J Environ Radioact, 2004, 75(2), 117 - 32 Evaluation of 14C abundance in soil respiration using acclerator mass spectrometry; Koarashi J et al.; To clarify the behavior of 14C in terrestrial ecosystems, 14C abundance in soil respiration was evaluated in an urban forest with a new method involving a closed chamber technique and 14C measurement by accelerator mass spectrometry (AMS) . Soil respiration had a higher Delta14C than the contemporary atmosphere . This indicates that a significant portion of soil respiration is derived from the decomposition of soil organic matter enriched in 14C by atmospheric nuclear weapons tests, with a notable time lag between atmospheric 14C addition and re-emission from soil . On the other hand, delta14C in soil respiration demonstrated that 14C abundance ratio itself in soil-respired CO2 is not always high compared with that in atmospheric CO2 because of the isotope fractionation during plant photosynthesis and microbial decomposition of soil organic matter . The Delta14C in soil respiration was slightly lower in August than in March, suggesting a relatively high contribution of plant root respiration and decomposition of newly accumulated and/or 14C-depleted soil organic matter to the total soil respiration in August. Chemosphere, 2004 Jul, 56(3), 299 - 304 Long-term effects of fertilization on the forms and availability of soil phosphorus in rice paddy; Lee CH et al.; The changes in total P accumulation and P compounds with time in the plough layer in a paddy soil in southern Korea were investigated in relation to the continuous application of chemical fertilizers (NPK), straw based compost (Compost), combination these two (NPK+Compost) for 31 years . Continuous fertilization increased the total and inorganic P contents in plough layers . In NPK, inorganic P fraction did not change with time, but organic P content increased significantly . Long-term application of chemical fertilizer together with compost accelerated the decrease in the organic P fraction, presumably due to promoting microbial activity in the plow layer, and then increased significantly inorganic P fraction . Compost application decreased the residual P and Fe-P fractions and then increased inorganic P fraction, in spite of continuous compost application . Increase in total, inorganic and extractable P with time may be closely related to the increase in the availability of accumulated P for rice growth. Chemosphere, 2004 Jul, 56(3), 257 - 63 Atrazine and simazine degradation in Pennisetum rhizosphere; Singh N et al.; The ability of rhizosphere of four plant species to promote the degradation of charcoal-fixed atrazine and simazine in cement blocks of a long-term contaminated soil when mixed with a normal soil at 1:1 ratio was tested . Of the four selected plants viz., rye grass (Lolium perenne), tall fescue (Festuca arundinacae), Pennisetum (Pennisetum clandestinum) and a spring onion (Allium sp.) used in this study, only P . clandestinum was able to survive in herbicide contaminated soil while other plants died within few days after germination/transplanting . Both atrazine and simazine were degraded at a faster rate in contaminated soil planted to P . clandestinum than in unplanted soil . Within 80 days, nearly 45% and 52% of atrazine and simazine, respectively, were degraded in soil planted to P . clandestinum while only 22% and 20% of the respective herbicide were degraded in the unplanted soil . During 80-day experimental period, both microbial biomass and soil dehydrogenase activity were significantly increased (7-fold) in soil planted to P . clandestinum over that in unplanted soil . The suspension of contaminated rhizosphere soil, planted to P . clandestinum exhibited an exceptional capability to degrade both atrazine (300 microg) and simazine (50 microg) in a mineral salts medium over that of non-rhizosphere soil suspension . Results indicate that P . clandestinum, a C4 plant, may be useful for remediation of soils contaminated with atrazine and simazine. J Chromatogr B Analyt Technol Biomed Life Sci, 2004 Jul 5, 806(2), 245 - 53 Liquid chromatography-mass spectrometry analysis of hydroxylated polycyclic aromatic hydrocarbons, formed in a simulator of the human gastrointestinal tract; Van de Wiele TR et al.; Described is a liquid chromatography-mass spectrometry (LC-MS) procedure for the determination of hydroxylated biotransformation products of polycyclic aromatic hydrocarbons (PAH) in the human gastrointestinal tract . The formation of hydroxylated PAHs was monitored upon incubation of PAHs with colon microbiota from the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) . The analytical method consisted of a biomass removal step followed by a solid phase extraction (SPE) step using C18 packed columns to remove non-digested food compounds and microbial metabolites that interfere with the detection of the target compounds . For quantification, 9-hydroxyphenanthrene (13)C(6)was used as the internal standard . The detection limits of the hydroxylated PAHs were generally in the range 0.36-14.09 microg x l(-1), based on a signal/noise ratio of 3:1 . The recovery of hydroxylated PAHs in intestinal suspension was variable ranging from 45 to 107%, with relative standard deviation (R.S.D.) between 5 and 17% . The analytical procedure was used to show the microbial production of 1-hydroxypyrene and 7-hydroxybenzo(a)pyrene, metabolites that may give colon incubated PAHs bioactive properties. Int J Immunopathol Pharmacol, 2004 May-Aug, 17(2), 127 - 34 Immune-signalling by orally-delivered probiotic bacteria: effects on common mucosal immunoresponses and protection at distal mucosal sites; Cross ML; Probiotics--orally-delivered preparations of non-pathogenic bacterial cells--have been reported to increase anti-microbial protection in the gastrointestinal tract environment, and offer a safe and effective non-pharmaceutical means for combating infectious diseases and certain other pathologies . There is also an increasing body of evidence to suggest that immunostimulation by probiotic bacteria in the gut can enhance immune protection at distal mucosal sites, such as the urogenital and respiratory tracts . This review summarises the current information, from both clinical and animal model studies, of a role for orally-delivered probiotics in modulating mucosal immunoresponses and protection at distal sites . While it is clear that probiotics hold promise in this area, research that is targeted toward identifying the mechanism driving stimulation of the common mucosal immune system, as well as patterns of mucosal tissue homing by immunocytes following probiotic-mediated signalling in the gut, is strongly encouraged. Muscle Nerve, 2004 Jun, 29(6), 873 - 7 Myositis in a patient with large granular leukocyte leukemia; Rosche B et al.; We describe the case of a 58-year-old patient with subacute progressive weakness in both legs accompanied by recurrent opportunistic infections . White cell count was normal, but immunophenotyping revealed an increased number of CD8(+) T cells and deficiency of natural killer cells, B cells, and CD4(+) T cells in the peripheral blood . Large granular leukocyte (LGL) leukemia was diagnosed based on a clonal T-cell receptor rearrangement . Muscle biopsy demonstrated severe myositis with extensive CD8(+) T-cell infiltrates . Since no evidence of microbial muscle infection was found, autoimmune myositis was diagnosed . Immunosuppressive treatment resulted in clinical improvement and normalization of creatine kinase (CK) serum levels . The immunological phenotype of the patient and the positive response to treatment adds further to the concept that CD8(+) T cells mediate disease in autoimmune myositis. Photochem Photobiol Sci, 2004 Jun, 3(6), 548 - 54 Epub 2004 Mar 18. Light-induced intramolecular charge movements in microbial rhodopsins in intact E . coli cells; Sineshchekov OA et al.; Microbial rhodopsins undergo cyclic photochemical reactions (photocycles) in which proton transfers and conformational changes result in charge displacements during transitions between photocycle intermediates . We report a new photoelectric method to monitor charge movements during rhodopsin photocycling with fast kinetic resolution in suspensions of intact E . coli cells . The method monitors electrical currents resulting from asymmetric photoexcitation of microbial rhodopsins by a unilateral laser flash, and kinetically resolves intramolecular charge movements . We investigated E . coli-expressed proton-transporting rhodopsins, specifically green- and blue-absorbing proteorhodopsins (GPR and BPR, respectively) from uncultivated marine plankton, and sensory rhodopsins, namely receptors from Natronomonas pharaonis and Anabaena (Nostoc) sp . PCC7120 . Kinetic components of the currents correlate with photochemical transformations of the pigments, and the integrated current measures net transport by the proton-pumping rhodopsins . The photoelectric measurements distinguish between known light-driven transporters and photosensors, and reveal differences in proton transfer reactions in the two tested proton pumps . Screening of nine newly identified proteorhodopsins reveals two with GPR-type charge movements, five with BPR-type, and two with the characteristics of the sensory rhodopsins . The approach developed in the present work provides a direct, rapid and informative method for studying electrogenic events in rhodopsin photocycles and also gives a clue to functions of newly found microbial rhodopsins in nature. Plant Cell Physiol, 2004 May, 45(5), 535 - 42 Secretion in unicellular marine phytoplankton: demonstration of regulated exocytosis in Phaeocystis globosa; Chin WC et al.; Almost half of the global photosynthetic activity is carried out in the ocean . During blooms, Phaeocystis can fix CO(2) at rates up to 40 g C m(-2) month(-1) . Most of this carbon is released as polysaccharides . However, the cellular mechanism whereby this huge amount of organic material is exported into the seawater remains unknown . A vaguely defined process of "exudation" is believed responsible for the release of these biopolymers . Here we report the first demonstration that Phaeocystis globosa does not "exude", but secretes microscopic gels . Secretion is stimulated by blue light (lambda = 470+/-20 nm), and it is transduced by a characteristic intracellular Ca(2+) signal that precedes degranulation . The polysaccharides that form the matrix of these gels remain in condensed phase while stored in secretory vesicles . Upon exocytosis, the exopolymer matrix undergoes a characteristic phase transition accompanied by extensive swelling resulting in the formation of microscopic hydrated gels . Owing to their tangled topology, once released into the seawater, the polymers that make these gels can reptate (axially diffuse), interpenetrate neighboring gels, and anneal them together forming massive mucilage accumulations that are characteristic of Phaeocystis blooms . These gel masses can supply a rich source of microbial substrates, disperse in the seawater, and/or eventually sediment to the ocean floor. Biotechnol Lett, 2004 Apr, 26(7), 607 - 10 Hydroxylation of 10-deoxoartemisinin to 15-hydroxy-10-deoxoartemisinin by Aspergillus niger; Parshikov IA et al.; The microbial hydroxylation of 10-deoxoartemisinin was investigated with the aim of obtaining preparative yields of hydroxy derivatives . During 14 d at 28 degrees C and pH 6.5 Aspergillus niger transformed 10-deoxoartemisinin (500 mg l(-1)) to 15-hydroxy-10-deoxoartemisinin (26%) and 7beta-hydroxy-10-deoxoartemisinin (69%). J Pediatr Gastroenterol Nutr, 2004 Jun, 39 Suppl 3, S719 - 22 CD1d-restricted T cell pathways at the epithelial-lymphocyte-luminal interface; Kaser A et al.; The mucosal-associated lymphoid tissues, including the gut-associated lymphoid tissues, represent a tightly regulated environment that, on the one hand, must resist microbial invasions and on the other hand, when perturbed, causes inflammation such as that associated with inflammatory bowel disease . One type of regulatory cellular subset that has recently gained attention in this compartment is the subset of T cells that are associated with CD1d-restricted responses . Recently, CD1d-restricted T cells have been increasingly appreciated to play a significant role in mucosal tissues of the intestine and lung, for example . In this review, we focus on recent observations in the characteristics of CD1d-restricted pathways in mucosal compartments after a brief introduction to the biology of CD1d and CD1d-restricted T cells. Curr Opin Otolaryngol Head Neck Surg, 2004 Jun, 12(3), 232 - 6 The hygiene theory: fact or fiction? Sheikh A, Strachan DP. PURPOSE OF REVIEW: The "hygiene hypothesis" offers a potentially credible and parsimonious explanation for the increasing prevalence of allergy noted in many westernized populations . The authors review recent evidence both for and against this hypothesis . RECENT FINDINGS: A strong body of epidemiologic evidence indicates that the original observations, namely of a birth order effect and increased risk of atopic disorders in those born into small, affluent households, are robust findings . Improved hygiene is believed to mediate its effect through decreased exposure to infectious agents in early life, and recent evidence has focused attention on the importance of the gastrointestinal microbial environment . In particular, infection with hepatitis A, Helicobacter pylori, and toxoplasma in those living in temperate climates, and geoheminths in those living in endemic areas, have been shown to be associated with reduced risk of atopic manifestations . It is postulated that these infections exert their effect through critically altering T-helper (Th)1/Th2 regulation, which is supported by the examination of the cytokine profiles of cord mononuclear cells when exposed to gastrointestinal flora and, furthermore, emerging evidence on the benefits of probiotics on symptoms of atopic dermatitis . Attempts to identify an inverse relation between Th1- and Th2-mediated disorders (as might be predicted by the Th1/Th2 paradigm) have, however, yielded conflicting results, raising the possibility that this model may be something of an oversimplification . SUMMARY: The hygiene hypothesis remains a credible but nonspecific explanation for observed variations over time, place and persons at risk for developing atopic allergic disorders . More prospective studies are needed to unravel which infectious agents exert a protective effect and the time period of importance for sensitization . The clinical implications of these advances in our understanding of the etiology of atopic allergic disorders are currently limited. J Clin Pathol, 2004 Jun, 57(6), 657 - 9 Chlamydia trachomatis serovar E isolates from patients with different clinical manifestations have similar courses of infection in a murine model: host factors as major determinants of C trachomatis mediated pathogenesis; Lyons JM et al.; BACKGROUND: Some investigators have proposed an association between certain Chlamydia trachomatis serovars and the clinical course of infection in humans . A recent study of over 1100 patients with culture confirmed and serotyped C trachomatis urogenital infection detected no such association . AIMS: To corroborate these results using a murine model of female genital tract infection . METHODS: Various parameters of infection were assessed in mice intravaginally infected with human genital isolates of C trachomatis serovar E from four cases with either a clear symptomatic or asymptomatic clinical course in both the patient and their partner . RESULTS: No differences were seen among the strains in the incidence or duration of infection, polymorphonuclear granulocyte responses, or upper genital tract progression . CONCLUSIONS: An investigation to determine the correlation between the clinical manifestations of different isolates of C trachomatis serovar E in humans and certain parameters of microbial pathogenesis in a mouse model failed to reveal an association between the measured parameters and the tendency of serovar E to produce symptomatic versus asymptomatic infections in humans . These findings suggest that differences in the clinical course of infection in humans seen with these strains may be more related to host factors than to genetic variation among strains. Mol Microbiol, 2004 Jun, 52(5), 1229 - 42 Structure, function and evolution of microbial adenylyl and guanylyl cyclases; Baker DA et al.; Cells respond to signals of both environmental and biological origin . Responses are often receptor mediated and result in the synthesis of so-called second messengers that then provide a link between extracellular signals and downstream events, including changes in gene expression . Cyclic nucleotides (cAMP and cGMP) are among the most widely studied of this class of molecule . Research on their function and mode of action has been a paradigm for signal transduction systems and has shaped our understanding of this important area of biology . Cyclic nucleotides have diverse regulatory roles in both unicellular and multicellular organisms, highlighting the utility and success of this system of molecular communication . This review will examine the structural diversity of microbial adenylyl and guanylyl cyclases, the enzymes that synthesize cAMP and cGMP respectively . We will address the relationship of structure to biological function and speculate on the complex origin of these crucial regulatory molecules . A review is timely because the explosion of data from the various genome projects is providing new and exciting insights into protein function and evolution. Pharmacogenomics, 2004 Jun, 5(4), 361 - 79 Pharmacogenomic strategies against resistance development in microbial infections; Ziebuhr W et al.; There are several promising new strategies against resistance development in microbial infections . This paper discusses typical experimental and bioinformatical strategies to study the impact of infectious challenges on host-pathogen interaction, followed by several novel approaches and sources for new pharmaceutical strategies against resistance development . Genomics reveals promising new targets by providing a better understanding of cellular pathways, through the identification of new pathways, and by identifying new intervention areas, such as phospholipids, glycolipids, innate immunity, and antibiotic peptides . Additional antibiotic resources come from new genomes, including marine organisms, lytic phages and probiotic strategies . A system perspective regards all interactions between the host, pathogen and environment to develop new pharmacogenomic strategies against resistance development. Antibiot Khimioter, 2004, 49(1), 14 - 6 {Effect of novel natural hypolipidemic compounds on human immunodeficiency virus}; Bibikova MV et al.; Target screening among microbial products resulted in isolation of hypolipidemic compounds tested for activity against HIV in culture of transferable lymphoblastoid cells MT-4 . The majority of the compounds showed antiviral activity . The highest antiviral effect was observed when before exposure to the virus the cells were preincubated for 1 hour in the presence of the isolated compounds . The compounds showed no effect when added to the cell culture preliminarily infected by HIV. Microb Ecol, 2004 Jul, 48(1), 139 - 44 Epub 2004 May 28. Determining parameters of the numerical response; Montagnes DJ et al.; The numerical response, the change in specific growth rate with food concentration, is a fundamental component of many aquatic microbial studies . Accurately and precisely determining the parameters of this response is essential to obtain useful data for both aut- and synec-ological studies . In this work we emphasize four points that are often ignored in designing numerical response experiments: (1) the inclusion of subthreshold concentrations (i.e., where growth rate is negative) in the experimental design; (2) an appropriate allocation of effort, i.e., the superiority of choosing more individual prey concentrations rather than replicating fewer; (3) the potential superiority of replicating experiments rather than simply replicating treatment in a single experiment; and (4) the placement of most measurements near the lower end of the concentration gradient, well below the asymptote, possibly following a geometric progression . We illustrate the first point by examining a small subset of published data on planktonic oligotrich ciliates and then, using a Monte Carlo simulation, rigorously evaluate the experimental design, supporting the remaining points. J Neurol, 2004 May, 251(5), 542 - 7 Increased prevalence of and gene transcription by Chlamydia pneumoniae in cerebrospinal fluid of patients with relapsing-remitting multiple sclerosis; Dong-Si T et al.; Microbial agents may play a role in the pathogenesis of multiple sclerosis (MS) . C . pneumoniae has been recently associated with MS; however, study results are at variance . We tested the hypothesis that Chlamydia pneumoniae-specific DNA and RNA are more often detected in cerebrospinal fluid (CSF) of patients with multiple sclerosis than patients with other neurological diseases (OND) . We investigated CSF samples from 84 patients with definite MS and 89 OND patients (n = 62 with normal CSF; n = 27 with pathological CSF) using a nested polymerase chain reaction (PCR) to detect ompA gene sequences of C . pneumoniae . In subjects with positive PCR, we probed for chlamydial heat shock protein 60-mRNA and 16S-rRNA by reverse transcriptase (rt)-PCR . C . pneumoniae-specific DNA was more often detected in MS patients (50 %) than in all OND patients combined (28.1%, p = 0.003) and in OND patients with normal CSF (24.2%, p = 0.003) but not than in OND patients with pathological CSF (37%, p = 0.24) . In relapsing-remitting MS (n = 55), the prevalence of C . pneumoniae DNA was higher (66.7 %) than in both OND subgroups (p <or= 0.05) . In MS patients (n = 20), chlamydial heat shock protein 60-mRNA (75%) and 16S-rRNA (70%) were more often detected than in OND patients (n = 16; 18.8%; p < 0.005).Although more often detected in remitting-relapsing MS, C . pneumoniae DNA in CSF is not specific for MS owing to its high prevalence in OND controls . However, the higher rate of gene transcription suggests a more active metabolism of C . pneumoniae in MS patients. J Biotechnol, 2004 Jun 10, 110(3), 313 - 22 Identification and characterization of a phytase of potential commercial interest; Casey A et al.; Phytases catalyse the hydrolytic degradation of phytic acid and its salts and are added to monogastric animal feed to ameliorate the negative environmental and nutritional consequences of dietary phytate . Screening of 58 microbial strains identified a phytase produced by Rhizopus oligosporus ATCC 22959 that displayed physicochemical characteristics likely to render it of potential industrial interest . The 124 kDa enzyme was purified to homogeneity by anion exchange chromatography, gel filtration and chromatofocusing . The monomeric glycosylated enzyme (30.5% total carbohydrate) displayed maximum activity at 65 degrees C and pH 5.0 . It displayed a Km of 10.4 microM, a Vmax of 1.32 nmols(-1) and a Kcat of 51 s(-1) . It is acid tolerant, retaining full activity after incubation at pH 2.0 for 6h . HPLC analysis indicated the enzyme's ability to almost completely degrade phytate . Substrate specificity studies showed its ability to dephosphorylate several additional phosphorylated molecules . Activity was unaffected or moderately stimulated by a range of metal ions with only Ca2+ exerting a modest (13%) inhibitory effect . The enzyme is significantly more thermostable at 80 degrees C and retains a significantly greater proportion of maximal activity at physiological temperatures than do two commercial phytases tested for comparative purposes . This may render it of industrial interest . J Biotechnol, 2004 Jun 10, 110(3), 251 - 6 The influence of cell and substratum surface hydrophobicities on microbial attachment; Liu Y et al.; This study investigated the role of hydrophobic/hydrophilic interaction between bacterial and support surfaces in microbial adhesion, and a model that correlates microbial adhesion and relative cell-hydrophobicity defined as the ratio of cell-support surface hydrophobicity over cell-support hydrophilicity was derived . This model quantitatively describes how cell hydrophobic and hydrophilic interactions affect microbial adhesion, and offers deep insights into the thermodynamic mechanisms of microbial adhesion . The proposed model was verified by literature data . It appears that a high cell-hydrophobicity strongly facilitates microbial adhesion on both hydrophobic and hydrophilic support surfaces . Cell, 2004 May 28, 117(5), 561 - 74 Inflammatory caspases: linking an intracellular innate immune system to autoinflammatory diseases; Martinon F et al.; Caspases not only play an essential role during apoptotic cell death, but a subfamily of them-the inflammatory caspases-are associated with immune responses to microbial pathogens . Activation of inflammatory caspases, such as caspase-1 and caspase-5, occurs upon assembly of an intracellular complex, designated the inflammasome . This results in the cleavage and activation of the proinflammatory cytokines IL-1beta and IL-18 . Mutations in one of the scaffold proteins of the inflammasome, NALP3/Cryopyrin, are associated with autoinflammatory disorders underscoring the importance of regulating inflammatory caspase activation. Rev Biol Trop, 2003 Mar, 51(1), 85 - 98 Heterotrophic microbial activity and organic matter degradation in coastal lagoons of Colombia; Gocke K et al.; In this study we measured the community respiration and the bacterial respiration as part of the overall degradation process of organic material . Additionally, the turnover rates of the pools of dissolved free glucose and acetate as representatives of the fraction of easily degradable low molecular organic solutes were determined . The study was performed in several coastal lagoons of the "Outer Delta of the Rio Magdalena" in northern Colombia . The lagoons can be separated into two groups: The first group contains highly productive brackish lagoons with chl a concentrations ranging from 62-130 micrograms/l . The second group consists of less productive freshwater lagoons with chl a between 5.5-19 micrograms/l . Turnover rates of glucose and acetate were very fast in the highly productive lagoons resulting in turnover times of less than 20 min for both compounds . In the less productive systems the cycling of glucose and acetate was much slower . Here the mean values of the turnover times were 2 hr for glucose and 1.5 hr for acetate . The rates of bacterial DNA-formation measured as thymidine incorporation differed significantly between both groups of lagoons, being very high (1.86-2.76 nmol/l/hr) in the highly productive and relatively low (0.073-0.55 nmol/l/hr) in the less productive group . Water column community respiration ranged between 122 and 16 micrograms C/l/hr with means of 88 micrograms C/l/hr in the highly and 19 micrograms C/l/hr in the less productive group . In the first group the mean values of the bacterial contribution to community respiration amounted to 37% and in the second group to 18% . The bacterial respiration was determined in an indirect way via bacterial biomass production and assuming a growth efficiency of 50% . It is discussed whether this relatively high growth efficiency allows reasonable results in both groups of lagoons. J Agric Food Chem, 2004 Jun 2, 52(11), 3617 - 25 Interactive effects of microbial transglutaminase and recombinant cystatin on the mackerel and hairtail muscle protein; Jiang ST et al.; Interactive effects of microbial transglutaminase (MTGase) and recombinant cystatin on the mackerel and hairtail water soluble protein (WSP), salt soluble protein (SSP), and muscle protein (MP) were investigated . According to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and enzymic activity analyses, cross-linking of mackerel and hairtail myosin heavy chain and low molecular mass compounds and formation of epsilon-(gamma-glutamyl)lysine cross-links were observed on samples with MTGase, while the recombinant cystatin could effectively inhibit the cathepsins and subsequently prevent degradation of proteins during setting . The cathepsins and MTGase activities in WSP, SSP, and MP solutions decreased, but the recombinant cystatin activity increased during setting at 45 degrees C. J Agric Food Chem, 2004 Jun 2, 52(11), 3385 - 8 Radiation-induced enhancement of antioxidant contents of soybean (Glycine max Merrill); Variyar PS et al.; Soybean samples were treated with gamma-radiation doses between 0.5 and 5 kGy for achieving insect disinfestation and microbial decontamination . Nutritional quality of soybeans with respect to antioxidant isoflavone content was tested in radiation-treated and untreated samples . Changes in major isoflavones such as genistein, diadzein, glycetein, and their glycosides were monitored by high-performance liquid chromatography . Interestingly, a decrease in content of glycosidic conjugates and an increase in aglycons were noted with increasing radiation dose . Antioxidant potential measured as percent 1,1-diphenyl-2-picrylhydrazyl scavenging activity showed an increasing trend with dose, indicating that radiation processing as a method of food preservation has a positive nutritional implication. Acta Crystallogr D Biol Crystallogr, 2004 Jun, 60(Pt 6), 1167 - 9 Epub 2004 May 21. Crystallization and preliminary X-ray analysis of alpha-isopropylmalate synthase from Mycobacterium tuberculosis; Koon N et al.; alpha-Isopropylmalate synthase catalyses the aldol condensation of alpha-ketoisovalerate and acetyl coenzyme A to produce alpha-isopropylmalate . This reaction is the first committed step of leucine biosynthesis, which is interrelated with the pathways for production of the other branched-chain amino acids, valine and isoleucine . The absence of these pathways in mammals suggests that these enzymes could be useful targets for drug design against microbial pathogens . The gene for alpha-IPMS in Mycobacterium tuberculosis (Rv3710) has been cloned, expressed in Escherichia coli, both in native and selenomethionine-substituted forms, and crystallized . The SeMet crystals are suitable for high-resolution X-ray structural analysis . These crystals are monoclinic, with unit-cell parameters a = 54.25, b = 154.73, c = 68.82 angstoms, space group P2(1) and two molecules in the asymmetric unit . X-ray diffraction data to 2.0 angstroms resolution have been collected . Mol Immunol, 2004 Jun, 41(2-3), 123 - 31 The anaphylatoxins bridge innate and adaptive immune responses in allergic asthma; Hawlisch H et al.; The complement system has long been recognized for its role as a lytic effector system that protects against microbial pathogens, as well as for its role in mediating acute and chronic inflammatory responses . Many of the inflammatory sequelae of complement activation can be related to the complement cleavage fragments C3a and C5a, the so-called anaphylatoxins (ATs) . Cloning and subsequent gene targeting of their corresponding receptors, as well as generation of specific C3a and C5a inhibitors, have fueled new interest in studies aimed at defining the roles of the anaphylatoxins in inflammatory diseases . Traditionally, the anaphylatoxins have been considered mediators of end-stage effector mechanisms . However, recent data from animal models of allergic asthma suggest that C3a and C5a provide a critical link between innate and adaptive immunity . This review is aimed at outlining our current knowledge of when and where anaphylatoxins contribute to and control the development of allergic asthma . The accumulated data suggest a model in which C3a and C5a play important but opposing roles during allergen-induced T-cell polarization: C3a promotes Th2 responses, whereas C5a prevents Th2 polarization . During the effector phase, both anaphylatoxins trigger the inflammatory response and contribute to bronchoconstriction. Bioresour Technol, 2004 Sep, 94(2), 159 - 67 Carbon, nitrogen and phosphorus mineralization in two soils amended with distillery yeast; Rezende LA et al.; The possibility of using yeast from alcohol distilleries as a source of nutrients in soil was investigated . The following treatments were used: no fertilization (control), 0.5% (w/w) yeast, 1% (w/w) yeast, and NPK . The decomposition of yeast was monitored for 90 days in two soils . The CO2 production and the microbial biomass were increased by an average of 1- to 3-fold by yeast incorporation compared to control . Protease activity also was enhanced 3- to 8-fold in the soils supplemented with yeast compared to control . The phosphatase activities were higher than control only during the first days . While nitrate contents increased in all treatments compared to control, available P only increased in the soils amended with 1% yeast or NPK by 45-119% and 309-489%, respectively . These results indicate that there exists an excellent potential for the use of yeast in the soil as a source of nitrate and available P for plant nutrition . FEMS Microbiol Lett, 2004 Jun 1, 235(1), 51 - 6 Hydroxylation of carbazoles by Aspergillus flavus VKM F-1024; Lobastova TG et al.; Carbazole was metabolized by Aspergillus flavus VKM F-1024 forming few monohydroxylated products . The structure of metabolites was determined by TLC, GC, MS and (1)H NMR analyses . 3-Hydroxycarbazole was revealed as a major bioconversion product, 1-hydroxy- and 2-hydroxycarbazoles were observed as minor products . In the presence of 1-benzoylindole, the hydroxylation position shifted toward preferable accumulation of 2-hydroxycarbazole and the formation of 2,6- and 2,7-dihydroxycarbazoles . This effect and microbial formation of these metabolites have never been reported before . At the conversion of N-acetyl- and N-benzoylcarbazoles, carbazole was the major product, while 1-, 2- and 3-monohydroxycarbazoles were formed in small amounts. Vet J, 2004 Jul, 168(1), 28 - 40 Current research on acute phase proteins in veterinary diagnosis: an overview; Murata H et al.; The acute phase proteins (APP) are a group of blood proteins that contribute to restoring homeostasis and limiting microbial growth in an antibody-independent manner in animals subjected to infection, inflammation, surgical trauma or stress . In the last two decades, many advances have been made in monitoring APP in both farm and companion animals for clinical and experimental purposes . Also, the mechanism of the APP response is receiving attention in veterinary science in connection with the innate immune systems of animals . This review describes the results of recent research on animal APP, with special reference to their induction and regulatory mechanisms, their biological functions, and their current and future applications to veterinary diagnosis and animal production. Microbes Infect, 2004 May, 6(6), 617 - 22 Syndecans and HIV-1 pathogenesis; Gallay P; The exploitation of receptors represents a common microbial strategy to survive in the hostile environment of the host . A growing body of evidence suggests that HIV-1 exploits a specific class of receptors-the syndecans-to facilitate colonization of the host. Leuk Res, 2004 Jul, 28(7), 667 - 71 Ajoene (natural garlic compound): a new anti-leukaemia agent for AML therapy; Hassan HT; The reputation of garlic (Allium sativum) as an effective remedy for tumours extends back to the Egyptian Codex Ebers of 1550 b.c . Several garlic compounds including allicin and its corresponding sulfide inhibit the proliferation and induce apoptosis of several human non-leukaemia malignant cells including breast, bladder, colorectal, hepatic, prostate cancer, lymphoma and skin tumour cell lines . Ajoene (4,5,9-trithiadodeca-1,6,11-triene-9-oxide) is a garlic-derived compound produced most efficiently from pure allicin and has the advantage of a greater chemical stability than allicin . Several clinical trials and in vitro studies of ajoene have demonstrated its best-known anti-thrombosis, anti-microbial and cholesterol lowering activities . Recently, topic application of ajoene has produced significant clinical response in patients with skin basal cell carcinoma . Ajoene was shown to inhibit proliferation and induce apoptosis of several human leukaemia CD34-negative cells including HL-60, U937, HEL and OCIM-1 . Also, ajoene induces 30% apoptosis in myeloblasts from chronic myeloid leukaemia patient in blast crisis . More significantly, ajoene profoundly enhanced the apoptotic effect of the two chemotherapeutic drugs: cytarabine and fludarabine in human CD34-positive resistant myeloid leukaemia cells through enhancing their bcl-2 inhibitory and caspase-3 activation activities . The two key anti-leukaemia biological actions of ajoene were the inhibition of proliferation and the induction of apoptosis . Studies have shown the anti-proliferation activity of ajoene to be associated with a block in the G2/M phase of cell cycle in human myeloid leukaemia cells . The apoptosis inducing activity of ajoene is via the mitochondria-dependent caspase cascade through a significant reduction of the anti-apoptotic bcl-2 that results in release of cytochrome c and the activation of caspase-3 . Since acute myeloid leukaemia (AML) is a heterogeneous malignant disease in which disease progression at the level of CD34-positive cells has a major impact on resistance to chemotherapy and relapse and the inability to undergo apoptosis is a crucial mechanism of multi-drug resistance in AML patients . The recent findings of the potent enhancing activity of ajoene on chemotherapy-induced apoptosis in CD34-positive resistant human myeloid leukaemia cells suggest a novel promising role for the treatment of refractory and/or relapsed AML patients as well as elderly AML patients . Further studies are warranted to evaluate similar enhancing effect for ajoene in blast cells from AML patients in primary cultures before its introduction in pilot clinical study. Brain Behav Immun, 2004 Jul, 18(4), 399 - 404 Sleep, but not febrile responses of Fisher 344 rats to immune challenge are affected by aging; Imeri L et al.; Sleep is altered in response to infection and immune challenge in humans and non-human animals . Although there are changes in sleep and facets of immune function with aging, sleep responses of aged subjects to immune challenge have received little, if any attention . To test the hypothesis that aging affects sleep responses to immune challenge, intracerebroventricular injections of interleukin 1 (IL-1) were given to young and aged rats and subsequent sleep-wake behavior was determined . Under basal conditions and in the absence of an immune challenge, sleep patterns of young (3 months) and aged (25-27 months) Fisher 344 rats did not differ . In young animals, IL-1 (2.5 ng) enhanced non-rapid eye movement (NREM) sleep, inhibited rapid eye movement (REM) sleep, and induced fever . In aged animals, IL-1 administration did not alter NREM sleep, but REM sleep was inhibited and brain temperature increased to the same extent observed in young animals . These results show that alterations in sleep following immune challenge are impacted by aging, whereas febrile responses are not . Since it has been postulated that enhanced NREM sleep may facilitate recovery from microbial infection, the present results also suggest that the lack of NREM sleep responses of aged rats to immune challenge may contribute to the increased infection-induced morbidity and mortality of aged organisms. Methods Mol Biol, 2004, 268, 411 - 5 Determination of bacterial adhesion to intestinal mucus; Gusils C et al.; The epithelial cells in the small intestine are covered by a relatively thick layer of mucus, secreted by specialized cells, which consists of mucin, many small associated proteins, glycoproteins, lipids, and glycolipids . The mucus contains receptors that recognize specific adhesion proteins . Adhesion or close association of bacteria to the epithelial cells may further contribute to competitive exclusion . In addition, bacterial adhesion to intestinal mucus and epithelia seems to be important for individual stability of microbial flora . Although the mucus layer covering the gastrointestinal tract has been recognized for many years, it has only recently been of interest in the study of the adhesion between mucus and bacteria . In this chapter, we describe a method for the study of colonization of the gastrointestinal mucus by bacteria and determine the possible effects on adhesion of pathogenic organisms. Science, 2004 May 21, 304(5674), 1151 - 4 Discovery and directed evolution of a glyphosate tolerance gene; Castle LA et al.; The herbicide glyphosate is effectively detoxified by N-acetylation . We screened a collection of microbial isolates and discovered enzymes exhibiting glyphosate N-acetyltransferase (GAT) activity . Kinetic properties of the discovered enzymes were insufficient to confer glyphosate tolerance to transgenic organisms . Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orders of magnitude from 0.87 mM-1 min-1 to 8320 mM-1 min-1 . From the fifth iteration and beyond, GAT enzymes conferred increasing glyphosate tolerance to Escherichia coli, Arabidopsis, tobacco, and maize . Glyphosate acetylation provides an alternative strategy for supporting glyphosate use on crops. Methods Mol Biol, 2004, 270, 151 - 72 RACE and RAGE cloning in parasitic microbial eukaryotes; Williams BA et al.; Many gene-cloning strategies and gene survey often provide partial sequence data . To exploit the information from these partial sequences numerous PCR-based approaches have been developed to clone full-length open reading frames . These approaches can be successful using small quantities of cDNA or genomic DNA as starting material and avoid the need to go through the complex and tedious process of constructing and screening gene libraries . Here we present two of these approaches, called RACE and RAGE, we used to successfully clone partial and full-length ORFs from amitochondriate parasitic microbial eukaryotes . The RACE approach uses cDNA as template for PCR cloning whereas RAGE uses genomic DNA . These two approaches were used to complement each other to provide full-length genes . The amitochondriate microbial eukaryotes we are investigating are of interest from both evolutionary and biomedical perspectives . We have investigated genes of mitochondrial origins in the obligate intracellular parasite called microsporidia . In these organisms spores are the only source of material that can be isolated from host cells and typically yield small amount of mRNA and genomic DNA for cloning . A full-length mitochondrial Hsp70 could be cloned and sequenced and specific antibody raised against a fusion protein . The highly specific antibody allowed us to demonstrate for the first time the presence of mitochondrial-like organelles in microsporidia. J Immunol, 2004 Jun 1, 172(11), 6954 - 60 Toxoplasma gondii triggers myeloid differentiation factor 88-dependent IL-12 and chemokine ligand 2 (monocyte chemoattractant protein 1) responses using distinct parasite molecules and host receptors; Del Rio L et al.; Toll-like receptors (TLR) that signal through the common adaptor molecule myeloid differentiation factor 88 (MyD88) are essential in proinflammatory cytokine responses to many microbial pathogens . In this study we report that Toxoplasma gondii triggers neutrophil IL-12 and chemokine ligand 2 (CCL2; monocyte chemoattractant protein 1) production in strict dependence upon functional MyD88 . Nevertheless, the responses are distinct . Although we identify TLR2 as the receptor triggering CCL2 production, parasite-induced IL-12 release did not involve this TLR . The production of both IL-12 and CCL2 was increased after neutrophil activation with IFN-gamma . However, the synergistic effect of IFN-gamma on IL-12, but not CCL2, was dependent upon Stat1 signal transduction . Although IL-10 was a potent down-regulator of Toxoplasma-triggered neutrophil IL-12 release, the cytokine had no effect on parasite-induced CCL2 production . Soluble tachyzoite Ag fractionation demonstrated that CCL2- and IL-12 inducing activities are biochemically distinct . Importantly, Toxoplasma cyclophilin-18, a molecule previously shown to induce dendritic cell IL-12, was not involved in neutrophil IL-12 production . Our results show for the first time that T . gondii possesses multiple molecules triggering distinct MyD88-dependent signaling cascades, that these pathways are independently regulated, and that they lead to distinct profiles of cytokine production. J Immunol, 2004 Jun 1, 172(11), 6922 - 30 Flagellin promotes myeloid differentiation factor 88-dependent development of Th2-type response; Didierlaurent A et al.; Activation of dendritic cells (DC) by microbial products via Toll-like receptors (TLR) is instrumental in the induction of immunity . In particular, TLR signaling plays a major role in the instruction of Th1 responses . The development of Th2 responses has been proposed to be independent of the adapter molecule myeloid differentiation factor 88 (MyD88) involved in signal transduction by TLRs . In this study we show that flagellin, the bacterial stimulus for TLR5, drives MyD88-dependent Th2-type immunity in mice . Flagellin promotes the secretion of IL-4 and IL-13 by Ag-specific CD4(+) T cells as well as IgG1 responses . The Th2-biased responses are associated with the maturation of DCs, which are shown to express TLR5 . Flagellin-mediated DC activation requires MyD88 and induces NF-kappaB-dependent transcription and the production of low levels of proinflammatory cytokines . In addition, the flagellin-specific response is characterized by the lack of secretion of the Th1-promoting cytokine IL-12 p70 . In conclusion, this study suggests that flagellin and, more generally, TLR ligands can control Th2 responses in a MyD88-dependent manner. J Immunol, 2004 Jun 1, 172(11), 6578 - 86 Mechanisms of Vdelta1 gammadelta T cell activation by microbial components; Das H et al.; There are two major subsets of gammadelta T cell in humans . Vgamma2Vdelta2 T cells predominate in the circulation and significantly expand in vivo during a variety of infectious diseases . Ags identified for the Vdelta2 T cells are nonpeptide phosphate, amine, and aminobisphosphonate compounds . In contrast, Vdelta1-encoded TCRs account for the vast majority of gammadelta T cells in tissues such as intestine and spleen . Some of these T cells recognize CD1c and MHC class I-related chain (MICA/B) molecules {correction} . These T cells are cytotoxic and use both perforin- and Fas-mediated cytotoxicity . A fundamental question is how these gammadelta T cells are activated during microbial exposure to carry out effector functions . In this study, we provide evidence for a mechanism by which Vdelta1 gammadelta T cells are activated by inflammatory cytokines in the context of the Vdelta1 TCR . Dendritic cells are necessary as accessory cells for microbial Ag-mediated Vdelta1 gammadelta T cell activation . Cytokine (IL-12), adhesion (LFA3/CD2, LFA1/ICAM1) and costimulatory (MHC class I-related chain (MICA/B) molecules/NK-activating receptor G2D) molecules play a significant role along with Vdelta1 TCR in this activation. J Antibiot (Tokyo), 2004 Mar, 57(3), 218 - 23 Structures of grixazone A and B, A-factor-dependent yellow pigments produced under phosphate depletion by Streptomyces griseus; Ohnishi Y et al.; A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) acts as a microbial hormone that induces morphological development and secondary metabolism in Streptomyces griseus . A diffusible yellow pigment is produced by S . griseus in an A-factor-dependent manner under phosphate depletion . Detailed analysis of the pigment production by S . griseus cultivated in minimal liquid medium containing different concentrations of phosphate showed that the pigment was actively produced in the presence of low concentrations of phosphate and the production of the pigment was completely repressed in the presence of 2.5 mM KH2PO4 . HPLC analysis of the culture supernatant showed that the pigment consisted of two major, structurally related compounds and they were produced at different ratios depending on the concentration of phosphate in the medium . The structures of the two major compounds, designated as grixazone A and B, were determined by spectroscopic analyses as 1-{{2-(acetylamino)-2-carboxyethyl}thio}-2-amino-3-oxo-8-formyl-3H-phenoxiazine and 1-{{2-(acetylamino)-2-carboxyethyl}thio}-2-amino-3-oxo-8-carboxyl-3H-phenoxiazine, respectively . Grixazone A was a novel compound, although grixazone B was reported in a patent as a parasiticide produced by Streptomyces sp . DSM3813. Protein Sci, 2004 Jun, 13(6), 1651 - 9 New enzymes from environmental cassette arrays: functional attributes of a phosphotransferase and an RNA-methyltransferase; Nield BS et al.; By targeting gene cassettes by polymerase chain reaction (PCR) directly from environmentally derived DNA, we are able to amplify entire open reading frames (ORFs) independently of prior sequence knowledge . Approximately 10% of the mobile genes recovered by these means can be attributed to known protein families . Here we describe the characterization of two ORFs which show moderate homology to known proteins: (1) an aminoglycoside phosphotransferase displaying 25% sequence identity with APH(7") from Streptomyces hygroscopicus, and (2) an RNA methyltransferase sharing 25%-28% identity with a group of recently defined bacterial RNA methyltransferases distinct from the SpoU enzyme family . Our novel genes were expressed as recombinant products and assayed for appropriate enzyme activity . The aminoglycoside phosphotransferase displayed ATPase activity, consistent with the presence of characteristic Mg(2+)-binding residues . Unlike related APH(4) or APH(7") enzymes, however, this activity was not enhanced by hygromycin B or kanamycin, suggesting the normal substrate to be a different aminoglycoside . The RNA methyltransferase contains sequence motifs of the RNA methyltransferase superfamily, and our recombinant version showed methyltransferase activity with RNA . Our data confirm that gene cassettes present in the environment encode folded enzymes with novel sequence variation and demonstrable catalytic activity . Our PCR approach (cassette PCR) may be used to identify a diverse range of ORFs from any environmental sample, as well as to directly access the gene pool found in mobile gene cassettes commonly associated with integrons . This gene pool can be accessed from both cultured and uncultured microbial samples as a source of new enzymes and proteins. J Med Microbiol, 2004 Jun, 53(Pt 6), 563 - 71 Changes in oral microbial profiles after periodontal treatment as determined by molecular analysis of 16S rRNA genes; Sakamoto M et al.; Terminal RFLP (T-RFLP) analysis was used to investigate changes in the oral microbiota in saliva and subgingival plaque samples from one patient with aggressive periodontitis (subject A) and two patients with chronic periodontitis (subjects B and C) before and 3 months after periodontal treatment . Substantial changes in the T-RFLP patterns of subgingival plaque samples of subjects B and C were noted after 3 months of improved oral hygiene and full-mouth supra- and subgingival scaling and root planing . However, there was little change in the subgingival microbiota of subject A . Although the proportions of terminal restriction fragments (T-RFs) larger than 1000 bp were notable in the T-RFLP patterns generated after digestion with HhaI of the samples from two subjects before treatment (subject B, 35.5 %; subject C, 29.6 %), the proportions of these T-RFs were significantly reduced or not detected after treatment (subject B, none; subject C, 4.1 %) . Real-time PCR showed a significant change in the proportions of target bacteria in subgingival plaque samples of subject B . After 3 months, the Porphyromonas gingivalis population was markedly reduced (3.1 x 10(-3) %), whereas the proportion of Porphyromonas gingivalis before treatment was 7.6 % . The proportions of Tannerella forsythensis, Treponema denticola and Treponema socranskii were also markedly diminished after treatment . Similarly, the proportion of the T-RF presumed to represent Porphyromonas gingivalis was 5.9 % and became undetectable after 3 months . Analysis of 16S rRNA gene clone libraries from subgingival plaque samples of subject B before and after treatment showed a notable change in the subgingival microbiota . These results were in agreement with the T-RFLP analysis data and showed that the T-RFs larger than 1000 bp represent Peptostreptococcus species . Our results indicate that T-RFLP analysis is useful for evaluation of the effects of medical treatment of periodontitis. Bioconjug Chem, 2004 May-Jun, 15(3), 491 - 7 Peptidyl linkers for protein heterodimerization catalyzed by microbial transglutaminase; Tanaka T et al.; Specific peptidyl linkers that result in the heterodimerization of functional proteins, which is catalyzed by microbial transglutaminase from Streptomyces mobaraensis (MTG), were generated based on a ribonuclease S-peptide using site-directed mutagenesis . The peptidyl linkers designated as Lys-tag and Gln-tag were designed to possess sole reactive Lys or Gln residue that was amenable for selective Lys-Gln cross-linkage of different proteins . Green fluorescent protein variants, ECFP and EYFP, were employed as model proteins, and those Lys- and Gln-tags were fused to the N-termini of ECFP and EYFP, respectively . As a result, we succeeded in solely obtaining the ECFP-EYFP heterodimer without forming multiply cross-linked byproducts . It was found that the reactivity of peptidyl linkers varied according to the type of amino acid to be replaced . Peptidyl linkers with a basic amino acid (Arg) exhibited the highest reactivity in the cross-linking reaction, suggesting the cationic residue substrate preference of MTG . Kinetic analysis utilizing fluorescent resonance energy transfer (FRET), that is only observed upon the heterodimeric ECFP-EYFP conjugation, revealed that the amino acid replacement contributed to the acceleration of cross-linking reactions by increasing catalytic turnover (k(cat)), rather than substrate binding affinity (K(m)) . Finally, using a ribonuclease S-protein, the manipulation of enzymatic protein cross-linking based on specific S-peptide:S-protein interactions was explored . Since newly designed Lys- and Gln-tags retained binding affinities to the S-protein, the heterodimerization was perfectly restrained by wrapping them with the S-protein . The results suggest the possibility of limited protein conjugation by tuning steric hindrance against the MTG . Tailoring enzymatic posttranslational modifications with either engineering peptidyl substrates or by taking specific peptide-protein interactions into consideration may facilitate the development of a new sequential protein conjugation method for the preparation of multifunctional protein. Commun Agric Appl Biol Sci, 2003, 68(4 Pt A), 3 - 16 Entomopathogenic nematodes in the European biocontrol market; Ehlers RU; In Europe total revenues in the biocontrol market have reached approximately 200 million Euros . The sector with the highest turn-over is the market for beneficial invertebrates with a 55% share, followed by microbial agents with approximately 25% . Annual growth rates of up to 20% have been estimated . Besides microbial plant protection products that are currently in the process of re-registration, several microbial products have been registered or are in the process of registration, following the EU directive 91/414 . Entomopathogenic nematodes (EPN) are exceptionally safe biocontrol agents . Until today, they are exempted from registration in most European countries, the reason why SMEs were able to offer economically reasonable nematode-based products . The development of technology for mass production in liquid media significantly reduced the product costs and accelerated the introduction of nematode products in tree nurseries, ornamentals, strawberries, mushrooms, citrus and turf . Progress in storage and formulation technology has resulted in high quality products which are more resistant to environmental extremes occurring during transportation to the user . The cooperation between science, industry and extension within the EU COST Action 819 has supported the development of quality control methods . Today four companies produce EPN in liquid culture, offering 8 different nematode species . Problems with soil insects are increasing . Grubs, like Melolontha melolontha and other scarabaeidae cause damage in orchards and turf . Since the introduction of the Western Corn Rootworm Diabrotica virgifera into Serbia in 1992, this pests as spread all over the Balkan Region and has reached Italy, France and Austria . These soil insect pests are potential targets for EPN . The development of insecticide resistance has opened another sector for EPN . Novel adjuvants used to improve formulation of EPN have enabled the foliar application against Western Flower Thrips and Plutella xylostella . To reach these markets, the product costs for EPN will have to further decrease in the future . One possibility to reduce application costs related with the use of EPN is the inoculative application to cause long term effects on pest populations. Am J Crit Care, 2004 May, 13(3), 235 - 41 Comparison of traditional and disposable bed baths in critically ill patients; Larson EL et al.; BACKGROUND: For bedridden patients unable to perform personal hygiene measures because of acute illness or chronic debilitation, the bed bath, with either the traditional basin or, more recently, disposable baths, has long been a measure for improving hygiene and costs . OBJECTIVE: To compare the traditional basin bed bath with a prepackaged disposable bed bath in terms of 4 outcomes: time and quality of bath, microbial counts on the skin, nurses' satisfaction, and costs . METHODS: Forty patients in surgical, medical, or cardiothoracic intensive care units received both types of bath on different days . Baths were observed, timed, and scored for quality . Cultures of the peri-umbilicus and groin were obtained before and after each bath . At the end of the study, nurses were interviewed about their preferences . RESULTS: Neither total quality scores nor microbial counts differed significantly between the 2 bath types . Significantly fewer products (P < .001) and less time were used, cost was lower, and nurses' ratings were significantly better with the disposable bath . CONCLUSION: The disposable bath is a desirable form of bathing for patients who are unable to bathe themselves in critical care and long-term care settings, and it may even be preferable to the traditional basin bath. Biopolymers, 2004, 76(3), 206 - 43 Beta2-amino acids-syntheses, occurrence in natural products, and components of beta-peptides1,2; Lelais G et al.; Although they are less abundant than their alpha-analogues, beta-amino acids occur in nature both in free form and bound to peptides . Oligomers composed exclusively of beta-amino acids (so-called beta-peptides) might be the most thoroughly investigated peptidomimetics . Beside the facts that they are stable to metabolism, exhibit slow microbial degradation, and are inherently stable to proteases and peptidases, they fold into well-ordered secondary structures consisting of helices, turns, and sheets . In this respect, the most intriguing effects have been observed when beta2-amino acids are present in the beta-peptide backbone . This review gives an overview of the occurrence and importance of beta2-amino acids in nature, placing emphasis on the metabolic pathways of beta-aminoisobutyric acid (beta-Aib) and the appearance of beta2-amino acids as secondary metabolites or as components of more complex natural products, such as peptides, depsipeptides, lactones, and alkaloids . In addition, a compilation of the syntheses of both achiral and chiral beta2-amino acids is presented . While there are numerous routes to achiral beta2-amino acids, their EPC synthesis is currently the subject of many investigations . These include the diastereoselective alkylation and Mannich-type reactions of cyclic- or acyclic beta-homoglycine derivatives containing chiral auxiliaries, the Curtius degradation, the employment of transition-metal catalyzed reactions such as enantioselective hydrogenations, reductions, C-H insertions, and Michael-type additions, and the resolution of rac . beta2-amino acids, as well as several miscellaneous methods . In the last part of the review, the importance of beta2-amino acids in the formation of beta-peptide secondary structures is discussed . Methods Mol Biol, 2004, 266, 29 - 45 Genome sequencing and annotation: an overview; Kuroda M et al.; Many microbial genome sequences have been determined, and more new genome projects are ongoing . Shotgun sequencing of randomly cloned short pieces of genomic DNA can provide a simple way of determining whole genome sequences . This process requires sequencing of many fragments, compilation of the separate sequences into one contiguous sequence, and careful editing of the assembled sequence . The genes present on the microbial genome are then predicted using clues derived from typical gene features, such as codon usage, ribosomal binding sequences, and bacterial initiation codons . Function of genes is predicted by homology searches performed against either public or well-established protein databases . This chapter discusses each of these stages in a genome-sequencing project. Mol Cell Proteomics, 2004 Aug, 3(8), 796 - 808 Epub 2004 May 17. Analysis of signal-dependent changes in the proteome of Drosophila blood cells during an immune response; Loseva O et al.; Innate immunity is based on the recognition of cell-surface molecules of infecting agents . Microbial substances, such as peptidoglycan, lipopolysaccharide, and beta-1,3-glucans, produce functional responses in Drosophila hemocytes that contribute to innate immunity . We have used two-dimensional gel electrophoresis and MS to resolve lipopolysaccharide-induced changes in the protein profile of a Drosophila hemocytic cell line . We identified 24 intracellular proteins that were up- or down-regulated, or modified, in response to immune challenge . Several proteins with predicted immune functions, including lysosomal proteases, actin-binding/remodeling proteins, as well as proteins involved in cellular responses to oxidative stress, were affected by the immune assault . Intriguingly, a number of the proteins identified in this study have recently been implicated in phagocytosis in higher vertebrates . We suggest that phagocytosis is activated in Drosophila hemocytes by the presence of microbial substances, and that this activation constitutes an evolutionarily conserved arm of innate immunity . In addition, a number of proteins involved in calcium-regulated signaling, mRNA processing, and nuclear transport were affected, consistent with a possible role in reprogramming of gene expression . In conclusion, the present proteome analysis identified many proteins previously not linked to innate immunity, demonstrating that differential protein profiling of Drosophila hemocytes is a valuable tool for identification of new players in immune-related cellular processes. Nahrung, 2004 Apr, 48(2), 104 - 9 Autoproteolysis rate of rainbow trout muscle proteins; Fik M et al.; Effect of some physicochemical agents (pH, temperature and incubation time) and iced storage of farmed rainbow trout (Oncorhynchus mykiss) on autoproteolysis of muscle proteins and quality (sensory assessment, instrumental texture, total bacterial counts) were determined . The results showed that the autoproteolysis rate proceeded with its highest intensity at pH 4.2 and temperature about 55 degrees C . The rate of protein hydrolysis and protease activity, as well as microbial contamination, gradually increased with prolonged periods of iced storage of fish . Properly iced trout immediately after its evisceration was acceptable in quality for up to 10 days. Arthritis Rheum, 2004 May, 50(5), 1624 - 35 Defective costimulatory function is a striking feature of antigen-presenting cells in an HLA-B27-transgenic rat model of spondylarthropathy; Hacquard-Bouder C et al.; OBJECTIVE: A disease resembling the human spondylarthropathies develops in HLA-B27-transgenic rats . This disease in rats is mediated by CD4+ T cells, but antigen-presenting cells (APCs) may also play a role . Dendritic cells (DCs) have been reported to be defective in allogeneic mixed lymphocyte culture in this model . Here, we further investigated the functional defect of APCs . METHODS: DCs and B cells from nontransgenic, HLA-B27 (33-3)-transgenic, and HLA-B7 (120-4)-transgenic rats were used to stimulate T cells . Surface expression of HLA-B transgene and rat molecules on APCs and the formation of conjugates between DCs and T cells were monitored by flow cytometry . RESULTS: We observed a strikingly defective stimulation of allogeneic and syngeneic T lymphocytes by APCs from HLA-B27 but not HLA-B7 rats, even if stimulation was driven in the presence of anti-T cell receptor (TCR) antibody . We found no evidence that HLA-B27 DCs were immature, lacked production of some diffusible factor, or produced an inhibitory factor for T cells . When comparing the levels of expression of class II major histocompatibility complex, CD2, intercellular adhesion molecule 1, lymphocyte function-associated antigen 1, B7, and CD40 molecules at the surface of DCs from 33-3, 120-4, and nontransgenic rats, we found little difference . However, HLA-B27-transgenic DCs formed fewer conjugates with T cells than did nontransgenic DCs . Furthermore, the proportion of conjugates formed between DCs and T cells, as well as the difference between nontransgenic and HLA-B27-transgenic DCs, were in large part reduced by blocking CD86 on DCs . CONCLUSION: We confirmed defective stimulation of T cells by APCs in HLA-B27 rats, the mechanism of which appears to implicate APC/T cell contact, independent of TCR engagement . In addition, decreased use of the CD86 costimulatory molecule by B27 DCs was observed . Impaired costimulatory function could result in a loss of tolerance toward microbial flora in this model. J Biol Chem, 2004 Jul 30, 279(31), 32728 - 36 Epub 2004 May 15. Nucleic acid is a novel ligand for innate, immune pattern recognition collectins surfactant proteins A and D and mannose-binding lectin; Palaniyar N et al.; Collectins are a family of innate immune proteins that contain fibrillar collagen-like regions and globular carbohydrate recognition domains (CRDs) . The CRDs of these proteins recognize various microbial surface-specific carbohydrate patterns, particularly hexoses . We hypothesized that collectins, such as pulmonary surfactant proteins (SPs) SP-A and SP-D and serum protein mannose-binding lectin, could recognize nucleic acids, pentose-based anionic phosphate polymers . Here we show that collectins bind DNA from a variety of origins, including bacteria, mice, and synthetic oligonucleotides . Pentoses, such as arabinose, ribose, and deoxyribose, inhibit the interaction between SP-D and mannan, one of the well-studied hexose ligands for SP-D, and biologically relevant d-forms of the pentoses are better competitors than the l-forms . In addition, DNA and RNA polymer-related compounds, such as nucleotide diphosphates and triphosphates, also inhibit the carbohydrate binding ability of SP-D, or approximately 60 kDa trimeric recombinant fragments of SP-D that are composed of the alpha-helical coiled-coil neck region and three CRDs (SP-D(n/CRD)) or SP-D(n/CRD) with eight GXY repeats (SPD(GXY)(8)(n/CRD)) . Direct binding and competition studies suggest that collectins bind nucleic acid via their CRDs as well as by their collagen-like regions, and that SP-D binds DNA more effectively than do SP-A and mannose-binding lectin at physiological salt conditions . Furthermore, the SP-D(GXY)(8)(n/CRD) fragments co-localize with DNA, and the protein competes the interaction between propidium iodide, a DNA-binding dye, and apoptotic cells . In conclusion, we show that collectins are a new class of proteins that bind free DNA and the DNA present on apoptotic cells by both their globular CRDs and collagen-like regions . Collectins may therefore play an important role in decreasing the inflammation caused by DNA in lungs and other tissues. Ann Bot (Lond), 2004 Jul, 94(1), 87 - 97 Epub 2004 May 14. Phenylpropanoids, phenylalanine ammonia lyase and peroxidases in elicitor-challenged cassava (Manihot esculenta) suspension cells and leaves; Gomez-Vasquez R et al.; BACKGROUND AND AIMS: Control of diseases in the key tropical staple, cassava, is dependent on resistant genotypes, but the innate mechanisms are unknown . The aim was to study phenylpropanoids and associated enzymes as possible defence components . METHODS: Phenylalanine ammonia-lyase (PAL), phenylpropanoids and peroxidases (POD) were investigated in elicited cassava suspension cells and leaves . Yeast elicitor was the most effective of several microbial and endogenous elicitors . Fungitoxicity was determined against the cassava pathogens Fusarium solani, F . oxysporum and the saprotroph Trichoderma harzianum . KEY RESULTS: A single and rapid (> or =2-3 min) oxidative burst, measured as hydrogen peroxide, occurred in elicited cells . PAL activity was induced maximally at 15 h and was preceded by PAL mRNA accumulation, which peaked at 9 h . Symplasmic POD activity increased four-fold in cells, 48 h post-elicitation . POD isoforms (2-7 isoforms, pI 3.1-8.8) were detected in elicited and unelicited cells, extracellular medium and leaves but two extracellular isoforms were enhanced post-elicitation . Also expression of a cassava peroxidase gene MecPOD1 increased in elicited cells . Only anionic forms oxidized scopoletin, with highest activity by isoform pI 3.6, present in all samples . Unidentified phenolics and possibly scopolin increased post-elicitation, but there was no enhancement of scopoletin, rutin or kaempferol-3-O-rutinoside concentration . Fungal germ tube elongation was inhibited more than germination by esculetin, ferulic acid, quercetin and scopoletin . T . harzianum was generally more sensitive than the pathogens and was inhibited by > or =50 microg mL(-1) of ferulic acid and quercetin and > or =10 microg mL(-1) of scopoletin . CONCLUSIONS: Phenolic levels in cells were not enhanced and were, theoretically, too low to be inhibitory . However, in combination and when oxidized they may contribute to defence, because oxidation of esculetin and scopoletin by peroxidase and of esculetin by tyrosinase enhanced their fungitoxicity up to 20-fold. Infect Dis Clin North Am, 2004 Jun, 18(2), 311 - 39, table of contents How the mighty have fallen: fatal infectious diseases of divine composers; Rietschel ET et al.; Their music is immortal, but famous composers of the last centuries were not . Up to 50 years ago, microbial infections were a major cause of mortality and showed composers no special mercy . They died of various infectious diseases . By application of modern intensive care measurements and effective antibiotics, many of them would have been saved . Disease and painful death brought the work of these divine artists to the level of immortal creations that both inspire and astonish the mortal audience. J Anim Sci, 2004 May, 82(5), 1518 - 27 Daily and alternate-day supplementation of urea or biuret to ruminants consuming low-quality forage: II . Effects on site of digestion and microbial efficiency in steers; Currier TA et al.; Five steers (491 +/- 21 kg BW) were used in an incomplete 5 x 4 Latin square with four 24-d periods to determine the influence of supplemental non-protein N (NPN) source and supplementation frequency (SF) on nutrient intake and site of digestion in steers consuming low-quality grass straw (4% CP) . Treatments (TRT) included an unsupplemented control and a urea- or biuret-containing supplement placed directly into the rumen daily (D) or every other day (2D) at 0700 . The NPN treatments were formulated to provide 90% of the estimated degradable intake protein requirement . Daily TRT were supplemented CP at 0.04% of BW/d, whereas the 2D TRT were supplemented at 0.08% of BW every other day . Therefore, all supplemented TRT received the same quantity of supplemental CP over a 2-d period . Forage OM intake was not affected (P > 0.05) by NPN supplementation, NPN source, or SF; however, total OM and N intake were increased (P < 0.01) with CP supplementation . Duodenal flow of N was greater (P = 0.04) with CP supplementation compared with the control . In addition, duodenal bacterial N flow was increased with CP supplementation (P = 0.04) and for biuret compared with urea (P < 0.01) . Bacterial efficiency (g bacterial N/kg OM truly digested in the rumen) was greater (P = 0.05) for biuret than for urea . Apparent total-tract N digestibility was increased with NPN supplementation (P < 0.01) but not affected by NPN source or SF . These results suggest that urea or biuret can be used effectively as a supplemental N source by steers consuming low-quality forage. J Air Waste Manag Assoc, 2002 Feb, 52(2), 237 - 43 Effect of solids concentration on bacterial leaching of heavy metals from sewage sludge; Cho KS et al.; Microbial metal leaching from sewage sludge (2-9% w/v) was carried out with the iron-oxidizing bacterium Thiobacillus ferrooxidans . Measurements of pH, oxidation-reduction potential, and concentration of Fe2+ indicated that T . ferrooxidans was effective in removing metals from an incubation bath containing less than 5% sludge solids concentration . Specifically, Cu leaching was completely suppressed at a high solids concentration of 9% (w/v) . Results indicated that the deactivation of T . ferrooxidans at a high sludge content was mainly due to the presence of inhibiting materials such as organic matter . A mixed culture of sulfur-oxidizing bacteria was obtained by enrichment from anaerobically digested sewage sludge to enhance the efficiency of the microbial leaching process . These bacteria were much more effective in metal leaching than was iron-oxidizing T . ferrooxidans . At 9% (w/v) solids concentration, the leaching efficiencies of Zn and Cu were 78% (2.66 g/kg dry sludge) and 59% (1.36 g/kg dry sludge), respectively . Therefore, when removing heavy metals from the anaerobically digested sewage sludge, the indigenous sulfur-oxidizing bacteria isolated in the current study were more efficient than T . ferrooxidans, especially at high sludge solids concentrations. Science, 2004 May 14, 304(5673), 1014 - 8 Regulation of phagosome maturation by signals from toll-like receptors; Blander JM et al.; In higher metazoans, phagocytosis is essential in host defense against microbial pathogens and in clearance of apoptotic cells . Both microbial and apoptotic cells are delivered on a common route from phagosomes to lysosomes for degradation . Here, we found that activation of the Toll-like receptor (TLR) signaling pathway by bacteria, but not apoptotic cells, regulated phagocytosis at multiple steps including internalization and phagosome maturation . Phagocytosis of bacteria was impaired in the absence of TLR signaling . Two modes of phagosome maturation were observed, constitutive and inducible; their differential engagement depended on the ability of the cargo to trigger TLR signaling. Environ Microbiol, 2004 Jun, 6(6), 622 - 37 Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), as determined by a 16S rDNA-based analysis, and related to physicochemical gradients; Koizumi Y et al.; The vertical and temporal changes in microbial communities were investigated throughout the water column and sediment of the saline meromictic Lake Kaiike by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA . Marked depth-related changes in microbial communities were observed at the chemocline and the sediment-water interface . However, no major temporal changes in the microbial community below the chemocline were observed during the sampling period, suggesting that the ecosystem in the anoxic zone of Lake Kaiike was nearly stable . Although the sequence of the most conspicuous DGGE band throughout the anoxic water and in the top of the microbial mat was most similar to that of an anoxic, photosynthetic, green sulphur bacterium, Pelodyction luteolum DSM273 (97% similarity), it represented a new phylotype . A comparison of DGGE banding patterns of the water column and sediment samples demonstrated that specific bacteria accumulated on the bottom from the anoxic water layers, and that indigenous microbial populations were present in the sediment . The measurements of bicarbonate assimilation rates showed significant phototrophic assimilation in the chemocline and lithoautotrophic assimilation throughout the anoxic water, but were not clearly linked with net sulphide turnover rates, indicating that sulphur and carbon metabolisms were not directly correlated. J Clin Periodontol, 2004 Jun, 31(6), 458 - 62 Atmospheric contamination during ultrasonic scaling; Timmerman MF et al.; OBJECTIVE: The aim of this study was to determine the microbial atmospheric contamination during initial periodontal treatment using a piezoelectric ultrasonic scaler in combination with either high-volume evacuation (HVE) or conventional dental suction (CDS) . METHODS: The study included 17 treatment sessions, consisting of a 40-min episode of continuous plaque and calculus removal using an ultrasonic unit (EMS) . The treatment sessions were carried out in six patients with generalized adult periodontitis and ranged from two to four sessions per patient according to their needs . The use of HVE and CDS was randomly assigned over the sessions within each patient . Before each treatment, the operating room was not used for 15 h . To measure baseline microbial air pollution two Petri dishes containing blood agar were exposed for 10 min to the air . At the start of each treatment session, two Petri dishes were exposed for 5 min at a distance of 40 cm from the mouth of the patients . After 20 min, this procedure was repeated . At a distance of 150 cm, two Petri dishes were exposed for 20 min followed by exposure of two new Petri dishes for the rest of the session . The plates were cultured aerobically and anaerobically for 3 and 7 days, respectively . RESULTS: The mean colony forming units (CFU) before treatment never exceeded 0.6 colonies per plate . At 40 cm, the mean CFU, when considering a period of 40 min, was 8.0 for HVE and 17.0 for CDS . The mean CFU at 150 cm during this period was 8.1 with HVE and 10.3 with the CDS . With reference to the Air Microbial Index the operatory atmosphere was considered to be in a good condition during 40 min of continuous use of the ultrasonic scaler in combination with both HVE and CDS . CONCLUSION: Within the restrictions of this study, only limited atmospheric microbial contamination is produced when using a piezoelectric ultrasonic scaler. Eur J Anaesthesiol, 2004 May, 21(5), 337 - 60 Management of septic shock: current concepts, with a particular emphasis on the role of source control, and future perspectives; Tsiotou AG et al.; Sepsis is an infection-induced syndrome characterized by a generalized inflammatory state . The normal reaction to infection involves a series of complex immunological processes . A potent, complex immunological cascade ensures a prompt protective response to microbial invasion in human beings . Although activation of the immune system during microbial invasion is generally protective, septic shock develops in a number of patients as a consequence of excessive or poorly regulated immune response to the offending organism . This unbalanced reaction may harm the host through a maladaptive release of endogenously generated inflammatory compounds . Early recognition of the syndrome is of key importance to promptly start appropriate management . Timely, aggressive resuscitation to preserve organ function remains a fundamental principle in the care of septic patients . The specific treatment is directed at identifying and treating the underlying disorder . The physician should investigate diligently for the presence of active infection using modern imaging methods and other diagnostic studies to localize the site of infection and to obtain adequate culture specimens from potential infective sources . Early administration of appropriate, effective antibiotic therapy is important in the management of septic patients . Infected fluid collections and/or infected necrotic tissues should be drained or debrided without delay . Adequate nutritional support is indicated in the management of the septic patient . A number of adjuvant therapies, aimed at blunting/downregulating the host immune response to bacterial infection are currently under intensive investigation; however, the complexity of immunological defences and the potential for complementary interaction of the different components of the inflammatory cascade make the development of these pharmacological interventions difficult. Orthopade, 2004 Apr, 33(4), 412 - 5 {Hygiene between tradition and implementation}; Hansis ML; The basis of evidence for hygiene rules implemented in hospitals is traditionally small . This is not only because there is little theoretical knowledge on the reciprocal influence between a single hygienic mistake/a single microbial input and the manifestation of a nosocomial infection . There are also not enough clinical studies, especially on complex hygiene questions, to determine whether special measures (e.g., septic rooms)can compensate for deficits in hygiene practice . Furthermore, it would be necessary to designate security buffers distinctly . In-house traditions are able to stabilize hygienic behavior in an excellent manner . They should be fostered and not disparaged as myths . Discussions of experts should not be conducted in public; that is disastrous for the everyday work of physicians in hospitals. Rev Med Liege, 2004 Mar, 59(3), 120 - 7 {How I treat...oropharyngeal mucositis associated with radiotherapy for head and neck cancer}; Piret P et al.; Oral mucositis the major acute effect of head and neck radiotherapy . According to the degree, irradiation may be compromised in dose and overall time with consequences on outcome . Up to now there is no standard accepted protocol . A strict program of local and general hygiene is mandatory . Analgesics are often required . Amifostine acts as a protector of salivary glands GM-CSF and G-CSF stimulate proliferation of mucosal basal cells . Sucralfate plays a barrier role . Camomile plant extract is anti-inflammatory, well tolerated and cheap . Povidone-iodine is better than chlorhexidine as an antiseptic agent . PTA lozenges with polymixin E, tobramycin and amphotericin B showed a marked power of selective microbial decontamination. Toxicology, 2004 May 20, 198(1-3), 255 - 62 Risk analysis of drinking water microbial contamination versus disinfection by-products (DBPs); Ashbolt NJ; Managing the provision of safe drinking water has a renewed focus in light of the new World Health Organization (WHO) water safety plans . Risk analysis is a necessary component to assist in selecting priority hazards and identifying hazardous scenarios, be they qualitative to quantitative assessments . For any approach, acute diarrhoeal pathogens are often the higher risk issue for municipal water supplies, no matter how health burden is assessed . Furthermore, potential sequellae (myocarditis, diabetes, reactive arthritis and cancers) only further increase the potential health burden of pathogens; despite the enormous uncertainties in determining pathogen exposures and chemical dose-responses within respective microbial and chemical analyses . These interpretations are currently being improved by Bayesian and bootstrapping approaches to estimate parameters for stochastic assessments . A case example, covering the health benefits of ozonation for Cryptosporidium inactivation versus potential cancers from bromate exposures, illustrated the higher risks from a pathogen than one of the most likely disinfection by-products (DBPs) . Such analyses help justify the industries long-held view of the benefits of multiple barriers to hazards and that microbial contamination of water supplies pose a clear public health risk when treatment is inadequate . Therefore, efforts to reduce potential health risks from DBP must not compromise pathogen control, despite socio-political issues. Cell, 2004 May 14, 117(4), 515 - 26 Instruction of distinct CD4 T helper cell fates by different notch ligands on antigen-presenting cells; Amsen D et al.; Antigen-presenting cells (APC) tailor immune responses to microbial encounters by stimulating differentiation of CD4 T cells into the Th1 and Th2 lineages . We demonstrate that APC use the Notch pathway to instruct T cell differentiation . Strikingly, of the two Notch ligand families, Delta induces Th1, while Jagged induces the alternate Th2 fate . Expression of these different Notch ligands on APC is induced by Th1- or Th2-promoting stimuli . Th2 differentiation has been considered a default process as APC-derived instructive signals are unknown . We demonstrate that Jagged constitutes an instructive signal for Th2 differentiation, which is independent of IL4/STAT6 . Th2 differentiation induced by APC is abrogated in T cells lacking the Notch effector RBPJkappa . Notch directs Th2 differentiation by inducing GATA3 and by directly regulating il4 gene transcription through RBPJkappa sites in a 3' enhancer. Expert Rev Mol Diagn, 2004 May, 4(3), 303 - 15 Development of rationally designed nucleic acid signatures for microbial pathogens; Cleland CA et al.; The detection and identification of microbial pathogens are critical challenges in clinical medicine and public health surveillance . Advances in genome analysis technology are providing an unprecedented amount of information about bacterial and viral organisms, and hold great potential for pathogen detection and identification . In this paper, a rational approach to the development and application of nucleic acid signatures is described based on phylogenetically informative sequence features, especially single nucleotide polymorphisms . The computational tools that are available to enable the development of the next generation of microbial molecular signatures for clinical diagnostics and infectious disease surveillance are reviewed and the impact on public health and national security will be discussed. Environ Manage . 2004 May 12; {Epub ahead of print} Biologically Defined Soil Organic Matter Pools as Affected by Rotation and Tillage; Doyle GL et al.; The importance of soil organic matter is well recognized; however, changes in C and N fractions are inadequately quantified . The objective of this study was to determine tillage and crop rotation effects on soil organic C and N fractions from a long-term (27-year) study in eastern Kansas . Cropping systems included continuous and rotation sequences of wheat ( Triticum aestivum L.), grain sorghum ( Sorghum bicolor (L.) Moench), and soybean ( Glycine max (L.) Merrill) on a Muir silt loam ( fine-silty, mixed, mesic Cumulic Haplustolls) . Tillage included conventional (CT), reduced (RT), and no-till (NT) . Total C and N (C(T) and N(T)) were determined on all treatments . Mineralizable C and N (C(o) and N(o)) and microbial biomass C and N were determined for the NT and CT soybean and sorghum rotations . Cropping systems that included wheat contained the greatest amount of C(T) and N(T) . Continuous wheat contained 2910 g C m(-2) and 287 g N m(-2), compared to 2225 g C m(-2) and 222 g N m(-2) (0-15 cm) for continuous soybean . No-tillage contained 1128 g C m(-2) and 109 g N m(-2) at 0-5 cm compared to 918 g C m(-2) and 87 g N m(-2) for CT . Sorghum contained 51% more C(o) than soybean, and NT accounted for 59% more C(o) than CT . More crop residue was produced and retained in rotations that included sorghum . No-tillage increased C 2440 kg ha(-1), while CT increased C 340 kg ha(-1) across all soybean/sorghum rotations . The highest sequestration rate (122 kg C ha(-1) y(-1)) was observed with NT sorghum and was equivalent to approximately 3.2% of the plant material (root and shoot, less gain harvest) remaining in the soil annually. J Microbiol Methods, 2004 Jun, 57(3), 379 - 90 The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria; Hahn MW et al.; We developed a novel method, the filtration-acclimatization method (FAM), which enables the isolation and cultivation of an important fraction of the bacterial diversity, which is not cultivable by standard methods . The method consists of a filtration step, which removes most of the readily cultivable bacteria able to overgrow slowly growing bacteria, and an acclimatization procedure that provides a slow transition from the low environmental substrate concentrations to the high concentration of standard microbial media . So far, we isolated in total 65 strains from surface freshwater habitats by utilizing FAM . The isolates are affiliated with Actinobacteria, Alpha-, Betaproteobacteria, Bacteroidetes, and Spirochaeta . All isolates are pure cultures and form visible colonies on agar plates with high substrate concentrations . For further analysis, strains sharing more than a 97% 16S rRNA gene sequence similarity were grouped into one taxon . Based on sequence similarities, 88% of the obtained taxa can be considered to be undescribed species (<97% similarity to closest species) . The highest similarity value of the taxa to the respective closest related species ranged from 87.7% to 99.8%, and was on average 94.5% . For comparison we isolated, by direct plating of water samples on a rich agar medium, a similar number of taxa . Amongst these taxa the percentage of taxa, which can be considered to be undescribed species, was only half of the percentage found for the taxa isolated by FAM . More importantly, it was amongst the taxa obtained by the standard method no taxon that was closer related to an uncultured bacterium than to an isolate, while 56% of the taxa isolated by FAM were closely related to uncultured bacteria. Am J Cardiovasc Drugs, 2004, 4(3), 169 - 77 Therapeutic potential of anticytokine therapy in congestive heart failure; Aukrust P et al.; Accumulating evidence indicates that inflammatory cytokines play a pathogenic role in congestive heart failure (CHF) by influencing heart contractility, inducing hypertrophy, and promoting apoptosis or fibrosis, contributing to the continuous myocardial remodeling process . While several stimuli may be operating such as heat-shock protein, microbial antigen, bacterial lipopolysaccharide, shear and oxidative stress, hypoxia and oxidized low-density lipoprotein (LDL), it seems that the inflammatory response to these stimuli may represent a common final pathogenic pathway in CHF regardless of the initial event . Traditional cardiovascular drugs seem to have little influence on the overall cytokine network, and immunomudulatory therapy has emerged as a possible new treatment modality in CHF . Several animal studies, and some clinical pilot studies, have suggested that down-regulation of inflammatory cytokines may improve cardiac performance . On the other hand, preliminary results from the placebo-controlled studies suggest no effect, or even adverse effect, of antitumor necrosis factor (TNF) therapy on mortality and hospitalization . Although somewhat disappointing, these negative results do not necessarily argue against the 'cytokine hypothesis' . These studies just underscore the difficulties and the challenges in developing treatment modalities that can modulate the cytokine network in CHF patients resulting in anti-inflammatory and beneficial net effects . Further research in this area will have to more precisely identify the most important actors in the immunopathogenesis of CHF in order to develop more specific immunomodulating agents for this disorder . However, at present the beneficial role of anticytokine therapy in patients with CHF remains unproven. Vet Rec, 2004 Apr 24, 154(17), 519 - 22 Dietary trials with a commercial chicken hydrolysate diet in 63 pruritic dogs; Loeffler A et al.; The owners of 63 pruritic dogs were instructed to feed them a chicken hydrolysate diet exclusively for six weeks as part of diagnostic investigations into non-seasonal pruritus . Ectoparasitism and microbial infections were eliminated during the dietary trial . The dogs' skin lesions, gastrointestinal signs and frequency of defecation were assessed and scores for pruritus were assigned before they started the diet and before and after they resumed their original diet . An adverse food reaction was diagnosed if the pruritus resolved while they were on the diet, but recurred when they resumed their original food regimen . Seventeen of the 63 dogs were withdrawn from the trial, including four which found the diet unpalatable; however, its palatability was reported to be good or excellent in 48 of the dogs . An adverse food reaction alone was diagnosed in nine (19.6 per cent) of the 46 dogs and another nine had an adverse food reaction and atopy . There were gastrointestinal signs in six of the nine dogs with an adverse food reaction, which resolved on the trial diet but recurred when they resumed their original diet. Protein Sci, 2004 Jun, 13(6), 1603 - 11 Epub 2004 May 07. Identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin E3; Walker D et al.; Colicin E3 is a cytotoxic ribonuclease that specifically cleaves 16S rRNA at the ribosomal A-site to abolish protein synthesis in sensitive Escherichia coli cells . We have performed extensive mutagenesis of the 96-residue colicin E3 cytotoxic domain (E3 rRNase), assayed mutant colicins for in vivo cytotoxicity, and tested the corresponding E3 rRNase domains for their ability to inactivate ribosome function in vitro . From 21 alanine mutants, we identified five positions where mutation resulted in a colicin with no measurable cytotoxicity (Y52, D55, H58, E62, and Y64) and four positions (R40, R42, E60, and R90) where mutation caused a significant reduction in cytotoxicity . Mutations that were found to have large in vivo and in vitro effects were tested for structural integrity through circular dichroism and fluorescence spectroscopy using purified rRNase domains . Our data indicate that H58 and E62 likely act as the acid-base pair during catalysis with other residues likely involved in transition state stabilization . Both the Y52 and Y64 mutants were found to be highly destabilized and this is the likely origin of the loss of their cytotoxicity . The identification of important active site residues and sequence alignments of known rRNase homologs has allowed us to identify other proteins containing the putative rRNase active site motif . Proteins that contained this active site motif included three hemagglutinin-type adhesins and we speculate that these have evolved to deliver a cytotoxic rRNase into eukaryotic cells during pathogenesis. FASEB J, 2004 Jul, 18(10), 1117 - 9 Epub 2004 May 07. Toll-like receptor 4 functions intracellularly in human coronary artery endothelial cells: roles of LBP and sCD14 in mediating LPS responses; Dunzendorfer S et al.; Endothelial cells are activated by microbial agonists through Toll-like receptors (TLRs) to express inflammatory mediators; this is of significance in acute as well as chronic inflammatory states such as septic shock and atherosclerosis, respectively . We investigated mechanisms of lipopolysaccharide (LPS)-induced cell activation in human coronary artery endothelial cells (HCAEC) using a combination of FACS, confocal microscopy, RT-PCR, and functional assays . We found that TLR4, in contrast to TLR2, is not only located intracellularly but also functions intracellularly . That being the case, internalization of LPS is required for activation . We further characterized the HCAEC LPS uptake system and found that HCAEC exhibit an effective LPS uptake only in the presence of LPS binding protein (LBP) . In addition to its function as a catalyst for LPS-CD14 complex formation, LBP enables HCAEC activation at low LPS concentrations by facilitating the uptake, and therefore delivery, of LPS-CD14 complexes to intracellular TLR4-MD-2 . LBP-dependent uptake involves a scavenger receptor pathway . Our findings may be of pathophysiological relevance in the initial response of the organism to infection . Results further suggest that LBP levels, which vary as LBP is an acute phase reactant, could be relevant to initiating inflammatory responses in the vasculature in response to chronic or recurring low LPS. FASEB J, 2004 Jul, 18(10), 1126 - 8 Epub 2004 May 07. Nitric oxide levels regulate macrophage commitment to apoptosis or necrosis during pneumococcal infection; Marriott HM et al.; Macrophages are resistant to constitutive apoptosis, but infectious stimuli can induce either microbial or host-mediated macrophage apoptosis . Phagocytosis and killing of opsonized pneumococci by macrophages are potent stimuli for host-mediated apoptosis, but the link between pneumococcal killing and apoptosis induction remains undefined . We now show phagocytosis of pneumococci by differentiated human monocyte-derived macrophages (MDM) results in up-regulation of inducible nitric oxide synthase (iNOS) and increased production of NO and reactive nitrogen species . NO accumulation in macrophages initiates an apoptotic program that involves NO-dependent mitochondrial membrane permeabilization, Mcl-1 down-regulation, and caspase activation and results in nuclear condensation and fragmentation . An inhibitor of mitochondrial permeability transition, bongkrekic acid, decreases pneumococcal-associated macrophage apoptosis . Conversely, inhibition of NO production using iNOS inhibitors decreases bacterial killing and shifts the cell death program from apoptosis to necrosis . Pneumolysin contributes to both NO production and apoptosis induction . After initial microbial killing, NO accumulation switches the macrophage phenotype from an activated cell to a cell susceptible to apoptosis . These results illustrate important roles for NO in the integration of host defense and regulation of inflammation in human macrophages. Mil Med, 2004 Apr, 169(4), 330 - 3 Identification of Francisella tularensis using real-time fluorescence polymerase chain reaction; McAvin JC et al.; A Francisella tularensis-specific, TaqMan probe-based, real-time fluorescence polymerase chain reaction (PCR) assay required approximately 60 minutes and consistently achieved a sensitivity of < or = 10 fg of F . tularensis genomic DNA (five genome equivalents) . Specificity testing against a genomic DNA cross-reaction panel comprised of 22 bacterial organisms representing closely related species, diverse genera, and human genomic DNA resulted in no false positives of significance . The assay was conducted on a field-deployable thermocycler, the R.A.P.I.D . ("Ruggedized" Advanced Pathogen Identification Device), a microbial identification system that can provide rapid and accurate identification F . tularensis. J Appl Genet, 2004, 45(2), 237 - 48 Role of epigenetic DNA alterations in the pathogenesis of systemic lupus erythematosus; Januchowski R et al.; Epigenetic alternations in genomic DNA encompass cytosine methylation in cytosine and guanine (CpG) dinucleotide islands, which are usually extended in the promoter and first exon of genes . The DNA methylation is carried out by DNA methyltransferases (DNMT) and it serves as an epigenetic method of gene expression modulation . The epigenetic alternations in genomic DNA have been implicated in the development of malignant and autoimmune diseases . The epigenetic aberration in regulatory DNA sequences may also be responsible for the emergence of changes in the immune system in patients with systemic lupus erythematosus (SLE) . The agents 5-azacytidine (azacitidine) and 5-aza-2'-deoxycytidine (decitabine) belong to inhibitors of methyltransferase . These compounds affect the methylation level of promoter sequences and cause phenotypic changes in peripheral blood mononuclear cells (PBMC), which are similar to those observed in PBMC of SLE patients . The lack of methylcytosine in CpG dinucleotides may be responsible for the antigenic properties of microbial DNA . The presence of low-apoptotic methylated DNA fragments has been identified in plasma of SLE patients . These DNA fragments exhibit antigenic properties and may elicit the humoral response responsible for the flare of SLE . The low methylation of CpG residues in the regulatory sequences may also contribute to the elevated expression of human endogenous retroviruses (HERVs) in PBMC of SLE patients . The HERV components exhibit a profound similarity with nuclear antigens and may be responsible for the enhancement of the production of anti-antinuclear antibodies (ANA) . Recent advances in the investigation of epigenetic DNA changes have formed the basis of improved understanding of etiopathogenesis of SLE, which may thereby facilitate improvement in therapeutic principles of this disease. Structure (Camb), 2004 May, 12(5), 775 - 84 Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase; Amaya MF et al.; Sialidases are a superfamily of sialic-acid-releasing enzymes that are of significant interest due to their implication as virulence factors in the pathogenesis of a number of diseases . However, extensive studies of viral and microbial sialidases have failed to provide a comprehensive picture of their mechanistic properties, in part because the structures of competent enzyme-substrate complexes and reaction intermediates have never been described . Here we report these structures for the Trypanosoma cruzi trans-sialidase (TcTS), showing that catalysis by sialidases occurs via a similar mechanism to that of other retaining glycosidases, but with some intriguing differences that may have evolved in response to the substrate structure. Biochem J, 2004 Aug 15, 382(Pt 1), 363 - 73 MT1-MMP mediates MUC1 shedding independent of TACE/ADAM17; Thathiah A et al.; MUC1, a transmembrane mucin, plays a critical role in embryo implantation, protection of mucosal epithelia from microbial and enzymic attack and various aspects of tumour progression . In some species, a decrease in uterine epithelial MUC1 protein and mRNA expression accompanies embryo implantation . In other species, such as rabbits and humans, MUC1 appears to be locally removed at blastocyst attachment sites, suggesting the action of a protease . We previously demonstrated that MUC1 is proteolytically released from the surface of a human uterine epithelial cell line, HES, and identified TACE/ADAM17 (where TACE stands for tumour necrosis factor-alpha converting enzyme and ADAM for A Disintegrin And Metalloprotease-like) as a constitutive and PMA-stimulated MUC1 sheddase {Thathiah, Blobel and Carson (2003) J . Biol . Chem . 274, 3386-3394} . Further characterization of the proteolytic activity(ies) mediating MUC1 release indicates that MUC1 shedding is also accelerated by the tyrosine phosphatase inhibitor pervanadate . Pervanadate, but not PMA, stimulates MUC1 shedding in TACE-deficient cells, indicating activation of a metalloproteolytic activity(ies) distinct from TACE . Pervanadate-stimulated MUC1 release is inhibited by the TIMP-2 (tissue inhibitor of metalloprotease-2) and TIMP-3, but is unaffected by TIMP-1, consistent with the MT-MMPs (membrane-type matrix metalloproteases) . Pervanadate stimulation of MUC1 shedding is absent from MUC1-transfected MT1-MMP-deficient fibroblasts, but is restored after MUC1 and MT1-MMP co-transfection . Furthermore, overexpression of MT1-MMP in HES cells enhances pervanadate-stimulated MUC1 release, and MT1-MMP co-localizes with MUC1 in vivo at the apical surface of receptive-phase human uterine epithelia . Taken together, these studies characterize a MUC1 sheddase activity in addition to TACE and identify MT1-MMP as a pervanadate-stimulated MUC1 sheddase. Ned Tijdschr Tandheelkd, 2004 Apr, 111(4), 120 - 7 {The odontogenic abscess . Aetiology, treatment and involvement in the orofacial region}; Spijkervet FK et al.; Odontogenic infections are a common problem in daily practice . Occasionally, an odontogenic infection evolves an abscess . This article discusses the aetiology, the treatment and the involvement of odontogenic abscesses in the oro-facial region . Their occurrence, course and treatment are depending on the patient's immune response, and on microbial and environmental factors. Biotechnol Bioeng, 2004 Jun 5, 86(5), 563 - 72 Production and characterization of liquid-core capsules made from cross-linked acrylamide copolymers for biotechnological applications; Wyss A et al.; A novel chemistry has been developed for the production of capsules composed of a hydrophobic liquid core surrounded by a cross-linked polyacrylamide/alginate membrane . These liquid-core capsules may be used in capsular perstraction for the removal of inhibitory products from bioprocesses and bioconversions . They have the advantage of having a high surface area to promote rapid mass transfer, while separation of the organic core phase from the aqueous environment by the capsule membrane prevents the formation of stable emulsions and potential problems associated with toxicity of the organic phase for microbial cells or enzymes . Monodisperse spherical liquid-core capsules of between 800 microm and 1.6 mm diameter, with high mechanical resistance, have been prepared by co-extrusion, using the jet break-up technique . Capsules produced from a solution of MBA/total monomer (5%) were found to be more elastic and have a higher burst force when exposed to chelating agents such as phosphate or citrate . The mechanical resistance was unaffected by buffer solutions in the pH range 4-9 and after sterilization at 121 degrees C for 20 min . Capsules having membranes composed of a copolymer of acrylamide and N-hydroxymethylacrylamide exhibited even higher mechanical stability toward chelating agents . Mar Biotechnol (NY) . 2004 May 6; {Epub ahead of print} Enzyme Inhibitors of Marine Microbial Origin with Pharmaceutical Importance; Imada C; Several enzyme inhibitors with various industrial uses were isolated from bacteria and actinomycetes living in the marine environment . These inhibitors are useful in medicine and agriculture . All the compounds, except the monoamine oxidase inhibitors, are novel, and their activities have been characterized. Appl Environ Microbiol, 2004 May, 70(5), 3180 - 2 Specific PCR assay for a tannin-tolerant selenomonas ruminantium isolate, derived from helicase coding sequences; Bishop R et al.; Sequences from a tannin-tolerant Selenomonas ruminantium isolate (EAT2) that hydrolyzes gallic acid were identified . Two exhibited identity to helicases with a wide phylogenetic distribution . PCR amplification by using primers from one helicase gene detected 2000 to 5000 EAT2 genome equivalents but did not amplify total gastrointestinal microbial DNA of nine other ungulate species. Appl Environ Microbiol, 2004 May, 70(5), 3041 - 6 Enhancing the thermal tolerance and gastric performance of a microbial phytase for use as a phosphate-mobilizing monogastric-feed supplement; Garrett JB et al.; The inclusion of phytase in monogastric animal feed has the benefit of hydrolyzing indigestible plant phytate (myo-inositol 1,2,3,4,5,6-hexakis dihydrogen phosphate) to provide poultry and swine with dietary phosphorus . An ideal phytase supplement should have a high temperature tolerance, allowing it to survive the feed pelleting process, a high specific activity at low pHs, and adequate gastric performance . For this study, the performance of a bacterial phytase was optimized by the use of gene site saturation mutagenesis technology . Beginning with the appA gene from Escherichia coli, a library of clones incorporating all 19 possible amino acid changes and 32 possible codon variations in 431 residues of the sequence was generated and screened for mutants exhibiting improved thermal tolerance . Fourteen single site variants were discovered that retained as much as 10 times the residual activity of the wild-type enzyme after a heated incubation regimen . The addition of eight individual mutations into a single construct (Phy9X) resulted in a protein of maximal fitness, i.e., a highly active phytase with no loss of activity after heating at 62 degrees C for 1 h and 27% of its initial activity after 10 min at 85 degrees C, which was a significant improvement over the appA parental phytase . Phy9X also showed a 3.5-fold enhancement in gastric stability. Appl Environ Microbiol, 2004 May, 70(5), 2722 - 7 Transformation of verapamil by Cunninghamella blakesleeana; Sun L et al.; A filamentous fungus, Cunninghamella blakesleeana AS 3.153, was used as a microbial model of mammalian metabolism to transform verapamil, a calcium channel antagonist . The metabolites of verapamil were separated and assayed by the liquid chromatography-ion trap mass spectrometry method . After 96 h of incubation, nearly 93% of the original drug was metabolized to 23 metabolites . Five major metabolites were isolated by semipreparative high-performance liquid chromatography and were identified by proton nuclear magnetic resonance and electrospray mass spectrometry . Other metabolites were characterized according to their chromatographic behavior and mass spectral data . The major metabolic pathways of verapamil transformation by the fungus were N dealkylation, O demethylation, and sulfate conjugation . The phase I metabolites of verapamil (introduction of a functional group) by C . blakesleeana paralleled those in mammals; therefore, C . blakesleeana could be a useful tool for generating the mammalian phase I metabolites of verapamil. Appl Environ Microbiol, 2004 May, 70(5), 2692 - 701 Responses of active bacterial and fungal communities in soils under winter wheat to different fertilizer and pesticide regimens; Girvan MS et al.; The composition of the active microbial (bacterial and fungal) soil community in an arable wheat field subjected to different management practices was examined at five times during a 1-year period . Field sections were fertilized either at good agricultural practice (GAP) levels or at reduced levels (0.5x GAP) and were inoculated with vesicular arbuscular mycorrhizae (VAM) at the same time . Field subsections were treated either with or without pesticides