Bacteriological

Ultrason Sonochem, 2004 Sep, 11(6), 379 - 84
The direct effect of ultrasound on the extraction of date syrup and its micro-organisms; Entezari MH et al.; In the date syrup industry, date fruits are mixed with a suitable amount of water at a temperature greater than 50 degrees C for about 1 h . This condition is not sufficient for killing the micro-organisms present in the fruit . In addition, Overheating for a long time can damages nutritious materials and also changes the final product's color . Ultrasound was applied for improving the quantity and quality of the extraction, and also to overcome the health problem . In this research, the following variables were examined: date fruit/water ratio, ultrasonic intensity and temperature . The results showed that sonication under the proper conditions can lead to a higher extraction in a shorter time with a better physical quality of the product . Most importantly, the sonication significantly decreased the microbial count in comparison to the classical method . This study also confirmed the presence of anti-microbial substances in date fruit, and that ultrasonic waves can accelerate their effects.

Anal Biochem, 2004 Sep 1, 332(1), 109 - 15
Enzyme-coupled assay of acetylxylan esterases on monoacetylated 4-nitrophenyl beta-D-xylopyranosides; Biely P et al.; Three different monoacetates of 4-nitrophenyl beta-D-xylopyranoside were tested as substrates for beta-xylosidase and for microbial carbohydrate esterases and a series of non-hemicellulolytic esterases . The acetyl group in 2-O-acetyl, 3-O-acetyl, and 4-O-acetyl 4-nitrophenyl beta-D-xylopyranoside makes the glycoside resistant to the action of beta-xylosidase (EC 3.2.1.37) . This fact was explored to introduce a new enzyme-coupled assay of acetylxylan esterases (EC 3.1.1.72) and other carbohydrate-deacetylating enzymes . The deacetylation converts the monoacetates into the substrate of beta-xylosidase, the auxiliary enzyme . The effect of the acetyl group migration along the xylopyranoid ring in aqueous media can be avoided by shortening the assay duration . The assay enables an easy examination of the positional specificity of the enzymes, which is important for classification of acetylxylan esterases and for elucidation of the structure-function relationship among carbohydrate esterases in general . Non-hemicellulolytic esterases showed different positional specificity of deacetylation than did acetylxylan esterases.

Clin Exp Rheumatol, 2004 Jul-Aug, 22(4), 433 - 40
Low density of CD1+ cells in the synovial tissue of patients with rheumatoid arthritis; Weidler C et al.; OBJECTIVE: CD1 molecules present microbial and self glycolipid antigens to a defined T cell subset with features of natural killer cells . CD1 molecules are up-regulated by inflammatory stimuli such as GM-CSF, and we would expect to find increased CD1 expression in the synovium of patients with rheumatoid arthritis (RA) as compared to osteoarthritis (OA) . This study was initiated to compare the density of CD1a+, CD1b+, and CD1c+ synovial cells in RA and OA patients . METHODS: Expression of CD1a+, CD1b+, and CD1c+ molecules in synovial tissue was assessed by semiquantitative immunohistochemistry . For comparison, serological, functional, and typical immunohistochemical markers of inflammation were detected . RESULTS: Although patients with RA as compared to OA had highly significantly increased signs of inflammation, the density of CD1a+, CD1b+, and CD1c+ synovial cells was similar This was also true for the density of CD1+ cells in relation to that of activated CD163+ macrophages . There was a high correlation between the densities of CD1a,b,c positive cells, which suggests the existence of similar regulatory pathways . In a combined analysis of RA and OA patients, there existed a negative association between prior NSAID therapy and the density of CD1a+, CD1b+, and CD1c+ synoviocytes in relation to CD163+ macrophages . This is interesting because a similar immunosuppressive aspect of NSAID has never been shown before and this might represent a hitherto unrecognized immunosuppressive aspect of NSAID . CONCLUSION: Considering the high synovial inflammation in patients with RA, the densities of CD1a+, CD1b+, and CD1c+ synovial cells were low compared to patients with OA . Further studies in RA patients are needed to clarify whether a defect in CD1 regulation may exist . Such a defect may lead to an insufficient immune response against microbial glycolipids, which would support smoldering or repeated inadequately responded infection.

Surgery, 2004 Aug, 136(2), 384 - 9
Beta-glucan affects leukocyte navigation in a complex chemotactic gradient; Tsikitis VL et al.; BACKGROUND: Polymorphonuclear leukocytes (PMNs) must traverse endogenous chemotactic gradients (interleukin 8 {IL-8}) before reaching target chemoattractants (fMLP {N-formylmethionine-leucine-phenylalanine}, C5a) produced at a site of bacterial infection . Complement receptor 3 (CR3; CD11b/CD18) contains 2 distinct binding sites, one that mediates adhesion and a lectin-like domain (LLD) that binds polysaccharides of microbial origin . This laboratory previously reported an increase in the chemotactic capacity of PMNs toward fMLP upon ligation of the CR3 LLD with beta-glucan, a CR3 agonist . Current studies sought to determine the effect of beta-glucan on PMN navigation toward other chemoattractants alone and in a competing chemotactic environment . METHODS: Migration was assessed by serum agarose overlay with the use of chambered slides containing or not, beta-glucan . Migration of human PMNs at 37 degrees C for 2 hours was evaluated toward C5a or IL-8 alone and in competing gradients . Selected groups were treated with anti-CR3-blocking antibodies . The number of chemotactic cells was quantified by microscopy . RESULTS: beta-glucan significantly enhanced chemotaxis toward C5a and suppressed that toward IL-8 in a CR3-dependent fashion . In the competing chemotactic gradient assays (C5a vs IL-8), beta-glucan further enhanced migration toward C5a while not affecting that toward IL-8 . CONCLUSIONS: beta-glucan selectively upregulates PMN chemotaxis toward C5a while suppressing chemotaxis toward IL-8 .

Environ Sci Technol, 2004 Jul 15, 38(14), 3877 - 84
Role of speciation in organotin toxicity to the yeast Candida maltosa; White JS et al.; Assessment of organometal pollution requires an understanding of the various processes that influence the bioavailability and toxicity of the contaminant . Organotins may exist as both cationic species and neutral hydroxides in aqueous solution, with the formation of chloride species in the presence of Cl- . Although these species have different chemical properties, there is very little information on the influence of speciation on organotin and microbial cell interactions . Tributyltin (TBT) and triphenyltin (TPT) interactions with the yeast Candida maltosa were investigated between pH 3.5 and 7.5 and in up to 0.5 M NaCl at pH 5.5 . Toxicity increased with both pH and NaCl concentration and the mechanisms of interaction depended on the species present in solution . TBT and TPT interacted by different mechanisms, as evidenced by action on membrane fluidity . Furthermore, there was a strong correlation between toxicity and overall octanol-water distribution ratio (D(OW)) of organotin compounds . Triorganotin cations are less toxic than triorganotin hydroxides, which are in turn less toxic than triorganotin chlorides . These findings underline the importance of speciation effects on organotin interactions in the environment.

J Vasc Surg, 2004 Aug, 40(2), 359 - 66
Genomic, serologic, and clinical case-control study of Chlamydia pneumoniae and peripheral artery occlusive disease; Linares-Palomino JP et al.; OBJECTIVES: Chlamydia pneumoniae has been related to atherosclerotic disease in both seroepidemiologic and genomic studies . We performed a case-control study to determine seropositivity and DNA detection in arteries of patients with peripheral artery occlusive disease and of healthy subjects . METHODS: The study included 64 patients with peripheral artery occlusive disease, and 50 control subjects who underwent varicose vein surgery, matched to the patient group for age, sex, and tobacco use . The fibrinogen level in all study subjects was measured as a marker of inflammation . Blood samples were taken from all subjects for determination of immunoglobulin (Ig) G elementary bodies (EB) against C pneumoniae with microimmunofluorescence (MIF) and enzyme-linked immunosorbent assay (ELISA), and of IgA EB with ELISA . The cutoff titers were 1:32 for MIF and 1.1 for ELISA . Biopsy specimens of arterial atheromatous plaque were obtained from patients, and of pudendal artery and saphenous vein from control subjects, and were studied with hemi-nested polymerase chain reaction . RESULTS: There were no differences in fibrinogen level between patients and controls . The prevalence of IgG anti-EB with MIF was 78% in patients and 24% in control subjects (P =.0001; odds ratio {OR}, 11.3; 95% confidence interval {CI}, 4.7-27.2) . Prevalence of IgG anti-EB with ELISA was 75% in patients and 16% in control subjects (P =.0001; OR, 15.7; 95% CI, 6.1-40) . There were no differences in IgA anti-EB titers . Bacterial DNA was detected in 67% of atheromatous plaques versus 12% of pudendal arteries (P =.0001) and 4% of saphenous veins . A weak correlation was found between seropositivity and the presence of intravascular DNA . CONCLUSIONS: Our results support the hypothesis that C pneumoniae is related to the pathogenesis of atherosclerotic peripheral artery occlusive disease . CLINICAL RELEVANCE: This study explored the infectious hypothesis in the context of the pathogenesis of atherosclerosis . This hypothesis has been supported by findings that certain infectious agents can cause or accelerate the course of diseases in which the possibility of a microbial cause was not previously proposed, as in the case of peptic ulcer and spongiform encephalopathy . The present study demonstrated the presence of Chlamydia pneumoniae and seropositivity in atheromatous plaques in patients with peripheral artery occlusive disease . These results contribute to a body of research that is opening up the possibility of treating atherosclerotic disease with antibiotic agents, and preventing it with immunization.

J Environ Radioact, 2004, 77(1), 1 - 27
Uranium mill tailings: nuclear waste and natural laboratory for geochemical and radioecological investigations; Landa ER; Uranium mill tailings (UMT) are a high volume, low specific activity radioactive waste typically disposed in surface impoundments . This review focuses on research on UMT and related earth materials during the past decade relevant to the assessment of: (1) mineral hosts of radionuclides; (2) the use of soil analogs in predicting long-term fate of radionuclides; (3) microbial and diagenetic processes that may alter radionuclide mobility in the surficial environment; (4) waste-management technologies to limit radionuclide migration; and (5) the impact of UMT on biota.

Dev Cell, 2004 Aug, 7(2), 217 - 28
EspFU is a translocated EHEC effector that interacts with Tir and N-WASP and promotes Nck-independent actin assembly; Campellone KG et al.; Several microbial pathogens including enteropathogenic E . coli (EPEC) exploit mammalian tyrosine-kinase signaling cascades to recruit Nck adaptor proteins and activate N-WASP-Arp2/3-mediated actin assembly . To promote localized actin "pedestal formation," EPEC translocates the bacterial effector protein Tir into the plasma membrane, where it is tyrosine-phosphorylated and binds Nck . Enterohemorrhagic E . coli (EHEC) also generates Tir-dependent pedestals, but in the absence of phosphotyrosines and Nck recruitment . To identify additional EHEC effectors that stimulate phosphotyrosine-independent actin assembly, we systematically generated EHEC mutants containing specific deletions in putative pathogenicity-islands . Among 0.33 Mb of deleted sequences, only one ORF was critical for pedestal formation . It lies within prophage-U, and encodes a protein similar to the known effector EspF . This proline-rich protein, EspFU, is the only EHEC effector of actin assembly absent from EPEC . Whereas EHEC Tir cannot efficiently recruit N-WASP or trigger actin polymerization, EspFU associates with Tir, binds N-WASP, and potently stimulates Nck-independent actin assembly.

Environ Sci Technol, 2004 Jul 1, 38(13), 3623 - 31
Deriving soil critical limits for Cu, Zn, Cd, and Pb: a method based on free ion concentrations; Lofts S et al.; We present a method to calculate critical limits of cationic heavy metals accounting for variations in soil chemistry . We assume the free metal ion concentration (Mfree) to be the most appropriate indicator of toxicity, combined with a protective effect of soil cations (e.g., H+, Ca2+) . Because soil metal cations tend to covary with pH, the concentration of Mfree exerting a given level of toxic effect (Mfree,toxic) can be expressed as a function of pH alone . We use linear regression equations to derive Mfree,toxic in toxicity experiments from soil pH, organic matter content, and endpoint soil metal . Chronic toxicity data from the literature, for plants, invertebrates, microbial processes, and fungi are interpreted in terms of an average log Mfree,toxic together with distributions of species sensitivity . This leads to critical limit functions to protect 95% of species, of the form log Mfree,CRIT = (pH + gamma . Appreciable effects of soil pH upon log Mfree,CRIT are found, with alpha = -1.21 (Cu), -0.34 (Zn), -0.43 (Cd), and -0.83 (Pb) . Critical limit functions in terms of the geochemically active soil metal (Msoil,CRIT), that pool of metal which controls the free ion concentration, have also been derived, with soil pH and organic matter content as variables . The pH effect on Msoil,CRIT is relatively small, with slopes of 0.05 (Cu), 0.19 (Zn), 0.16 (Cd), and 0.20 (Pb), since the effect of pH on Mfree,CRIT is countered by the variation of Mfree with pH.

J Infect Dis, 2004 Sep 1, 190(5), 946 - 56 Epub 2004 Jul 30.
Transcription profile of Helicobacter pylori in the human stomach reflects its physiology in vivo; Boonjakuakul JK et al.; BACKGROUND: Little is known about levels of expression of Helicobacter pylori genes in the human host . We therefore developed a quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) assay to measure transcript profiles of H . pylori in the human stomach . METHODS: In vivo expression of 16 genes on the cag pathogenicity island and of 18 putative virulence genes was quantitated by isolation of total RNA directly from infected human gastric mucosa . The results were compared with in vitro expression determined from H . pylori cells grown in culture . RESULTS: The highest levels of expression were found for cag1 and cag25 and for genes, such as urease and catalase, that may be important for bacterial homeostasis in the relatively hostile environment of the gastric mucosa . Transcript abundance, relative to 16S rRNA, was lower in vivo than in vitro, which suggests that H . pylori cells are in stationary phase in the gastric environment . This was particularly apparent for cagA . Since CagA is arguably of unique importance, in terms of interaction with the host, tight control of its in vivo expression might be particularly important . CONCLUSIONS: qRT-PCR is a powerful tool to measure gene expression in human or animal tissue that contains minute amounts of microbial mRNA, and the results reflect on the physiology of the pathogen in its natural host.

J Immunol, 2004 Aug 15, 173(4), 2725 - 35
The induction of acute ileitis by a single microbial antigen of Toxoplasma gondii; Rachinel N et al.; The role of specific microbial Ags in the induction of experimental inflammatory bowel disease is poorly understood . Oral infection of susceptible C57BL/6 mice with Toxoplasma gondii results in a lethal ileitis within 7-9 days postinfection . An immunodominant Ag of T . gondii (surface Ag 1 (SAG1)) that induces a robust B and T cell-specific response has been identified and a SAG1-deficient parasite (Deltasag1) engineered . We investigated the ability of Deltasag1 parasite to induce a lethal intestinal inflammatory response in susceptible mice . C57BL/6 mice orally infected with Deltasag1 parasites failed to develop ileitis . In vitro, the mutant parasites replicate in both enterocytes and dendritic cells . In vivo, infection with the mutant parasites was associated with a decrease in the chemokine and cytokine production within several compartments of the gut-associated cell population . RAG-deficient (RAG1(-/-)) mice are resistant to the development of the ileitis after T . gondii infection . Adoptive transfer of Ag-specific CD4(+) effector T lymphocytes isolated from C57BL/6-infected mice into RAG(-/-) mice conferred susceptibility to the development of the intestinal disease . In contrast, CD4(+) effector T lymphocytes from mice infected with the mutant Deltasag1 strain failed to transfer the pathology . In addition, resistant mice (BALB/c) that fail to develop ileitis following oral infection with T . gondii were rendered susceptible following intranasal presensitization with the SAG1 protein . This process was associated with a shift toward a Th1 response . These findings demonstrate that a single Ag (SAG1) of T . gondii can elicit a lethal inflammatory process in this experimental model of pathogen-driven ileitis.

J Immunol, 2004 Aug 15, 173(4), 2211 - 5
Regulatory cells and infectious agents: detentes cordiale and contraire; Rouse BT et al.; This brief review describes the types of interactions that occur between CD4(+)CD25(+) regulatory T cells (Treg) and microbial pathogens . These interactions range from one of mutual benefit (detente cordiale) such as occurs in Leishmania major infection of resistant mouse strains, to instances where the Treg response appears to mainly favor the pathogen and be detrimental to the host (detente contraire) . Examples of the latter include chronic persistent infections with retroviruses, perhaps including HIV, and hepatitis C virus . The Treg response also hampers the effectiveness of immunity against some acute virus infections such as HSV . Evidence is also discussed showing that Treg can play a benevolent role to limit the severity of bystander tissue damage in circumstances where the immune response to pathogens is immunopathological . Finally, emerging approaches are discussed that either blunt or activate Treg and that could be used practically to manage host-pathogen interaction.

Appl Environ Microbiol, 2004 Aug, 70(8), 4930 - 40
Dominant microbial composition and its vertical distribution in saline meromictic Lake Kaiike (Japan) as revealed by quantitative oligonucleotide probe membrane hybridization; Koizumi Y et al.; Vertical distributions of dominant bacterial populations in saline meromictic Lake Kaiike were investigated throughout the water column and sediment by quantitative oligonucleotide probe membrane hybridization . Three oligonucleotide probes specific for the small-subunit (SSU) rRNA of three groups of Chlorobiaceae were newly designed . In addition, three general domain (Bacteria, Archaea, and Eukarya)-specific probes, two delta-Proteobacteria-specific probes, a Chlorobiaceae-specific probe, and a Chloroflexi-specific probe were used after optimization of their washing conditions . The abundance of the sum of SSU rRNAs hybridizing with probes specific for three groups of Chlorobiaceae relative to total SSU rRNA peaked in the chemocline, accounting for up to 68% . The abundance of the delta-proteobacterial SSU rRNA relative to total SSU rRNA rapidly increased just below the chemocline up to 29% in anoxic water and peaked at the 2- to 3-cm sediment depth at ca . 34% . The abundance of SSU rRNAs hybridizing with the probe specific for the phylum Chloroflexi relative to total SSU rRNA was highest (31 to 54%) in the top of the sediment but then steeply declined with depth and became stable at 11 to 19%, indicating the robust coexistence of sulfate-reducing bacteria and Chloroflexi in the top of the sediment . Any SSU rRNA of Chloroflexi in the water column was under the detection limit . The summation of the signals of group-specific probes used in this study accounted for up to 89% of total SSU rRNA, suggesting that the DGGE-oligonucleotide probe hybridization approach, in contrast to conventional culture-dependent approaches, was very effective in covering dominant populations.

Appl Environ Microbiol, 2004 Aug, 70(8), 4800 - 6
Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis; Yu Z et al.; Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial diversity and community structure, but no systematic comparison has been made of the DGGE profiles obtained when different hypervariable (V) regions are amplified from the same community DNA samples . We report here a study to make such comparisons and establish a preferred choice of V region(s) to examine by DGGE, when community DNA extracted from samples of digesta is used . When the members of the phylogenetically representative set of 218 rrs genes archived in the RDP II database were compared, the V1 region was found to be the most variable, followed by the V9 and V3 regions . The temperature of the lowest-melting-temperature (T(m(L))) domain for each V region was also calculated for these rrs genes, and the V1 to V4 region was found to be most heterogeneous with respect to T(m(L)) . The average T(m(L)) values and their standard deviations for each V region were then used to devise the denaturing gradients suitable for separating 95% of all the sequences, and the PCR-DGGE profiles produced from the same community DNA samples with these conditions were compared . The resulting DGGE profiles were substantially different in terms of the number, resolution, and relative intensity of the amplification products . The DGGE profiles of the V3 region were best, and the V3 to V5 and V6 to V8 regions produced better DGGE profiles than did other multiple V-region amplicons . Introduction of degenerate bases in the primers used to amplify the V1 or V3 region alone did not improve DGGE banding profiles . Our results show that DGGE analysis of gastrointestinal microbiomes is best accomplished by the amplification of either the V3 or V1 region of rrs genes, but if a longer amplification product is desired, then the V3 to V5 or V6 to V8 region should be targeted.

Appl Environ Microbiol, 2004 Aug, 70(8), 4756 - 65
Determining rates of change and evaluating group-level resiliency differences in hyporheic microbial communities in response to fluvial heavy-metal deposition; Feris KP et al.; Prior field studies by our group have demonstrated a relationship between fluvial deposition of heavy metals and hyporheic-zone microbial community structure . Here, we determined the rates of change in hyporheic microbial communities in response to heavy-metal contamination and assessed group-level differences in resiliency in response to heavy metals . A controlled laboratory study was performed using 20 flowthrough river mesocosms and a repeated-measurement factorial design . A single hyporheic microbial community was exposed to five different levels of an environmentally relevant metal treatment (0, 4, 8, 16, and 30% sterilized contaminated sediments) . Community-level responses were monitored at 1, 2, 4, 8, and 12 weeks via denaturing gradient gel electrophoresis and quantitative PCR using group-specific primer sets for indigenous populations most closely related to the alpha-, beta-, and gamma-proteobacteria . There was a consistent, strong curvilinear relationship between community composition and heavy-metal contamination (R(2) = 0.83; P < 0.001), which was evident after only 7 days of metal exposure (i.e., short-term response) . The abundance of each phylogenetic group was negatively affected by the heavy-metal treatments; however, each group recovered from the metal treatments to a different extent and at a unique rate during the course of the experiment . The structure of hyporheic microbial communities responded rapidly and at contamination levels an order of magnitude lower than those shown to elicit a response in aquatic macroinvertebrate assemblages . These studies indicate that hyporheic microbial communities are a sensitive and useful indicator of heavy-metal contamination in streams.

Asia Pac J Clin Nutr . 2004;13(Suppl):S162.
Watermelon juice concentrate; Ghazizadeh M et al.; Production of watermelon is in great amount in Iran during summer time . Consumption of this fruit is recommended by health and nutrition authorities . Findings from USDA scientists indicate that watermelon contains high levels of lycopene an antioxidant that may help the body fight against cancer and other chronic diseases . Thus it can be considered as a functional food - one that may help prevent certain diseases . However, production of this fruit in some parts of country is in excess of its consumption, so large amounts are spoiled and wasted . Therefore, in this study we tried to process two kinds of watermelons and to formulate their juice and concentrate which preserves its flavor, appearance and nutrient contents . Seventy two Charleston Gray and local variety of Khorasan watermelon samples were analyzed . Water content of local watermelon and Charleston Gray were 55.9 % +/- 3.1 and 58 % +/- 1.12 respectively, rind 34.3 % +/- 0.7 and 31.8 % +/- 1.56 (N.S), seeds 4.8% +/- 1.29 and 2.3 %+/- 0.32 (P<002) and pulps were 4.9% +/- 1/39 and 7.9 % +/- 0.45 (P<0.001) . Sixty different formulae from a mixture of watermelon Juice and food additives (30 formulae of each variety) were prepared and their organoleptic characteristics underwent preliminary investigation by category scale . Three formulae from each variety were selected (A, B and C) and their organoleptic characteristics were evaluated . The suitable formula for each variety was nominated by test panel . The formula A of Charleston Gray variety including 100 ml Juice, 4gr sugar and 0.1 gr citric acid with 68.3% acceptability and the formula B of local variety including 100ml juice, 5 gr Sugar and 0.2 gr citric acid with 30.4 % acceptability were selected as preferred samples . The selected formula of Charleston Gray variety was concentrated (up to Brix 54) and packed . Changes of chemical, microbial and organoleptic characteristics in different condition (room, refrigerator and freezer) during 0, 15, 30, 45, . 90 days storage were determined . Ninety days storage in different temperatures did not cause notable changes of chemical, microbial and organoleptic characteristics.

Asia Pac J Clin Nutr . 2004 Aug;13(Suppl):S91.
The efficacy of phytase in corn soybean meal based broiler diets; Mulyantini NG et al.; Background - To overcome the inability of poultry to utilise phosphorus bound to phytate in plant feed ingredients, phytase of microbial origin is added to poultry diets . This has the added advantage of reducing phosphorus build up in manure . Objective - To examine the efficacy of two commercial phytase sources on the performance of broiler chickens fed corn soybean meal based diets . Design - Day-old, male broiler chicks (Ross) were allocated to 30 pens in a completely randomised experimental design with each diet offered to 6 pens of 50 chicks per pen . The 6 experimental mash diets were formulated as: 1) standard Phosphorus (P), 2) low-P, 3) low-P + phytase A at 500 U/kg feed, and 4) low-P + phytase A at 1000 U/kg feed, 5) low-P + phytase B at 500 U and 6) low-P + phytase B at 1000 U/kg feed . A starter diet was fed from day old to day 22 and a finisher diet from day 23 to day 42 . The standard-P starter and finisher diets contained 0.4% and 0.32% available phosphorous respectfully compared to 0.28% and 0.20% in the low-P diets . Outcomes - At the completion of the study body weight of the birds fed the standard-P diet were significantly (P<0.05) heavier than those fed the unsupplemented low-P diets . There was no significant difference in body weight between the groups fed the standard-P diet and the phytase supplemented diets . Feed conversion ratio was not significantly affected by phytase supplementation . Conclusion - The performance of broilers fed low phosphorus corn soybean meal based diets can be significantly improved by phytase supplementation . Both sources of phytase gave similar results, and can replace approximately 50% dicalcium phosphate in diets, without affecting broiler performance.

Parasitol Res . 2004 Jul 31; {Epub ahead of print}
The involvement of an integrin-like protein and protein kinase C in amoebic adhesion to fibronectin and amoebic cytotoxicity; Han KL et al.; Adherence of a pathogen to the host cell is one of the critical steps in microbial infections . Naegleria fowleri, a causative agent of primary amoebic meningoencephalitis in humans, is expected to interact with extracellular components of the host, such as fibronectin, in a receptor-mediated mode . In this study, we investigated the interaction between N . fowleri and fibronectin to understand its cytopathology . In binding assays using immobilized fibronectin, the number of amoebae bound to fibronectin was increased compared to the controls, and was dependent on the amount of coated fibronectin present . A fibronectin binding protein of 60 kDa was found in extracts of N . fowleri . Western blot and immunolocalization assays using integrin alpha(5)/FnR antibodies showed that a 60 kDa protein reacted with the antibodies in extracts of N . fowleri, which was localized on the surface of N . fowleri . Preincubation of N . fowleri with the integrin antibodies significantly inhibited amoebic binding to fibronectin and cytotoxicity to the CHO cells . Additionally, protein kinase C activity was detected in the extract of N . fowleri . When N . fowleri was pretreated with protein kinase C activator or inhibitor, the abilities of amoebic adhesion to fibronectin and cytotoxicity to the host cells were markedly affected compared to untreated amoebae . These results suggest that an amoebic integrin-like receptor and protein kinase C play important roles in amoebic cellular processes in response to fibronectin.

Genome Res, 2004 Aug, 14(8), 1669 - 75
cpnDB: a chaperonin sequence database; Hill JE et al.; Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes . Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms . Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers . Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies . The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea . The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera . As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage . We built cpnDB from open source tools and it is available at

Cancer Res, 2004 Aug 1, 64(15), 5518 - 24
Modern criteria to establish human cancer etiology; Carbone M et al.; The Cancer Etiology Branch of the National Cancer Institute hosted a workshop, "Validation of a causal relationship: criteria to establish etiology," to determine whether recent technological advances now make it possible to delineate improved or novel criteria for the rapid establishment for cancer causation . The workshop was held in Washington, D.C., December 11-12, 2003, and participants were among the international leaders in the fields of epidemiology, chemistry, biochemistry, microbiology, virology, environmental and chemical carcinogenesis, immunology, pathology, molecular pathology, genetics, oncology, and surgical oncology . There was a general consensus that the rapid identification of human carcinogens and their removal (when possible) or the establishment of specific preventive and therapeutic measures was the most desirable and effective way to have a rapid and positive impact in the fight against cancer . From a clinical perspective, it may be as important to target initiators, cocarcinogens and promoters, if by removing any one of them tumor growth can be prevented . Future studies should focus on interactions among and between different biological, chemical, and physical agents . Analyses of single agents can at times miss their carcinogenic potential when such agents are carcinogenic only in subgroups of individuals because of their genetic background, diet, exposure to other carcinogens, or microbial infection . Epidemiology, molecular pathology (including chemistry, biochemistry, molecular biology, molecular virology, molecular genetics, epigenetics, genomics, proteomics, and other molecular-based approaches), and animal and tissue culture experiments should all be seen as important integrating evidence in the determination of human carcinogenicity . Concerning the respective roles of epidemiology and molecular pathology, it was noted that epidemiology allows the determination of the overall effect of a given carcinogen in the human population (e.g., hepatitis B virus and hepatocellular carcinoma) but cannot prove causality in the individual tumor patient . Molecular pathology cannot determine the overall impact of a carcinogen in the population but can at times prove causality in the individual tumor patient {such as the detection of high-risk human papillomavirus (HPV) in a cervical carcinoma biopsy} . This is possible when molecular techniques have shown that the agent is required for transformation or malignant growth of human cells (such as antisense HPV strategies showing the requirement for the expression of HPV proteins for tumor cell growth) and when there is supportive experimental animal evidence . Ideally, epidemiology and molecular pathology information together with experimental evidence in animals should be available for the most reliable identification of human carcinogens . All sets of data are not always available, and a rapid identification of human carcinogens is in the best public health interest . Swift validation of a causal relationship when followed by a rapid deployment of preventive and therapeutic approaches should lead to a favorable public health impact (such as hepatitis B virus vaccination to prevent hepatocellular carcinoma).

Mutat Res, 2004 Aug 18, 552(1-2), 101 - 17
Emerging contaminants--pesticides, PPCPs, microbial degradation products and natural substances as inhibitors of multixenobiotic defense in aquatic organisms; Smital T et al.; The environmental presence of chemosensitizers or inhibitors of the multixenobiotic resistance (MXR) defense system in aquatic organisms could cause increase in intracellular accumulation and toxic effects of other xenobiotics normally effluxed by MXR transport proteins (P-glycoprotein (P-gps), MRPs) . MXR inhibition with concomitant detrimental effects has been shown in several studies with aquatic organisms exposed to both model MXR inhibitors and environmental pollutants . The presence of MXR inhibitors has been demonstrated in environmental samples from polluted locations at concentrations that could abolish P-gp transport activity . However, it is not clear whether the inhibition observed after exposure to environmental samples is a result of saturation of MXR transport proteins by numerous substrates present in polluted waters or results from the presence of powerful MXR inhibitors . And are potent environmental MXR inhibitors natural or man-made chemicals? As a consequence of these uncertainties, no official action has been taken to monitor and control the release and presence of MXR inhibitors into aquatic environments . In this paper we present our new results addressing these critical questions . Ecotoxicological significance of MXR inhibition was supported in in vivo studies that demonstrated an increase in the production of mutagenic metabolites by mussels and an increase in the number of sea urchin embryos with apoptotic cells after exposure to model MXR inhibitors . We also demonstrated that MXR inhibitors are present among both conventional and emerging man-made pollutants: some pesticides and synthetic musk fragrances show extremely high MXR inhibitory potential at environmentally relevant concentrations . In addition, we emphasized the biological transformation of crude oil hydrocarbons into MXR inhibitors by oil-degrading bacteria, and the risk potentially caused by powerful natural MXR inhibitors produced by invasive species.

Waste Manag, 2004, 24(7), 673 - 9
Biodegradable organic matter in municipal solid waste incineration bottom ash; Zhang S et al.; For investigation of the behavior of municipal solid waste incineration bottom ash in landfill, we have analysed bottom ash samples taken after the quench tank as well as after five months of storage in the laboratory for elements and organic constituents . Water extractable organic carbon, particulate organic carbon, amino acids, hexosamines and carbohydrates considerably decreased during the five months of storage and their spectra revealed microbial reworking . This shows that the organic matter present in the bottom ash after incineration can provide a substrate for microbial activity . The resulting changes of the physico-chemical environment may effect the short-term behavior of the bottom ash in landfill .

Bioresour Technol, 2004 Dec, 95(3), 287 - 91
Single cell oil (SCO) production by Mortierella isabellina grown on high-sugar content media; Papanikolaou S et al.; Mortierella isabellina cultivated in nitrogen-limited media presented remarkable cell growth (up to 35.9 g/l) and high glucose uptake even with high initial sugar concentrations (e.g . 100 g/l) in media . After nitrogen depletion, significant fat quantities were accumulated inside the fungal mycelia (50-55%, wt/wt oil in dry biomass), resulting in a notable single cell oil production of 18.1 g/l of culture medium . Total dry biomass and lipid yields presented greatly increased values (0.34 and 0.17 g respectively per gram of glucose consumed) . The microbial lipid produced contained gamma-linolenic acid (GLA) at a concentration of 3.5+/-1.0%, wt/wt, which corresponded to 16-19 mg GLA per gram of dry microbial mass and a maximum concentration of 0.801 g GLA per liter of culture medium.

Autoimmun Rev, 2004 Jul, 3(5), 394 - 400
Inflammatory bowel disease: the role of environmental factors; Danese S et al.; Environmental factors are essential components of the pathogenesis of inflammatory bowel disease (IBD) and primarily responsible for its growing incidence around the globe . Epidemiological, clinical and experimental evidence support an association between IBD and a large number of seemingly unrelated environmental factors, which include smoking, diet, drugs, geographical and social status, stress, microbial agents, intestinal permeability and appendectomy . Data supporting the involvement of each of these factors in predisposing to, triggering, or modulating the course or outcome of IBD vary from strong to tenuous . Smoking and the enteric bacterial flora are the ones for which the most solid evidence is currently available . Smoking increases the risk of Crohn's disease (CD) and worsens its clinical course, but has a protective effect in ulcerative colitis (UC) . Presence of enteric bacteria is indispensable to develop gut inflammation in most animal models of IBD, and modulation of the quantity or quality of the flora can be beneficial in patients with IBD . Surprisingly, evidence for a major role of the diet in inducing or modifying IBD is limited, while that for nonsteroidal anti-inflammatory drugs is more convincing than for oral contraceptives . Northern geographic location, and a high social, economical, educational or occupational status increase the risk of IBD, an observation fitting the hygiene hypothesis for allergic and autoimmune diseases . Stress is also associated with IBD, but more as a modifier than an inducing factor, and its contribution is more obvious in IBD animal models than human IBD . Finally, an increased intestinal permeability may increase the risk for developing CD, whereas an appendectomy lowers the risk of developing UC.

Microb Cell Fact . 2004 Aug 2;3(1):10.
Use and improvement of microbial redox enzymes for environmental purposes; Garcia-Arellano H et al.; Industrial development may result in the increase of environmental risks . The enzymatic transformation of polluting compounds to less toxic or even innocuous products is an alternative to their complete removal . In this regard, a number of different redox enzymes are able to transform a wide variety of toxic pollutants, such as polynuclear aromatic hydrocarbons, phenols, azo dyes, heavy metals, etc . Here, novel information on chromate reductases, enzymes that carry out the reduction of highly toxic Cr(VI) to the less toxic insoluble Cr(III), is discussed . In addition, the properties and application of bacterial and eukaryotic proteins (lignin-modifying enzymes, peroxidases and cytochromes) useful in environmental enzymology is also discussed.

Lett Appl Microbiol, 2004, 39(3), 306 - 9
Kinetics and effects of trace elements and electron complexes on 2-keto-4-methylthiobutyric acid-dependent biosynthesis of ethylene in soil; Arshad M et al.; AIMS: 2-Keto-4-methylthiobutyric acid (KMBA) is an established intermediate in microbial biosynthesis of ethylene from methionine . This study demonstrates the kinetics and effects of trace elements and electron complexes on substrate (KMBA)-derived C2H4 biosynthesis in soil . METHODS AND RESULTS: We have previously reported KMBA-dependent C2H4 production in soil . We studied the kinetics and effects of various trace elements and electron complexes on KMBA-derived C2H4 biosynthesis in soil by gas chromatography . Kinetic analysis revealed that ethylene forming enzyme (EFE) reaction was linear (R2 = 0.9448) when velocity of reaction (V) was plotted against substrate {S} over the range from 2.5 to 10 mmol l(-1) and thus followed a first order reaction . Application of three linear transformations of the Michaelis-Menten equation indicated high affinity of EFE for the substrate because Km values ranged between 5.4 and 6.67 mmol l(-1) and Vmax of reaction was between 22.4 and 35.7 nmol kg(-1) soil 120 cm(-1) . Most of the trace elements exhibited positive effects on KMBA-dependent C2H4 production in soil . Maximum stimulatory effect on C2H4 biosynthesis was observed in response to Co(II) application, while Fe(III) inhibited the biotransformation of KMBA into C2H4 . Contrarily, most of the tested electron complexes inhibited KMBA-derived C2H4 biosynthesis in the soil . However, lower concentrations (1.0 mmol l(-1)) of mannitol and hydroquinone were stimulatory to C2H4 production in soil compared with controls (substrate only) . Conclusions: The results revealed that both kind and concentration of trace elements and electron complexes affected the substrate-dependent production of C2H4 in soil with different degrees of efficacy . SIGNIFICANCE AND IMPACT OF THE STUDY: The C2H4 in the root environment could be physiologically active even at low concentrations, so knowledge regarding various factors which regulate C2H4 biosynthesis in soil could be of significance for plant growth and development.

J AOAC Int, 2004 May-Jun, 87(3), 587 - 91
Rapid fluorescence screening assay for tetracyclines in chicken muscle; Schneider MJ et al.; A simple, rapid fluorescence assay was developed for screening tetracyclines in chicken muscle at the U.S . tolerance level (2 mg/kg) . The method requires only a homogenization of the tissue in acetonitrile-ammonium hydroxide, centrifugation, addition of Mg+2, and another centrifugation before fluorescence of the supernatant is measured at 505 nm (excitation at 385 nm) . Comparison of the fluorescence of control chicken muscle extracts with extracts from muscle fortified with either 2 mg/kg tetracycline, oxytetracycline, or chlortetracycline showed no overlap . A threshold level set at the average fluorescence for a series of fortified 2 mg/kg samples minus 3sigma minimized false-negative responses to provide a successful screening method . The method was tested with blinded samples as controls or samples fortified with tetracycline, oxytetracycline, or chlortetracycline in order to demonstrate its utility . This approach can provide an alternative to microbial screening assays.

Int J Oral Maxillofac Surg, 2004 Apr, 33(3), 221 - 34
Recurrent aphthous ulcers today: a review of the growing knowledge; Natah SS et al.; Recurrent aphthous ulcers represent a very common but poorly understood mucosal disorder . They occur in men and women of all ages, races and geographic regions . It is estimated that at least 1 in 5 individuals has at least once been afflicted with aphthous ulcers . The condition is classified as minor, major, and herpetiform on the basis of ulcer size and number . Attacks may be precipitated by local trauma, stress, food intake, drugs, hormonal changes and vitamin and trace element deficiencies . Local and systemic conditions, and genetic, immunological and microbial factors all may play a role in the pathogenesis of recurrent aphthous ulceration (RAU) . However, to date, no principal cause has been discovered . Since the aetiology is unknown, diagnosis is entirely based on history and clinical criteria and no laboratory procedures exist to confirm the diagnosis . Although RAU may be a marker of an underlying systemic illness such as coeliac disease, or may present as one of the features of Behcet's disease, in most cases no additional body systems are affected, and patients remain otherwise fit and well . Different aetiologies and mechanisms might be operative in the aetiopathogenesis of aphthous ulceration, but pain, recurrence, self-limitation of the condition, and destruction of the epithelium seem to be the ultimate outcomes . There is no curative therapy to prevent the recurrence of ulcers, and all available treatment modalities can only reduce the frequency or severity of the lesions.

Biotechnol Bioeng, 2004 Aug 20, 87(4), 516 - 24
Metabolic engineering and protein directed evolution increase the yield of L-phenylalanine synthesized from glucose in Escherichia coli; Baez-Viveros JL et al.; L-phenylalanine (L-Phe) is an aromatic amino acid with diverse commercial applications . Technologies for industrial microbial synthesis of L-Phe using glucose as a starting raw material currently achieve a relatively low conversion yield (Y(Phe/Glc)) . The purpose of this work was to study the effect of PTS (phosphotransferase transport system) inactivation and overexpression of different versions of feedback inhibition resistant chorismate mutase-prephenate dehydratase (CM-PDT) on the yield (Y(Phe/Glc)) and productivity of L-Phe synthesized from glucose . The E . coli JM101 strain and its mutant derivative PB12 (PTS(-)Glc(+) phenotype) were used as hosts . PB12 has an inactive PTS, but is capable of transporting and phosphorylating glucose by using an alternative system constituted by galactose permease (GalP) and glucokinase activities (Glk) . JM101 and PB12 were transformed with three plasmids, harboring genes that encode for a feedback inhibition resistant DAHP synthase (aroG(fbr)), transketolase (tktA) and either a truncated CM-PDT (pheA(fbr)) or its derived evolved genes (pheA(ev1) or pheA(ev2)) . Resting-cells experiments with these engineered strains showed that JM101 and PB12 strains expressing either pheA(ev1) or pheA(ev2) genes produced l-Phe from glucose with Y(Phe/Glc) of 0.21 and 0.33 g/g, corresponding to 38 and 60% of the maximum theoretical yield (0.55 g/g), respectively . In addition, in both engineered strains the reached q(Phe) high levels of 40 mg/g-dcw.h . The metabolic engineering strategy followed in this work, including a strain with an inactive PTS, resulted in a positive impact over the Y(Phe/Glc), enhancing it nearly 57% compared with its PTS(+) counterpart . This is the first report wherein PTS inactivation was a successful strategy to improve the Y(Phe/Glc).

Rev Hosp Clin Fac Med Sao Paulo, 2004 May-Jun, 59(3), 138 - 44 Epub 2004 Jul 28.
Involvement of C4 allotypes in the pathogenesis of human diseases; Samano ES et al.; The complement system is an important humoral defense mechanism that plays a relevant role against microbial agents, inflammatory response control, and immunocomplex clearance . Classical complement pathway activation is antibody-dependent . The C4 component participates in the initial step of activation, and C4 expression is determined by 2 pairs of allotypes: C4A and C4B . Deficiencies in C4 allotypes have been associated with several diseases . The aim of the present review is evaluate the reported data in the literature regarding specific C4A and C4B deficiencies and characterize their clinical relevance . We searched the MEDLINE and LILACS databases . Papers referring to total C4 deficiency without allotype evaluation and case reports of primary C4 deficiency were not included . Deficiencies in C4 allotypes have been associated with Mycobacterium leprae infection, erythema nodosum, systemic sclerosis with anti-topoisomerase I antibodies, intermediate congenital adrenal hyperplasia with DR5 genotype, diabetes mellitus type 1 with DR3,4 genotype, and diabetes mellitus with antibodies against islet cells . C4 allotype deficiency is also related to C4B deficiency and autoimmune-associated diseases, such as systemic lupus erythematosus, or diseases with an autoimmune component, such as autism . Some reports associate C4A with thyroiditis after delivery as well as limited and systemic sclerosis without anti-topoisomerase I antibodies . However, the studies with C4A and C4B have been concentrated in isolated populations, and some of the studies could not be reproduced by other authors.

Rev Inst Med Trop Sao Paulo, 2004 May-Jun, 46(3), 119 - 26 Epub 2004 Jul 20.
The influence of the human genome on chronic viral hepatitis outcome; de Andrade DR Jr et al.; The mechanisms that determine viral clearance or viral persistence in chronic viral hepatitis have yet to be identified . Recent advances in molecular genetics have permitted the detection of variations in immune response, often associated with polymorphism in the human genome . Differences in host susceptibility to infectious disease and disease severity cannot be attributed solely to the virulence of microbial agents . Several recent advances concerning the influence of human genes in chronic viral hepatitis B and C are discussed in this article: a) the associations between human leukocyte antigen polymorphism and viral hepatic disease susceptibility or resistance; b) protective alleles influencing hepatitis B virus (HBV) and hepatitis C virus (HCV) evolution; c) prejudicial alleles influencing HBV and HCV; d) candidate genes associated with HBV and HCV evolution; d) other genetic factors that may contribute to chronic hepatitis C evolution (genes influencing hepatic stellate cells, TGF-beta 1 and TNF-alpha production, hepatic iron deposits and angiotensin II production, among others) . Recent discoveries regarding genetic associations with chronic viral hepatitis may provide clues to understanding the development of end-stage complications such as cirrhosis or hepatocellular carcinoma . In the near future, analysis of the human genome will allow the elucidation of both the natural course of viral hepatitis and its response to therapy.

J Cell Sci, 2004 Aug 1, 117(Pt 17), 4007 - 14
Lateral diffusion of Toll-like receptors reveals that they are transiently confined within lipid rafts on the plasma membrane; Triantafilou M et al.; The innate immune system utilises pattern recognition receptors in order to recognise microbial conserved molecular patterns . The family of Toll-like receptors (TLRs) has been shown to act as the main pattern recognition receptors for the innate immune system . Using biochemical as well as fluorescence imaging techniques, TLR2 and TLR4 were found to be recruited within microdomains upon stimulation by bacterial products . Furthermore their lateral diffusion in the cell membrane as determined by fluorescence recovery after photobleaching revealed that upon stimulation by bacterial products TLRs encounter barriers to their lateral movement, thus supporting the notion that specialised domains on the plasma membrane facilitate the innate recognition.

Environ Toxicol Chem, 2004 Mar, 23(3), 613 - 20
Glycosidation of chlorophenols by Lemna minor; Day JA et al.; Metabolic fate of xenobiotics in plant tissues has an important role in the ultimate fate of these compounds in natural and engineered systems . Chlorophenols are an important class of xenobiotics used in a variety of biocides and have been shown to be resistant to microbial degradation . Three chlorophenyl glycosides were extracted from tissues of Lemna minor exposed to 2,4-dichlorophenol (DCP) . The products were identified as 2,4-dichlorophenyl-beta-D-glucopyranoside (DCPG), 2,4-dichlorophenyl-beta-D-(6-O-malonyl)-glucopyranoside (DCPMG) and 2,4-dichlorophenyl-beta-D-glucopyranosyl-(6 --> 1)-beta-D-apiofuranoside (DCPAG) . Identification was based on reverse phase retention (C18), electrospray mass spectra collected in negative and positive mode (ESI-NEG and ESI-POS, respectively), and nuclear magnetic resonance (NMR) spectra comparisons to reference materials synthesized in the laboratory . Liquid chromatography-mass spectrometry (LC-MS) analysis of plants exposed to 2,4,5-trichlorophenol (TCP) formed analogous compounds: 2,4,5-trichlorophenyl-beta-D-glucopyranoside (TCPG), 2,4,5-trichlorophenyl-beta-D-(6-O-malonyl)-glucopyranoside (TCPMG) and 2,4,5-trichlorophenyl-beta-D-glucopyranosyl-(6 --> 1)-beta-D-apiofuranoside (TCPAG) . Enzyme catalyzed hydrolysis with beta-glucosidase was ineffective in releasing the beta-glucosides with chemical modifications at C6 . Presence of these glucoconjugates confirmed that L . minor was capable of xenobiotic uptake and transformation . Identification of these products suggested that chlorophenols were incorporated into vacuoles and cell walls of L . minor.

Nahrung, 2004 Jun, 48(3), 165 - 8
Casein gelation under simultaneous action of transglutaminase and glucono-delta-lactone; Menendez O et al.; Casein solutions (5% w/v) were treated with microbial transglutaminase (MTG) and glucono-delta-lactone (GDL) under varying conditions in order to obtain gels . Storage modulus (G') and gelation time of the gels were measured by oscillation rheometry, while protein cross-linking was determined by gel permeation chromatography . The addition of only GDL to milk resulted in very weak gels, while MTG on its own was not able to create gel networks . Simultaneous action of both ingredients led to gels, the firmness of which was linearly related to the added amount of MTG, but passed through a maximum with rising GDL concentrations . Using chromatographical analysis, increasing G' values were interrelated with the formation of MTG-induced oligomers . The gelation time was directly proportional to the GDL concentration but not influenced by the addition of MTG within the studied range of concentration.

Annu Rev Phytopathol, 2004, 42, 35 - 59
Assessment and management of soil microbial community structure for disease suppression; Mazzola M; Identification of the biological properties contributing to the function of suppressive soils is a necessary first step to the management of such systems for use in the control of soilborne diseases . The development and application of molecular methods for the characterization and monitoring of soil microbial properties will enable a more rapid and detailed assessment of the biological nature of soil suppressiveness . Although suppressive soils have provided a wealth of microbial resources that have subsequently been applied for the biological control of soilborne plant pathogens, the full functional capabilities of the phenomena have not been realized in production agricultural ecosystems . Cultural practices, such as the application of soil amendments, have the capacity to enhance disease suppression, though the biological modes of action may vary from that initially resident to the soil . Plants have a distinct impact on characteristics and activity of resident soil microbial communities, and therefore play an important role in determining the development of the disease-suppressive state . Likewise, plant genotype will modulate these same biological communities, and should be considered when developing strategies to exploit the potential of such a natural disease control system . Implementation of consistently effective practices to manage this resource in an economically and environmentally feasible manner will require more detailed investigation of these biologically complex systems and refinement of currently available methodologies.

Anal Chem, 2004 Aug 1, 76(15), 4452 - 8
Raman microscopic analysis of single microbial cells; Huang WE et al.; We demonstrate the utility of the Raman confocal microscope to generate a spectral profile from a single microbial cell and the use of this approach to differentiate bacterial species . In general, profiles from different bacterial taxa shared similar peaks, but the relative abundances of these components varied between different species . The use of multivariate methods subsequently allowed taxa discrimination . Further investigations revealed that the single-cell spectra could be used to differentiate between growth phases of a single species, but these differences did not obscure the overall interspecies discrimination . Finally, we tested the efficacy of the method as a means to identify cells responsible for the uptake of a specific substrate . A single strain was grown in media containing incrementally varying ratios of (13)C(6) to (12)C(6) glucose, and it was found that (13)C incorporation shifted characteristic peaks to lower wavenumbers . These findings suggest that Raman microscopy has significant potential for studies requiring the taxonomic identity and functioning of single microbial cells to be determined.

Am J Rhinol, 2004 May-Jun, 18(3), 151 - 6
Multi-use Venturi nasal atomizer contamination in a clinical rhinologic practice; Dubin MG et al.; INTRODUCTION: Cross-contamination of Venturi atomizers has been reported . METHODS: In phase I, 16 atomizers were sterilized and refilled with either 1% lidocaine or 0.1% Tyzine (day 0) . During phase II, atomizers were wiped with isopropyl alcohol wipes between uses . In both phases, on days 7, 14, 21, and 28, the contents of the atomizer were sprayed onto two culture media . If a culture was found positive, cultures from the nozzle, lumen, and solution were taken and cultured in depth . RESULTS: Twelve lidocaine bottles and three Tyzine bottles were initially positive . There were more positive cultures from lidocaine bottles than Tyzine bottles at 2 weeks (p = 0.02) . After wiping with isopropyl alcohol, contamination was significantly reduced in the lidocaine bottles at 2 weeks (p = 0.02) . CONCLUSION: Microbial contamination of questionable clinical significance may occur with nasal atomizers . Regardless of this significance, wiping the devices with isopropyl alcohol can eliminate microbial growth for a 2-week interval.

Prikl Biokhim Mikrobiol, 2004 May-Jun, 40(3), 366 - 9
{Effects of treatment with a composite preparation (2-chloroethylphosphonic acid and methacide) or butylated hydroxyanisole on ethylene release in apples}; Chernykh AS et al.; We studied the effect of a Russian composite preparation (2-chloroethylphosphonic acid and methacide) and butylated hydroxyanisole on ethylene release in whole fruit and peel disks of two apple cultivars, Antonovka obyknovennaya (Antonovka) and Simirenko's rennet (Simirenko) . Treatment with the composite preparation was followed by an increase in ethylene release from whole apples and peel disks . The development of microbial infection (fruit rot) in whole apples became less pronounced after the treatment . Treatment of whole apples with the antioxidant butylated hydroxyanisole (BHA) increased the intensity of ethylene release during the first subsequent days; thereafter, ethylene release decreased and was 10-15% lower than in the control on days 10-12 . In model experiments, BHA decreased ethylene release from apple peel disks below control levels as early as on day 1 after the treatment . Antonovka apples gave quick responses to the treatment . In the late-ripening Simirenko apples, the response persisted for a longer period . Our results suggest that treatment with physiologically active preparations affects ethylene release, ripening, and preservation of apples in storage.

Int J Food Microbiol, 2004 Sep 1, 95(2), 169 - 75
Predictive modelling of growth and measurement of enzymatic synthesis and activity by a cocktail of Brochothrix thermosphacta; Braun P et al.; The possibility was examined of developing a predictive model that combined microbial growth (increase in cellular number) and extracellular enzyme activity of a cocktail of three strains of Brochothrix thermosphacta . Estimations of growth and enzyme activity were made within a three-dimensional matrix of conditions: temperature 2-20 degrees C, pH value 4.0-7.5 and water activity (a(w)) 0.95-0.995 . A model which predicted growth based on increases in cell number was constructed . No extracellular lipases were detected, but slight proteolytic reactions were observed . Although it was not possible to model protease activity, the growth model and information relating to enzyme activity will be made freely available in a database on the Internet.

Clin Experiment Ophthalmol, 2004 Aug, 32(4), 349 - 53
Evaluation of surveillance methods for an epidemiological study of contact lens related microbial keratitis; Keay L et al.; PURPOSE: To evaluate surveillance methods in a pilot epidemiological study of contact lens related microbial keratitis (MK) cases identified by ophthalmic practitioners in Australia and New Zealand between May and August 2003 inclusive . METHODS: Twelve ophthalmologists and 55 optometrists from rural and metropolitan locations were sent a study information pack with postal reporting forms . After 2 months, practitioners were emailed a link to a website for Internet reporting . After 4 months, practitioners were prompted by email and then by telephone if a response was not received . Passive response rates were the rate of returns after posting information and emailing the website link . Active response rates included personalized email and telephone follow-up . RESULTS: Ten cases of MK were identified by optometrists and five by ophthalmologists . The passive response rates were 79% and 58% for the first and second reporting periods, respectively . There was a lower response rate in the second reporting period compared to the first (P = 0.02) . With active surveillance the response rate increased to 97% and 96% . A large proportion of optometrists (62%) and ophthalmologists (55%) used the website for at least one reporting period . Internet reporting was used by all New Zealand practitioners (5/5) . CONCLUSIONS: A surveillance study to estimate the incidence of contact lens related MK in Australia and New Zealand is feasible and acceptable . Internet-based reporting offers a reliable, rapid and cost-effective means of running a large scale, international surveillance study . Active surveillance methods are necessary to enhance reporting rates.

J Appl Microbiol, 2004, 97(3), 546 - 56
Assessment of the rind microbial diversity in a farmhouse-produced vs a pasteurized industrially produced soft red-smear cheese using both cultivation and rDNA-based methods; Feurer C et al.; AIMS: The diversity of the surface flora of two French red-smear soft cheeses was examined by cultivation-dependent and cultivation-independent methods to assess their composition and to evaluate the accuracy of both approaches . METHODS AND RESULTS: Culture-independent methods used involved 16S ribosomal DNA gene cloning and sequencing and single-strand conformation polymorphism analysis (SSCP) . The culture-dependent method used involved direct culture and macroscopic observation, polymerase chain reaction of the 16S rRNA gene from DNA extracted from single colonies followed by complete sequencing of the gene . Only few species were recovered by both approaches either in the pasteurized and the farmer cheese . A large diversity of isolates or 16S rDNA sequences related to marine bacteria was identified at the surface of both cheeses . CONCLUSIONS: The results indicated that all three techniques were informative and complementary to allow a more accurate representativeness of the cheese surface biodiversity . SIGNIFICANCE AND IMPACT OF THE STUDY: Cultivation and molecular methods have to be combined in order to obtain an extended view of the bacterial populations of complex ecosystems .

J Exp Med, 2004 Aug 2, 200(3), 273 - 6 Epub 2004 Jul 26.
Suppressor T cells in human diseases; Baecher-Allan C et al.; Although central and peripheral tolerance are important for the regulation of human immune responses to self- and microbial antigens, an important role of suppressor CD4(+) CD25(+) T cells is suggested from the recent investigations of human autoimmune diseases and HIV . These new data provide increasing evidence that altered function of CD4(+) CD25(+) T cells may be an important factor in a wide range of human inflammatory and infectious diseases.

J Microbiol Methods, 2004 Sep, 58(3), 297 - 302
First use of two-dimensional polyacrylamide gel electrophoresis to determine phylogenetic relationships; Dopson M et al.; Methods for microbial classification are not always capable of distinguishing between isolates at the species level . We have previously characterised four Ferroplasma isolates that were >98.9% similar at the 16S rDNA level, the isolates showed marked phenotypic differences, and one isolate was borderline on the 70% species boundary from DNA-DNA similarity data . In this study we have used statistical comparisons of two-dimensional polyacylamide gel electrophoresis gels for classification of closely related isolates . From the protein profile similarities an un-rooted tree was constructed that was congruent with a tree derived from DNA-DNA similarities.

J Med Assoc Thai, 2004 Jun, 87(6), 697 - 703
Microbial air quality in mass transport buses and work-related illness among bus drivers of Bangkok Mass Transit Authority; Luksamijarulkul P et al.; The air quality in mass transport buses, especially air-conditioned buses may affect bus drivers who work full time . Bus numbers 16, 63, 67 and 166 of the Seventh Bus Zone of Bangkok Mass Transit Authority were randomly selected to investigate for microbial air quality . Nine air-conditioned buses and 2-4 open-air buses for each number of the bus (36 air-conditioned buses and 12 open-air buses) were included . Five points of in-bus air samples in each studied bus were collected by using the Millipore A ir Tester Totally, 180 and 60 air samples collected from air-conditioned buses and open-air buses were cultured for bacterial and fungal counts . The bus drivers who drove the studied buses were interviewed towards histories of work-related illness while working . The results revealed that the mean +/- SD of bacterial counts in the studied open-air buses ranged from 358.50 +/- 146.66 CFU/m3 to 506 +/- 137.62 CFU/m3; bus number 16 had the highest level . As well as the mean +/- SD of fungal counts which ranged from 93.33 +/- 44.83 CFU/m3 to 302 +/- 294.65 CFU/m3; bus number 166 had the highest level . Whereas, the mean +/- SD of bacterial counts in the studied air-conditioned buses ranged from 115.24 +/- 136.01 CFU/m3 to 244.69 +/- 234.85 CFU/m3; bus numbers 16 and 67 had the highest level . As well as the mean +/- SD of fungal counts which rangedfrom 18.84 +/- 39.42 CFU/m3 to 96.13 +/- 234.76 CFU/m3; bus number 166 had the highest level . When 180 and 60 studied air samples were analyzed in detail, it was found that 33.33% of the air samples from open-air buses and 6.11% of air samples from air-conditioned buses had a high level of bacterial counts (> 500 CFU/m3) while 6.67% of air samples from open-air buses and 2.78% of air samples from air-conditioned buses had a high level of fungal counts (> 500 CFU/m3) . Data from the history of work-related illnesses among the studied bus drivers showed that 91.67% of open-air bus drivers and 57.28% of air-conditioned bus drivers had symptoms of work-related illnesses, p = 0.0185.

Appl Microbiol Biotechnol . 2004 Jul 20; {Epub ahead of print}
Microbial population dynamics during fed-batch operation of commercially available garbage composters; Narihiro T et al.; Microbial populations in terms of quantity, quality, and activity were monitored during 2 months of start-up operation of commercially available composters for fed-batch treatment of household biowaste . All the reactors, operated at a waste-loading rate of 0.7 kg day(-1) (wet wt), showed a mass reduction efficiency of 88-93% . The core temperature in the reactors fluctuated between 31show $132# degrees show $132#C and 58show $132# degrees show $132#C due to self-heating . The pH declined during the early stage of operation and steadied at pH 7.4-9.3 during the fully acclimated stage . The moisture content was 48-63% early in the process and 30-40% at the steady state . Both direct total counts and plate counts of bacteria increased via two phases (designated phases I, II) and reached an order of magnitude of 10(11) cells g(-1) (dry wt) at the steady state . Microbial community changes during the start-up period were studied by culture-independent quinone profiling and denatured gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA . In all the reactors, ubiquinones predominated during phase I, whereas partially saturated menaquinones became predominant during phase II . This suggested that there was a drastic population shift from ubiquinone-containing Proteobacteria to Actinobacteria during the start-up period . The DGGE analysis of the bacterial community in one of the reactors also demonstrated a drastic population shift during phase I and the predominance of members of the phyla Proteobacteria and Bacteroidetes during the overall period . But this molecular analysis failed to detect actinobacterial clones from the reactor at any stage.

Water Res, 2004 Aug-Sep, 38(14-15), 3449 - 57
Neural networks provide superior description of Giardia lamblia inactivation by free chlorine; Haas CN; Use of conventional models to describe data on microbial inactivation during disinfection suffers from limitations with respect to flexibility and direct quantitative incorporation of water quality variables . This paper develops an approach to analysis of such data using neural networks (NNs) . Using the data on free chlorine inactivation of Giardia lamblia previously reported, it was found that the use of an NN with a single hidden layer and four hidden neurons provided a superior (better) fit to the data with a reduced number of model parameters when compared to the fitting of this data using a conventional approach . Therefore, the use of NN models should be considered in the future assessment of microbial inactivation during disinfection . Incorporation of additional facets of the disinfection process, such a disinfectant decay, needs to be considered in subsequent development of this approach.

Water Res, 2004 Aug-Sep, 38(14-15), 3442 - 8
Dynamics and influencing factors of heterotrophic bacterial utilization of acetate in constructed wetlands treating woodwaste leachate; Tao W et al.; 14C-acetate was used as a tracer of substrates for heterotrophic bacteria to investigate the dynamics and influencing factors of bacterial activity in surface flow wetlands treating woodwaste leachate . Epiphytic assimilation and mineralization of acetate increased considerably over three weeks of microbial colonization . No significant longitudinal variation in acetate uptake was found . The temporal variation of bacterial activity was neither correlated to water temperature nor acetic acid concentration . Mineralization percentage varied significantly with acetate uptake rate . Acetate uptake rates of bacterioplankton (408+/-258 microg L(-1) h(-1)), epiphyton (67.7+/-41.7 mg m(-2) h(-1)) and sedimentary bacteria (26.7+/-25.6 microg g(-1) h(-1)) were influenced by the concentrations of organic substrates and inorganic nutrients . Sedimentary bacteria contributed to the majority (55-73%) of the total heterotrophic acetate uptake, while epiphytic bacteria played only a minor role (1-3%) . The acetate mineralization percentage of sediment (16%) was much lower than that of water (55%) and epiphyton (64%) . Addition of ammonium nitrate fertilizer increased acetate uptake rates significantly, especially for sediment . No remarkable changes in mineralization percentage and the relative importance of water, sediment and epiphyton were found due to fertilization.

Parasitol Today, 1994, 10(4), 154 - 7
Borrelia burgdorferi and the macrophage: Routine annihilation but occasional haven?
Montgomery RR, Malawista SE.
Borrelia burgdorferi, the agent for Lyme disease, has a typical pattern of bacterial interaction with phagocytes: attachment, stimulation o f release o f inflammatory mediators and, in most cases, ingestion and killing . Spirochetes are killed extracellulorly by antibody plus complement via the classical pathway, as well as by phagocytes through apparently nonoxidative means . Yet rare persistent spirochetes (mutants?) have been identified both in patients' tissues and in cells grown in vitro . Ruth Montgomery and Stephen Malawista here ask: are some Borrelia wolves in sheeps' clothing, evading macrophage anti-microbial action?

Parasitol Today, 1994, 10(8), 324 - 7
MVR-PCR analysis of hypervariable DNA sequence variation; Arnot DE et al.; Techniques for accurate marking of infectious microbial agents circulating in populations would be very useful to epidemiologists . In this article, David Arnot, Cally Roper and Ali Sultan review recent progress in transferring MVR-PCR DNA finger-printing techniques from human forensic medicine to parasitology.

BMC Immunol . 2004 Jul 26;5(1):15.
Age-associated alterations in CXCL1 chemokine expression by murine B cells; Hu L et al.; BACKGROUND: The CXCL1 chemokines, macrophage inflammatory protein-2 (MIP-2) and cytokine-induced neutrophil chemoattractant (KC), have been shown to play a role in a number of pathophysiological disease states including endotoxin-induced inflammation and bacterial meningitis . While the expression of these chemokines has been identified in a variety of cell types in the mouse, little is known about their expression with murine B-lymphocytes . RESULTS: Here, we demonstrate that highly purified murine splenic B cells are capable of expressing both MIP-2 and KC protein and mRNA upon activation with lipopolysaccharide (LPS) but not in response to anti-micro and anti-CD40 in combination with interleukin-4 (IL-4) stimulation . Moreover, these chemokines are expressed at higher levels in B cells derived from young (4 m) compared to old (24-29 m) mice . Upon fractionation into distinct B-cell subsets, we found that the expression of MIP-2 and KC by aged follicular (FO) B cells is significantly decreased when compared to the same cells from younger mice, while only MIP-2 production was found to be diminished in aged marginal zone (MZ) B cells . Interestingly, MIP-2 and KC production by newly formed (NF) B cells did not significantly differ with age . Moreover, the potential relevance of these findings is supported by the poor ability of LPS-activated aged B cells to specifically mediate CXCL1-dependent leukocyte recruitment when compared to younger B cells . CONCLUSION: Overall, the decreased expression of CXCL1 chemokines by aged B cells in response to LPS may have potential implications on the secondary recruitment of leukocytes to sites of microbial infections and inflammation possibly contributing to the increased susceptibility of older subjects to pathogen challenge.

J Chem Ecol, 2004 May, 30(5), 1067 - 82
Allelochemicals of Polygonella myriophylla: chemistry and soil degradation; Weidenhamer JD et al.; Gallic acid and hydroquinone have been identified as the major allelochemicals of the known allelopathic plant Polygonella myriophylla . Both of these compounds occur in the foliage as glycosides . Quercetin and rhamnetin were identified as the major flavonoid constituents, but in much lower concentration . The behavior of gallic acid, hydroquinone, the hydroquinone glycoside arbutin, and benzoquinone in sterile and nonsterile soil from beneath Polygonella was investigated . Sterilization effectively stabilized arbutin, hydroquinone, and gallic acid . Concentrations of benzoquinone rapidly diminished in sterilized soil, and the compound was almost completely gone after 7 days . In nonsterile soils, all four compounds degraded rapidly . The order of persistence was hydroquinone > benzoquinone > gallic acid > arbutin . Persistence was rate-dependent . Arbutin degraded to hydroquinone, and benzoquinone formed as a degradation product of hydroquinone . Hydroquinone was also observed as a degradation product of benzoquinone . Benzoquinone degrades rapidly by nonmicrobial oxidative processes . These results support the hypothesis that microbial and nonmicrobial oxidative transformations of soil allelochemicals are crucial in mediating the allelopathic effects of Polygonella myriophylla.

Protein Sci, 2004 Aug, 13(8), 2108 - 19
Biophysical and kinetic analysis of wild-type and site-directed mutants of the isolated and native dehydroquinate synthase domain of the AROM protein; Park A et al.; Dehydroquinate synthase (DHQS) is the N-terminal domain of the pentafunctional AROM protein that catalyses steps 2 to 7 in the shikimate pathway in microbial eukaryotes . DHQS converts 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate in a reaction that includes alcohol oxidation, phosphate beta-elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation . Kinetic analysis of the isolated DHQS domains with the AROM protein showed that for the substrate DAHP the difference in Km is less than a factor of 3, that the turnover numbers differed by 24%, and that the Km for NAD+ differs by a factor of 3 . Isothermal titration calorimetry revealed that a second (inhibitory) site for divalent metal binding has an approximately 4000-fold increase in KD compared to the catalytic binding site . Inhibitor studies have suggested the enzyme could act as a simple oxidoreductase with several of the reactions occurring spontaneously, whereas structural studies have implied that DHQS participates in all steps of the reaction . Analysis of site-directed mutants experimentally test and support this latter hypothesis . Differential scanning calorimetry, circular dichroism spectroscopy, and molecular exclusion chromatography demonstrate that the mutant DHQS retain their secondary and quaternary structures and their ligand binding capacity . R130K has a 135-fold reduction in specific activity with DAHP and a greater than 1100-fold decrease in the kcat/Km ratio, whereas R130A is inactive.

Swed Dent J, 2004, 28(2), 67 - 76
The microbial outcome observed with polymerase chain reaction in subjects with recurrent periodontal disease following local treatment with 25% metronidazole gel; Jansson H et al.; The aim of this study was to evaluate the microbial outcome in patients with recurrent periodontal disease following treatment with 25% metronidazole gel using the polymerase chain reaction (PCR) . Twenty subjects in a maintenance care program but with recurrent periodontal disease participated . Three months after scaling and root planing a total of 40 sites, 2 in each patient, with pocket probing depth of > or = 5 mm were selected . One site randomly selected was treated with 25% metronidazole gel (test) and the other site with a placebo gel (control) . A bacterial sample was collected on paperpoint from each test and control site at baseline and 12 weeks after treatment . The following pathogens were analysed and detected with PCR:Actinobacillus actinomycetemcomitans (A.a.), Porphyromonas gingivalis (P.g.) and Prevotella nigrescens (P.n.) . At baseline, A.a., P.g . and P.n . were detected in 30, 60 and 70% of all test sites and in 32, 58 and 21% of all control sites . There was a statistically significant difference between the test and control sites for P.n . at baseline . The major difference after treatment with 25% metronidazole gel was the increase of positive control sites for P.g . and P.n . However, there were no statistically significant differences in the occurrence rate of A.a., P.g . and P.n . at test and control sites after treatment . This study has shown that 25% metronidazole gel treatment did not seem to influence the microbial outcome, when PCR was used to analyse the presence/absence of A.a., P.g . and P.n . in this group of subjects with recurrent periodontal disease.

EMBO Rep, 2004 Aug, 5(8), 825 - 30 Epub 2004 Jul 23.
HMGB1 is an endogenous immune adjuvant released by necrotic cells; Rovere-Querini P et al.; Immune responses against pathogens require that microbial components promote the activation of antigen-presenting cells (APCs) . Autoimmune diseases and graft rejections occur in the absence of pathogens; in these conditions, endogenous molecules, the so-called 'innate adjuvants', activate APCs . Necrotic cells contain and release innate adjuvants; necrotic cells also release high-mobility group B1 protein (HMGB1), an abundant and conserved constituent of vertebrate nuclei . Here, we show that necrotic HMGB1(-/-) cells have a reduced ability to activate APCs, and HMGB1 blockade reduces the activation induced by necrotic wild-type cell supernatants . In vivo, HMGB1 enhances the primary antibody responses to soluble antigens and transforms poorly immunogenic apoptotic lymphoma cells into efficient vaccines.

J Inorg Biochem, 2004 Aug, 98(8), 1331 - 7
Inhibition of alcohol dehydrogenase by bismuth; Jin L et al.; Bismuth compounds have been widely used for the treatment of ulcers and Helicobacter pylori infection, and enzyme inhibition was thought to be crucial for bismuth anti-microbial activity . We have investigated the interaction of colloidal bismuth subcitrate (CBS) with alcohol dehydrogenase and our results demonstrate that bismuth can effectively inhibit the enzyme . Kinetic analysis revealed that CBS acted as a non-competitive inhibitor of yeast alcohol dehydrogenase . Both UV-vis and fluorescence data show that interaction of CBS with the enzyme exhibits biphasic processes . Bismuth can replace only half of Zn(II) from the enzyme (i.e., about one Zn(II) per monomer) . Surprisingly, binding of CBS also induces the enzyme dissociation from its native form, tetramer into dimers . The inhibition of Bi(III) on the enzyme is probably due to its direct interference with the zinc sites . This study is likely to provide an insight into the mechanism of action of bismuth drugs.

Clin Exp Immunol, 2004 Aug, 137(2), 253 - 62
DNA vaccination encoding glutamic acid decarboxylase can enhance insulitis and diabetes in correlation with a specific Th2/3 CD4 T cell response in non-obese diabetic mice; Gauvrit A et al.; DNA vaccination encoding beta cell autoantigens has been shown very recently to prevent type I diabetes in non-obese diabetic (NOD) mice . However, DNA vaccination encoding microbial or reporter antigens is known to induce specific long-lasting CD4 Th1 and strong cytolytic CD8 T cell responses . As this immune phenotype is associated strongly with beta cell destruction leading to diabetes, we have chosen to study the effects of plasmids encoding glutamic acid decarboxylase (GAD), a crucial beta cell autoantigen, in female NOD mice that developed a 'moderate' diabetes incidence . In the present study, 3-week-old female NOD mice were vaccinated twice in tibialis muscles with plasmid-DNA encoding 65-kDa GAD or betagalactosidase . In GAD-DNA immunized mice, diabetes cumulative incidence (P < 3.10(-3)) and insulitis (P < 7.10(-3)) increased significantly . Simultaneously, DNA immunization induced GAD-specific CD4 T cells secreting interleukin (IL)-4 (P < 0.05) and transforming growth factor (TGF)-beta (P = 0.03) . These cells were detected in spleen and in pancreatic lymph nodes . Furthermore, vaccination produced high amounts of Th2 cytokine-related IgG1 (P < 3.10(-3)) and TGF-beta-related IgG2b to GAD (P = 0.015) . Surprisingly, diabetes onset was correlated positively with Th2-related GAD-specific IgG1 (P < 10(-4)) and TGF-beta-related IgG2b (P < 3.10(-3)) . Moreover, pancreatic lesions resembled Th2-related allergic inflammation . These results indicate, for the first time, that GAD-DNA vaccination could increase insulitis and diabetes in NOD mice . In addition, our study suggests that Th2/3 cells may have potentiated beta cell injury.

Immunology, 2004 Aug, 112(4), 651 - 60
Enteroaggregative Escherichia coli flagellin-induced interleukin-8 secretion requires Toll-like receptor 5-dependent p38 MAP kinase activation; Khan MA et al.; Enteroaggregative Escherichia coli (EAEC) is an emerging enteric pathogen that causes acute and chronic diarrhoea in a number of clinical settings . EAEC diarrhoea involves bacterial aggregation, adherence to intestinal epithelial cells and elaboration of several toxigenic bacterial mediators . Flagellin (FliC-EAEC), a major bacterial surface protein of EAEC, causes interleukin (IL)-8 release from several epithelial cell lines . The host response to flagellins from E . coli and several other bacteria is mediated by Toll-like receptor 5 (TLR5), which signals through nuclear factor kappa B (NF-kappaB) to induce transcription of pro-inflammatory cytokines . p38 mitogen-activating protein (MAP) kinase (MAPK) is a member of a family of stress-related kinases that influences a diverse range of cellular functions including host inflammatory responses to microbial products . We studied the role of p38 MAPK in FliC-EAEC-induced IL-8 secretion from Caco-2 human intestinal epithelial cells and THP-1 human monocytic cells . We found that IL-8 secretion from both cell types is dependent on p38 MAPK, which is phospho-activated in response to FliC-EAEC . The role of TLR5 in p38 MAPK-dependent IL-8 secretion was verified in HEp-2 cells transiently transfected with a TLR5 expression construct . Activation of interleukin-1 receptor-associated kinase (IRAK) was also observed in Caco-2 and TLR5-transfected HEp-2 cells after exposure to FliC-EAEC . Finally, we demonstrated that pharmacological inhibition of p38 MAPK reduced IL-8 transcription and mRNA levels, but did not affect NF-kappaB activation . Collectively, our results suggest that TLR5 mediates p38 MAPK-dependent IL-8 secretion from epithelial and monocytic cells incubated with FliC-EAEC, and that this effect requires IL-8 promoter activation independent of NF-kappaB nuclear migration.

Biochem Soc Trans, 2004 Aug, 32(Pt 4), 629 - 32
Functional domains of HSP70 stimulate generation of cytokines and chemokines, maturation of dendritic cells and adjuvanticity; Lehner T et al.; Microbial HSP70 (heat-shock protein 70) consists of three functionally distinct domains: an N-terminal 44 kDa ATPase portion (amino acids 1-358), followed by an 18 kDa peptide-binding domain (amino acids 359-494) and a C-terminal 10 kDa fragment (amino acids 495-609) . Immunological functions of these three different domains in stimulating monocytes and dendritic cells have not been fully defined . However, the C-terminal portion (amino acids 359-610) stimulates the production of CC chemokines, IL-12 (interleukin-12), TNFalpha(tumour necrosis factor alpha), NO and maturation of dendritic cells and also functions as an adjuvant in the induction of immune responses . In contrast, the ATPase domain of microbial HSP70 mostly lacks these functions . Since the receptor for HSP70 is CD40, which with its CD40 ligand constitutes a major co-stimulatory pathway in the interaction between antigen-presenting cells and T-cells, HSP70 may function as an alternative ligand to CD40L . HSP70-CD40 interaction has been demonstrated in non-human primates to play a role in HIV infection, in protection against Mycobacterium tuberculosis and in conversion of tolerance to immunity.

Biochem Soc Trans, 2004 Aug, 32(Pt 4), 622 - 5
Peptides complexed with the protein HSP70 generate efficient human cytolytic T-lymphocyte responses; Javid B et al.; Microbial HSPs (heat-shock proteins) are implicated in the induction of the innate and adaptive arms of the immune response . We set out to determine whether peptides complexed with HSP70 generate efficient CTL (cytolytic T-lymphocyte) responses . Human dendritic cells pulsed with peptide-loaded microbial HSP70 complexes generate potent antigen-specific CTL responses . Using fluorescence anisotropy, we have calculated the peptide-binding affinity of mycobacterial HSP70 (K(D)=14 microM) and show that 120 pM HSP70-bound peptide is sufficient to generate a peptide-specific CTL response that is four orders of magnitude more efficient than the peptide alone . Through the generation of mycobacterial HSP70 truncations, we find that the minimal 136 amino acid, mycobacterial HSP70 peptide-binding domain is sufficient to generate CTL responses . The design of an HSP70 mutant, in which the peptide-binding site of HSP70 is filled with a bulky hydrophobic residue, leads to a large decrease in the peptide-binding affinity . This mutant HSP70 retains stimulatory capacity but is unable to generate CTL and has separated antigen delivery from immunostimulation of dendritic cells.

Thromb Haemost, 2004 Aug, 92(2), 288 - 97
Aberrant mucosal wound repair in the absence of secretory leukocyte protease inhibitor; Angelov N et al.; Secretory leukocyte protease inhibitor (SLPI) is a cationic serine protease inhibitor with anti-microbial and anti-inflammatory properties found in large quantities in mucosal fluids, including saliva . SLPI is expressed during cutaneous wound healing, however, its role in oral wound repair is unknown . We have used a novel approach involving a murine buccal mucosal acute wound model to investigate the role of SLPI in oral healing . In parallel to the observed cutaneous healing phenotype, an absence of SLPI results in markedly impaired oral wound healing associated with increased inflammation and raised elastase activity . Moreover, matrix deposition was decreased, while MMP activity was enhanced in the oral SLPI null wounds suggesting deregulated proteolysis . Intriguingly, regardless of genotype, reduced collagen deposition was observed in oral compared to dermal wounds, associated with reduced TGF-beta expression and decreased fibroblast collagen expression in vitro . We propose that SLPI is a pivotal endogenous factor necessary for optimal tissue repair including intra-oral wound healing . In addition, our model provides a unique opportunity to delineate the cellular and molecular mechanisms underlying the differences between dermal scarring and oral scar-free healing.

Lab Chip, 2004 Aug, 4(4), 337 - 41 Epub 2004 Apr 05.
Filter-based microfluidic device as a platform for immunofluorescent assay of microbial cells; Zhu L et al.; A filter-based microfluidic device was combined with immunofluorescent labeling as a platform to rapidly detect microbial cells . The coin-sized device consisted of micro-chambers, micro-channels and filter weirs (gap = 1-2 microm), and was demonstrated to effectively trap and concentrate microbial cells (i.e., Cryptosporidium parvum and Giardia lamblia), which were larger in size than the weir gap . After sample injection, a staining solution containing fluorescently-labeled antibodies was continuously provided into the device (flow rate = 20 microl min(-1)) to flush the microbial cells toward the weirs and to accelerate the fluorescent labeling reaction . Using a staining solution that was 10 to 100 times more dilute than the recommended concentration used in a conventional glass method, those target cells with a fluorescent signal-to-noise ratio of 12 could be microscopically observed at single-cell level within 2 to 5 min prior to secondary washing.

J Biochem (Tokyo), 2004 Jul, 136(1), 81 - 7
Protective properties of neoechinulin A against SIN-1-induced neuronal cell death; Maruyama K et al.; Peroxynitrite (ONOO-) is thought to be involved in the neurodegenerative process . To screen for neuroprotective compounds against ONOO- -induced cell death, we developed 96-well based assay procedures for measuring surviving cell numbers under oxidative stress caused by 3-(4-morpholinyl) sydnonimine hydrochloride (SIN-1), a generator of ONOO-, and sodium N,N-dietyldithiocarbamate trihydrate (DDC), an inhibitor of Cu/Zn superoxide (O2-) dismutase . Using these procedures, we obtained a microbial metabolite that rescued primary neuronal cells from SIN-1-induced damage, but not from DDC-induced damage . By NMR analysis, the compound was identified as neoechinulin A, an antioxidant compound that suppresses lipid oxidation . We found that the compound rescues neuronal cells such as primary neuronal cells and differentiated PC12 cells from damage induced by extracellular ONOO- . However, non-neuronal cells, undifferentiated PC12 cells and cells of the fibroblast cell line 3Y1 were not rescued . Neoechinulin A has scavenging, neurotrophic factor-like and anti-apoptotic activities . This compound specifically scavenges ONOO-, but not O2- or nitric oxide (NO) . Similar to known neuroprotective substances such as nerve growth factor and extracts of Gingko biloba leaves, neoechinulin A inhibits the SIN-1-induced activation of caspase-3-like proteases and increases NADH-dehydrogenase activity . These results suggest that neoechinulin A might be useful for protecting against neuronal cell death in neurodegenerative diseases.

Chemosphere, 2004 Sep, 56(10), 999 - 1009
Abiotic reductive dechlorination of chlorinated ethylenes by iron-bearing phyllosilicates; Lee W et al.; Abiotic reductive dechlorination of chlorinated ethylenes (tetrachloroethylene (PCE), trichloroethylene (TCE), cis-dichloroethylene (c-DCE), and vinylchloride (VC)) by iron-bearing phyllosilicates (biotite, vermiculite, and montmorillonite) was characterized to obtain better understanding of the behavior of these contaminants in systems undergoing remediation by natural attenuation and redox manipulation . Batch experiments were conducted to evaluate dechlorination kinetics and some experiments were conducted with addition of Fe(II) to simulate impact of microbial iron reduction . A modified Langmuir-Hinshelwood kinetic model adequately described reductive dechlorination kinetics of target organics by the iron-bearing phyllosilicates . The rate constants stayed between 0.08 (+/-10.4%) and 0.401 (+/-8.1%) day(-1) and the specific initial reductive capacity of iron-bearing phyllosilicates for chlorinated ethylenes stayed between 0.177 (+/-6.1%) and 1.06 (+/-7.1%) microM g(-1) . The rate constants for the reductive dechlorination of TCE at reactive biotite surface increased as pH (5.5-8.5) and concentration of sorbed Fe(II) (0-0.15 mM g(-1)) increased . The appropriateness of the model is supported by the fact that the rate constants were independent of solid concentration (0.0085-0.17 g g(-1)) and initial TCE concentration (0.15-0.60 mM) . Biotite had the greatest rate constant among the phyllosilicates both with and without Fe(II) addition . The rate constants were increased by a factor of 1.4-2.5 by Fe(II) addition . Between 1.8% and 36% of chlorinated ethylenes removed were partitioned to the phyllosilicates . Chloride was produced as a product of degradation and no chlorinated intermediates were observed throughout the experiment.

Cloning Stem Cells, 2004, 6(2), 172 - 7
Nutritional value of milk and meat products derived from cloning; Tome D et al.; The development and use of milk and meat products derived from cloning depends on their safety and on the nutritional advantages they can confer to the products as perceived by consumers . The development of such products thus implies (i) to demonstrate their safety and security, (ii) to show that their nutritional value is equivalent to the traditional products, and (iii) to identify the conditions under which cloning could allow additional nutritional and health benefit in comparison to traditional products for the consumers . Both milk and meat products are a source of high quality protein as determined from their protein content and essential amino acid profile . Milk is a source of calcium, phosphorus, zinc, magnesium and vitamin B2 and B12 . Meat is a source of iron, zinc and vitamin B12 . An important issue regarding the nutritional quality of meat and milk is the level and quality of fat which usually present a high content in saturated fat and some modification of the fat fraction could improve the nutritional quality of the products . The role of the dietary proteins as potential allergens has to be taken into account and an important aspect regarding this question is to evaluate whether the cloning does not produce the appearance of novel allergenic structures . The presence of bio-activities associated to specific components of milk (lactoferrin, immunoglobulins, growth factors, anti-microbial components) also represents a promising development . Preliminary results obtained in rats fed cow's milk or meat-based diets prepared from control animals or from animals derived from cloning did not show any difference between control and cloning-derived products.

Am Nat, 2004 Jun, 163(6), E126 - 35 Epub 2004 May 06.
Evolution of cross-feeding in microbial populations; Pfeiffer T; Although limited by a single resource, microbial populations that grow for long periods in continuous culture (chemostat) frequently evolve stable polymorphisms . These polymorphisms may be maintained by cross-feeding, where one strain partially degrades the primary energy resource and excretes an intermediate that is used as an energy resource by a second strain . It is unclear what selective advantage cross-feeding strains have over a single competitor that completely degrades the primary resource . Here we show that cross-feeding may evolve in microbial populations as a consequence of the following optimization principles: the rate of ATP production is maximized, the concentration of enzymes of the pathway is minimized, and the concentration of intermediates of the pathway is minimized.

J Immunol, 2004 Aug 1, 173(3), 2060 - 7
Platelet factor 4/CXCL4 induces phagocytosis and the generation of reactive oxygen metabolites in mononuclear phagocytes independently of Gi protein activation or intracellular calcium transients; Pervushina O et al.; Platelet factor 4 (PF-4), a platelet-derived CXC chemokine, is known to prevent human monocytes from apoptosis and to promote differentiation of these cells into HLA-DR(-) macrophages . In this study, we investigated the role of PF-4 in the control of acute monocyte proinflammatory responses involved in the direct combat of microbial invaders . We show that PF-4 increases monocyte phagocytosis and provokes a strong formation of oxygen radicals but lacks a chemotactic activity in these cells . Compared with FMLP, PF-4-induced oxidative burst was later in its onset but was remarkably longer in its duration (lasting for up to 60 min) . Furthermore, in PF-4-prestimulated cells, FMLP- as well as RANTES-induced burst responses became synergistically enhanced . As we could show, PF-4-mediated oxidative burst in monocytes does not involve Gi proteins, elevation of intracellular free calcium concentrations, or binding to CXCR3B, a novel PF-4 receptor recently discovered on endothelial cells . Moreover, we found that PF-4 acts on macrophages in a dual manner . On the one hand, very similar to GM-CSF or M-CSF, PF-4 treatment of monocytes generates macrophages with a high capacity for unspecific phagocytosis . On the other hand, short term priming of GM-CSF-induced human macrophages with PF-4 substantially increases their capability for particle ingestion and oxidative burst . A comparable effect was also observed in murine bone marrow-derived macrophages, indicating cross-reactivity of human PF-4 between both species . Taken together, PF-4 may play a crucial role in the induction and maintenance of an unspecific immune response.

J Immunol, 2004 Aug 1, 173(3), 1966 - 77
Characterization of a Mycobacterium tuberculosis peptide that is recognized by human CD4+ and CD8+ T cells in the context of multiple HLA alleles; Shams H et al.; The secreted Mycobacterium tuberculosis 10-kDa culture filtrate protein (CFP)10 is a potent T cell Ag that is recognized by a high percentage of persons infected with M . tuberculosis . We determined the molecular basis for this widespread recognition by identifying and characterizing a 15-mer peptide, CFP10(71-85), that elicited IFN-gamma production and CTL activity by both CD4(+) and CD8(+) T cells from persons expressing multiple MHC class II and class I molecules, respectively . CFP10(71-85) contained at least two epitopes, one of 10 aa (peptide T1) and another of 9 aa (peptide T6) . T1 was recognized by CD4(+) cells in the context of DRB1*04, DR5*0101, and DQB1*03, and by CD8(+) cells of A2(+) donors . T6 elicited responses by CD4(+) cells in the context of DRB1*04 and DQB1*03, and by CD8(+) cells of B35(+) donors . Deleting a single amino acid from the amino or carboxy terminus of either peptide markedly reduced IFN-gamma production, suggesting that they are minimal epitopes for both CD4(+) and CD8(+) cells . As far as we are aware, these are the shortest microbial peptides that have been found to elicit responses by both T cell subpopulations . The capacity of CFP10(71-85) to stimulate IFN-gamma production and CTL activity by CD4(+) and CD8(+) cells from persons expressing a spectrum of MHC molecules suggests that this peptide is an excellent candidate for inclusion in a subunit antituberculosis vaccine.

J Neuroimmunol, 2004 Aug, 153(1-2), 7 - 15
Innate immunity in the retina: Toll-like receptor (TLR) signaling in human retinal pigment epithelial cells; Kumar MV et al.; Toll-like receptors (TLRs) are crucial components of innate immunity that participate in host defense against microbial pathogens . We evaluated the expression and function of TLRs in human retinal pigment epithelial (RPE) cells . Real time PCR analysis revealed gene expression for TLRs 1-7, 9, and 10 in RPE cells . TLRs 1 and 3 were the most highly expressed TLRs . Protein expression for TLRs 2, 3, and 4 was observed on RPE cells and this expression was augmented by treatment with poly I:C or interferon-gamma (IFN-gamma) . TLR 3 is the receptor for dsRNA, an intermediate of virus replication . Because RPE cells express TLR 3 and are frequently the site of virus replication within the retina, we evaluated TLR 3 signaling . RPE cells treated with poly I:C produced IFN-beta but not IFN-alpha, and this was inhibited by the treatment of RPE cells with anti-TLR 3 antibody . Human recombinant IFN-beta was shown to be biologically active on RPE cells by inhibiting viral replication . Poly I:C treatment of RPE resulted in an increase in the production of IL-6, IL-8, MCP-1, and sICAM-1 . The presence of TLRs on RPE cells and the resultant TLR signaling in RPE cells suggest that these molecules may play an important role in innate and adaptive immune responses within the retina.

Brain Behav Immun, 2004 Sep, 18(5), 458 - 67
Acute stress effects on local Il-1beta responses to pathogens in a human in vivo model; Deinzer R et al.; The combined effects of stress and antigen on interleukin-1beta (Il-1beta) have rarely been studied locally at the site of microbial challenges in vivo, so far . We here propose a model for the analysis of such effects in humans and examine its utility for acute stress trials . Twelve students (6 male, 6 female) refrained from oral hygiene in two antagonistic quadrants for 28 days to allow for increasing bacterial stimulation of the respective gingival sites due to accumulation of microbial plaque . Good oral hygiene was maintained in the remaining quadrants . At day 27 and 28 students were subjected to either stress ('public speech') or a control condition, in a cross-over design . Samples of gingival crevicular fluid (GCF) which emerges between the tooth surface and the gingival epithelium as transudate of healthy and exudate of inflamed gingival tissue, were taken immediately after stress and 60 min later for Il-1beta analysis . Salivary cortisol was assessed to prove the validity of the stress protocol . Stress induced a profound increase of salivary cortisol (p=.001) . Repeated measures (stress x time x hygiene) ANOVA with gender as between factor revealed significant stress (p=.014) and hygiene (p=.038) effects on GCF-Il-1beta concentrations and tentatively significant hygiene x time (p = .097) and stress x time x hygiene x gender (p=.107) interactions . Stress induced an increase of Il-1beta as did plaque accumulation . The merits of the proposed model are discussed . It is concluded that it is well suited for the assessment of the effects of stress on inflammatory responses in vivo in humans.

J Struct Funct Genomics, 2004, 5(1-2), 111 - 8
Automation of protein purification for structural genomics; Kim Y et al.; A critical issue in structural genomics, and in structural biology in general, is the availability of high-quality samples . The additional challenge in structural genomics is the need to produce high numbers of proteins with low sequence similarities and poorly characterized or unknown properties . 'Structural-biology-grade' proteins must be generated in a quantity and quality suitable for structure determination experiments using X-ray crystallography or nuclear magnetic resonance (NMR) . The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples . The purification procedure must yield a homogeneous protein and must be highly reproducible in order to supply milligram quantities of protein and/or its derivative containing marker atom(s) . At the Midwest Center for Structural Genomics we have developed protocols for high-throughput protein purification . These protocols have been implemented on AKTA EXPLORER 3D and AKTA FPLC 3D workstations capable of performing multidimensional chromatography . The automated chromatography has been successfully applied to many soluble proteins of microbial origin . Various MCSG purification strategies, their implementation, and their success rates are discussed in this paper.

Eur J Obstet Gynecol Reprod Biol, 2004 Aug 10, 115(2), 159 - 60
Infectious and inflammatory mechanisms in preterm birth and cerebral palsy; Jacobsson B; OBJECTIVE: In a thesis examine infectious and inflammatory mechanisms involved in preterm birth and cerebral palsy . STUDY DESIGN: Four cross-sectional studies and a case control study . RESULTS: Microbial invasion of the amniotic cavity and inflammation in this population of Swedish women in preterm labor and preterm prelabor rupture of membranes was similar to that reported in data from populations with a higher incidence of preterm birth . Our data support an association between antenatal infection/inflammation and cerebral palsy . CONCLUSIONS: Infectious and inflammatory mechanisms are involved in preterm birth and cerebral palsy in a population with low incidence of preterm birth.

J Chromatogr B Analyt Technol Biomed Life Sci, 2004 Sep 5, 808(2), 249 - 54
Characterization of spirochetal isolates from arthropods collected in South Moravia, Czech Republic, using fatty acid methyl esters analysis; Cechova L et al.; Aim of this study was to evaluate cellular fatty acid analysis for characterization of spirochetes . Strains were isolated from arthropods collected in South Moravia, Czech Republic . Fatty acid methyl esters (FAME) profile was determined for five Borrelia burgdorferi sensu lato (s.l.) strains isolated from Ixodes ricinus ticks, one "Spironema culicis" strain recovered from mosquito Culex pipiens and seven spirochetal strains (not identified yet) isolated from mosquitoes and blackflies . Analysis was performed using a gas chromatography column in conjunction with Microbial Identification System Sherlock (MIDI Inc., Newark, DE, USA) . Results obtained on the basis of cluster analysis of FAME profiles showed, that the B . burgdorferi sensu lato isolates could be well separated from other spirochetal isolates . We recommended method used in this study as a useful tool for preliminary identification of spirochetes isolated from ticks and dipterans.

Rheum Dis Clin North Am, 2004 Aug, 30(3), 559 - 74, ix
The stimulation of Toll-like receptors by nuclear antigens: a link between apoptosis and autoimmunity; Marshak-Rothstein A et al.; As immunologists have long understood, effective responses to foreign antigens require adjuvants . It is now apparent that the initiation of autoimmune disease is comparably facilitated by adjuvant activity . In the case of antinuclear antibodies, it seems that DNA itself can serve as an endogenous adjuvant . Similar to many of the microbial adjuvants, mammalian DNA mediates its effect through a Toll-like receptor--in this case, TLR9.

J Steroid Biochem Mol Biol, 2004 Jun, 91(1-2), 87 - 98
Novel cytotoxic bufadienolides derived from bufalin by microbial hydroxylation and their structure-activity relationships; Ye M et al.; Microbial transformation was used to prepare novel cytotoxic bufadienolides . Twelve products (3-14) were obtained from bufalin (1) by the fungus Mucor spinosus . Their structures were elucidated by high-resolution mass spectroscopy (HR-MS) and extensive NMR techniques, including 1H NMR, 13C NMR, DEPT, 1H-1H correlation spectroscopy (COSY), two dimensional nuclear Overhauser effect correlation spectroscopy (NOESY), heteronuclear multiple quantum coherence (HMQC), and heteronuclear multiple bond coherence (HMBC) . Compounds 3, 4, 9 and 11-14 are new mono- or dihydroxylated derivatives of bufalin with novel oxyfunctionalities at C-1beta, C-7beta, C-11beta, C-12beta and C-16alpha positions . The in vitro cytotoxic activities against human cancer cell lines of 3-14, together with 16 biotransformed products derived from cinobufagin (15-30) were determined by the MTT method, and their structure-activity relationships (SAR) were discussed.

Biochemistry, 2004 Jul 27, 43(29), 9361 - 71
Solution NMR structure and X-ray absorption analysis of the C-terminal zinc-binding domain of the SecA ATPase; Dempsey BR et al.; The solution NMR structure of a 22-residue Zn(2+)-binding domain (ZBD) from Esherichia coli preprotein translocase subunit SecA is presented . In conjunction with X-ray absorption analysis, the NMR structure shows that three cysteines and a histidine in the sequence CXCXSGX(8)CH assume a tetrahedral arrangement around the Zn(2+) atom, with an average Zn(2+)-S bond distance of 2.30 A and a Zn(2+)-N bond distance of 2.03 A . The NMR structure shows that ND1 of His20 binds to the Zn(2+) atom . The ND1-Zn(2+) bond is somewhat strained: it makes an angle of approximately 17 degrees with the plane of the ring, and it also shows a significant "in-plane" distortion of 13 degrees . A comprehensive sequence alignment of the SecA-ZBD from many different organisms shows that, along with the four Zn(2+) ligands, there is a serine residue (Ser12) that is completely conserved . The NMR structure indicates that the side chain of this serine residue forms a strong hydrogen bond with the thiolate of the third cysteine residue (Cys19); therefore, the conserved serine appears to have a critical role in the structure . SecB, an export-specific chaperone, is the only known binding partner for the SecA-ZBD . A phylogenetic analysis using 86 microbial genomes shows that 59 of the organisms carry SecA with a ZBD, but only 31 of these organisms also possess a gene for SecB, indicating that there may be uncharacterized binding partners for the SecA-ZBD.

Pest Manag Sci, 2004 Jul, 60(7), 703 - 9
Tebuconazole dissipation and metabolism in Tifton loamy sand during laboratory incubationt; Strickland TC et al.; The fungicide tebuconazole is widely used to control soil-borne and foliar diseases in peanuts and other crops . No published data are currently available on the extent and rate at which this compound degrades in soil . Unpublished data summarized in registration documents suggest that the compound is persistent, with 300-600 days half-life . We conducted a 63-day laboratory incubation to evaluate tebuconazole's dissipation kinetics and impact on soil microbial activity in Tifton loamy sand . Tifton soils support extensive peanut production in the Atlantic Coastal Plain region of Georgia and Alabama . Products containing tebuconazole are applied to an estimated 50% of the peanut acreage in the region . At the end of the incubation, 43 (+/-42)% of the parent compound was recovered in soil extracts . The first-order kinetic model, which gave a good fit to the dissipation data (r2 = 0.857), yielded a soil half-life (t1/2) of 49 days . This is 6-12 times more rapid than t1/2 values described in unpublished tebuconazole registration documents . Four degradates were identified . Tentative structural assignments indicated that degradates were derived from hydroxylation of the parent compound and/or chlorophenyl ring cleavage . Cleavage products showed a steady increase during the incubation, and on a molar basis were equal to 63% of the time zero tebuconazole concentration . No significant effect on soil microbial biomass was observed, indicating that when the compound is applied at normal agronomic rate it does not impact soil metabolic activity . Use of the soil-half life data derived in this study should improve the accuracy oftebuconazole fate assessments for Coastal Plain peanut production . The study also indicated that environmental assessment of selected degradates may be needed to fully evaluate risks of tebuconazole use.

Pest Manag Sci, 2004 Jul, 60(7), 645 - 54
Degradation and leaching potential of pesticides in biobed systems; Fogg P et al.; Biobeds provide a potential solution to pesticide contamination of surface waters arising from the farmyard . Previous work has shown that biobeds can effectively treat spills and splashes of pesticide . This study investigated the potential for biobeds to treat much larger volumes and amounts of pesticide waste not only arising from spills but also from washing processes . Two systems were assessed using a range of pesticides at the semi-field scale, ie a lined biobed system and an unlined system . Studies using the lined biobeds demonstrated that water management was crucial, with biobeds needing to be covered to exclude rain-water . Once covered, the top of the biobed became hydrophobic, restricting moisture loss and resulting in saturated conditions at depth . The drying out of the top layer coincided with a measured decrease in microbial biomass in the treated biobeds . Applied pesticides were effectively retained within the 0-5 cm layer . Whilst all pesticides tested degraded, low moisture content and microbial activity meant degradation rates were low . Studies using unlined biobeds showed that only the most mobile pesticides leached, and for these > 99% was removed by the system, with a significant proportion degraded within 9 months . Peak concentrations of the two most mobile pesticides did however exceeded the limits that are likely to be required by regulatory bodies . However, it is thought that these limits could be reached by optimisation of the system.

Water Sci Technol, 2004, 49(10), 251 - 8
Sustainable sludge management in developing countries; Jimenez B et al.; Worldwide, unsanitary conditions are responsible for more than three million deaths annually . One of the reasons is the low level of sanitation in developing countries . Particularly, sludge from these regions has a high parasite concentration and low heavy metal content even though the available information is limited . Different issues needed to achieve a sustainable sludge management in developing nations are analysed . Based on this analysis some conclusions arise: sludge management plays an important role in sanitation programs by helping reduce health problems and associated risks; investments in sanitation should consider sludge management within the overall projects; the main restriction for reusing sludge is the high microbial concentration, which requires a science-based decision on the treatment process, while heavy metals are generally low; adequate sludge management needs the commitment of those sectors involved in the development and enforcement of the regulations as well as those that are directly related to its generation, treatment, reuse or disposal; current regulations have followed different approaches, based mainly on local conditions, but they favour sludge reuse to fight problems like soil degradation, reduced crop production, and the increased use of inorganic fertilizers . This paper summarises an overview of these issues.

Dig Dis Sci, 2004 May, 49(5), 878 - 82
Comparative studies of superoxide production by microbial wall product-primed neutrophils in ulcerative colitis; Nielsen SE et al.; A diminished tolerance to the normal gut bacterial flora has been suggested to be pathogenic in ulcerative colitis (UC) and the aim of this study was to evaluate the priming effect of selected bacterial wall products on UC neutrophil granulocytes . Neutrophils from 10 UC patients and 10 healthy controls were primed with bacterial lipoprotein (BLP) or lipopolysaccharide (LPS) and subsequently activated . Extracellular superoxide production was measured by the cytochrome c reduction assay . Priming neutrophils with BLP or LPS dose dependently increased the superoxide production in both UC and controls (P < 0.01), and BLP was more potent than LPS (P < 0.05) . No differences were found between UC and controls . UC neutrophils do not seem to have an intrinsic abnormality with reduced tolerance to bacterial substances . However, bacterial wall products such as BLP modify neutrophil tissue-destruction mechanisms and might be pivotal for perpetuation of chronic colonic inflammation.

Microb Ecol, 2004 Jan, 47(1), 104 - 13
The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil; Griffiths BS et al.; Soil collected from an upland pasture was manipulated experimentally in ways shown previously to alter microbial community structure . One set of soil was subjected to chloroform fumigation for 0, 0.5, 2, or 24 h and the other was sterilised by gamma-irradiation and inoculated with a 10(-2), 10(-4), 10(-6), or 10(-8) dilution of a soil suspension prepared from unsterilized soil . Following incubation for 8 months, to allow for the stabilization of microbial biomass and activity, the resulting microbial community structure (determined by PCR-DGGE of bacterial specific amplification products of total soil DNA) was assessed . In addition, the functional stability (defined here as the resistance and resilience of short-term decomposition of plant residues to a transient heat or a persistent copper perturbation) was determined . Changes in the active bacterial population following perturbation (determined by RT-PCR-DGGE of total soil RNA) were also monitored . The manipulations resulted in distinct shifts in microbial community structure as shown by PCR-DGGE profiles, but no significant decreases in the number of bands . These shifts in microbial community structure were associated with a reduction in functional stability . The clear correlation between altered microbial community structure and functional stability observed in this upland pasture soil was not evident when the same protocols were applied to soils in other studies . RT-PCR-DGGE profiles only detected a shift in the active bacterial population following heat, but not copper, perturbation . We conclude that the functional stability of decomposition is related to specific components of the microbial community.

Microb Ecol, 2004 Jan, 47(1), 59 - 67
Archaeal community structure and pathway of methane formation on rice roots; Chin KJ et al.; The community structure of methanogenic Archaea on anoxically incubated rice roots was investigated by amplification, sequencing, and phylogenetic analysis of 16S rRNA and methyl-coenzyme M reductase (mcrA) genes . Both genes demonstrated the presence of Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Rice cluster I, an uncultured methanogenic lineage . The pathway of CH4 formation was determined from the 13C-isotopic signatures of the produced CH4, CO2 and acetate . Conditions and duration of incubation clearly affected the methanogenic community structure and the pathway of CH4 formation . Methane was initially produced from reduction of CO2 exclusively, resulting in accumulation of millimolar concentrations of acetate . Simultaneously, the relative abundance of the acetoclastic methanogens (Methanosarcinaceae, Methanosaetaceae), as determined by T-RFLP analysis of 16S rRNA genes, was low during the initial phase of CH4 production . Later on, however, acetate was converted to CH4 so that about 40% of the produced CH4 originated from acetate . Most striking was the observed relative increase of a population of Methanosarcina spp . (but not of Methanosaeta spp.) briefly before acetate concentrations started to decrease . Both acetoclastic methanogenesis and Methanosarcina populations were suppressed by high phosphate concentrations, as observed under application of different buffer systems . Our results demonstrate the parallel change of microbial community structure and function in a complex environment, i.e., the increase of acetoclastic Methanosarcina spp . when high acetate concentrations become available.

Microb Ecol, 2004 Jan, 47(1), 9 - 17
Abundance, distribution, and diversity of viruses in alkaline, hypersaline Mono Lake, California; Jiang S et al.; Mono Lake is a large (180 km2), alkaline (pH approximately 10), moderately hypersaline (70-85 g kg(-1)) lake lying at the western edge of the Great Basin . An episode of persistent chemical stratification (meromixis) was initiated in 1995 and has resulted in depletion of oxygen and accumulation of ammonia and sulfide beneath the chemocline . Although previous studies have documented high bacterial abundances and marked seasonal changes in phytoplankton abundance and community composition, there have been no previous reports on the occurrence of viruses in this unique lake . Based on the high concentrations and diversity of microbial life in this lake, we hypothesized that planktonic viruses are also abundant and diverse . To examine the abundance and distribution of viruses and bacteria, water samples were collected from four stations along 5 to 15 vertical depths at each station . Viral abundance ranged from 1 x 10(8) to 1 x 10(9) mL(-1), among the highest observed in any natural aquatic system examined so far . Increases (p < 0.1) in viral densities were observed in the anoxic bottom water at multiple stations . However, regression analysis indicated that viral abundance could not be predicted by any single environmental parameter . Pulsed field gel electrophoresis revealed a diverse viral community in Mono Lake with genome sizes ranging from approximately 14 to >400 kb with most of the DNA in the 30 to 60 kb size range . Cluster analysis grouped the anoxic bottom-water viral community into a unique cluster differentiating it from surface and mid-water viral communities . A hybridization study using an indigenous viral isolate as a probe revealed an episodic pattern of temporal phage distribution with strong niche stratification between oxic and anoxic waters.

Microb Ecol, 2004 Jan, 47(1), 1 - 8
Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste; Stopar D et al.; Epifluorescence microscopy and transmission electron microscopy were applied to study virioplankton community in the Gulf of Trieste (northern Adriatic Sea) . The total viral abundance was in a range between 2.5 x 10(9)/L and 2.9 x 10(10)/L and was positively correlated with trophic status of the environment . Viruslike particles were significantly correlated with bacterial abundance in all samples studied . Correlations with other physicochemical or biological parameters were not significant . The data suggest that, because of the substantial fraction of tailed viruses present (26%), bacteriophages are an important component of the virioplankton community in the Gulf of Trieste . The abundance of viruslike particles in the seawater changed at hour intervals in a range from 1.3 x 10(9)/L to 5.1 x 10(9)/L . A significant fraction (71%) of the bacterial isolates was inducible in vitro by mitomycin C, and a high occurrence (51%) of lysogenic isolates with more than one phage morphotype present in the lysate was detected . The presence of lysogenic bacteria in the seawater was confirmed in situ with a mitomycin C induction experiment on the natural bacterial population . Results suggest that virioplankton is an abundant component of the microbial community in the Gulf of Trieste.

J Dairy Sci, 2004 Apr, 87(4), 797 - 809
Invited review: formation of keratins in the bovine claw: roles of hormones, minerals, and vitamins in functional claw integrity; Tomlinson DJ et al.; Keratins are the characteristic structural proteins of the highly cornified epidermis of the skin, feathers, and hoof . Keratin proteins provide the structural basis for the unique properties of the biomaterial horn and its protective function against a wide range of environmental factors . Hoof horn is produced through a complex process of differentiation (keratinization) of epidermal cells . Formation and biochemical binding of keratin proteins and synthesis and exocytosis of intercellular cementing substance (ICS) are the hallmarks of keratinization . It is finalized by the programmed death of the living epidermal cells, i.e., cornification, that turns the living epidermal cells into dead horn cells . The latter become connected by the intercellular cementing substance . The functional integrity of hoof horn essentially depends on a proper differentiation, i.e., keratinization of hoof epidermal cells . Keratinization of hoof epidermis is controlled and modulated by a variety of bioactive molecules and hormones . This process is dependent on an appropriate supply of nutrients, including vitamins, minerals, and trace elements . Regulation and control of differentiation and nutrient flow to the epidermal cells play a central role in determining the quality and, consequently, the functional integrity of hoof horn . Decreasing nutrient supply to keratinizing epidermal cells leads to horn production of inferior quality and increased susceptibility to chemical, physical, or microbial damage from the environment . A growing body of evidence suggests that hormones, vitamins, minerals, and trace elements play critical roles in the normal development of claw horn and correct keratin formation.

J Dairy Sci, 2004 Apr, 87(4), 777 - 84
ADSA Foundation Scholar Award: defining dairy flavors; Drake M; Production and consumption of dairy foods continue to increase annually . Further, new ingredient applications for dairy foods continue to expand . With continued production and consumption, there is also increased competition . Increased competition exists regionally, nationally, and globally . Processors as well as product developers must find ways to maximize existing markets and expand into new markets . A consistent high quality product is necessary to maintain competitiveness . Although microbial safety and stability are key ways to define quality, flavor is one method of defining quality that is often assumed or overlooked . The aggressive and competitive nature of today's market demands more precise and powerful tools for defining flavor and flavor quality . Traditional as well as more recent methods for evaluating dairy flavor are reviewed . The application of defining sensory flavors to fundamental research on flavor chemistry, product understanding, and effective marketing is addressed.

Eur J Immunol, 2004 Aug, 34(8), 2286 - 92
IL-8 induces a specific transcriptional profile in human neutrophils: synergism with LPS for IL-1 production; Martinez FO et al.; IL-8 is an inflammatory CXC chemokine involved in neutrophil recruitment and activation in various inflammatory conditions . The transcriptional profile induced by IL-8 in human neutrophils was analyzed using high-density oligonucleotide arrays and compared with that of the prototypic phagocyte activator LPS . As expected, LPS induced a major effect on the cell transcriptome, upregulating 116 (0.93%) and downregulating 70 (0.56%) of the transcripts . IL-8 induced a less profound modulation of the cell transcriptome, with upregulation of 30 (0.25%) and downregulation of 6 (0.04%) of the transcripts . Although the two proinflammatory mediators induced partially overlapping transcriptional profiles (50.0% of IL-8-responsive genes were concordantly regulated by LPS), IL-8 also modulated a significant number of genes unresponsive to LPS, including soluble mediators, membrane receptors, signaling molecules, and regulators of transcription and translation . A set of IL-8-inducible genes was related to cell motility, possibly a strategy to prepare for migration into tissues . Analysis of the IL-8-responsive gene IL-1beta at the protein level revealed that transcript induction was not followed by protein production . Neutrophils stimulated with IL-8, however, showed a significant increase in IL-1beta secretion after subsequent exposure to LPS . Thus, the effect of IL-8 at the transcriptional level could provide a synergistic effect with microbial products for neutrophil activation.

J Histochem Cytochem, 2004 Aug, 52(8), 1107 - 12
Immunohistochemical demonstration of carbonic anhydrase isoenzyme VI (CA VI) expression in rat lower airways and lung; Leinonen JS et al.; Carbonic anhydrase isoenzyme VI (CA VI), which is transported in high concentrations in saliva and milk into the alimentary tract, is an important element of mucosal protection in the upper alimentary tract . Like alimentary tract mucosa, the respiratory tract mucosa is also exposed to heavy microbial, physical, and chemical stress . The protective and renewal-promoting factors present in the surface mucus of the respiratory tract are mainly produced by the seromucous tracheobronchial glands . Here we studied the secretion of CA VI by these glands in adult and developing rats using immunohistochemical techniques . The serous acinar and duct cells of the tracheobronchial glands stained for CA VI . The presence of the enzyme also in the duct content indicates its active secretion into the surface mucus . CA VI was also visible in the secretory cells and at the base of the ciliated cells of the tracheobronchial surface epithelium . Moreover, the Clara cells of the bronchiolar surface epithelium stained for CA VI . These findings are consistent with the hypothesis that CA VI has a mucosa-protective role not only in the gastrointestinal tract but also in the respiratory tract, where CA VI may act as a pivotal pH neutralizer and growth factor.

Cornea, 2004 Aug, 23(6), 632 - 4
Congenital alacrima in Pierre Robin sequence; Arya SK et al.; PURPOSE: To report the presence of congenital alacrima in a patient with Pierre Robin (PR) sequence . METHODS: A 6-month-old child with diagnosed PR sequence presented to us with dysfunctional lacrimation present since birth . The child subsequently developed bilateral corneal ulcers . This unusual presentation and its management are described in detail, and other ocular associations of the PR sequence are discussed . RESULTS: Continuous tear supplementation and appropriate treatment with antibiotics controlled the microbial infection . However, the long-term prognosis for visual rehabilitation remained poor in this patient because of the presence of central corneal opacities, persistent dry eye, which would preclude future optical keratoplasty, and possible sensory deprivation amblyopia . CONCLUSIONS: Alacrima can cause significant ocular morbidity, because persistent ocular surface dryness can be very difficult to manage . Lifelong tear supplementation may be necessary . The association or coexistence of congenital alacrima and the Pierre Robin sequence has not been described before this report.

Cell Tissue Bank, 2000, 1(1), 45 - 53
Fetal tissue banking for transplantation: characteristics of the donor population and considerations for donor and tissue screening; Newman-Gage H et al.; We initiated this study to evaluate the suitability for therapeutic use in transplantation of tissues obtained from human abortuses . We have developed protocols for the collection, handling and preservation of hepatic stem cells from electively aborted embryos and have developed methods for assessment of the cells so derived and processed . In this paper we present our findings regarding screening of potential donors, acquisition of fetal tissues, and assessment of the tissues for potentially infectious contaminants . We assess the suitability of the tissue donors according to current standards used for donors of commonly transplanted tissues (e.g., bone grafts, skin grafts and heart valves) and present data regarding the real availability of tissues from elective abortion procedures that would meet those standard tissue banking criteria.We specifically evaluated the donor's willingness to provide a blood sample for testing, conducted a detailed interview similar to those used for typical organ and tissue donors, and assessed the type and incidence of contamination in collected tissues . We find that although many women are willing to consent to use of the tissues for transplantation, attrition from the study for various reasons results in few fetal organs ultimately realistically available for transplantation . Typical reasons for attrition include: unwillingness to have a blood sample drawn or tested, positive serology results, social/medical high risk factors for acquisition of transmissible disease, no identifiable organs available, and unacceptable microbial contamination . Thus, although it might seem that due to the numbers of abortions performed annually, that there would be substantial numbers of suitable tissues available, only a small proportion are truly suitable for transplantation.

Cell Tissue Bank, 2004, 5(1), 37 - 44
The measurement of water activity in allogeneic skin grafts preserved using high concentration glycerol or propylene glycol; Ross A et al.; In the presence of free water, many degradation reactions can occur within stored tissues including enzymatic digestion, oxidation (peroxidation) and hydrolytic reactions, as well as the detrimental effects of microbial growth, therefore most long-term banking techniques are designed to avoid free water . One method currently used for banking of skin grafts is the use of high concentration (85%) glycerol as a preservative . In this case, the glycerol was assumed to dehydrate the skin by osmosis and diffusion out of the cells and skin matrix respectively . We have recently shown that this assumption is incorrect and the converse occurs, i.e . glycerol enters the skin and sequesters the water . It was therefore essential to determine whether enough water had been immobilised to prevent degradation of the tissue . Using an instrument (Pawkit) designed to measure water activity (aw) it was shown that a stepwise reduction in aw was achieved when the skin was immersed in 50 and 85% glycerol or propylene glycol, respectively . At the end of the glycerolisation process, the final aw was shown to be circa 0.3 . An aw of 0.3 is known to minimise lipid peroxidation and reduce other degradation reaction rates to very low levels . It was concluded that the current glycerolisation protocol results in effective sequestration of water avoiding degradation of the skin during storage . The method presented should be used as a quality control step to confirm adequacy of preservation for each batch of glycerolised skin.

Cell Tissue Bank, 2004, 5(1), 3 - 21
Banking of non-viable skin allografts using high concentrations of glycerol or propylene glycol; Huang Q et al.; The aims of this study were to investigate the kinetics of the current glycerol banking method for the preservation of non-viable skin allografts; to improve it with respect to efficiency and microbial safety; and to investigate the possibility of using propylene glycol in place of glycerol to provide a more rapid process . Skin grafts were preserved in 98% v/v glycerol (GLY) according to the method used in the Sheffield Skin Bank . During the addition and removal processes, the amounts of GLY and water in the skin were determined using the Karl Fischer method and HPLC respectively . Propylene glycol (PG) was investigated as an alternative to glycerol with the object of shortening the process . To avoid the need for prolonged storage in glycerol to disinfect the tissue, and to improve the effectiveness of disinfection, exposure to peracetic acid (PAA) was included and its influence on the kinetics of the preservation process was evaluated . The histological and ultrastructural appearances of skin that had been banked by these methods was also investigated . It was found that the permeation of GLY in skin probably involves two processes: diffusion and binding; the rate of transport was attenuated as the GLY concentration in the skin increased . The current incubation time could be shortened, but an inconveniently prolonged washout process was required . The substitution of PG for GLY accelerated the whole process, particularly the removal process, making the method more convenient for the emergency use of skin grafts in the clinic . The penetration of PG also involved diffusion and binding, but there was no attenuation of transport as the concentration increased . The addition of PAA sterilisation did not alter the transport of GLY or PG . Structural integrity was also maintained with the new banking treatments . An improved banking method can now be proposed; it can be completed in only one working day and the risk of disease transmission is reduced.

Proc Natl Acad Sci U S A, 2004 Jul 27, 101(30), 10990 - 4 Epub 2004 Jul 15.
Integration of Caenorhabditis elegans MAPK pathways mediating immunity and stress resistance by MEK-1 MAPK kinase and VHP-1 MAPK phosphatase; Kim DH et al.; The p38 and JNK classes of mitogen-activated protein kinases (MAPKs) have evolutionarily conserved roles in the control of cellular responses to microbial and abiotic stresses . The mechanisms by which crosstalk between distinct p38 and c-Jun N-terminal kinase (JNK) MAPK pathways occurs with resultant integration of signaling information have been difficult to establish, particularly in the context of whole organism physiology . In Caenorhabditis elegans a PMK-1 p38 MAPK pathway is required for resistance to bacterial infection, and a KGB-1 JNK-like MAPK pathway has recently been shown to mediate resistance to heavy metal stress . Here, we show that two components of the KGB-1 pathway, MEK-1 MAPK kinase (MAPKK), a homolog of mammalian MKK7, and VHP-1 MAPK phosphatase (MKP), a homolog of mammalian MKP7, also regulate pathogen resistance through the modulation of PMK-1 activity . The regulation of p38 and JNK-like MAPK pathways mediating immunity and heavy metal stress by common MAPKK and MKP signaling components suggests pivotal roles for MEK-1 and VHP-1 in the integration of diverse stress signals contributing to pathogen resistance in C . elegans . In addition, these data point to mechanisms in multicellular organisms by which signals transduced by distinct MAPK pathways may be subject to physiological integration at the level of regulation of MAPK activity by MAPKKs and MKPs.

Bioinformatics, 2004 Dec 12, 20(18), 3682 - 6 Epub 2004 Jul 15.
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data; Hallin PF et al.; SUMMARY: Currently, new bacterial genomes are being published on a monthly basis . With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis . More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists . In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics . DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page . Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout . Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes . Currently, these results counts to more than 220 pieces of information . The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content . The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center . This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues . AVAILABILITY: A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via SUPPLEMENTARY INFORMATION: This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase.

Am J Physiol Heart Circ Physiol, 2004 Nov, 287(5), H2241 - 51 Epub 2004 Jul 15.
Selective decontamination of the digestive tract attenuated the myocardial inflammation and dysfunction that occur with burn injury; Horton JW et al.; This study examined the effects of oral antibiotics to selectively decontaminate the digestive tract (SDD) on postburn myocardial signaling, inflammation, and function . We hypothesized that antibiotic therapy to eliminate pathogens from the gastrointestinal (GI) tract would reduce myocardial inflammatory responses and improve postburn myocardial performance . Sprague-Dawley rats received polymyxin E (15 mg), tobramycin (6 mg), and 5-flucytosin (100 mg) by oral gavage twice daily for 3 days preburn and 24 h postburn . Experimental groups included 1) sham burn given vehicle (3 ml water), 2) sham plus SDD, 3) burn over 40% total body surface area (TBSA) plus SDD, and 4) burn over 40% TBSA given vehicle . All burns received lactated Ringer solution (4 mg.kg(-1).%burn(-1)); myocardial signaling (PKCepsilon/p38 MAPK/NF-kappaB) was studied 2, 4, and 24 h postburn; and cytokine secretion (systemic and myocyte secreted cytokines, ELISA) and cardiac function were examined 24 h postburn . Vehicle-treated burn injury increased myocardial PKCepsilon/p38 MAPK expression, promoted NF-kappaB nuclear translocation, promoted TNF-alpha, IL-1beta, IL-6, and IL-10 secretion, and impaired myocardial function . SDD attenuated burn-related proinflammatory myocardial signaling, cytokine secretion, and myocardial contractile defects . Our data suggest that burn-related loss of GI barrier function and translocation of microbial products serve as upstream mediators of postburn myocardial inflammatory signaling and dysfunction.

Metab Eng, 2004 Jul, 6(3), 220 - 8
Inverse metabolic engineering with phosphagen kinase systems improves the cellular energy state; Sauer U et al.; Inverse metabolic engineering attempts to identify or construct desired phenotypes of applied interest to endow them on appropriate host organisms . A particular desirable phenotype is the ATP homeostasis exhibited by animal cells with high and variable ATP turnover through temporal and spatial energy buffering . This buffering is achieved by phosphagen kinase systems that consist of a specific kinase and its cognate phosphagen, which functions as a large pool of 'high-energy phosphates' that are used to replenish ATP during periods of high energetic demand . This review discusses recent advances and potentials of inverse metabolic engineering of cell types that do not normally contain such systems--bacteria, yeast, plants, and liver--with creatine or arginine kinase systems . Examples are discussed that illustrate how microbial metabolism can be tailored for large-scale industrial processes with imperfect mixing and how the liver can be protected from metabolic insults or stimulated for better regeneration.

Metab Eng, 2004 Jul, 6(3), 197 - 203
Amino acid stabilization for cell-free protein synthesis by modification of the Escherichia coli genome; Michel-Reydellet N et al.; Cell-free biology provides a unique opportunity to assess and to manipulate microbial systems by inverse metabolic engineering . We have applied this approach to amino acid metabolism, one of the systems in cell-free biology that limits protein synthesis reactions . Four amino acids (arginine, tryptophan, serine and cysteine) are depleted during a 3-h batch cell-free protein synthesis reaction under various conditions . By modifying the genome of the Escherichia coli strain used to make the cell extract, we see significant stabilization of arginine, tryptophan and serine . Cysteine, however, continues to be degraded . Cell-free protein synthesis with the modified cell extract produces increased yields of the cysteine-free protein Outer Membrane Protein T (OmpT).

Eur J Neurosci, 2004 Aug, 20(3), 658 - 70
Anatomical and functional evidence for a role of arginine-vasopressin (AVP) in rat olfactory epithelium cells; Levasseur G et al.; The olfactory epithelium (OE) is composed of olfactory sensory neurons (OSNs) and sustentacular cells; it lies in the nasal cavity where it is protected by a thin mucus layer . The finely regulated composition of this mucus provides OSN with a suitable ionic environment . To maintain the functional integrity of the epithelium despite permanent physical, chemical and microbial aggressions, both OSNs and surrounding sustentacular cells are continuously renewed from globose basal cells . Moreover, the sense of smell is involved in so numerous behaviours (feeding, reproduction, etc.) that it has to cross-talk with the endocrine and neuroendocrine systems . Thus, besides its sensory function, the olfactory epithelium is thought to undergo a lot of complex regulatory processes . We therefore studied the effects of various neuropeptides on primary cultures of Sprague-Dawley rat olfactory epithelium cells . We found that arginine-vasopressin (AVP) triggered a robust, dose-dependent calcium increase in these cells . The cell response was essentially ascribed to the V1a AVP receptor, whose presence was confirmed by RT-PCR and immunolabelling . In the culture, V1a but not V1b receptors were present, mainly localized in neurons . In the epithelium, both subtypes were found differentially distributed . V1a-R were localized mainly in globose basal cells and at the apical side of the epithelium, in the area of the dendritic knobs of OSNs . V1b-R were strongly associated with Bowman's gland cells and globose basal cells . These localizations suggested potential multifaceted roles of a hormone, AVP, in the olfactory epithelium.

J Indian Soc Pedod Prev Dent, 2004 Mar, 22(1), 33 - 5
A comparative evaluation of an ultrasonic and a manual toothbrush on the oral hygiene status and stain removing efficacy; Vandana KL et al.; The efficacy of ultrasonic toothbrush and a manual toothbrush was compared on the oral hygiene status and on microbial parameters . 26 dental students from the College of Dental Sciences Davangere, Karnataka, were selected for this single blind study of 4 weeks duration . The participants were in the age group of 18-25 years . The brushes were randomly allotted by the co-investigator, who also supervised the brushing technique throughout the study period . The subjects were instructed to refrain from brushing their teeth for 12-14 hours prior to each follow up visit . The main investigator assessed all the clinical parameters at baseline, 14th, 21st and 28th day . Statistical analysis was carried out by an independent statistician who remained blind to the test products . Each of the tooth brushes tested, showed significant reductions in all the clinical parameters between 0 and 28th day . The reductions within the groups were significant although no significant differences between the groups were found . The reductions in stain index, bleeding index and gingival index was higher in ultrasonic toothbrush compared to manual toothbrush . It is concluded that ultrasonic toothbrush is safe and effective in the removal of plaque, stains, reduction of gingival inflammation and gingival bleeding.

Planta Med, 2004 Jul, 70(7), 637 - 41
Microbial metabolism of pseudoprotodioscin; Dong M et al.; Microbial transformation of the furostanol saponin pseudoprotodioscin ( 1) using Aspergillus fumigatus resulted in the isolation of two new steroidal metabolites, 3- O-{bis- alpha- L-rhamnopyranosyl-(1-->2 and 1-->4)- beta- D-glucopyranosyl}-22 R,25 R-spirost-5-ene-3 beta,20 alpha-diol ( 2) and 3- O-{bis- alpha- L-rhamnopyranosyl-(1-->2 and 1-->4)- beta- D-glucopyranosyl}-25 R-furost-5-ene-3 beta,22 alpha,26-triol ( 3), in addition to the previously reported steroidal saponins: dioscin ( 4) and progenin II ( 5) . The structure elucidation of these metabolites was based primarily on 1D and 2D NMR analyses . Metabolites 2 - 5 showed significant cytotoxicity against cancer cell lines A375, L929, and HeLa with IC (50) values ranging from 1.18 microM to 17.88 microM.

J Clin Invest, 2004 Jul, 114(2), 270 - 9
Inhibition of experimental asthma by indoleamine 2,3-dioxygenase; Hayashi T et al.; Epidemiological evidence points to the inverse relationship between microbial exposure and the prevalence of allergic asthma and autoimmune diseases in Westernized countries . The molecular basis for this observation has not yet been completely delineated . Here we report that the administration of certain toll-like receptor (TLR) ligands, via the activation of innate immunity, induces high levels of indoleamine 2,3-dioxygenase (IDO), the rate-limiting enzyme of tryptophan catabolism in various organs . TLR9 ligand-induced pulmonary IDO activity inhibits Th2-driven experimental asthma . IDO activity expressed by resident lung cells rather than by pulmonary DCs suppressed lung inflammation and airway hyperreactivity . Our results provide a mechanistic insight into the various formulations of the hygiene hypothesis and underscore the notion that activation of innate immunity can inhibit adaptive Th cell responses.

Nature, 2004 Jul 15, 430(6997), 335 - 8
Hydrological response to a seafloor spreading episode on the Juan de Fuca ridge; Davis E et al.; Seafloor hydrothermal systems are known to respond to seismic and magmatic activity along mid-ocean ridges, often resulting in locally positive changes in hydrothermal discharge rate, temperature and microbial activity, and shifts in composition occurring at the time of earthquake swarms and axial crustal dike injections . Corresponding regional effects have also been observed . Here we present observations of a hydrological response to seafloor spreading activity, which resulted in a negative formation-fluid pressure transient during and after an earthquake swarm in the sediment-sealed igneous crust of the Middle Valley rift of the northernmost Juan de Fuca ridge . The observations were made with a borehole seal and hydrologic observatory originally established in 1991 to study the steady-state pressure and temperature conditions in this hydrothermally active area . The magnitude of the co-seismic response is consistent with the elastic strain that would be expected from the associated earthquakes, but the prolonged negative pressure transient after the swarm is surprising and suggests net co-seismic dilatation of the upper, permeable igneous crust . The rift valley was visited four weeks after the onset of the seismic activity, but no signature of increased hydrothermal activity was detected in the water column . It appears that water, not magma, filled the void left by this spreading episode.

Mol Biol Evol, 2004 Oct, 21(10), 1981 - 91 Epub 2004 Jul 14.
Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates; Bordenstein SR et al.; The highly specialized genomes of bacterial endosymbionts typically lack one of the major contributors of genomic flux in the free-living microbial world-bacteriophages . This study yields three results that show bacteriophages have, to the contrary, been influential in the genome evolution of the most prevalent bacterial endosymbiont of invertebrates, Wolbachia . First, we show that bacteriophage WO is more widespread in Wolbachia than previously recognized, occurring in at least 89% (35/39) of the sampled genomes . Second, we show through several phylogenetic approaches that bacteriophage WO underwent recent lateral transfers between Wolbachia bacteria that coinfect host cells in the dipteran Drosophila simulans and the hymenopteran Nasonia vitripennis . These two cases, along with a previous report in the lepidopteran Ephestia cautella, support a general mechanism for genetic exchange in endosymbionts--the "intracellular arena" hypothesis--in which genetic material moves horizontally between bacteria that coinfect the same intracellular environment . Third, we show recombination in this bacteriophage; in the region encoding a putative capsid protein, the recombination rate is faster than that of any known recombining genes in the endosymbiont genome . The combination of these three lines of genetic evidence indicates that this bacteriophage is a widespread source of genomic instability in the intracellular bacterium Wolbachia and potentially the invertebrate host . More generally, it is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts . Gene transfer by bacteriophages could drive significant evolutionary change in the genomes of intracellular bacteria that are typically considered highly stable and prone to genomic degradation.

Oncol Nurs Forum, 2004 Jul 13, 31(4), 717 - 25 Print 2004 Jul.
Evidence-based nursing practice to prevent infection in hospitalized neutropenic patients with cancer; Larson E et al.; PURPOSE/OBJECTIVES: To review studies that have assessed the effectiveness of selected nursing interventions used in hospitals to prevent healthcare-associated infections in neutropenic patients with cancer . DATA SOURCES: Literature review of low microbial diets, protective clothing and environments, personal hygiene, and oral care in English-language articles from PubMed; the Cumulative Index of Nursing and Allied Health Literature; the National Guideline Clearinghouse, 1980-June 2003; and Cochrane Database of Systematic Reviews . DATA SYNTHESIS: Few studies have demonstrated the effectiveness of low microbial food and water and protective environments and clothing in reducing infections in neutropenic patients with cancer, and hospitals vary in these practices . Skin antisepsis reduces microbial counts, but data regarding the effect on infections are lacking . Many studies were characterized by insufficient sample sizes or use of multiple interventions . CONCLUSIONS: Major gaps exist in empirical evidence regarding which nursing interventions might be helpful in preventing or controlling healthcare-associated infections in neutropenic patients . IMPLICATIONS FOR NURSING: Although the evidence base for clinical practices such as a low microbial diet, protective environments and clothing, and special skin antisepsis regimens is weak, some of these practices seem prudent and reasonable . Until further evidence is available, clinicians can use consensus guidelines and should assist in identifying clinical practices that require additional research . Ultimately, interventions with little or no demonstrated efficacy should be examined systematically or abandoned . Additional studies of sufficient sample size regarding nursing practices such as the role of protective environments, room placement, antiseptic bathing, and prevention and treatment of oral complications are indicated . Because of difficulties in randomization and risk stratification, rigorous observational studies often may be an acceptable alternative to clinical trials.

FEBS Lett, 2004 Jul 16, 570(1-3), 1 - 6
Miraculous catch of iron-sulfur protein sequences in the Sargasso Sea; Meyer J; Recent shotgun sequencing of filtered Sargasso Sea water samples has yielded data in astounding amount and diversity . Iron-sulfur proteins, which are ancient, diverse and ubiquitous, have been implemented here to further probe the sequence diversity of the Sargasso Sea database (SSDB) . Sequence searches and comparisons confirm that the SSDB by and large equals in diversity the combined currently available databases . The data thus suggest that microbial diversity has so far been underestimated by orders of magnitude.

FEMS Microbiol Lett, 2004 Jul 15, 236(2), 249 - 56
Global distribution of nearly identical phage-encoded DNA sequences; Breitbart M et al.; Phages, the most abundant biological entities on the planet, play important roles in biogeochemical cycling, horizontal gene transfer, and defining microbial community composition . However, very little is known about phage diversity or biogeography, and there has not yet been a systematic effort to compare the phages found in different ecosystems . Here, we report that T7-like Podophage DNA polymerase sequences occur in every major biome investigated, including marine, freshwater, sediment, terrestrial, extreme, and metazoan-associated . The majority of these sequences belong to a unique clade that is only distantly related to cultured isolates . Some identical T7-like phage-encoded DNA polymerase genes from this clade were >99% conserved at the nucleotide level in multiple different environments, suggesting that these phages are moving between biomes in recent evolutionary time and that the global genomic pool for T7-like phages may be smaller than previously hypothesized.

Int Immunopharmacol, 2004 Sep, 4(9), 1209 - 15
Pharmacokinetics of fungal (1-3)-beta-D-glucans following intravenous administration in rats; Rice PJ et al.; Glucans are microbial cell wall carbohydrates that are shed into the circulation of patients with infections . Glucans are immunomodulatory and have structures that are influenced by bacterial or fungal species and growth conditions . We developed a method to covalently label carbohydrates with a fluorophore on the reducing terminus, and used the method to study the pharmacokinetics following intravenous administration of three highly purified and characterized glucans (glucan phosphate, laminarin and scleroglucan) that varied according to molecular size, branching frequency and solution conformation . Elimination half-life was longer (3.8+/-0.8 vs . 2.6+/-0.2 and 3.1+/-0.6 h) and volume of distribution lower (350+/-88 ml/kg vs . 540+/-146 and 612+/-154 ml/kg) for glucan phosphate than for laminarin and scleroglucan . Clearance was lower for glucan phosphate (42+/-6 ml/kg h) than for laminarin (103+/-17 ml/kg h) and scleroglucan (117+/-19 ml/kg h) . Since plasma levels at steady state are inversely related to clearance, these differences suggest that pharmacokinetics could favor higher blood levels of glucans with certain physicochemical properties.

Chest, 2004 Jul, 126(1), 95 - 9
Mannose-binding lectin gene polymorphism is a modulating factor in repeated respiratory infections; Gomi K et al.; STUDY OBJECTIVE: To clarify how mannose-binding lectin (MBL) participates in the pulmonary defense system . DESIGN: Multicenter retrospective study . PARTICIPANTS: Sixty-two patients with unexplained recurrent respiratory infections, 50 patients with nontuberculous mycobacterial infection, 23 patients with aspergillosis, and 49 patients with diffuse panbronchiolitis (DPB) . For controls, 52 blood samples were provided by the Blood Donation Center of the Japanese Red Cross Society . For BAL fluid (BALF) evaluation, there were five patients with acute phase pneumonia and five healthy volunteers . MEASUREMENT AND RESULTS: We demonstrated that MBL protein could be directly measured in the BALF from the lungs of patients with pneumonia by means of enzyme-linked immunosorbent assay . Furthermore, we demonstrated that the prevalence of the codon 54 mutation of the MBL gene in 62 patients having repeated respiratory infections was significantly higher compared with healthy control subjects (54.8% vs 32.7%) . The prevalence of the MBL mutant genotype among patients with DPB was higher (51.1%) than in the rest of the patients . In contrast, the prevalence of the MBL mutant genotype among patients with nontuberculous mycobacteria or Aspergillus chronic infection was not significantly different from that in control subjects (44.0% and 34.8%) . CONCLUSIONS: Our results suggest that MBL may play an important role in modulating the inflammatory response against repeated microbial infections.

J Environ Biol, 2003 Oct, 24(4), 429 - 35
Landfill leachate-induced toxicity in mice; Bakare AA et al.; Microbial, plant and studies in aquatic animals have shown that landfill leachate is toxic . However, more information about its effects in terrestrial animals is required . As a part of ongoing research into the toxic effects of landfill leachate in Nigeria, we evaluated the acute effects of raw and simulated leachates from Abadina, Orita-Aperin and Oworonsoki dump sites, all in Southwest Nigeria, in mice . Raw leachates were obtained directly from the dumps while the simulated leachates were obtained from the solid wastes in the laboratory by using the ASTM method . The samples were designated Abadina raw leachate (ARL), Orita-Aperin raw leachate (OARL) and Oworonsoki raw leachate (OWRL); and Abadina simulated leachate (ASL), Orita-Aperin simulated leachate (OASL) and Oworonsoki simulated leachate (OWSL) . Their physico-chemical properties were determined in accordance with standard analytical methods . Young male mice (12-15 wk) weighing 24-31 g were exposed to 1%, 5%, 10%, 25%, 50% and 100% concentrations of each test samples for 5 consecutive days and were observed for a period of 96 h for toxic response . Mortality recorded at different times for each sample at the various concentrations was mostly within the last 48 h of the exposure period . The LC50 obtained are 100% for both ARL and OARL, and 50% for OWRL; and 83.50% and 50% for ASL and OWSL, respectively . It was indeterminate for OASL . Apart from this, other toxic effects like weight loss, sluggishness, loss of hair and reduced food intake were observed . The investigated samples were ranked as OWRL > OWSL > ASL > OARL > ARL > OASL . The observed effects were due to the toxic constituents present in the leachate samples . This suggests that the mixtures have the potential to cause harmful effect to public health and our environment through seepage into ground or surface water.

Nat Med, 2004 Aug, 10(8), 871 - 5 Epub 2004 Jul 11.
An efficient method to make human monoclonal antibodies from memory B cells: potent neutralization of SARS coronavirus; Traggiai E et al.; Passive serotherapy can confer immediate protection against microbial infection, but methods to rapidly generate human neutralizing monoclonal antibodies are not yet available . We have developed an improved method for Epstein-Barr virus transformation of human B cells . We used this method to analyze the memory repertoire of a patient who recovered from severe acute respiratory syndrome coronavirus (SARS-CoV) infection and to isolate monoclonal antibodies specific for different viral proteins, including 35 antibodies with in vitro neutralizing activity ranging from 10(-8)M to 10(-11)M . One such antibody confers protection in vivo in a mouse model of SARS-CoV infection . These results show that it is possible to interrogate the memory repertoire of immune donors to rapidly and efficiently isolate neutralizing antibodies that have been selected in the course of natural infection.

Keio J Med, 2004 Jun, 53(2), 78 - 84
Osteoclasts, mononuclear phagocytes, and c-Fos: new insight into osteoimmunology; Matsuo K et al.; Osteoimmunology is the emerging concept that certain molecules link the skeletal and immune systems . The transcription factor c-Fos, a component of activator protein-1 (AP-1), is essential for osteoclast differentiation . Mice lacking c-Fos are osteopetrotic owing to impaired osteoclast development . Recent studies suggest that in contrast to this positive role in osteoclastogenesis, c-Fos expression inhibits differentiation and activation of mononuclear phagocytes . Here, we focus on the contrasting roles of c-Fos in the bone and immune lineages . Both osteoclasts and mononuclear phagocytes are derived from common myeloid precursors . Osteoclasts resorb bone, whereas macrophages and myeloid dendritic cells phagocytose microbial pathogens, initiating innate and adaptive immunity . Differentiation of the common precursors into either bone or immune lineage is determined by ligand binding to cell-surface receptors, particularly receptor activator of NF-kappa B (RANK) for osteoclasts, or Toll-like receptors (TLRs) for mononuclear phagocytes . Both RANK and TLRs activate the dimeric transcription factors NF-kappa B and AP-1 . Yet, c-Fos/AP-1 plays a positive role in osteoclasts but a negative role in macrophages and dendritic cells . Further study is necessary to clarify this dual role of c-Fos.

Proc Natl Acad Sci U S A, 2004 Jul 20, 101(29), 10560 - 5 Epub 2004 Jul 09.
The Spn4 gene of Drosophila encodes a potent furin-directed secretory pathway serpin; Richer MJ et al.; Proprotein convertases (PCs) are an important class of host-cell serine endoproteases implicated in many physiological and pathological processes . Owing to their expanding roles in the proteolytic events required for generating infectious microbial pathogens and for tumor growth and invasiveness, there is increasing interest in identifying endogenous PC inhibitors . Here we report the identification of Spn4A, a previously uncharacterized secretory pathway serine protease inhibitor (serpin) from Drosophila melanogaster that contains a consensus furin cleavage site, -Arg(P4)-Arg-Lys-Arg(P1) downsream-, in its reactive site loop (RSL) . Our biochemical and kinetics analysis revealed that recombinant Spn4A inhibits human furin (K(i), 13 pM; k(ass), 3.2 x 10(7) M(-1) x s(-1)) and Drosophila PC2 (K(i), 3.5 nM; k(ass), 9.2 x 10(4) M(-1) x s(-1)) by a slow-binding mechanism characteristic of serpin molecules and forms a kinetically trapped SDS-stable complex with each enzyme . For both PCs, the stoichiometry of inhibition by Spn4A is nearly 1, which is characteristic of known physiological serpin-protease interactions . Mass analysis of furin-Spn4A reaction products identified the actual reactive site center of Spn4A to be -Arg(P4)-Arg-Lys-Arg(P1)-downstream- . Moreover, we demonstrate that Spn4A's highly effective PC inhibition properties are critically dependent on the unusual length of its RSL, which is composed of 18 aa instead of the typical 17-residue RSL found in most other inhibitory serpins . The identification of Spn4A, the most potent and effective natural serpin of PCs identified to date, suggests that Spn4A could be a prototype of endogenous serpins involved in the precise regulation of PC-dependent proteolytic cleavage events in the secretory pathway of eukaryotic cells.

J Environ Radioact, 2004, 76(1-2), 265 - 72
Seasonal changes of redox potential and microbial activity in two agricultural soils of tropical Australia: some implications for soil-to-plant transfer of radionuclides; Twining JR et al.; Very little is known of the factors controlling soil-to-plant transfer of radionuclides in tropical environments . As part of an IAEA/FAO coordinated research project (CRP) designed to elucidate some of those factors, near-surface samples of two agricultural red-earth soils (Blain and Tippera) were collected from a study site in the Northern Territory . The climate is tropical monsoonal with crops being grown over the wet season from December to March/April . It is important to understand soil variables that may be related to this dramatic seasonality . In this investigation, soil redox state and microbial populations were assessed before and after the growing season with a view to generating hypotheses for future evaluation . The X-ray absorption near edge structure (XANES) technique was used to determine overall changes in the solid-state redox speciation of Fe and Mn in soils across the growing period . Fe speciation did not change but approximately 10% of the total Mn was oxidised from Mn(II) to Mn(III) and Mn(IV) in both soils between October 1999 and April 2000 . An apparent disconnect between Fe and Mn was not unexpected given the >10 times higher concentration of Fe in the soils compared with Mn . These results have implications for the bioavailability of redox sensitive radionuclides such as Tc and Pu . Similarly, microbial population estimates were derived before and after the growing period . Total bacterial populations did not vary from 10(6) to 10(7) colonies per gram . Fungal populations increased over the growing season from 3-6 x 10(5) to 1-4 x 10(6) colonies per gram of soil . Fungi have the potential to decrease soil pH and hence increase the bioavailability of radionuclides such as Cs . In addition, fungi act to facilitate plant nutrition . This could lead to enhanced accumulation of nutrient analogues (e.g . Sr and Ra for Ca; Tc for Mn), but this effect may be masked by improved biomass production.

Biomacromolecules, 2004 Jul-Aug, 5(4), 1270 - 9
Mechanical properties of biomimetic tissue adhesive based on the microbial transglutaminase-catalyzed crosslinking of gelatin; McDermott MK et al.; Fibrin sealants are a type of soft tissue adhesive that employs biochemical reactions from the late stages of the blood coagulation cascade . Intrinsic to these adhesives are a structural protein and a transglutaminase crosslinking enzyme . We are investigating an alternative biomimetic adhesive based on gelatin and a calcium-independent microbial transglutaminase (mTG) . Rheological measurements show that mTG catalyzes the conversion of gelatin solutions into hydrogels, and gel times are on the order of minutes depending on the gelatin type and concentration . Tensile static and dynamic loading of the adhesive hydrogels in bulk form demonstrated that the Young's modulus ranged from 15 to 120 kPa, and these bulk properties were comparable to those reported for hydrogels obtained from fibrin-based sealants . Lap-shear adhesion tests of porcine tissue were performed using a newly published American Society for Testing and Materials (ASTM) standard for tissue adhesives . The gelatin-mTG adhesive bound the opposing tissues together with ultimate adhesive strengths of 12-23 kPa which were significantly higher than the strength observed for fibrin sealants . Even after failure, strands of the gelatin-mTG adhesive remained attached to both of the opposing tissues . These results suggest that gelatin-mTG adhesives may offer the benefits of fibrin sealants without the need for blood products.

Indian J Exp Biol, 2003 May, 41(5), 391 - 402
Properties of biophotons and their theoretical implications; Popp FA; The word "biophotons" is used to denote a permanent spontaneous photon emission from all living systems . It displays a few up to some hundred photons/(s x cm2) within the spectral range from at least 260 to 800 nm . It is closely linked to delayed luminescence (DL) of biological tissues which describes the long term and ultra weak reemission of photons after exposure to light illumination . During relaxation DL turns continuously into the steady state biophoton emission, where both, DL and biophoton emission exhibit mode coupling over the entire spectrum and a Poissonian photo count distribution . DL is representing excited states of the biophoton field . The physical properties indicate that biophotons originate from fully coherent and sometimes even squeezed states . The physical analysis provides thermodynamic and quantum optical interpretation, in order to understand the biological impacts of biophotons . Biological phenomena like intracellular and intercellular communication, cell growth and differentiation, interactions among biological systems (like "Gestaltbildung" or swarming), and microbial infections can be understood in terms of biophotons . "Biophotonics", the corresponding field of applications, provide a new powerful tool for assessing the quality of food (like freshness and shelf life), microbial infections, environmental influences and for substantiating medical diagnosis and therapy.

Insect Biochem Mol Biol, 2004 Jul, 34(7), 673 - 8
Immune responses in Anopheles gambiae; Levashina EA; Transmission of human malaria requires a successful development of Plasmodium parasites in anopheline mosquitoes . Insects have developed efficient immune responses to oppose microbial and eukaryotic invaders . The completion of the sequencing of the Anopheles genome provides a wealth of information on putative immune genes that are homologous to components of the Drosophila and mammalian immune systems . In this review, we will summarize our present knowledge of immune responses in the mosquito Anopheles gambiae and attempt a comparative analysis of insect immune systems.

Lett Appl Microbiol, 2004, 39(2), 163 - 8
Co-composting of PAH-contaminated soil with poultry manure; Atagana HI; AIMS: To investigate the effects of co-composting poultry manure with soil contaminated with different concentrations of polycyclic aromatic hydrocarbons (PAHs), on the degradation of selected PAHs in a static-pile compost system . METHODS: Mispah form (Food & Agricultural Organisation, FAO : lithosol) soil contaminated with PAHs was co-composted with poultry manure for 19 months . The soil was mixed with wood chips in a ratio of 1:1 to improve aeration and then mixed with poultry manure in a ratio of 4:1 . A data logger measured temperature monthly . Residual concentrations of selected PAHs in the compost were determined monthly by gas chromatography/flame ionisation detection (GC/FID) . Moisture, pH, ash content and C:N ratios were also monitored monthly . Microbial activity was measured by measuring CO(2) evolution . CONCLUSIONS: The results obtained in this experiment have shown that co-composting poultry manure with PAH-contaminated soil is capable of removing large concentrations of high molecular weight PAH from contaminated soil to levels below 1 mg kg(-1) in 19 months . SIGNIFICANCE AND IMPACT OF THE STUDY: The paper adds to the body of knowledge necessary for the development of a cost effective technology for the remediation of soil contaminated with high molecular weight PAHs by providing information on the behaviour of selected PAHs and factors such as nutrient ratio, temperature and pH during composting.

Lett Appl Microbiol, 2004, 39(2), 148 - 55
Rapid and quantitative detection of the microbial spoilage in chicken meat by diffuse reflectance spectroscopy (600-1100 nm); Lin M et al.; AIMS: To evaluate the feasibility of visible and short-wavelength near-infrared (SW-NIR) diffuse reflectance spectroscopy (600-1100 nm) to quantify the microbial loads in chicken meat and to develop a rapid methodology for monitoring the onset of spoilage . METHODS AND RESULTS: Twenty-four prepackaged fresh chicken breast muscle samples were prepared and stored at 21 degrees C for 24 h . Visible and SW-NIR was used to detect and quantify the microbial loads in chicken breast muscle at time intervals of 0, 2, 4, 6, 8, 10, 12 and 24 h . Spectra were collected in the diffuse reflectance mode (600-1100 nm) . Total aerobic plate count (APC) of each sample was determined by the spread plate method at 32 degrees C for 48 h . Principal component analysis (PCA) and partial least squares (PLS) based prediction models were developed . PCA analysis showed clear segregation of samples held 8 h or longer compared with 0-h control . An optimum PLS model required eight latent variables for chicken muscle (R = 0.91, SEP = 0.48 log CFU g(-1)) . CONCLUSIONS: Visible and SW-NIR combined with PCA is capable of perceiving the change of the microbial loads in chicken muscle once the APC increases slightly above 1 log cycle . Accurate quantification of the bacterial loads in chicken muscle can be calculated from the PLS-based prediction method . SIGNIFICANCE AND THE IMPACT OF THE STUDY: Visible and SW-NIR spectroscopy is a technique with a considerable potential for monitoring food safety and food spoilage . Visible and SW-NIR can acquire a metabolic snapshot and quantify the microbial loads of food samples rapidly, accurately, and noninvasively . This method would allow for more expeditious applications of quality control in food industries.

Z Naturforsch {C}, 2004 Mar-Apr, 59(3-4), 209 - 14
Microbial transformations of alpha-santonin; Ata A et al.; Fungal biotransformations of alpha-santonin (1) were conducted with Mucor plumbeus (ATCC 4740), Cunninghamella bainieri (ATCC 9244), Cunninghamella echinulata (ATCC 9245), Curvularia lunata (ATCC 12017) and Rhizopus stolonifer (ATCC 10404) . Rhizopus stolonifer (ATCC 10404) metabolized compound 1 to afford 3,4-epoxy-alpha-santonin (2) and 4,5-dihydro-alpha-santonin (3) while Cunninghamella bainieri (ATCC 9244), Cunninghamella echinulata (ATCC 9245) and Mucor plumbeus (ATCC 4740) were capable of metabolizing compound 1 to give a reported metabolite, 1,2-dihydro-alpha-santonin (4) . The structures of these transformed metabolites were established with the aid of extensive spectroscopic studies . These fungi regiospecifically reduced the carbon-carbon double bond in ring A of alpha-santonin.

Am J Dent, 2004 Feb, 17(1), 56 - 60
Effect of ozone on the oral microbiota and clinical severity of primary root caries; Baysan A et al.; PURPOSE: To assess the effect of ozone on the microbial flora and clinical severity of primary root caries . METHODS: 26 patients with 70 primary root carious lesions (PRCLs) were entered . Each PRCL was classified in terms of color, cavitation, size, hardness, distance from the gingival margin and severity . Overlying plaque was then removed and each lesion dried . A biopsy was taken from half of each PRCL using a sterile excavator . Subsequently, the remaining lesions were exposed to ozone gas for a period of either 10 seconds (n = 35) or 20 seconds (n = 35) and a further biopsy was taken . RESULTS: Using a paired Student t-test, a significant (P < 0.001) difference (mean +/- SE) in total micro-organisms was observed in the ozone-treated samples after either a 10 seconds (log10 4.35 +/- 0.49) or 20 seconds (log10 0.46 +/- 0.26) ozone application compared with the control samples (log10 7.00 +/- 0.24) and (log10 6.00 +/- 0.21) respectively . Using Pearson's correlation tests, there were significant correlations for the reduction in total micro-organisms after 10 seconds of ozone application with cavitation, size, distance from gingival margin and severity of PRCLs (P < 0.05) . In conclusion, ozone application either for 10 or 20 seconds dramatically reduced most of the micro-organisms in PRCLs without any side effects recorded at recall intervals between 3 and 5.5 months . Out of the 65 PRCLs reviewed, 33 lesions had become hard, 27 lesions reversed to severity index 1 from severity index 2, and five lesions remained the same following ozone application for a period of either 10 or 20 seconds.

Hum Mutat, 2004 Aug, 24(2), 178 - 84
Bayesian approach to discovering pathogenic SNPs in conserved protein domains; Cai Z et al.; The success rate of association studies can be improved by selecting better genetic markers for genotyping or by providing better leads for identifying pathogenic single nucleotide polymorphisms (SNPs) in the regions of linkage disequilibrium with positive disease associations . We have developed a novel algorithm to predict pathogenic single amino acid changes, either nonsynonymous SNPs (nsSNPs) or missense mutations, in conserved protein domains . Using a Bayesian framework, we found that the probability of a microbial missense mutation causing a significant change in phenotype depended on how much difference it made in several phylogenetic, biochemical, and structural features related to the single amino acid substitution . We tested our model on pathogenic allelic variants (missense mutations or nsSNPs) included in OMIM, and on the other nsSNPs in the same genes (from dbSNP) as the nonpathogenic variants . As a result, our model predicted pathogenic variants with a 10% false-positive rate . The high specificity of our prediction algorithm should make it valuable in genetic association studies aimed at identifying pathogenic SNPs .

Internist (Berl), 2004 Aug, 45(8), 912 - 22
{Adult-onset primary immunodeficiencies}; Gadola S et al.; Different individuals with the same kind of primary immunodeficiency may start having symptoms from early childhood on, or alternatively much later in adult life, or never . The differences in phenotype can only partly be deduced from genotype-analysis or--in case of female patients with X-linked diseases--from age-related skewing of lyonisation . The role of compensatory immune mechanisms is less clear . The microbial spectrum of infections is usually the same for both adult and infantile forms of a special primary immunodeficiency syndrome . Yet, many of the adult forms are associated with non-infectious complications, such as granuloma formation, autoimmunity or tumors . Besides standard antibiotic treatment and IgG replacement therapy, there are now different cytokine- or enzyme-replacement regimens available for some of the primary immunodeficiencies . However, exact diagnostic classification of the immunodeficiency should be obtained before such treatment modalities are used . Adult primary immunodeficiency syndromes therefore represent a challenge to both clinicians and molecular biologists.

Nature, 2004 Jul 8, 430(6996), 218 - 22
Regulation of Toll/IL-1-receptor-mediated gene expression by the inducible nuclear protein IkappaBzeta; Yamamoto M et al.; Toll-like receptors (TLRs) recognize microbial components and trigger the inflammatory and immune responses against pathogens . IkappaBzeta (also known as MAIL and INAP) is an ankyrin-repeat-containing nuclear protein that is highly homologous to the IkappaB family member Bcl-3 (refs 1-6) . Transcription of IkappaBzeta is rapidly induced by stimulation with TLR ligands and interleukin-1 (IL-1) . Here we show that IkappaBzeta is indispensable for the expression of a subset of genes activated in TLR/IL-1R signalling pathways . IkappaBzeta-deficient cells show severe impairment of IL-6 production in response to a variety of TLR ligands as well as IL-1, but not in response to tumour-necrosis factor-alpha . Endogenous IkappaBzeta specifically associates with the p50 subunit of NF-kappaB, and is recruited to the NF-kappaB binding site of the IL-6 promoter on stimulation . Moreover, NF-kappaB1/p50-deficient mice show responses to TLR/IL-1R ligands similar to those of IkappaBzeta-deficient mice . Endotoxin-induced expression of other genes such as Il12b and Csf2 is also abrogated in IkappaBzeta-deficient macrophages . Given that the lipopolysaccharide-induced transcription of IkappaBzeta occurs earlier than transcription of these genes, some TLR/IL-1R-mediated responses may be regulated in a gene expression process of at least two steps that requires inducible IkappaBzeta.

J Immunol, 2004 Jul 15, 173(2), 1219 - 23
Microbial DNA induces a host defense reaction of human respiratory epithelial cells; Platz J et al.; Epithelial cells represent the initial site of bacterial colonization in the respiratory tract . TLR9 has been identified in B cells and CD 123(+) dendritic cells and found to be involved in the recognition of microbial DNA . It was the aim of the study to investigate the role of TLR9 in the host defense reactions of the respiratory epithelium . Respiratory epithelial cell lines (IHAEo(-), Calu-3) or fully differentiated primary human cells as air-liquid interface cultures were stimulated with bacterial DNA or synthetic oligonucleotides containing CpG motifs (CpG oligodeoxynucleotides) . Expression of TLR9, cytokines, and human beta-defensin 2 was determined by quantitative RT-PCR or by ELISA . We found that TLR9 is expressed by respiratory epithelial cell lines and fully differentiated primary epithelial cells at low levels . Stimulation of the above-mentioned cells with bacterial DNA or CpG oligodeoxynucleotide resulted in an inflammatory reaction characterized by a dose-dependent up-regulation of cytokines (IL-6, IL-8) and human beta-defensin 2 . Up-regulation of NF-kappaB in epithelial cells in response to the CpG motif containing DNA was inhibited by overexpression of a dominant negative form of MyD88 . These results provide clear evidence that the human respiratory epithelium is capable of detecting microbial DNA by TLR9 . The respiratory epithelium has an important function in triggering innate immune responses and therefore represents an interesting target for anti-inflammatory therapy.

Appl Environ Microbiol, 2004 Jul, 70(7), 4242 - 8
Molecular analysis of carbon monoxide-oxidizing bacteria associated with recent Hawaiian volcanic deposits; Dunfield KE et al.; Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase . The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest . PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans . PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ . On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct . Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers . On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations . Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration . Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.

Clin Immunol, 2004 Aug, 112(2), 190 - 9
Beta-2-glycoprotein-I, infections, antiphospholipid syndrome and therapeutic considerations; Blank M et al.; Evidence supports the association between infectious agents, antiphospholipid syndrome (APS), and the presence of antiphospholipid antibodies and anti-beta2-glycoprotein-I (beta2GPI) antibodies . Several mechanisms have been proposed to explain the role of bacteria/viruses in induction of an autoimmune condition, such as molecular mimicry between structures of a pathogen and self antigen and bystander activation or bacterial/viral superantigens . Protein databases reveal high homologies between the beta2GPI-related synthetic peptides and infectious agents . Studies employing experimental APS models proved molecular mimicry between beta2GPI-related synthetic peptides, which serve as target epitopes for anti-beta2GPI Abs, and structures within bacteria, viruses (e.g., CMV), and tetanus toxoid . Any explanation of how microbial infections might induce APS must take into account the genetic predisposition . In this paper, we discuss the association of antiphospholipid antibodies, infectious states, and molecular mimicry as a proposed mechanism for development of APS.

J Appl Microbiol, 2004, 97(2), 395 - 401
Efficiency of Calamintha officinalis essential oil as preservative in two topical product types; Nostro A et al.; AIMS: To verify the efficiency of Calamintha officinalis essential oil as natural preservative in two current formulations . METHODS AND RESULTS: The 1.0 and 2.0% (v/v) C . officinalis essential oil was assayed for its preservative activity in two product types (cream and shampoo) . The microbial challenge test was performed following the standards proposed by the European Pharmacopoeia Commission (E.P.) concerning topical preparations using standard micro-organisms and in addition wild strains, either in single or mixed cultures were used . The results clearly demonstrated that the C . officinalis essential oil at 2.0% concentration reduced the microbial inoculum satisfying the criterion A of the E.P . in the cream formulation and the criterion B in the shampoo formulation . Standard and wild strains showed a behaviour similar, both in cream and in shampoo formulation, with no significant difference (gerarchic variance, P > 0.05) . CONCLUSION: C . officinalis essential oil confirmed its preservative properties but at higher concentration than that shown in previous studies on cetomacrogol cream . SIGNIFICANCE AND IMPACT OF THE STUDY: The nature of the formulation in which an essential oil is incorporated as preservative could have considerable effect on its efficacy.

J Appl Microbiol, 2004, 97(2), 378 - 83
Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences; Shin EC et al.; AIMS: To examine the diversity of protozoa in the rumen contents of cow . METHODS AND RESULTS: Protozoa that inhabit the rumen were detected by PCR using protozoan-specific primers . Libraries of protozoan rDNA sequences were constructed from rumen fluid, solid tissues and epithelium . Twenty-three clones isolated from rumen fluid fell into two genera identified as Entodinium (69.6% of clones) and Epidinium (31.4% of clones) . Of the clones isolated from rumen fluid, a moderate number were unidentifiable (30.4%) . CONCLUSIONS: The predominant protozoan genus identified in the whole rumen belonged to the Entodinium group (81.1%) . Protozoa were not detected in the rumen epithelium . SIGNIFICANCE AND IMPACT OF THE STUDY: These findings suggest that rumen fluid and solid tissues contain different protozoan populations that may play specific roles in rumen function . Quantitative PCR techniques and a more specific set of phylogenetic probes that distinguish between protozoan species are needed to determine the significance of newly identified groups and to determine the distribution of identified protozoan clusters in rumen microbial communities.

Cancer Nurs, 2004 May-Jun, 27(3), 183 - 205
Prevention and treatment of oropharyngeal mucositis following cancer therapy: are there new approaches?
Kwong KK.
Oropharyngeal mucositis is an acute and distressing toxic effect of chemotherapy and head and neck irradiation . This oral sequela significantly impairs the daily functioning and quality of life of patients . The biological basis of mucositis is quite complex, involving sequential interaction of chemotherapeutic drugs or irradiation on mitosis of proliferating epithelium, a number of cytokines, and elements of oral microbial environment . Various interventions based on biological attenuation have been tested for mucositis . Such interventions have been reviewed elsewhere; however, most reviews focus on biomedical outcomes . Little attention has been paid to mucositis outcomes with oral morbidity or psychosocial aspects . The purpose of this article is to review the current research studies on the prevention and treatment of oropharyngeal mucositis following chemotherapy, radiotherapy, and bone marrow transplantation with an emphasis on biomedical, oral symptomatic, and functional impairment outcomes . In addition, further avenues of mucositis management, including psychotherapeutic intervention and integrated and stage-based treatment approaches are discussed.

Am J Trop Med Hyg, 2004 Jul, 71(1), 24 - 8
Relationship of anti-microbial activity of tetracyclines to their ability to block the l3 to L4 molt of the human filarial parasite brugia malayi; Rajan TV; The nematode parasites Wuchereria bancrofti, Brugia malayi, and B . timori cause a human disease known as lymphatic filariasis, which afflicts approximately 120 million people worldwide . These organisms are known to contain endosymbiotic bacteria (Wolbachia) that are related to rickettsiae . It has been previously reported that tetracycline blocks the L3 to L4 molt of the filarial parasite B . malayi, and suggested that this was related to their known anti-rickettsial activity . However, this interpretation was tempered by several observations . First, Wolbachia DNA could still be detected in nematodes from tetracycline-treated cultures . In addition, chloramphenicol, which has anti-rickettsial and anti-chlamydial activity, failed to inhibit the molt . These observations could not rule out the possibility that the anti-molting activity of tetracycline is due to pharmacologic activities unrelated to its anti-rickettsial functions . This study shows that chemically modified tetracycline, which does not to have anti-microbial activity, also blocks molting.

Ann Intern Med, 2004 Jul 6, 141(1), 9 - 15
Plasma level of a triggering receptor expressed on myeloid cells-1: its diagnostic accuracy in patients with suspected sepsis; Gibot S et al.; BACKGROUND: Previous experimental studies have suggested that the triggering receptor expressed on myeloid cells-1 (TREM-1) is specifically upregulated in the presence of microbial products . OBJECTIVE: To evaluate the diagnostic value of plasma levels of the soluble form of TREM-1 in patients admitted with clinical suspicion of infection . DESIGN: Prospective, noninterventional study conducted between July and September 2003 . SETTING: Medical adult intensive care unit at a university hospital in France . PARTICIPANTS: 76 consecutive newly admitted patients who presented with clinically suspected infection and fulfilled at least 2 criteria of the systemic inflammatory response syndrome . MEASUREMENTS: Sensitivity and specificity of plasma soluble TREM-1 levels at admission for the diagnosis of infection . Two independent intensivists blinded to the results of soluble TREM-1 assays retrospectively classified patients as having the systemic inflammatory response syndrome, sepsis, severe sepsis, or septic shock . RESULTS: The systemic inflammatory response syndrome was diagnosed in 29 patients (38%), and sepsis, severe sepsis, or septic shock was diagnosed in the remaining 47 (62%) . A plasma soluble TREM-1 level higher than 60 ng/mL was more accurate than any other clinical or laboratory finding for indicating infection (sensitivity, 96% {95% CI, 92% to 100%}; specificity, 89% {CI, 82% to 95%}; positive likelihood ratio, 8.6 {CI, 3.8 to 21.5}; negative likelihood ratio, 0.04 {CI, 0.01 to 0.2}) . LIMITATIONS: The study did not enroll patients with mild infections not requiring intensive care unit hospitalization, patients older than 80 years of age, or patients who were immunocompromised . CONCLUSION: In newly admitted critically ill patients, measurement of plasma levels of soluble TREM-1 could help to rapidly identify those with infection.

Drug Metab Rev, 2004 May, 36(2), 363 - 75
Physiological roles of xanthine oxidoreductase; Harrison R; Xanthine oxidoreductase (XOR) is a major protein component of the milk fat globule membrane (MFGM) surrounding fat droplets in milk and its enzymology is well characterised . The enzyme is widely distributed in mammalian tissues and is generally accepted to be a key enzyme of purine catabolism . It catalyses the oxidation of a wide range of substrates and can pass electrons to molecular oxygen, generating reactive oxygen species (ROS); similar reduction of nitrite yields reactive nitrogen species (RNS) . While XOR has been implicated in ischemia-reperfusion injury, its involvement in normal physiological processes has been less studied . It is argued here that XOR-derived ROS and RNS play a role in innate immunity, specifically in the inflammatory response and in anti-microbial defense of the gastrointestinal tract . XOR-derived species could also be involved in signalling . Additionally, XOR is likely to play a part in metabolism of xenobiotics and has recently been shown to mediate the secretion of milk fat globules . The human enzyme has only relatively recently been characterized . The enzyme purified from breast milk shows very low enzymatic activity, and it is suggested that human XOR has evolved so as to be regulated by an exceptional range of pre- and posttranslational mechanisms.

J Chromatogr B Analyt Technol Biomed Life Sci, 2004 Aug 25, 808(1), 69 - 73
Fungal mycelium--the source of chitosan for chromatography; Kucera J; Mycelium of the mold Aspergillus niger was used as a raw material for the preparation of microbial chitosan . Aspergillus niger, the mold used for the production of citric acid, contains approx . 15% of chitin, which can be separated, transformed into chitosan, and used as a sorbent for chromatography . The main advantage of this material in comparison with krill chitosan is the uniformity of particle size leading to the low back-pressure in the column . The other advantage is the fact, that original fibrous structure of mycelial pellets could be stabilized before chitosan preparation by cross-linking with glutaraldehyde . The product prepared by this way -- crosslinked chitosan of uniform particle size, is highly porous, with high water regain and, as a result, low sedimentation velocity . Low sedimentation velocity is not disadvantage in chromatographic application, but may form some problems in batchwise operation . Chitosan as a polymer of glucosamine is anion exchanger in nature and the chromatographic properties of this anion exchanger was demonstrated by the chromatography of bovine blood plasma, glucose oxidase, and chicken pepsinogen . In all cases, the course of chromatography on crosslinked chitosan was compared with the chromatography on MONO Q (bovine blood plasma) or DEAE-cellulose (glucose oxidase, chicken pepsinogen) under the same protocol.

Cell Microbiol, 2004 Aug, 6(8), 783 - 93
Enteropathogenic Escherichia coli infection leads to appearance of aberrant tight junctions strands in the lateral membrane of intestinal epithelial cells; Muza-Moons MM et al.; Infection of intestinal epithelial cells with enteropathogenic Escherichia coli (EPEC) disrupts tight junction (TJ) architecture and barrier function . The aim of this study was to determine the impact of EPEC on TJ protein interactions and localization . Human intestinal epithelial cells (T84) were infected for 1, 3 or 6 h with EPEC . To probe the TJ protein-protein interactions, co-immunoprecipitations were performed . The associations between ZO-1, occludin and claudin-1 progressively decreased after infection . Corresponding morphological changes were analysed by immunofluorescence confocal microscopy . Tight junction proteins progressively lost their apically restricted localization . Freeze-fracture electron microscopy revealed the appearance of aberrant strands throughout the lateral membrane that contained claudin-1 and occludin as determined by immunogold labelling . These structural alterations were accompanied by a loss of barrier function . Mutation of the gene encoding EspF, important in the disruption of TJs by EPEC, prevented the disruption of TJs . Tight junction structure normalized following eradication of EPEC with gentamicin and overnight recovery . This is the first demonstration that a microbial pathogen can cause aberrant TJ strands in the lateral membrane of host cells . We speculate that the disruption of integral and cytoplasmic TJ protein interactions following EPEC infection allows TJ strands to form or diffuse into the lateral plasma membrane.

Biotechnol Bioeng, 2004 Jul 20, 87(2), 200 - 12
Mono and diterpene production in Escherichia coli; Reiling KK et al.; Mono- and diterpenoids are of great industrial and medical value as specialty chemicals and pharmaceuticals . Production of these compounds in microbial hosts, such as Escherichia coli, can be limited by intracellular levels of the polyprenyl diphosphate precursors, geranyl diphosphate (GPP), and geranylgeranyl diphosphate (GGPP) . To alleviate this limitation, we constructed synthetic operons that express three key enzymes for biosynthesis of these precursors: (1) . DXS,1-deoxy-d-xylulose-5-phosphate synthase; (2) . IPPHp, IPP isomerase from Haematococcus pluvialis; and (3) . one of two variants of IspA, FPP synthase that produces either GPP or GGPP . The reporter plasmids pAC-LYC and pACYC-IB, which encode enzymes that convert either FPP or GGPP, respectively, to the pigment lycopene, were used to demonstrate that at full induction, the operon encoding the wild-type FPP synthase and mutant GGPP synthase produced similar levels of lycopene . To synthesize di- or monoterpenes in E . coli using the GGPP and GPP encoding operons either a diterpene cyclase {casbene cyclase (Ricinus communis L) and ent-kaurene cyclase (Phaeosphaeria sp . L487)} or a monoterpene cyclase {3-carene cyclase (Picea abies)} was coexpressed with their respective precursor production operon . Analysis of culture extracts or headspace by gas chromatography-mass spectrometry confirmed the in vivo production of the diterpenes casbene, kaur-15-ene, and kaur-16-ene and the monoterpenes alpha-pinene, myrcene, sabinene, 3-carene, alpha-terpinene, limonene, beta-phellandrene, alpha-terpinene, and terpinolene . Construction and functional expression of GGPP and GPP operons provides an in vivo precursor platform host for the future engineering of di- and monoterpene cyclases and the overproduction of terpenes in bacteria .

J Microbiol Methods, 2004 Aug, 58(2), 251 - 62
The development of a DNA microarray-based assay for the characterization of commercially formulated microbial products; Dubois JW et al.; Commercially formulated bioproducts containing a complex consortia of bacteria as an active ingredient pose a significant challenge for regulatory agencies and companies seeking to assess the safety and efficacy of these bioproducts . The main challenge stems from how to characterize the bacterial composition of these products, for which there is presently a lack of suitable methods . A prototype DNA microarray composed of oligonucleotide probes for functional genes, virulence factors, and taxonomic genes for a number of bacterial species was developed to examine the utility of microarray technology as a molecular tool for characterizing consortia bioproducts . The genomic DNA from four different products was extracted by two methods and examined with the microarray prototype and by denaturing gradient gel electrophoresis (DGGE) . Although the identity of the consortial species remains unknown, the microarray assay provided unique and reproducible hybridization patterns for all four products, and agreed with the fingerprints generated by DGGE . The ability to differentiate between a variety of consortia products demonstrates that DNA microarrays have the potential to be a powerful tool in monitoring complex microbial communities.

Environ Pollut, 2004 Sep, 131(2), 263 - 73
Biotransformation of 2,4,6-trinitrotoluene (TNT) by enchytraeids (Enchytraeus albidus) in vivo and in vitro; Dodard SG et al.; 2,4,6-Trinitrotoluene (TNT) is toxic to soil invertebrates, but little is known about its toxicokinetic behavior in soil . Tissue residue analysis was used to evaluate whether the presence of TNT and its reduced metabolites in soil invertebrates was due to uptake of these compounds from the soil into the organism, or due to microbial transformation of TNT associated with the organism followed by uptake . Adult white potworms (Enchytraeus albidus) were exposed to non-lethal concentrations of TNT in amended artificial soil for 21 d, or to TNT in solution for 20 h . Soil exposure studies confirmed earlier reports that TNT was transformed in enchytraeids in vivo to 2- and 4-aminodinitrotoluenes . However, enchytraeid exposure to TNT in solution led to the additional presence of 2,4-diaminonitrotoluene as well as 2- and 4- hydroxyamino-dinitrotoluenes and azoxy-compounds, suggesting that TNT can be metabolized in vivo in the absence of soil . Incubation of unexposed enchytraeid homogenates with TNT led to a protein-dependent appearance of these metabolites in vitro after > or =16 h incubation . Cellular fractionation studies indicated that most of this activity resided in the 8000 x g pellet, and was completely inhibited by broad-spectrum antibiotics . These studies demonstrate that enchytraeids can transform TNT in vivo and in vitro, at least in part, by bacteria associated with the host organism.

J Chromatogr A, 2004 Jun 4, 1038(1-2), 11 - 8
Development of a rapid and accurate method for the determination of key compounds of pig odor; Willig S et al.; Sampling of odor substances in the emissions from swine production facilities is still the limiting step for routine odor quantification . Solid sorption techniques based on cartridges were developed for three categories of substances (indoles, volatile fatty acids and methylthiol) and were standardized to a sampling time of 15 min . These cartridges also trap dust particles which transport odor substances . Quantification was performed by RP-HPLC or GC . Reliability criteria revealed excellent values for sensitivity (lower ppb level) and repeatability (R.S.D . < 10%), thus they are comparable to fiber solid-phase micro extraction sorption techniques . Parallel determinations in feces and air revealed high correlations (r = 0.99, P < 0.01), so that microbial processes during digestion determine odor quality and hence provide a possibility to reduce odor via feeding.

Aviakosm Ekolog Med, 2004, 38(2), 57 - 8
{Air decontamination and the fine filtration system "Potok 150MK"}; Kapustina EA et al.; Longevity of space stations is dependent on efficiency and robustness of the life support systems . The article describes the principle of operation of air decontamination system Potok 150MK intended for providing microbial safety of the orbital station environment . High quality of air disinfection and decontamination has been demonstrated aboard SS Mir and the International space station.

Morfologiia, 2004, 125(2), 78 - 85
{In Process Citation}
Is the nectar redox cycle a floral defense against microbial attack?
Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USAMany angiosperms use a remarkable reproductive strategy that relies on attracting animals (insect, avian or mammalian pollinators) to transfer pollen between plants . Relying on other organisms for sexual reproduction seems evolutionarily untenable, but the great diversity of angiosperms illustrates how highly successful this strategy is . To attract pollinators, plants offer a variety of rewards . Perhaps the primary floral reward is floral nectar . Plant nectar has long been considered a simple sugar solution but recent work has demonstrated that nectar is a complex biological fluid containing significant and important biochemistry with the potential function of inhibiting microbial growth . These results lead the way to novel insights into the mechanisms of floral defense and the co-evolution of angiosperms and their pollinators.

Curr Opin Plant Biol, 2004 Aug, 7(4), 356 - 64
Strategies used by bacterial pathogens to suppress plant defenses; Abramovitch RB et al.; Plant immune systems effectively prevent infections caused by the majority of microbial pathogens that are encountered by plants . However, successful pathogens have evolved specialized strategies to suppress plant defense responses and induce disease susceptibility in otherwise resistant hosts . Recent advances reveal that phytopathogenic bacteria use type III effector proteins, toxins, and other factors to inhibit host defenses . Host processes that are targeted by bacteria include programmed cell death, cell wall-based defense, hormone signaling, the expression of defense genes, and other basal defenses . The discovery of plant defenses that are vulnerable to pathogen attack has provided new insights into mechanisms that are essential for both bacterial pathogenesis and plant disease resistance.

BMC Bioinformatics . 2004 Jul 01;5(1):86.
mlstdbNet - distributed multi-locus sequence typing (MLST) databases; Jolley KA et al.; BACKGROUND: Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments . The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet . RESULTS: The software enables multiple isolate databases to query a single profiles database that contains allelic profile and sequence definitions . This separation enables isolate databases to be established by individual laboratories, each customized to the needs of the particular project and with appropriate access restrictions, while maintaining the benefits of a single definitive source of profile and sequence information . Databases are described by an XML file that is parsed by a Perl CGI script . The software offers a large number of ways to query the databases and to further break down and export the results generated . Additional features can be enabled by installing third-party (freely available) tools . CONCLUSION: Development of a distributed structure for MLST databases offers scalability and flexibility, allowing participating centres to maintain ownership of their own data, without introducing duplication and data integrity issues.

Environ Toxicol Chem, 2004 Jul, 23(7), 1600 - 9
Estimation of microbial reductive transformation rates for chlorinated benzenes and phenols using a quantitative structure-activity relationship approach; Tebes-Stevens CL et al.; A set of literature data was used to derive several quantitative structure-activity relationships (QSARs) to predict the rate constants for the microbial reductive dehalogenation of chlorinated aromatics . Dechlorination rate constants for 25 chloroaromatics were corrected for the effects of hydrophobic partitioning and adjusted for the observed distribution of product species . A number of physicochemical properties and molecular parameters were considered for inclusion in the QSARs . Multivariate statistical analyses were used to select the optimal set of descriptors to minimize multicollinearity between the descriptors, as well as to minimize the p-value of the regression coefficients . The final QSAR included four descriptors: The logarithm of the octanol-water partition coefficient (Kow), the summation of the Hammett sigma constants, and the sigma induction constants in the ortho and meta positions relative to the transformation reaction center . The predictive ability of this QSAR was evaluated using 24 site-specific rate constants that were measured in five separate studies and were not used to derive the expression . The peer-reviewed literature was screened carefully to ensure that all rate constant data were representative of environmentally relevant conditions.

Nature, 2004 Jul 1, 430(6995), 75 - 8
Microbialite resurgence after the Late Ordovician extinction; Sheehan PM et al.; Microbialites, including biogenic stromatolites, thrombolites and dendrolites, were formed by various microbial mats that trapped and bound sediments or formed the locus of mineral precipitation . Microbialites were common and diverse during the Proterozoic, but declined in abundance and morphological diversity when multicellular life diversified during the Cambrian Radiation . A second decline occurred during the Ordovician Radiation of marine animals, and from then until the present microbialites have been confined largely to high-stress environments where multicellular organisms are rare . The microbialite declines in the Phanerozoic are attributed to disruption of the mats by animals . A resurgence of stromatolite abundance and size during reduced animal diversity after the Permian extinction has been documented anecdotally . Here we show, with statistical support, that a microbialite resurgence also occurred after the Late Ordovician extinction event in western North America . The resurgences were associated with loss of mat-inhibiting animals, providing insights into shallow-water community structures after extinction events.

Enferm Infecc Microbiol Clin, 2004 Jun-Jul, 22(6), 355 - 60
{Applications of PCR techniques for molecular epidemiology of infectious diseases}; Fernandez-Cuenca F; The development of new PCR-based typing methods in the last years have supposed an important advance in the study of infectious diseases . Arbitrarily primed PCR (AP-PCR) and repetitive element sequence-based PCR (rep-PCR) are the most widely used PCR-based fingerprinting methods for bacteria and fungi . Major advantages of these methods are flexibility, technical simplicity and high discriminatory power . The AP-PCR presents problems of low inter-run and inter-laboratory reproducibility which make necessary the optimization of the protocol and reagents . PCR-RFLP is based in the enzymatic digestion of polymorphic genes amplified by PCR . This method is easy to perform and discriminatory, although less than AP-PCR or rep-PCR . Amplified fragment length polymorphism (AFLP) is a highly reproducible and discriminatory typing method based on the amplification by PCR of restriction fragments obtained from chromosomic DNA . This method is more discriminative and reproducible than AP-PCR, rep-PCR and PCR-RFLP, but it is more time-consuming and expensive, and requires specialised personnel . Most of these PCR-based typing methods are less time-consuming, rapid and easy to perform and of interpretation than pulsed-field gel electrophoresis (PFGE; gold standard method for typing most bacterium and fungi), but they usually are less discriminative and reproducible than PFGE, depending on the species studied and the method of PCR used . In summary, there are several PCR-based methods which are useful as a primary approach to the study of the clonal relationship among microbial isolates . The selection of the method to be used depend on technical (rapid, low time-consuming, easy to perform and to interpret, reproducible and discriminatory) and economical (low cost) factors.

Ying Yong Sheng Tai Xue Bao, 2004 Mar, 15(3), 487 - 92
{Effects of different organic materials and their composting levels on soil microbial community}; Kong W et al.; In this paper, a pot experiment with tomato and different organic material amendment was installed in a greenhouse, and the diversity of soil microbial communities and their utilization pattern of amine, amino acid, carbohydrate, carboxylic acid, polymer and miscellaneous were assessed by Biolog method at 60 days after amendment . The results showed that organic material amendment could improve soil microbial community diversity . Fresh distiller grain amendment was a little bit better than its 10 days composting, and the composting level of cow manure had a significant positive or negative effect on the microbial diversity . Among the six carbon sources, the utilization of carbohydrate by soil microbial communities was the highest, and the microbial communities in soils amended with distiller grain had a significantly higher utilization of polymer, relative to those in soils amended with cow manure.

Ying Yong Sheng Tai Xue Bao, 2004 Mar, 15(3), 469 - 72
{Effect of crop-residue incorporation on soil CO2 emission and soil microbial biomass}; Qiang X et al.; In a wheat-corn cropping system, the crop residues were crushed and incorporated into soil after harvest . The soil respiration and soil microbial biomass were compared one year later with soil that had doubled amount of residues incorporation or had no incorporated residues . The soil respiration was increased by the residue incorporation and the effect was more apparent when the incorporated residue amount was doubled . The soil microbial biomass was also increased by the residue incorporation . But the effect of the incorporated residue quantity was not significant . Seasonally, the maximum soil respiration appeared earlier than the maximum microbial biomass, but soon turned to decrease . The microbial biomass maintained the high level for a longer period, indicating there was maintenance respiration and biosynthetic respiration as well . The residue incorporation was suggested as a measure to increase the soil fertility, but doubling the amount of residue incorporation seems not necessary.

Ying Yong Sheng Tai Xue Bao, 2004 Mar, 15(3), 449 - 52
{Effect of incorporating corn residues into soil on nitrogen transformation in soil-plant ecosystem}; Wang S et al.; Appropriate field management of crop residues can help to enhance soil productivity and nutrient recycling, and to minimize greenhouse gas emission . In this paper, a 15N tracer pot experiment was installed to study the effect of incorporating corn stalk and stubble into black soil on the nitrogen transformation in soil-plant ecosystem . The results indicated that compared with single application of N fertilizer, incorporation of corn stalk and stubble could increase soil nitrogen content and enhance its availability, and increase soil microbial nitrogen content . It also promoted the transfer of nitrogen in corn into its kernel, so as to increase the nitrogen use efficiency . Simultaneously, it reduced the content of soil NO3(-)-N, and decreased the fertilizer nitrogen loss by 4.7-5.6%.

Folia Microbiol (Praha), 2004, 49(2), 183 - 6
Obstacles to flow cytometric analysis of rumen microbial samples; Lipoglavsek L et al.; Several methods were tested that would improve the fluorescence signal from hybridized rumen bacterial cells . Disruption of cell envelopes by lysozyme, EDTA, proteinase K and/or SDS caused only a minor increase in fluorescence signal . Use of helper unlabeled oligonucleotide probes was successful only with the Puni{H672} probe which, however, when used with specific PBBl4-labeled probe, gave fluorescence signal drop . No substantial rise in fluorescence signal was also observed with cells subjected to growth-without-cell-division treatment . Further improvements are needed to make the fluorescent in situ hybridization (FISH)-flow cytometry combination applicable to rumen bacteria.

Physiol Genomics, 2004 Sep 16, 19(1), 22 - 31 Epub 2004 Jun 29.
Impact of commensal microbiota on murine gastrointestinal tract gene ontologies; Mutch DM et al.; The gastrointestinal tract (GIT) of eukaryotes is colonized by a vast number of bacteria, where the commensal microbiota play an important role in defining the healthy gut . To investigate the influence of commensal bacteria on multiple regions of the host GIT transcriptome, the gene expression profiles of the corpus, jejunum, descending colon, and rectum of conventional (n = 3) and germ-free mice (n = 3) were examined using the Affymetrix Mu74Av2 GeneChip . Differentially regulated genes were identified using the global error assessment model, and a novel method of Gene Ontology (GO) clustering was used to identify significantly modulated biological functions . The microbiota modify the greatest number of genes in the jejunum (267 genes with an alpha < 0.001) and the fewest in the rectum (137 genes with an alpha < 0.001) . Clustering genes by GO biological process and molecular function annotations revealed that, despite the large number of differentially regulated genes, the residential microbiota most significantly modified genes involved in such biological processes as immune function and water transport all along the length of the mouse GIT . Additionally, region-specific communication between the host and microbiota were identified in the corpus and jejunum, where tissue kallikrein and apoptosis regulator activities were modulated, respectively . These findings identify important interactions between the microbiota and the mouse gut tissue transcriptome and, furthermore, suggest that interactions between the microbial population and host GIT are implicated in the coordination of region-specific functions.

Theor Popul Biol, 2004 Aug, 66(1), 37 - 51
The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model; Jost C et al.; Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains . However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs-organisms that both photosynthesize and graze . We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients-autotrophs-herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs . This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics . The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions . However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime . Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

Toxicon, 2004 Jul, 44(1), 107 - 9
Isolation of Adda from microcystin-LR by microbial degradation; Harada K et al.; The intact Adda was isolated from microcystin-LR by a microbial degradation using an isolated Sphingomonas strain, B-9 . The reaction of microcystin-LR with cell extract of this strain proceeded smoothly to give the final degradation product by way of two intermediates, linearized microcystin-LR and a tetrapeptide . The purified Adda that was structurally characterized using various spectral data did not show the toxicity to mice or inhibition to protein phosphatase activity in contrast to the native toxin.

J Environ Qual, 2004 May-Jun, 33(3), 984 - 93
Overland and near-surface transport of Cryptosporidium parvum from vegetated and nonvegetated surfaces; Trask JR et al.; Understanding microbial pathogen transport patterns in overland flow is important for developing best management practices for limiting microbial transport to water resources . Knowledge about the effectiveness of vegetative filter strips (VFS) to reduce pathogen transport from livestock confinement areas is limited . In this study, overland and near-surface transport of Cryptosporidium parvum has been investigated . Effects of land slopes, vegetation, and rainfall intensities on oocyst transport were examined using a tilting soil chamber with two compartments, one with bare ground and the other with brome (Bromus inermis Leyss.) vegetation . Three slope conditions (1.5, 3.0, and 4.5%) were used in conjunction with two rainfall intensities (25.4 and 63.5 mm/h) for 44 min using a rainfall simulator . The vegetative surface was very effective in reducing C . parvum in surface runoff . For the 25.4 mm/h rainfall, the total percent recovery of oocysts in overland flow from the VFS varied from 0.6 to 1.7%, while those from the bare ground condition varied from 4.4 to 14.5% . For the 63.5 mm/h rainfall, the recovery percentages of oocysts varied from 0.8 to 27.2% from the VFS, and 5.3 to 59% from bare-ground conditions . For all slopes and rainfall intensities, the total (combining both surface and near-surface) recovery of C . parvum oocysts was considerably less from the vegetated surface than those from the bare-ground conditions . These results indicate that the VFS can be a best management practice for controlling C . parvum in runoff from animal production facilities.

J Environ Qual, 2004 May-Jun, 33(3), 816 - 24
Impact of genetically modified crops and their management on soil microbially mediated plant nutrient transformations; Motavalli PP et al.; One of the potential environmental effects of the recent rapid increase in the global agricultural area cultivated with transgenic crops is a change in soil microbially mediated processes and functions . Among the many essential functions of soil biota are soil organic matter decomposition, nutrient mineralization and immobilization, oxidation-reduction reactions, biological N fixation, and solubilization . However, relatively little research has examined the direct and indirect effects of transgenic crops and their management on microbially mediated nutrient transformations in soils . The objectives of this paper are to review the available literature related to the environmental effects of transgenic crops and their management on soil microbially mediated nutrient transformations, and to consider soil properties and climatic factors that may affect the impact of transgenic crops on these processes . Targeted genetic traits for improved plant nutrition include greater plant tolerance to low Fe availability in alkaline soils, enhanced acquisition of soil inorganic and organic P, and increased assimilation of soil N . Among the potential direct effects of transgenic crops and their management are changes in soil microbial activity due to differences in the amount and composition of root exudates, changes in microbial functions resulting from gene transfer from the transgenic crop, and alteration in microbial populations because of the effects of management practices for transgenic crops, such as pesticide applications, tillage, and application of inorganic and organic fertilizer sources . Possible indirect effects of transgenic crops, including changes in the fate of transgenic crop residues and alterations in land use and rates of soil erosion, deserve further study . Despite widespread public concern, no conclusive evidence has yet been presented that currently released transgenic crops, including both herbicide and pest resistant crops, are causing significant direct effects on stimulating or suppressing soil nutrient transformations in field environments . Further consideration of the effects of a wide range of soil properties, including the amount of clay and its mineralogy, pH, soil structure, and soil organic matter, and variations in climatic conditions, under which transgenic crops may be grown, is needed in evaluating the impact of transgenic crops on soil nutrient transformations . Future environmental evaluation of the impact of the diverse transgenic crops under development could lead to an improved understanding of soil biological functions and processes.

Int J Phytoremediation, 2004, 6(1), 1 - 15
Artificial inoculation-perspectives in tailings phytostabilization; Petrisor IG et al.; Intensive mining and processing activities worldwide resulted in the generation of huge amounts of waste (tailings), generally characterized as toxic, radioactive, and/or hazardous . The exposure potential and, hence, the risk posed by such wastes is enhanced by a general lack of vegetation . Phytostabilization has proven to be efficient in reducing this risk . However, establishing vegetation on tailing dumps may be expensive due to the intensive use of amendments and chemical fertilizers . In this article, investigations on artificial inoculation of mine tailings with bacterial strains as a means to improve the development of vegetative covers and reduce application cost by eliminating chemical fertilization are presented and discussed . The development of plants and microbial communities from tailings, as well as the impact of inoculation on metal uptake in plants, were studied . Experiments were carried out in greenhouse using two types of mine tailings (phosphogypsum and sulphidic tailings) from the Romanian Black Sea coast . Indigenous herbaceous plants were cultivated on tailings with the addition of chemical fertilizers versus bacterial inoculation . After a 6-month experimental period, excellent plant growth, which is associated with a rich microbial community, was observed in all inoculated treatments, in contrast with poor plant growth and microbiota from the chemical fertilization treatments alone . Additionally, artificial inoculation improved plant resistance to heavy metals by reducing the uptake of some toxic metals . Once a rich microbial community is established, inoculation may be discontinued . Based on these results, efficient and cost-effective phytostabilization schemes can be proposed.

Environ Sci Technol, 2004 Jun 1, 38(11), 3131 - 8
Reactive transport modeling of column experiments for the remediation of acid mine drainage; Amos RT et al.; Reactive transport modeling was used to evaluate the performance of two similar column experiments . The experiments were designed to simulate the treatment of acid mine drainage through microbially mediated sulfate reduction and subsequent sulfide mineral precipitation by means of an organic carbon permeable reactive barrier . Principal reactions considered in the simulations include microbially mediated reduction of sulfate by organic matter, mineral dissolution/precipitation reactions, and aqueous complexation/hydrolysis reactions . Simulations of column 1, which contained composted leaf mulch, wood chips, sawdust, and sewage sludge as an organic carbon source, accurately predicted sulfate concentrations in the column effluent throughout the duration of the experiment using a single fixed rate constant for sulfate reduction of 6.9 x 10(-9) mol L(-1) s(-1) . Using the same reduction rate for column 2, which contained only composted leaf mulch and sawdust as an organic carbon source, sulfate concentrations at the column outlet were overpredicted at late times, suggesting that sulfate reduction rates increased over the duration of the column experiment and that microbial growth kinetics may have played an important role . These modeling results suggest that the reactivity of the organic carbon treatment material with respect to sulfate reduction does not significantly decrease over the duration of the 14-month experiments . The ability of the columns to remove ferrous iron appears to be strongly influenced by the precipitation of siderite, which is enhanced by the dissolution of calcite . The simulations indicate that while calcite was available in the column, up to 0.02 mol L(-1) of ferrous iron was removed from solution as siderite and mackinawite . Later in the experiments after approximately 300 d, when calcite was depleted from the columns, mackinawite became the predominant iron sink . The ability of the column to remove ferrous iron as mackinawite was estimated to be approximately 0.005 mol L(-1) for column 1 . As the precipitation of mackinawite is sulfide limited at later times, the amount of iron removed will ultimately depend on the reactivity of the organic mixture and the amount of sulfate reduced.

Z Rheumatol, 2004 Jun, 63(3), 187 - 92
{Pathogenesis of ankylosing spondylitis-mechanisms of disease manifestation and chronicity}; Marker-Hermann E et al.; Despite intensive research during the last three decades, it is still not clear which precise mechanisms determine the interactions between host factors (HLA-B27 and other genes, cytokines, T lymphocytes) and microbial factors leading to the manifestation and chronicity of ankylosing spondylitis (AS) . Rheumatologists and histopathologists have focused their interest on decoding the immune-mediated inflammatory processes and on studying new bone formation and ankylosis . Concerning the genetic basis of AS, there is considerable effort in large genome-wide and candidate gene analyses to discover new genes that are associated with AS . Moreover, such genetic studies could identify genomic regions that determine clinical manifestations and the course of disease.

J Mol Biol, 2004 Jul 16, 340(4), 909 - 17
Crystal structure of the Drosophila peptidoglycan recognition protein (PGRP)-SA at 1.56 A resolution; Reiser JB et al.; Peptidoglycan recognition proteins (PGRPs) form a recently discovered protein family, which is conserved from insect to mammals and is implicated in the innate immune system by interacting with/or degrading microbial peptidoglycans (PGNs) . Drosophila PGRP-SA is a member of this family of pattern recognition receptors and is involved in insect Toll activation . We report here the crystal structure of PGRP-SA at 1.56 A resolution, which represents the first example of a "recognition" PGRP . Comparison with the catalytic Drosophila PGRP-LB reveals an overall structure conservation with an L-shaped hydrophilic groove that is likely the PGN carbohydrate core binding site, but further suggests some possible functional homology between recognition and catalytic PGRPs . Consistent with sequence analysis, PGRP-SA does not contain the canonical zinc-binding residues found in catalytic PGRPs . However, substitution of the zinc-binding cysteine residue by serine, along with an altered coordinating histidine residue, assembles a constellation of residues that resembles a modified catalytic triad . The serine/histidine juxtaposition to a threonine residue and a carbonyl oxygen atom, along with conservation of the catalytic water molecule found in PGRP-LB, tantalizingly suggests some hydrolytic function for this member of receptor PGRPs.

Biometals, 2004 Jun, 17(3), 203 - 8
Lactoferrin: role in iron homeostasis and host defense against microbial infection; Ward PP et al.; The transferrin family of non-heme iron binding glycoproteins are believed to play a central role in iron metabolism and have been implicated in iron transport, cellular iron delivery and control of the level of free iron in external secretions . Lactoferrin (LF) is a member of this family that is widely localized in external fluids including milk and mucosal secretions, in addition to being a prominent component of the secondary granules of neutrophils . Although structurally related to transferrin, LF appears to have a broader functional role mediated by both iron dependent and iron independent mechanisms . In this review, we will focus on our current understanding on the role of LF in regulating iron homeostasis and its role in host protection against microbial infection at the mucosal surface . In addition, recent insights obtained from analyzing the phenotypic consequences of LF ablation in lactoferrin knockout mice (LFKO), which challenge the long held dogma that LF is required for intestinal iron absorption in the neonate, are summarized.

Eur J Clin Microbiol Infect Dis, 2004 Jul, 23(7), 539 - 44 Epub 2004 Jun 22.
Markers of bacteremia in febrile neutropenic patients with hematological malignancies: procalcitonin and IL-6 are more reliable than C-reactive protein; von Lilienfeld-Toal M et al.; Since neutropenic patients with hematological malignancies are at high risk of contracting life-threatening infections, specific markers of infection are needed in cases of febrile neutropenia . The study presented here assessed serum concentrations of C-reactive protein (CRP), procalcitonin (PCT) and interleukin-6 (IL-6) in samples obtained from 31 febrile neutropenic patients . A total of 53 episodes were evaluated, and 18 of these were associated with positive blood culture results . Procalcitonin and IL-6 concentrations differed significantly between bacteremic and non-bacteremic episodes . Procalcitonin values were 0.22 ng/ml {interquartile range (IR), 0.15-1.9} for patients with pneumonia without bacteremia, 0.22 ng/ml (IR, 0.16-0.55) for patients with fever of unknown origin, 0.2 ng/ml (IR, 0.13-0.57) for patients with non-microbial fever and 1.8 ng/ml (IR, 0.35-5.3) for patients with bacteremia . The differences between bacteremic and non-bacteremic episodes had a P-value of 0.003 using the Mann-Whitney test . For IL-6 the median values were 301 pg/ml (IR, 152-1,879) for patients with pneumonia without bacteremia, 207 pg/ml (IR, 94-445) for patients with fever of unknown origin, 177 pg/ml (IR, 142-208) for patients with non-microbial fever and 942 pg/ml (IR, 181-2,807) for patients with bacteremia . Using the Mann-Whitney test, the differences between bacteremic and non-bacteremic episodes were P=0.006 . No differences were found in CRP concentrations . Cutoff levels to distinguish between bacteremic and non-bacteremic episodes were chosen using receiver operating characteristic curves: 0.62 ng/ml for PCT and 297 pg/ml for IL-6 . Negative predictive values were 84% for PCT and 70% for IL-6 . The results indicate that PCT and IL-6 are more reliable markers than CRP for predicting bacteremia in patients with febrile neutropenia.

Mycorrhiza, 2004 Aug, 14(4), 271 - 5 Epub 2004 Jun 25.
Rapid and reliable DNA extraction techniques from trypan-blue-stained mycorrhizal roots: comparison of two methods; Ishii S et al.; Two improved DNA extraction techniques from trypan-blue-stained root fragments were developed and compared for rapid and reliable analyses . In Method A, 1 cm trypan-blue-stained mycorrhizal root fragments were individually isolated, crushed by bead beating, and purified with Chelex-100 (Bio-Rad) . In Method B, DNA extraction was carried out using an UltraClean microbial DNA isolation kit (MoBio Laboratories) . DNA was extracted from the mycorrhizal roots of four plant species, quantified by UV absorbance, and PCR-amplified with primers specific to arbuscular mycorrhizal fungi . Although PCR inhibitors might still exist when using Method A, appropriate dilution and employment of nested-PCR overcame this problem . Method B removed PCR inhibitors, but sometimes, depending on the mycorrhizal colonization within the root fragments, it also required nested PCR . In conclusion, both methods enabled us to handle many samples in a short time . Method B provided greater reliability and Method A provided better cost performance . Both techniques can be useful for PCR-based applications to identify species and estimate species composition after measuring mycorrhizal colonization rate with trypan blue staining.

Oecologia, 2004 Aug, 140(4), 617 - 25 Epub 2004 Jun 19.
Successional changes in soil nitrogen availability, non-symbiotic nitrogen fixation and carbon/nitrogen ratios in southern Chilean forest ecosystems; Perez CA et al.; Vast areas of southern Chile are now covered by second-growth forests because of fire and logging . To study successional patterns after moderate-intensity, anthropogenic fire disturbance, we assessed differences in soil properties and N fluxes across a chronosequence of seven successional stands (2-130 years old) . We examined current predictions of successional theory concerning changes in the N cycle in forest ecosystems . Seasonal fluctuations of net N mineralization (N(min)) in surface soil and N availability (N(a); N(a)=NH4+-N+NO3--N) in upper and deep soil horizons were positively correlated with monthly precipitation . In accordance with theoretical predictions, stand age was positively, but weakly related to both N(a) ( r(2)=0.282, P<0.001) and total N (N(tot); r(2)=0.192, P<0.01), and negatively related to soil C/N ratios ( r(2)=0.187, P<0.01) in surface soils . A weak linear increase in soil N(min) (upper plus deep soil horizons) was found across the chronosequence ( r(2)=0.124, P<0.022) . N(min) occurred at modest rates in early successional stands, suggesting that soil disturbance did not impair microbial processes . The relationship between N fixation (N(fix)) in the litter layer and stand age best fitted a quadratic model ( r(2)=0.228, P<0.01) . In contrast to documented successional trends for most temperate, tropical and Mediterranean forests, non-symbiotic N(fix) in the litter layer is a steady N input to unpolluted southern temperate forests during mid and late succession, which may compensate for hydrological losses of organic N from old-growth ecosystems.

Theor Appl Genet, 2004 Sep, 109(5), 922 - 32
Pine genes regulated by the necrotrophic pathogen Fusarium circinatum; Morse AM et al.; A targeted genomics approach was used to construct a cDNA array of potential pathogen-regulated genes for investigating host-pathogen interactions in pine trees (Pinus species) . This array, containing a nonredundant set of 311 cDNAs, was assembled by combining smaller sets of cDNAs generated by differential display or suppression subtraction hybridization using a variety of pathogen treatments and elicitors . The array was probed to identify host genes regulated by Fusarium circinatum, a necrotrophic fungus that incited pitch canker disease on pine stems . A set of 29 cDNAs were induced during the disease state . Notably, cDNAs on the array that were derived from experiments with fusiform rust, incited by Cronartium quercuum f . sp . fusiforme (a biotrophic fungus) were unregulated by Fusarium . the results imply distinct genetic responses in pine to diseases incited by necrotrophs and biotrophs . This cDNA collection expands the genomics toolkit for understanding interactions between conifers and their microbial associates in forest ecosystems.

J Clin Gastroenterol, 2004 Jul, 38(6 Suppl), S84 - 5
The role of probiotics in the clinical management of food allergy and atopic dermatitis; Miraglia del Giudice M et al.; The probiotics are cultures of potentially beneficial bacteria that positively affects host by enhancing the microbial balance and therefore restore the normal intestinal permeability and gut microecology, improve the intestine's immunologic barrier function and reduce the generation of proinflammatory cycochines characteristics of allergic inflammation . The authors made a survey of the most relevant studies concerning the use of probiotics in the food allergy, atopic dermatitis, and in primary prevention of atopy . On the basis of these trials probiotic therapy alleviates allergic inflammation as demonstrated by the control of clinical symptoms and the reduction of local and systemic inflammatory markers.

J Virol, 2004 Jul, 78(14), 7852 - 60
Epstein-Barr virus latent membrane protein LMP-2A is sufficient for transactivation of the human endogenous retrovirus HERV-K18 superantigen; Sutkowski N et al.; Superantigens are microbial proteins that strongly stimulate T cells . We described previously that the Epstein-Barr virus (EBV) transactivates a superantigen encoded by the human endogenous retrovirus, HERV-K18 . We now report that the transactivation is dependent upon the EBV latent cycle proteins . Moreover, LMP-2A is sufficient for induction of HERV-K18 superantigen activity.

Prog Retin Eye Res, 2004 Jul, 23(4), 449 - 74
Changes in the tear film and ocular surface from dry eye syndrome; Johnson ME et al.; Dry eye syndrome (DES) refers to a spectrum of ocular surface diseases with diverse and frequently multiple aetiologies . The common feature of the various manifestations of DES is an abnormal tear film . Tear film abnormalities associated with DES are tear deficiency, owing to insufficient supply or excessive loss, and anomalous tear composition . These categorizations are artificial, as in reality both often coexist . DES disrupts the homeostasis of the tear film with its adjacent structures, and adversely affects its ability to perform essential functions such as supporting the ocular surface epithelium and preventing microbial invasion . In addition, whatever the initial trigger, moderate and severe DES is characterized by ocular surface inflammation, which in turn becomes the cause and consequence of cell damage, creating a self-perpetuating cycle of deterioration . Progress has been made in our understanding of the aetiology and pathogenesis of DES, and these advances have encouraged a proliferation of therapeutic options . This article aims to amalgamate prevailing ideas of DES development, and to assist in that, relevant aspects of the structure, function, and production of the tear film are reviewed . Additionally, a synopsis of therapeutic strategies for DES is presented, detailing treatments currently available, and those in development.

Acta Biochim Pol, 2004, 51(2), 539 - 44
Differentiated Paju cells have increased resistance to toxic effects of potassium ionophores; Teplova V et al.; In this study we have investigated the impact of differentiation of neuronal cells on their sensitivity to microbial toxins . We used the human neural crest-derived tumor cell line Paju, which can be induced to differentiation in vitro by treatment with phorbol 12-myristate 13-acetate . Addition of the highly toxic potassium ionophores cereulide (4.5 and 9.0 ng/ml) or valinomycin (20 ng/ml), to cultures of undifferentiated Paju cells caused collapse of the mitochondrial membrane potential - measured with the fluorescent probe 5,5',6,6'-tetrachloro-1,1',3,3'-tetrabenzimidazole carbocyanine iodide (JC-1) followed by detachment of the cells and their apoptotic death . After induced differentiation of the Paju cells, their mitochondria retained the membrane potential upon exposure to the toxins and the cells displayed increased resistance to apoptosis as compared with undifferentiated cells . This effect may be caused by an elevated expression of the anti-apoptotic protein Bcl-2 and of the neuroprotective factor, stanniocalcin, in differentiated cells.

Ecotoxicology, 2004 Apr, 13(3), 245 - 60
Effects of the agricultural pesticides atrazine, chlorothalonil, and endosulfan on South Florida microbial assemblages; Downing HF et al.; One of the most impacted watersheds in the US in terms of pesticide usage is South Florida, which drains through a series of canals into the Florida Everglades and Florida Bay . Single species responses to pesticide exposure are well documented; however, little is known about community level responses to pesticides, especially at lower trophic levels . Microbial assemblages at two sites along the C-111 canal in the Dade County agricultural area in October 1999 (wet season, limited pesticide application) and in February 2000 (dry season, heavy pesticide application) were colonized onto artificial substrates, transported to the laboratory and exposed to atrazine (20 and 200 microg/l), chlorothalonil (2 and 20 microg/l), or endosulfan (1 and 10 microg/l) . Structural and functional responses were measured at 24 h and 168 h post-dose . Regardless of site, season or exposure time, the highest atrazine dose (200 microg/l) significantly reduced chlorophyll a, phototrophic carbon assimilation and bacterial biomass, but stimulated heterotrophic bacterial productivity . Chlorophyll a was also significantly reduced by 20 microg/l atrazine (October only) . The lowest endosulfan dose (1 microg/l) significantly increased phototrophic carbon assimilation . The highest chlorothalonil dose (20 microg/l) stimulated heterotrophic bacterial productivity (October only) . An overall decrease in the number of protist taxa was observed with all pesticide treatments . Atrazine significantly decreased the relative abundance of chlorophytes and chrysophytes and increased the number of diatom and heterotrophic protist taxa . Chlorothalonil significantly increased the relative abundance of diatoms and chlorophytes, while chrysophytes and heterotrophic protists decreased . Endosulfan also significantly reduced diatom abundance, as well as decreasing the number of chrysophyte, cryptophyte and dinoflagellate taxa . Although previous agricultural pesticide exposure was greater at site C than at site E, the microbial assemblages at site C did not exhibit increased resistance to a subsequent dose of the pesticides.

Cell Struct Funct, 1999 Oct, 24(5), 237 - 46
Rearrangements of actin cytoskeleton during infection with Escherichia coli O157 in macrophages; Shimada O et al.; The lamina propria of the large intestine is rich in macrophages, and they might be one of the first lines of the host defense in enterohemorrhagic Escherichia coli (EHEC) O157:H7 infection . Although macrophages were infected with them, they can survive the EHEC O157 infection . We examined the structural rearrangements of the actin cytoskeleton during the microbial infection process . Macrophage actin filaments were rearranged in the following sequence; 1) disappearance of the actin filament bundles in the cytoplasm, 2) accumulation of actin filaments under the cell surface, and 3) construction of actin networks underlying the endosome membrane . Before infection, actin filaments were distributed under the cell surface and in bundles located in the macrophage cytoplasm . Within 2 min, infection caused a rapid and marked loss of the actin filament bundles that had run parallel to the long axis of the cell . Concomitant with the loss, actin filaments became more markedly distributed under the cell surface . In the formation of the endosome, new networks of actin filaments were constructed below the phagosome membrane . The networks contained a large amount of actin as well as a fodrin-like immunoreactivity . The thickness of the networks reached about 400 nm under the phagosome membrane . The actin networks disappeared again after the bacterial digestion . The results of this study showed that actin filaments undergo three major rearrangements of the actin filaments during the infection in macrophages, and suggested that the third rearrangement is mediated by actin-binding proteins, such as a fodrin-like molecules . These morphological changes in macrophages were not clear after infection with other strains of Escherichia coli.

Plant Cell Physiol, 2004 Jun, 45(6), 770 - 80
Up-regulation and localization of asparagine synthetase in tomato leaves infected by the bacterial pathogen Pseudomonas syringae; Olea F et al.; Nitrogen metabolism is one aspect of basic metabolism, which is still quite unknown in the field of plant-pathogen interactions . Evidence derived from previous studies conducted in our laboratory strongly suggests that during microbial pathogenesis an important nitrogen mobilization process takes place in diseased tissues . Here we describe the expression pattern of asparagine synthetase (AS; EC 6.3.5.4) in tomato leaves infected by the bacterial pathogen Pseudomonas syringae pv . tomato . Using an homologous AS cDNA probe isolated by RT-PCR from infected leaves, we have observed a high level induction of AS expression during the course of infection . Concomitantly, a single AS polypeptide also accumulated in response to bacterial infection . Furthermore, immunohistochemical analysis of AS in infected leaves revealed a strong immunostaining in phloem cells of the main vascular bundles and in secondary veins of the leaf blade . These data correlate with those previously reported for expression of a cytosolic isoform of glutamine synthetase (GS1) also induced during development of the infectious process . Taken together, our results suggest the existence of a GS1/AS pathway representing a metabolic route for transferring ammonium released from protein catabolism into asparagine, an amino acid that may have a major role in nitrogen mobilization from diseased tissues.

Nucleic Acids Res, 2004 Jul 1, 32(Web Server issue), W59 - 63
MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments; Ray WC; Many powerful tools have been created to detect and describe the similarities between nucleic acid or protein sequences . Frequently these take the form of a sequence consensus, expressing simple most popular positional identities, positional identities with allowances for varying positions or some type of statistical description of the positional frequency characteristics of the defining sequence family . Despite the fact that some provide intuitively interpretable descriptions of the consensuses themselves, they typically do not give the viewer any information about regions of the sequence that might have inter-positional dependencies, and that therefore do not obey a strict consensus behavior . Herein, we present MAVL (Multiple Alignment Variation Linker) and StickWRLD . MAVL is our web-based application for detecting and displaying both positive and negative inter-positional correlations in nucleic acid sequences . MAVL examines all positional pairs in each of a collection of pre-aligned sequences and determines any pairs that occur with either greater or lesser frequency than a positional frequency matrix would predict . These data are then composited into a StickWRLD representation and supplied back to the user as a VRML (virtual reality modeling language) file . MAVL and StickWRLD can be accessed at A tutorial that explains MAVL features and demonstrates typical user interactions with StickWRLD graphs is available at This tutorial is quite large; please be patient while it loads.

J Biol Chem, 2004 Sep 3, 279(36), 37436 - 44 Epub 2004 Jun 22.
BCL10 mediates lipopolysaccharide/toll-like receptor-4 signaling through interaction with Pellino2; Liu Y et al.; Toll-like receptor (TLR) pathways signal through microbial components stimulation to induce innate immune responses . Herein, we demonstrate that BCL10, a critical molecule that signals between the T cell receptor and IkappaB kinase complexes, is involved in the innate immune system and is required for appropriate TLR4 pathway and nuclear factor-kappaB (NF-kappaB) activation . In response to lipopolysaccharide (LPS) stimulation, BCL10 was recruited to TLR4 signaling complexes and associated with Pellino2, an essential component down-stream of BCL10 in the TLR4 pathway . In a BCL10-deficient macrophage cell line, LPS-induced NF-kappaB activation was consistently defective, whereas activator protein-1 and Elk-1 signaling was intact . In addition, we found that BCL10 was targeted by SOCS3 for negative regulation in LPS signaling . The recruitment of BCL10 to TLR4 signaling complexes was attenuated by induced expression of SOCS3 in a feedback loop . Furthermore, ectopic SOCS3 expression blocked the interaction between BCL10 and Pellino2 together with BCL10-generated NF-kappaB activation and inducible nitric-oxide synthase expression . Together, these data define an important role of BCL10 in the innate immune system.

Infect Immun, 2004 Jul, 72(7), 3951 - 60
Murine oviduct epithelial cell cytokine responses to Chlamydia muridarum infection include interleukin-12-p70 secretion; Johnson RM; Epithelial cells play an important role in host defense as sentinels for invading microbial pathogens . Chlamydia trachomatis is an intracellular bacterial pathogen that replicates in reproductive tract epithelium . Epithelial cells lining the reproductive tract likely play a key role in triggering inflammation and adaptive immunity during Chlamydia infections . For this report a murine oviduct epithelial cell line was derived in order to determine how epithelial cells influence innate and adaptive immune responses during Chlamydia infections . As expected, oviduct epithelial cells infected by Chlamydia muridarum produced a broad spectrum of chemokines, including CXCL16, and regulators of the acute-phase response, including interleukin-1alpha (IL-1alpha), IL-6, and tumor necrosis factor alpha . In addition, infected epithelial cells expressed cytokines that augment gamma interferon (IFN) production, including IFN-alpha/beta and IL-12-p70 . To my knowledge this is the first report of a non-myeloid/lymphoid cell type making IL-12-p70 in response to an infection . Equally interesting, infected epithelial cells significantly upregulated transforming growth factor alpha precursor expression, suggesting a mechanism by which they might play a direct role in the pathological scarring seen as a consequence of Chlamydia infections . Data from these in vitro studies predict that infected oviduct epithelium contributes significantly to host innate and adaptive defenses but may also participate in the immunopathology seen with Chlamydia infections.

Chemosphere, 2004 Aug, 56(5), 475 - 80
Formation of chloromethoxybenzaldehyde during composting of organic household waste; Eklind Y et al.; Standardized household waste was mixed with different litter amendments, straw, leaves, hardwood shavings, softwood shavings, paper, and sphagnum peat, resulting in six compost mixtures . In addition non-amended household waste was composted . Composting was done in small rotatable bins and compost samples were taken on a regular basis until day 590 . Extraction and analysis of wet compost samples showed no evidence for the presence of chloroorganic compounds . Drying and re-wetting of compost samples, however, revealed that chloromethoxybenzaldehyde (CMBA) was formed in all composts at concentrations varying between 5.6 and 73.4 microg kg(-1) dry matter . CMBA was not present in the original materials . During composting, there was a clear positive relation between formation of CMBA and microbial activity, as indicated by C losses and temperature . Formation took place during the most intensive phase of composting when C losses were highest . Under anaerobic conditions, however, which prevailed initially in the non-amended compost, no CMBA was formed . Calculation of total amounts of CMBA in composts revealed that there was a small decrease during storage in the hardwood, peat, and softwood composts . However, all composts contained CMBA after 590 days . The mean concentration was 33.4 microg kg(-1) dry matter (s.d . = 21.9) . Possible biocidal effects of composts when used in cultivation may be explainable by the presence of natural toxic compounds formed during composting.

Chemosphere, 2004 Aug, 56(6), 619 - 30
Effects of bacterial activities on the release of heavy metals from contaminated dredged sediments; Lors C et al.; The potential impact of indigenous bacterial processes on the release of heavy metals from dredged sediment deposits was investigated . Batch re-suspension experiments were conducted in order to investigate the release of Zn, Cd, Cu and Pb from a polluted anoxic sediment submitted to oxidative perturbations . The concentrations of heavy metals, sulphate and dissolved organic carbon (DOC) were periodically recorded, and cell counts were performed to follow the evolution of several bacterial species . The specific effects of microbial processes were quantified by performing re-suspension assays on sterilised samples . Moreover, the effect of an initial acidification of the system was studied . The results showed that metal release was mainly due to oxidation of sulphide minerals contained in the sediment . Sulphur-oxidising bacteria such as Acidithiobacillus thiooxidans were identified to play a major role in the process, by enhancing the oxidation kinetic . However, the acid production resulting from these reactions was almost totally buffered by the dissolution of the calcite present in the sediment . Copper was released to a lesser extent, and a strong association with organic matter was observed . Lead was not observed in solution, because of its low solubility at neutral conditions and of its re-adsorption on the solid phase . The initial acidification of the system resulted in an faster growth of the acidophilic A . thiooxidans . A subsequent pH drop originating from microbial processes was then observed during the first stages of the experiment . As a consequence, drastic increases in metal (Zn, Cd) release were observed.

Chemosphere, 2004 Aug, 56(6), 519 - 30
Degradation of picric acid and 2,6-DNT in marine sediments and waters: the role of microbial activity and ultra-violet exposure; Nipper M et al.; Bio- and photo-transformation of two munitions and explosives of concern, 2,6-dinitrotoluene (2,6-DNT) and 2,4,6-trinitrophenol (picric acid) were assessed in spiked marine sediments and water . A sandy and a fine-grained sediment, with 0.25% and 1.1% total organic carbon, respectively, were used for biotransformation assessments at 10 and 20 degrees C . Sterilized sediments were used as controls for biotic vs . abiotic transformation . Transformation products were analyzed by HPLC, GC/MS and LC/MS . Biotransformation in sediments started soon after the initial contact of the chemicals with the sediments and proceeded for several months, with rates in the following sequence: fine-grain at 20 degrees C > fine-grain at 10 degrees C > sand at 20 degrees C > sand at 10 degrees C . The biotransformation paths seemed to be similar for all conditions . The major biotransformation product of 2,6-DNT was 2-amino-6-nitrotoluene (2-A-6-NT) . 2-Nitrotoluene (2-NT) and other minor components, including N,N-dimethyl-3-nitroaniline, benzene nitrile, methylamino-2-nitrosophenol and diaminophenol, were also identified . After more prolonged incubation these chemicals were replaced by high molecular weight polymers . Several breakdown products of picric acid were identified by GC/MS, including 2,4-dinitrophenol, amino dinitrophenols, 3,4-diamino phenol, amino nitrophenol and nitro diaminophenol . Photo-transformation of 2,6-DNT and picric acid in seawater was assessed under simulated solar radiation (SSR) . No significant photolysis of picric acid in seawater was observed for up to 47 days, but photo-transformation of 2,6-DNT began soon after the initial exposure to SSR, with 89% being photo-transformed in 24 h and none remaining after 72 h . High molecular weight chemicals were generated, with mass spectra ranging from molecular weight 200-500 compared to 182 for DNT, and the color of the stock solution changed from clear to orange . Complexity of the mass spectra and mass differences among fragments suggest that multiple polymers were produced and were co-eluting during the LC/MS analyses.

Best Pract Res Clin Anaesthesiol, 2004 Sep, 18(3), 455 - 75
The systemic inflammatory response syndrome; Weigand MA et al.; Sepsis and septic shock are the leading causes of death in intensive care units in developed countries despite recent advances in critical care medicine . Sepsis is the systemic inflammatory response to infection frequently associated with hypoperfusion followed by tissue injury and organ failure . The activation of monocytes/macrophages and neutrophils, with the consecutive release of pro-inflammatory mediators and activation of the coagulation cascade, seems to play a key role in the pathogenesis of sepsis . Elimination of the septic focus, anti-microbial therapy and supportive treatment are the cornerstones of sepsis therapy . In addition, the application of small doses hydrocortisone to patients with refractory septic shock and the treatment of patients with septic multiple organ failure with activated protein C are two adjunctive therapeutic strategies . Promising new experimental treatment options are interference with MIF, HMGB1, C5a or TREM-1 signal transduction pathways and an inhibition of apoptosis, which may further improve the prognosis of septic patients in the future.

Best Pract Res Clin Anaesthesiol, 2004 Sep, 18(3), 385 - 405
Mechanisms of the inflammatory response; Sherwood ER et al.; The physiological alterations induced by acute inflammation present significant management challenges for anaesthesiologists . Major surgery, trauma, burns and sepsis all have large inflammatory components . Acute inflammation is characterized by vasodilatation, fluid exudation and neutrophil infiltration . These processes are activated and amplified by a series of intracellular and extracellular factors that tightly co-ordinate the inflammatory process . The innate immune system responds rapidly to infection or injury . Macrophages, natural killer cells, CD8 + T-lymphocytes and neutrophils provide an early response to injurious factors in an effort to contain and eliminate harmful stimuli . The adaptive immune response requires prior exposure to microbial antigens, is mediated primarily by CD4 + T-lymphocytes and serves to further amplify acute inflammation . Although acute inflammation is fundamentally beneficial, severe inflammation can precipitate the systemic inflammatory response syndrome . This syndrome is characterized by hyperinflammation and can cause organ injury, shock and death in its most severe forms . Overall, our understanding of inflammation has increased tremendously during the past 20 years . However, these basic science advances have not yet translated into widespread benefit for patients suffering from trauma, sepsis and systemic inflammation.

Environ Sci Technol, 2004 May 15, 38(10), 2813 - 21
Historical variations in the stable isotope composition of mercury in Arctic lake sediments; Jackson TA et al.; The stable isotope composition of mercury (Hg) in a dated core from the anoxic zone of a saline, meromictic Arctic lake was found to vary as a complex function of the age and chemical composition of the sediment . Throughout the stratigraphic sequence, which spans the years 1899-1997, the ratios 198Hg/202Hg, 199Hg/202Hg, 200Hg/202Hg, 201Hg/202Hg, and 204Hg/202Hg expressed as delta-values (per mil deviations relative to a standard) reveal enrichment in 198Hg, 199Hg, 200Hg, and 201Hg, with depletion in 204Hg, the degree of enrichment varying inversely with atomic mass . A plot of delta198Hg, delta199Hg, delta200Hg, and delta201Hg against depth gave parallel profiles characterized by large, regular undulations superimposed on an overall trend toward increase with depth (i.e . age), and the delta204Hg profile is a mirror image of them . The delta198Hg, delta199Hg, delta200Hg, and delta201Hg values of the oldest (1899-1929) strata vary inversely with NH2OH.HCl/HNO3-extractable manganese concentration, but those of the youngest (1963-1997) strata give a positive correlation; intermediate (1936-1956) strata show no correlation and negligible variation in delta-values, possibly signifying a transition phase in which the two opposite trends offset each other . The delta-values show similar but weaker relationships with organic carbon . The results strongly suggest fractionation of Hg isotopes by microbial activities linked to oxidation-reduction reactions in the lake, although effects of isotopic signatures indicative of the sources of the Hg have not been ruled out . The radical change in the nature of the relationship between 6-values and sediment chemistry over time may reflect environmental and biotic changes that altered the isotope-fractionating processes . These findings imply that variations in the isotopic makeup of Hg, together with related physical, chemical, and biological data, could yield important new information about the biogeochemical cycle of Hg.

Invest Clin, 2004 Jun, 45(2), 131 - 5
{Acute non-specific splenitis as indicator of systemic infection . Assessment of 71 autopsy cases}; Arismendi-Morillo GJ et al.; Classic pathology textbooks claim that acute splenitis reflects septic states, nevertheless, the evidence upon which that association is based remains unclear . We assessed the occurrence of acute splenitis, as an indicator of systemic infection, in 34 autopsies performed in patients in whom the cause of death was due to multiple organ dysfunction syndrome, secondary to sepsis (group A); and in 37 cases of death by non-infectious causes (group B) . These necropsies were done during the period January 31, 1999-December 31, 2000, at the Pathology Department of the Hospital General del Sur "Dr . Pedro Iturbe", Maracaibo, Venezuela . Acute splenitis was observed in 79% of the cases in group A, whereas it was absent in group B (p < 0.001) . Thirty three (97%) of the patients of group A did not receive antibiotic therapy, and died within the first 24 hours following admission . Our results suggest that based on a proper clinical-pathological correlation, non-specific acute splenitis constitutes a finding that reflects a septic state, at least in cases that do not receive anti-microbial therapy.

Wei Sheng Yan Jiu, 2004 May, 33(3), 386 - 8
{Quality standards and hygienic problems of bottled drinking-water}; Zhao Q et al.; The consumption of bottled drinking-water increases worldwide and relevant regulation for inspection and supervision work of bottled drinking-water were established in many countries . However, regulation mentioned above is lower than that for tap water . The hygienic problems of bottled drinking-water is emphasized, especially on microbial contamination . In this paper, some issues in regards were reviewed and discussed.

Proteins, 2004 Aug 1, 56(2), 261 - 76
Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase; Giraldo J et al.; The microbial ribonuclease barnase exhibits low catalytic activity toward GpN dinucleotides, where G is guanosine, p is phosphate and N represents any nucleoside . When a phosphate is added to the 3'-end, as in GpNp, substrate affinity is enhanced by one order of magnitude, and the catalytic rate by two . In order to gain insight into this phenomenon, we analyzed the nucleotide conformations and protein-nucleotide interactions of 4 ns molecular dynamics (MD) trajectories of complexes of barnase with guanylyl(3'-5') adenosine (GpA) and guanylyl(3'-5') adenosine 3'-monophosphate (GpAp), respectively, in the presence of solvent and counter ions . We found that, in a majority of the bound GpA conformations, the guanine base was firmly bound to the recognition site . The phosphate and adenosine moieties pointed into the solvent, and interactions with key catalytic residues were absent . In contrast, the bound GpAp adopted conformations in which all of the nucleotide portions remained tightly bound to the enzyme and interactions with key catalytic residues were maintained . These observations indicate that, for GpA, a significant proportion of the bound nucleotide adopts non-productive conformations and that adding the terminal phosphate as in GpAp shifts the equilibrium of the bound conformations towards structures capable of undergoing catalysis . Incorporating this property into the kinetic equations yields an increase in both the apparent rate constant (kcat) and the apparent dissociation constant (K(M)) for GpAp versus GpA . The increase in K(M), caused by the presence of additional non-productive binding modes for GpA, should however be counterbalanced by the propensity of free GpA to adopt folded conformations in solution, which are unable to bind the enzyme and by the tighter binding of GpAp (Giraldo J, Wodak SJ, Van Belle D . Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods . J Mol Biol 1998; 283:863-882) . Addition of the terminal phosphate is shown to significantly influence the collective motion of the enzyme in a manner that fosters interactions with key catalytic residues, representing a further likely contribution to the catalytic rate enhancement .

Khirurgiia (Mosk), 2004, (6), 12 - 6
{Effectiveness of external drainage of the common bile duct}; Cherkasov VA et al.; Influence of different methods of external drainage of the biliary tract on dynamics of inflammation in the biliary tracts was evaluated based on the data examination of bioimpedance, specific electric conductivity and general microbial number of bile received during surgery and from drainage of the common bile duct during 9 days after surgery in 197 patients with cholelithiasis complicated by bile outflow disturbances . It is demonstrated that each type of external drainage has own indications depending on the degree of bacterial contamination, macroscopic structure, biophysical parameters of bile, and planned treatment policy after surgery . Right fixation of the drainage tube in the common bile duct improves immediate results of surgical treatment of patients with cholelithiasis.

J Immunol, 2004 Jul 1, 173(1), 437 - 45
The major surface protein of Wolbachia endosymbionts in filarial nematodes elicits immune responses through TLR2 and TLR4; Brattig NW et al.; More than 150 million humans in tropical countries are infected by filarial nematodes which harbor intracellular bacterial endosymbionts of the genus Wolbachia (Rickettsiales) . These bacteria have been implicated in adverse effects of drug treatment in filariasis . The present study provides evidence that purified major Wolbachia surface protein (rWSP) acts as an inducer of the innate immune system through TLR2 and TLR4: 1) recombinant, stringently purified rWSP elicited the release of TNF-alpha, IL-12, and IL-8 from cultured blood cells of both Onchocerca volvulus-infected and uninfected people; 2) the inflammatory response to rWSP challenge was TLR2- and TLR4-dependent as demonstrated with TLR-transfected fibroblastoid cells, as well as macrophages and dendritic cells from functional TLR-deficient mice; 3) blood cells of onchocerciasis patients exposed to rWSP also generated down-regulating mediators IL-10 and PGE(2) after 6 days of culture; 4) furthermore, rWSP-reactive IgG1 Abs were present in sera of O . volvulus-infected people but not in those of uninfected Europeans . The lack of rWSP-reactive IgE and IgG4 in serum indicated a bias toward a Th1-type adaptive immune response . Abs against rWSP stained endobacteria in living and degenerating adult O . volvulus filariae, tissue microfilariae and host tissue macrophages that apparently had engulfed microfilariae . Thus, filarial helminths, through products of their endobacteria such as WSP, acquire characteristics of a typical microbial pathogen inducing immune responses via TLR2 and TLR4.

Bull Math Biol, 2004 Jul, 66(4), 865 - 78
Bottom-up excitable models of phytoplankton blooms; Huppert A et al.; A simple nutrient-phytoplankton model is used to explore the dynamics of phytoplankton blooms . The model exhibits excitable behaviour in the sense that a large scale outbreak can only be triggered when a critical nutrient threshold is exceeded . The model takes into account several features often neglected but whose combined effect proves very important: (i) rapid nutrient recycling associated with the microbial loop and patch formation; (ii) self-shading; and (iii) a bottom-up approach, whereby nutrient levels are responsible for both the triggering and the demise of the bloom . Although the literature is replete with studies of 'top-down' models in which zooplankton grazing control the triggering and demise of the bloom, bottom-up models are nevertheless appropriate in many circumstances . We provide a full mathematical investigation of the effects of these three different features in an excitable system framework.

Environ Pollut, 2004 Sep, 131(1), 45 - 54
Treatment of atrazine by integrating photocatalytic and biological processes; Chan CY et al.; This research examines the degradation of atrazine by photocatalytic oxidation (PCO) under different experimental conditions . Deisopropylatrazine, deethylatrazine and deethyldeisopropylatrazine were formed as major intermediates based on gas chromatography-mass spectrometry . The reaction mixture was found to be toxic towards two bioassays, i.e . the Microtox and amphipods survival tests even when atrazine was completely degraded by PCO within 2 h under optimized conditions . The results indicate that adding H2O2 could significantly enhance the degradation of atrazine by PCO . Ammeline, ammelide and cyanuric acid (CA) became the major intermediates/products as detected by high performance liquid chromatography from 6th to the 40th h of PCO treatment . After 72 h PCO treatment, only CA was detectable in the reaction mixture . Further degradation of CA was carried out by a newly isolated CA-degrading bacterium, Sphingomonas capsulata . The photochemical pretreatment integrated with microbial degradation lead to the complete degradation and detoxification of atrazine.

Acta Odontol Latinoam, 2001, 14(1-2), 35 - 9
Effects of handling and storage on sterile dental instruments; Rosa AC et al.; The microbial contamination post-sterilization of dental instruments has been the object of permanent study . The aim of the present study was to evaluate factors affecting long-term sterility of dental instruments sterilized in the dry-oven or autoclave at the Central Sterilizing Service of the School of Dentistry, University of Buenos Aires stored under room temperature and humidity conditions . Half of the 192 samples were placed in standard closed metal containers and sterilized in a dry-oven (D.O), and the remaining half were placed in perforated metal containers and sterilized in an autoclave (A) . All the samples were placed in sterilizing paper bags for medical use . Post sterilization, each group (DO and A) was divided into: Group I: minimal handling (control); Group II: wrapping torn mechanically (1 cm); Group III: wrapping torn manually (1 cm) . All the samples were stored a closed cabinet . Contamination was evaluated at 30 and 180 days, by seeding under aerobic and anaerobic conditions . Temperature was monitored throughout the experiment, and ranged between 20 degrees C and 31 degrees C (x: 24 degrees C +/- 3.9) . Humidity was measured with a digital hygrometer, and ranged between 40% and 60% (x: 54% +/- 10) . Group I evidenced no microbial contamination, unlike Groups II and III . Our results evidence that 1) dry oven or autoclave sterilized material that is handled properly during storage remains sterile regardless of variations in temperature and humidity; 2) improper handling affects sterility, and contamination is time-dependent.

Res Microbiol, 2004 Jun, 155(5), 319 - 27
Dynamics of insertion sequence elements during experimental evolution of bacteria; Schneider D et al.; We review the intersection between two areas of microbial evolution that were research foci of Michel Blot . One focus is the behavior of insertion sequence (IS) elements, including their role in promoting the evolutionary adaptation of their hosts . The other focus is experimental evolution, an approach that allows the dynamics of genomic and phenotypic change to be observed in the laboratory . This review shows that IS elements are useful as markers for detecting genomic change over experimental time scales and, moreover, that IS elements generate some of the beneficial mutations that increase organismal fitness.

Res Microbiol, 2004 Jun, 155(5), 311 - 8
Microbial evolution in laboratory environments; Adams J; The classical model of evolutionary change in microbial populations is evaluated in terms of recent evidence obtained from genetic and molecular analysis of evolving laboratory populations in simple, defined homogeneous environments . Patterns of change are observed which cannot be predicted from the classical model . These observations highlight the value of the study of evolving laboratory populations, which allow a degree of analysis typically not possible for natural populations.

Tuberculosis (Edinb), 2004, 84(3-4), 144 - 58
Resistance and susceptibility to tuberculosis analysed at the transcriptome level: lessons from mouse macrophages; Keller C et al.; Gene expression patterns associated with resistance and susceptibility to tuberculosis (TB) were investigated at the macrophage level in the well-defined mouse model of infection . Oligonucleotide microarrays were used to analyse the regulation of gene expression in murine bone marrow-derived macrophages infected with Mycobacterium tuberculosis . Four mouse strains, known to differ in terms of growth permissiveness for M . tuberculosis in infected tissues, in the development of pulmonary pathology, and in the rate of premature death due to tuberculosis, were compared: C57BL/6 and BALB/c representing resistant, DBA/2 and CBA/J representing susceptible mouse strains . Genes (55) were regulated more than two-fold in macrophages of all strains investigated following M . tuberculosis infection . Importantly, 18 genes were commonly regulated only in macrophages of the two resistant strains upon infection, and 102 genes were commonly regulated exclusively in macrophages of the two susceptible strains . Using this approach, we have therefore identified more than 100 genes potentially associated with resistance and susceptibility, respectively, to TB at the macrophage level . A tentative interpretation of our microarray data suggests that macrophages from susceptible mice predominantly stimulate the recruitment of cells that contribute disproportionately to tissue damage rather than to microbial elimination . In conclusion, microarray gene chips are useful tools for generating new hypotheses about resistance and susceptibility to TB, and the mouse model can now be used to subject candidate genes identified by this approach to further functional analyses.

Vet Immunol Immunopathol, 2004 Aug, 100(3-4), 187 - 95
Interaction of antigen presenting cells with mycobacteria; Hope JC et al.; The interaction of mycobacteria with antigen presenting cells is a key feature in the pathogenesis of tuberculosis and the outcome of this interaction is pivotal in determining whether immunity or disease ensues . Human and mouse macrophages and dendritic cells (DC) have been shown to become infected with mycobacteria and to produce a response to infection that reflects their suggested role in immunity . Thus, macrophages elicit anti-microbial mechanisms for elimination of mycobacteria and DC up-regulate expression of molecules that aid their stimulation of T lymphocytes . We have examined the effects of infection with the avirulent strain Mycobacterium bovis BCG and with virulent M . bovis on bovine antigen presenting cells . Differences in the intracellular survival of bacteria within DC and macrophages were observed with higher numbers of bacteria maintained within DC following infection compared to macrophages . BCG was killed more effectively than M . bovis . Alterations in the expression of cell surface molecules involved in antigen presentation and the stimulation of T cells, including MHC II and CD40, were observed following infection of bovine antigen presenting cells . In addition infected DC secreted IL-12, TNFalpha and IL-10 whereas macrophages produced TNFalpha, IL-10 and little IL-12 . Generally responses were more marked when virulent M . bovis was used compared to BCG . These studies indicate that infection of bovine antigen presenting cells by mycobacterial species results in the induction of both innate and adaptive immune responses that are critical for the outcome of infection.

Poult Sci, 2004 Jun, 83(6), 962 - 70
Evaluation of microbial phytase in broiler diets; Dilger RN et al.; Two trials were conducted to evaluate the efficacy of a new microbial phytase (Phyzyme XP) for broiler chicks . Trial 1 used 192 8-d-old male broilers in a 14-d trial to assess growth and nutrient utilization . Dietary treatments (221.9 g/kg CP) included a positive control {5.0 g/kg nonphytate P (NPP)}, negative control (1.2 g/kg NPP), and negative control plus 500 or 1,000 phytase units/kg of diet . Phytase addition increased weight gain, feed intake, feed efficiency, and tibia and toe ash (linear, P < 0.01) with tibia ash also responding quadratically (P < 0.05) . Apparent ileal digestibility of P (linear and quadratic, P < 0.05), tryptophan, and valine (linear, P < 0.05) also increased . Linear and quadratic responses were observed for retention of DM, nitrogen, P, and several amino acids (P < 0.05) with added phytase . Trial 2 utilized 576 1-d-old male broilers over a 42-d period to evaluate growth performance . Diets were formulated for starter (222.7 g/kg CP) and grower (201.5 g/kg CP) phases and included a positive control (starter and grower, 5.0 and 3.8 g/kg NPP, respectively); negative control (starter and grower, 2.4 and 1.8 g/kg NPP, respectively); negative control plus 500, 750, or 1,000 phytase units/kg; and negative control plus 500 phytase units/kg of Natuphos phytase . Phytase increased weight gain and feed intake (starter, grower, overall) as well as feed efficiency during the starter period (linear, P < 0.05) . Feed intake was also improved during the grower period and overall (quadratic, P < 0.05) . Tibia and toe ash of birds fed for the first 21 d increased (linear, P < 0.05) with tibia ash also increasing quadratically (P < 0.05) . Overall, tibia and toe ash were improved due to phytase addition (linear and quadratic, P < 0.05) . In conclusion, this microbial phytase, derived from Escherichia coli and expressed in Schizosaccaromyces pombe, elicited improved growth performance, bone mineralization, and P utilization in broiler chicks.

Allerg Immunol (Paris), 2004 May, 36(5), 182 - 5
Indoor moisture and mold-related health problems; Johanning E; Moisture, microbial and in particular mold related indoor exposure and health problems in homes, offices, and public buildings (Kindergartens, schools, library, and hospitals) have been gaining recognition as one of the most common indoor environmental health issues . Proper recognition of microbial related health problems and the differential diagnosis of sick building syndrome (SBS) or building related illness (BRI) are important for early and effective exposure intervention, treatment, referral and prevention of more serious illness.

Waste Manag Res, 2004 Apr, 22(2), 93 - 9
Microbial biomass in a soil amended with different types of organic wastes; Jedidi N et al.; Application of different types of organic wastes may have a marked effect on soil microbial biomass and its activity . The objective of this study was to quantify the amount of microbial biomass in a loamy-clayey soil, amended with different types of organic waste residues (composts of municipal solid waste of different ages, sewage sludge and farmyard manure) and incubated for 8 weeks at 25 degrees C and two-thirds of field capacity, using the fumigation-extraction method . Both microbial biomass-C and -N (BC and BN, respectively) appeared to be dependent on the type of organic waste residues, on their degree of stability, and on their chemical characteristics . In general, organic wastes increased the microbial biomass-C content in the soil and the microbial BC was positively correlated with the organic C content, the C/N, neutral detergent fibre/N (NDF/N) and acid detergent fibre/N (ADF/ N) ratios . The microbial biomass content decreased according to the period of incubation, especially when the compost used was immature . The microbial biomass-N was positively correlated with the total N and percentage of hemicellulose . The microbial biomass-C was linearly related with the microbial biomass-N and the ratio BC/BN was exponentially related with the BC.

J Org Chem, 2004 Jun 25, 69(13), 4471 - 6
Phytoalexins from the crucifer rutabaga: structures, syntheses, biosyntheses, and antifungal activity; Pedras MS et al.; Phytoalexins are inducible chemical defenses produced de novo by plants in response to diverse forms of stress, including microbial attack . Our search for phytoalexins from economically important crucifers lead us to examine rutabaga tubers (Brassica napus L . ssp . rapifera) . Three new phytoalexins, named isalexin (9), brassicanate A (10), and rutalexin (11), were isolated together with five known phytoalexins, brassinin (4), 1-methoxybrassinin (5), spirobrassinin (13), brassicanal A (14), and brassilexin (15) . The chemical structures of the new phytoalexins were proven by syntheses, and their biological activity against four plant pathogens were determined . Biosynthetic studies using tetra- and pentadeuterated precursors established that indolyl-3-acetaldoxime (22) and brassinin (4) are precursors of brassicanate A (10) and rutalexin (11) and that cyclobrassinin (23) is a biosynthetic precursor of rutalexin (11), whereas tryptamine (24) is not a precursor of rutabaga phytoalexins.

Huan Jing Ke Xue, 2004 Mar, 25(2), 73 - 6
{Formation of an acetic-acid type microbial metabolism pathway and its stability during the course of sulfate-reduction}; Wang AJ et al.; Continuous-flow experiment was conducted in an acidogenic sulfate-reducing reactor supplied with molasses as sole carbon resource and sulfate sodium as electron acceptor . The composition of Volatile fat acid(VFA) in terminal liquid products, the distribution of acetic acid, the existence of microbial populations and the interspecific relationship between sulfate-reducing bacteria (SRB) and acidogenic bacteria (AB) were investigated in different experimental stages when sulfate removal rate and gas production maintained at a relatively stable status . The experimental results showed that an acetic-acid type microbial metabolism pathway was formed based on the fact that the proportion of acetic acid in terminal liquid products was as high as 50% to 82% . It was also explained the formation of acetic-acid type microbial metabolism pathway was resulted from acetic acid accumulation in the terminal liquid products, which was subjected to the bio-chain cooperation relationship between populations of SRB and AB, and the incomplete-oxidation of organic substance in acidogenic-phase reactor of two-phase anaerobic treatment process . It was also presented that the formation of acetic-acid type microbial metabolism pathway depended on the capability of acetic-acid utilized-SRB (ASRB) population competing against other populations and its ability of acetic acid consumption . Furthermore, this kind of metabolism pathway could offer suitable carbon resource for methane producing reactor in the two-phase anaerobic treatment process, and has significant effect on the sulfate removal rate of the whole treatment system and its running stability.

J Occup Environ Hyg, 2004 Jan, 1(1), 1 - 6
Potentially pathogenic, slow-growing mycobacteria released into workplace air during the remediation of buildings; Rautiala S et al.; Construction workers' exposure to airborne viable mycobacteria was studied during the remediation of three moldy and two nonmoldy buildings . Furthermore, the concentrations of airborne fungal and actinobacterial spores were determined . The samples for the microbial analyses were collected using a six-stage impactor and an all-glass impinger sampler, and by filter sampling . Specific mycobacteria media and nonselective media were used for the cultures . The samples were cultured for the total numbers of rapidly growing and slow-growing mycobacteria, and the isolates obtained were identified to the genus or species level . Mycobacteria were recovered from the air during the remediation of two of the moldy buildings and one nondamaged building . Concentrations of mycobacteria up to 160 cfu/m3 were detected . A total of 43 mycobacterial isolates was recovered . Most of the isolates were slow-growers, only two rapid-growing strains being detected . The 38 identified isolates belonged to potentially pathogenic species, including Mycobacterium avium complex, M . scrofulaceum, and M . fortuitum, and to saprophytic species, including M . nonchromogenicum and M . terrae . Mycobacteria were the most often detected in samples taken with a six-stage impactor . They were found in buildings with both high and low concentrations of fungi . In conclusion, mycobacteria, both potentially pathogenic and saprophytic species, may be released into the indoor air during the remediation of buildings.

Shock, 2004 Jul, 22(1), 11 - 5
Early activation of gammadelta T lymphocytes in patients with severe systemic inflammatory response syndrome; Matsushima A et al.; Innate immunity plays an important role in host defense after severe insult . gammadelta T lymphocytes are recognized as the first line of defense against microbial invasion . In this study, we evaluated gammadelta T lymphocytes in the peripheral blood of patients with severe systemic inflammatory response syndrome (SIRS), and examined on role of these cells . Thirty-seven patients with severe SIRS (SIRS criteria and serum C-reactive protein > or = 10 mg/dL) and 27 healthy volunteers were studied . Severe SIRS was caused by trauma in 14 patients (Injury Severity Score of 30.1 +/- 10.8) and by sepsis in 23 patients . The counts of gammadelta and alphabeta T lymphocytes were determined by flow cytometry of cells stained with monoclonal antibodies to gammadelta and alphabeta T lymphocyte receptors . The activation of these cells was evaluated by flow cytometry of cells stained with monoclonal antibodies to CD69 and HLA-DR . Serial counts and activation of gammadelta and alphabeta T lymphocytes were also determined in eight trauma patients (Injury Severity Score of 31.0 +/- 13.5) during a 2-week observation period . The count of gammadelta T lymphocytes in the peripheral blood of SIRS patients (30.1 +/- 6.0/microL) was significantly lower (P < 0.05) than that of the healthy volunteers (104.3 +/- 10.9/microL) . The expression of CD69, an index of early activation of T lymphocytes, was significantly greater on gammadelta T lymphocytes from SIRS patients (patients 23.9% +/- 3.4%, healthy controls 4.8% +/- 0.6%, P < 0.05) . In trauma patients, the expression of CD69 on gammadelta T lymphocytes increased rapidly within 48 h after injuries . In conclusion, gammadelta T lymphocytes are activated and decreased in the peripheral blood of severe SIRS patients . In trauma patients, the activation of gammadelta T lymphocytes occurs in the fairly acute phase after injuries . These results suggest a significant role for gammadelta T lymphocytes as early responders after severe insult.

Curr Opin Rheumatol, 2004 Jul, 16(4), 406 - 10
Bacteria and human autoimmunity: the case of primary biliary cirrhosis; Selmi C et al.; PURPOSE OF REVIEW: Primary biliary cirrhosis is a chronic inflammatory disease of the intrahepatic bile ducts that eventually leads to liver cirrhosis and organ failure, in which several observations suggest an autoimmune origin . Similarly to other autoimmune diseases, microbial mediated molecular mimicry is the most widely studied trigger that may break immunologic tolerance in primary biliary cirrhosis . RECENT FINDINGS: The hypothesis of a bacterial role in the cause of primary biliary cirrhosis has received recent attention, based on in vitro data and the identification of a unique xenobiotic-metabolizing bacterium that modulates naturally occurring environmental estrogens, namely, Novosphingobium aromaticivorans . SUMMARY: The evidence indicates that bacteria, through different mechanisms, may precipitate autoimmunity in primary biliary cirrhosis and other autoimmune diseases . These data have several implications.

Immunol Rev, 2004 Apr, 198, 149 - 68
Insights into the anti-microbial defense of marine invertebrates: the penaeid shrimps and the oyster Crassostrea gigas; Bachere E et al.; Research on innate immunity of the penaeid shrimps and the oyster Crassostrea gigas is motivated greatly by economical necessities . Indeed, the aquaculture of these organisms is now limited by the development of infectious diseases . Studying anti-microbial peptides/proteins (AMPs), which are effector molecules of the host defense, is particularly attractive not only for progressing basic knowledge on immunity but also because they offer various possible applications for disease management in aquaculture . AMPs are explored with a global approach,considering their structure, properties, function, gene expression, and tissue distribution during the response to infections . In shrimp, investigations of the penaeidins, which are constitutively expressed peptides, have highlighted the importance of hemocytes and hematopoiesis as major elements of the immune response, providing both local and systemic reactions . The activation of hematopoiesis must be regarded as a regulatory way for the expression and distribution of constitutively expressed immune effectors . As complementary approaches, genomics and gene profiling are promising to deepen our understanding of the anti-microbial defense of the oyster and the shrimp . However, real progress will depend also on the characterization of hemocyte lineages and hematopoiesis of these marine invertebrates as well as on the ontogenesis of their immune systems.

Immunol Rev, 2004 Apr, 198, 116 - 26
The prophenoloxidase-activating system in invertebrates; Cerenius L et al.; A major innate defense system in invertebrates is the melanization of pathogens and damaged tissues . This important process is controlled by the enzyme phenoloxidase (PO) that in turn is regulated in a highly elaborate manner for avoiding unnecessary production of highly toxic and reactive compounds . Recent progress, especially in arthropods, in the elucidation of mechanisms controlling the activation of zymogenic proPO into active PO by a cascade of serine proteinases and other factors is reviewed . The proPO-activating system (proPO system) is triggered by the presence of minute amounts of compounds of microbial origins, such as beta-1,3-glucans, lipopolysaccharides, and peptidoglycans, which ensures that the system will become active in the presence of potential pathogens . The presence of specific proteinase inhibitors prevents superfluous activation . Concomitant with proPO activation, many other immune reactions will be produced, such as the generation of factors with anti-microbial, cytotoxic, opsonic, or encapsulation-promoting activities.

Immunol Rev, 2004 Apr, 198, 97 - 105
Innate immune responses of a lepidopteran insect, Manduca sexta; Kanost MR et al.; Many innate immune mechanisms are conserved throughout the animal kingdom . Manduca sexta, a widely used model for insect biochemical research, employs these mechanisms to defend against invading pathogens and parasites . We have isolated from M . sexta hemolymph a group of proteins (hemolin, peptidoglycan recognition proteins, beta-1,3-glucan recognition proteins, and C-type lectins), which serve as a surveillance mechanism by binding to microbial surface molecules (e.g . peptidoglycan, lipopolysaccharide, lipoteichoic acid, and beta-1,3-glucan) . The binding triggers diverse responses such as phagocytosis, nodule formation, encapsulation, melanization, and synthesis of anti-microbial peptides/proteins . Some of these responses are mediated and coordinated by serine proteinase cascades, analogous to the complement system in mammals . Our current research is focused on the proteolytic activation of prophenoloxidase (proPO)--a reaction implicated in melanotic encapsulation, wound healing, and protein cross-linking . We have isolated three proPO-activating proteinases, each of which requires serine proteinase homologs as a cofactor for generating active phenoloxidase . The proteinases and proteinase-like molecules, containing one to two clip domains at their amino-terminus, are acute-phase proteins induced upon an immune challenge . Inhibitory regulation of the proteinases by serpins and association of the proteinase homologs with a bacteria-binding lectin are important for ensuring a localized defense response . Additional serine proteinases expressed in M . sexta hemocytes and fat body have been discovered . Future research efforts will be aimed at elucidating the proteinase cascade for proPO activation and investigating the roles of proteinases in other immune responses such as processing of plasmatocyte-spreading peptide.

J Biomed Mater Res, 2004 Jul 15, 70B(1), 1 - 20
In vitro tobramycin elution analysis from a novel beta-tricalcium phosphate-silicate-xerogel biodegradable drug-delivery system; DiCicco M et al.; This in vitro research analyzed local tobramycin elution characteristics from a novel, biodegradable drug delivery system, consisting of a beta-TCP bone substitute, VITOSS trade mark, encapsulated with silicate xerogel prepared by the sol-gel process . Tobramycin elution from silicate-xerogel-encapsulated VITOSS was compared directly with non-silicate-xerogel-encapsulated VITOSS to assess whether xerogels are effective in delivering greater tobramycin quantities in a controllable, sustained manner crucial for microbial inhibition . Tobramycin elution characteristics indicate an initial release maximum during the first 24 h that diminishes gradually several days after impregnation . The copious tobramycin quantity eluted from the VITOSS/silicate-xerogel systems is attributed to various factors: the intrinsic ultraporosity and hydrophilicity of VITOSS, the ability of tobramycin to completely dissolve in aqueous media, tobramycin complexation with highly polar SO(4) (2-) salts that further assist dissolution, and ionic exchanges between VITOSS and the environment . Silicate-xerogel-encapsulated VITOSS eluted 60.65 and 61.31% of impregnated tobramycin, whereas non-silicate-xerogel-encapsulated VITOSS eluted approximately one-third less impregnated tobramycin, at 21.53 and 23.60% . These results suggest that silicate xerogel optimizes tobramycin elution because of its apparent biodegradability . This mechanism occurs through xerogel superficial acidic sites undergoing exchanges with various ions present in the leaching buffer . Tobramycin elution kinetics were evaluated, and demonstrate that first-order elution rate constants are considerably less when silicate xerogels are employed, following a more uniform exponential decay-type mechanism, thus bolstering controlled release . Overall, tobramycin elution rates adhere to linear-type Higuchi release profiles . Elution rate constants are initially first order, and taper into zero-order elution kinetics in the latter stages of release . Because VITOSS and silicate xerogel are completely biodegradable, essentially all impregnated tobramycin will be delivered to the surgical site after implantation .

Pest Manag Sci, 2004 Jun, 60(6), 550 - 5
Microbial biomass and activity on railway track and embankments; Cederlund H et al.; The spatial distribution of microbial biomass and microbial activity was studied in two Swedish railway embankments (located close to Mora and Nassjo) . Basal respiration and substrate-induced respiration (SIR) as well as the active (r) and dormant (K) fractions of the microbial biomass were determined in samples taken from the surface layer of the ballast . The SIR, r, K and basal respiration values were all of an overall low magnitude, but were highly variable over short distances on the track . Both the biomass and basal respiration were higher on the sides of the embankment than in the middle of the tracks . SIR, K and basal respiration were correlated to the organic matter content as measured by loss on ignition, whereas r was not . None of the parameters correlated with pH . It is proposed that organic matter content could be used as a predictor for microbial biomass in railway embankments.

Pest Manag Sci, 2004 Jun, 60(6), 544 - 9
The fate of imazapyr in a Swedish railway embankment; Borjesson E et al.; The long-term fate of the herbicide imazapyr {2-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)nicotinic acid} applied to a Swedish railway embankment was studied . Imazapyr was applied at 750 and 1500 g ha(-1) by a spraying train used for full-scale herbicide treatment operations . Soil and groundwater were sampled twice a year for 8 years after application of the herbicide, and the dissipation of imazapyr was studied by HPLC analysis of the residues in soil and groundwater . A clean-up procedure including solid-phase extraction was performed prior to detection by HPLC . Recoveries of imazapyr from soil and water samples were 76-98% and 61-90%, respectively, and detection levels were 0.003 mg kg(-1) and 0.05 microg litre(-1), respectively . Sorption, desorption and microbial amount and activity were also measured at the two locations . The organic matter content correlated positively and the pH negatively to the adsorption of imazapyr on soil, and increasing organic matter contents decreased desorption . Apart from the 0-10-cm top layers of both sites, the microbial amount and activity were small . The main proportion of imazapyr was found in the upper 30 cm of the soil, and degraded with a half-life in the range 67-144 days . Small amounts were transported to lower soil layers and to the groundwater in proportion to the amounts applied . Traces of imazapyr were detected in the groundwater even 8years after application . It was concluded that environmental risks from the use of herbicides on railway embankments could be reduced by including adsorption layers in the embankment during their construction and by reducing the dose of the herbicide used.

Mikrobiologiia, 2004 Mar-Apr, 73(2), 271 - 83
{Intensities of microbial production and oxidation of methane in bottom sediments and water mass of the Black Sea}; Gal'chenko VF et al.; Intensities of biogeochemical (microbial) processes of methane production and methane oxidation were determined in bottom sediments and water column of the Black Sea . Aerobic bacterial oxidation of methane is confined to the upper 20-30 cm of Holocene bottom sediments of the shelf (0.7-259 ng C/(dm3 day)) and oxygenated waters (0.2-45 ng C/(dm3 day)) . In reduced sediments of the deep-sea zone and in the hydrogen sulfide-containing water column, considerable intensities of anaerobic methane oxidation were recorded, comparable to or exceeding the intensities of methane oxidation in oxygenated layers . From one fourth to one half of the methane formed in bottom sediments was oxidized immediately therein . The major part of the remaining methane was oxidized in the water column, and a smaller portion arrived in the atmosphere.

Mikrobiologiia, 2004 Mar-Apr, 73(2), 204 - 10
{Protection of Saccharomyces cerevisiae against oxidative and radiation-caused damage by alkyl hydroxybenzenes}; Stepanenko IIu et al.; The effects of C7-alkylhydroxybenzene (C7-AHB) and p-hydroxyethylphenol (tyrosol), chemical analogs of microbial anabiosis autoregulators, on the viability of yeast cells under oxidative stress were investigated . The stress was caused by reactive oxygen species (ROS) produced under gamma irradiation of cell suspensions using doses of 10-150 krad at an intensity of 194 rad/s or by singlet oxygen generated in cells photosensibilized with chlorin e6 (10 micrograms/l) . C7-AHB was found to exert a protective effect . The addition of 0.05-0.16 vol% of C7-AHB to cell suspensions 30 min before irradiation protected yeast cells from gamma radiation (50 krad) . The protective effect of C7-AHB manifested itself both in the preservation of cell viability during irradiation and in the recovery of their capacity to proliferate after irradiation . In our studies on photodynamic cell inactivation, the fact that the phenolic antioxidant C7-AHB protects cells from intracellular singlet oxygen was revealed for the first time . The analysis of difference absorption spectra of oxidized derivatives of C7-AHB demonstrated that the protective mechanism of C7-AHB involves the scavenging of ROS resulting from oxidative stress . The fact that tyrosol failed to perform a photoprotective function suggests that the antioxidant properties of microbial C7-AHB are not related to their chaperon functions . The results obtained make an important addition to the spectrum of known antioxidant and antistress effects of phenolic compounds.

Methods Mol Biol, 2004, 283, 109 - 23
Synthesis of hapten-protein conjugates using microbial transglutaminase; Meusel M; Hapten-protein conjugates are essential in many immunochemical assays and in particular in assays using titration or competitive assay formats . By exploitation of the catalytic properties of the microbial transglutaminase from Streptoverticillium mobarense species (MTGase), that is, acyl transfer between gamma-carboxamide groups and various primary amines, new techniques for the enzymatic modification of proteins were developed . One example of bioconjugation is the biotinylation of antibodies for immunochemical applications using two species of activated biotin . In this case, the activated biotin acts as the acyl acceptor and is coupled to the glutamine residues of a monoclonal antibody . Because of the substrate specificity of the MTGase with regard to the limited number of glutamine residues and the surrounding microenvironment, only a limited number of binding sites on the target protein are available; the proposed method is thus particularly suitable when only a few biotin molecules need to be attached . Another example for the modification of proteins is the synthesis of hapten-protein conjugates used in competitive-type immunoassays . Methods for the synthesis of 2,4-D-casein conjugates (2,4-diclorophenoxyacetic acid, a herbicide) are presented . Various approaches, including a batch procedure and two in situ procedures, are described.

Int J Pharm, 2004 Jul 8, 278(2), 391 - 406
Bioadhesive, rheological, lubricant and other aspects of an oral gel formulation intended for the treatment of xerostomia; Kelly HM et al.; Xerostomia is commonly known as 'dry mouth' and is characterised by a reduction or loss in salivary production . A bioadhesive gel for its localised treatment was formulated to help enhance the residence time of the product, based on the polymer Carbopol 974P . The bioadhesion of various formulations was evaluated on different mucosal substrates, as simulations of the oral mucosa of xerostomic patients . Depending on the type of model substrate used, the mechanism of bioadhesion could alter . When the rheology of various formulations was examined, changes in bioadhesion were more easily interpreted, as the presence of other excipients caused an alteration in the rheological profile, with a change from a fully expanded and partially cross-linked system to an entangled system . Improving the lubricity of the product was considered important, with optimum incorporation of vegetable oil causing a desirable lowering of the observed friction of the product . The final complex formulation developed also contained salivary levels of electrolytes to help remineralisation of teeth, fluoride to prevent caries, zinc to enhance taste sensation, triclosan as the main anti-microbial/anti-inflammatory agent and non-cariogenic sweeteners with lemon flavour to increase the palatability of the product while stimulating any residual salivary function.

Curr Opin Microbiol, 2004 Jun, 7(3), 296 - 307
Metabolomics and systems biology: making sense of the soup; Kell DB; Novel techniques for acquiring metabolomics data continue to emerge . Such data require proper storage in suitably configured databases, which then permit one to establish the size of microbial metabolomes (hundreds of major metabolites) and allow the nature, organisation and control of metabolic networks to be investigated . A variety of algorithms for metabolic network reconstruction coupled to suitable modelling algorithms are the ground substances for the development of metabolic network and systems biology . Even qualitative models of metabolic networks, when subject to stoichiometric constraints, can prove highly informative, and are the first step to the quantitative models, which alone can allow the true representation of complex biochemical systems.

Curr Opin Microbiol, 2004 Jun, 7(3), 267 - 73
Emerging foundations: nano-engineering and bio-microelectronics for environmental biotechnology; Sayler GS et al.; The growth of nanotechnology, the emergence of 'nanobiotechnology', and the incorporation of living organisms in biomicroelectronic devices are revolutionizing the interdisciplinary opportunities for microbiologists to participate in understanding, developing and exploiting microbial processes in and from the environment.

Curr Opin Microbiol, 2004 Jun, 7(3), 262 - 6
Recent applications of biosurfactants as biological and immunological molecules; Cameotra SS et al.; The interest in microbial biosurfactants has steadily increased during the past decade . In addition to the classical application as emulsifiers of hydrocarbons, they can be used in environmental protection, crude-oil recovery, food-processing industries and in various fields of biomedicine . Biosurfactants have several advantages over chemical surfactants including lower toxicity and higher biodegradability, and are likely to become molecules of the future in areas such as biomedicine and therapeutics . Here, we discuss the role and applications of biosurfactants (mainly glycolipids and lipopeptides) focusing on medicinal and therapeutic perspectives.

Curr Opin Microbiol, 2004 Jun, 7(3), 210 - 20
Molecular microbial ecology: land of the one-eyed king; Forney LJ et al.; Studies of microbial biodiversity have made astounding discoveries of late due to the use of methodologies based on phylogenetic analyses of small subunit ribosomal RNA sequences . Although there are limitations to these methods, they can nonetheless be very useful if these limitations are kept in mind . These limitations range from technical problems such as obtaining representative genomic DNA and suitable primers, to conceptual problems such as defining and using meaningful taxonomic units of diversity (species) . Here we discuss several of the limitations inherent in studies of microbial diversity that must be considered when interpreting the results obtained using these approaches.

Immunology, 2004 Jul, 112(3), 369 - 77
Polyinosinic-polycytidylic acid-mediated stimulation of human gammadelta T cells via CD11c dendritic cell-derived type I interferons; Kunzmann V et al.; The recognition of pathogen-associated molecular patterns (PAMPs) by the innate immune system is a crucial step in inducing effective immune responses . Double-stranded RNA {mimicked by polyinosinic-polycytidylic acid (poly(I:C)}, synthesized by various types of viruses, represents one important member of these immunostimulatory microbial components . Here we report that poly(I:C) has potent gammadelta T-cell costimulatory capacity . Within peripheral blood mononuclear cells, poly(I:C)-stimulated gammadelta T cells expressed increased levels of CD69 and exhibited significantly enhanced antigen-mediated proliferation in response to isopentenylpyrophosphate (IPP) . Among several recombinant cytokines tested, type I interferons (IFN-alpha, IFN-beta) and interleukin-15 (IL-15) showed a similar activation pattern of gammadelta T cells . gammadelta T-cell clones and purified gammadelta T cells did not respond to poly(I:C), indicating indirect effects of this compound . Depletion of CD11c(+) dendritic cells (DC), which express Toll-like receptor 3 (TLR3), known to recognize poly(I:C), abrogated poly(I:C)-mediated stimulation of gammadelta T cells . In addition, the supernatant of poly(I:C)-treated CD11c(+) DC was able to mimic the stimulatory effects of poly(I:C) on gammadelta T cells . Experiments with neutralizing antibodies indicated that type I IFNs, but not IL-15, contributed to the poly(I:C)-mediated activation of gammadelta T cells . In conclusion, gammadelta T-cell activation by immunostimulatory double-stranded RNA, such as poly(I:C), is indirectly mediated via type I IFNs derived from TLR3-expressing CD11c(+) DCs . These results suggest that upon confrontation with certain viruses, gammadelta T cells can be rapidly activated by type I interferons and may contribute to effective antiviral responses.

Arch Anim Nutr, 2004 Apr, 58(2), 117 - 35
Nutrient supply to dairy cows from processed white lupines; Yu P et al.; The objective of this study was to compare the DVE/OEB system (DVE = truly absorbed protein in the small intestine; OEB = degraded protein balance (DPB) in Dutch) and the NRC-2001 model in the prediction of supply of protein to dairy cows from processed white lupines (Lupinus albus L.) . Comparisons were made in terms of (1) ruminally synthesized microbial CP, (2) truly absorbed protein in the small intestine, and (3) degraded protein balance . In addition, the systematic investigation of roasting of the white lupines at various temperatures (110, 130, or 150 degrees C) and times (15, 30 or 45 min) on manipulation of digestive behaviour and the potential nutrient supply to dairy cows were also carried out, to obtain information on best processing conditions as intestinal protein sources (to achieve target values for potential high net absorbable protein in the small intestine while holding any N loss in the rumen to a low level) . The results showed that the predicted values from the DVE/OEB system and the NRC-2001 model had significant correlations with high R ( > 0.83) values . However, using the DVE/OEB system, the overall average microbial protein supply based on available energy was 11% higher and the truly absorbed protein in the small intestine was 7% higher than that predicted by the NRC-2001 model . The difference was also found in the prediction of the degraded protein balances (DPB), which was 8% higher based on data from the NRC-2001 model . These differences are due to considerably different factors used in calculations in the two models, although both are based on similar principles . This indicates that a further refinement is needed for a modern protein evaluation and prediction system . In addition, this study showed that the roasting at higher temperature and time was effective in shifting protein degradation from rumen to intestines and it increased the DVE or MP values without reaching the negative degraded protein balance . The processing at 15 degrees C for 30 or 45 min might be the best treatments for white lupine due to its higher DVE and MP values and the very low DPB values.

Yi Chuan Xue Bao, 2004 Mar, 31(3), 231 - 5
{Differential expression of apoptosis-related gene induced by clinical and laboratory Mycobacterium tuberculosis strain in macrophages U937 revealed by oligonucleotide microarray}; Hu CH et al.; Tuberculosis(TB) remains one of the major problems in global health . Macrophage (MPhi) apoptosis, induced by Mycobacterium tuberculosis (Mtb), is a cornerstone of effective innate microbial defense mechanism . Elucidation of the complex apoptosis-related gene expression may facilitate understanding the mechanism and regulation of macrophage apoptosis in response to Mtb, and contribute to developing novel measures to counter TB . DNA microarray containing 19,200 gene or gene fragments was used to compare the macrophage cell line U937 gene expression response to the clinical and laboratory Mtb infection . Northern blotting and RT-PCR were used to confirm the microarray results . Mtb H37Rv infection were found to downregulate the bcl-2, vitamin D receptor, interferon regulatory factor 3, cytochrome c oxidase, gene expression by 2-, 3-, 3-, 2.5-fold, respectively, while the clinical strain infection leads to upregulate the SOD2, SOD3, serine protease, toll-like receptor 2, signal transducer and activator (STAT1), hypoxia-inducible factor 22, 2.9-, 2.5-, 2.5-, 2.2-, 2.4-, 5.9-fold respectively . The findings suggest that the clinical strain infection tends to override the macrophage apoptosis by which the host attempt to limit the growth of the invader . The research on the complex factors network involved in the interaction will benefit the vaccine and novel drug target development.

Water Sci Technol, 2004, 49(7), 73 - 83
The global change of continental aquatic systems: dominant impacts of human activities; Meybeck M; Continental aquatic systems, particularly rivers, are exposed to major changes due to human pressures . Some changes are voluntary such as flow regulation and the fragmentation of river courses, both due to damming, or the water consumption particularly in dry regions, which results in a partial to complete dry-up of some rivers (neo-arheism) . Other changes result from indirect impacts of other human activities, and include: sediment unbalance of river systems, chemical contamination, acidification, eutrophication, thermal unbalance, radioactive contamination, microbial contamination, and aquatic species introduction/invasion . These changes can be regarded as syndromes which have now reached a global amplitude, even in less populated regions, as the result of damning, mining and of long-range atmospheric pollution, thus defining a new era, the Anthropocene, where continental aquatic systems are no longer controlled by earth systems processes but by human activities . Each region of the globe has developed specific patterns of syndromes trajectories that can be reconstructed from historical analysis and through environmental archives . These trajectories reveal multiple types of human responses to aquatic environmental issues (e.g . water quality), usually lasting 10 to 50 years for the successful ones . The reactions of the earth system to such major changes of fluxes (water, energy, nutrients, carbon, pollutants) via the continental waterscape, the land-ocean interactions, the water bodies-atmosphere interactions, are likely to take place over a longer time scale (100-1,000 years) yet are poorly addressed by scientists and not considered in Integrated Water Management, particularly as concerns the coastal zone.

J Infect Dis, 2004 Jul 1, 190(1), 192 - 8 Epub 2004 Jun 08.
Immunosuppression affects the severity of experimental Fusarium solani keratitis; Wu TG et al.; We have established a mouse model of corneal fusariosis that permits the evaluation of fungal infection and pathogenesis . Corneas of immunocompetent and cyclophosphamide-treated adult BALB/c mice were topically inoculated with Fusarium solani after corneal scarification . Eyes were scored for corneal involvement daily for 8 days and at 2 weeks after infection . Eyes were enucleated at various time points for quantitative fungal recovery and histopathological examination . An inoculum-dose response was observed in cyclophosphamide-treated mice, and fungi were recovered from the infected eyes by quantitative microbial culturing . Treatment with cyclophosphamide increased disease severity and delayed fungal clearance . Fungal hyphae, inflammatory cells, and stromal edema were histologically evident within corneal tissue and correlated with disease severity . Although the mouse cornea resists fungal infections, F . solani keratitis could be induced in immunosuppressed mice after surface scarification, which resulted in infection and clinical disease that could be evaluated both in vivo and in vitro.

Biomed Pharmacother, 2004 Jun, 58(5), 325 - 37
Autoimmunity induced by adjuvant hydrocarbon oil components of vaccine; Kuroda Y et al.; Adjuvant oils such as Bayol F (Incomplete Freund's adjuvant: IFA) and squalene (MF59) have been used in human and veterinary vaccines despite poor understanding of their mechanisms of action . Several reports suggest an association of vaccination and various autoimmune diseases, however, few were confirmed epidemiologically and the risk of vaccination for autoimmune diseases has been considered minimal . Microbial components, not the adjuvant components, are considered to be of primary importance for adverse effects of vaccines . We have reported that a single intraperitoneal injection of the adjuvant oils pristane, IFA or squalene induces lupus-related autoantibodies to nRNP/Sm and -Su in non-autoimmune BALB/c mice . Induction of these autoantibodies appeared to be associated with the hydrocarbon's ability to induce IL-12, IL-6, and TNF-alpha, suggesting a relationship with hydrocarbon's adjuvanticity . Whether this is relevant in human vaccination is a difficult issue due to the complex effects of vaccines and the fact that immunotoxicological effects vary depending on species, route, dose, and duration of administration . Nevertheless, the potential of adjuvant hydrocarbon oils to induce autoimmunity has implications in the use of oil adjuvants in human and veterinary vaccines as well as basic research .

Vaccine, 2004 Jun 30, 22(20), 2651 - 9
A plasmid immunization construct encoding urease B of Helicobacter pylori induces an antigen-specific antibody response and upregulates the expression of beta-defensins and IL-10 in the stomachs of immunized mice; Hatzifoti C et al.; The objectives of this study were to investigate the efficacy of a prototype DNA immunization construct encoding the urease B subunit enzyme of Helicobacter pylori (H . pylori) for inducing adaptive and innate immune responses in mice immunized via intramuscular or subcutaneous routes and to further explore the adjuvant effects of the CpG motifs in the vector . Antibody, cytokine, and beta-defensin profiles were assessed in the stomachs of immunized animals: experiments were terminated 3 months after immunization because there was a significant increase in the anti-H . pylori urease B antibody response at Week 6 in mice immunized with the urease B construct . A long lasting expression of IL-10 mRNA was noted . Furthermore, a marked and sustained increase in the mRNA expression of beta-defensins was also observed, particularly beta1 . This study demonstrates that an H . pylori urease B DNA construct can induce innate as well as adaptive immune responses in the stomachs of immunized mice . Upregulation of beta-defensin gene expression followed immunization and we believe that this is the first report of a DNA vaccine inducing innate anti-microbial responses . Such complex molecular interactions that modulate both innate and adaptive immune responses may be of critical importance in the control of mucosal pathogens, such as H . pylori.

Curr Opin Biotechnol, 2004 Jun, 15(3), 175 - 80
Emerging waterborne pathogens: can we kill them all?
Nwachcuku N, Gerba CP.
The rapid emergence of Cryptosporidium parvum and Escherichia coli 0157:H7 have created a threat to the drinking water industry and there is a growing need to develop a strategy for recognizing potential emerging waterborne pathogens . Globalization of trade, changing population demographics and changes in treatment technology have been driving factors in the emergence of these new pathogens . An understanding of disinfectant action and microbial resistance to treatment processes is needed to better identify those pathogens likely to be of greatest concern . Recent research on microbial resistance to treatment and disinfection demonstrates that the microbial surface structure and composition and the nature of the genome are key to determining the potential for waterborne transmission of emerging pathogens.

Apoptosis, 2004 Jul, 9(4), 399 - 413
Modulation of phagocyte apoptosis by bacterial pathogens; DeLeo FR; Phagocytic leukocytes such as neutrophils and macrophages are essential for the innate immune response against invading bacteria . Binding and ingestion of bacteria by these host cells triggers potent anti-microbial activity, including production of reactive oxygen species . Although phagocytes are highly adept at destroying bacteria, modulation of leukocyte apoptosis or cell death by bacteria has emerged as a mechanism of pathogenesis . Whereas induction of macrophage apoptosis by pathogens may adversely affect the host immune response to infection, acceleration of neutrophil apoptosis following phagocytic interaction with bacteria appears essential for the resolution of infection . This idea is supported by the finding that some bacterial pathogens alter normal phagocytosis-induced neutrophil apoptosis to survive and cause disease . This review summarizes what is currently known about modulation of phagocyte apoptosis by bacteria and describes a paradigm whereby bacteria-induced neutrophil apoptosis plays a role in the resolution of infection .

J Clin Periodontol, 2004 Jul, 31(7), 497 - 500
Critical soft tissue parameters of the zygomatic implant; Al-Nawas B et al.; AIM: Zygomatic implants have been introduced for the rehabilitation of patients with severe bone defects of the maxilla . The soft tissue aspects of the palatal emergence situation have not been described yet . The aim of this study was to evaluate the incidence and clinical impact of possible periimplant alterations of zygomatic implants . MATERIALS AND METHODS: From 1998 to 2001 all patients with zygomatic implants were included into this study (24 patients, 37 zygomatic implants) . One implant was lost in the loading phase giving a survival rate of 97% . Fourteen patients with 20 zygomatic implants fulfilled the inclusion criteria and were all available for the recall examination . Thirteen zygomatic implants were inserted in cases of severe maxillary atrophy, seven in cases of tumour-resection of the maxilla . Clinical examination and microbial analysis using a DNA probe was performed . The implants had a mean time in situ of 598 days (min: 326, max: 914) . RESULTS: Colonisation with periodontal pathogens was found at four of the 20 implants . A positive microbiologic result of the periimplant pocket and the maximum pocket probing depth were not statistically related . Nine of the 20 implants showed bleeding on probing, four of these had positive microbiologic results . At sites without bleeding on probing only negative microbiologic samples were found (p=0.026) . The mean palatal and mesial probing depth was 1 mm deeper than at the vestibular and distal aspect . Thus at nine out of the 20 implants both, bleeding on probing and pocket probing depth >/=5 mm indicated soft tissue problems resulting in a success rate of only 55% . The patient's history (tumor versus atrophy) or smoking habits seemed not to have influence the situation . CONCLUSION: These soft tissue problems should be taken into account if zygomatic implants are considered as an alternative therapy option in the maxilla.

Ann Allergy Asthma Immunol, 2004 May, 92(5), 545 - 8
Soluble CD14 as a predictor of subsequent development of recurrent wheezing in hospitalized young children with respiratory syncytial virus-induced bronchiolitis; Soferman R et al.; BACKGROUND: Respiratory syncytial virus (RSV) infection in infancy that causes severe bronchiolitis had been implicated as potentially responsible for the subsequent development of asthma . The CD14 receptor responds to the microbial burden in the environment and modulates the development of the allergic phenotype . OBJECTIVE: To investigate the relationship between the serum level of soluble CD14 (sCD14) in children hospitalized because of RSV-induced bronchiolitis and the subsequent development of recurrent wheezing . METHODS: Serum levels of sCD14 were measured in 21 children younger than 14 months who were hospitalized because of RSV-induced bronchiolitis . The diagnosis of significant wheezing was evaluated by recurrent episodes of coughing, wheezing, and respiratory distress, which were relieved by inhalation of beta-agonists and corticosteroids . RESULTS: Of the 21 children, 19 were followed up for 12 months . The mean sCD14 serum level of 14,521 +/- 1,773 pg/mL in the group of 6 children who did not exhibit recurrent wheezing was significantly higher than the level of 11,243 +/- 3,264 pg/mL in the group of 13 children who exhibited significant recurrent wheezing (P < .05) . The subsequent development of recurrent wheezing was not influenced by positive family history of asthma, number of siblings, sex, or breast-feeding . CONCLUSION: A follow-up period of 12 months in this small pilot group showed that high serum levels of sCD14 modulate the influence of RSV on subsequent recurrent episodes of wheezing.

Immunity, 2004 Jun, 20(6), 757 - 67
NKG2D blockade prevents autoimmune diabetes in NOD mice; Ogasawara K et al.; NKG2D is an activating receptor on CD8(+) T cells and NK cells that has been implicated in immunity against tumors and microbial pathogens . Here we show that RAE-1 is present in prediabetic pancreas islets of NOD mice and that autoreactive CD8(+) T cells infiltrating the pancreas express NKG2D . Treatment with a nondepleting anti-NKG2D monoclonal antibody (mAb) during the prediabetic stage completely prevented disease by impairing the expansion and function of autoreactive CD8(+) T cells . These findings demonstrate that NKG2D is essential for disease progression and suggest a new therapeutic target for autoimmune type I diabetes.

Acta Paediatr, 2004 Apr, 93(4), 534 - 9
Human neutrophil lipocalin: normal levels and use as a marker for invasive infection in the newborn; Bjorkqvist M et al.; AIM: To evaluate human neutrophil lipocalin (HNL) as a marker of neonatal invasive infection and determine the normal serum levels of HNL in newborns . METHODS: HNL is released from neutrophil granulocytes and is regarded as a specific marker of neutrophil activity . In 81 newborns < or = 28 d of age with signs of infection on a total of 87 occasions, HNL and C-reactive protein (CRP) were measured at inclusion and on the three following days . As controls, term healthy newborns were recruited at birth (cord blood, n = 45) and at ages 3-5 d (n = 46) . Serum HNL was measured by a radioimmunoassay . RESULTS: 25/87 episodes were classified as infection and 62 as non-proven infection . HNLmax was significantly higher in the infected group (mean 587.6 microg/l) than in the non-proven infected group (mean 217.7 microg/, p < 0.001) . HNL peaked at inclusion, 1 d earlier than CRP . In the healthy controls . HNL was the same at 3-5 d of age as at birth (mean 82.4-81.7 microg/l) and similar to normal adult levels . CONCLUSIONS: The release of HNL is not increased in healthy newborns at birth, but neonatal neutrophils rapidly release HNL upon microbial stimulation in vivo . HNL might be useful as an early marker of neonatal infection.

Zh Mikrobiol Epidemiol Immunobiol, 2004 Mar-Apr, (2), 79 - 81
{Microbial ecology and the state of the gastrointestinal mucosa in patients with allergic diseases}; Gracheva NM et al.; Patients with allergic diseases of the skin and the respiratory system were found to have a high rate of disturbances in the microbial ecology of the gastrointestinal tract and the involvement of all its sections into the pathological process . On the mucous membrane of different sections of the digestive tract spiral-like bacteria were detected in a large percentage of cases . The possibility of the fact that the development and maintenance of the allergic process were evidently linked with the detected changes in the microbial ecology and pathomorphological features of the gastrointestinal mucosa could hardly be excluded, which made it necessary to make corrections in the therapeutic process.

J Vet Med Sci, 2004 May, 66(5), 515 - 20
Effect of tissue deterioration on postmortem BSE diagnosis by immunobiochemical detection of an abnormal isoform of prion protein; Hayashi H et al.; Surveillance for bovine spongiform encephalopathy (BSE) in fallen stock in Japan is conducted with a commercial enzyme-linked immunosorbent assay (ELISA) for mass screening, with Western blotting (WB) and immunohistochemistry performed for confirmation of the ELISA . All tests are based on immunological detection of an abnormal isoform of the prion protein (PrP(Sc)) in brain tissues, which have sometimes deteriorated by the time samples from fallen stock reach a diagnostic laboratory . To evaluate BSE surveillance procedures for fallen stock, we examined PrP(Sc) detection from artificially deteriorated BSE-affected bovine brain tissues with a commercial ELISA kit and compared the results with those of WB . The optical density (OD) values of the ELISA decreased with advancing deterioration of the tissues, whereas no reduction in the signal for PrP(Sc) was observed in WB, even when performed after 4 days of incubation at 37 degrees C . The progressive decrease in the OD values in the ELISA appear to be caused by a partial loss of the N-terminal moiety of PrP(Sc) due to digestion by endogeneous and/or contaminated microbial enzymes, and by the presence of ELISA inhibitors that are generated in deteriorated tissues . These results suggest that WB is the most reliable test for fallen stock, especially for cattle brains within decaying carcasses.

J Immunol, 2004 Jun 15, 172(12), 7684 - 93
The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing; Theilgaard-Monch K et al.; To investigate the cellular fate and function of polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds, we used a human skin-wounding model and microarray technology to define differentially expressed genes in PMNs from peripheral blood, and PMNs that had transmigrated to skin lesions . After migration to skin lesions, PMNs demonstrated a significant transcriptional response including genes from several different functional categories . The up-regulation of anti-apoptotic genes concomitant with the down-regulation of proapoptotic genes suggested a transient anti-apoptotic priming of PMNs . Among the up-regulated genes were cytokines and chemokines critical for chemotaxis of macrophages, T cells, and PMNs, and for the modulation of their inflammatory responses . PMNs in skin lesions down-regulated receptors mediating chemotaxis and anti-microbial activity, but up-regulated other receptors involved in inflammatory responses . These findings indicate a change of responsiveness to chemotactic and immunoregulatory mediators once PMNs have migrated to skin lesions and have been activated . Other effects of the up-regulated cytokines/chemokines/enzymes were critical for wound healing . These included the breakdown of fibrin clots and degradation of extracellular matrix, the promotion of angiogenesis, the migration and proliferation of keratinocytes and fibroblasts, the adhesion of keratinocytes to the dermal layer, and finally, the induction of anti-microbial gene expression in keratinocytes . Notably, the up-regulation of genes, which activate lysosomal proteases, indicate a priming of skin lesion-PMNs for degradation of phagocytosed material . These findings demonstrate that migration of PMNs to skin lesions induces a transcriptional activation program, which regulates cellular fate and function, and promotes wound healing.

J Immunol, 2004 Jun 15, 172(12), 7642 - 6
Rac1 and Toll-IL-1 receptor domain-containing adapter protein mediate Toll-like receptor 4 induction of HIV-long terminal repeat; Equils O et al.; Opportunistic infections, common in HIV-1-infected patients, increase HIV replication; however, the intracellular signaling mechanisms involved are not clearly known . We have shown that Toll-like receptor 2 (TLR2), TLR4, and TLR9 mediate microbial Ag-induced HIV-long terminal repeat (HIV-LTR) trans-activation and HIV-1 replication, and that LPS-induced HIV-LTR trans-activation is mediated through myeloid differentiation adapter protein . Recently, Toll-IL-1R domain-containing adapter protein (TIRAP) has been identified as an adapter molecule that mediates responses to TLR2 and TLR4 ligands, and TIRAP was suggested to provide signaling specificity for different TLRs . Rac1, a small GTP-binding protein that is activated upon LPS stimulation of macrophages, activates phosphatidylinositol 3-kinase and Akt and leads to NF-kappaB activation . The roles of Rac1 and TIRAP in LPS activation of HIV replication is not known . In the present study we show that LPS stimulation of human microvessel endothelial cells leads to Rac1 activation . Constitutively active Rac1 (Rac1V12) simulated the effect of LPS to activate HIV-LTR, whereas the expression of dominant negative Rac1 (Rac1N17) partially blocked LPS-induced HIV-LTR trans-activation . Rac1V12-induced HIV-LTR activation was independent of myeloid differentiation adapter protein, and dominant negative TIRAP blocked Rac1V12-induced HIV-LTR trans-activation . In this study we show for the first time that activation of Rac1 leads to HIV-LTR trans-activation, and this is mediated through TIRAP . Together these results underscore the importance of Rac1 and TIRAP in TLR4 activation of HIV replication and help delineate the signaling pathways induced by TLRs to mediate microbial Ag-induced HIV replication and HIV pathogenesis.

J Immunol, 2004 Jun 15, 172(12), 7399 - 407
Activation of naive CD4+ T cells in vivo by a self-peptide mimic: mechanism of tolerance maintenance and preservation of immunity; Choi JY et al.; Intrathymic selection generates a peripheral repertoire of CD4(+) T cells with receptors that retain low affinity for self-peptide MHC complexes . Despite self-recognition, T cells remain tolerant even in the setting of microbial challenge and resultant costimulatory signals . We demonstrate here a novel mechanism for tolerance maintenance under conditions of self-recognition and strong costimulation . TCR engagement in vivo with a low-avidity peptide, as a mimic of self, provided with poly(I:C) (dsRNA) led to division of naive T cells that was dependent upon costimulatory signals; however, the dividing cells rapidly underwent deletion . By contrast, the surviving cells that were activated as evidenced by up-regulation of CD69 did not become effectors upon restimulation with the same ligand and maintained an effective response against agonist peptide . We suggest TCR engagement with self-peptide MHC complexes promotes tolerance maintenance during pathogen challenge, while preserving efficient reactivity for subsequent encounter with foreign Ags.

J Immunol, 2004 Jun 15, 172(12), 7297 - 305
Expression of human CD1d molecules protects target cells from NK cell-mediated cytolysis; Campos-Martin Y et al.; The cytotoxic activity of NK cells can be inhibited by classical and nonclassical MHC molecules . The CD1 system is formed by a family of glycoproteins that are related to classical MHC . CD1a, b, and c molecules present lipids or glycolipids to T cells and are involved in defense against microbial infections, especially mycobacteria . It has been shown recently that these molecules can inhibit target cell lysis by human NK cells . It has also been shown that mouse CD1d molecules can protect cells from NK cell-mediated cytotoxicity . In the present study, we describe how human CD1d, orthologous to murine CD1 molecules, can inhibit NK cell-mediated cytolysis . We have expressed CD1d in the HLA class I-deficient cell lines L721.221 and C1R . The inhibitory effect is observed when effector NK cells from different donors are used, as well as in different cell lines with NK activity . The inhibitory effect was reversed by incubating the target cells with a mAb specific for human CD1d . Incubation of target cells with the ligands for CD1d, alpha-galactosylceramide (alpha-GalCer), and beta-GalCer abolishes the protective effect of CD1d in our in vitro killing assays . Staining the effector cells using CD1d tetramers loaded with alpha-GalCer was negative, suggesting that the putative inhibitory receptor does not recognize CD1d molecules loaded with alpha-GalCer.

Tohoku J Exp Med, 2004 May, 203(1), 1 - 8
Elimination of intraluminal colonization by antibiotic lock in catheters; Oncu S et al.; Antibiotic lock (AL) technique for catheter related infection encompasses the filling of a catheter lumen with high concentrations of antibiotics for hours . The goal of AL therapy is to decontaminate the intraluminal surface of the catheter . However the duration of antibiotic therapy is not established . An in vitro model was designed to establish the time needed to eliminate intraluminal microbial colonization and to evaluate the efficacy of vancomycin in comparison with teicoplanin by using laboratory AL model . Human plasma was instilled into the catheters to allow deposition of fibrin and other products on the catheter wall . After 48 hours, the catheters were drained and inoculated with bacteria in tryptic soy broth . The catheters were then drained and filled with either (a) vancomycin saline solution (VSS) lock (b) teicoplanin saline solution (TSS) lock or (c) saline solution (SS) as the control and then incubated for 12 hours . After 12 hours incubation all the catheter were drained and filled with human plasma . Instillation of human plasma and AL was alternated every 12 hours to simulate clinical conditions . For each day three catheters, locked with VSS, TSS and SS were cultured for colony count . Microbial counts were expressed as total colony-forming units per longitudinal centimeters of catheter surface . A significant decrease in intraluminal catheter colonization started as early as day 1 . At the end of 7th day catheters treated with VSS and TSS lock were completely sterile . The decrease of intraluminal colonization was similar in catheters treated with VSS and TSS lock . Also the decrease of intraluminal colonization were similar in catheter colonized with slime forming S . epidermidis and nonslime-forming S . epidermidis.

Chembiochem, 2004 Apr 2, 5(4), 437 - 44
Loading of the antigen-presenting protein CD1d with synthetic glycolipids; Wallner FK et al.; CD1 proteins present mammalian and microbial lipid and glycolipid antigens to different subsets of T cells . Few such antigens have been identified and the binding of these to CD1 molecules has mainly been studied by using responding T cells in cellular assays or recombinant solid-phase CD1 proteins . In the present study we use four different glycolipids, some of which contain tumor-associated carbohydrate antigens, to develop a procedure to easily detect binding of glycolipids to CD1 proteins on viable cells . Two of these glycolipids are novel glycoconjugates containing alpha-D-N-acetylgalactosamine (alpha-GalNAc) that were prepared by a combined solution and solid-phase approach . The key step, a Fischer glycosylation of 9-fluorenylmethoxycarbonylaminoethanol with GalNAc, furnished the alpha-glycoside 4 in 34% yield . Cells were incubated with glycolipids and stained with monoclonal antibodies specific for the carbohydrate part . The level of glycolipid bound to cells was then determined by flow cytometry with a secondary antibody labeled with fluorescein isothiocyanate . All four glycolipids were found to bind to CD1d but with different selectivity . The loading was dose dependent and could be inhibited by an established CD1d ligand, alpha-galactosylceramide . Through use of this procedure, glycolipids were selectively loaded onto CD1d expressed on professional antigen-presenting cells for future use as cellular vaccines . Moreover, the glycolipids described in this study represent novel CD1d-binding ligands that will be useful derivatives in the study of CD1d-dependent immune responses, for example, against tumors.

Microbiology, 2004 Jun, 150(Pt 6), 1629 - 36
Substrate recognition by nonribosomal peptide synthetase multi-enzymes; Lautru S et al.; Nonribosomal peptide synthetases (NRPSs) are giant multi-domain enzymes that catalyse the biosynthesis of many commercially important peptides produced by bacteria and fungi . Several studies over the last decade have shown that many of the individual domains within NRPSs exhibit significant substrate selectivity, which impacts on our ability to engineer NRPSs to produce new bioactive microbial peptides . Adenylation domains appear to be the primary determinants of substrate selectivity in NRPSs . Much progress has been made towards an empirical understanding of substrate selection by these domains over the last 5 years, but the molecular basis of substrate selectivity in these domains is not yet well understood . Perhaps surprisingly, condensation domains have also been reported to exhibit moderate to high substrate selectivity, although the generality of this observation and its potential impact on engineered biosynthesis experiments has yet to be fully elucidated . The situation is less clear for the thioesterase domains, which seem in certain cases to be dedicated to the hydrolysis/cyclization of their natural substrate, whereas in other cases they are largely permissive.

Int Immunol, 2004 Jul, 16(7), 961 - 9 Epub 2004 Jun 07.
Lipid A antagonist, lipid IVa, is distinct from lipid A in interaction with Toll-like receptor 4 (TLR4)-MD-2 and ligand-induced TLR4 oligomerization; Saitoh S et al.; Toll-like receptor 4 (TLR4) and MD-2 recognizes lipid A, the active moiety of microbial lipopolysaccharide (LPS) . Little is known about mechanisms for LPS recognition by TLR4-MD-2 . Here we show ligand-induced TLR4 oligomerization, homotypic interaction of TLR4, which directly leads to TLR4 signaling . Since TLR4 oligomerization normally occurred in the absence of the cytoplasmic portion of TLR4, TLR4 oligomerization works upstream of TLR4 signaling . Lipid IVa, a lipid A precursor, is agonistic on mouse TLR4-MD-2 but turns antagonistic on chimeric mouse TLR4-human MD-2, demonstrating that the antagonistic activity of lipid IVa is determined by human MD-2 . Binding studies with radioactive lipid A and lipid IVa revealed that lipid IVa is similar to lipid A in dose-dependent and saturable binding to mouse TLR4-human MD-2 . Lipid IVa, however, did not induce TLR4 oligomerization, and inhibited lipid A-dependent oligomerization of mouse TLR4-human MD-2 . Thus, lipid IVa binds mouse TLR4-human MD-2 but does not trigger TLR4 oligomerization . Binding study further revealed that the antagonistic activity of lipid IVa correlates with augmented maximal binding to mouse TLR4-human MD-2, which was approximately 2-fold higher than lipid A . Taken together, lipid A antagonist lipid IVa is distinct from lipid A in binding to TLR4-MD-2 and in subsequent triggering of TLR4 oligomerization . Given that the antagonistic activity of lipid IVa is determined by MD-2, MD-2 has an important role in a link between ligand interaction and TLR4 oligomerization.

Appl Environ Microbiol, 2004 Jun, 70(6), 3541 - 51
Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery; Filion M et al.; Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis . Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs) . A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced . Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa . For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments . Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P . mariana seedlings were different . The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices . Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones . The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.

Toxicol Lett, 2004 Jul 15, 151(2), 375 - 87
Involvement of cytochrome P450 1A in sanguinarine detoxication; Vrba J et al.; Sanguinarine (SA), a member of the benzo{c}phenanthridine alkaloids, is a potent anti-microbial agent with anti-inflammatory and anti-neoplastic properties . However, toxicity of the alkaloid severely limits its medical applications . Recent report by Williams et al . implicated rat hepatic cytochrome P450 (CYP) 1A2 as a likely modulator of SA toxicity . Indeed, the in vitro toxicity of SA in primary culture of rat hepatocytes and human hepatic cell line HepG2, demonstrated as lactate dehydrogenase leakage and metabolic capability (MTT assay), was diminished following induction of CYP1A by 2,3,7,8-tetrachlorodibenzo-p-dioxin, 3-methylcholanthrene, and beta-naphtoflavone . Using microsomes containing recombinant CYP1A1 or CYP1A2 we show that SA causes non-competitive inhibition of the former and competitive inhibition of the latter as assessed by ethoxyresorufin de-ethylation (EROD) . In human hepatic microsomes SA exhibits competitive inhibition of EROD activity with apparent K(i) of 2 microM, a value identical to that observed for CYP1A2 inhibition in recombinant system . Pre-incubation of SA with human liver microsomes resulted in time-dependent, but not dose-dependent decline in EROD activity suggesting CYP1A2 inhibition is not mechanism based . SA also inhibits activity of NADPH:CYP reductase, an enzyme required for CYP activity, with IC(50) very similar to that observed for EROD inhibition . Tentative mechanism for CYP1A involvement in decreased in vitro SA toxicity is discussed.

Dev Comp Immunol, 2004 Jul 1, 28(9), 911 - 25
Molecular cloning and sequencing of Japanese pufferfish (Takifugu rubripes) NADPH oxidase cDNAs; Inoue Y et al.; The superoxide-producing NADPH oxidase complex of phagocytes plays a crucial role in host defenses against microbial infection . NADPH oxidase consists of a membrane heterodimeric protein, composed of gp91phox and p22phox, and cytosolic proteins, p40phox, p47phox and p67phox . In the present study, cDNAs of all the components of NADPH oxidase were cloned from peripheral white blood cells of the Japanese pufferfish utilizing the reverse transcription-polymerase chain reaction . The sequences of these cDNAs showed that the pufferfish gp91phox, p22phox, p40phox, p47phox and p67phox clones contained open reading frames encoding 565, 186, 348, 423 and 495 amino acids, respectively . Comparison of the deduced amino acid sequences showed that the pufferfish gp91phox, p22phox, p40phox, p47phox and p67phox sequences shared 68.0, 61.8, 53.8, 54.7 and 41.9% identity with those of human components, respectively . gp91phox has three potential N-linked glycosylation sites . gp91phox and p22phox have six and three hydrophobic regions, respectively, that are predicted to be transmembrane regions . p47phox and p67phox have two potential Src homology 3 domains and p40phox has one . The functional domains are highly conserved in many animals, though the sequence of the components of the pufferfish showed low homology with that of mammals . The Fugu NADPH oxidase genes were expressed in various tissues of unstimulated fish . The level of gp91phox, p47phox and p67phox expression were high only in the blood and kidney, while p22phox and p40phox were constitutively expressed in a wide range of tissues . These results suggest that Japanese pufferfish NADPH oxidase components possess functional activities similar to those of human.

Clin Nephrol, 2004 May, 61(5), 324 - 36
Effect of advanced glycation end products on endotoxin-induced TNF-alpha, IL-1beta and IL-8 in human peripheral blood mononuclear cells; Reznikov LL et al.; BACKGROUND/AIMS: Advanced glycated end products (AGE) are endogenous proteins that have formed covalent complexes with sugars by a nonenzymatic process . Being proinflammatory molecules, AGE are thought to contribute to chronic systemic and local inflammatory processes associated with pathological changes in various diseases . In patients with end-stage renal disease, AGE are believed to play a role in the progression of atherosclerosis and worsening of renal failure . In patients receiving hemodialysis, AGE are thought to contribute to the inflammatory components of the therapy, particularly in diabetic patients . METHODS: In the present study, AGE were produced using 5% human serum albumin (HSA) and 50% glucose, both used for intravenous infusion into humans and both released after strict control for endotoxin content . The presence of AGE formed by HSA and glucose was confirmed using 2 independent assays . The inflammatory properties of these AGE were assessed using synthesis and release of the proinflammatory cytokines interleukin-1 (IL-1), tumor necrosis factor (TNF) and IL-8, a chemokine . RESULTS: Alone, AGE did not induce these cytokines from peripheral blood mononuclear cells (PBMC) obtained from 14 healthy human donors . However, in the presence of 1 or 10 ng/ml of endotoxin, AGE augmented the production of IL-1 and TNF above that induced by endotoxin alone . Although the amount of augmentation of LPS-induced cytokines by AGE varied between the blood donors, the response was consistently observed and reached statistical significance . The augmentation of cytokine production was confirmed using AGE prepared with different lots of HSA and glucose . CONCLUSION: These results demonstrate that in the strict absence ofendotoxins, AGE are formed that do not stimulate cytokine production from PBMC of healthy donors, however, AGE significantly augment the synthesis and release of proinflammatory cytokine in the presence of low concentrations of endotoxins . The data suggest that renal replacement therapies should consider the role of microbial products in potentiating the biological consequences of naturally formed AGE and their potential to contribute to systemic and local inflammation in renal replacement therapies . Therefore, although the formation of AGE is unavoidable, excluding microbial products during renal replacement therapy should reduce the pathological consequences of AGE.

Sichuan Da Xue Xue Bao Yi Xue Ban, 2004 May, 35(3), 364 - 6
{Effect of tea polyphenol on the demineralization and remineralization of enamel in vitro}; Li JY et al.; OBJECTIVE: To investigate the effect of tea polyphenol (TP) on the mineralization behaviour of enamel in two sterile, in vitro systems . METHODS: In the demineralization study, sound enamel sections were pH-cycled . Treatments were 2000 mg/L TP, 200 mg/L TP, 2000 mg/L TP + 100 mg/L fluoride, 100 mg/L fluoride, and deionized water . In the remineralization study, surface-softened enamel was used and pH-cycled as above . Test treatments were 2000 mg/L TP, 2000 mg/L TP + 250 mg/L fluoride, 250 mg/L fluoride, and deionized water . The acidic buffers were retained for calcium analysis . The enamel was analysed before and after pH-cycling by microhardness . RESULTS: In the demineralization study, the calcium depletion rates(CDR) were (0.43 +/- 0.05), (0.49 +/- 0.006), (0.21 +/- 0.02), (0.21 +/- 0.03) and (0.50 +/- 0.11) microgram/(mm2.h) respectively . The Knoop hardness values(KHV) percent reduction were 94.19 +/- 3.50, 96.62 +/- 0.63, 74.74 +/- 4.09, 77.79 +/- 3.11 and 97.32 +/- 4.03 respectively . There were no significant differences within either the TP-only groups or the fluoride groups, but the fluoride groups were significantly more efficacious than the TP-only groups (P < 0.05) . In the remineralization study, the KHV percent increase were -11.96 +/- 10.1, -21.32 +/- 11.3, -49.52 +/- 24.6 and -4.24 +/- 8.51 respectively . Notably more remineralization was observed in the fluoride group . There were no significant differences between the other groups (P > 0.05) . CONCLUSION: The data of this in vitro study suggest that TP has no effect on de/remineralization of enamel blocks and there is no synergetic action of TP and fluoride in a sterile system . This finding supports the proposition that tea polyphenols exert an anti-caries effect via an anti-microbial mode-of-action.

Immunol Res, 2004, 29(1-3), 55 - 68
Intestinal epithelial cell regulation of mucosal inflammation; Yu Y et al.; The intestinal epithelium serves as one of human's primary interfaces with the outside world . This interface is very heavily colonized with bacteria and yet permits absorption of life-sustaining nutrients while protecting the tissues below from microbial onslaught . Although the gut epithelium had been classically thought to achieve this function primarily by functioning as a passive, albeit highly selective, barrier, research over the last decade has demonstrated that in fact the epithelium plays a very active role in protecting the host from the bacteria that colonize it . As a consequence of its mediation of mucosal immunity, intestinal epithelial dysfunction appears to be central to diseases associated with aberrant gut mucosal immune responses such as inflammatory bowel disease (IBD) . This article reviews: (1) how the gut epithelium participates in regulating innate immune inflammatory responses to enteric pathogens, (2) how these responses may regulate the adaptive immune system, (3) mechanisms that may resolve acute inflammation, and (4) how epithelial dysfunction may participate in regulating both the active and chronic phases of IBD.

Environ Toxicol Chem, 2004 May, 23(5), 1211 - 8
Comparison of two screening bioassays, based on the frog sciatic nerve and yeast cells, for the assessment of herbicide toxicity; Papaefthimiou C et al.; Two different test systems, one based on the isolated sciatic nerve of an amphibian and the other on a microbial eukaryote, were used for the assessment of herbicide toxicity . More specifically, we determined the deleterious effects of increasing concentrations of herbicides of different chemical classes (phenoxyacetic acids, triazines, and acetamides), and of 2,4-dichlorophenol (2,4-DCP), a degradation product of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), on electrophysiological parameters and the vitality of the axons of the isolated sciatic nerve of the frog (Rana ridibunda) and on the growth curve of the yeast Saccharomyces cerevisiae based on microtiter plate susceptibility assays . The no-observed-effect-concentration (NOEC), defined as the maximum concentration of the tested compound that has no effect on these biological parameters, was estimated . In spite of the different methodological approaches and biological systems compared, the NOEC values were identical and correlated with the lipophilicity of the tested compounds . The relative toxicity established here, 2,4-DCP > alachlor, metolachlor >> metribuzin > 2,4-D, 2-methyl-4-chlorophenoxyacetic acid (MCPA), correlates with the toxicity indexes reported in the literature for freshwater organisms . Based on these results, we suggest that the relatively simple, rapid, and low-cost test systems examined here may be of interest as alternative or complementary tests for toxicological assessment of herbicides.

Environ Toxicol Chem, 2004 May, 23(5), 1164 - 71
Distribution of atrazine into three chemical fractions: impact of sediment depth and organic carbon content; Smalling KL et al.; The fate and transport of organic contaminants in aquatic sediments are impacted largely by microbial degradation and sorption to organic matter . Atrazine, a pre-emergent herbicide, has the potential to contaminate groundwater because of its slight water solubility, long half-life, and sorption to organic matter . Mineralization and distribution of 14C-atrazine into three chemical fractions were monitored over time in surface and subsurface coastal aquatic sediments of different land use . Sediments were extracted with an organic solvent followed by an alkali hydrolysis, and 14C activity was measured in the aqueous, solvent, and basic fractions (representing nonsorbed compounds, loosely sorbed compounds, and humic or fulvic acid bound compounds, respectively) . Limited mineralization of atrazine occurred (< 4%) . The 14C activity in the aqueous and basic fractions increased over time, was greater in surface versus subsurface sediments, and was positively correlated with sediment organic carbon (SOC) content, indicating greater biological and chemical activity . Total 14C recovered ranged from 50 to 90%, was less in surface versus subsurface sediments, and was not correlated with SOC after 80 d . These results suggest that in native aquatic surface sediments, atrazine sorption plays a major role, whereas in subsurface sediments atrazine may be available for degradation and transport to shallow groundwater.

Environ Toxicol Chem, 2004 May, 23(5), 1145 - 55
Effect of sediment on the fate of metolachlor and atrazine in surface water; Rice PJ et al.; In aquatic environments, pesticides can partition between the dissolved phase and particulate phase depending on the type of suspended sediment present and the physical and chemical properties of the pesticides and water . Particulate matter and sediment can alter the bioavailability of contaminants to organisms and therefore influence their toxicity and availability for microbial degradation . Experiments were conducted to determine the degradation of atrazine (6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2.4-diamine) and metolachlor (2-chloro-N-(2-ethyl-6-methylphenyl)-N-(methooxyprop-2-yl)acetamide) in surface water, and to evaluate the contribution of sediment to their dissipation . Sediment significantly reduced concentrations of atrazine and metolachlor in the surface water as a result of greater degradation, evident by increased quantities of degradates in the surface water, and the partitioning of the herbicide or herbicide degradates in the sediment . First-order 50% dissipation time (DT50) values for atrazine and metolachlor were 42 and 8 d in the surface water-sediment incubation systems, which were almost four times less than the DT50s calculated for the sediment-free systems . The results of this research illustrate the importance of sediment in the fate of pesticides in surface water . Greater comprehension of the role of sediment to sequester or influence degradation of agrichemicals in aquatic systems will provide a better understanding of the bioavailability and potential toxicity of these contaminants to aquatic organisms.

Int Microbiol, 2004 Mar, 7(1), 19 - 25
Distribution of phototrophic populations and primary production in a microbial mat from the Ebro Delta, Spain; Martinez-Alonso M et al.; Microbial mats arising in the sand flats of the Ebro Delta (Tarragona, Spain) were investigated during the summer season, when the community was highly developed . These mats are composed of three pigmented layers of phototrophic organisms, an upper brown layer mainly composed of Lyngbya aestuarii and diatoms, an intermediate green layer of the cyanobacterium Microcoleus chthonoplastes, and an underlying pink layer of a so-far unidentified purple sulfur bacterium . In the photic zone, oxygenic phototrophs constitute about 58% of total photosynthetic biomass, measured as biovolume, and anoxygenic phototrophs represent 42% . Diatoms constitute 11.8% of the oxygenic biomass, M . chthonoplastes 61.2%, and L . aestuarii and coccoid cyanobacteria 20.6 and 6.4%, respectively . In this laminated community, organic matter has an autochthonous origin, and photosynthesis is the most important source of organic carbon . Oxygen production reaches up to 27.2 mmol O(2) m(-2) h(-1), measured at 1000 microE m(-2) s(-1) light intensity, whereas oxidation of sulfide in the light has been calculated to be 18.6 mmol S m(-2) h(-1) . This amount represents 26% of the total photosynthetic production in terms of photoassimilated carbon, demonstrating the important role of anoxygenic phototrophs as primary producers in the pink layer of Ebro Delta microbial mats.

Arch Immunol Ther Exp (Warsz), 2004 Mar-Apr, 52(2), 104 - 12
Leucine-rich repeats in host-pathogen interactions; Kedzierski L et al.; Leucine-rich repeats (LRRs) are versatile binding motifs found in a variety of proteins and are involved in protein-protein interactions . The LRR domain is composed of repeats forming a characteristic solenoid horse-shoe structure, which provides a scaffold for numerous insertions involved in binding to pathogen-associated molecular patterns and surface receptors . LRRs have been shown to be involved in the host defense systems of both plants (resistance genes) and mammals (Toll-like receptors and nucleotide-binding oligomerisation domain proteins), where they sense specific pathogen-associated molecules and activate the innate immune system . Paradoxically, LRRs have also been shown to be part of microbial virulence factors involved in the interaction with host cells and establishment of infection . The potential of LRRs to bind a vast array of structurally unrelated ligands and their well-documented involvement in microbial pathogenesis make them a potential target for vaccines and new drugs . The recent identification of LRRs in the obligate intracellular protozoan parasite Leishmania and their participation in the macrophage-parasite interaction have added new insight into the role of LRRs in the host cell invasion.

Int Arch Allergy Immunol, 2004 Jul, 134(3), 179 - 85 Epub 2004 Jun 01.
The regulatory role of dendritic cells in the immune response; Granucci F et al.; Dendritic cells (DCs) are key regulators of immune reactions . They control early innate responses, regulate long-lasting adaptive immunity and contribute to the maintenance of self-tolerance . DCs continuously monitor the environment through a multifaceted innate antigen receptor repertoire and, in response to perturbations, start a complex genetic reprogramming that leads to a complete activation of innate and, then, adaptive immune responses . This review discusses how DCs become efficient activators of NK and, subsequently, T cells following a microbial encounter .

J Pept Res, 2004 Jun, 63(6), 469 - 76
A theta-defensin composed exclusively of D-amino acids is active against HIV-1; Owen SM et al.; The ability of certain theta-defensins, including retrocyclin-1, to protect human cells from infection by HIV-1 marks them as potentially useful molecules . Theta-defensins composed of L-amino acids are likely to be unstable in environments that contain host and microbial proteases . This study compared the properties of two enantiomeric theta-defensins, retrocyclin-1, and RC-112 . Although these peptides have identical sequences, RC-112 is composed exclusively of D-amino acids, whereas retrocyclin-1 contains only L-amino acids . We compared the ability of these peptides to protect JC53-BL human cells from infection by 30 primary HIV-1 isolates . JC53-BL cells are modified HeLa cells that express surface CD4, CXCR4, and CCR5 . They also contain reporter cassettes that are driven by the HIV-1 LTR, and express beta-galactosidase and luciferase . The HIV-1 isolates varied in co-receptor specificity and included subtypes A, B, C, D, CRF01-AE, and G . RC-112 was several fold more potent than retrocyclin-1 across the entire HIV-1 panel . Although RC-112 bound immobilized gp120 and CD4 with lower affinity than did retrocyclin-1, surface plasmon resonance experiments performed with 1 microg/mL of RC-112 and retrocyclin-1 revealed that both glycoproteins were bound to a similar extent . The superior antiviral performance of RC-112 most likely reflected its resistance to degradation by surface-associated or secreted proteases of the JC53-BL target cells . Theta-defensins composed exclusively of D-amino acids merit consideration as starting points for designing microbicides for topical application to the vagina or rectum.

Proteomics, 2004 Jun, 4(6), 1779 - 88
Cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, Sphingopyxis alaskensis; Ostrowski M et al.; Sphingopyxis (formerly Sphingomonas) alaskensis is a model bacterium for studying adaptation to oligotrophy (nutrient-limitation) . It has a unique physiology which is fundamentally different to that of the well studied bacteria such as Escherichia coli . To begin to identify the genes involved in its physiological responses to nutrient-limited growth and starvation, we developed high resolution two-dimensional electrophoresis (2-DE) methods and determined the identity of 12 proteins from a total of 21 spots using mass spectrometric approaches and cross-species matching . The best matches were to Novosphingobium aromaticivorans; a terrestrial, hydrocarbon degrading bacterium which was previously classified in the genus Sphingomonas . The proteins identified are involved in fundamental cellular processes including protein synthesis, protein folding, energy generation and electron transport . We also compared radiolabelled and silver-stained 2-DE gels generated with the same protein samples and found significant differences in the protein profiles . The use of both methods increased the total number of proteins with differential spot intensities which could be identified from a single protein sample . The ability to effectively utilise cross-species matching from radiolabelled and silver-stained gels provides new approaches for determining the genetic basis of microbial oligotrophy.

Ann Neurol, 2004 Jun, 55(6), 840 - 4
Role of cerebral lateralization in control of immune processes in humans; Meador KJ et al.; Cerebral lateralization may be important in neural control of immune function . Animal studies have demonstrated differential effects of left and right brain lesions on immune function, but human studies are inconclusive . Here, we show that resections in the language dominant hemisphere of patients with epilepsy reduce lymphocytes, total T cells, and helper T cells . In contrast, resections in the language nondominant hemisphere increased the same cellular elements . T-cell responses to mitogens and microbial antigens were not differentially affected . Left/right arm histamine skin response ratios were altered in patients with left cerebral epileptic focus, and flare skin responses were reduced by left cerebral resections in contrast with an increase after right cerebral resections . The findings demonstrate a differential role of the left and right cerebral hemispheres on immune functions in humans.

J Biol Chem, 2004 Aug 13, 279(33), 34589 - 94 Epub 2004 Jun 01.
Four N-linked glycosylation sites in human toll-like receptor 2 cooperate to direct efficient biosynthesis and secretion; Weber AN et al.; Most higher organisms have a system of innate immune defense that is mediated by a group of evolutionarily related, germ line-encoded receptors, so-called Toll-like receptors . In mammals Toll-like receptors signal in response to pathogen-associated microbial structures . For example, Toll-like receptor 2 appears to mediate responses to bacterial peptidoglycan and acylated lipoproteins and Toll-like receptor 4 to bacterial lipopolysaccharide . However, the structural principles that underlie recognition of these structures are poorly understood . Toll-like receptors have leucine-rich repeats in their extracellular domains and are thus believed to adopt solenoid structures, similar to that found in platelet glycoprotein Ib . Additionally, all Toll-like receptors contain N-linked glycosylation consensus sites, and Toll-like receptor 4 requires glycosylation for function . Toll-like receptor glycosylation is also likely to influence receptor surface representation, trafficking, and pattern recognition . Using circular dichroism spectroscopy, we show here that purified human Toll-like receptor 2 and 4 proteins have secondary structure contents similar to glycoprotein Ib . We have also analyzed where consensus glycosylation sites are located in the extracellular domains of other human Toll-like receptors . We found that there are significant differences in the location and degree of conservation between sites in different Toll-like receptors . Using site-directed mutagenesis, we have found that in Toll-like receptor 2 extracellular domain all four predicted glycosylation sites are substituted, although one site is inefficiently core-glycosylated and its removal drastically affects secretion . The remaining Toll-like receptor 2 glycosylation sites also contribute to efficient protein secretion, albeit to a lesser degree.

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