Microbial

Org Lett, 2003 May 15, 5(10), 1749 - 52
Biomimetic synthesis of gramicidin s and analogues by enzymatic cyclization of linear precursors on solid support; Wu X et al.; {reaction: see text} Gramicidin S is a potent decapeptide antibiotic with high hemolytic activity but is unlikely to provoke microbial resistance . Here we demonstrate that gramicidin thioesterase (GrsB TE) correctly cyclizes immobilized linear decapeptide precursors into head-to-tail products, indicating its suitability for parallel solid-phase synthesis of gramicidin analogues from linear precursors on solid support . This chemoenzymatic method will enable the optimization of the therapeutic index of the natural product to fight microbial resistance.

Biol Proced Online, 1998 May 14, 1, 40 - 47
Methods for microbial DNA extraction from soil for PCR amplification; Yeates C et al.; Amplification of DNA from soil is often inhibited by co-purified contaminants . A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1) . DNA is also suitable for PCR amplification using various DNA targets . DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation . This method was compared to other DNA extraction methods with regard to DNA purity and size.

J Immunol, 2003 May 15, 170(10), 5075 - 81
Early IL-2 production by mouse dendritic cells is the result of microbial-induced priming; Granucci F et al.; Dendritic cells (DCs) are professional APCs able to initiate innate and adaptive immune responses against invading pathogens . Different properties such as the efficient Ag processing machinery, the high levels of expression of costimulatory molecules and peptide-MHC complexes, and the production of cytokines contribute in making DCs potent stimulators of naive T cell responses . Recently we have observed that DCs are able to produce IL-2 following bacterial stimulation, and we have demonstrated that this particular cytokine is a key molecule conferring to early bacterial activated DCs unique T cell priming capacity . In the present study we show that many different microbial stimuli, but not inflammatory cytokines, are able to stimulate DCs to produce IL-2, indicating that DCs can distinguish a cytokine-mediated inflammatory process from the actual presence of an infection . The capacity to produce IL-2 following a microbial stimuli encounter is a feature shared by diverse DC subtypes in vivo, such as CD8 alpha(+) and CD8 alpha(-) splenic DCs and epidermal Langerhans cells . When early activated DCs interact with T cells, IL-2 produced by DCs is enriched at the site of cell-cell contact, confirming the importance of DCs-derived IL-2 in T cell activation.

J Immunol, 2003 May 15, 170(10), 5008 - 17
Superantigen-induced regulatory T cells display different suppressive functions in the presence or absence of natural CD4+CD25+ regulatory T cells in vivo; Grundstrom S et al.; Repeated exposures to both microbial and innocuous Ags in vivo have been reported to both eliminate and tolerize T cells after their initial activation and expansion . The remaining tolerant T cells have been shown to suppress the response of naive T cells in vitro . This feature is reminiscent of natural CD4(+)CD25(+) regulatory T cells . However, it is not known whether the regulatory function of in vivo-tolerized T cells is similar to the function of natural CD4(+)CD25(+) regulatory T cells . In this study, we demonstrate that CD4(+)CD25(+) as well as CD4(+)CD25(-) T cells isolated from mice treated with superantigen three consecutive times to induce tolerance were functionally comparable to natural CD4(+)CD25(+) regulatory T cells, albeit more potent . The different subpopulations of in vivo-tolerized CD4(+) T cells efficiently down-modulated costimulatory molecules on dendritic cells, and their suppressive functions were strictly cell contact dependent . Importantly, we demonstrate that conventional CD4(+)CD25(-) T cells could also be induced to acquire regulatory functions by the same regimen in the absence of natural regulatory T cells in vivo, but that such regulatory cells were functionally different.

Nutr Cancer, 2002, 44(2), 189 - 91
Food-borne radiolytic compounds (2-alkylcyclobutanones)may promote experimental colon carcinogenesis; Raul F et al.; Food irradiation is acknowledged as a safe process to improve food quality by reducing microbial contamination . Information on the toxicological potential of 2-alkylcyclobutanones (2-ACBs), radiolytic derivatives of triglycerides found exclusively in irradiated food, is scarce . Wistar rats received daily a solution of highly pure 2-tetradecylcyclobutanone (2-tDCB) or 2-(tetradec-5-enyl)-cyclobutanone (2-tDeCB) at a concentration of 0.005% in 1% ethanol as drinking fluid, while control animals received 1% ethanol . All animals received a single intraperitoneal injection of the chemical carcinogen azoxymethane (AOM) at Weeks 3 and 4 . At 3 mo after AOM injection, no significant changes were observed in the total number of preneoplastic lesions in the colon of AOM controls and 2-ACB-treated animals . After 6 mo, the total number of tumors in the colon was threefold higher in the 2-ACB-treated animals than in the AOM controls . The colon of four of six AOM control rats exhibited only one small tumor ( &6 mm3) . Multiple tumors were observed in four and three of six animals treated with 2-tDCB or 2-tDeCB, respectively . Medium (6 < S < 25 mm3) and larger (>25 mm3) tumors were detected only in 2-ACB-treated animals . This is the first demonstration that a compound found exclusively in irradiated dietary fats may promote colon carcinogenesis in animals treated with a chemical carcinogen.

Environ Monit Assess, 2003 May, 84(1-2), 71 - 84
Biotic landfill cover treatments for mitigating methane emissions; Hilgeri H et al.; Landfill methane (CH4) emissions have been cited as one of the anthropogenic gas releases that can and should be controlled to reduce global climate change . This article reviews recent research that identifies ways to enhance microbial consumption of the gas in the aerobic portion of a landfill cover . Use of these methods can augment CH4 emission reductions achieved by gas collection or provide a sole means to consume CH4 at small landfills that do not have active gas collection systems . Field studies indicate that high levels of CH4 removal can be achieved by optimizing natural soil microbial processes . Further, during biotic conversion, not all of the CH4 carbon is converted to carbon dioxide (CO2) gas and released to the atmosphere; some of it will be sequestered in microbial biomass . Because biotic covers can employ residuals from other municipal processes, financial benefits can also accrue from avoided costs for residuals disposal.

Ambio, 2003 Mar, 32(2), 87 - 90
Hypersaline cyanobacterial mats as indicators of elevated tropical hurricane activity and associated climate change; Paerl HW et al.; The Atlantic hurricanes of 1999 caused widespread environmental damage throughout the Caribbean and US mid-Atlantic coastal regions . However, these storms also proved beneficial to certain microbial habitats; specifically, cyanobacteria-dominated mats . Modern mats represent the oldest known biological communities on earth, stromatolites . Contemporary mats are dominant biological communities in the hypersaline Bahamian lakes along the Atlantic hurricane track . We examined the impacts of varying levels of hypersalinity on 2 processes controlling mat growth, photosynthesis and nitrogen fixation, in Salt Pond, San Salvador Island, Bahamas . Hypersalinity (> 5 times seawater salinity) proved highly inhibitory to these processes . Freshwater input from Hurricane Floyd and other large storms alleviated this salt-inhibition . A predicted 10 to 40 year increase in Atlantic hurricane activity accompanied by more frequent "freshening" events will enhance mat productivity, CO2 sequestration and nutrient cycling . Cyanobacterial mats are sensitive short- and long-term indicators of climatic and ecological changes impacting these and other waterstressed environments.

Appl Environ Microbiol, 2003 May, 69(5), 2942 - 9
Stable carbon isotope fractionation by sulfate-reducing bacteria; Londry KL et al.; Biogeochemical transformations occurring in the anoxic zones of stratified sedimentary microbial communities can profoundly influence the isotopic and organic signatures preserved in the fossil record . Accordingly, we have determined carbon isotope discrimination that is associated with both heterotrophic and lithotrophic growth of pure cultures of sulfate-reducing bacteria (SRB) . For heterotrophic-growth experiments, substrate consumption was monitored to completion . Sealed vessels containing SRB cultures were harvested at different time intervals, and delta(13)C values were determined for gaseous CO(2), organic substrates, and products such as biomass . For three of the four SRB, carbon isotope effects between the substrates, acetate or lactate and CO(2), and the cell biomass were small, ranging from 0 to 2 per thousand . However, for Desulfotomaculum acetoxidans, the carbon incorporated into biomass was isotopically heavier than the available substrates by 8 to 9 per thousand . SRB grown lithoautotrophically consumed less than 3% of the available CO(2) and exhibited substantial discrimination (calculated as isotope fractionation factors {alpha}), as follows: for Desulfobacterium autotrophicum, alpha values ranged from 1.0100 to 1.0123; for Desulfobacter hydrogenophilus, the alpha value was 0.0138, and for Desulfotomaculum acetoxidans, the alpha value was 1.0310 . Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO(2) resulted in biomass with a delta(13)C composition intermediate to that of the substrates . The extent of fractionation depended on which enzymatic pathways were used, the direction in which the pathways operated, and the growth rate, but fractionation was not dependent on the growth phase . To the extent that environmental conditions affect the availability of organic substrates (e.g., acetate) and reducing power (e.g., H(2)), ecological forces can also influence carbon isotope discrimination by SRB.

Appl Environ Microbiol, 2003 May, 69(5), 2893 - 8
Cyanobacterial ecotypes in different optical microenvironments of a 68 degrees C hot spring mat community revealed by 16S-23S rRNA internal transcribed spacer region variation; Ferris MJ et al.; We examined the population of unicellular cyanobacteria (Synechococcus) in the upper 3-mm vertical interval of a 68 degrees C region of a microbial mat in a hot spring effluent channel (Yellowstone National Park, Wyoming) . Fluorescence microscopy and microsensor measurements of O(2) and oxygenic photosynthesis demonstrated the existence of physiologically distinct Synechococcus populations at different depths along a light gradient quantified by scalar irradiance microprobes . Molecular methods were used to evaluate whether physiologically distinct populations could be correlated with genetically distinct populations over the vertical interval . We were unable to identify patterns in genetic variation in Synechococcus 16S rRNA sequences that correlate with different vertically distributed populations . However, patterns of variation at the internal transcribed spacer locus separating 16S and 23S rRNA genes suggested the existence of closely related but genetically distinct populations corresponding to different functional populations occurring at different depths.

Appl Environ Microbiol, 2003 May, 69(5), 2664 - 73
Large-scale spatial distribution of virioplankton in the Adriatic Sea: testing the trophic state control hypothesis; Corinaldesi C et al.; Little is known concerning environmental factors that may control the distribution of virioplankton on large spatial scales . In previous studies workers reported high viral levels in eutrophic systems and suggested that the trophic state is a possible driving force controlling the spatial distribution of viruses . In order to test this hypothesis, we determined the distribution of viral abundance and bacterial abundance and the virus-to-bacterium ratio in a wide area covering the entire Adriatic basin (Mediterranean Sea) . To gather additional information on factors controlling viral distribution on a large scale, functional microbial parameters (exoenzymatic activities, bacterial production and turnover) were related to trophic gradients . At large spatial scales, viral distribution was independent of autotrophic biomass and all other environmental parameters . We concluded that in contrast to what was previously hypothesized, changing trophic conditions do not directly affect virioplankton distribution . Since virus distribution was coupled with bacterial turnover times, our results suggest that viral abundance depends on bacterial activity and on host cell abundance.

Appl Environ Microbiol, 2003 May, 69(5), 2631 - 7
Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization; Pernthaler J et al.; We describe here an automated system for the counting of multiple samples of double-stained microbial cells on sections of membrane filters . The application integrates an epifluorescence microscope equipped with motorized z-axis drive, shutters, and filter wheels with a scanning stage, a digital camera, and image analysis software . The relative abundances of specific microbial taxa are quantified in samples of marine picoplankton, as detected by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition . Pairs of microscopic images are automatically acquired from numerous positions at two wavelengths, and microbial cells with both general DNA and FISH staining are counted after object edge detection and signal-to-background ratio thresholding . Microscopic fields that are inappropriate for cell counting are automatically excluded prior to measurements . Two nested walk paths guide the device across a series of triangular preparations until a user-defined number of total cells has been analyzed per sample . A backup autofocusing routine at incident light allows automated refocusing between individual samples and can reestablish the focal plane after fatal focusing errors at epifluorescence illumination . The system was calibrated to produce relative abundances of FISH-stained cells in North Sea samples that were comparable to results obtained by manual evaluation . Up to 28 preparations could be analyzed within 4 h without operator interference . The device was subsequently applied for the counting of different microbial populations in incubation series of North Sea waters . Automated digital microscopy greatly facilitates the processing of numerous FISH-stained samples and might thus open new perspectives for bacterioplankton population ecology.

Appl Environ Microbiol, 2003 May, 69(5), 2555 - 62
Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure; Egert M et al.; Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in molecular microbial ecology . In this study, we show that besides expected terminal restriction fragments (T-RFs), additional secondary T-RFs occur in T-RFLP analysis of amplicons from cloned 16S rRNA genes at high frequency . A total of 50% of 109 bacterial and 78% of 68 archaeal clones from the guts of cetoniid beetle larvae, using MspI and AluI as restriction enzymes, respectively, were affected by the presence of these additional T-RFs . These peaks were called "pseudo-T-RFs" since they can be detected as terminal fluorescently labeled fragments in T-RFLP analysis but do not represent the primary terminal restriction site as indicated by sequence data analysis . Pseudo-T-RFs were also identified in T-RFLP profiles of pure culture and environmental DNA extracts . Digestion of amplicons with the single-strand-specific mung bean nuclease prior to T-RFLP analysis completely eliminated pseudo-T-RFs . This clearly indicates that single-stranded amplicons are the reason for the formation of pseudo-T-RFs, most probably because single-stranded restriction sites cannot be cleaved by restriction enzymes . The strong dependence of pseudo-T-RF formation on the number of cycles used in PCR indicates that (partly) single-stranded amplicons can be formed during amplification of 16S rRNA genes . In a model, we explain how transiently formed secondary structures of single-stranded amplicons may render single-stranded amplicons accessible to restriction enzymes . The occurrence of pseudo-T-RFs has consequences for the interpretation of T-RFLP profiles from environmental samples, since pseudo-T-RFs may lead to an overestimation of microbial diversity . Therefore, it is advisable to establish 16S rRNA gene sequence clone libraries in parallel with T-RFLP analysis from the same sample and to check clones for their in vitro digestion T-RF pattern to facilitate the detection of pseudo-T-RFs.

J Microbiol Methods, 2003 Jul, 54(1), 121 - 5
Variation between observed and true Terminal Restriction Fragment length is dependent on true TRF length and purine content; Kaplan CW et al.; Terminal Restriction Fragment (TRF) pattern analysis has become a widely used and informative tool for studying microbial communities . Variation between sequence-determined or true TRF length and observed TRF length (TRF drift) has been previously reported and can significantly affect identification of bacterial species using TRF lengths predicted from sequence databases . In this study TRF drift was determined for 21 bacterial species using an ABI 310 Genetic Analyzer . TRF drift was positively correlated with true TRF length and negatively correlated with TRF purine content . This implies that subtle differences in molecular weight, whether from purine content or dye label, can significantly affect the observed TRF length.

J Microbiol Methods, 2003 Jul, 54(1), 13 - 20
Evaluation of QIAamp DNA Stool Mini Kit for ecological studies of gut microbiota; Li M et al.; Cell lysis efficiency and the quality of DNA extracts from complex bacterial ecosystems are two major concerns in molecular ecological studies of gut microbiota . In this study, we use PCR-denaturing gradient gel electrophoresis (DGGE) DNA profiling, random cloning and sequence analysis of 16S rRNA genes to compare the QIAamp DNA Stool Mini Kit with the bead beating technique in the preparation of DNA extracts from gut microbiota of pigs . We also developed a washing procedure that can release more than 93% of bacterial cells attached to the gut mucosa . Both the QIAamp kit and bead beating method lysed approximately 95% of bacterial cells . PCR-DGGE DNA profiles of ileal and cecal microbiota from both digesta and mucosa that were generated from the DNA extracts using the two methods were nearly identical . Random cloning and sequence analysis also demonstrated the high quality of DNA extracts using the two methods . Two random clone sets of 16S rRNA genes generated from the DNA extracts had a similar degree of bacterial diversity . Different preparations of DNA extract from a single sample using the QIAamp kit consistently produced similar PCR-DGGE DNA profiles with similarity indexes higher than 99% . Our data suggest the appropriateness of the QIAamp DNA Stool Mini Kit for the studies of gut microbial ecology and the effectiveness of the QIAamp kit in processing multiple samples for cell lysis and DNA extraction.

Cell, 2003 May 2, 113(3), 343 - 55
Molecular basis of phosphorylation-induced activation of the NADPH oxidase; Groemping Y et al.; The multi-subunit NADPH oxidase complex plays a crucial role in host defense against microbial infection through the production of reactive oxygen species . Activation of the NADPH oxidase requires the targeting of a cytoplasmic p40-p47-p67(phox) complex to the membrane bound heterodimeric p22-gp91(phox) flavocytochrome . This interaction is prevented in the resting state due to an auto-inhibited conformation of p47(phox) . The X-ray structure of the auto-inhibited form of p47(phox) reveals that tandem SH3 domains function together to maintain the cytoplasmic complex in an inactive form . Further structural and biochemical data show that phosphorylation of p47(phox) activates a molecular switch that relieves the inhibitory intramolecular interaction . This permits p47(phox) to interact with the cytoplasmic tail of p22(phox) and initiate formation of the active, membrane bound enzyme complex.

J Nutr, 2003 May, 133(5 Suppl 2), 1668S - 1673S
Micronutrients and intrauterine infection, preterm birth and the fetal inflammatory response syndrome; Romero R et al.; Prematurity is the leading cause of perinatal morbidity and mortality worldwide . Intrauterine infection has emerged as a major cause of premature labor and delivery . It has been estimated that 25% of all preterm deliveries occur to mothers who have microbial invasion of the amniotic cavity, although these infections are mostly subclinical in nature . This article describes the pathways leading to intrauterine infection, microbiology, frequency and clinical consequences of infection . The pathophysiology of the fetal inflammatory response syndrome is reviewed, as is its relationship to long-term handicap, such as cerebral palsy and bronchopulmonary dysplasia . A possible role for two micronutrients, vitamins C and E, in the prevention of the preterm prelabor rupture of membranes and the consequences of fetal inflammation is considered . Research needs are listed.

J Nutr, 2003 May, 133(5 Suppl 1), 1506S - 9S
Trace mineral bioavailability in ruminants; Spears JW; Absorption of selenium and copper is much lower in ruminants than in nonruminants . The low absorption of these minerals in ruminants is due to modifications that occur in the rumen environment . Selenium bioavailability is reduced by high dietary sulfur and the presence of cyanogenetic glycosides in certain legumes . Feeding organic selenium from selenomethionine or selenized yeast results in much higher tissue and milk selenium concentrations than are obtained with selenite . High dietary molybdenum in combination with moderate to high dietary sulfur results in formation of thiomolybdates in the rumen . Thiomolybdates greatly reduce copper absorption, and certain thiomolybdate species can be absorbed and interfere systemically with copper metabolism . Independent of molybdenum, high dietary sulfur reduces copper absorption perhaps via formation of copper sulfide . High dietary iron also reduces copper bioavailability . Dietary factors that affect bioavailability of zinc in ruminants are not well defined . Phytate does not affect zinc absorption in ruminants because microbial phytase in the rumen degrades phytate . Manganese is very poorly absorbed in ruminants, and limited research suggests that high dietary calcium and phosphorus may reduce manganese absorption.

Biosci Biotechnol Biochem, 2003 Feb, 67(2), 291 - 4
Structure of folding intermediates at pH 4.0 and native state of microbial transglutaminase; Yokoyama K et al.; Recombinant microbial transglutaminase has been expressed in Escherichia coli as insoluble inclusion bodies . After we searched for refolding conditions, refolding of the protein could be done by first dilution of the unfolded enzyme in a buffer at pH 4.0, and then by titration of the pH from 4.0 to 6.0 . CD analysis showed that a burst of secondary structure formation occurred within the dead time of the experiment and accounted for 75% of the signal change in the far UV CD, with little tertiary structure being formed . This burst was followed by slow rearrangement of the secondary structure accompanied by formation of tertiary structure . The secondary and tertiary structures of the final sample at pH 4.0, corresponding to the folding intermediate, were different from these structures at pH 6.0 . Once the native structure was obtained, acidification of the native protein to pH 4.0 did not lead to a structure like that of the folding intermediate . Sedimentation velocity analysis showed that the folding intermediate had an expanded structure and contained no other structure species including large aggregates.

J Clin Invest, 2003 May, 111(9), 1297 - 308
Toll-like receptor-dependent production of IL-12p40 causes chronic enterocolitis in myeloid cell-specific Stat3-deficient mice; Kobayashi M et al.; Stat3 plays an essential role in IL-10 signaling pathways . A myeloid cell-specific deletion of Stat3 resulted in inflammatory cytokine production and development of chronic enterocolitis with enhanced Th1 responses in mice . In this study, we analyzed the mechanism by which a Stat3 deficiency in myeloid cells led to the induction of chronic enterocolitis in vivo . Even in the absence of Stat1, which is essential for IFN-gamma signaling pathways, Stat3 mutant mice developed chronic enterocolitis . TNF-alpha/Stat3 double-mutant mice developed severe chronic enterocolitis with enhanced Th1 cell development . IL-12p40/Stat3 double-mutant mice, however, showed normal Th1 responses and no inflammatory change in the colon . RAG2/Stat3 double-mutant mice did not develop enterocolitis, either . These findings indicate that overproduction of IL-12p40, which induces potent Th1 responses, is essential for the development of chronic enterocolitis in Stat3 mutant mice . Furthermore, enterocolitis was significantly improved and IFN-gamma production by T cells was reduced in TLR4/Stat3 double-mutant mice, indicating that TLR4-mediated recognition of microbial components triggers aberrant IL-12p40 production by myeloid cells, leading to the development of enterocolitis . Thus, this study clearly established a sequential innate and acquired immune mechanism for the development of Th1-dependent enterocolitis.

Ann N Y Acad Sci, 2003 Apr, 987, 15 - 25
Dendritic cell function in vivo during the steady state: a role in peripheral tolerance; Steinman RM et al.; The avoidance of autoimmunity requires mechanisms to actively silence or tolerize self reactive T cells in the periphery . During infection, dendritic cells are not only capturing microbial antigens, but also are processing self antigens from dying cells as well as innocuous environmental proteins . Since the dendritic cells are maturing in response to microbial and other stimuli, peptides will be presented from both noxious and innocuous antigens . Therefore it would be valuable to have mechanisms whereby dendritic cells, prior to infection, establish tolerance to those self and environmental antigens that can be processed upon pathogen encounter . In the steady state, prior to acute infection and inflammation, dendritic cells are in an immature state and not fully differentiated to carry out their known roles as inducers of immunity . These immature cells are not inactive, however . They continuously circulate through tissues and into lymphoid organs, capturing self antigens as well as innocuous environmental proteins . Recent experiments have provided direct evidence that antigen-loaded immature dendritic in vivo silence T cells either by deleting them or by expanding regulatory T cells . In this way, it is proposed that the immune system overcomes at least some of the risk of developing autoimmunity and chronic inflammation . It is proposed that dendritic cells play a major role in defining immunologic self, not only centrally in the thymus but also in the periphery.

Water Res, 2003 May, 37(10), 2408 - 18
The use of vegetation to remediate soil freshly contaminated by recalcitrant contaminants; Sung K et al.; The use of vegetation to remediate soil contaminated by recalcitrant hydrocarbons was tested under field conditions . Specifically, an evaluation was made of the effectiveness of deep rooting grasses, Johnsongrass and Canadian wild rye in the dissipation of TNT and PBB's in the soils freshly contaminated to an initial concentration of 10.17+/-1.35 for TNT and 9.87+/-1.23 mg/kg for PBB . The experiment used 72 (1.5m long and 0.1m diameter) column lysimeters with four treatments: Johnsongrass; wild rye grass; a rotation of Johnsongrass and wild rye grass; and unplanted fallow conditions . In the laboratory, immunoassay test procedures determined the TNT and PBB concentrations in the soil, leachate, herbage and root samples . The root characteristics such as total root length, rooting density, and root surface area were quantified to a depth of 1.5m . Changes in microbial biomass were assessed for both rhizosphere soil and the bulk soil during the 2-year study . The largest and most rapid loss in soil chemical concentration was for TNT, which decreased to less than 250 microg/kg, the detection limit, by 93 days after germination . The PBB was at or near the detection limit of 500 microg/kg by 185 days after germination . There was no perceptible difference in contaminant concentration in the soil between the vegetation treatments and/or with depth.

Nutr Rev, 2003 Mar, 61(3), 91 - 9
Probiotics: considerations for human health; Sanders ME; Evidence for the role of probiotics in maintenance of health or prevention of disease is mounting and is supported in some cases by blinded, placebo-controlled human trials . Today, in an era of antibiotic-resistant pathogens and other looming microbial threats, the value of prevention of infection is recognized . Probiotics may play an important role in helping the body protect itself from infection, especially along the colonized mucosal surfaces of the gastrointestinal tract . Probiotic products are available in many different forms worldwide, including pills, powders, foods, and infant formula . In some cases, general health claims are made that cannot be substantiated for the specific strains and levels being used and consumers must therefore beware.

Neuropathology, 2003 Mar, 23(1), 1 - 8
Role of Chlamydia pneumoniae-infected macrophages in atherosclerosis developments of the carotid artery; Kuroda S et al.; Chlamydia pneumoniae (C . pneumoniae) infection has been recently accepted as an important cause of atherosclerosis . However, the precise mechanisms remain unclear . The present study was aimed to clarify the distribution link among C . pneumoniae, chlamydial HSP 60, and activated macrophages . Atheromatous carotid plaques were obtained from 40 consecutive carotid endarterectomies (CEA) . The specimens were prepared for HE and elastica-van Gieson staining . Parallel sections were stained immunocytochemically with monoclonal antibodies for a C . pneumoniae-specific antigen, chlamydial HSP 60, activated macrophages, and smooth muscle cells . Immunoreactivity for the C . pneumoniae-specific antigen was observed within the endothelial cells, activated macrophages, and smooth muscle cells in 36 of 40 specimens (90%) . Chlamydial HSP 60 was found in all specimens positive for the C . pneumoniae-specific antigen, and mainly co-localized with the C . pneumoniae-specific antigen within the activated macrophages . The present results suggest that C . pneumoniae is a key microbial organ that causes atheroma developments in the carotid artery . Chlamydia pneumoniae-infected macrophages may come into the arterial intima and mediate inflammatory and autoimmune processes through the production of chlamydial HSP 60, leading to atherosclerosis.

Ying Yong Sheng Tai Xue Bao, 2003 Jan, 14(1), 148 - 50
{Micro-ecology in animal stomach and digestive tracts--theory and practice}; Tan Z; The origin, development and practical use of animal micro-ecology community in the gastrointestinal tract of domestic animals were reviewed, and the microbial species, features, and their function mechanism were introduced . Meanwhile, the relationship of micro-ecological theory, microbial additives and their practical use in animal feeding were emphatically discussed.

Ying Yong Sheng Tai Xue Bao, 2003 Jan, 14(1), 79 - 84
{Degradation of metsulfuron-methyl in soils . I . Effect of soil properties}; Wang H et al.; The ANOVA results showed that degradation of metsulfuron-methyl was different among various soils . Five principal factors were selected by principal factor analysis and they represented 90.4% of total information . The multivariate regression equations were established between soil properties and metsulfuron-methyl residues after stepwise regression analysis . The partial correlation and path analysis indicated that soil pH and microbial activity were the most significant factors controlling the degradation of metsulfuron-methyl in soils.

Appl Biochem Biotechnol, 2003 Spring, 105 -108, 27 - 41
Microbial pretreatment of biomass: potential for reducing severity of thermochemical biomass pretreatment; Keller FA et al.; Typical pretreatment requires high-energy (steam and electricity) and corrosion-resistant, high-pressure reactors . A review of the literature suggests that fungal pretreatment could potentially lower the severity requirements of acid, temperature and time . These reductions in severity are also expected to result in less biomass degradation and consequently lower inhibitor concentrations compared to conventional thermochemical pretreatment . Furthermore, potential advantages of fungal pretreatment of agricultural residues, such as corn stover, are suggested by its effectiveness in improving the cellulose digestibility of many types of forage fiber and agricultural wastes . Our preliminary tests show a three- to five-fold improvement in enzymatic cellulose digestibility of corn stover after pretreatment with Cyathus stercoreus; and a ten- to 100-fold reduction in shear force needed to obtain the same shear rate of 3.2 to 7 rev/s, respectively, after pretreatment with Phanerochaete chrysosporium.

J Androl, 2003 May-Jun, 24(3), 448 - 55
Male genital tract inflammation: The role of selected interleukins in regulation of pro-oxidant and antioxidant enzymatic substances in seminal plasma; Sanocka D et al.; Human semen contains spermatozoa as well as populations of round nonspermatozoal cells primarily consisting of leukocytes . Activation of white blood cells present in the seminal plasma during genital tract inflammation and cellular reactions against microbial agents may provoke a release of a variety of products such as cytokines and reactive oxygen species . The aim of this study was to evaluate whether a panel of selected cytokines (interleukin {IL}-1 beta, IL-6, IL-8, and tumor necrosis factor-alpha {TNF alpha}) detectable in seminal plasma during male genital tract inflammation could be considered as mediators between altered semen parameters and changed levels of pro-oxidant and antioxidant substances . Studies using chemiluminometric, spectrophotometric, and enzyme-linked immunosorbent assay methods indicate that proinflammatory cytokines such as IL-1 beta, IL-6, IL-8, and TNF alpha may modulate pro-oxidant and antioxidant activities in the male genital tract . The data also suggest that the function of pro-oxidant and antioxidant systems in semen may directly influence basic semen parameters . The elevated numbers of leukocytes present in semen during male genital tract inflammation without an associated contribution of cytokines and semen antioxidant capacity appear to be of little prognostic value in evaluating male fertilization potential.

J Agric Food Chem, 2003 May 7, 51(10), 3043 - 8
Influence of microbial inoculation (Pseudomonas sp . strain ADP), the enzyme atrazine chlorohydrolase, and vegetation on the degradation of atrazine and metolachlor in soil; Zhao S et al.; The concentrations of atrazine in the freshly added soils and the soils that had been incubated for 50 days significantly decreased 1 day after the addition of the enzyme atrazine chlorohydrolase or the soil bacterium Pseudomonas sp . strain ADP as compared with those in the uninoculated soils . Atrazine chlorohydrolase or ADP had no effect on the degradation of metolachlor . The half-lives of atrazine in the freshly added soils and in the aged soils after the treatment with atrazine chlorohydrolase or ADP markedly decreased as compared with those in the uninoculated soils . The half-lives of metolachlor in the aged soils were much longer than those of freshly added metolachlor . The percentage atrazine degraded in the freshly treated soils was much higher than that in the aged soils . This indicates that aging significantly decreased the bioavailability of atrazine . Vegetation significantly decreased the concentration of metolachlor . However, vegetation showed no effect on the degradation of atrazine.

J Cell Biol, 2003 Apr 28, 161(2), 249 - 55
Helicobacter pylori CagA protein targets the c-Met receptor and enhances the motogenic response; Churin Y et al.; Infection with the human microbial pathogen Helicobacter pylori is assumed to lead to invasive gastric cancer . We find that H . pylori activates the hepatocyte growth factor/scatter factor receptor c-Met, which is involved in invasive growth of tumor cells . The H . pylori effector protein CagA intracellularly targets the c-Met receptor and promotes cellular processes leading to a forceful motogenic response . CagA could represent a bacterial adaptor protein that associates with phospholipase Cgamma but not Grb2-associated binder 1 or growth factor receptor-bound protein 2 . The H . pylori-induced motogenic response is suppressed and blocked by the inhibition of PLCgamma and of MAPK, respectively . Thus, upon translocation, CagA modulates cellular functions by deregulating c-Met receptor signaling . The activation of the motogenic response in H . pylori-infected epithelial cells suggests that CagA could be involved in tumor progression.

Arthritis Res Ther, 2003, 5(2), R114 - 21 Epub 2003 Feb 03.
The VH gene repertoire of splenic B cells and somatic hypermutation in systemic lupus erythematosus; Fraser NL et al.; In systemic lupus erythematosus (SLE) it has been hypothesized that self-reactive B cells arise from virgin B cells that express low-affinity, nonpathogenic germline V genes that are cross-reactive for self and microbial antigens, which convert to high-affinity autoantibodies via somatic hypermutation . The aim of the present study was to determine whether the VH family repertoire and pattern of somatic hypermutation in germinal centre (GC) B cells deviates from normal in SLE . Rearranged immunoglobulin VH genes were cloned and sequenced from GCs of a SLE patient's spleen . From these data the GC V gene repertoire and the pattern of somatic mutation during the proliferation of B-cell clones were determined . The results highlighted a bias in VH5 gene family usage, previously unreported in SLE, and under-representation of the VH1 family, which is expressed in 20-30% of IgM+ B cells of healthy adults and confirmed a defect in negative selection . This is the first study of the splenic GC response in human SLE.

Asian Pac J Cancer Prev, 2002, 3(3), 225 - 230
Elimination of Deleterious Effects of Free Radicals in Murine Skin Carcinogenesis by Black Tea Infusion, Theaflavins & Epigallocatechin Gallate; Saha P et al.; In recent years, numerous reports have been published on the identification of novel, naturally occurring antioxidants from plants, animals, microbial sources and processed food products . Most natural antioxidants are phenolic compounds, which have a modulatory role on physiological functions and biotransformation reactions involved in the detoxification process, thereby affording protection from cytotoxic, genotoxic and metabolic actions of environmental toxicants . As part of our program on evaluation of food, beverage and traditional medicinal plants for their anticarcinogenic activity, the present report deals with the evaluation of aqueous infusion of Black tea (Camellia sinensis), Black tea extract (80% Theaflavins) & EGCG on mice exposed to the chemical carcinogen DMBA . All the four detoxification enzymes studied viz, GST, GPx, SOD and CAT were found to be activated to different degrees following treatment with black tea and two of its active compounds . The activation of the enzymes was accompanied by significant reduction in lipid peroxidation . The effect on apoptosis and cell proliferation was also studied in mice skin following administration of DMBA . Theaflavins, and EGCG significantly inhibited cell proliferation and induced apoptosis . The observation suggests chemopreventive potential of black tea infusion, black tea extract Theaflavins and the compound EGCG.

Vet Res Commun, 2003 Feb, 27(2), 111 - 24
Biochemical changes in apparently normal sheep from flocks affected by polioencephalomalacia; Ramos JJ et al.; Blood samples were obtained for determination of the activities of lactate, pyruvate and erythrocyte transketolase, and faeces as samples for estimation of thiaminase, from 190 apparently healthy sheep from 19 flocks in which at least one animal had been diagnosed with polioencephalomalacia (PEM), from 59 control animals and from 7 affected by PEM . Feed and pasture grass samples were collected for thiaminase analysis and thiaminase was assayed in ryegrass and fescue . Decreased erythrocyte transketolase activity, accompanied by a corresponding rise in the thiamin pyrophosphate effect, and estimation of the thiaminase content in faeces, may be useful diagnostic procedures by which to identify periods of greater risk, during which animals could develop PEM . The changes in the diet probably acted as a primary factor for microbial production of thiaminases in replacement ewes . In these, the prevalence was higher in the spring months.

Bioessays, 2003 May, 25(5), 478 - 88
Subversion of the chemokine world by microbial pathogens; Liston A et al.; It is well known that microbial pathogens are able to subvert the host immune system in order to increase microbial replication and propagation . Recent research indicates that another arm of the immune response, that of the chemokine system, is also subject to this sabotage, and is undermined by a range of microbial pathogens, including viruses, bacteria, and parasites . Currently, it is known that the chemokine system is being challenged by a number of mechanisms, and still more are likely to be discovered with further research . Here we first review the general mechanisms by which microbial pathogens bypass mammalian chemokine defences . Broadly, these can be grouped as viral chemokine interacting proteins, microbial manipulation of host chemokine and chemokine receptor expression, microbial blockade of host chemokine receptor signalling, and the largely hypothetical mechanisms of microbial enhancement of host anti-chemokine networks (including digestion, antagonism, and neutralisation of host chemokines and chemokine receptors) . We then discuss the potential results of these interactions in terms of outcome of infection .

J Med Biogr, 2003 May, 11(2), 81 - 6
Henry Wade (1876-1955) and cancer research: early years in the life of a pioneer of urological surgery; Gardner DL; This paper describes the microscopic studies of human and experimental cancers made by Henry Wade during the years 1904-9 . William Ford Robertson, his mentor, and Wade claimed to have discovered a microbial cause of human cancer . The claim was at once fiercely disputed . Wade turned to the investigation of a transmissible sarcoma of the dog, during which he demonstrated an early form of immune transplant rejection . He also undertook studies of Hodgkin's disease . Later in life, Wade established urological surgery at the Royal Infirmary of Edinburgh and became President of the Royal College of Surgeons of Edinburgh.

Mol Biol Evol, 2003 Jun, 20(6), 945 - 54 Epub 2003 Apr 25.
On the nature of gene innovation: duplication patterns in microbial genomes; Hooper SD et al.; Gene duplication is considered a major force in gene family expansion and gene innovation . As gene copies assume novel functions, they must avoid periods of neutrality or be deleted from the genome . Current opinions state that copies avoid neutrality through gene dosage effects . These copies are therefore selected from an early stage . This study concentrates on the flow of copies from recent duplication to gene innovation . We have studied 21 microbial genomes using amino acid divergence to describe paralog evolution in the long-term perspective . Five of these were studied in closer detail using nucleotide divergence for a shorter perspective . It was found that rates of duplication and deletion are high, with only a small fraction of duplications retained and apparently selected . This leads to a steady accumulation of paralogs, which seems to be of a similar magnitude in most of the genomes . Furthermore, it is found that genes of high expression level, as measured by their codon bias, are strongly underrepresented among the most recent duplications . Based on these and other observations, it is suggested that gene innovation is driven by amplification of weak, ancillary functions rather than strong, established functions.

Asian Pac J Cancer Prev, 2000, 1(4), 311 - 317
Chemopreventive Activity of Porphyrin Derivatives Against 6-Sulfooxymethylbenzo{a}pyrene Mutagenicity; Cho YS et al.; Porphyrins exhibit potent antimutagenic activity in the range of assays in vitro and in vivo . The antimutagenic activities of porphyrin derivatives including phthalocyanines (Pcs) were investigated using 6-sulfooxymethylbenzo{a}pyrene (SMBP) and its proximate metabolite 6-hydroxymethylbenzo{a}pyrene (HMBP) in the Ames assay and hypoxanthine:guanine phosphoribosyl transferase (hprt) point mutation assay in V79 cells . Pcs, irrespective of coordinated metal, showed highly antimutagenic activity against both HMBP and SMBP in the Ames assay . However, their inhibitory effects against HMBP were in general less dramatic than against SMBP . Treatment with chlorophyllin (CHL) and protoporphyrin reduced the mutation frequency to 24.8% and 19.1% of that with SMBP, and 56.5% and 40.7% of that with HMBP, respectively . Hemin, biliverdin and chlorophylls had a lower antimutagenic activity compared with other porphyrin derivatives although they still retained inhibitory capacity against SMBP . The results of the Ames test for SMBP were extended to the mammalian system to confirm the antimutagenicity of porphyrin derivatives . The antimutagenic strength of porphyrin derivatives was in order of hemin, Pcs, CHL and protoporphyrin . Biliverdin, chlorophyll a and chlorophyll b had a little effect against HMBP and SMBP . Among the compounds tested here, hemin had a strong inhibitory effect against SMBP-induced mutation in V79 cells while Pcs were most effective in the microbial system . It is assumed that these discrepancies are partly due to differences in membrane permeability to the chemicals, their metabolisms and chromosomal organization . Furthermore, carcinogen-DNA binding in calf thymus DNA and plasmid was carried out with a series of porphyrin derivatives to understand their protective mechanism . Most of the porphyrin derivatives exhibited inhibitory activity against SMBP with a variety of degrees . A significant reduction of SMBP-mediated DNA damage by Pcs was confirmed on agarose electrophoresis . There was little correlation between the levels of SMBP-DNA adducts and their modulation in mutation frequencies, indicating that porphyrin compounds somehow affect the antioxidant function and the reactivity of SMBP to cellular components.

Cell Tissue Res, 2003 May, 312(2), 249 - 63 Epub 2003 Apr 25.
The mode of action of acute and chronic concentrations of waterborne Cd in the digestive gland of the acclimated infested freshwater crab ( Potamonautes warreni); Schuwerack PM et al.; Cadmium (Cd) uptake, transport and accumulation were investigated in the digestive gland of the freshwater crab, Potamonautes warreni, acclimated in its natural habitat to stresses, such as microbial gill infestations, Cd(2+) and NH(4)(+), and subsequently exposed to increasing concentrations of Cd in the laboratory for up to 21 days . Cd exposure (0.2 mg l(-1)) for 7-14 days led to Cd permeating cell membranes in a particulate form; it was adsorbed intracellularly to endocytotic circulating amoebocytes, lipid droplets and Golgi vesicles in R-cells . Cd also caused dissociation of the fibrillar rough endoplasmic reticulum (RER) and an increase in phagocytotic activity in F- and B-cells . After 21 days, Cd accumulated as crystal deposits on the basal membranes of cells in the haemolymph space and along the microvilli of cells lining the tubular lumen . Elevated Cd concentrations were found in the cytosol, amoebocytes, Golgi vesicles and P/Ca granules in R-cells . Chronic exposure to higher concentrations of Cd (0.5 and 1.0 mg l(-1)) increased crystal deposition, whereas concentrations of Cd, copper and iron decreased in the cell membranes and in amoebocytes and increased in Golgi vesicles . Reduced lipid content, swollen nuclei with vesiculated nucleoli and enhanced activity of RER in R-cells were also noted . Cd was stored in the P/Ca and Ca granules of B-cells . Acute exposure to Cd (2.0 mg l(-1) for 48 h) caused metal granule accumulation along cells lining the tubular lumen and cellular dissociation, with acidosis and necrosis in the cytoplasm and Cd deposits in mitochondria . Cd accumulated in the cells of the digestive gland in a time-, concentration- and cell-type-specific fashion.

Dement Geriatr Cogn Disord, 2003, 16(1), 35 - 8
T cell response to amyloid-beta and to mitochondrial antigens in Alzheimer's disease; Giubilei F et al.; Despite the vast amount of literature on non-specific immune mechanisms in Alzheimer's disease (AD), little is known about the role of antigen-specific immune responses . We investigated T cell reactivity to fragment 1-42 of amyloid-beta (Abeta) and to N-terminal peptides of human mitochondrial and control microbial proteins . Thirty subjects with a diagnosis of probable AD according to NINCDS-ADRDA criteria and 30 sex- and age-matched healthy controls were enrolled . T cell responses to Abeta fragment showed no significant differences between AD patients and controls . By contrast, the mean number of positive T cell responses to both human mitochondrial and microbial peptides was significantly decreased in AD patients compared to control subjects . No significant correlation was found between T cell responses and both the severity of cognitive impairment and duration of the disease . Our results suggest that antigen-specific immune responses are impaired in AD . Protective immune responses to harmful amyloidogenic substances may also be impaired, thus favoring their accumulation in the brain .

J Biol Chem, 2003 Jul 4, 278(27), 24491 - 9 Epub 2003 Apr 24.
The molecular basis for the pH-activation mechanism in the channel-forming bacterial colicin E1; Musse AA et al.; The in vitro activity of the channel-forming bacteriocins such as colicin E1 in model membranes requires the specific activation of the protein by an acidic environment in the presence of a membrane potential . Acid activation of the C-terminal domain results in the formation of an insertion-competent intermediate with an enhanced ability to penetrate and perforate cell membranes . We report novel findings of this activation process through the design and study of mutant proteins involving the replacement of conserved Asp residues Asp-408, Asp-410, and Asp-423 within helices 5a and 4 in the colicin E1 channel domain that resulted in enhanced membrane binding, bilayer insertion rates, and ion channel activities at near neutral pH values . This activation process involves the destabilization of a critical salt bridge (Asp-410 and Lys-406) and H-bonds (Asp-408 and Ser-405 main chain; Asp-423 and Lys-420 main chain) . The helix-to-coil transition of this motif was identified previously by time-resolved Trp fluorescence measurements (Merrill, A . R., Steer, B . A., Prentice, G . A., Weller, M . J., and Szabo, A . G . (1997) Biochemistry 36, 6874-6884), and here we use this approach to demonstrate that disruption of the helical structure of helices 4 and 5a results in a shift in this equilibrium to favor the coil state . Finally, we show that the essential components of the pH trigger motif are conserved among the channel-forming colicins and that it likely exists within other bacterial proteins and may even have evolved into more sophisticated devices in a number of microbial species.

J Leukoc Biol, 2003 May, 73(5), 639 - 49
Migration of human blood dendritic cells across endothelial cell monolayers: adhesion molecules and chemokines involved in subset-specific transmigration; de la Rosa G et al.; Distinct subsets of dendritic cells (DCs) are present in blood, probably "en route" to different tissues . We have investigated the chemokines and adhesion molecules involved in the migration of myeloid (CD11c(+)) and plasmacytoid (CD123(+)) human peripheral blood DCs across vascular endothelium . Among blood DCs, the CD11c(+) subset vigorously migrated across endothelium in the absence of any chemotactic stimuli, whereas spontaneous migration of CD123(+) DCs was limited . In bare cell migration assays, myeloid DCs responded with great potency to several inflammatory and homeostatic chemokines, whereas plasmacytoid DCs responded poorly to all chemokines tested . In contrast, the presence of endothelium greatly favored transmigration of plasmacytoid DCs in response to CXCL12 (stromal cell-derived factor-1) and CCL5 (regulated on activation, normal T expressed and secreted) . Myeloid DCs exhibited a very potent transendothelial migration in response to CXCL12, CCL5, and CCL2 (monocyte chemoattractant protein-1) . Furthermore, we explored whether blood DCs acutely switch their pattern of migration to the lymph node-derived chemokine CCL21 (secondary lymphoid-tissue chemokine) in response to microbial stimuli {viral double-stranded (ds)RNA or bacterial CpG-DNA} . A synthetic dsRNA rapidly enhanced the response of CD11c(+) DCs to CCL21, whereas a longer stimulation with CpG-DNA was needed to trigger CD123(+) DCs responsive to CCL21 . Use of blocking monoclonal antibodies to adhesion molecules revealed that both DC subsets used platelet endothelial cell adhesion molecule-1 to move across activated endothelium . CD123(+) DCs required beta(2) and beta(1) integrins to transmigrate, whereas CD11c(+) DCs may use integrin-independent mechanisms to migrate across activated endothelium.

J Leukoc Biol, 2003 May, 73(5), 591 - 9
Diminished production of anti-inflammatory mediators during neutrophil apoptosis and macrophage phagocytosis in chronic granulomatous disease (CGD); Brown JR et al.; Genetic defects in the phagocyte nicotinamide adenine dinucleotide phosphate (NADPH)-oxidase enzyme system result in chronic granulomatous disease (CGD) . In addition to recurrent, life-threatening infections, patients with CGD frequently present with sterile inflammatory complications, suggesting that NADPH-oxidase deficiency predisposes to these responses in the absence of persistent microbial infection . The mechanisms involved in the aberrant, inflammatory process are unknown . In this study, we have shown that neutrophils isolated from CGD patients, which are more resistant to spontaneous apoptosis in vitro, also produce significantly less of the anti-inflammatory mediator cyclopentenone prostaglandin D(2) (PGD(2)) . In addition, during phagocytosis of opsonized and nonopsonized apoptotic targets, CGD macrophages are severely compromised in their ability to produce PGD(2) and transforming growth factor-beta (TGF-beta) . We suggest that delayed apoptosis of inflammatory cells, such as neutrophils and deficient production of the anti-inflammatory mediators PGD(2) and TGF-beta during macrophage clearance of apoptotic debris and invading pathogens, contributes to persistence of inflammation in CGD.

Curr Opin Chem Biol, 2003 Apr, 7(2), 273 - 8
Recent efforts in engineering microbial cells to produce new chemical compounds; de Boer AL et al.; In the process of evolution, variation and combination of basic building blocks has led to an astonishing wealth of secondary metabolites . Recently, the same evolutionary tools have been used to create novel compounds that have not been found in nature.

Environ Pollut, 2003, 124(2), 331 - 9
Influence of arsenic co-contamination on DDT breakdown and microbial activity; Van Zwieten L et al.; The impacts of arsenic co-contamination on the natural breakdown of 1,1,l1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) in soil are investigated in a study of 12 former cattle dip sites located in northeastern NSW, Australia . This study examines the relationship between the intrinsic breakdown of DDT to 1,1 -dichloro-2,2-bis(4-chlorophenyl)ethane (DDD) and 1,l-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE), and the impacts of arsenic co-contamination on this breakdown . Between-site analysis demonstrated that arsenic at 2000 mg/kg gave a 50% reduction in the concentration of DDD compared to background arsenic of 5 mg/kg.Within-site analysis also showed the ratio of DDT:DDD increased in soils as arsenic concentrations increased . This within-site trend was also apparent with the DDT:DDE ratio, suggesting inhibition of DDT breakdown by arsenic co-contamination . Microbial activity was inhibited as residues of total DDTs and arsenic increased . Hence arsenic co-contamination and high concentrations of DDT in soil may result in an increased persistence of DDT in the environment studied.

Environ Microbiol, 2003 May, 5(5), 370 - 82
The bacterial ecology of a plague-like disease affecting the Caribbean coral Montastrea annularis; Pantos O et al.; The bacterial communities associated with the Caribbean coral Montastrea annularis showing tissue lesions indicative of a White Plague (WP)-like disease were investigated . Two molecular screening techniques using bacterial 16S rDNA genes were used and demonstrated distinct differences between the bacterial communities of diseased and non-diseased coral tissues, and also in relation to the proximity of tissue lesions on diseased corals . Differences between non-diseased corals and the apparently healthy tissues remote from the tissue lesion in affected corals indicates a 'whole coral' response to a relatively small area of infection with a perturbation in the normal microbial flora occurring prior to the onset of visible signs of disease . These whole organism changes in the microbial flora may serve as a bioindicator of environmental stress and disease . There were striking similarities between the 16S rDNA sequence composition associated with the WP-like disease studied here and that previously reported in association with black band disease (BBD) in coral . Similarities included the presence of a potential pathogen, an alpha-proteobacterium identified as the causal agent of juvenile oyster disease (JOD) . The WP-like disease studied here is apparently different to WP Type ii because the bacterial species previously identified as the causal agent of WP Type ii was not detected, although the symptoms of the two diseases are similar.

Rozhl Chir, 2003 Feb, 82(2), 67 - 71
{Preemptive antimycotic therapy in critically ill patients}; Havlicek K et al.; This article presents the results of the first year of the grant study that deal with preemptive treatment of yeast infection in surgical ICU . This research included patients with a large number of risk factors (ten and more) . These risk factors indicated in the chart . 147 patients reached a score of ten and more points . This number was divided in two groups . In the first group there were 87 patients who received treatment of itraconazol by prescribed scheme . They were hospitalized in ICU for 11.6 days, on average . The first group did not display any positive hemoculture and also other microbial culture from intravenous cannula . No patients fell from ill candida sepsis . Itraconazol was not administered to the 60 patients, who were hospitalizated 11.8 days, on average . Positive hemoculture or yeast sepsis with connection invasive yeast infection was proven in six cases (10%) . No patient died in direct connection with yeast infection in either groups . The presented results show a reduction in the number of developing yeast infections and mainly yeast sepsis in patients undergoing preemptive treatment with itraconazol.

Zh Mikrobiol Epidemiol Immunobiol, 2000 Jul-Aug, (4 Suppl), 65 - 71
{Role of active forms of oxygen generated by phagocytes in the pathogenesis of diseases}; Riabichenko EV et al.; The review deals with the analysis of the properties of active forms of oxygen (AFO), generated by phagocytic cells, and their role in the development of a number of human diseases . Bacterial and viral infections contribute to the activation of the oxidizing metabolism of phagocytes . In the process of this metabolism the formation of toxic oxygen and nitrogen metabolites occurs . The defect of the system of activation calls prolonged microbial persistence whose most severe manifestation is chronic granulomatosis . On the contrary, the uncontrolled production of oxidants cause tissue lesions . The role of AFO in the pathogenesis of cardiovascular diseases, peptic ulcer, the syndrome of respiratory insufficiency and bronchial asthma is discussed.

Naturwissenschaften, 2003 Apr, 90(4), 173 - 9 Epub 2003 Apr 01.
A novel sex-specific and inducible monoterpene synthase activity associated with a pine bark beetle, the pine engraver, Ips pini; Martin D et al.; Ecological interactions of conifers and coniferophagous bark beetles are determined in part by terpenoids (isoprenoids), which are major defense metabolites of conifer oleoresin . Curiously, similar compounds are important aggregation pheromones of conifer-attacking bark beetles . Terpene synthases are responsible for generating the enormous variety of terpenoid carbon skeletons found in nature . These catalysts convert short-chain prenyl diphosphates to a diverse assortment of hemiterpene, monoterpene, sesquiterpene, and diterpene natural products . While terpene synthases have frequently been characterized from plant and microbial sources, they have not yet been described in animals . Here we report the discovery of a monoterpene synthase activity in an insect, the pine engraver, Ips pini (Say) (Coleoptera: Scolytidae) . Cell-free assays of I . pini revealed that geranyl diphosphate (GDP) is converted to the acyclic monoterpene myrcene in whole-body extracts from males, but not females . Furthermore, the monoterpene synthase activity in males can be induced by prior treatment with juvenile hormone III (JH III) or by feeding on phloem from the host trees, Jeffrey pine (Pinus jeffreyi Grev . & Balf.) or red pine (Pinus resinosa Ait.) . The sex-specificity and endocrine induction of this activity argue for its involvement in the biosynthesis of monoterpenoid pheromones mediated by enzymes from insect tissue . This discovery is the first example of a monoterpene synthase in the Metazoa and evokes exciting new questions about the origin, evolution, and occurrence of terpene synthases.

Intensive Care Med, 2003 Jun, 29(6), 923 - 8 Epub 2003 Apr 24.
Calcitonin gene related peptide and N-procalcitonin modulate CD11b upregulation in lipopolysaccharide activated monocytes and neutrophils; Monneret G et al.; OBJECTIVE: Circulating levels of calcitonin gene related peptide (CGRP) and calcitonin precursors, including procalcitonin (PCT) and its free aminopeptide N-procalcitonin (N-PCT), have been found dramatically increased in septic patients . PCT is known to attenuate the chemotaxis of monocytes in response to chemoattractants . This study examined whether CGRP and N-PCT modulate the LPS-induced expression of CD11b, which is one of the major integrins involved in monocyte and neutrophil chemotaxis during a response to microbial infections . DESIGN AND SETTING: In vitro cell culture study in the immunology laboratory of a university hospital . PARTICIPANTS: Healthy volunteers . MEASUREMENTS AND RESULTS: We assessed the effects of N-PCT and CGRP on CD11b expression on monocytes and neutrophils after LPS (2 ng/ml) or fMLP (10(-8) M) challenges . We used a human whole blood model, and measurements were made by flow cytometry . Both peptides in a dose-dependent manner decreased the LPS- and fMLP-induced rise in CD11b in monocytes and neutrophils . As these peptides are thought to act by raising cAMP, we also mimicked their effects with the use of rolipram and forskolin and found similar results . CONCLUSIONS: These findings are in line with recent studies demonstrating anti-inflammatory properties for this family of peptides . CGRP and calcitonin precursors may function as factors suppressing the propagation of inflammation through the inhibition of several processes involved during a response to a bacterial stimulus.

Sci Total Environ, 2003 May 20, 307(1-3), 167 - 78
The roles of natural organic matter in chemical and microbial reduction of ferric iron; Chen J et al.; Although natural organic matter (NOM) is known to be redox reactive, the roles and effectiveness of specific functional groups of NOM in metal reduction are still a subject of intense investigation . This study entails the investigation of the Fe(III) reduction kinetics and capacity by three fractionated NOM subcomponents in the presence or absence of the dissimilatory metal reducing bacterium Shewanella putrefaciens CN32 . Results indicate that NOM was able to reduce Fe(III) abiotically; the reduction was pH-dependent and varied greatly with different fractions of NOM . The polyphenolic-rich NOM-PP fraction exhibited the highest reactivity and oxidation capacity at a low pH (<4) as compared with the carbohydrate-rich NOM-CH fraction and a soil humic acid (soil HA) in reducing Fe(III) . However, at a pH>4, soil HA showed a relatively high oxidation capacity, probably resulting from its conformational and solubility changes with an increased solution pH . In the presence of S . putrefaciens CN32, all NOM fractions were found to enhance the microbial reduction of Fe(III) under anaerobic, circumneutral pH conditions . Soil HA was found to be particularly effective in mediating the bioreduction of Fe(III) as compared with the NOM-PP or NOM-CH fractions . NOM-CH was the least effective because it was depleted in both aromatic and polyphenolic organic contents . However, because both soil HA and NOM-PP contain relatively high amounts of aromatic and phenolic compounds, results may indicate that low-molecular-weight polyphenolic organics in NOM-PP were less effective in mediating the bioreduction of Fe(III) at circumneutral pH than the high-molecular-weight polycondensed, conjugated aromatics present in soil HA . These research findings may shed additional light in understanding of the roles and underlying mechanisms of NOM reactions with contaminant metals, radionuclides, and other toxic chemicals in the natural environment.

J Virol Methods, 2003 May, 109(2), 171 - 6
Determination of hepatitis C virus genotype by Pyrosequencing; Elahi E et al.; A simple sequencing-based assay is described for genotyping of hepatitis C virus (HCV) . RT-PCR was employed to amplify a 237-nucleotide-long fragment from the 5' untranslated region (UTR) of the genome using one biotinylated and one normal primer . Subsequent to capture of the PCR products on streptavidin-coated beads, single-stranded DNA separation, and hybridization of sequencing primer, Pyrosequencing was performed . The genotype of 98 samples out of which 77 samples were from American veterans and 21 samples were from Iran was determined . The samples from the American veterans contained six different subtypes, while five subtypes were found in Iranian samples . For rapid population-specific HCV subtyping, a multiplex assay was developed . This study demonstrates the suitability of this technology for low-cost, high throughput and accurate microbial genotyping.

J Matern Fetal Neonatal Med, 2003 Jan, 13(1), 32 - 8
Differences in the fetal interleukin-6 response to microbial invasion of the amniotic cavity between term and preterm gestation; Yoon BH et al.; BACKGROUND/OBJECTIVE: Fetal inflammatory response has been implicated as a mechanism of multi-system organ injury in preterm and term neonates . Microbial invasion of the amniotic cavity (MIAC) is frequently associated with a fetal inflammatory response . However, there are no studies comparing the fetal response to MIAC in term and preterm gestations . The purpose of this study was to compare the umbilical cord plasma interleukin-6 (IL-6) concentrations in term and preterm neonates in the presence or absence of MIAC . STUDY DESIGN: Umbilical cord blood was obtained at birth from 252 neonates whose mothers had an amniocentesis within 48 h of delivery (preterm delivery, n = 62; term delivery, n = 190) . MIAC was defined as a positive amniotic fluid culture for bacteria or genital mycoplasmas . IL-6 was measured by a sensitive and specific immunoassay . RESULTS: The median IL-6 concentration in umbilical cord plasma was significantly higher in preterm neonates than in term neonates (median 13.4 pg/ml, range 0.1-676 pg/ml vs . median 3.2 pg/ml, range 0.1-408 pg/ml; p < 0.0001) . In the context of MIAC, the median umbilical cord plasma IL-6 concentration was significantly higher in preterm than in term neonates (median 31.6 pg/ml, range 1.4-676 pg/ml vs . median 11.7 pg/ml, range 1.3-82 pg/ml, respectively; p < 0.05) . Neonates born to mothers with a positive amniotic fluid culture had a significantly higher median IL-6 concentration than neonates born to mothers with a negative amniotic fluid culture (preterm: median 31.6, range 1.4-676 pg/ml vs . median 8.0, range 0.1-656 pg/ml; p < 0.05 and term: median 11.7, range 1.3-82 pg/ml vs . median 3.1, range 0.1-408 pg/ml; p < 0.01, respectively) . CONCLUSIONS: The preterm fetus is capable of mounting a systemic cytokine response as measured by IL-6 in its peripheral blood . In the setting of MIAC, a fetal IL-6 response is higher in preterm than in term gestation.

Int J Periodontics Restorative Dent, 2003 Apr, 23(2), 121 - 7
The clinical relevance of microbiologic testing . Part 2: a comparative analysis of microbiologic samples secured simultaneously from the same sites and cultured in the same laboratory; Salkin LM et al.; A field study using four different private periodontal practices and two independent laboratories was conducted to compare two microbiologic cultures sampled simultaneously from the same sites in 20 individual patients . Both paired samples were submitted separately to one of the two independent laboratories for bacterial identification and antibiotic sensitivity testing . The results from the two samples were quite variable . In only two instances did both specimens reveal the presence of identical bacterial species, but these specimens differed in both threshold levels and antibiotic sensitivity . When only bacteria above threshold levels were compared, total agreement was found in 11 of 20 cases . When examining antibiotic sensitivity, using 100% kill as the ideal, agreement between the two specimens was inconsistent The use or nonuse of tetracycline was in agreement 85% of the time, amoxicillin 75% of the time, metronidazole 70% of the time, and amoxicillin-metronidazole in combination 85% of the time . The two specimens agreed on the empirical use of amoxicillin 45% of the time, tetracycline 60% of the time, and metronidazole 60% of the time . The empirical use of amoxicillin-metronidazole in combination yielded 80% agreement when the results of both specimens were combined . The empirical use of amoxicillin-metronidazole combination therapy may be more clinically sound and cost effective than culturing and antibiotic selection based on the culture from any single microbiologic testing laboratory . This supports the data from a previous study that examined specimens secured simultaneously from the same site and submitted to two different testing laboratories . The failure of microbial testing to achieve a higher level of consistency between samples leaves the clinical efficacy of microbial testing in question.

J Vet Med B Infect Dis Vet Public Health, 2003 Feb, 50(1), 27 - 30
Differences in antibiotic resistance in Escherichia coli, isolated from East-European swine herds with or without prophylactic use of antibiotics; Docic M et al.; The aim of the study was to compare the resistance patterns of Escherichia coli isolates from pig herds with or without prophylactic use of anti-microbial substances . The presented pig units received either antibiotics or oregano as preventive feed additives . The trial was performed from April to October 2001, in the large 'country-corner', Hungary-Rumania-Serbia . Thirty of 39 evaluated herds suffered E . coli O139 K88 ac or ad LT STb caused losses, the remaining were negative for E . coli O139 . Thirteen of the selected 30 herds produced with oregano feed supplementation (Oregpig Pecs, Hungary) antibiotic-free pigs . These units had no history of prophylactic antibiotic use since 1995 . The remaining 17 herds routinely used prophylactic antibiotic feed supplementation . In each herd, pigs of four different age groups (suckling piglets, weaners . fattening swine and breeding sows), showing the clinical symptoms of wasting, were investigated . E . coli O139 K88 ac or ad LT STb were tested for their resistance to antibiotics, available in this region . Oregano-fed herds demonstrated high significantly (P < 0.001) lower MICs (microg/ml) for ampicillin, doxycyclin, enrofloxacin, gentamycin, oxytetracyclin and sulfamethacin compared to herds with prophylactic use of antibiotics . Resistance to ceftiofur revealed significant (P < 0.05) differences between the antibiotic- or oregano-treated units . The present results confirm literature data, that prophylactic use of antibiotics likely plays a role in inducing resistance of E . coli and other intestinal bacteria . Thus, imposing greater restrictions on antibiotic use in animal agriculture is likely to reduce but not eliminate the occurrence of resistant isolates.

Pneumonol Alergol Pol, 2002, 70(9-10), 450 - 7
{Evaluation of Bactec MGIT 960 fluorescent method in diagnosis of tuberculosis}; Augustynowicz-Kopec E et al.; We evaluated the fluorescent Bactec MGIT 960 the new system in Poland, which is a fully automated, non-invasive, system for growth and detection of Mycobacterium with a capacity to incubate and continuously monitor 960 of 7-ml culture tubes . This system is equipped with special oxygen-quenching fluorescent sensor, which permits to continuously monitoring of microbial growth . Processed specimens were inoculated into Bactec MGIT 960, Bactec 460 Tb and MB/BacT as well as on to Lowenstein-Jensen slants . The greatest number of isolates of M . tuberculosis complex was recovered by using Bactec MGIT 960 system (49/19.5%) . Other systems detected M . tuberculosis complex as follows: Bactec 460 Tb (47/18.7%), MB/BacT (43/17/1%), L-J (38/15.1%) . Detection mean time of mycobacterial growth in smear-positive specimens were 15.4 days for Bactec MGIT 960, 16.2 days for Bactec 460 Tb, 15.1 days for MB/BacT and 28.2 days for L-J medium The rates of contamination for each of the system were: 3.8% for Bactec MGIT 960 and Bactec 460 Tb, 3.6% for MB/BacT and 2.9% for L-J . In conclusion Bactec MGIT 960 system is a valuable alternative of radiometric, semi automated Bactec 460 Tb system.

Immunology, 2003 May, 109(1), 102 - 8
A differential requirement for phosphoinositide 3-kinase reveals two pathways for inducible upregulation of major histocompatibility complex class II molecules and CD86 expression by murine B lymphocytes; Marshall-Clarke S et al.; Constitutive expression of major histocompatibility complex class II molecules (MHC II) is restricted to dendritic cells, cells of the macrophage lineage and B lymphocytes . In all three lineages, peptide fragments of captured antigen are loaded into newly synthesized MHC II molecules . In B-lineage cells, MHC II synthesis is dramatically increased on encounter with antigen, by T-cell-derived signals and by microbial products . We have previously shown that immature B cells fail to hyperexpress MHC II after antigen receptor {B-cell receptor (BCR)} ligation, but are responsive to other stimuli . Expression of the costimulatory molecule, CD86, was similarly regulated . This suggested the existence of two pathways regulating expression of these important molecules . Here we present data supporting this hypothesis . We show that activity of the enzyme phosphatidylinositol 3-kinase is critical for MHC II hyperexpression and induction of CD86 in response to ligation of the BCR or CD38, but not for responses to other stimuli including interleukin-4, lipopolysaccharide and CD40 ligation.

J Environ Qual, 2003 Mar-Apr, 32(2), 702 - 10
Nutrient and hydrology effects on soil respiration in a northern Everglades marsh; DeBusk WF et al.; Microbial respiration in peat and overlying plant litter, as influenced by water level and phosphorus enrichment, was evaluated for an Everglades (Florida, USA) marsh ecosystem by measuring CO2 and CH4 release from soil-water microcosms . Intact cores of peat, overlying plant litter, and surface water were collected at seven locations in cattail (Typha domingensis Pers.) and sawgrass (Cladium jamaicense Crantz) stands along a phosphorus (P) enrichment gradient in Water Conservation Area 2A (WCA-2A) . Each soil-water microcosm was outfitted with a controlled air circulation system whereby outflow gas from the headspace could be analyzed for CO2 and CH4 to determine flux of C from the soil-water column to the atmosphere . Gaseous C flux was determined for flooded conditions (10-cm water depth) and for water levels of 0, 5, 10, and 15 cm below the peat surface . Overall, decreasing water level resulted in significantly increased C flux, although rates were significantly higher under flooded conditions than under nonflooded, saturated-soil conditions, presumably due to O2 availability associated with algal photosynthesis within the litter layer in the water column . Carbon flux decreased significantly for sites increasingly distant from the primary hydrologic and nutrient inflows to WCA-2A . The microcosm study demonstrated that the C turnover rate was significantly increased by accelerated nutrient loading to the marsh, and was further enhanced by decreasing water level under drained conditions . Our results also demonstrated that photosynthesis within the water column is a potentially important regulator of C mineralization rate in the litter layer of the marsh system.

J Environ Qual, 2003 Mar-Apr, 32(2), 441 - 6
Characterization of selenate removal from drainage water using rice straw; Zhang Y et al.; Removal of selenium (Se) from agricultural drainage water is very important for protecting wildlife in wetland systems . We conducted a series of experiments on selenite {Se(IV)} adsorption and selenate {Se(VI)} reduction to determine Se removal from drainage water amended with 1000 microg/L of Se(VI) or Se(IV) and 5 g of rice (Oryza sativa L.) straw . Under sterile conditions, the added Se(IV) was not adsorbed to the rice straw within 2 d of the experiment and the added Se(VI) was not reduced within 14 d . In contrast, added Se(VI) in a nonsterile rice-straw solution was reduced rapidly, from 930 microg/L at Day 3 to 20 microg/L at Day 5, with an increase in unprecipitated elemental Se {Se(0)} and total Se(0) . In the last several days of the experiments, unprecipitated Se(0) was the major Se form in the rice-straw solution, with a small amount of organic Se(-II) . This study showed that Se removal from drainage water in the presence of rice straw involves a two-step process . The first is the microbial reduction of Se(VI) to Se(IV) and then to colloidal Se(0) . The second is flocculation and precipitation of colloidal Se(0) to the bottom of the experimental flasks and the surface of rice straw.

Huan Jing Ke Xue, 2003 Jan, 24(1), 157 - 60
{Composting technology of municipal solid waste with inoculation agent}; Xi B et al.; This paper introduced composting technology of municipal solid wastes (MSW) with inoculation agent, used complex microbial community, ordure of horse, composting, soil of garden and sewage sludge as inoculation agent, the temperature, oxygen consumption rate, organic matters degradation rate and outlet H2S gas were detected and analyzed in composting process . The experimental results indicated that adding inoculation agent to municipal solid wastes were proper for enhancing the composting temperature, oxygen consumption rate and controlling well H2S gas . Especially, when adding complex microbial community or ordure of horse as inoculation were effective to compose organic matter and speed up composting into humus . Therefore, adding inoculation agent to MSW greatly influence the rate of organic degradation and was useful to improve composting conditions.

Huan Jing Ke Xue, 2003 Jan, 24(1), 46 - 51
{Change of organic carbon pools and the responses to soil warming during laboratory incubations under different temperatures of 3 kinds of paddy soils in Tai Lake Region, China}; Zhou Y et al.; Change of soil organic carbon (SOC) storage under global warming scenarios was paid much attention of the soil and global change studies . To address the features of SOC loss of paddy soils in response to global warming, the authors used 3 representative paddy soils from the Tai Lake region, China to incubate at laboratory respectively under 20 degrees C and 25 degrees C and the change dynamics of total organic carbon(TOC), soluble organic carbon (DOC) and microbial biomass carbon (MBC) were monitored in time intervals . The TOC dynamics could be described with primary reaction equations with the constants varied with soil types and incubation temperature . While soil warming strengthened TOC loss of a Fe-leached Stagnic Anthrosol and a Gleyic Stagnic Anthrosol, no significant difference of TOC was detected in a Fe-accumulic Stagnic Anthosol under different temperature incubations . Q10 quotient, a measurement of soil SOC sensitivity to warming, of the studied soils decreased in the order: 11.1-14.1 for the Gleyic Stagnic Anthrosol < 4.4-4.6 for Fe-leached Stagnic Anthrosol < 0.63-0.73 for the Fe-accumulic Stagnic Anthosol . This indicated that paddy soils could be a group of human managed soils with sensitive response to global warming, whereas the inter-soil group difference in this sensitivity may be greater than that existing between the soils from different eco-zones . The different patterns of DOC and MBC change during the incubation of the 3 studied soils were indicative of different features of soil microbial community of the studied 3 types of paddy soils, which influenced the carbon bio-availability under different temperatures . Thus, change of SOC pools due to soil warming can be accounted for not only by nature of SOC of the soils but changes of microbial activity and even the community associated with soil properties . This study evidences that SOC loss due to soil warming is not a temperature-controlled kinetically decomposition process at least . Further studies should be dedicated on the SOC loss in relation to the interactions between SOC-soil minerals-soil micro-biota.

J Immunol, 2003 May 1, 170(9), 4717 - 23
CpG oligodeoxynucleotides protect normal and SIV-infected macaques from Leishmania infection; Verthelyi D et al.; Oligodeoxynucleotides containing CpG motifs (CpG ODNs) mimic microbial DNA and activate effectors of the innate immune response, which limits the spread of pathogens and promotes an adaptive immune response . CpG ODNs have been shown to protect mice from infection with intracellular pathogens . Unfortunately, CpG motifs that optimally stimulate humans are only weakly active in mice, mandating the use of nonhuman primates to monitor the activity and safety of "human" CpG ODNs in vivo . This study demonstrates that CpG ODN treatment of rhesus macaques significantly reduces the severity of the lesions caused by a challenge with Leishmania: Leishmania superinfection is common in immunocompromised hosts, particularly those infected with HIV . This study shows that PBMCs from HIV-infected subjects respond to stimulation with CpG ODNs . To determine whether CpG ODNs can protect retrovirus-infected primates, SIV-infected macaques were treated with CpG ODNs and then challenged with Leishmania: Both lesion size and parasite load were significantly reduced in the CpG-treated animals . These findings support the clinical development of CpG ODNs as immunoprotective agents in normal and HIV-infected patients.

Biosens Bioelectron, 2003 May, 18(5-6), 841 - 6
Market analysis of biosensors for food safety; Alocilja EC et al.; This paper is presented as an overview of the pathogen detection industry . The review includes pathogen detection markets and their prospects for the future . Potential markets include the medical, military, food, and environmental industries . Those industries combined have a market size of $563 million for pathogen detecting biosensors and are expected to grow at a compounded annual growth rate of 4.5% . The food market is further segmented into different food product industries . The overall food-pathogen testing market is expected to grow to $192 million and 34 million tests by 2005 . The trend in pathogen testing emphasizes the need to commercialize biosensors for the food safety industry as legislation creates new standards for microbial monitoring . With quicker detection time and reusable features, biosensors will be important to those interested in real time diagnostics of disease causing pathogens . As the world becomes more concerned with safe food and water supply, the demand for rapid detecting biosensors will only increase.

Biosens Bioelectron, 2003 May, 18(5-6), 667 - 74
Combined physico-chemical and biological sensing in environmental monitoring; Bhatia R et al.; Single-use conductivity and microbial sensors were used to investigate the effect of both species (chloride, nitrate, and sulphate) and concentration/osmolarity of anions on the metabolic activity of Escherichia coli . A new disposable, single-use conductivity sensor is described which is compatible with the CellSense mediated amperometric biosensor system . The effect of changing salinity and nitrate concentration on the response of E . coli to 3,5-dichlorophenol and mercuric chloride was determined . The implications for toxicity assessment of a hybrid sensing system, allowing the simultaneous monitoring of physico-chemical and biological data, are discussed.

Biosens Bioelectron, 2003 May, 18(5-6), 541 - 6
High-density, microsphere-based fiber optic DNA microarrays; Epstein JR et al.; A high-density fiber optic DNA microarray has been developed consisting of oligonucleotide-functionalized, 3.1-microm-diameter microspheres randomly distributed on the etched face of an imaging fiber bundle . The fiber bundles are comprised of 6000-50000 fused optical fibers and each fiber terminates with an etched well . The microwell array is capable of housing complementary-sized microspheres, each containing thousands of copies of a unique oligonucleotide probe sequence . The array fabrication process results in random microsphere placement . Determining the position of microspheres in the random array requires an optical encoding scheme . This array platform provides many advantages over other array formats . The microsphere-stock suspension concentration added to the etched fiber can be controlled to provide inherent sensor redundancy . Examining identical microspheres has a beneficial effect on the signal-to-noise ratio . As other sequences of interest are discovered, new microsphere sensing elements can be added to existing microsphere pools and new arrays can be fabricated incorporating the new sequences without altering the existing detection capabilities . These microarrays contain the smallest feature sizes (3 microm) of any DNA array, allowing interrogation of extremely small sample volumes . Reducing the feature size results in higher local target molecule concentrations, creating rapid and highly sensitive assays . The microsphere array platform is also flexible in its applications; research has included DNA-protein interaction profiles, microbial strain differentiation, and non-labeled target interrogation with molecular beacons . Fiber optic microsphere-based DNA microarrays have a simple fabrication protocol enabling their expansion into other applications, such as single cell-based assays.

Environ Int, 2003 Jul, 29(4), 437 - 50
Soil erosion and the global carbon budget; Lal R; Soil erosion is the most widespread form of soil degradation . Land area globally affected by erosion is 1094 million ha (Mha) by water erosion, of which 751 Mha is severely affected, and 549 Mha by wind erosion, of which 296 Mha is severely affected . Whereas the effects of erosion on productivity and non-point source pollution are widely recognized, those on the C dynamics and attendant emission of greenhouse gases (GHGs) are not . Despite its global significance, erosion-induced carbon (C) emission into the atmosphere remains misunderstood and an unquantified component of the global carbon budget . Soil erosion is a four-stage process involving detachment, breakdown, transport/redistribution and deposition of sediments . The soil organic carbon (SOC) pool is influenced during all four stages . Being a selective process, erosion preferentially removes the light organic fraction of a low density of <1.8 Mg/m(3) . A combination of mineralization and C export by erosion causes a severe depletion of the SOC pool on eroded compared with uneroded or slightly eroded soils . In addition, the SOC redistributed over the landscape or deposited in depressional sites may be prone to mineralization because of breakdown of aggregates leading to exposure of hitherto encapsulated C to microbial processes among other reasons . Depending on the delivery ratio or the fraction of the sediment delivered to the river system, gross erosion by water may be 75 billion Mg, of which 15-20 billion Mg are transported by the rivers into the aquatic ecosystems and eventually into the ocean . The amount of total C displaced by erosion on the earth, assuming a delivery ratio of 10% and SOC content of 2-3%, may be 4.0-6.0 Pg/year . With 20% emission due to mineralization of the displaced C, erosion-induced emission may be 0.8-1.2 Pg C/year on the earth . Thus, soil erosion has a strong impact on the global C cycle and this component must be considered while assessing the global C budget . Adoption of conservation-effective measures may reduce the risks of C emission and sequester C in soil and biota.

Cell, 2003 Apr 18, 113(2), 171 - 82
Origins of highly mosaic mycobacteriophage genomes; Pedulla ML et al.; Bacteriophages are the most abundant organisms in the biosphere and play major roles in the ecological balance of microbial life . The genomic sequences of ten newly isolated mycobacteriophages suggest that the bacteriophage population as a whole is amazingly diverse and may represent the largest unexplored reservoir of sequence information in the biosphere . Genomic comparison of these mycobacteriophages contributes to our understanding of the mechanisms of viral evolution and provides compelling evidence for the role of illegitimate recombination in horizontal genetic exchange . The promiscuity of these recombination events results in the inclusion of many unexpected genes including those implicated in mycobacterial latency, the cellular and immune responses to mycobacterial infections, and autoimmune diseases such as human lupus . While the role of phages as vehicles of toxin genes is well established, these observations suggest a much broader involvement of phages in bacterial virulence and the host response to bacterial infections.

Immunity, 2003 Apr, 18(4), 499 - 511
Feedback regulation of pathogen-specific T cell priming; Wong P et al.; MHC class I-restricted antigen presentation is an essential step in the priming of CD8 T lymphocytes during immune responses to infection . While microbial growth and clearance have been accurately measured in mammalian hosts, the duration of functional antigen presentation during infection remains undefined in vivo . Herein we characterize the activation of naive and memory T cells at different times during bacterial infection . Surprisingly, the host's ability to prime T cells is of much shorter duration than bacterial infection, inversely correlating with the development of pathogen-specific cytolytic T lymphocytes . Our studies demonstrate a feedback mechanism that limits the duration of effective in vivo antigen presentation, thereby modulating T cell responses by temporally restricting recruitment of naive T cells into the immune response.

Implant Dent, 2003, 12(1), 41 - 6
Management of the implant periapical lesion: a case report; Oh TJ et al.; The implant periapical lesion (IPL), a possible cause for implant failure, may occur from the presence of pre-existing microbial pathology such as endodontic/periodontal lesions . This case report presents a case history related to IPL, which was caused by a pre-existing endodontic lesion . In addition, other possible causes such as surgical trauma and the management strategies of IPL are suggested . For the treatment of the infected form of IPL, a sequential surgical therapy can be utilized . This includes surgical removal of the implant or implant apical region, thorough debridement of the infected lesion, systemic antibiotics, and/or guided bone regeneration . The implant therapy should be directed to minimize the occurrence or consequences of IPL by careful diagnosis, systematic treatment planning, and appropriate treatment procedures.

Microb Ecol, 2003 May, 45(4), 340 - 52 Epub 2003 Apr 28.
The pinyon rhizosphere, plant stress, and herbivory affect the abundance of microbial decomposers in soils; Kuske CR et al.; In terrestrial ecosystems, changes in environmental conditions that affect plant performance cause a cascade of effects through many trophic levels . In a 2-year field study, seasonal abundance measurements were conducted for fast-growing bacterial heterotrophs, humate-degrading actinomycetes, fungal heterotrophs, and fluorescent pseudomonads that represent the decomposers in soil . Links between plant health and soil microbiota abundance in pinyon rhizospheres were documented across two soil types: a dry, nutrient-poor volcanic cinder field and a sandy-loam soil . On the stressful cinder fields, we identified relationships between soil decomposer abundance, pinyon age, and stress due to insect herbivory . Across seasonal variation, consistent differences in microbial decomposer abundance were identified between the cinders and sandy-loam soil . Abundance of bacterial heterotrophs and humate-degrading actinomycetes was affected by both soil nutritional status and the pinyon rhizosphere . In contrast, abundance of the fungal heterotrophs and fluorescent pseudomonads was affected primarily by the pinyon rhizosphere . On the cinder field, the three bacterial groups were more abundant on 150-year-old trees than on 60-year-old trees, whereas fungal heterotrophs were unaffected by tree age . Fungal heterotrophs and actinomycetes were more abundant on insect-resistant trees than on susceptible trees, but the opposite was true for the fluorescent pseudomonads . Although all four groups were present in all the environments, the four microbial groups were affected differently by the pinyon rhizosphere, by tree age, and by tree stress caused by the cinder soil and insect herbivory.

Microb Ecol, 2003 May, 45(4), 411 - 8 Epub 2003 Apr 22.
Detritus processing and microbial dynamics of an aquatic macrophyte and terrestrial leaf in a thermally constant, spring-fed stream; Schlickeisen E et al.; Past studies of organic matter processing in stream ecosystems have focused on the fate of allochthonous terrestrial leaf detritus . In streams with a reduced canopy, submerged macrophytes may provide a significant source of organic matter to the microbial community and higher trophic levels . We compared mass loss patterns and microbial dynamics between a submerged macrophyte, Sagittaria platyphylla, and a deciduous leaf, Populus deltoides . Mass loss rates were higher for the submerged macrophyte, though exponential decay values indicated that both are "fast" decomposers . Bacterial abundance was not significantly different between plant types, but bacterial productivity was significantly higher in Sagittaria . Although fungal biomass was higher overall for Populus, it was not significantly different from that of Sagittaria until day 30 . Relative to fungi, bacteria made up 4% and 7% of the peak microbial biomass on Populus and Sagittaria, respectively . Aquatic hyphomycete sporulation was detected only on Populus . These results suggest that in systems where submerged macrophytes are abundant, they can provide a carbon source quantitatively comparable to that of riparian leaf detritus, but that qualitative differences in leaf structural composition cause a shift toward a more significant role for bacterial decomposers.

J Allergy Clin Immunol, 2003 Apr, 111(4), 813 - 7
Association between polymorphisms in caspase recruitment domain containing protein 15 and allergy in two German populations; Kabesch M et al.; BACKGROUND: Early exposure to microbial matter such as LPS may influence the development of asthma and allergies by activation of innate immunity pathways as indicated by studies in farming environments . Recently, polymorphisms in caspase recruitment domain containing protein 15 (CARD15), an intracellular LPS receptor protein, have been associated with Crohn's disease . Because these polymorphisms lead to changes in LPS recognition, they may affect the development of asthma and allergies . OBJECTIVE: We genotyped a large population of German schoolchildren (N = 1872) from East and West Germany for 3 functional relevant CARD15 polymorphisms for their role in the development of asthma and allergy . METHODS: By use of parental questionnaires, skin prick testing, pulmonary function tests, bronchial challenge tests, and measurements of serum IgE levels, children were phenotyped for the presence of atopic diseases . Genotyping was performed with PCR-based restriction enzyme assays . To assess associations between atopic phenotypes and genotypes standard statistical procedures were applied . RESULTS: Children with the polymorphic allele C2722 had a more than 3-fold risk to develop allergic rhinitis (P <.001) and an almost 2-fold risk for atopic dermatitis (P <.05) . Furthermore, the T2104 allele was associated with an almost 2-fold risk for allergic rhinitis (P <.05) . When a C insertion at position 3020 was present, the risk of atopy increased by 50% (P <.05) and serum IgE levels were elevated (P <.01) . CONCLUSION: The shared genetic background between Crohn's disease and atopy may indicate that an impaired recognition of microbial exposures results in an insufficient downregulation of excessive immune responses, giving rise to either T(H)2 dominated allergies or T(H)1 related Crohn's disease.

Infect Immun, 2003 May, 71(5), 2525 - 33
Identification of a Treponema pallidum laminin-binding protein; Cameron CE; Host extracellular matrix (ECM) components represent ideal microbial adhesion targets that many pathogens use for colonization of tissues and initiation of infection . This study investigated the interaction of the spirochete Treponema pallidum with the ECM component laminin . To identify candidate laminin-binding adhesins, the T . pallidum genome was analyzed to predict open reading frames that encode putative outer membrane proteins, as these proteins interact directly with host ECM components . Subsequent recombinant expression of these proteins and analysis of their laminin-binding potential identified one protein, Tp0751, that demonstrated specific attachment to laminin . Tp0751 attached to laminin in a dose-dependent, saturable manner but did not attach to the ECM component collagen type I or IV or to the negative control proteins fetuin or bovine serum albumin . Sodium metaperiodate treatment of laminin reduced the Tp0751-laminin interaction in a concentration-dependent manner, suggesting that oligosaccharides play a role in this interaction . In addition, Tp0751-specific antibodies were detected in serum samples collected from both experimental and natural syphilis infections, indicating that Tp0751 is expressed in vivo during the course of infection . Collectively, these experiments identified Tp0751 as a laminin-binding protein that is expressed during infection and may be involved in attachment of T . pallidum to host tissues.

Biotechniques, 2003 Apr, 34(4), 790 - 4, 796, 798 passim
Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity; Crosby LD et al.; Molecular tools based on rRNA (rrn) genes are valuable techniques for the study of microbial communities . However, the presence of operon copy number heterogeneity represents a source of systematic error in community analysis . To understand the types and magnitude of such bias, four commonly used rrn-based techniques were used to perform an in silico analysis of a hypothetical community comprised organisms from the Comprehensive Microbial Resource database . Community profiles were generated, and diversity indices were calculated for length heterogeneity PCR, automated ribosomal integenic spacer analysis, denaturing gradient gel electrophoresis, and terminal RFLP (using RsaI, MspI, and HhaI) . The results demonstrate that all techniques present a quantitative bias toward organisms with higher copy numbers . In addition, techniques may underestimate diversity by grouping similar ribotypes or overestimate diversity by allowing multiple signals for one organism . The results of this study suggest that caution should be used when interpreting rrn-based community analysis techniques.

Arterioscler Thromb Vasc Biol, 2003 Jun 1, 23(6), 1060 - 5 Epub 2003 Apr 17.
Cross-reactive B-cell epitopes of microbial and human heat shock protein 60/65 in atherosclerosis; Perschinka H et al.; OBJECTIVE: Growing evidence suggests that immune reactions to heat shock protein 60 (HSP60) are involved in atherogenesis . Because of the high phylogenetic conservation between microbial and human HSP60, bacterial infections might be responsible for breaking the tolerance to self-HSP60, which is expressed on the surface of stressed arterial endothelial cells . METHODS AND RESULTS: We purified serum antibodies to Escherichia coli HSP60 (GroEL), the 60-kD chlamydial HSP, and HSP65 of Mycobacterium tuberculosis by affinity chromatography from clinically healthy subjects with sonographically proven carotid atherosclerosis . Reactivity of the purified antibodies with overlapping human HSP60 peptides was measured, and 8 shared common epitopes, recognized by all anti-bacterial HSP60/65 antibodies, were identified . Antisera specific for these cross-reactive epitopes were produced by immunizing rabbits with peptides derived from human HSP60 . By immunohistochemistry, the epitopes were found to be present in the arterial wall of young subjects during the earliest stages of the disease . CONCLUSIONS: Antibodies to microbial HSP60/65 recognize specific epitopes on human HSP60 . These cross-reactive epitopes were shown to serve as autoimmune targets in incipient atherosclerosis and might provide further insights into the mechanisms of early atherogenesis.

FEMS Yeast Res, 2002 Jan, 1(4), 291 - 8
Endogenous prolyl 4-hydroxylation in Hansenula polymorpha and its use for the production of hydroxylated recombinant gelatin; de Bruin EC et al.; Several yeast systems have recently been developed for the recombinant production of gelatin and collagen . Amino acid sequence-specific prolyl 4-hydroxylation is essential for the gel-forming capacity of gelatin and for the proper folding of (pro)collagen . This post-translational modification is generally considered to be absent in microbial eukaryotic systems and therefore co-expression of heterologous (human or animal) prolyl 4-hydroxylase would be required . However, we found that the well-known protein expression host Hansenula polymorpha unexpectedly does have the endogenous capacity for prolyl 4-hydroxylation . Without co-expression of a heterologous prolyl 4-hydroxylase, both an endogenous collagen-like protein and a heterologously expressed collagen fragment were found to be sequence-specifically hydroxylated.

Water Sci Technol, 2003, 47(5), 181 - 8
Image analysis, methanogenic activity measurements, and molecular biological techniques to monitor granular sludge from an EGSB reactor fed with oleic acid; Pereira MA et al.; Morphological changes in anaerobic granular sludge fed with increasing loads of oleic acid were quantified by image analysis . The combination of this technique with data on the accumulation of adsorbed long chain fatty acid and with the molecular characterization of microbial community gave insight into the mechanisms of sludge disintegration, flotation and washout . It was found that the bacterial domain was more affected than the archaeal domain during this process . However, no acetoclastic activity and onlya residual hydrogenotrophic activity were detected in the sludge at the end of the operation.

J Immunol, 2003 Apr 15, 170(8), 4102 - 10
A subset of Toll-like receptor ligands induces cross-presentation by bone marrow-derived dendritic cells; Datta SK et al.; Dendritic cells (DCs) are capable of cross-presenting exogenous Ag to CD8(+) CTLs . Detection of microbial products by Toll-like receptors (TLRs) leads to activation of DCs and subsequent orchestration of an adaptive immune response . We hypothesized that microbial TLR ligands could activate DCs to cross-present Ag to CTLs . Using DCs and CTLs in an in vitro cross-presentation system, we show that a subset of microbial TLR ligands, namely ligands of TLR3 (poly(inosinic-cytidylic) acid) and TLR9 (immunostimulatory CpG DNA), induces cross-presentation . In contrast to presentation of Ag to CD4(+) T cells by immature DCs, TLR-induced cross-presentation is mediated by mature DCs, is independent of endosomal acidification, and relies on cytosolic Ag processing machinery.

Biol Bull, 2003 Apr, 204(2), 192 - 5
Viral influence on aquatic bacterial communities; Fuhrman JA et al.; Bacterial viruses, or bacteriophages, have numerous roles in marine systems . Although they are now considered important agents of mortality of bacteria, a second possible role of regulating bacterial community composition is less well known . The effect on community composition derives from the presumed species-specificity and density-dependence of infection . Although models have described the "kill the winner" hypothesis of such control, there are few observational or experimental demonstrations of this effect in complex natural communities . We report here on some experiments that demonstrate that viruses can influence community composition in natural marine communities . Although the effect is subtle over the time frame suitable for field experiments (days), the cumulative effect over months or years would be substantial . Other virus roles, such as in genetic exchange or microbial evolution, have the potential to be extremely important, but we know very little about them.

Biol Bull, 2003 Apr, 204(2), 186 - 91
Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation; Teske A et al.; Genomic markers for anaerobic microbial processes in marine sediments-sulfate reduction, methanogenesis, and anaerobic methane oxidation-reveal the structure of sulfate-reducing, methanogenic, and methane-oxidizing microbial communities (including uncultured members); they allow inferences about the evolution of these ancient microbial pathways; and they open genomic windows into extreme microbial habitats, such as deep subsurface sediments and hydrothermal vents, that are analogs for the early Earth and for extraterrestrial microbiota.

Biol Bull, 2003 Apr, 204(2), 168 - 73
Complexity in natural microbial ecosystems: the Guerrero Negro experience; Spear JR et al.; The goal of this project is to describe and understand the organismal composition, structure, and physiology of microbial ecosystems from hypersaline environments . One collection of such ecosystems occurs at North America's largest saltworks, the Exportadora de Sal, in Guerrero Negro, Baja California Sur . There, seawater flows through a series of evaporative basins with an increase in salinity until saturation is reached and halite crystallization begins . Several of these ponds are lined with thick (10 cm) microbial mats that have received some biological study . To determine the nature and extent of diversity of the microbial organisms that constitute these ecosystems, we are conducting a phylogenetic analysis using molecular approaches, based on cloning and sequencing of small subunit (SSU) rRNA genes (16S for Bacteria and Archaea, 18S for Eukarya) . In addition, we report preliminary results on the microbial composition of a laminated community that occurs in a crystallized gypsum-halite matrix in near-saturated salt water . Exposure of the interior of these large (kilogram) wet, endoevaporite crystals reveals a multitude of colors: layers of yellow, green, pink, and purple microbiota . To date, analyses of these two environments indicate the ubiquitous dominance of uncultured organisms of phylogenetic kinds not generally thought to be associated with hypersaline environments.

Biol Bull, 2003 Apr, 204(2), 160 - 7
Biogeochemistry of hypersaline microbial mats illustrates the dynamics of modern microbial ecosystems and the early evolution of the biosphere; Des Marais DJ; Photosynthetic microbial mats are remarkably complete self-sustaining ecosystems at the millimeter scale, yet they have substantially affected environmental processes on a planetary scale . These mats may be direct descendents of the most ancient biological communities in which even oxygenic photosynthesis might have developed . Photosynthetic mats are excellent natural laboratories to help us to learn how microbial populations associate to control dynamic biogeochemical gradients.

Protein Expr Purif, 2003 Apr, 28(2), 220 - 3
Compaction agent clarification of microbial lysates; DeWalt BW et al.; Recombinant proteins are often purified from microbial lysates containing high concentrations of nucleic acids . Pre-purification steps such as nuclease addition or precipitation with polyethyleneimine or ammonium sulfate are normally required to reduce viscosity and to eliminate competing polyanions before anion exchange chromatography . We report that small polycationic compaction agents such as spermine selectively precipitate nucleic acids during or after Escherichia coli lysis, allowing DNA and RNA to be pelleted with the insoluble cell debris . Analysis by spectrophotometry and protein assay confirmed a significant reduction in the concentration of nucleic acids present, with preservation of protein . Lysate viscosity is greatly reduced, facilitating subsequent processing . We have used 5mM spermine to remove nucleic acids from E . coli lysate in the purification of a hexahistidine-tagged HIV reverse transcriptase.

Int J Biol Markers, 2003 Jan-Mar, 18(1), 57 - 61
Signaling protein networks as targets of new antineoplastic drugs; Alberti S et al.; In-depth analysis of molecular regulatory networks in cancer holds the promise of improved knowledge of the pathophysiology of tumor cells so that it will become possible to design a detailed molecular tumor taxonomy . This knowledge will also offer new opportunities for the identification and validation of key molecular tumor targets to be exploited for novel therapeutic approaches . Some signaling proteins have already been identified as such, e.g . c-Myc, Cyclin D1, Bcl-XL, kinases and some nuclear receptors . This has led to the successful development of a few function-modulatory drugs (Glivec, SERM, Iressa), providing proof-of-principle of the validity of this approach . Further developments are likely to derive from "-omic" approaches, aimed at the understanding of signaling networks and of the mechanism of action of newfound lead molecules . High-throughput screening of small drug-like molecules from combinatorial chemical libraries or from microbial extracts will identify novel, "intelligent" drug candidates . An additional medicinal chemistry strategy (via 40-50 unit rosary-bead chains) has the potential to be much more effective than small molecules in interfering with protein-protein interactions . This may lead to considerably higher selectivity and effectiveness compared with historical approaches in drug discovery.

J Am Dent Assoc, 2003 Mar, 134(3), 325 - 30; quiz 339
Surface contamination in the dental operatory: a comparison over two decades; Williams HN et al.; BACKGROUND: This study compares surface bacterial contamination levels in a large teaching clinic in 1998 with that of a 1976 study in the same clinic to determine if renovation and more stringent infection control, or IC, practices have made a difference . METHODS: The authors obtained samples from surfaces in clinic operatories--including the light handle covers, jacket cuffs, sinks and floors--in the morning and afternoon . They compared the bacterial counts from these samples with those from the 1976 study . Data were analyzed using the matched pairs t tests and independent t tests . RESULTS: In both the 1976 and 1998 studies, mean bacterial counts were higher at the end of the day than in the morning; however, the differences were only significant in the 1976 study . Comparisons between the 1998 and 1976 counts revealed significant differences for the floor, headrest, light handle covers and clinic jacket cuffs . CONCLUSIONS: Improvements in clinic design and equipment, as well as IC procedures and practices resulted in a lower level of surface bacterial contamination in 1998 than in 1976 in a large teaching clinic . Clinical Implications . Attention to clinic design and furnishings and adherence to recommended IC practices can reduce microbial surface contamination, thereby reducing the risk of causing cross-infection and making dental practice safer.

J Gastroenterol, 2003 Mar, 38 Suppl 15, 63 - 6
The future of IBD treatment; Podolsky DK; Throughout most of the past 50 years, treatment of Crohn's disease and ulcerative colitis has been dominated by the use of agents whose efficacy was defined on an empiric basis . Many of these, including most especially 5-amino salicylic acid (5-ASA)-based agents and corticosteroids, remain mainstays of current treatment even as research is catching up with clinical experience to define the mechanistic basis of their efficacy . Other agents, also of established utility in at least a subset of patients, were developed on the basis of general inferences about disease pathogenesis . These agents are exemplified by antibiotics (metronidazole) and immunosuppressive agents (azathioprine/6-mercaptopurine, methotrexate, and cyclosporine); attention was directed on the assumption of the general likely importance of microbial species and immunoactivation, respectively . However, the rapid progress, even if still incomplete in understanding of pathophysiological mechanisms that play a role in IBD, has transformed the development of new therapeutic agents, enabling the development of several agents now available or currently in advanced clinical development . It is notable that each of the major overall thrusts in development of new therapeutic strategies parallels, and may be reasonably viewed as the partial outgrowth of, dominant areas of progress in understanding of disease mechanisms relevant to IBD.

Cas Lek Cesk, 2003 Feb, 142(2), 75 - 9
{Molecular diagnosis of infections}; Benedik J et al.; Molecular diagnostics (detection of nucleic acids by molecular genetics techniques) become more valuable in clinical diagnosis of disease . Apart from the already long-time used genetic techniques for detection of congenital anomalies, current use of molecular techniques includes detection of microbial pathogens . The character of these techniques increases the possibility of achieving diagnosis in cases where classical cultivation is not possible, is not reliable or is not fast enough . As with every new approach, molecular diagnostics have faced encountered reactions from the scientific community . Some scientists tend to overestimate the value of molecular diagnostic techniques, while sceptics, sometimes influenced by a biased or incomplete knowledge of the technology, think it is of little value . In this work, on the basis of literature and our own data from more than 5 years of experience with these methods, we have assessed the pros and cons of the use of molecular diagnostics of infectious diseases in the light of their potential use in clinical practice.

Proc Natl Acad Sci U S A, 2003 Apr 29, 100(9), 5336 - 41 Epub 2003 Apr 15.
PD-L1 and PD-L2 are differentially regulated by Th1 and Th2 cells; Loke P et al.; PD-L1 and PD-L2 are ligands for PD-1, a costimulatory molecule that plays an inhibitory role in regulating T cell activation in the periphery . We find that PD-L1 is highly expressed on inflammatory macrophages as compared with resident peritoneal macrophages but can be induced on resident macrophages by classical activation stimuli such as lipopolysaccharide, IFN-gamma, and polyinosinic-polycytidylic acid . Further up-regulation of PD-L1 on inflammatory macrophages can also be induced by subsequent exposure to lipopolysaccharide and IFN-gamma . In contrast, PD-L2 is not expressed on inflammatory macrophages but can be induced by alternative activation via IL-4 . Although PD-L1 is highly inducible on a variety of antigen-presenting cell lines as well as resident macrophages, PD-L2 is most significantly inducible only on inflammatory macrophages . PD-L1 up-regulation depends on TLR4 and STAT1, whereas PD-L2 expression depends on IL-4R alpha and STAT6 . Consistent with these results, T helper 1T helper 2 (Th1/Th2) cells also differentially up-regulate PD-L1 and PD-L2 expression on inflammatory macrophages . Hence, Th1 cells as well as microbial products can enhance PD-L1 expression on many different macrophage populations, whereas Th2 cells instruct only inflammatory macrophages to up-regulate PD-L2 . These results suggest that PD-L1 and PD-L2 might have different functions in regulating type 1 and type 2 responses.

Water Res, 2003 Apr, 37(8), 1818 - 30
Nitrate removal in zero-valent iron packed columns; Westerhoff P et al.; Nitrate removal by laboratory and field continuous-flow zero-valent iron (Fe(0)) packed bed columns was evaluated for different influent water qualities (pH, dissolved oxygen (DO), nitrate concentration) and several months of operation (600-1500 bed volumes (BVs)) . In contrast to previous batch experiments with Fe(0) where nitrate was stoichiometrically converted to ammonium, only 70% of the applied nitrogen was recovered as nitrate, ammonium, or nitrite (<0.1mg/L) during shorter-term column tests (2-20 BVs) and less than 25% of the applied nitrogen was recovered during longer-term field testing (500-1000 BVs) at elevated nitrate levels (approximately 25mg N/L) . Nitrate removal was accompanied by a pH increase, DO decrease, and soluble iron increase . During longer-term operation (500-1500 BVs) iron and calcium precipitates were observed, by SEM and EDX analyses, to form in the packed columns . Precipitation led to cementation and reduction in permeability for the Fe(0)/sand media in the packed column . Different abiotic and microbial-mediated mechanisms may be involved during shorter- and longer-term operation of Fe(0) systems and the role of iron precipitates should be further evaluated.

J Endotoxin Res, 2002, 8(6), 477 - 81
Modulating macrophage function with IgG immune complexes; Anderson CF et al.; Macrophages respond to bacterial products by releasing a large array of inflammatory mediators . We demonstrate that, in the presence of IgG immune complexes, macrophages produce high levels of IL-10 and virtually no IL-12, when they are exposed to bacterial products . The production of IL-10 by these cells can dampen innate inflammatory responses to microbial products, such as LPS . This alteration in macrophage cytokine production can also influence an adaptive immune response, preferentially inducing Th2-type immunity . Thus, immune complexes change the physiology of activated macrophages, converting them to anti-inflammatory cells that induce Th2-like immune responses . We have termed these cells type II activated macrophages.

J Appl Microbiol, 2003, 94(5), 816 - 25
Study of temperature-growth interactions of entomopathogenic fungi with potential for control of Varroa destructor (Acari: Mesostigmata) using a nonlinear model of poikilotherm development; Davidson G et al.; AIMS: To investigate the thermal biology of entomopathogenic fungi being examined as potential microbial control agents of Varroa destructor, an ectoparasite of the European honey bee Apis mellifera . METHODS AND RESULTS: Colony extension rates were measured at three temperatures (20, 30 and 35 degrees C) for 41 isolates of entomopathogenic fungi . All of the isolates grew at 20 and 30 degrees C but only 11 isolates grew at 35 degrees C . Twenty-two isolates were then selected on the basis of appreciable growth at 30-35 degrees C (the temperature range found within honey bee colonies) and/or infectivity to V . destructor, and their colony extension rates were measured at 10 temperatures (12.5-35 degrees C) . This data were then fitted to Schoolfield et al . {J Theor Biol (1981)88:719-731} re-formulation of the Sharpe and DeMichele {J Theor Biol (1977)64:649-670} model of poikilotherm development . Overall, this model accounted for 87.6-93.9% of the data variance . Eleven isolates exhibited growth above 35 degrees C . The optimum temperatures for extension rate ranged from 22.9 to 31.2 degrees C . Only three isolates exhibited temperature optima above 30 degrees C . The super-optimum temperatures (temperature above the optimum at which the colony extension rate was 10% of the maximum rate) ranged from 31.9 to 43.2 degrees C . CONCLUSIONS: The thermal requirements of the isolates examined against V . destructor are well matched to the temperatures in the broodless areas of honey bee colonies, and a proportion of isolates, should also be able to function within drone brood areas . SIGNIFICANCE AND IMPACT OF THE STUDY: Potential exists for the control of V . destructor with entomopathogenic fungi in honey bee colonies . The methods employed in this study could be utilized in the selection of isolates for microbial control prior to screening for infectivity and could help in predicting the activity of a fungal control agent of V . destructor under fluctuating temperature conditions.

Nat Med, 2003 May, 9(5), 525 - 32 Epub 2003 Apr 14.
Activation and regulation of Toll-like receptors 2 and 1 in human leprosy; Krutzik SR et al.; The expression and activation of Toll-like receptors (TLRs) was investigated in leprosy, a spectral disease in which clinical manifestations correlate with the type of immune response mounted toward Mycobacterium leprae . TLR2-TLR1 heterodimers mediated cell activation by killed M . leprae, indicating the presence of triacylated lipoproteins . A genome-wide scan of M . leprae detected 31 putative lipoproteins . Synthetic lipopeptides representing the 19-kD and 33-kD lipoproteins activated both monocytes and dendritic cells . Activation was enhanced by type-1 cytokines and inhibited by type-2 cytokines . In addition, interferon (IFN)-gamma and granulocyte-macrophage colony-stimulating factor (GM-CSF) enhanced TLR1 expression in monocytes and dendritic cells, respectively, whereas IL-4 downregulated TLR2 expression . TLR2 and TLR1 were more strongly expressed in lesions from the localized tuberculoid form (T-lep) as compared with the disseminated lepromatous form (L-lep) of the disease . These data provide evidence that regulated expression and activation of TLRs at the site of disease contribute to the host defense against microbial pathogens.

Water Res, 2003 May, 37(9), 2242 - 7
Biodegradable fraction of organic carbon estimated under oxic and anoxic conditions; Tusseau-Vuillemin MH et al.; The biodegradability of water samples is usually estimated with bioassays under oxic conditions . In order to overcome some of the drawbacks linked to the incubation of the samples in aerobic batches, a new protocol is proposed and tested, which is based on an organic carbon (OC) balance after a 45 days incubation under anoxic conditions with excess nitrate . The biodegradable fractions of organic matter obtained with the anoxic protocol are slightly lower than those obtained under oxic conditions . Several possible reasons for a systematic underestimation of the biodegradable organic matter under anoxic conditions are evaluated and discussed: a reduced microbial metabolic potential, significantly reduced degradation rates for the slowly biodegradable organic matter, an additional production of refractory organic compounds during the incubation, or the inhibition of the recycling of the organic matter stored in bacterial biomass . Nevertheless, the 7% difference observed on the biodegradable total OC estimations keeps low enough so that the anoxic protocol can be proposed as a convenient alternative to the oxic one.

J Mol Biol, 2003 Apr 25, 328(2), 335 - 63
Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases; Yadav G et al.; Modular polyketide synthases (PKSs) are large multi-enzymatic, multi-domain megasynthases, which are involved in the biosynthesis of a class of pharmaceutically important natural products, namely polyketides . These enzymes harbor a set of repetitive active sites termed modules and the domains present in each module dictate the chemical moiety that would add to a growing polyketide chain . This modular logic of biosynthesis has been exploited with reasonable success to produce several novel compounds by genetic manipulation . However, for harnessing their vast potential of combinatorial biosynthesis, it is essential to develop knowledge based in silico approaches for correlating the sequence and domain organization of PKSs to their polyketide products . In this work, we have carried out extensive sequence analysis of experimentally characterized PKS clusters to develop an automated computational protocol for unambiguous identification of various PKS domains in a polypeptide sequence . A structure based approach has been used to identify the putative active site residues of acyltransferase (AT) domains, which control the specificities for various starter and extender units during polyketide biosynthesis . On the basis of the analysis of the active site residues and molecular modelling of substrates in the active site of representative AT domains, we have identified a crucial residue that is likely to play a major role in discriminating between malonate and methylmalonate during selection of extender groups by this domain . Structural modelling has also explained the experimentally observed chiral preference of AT domain in substrate selection . This computational protocol has been used to predict the domain organization and substrate specificity for PKS clusters from various microbial genomes . The results of our analysis as well as the computational tools for prediction of domain organization and substrate specificity have been organized in the form of a searchable computerized database (PKSDB) . PKSDB would serve as a valuable tool for identification of polyketide products biosynthesized by uncharacterized PKS clusters . This database can also provide guidelines for rational design of experiments to engineer novel polyketides .

Clin Microbiol Infect, 2003 Jan, 9(1), 15 - 32
Microbial natural products as a source of antifungals; Vicente MF et al.; The vast number and variety of chemotherapeutic agents isolated from microbial natural products and used to treat bacterial infections have greatly contributed to the improvement of human health during the past century . However, only a limited number of antifungal agents (polyenes and azoles, plus the recently introduced caspofungin acetate) are currently available for the treatment of life-threatening fungal infections . Furthermore, the prevalence of systemic fungal infections has increased significantly during the past decade . For this reason, the development of new antifungal agents, preferably with novel mechanisms of action, is an urgent medical need . A selection of antifungal agents in early stages of development, produced by micro-organisms, is summarized in this review . The compounds are classified according to their mechanisms of action, covering inhibitors of the synthesis of cell wall components (glucan, chitin and mannoproteins), of sphingolipid synthesis (serine palmitoyltransferase, ceramide synthase, inositol phosphoceramide synthase and fatty acid elongation) and of protein synthesis (sordarins) . In addition, some considerations related to the chemotaxonomy of the producing organisms and some issues relevant to antifungal drug discovery are also discussed.

J Microbiol Methods, 2003 Jun, 53(3), 423 - 5
Sulfoacetaldehyde bisulfite adduct is a substrate for enzymes presumed to act on sulfoacetaldehyde; Gritzer RF et al.; Sulfoacetaldehyde, an intermediate of interest to those studying microbial metabolism of sulfonates, is commonly synthesized as the bisulfite adduct . A published method presumed to convert this to the free aldehyde (and cited several times elsewhere in the literature) has been shown to be ineffective; this had not been realized by its users because the enzymes under study recognize the adduct as a substrate.

J Microbiol Methods, 2003 Jun, 53(3), 365 - 75
The edaphic quantitative protargol stain: a sampling protocol for assessing soil ciliate abundance and diversity; Acosta-Mercado D et al.; It has been suggested that species loss from microbial groups low in diversity that occupy trophic positions close to the base of the detrital food web could be critical for terrestrial ecosystem functioning . Among the protozoans within the soil microbial loop, ciliates are presumably the least abundant and of low diversity . However, the lack of a standardized method to quantitatively enumerate and identify them has hampered our knowledge about the magnitude of their active and potential diversity, and about the interactions in which they are involved . Thus, the Edaphic Quantitative Protargol Staining (EQPS) method is provided to simultaneously account for ciliate species richness and abundance in a quantitative and qualitative way . This direct method allows this rapid and simultaneous assessment by merging the Non-flooded Petri Dish (NFPD) method {Prog . Protistol . 2 (1987) 69} and the Quantitative Protargol Stain (QPS) method {Montagnes, D.J.S., Lynn, D.H., 1993 . A quantitative protargol stain (QPS) for ciliates and other protists . In: Kemp, P.F., Sherr, B.F., Sherr, E.B., Cole, J.J . (Eds.), Handbook of Methods in Aquatic Microbial Ecology . Lewis Publishers, Boca Raton, FL, pp . 229-240} . The abovementioned protocols were refined by experiments examining the spatial distribution of ciliates under natural field conditions, sampling intensity, the effect of storage, and the use of cytological preparations versus live observations . The EQPS could be useful in ecological studies since it provides both a "snapshot" of the active and effective diversity and a robust estimate of the potential diversity.

Water Res, 2003 Feb, 37(3), 551 - 60
Anaerobic microbial and photochemical degradation of 4,4'-dibromodiphenyl ether; Rayne S et al.; The anaerobic microbial and photochemical degradation pathways of 4,4'-dibromodiphenyl ether (BDE15) were examined . BDE15 was reductively debrominated within a fixed-film plug-flow biological reactor at hydraulic retention times of 3.4 and 6.8 h, leading to exclusive production of 4-bromodiphenyl ether (BDE3) and diphenyl ether (DE) . A suite of potential BDE15 metabolites arising from reductive debromination, hydroxylation, and methoxylation of the aromatic C-Br and C-H bonds were not observed . Following initial debromination of BDE15, degradation of BDE3 to DE readily occurs, suggesting the rate-limiting step for anaerobic BDE15 degradation is conversion of BDE15 to BDE3 . The photochemical degradation of BDE15 was also examined in organic (CH3CN and CH3OH) and aqueous (H2O:CH3CN; 1:1 v/v) solvent systems at 300 nm . Only photochemically induced reductive debromination was found to occur via homolytic C-Br bond cleavage, with no evidence of C-O bond cleavage or products arising from heterolytic bond cleavage.

Water Res, 2003 Feb, 37(3), 533 - 8
Effects of stream acidification on fungal biomass in decaying beech leaves and leaf palatability; Dangles O et al.; We examined the effect of surface water acidification on rates of decomposition, ergosterol concentrations (as a measure of fungal biomass), and palatability to shredders of common beech leaves (Fagus sylvatica L.) in five mountain streams (pH 4.7-7.1) . Leaf decomposition was significantly faster in the circumneutral streams (pH 6.4-7.1; k > or = 0.00175 d(-1)), when compared to acidic streams (pH 4.7-4.9; k < or = 0.00100 d(-1)) . Fungal biomass showed no particular trend along the acidification gradient except that it peaked earlier in the stream closest to neutrality . Leaf palatability, measured as the feeding activity of the leaf-shredding amphipod Gammarus fossarum Koch, varied with the exposure time in the streams . Except for the higher palatability of leaves exposed during 6 weeks at the highest pH, patterns among streams were mostly similar . These results suggest that reduced processing rates in the most acidic streams were not related to differences in fungal biomass associated with decomposing leaves and that microbial conditioning was only slightly delayed by acidification . Possible effects of low pH and related variables (Ca, Al) on microbial decomposition and detritivorous macroinvertebrates are discussed to clarify the inhibition of beech leaf decomposition in the studied systems.

Pediatr Allergy Immunol, 2002, 13 Suppl 15, 19 - 22
Fetal immune responsiveness and routes of allergic sensitization; Jones CA et al.; There is much interest in the role of early-life events in the subsequent development of atopy and/or atopic disease . Despite the ongoing debate about the intrauterine exposure of the fetus to environmental allergens and the establishment of T-cell memory, it is clear that the immunological response of the neonate at risk of atopy is more immature than that of the neonate likely to be non-atopic . The reasons for this remain unknown, but might reflect maternally transmitted signals that adapt the neonatal immune response . An inadvertent consequence of this might be an inappropriate host response to environmental signals such as those from microbial products during early post-natal life that result in an inability to dampen neonatal T helper 2-skewed responses . The developing gastrointestinal tract and theexogenous factors that impact on this, such as microbial flora and breast milk, should therefore be a focus of investigation.

Chemosphere, 2003 Feb, 50(6), 855 - 61
Changes in soil microbial biomass and Zn extractability over time following zn addition to a paddy soil; Jiang XJ et al.; A laboratory incubation study was conducted using a paddy soil spiked with two quantities of Zn as soluble Zn(NO3)2 and unamended controls . Three single extractants (1 M ammonium acetate (pH 7.0), 0.43 M acetic acid and 0.05 M EDTA) were used to assess the bioavailability of Zn . Biological community assessments were made microbial biomass (chloroform fumigation), soil basal respiration and dehydrogenase activity . During the 84-day period of the experiment, addition of Zn at both 500 and 1,000 mg kg(-1) had little detectable effect on soil pH . The concentration of NH4OAc-extractable Zn decreased rapidly within the initial six weeks . The concentration of HOAc-extractable Zn showed no decrease during 84 days incubation . EDTA-extractable Zn was greater than NH4OAc- and HOAc-extractable fractions, and showed a similar trend to NH4OAc-extractable after incubation . Microbial biomass, soil basal respiration and dehydrogenase activity all decreased over time during 84 days incubation . Addition of Zn resulted in a significant increase in specific respiration (qCO2) . Microbial biomass and dehydrogenase activity did not appear to be influenced by added Zn, probably due to the strong buffering capacity of the soil . The Zn extracted by EDTA, HOAc and NH4OAc showed close relationships with each other (p < 0.001) . Zinc extracted by 0.05 M EDTA and NH4OAc were highly correlated with soil basal respiration and specific respiration rate (p < 0.01) . The results suggest that NH4OAc-extractable Zn combined with soil specific respiration could be used as parameters for risk assessment.

Curr Opin Pulm Med, 2003 May, 9(3), 199 - 209
Septic shock, multiple organ failure, and acute respiratory distress syndrome; Sharma S et al.; In 1914, Schottmueller wrote "Septicemia is a state of microbial invasion from a portal of entry into the blood stream which causes signs of illness." In the last few decades, the evidence that sepsis results from an exaggerated systemic inflammatory host response induced by infecting organisms is compelling; inflammatory mediators are the key players in the pathogenesis of septic shock and multiorgan failure . Sepsis and its sequelae represent a continuum of clinical syndrome encompassing systemic inflammation, coagulopathy, and hemodynamic abnormalities . Severe sepsis and septic shock continue to be the major causes of morbidity and mortality in the United States; sepsis deaths currently match mortality from myocardial infarction . Despite significant advances in our understanding of the pathophysiology and technological innovations in the supportive management, mortality from septic shock remains excessive . After many disappointments with strategies to manipulate the inflammatory response, modulation of coagulation cascade to decrease sepsis mortality has become a clinical reality . This review will highlight and discuss recent advances in the pathophysiology and management of sepsis.

J Clin Microbiol, 2003 Apr, 41(4), 1447 - 53
Evaluation of the MicroSeq system for identification of mycobacteria by 16S ribosomal DNA sequencing and its integration into a routine clinical mycobacteriology laboratory; Hall L et al.; An evaluation of the MicroSeq 500 microbial identification system by nucleic acid sequencing and the Mayo Clinic experience with its integration into a routine clinical laboratory setting are described . Evaluation of the MicroSeq 500 microbial identification system was accomplished with 59 American Type Culture Collection (ATCC) strains and 328 clinical isolates of mycobacteria identified by conventional and 16S ribosomal DNA sequencing by using the MicroSeq 500 microbial identification system . Nucleic acid sequencing identified 58 of 59 (98.3%) ATCC strains to the species level or to the correct group or complex level . The identification results for 219 of 243 clinical isolates (90.1%) with a distance score of <1% were concordant with the identifications made by phenotypic methods . The remaining 85 isolates had distance scores of >1%; 35 (41.1%) were identified to the appropriate species level or group or complex level; 13 (15.3%) were identified to the species level . All 85 isolates were determined to be mycobacterial species, either novel species or species that exhibited significant genotypic divergence from an organism in the database with the closest match . Integration of nucleic acid sequencing into the routine mycobacteriology laboratory and use of the MicroSeq 500 microbial identification system and Mayo Clinic databases containing additional genotypes of common species and added species significantly reduced the number of organisms that could not be identified by phenotypic methods . The turnaround time was shortened to 24 h, and results were reported much earlier . A limited number of species could not be differentiated from one another by 16S ribosomal DNA sequencing; however, the method provides for the identification of unusual species and more accurate identifications and offers the promise of being the most accurate method available.

FEBS Lett, 2003 Apr 10, 540(1-3), 15 - 20
Cytotoxic ribonucleases: molecular weapons and their targets; Makarov AA et al.; Many ribonucleases (RNases) are highly cytotoxic . In some cases, they attack selectively malignant cells, triggering apoptotic response, and therefore are considered as alternative chemotherapeutic drugs . Factors that determine the cytotoxicity of RNases, primarily of those of microbial origin, are reviewed here . These factors include catalytic activity, ability to escape natural inhibitors, stability, and efficiency of internalization . The latter is, in turn, determined by positive charge on the molecule and interaction with cell membrane . Cellular targets and molecular determinants of RNases decisive for their cytotoxic action are characterized .

J Heart Lung Transplant, 2003 Apr, 22(4), 492 - 7
Successful management of disseminated Nocardia transvalensis infection in a heart transplant recipient after development of sulfonamide resistance: case report and review; Lopez FA et al.; Nocardia transvalensis is a rarely reported cause of clinically significant disease, and, to our knowledge, has not been reported previously as a cause of infection in the cardiac transplant population . We report a case of N transvalensis new taxon-2 pulmonary infection that disseminated to the brain and skin in a cardiac transplant recipient despite adequate sulfonamide serum levels . Subsequent isolates were resistant to sulfonamides, and molecular ribotyping of the primary and subsequent isolates confirmed that these were the same N transvalensis new taxon-2 strain . The taxonomic and diagnostic considerations, as well as the clinical significance of anti-microbial-resistant nocardia, are reviewed and discussed herein.

Clin Exp Allergy, 2003 Apr, 33(4), 501 - 6
The economic burden of antibiotic treatment of penicillin-allergic patients in internal medicine wards of a general tertiary care hospital; Sade K et al.; BACKGROUND: Penicillin allergy poses a major problem in the management of infectious diseases . OBJECTIVE: We estimated the costs and usage of antibiotic treatment of 'penicillin-allergic' patients in comparison to non-allergic patients in a tertiary care hospital . MATERIALS AND METHODS: The study was based on the records of 118 randomly chosen in-hospital patients labelled as being 'allergic to penicillin' and who were treated with antibiotics . The antibiotic selection and cost of the patients with alleged penicillin allergy were compared to 118 matched patients without an antibiotic allergy (controls) . RESULTS: During in-hospital treatment, the mean antibiotic cost for penicillin-allergic patients was 63% higher than the cost for the controls . In addition, there was a 38% higher cost of the recommended anti-microbial treatment regimen to be followed upon discharge by the former compared to the latter . CONCLUSIONS: Penicillin-allergic patients were more likely to receive broader spectrum antibiotics compared to the non-allergic ones . Since many of the patients who are labelled as being 'allergic to penicillin' are, in fact, not allergic to it, inaccurate reporting of penicillin allergies may have costly economic and epidemiologic repercussions in addition to more toxic effects which can occur when choosing alternative drugs in case of penicillin allergy.

Clin Exp Allergy, 2003 Apr, 33(4), 427 - 34
Which factors explain the lower prevalence of atopy amongst farmers' children?
Remes ST, Iivanainen K, Koskela H, Pekkanen J.
BACKGROUND: The inverse association between farming and atopy in children has been attributed to microbial exposure, especially through livestock . Very little is known about other potential explanatory factors . OBJECTIVE: To explore potential differences in lifestyle and environmental factors between farmer and non-farmer families, and whether these factors could explain the association between farming and childhood atopy . METHODS: A cross-sectional study, including 366 farmers' and 344 non-farmers' children in eastern Finland . Information regarding exposure and background characteristics was gathered by a written questionnaire . Atopy was defined as having one or more positive skin prick test reactions (> 3 mm) against the six common aeroallergens . RESULTS: Regardless of the current farming type, atopy was less frequent among the farmers' children than the non-farmers' children (aOR 0.56, 95% CI 0.40-0.78) . Remarkable differences were seen in many lifestyle factors (including diet) between the farmer and non-farmer families, but only a few of the explored factors were associated with atopy . The frequency of current livestock contacts seemed to have an inverse, dose-dependent association with atopy (aOR 0.46, 95% CI 0.22-0.97 for daily vs . no contact) . Having lived on a dairy farm in infancy (aOR 0.51, 95% CI 0.28-0.93), or having had cats or dogs in infancy (aOR 0.60, 95% CI 0.42-0.85), decreased the risk of atopy at school age . The inverse association between farming and atopy was not explained by the sociodemographic factors, or by differences in conventional risk factors of atopy . Animal contacts explained partially, but not completely, the association . CONCLUSION: Higher frequency of animal contacts is one factor, but probably not the only one, explaining the inverse association of farming and atopy in children . The importance of early life exposures may have recently been over-emphasized, and current exposures discounted, when studying the risk factors of childhood atopy.

Environ Sci Technol, 2003 Mar 15, 37(6), 1159 - 62
Microbial sulfate reduction at low pH in sediments of an acidic lake in Argentina; Koschorreck M et al.; We measured sulfate reduction in the acidic (pH < or = 3) sediment of an Argentinean lake influenced by volcanism . Sulfate reduction rates of 2.04 mmol m(-2) d(-1) were determined with a 35SO4(2-) core injection method and confirmed by batch incubations and from H2S measurements in the sediment . H2S production stopped when iron reduction was stimulated by addition of ferric iron . The results suggest that sulfate reduction at pH values around 3 is possible and can probably be used in biotechnological strategies if competing microbial processes are inhibited and electron donors are highly available.

Environ Sci Technol, 2003 Mar 15, 37(6), 1100 - 7
Changes in enantiomeric fractions during microbial reductive dechlorination of PCB132, PCB149, and araclor 1254 in Lake Hartwell sediment microcosms; Pakdeesusuk U et al.; The enantioselectivity of microbial reductive dechlorination of chiral PCBs in sediments from Lake Hartwell, SC, was determined by microcosm studies and enantiomer-specific GC analysis . Sediments from two locations in the vicinity of the highest levels of PCB contamination were used as inocula . Dechlorination activity was monitored by concentration decreases in the spiked chiral PCBs and formation of dechlorination products using both achiral and chiral chromatography . Live microcosms spiked with PCB132 (234-236) exhibited dechlorination of PCB132 to PCB91 (236-24) and PCB51 (24-26) . Meta dechlorination was the dominant mechanism . Microcosms spiked with PCB149 (245-236) exhibited preferential para dechlorination of PCB149 to PCB95 (236-25), followed by meta dechlorination to PCB53 (25-26) and subsequently PCB19 (26-2) . Dechlorination of chiral PCB132 and PCB149 was not enantioselective . In Aroclor 1254-spiked microcosms, reductive dechlorination of PCB149 also was nonenantioselective . These results suggest that dechlorinating enzymes responsible for the dehalogenation of the chiral PCB132 and PCB149 congeners bind the two enantiomers equally . Reductive dechlorination of PCB91 and PCB95, however, occurred in an enantioselective manner, indicating that the dechlorinating enzymes for these PCBs are enantiomer-specific . The chlorine substitution pattern on the biphenyl ring appears to influence whether reductive dechlorination of chiral PCB congeners is enantioselective . Enantioselective PCB dechlorination by the microbial population of Lake Hartwell sediments occurs for select chiral PCBs; thus, certain chiral PCBs might be useful as markers for in situ reductive dechlorination.

Environ Sci Technol, 2003 Mar 15, 37(6), 1093 - 9
Sources of sulfate supporting anaerobic metabolism in a contaminated aquifer; Ulrich GA et al.; Field and laboratory techniques were used to identify the biogeochemical factors affecting sulfate reduction in a shallow, unconsolidated alluvial aquifer contaminated with landfill leachate . Depth profiles of 35S-sulfate reduction rates in aquifer sediments were positively correlated with the concentration of dissolved sulfate . Manipulation of the sulfate concentration in samples revealed a Michaelis-Menten-like relationship with an apparent Km and Vmax of approximately 80 and 0.83 microM SO4(-2) x day(-1), respectively . The concentration of sulfate in the core of the leachate plume was well below 20 microM and coincided with very low reduction rates . Thus, the concentration and availability of this anion could limit in situ sulfate-reducing activity . Three sulfate sources were identified, including iron sulfide oxidation, barite dissolution, and advective flux of sulfate . The relative importance of these sources varied with depth in the alluvium . The relatively high concentration of dissolved sulfate at the water table is attributed to the microbial oxidation of iron sulfides in response to fluctuations of the water table . At intermediate depths, barite dissolves in undersaturated pore water containing relatively high concentrations of dissolved barium (approximately 100 microM) and low concentrations of sulfate . Dissolution is consistent with the surface texture of detrital barite grains in contact with leachate . Laboratory incubations of unamended and barite-amended aquifer slurries supported the field observation of increasing concentrations of barium in solution when sulfate reached low levels . At a deeper highly permeable interval just above the confining bottom layer of the aquifer, sulfate reduction rates were markedly higher than rates at intermediate depths . Sulfate is supplied to this deeper zone by advection of uncontaminated groundwater beneath the landfill . The measured rates of sulfate reduction in the aquifer also correlated with the abundance of accumulated iron sulfide in this zone . This suggests that the current and past distributions of sulfate-reducing activity are similar and that the supply of sulfate has been sustained at these sites.

J Chromatogr A, 2002 Aug 23, 967(2), 219 - 34
Flow field-flow fractionation and characterization of ionic and neutral polysaccharides of vegetable and microbial origin; Benincasa MA et al.; The flow field-flow fractionation (FlFFF) analysis of a variety of neutral as well as ionic polysaccharides from plants and micro-organisms shows the generally broad distribution in molecular size of these polymers . This result is also obtained on a commercial sample of pullulan whose size distribution appears much wider than that of any of five standard fractions of the same polymer . Clear evidence of some physico-chemical properties of the polysaccharides is given by the study of the effect of the carrier ionic strength on salep, oxidized salep and konjac, carboxymethylcellulose and hyaluronic acid . While neutral polysaccharides, regardless of their origin, only slightly change size distribution in the presence of a simple electrolyte in solution, charged polymers, either naturally charged or chemically ionized, consistently exhibit very low retention levels in water which dramatically increase even at low salt concentrations . Exclusion mechanisms, including steric effects, are shown to be responsible for the anticipated retention times in water of these species that assume the expected statistical coil behavior only when electric charges are screened by the added electrolyte . Under these conditions, higher retention levels are obtained because the volume adjacent to the accumulation wall becomes more accessible to the sample during relaxation . On the basis of these findings, the elution behavior of a number of polysaccharide samples in-laboratory obtained from the fungus Aureobasidium pullulans under different incubation conditions is attributed to the presence of species varying in physico-chemical properties and molecular size.

Pract Proced Aesthet Dent, 2002 Nov-Dec, 14(9), suppl 3 - 10; quiz 11
Using host response modifiers in the treatment of periodontal disease; Novak MJ et al.; Periodontal disease is the result of a complex interaction between microbial plaque, the host's inflammatory response to the plaque, and host modifying factors (e.g., smoking, diabetes, genetics) that may have an impact on the disease process . It is known that plaque initiates periodontal disease but that the host response is responsible for the destruction of periodontal tissues . This article describes why host response modifiers may be used to help control inflammation and tissue destruction as part of the initial phase of periodontal therapy in selected patient groups.

Eksp Klin Gastroenterol, 2002, (6), 16 - 21, 111
{Features of mucosal flora associated with relapsed ulcer and acute erosive-ulcer damage of the gastroduodenal zone in an unstable course of myocardial ischemia}; Osadchii VA et al.; The findings indicate that erosive and ulcerous lesions of the gastroduodenal zone in case of an unstable course of ischemic heart disease are accompanied by an increase in the microbial semination of its mucous coat and induction of enzymatic activity of bacteria and fungi . The pathomicrobiocenosis being formed there can reinforce inflammatory and necrotic changes and inhibit their elimination . This should be taken into consideration when studying the pathogenesis mechanisms of erosive and ulcerous stomach and duodenal lesions in case of an unstable course of ischemic disease and developing methods for their prevention and treatment.

Parasitol Res, 2003 Aug, 90(5), 349 - 54 Epub 2003 Mar 27.
Ultrastructure and bacterial infection of wounds in honey bee ( Apis mellifera) pupae punctured by Varroa mites; Kanbar G et al.; The damage to western honey bee, Apis mellifera, colonies caused by the originally Asian ectoparasitic mite Varroa destructor is mainly a consequence of the infestation of host bee pupae . In the capped brood cell, female mites puncture the host's integument at preferred sites in order to suck haemolymph . Due to repeated feeding by the mother mite and her progeny, these perforations are kept open until shortly before the imaginal moult of the bee . Thereafter scarring takes place, thus preventing microbial infection after the adult bee has emerged from the protected environment of the sealed brood cell . However, colonies of various bacteria were found in the open wounds of about 15-30% of all inspected host pupae with an abundance depended on the level of host brood cell infestation by the mite . The small punctures of the pupal integument are difficult to detect but, by vital staining with trypan blue, the wounds can be visualised . The ultrastructure of the pupal wounds, the bacterial colonies and the scarring process are documented by a series of scanning electron micrographs.

J Am Chem Soc, 2003 Apr 16, 125(15), 4444 - 50
Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA; Yu L et al.; A method is described for the NMR-based screening for the discovery of aminoglycoside mimetics that bind to Escherichia coli A-site RNA . Although aminoglycosides are clinically useful, they exhibit high nephrotoxicity and ototoxicity, and their overuse has led to the development of resistance to important microbial pathogens . To identify a new series of aminoglycoside mimetics that could potentially overcome the problems associated with toxicities and resistance development observed with the aminoglycosides, we have prepared large quantities of E . coli 16 S A-site RNA and conducted an NMR-based screening of our compound library in search for small-molecule RNA binders against this RNA target . From these studies, several classes of compounds were identified as initial hits with binding affinities in the range of 70 microM to 3 mM . Lead optimization through synthetic modifications of these initial hits led to the discovery of several small-molecule aminoglycoside mimetics that are structurally very different from the known aminoglycosides . Structural models of the A-site RNA/ligand complexes were prepared and compared to the three-dimensional structures of the RNA/aminoglycoside complexes.

Ying Yong Sheng Tai Xue Bao, 2002 Dec, 13(12), 1637 - 41
{Effect of earthworm inoculation on soil carbon and nitrogen dynamics and on crop yield with application of corn residues}; Li H et al.; This study was carried out in the Experimental Station of Nanjing Agricultural University, which is in a subtropical monsoon region characterized by a warm-wet spring and a hot-dry summer . The annual average temperature, precipitation and evaporation are 15.6 degrees C, 1010 mm and 1560 mm, respectively . In 1999, the experimental plots (2.8 m x 1.0 m x 0.6 m) were established by concrete frame . Soil in the plots was orthic aquisols collected from Rugao County, Jiangsu Province . Crop rotation was upland rice and winter wheat . At the beginning of the first crop (rice) season, earthworms (Pheretima sp.) were inoculated at a density of 10.m-2 and 20.m-2, respectively, in the plots with an application of corn residues at the rate of 1500 g.m-2(750 g.m-2 in the following seasons) . The responses of soil carbon and nitrogen and crop yield to earthworm activity were investigated from 1999 to 2001 . The results showed that earthworms had no significant influences on total soil carbon and nitrogen content, which implied that there was no depletion of soil carbon and nitrogen pools in the presence of earthworms . The maintenance of soil carbon might be explained by low assimilation efficiency of organic matter by earthworms, and by the compensation of carbon returning from plant production enhancement . Soil mineral nitrogen, soil microbial biomass carbon and microbial biomass nitrogen were increased, and nitrogen mineralization was strengthened by earthworm activities, which was more obvious at jointing/booting and heading stages . In comparison with no-worm treatments, the yield of rice wheat increased by 9.3% and 5.1%, respectively, in the treatments inoculated with earthworms . It was concluded that earthworm was very important in promoting nitrogen recycling of crop residues and plant productivity, and in keeping the balance of soil carbon pool as well.

Br J Nurs, 2003 Mar 13-26, 12(5), 274 - 80, 282, 284
Reducing infections associated with central venous catheters; Rickard NA; The cost of infections in central venous catheters (CVCs) is high both to the NHS and to the patients and their carers . This article discusses reduction of infection in patients with CVCs . Adding to the debate on how to do this, three interlinked factors are discussed: (1) the virulence of the invading micro-organisms, (2) the environment for microbial growth, and (3) the host defence mechanisms . The article encourages healthcare workers to use interprofessional groups to write, update frequently, and discuss protocols designed to reduce infections . The discussion and updating of the protocols, based on local experience, monitoring actions and infection rates within the interprofessional group, will assist in the reduction of infection.

Trends Biotechnol, 2003 Apr, 21(4), 162 - 9
Genome-scale microbial in silico models: the constraints-based approach; Price ND et al.; Genome sequencing and annotation has enabled the reconstruction of genome-scale metabolic networks . The phenotypic functions that these networks allow for can be defined and studied using constraints-based models and in silico simulation . Several useful predictions have been obtained from such in silico models, including substrate preference, consequences of gene deletions, optimal growth patterns, outcomes of adaptive evolution and shifts in expression profiles . The success rate of these predictions is typically in the order of 70-90% depending on the organism studied and the type of prediction being made . These results are useful as a basis for iterative model building and for several practical applications.

Trends Biotechnol, 2003 Apr, 21(4), 152 - 6
Mining genomic databases to identify novel hydrogen producers; Kalia VC et al.; The realization that fossil fuel reserves are limited and their adverse effect on the environment has forced us to look into alternative sources of energy . Hydrogen is a strong contender as a future fuel . Biological hydrogen production ranges from 0.37 to 3.3 moles H(2) per mole of glucose and, considering the high theoretical values of production (4.0 moles H(2) per mole of glucose), it is worth exploring approaches to increase hydrogen yields . Screening the untapped microbial population is a promising possibility . Sequence analysis and pathway alignment of hydrogen metabolism in complete and incomplete genomes has led to the identification of potential hydrogen producers.

Curr Med Chem, 2003 May, 10(9), 787 - 96
Novel marine and microbial natural product inhibitors of vacuolar ATPase; Beutler JA et al.; Vacuolar-ATPase (V-ATPase) has been proposed as a drug target in osteoporosis due to its involvement in bone resorption, and as a target in cancer due to potential involvement in tumor invasion and metastasis . The classical selective inhibitors of V-ATPase are microbial macrolides of the bafilomycin and concanamycin class . These inhibitors have proven to be too toxic for therapeutic use, however recent structure-activity studies on bafilomycins, and the isolation of novel macrolide structures from marine sources, have provided new avenues for development of potentially less toxic V-ATPase inhibitors . The novel salicylihalamide and lobatamide series of compounds were predicted to share a common mechanism of action based on the patterns of cytotoxicity produced in the NCI 60-cell cancer screen . They have subsequently been shown to selectively interact with mammalian V-ATPases, but not with fungal V-ATPases . With the recent achievement of total syntheses of salicylihalamide, lobatamide, and related compounds, the elaboration of congeners with specificity for particular enzyme isoforms may provide drug candidates which are less toxic . This review summarizes recent advances in V-ATPase inhibition and the prospects for further progress.

Curr Med Chem, 2003 May, 10(9), 727 - 32
Development and application of bioprobes for Mammalian cell cycle analyses; Osada H; In this review, I have mainly described the cell cycle inhibitors isolated from microbial metabolites . Once the molecular target of the inhibitor is determined, the inhibitor can be used as bioprobe to dissect the diverse aspect of biological functions in chemical biology research . Reveromycin A and phosmidosine inhibited the protein synthesis of mammalian cells and arrested the cell cycle at G1 phase . Lucilactaene arrested cells at G1 phase through restoration of mutant p53 . Tryprostatin A inhibited the microtubule polymerization by interfering with the interaction between tubulin and microtubule associating protein . On the contrary, cyclotryprostatin D, structurally related to tryprostatin A, enhanced the tubulin polymerization . Terpendole E inhibited the motor activity of mitotic kinesin, Eg5 and induced monoastral spindle in M phase.

Curr Med Chem, 2003 Jun, 10(12), 1065 - 76
Development of tridentate iron chelators: from desferrithiocin to ICL670; Nick H et al.; Successful treatment of beta-thalassemia requires two key elements: blood transfusion and iron chelation . Regular blood transfusions considerably expand the lifespan of patients, however, without the removal of the consequential accumulation of body iron, few patients live beyond their second decade . In 1963, the introduction of desferrioxamine (DFO), a hexadentate chelator, marked a breakthrough in the treatment of beta-thalassemia . DFO significantly reduces body iron burden and iron-related morbidity and mortality . DFO is still the only drug for general use in the treatment of transfusion dependent iron overload . However, its very short plasma half-life and poor oral activity necessitate special modes of application (subcutaneous or intravenous infusion) which are inconvenient, can cause local reactions and are difficult to be accepted by many patients . Over the past four decades, many different laboratories have invested major efforts in the identification of orally active iron chelators from several hundreds of molecules of synthetic, microbial or plant origin . The discovery of ferrithiocin in 1980, followed by the synthesis of the tridentate chelator desferrithiocin and proof of its oral activity raised a lot of hope . However, the compound proved to be toxic in animals . Over a period of about fifteen years many desferrithiocin derivatives and molecules with broader alterations led to the discovery of numerous new compounds some of which were much better tolerated and were more efficacious than desferrithiocin in animals, however, none was safe enough to proceed to the clinical use . The discovery of a new chemical class of iron chelators: The bis-hydroxyphenyltriazoles re-energized the search for a safe tridentate chelator . The basic structure of this completely new chemical class of iron chelators was discovered by a combination of rational design, intuition and experience . More than forty derivatives of the triazole series were synthesized at Novartis . These compounds were evaluated, together with more than 700 chelators from various chemical classes . Using vigorous selection criteria with a focus on tolerability, the tridentate chelator 4-{(3,5-Bis-(2-hydroxyphenyl)-1,2,4)triazol-1-yl}-benzoic acid (ICL670) emerged as an entity which best combined high oral potency and tolerability in animals . ICL670 is presently being evaluated in the clinic.

Int Ophthalmol, 2001, 24(4), 195 - 8
Causes of blindness in Northern Tanzania: a hospital and rural health centre based study; Poole TR; OBJECTIVE: To identify the main causes of blindness in Northern Tanzania . METHODS: Ophthalmic patients at the Kilimanjaro Christian Medical Centre and on outreach clinics in the Kilimanjaro region of Northern Tanzania were examined . The cause of blindness was documented for any eye seeing less than 3/60 Snellen . If more than one factor contributed to the visual loss, the single factor deemed to be the most visually disabling was documented . RESULTS: 1045 blind eyes of 781 patients were examined . 264 patients were bilaterally blind . The main cause of bilateral blindness was cataract {39%} . The other chief causes of blindness were glaucoma, trauma and corneal scarring . The most important cause of corneal scarring, approximately half the cases, was microbial keratitis . Refractive error alone was responsible for 4.2% of bilateral blindness, of which 2.7% was uncorrected post-cataract surgery aphakia . CONCLUSIONS: Treatable causes of blindness, including cataract and refractive error account for over a third of all blindness in Northern Tanzania . Trauma, glaucoma and microbial keratitis are other important causes of blindness in the region.

Eur J Public Health, 2003 Mar, 13(1), 87 - 9
Safe water for the Aral Sea Area: could it get any worse?
Small I, Falzon D, van der Meer JB, Ford N.
The environmental adversities around the Aral Sea in Central Asia have been the subject of recent research . Attempts at sustainable provision of palatable drinking water in low chemical and microbial contaminants for the 4 million people in the two countries around the Aral littoral have been largely unsuccessful . In the last few years, severe drought has further depleted the amount of available water . This shortage has negatively impacted on agriculture, and accentuated the out migration of people . An appeal is made to assist the local population in this arid area to cope with the acute and chronic deterioration of water security.

Life Sci Space Res, 1976, 14, 195 - 9
Pioneer 10 and 11 Jovian encounters: radiation dose and biological lethality; Miller MW et al.; In their recent Jupiter flybys Pioneer 10 and Pioneer 11 passed through a belt of intense particulate radiation . For Pioneer 10 the radiation dose on the craft's outer surface was at least 5 x 10(5) rads from electrons plus 1.0 x 10(6) rads from protons; the radiation dose inside the craft (0.3 cm aluminum) was approximately 4.5 x 10(5) rads . For Pioneer 11 the surface dose was at least 1.3 x 10(5) rads from electrons plus 3 x 10(5) rads from protons; the interior radiation dose was approximately 1.2 x 10(5) rads . Significant survival of microbial spores would be possible at these calculated doses; however, even the interior dose of Pioneer 11 would be lethal to man and most multicellular biological organisms.

Proc Natl Acad Sci U S A, 2003 Apr 15, 100(8), 4639 - 43 Epub 2003 Apr 03.
Positive selection in the egg receptor for abalone sperm lysin; Galindo BE et al.; The mechanism of speciation is a central problem in evolutionary biology . In free-spawning animals with no complex mating behavior, prezygotic reproductive isolation (speciation) could result from the rapid divergence of genes coding for sperm and egg proteins that bind each other during fertilization . In abalone, sperm lysin evolves rapidly by positive Darwinian selection . The egg vitelline envelope receptor for lysin had previously been shown to evolve neutrally and be subjected to concerted evolution . Several mathematical simulations predict that both male and female reproductive proteins should evolve rapidly by positive selection . Here we report that the sequence diversity of the amino-terminal end of the egg vitelline envelope receptor for lysin has been promoted by positive Darwinian selection . These data provide molecular support for theoretical models showing that the two sexes are locked in a "coevolutionary chase" that could be driven by processes such as sexual selection, sexual conflict, or microbial attack (pathogen avoidance) . The result of this continuous coevolution of the gamete recognition system could be the splitting of one population into two that are reproductively isolated (speciation).

Appl Environ Microbiol, 2003 Apr, 69(4), 2377 - 82
Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays; El Fantroussi S et al.; Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification . In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities . The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.

Appl Environ Microbiol, 2003 Apr, 69(4), 1928 - 35
mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil; Burgmann H et al.; The study of free-living nitrogen-fixing organisms in bulk soil is hampered by the great diversity of soil microbial communities and the difficulty of relating nitrogen fixation activities to individual members of the diazotroph populations . We developed a molecular method that allows analysis of nifH mRNA expression in soil in parallel with determinations of nitrogen-fixing activity and bacterial growth . In this study, Azotobacter vinelandii growing in sterile soil and liquid culture served as a model system for nifH expression, in which sucrose served as the carbon source and provided nitrogen-limited conditions, while amendments of NH(4)NO(3) were used to suppress nitrogen fixation . Soil RNA extraction was performed with a new optimized direct extraction protocol that yielded nondegraded total RNA . The RNA extracts were of high purity, free of DNA contamination, and allowed highly sensitive and specific detection of nifH mRNA by a reverse transcription-PCR . The level of nifH gene expression was estimated by PCR amplification of reverse-transcribed nifH mRNA fragments with A . vinelandii-specific nifH primers . This new approach revealed that nifH gene expression was positively correlated with bulk nitrogen fixation activity in soil (r(2) = 0.72) and in liquid culture (r(2) = 0.84) and therefore is a powerful tool for studying specific regulation of gene expression directly in the soil environment.

Environ Int, 2003 Jun, 29(2-3), 393 - 9
Importance of atmospherically deposited nitrogen to the annual nitrogen budget of the Neuse River estuary, North Carolina; Whitall D et al.; Wet deposition of nitrogen, as NH(4)(+), NO(3)(-), and organic N, contributes up to 50% of the total externally supplied or 'new' N flux to the Neuse River Estuary (North Carolina) . Excessive nitrogen (N) loading to N-sensitive waters such as the Neuse River Estuary has been linked to changes in microbial and algal community composition and function (harmful algal blooms), hypoxia/anoxia, and fish kills . In a 4-year study from July 1996 to July 2000, the weekly wet deposition of NH(4)(+), NO(3)(-), and dissolved organic N was calculated, based on concentration and precipitation measurements, at 11 sites on a northwest-southeast transect in the watershed . Data from this period indicate that the annual mean total wet atmospherically deposited (AD)-N flux was 11 kg ha(-1) year(-1) . Deposition was fairly evenly distributed between nitrate, ammonium, and organics (32%, 32%, and 36%, respectively) . Seasonally, the summer (June-August) months contained the highest weekly wet total N deposition; this trend was not driven by precipitation amount . Estimates of watershed N retention and in-stream riverine processing revealed that the AD-N flux contributed an estimated 20% (range of 15-51%) of the total 'new' N flux to the estuary, with direct deposition of N to the estuary surface accounting for 6% of the total 'new' N flux . This study did not measure the dry depositional flux, which may double the contribution of AD-N to the estuary . The AD-N is an important source of 'new' N to the Neuse River Estuary as well as other estuarine and coastal ecosystems downwind of major emission sources . As such, AD-N should be included in effective nutrient mitigation and management efforts for these N-sensitive waters.

J Altern Complement Med, 2003 Feb, 9(1), 133 - 41
Controlled clinical trials evaluating the homeopathic treatment of people with human immunodeficiency virus or acquired immune deficiency syndrome; Ullman D; CONTEXT: Homeopathic medicine developed significant popularity in the nineteenth century in the United States and Europe as a result of its successes treating the infectious disease epidemics during that era . Homeopathic medicine is a medical system that is specifically oriented to using nanopharmacologic and ultramolecular doses of medicines to strengthen a person's immune and defense system rather than directly attacking the microbial agents . OBJECTIVES: To review the literature referenced in MEDLINE and in nonindexed homeopathic journals for placebo-controlled clinical trials using homeopathic medicines to treat people with AIDS or who are human immunodeficiency virus (HIV)-positive and to consider a different theoretical and methodological approach to treating people with the viral infection . FINDINGS: A total of five controlled clinical trials were identified . A double-blinded, placebo-controlled study was conducted on 50 asymptomatic HIV-positive subjects (stage II) and 50 subjects with persistent generalized lymphadenopathy (stage III) in whom individualized single-remedy homeopathic treatment was provided . A separate body of preliminary research was conducted using homeopathic doses of growth factors . Two randomized double-blinded, placebo-controlled studies were conducted with a total of 77 people with AIDS who used only natural therapies over a 8-16-week period . Two other studies were conducted over a 2.5-year period with 27 subjects in an open-label format . SETTINGS: The first study was conducted by the Regional Research Institute for Homeopathy in Mumbai, India, under the Central Council for Research in Homeopathy, with the approval of the Ministry of Health and Family Welfare, Government of India . The second body of studies was conducted in clinic settings in California, Oregon, Arizona, Hawaii, New York, and Washington . RESULTS: The first study found no statistically significant improvement in CD4 T-lymphocytes, but did find statistically significant pretest and post-test results in subjects with stage III AIDS, in CD4 (p = 0.008) and in CD8 (p = 0.04) counts . The second group of studies found specific physical, immunologic, neurologic, metabolic, and quality-of-life benefits, including improvements in lymphocyte counts and functions and reductions in HIV viral loads . CONCLUSIONS: As a result of the growing number of people with drug-resistant HIV infection taking structured treatment interruptions, homeopathic medicine may play a useful role as an adjunctive and/or alternative therapy.

Biotechnol Prog, 2003 Mar-Apr, 19(2), 352 - 60
Hydrolysis of proteins by immobilized-stabilized alcalase-glyoxyl agarose; Tardioli PW et al.; This paper presents stable Alcalase-glyoxyl derivatives, to be used in the controlled hydrolysis of proteins . They were produced by immobilizing-stabilizing Alcalase on cross-linked 10% agarose beads, using low and high activation grades of the support and different immobilization times . The Alcalase glyoxyl derivatives were compared to other agarose derivatives, prepared using glutaraldehyde and CNBr as activation reactants . The performance of derivatives in the hydrolysis of casein was also tested . At pH 8.0 and 50 degrees C, Alcalase derivatives produced with 1 h of immobilization time on agarose activated with glutaraldehyde, CNBr, and low and high glyoxyl groups concentration presented half-lives of ca . 10, 29, 60, and 164 h, respectively . More extensive immobilization monotonically led to higher stabilization . The most stabilized Alcalase-glyoxyl derivative was produced using 96 h of immobilization time and high activation grade of the support . It presented half-life of ca . 23 h, at pH 8.0 and 63 degrees C and was ca . 500-fold more stable than the soluble enzyme . Thermal inactivation of all derivatives followed a single-step non-first-order kinetics . The most stable derivative presented ca . 54% of the activity of the soluble enzyme for the hydrolysis of casein and of the small substrate Boc-Ala-ONp . This behavior suggests that the decrease in activity was due to enzyme distortion but not to wrong orientation . The hydrolysis degree of casein at 80 degrees C with the most stabilized enzyme was 2-fold higher than that achieved using soluble enzyme, as a result of the thermal inactivation of the latter . Therefore, the high stability of the new Alcalase-glyoxyl derivative allows the design of continuous processes to hydrolyze proteins at temperatures that avoid microbial growth.

Am Nat, 2003 Feb, 161(2), 310 - 25
Mutualistic asexual endophytes in a native grass are usually parasitic; Faeth SH et al.; Asexual systemic fungi that live symbiotically within grasses are viewed as strong mutualists on the basis of theory and empirical studies of introduced agronomic grasses . Evolutionary theory predicts that microbial symbionts that lose sexuality and rely on propagules of their hosts for transmission should evolve to benefit their hosts . Fungal endophytes of some cultivated turf and pasture grasses are well known for increasing plant performance and competitive abilities, especially under stress, and increasing resistance to herbivores, pathogens, and root-feeders by virtue of fungal alkaloids . The assumption of mutualism, however, has rarely been tested in native grasses, which often harbor high but variable frequencies of systemic asexual endophytes . We tested the effect of Neotyphodium infections for the native grass Arizona fescue in a 3-yr field experiment . We strictly controlled host genotype and manipulated soil moisture and nutrients . Infection generally decreased host growth in terms of plant volume, number of tillers, and dry mass of shoots and roots . Infected plants also showed decreased reproduction in terms of number and mass of seeds, and the seeds produced by infected plants had lower germination success than plants without their endophytes, suggesting that the negative effects of the symbiont are transferred to the next generation . Plant genotype strongly influenced host's growth and reproduction and interacted with the presence of the endophyte, but the interaction was usually in the direction of negative effects . Our results challenge the notion that systemic asexual endophytes must be plant mutualists for infections to persist in nature . We propose other hypotheses to explain the variable but usually high endophyte frequencies in natural populations of grasses.

Can J Microbiol, 2003 Jan, 49(1), 15 - 27
Phylogenetic analysis of bacterial populations in an anaerobic microbial consortium capable of degrading saturation concentrations of tetrachloroethylene; Dennis PC et al.; An anaerobic microbial consortium able to biodegrade saturation levels of perchloroethylene (PCE) in a column containing a source zone of PCE was examined phylogenetically to determine microbial community structure and spatial variation in relation to the PCE source . The consortium was comprised of at least 34 members with 7 organisms sharing affiliations with known respiratory or cometabolic dechlorinators . Seven other organisms had their closest phylogenetic relative detected in other environments containing chlorinated compounds . Based on denaturing gradient gel electrophoresis, significant Bacteria were Dehalococcoides ethenogenes, Shewanella putrefaciens, and an Acetobacterium species . Spatial variations in community structure of the consortium relative to the PCE source zone were observed . A Pseudomonas species was predominant in a zone 30 cm from the PCE source . A Methanothrix species was predominant at points over 85 cm from the source zone . A Trichlorobacter species was detected where PCE concentrations were highest, up to 85 cm from the PCE source, whereas D . ethenogenes was ubiquitous to over 128 cm from the PCE source.

Eur J Immunol, 2003 Apr, 33(4), 827 - 33
Toll-like receptor expression in murine DC subsets: lack of TLR7 expression by CD8 alpha+ DC correlates with unresponsiveness to imidazoquinolines; Edwards AD et al.; Toll-like receptors (TLR) recognize microbial and viral patterns and activate dendritic cells (DC) . TLR distribution among human DC subsets is heterogeneous: plasmacytoid DC (PDC) express TLR1, 7 and 9, while other DC types do not express TLR9 but express other TLR . Here, we report that mRNA for most TLR is expressed at similar levels by murine splenic DC sub-types, including PDC, but that TLR3 is preferentially expressed by CD8 alpha(+) DC while TLR5 and TLR7 are selectively absent from the same subset . Consistent with the latter, TLR7 ligand activates CD8 alpha(-) DC and PDC, but not CD8 alpha(+) DC as measured by survival ex vivo, up-regulation of surface markers and production of IL-12p40 . These data suggest that the dichotomy in TLR expression between plasmacytoid and non-plasmacytoid DC is not conserved between species . However, lack of TLR7 expression could restrict the involvement of CD8 alpha(+) DC in recognition of certain mouse pathogens.

Clin Orthop, 2003 Apr, (409), 317 - 24
Blood and marrow cultures as indicators of bone contamination in cadaver donors; Martinez OV et al.; Of 770 cadaver bone donors evaluated, 185 had positive blood or ilium marrow aspirate cultures . These donors were matched with an immediately preceding or subsequent donor with negative blood and marrow cultures . Donors with cultures positive for skin contaminants only were not included in the study . Samples of the blood and bone marrow, surface swab cultures, and cultures of tissue samples of the excised skeletal tissues were obtained at the time of tissue procurement . There were 88 (48%) donors with similar microbial species recovered from the blood and ilium marrow . These donors had a higher rate of positive bone cultures (30%) than donors with positive blood (15%) or marrow cultures only (11%) or donors with negative blood and marrow culture results (7.3%) . Recovery of similar isolates from the blood and marrow had a positive predictive value of 72% for the isolation of the same types of organisms from the excised tissues compared with 38% for donors with positive blood cultures only . Although not absolute predictors of tissue contamination, combined blood and bone marrow cultures were more reliable indicators of tissue contamination than blood cultures alone.

Exp Biol Med (Maywood), 2003 Apr, 228(4), 424 - 33
Gastrointestinal and microbial responses to sulfate-supplemented drinking water in mice; Deplancke B et al.; There is increasing evidence that hydrogen sulfide (H2S), produced by intestinal sulfate-reducing bacteria (SRB), may be involved in the etiopathogenesis of chronic diseases such as ulcerative colitis and colorectal cancer . The activity of SRB, and thus H2S production, is likely determined by the availability of sulfur-containing compounds in the intestine . However, little is known about the impact of dietary or inorganic sulfate on intestinal sulfate and SRB-derived H2S concentrations . In this study, the effects of short-term (7 day) and long-term (1 year) inorganic sulfate supplementation of the drinking water on gastrointestinal (GI) sulfate and H2S concentrations (and thus activity of resident SRBs), and the density of large intestinal sulfomucin-containing goblet cells, were examined in C3H/HeJBir mice . Additionally, a PCR-denaturing gradient gel electrophoresis (DGGE)-based molecular ecology technique was used to examine the impact of sulfate-amended drinking water on microbial community structure throughout the GI tract . Average H2S concentrations ranged from 0.1 mM (stomach) to 1 mM (cecum) . A sulfate reduction assay demonstrated in situ production of H2S throughout the GI tract, confirming the presence of SRB . However, H2S generation and concentrations were greatest in the cecum and colon . Sulfate supplementation of drinking water did not significantly increase intestinal sulfate or H2S concentrations, suggesting that inorganic sulfate is not an important modulator of intestinal H2S concentrations, although it altered the bacterial profiles of the stomach and distal colon of 1-year-old mice . This change in colonic bacterial profiles may reflect a corresponding increase in the density of sulfomucin-containing goblet cells in sulfate-supplemented compared with control mice.

Exp Biol Med (Maywood), 2003 Apr, 228(4), 331 - 2
Introduction to the food safety concerns of verotoxin-producing Escherichia coli; Hussein HS et al.; Verotoxin-producing Escherichia coli (VTEC) have emerged in the past two decades as food-borne pathogens that can cause major outbreaks of human illnesses worldwide . The number of outbreaks has increased in recent years due to changes in food production and processing systems, eating habits, microbial adaptation, and methods of VTEC transmission . The human illnesses range from mild diarrhea to hemolytic uremic syndrome (HUS) that can lead to death . The VTEC outbreaks have been attributed to O157:H7 and non-O157:H7 serotypes of E . coli . These E . coli serotypes include motile (e.g., O26:H11 and O104:H21) and nonmotile (e.g., O111:H-, O145:H-, and O157:H-) strains . In the United States, E . coli O157:H7 has been the major cause of VTEC outbreaks . Worldwide, however, non-O157:H7 VTEC (e.g., members of the O26, O103, O111, O118, O145, and O166 serogroups) have caused approximately 30% of the HUS cases in the past decade . Because large numbers of the VTEC outbreaks have been attributed to consumption of ruminant products (e.g., ground beef), cattle and sheep are considered reservoirs of these food-borne pathogens . Because of the food safety concern of VTEC, a global perspective on this problem is addressed (Exp Biol Med Vol . 228, No . 4) . The first objective was to evaluate the known non-O157:H7 VTEC strains and the limitations associated with their detection and characterization . The second objective was to identify the VTEC serotypes associated with outbreaks of human illnesses and to provide critical evaluation of their virulence . The third objective was to determine the rumen effect on survival of E . coli O157:H7 as a VTEC model . The fourth objective was to explore the role of intimins in promoting attaching and effacing lesions in humans . Finally, the ability of VTEC to cause persistent infections in cattle was evaluated.

Sci Total Environ, 2003 Apr 15, 305(1-3), 207 - 16
Factors affecting removal of selenate in agricultural drainage water utilizing rice straw; Zhang Y et al.; Microbial reduction of selenate {Se(VI)} to elemental selenium {Se(0)} is a useful technique for removing Se from agricultural drainage water . A series of batch experiments were conducted in the laboratory to determine the effects of pH (5-10), NO(3)(-) (100-500 mg/l), and SO(4)(2-) (0-5000 mg/l) on the removal of Se(VI) from drainage water with 1000 microg/l of Se(VI) and different amounts (1-4 g) of rice straw . Results showed that rice straw was very effective in creating a reducing environment (Eh=-205 to -355 mV) in the first 3 days of the pH-effect experiments . The optimum conditions for rapid Se(VI) removal from drainage water were a pH range of 6-9, high amounts of SO(4)(2-) (1000-5000 mg/l), low amounts of NO(3)(-) (100 mg/l) and high amounts of rice straw (3-4 g) . Under these conditions, it took 5-7 days to reduce 93-95% of the added Se(VI) to Se(0) . This study indicates that rice straw may be an inexpensive reducing agent to remediate Se(VI)-dominant San Joaquin Valley drainage water in the field.

FEMS Microbiol Lett, 2003 Mar 28, 220(2), 229 - 33
Evaluation of electron-shuttling compounds in microbial ferric iron reduction; Straub KL et al.; Iron-reducing bacteria can transfer electrons to ferric iron oxides which are barely soluble at neutral pH, and electron-shuttling compounds or chelators are discussed to be involved in this process . Experiments using semipermeable membranes for separation of ferric iron-reducing bacteria from ferric iron oxides do not provide conclusive results in this respect . Here, we used ferrihydrite embedded in 1% agar to check for electron-shuttling compounds in pure and in enrichment cultures . Geobacter sulfurreducens reduced spatially distant ferrihydrite only in the presence of anthraquinone-2,6-disulfonate, a small molecule known to shuttle electrons between the bacterial cell and ferrihydrite . However, indications for the production and excretion of electron-shuttling compounds or chelators were found in ferrihydrite-containing agar dilution cultures that were inoculated with ferric iron-reducing enrichment cultures.

Chemosphere, 2003 Jun, 51(8), 663 - 8
Dimethylphthalate hydrolysis by specific microbial esterase; Vega D et al.; TWO BACTERIAL STRAINS: Arthrobacter sp . and Sphingomonas paucimobilis were isolated from soil by enrichment cultures using dimethylphthalate (DMP) or monomethylphthalate (MMP) as sole carbon source, respectively . DMP was rapidly transformed by an Arthrobacter sp . culture with formation of MMP and phthalic acid (PA) which is further degraded . This strain was unable to hydrolyse MMP . A mechanism of degradation of DMP was proposed with two ways: DMP-->PA and DMP-->MMP . The S . paucimobilis strain hydrolyses only MMP and a coculture of the two strains allowed a complete degradation of DMP.

J Environ Manage, 2003 Mar, 67(3), 255 - 66
Assessing soil biodiversity across Great Britain: national trends in the occurrence of heterotrophic bacteria and invertebrates in soil; Black HI et al.; An assessment of the biodiversity of soils was a component of the Countryside Survey 2000 (CS2000) . This was the first integrated survey of soil biota and chemical properties at a national scale . A total of 1052 soil samples were collected across Great Britain during CS2000 and analysed for a range of soil microbial and invertebrate characteristics resulting in the production of a series of robust datasets . A principal objective was to use these datasets to investigate relationships between soil biota and environmental factors such as geographical location, vegetation, land use, land cover, soil type and pollutant levels as first stages in characterising the inherent biodiversity of British soils and investigating the potential of soil biodiversity as indicators of soil health at a regional or national scale . Preliminary results for culturable heterotrophic, invertebrate taxa, Acari, Collembola and Oribatid mites are presented here to illustrate the nature of the data collected and the patterns of soil biodiversity in relation to large-scale regional, vegetation and soil characteristics across the British countryside.

J Int Acad Periodontol, 2000 Jan, 2(1), 19 - 23
Some risk factors for the progression of periodontal disease; Skaleric U et al.; Inflammatory periodontal disease is one of the most common diseases of mankind . Gingival inflammation is widespread, but advanced periodontitis is limited to relatively small subgroups of the population . Gingivitis is initiated by microbial plaque deposits on the dento-gingival interface but progression to periodontitis is modified by several environmental, behavioural, biological and health care variables . This paper reviews the reports dealing with some risk factors for periodontal disease published in recent years and compares the data with findings in a Ljubljana population . It is concluded that male smokers with lower education and low frequency of tooth brushing represent a risk population for progression of periodontal disease . Marital status and body mass need further study to be proved as risk factors for periodontitis . A socioecological model proposed by Hansen et al . (1993) should be used for understanding the interplay of different risk factors for progression of periodontal disease.

J Int Acad Periodontol, 2000 Apr, 2(2), 49 - 55
Negative effects of chronic inflammatory periodontal disease on diabetes mellitus; Nishimura F et al.; Periodontal disease is the result of a complex interplay of bacterial infection and host responses, and is often modified by various systemic diseases such as diabetes mellitus . Such diseases are capable of affecting the periodontium and/or the treatment of periodontal disease . However, recent research has changed our concept of how periodontal disease should be treated . Here we present several concerns directed towards the periodontal therapy of patients with diabetes mellitus based on our studies . When treating periodontitis patients who have diabetes mellitus it is important to consider the type of diabetes . Patients with non-insulin dependent diabetes mellitus can be further classified according to the degree of insulin resistance, since recent epidemiological studies have suggested that successful anti-microbial therapy might result in improved insulin resistance in highly insulin resistant patients . Because the major contributing factor for insulin resistance is currently considered to be the proinflammatory cytokine tumor necrosis factor-alpha (TNF-alpha), and because periodontal surgery may cause transient bacteremia which may up-regulate the serum TNF-alpha level, which in turn suppresses insulin action, patients should be strictly treated non-surgically and their serum TNF-alpha levels should be periodically monitored . On the other hand, diabetic patients positive for serum anti-glutamate decarboxylase auto-antibody should be examined for the source of this antibody, since 1) gingival and periodontal ligament fibroblasts were found to express glutamate decarboxylase, and 2) some otherwise healthy periodontitis patients develop anti-glutamate decarboxylase antibody . Thus, chronic periodontitis may influence the level of this antibody which is widely used as a predictive marker for slowly progressive insulin dependent diabetes mellitus . Not only is periodontal disease thereby affected by systemic diseases, but carefully managed periodontal therapy may also have a positive effect on the general health of patients with systemic diseases.

Nat Immunol, 2003 May, 4(5), 485 - 90 Epub 2003 Mar 31.
Molecular mimicry of a CCR5 binding-domain in the microbial activation of dendritic cells; Aliberti J et al.; Toxoplasma gondii releases factors that potently stimulate production of interleukin-12 (IL-12) from dendritic cells (DCs) . Purification of this activity showed that cyclophilin-18 (C-18) was its principal component, and antibodies generated against recombinant C-18 inhibited tachyzoite extract-induced synthesis of IL-12 . Recombinant C-18 showed high affinity for and triggered cell signaling through CCR5, a chemokine receptor important in parasite-induced IL-12 production by DCs . These findings suggest that the unusual potency of T . gondii in inducing IL-12 from DCs results from its synthesis of a unique chemokine mimic that signals through CCR5 . The ability to generate this strong protective response may benefit parasite transmission by preventing the protozoan from overwhelming its intermediate hosts.

Mol Biotechnol, 2003 Mar, 23(3), 259 - 70
Complement components and their autoantibodies; Norsworthy P et al.; The purpose of the immune system is to defend the host from constantly changing microbial pathogens . Autoimmune diseases develop as a consequence of the production of antibodies and/or cells that react with self-antigens, and may recruit other effector mechanisms that result in tissue damage . Thus, in this context, autoimmunity represents an immune response to self-antigens that is sufficient to cause disease . This article is specifically devoted to autoantibodies directed against complement components.

CNS Drugs, 2003, 17(4), 235 - 72
Propofol: a review of its use in intensive care sedation of adults; McKeage K et al.; Propofol (Diprivan) is a phenolic derivative with sedative and hypnotic properties but is unrelated to other sedative/hypnotic agents . Formulated as an oil-in-water emulsion for intravenous use, it is highly lipophilic and rapidly crosses the blood-brain barrier resulting in a rapid onset of action . Emergence from sedation is also rapid because of a fast redistribution into peripheral tissues and metabolic clearance . The depth of sedation increases in a dose-dependent manner . In well designed clinical trials in patients receiving sedation in the intensive care unit (ICU) for a variety of indications, propofol provided adequate sedation for a similar proportion of time to midazolam, but the rate of recovery was faster with propofol . Even after periods of prolonged sedation (>72 hours), propofol was generally associated with a faster time to recovery than midazolam . Propofol facilitated better predictability of recovery and an improved control of the depth of sedation in response to titration than midazolam . In patients sedated following head trauma, propofol reduced or maintained intracranial pressure . Propofol is associated with generally good haemodynamic stability but induces a dose-dependent decrease in blood pressure and heart rate . Bolus administration may cause transient hypotension, and slow initial infusions are recommended in most patients . Serum triglyceride concentrations should be monitored during prolonged infusions (>3 days) because of the risk of hypertriglyceridaemia . The administration of 2% propofol can reduce this risk . Strict aseptic technique must be used during the handling of the product to prevent accidental extrinsic microbial contamination . Despite a higher acquisition cost with propofol, most studies of short-term sedation (approximately <3 days) showed that overall costs were lower with propofol than with midazolam, because a faster time to extubation reduced total ICU costs . However, as the period of sedation increased, the cost difference decreased . CONCLUSION: The efficacy of propofol in the sedation of adults in the ICU is well established, and clinical trials have demonstrated a similar quality of sedation to midazolam . Because of a rapid distribution and clearance, the duration of action of propofol is short and recovery is rapid . Emergence from sedation is more rapid with propofol than with midazolam, even after long-term administration (>72 hours), which enables better control of the depth of sedation in response to titration and more predictable recovery times . Thus, for the ICU sedation of adults in a variety of clinical settings, propofol provides effective sedation with a more rapid and predictable emergence time than midazolam.

West Afr J Med, 2002 Oct-Dec, 21(4), 302 - 4
Microbial isolates in open fractures seen in the accident and emergency unit of a teaching hospital in a developing country; Alonge TO et al.; In this prospective study, superficial and deep swabs of all open fractures seen at the accident and emergency unit of our hospital between January and June 2000 were taken (before wound debridement was done or anitibiotics commenced) . Routine microscopy, culture and sensitivities for aerobic and anaerobic organisms were carried out on these specimens . The organisms were cultured and identified using standard techniques and the antibiotic sensitivity testing was carried out using the disc diffusion method of Stokes . Within six hours of injury, single-organism isolates were commonly found whilst after 48 hours a mixed or poly-microbial organism load were isolated . In 90% of the positive isolates, the organisms isolated form the superficial and the deep swabs were the same . The antibiotic sensitivity pattern of all the isolates shows that pefloxacin, ciprofloxacin and ceftriaxone were more effective compared to cefuroxime and amoxycillin which had substantial resistance to most of the isolates . 41 fractures were followed to union and 4 (9.7%) developed osteomyelitis.

J Investig Med, 2003 Feb, 51 Suppl 1, S6 - 11
Human challenge studies with infectious agents; Kotloff KL; Experimental inoculation of healthy volunteers with infectious agents has been practiced by investigators for many years to elucidate mechanisms of microbial virulence, disease pathogenesis, host immunity, and vaccine efficacy . Establishing these models requires detailed attention to scientific, ethical, and medical principles to ensure the safety of the participants and their community contacts and to generate valid observations that can be generalized to natural infections . This discussion provides examples of the potential values and applications of human challenge studies, addresses issues that must be considered in establishing a new challenge model, and examines the limitations of human data generated in this experimental setting.

Life Sci Space Res, 1970, 8, 90 - 8
Detection of iron-porphyrin proteins with a biochemiluminescent method in search of extraterrestrial life; Sotnikov GG; Iron-porphyrin proteins (catalase, peroxidase, hemoglobin, cytochrome C) represent an important group of redoxenzymes which have vitally important functions in micro-organisms . A biochemiluminescent method was employed for the detection of iron-porphyrin proteins . The reaction of luminol oxidation with H2O2 is accompanied by chemiluminescence . The rate of hydrogen peroxide decomposition increased 10(5)-10(7) -fold in the presence of the above enzymes as compared with ferrous (or ferric) ions . Possible application of this reaction for the detection of iron-porphyrin proteins of microbial origin was studied . Other authors have suggested this reaction for the detection of extraterrestrial life . Kinetics of the above reaction in the presence of iron-porphyrin proteins were shown to differ both in amplitude and duration of the signal from the pattern observed in the presence of non-hemin catalysts . The reaction pattern in the presence of mixed-soil populations is similar to those observed with pure bacterial cultures and individual iron-porphyrin proteins . Photometric tests revealed that among preparations studied the addition of 0.01% lysozyme was the most effective in destroying cell walls in microbial populations . However, removal of cell walls is not a necessary prerequisite for the detection of iron porphyrin since, for effective luminol oxidation with H2O2 the medium should be kept at pH 12.0 . Pretreatment of microbial suspensions with ultrasound increased 2-fold the total signal due to iron porphyrins . The above method gives a reproducible signal indicating the presence of iron porphyrins when sterile nutrient media were innoculated with desert soil samples (Repeteck, Kara-Kum) and incubated for 13 hr . The device was able to detect the presence of no less than 10(5) - 10(6) cells per ml . The addition of limonite (Fe2O3 X nH2O) does not result in the appearance of an appreciable signal in the luminol + H2O2 system.

Life Sci Space Res, 1970, 8, 59 - 61
Multiplication of certain soil micro-organisms under simulated Martian conditions; Imshenetsky AA et al.; According to earlier observations, severe UV irradiation kills all micro-organisms in a chamber with simulated Martian conditions . However, even a thin soil layer protects buried micro-organisms from UV irradiation . The chief limiting factor for microbial multiplication under simulated Martian conditions seems to be soil humidity . Several micro-organisms were isolated from harsh environments (e.g., from Arctic, Antarctic desert and high-mountain soil samples) . A strain of an oligonitrophilic mycococcus, isolated from Dixon Island, proved to be most resistant to low humidity . It multiplied in a mixture of limonite (maximal hygroscopical humidity 3.8%) + 2% (w/w) garden soil kept in a chamber simulating Martian conditions . Total cell count increased 7.6-fold and, in some experiments, 26-fold in 14 days . The oligonitrophilic mycococcus was able to grow even at a humidity level of 2.5%, that is less than maximal hygroscopical (3.8%) . Under these conditions cell count increased 10-fold in 36 days . Thus, it was shown that even in Earth soils there are xerophytic micro-organisms which are able to multiply in limonite of low humidity . These data might correct our current concepts concerning microbial water requirements . One might speculate that Martian micro-organisms belong to xerophytic species.

Eur J Oral Sci, 2002 Oct, 110(5), 345 - 52
Periodontal microbiota and clinical periodontal status in a rural sample in southern Thailand; Papapanou PN et al.; We sought to determine (i) the association of subgingival bacterial profiles to clinical periodontal status in a population with limited access to dental care in Thailand, and (ii) the external validity of our earlier findings from a similar study in rural China . We examined 356 subjects, 30-39 yr old and 50-59 yr old, with respect to clinical periodontal status and subgingival plaque at maximally 14 sites per subject . Checkerboard hybridizations were used to analyse a total of 4343 samples . The prevalence of the 27 species investigated ranged between 87.2% and 100% . Discriminant analysis based on microbial profiles classified correctly 67.5% of all deep (> or = 5 mm) and 64.2% of all shallow sites, and 67.4% of all subjects with and 69.3% of all subjects without > or = 3 deep pockets . High colonization by 'red complex' bacteria was four times as likely (95% Confidence Limits (CL) 2.5-6.6) in subjects with > or = 10 sites with attachment loss of > or = 5 mm, and 4.3 times as likely (95% CL 2.6-7.1) in subjects with > or = 30 such sites . The data confirmed (i) the ubiquitous prevalence of the bacteria investigated in subjects with no regular access to dental care; and (ii) the high odds for periodontal pathology conferred by increased levels of specific periodontal bacteria.

Blood, 2003 Jul 15, 102(2), 672 - 81 Epub 2003 Mar 27.
Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites; Chaussabel D et al.; Monocyte-derived dendritic cells (DCs) and macrophages (Ms) generated in vitro from the same individual blood donors were exposed to 5 different pathogens, and gene expression profiles were assessed by microarray analysis . Responses to Mycobacterium tuberculosis and to phylogenetically distinct protozoan (Leishmania major, Leishmania donovani, Toxoplasma gondii) and helminth (Brugia malayi) parasites were examined, each of which produces chronic infections in humans yet vary considerably in the nature of the immune responses they trigger . In the absence of microbial stimulation, DCs and Ms constitutively expressed approximately 4000 genes, 96% of which were shared between the 2 cell types . In contrast, the genes altered transcriptionally in DCs and Ms following pathogen exposure were largely cell specific . Profiling of the gene expression data led to the identification of sets of tightly coregulated genes across all experimental conditions tested . A newly devised literature-based clustering algorithm enabled the identification of functionally and transcriptionally homogenous groups of genes . A comparison of the responses induced by the individual pathogens by means of this strategy revealed major differences in the functionally related gene profiles associated with each infectious agent . Although the intracellular pathogens induced responses clearly distinct from the extracellular B malayi, they each displayed a unique pattern of gene expression that would not necessarily be predicted on the basis of their phylogenetic relationship . The association of characteristic functional clusters with each infectious agent is consistent with the concept that antigen-presenting cells have prewired signaling patterns for use in the response to different pathogens.

Blood, 2003 Jul 15, 102(2), 585 - 91 Epub 2003 Mar 27.
Ontogeny and innate properties of neonatal dendritic cells; Sun CM et al.; We investigated whether a developmental immaturity of the dendritic cells (DCs) compartment could contribute to the high susceptibility to infections observed in newborns . DCs are among the first cells to colonize the spleen, but the ontogeny of DC subsets follows distinct steps . At birth, plasmacytoid DCs and CD4-CD8alpha- DCs are found in the spleen, whereas CD8alpha+ and CD4+ DCs are not present . Then, the CD8alpha+ DC compartment quickly develops and reaches an adult size by day 7, whereas the CD4+ DC compartment slowly increases to become predominant by the age of 3 weeks . The production of interleukin (IL)-12p70 by DCs is particularly efficient after birth, reflecting the stronger capacity of the neonatal CD8alpha- DCs to secrete IL-12 compared with its adult counterpart . Like-wise, neonatal DCs produced type I and II interferons . In vivo, following microbial stimulation, up-regulation of major histocompatibility complexes (MHCs) and of costimulatory molecules on DCs was induced clearly showing the activation of neonatal DCs in the neonatal environment . Therefore, despite a markedly different DC subset composition in early life compared with the adult DC compartment, neonatal DCs are fully competent in their innate immune functions.

Sci Total Environ, 2003 Mar 20, 304(1-3), 305 - 13
Methylmercury in rivers draining cultivated watersheds; Balogh SJ et al.; Total mercury (THg) concentrations in streams draining cultivated watersheds in Minnesota, USA are strongly correlated with total suspended sediment (TSS) concentrations, varying widely in response to precipitation-driven inputs of soil-derived suspended sediments . Methylmercury (MeHg) concentrations in these waterways have not been studied, and little is known about mercury uptake mechanisms in resident fish populations . To begin to identify factors influencing MeHg concentrations and loadings in these streams, we measured THg and MeHg concentrations in unfiltered whole water samples from the Minnesota River and two of its major tributaries, the Blue Earth and Le Sueur Rivers . Land use in the watersheds of these rivers is over 90% row-crop agriculture, and extensive artificial drainage systems deliver runoff and associated solids quickly to local streams and rivers . THg concentrations were elevated (>10 ng/l) during much of Spring 2000 and part of the summer when runoff from precipitation events increased stream discharge and carried soil materials into the streams . Reduced precipitation resulted in low flow conditions from August through October, and THg concentrations decreased to <4.0 ng/l in all three rivers . MeHg concentrations in the Le Sueur River ranged from 0.07 to 0.42 ng/l between June and December . Higher MeHg concentrations (>0.2 ng/l) were measured during summer months when THg and TSS concentrations were high after precipitation events . Elevated MeHg concentrations were also observed in late October after leaf litter inputs . Conditions on the Blue Earth River were different, with elevated MeHg concentrations (>0.5 ng/l) observed during low flow in August and September . These higher concentrations coincided with a period of enhanced microbial growth stimulated by high late-summer temperatures . A late-October increase in MeHg concentration attributed to leaf litter inputs was also observed in this river . MeHg concentration trends in the Minnesota River were similar to those in the Blue Earth River . Indicators of biological productivity (chlorophyll a, volatile suspended solids, and total Kjeldahl nitrogen) were higher in the Blue Earth and Minnesota Rivers compared to the Le Sueur River, which may signal a connection between higher biological activity and increased MeHg concentrations.

Int J STD AIDS, 2003 Feb, 14(2), 114 - 8
Evaluation of a novel diagnostic test for bacterial vaginosis: 'the electronic nose'; Hay P et al.; The objectives were, first, to determine the sensitivity and specificity of the Osmetech Microbial Analyser (OMA) for the diagnosis of bacterial vaginosis (BV) and, secondly, to determine the factors that interfere with the performance of the test . Women presenting to a genitourinary medicine clinic underwent routine screening for genital infections . Additional swabs were tested on the OMA, and by Nugent scoring . The optimum method for sampling was determined on the first 372 samples . BV was diagnosed in 182 (27%) of the remaining 665 subjects by Amsel criteria, and 188 (29%) of 642 women with evaluable Gram-stains . The sensitivity and specificity of the OMA were 81.45% and 76.1% compared to Amsel criteria and 82.9% and 77.3% compared to Gramstain . Further refinements to improve the sensitivity and specificity of the OMA are required to provide an accurate near patient testing method.

Environ Microbiol, 2003 Apr, 5(4), 309 - 20
Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock; Takai K et al.; Subsurface microbial community structure in relation to geochemical gradients and lithology was investigated using a combination of molecular phylogenetic and geochemical analyses . Discreet groundwater and substratum samples were obtained from depths ranging from 182 to 190 m beneath the surface at approximately 10-cm intervals using a multilevel sampler (MLS) that straddled Cretaceous shale and sandstone formations at a site in the southern San Juan Basin in New Mexico . DNA and RNA were extracted directly from quartzite sand substratum loaded into individual cells of the MLS and colonized in situ . Polymerase chain reaction (PCR)-mediated T-RFLP analysis of archaeal rRNA genes (rDNA) in conjunction with partial sequencing analysis of archaeal rDNA libraries and quantitative RNA hybridization with oligonucleotide probes were used to probe community structure and function . Although total microbial populations remained relatively constant over the entire depth interval sampled, significant shifts in archaeal populations, predominantly methanogens, were observed . These shifts coincided with the geochemical transition from relatively high methane (26 mM), low sulphate (< 3 mg l(-1)) conditions in the region adjacent to the organic matter-rich shale to relatively low-methane (< 0.5 mM), high-sulphate (48 mg l(-1)) conditions in the organic-poor sandstone beneath the shale . These results indicated that active, phylogenetically diverse archaeal communities were present in the subsurface Cretaceous rock environment at this site and that major archaeal clades shifted dramatically over scales of tens of centimetres, corresponding to changes in the lithology and geochemical gradients.

Environ Microbiol, 2003 Apr, 5(4), 296 - 308
Dimethyl sulphide and methanethiol formation in microbial mats: potential pathways for biogenic signatures; Visscher PT et al.; Mechanisms of dimethyl sulphide (DMS) and methanethiol (MT) production and consumption were determined in moderately hypersaline mats, Guerrero Negro, Mexico . Biological pathways regulated the net flux of DMS and MT as revealed by increases in flux resulting from decreased salinity, increased temperature and the removal of oxygen . Dimethylsulphoniopropionate (DMSP) was not present in these microbial mats and DMS and MT are probably formed by the reaction of photosynthetically produced low-molecular weight organic carbon and biogenic hydrogen sulphide derived from sulphate reduction . These observations provide an alternative to the notion that DMSP or S-containing amino acids are the dominant precursors of DMS in intertidal sediment systems . The major sink for DMS in the microbial mats was biological consumption, whereas photochemical oxidation to dimethylsulphoxide was the major sink for DMS in the overlying water column . Diel flux measurements demonstrated that significantly more DMS is released from the system during the night than during the day . The major consumers of DMS in the presence of oxygen were monooxygenase-utilizing bacteria, whereas under anoxic conditions, DMS was predominantly consumed by sulphate-reducing bacteria and methanethiol was consumed by methanogenic bacteria . Aerobic and anaerobic consumption rates of DMS were nearly identical . Mass balance estimates suggest that the consumption in the water column is likely to be smaller than net the flux from the mats . Volatile organic sulphur compounds are thus indicators of high rates of carbon fixation and sulphate reduction in these laminated sediment ecosystems, and atmospheric sulphur can be generated as a biogenic signature of the microbial mat community.

J Nat Prod, 2003 Mar, 66(3), 392 - 7
Microbial transformation of 18-hydroxy-9,13-epi-ent-pimara-7,15-diene by Gibberella fujikuroi; Fraga BM et al.; The incubation of the diterpene 18-dihydroxy-9,13-epi-ent-pimara-7,15-diene (3) with the fungus Gibberella fujikuroi gave 14 metabolites, 4 and 6-18 . The carbons functionalized were the C-20 methyl and all the secondaries, except C-12 . The main reaction observed was the epoxidation of the 7,8-double bond, which rearranged to form 7-keto derivatives, such as 10-17, or the allylic alcohol 18 . Compound 9 was the only one obtained in which the 7,8-double bond of the substrate remained unaltered . This work confirms that, in the feeding of this type of diterpene with this fungus, the oxidation at C-19, typical of the biosynthesis of gibberellins from ent-kaur-16-ene, is inhibited.

J Nat Prod, 2003 Mar, 66(3), 350 - 6
Biotransformations of the cardiovascular drugs mexrenone and canrenone; Preisig CL et al.; Microbial transformation studies of the cardiovascular drugs mexrenone (1) and canrenone (2) were conducted . Thirty-nine biotransformations of mexrenone and 84 biotransformations of canrenone were analyzed . Metabolism of the substrate was observed in the majority of these cases . Several monohydroxylated derivatives were detected by HPLC-MS-UV and subsequently identified . Two new mexrenone derivatives, 11alpha- (3) and 12beta-hydroxymexrenone (4), and the known metabolite 6beta-hydroxymexrenone (5) were isolated as major products produced by the Beauveria bassiana ATCC 13144 bioconversion (3) and the Mortierella isabellina bioconversion (4 and 5), respectively . Single-elimination products were also sought; however, only the production of the known metabolite Delta(1,2)-mexrenone (6) by several bacteria was confirmed . One new monohydroxylated derivative of canrenone, 9alpha-hydroxycanrenone (7), was isolated as a major product from the Corynespora cassiicola bioconversion . Structure elucidation of all metabolites was based on NMR and HRMS analyses.

Swiss Surg, 2003, 9(1), 9 - 14
{Perioperative antibiotic prophylaxis at the Clinic of Reconstructive Surgery of the Zurich University Hospital}; Spicher I et al.; With the goal of ensuring maximal safety, surgeons tend to apply antibiotic prophylaxis generously to patients undergoing selective operative procedures . However, the indiscriminate or inappropriate use of prophylactic antibiotics i) leads to the selection of resistant microbial organisms and ii) results in an increase in general medical treatment costs . Given this controversy, the clinic of reconstructive surgery implemented in 1999 a set of guidelines for the proper use of antibiotics . Antibiotic prophylaxis was defined as a pre- or perioperative application of antibiotics as a single to maximum triple-shot dose . It was recommended only for operations involving special risk factors or the implantation of alloplastic material . The recommended medication of choice was the widely-accepted standard first-generation cephalosporin product Cefazolin . We have carried out a quality control trial to analyse prospectively our own experience with the implementation of these guidelines and to compare results with a retrospective group of patients . A total of 792 patients (441 in the retrospective group, 351 in the prospective group) were enrolled in the study . About one third of all patients received an antibiotic prophylaxis . Of these, about 3/4 received the antibiotic prophylaxis without having one of the above-mentioned indications . We observed that 35% of all prophylaxis were given for breast surgery, followed by surgery for scar revisions and lipodystrophy . The most commonly used antibiotic was Cefuroxim rather than Cefazolin . There was no significant reduction in the general application of antibiotic prophylaxis yet apparent in the prospective group . However, there was a clear increase in the use of Cefazolin from 0.2% to 13.2% . We conclude that guidelines can be created to reduce the incidence of uninformed and inappropriate decisions, but their implementation requires time, motivation, and thorough and repeated information campaigns.

J Perinat Med, 2003, 31(1), 12 - 22
Matrix metalloproteinase 3 in parturition, premature rupture of the membranes, and microbial invasion of the amniotic cavity; Park KH et al.; OBJECTIVE: Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that are expressed in many inflammatory conditions and contribute to connective tissue breakdown . Stromelysin 1 {matrix metalloproteinase 3 (MMP-3)}, a novel member of this family, is produced in the context of infection and is able to activate the latent forms of other MMPs . The purpose of this study was to determine if parturition (either term or preterm), premature rupture of the membranes (PROM), and microbial invasion of the amniotic cavity are associated with changes in amniotic fluid concentrations of MMP-3 . STUDY DESIGN: A cross-sectional study was conducted, which included women who underwent transabdominal amniocentesis (n = 365) in the following categories: (1) mid-trimester with a subsequent normal pregnancy outcome (n = 84) and a subsequent fetal loss (n = 10); (2) preterm labor with intact membranes without microbial invasion of the amniotic cavity who delivered at term (n = 36), or prematurely (n = 50), and preterm labor with microbial invasion of the amniotic cavity (n = 25); (3) preterm PROM with (n = 25) and without (n = 26) microbial invasion of the amniotic cavity; (4) term with intact membranes in the absence of microbial invasion of the amniotic cavity, in labor (n = 52) and not in labor (n = 31); and (5) term with PROM in the absence of microbial invasion of the amniotic cavity and not in labor (n = 26) . MMP-3 concentrations in amniotic fluid were measured by a sensitive and specific immunoassay that was validated for amniotic fluid . MMP-3 concentrations were normalized using logarithmic transformation for statistical analysis . Parametric statistics were used and a p value < 0.05 was considered statistically significant . RESULTS: (1) MMP-3 was detected in 99.5% (363/365) of amniotic fluid samples, and its concentration did not change with advancing gestational age . (2) Spontaneous parturition at term and preterm was associated with a significant increase in amniotic fluid MMP-3 concentrations (p = 0.04 and p = 0.002, respectively) . (3) Spontaneous rupture of membranes in term and preterm gestations was not associated with significant changes in amniotic fluid MMP-3 concentrations . (4) Intra-amniotic infection was associated with a significant increase in amniotic fluid MMP-3 concentrations in both women with preterm labor and intact membranes (p = 0.03), and women with preterm PROM (p = 0.02) . (5) Subsequent fetal loss after genetic amniocentesis was not associated with significant changes in mid-trimester concentrations of amniotic fluid MMP-3 . CONCLUSIONS: (1) MMP-3 is a physiologic constituent of amniotic fluid . (2) MMP-3 may play a role in the mechanisms of human parturition and in the regulation of the host response to intrauterine infection.

Rapid Commun Mass Spectrom, 2003, 17(7), 660 - 71
Confirmatory analysis of beta-lactam antibiotics in kidney tissue by liquid chromatography/electrospray ionization selective reaction monitoring ion trap tandem mass spectrometry; Fagerquist CK et al.; Eleven beta-lactam antibiotics were analyzed in fortified and incurred beef kidney tissue using high-performance liquid chromatography/electrospray ionization/selective reaction monitoring-ion trap tandem mass spectrometry (LC/ESI-SRM-MS(n)) . The analytes included: deacetylcephapirin, amoxicillin, cephapirin, desfuroylceftiofur cysteine disulfide (DCCD, a biomarker of ceftiofur), ampicillin, cefazolin, Pen G, oxacillin, cloxacillin, naficillin and dicloxicillin . Analytes were extracted with acetonitrile and water . Clean-up was performed by solid-phase extraction . Limits of confirmation in fortified tissue are as follows (tolerances or target levels in parentheses): deacetylcephapirin: 10-50 ng/g (100 ng/g); amoxacillin: 50-100 ng/g (10 ng/g); cephapirin: 10 ng/g (100 ng/g); DCCD: 500 ng/g (8000 ng/g); ampicillin: 10 ng/g (10 ng/g); cefazolin: 10 ng/g (10-50 ng/g); Pen G: 10 ng/g (50 ng/g); oxacillin: 10 ng/g (10-50 ng/g); cloxacillin: 10 ng/g (10 ng/g); naficillin: 10 ng/g (10-50 ng/g); dicloxacillin: 100-500 ng/g (10-50 ng/g) . The present method was also tested on incurred kidney tissue that had previously been analyzed using a microbial assay . Good correspondence was found between the results from this new method and the bioassay . However, the present method is much more specific and, in several cases, more sensitive than the bioassay . In addition, the time of analysis is significantly shorter than the bioassay . We also found that SRM MS(n) was superior in the analysis of unknown incurred tissue than full spectrum MS(n) . We also obtained an MS/MS spectrum of DCCD that is significantly at variance with previously published fragmentation spectra.

Toxicol Sci, 2003 Apr, 72(2), 331 - 8
Effect of preexposure to ultrafine carbon black on respiratory syncytial virus infection in mice; Lambert AL et al.; Epidemiological studies have indicated that exposure to elevated levels of particulate matter exacerbates several pulmonary diseases, including asthma, bronchitis, and viral infections . Respiratory syncytial virus (RSV) is the major cause of bronchiolitis and pneumonia in infants and may lead to the development of asthma in childhood . To determine whether particle exposure modulates the immune response to RSV, eight-week-old female BALB/c mice received an intratracheal (i.t.) instillation of either 40 micro g ultrafine carbon black (CB) particles or vehicle . The following day, mice were i.t . instilled with either 106 pfu RSV or uninfected media . End points were examined 1, 2, 4, 7, and 10 days during RSV infection . Compared with RSV alone, tumor necrosis factor-alpha (TNF-alpha) protein was reduced in the bronchoalveolar lavage fluid (BALF) on days 1 and 2 of infection; there was also a reduction in BALF lymphocyte numbers on day 4, which correlated with reductions in both IFN-gamma-inducible protein (IP-10), lymphotactin, and IFN-gamma mRNAs in the lungs of RSV + CB mice . Multiprobe ribonuclease protection assays of RSV + CB lung tissue showed no changes in the RSV-associated chemokines regulated upon activation, normal T cell expressed and secreted (RANTES), eotaxin, monocyte chemoattractant protein (MCP-1), macrophage inflammatory protein (MIP)-1 alpha or MIP-1 beta . Viral titers in RSV + CB mice were lower than RSV on days 2-4 of infection . By day 7 of infection, however, neutrophil numbers, proinflammatory cytokine mRNA expression, and protein levels of TNF-alpha and the Th2 cytokine interleukin (IL)-13 were increased in the lungs of RSV + CB mice, indicating an exacerbation of infection . These data indicate that preexposure to ultrafine particles induces an inflammatory milieu promoting allergic immune responses rather than IFNgamma production necessary for microbial defense.

Acta Trop, 2003 Mar, 85(3), 375 - 90
Leishmania model for microbial virulence: the relevance of parasite multiplication and pathoantigenicity; Chang KP et al.; Leishmanial mechanisms of virulence have been proposed previously to involve two different groups of parasite molecules . One group consists of largely surface and secretory products, and the second group includes intracellular molecules, referred to as 'pathoantigens' . In the first group are invasive/evasive determinants, which protect not only parasites themselves, but also infected host cells from premature cytolysis . These determinants help intracellular amastigotes maintain continuous infection by growing at a slow rate in the parasitophorous vacuoles of host macrophages . This is illustrated in closed in vitro systems, e.g . Leishmania amazonensis in macrophage cell lines . Although individual macrophages may become heavily parasitized at times, massive destruction of macrophages has not been observed to result from uncontrolled parasite replication . This is thus unlikely to be the direct cause of virulence manifested as the clinical symptoms seen in human leishmaniasis . Of relevance is likely the second group of immunopathology-causing parasite 'pathoantigens' . These are highly conserved cytoplasmic proteins, which have been found to contain Leishmania-unique epitopes immunologically active in leishmaniasis . How these intracellular parasite antigens become exposed to the host immune system is accounted for by periodic cytolysis of the parasites during natural infection . This event is notable with a small number of parasites, even as they grow in an infected culture . The cytolysis of these parasites to release 'pathoantigens' may be inadvertent or medicated by specific mechanisms . Information on the pathoantigenic epitopes is limited . T-cell epitopes have long been recognized, albeit ill-defined, as important in eliciting CD4+ cell development along either the Th1 or Th2 pathway . Their operational mechanisms in suppressing or exacerbating cutaneous disease are still under intensive investigation . However, immune response to B-cell epitopes of such 'pathoantigens' is clearly futile and counterproductive . Their intracellular location within the parasites renders them inaccessible to the specific antibodies generated . One example is the Leishmania K39 epitope, against which antibodies are produced in exceedingly high titers, especially in Indian kala-azar . Here, we consider the hypothetical emergence of this pathoantigenicity and its potential contributions to the virulent phenotype in the form of immunopathology . Microbial virulence may be similarly explained in other emerging and re-emerging infectious diseases . Attenuation of microbial virulence may be achieved by genetic elimination of pathoantigenicity, thereby providing mutants potentially useful as avirulent live vaccines for immunoprophylasis of infectious diseases.

J Chromatogr B Analyt Technol Biomed Life Sci, 2003 Apr 5, 787(1), 77 - 89
Proteomics: general strategies and application to nutritionally relevant proteins; Kvasnicka F; Proteomics as a subset of applied genomics technologies will be a key area of biology during the first decade or two of the new Millennium, and that it will have major impact, both directly and indirectly, on nutritional science . The aim of this review is to summarize information about general strategies of proteome and its application to important food proteins (plant, animal, and microbial) . Methods are also described for protein separation, identification and determination . This article covers papers published within the last decade .

Photochem Photobiol Sci, 2003 Jan, 2(1), 16 - 28
Health effects from stratospheric ozone depletion and interactions with climate change; de Gruijl FR et al.; The potential health effects of elevated levels of ambient UV-B radiation are diverse, and it is difficult to quantify the risks, especially as they are likely to be considerably modified by human behaviour . Nevertheless epidemiological and experimental studies have confirmed that UV radiation is a definite risk factor for certain types of cataract, with peak efficacy in the UV-B waveband . The causal link between squamous cell carcinoma and cumulative solar UV exposure has been well established . New findings regarding the genetic basis of skin cancer, including studies on genetically modified mice, have confirmed the epidemiological evidence that UV radiation contributes to the formation of basal cell carcinomas and cutaneous melanomas, For the latter, animal models have demonstrated that UV exposure at a very young age is more detrimental than exposure in adulthood . Although suppression of certain immune responses has been recognised following UV exposure, the impact of this suppression on the control of infectious and autoimmune diseases is largely unknown . However, studies on several microbial infections have indicated significant consequences in terms of symptoms or reactivation of disease . The possibility that the immune response to vaccination could be depressed by UV-B exposure is of considerable concern . Newly emerging possibilities regarding interactions between ozone depletion and global climate change further complicate the risk assessments for human health but might result in an increased incidence of cataracts and skin cancer, plus alterations in the patterns of certain categories of infectious and other diseases.

Ground Water, 2003 Mar-Apr, 41(2), 247 - 57
MODFLOW/MT3DMS-based reactive multicomponent transport modeling; Prommer H et al.; This paper presents a three-dimensional, MODFLOW/MT3DMS-based reactive multicomponent transport model for saturated porous media . Based on a split-operator technique, the model, referred to as PHT3D, couples the transport simulator MT3DMS and the geochemical modeling code PHREEQC-2 . Through the flexible, generic nature of PHREEQC-2, PHT3D can handle a broad range of equilibrium and kinetically controlled reactive processes, including aqueous complexation, mineral precipitation/dissolution, and ion exchange . The diversity of potential applications is demonstrated through simulation of five existing literature benchmarks and a new three-dimensional sample problem . The model might be applied to simulate the geochemical evolution of pristine and contaminated aquifers as well as their cleanup . The latter problem class includes the natural and enhanced attenuation/remediation schemes of a wide range of organic and inorganic contaminants . Processes/reactions not included in the standard PHREEQC-2 database but typical for this type of application (e.g., NAPL dissolution, microbial growth/decay) can be defined and included via the extensible PHREEQC-2 database file.

Inflamm Bowel Dis, 2003 Jan, 9(1), 28 - 33
Meeting summary: Signal transduction pathways in immune and inflammatory cells . November 30-December 3, 2000, Amelia Island, Florida, U.S.A; Plevy S et al.; Throughout this symposium, recurrent themes were highlighted that may provide important clues to the pathogenesis of mucosal inflammation and IBD . First, the mucosal immune system is unique: Studies describing signaling paradigms in peripheral immunocytes should be re-explored in the gut where the rules that govern cell signaling may not be the same . Paradigms are a point of departure to characterize similarities and differences in mucosal immunity . A good example is a differential requirement for costimulation through CD2 in lamina propria T cells compared with peripheral T cells . Furthermore, a new definition of T-cell "costimulation" is beginning to emerge . Costimulatory molecules may function to overcome physical barriers by allowing cognate interactions between other molecules or by targeting signaling complexes to membrane microdomains . This concept also relates to another recurrent theme: Interactions between signaling pathways and the cytoskeleton are functionally important . Finally, we were introduced to the novel concept of metabolic parameters as a readout for signal transduction in the immune system . In the recent past, cell signaling has been viewed as a linear exercise, connecting a cell surface receptor to a series of intermediate molecules to a program of gene expression . However, signal transduction is in fact a three-dimensional exercise in cell biology . The future challenge, as pointed out in the keynote address, is to integrate reductionist models into reality and describe networks of signal transduction pathways in complex biosystems . "Threshold" responses were emphasized, with a small incremental increase or decrease in enzymatic activity leading to an on-off phenomenon referred to as a "molecular switch." In IBD, minute genetically determined differences in enzymatic activity may be critical . This point emphasizes the power of a genetic approach in IBD . Without strong genetic evidence, it is unlikely that fuctional assays will clarify the importance of small differences in enzymatic activity that may have dramatic biologic consequences . This symposium identified recently described signal transduction molecules that may be attractive therapeutic targets in IBD . Characterization of signaling molecules such as SLP-76, SLAM, SAP, and Fyb in the mucosal immune system will be an important area of future research . Ultimately, well-developed scientific hypotheses need to be tested in human beings . This paradigm was perhaps best illustrated by PPARgamma, where reductionist models and mouse experiments have recently lead to small trials suggesting proof of concept in human IBD . This meeting also emphasized a renewed interest in innate immunity in IBD and inflammation research . The role of enteric flora in initiating and perpetuating inflammation in animal models of IBD suggests at some level the importance of the innate immune response . The role of TLRs and bacterial interactions were discussed, as was NF-kappaB as the prominent transcription factor target of innate immune activation . Numerous bridges between innate and adaptive immunity were highlighted, including IL-10, IL-12, IL-18, and IFN-gamma . Their production during an innate immune response can profoundly affect functional T-cell responses in humans . In conclusion, the challenge of understanding signal transduction in IBD is one of integrating well-characterized inflammatory pathways into a complex biologic system that is inhabited by diverse cell types that communicate, and is characterized by interactions with a complex microbial environment . Making sense of this complexity is a daunting task that will require a multifactorial approach utilizing reductionist systems, mouse models, genetic studies, and ultimately human clinical trials.

Int J Phytoremediation, 2002, 4(2), 157 - 68
Remediation of benzo{a}pyrene and chrysene-contaminated soil with industrial hemp (Cannabis sativa); Campbell S et al.; The phytoremediation, with industrial hemp (Cannabis sativa), of a Hawaiian silty clay soil contaminated with two polycyclic aromatic hydrocarbons (PAHs), chrysene and benzo{a}pyrene, was studied . Hemp showed a very high tolerance to the contaminants . The growth rates of hemp, compared with control, in soils fortified with chrysene and benzo{a}pyrene at concentrations of each varying from 25 to 200 micrograms/g were consistently above 100% . The plants grew from seed for 45 days in soil fortified with PAHs at concentrations of 25, 50, and 75 micrograms/g . Controls were pots with contaminated soil but no plant . PAHs levels were significantly reduced in all pots (control and seeded pots), expect for one set at a high concentration of chrysene, which may be due to uneven spiking . A time course study over 28 days was done to monitor changes of microbial count and levels of chrysene . Little changes were observed for the total microbial count in the soil, and the concentration of chrysene in the soil decreased slightly in the pots containing plants . However, the chrysene levels in those pots were consistently lower than those in the pots without plants.

Nucleic Acids Res . 2003 Apr 1;31(7):e39.
Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments; Zipper H et al.; DNA quantification of soils and sediments is useful for the investigation of microbial communities and for the acquisition of their genomes that are exploited for the production of natural products . However, in such samples DNA quantification is impaired by humic acids (HA) . Due to its lack of specificity and sensitivity, UV spectrophotometry cannot be applied . Consequently, fluorimetric assays applying Hoechst (H) 33258 or PicoGreen (PG) are used . Here, we investigated the SYBR Green I (SG) assay, which was also affected by HA, but was found to be 25- and 1.7-fold more sensitive compared to the H 33258 and PG assays, respectively . Spectrophotometric, fluorimetric and quenching studies as well as gel mobility shift assays suggested that the effect of HA on the SG assay was based on an inner filter effect, collisional quenching and binding of SG to HA . As to the latter finding, the standard 6250-fold dilution of the SG reagent was optimised to a 2000-fold dilution . Although the sensitivity of the optimised SG assay was reduced by a factor of 1.3, the interfering effect of HA could be reduced up to 22-fold . A significant reduction of HA interferences by lowering the pH of the assay was not observed . Finally, the performance of the modified SG assay and the corresponding evaluation methods were verified by the determination of DNA recoveries and concentrations of standards and environmental samples in comparison to the PG assay.

Nucleic Acids Res, 2003 Apr 1, 31(7), 1805 - 12
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes; Roberts RJ et al.; A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products . It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.

J Exp Bot, 2003 Apr, 54(385), 1183 - 91
Isolation and characterization of a cDNA encoding a lipid transfer protein expressed in 'Valencia' orange during abscission; Wu Z et al.; The genetics and expression of a lipid transfer protein (LTP) gene was examined during abscission of mature fruit of 'Valencia' orange . A cDNA encoding an LTP, CsLTP, was isolated from a cDNA subtraction library constructed from mature fruit abscission zones 48 h after application of a mature fruit-specific abscission agent, 5-chloro-3-methyl-4-nitro-pyrazole (CMN-pyrazole) . A full-length cDNA clone of 652 nucleotides was isolated using 5' and 3' RACE followed by cDNA library screening and PCR amplification . The cDNA clone encoded a protein of 155 amino acid residues with a molecular mass and isoelectric point of 9.18 kDa and 9.12, respectively . A partial genomic clone of 505 nucleotides containing one intron of 101 base pairs was amplified from leaf genomic DNA . Southern blot hybridization demonstrated that at least two closely related CsLTP genes are present in 'Valencia' orange . Temporal expression patterns in mature fruit abscission zones were examined by northern hybridization . Increased expression of CsLTP mRNA was detected in RNA of mature fruit abscission zones 6, 24, 48, and 72 h after application of a non-specific abscission agent, ethephon . Low expression of CsLTP transcripts was observed after treatment of CMN-pyrazole until 24 h after application . After this time, expression markedly increased . The results suggest that CsLTP has a role in the abscission process, possibly by assisting transport of cutin monomers to the fracture plane of the abscission zone or through its anti-microbial activity by reducing the potential of microbial attack.

Infect Immun, 2003 Apr, 71(4), 1733 - 9
Modification in the ppk gene of Helicobacter pylori during single and multiple experimental murine infections; Ayraud S et al.; The bacterial pathogen Helicobacter pylori is highly adapted to the human stomach, and a high level of polymorphism is observed among clinical isolates . This polymorphism may be the consequence of adaptive changes during colonization, making a strain better able to survive, to evade the immune system, and to provoke a chronic infection . To investigate the mechanisms involved in the acquisition of diversity in H . pylori, mouse models of single infections, coinfections, and superinfections were developed . These experimental infections were conducted with strain SS1, well known to be mouse adapted, and with two strains freshly isolated from infected patients: Hp141 and Hp145 . Genetic modifications occurring in these strains were studied over time by comparing randomly selected colonies of the emerging strains to those of the infecting strains by using randomly amplified polymorphic DNA fingerprinting with six different primers and by using PCR to amplify the vacA and cagA genes . We showed that, regardless of the number of infecting strains, only one emerged from the animals and that the establishment of a first strain thwarted the implantation of a second strain . During both a single infection and a coinfection with SS1, Hp141 was replaced by a genetic variant (Hp141v) that overcame SS1 in coinfection experiments . Hp141v exhibited a deletion of a 102-bp repeated sequence within the ppk gene, which encodes polyphosphate kinase (PPK), an enzyme involved in the physiological adaptation of the microbial cell to nutritional and environmental stresses . The deletion led to higher enzymatic activity of PPK, and the variant exhibited a better capacity to colonize mice . Considering that the modified gene is known to be involved in adaptation to a new environment, our results are consistent with an adaptive change in strain Hp141 and suggest that PPK is an important virulence factor in H . pylori.

J Dent, 2003 Feb, 31(2), 153 - 7
The efficacy of a toothbrush disinfectant spray-an in vitro study; Neal PR et al.; Objectives . Toothbrushes are contaminated by micro-organisms which may be sources of infection, re-infection or cross infection . The object of this research is to test the efficacy of a proprietary toothbrush spray disinfectant (Brushtox((R))) against specific test bacteria and fungi and to consider its potential.Methods . Three bacteria and two fungi representing a broad microbial spectrum with relevance to oral bacteria were used in four laboratory tests including an in vitro toothbrush disinfection test.Results . Brushtox proved to be almost 100% effective in three tests and showed significant inhibitory action in the standard agar diffusion test.Conclusion . Brushtox is an effective disinfectant agent for bacteria and fungi on toothbrushes . The solution may be valuable in the control of a wide variety of oral infections and secondary infections, especially in frail or debilitated individuals or those on immuno-suppressive therapy, and also in healthy individuals.

Biochem Soc Trans, 2003 Apr, 31(2), 340 - 2
Glucosaminyl N-deacetylase/N-sulphotransferases in heparan sulphate biosynthesis and biology; Kjellen L; During the biosynthesis of heparan sulphate (HS) in the Golgi compartment, the first modification enzyme, glucosaminyl N-deacetylase/N-sulphotransferase (NDST), starts to work on the growing HS polysaccharide chain . This enzyme defines the overall design of the sulphation pattern, which will determine the ability of the HS chain to interact with target molecules . NDST removes acetyl groups from glucosamine residues and replaces them with sulphate groups . These N-sulphate groups are essential for further modification during biosynthesis; without N-sulphation, no O-sulphation or conversion of glucuronic acid into iduronic acid will occur . Four NDST isoforms, transcribed from four genes, have been identified . Much of our work is concentrated on how the enzymes are organized within the Golgi compartment and the identification of interacting partners . In addition, we study mice in which the gene encoding NDST-1 or NDST-2 has been knocked out . NDST-1 knockout mice with altered HS structure die at birth due to lung failure, whereas lack of NDST-2 results in abnormal mast cells . Since NDSTs have a key role in HS design (see above), these mice can be used to study HS function . Areas of interest are cell differentiation, growth, inflammation, cancer, lipid metabolism and microbial infection.

Int Endod J, 2002 Dec, 35(12), 964 - 78
Temporization for endodontics; Naoum HJ et al.; Teeth undergoing root-canal therapy are susceptible to microbial contamination from oral fluids both during and after treatment . With the exception of single-visit treatment, the use of a temporary restoration is mandatory . This review aims to provide an overview of the materials and techniques used for short- and long-term restorations during and immediately after endodontic treatment, and to make clinical recommendations . Further research is necessary to determine the effectiveness of temporary restorations in the conditions of the oral environment, especially with respect to leakage and functional demands.

Bioresour Technol, 2003 Jan, 86(2), 183 - 8
Purification and characterization of extracellular phytase from Aspergillus niger ATCC 9142; Casey A et al.; Extracellular phytase produced by Aspergillus niger ATCC 9142 was purified to homogeneity by employing an initial ultrafiltration step, followed by chromatography using ion exchange, gel filtration and chromatofocusing steps . The purified enzyme was an 84 kDa, monomeric protein . It possessed a temperature optimum of 65 degrees C, and a pH optimum of 5.0 . Km and Vmax values of 100 microM and 7 nmol/s, respectively, were recorded and these values fall well within the range of those previously reported for microbial phytases . Substrate specificity studies indicated that, while the enzyme could hydrolyse a range of non-phytate-based phosphorylated substrates, its preferred substrate was phytate . Phytase activity was moderately stimulated in the presence of Mg2+, Mn2+, Cu2+, Cd2+, Hg2+, Zn2+ and F- ions . Activity was not significantly affected by Fe2- or Fe3- and was moderately inhibited by Ca2+ . The enzyme displayed higher thermostability at 80 degrees C than did two commercial phytase products . Initial characterisation of the purified enzyme suggested that it could be a potential candidate for use as an animal feed supplement.

Am J Pathol, 2003 Apr, 162(4), 1221 - 7
Expression and regulation of Toll-like receptor 2 in rheumatoid arthritis synovium; Seibl R et al.; Toll-like receptors (TLRs) are involved in mediating cell activation on stimulation with microbial constituents . We investigated the role for TLRs in synovial fibroblast (SF) activation in rheumatoid arthritis (RA) . We analyzed whether stimulation with interleukin-1 beta and tumor necrosis factor-alpha, cytokines present in RA synovium, influences expression of TLR genes in SFs . The effects were compared with those of treatment with lipopolysaccharide and a synthetic lipopeptide (sBLP) . Gene expression was examined using quantitative polymerase chain reaction . TLR2-mediated cell activation was investigated by electromobility shift assay for nuclear factor-kappa B . To localize TLR2 expression in joint tissue sections of RA patients were stained using in situ hybridization . Expression of TLR2 in RA SFs was increased after treatment with interleukin-1 beta, tumor necrosis factor-alpha, lipopolysaccharide, and sBLP . Nuclear factor-kappa B translocation in SFs was triggered by TLR2-mediated cell stimulation . Synovial tissues from RA joints expressed TLR2 predominantly at sites of attachment and invasion into cartilage and bone . The observed elevated expression of TLR2 in RA SFs could be a consequence of direct exposure to microbial compounds or of the presence of inflammatory mediators in the joint . TLR-associated signaling pathways may contribute to the pathogenesis of RA, either by initiating or perpetuating activation of SFs.

Tree Physiol, 2000 Jun, 20(11), 745 - 753
Estimating CO(2) flux from snowpacks at three sites in the Rocky Mountains; McDowell NG et al.; Soil surface CO(2) flux (F(s)) is the dominant respiratory flux in many temperate forest ecosystems . Snowpacks increase this dominance by insulating the soil against the low temperature to which aboveground components are exposed . However, measurement of F(s) in winter may be impeded by snow cover . Likewise, developing annual F(s) models is complicated by seasonal variation in root and microbial metabolism . We compared three methods of measuring sub-snow F(s): (1) dynamic chamber measurements at the upper snowpack surface (F(snow)), (2) dynamic chamber measurements at the soil surface via snowpits (F(soil)), and (3) static estimates based on measured concentrations of carbon dioxide ({CO(2)}) and conductance properties of the snowpack (F(diffusional)) . Methods were compared at a mid-elevation forest in northeastern Washington, a mid-elevation forest in northern Idaho, and a high-elevation forest and neighboring meadow in Wyoming . The methods that minimized snowpack disturbance, F(diffusional) and F(snow), yielded similar estimates of F(s) . In contrast, F(soil) yielded rates two to three times higher than F(snow) at the forested sites, and seven times higher at the subalpine meadow . The ratio F(soil)/F(snow) increased with increasing snow depth when compared across all sites . Snow removal appears to induce elevated soil flux as a result of lateral CO(2) diffusion into the pit . We chose F(snow) as our preferred method and used it to estimate annual CO(2) fluxes . The snowpack was present for 36% of the year at this site, during which time 132 g C m(-2), or 17% of the annual flux, occurred . We conclude that snowpack CO(2) flux is quantitatively important in annual carbon budgets for these forests and that the static and dynamic methods yield similar and reasonable estimates of the flux, as long as snowpack disturbance is minimized.

Protein Expr Purif, 2003 Mar, 28(1), 182 - 9
Purification and properties of 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase involved in microbial degradation of carbazole; Riddle RR et al.; Hydrolysis following meta-ring cleavage by a dioxygenase is a well-known step in aromatic compound metabolism . The 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase from Pseudomonas LD2 is a new member of the small group of characterized aromatic hydrolases that catalyze the cleavage of C-C bonds . In this study, the His(6)-tagged 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid (HOPDA) hydrolase was purified from a recombinant Escherichia coli strain utilizing immobilized metal affinity chromatography . 2-Hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase is a colorless homodimer with no cofactor requirement . The enzyme actively converted HOPDA into benzoic acid and 2-hydroxypenta-2,4-dienoic acid . The enzyme exhibited activity between pH 6.5 and 10.5 with a maximum activity at pH 7.0 . The optimum temperature at pH 7.0 was 60 degrees C . The calculated K'(m) for HOPDA was 4.6 microM, the V(max) was 3.3 micromol min(-1), and the K(s) was 70.0 microM . This corresponds to a maximum specific turnover rate of 1300 HOPDAs(-1)dimer(-1) . The deduced amino acid sequence of CarC showed 30.3, 31.3, and 31.8% identity with TodF (P . putida F1), XylF (P . putida), and DmpD (Pseudomonas sp . CF600), respectively, which are meta-cleavage compound hydrolases from other Pseudomonads . The amino acid sequence Gly-X-Ser-X-Gly, which is highly conserved in these hydrolases, is also found in CarC . Lysates from a strain expressing enzyme in which the putative active site serine is mutated to alanine showed a significant reduction in activity.

Appl Occup Environ Hyg, 2003 Jan, 18(1), 41 - 50
Rapid detection and determination of the aerodynamic size range of airborne mycobacteria associated with whirlpools; Schafer MP et al.; Novel environmental air and water mycobacteria sampling and analytical methods are needed to circumvent difficulties associated with the use of culture-based methodologies . To implement this objective, a commercial, clinical, genus DNA amplification method utilizing the polymerase chain reaction (PCR) was interfaced with novel air sampling strategies in the laboratory . Two types of air samplers, a three-piece plastic, disposable filter cassette and an eight-stage micro-orifice uniform deposit impactor (MOUDI), were used in these studies . In both samplers, 37-mm polytetrafluoroethylene (PTFE) filters were used . Use of the MOUDI sampler permitted the capture of airborne mycobacteria in discrete size ranges, an important parameter for relating the airborne mycobacteria cells to potential respirable particles (aerodynamic diameter <10 microm) capable of causing health effects . Analysis of the samples was rapid, requiring only 1-1.5 days, as no microbial culturing or DNA purification was required . This approach was then used to detect suspected mycobacteria contamination associated with pools at a large public facility . PCR was also used to analyze various water samples from these pools . Again, no culturing or sample purification was required . Water samples taken from all ultraviolet light/hydrogen peroxide-treated whirlpools tested positive for the presence of mycobacteria . No mycobacteria were detected in the chlorine-treated pools and the water main supply facility . All air samples collected in the proximity of the indoor whirlpools and the associated changing rooms were strongly positive for airborne mycobacteria . The airborne mycobacteria particles were predominantly collected on MOUDI stages 1-6 representing an aerodynamic size range of 0.5 to 9.9 microm . In conclusion, using this approach permits the rapid detection of mycobacteria contamination as well as the routine monitoring of suspected pools . The approach circumvents problems associated with culture-based methods such as fungal overgrowth on agar plates, and the presence of nonculturable or difficult to culture mycobacteria strains.

Int Rev Immunol, 2002 Nov-Dec, 21(6), 497 - 513
Female sex hormones as regulatory factors in the vaginal immune compartment; Rakasz E et al.; Sexually transmitted diseases (STD) are now considered to be among the most common human infections . The incidence of STD is on the rise, which is partly due to frequent transmission during the asymptomatic phase of infection . The compounded cost of STD just in the United States is estimated to exceed $10 billion annually . STD are particularly prevalent in teenagers and young adults and the health problems caused by these diseases tend to be more severe and more frequent in woman than in men . Despite considerable efforts, a vaccine that provides protective immunity against sexually transmitted diseases in humans has not been developed . Nonetheless, research in animal models indicates that strong local and regional immune responses can influence the outcome of vaginal challenge with microbial pathogens . Vaginal immunity is an area of basic immunology that has received relatively little attention, but it is already clear that the mucosal and regional immunology of the vagina has unique features . The present review summarizes some of the anatomical, physiological and immunological features of the vagina and uterus that distinguish humans, non-human primates, rats and mice . These interspecies differences need to be taken into account in laboratory efforts to develop effective vaccines for STD in humans.

J Dairy Sci, 2003 Feb, 86(2), 486 - 97
Relationships between flavoring capabilities, bacterial composition, and geographical origin of natural whey cultures used for traditional water-buffalo mozzarella cheese manufacture; Mauriello G et al.; Natural whey cultures (NWC) (n = 29) used for traditional water-buffalo Mozzarella cheese manufacture and arising from different geographical areas of production were characterized and grouped on the basis of their capability to develop neutral volatile compounds and according to their microbial diversity as revealed by molecular analysis . The flavoring properties of NWC were studied in dairy microcosms resembling the specific technological procedure used in the traditional water-buffalo Mozzarella cheese-making . Neutral volatile compounds were identified by high-resolution gas chromatography (HRGC)-mass spectrometry analysis while information on the microbial diversity occurring in the NWC was retrieved by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rDNA after direct DNA extraction . Neoformation volatile substances (n = 27) were found; 23 were identified and some of them recognized as odor-conferring molecules . Eight different bands, referable to eight microbial species, were obtained by PCR-DGGE analysis of the NWC . Statistical analyses were applied to PCR-DGGE and HRGC data . Interestingly, the flavoring capabilities and the microbial diversity of the NWC proved to be closely linked and both related to the geographical origin of the NWC . These results suggested a possible use of the molecular characterization of the dairy products to support the traceability criteria of typical dairy products like water-buffalo Mozzarella cheese.

Oecologia, 2003 Feb, 134(3), 388 - 96 Epub 2003 Jan 09.
Microbial impacts on plant-herbivore interactions: the indirect effects of a birch pathogen on a birch aphid; Johnson SN et al.; The role of indirect interactions in structuring communities is becoming increasingly recognised . Plant fungi can bring about changes in plant chemistry which may affect insect herbivores that share the same plant, and hence the two may interact indirectly . This study investigated the indirect effects of a fungal pathogen ( Marssonina betulae) of silver birch ( Betula pendula) on an aphid ( Euceraphis betulae), and the processes underpinning the interaction . There was a strong positive association between natural populations of the aphid and leaves bearing high fungal infection . In choice tests, significantly more aphids settled on leaves inoculated with the fungus than on asymptomatic leaves . Individual aphids reared on inoculated leaves were heavier, possessed longer hind tibiae and displayed enhanced embryo development compared with aphids reared on asymptomatic leaves; population growth rate was also positively correlated with fungal infection when groups of aphids were reared on inoculated branches . Changes in leaf chemistry were associated with fungal infection with inoculated leaves containing higher concentrations of free-amino acids . This may reflect a plant-initiated response to fungal attack in which free amino acids from the degradation of mesophyll cells are translocated out of infected leaves via the phloem . These changes in plant chemistry are similar to those occurring during leaf senescence, and are proposed as the mechanistic basis for the positive interaction between the fungus and aphid.

J Immunol, 2003 Apr 1, 170(7), 3468 - 77
CpG-A oligonucleotides induce a monocyte-derived dendritic cell-like phenotype that preferentially activates CD8 T cells; Krug A et al.; Human B cells and plasmacytoid dendritic cells recognize CpG motifs within microbial DNA via Toll-like receptor 9 . Two functionally distinct types of CpG motif containing oligonucleotides (CpG ODN) have been described, CpG-A and CpG-B . In contrast to CpG-B, CpG-A induces high amounts of type I IFN (IFN-alpha and IFN-beta) in plasmacytoid dendritic cells . In the present study, we examined the effects of CpG-A on human primary monocytes . In PBMC stimulated with CpG-A and GM-CSF, monocytes showed excellent survival, increased in size and granularity, and within 3 days developed a dendritic cell-like phenotype that was characterized by down-regulation of CD14, partial up-regulation of CCR7, and an increased surface expression of costimulatory and Ag-presenting molecules . This effect could be inhibited by a combination of blocking Abs to type I IFN, and no such CpG-A-induced changes were observed in purified monocytes . Although IL-12 production by this dendritic cell-like phenotype required additional stimulation with CD40 ligand, this cell type spontaneously up-regulated IL-15 expression . Consistent with the known effect of IL-15 on effector and memory CD8 T cells, the frequency of CCR7(-)/CD45RA(-) CD8 T cells was selectively increased in allogeneic T cell assays . Furthermore, this dendritic cell type was more potent to support both the generation and the IFN-gamma production of autologous influenza matrix peptide-specific memory CD8 T cells as compared with dendritic cells generated in the presence of GM-CSF and IL-4 . In conclusion, monocytes exposed to the cytokine milieu provided by CpG-A rapidly develop a dendritic cell-like phenotype that is well equipped to support CD8 T cell responses.

J Immunol, 2003 Apr 1, 170(7), 3451 - 4
Cutting edge: a Toll-like receptor 2 polymorphism that is associated with lepromatous leprosy is unable to mediate mycobacterial signaling; Bochud PY et al.; Toll-like receptors (TLRs) are key mediators of the innate immune response to microbial pathogens . We investigated the role of TLRs in the recognition of Mycobacterium leprae and the significance of TLR2Arg(677)Trp, a recently discovered human polymorphism that is associated with lepromatous leprosy . In mice, TNF-alpha production in response to M . leprae was essentially absent in TLR2-deficient macrophages . Similarly, human TLR2 mediated M . leprae-dependent activation of NF-kappaB in transfected Chinese hamster ovary and human embryonic kidney 293 cells, with enhancement of this signaling in the presence of CD14 . In contrast, activation of NF-kappaB by human TLR2Arg(677)Trp was abolished in response to M . leprae and Mycobacterium tuberculosis . The impaired function of this TLR2 variant provides a molecular mechanism for the poor cellular immune response associated with lepromatous leprosy and may have important implications for understanding the pathogenesis of other mycobacterial infections.

AAPS PharmSci . 2002;4(4):E33.
Evolving importance of biologics and novel delivery systems in the face of microbial resistance; Bowersock TL; Methods to control infectious diseases in livestock are growing in importance . As the size of the average farm increases - for poultry, dairy and beef cattle, swine, and fish - the risk of rapid spread of infectious diseases increases as well . This increases the need for alternative methods of control of infectious agents . Improvements in specific immunogens, adjuvants, and delivery systems are needed to meet the demand for vaccines to ensure a healthy and safe meat supply . This article explores the challenges, trends, and recent advances in the control of infectious diseases through the use of biologics.

Eur J Immunol, 2003 Feb, 33(2), 381 - 91
A novel ligand for the NKG2D receptor activates NK cells and macrophages and induces tumor immunity; Diefenbach A et al.; NK cells are involved in the immune response against viral and microbial infections and tumors . In contrast to B and T cells, NK cells employ various modes of immune recognition . An important mode of immune recognition employed by NK cells is "induced self recognition" exemplified by the NKG2D receptor-ligand system . The NKG2D immunoreceptor, expressed by NK cells, and by activated CD8+ T cells and macrophages, recognizes one of several cell surface ligands that are distantly related to MHC class I molecules (i.e . H60 and Rae1 proteins in mice, and MHC class I chain-related proteins and UL-16-binding proteins in humans) . These ligands are not expressed abundantly by most normal cells but are up-regulated on cells exposed to various forms of cellular insults . Here we report the cloning of another ligand for NKG2D; transcripts of this ligand are found in a wide variety of tissues and in various tumor cells . Cross-linking of NKG2D with the novel ligand potently activated NK cells and macrophages . Tumor cells ectopically expressing the molecule were efficiently rejected by naive mice, and induced strong protective immunity to the parental, ligand-negative tumor cells.

Immunol Allergy Clin North Am, 2003 Feb, 23(1), 117 - 32
Atherosclerosis as a paradigmatic disease of the elderly: role of the immune system; Knoflach M et al.; When a new hypothesis about the etiology and pathogenesis of a disease is developed, there is always the danger that it will be presented as the only acceptable explanation for the occurrence of a given pathologic condition . In view of the well-proven multifactoral pathogenesis of atherosclerosis, we would like to emphasize that we are not postulating that immunity to HSP60 is the only cause of atherogenesis, especially in the later stages where there are clinically-apparent sequelae, such as myocardial infarction, stroke, and other atherosclerosis-dependent symptoms . In this article, we summarized some of the experimental and clinical data that we and others have collected in support of the concept that atherosclerosis is a good example of pleotropic antagonism, and postulated that age-dependent diseases are the price we pay for genetic traits established by natural selection to assure maximum survival until the age of reproduction, the effects of which may, however, become deleterious later in life . In the present case, the cost we pay for protective immunity to microbial and altered autologous HSP60 is the risk of cross-reactivity with HSP60 expressed by arterial endothelial cells that are subjected to stress factors already known as classical atherosclerosis risk factors . We showed that the first inflammatory stage of atherosclerosis starts early in life, long before it becomes clinically apparent . More severe lesions that lead to atherosclerosis-dependent organ-specific or systemic symptoms will only occur if classical atherosclerosis risk factors, especially those involving the cholesterol metabolism, remain present.

FEMS Microbiol Lett, 2003 Mar 14, 220(1), 29 - 33
The effect of soil: water ratios on the mineralisation of phenanthrene: LNAPL mixtures in soil; Doick KJ et al.; Contamination of soil by polycyclic aromatic hydrocarbons is frequently associated with non-aqueous-phase liquids . Measurement of the catabolic potential of a soil or determination of the biodegradable fraction of a contaminant can be done using a slurried soil respirometric system . This work assessed the impact of increasing the concentration of transformer oil and soil:water ratio on the microbial catabolism of {(14)C}phenanthrene to (14)CO(2) by a phenanthrene-degrading inoculum . Slurrying (1:1, 1:2, 1:3 and 1:5 soil:water ratios) consistently resulted in statistically higher rates and extents of mineralisation than the non-slurried system (2:1 soil:water ratio; P<0.01) . The maximum extents of mineralisation observed occurred in the 1:2-1:5 soil:water ratio microcosms irrespective of transformer oil concentration . Transformer oil concentrations investigated displayed no statistically significant effect on total mineralisation (P>0.05) . Soil slurries 1:2 or greater, but less than 1:5 (soil:water), are recommended for bioassay determinations of total contaminant bioavailability due to greater overall mineralisation and improved reproducibility.

J Biomol Struct Dyn, 2003 Apr, 20(5), 687 - 92
RNA binding efficacy of theophylline, theobromine and caffeine; Johnson IM et al.; The binding of naturally occurring methylxanthines such as theophylline, theobromine and caffeine to nucleic acids are reckoned to be pivotal as they are able to modulate the cellular activities . We explore the interaction of yeast RNA binding efficacy of the above xanthine derivatives by using UV absorption differential spectroscopy and Fourier Transform Infrared (FTIR) spectroscopy . Both the analyses show discrimination in their binding affinity to RNA . The differential UV-spectrum at P/D 3.3 reveals the greater RNA binding activity for theophylline (85 +/- 5%), whereas moderate and comparatively less binding activity for theobromine (45 +/- 5%) and caffeine (30 +/- 5%) and the binding activity was found to depend on concentration of the drugs . In FTIR analysis we observed changes in the amino group (NH) of RNA complexed by drugs, where the NH band is found to become very broad, indicating hydrogen bonding (H-bonding) with theophylline (3343.4 cm(-1)), theobromine (3379.8 cm(-1)) and caffeine (3343 cm(-1)) as compared to the free RNA (3341.6 cm(-1)) . Furthermore in RNA-theophylline complex, it is observed that the carbonyl (C=O) vibration frequency (nu(C=O)) of both drug (nu(C=O)=1718, 1666 cm(-1)) as well as RNA (nu(C=O)=1699, 1658 cm(-1)) disappeared and a new vibration band appeared around 1703 cm(-1), indicating that the C=O and NH groups of drug and RNA are effectively involved in H-bonding . Whereas in RNA-theobromine and RNA-caffeine complexes, we found very little changes in C=O frequency and only broadening of the NH band of RNA due to complexation is observed in these groups . The changes in the vibrations of G-C/A-U bands and other bending frequencies are discussed . Thus the discrimination in the binding affinity of methylxanthines with RNA molecule shows that strong RNA binding drugs like theophylline can selectively be delivered to RNA targets of microbial pathogens having the mechanism of RNA catalysis.

Bioconjug Chem, 2003 Mar-Apr, 14(2), 351 - 7
S-peptide as a potent peptidyl linker for protein cross-linking by microbial transglutaminase from Streptomyces mobaraensis; Kamiya N et al.; We have found that ribonuclease S-peptide can work as a novel peptidyl substrate in protein cross-linking reactions catalyzed by microbial transglutaminase (MTG) from Streptomyces mobaraensis . Enhanced green fluorescent protein tethered to S-peptide at its N-terminus (S-tag-EGFP) appeared to be efficiently cross-linked by MTG . As wild-type EGFP was not susceptible to cross-linking, the S-peptide moiety is likely to be responsible for the cross-linking . A site-directed mutation study assigned Gln15 in the S-peptide sequence as the sole acyl donor . Mass spectrometric analysis showed that two Lys residues (Lys5 and Lys11) in the S-peptide sequence functioned as acyl acceptors . We also succeeded in direct monitoring of the cross-linking process by virtue of fluorescence resonance energy transfer (FRET) between S-tag-EGFP and its blue fluorescent color variant (S-tag-EBFP) . The protein cross-linking was tunable by either engineering S-peptide sequence or capping the S-peptide moiety with S-protein, the partner protein of S-peptide for the formation of ribonuclease A . The latter indicates that S-protein can be used as a specific inhibitor of S-peptide-directed protein cross-linking by MTG . The controllable protein cross-linking of S-peptide as a potent substrate of MTG will shed new light on biomolecule conjugation.

J Proteome Res, 2003 Jan-Feb, 2(1), 89 - 93
Solubilization of trichloroacetic acid (TCA) precipitated microbial proteins via naOH for two-dimensional electrophoresis; Nandakumar MP et al.; In preparing intracellular microbial samples for one- or two-dimensional electrophoresis, trichloroacetic acid (TCA) precipitation is frequently used to remove interfering compounds . Solubilization of TCA precipitate typically requires the addition of a number of chaotropes or detergents, in a multistep process, that requires hours to carry out . In this study, a simple, rapid, one-step method to solubilize TCA precipitated proteins is presented . Precipitated proteins are pretreated with 0.2 M NaOH for less than 5 min, followed by addition of standard sample solubilization buffer (SSSB) . When compared to solubilization with SSSB alone, NaOH pretreatment of TCA-precipitated intracellular protein from Aspergillus oryzae and Escherichia coli shows an approximate 5-fold increase in soluble protein . In addition, two-dimensional gel electrophoresis on resolubilized proteins shows an equivalent number of proteins in samples with and without NaOH pretreatment.

J Allergy Clin Immunol, 2003 Mar, 111(3), 471 - 8
Hygiene hypothesis: fact or fiction?
Liu AH, Murphy JR.
The hygiene hypothesis of asthma and allergy has recently received a swell of popularity and published supporting evidence, and has been extended to autoimmune conditions of childhood . Broadly stated, naturally occurring infections and microbial exposures might essentially immunize against the development of asthma and allergic and autoimmune diseases . If true, then reductions in nature's immunotherapy over the past century might be a major factor in the global increase of these conditions (eg, the higher prevalence of asthma and allergies in urban metropolitan areas compared with rural and farm communities) and might lead to new therapies for these conditions . Although such a unifying hypothesis has great appeal, currently it is only speculation about what might be at the end of the investigative road . How close are the current studies to establishing a causal relationship between microbial exposures and a reduction in allergic, asthmatic, and autoimmune disease prevalence? A systematic epidemiologic appraisal of the current hygiene hypothesis evidence can provide a critical analysis of what is currently known and an investigative blueprint for future studies that can ultimately prove causation and improve recommendations, interventions, and therapies.

J Chromatogr A, 2003 Mar 7, 989(1), 109 - 18
Direct enzyme adsorption from an unclarified microbial feedstock using suspended bed chromatography; Ling TC et al.; Suspended bed chromatography (SBC) is a new hybrid technique concomitantly benefiting from batch adsorption, the process advantages of an enclosed system, and its compatibility with established commercial chromatographic contactors and adsorbents . SBC was evaluated in the anion-exchange capture and chromatographic fractionation of native glyceraldehyde-3-phosphate dehydrogenase (G3PDH) from the complex mixture of molecular and particulate moieties that constitute wet-milled bakers' yeast . Method scouting established operating conditions exploiting Whatman Express-Ion Exchanger Q at pH 7.5 and a disrupted biomass concentration equivalent to 3.5% (wet mass/v original intact cells) . Partially purified G3PDH was recovered directly from the yeast disruptate in a scaled-down process developed at 1/756 process scale . This was used to establish operating parameters to facilitate process scale-up to exploit a 44 cm I.D . Millipore IsoPak column, 18 kg (swollen mass) of Express-Ion Q anion-exchange cellulose and 275 1 of 3.5% (wet w/v) bakers' yeast disruptate . The generic utility of SBC was demonstrated for direct product adsorption from feedstocks characterised by a modest content of bioparticulates (equivalent to < 4% (wet w/v) disrupted cells) . Analyses illustrated an enrichment of G3PDH in respect of enzyme concentration and significant reduction in product turbidity and Pico-Green reactivity (correlated with double stranded (ds) DNA content) . The application niche for this new approach to primary protein recovery is discussed with particular reference to the downstream processing of coarsely clarified whole broths, cell disruptates and biological extracts.

Mol Cell Biol, 2003 Apr, 23(7), 2501 - 14
Modulation of Rab5 and Rab7 recruitment to phagosomes by phosphatidylinositol 3-kinase; Vieira OV et al.; Phagosomal biogenesis is central for microbial killing and antigen presentation by leukocytes . However, the molecular mechanisms governing phagosome maturation are poorly understood . We analyzed the role and site of action of phosphatidylinositol 3-kinases (PI3K) and of Rab GTPases in maturation using both professional and engineered phagocytes . Rab5, which is recruited rapidly and transiently to the phagosome, was found to be essential for the recruitment of Rab7 and for progression to phagolysosomes . Similarly, functional PI3K is required for successful maturation . Remarkably, inhibition of PI3K did not preclude Rab5 recruitment to phagosomes but instead enhanced and prolonged it . Moreover, in the presence of PI3K inhibitors Rab5 was found to be active, as deduced from measurements of early endosome antigen 1 binding and by photobleaching recovery determinations . Though their ability to fuse with late endosomes and lysosomes was virtually eliminated by wortmannin, phagosomes nevertheless recruited a sizable amount of Rab7 . Moreover, Rab7 recruited to phagosomes in the presence of PI3K antagonists retained the ability to bind its effector, Rab7-interacting lysosomal protein, suggesting that it is functionally active . These findings imply that (i) dissociation of Rab5 from phagosomes requires products of PI3K, (ii) PI3K-dependent effectors of Rab5 are not essential for the recruitment of Rab7 by phagosomes, and (iii) recruitment and activation of Rab7 are insufficient to induce fusion of phagosomes with late endosomes and lysosomes . Accordingly, transfection of constitutively active Rab7 did not bypass the block of phagolysosome formation exerted by wortmannin . We propose that Rab5 activates both PI3K-dependent and PI3K-independent effectors that act in parallel to promote phagosome maturation.

Ann Occup Hyg, 2003 Apr, 47(3), 187 - 200
Bioaerosol health effects and exposure assessment: progress and prospects; Douwes J et al.; Exposures to bioaerosols in the occupational environment are associated with a wide range of health effects with major public health impact, including infectious diseases, acute toxic effects, allergies and cancer . Respiratory symptoms and lung function impairment are the most widely studied and probably among the most important bioaerosol-associated health effects . In addition to these adverse health effects some protective effects of microbial exposure on atopy and atopic conditions has also been suggested . New industrial activities have emerged in recent years in which exposures to bioaerosols can be abundant, e.g . the waste recycling and composting industry, biotechnology industries producing highly purified enzymes and the detergent and food industries that make use of these enzymes . Dose-response relationships have not been established for most biological agents and knowledge about threshold values is sparse . Exposure limits are available for some contaminants, e.g . wood dust, subtilisins (bacterial enzymes) and flour dust . Exposure limits for bacterial endotoxin have been proposed . Risk assessment is seriously hampered by the lack of valid quantitative exposure assessment methods . Traditional culture methods to quantify microbial exposures have proven to be of limited use . Non-culture methods and assessment methods for microbial constituents {e.g . allergens, endotoxin, beta(1-->3)-glucans, fungal extracellular polysaccharides} appear more successful; however, experience with these methods is generally limited . Therefore, more research is needed to establish better exposure assessment tools and validate newly developed methods . Other important areas that require further research include: potential protective effects of microbial exposures on atopy and atopic diseases, inter-individual susceptibility for biological exposures, interactions of bioaerosols with non-biological agents and other potential health effects such as skin and neurological conditions and birth effects.

Curr Issues Mol Biol, 2003 Jan, 5(1), 9 - 15
Using flow cytometry to quantify microbial heterogeneity; Davey HM et al.; Flow cytometry is a powerful technique for the study of single cells, and thus it is of particular utility in the study of heterogeneity in microbial populations . This review seeks to highlight the role of flow cytometric analyses in studies of microbial heterogeneity, drawing wherever possible on recently published research articles . Whilst microbial heterogeneity is well documented in both natural and laboratory environments, the underlying causes are less well understood . Possible sources for the heterogeneity that is observed in microbial systems are discussed, together with the flow cytometric tools that aid its study . The role of flow cytometry in molecular biology is discussed with reference to gene reporter systems, which enable heterogeneity of gene expression to be monitored . With the recent sequencing of a variety of microbial genomes, it is anticipated that flow cytometry will have an increasing role to play in studying the effects of gene expression and mutation on heterogeneity, and in resolving the interactions of genetics and physiology.

Curr Issues Mol Biol, 2003 Jan, 5(1), 1 - 8
Direct extraction of DNA from soils for studies in microbial ecology; Schneegurt MA et al.; Molecular analyses for the study of soil microbial communities often depend on the extraction of DNA directly from soils . These extractions are by no means trivial, being complicated by humic substances that are inhibitory to PCR and restriction enzymes or being too highly colored for blot hybridization protocols . Many different published protocols exist, but none have been found to be suitable enough to be generally accepted as a standard . Most direct extraction protocols start with relatively harsh cell breakage steps such as bead-beating and freeze-thaw cycles, followed by the addition of detergents and high salt buffers and/or enzymic digestion with lysozyme and proteases . After typical organic extraction and alcohol precipitation, further purification is usually needed to remove inhibitory substances from the extract . The purification steps include size-exclusion chromatography, ion-exchange chromatography, silica gel spin columns, and cesium chloride gradients, among others . A direct DNA extraction protocol is described that has been shown to be effective in a wide variety of soil types . This protocol is experimentally compared to several published protocols.

Science, 2003 Mar 14, 299(5613), 1694 - 7
Dispelling the myths--biocatalysis in industrial synthesis; Schoemaker HE et al.; Biocatalysis has emerged as an important tool in the industrial synthesis of bulk chemicals, pharmaceutical and agrochemical intermediates, active pharmaceuticals, and food ingredients . However, the number and diversity of the applications are modest, perhaps in part because of perceived or real limitations of biocatalysts, such as limited enzyme availability, substrate scope, and operational stability . Recent scientific breakthroughs in genomics, directed enzyme evolution, and the exploitation of biodiversity should help to overcome these limitations . As a result, we expect many new industrial applications of biocatalysis to be realized, from single-step enzymatic conversions to customized multistep microbial synthesis by means of metabolic pathway engineering.

Environ Sci Technol, 2003 Feb 15, 37(4), 707 - 12
Degradation of racemic and enantiopure metalaxyl in tropical and temperate soils; Monkiedje A et al.; The degradation of the racemic mixture and the enantiomers of metalaxyl in typical soils from Germany and Cameroon has been studied . Formulated and unformulated R-metalaxyl were studied as well as racemic (rac) metalaxyl in controlled incubation experiments . The kinetics of the degradation or transformation were determined by means of reversed phase HPLC, while the enantiomeric ratios were measured by HPLC with a chiral Whelk O1 column . The degradation followed first-order kinetics (R2 > or = 0.96) . Higher metalaxyl acid metabolite concentrations were found in German soil than in Cameroonian soil . The enantiomers of the fungicide each had different degradation rates in both soils, with half-lives ranging from 17 to 38 days . All forms of metalaxyl had lower degradation rates in the Cameroonian soil than in the German soil . The degradation . of the R-enantiomer was much faster than the S-enantiomer in the German soil and slower than the S-enantiomer in the Cameroonian soil suggesting that different microbial populations, which may be using different enzymes, have different degradation preferences . The results for the major differences in the degradation of the enantiomers may have some implication for the frequency of use as well as the environmental assessment for chiral pesticides.

Nat Prod Rep, 2003 Feb, 20(1), 137 - 66
The C7N aminocyclitol family of natural products; Mahmud T; This review covers microbial secondary metabolites classified in the family of C7N aminocyclitols, a relatively new class of natural products that is increasingly gaining recognition due to their significant biomedical and agricultural uses . Their discovery and structure determinations, their biosynthetic origin, biological properties, chemical synthesis, as well as their further development for pharmaceutical uses are described . The literature from 1970 to July 2002 is reviewed, with 269 references cited.

Anaesth Intensive Care, 2003 Feb, 31(1), 28 - 33
Intermittent enteral nutrition--a comparative study examining the effect on gastric pH and microbial colonization rates; Gowardman J et al.; In a prospective randomized study we aimed to examine the effect on gastric pH and microbial colonization of enteral nutrition (EN) delivered both by intermittent and continual infusion . Forty-three mechanically ventilated patients were randomized to receive EN by one of three methods, intermittent or continual gastric or continual jejunal . We sampled gastric aspirate for pH and culture in all patients at 0600 hours and pH in gastric intermittent feeders at 2200 hours daily . Patients were studied for 12 days or until extubated . Data was obtained on 41 patients, of whom 73% had a diagnosis of trauma . Median APACHE II score was 17 and ventilation time 11 days . Twelve patients received gastric continuous, 15 gastric intermittent and 14 jejunal nutrition . No significant difference was observed between the three groups with regard to median 0600 pH (P = 0.16) . This was lowest in the jejunal group (3.2) followed by the gastric intermittent group (4.0) and then gastric continuous group (5.0) . With overnight cessation of EN in the gastric intermittent group, the median pH fell from 5.2 at 2200 to 4.0 at 0600 (P = 0.01) with no effect on gastric colonization . The probability of gastric colonization over time however was significantly lower in the jejunal group compared with the two gastric groups (Log rank test, P = 0.02) . These results demonstrate that in a patient population consisting predominantly of trauma, overnight cessation of EN made no overall difference to 0600 gastric pH or colonization rates . The preservation of pH and lowered colonization in those given jejunal feeding may have implications in the pathogenesis of ventilator-associated infection and may warrant further study using larger patient numbers.

Hautarzt, 2003 Mar, 54(3), 209 - 14 Epub 2003 Feb 12.
{Latest aspects in psoriasis pathogenesis}; Prinz JC; During recent years the understanding of psoriasis pathogenesis has changed essentially . Psoriasis is now considered as a T cell mediated inflammation of the skin . Genetic predisposition and microbial environment cooperate in the induction of an antigen-specific T cell mediated immune response which may persist lifelong . The phenotype of the psoriatic inflammation is determined by the particular functional differentiation of the pathogenic T cells . The progress in understanding the pathogenesis of psoriasis has identified T cells and T cell-derived cytokines as targets for causal treatment approaches that in the near future will change psoriasis therapy considerably.

Nature, 2003 Mar 13, 422(6928), 164 - 9
Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1; Treiner E et al.; The evolutionary conservation of T lymphocyte subsets bearing T-cell receptors (TCRs) using invariant alpha-chains is indicative of unique functions . CD1d-restricted natural killer T (NK-T) cells that express an invariant Valpha14 TCRalpha chain have been implicated in microbial and tumour responses, as well as in auto-immunity . Here we show that T cells that express the canonical hValpha7.2-Jalpha33 or mValpha19-Jalpha33 TCR rearrangement are preferentially located in the gut lamina propria of humans and mice, respectively, and are therefore genuine mucosal-associated invariant T (MAIT) cells . Selection and/or expansion of this population requires B lymphocytes, as MAIT cells are absent in B-cell-deficient patients and mice . In addition, we show that MAIT cells are selected and/or restricted by MR1, a monomorphic major histocompatibility complex class I-related molecule that is markedly conserved in diverse mammalian species . MAIT cells are not present in germ-free mice, indicating that commensal flora is required for their expansion in the gut lamina propria . This indicates that MAIT cells are probably involved in the host response at the site of pathogen entry, and may regulate intestinal B-cell activity.

Nature, 2003 Mar 13, 422(6928), 150 - 4
Self-organization of dissolved organic matter to micelle-like microparticles in river water; Kerner M et al.; In aquatic systems, the concept of the 'microbial loop' is invoked to describe the conversion of dissolved organic matter to particulate organic matter by bacteria . This process mediates the transfer of energy and matter from dissolved organic matter to higher trophic levels, and therefore controls (together with primary production) the productivity of aquatic systems . Here we report experiments on laboratory incubations of sterile filtered river water in which we find that up to 25% of the dissolved organic carbon (DOC) aggregates abiotically to particles of diameter 0.4-0.8 micrometres, at rates similar to bacterial growth . Diffusion drives aggregation of low- to high-molecular-mass DOC and further to larger micelle-like microparticles . The chemical composition of these microparticles suggests their potential use as food by planktonic bacterivores . This pathway is apparent from differences in the stable carbon isotope compositions of picoplankton and the microparticles . A large fraction of dissolved organic matter might therefore be channelled through microparticles directly to higher trophic levels--bypassing the microbial loop--suggesting that current concepts of carbon conversion in aquatic systems require revision.

Euro Surveill, 2000 Dec, 5(12), 135 - 138
Bacterial resistance to antibiotics in France : a public health priority; Aubry Damon H et al.; For a few years, France has been faced to a rapid spread of anti-microbial resistance in hospitals and in general practice despite the many recommendations issued to solve this problem . In 1999, the Institut de Veille Sanitaire conducted a collective expe

Wound Repair Regen, 2003 Mar-Apr, 11(2), 104 - 9
Treatment of periprosthetic soft tissue infection of the groin following vascular surgical procedures by means of a polyvinyl alcohol-vacuum sponge system; Pinocy J et al.; Deep groin infections after prosthetic vascular surgical procedures represent a serious complication of surgical practice . Septicemia and/or erosive hemorrhage can both be consequences . In this situation, removal of the graft appears to be the only option . However, if the infection is detected early (type Szilagyi III), local treatment to eradicate the infection could serve as an alternative . Twenty-four patients with confirmed infection of the soft tissue adjacent to the prosthetic material in the groin were treated locally by implantation of a vacuum sponge system . Duration of this treatment was 2 weeks . All patients showed excellent tissue granulation of the wound area and the microbial stains were negative at the end of therapy . In 21 patients the wound could be primarily closed after explantation of the sponge . Three patients underwent open treatment because of a skin defect . After 12 months, the wounds had healed well in all patients . Histologic evaluation revealed a physiological healing process . Deep soft tissue infections of the groin adjacent to prosthetic vascular material (type Szilagyi III) can be treated effectively and safely with the vacuum sponge system . The treatment is inexpensive, easy to perform, and the initial vascular reconstruction can be preserved.

Shock, 2003 Mar, 19(3), 252 - 6
Antioxidant amplifies antibiotic protection in the cecal ligation and puncture model of microbial sepsis through interleukin-10 production; Kotake Y et al.; Preadministration of antioxidants such as pyrrolidine dithiocarbamate (PDTC) and phenyl N-tert-butyl nitrone (PBN) protects animals from lethality in sepsis models . However, the requirement of preadministration greatly diminishes the clinical significance of these studies . Although the synthetic antioxidant PBN has been shown to effectively protect rodents from lethality in endotoxemia (lipopolysaccharide {LPS} model), preliminary screening indicates that pre- or postadministration of PBN does not protect in the rat cecal ligation and puncture (CLP) model . We show in this report that in a rat CLP model, the administration of PBN (150 mg/kg, 30 min after CLP) followed by the antibiotic imipenem (IMP; 10 mg/kg, 1 h after CLP) significantly increased survival compared with other single treatment groups . Previously, we have shown that PBN's protection in a rat LPS model is mediated by the overproduction of the anti-inflammatory cytokine interleukin (IL)-10 . We show in this study that the increase in survival found in the PBN + IMP-treated group was abrogated by immunoneutralization with anti-IL-10 antibody, indicating that endogenous IL-10 is an effective protective factor . Plasma LPS levels were shown to be elevated after imipenem treatment, and the increased LPS level could have assisted to overproduce endogenous IL-10, as in the case of the PBN-treated LPS model . Statistical analysis indicated that the increase of IL-10 in PBN + IMP-treated group at early time period has significant association to the improvement of survival.

OMICS, 2002, 6(4), 287 - 303
Genomes to Life "Center for Molecular and Cellular Systems": a research program for identification and characterization of protein complexes; Buchanan MV et al.; Goal 1 of Department of Energy's Genomes to Life (GTL) program seeks to identify and characterize the complete set of protein complexes within a cell . Goal 1 forms the foundation necessary to accomplish the other objectives of the GTL program, which focus on gene regulatory networks and molecular level characterization of interactions in microbial communities . Together this information would allow cells and their components to be understood in sufficient detail to predict, test and understand the responses of a biological system to its environment . The Center for Molecular and Cellular Systems has been established to identify and characterize protein complexes using high through-put analytical technologies.A dynamic research program is being developed that supports the goals of the Center by focusing on the development new capabilities for sample preparation and complex separations, molecular level identification of the protein complexes by mass spectrometry, characterization of the complexes in living cells by imaging techniques, and bioinformatics and computational tools for the collection and interpretation of data and formation of databases and tools to allow the data to be shared by the biological community.

Chest, 2003 Mar, 123(3 Suppl), 385S - 90S
Is asthma an infectious disease?: Thomas A . Neff lecture; Lemanske RF Jr; Respiratory tract infections caused by viruses, Chlamydia, and Mycoplasma have been implicated in the pathogenesis of asthma . Of these respiratory pathogens, viruses have been demonstrated to be associated with asthma epidemiologically in at least two ways . First, during infancy, certain viruses have been implicated as potentially being responsible for the inception of the asthmatic phenotype . Second, in patients with established asthma, particularly children, viral upper respiratory tract infections play a significant role in producing acute exacerbations of airway obstruction that may result in frequent outpatient visits or in hospitalizations . For infections with other microbial agents, recent attention has focused on Chlamydia and Mycoplasma as potential contributors to both exacerbations and the severity of chronic asthma in terms of loss of lung function or medication requirements . In an attempt to address the question posed in the title, this article will briefly review these various associations as they pertain to the pathogenesis of asthma in both children and adults.

Curr Rheumatol Rep, 2003 Apr, 5(2), 136 - 41
Infectious etiology of vasculitis: diagnosis and management; Mohan N et al.; Vasculitides are a heterogeneous group of syndromes characterized by inflammation of the vessel wall . Several microbial pathogens have been known or suspected to cause vasculitis, and the development of molecular biology has promoted the search and confirmation of infectious agents in idiopathic vasculitis . Though several agents present primarily as an infectious process with vasculitis as an occasional manifestation, vasculitis may be the major manifestation of disease . Less definitive, and more controversial, is the role of infection and inflammation of the vessel wall in the pathogenesis of atherosclerotic disease . Clinical features can be nonspecific, and a high index of suspicion is required in order to make a diagnosis of vasculitis . Infection should always be excluded based on appropriate cultures and serologic assays, and, if confirmed, early and aggressive treatment should be instituted . However, in many instances, especially if there is a delay in the diagnosis, surgical intervention becomes necessary to treat the associated anatomic and physiologic sequelae.

Scanning, 2003 Jan-Feb, 25(1), 1 - 7
The biomass dynamics of cyanobacteria in an annual cycle determined by confocal laser scanning microscopy; Sole A et al.; We recently published a method for estimating cyanobacteria biomass in delta microbial mats from the Ebro river using confocal laser scanning microscopy (CLSM) . The present paper uses this method for identifying different groups of cyanobacteria and for determining their biomass dynamics . Microcoleus chthonoplastes and the Lyngbya-Oscillatoria were the most important contributors to the cyanobacterial biomass throughout the study . Biomass values ranged from 1.29 to 6.55 mgC/cm2 sediment for Microcoleus chthonoplastes, and from 128 microgC/cm2 to 3.16 mgC/cm2 sediment for Lyngbya-Oscillatoria . This technique is useful for determining biomass and for studying filamentous cyanobacteria as well as ramified eukaryotic cells . Confocal serial sections through the samples can be obtained . Two-dimensional images from the samples can be used to calculate the biomass of individual cells.

Proc Natl Acad Sci U S A, 2003 Mar 18, 100(6), 3455 - 60 Epub 2003 Mar 07.
Gene-environment interaction modulated by allelic heterogeneity in inflammatory diseases; Chamaillard M et al.; CARD15 is a major susceptibility gene for a frequent multifactorial chronic inflammatory bowel disorder, Crohn disease (CD) . By using NF-kappaB activation assays, the cytosolic CARD15 was shown to efficiently detect bacterial peptidoglycan (PGN), reminiscent of the PGN recognition protein surveillance mechanism in Drosophila . The 3 CD-associated variants and 13 additional variants carried by CD patients demonstrated impaired PGN-dependent response revealing null, hypomorphic, or dominant-negative properties . Quantitative parametrization of this response, computed from the patients' CARD15 genotypes, was predictive of several variable CD manifestations . In contrast, CARD15 alleles associated with Blau's syndrome promoted PGN-independent NF-kappaB activation, an observation that accounts for the minimal microbial input in the etiology of this dominant, monogenic inflammatory disorder affecting solely aseptic sites.

Annu Rev Nutr, 2003, 23, 203 - 27 Epub 2003 Feb 26.
Nutritional regulation of milk fat synthesis; Bauman DE et al.; Certain diets cause a marked reduction in milk fat production in ruminants . Commonly referred to as milk fat depression (MFD), the mechanism involves an interrelationship between rumen microbial processes and tissue metabolism . Numerous theories to explain this interrelationship have been proposed and investigations offer little support for theories that are based on a limitation in the supply of lipogenic precursors . Rather, the basis involves alterations in rumen biohydrogenation of dietary polyunsaturated fatty acids and a specific inhibition of mammary synthesis of milk fat . The biohydrogenation theory proposes that under certain dietary conditions, typical pathways of rumen biohydrogenation are altered to produce unique fatty acid intermediates that inhibit milk fat synthesis . Trans-10, cis-12 conjugated linoleic acid (CLA) has been identified as one example that is correlated with the reduction in milk fat . Investigations with pure isomers have shown that trans-10, cis-12 CLA is a potent inhibitor of milk fat synthesis, and similar to diet-induced MFD, the mechanism involves a coordinated reduction in mRNA abundance for key enzymes involved in the biochemical pathways of fat synthesis . A more complete identification of these naturally produced inhibitors of fat synthesis and delineation of cellular mechanisms may offer broader opportunities for application and understanding of the regulation of lipid metabolism.

J Immunol, 2003 Mar 15, 170(6), 3171 - 9
Dendritic cell (DC)-based protection against an intracellular pathogen is dependent upon DC-derived IL-12 and can be induced by molecularly defined antigens; Berberich C et al.; Upon loading with microbial Ag and adoptive transfer, dendritic cells (DC) are able to induce immunity to infections . This offers encouragement for the development of DC-based vaccination strategies . However, the mechanisms underlying the adjuvant effect of DC are not fully understood, and there is a need to identify Ag with which to arm DC . In the present study, we analyzed the role of DC-derived IL-12 in the induction of resistance to Leishmania major, and we evaluated the protective efficacy of DC loaded with individual Leishmania Ag . Using Ag-pulsed Langerhans cells (LC) from IL-12-deficient or wild-type mice for immunization of susceptible animals, we showed that the inability to release IL-12 completely abrogated the capacity of LC to mediate protection against leishmaniasis . This suggests that the availability of donor LC-derived IL-12 is a requirement for the development of protective immunity . In addition, we tested the protective effect of LC loaded with Leishmania homolog of receptor for activated C kinase, gp63, promastigote surface Ag, kinetoplastid membrane protein-11, or Leishmania homolog of eukaryotic ribosomal elongation and initiation factor 4a . The results show that mice vaccinated with LC that had been pulsed with selected molecularly defined parasite proteins are capable of controlling infection with L . major . Moreover, the protective potential of DC pulsed with a given Leishmania Ag correlated with the level of their IL-12 expression . Analysis of the cytokine profile of mice after DC-based vaccination revealed that protection was associated with a shift toward a Th1-type response . Together, these findings emphasize the critical role of IL-12 produced by the sensitizing DC and suggest that the development of a DC-based subunit vaccine is feasible.

J Immunol, 2003 Mar 15, 170(6), 2833 - 42
IL-1 receptor-associated kinase 1 regulates susceptibility to organ-specific autoimmunity; Deng C et al.; Infections often precede the development of autoimmunity . Correlation between infection with a specific pathogen and a particular autoimmune disease ranges from moderately strong to quite weak . This lack of correspondence suggests that autoimmunity may result from microbial activation of a generic, as opposed to pathogen-specific host-defense response . The Toll-like receptors, essential to host recognition of microbial invasion, signal through a common, highly conserved pathway, activate innate immunity, and control adaptive immune responses . To determine the influence of Toll/IL-1 signaling on the development of autoimmunity, the responses of wild-type (WT) mice and IL-1R-associated kinase 1 (IRAK1)-deficient mice to induction of experimental autoimmune encephalomyelitis were compared . C57BL/6 and B6.IRAK1-deficient mice were immunized with MOG 35-55/CFA or MOG 35-55/CpG DNA/IFA . WT animals developed severe disease, whereas IRAK1-deficient mice were resistant to experimental autoimmune encephalomyelitis, exhibiting little or no CNS inflammation . IRAK1-deficient T cells also displayed impaired Th1 development, particularly during disease induction, despite normal TCR signaling . These results suggest that IRAK1 and the Toll/IL-1 pathway play an essential role in T cell priming, and demonstrate one means through which innate immunity can control subsequent development of autoimmunity . These findings may also help explain the association between antecedent infection and the development or exacerbations of some autoimmune diseases.

Clin Diagn Lab Immunol, 2003 Mar, 10(2), 308 - 14
Elevated levels of matrix metalloproteinase 9 and tissue inhibitor of metalloproteinase 1 during the acute phase of Kawasaki disease; Chua PK et al.; Kawasaki disease (KD) is an acute, self-limiting, multisystem vasculitis of unknown etiology affecting infants and young children . Unless treated promptly with high-dose intravenous gamma globulin and aspirin, patients frequently develop coronary aneurysms . Previously, matrix metalloproteinase 9 (MMP-9), which is secreted complexed to tissue inhibitor of metalloproteinase 1 (TIMP-1), has been implicated in abdominal aortic aneurysm formation . Since the clinical and pathological features of KD include inflammation and weakening of blood vessels, we analyzed acute- and convalescent-phase paired plasma or serum samples from 31 KD patients, 7 patients who did not completely meet the criteria for KD, and 26 non-KD controls (9 febrile and 17 afebrile patients) for pro-MMP-9 (92 kDa) enzyme activity by gelatin zymography and for active MMP-9 (83 kDa), pro-MMP-9, and TIMP-1 protein levels by enzyme-linked immunosorbent assay . Statistical analysis was performed by using Student t tests, linear regression, and the Wilcoxon rank-sum test . Markedly elevated pro-MMP-9 enzymatic activity, pro-MMP-9 protein levels, and TIMP-1 protein levels were found during the acute phase of illness in patients with clinically established KD and in patients who were suspected of having KD but did not meet all of the criteria . There was no significant difference in active MMP-9 levels . Furthermore, pro-MMP-9 and TIMP-1 protein levels were significantly elevated among KD patients, compared to those of febrile and afebrile non-KD controls . The significantly elevated pro-MMP-9 enzyme and protein levels during the acute phase of KD may reflect vascular remodeling or an inflammatory response to a microbial agent, suggesting a pathophysiological role for MMP-9 in coronary aneurysm formation.

OMICS, 2002, 6(4), 349 - 62
Target selection for structural genomics: a single genome approach; Grigoriev IV et al.; We describe our strategy for selecting targets for protein structure determination in context of structural genomics of a single genome . In the course of target selection, we have studied two of the smallest microbial genomes, Mycoplasma genitalium and Mycoplasma pneumoniae . To our surprise, we found that only 71 Mycoplasma genes or their orthologues can be considered as easy targets for high-throughput structural studies--far fewer than expected . We discuss the methods and criteria used for target selection and the reasons explaining rarity of easy targets . First, despite the common opinion that protein folds can be predicted for only 30-50% of genes, the number of "truly unknown" structures is less than one-third . Second, due to the different codon usage, two thirds of Mycoplasma proteins cannot be directly expressed in E . coli in high-throughput manner and require substitution by their homologues from other organisms . Third, membrane or large multi-domain proteins are difficult targets because of solubility and size issues and often require identification and structure determination of protein domains . Finally, we propose different approaches to address the difficult targets.

Z Rheumatol, 2003 Feb, 62(1), 10 - 5
{Therapy of pulmonary involvement of rheumatic diseases}; Graninger W; Pulmonary manifestations of rheumatologic diseases occur as an effect of immunological damage to the parenchyma and to the vasculature of the lung . Hence an intensive immunosuppressive management including the use of corticosteroids and cyclophosphamide as well as extracorporeal apheresis procedures has been suggested and found to be efficacious in small series of patients . Pulmonary hypertension secondary to inflammatory rheumatological disease is a well known complication of scleroderma and lupus . The new advent in the treatment of such conditions like bosentan or epoprostenol and their second generation followers opens new prospects towards the hitherto very dark prognosis for these patients . The most frequent pulmonary problem in rheumatological patients will be the increasingly frequent occurrence of microbial pneumonias due to aggressive therapeutic immunosuppression.

J Lab Clin Med, 2003 Mar, 141(3), 159 - 67
Infection control during gastrointestinal endoscopy; Nelson DB; Infection-control issues during gastrointestinal endoscopy, which are becoming increasingly important, can generally be divided into three major areas: (1) infectious complications resulting from a patient's own microbial flora (autologous), (2) infections transmitted from patient to patient by way of the endoscope (exogenous), and (3) infections transmitted between the patient and the health-care provider . The mean frequency of postprocedure bacteremia ranges from 0.5% for flexible sigmoidoscopy to 2.2% for colonoscopy, 4.2% for esophagogastroduodenoscopy, 8.9% for variceal ligation, 11% for endoscopic retrograde cholangiopancreatography, 15.4% for variceal sclerotherapy, and 22.8% for esophageal dilation . Although postprocedure bacteremia is not uncommon, it seldom results in infectious complications . Exogenous infections transmitted during endoscopy, which are extremely rare, generally result from failure to follow accepted guidelines for the cleaning and disinfection of gastrointestinal endoscopes, underscoring the importance of meticulous attention to endoscope reprocessing . Finally, although the risk of patient-staff transmission of infection is also rare, standard infection-control recommendations are important in protecting both patients and health-care providers.

Microbiology, 2003 Feb, 149(Pt 2), 459 - 69
Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community; Rossetti S et al.; The reductive dechlorination (RD) of tetrachloroethene (PCE) to vinyl chloride (VC) and, to a lesser extent, to ethene (ETH) by an anaerobic microbial community has been investigated by studying the processes and kinetics of the main physiological components of the consortium . Molecular hydrogen, produced by methanol-utilizing acetogens, was the electron donor for the PCE RD to VC and ETH without forming any appreciable amount of other chlorinated intermediates and in the near absence of methanogenic activity . The microbial community structure of the consortium was investigated by preparing a 16S rDNA clone library and by fluorescence in situ hybridization (FISH) . The PCR primers used in the clone library allowed the harvest of 16S rDNA from both bacterial and archaeal members in the community . A total of 616 clones were screened by RFLP analysis of the clone inserts followed by the sequencing of RFLP group representatives and phylogenetic analysis . The clone library contained sequences mostly from hitherto undescribed bacteria . No sequences similar to those of the known RD bacteria like 'Dehalococcoides ethenogenes' or Dehalobacter restrictus were found in the clone library, and none of these bacteria was present in the RD consortium according to FISH . Almost all clones fell into six previously described phyla of the bacterial domain, with the majority (56.6 %) being deep-branching members of the Spirochaetes phylum . Other clones were in the Firmicutes phylum (18.5 %), the Chloroflexi phylum (16.4 %), the Bacteroidetes phylum (6.3 %), the Synergistes genus (1.1 %) and a lineage that could not be affiliated with existing phyla (1.1 %) . No archaeal clones were found in the clone library . Owing to the phylogenetic novelty of the microbial community with regard to previously cultured micro-organisms, no specific microbial component(s) could be hypothetically affiliated with the RD phenotype . The predominance of Spirochaetes in the microbial consortium, the main group revealed by clone library analysis, was confirmed by FISH using a purposely developed probe.

Ophthalmology, 2003 Mar, 110(3), 457 - 65
A phase III clinical trial of 0.5% levofloxacin ophthalmic solution versus 0.3% ofloxacin ophthalmic solution for the treatment of bacterial conjunctivitis; Schwab IR et al.; OBJECTIVE: To compare the efficacy and safety of 0.5% levofloxacin ophthalmic solution (QUIXIN) with 0.3% ofloxacin ophthalmic solution for the treatment of bacterial conjunctivitis . DESIGN: Prospective, randomized, active-controlled, double-masked, multicenter study . PARTICIPANTS: Four hundred twenty-three patients with a clinical diagnosis of bacterial conjunctivitis were enrolled . METHODS: Patients were randomly assigned to receive either 0.5% levofloxacin (n = 211) or 0.3% ofloxacin (n = 212) for 5 days (every 2 hours on days 1 and 2 and every 4 hours on days 3-5) . Conjunctival cultures were obtained, and ocular signs and symptoms were evaluated on day 1 (baseline), days 3 to 5 (interim), and days 6 to 10 (final) . End point was defined as the last evaluable observation . MAIN OUTCOME MEASURES: Primary microbial and clinical outcomes were based on culture results and resolution of cardinal signs, respectively . Secondary efficacy assessments included evaluations of ocular signs and symptoms . RESULTS: Two hundred eight patients (levofloxacin, n = 109; ofloxacin, n = 99) were evaluated for efficacy . Microbial eradication rates were significantly greater in the 0.5% levofloxacin treatment group compared with the 0.3% ofloxacin group at both the final visit (89% vs . 80%, P = 0.034) and at end point (90% vs . 81%; P = 0.038) . Treatment with 0.5% levofloxacin was significantly more effective in resolving photophobia than was 0.3% ofloxacin treatment (94% vs . 73%, P = 0.006) . Both study medications were well tolerated, with a low incidence of adverse events . CONCLUSIONS: Although clinical cure rates in the 0.5% levofloxacin and 0.3% ofloxacin treatment groups were similar, a 5-day treatment regimen with 0.5% levofloxacin achieved microbial eradication rates that were statistically superior to those attained with 0.3% ofloxacin . Despite the higher concentration of active drug in 0.5% levofloxacin versus 0.3% ofloxacin, there was no difference between treatment groups in the incidence of treatment-related adverse events.

Allergy, 2003 Feb, 58(2), 150 - 3
The effect of storage on allergen and microbial agent levels in frozen house dust; Fahlbusch B et al.; BACKGROUND: House dust samples collected for exposure studies are often stored for variable time periods until analysis . However, there is currently no information on the effects of dust storage on the content of biocontaminants . Therefore, associations were analysed between the levels of mite allergens (Der p 1, Der f 1), cat allergen (Fel d 1) and microbial components (endotoxin, beta(1-->3)-glucan) on the one hand and the storage duration of dust samples at -20 degrees C on the other hand . METHODS: Within the framework of a study on the influences of INdoor factors and Genetics on Asthma (INGA), dust samples were collected from living room floors between June 1995 and August 1998 and extracted according to a standardized protocol . The concentrations of Der p 1, Der f 1, Fel d 1 and beta(1-->3)-glucan were determined with specific enzyme immunoassays . Endotoxin content was quantified using a chromogenic kinetic Limulus amoebocyte lysate (LAL) test . All concentrations were expressed per gram of dust RESULTS: Dust samples (n = 1236) were obtained from 655 homes in Hamburg, Hettstedt, Zerbst and Bitterfeld . Storage duration (range 8-298 days) was grouped into four categories (<or= 60 d; 61-90 d; 91-120 d; > 120 d) . After adjustment for city of residence and season of dust sampling, means ratios comparing categories 2-4 to the first category were not statistically significant for Der p 1, Der f 1, endotoxin and beta(1-->3 glucan) . However, Fel d 1 concentrations significantly declined with increased storage times of dust samples . CONCLUSIONS: Storage of house dust at -20 degrees C for up to 10 months has no effect on mite allergen, endotoxin and beta(1-->3)-glucan levels . A potential loss of Fel d 1 during storage of frozen dust samples needs further investigations by repeated measurements of allergen in identical dust samples.

Dermatol Clin, 2003 Jan, 21(1), 195 - 205
Oral manifestations of erythema multiforme; Ayangco L et al.; Erythema multiforme is a reactive mucocutaneous disorder in a disease spectrum that comprises a self-limited, mild, exanthematic, cutaneous variant with minimal oral involvement (EM minor) to a progressive, fulminating, severe variant with extensive mucocutaneous epithelial necrosis (SJS and TEN) . Significant differences exist among EM minor, EM major, SJS, and TEN with regards to severity and clinical expression; however, all variants share two common features: typical or less typical cutaneous target lesions and satellite-cell or more widespread necrosis of the epithelium . These features are considered to be sequelae of a cytotoxic immunologic attack on keratinocytes expressing non-self-antigens . These antigens are primarily microbial (viruses) or drugs and in rare instances histocompatibility antigens {5} . Although the precise pathogenesis is unknown, there is a tendency to consider EM both minor and major as part of one spectrum that is most often triggered by viral infections, and SJS and TEN as a separate one most often elicited by drugs with EM major and SJS representing a bridge in the continuum of EM . The oral manifestations of the spectrum of EM range from tender superficial erythematous and hyperkeratotic plaques to painful deep hemorrhagic bullae and erosions . Other mucosal surfaces including ocular, nasal, pharyngeal, laryngeal, upper respiratory, and anogenital may be involved . Scarring sequelae from ocular and pharyngeal involvement cause morbidity . The oral EM variant is an underrecognized form of EM . Most patients have chronic or recurrent oral lesions only, but one third have oral and lip lesions and one quarter have oral, lip, and skin lesions . This variant is a reaction pattern similar to EM minor, EM major, SJS, and TEN . The diagnosis of oral EM is one of exclusion . Careful clinical evaluation for other chronic mucocutaneous diseases, such as pemphigus, paraneoplastic pemphigus, mucous membrane pemphigoid, and lichen planus, is a necessary component of the diagnosis . The value of a biopsy specimen studied by both routine histopathologic and immunopathologic methods is fundamental to excluding the other causes for this variant of EM.

Appl Environ Microbiol, 2003 Mar, 69(3), 1847 - 53
Cr(VI) reduction by sulfidogenic and nonsulfidogenic microbial consortia; Arias YM et al.; In time course experiments, bacterial community compositions were compared between a sulfidogenic and two nonsulfidogenic Cr(VI)-reducing consortia enriched from metal-contaminated sediments . The consortia were subjected to 0 and 0.85 mM or 1.35 mM Cr(VI), and Cr(VI) reduction, growth, and denaturing gradient gel electrophoresis profiles of PCR products of small-subunit (16S) ribosomal genes were compared . Results showed that although Cr(VI) was completely reduced by the three consortia, Cr(VI) inhibited cell growth, with sulfate-reducing bacteria being particularly sensitive to Cr(VI) toxicity relative to other bacteria in the consortia.

Appl Environ Microbiol, 2003 Mar, 69(3), 1548 - 55
Electricity production by Geobacter sulfurreducens attached to electrodes; Bond DR et al.; Previous studies have suggested that members of the Geobacteraceae can use electrodes as electron acceptors for anaerobic respiration . In order to better understand this electron transfer process for energy production, Geobacter sulfurreducens was inoculated into chambers in which a graphite electrode served as the sole electron acceptor and acetate or hydrogen was the electron donor . The electron-accepting electrodes were maintained at oxidizing potentials by connecting them to similar electrodes in oxygenated medium (fuel cells) or to potentiostats that poised electrodes at +0.2 V versus an Ag/AgCl reference electrode (poised potential) . When a small inoculum of G . sulfurreducens was introduced into electrode-containing chambers, electrical current production was dependent upon oxidation of acetate to carbon dioxide and increased exponentially, indicating for the first time that electrode reduction supported the growth of this organism . When the medium was replaced with an anaerobic buffer lacking nutrients required for growth, acetate-dependent electrical current production was unaffected and cells attached to these electrodes continued to generate electrical current for weeks . This represents the first report of microbial electricity production solely by cells attached to an electrode . Electrode-attached cells completely oxidized acetate to levels below detection (<10 micro M), and hydrogen was metabolized to a threshold of 3 Pa . The rates of electron transfer to electrodes (0.21 to 1.2 micro mol of electrons/mg of protein/min) were similar to those observed for respiration with Fe(III) citrate as the electron acceptor (E(o)' =+0.37 V) . The production of current in microbial fuel cell (65 mA/m(2) of electrode surface) or poised-potential (163 to 1,143 mA/m(2)) mode was greater than what has been reported for other microbial systems, even those that employed higher cell densities and electron-shuttling compounds . Since acetate was completely oxidized, the efficiency of conversion of organic electron donor to electricity was significantly higher than in previously described microbial fuel cells . These results suggest that the effectiveness of microbial fuel cells can be increased with organisms such as G . sulfurreducens that can attach to electrodes and remain viable for long periods of time while completely oxidizing organic substrates with quantitative transfer of electrons to an electrode.

Eur J Med Chem, 2003 Feb, 38(2), 123 - 40
Rebeccamycin analogues as anti-cancer agents; Prudhomme M; Rebeccamycin, a microbial metabolite possessing a maleimide indolo{2,3-a}carbazole framework with a carbohydrate moiety attached to one of the indole nitrogens, is a well-known topoisomerase I inhibitor . This review reports the various total syntheses of rebeccamycin and structure-activity relationship studies on rebeccamycin analogues . Rebeccamycin analogues were prepared either by semi-synthesis from the natural metabolite or by total synthesis . Different families of rebeccamycin analogues were obtained by modifications at the imide heterocycle, dechlorination and substitutions on the indole moieties, modifications of the sugar residue, construction of dimers, coupling the sugar unit to the second indole nitrogen, changing indolo{2,3-a}carbazole skeleton to indolo{2,3-c}carbazole, replacing one or both indole moieties by 7-azaindole units . The biological activities of the rebeccamycin analogues are described . According to their chemical structure, the analogues can inhibit topoisomerase I and/or kinases . From the structure-activity relationships, some important rules were established . Several compounds exhibit stronger antiproliferative activities than the natural metabolite with IC(50) values in the nanomolar range . Some analogues, especially those possessing azaindole moieties, are much more selective than rebeccamycin toward the tumour cell lines tested.

J Neuroimmunol, 2003 Mar, 136(1-2), 1 - 8
Infectious agents and multiple sclerosis--are Chlamydia pneumoniae and human herpes virus 6 involved?
Swanborg RH, Whittum-Hudson JA, Hudson AP.
A good deal of evidence suggests an infectious component in the development of multiple sclerosis (MS) and, to date, some 20 bacteria and viruses have been associated with the disease . Recent independent sets of studies have implicated the respiratory bacterium Chlamydia pneumoniae and human herpes virus 6 (HHV-6) in the pathogenesis of MS . However, as is the case for essentially all earlier microbial associations, experimental evidence linking either this bacterium or this virus to MS is equivocal . We review the published reports concerning involvement of C . pneumoniae and HHV-6 in MS, and data relating to possession of the APOE epsilon 4 allele, which some studies indicate might influence how these or other pathogens affect disease genesis . Based on the large set of inconsistent observations available and given important new information regarding the neuropathology of MS, we contend that no conclusion is possible at this point regarding the potential role of either C . pneumoniae or HHV-6 in MS . We therefore propose future studies that should clarify whether, and if so how, these and other organisms function in the pathogenesis of this disease.

Poult Sci, 2003 Feb, 82(2), 235 - 41
Serum levels of mannan-binding lectin in chickens prior to and during experimental infection with avian infectious bronchitis virus; Juul-Madsen HR et al.; Mannan-binding lectin (MBL) is a glycoprotein and a member of the C-type lectin super family, the collectin family, and the acute phase protein family . The MBL exerts its function by directly binding to microbial surfaces through its carbohydrate recognition domains, followed by direct opsonization or complement activation via MBL-associated serine proteases (MASP)-1 and -2 . Thus, MBL plays a major role in the first-line innate defense against pathogens . We investigated the MBL concentrations in serum during experimental infectious bronchitis virus (IBV) infections in chickens . The results showed that the acute phase MBL response to infection with IBV was, to a degree (P < 0.0068), dependent on whether the chickens were inoculated after 12 h of rest (dark) or after 12 h of activity (light) . The acute phase response in chickens challenged after 12 h of activity peaked after 4.6 d with an increase of 24%, whereas the acute phase response in chickens challenged after 12 h of rest peaked after 3.1 d with an increase of 51% . The specific antibody titer against IBV was also tested, and a difference (P < 0.0091) between the two experimental groups was found with peak titer values of 6,816 and 4,349 . However, the highest value was found in chickens inoculated after 12 h of activity . Thus, an inverse relation exists between the MBL response and the IBV specific antibody response . The ability of MBL to activate the complement cascade was tested in a heterologous system by deposition of human C4 on the chicken MBL/MASP complex . The complement activation was directly associated with the concentration of MBL in serum, indicating neutralization of the virus before the humoral antibody response took over.

Biocell, 2002 Dec, 26(3), 369 - 74
Stimulation of jasmonic acid production in Zea mays L . infected by the maize rough dwarf virus-Río Cuarto . Reversion of symptoms by salicylic acid; Vigliocco A et al.; In the present paper we study the possible biological relevance of endogenous jasmonic acid (JA) and exogenous salicylic acid (SA) in a plant-microbial system maize-virus . The virus disease "Mal de Rio Cuarto" is caused by the maize rough dwarf virus-Rio Cuarto . The characteristic symptoms are the appearance of galls or "enations" in leaves, shortening of the stem internodes, poor radical system and general stunting . Changes in JA and protein pattern in maize control and infected plants of a virus-tolerant cultivar were investigated . Healthy and infected-leaf discs were collected for JA measurement at different post-infection times (20, 40, 60 and 68 days) . JA was also measured in roots on day 60 after infection . For SDS-PAGE protein analysis, leaf discs were also harvested on day 60 after infection . Infected leaves showed higher levels of JA than healthy leaves, and the rise in endogenous JA coincided with the enation formation . The soluble protein amount did not show differences between infected and healthy leaves; moreover, no difference in the expression of soluble protein was revealed by SDS-PAGE . Our results show that the octadecanoid pathway was stimulated in leaves and roots of the tolerant maize cultivar when infected by this virus . This finding, together with fewer plants with the disease symptoms, suggest that higher foliar and roots JA content may be related to disease tolerance . SA exogenous treatment caused the reversion of the dwarfism symptom.

Chem Biol, 2003 Feb, 10(2), 131 - 7
A novel action of terpendole E on the motor activity of mitotic Kinesin Eg5; Nakazawa J et al.; To reveal the mechanism of mitosis, the development of M phase-specific inhibitors is an important strategy . We have been screening microbial products to find specific M phase inhibitors that do not directly target tubulins, and rediscovered terpendole E (TerE) as a novel Eg5 inhibitor . TerE did not affect microtubule integrity in interphase, but induced formation of a monoastral spindle in M phase . TerE inhibited both motor and microtubule-stimulated ATPase activities of human Eg5, but did not affect conventional kinesin from either Drosophila or bovine brain . Although terpendoles have been reported as inhibitors of acyl-CoA:cholesterol O-acyltransferase (ACAT), the Eg5 inhibitory activity of TerE was independent of ACAT inhibition . Taken together, we demonstrate that TerE is a novel Eg5 inhibitor isolated from a fungal strain.

Bioresour Technol, 2003 Jul, 88(3), 197 - 206
Comparative efficacy of three epigeic earthworms under different deciduous forest litters decomposition; Manna MC et al.; An experiment was conducted during 1998-1999, in a deciduous forest located in the semi-arid tropics of central India, to evaluate the suitability of different forest litters as food material for the tropical epigeic earthworms i.e . Eisenia fetida (Savigny), Perionyx excavatus (Perrier) and Dicogaster bolaui (michaelsen) . The aim was to examine the influence of these earthworms on the decomposition processes of three types of forest litters i.e . Tectona grandis (teak), Madhuca indica (mahua) and Butea monosperma (palas), on the maintenance of quality in a vermicomposting system, and to assess the effect of applications of in situ prepared vermicomposts on the growth of forest trees . The results indicated that T . grandis litter was the most suitable food material for the earthworms possibly because it contained high reserves of mineral nutrients . Comparisons of the survival and reproduction rates of the three epigeic earthworm species indicated that a higher reproduction rate was maintained for E . fetida compared to P . excavatus and D . bolaui in the decomposition of these forest litters . The rates of growth and population increases of E . fetida approximately doubled after 12 weeks of litter decomposition . The litter decomposition process was associated strongly with the quality of the materials and their chemical composition . Irrespective of earthworm inoculations, the levels of available nutrient such as NH(4)-N, NO(3)-N, available P and K increased significantly (p</=0.05) in the order T . grandis litter compost>M . indica litter compost>B . monosperma litter compost . The mature decomposed litter had lower C/N ratios (11.3-24.8:1), water-soluble carbon (0.30-0.58%), water-soluble carbohydrates (0.35-0.71%) and larger cation exchange capacity/total organic carbon ratios than the values in the parent forest litter . The lignin content increased with maturation with a concomitant decrease in cellulose resulting in higher lignin/cellulose ratios.Application of all three vermicomposts to forest trees significantly improved their heights and diameters over those of control trees, although the increases were lower than those resulting from the chemical fertilizer applications . However, soil biological activities i.e . soil respiration, soil microbial biomass carbon and dehydrogenase activity were greater by application of vermicomposts over that after application of inorganic fertilizer in a new plantation of T . grandis.

Crit Care, 2003 Feb, 7(1), 23 - 38 Epub 2002 Dec 20.
Bench-to-bedside review: functional relationships between coagulation and the innate immune response and their respective roles in the pathogenesis of sepsis; Opal SM et al.; The innate immune response system is designed to alert the host rapidly to the presence of an invasive microbial pathogen that has breached the integument of multicellular eukaryotic organisms . Microbial invasion poses an immediate threat to survival, and a vigorous defense response ensues in an effort to clear the pathogen from the internal milieu of the host . The innate immune system is able to eradicate many microbial pathogens directly, or innate immunity may indirectly facilitate the removal of pathogens by activation of specific elements of the adaptive immune response (cell-mediated and humoral immunity by T cells and B cells) . The coagulation system has traditionally been viewed as an entirely separate system that has arisen to prevent or limit loss of blood volume and blood components following mechanical injury to the circulatory system . It is becoming increasingly clear that coagulation and innate immunity have coevolved from a common ancestral substrate early in eukaryotic development, and that these systems continue to function as a highly integrated unit for survival defense following tissue injury . The mechanisms by which these highly complex and coregulated defense strategies are linked together are the focus of the present review.

Biochem J, 2003 Jun 1, 372(Pt 2), 399 - 405
Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var . Soisson); Payan F et al.; A novel class of proteinaceous inhibitors exhibiting specificity towards microbial xylanases has recently been discovered in cereals . The three-dimensional structure of xylanase inhibitor protein I (XIP-I) from wheat (Triticum aestivum, var . Soisson) was determined by X-ray crystallography at 1.8 A (1 A=0.1 nm) resolution . The inhibitor possesses a (beta/alpha)(8) barrel fold and has structural features typical of glycoside hydrolase family 18, namely two consensus regions, approximately corresponding to the third and fourth barrel strands, and two non-proline cis -peptide bonds, Ser(36)-Phe and Trp(256)-Asp (in XIP-I numbering) . However, detailed structural analysis of XIP-I revealed several differences in the region homologous with the active site of chitinases . The catalytic glutamic acid residue of family 18 chitinases {Glu(127) in hevamine, a chitinase/lysozyme from the rubber tree (Hevea brasiliensis)} is conserved in the structure of the inhibitor (Glu(128)), but its side chain is fully engaged in salt bridges with two neighbouring arginine residues . Gly(81), located in subsite -1 of hevamine, where the reaction intermediate is formed, is replaced by Tyr(80) in XIP-I . The tyrosine side chain fills the subsite area and makes a strong hydrogen bond with the side chain of Glu(190) located at the opposite side of the cleft, preventing access of the substrate to the catalytic glutamic acid . The structural differences in the inhibitor cleft structure probably account for the lack of activity of XIP-I towards chitin.

J Environ Sci Health B, 2003 Mar, 38(2), 211 - 9
Extractable soil lipids and microbial activity as affected by Bt and non Bt maize grown on a silty clay loam soil; Dinel H et al.; Pyrolysis-gas (Py-GC) chromatography was used to characterize extractable lipids from Bt and non-Bt maize shoots and soils collected at time of harvesting . Py-GC-MS (mass spectrometry) showed that the concentrations of total alkenes identified in non-Bt shoots and soils were 47.9 and 21.3% higher than in Bt maize shoots and soils, respectively . N-alkanes identified were of similar orders of magnitude in Bt and non-Bt maize shoots, but were 28.6% higher in Bt than in non-Bt soils . Bt maize shoots contained 29.7% more n-fatty acids than non-Bt maize shoots, whereas the concentrations of n-fatty acids in Bt soils were twice as high as those in non-Bt soils . Concentrations of unsaturated fatty acids in Bt maize shoots were 22.1% higher than those in non-Bt maize shoots, while concentrations of unsaturated fatty acids were 22.5% higher in non-Bt than in Bt soils . The cumulative CO2-C evolved from soils under Bt and non-Bt crops was 30.5% lower under Bt as compared to non-Bt crops, whereas when maize shoots were added to Bt and non-Bt soils, the decrease in CO2-C evolved were 16.5 and 23.6%, respectively . Our data showed that the cultivation of Bt maize significantly increased the saturated to unsaturated lipid ratios in soils which appeared to negatively affect microbial activity.

J Exp Med, 2003 Mar 3, 197(5), 585 - 99
Compartmentalized production of CCL17 in vivo: strong inducibility in peripheral dendritic cells contrasts selective absence from the spleen; Alferink J et al.; Dendritic cells (DCs)(*) fulfill an important regulatory function at the interface of the innate and adaptive immune system . The thymus and activation-regulated chemokine (TARC/CCL17) is produced by DCs and facilitates the attraction of activated T cells . Using a fluorescence-based in vivo reporter system, we show that CCL17 expression in mice is found in activated Langerhans cells and mature DCs located in various lymphoid and nonlymphoid organs, and is up-regulated after stimulation with Toll-like receptor ligands . DCs expressing CCL17 belong to the CD11b(+)CD8(-)Dec205(+) DC subset, including the myeloid-related DCs located in the subepithelial dome of Peyer's patches . CCL17-deficient mice mount diminished T cell-dependent contact hypersensitivity responses and display a deficiency in rejection of allogeneic organ transplants . In contrast to lymphoid organs located at external barriers of the skin and mucosa, CCL17 is not expressed in the spleen, even after systemic microbial challenge or after in vitro stimulation . These findings indicate that CCL17 production is a hallmark of local DC stimulation in peripheral organs but is absent from the spleen as a filter of blood-borne antigens.

Food Chem Toxicol, 2003 Apr, 41(4), 551 - 4
Occurrence of preformed volatile nitrosamines in preparations of some Nigerian medicinal plants: a preliminary report; Atawodi SE; Preparations of some tropical plants of medicinal importance collected from the savannah vegetational belt of Nigeria were analysed for preformed volatile N-nitrosamines . N-nitrosamines were analyzed by chemiluminescence detection on a thermal energy analyzer (TEA) following gas chromatographic (GC) separation . Only N-nitrosodimethylamine (NDMA) in the range of 1.2-3.4 microg/kg was detected in four out of the 29 sample preparations . These preliminary data suggest that medicinal plant preparations may be due in part to microbial contamination, contributing to N-nitroso compound burden in many developing countries where ethnomedicine in still widely practised .

Food Chem Toxicol, 2003 Apr, 41(4), 523 - 9
Safety evaluation of a hexose oxidase expressed in Hansenula polymorpha; Cook MW et al.; A programme of studies was conducted to establish the safety of hexose oxidase (HOX) from Chondrus crispus expressed in the yeast Hansenula polymorpha to be used as a processing aid in the food industry . Rat feeding studies were conducted to assess acute and subchronic oral toxicity . In addition, the potential of the enzyme to cause mutagenicity and chromosomal aberrations was assessed in microbial and tissue culture in vitro studies . Acute and subchronic oral toxicity was not detected at the highest dosage recommended by OECD guidelines . There was no evidence of mutagenic potential or chromosomal aberrations . The no-observed-adverse-effect level (NOAEL) derived from the 13-week study was 5000 units/kg body weight/day . In conclusion it can be considered a safe processing aid for use in the food industry .

Biochem Biophys Res Commun, 2003 Mar 14, 302(3), 539 - 44
Dykellic acid inhibits drug-induced caspase-3-like protease activation; Lee SH et al.; Dykellic acid is a novel microbial metabolite isolated from the broth of Westerdykella multispora F50733 . Investigations on the molecular function of dykellic acid revealed that this compound partially inhibits calcium influx, resulting in a decrease in Ca(2+)-dependent endonuclease activation and DNA fragmentation induced by camptothecin . In our experiments, active caspase-3-like protease cleavage of procaspase-3, PARP, and cytosolic cytochrome c was inhibited by dykellic acid in a concentration-dependent manner when the apoptosis was induced by camptothecin as well as doxorubicin . We confirmed that dykellic acid did not bind to camptothecin using surface plasmon resonance analysis . These results suggest that dykellic acid inhibits drug-induced apoptosis via a caspase-3-like protease-suppressing mechanism . Our data provide important information on the mechanism of action of dykellic acid and indicate that this compound may be employed in the treatment of specific caspase-3-like protease-mediated diseases.

Clin Exp Allergy, 2003 Mar, 33(3), 295 - 300
Endotoxin levels in Estonian and Swedish house dust and atopy in infancy; Bottcher MF et al.; BACKGROUND: Immune responses, including those to allergens, may be T helper (Th)2 skewed in newborns . In order to redress the fetal Th1/Th2 imbalance, Th1-stimulating factors, such as bacterial endotoxin, may be required . The increasing prevalence and severity of atopic diseases in industrialized countries, which are in marked contrast with the low prevalence of allergy among children in the formerly socialist countries of Europe, have been suggested to be caused by a reduced microbial stimulation . AIM: To relate the endotoxin levels in house dust from two countries with a low (Estonia) and a high (Sweden) prevalence of allergy to the development of atopic disease and sensitization in the children during the first 2 years of life . METHODS: The study included 108 children from Tartu, Estonia and 111 children from Linkoping, Sweden . Skin prick tests were performed at 3, 6, 12 and 24 months of age, and questionnaires were distributed to the families . At 24 months, a paediatrician examined the children . Dust samples were collected from mattresses and carpets and the endotoxin concentration was determined by a chromogenic Limulus assay . RESULTS: The endotoxin levels were higher in Estonian than in Swedish house dust (median levels 29 (range 0.25-280) and 14 (range 0.25-99) EU/mg dust, respectively, P < 0.001) . Furthermore, the levels were inversely related to the development of atopic disease and sensitization in the Swedish, but not in the Estonian, children . CONCLUSIONS: The low prevalence of atopic disease in Estonia may, at least in part, be related to the high endotoxin levels in this country . The findings support that high levels of endotoxin, or other bacterial products with Th1-stimulating properties, might protect children from developing atopic disease.

J Dairy Sci, 2003 Jan, 86(1), 344 - 50
Reassessment of biases in predicted nitrogen flows to the duodenum by NRC 2001; St-Pierre NR; The appearance of numerous plots in recent literature from which the residuals are plotted against observed values (Y) to assess a model's potential bias raises this question: should residuals be regressed against Y or against predicted values (Y)? The answer requires knowing the expected relationship under the assumption of an unbiased model . The objectives of this paper are: 1) to derive the expected relationship between residuals, Y, and Y; 2) to determine whether Y or Y should be used for the assessment of bias; and 3) to reassess the extent of mean and linear bias in the prediction of N flows to the duodenum by the NRC (2001) . In the simplest case, we can assume a true model of the form Y = Xbeta + epsilon . This model is estimated by Y = Xb + e, and Y = Xb . The correlation between the residual vector e and the vector of observations Y can easily be derived . The numerator of the correlation coefficient is shown to be equal to e'e, the residual sum of squares . The denominator of this correlation is equal to the square root of e'e multiplied by the total sum of squares . Algebraic simplifications show that the correlation between e and Y is equal to the square root of (1-R2) . That is, under the assumption of an unbiased model, the residuals are correlated with the observed values and the slope of e regressed on Y is equal to (1-R2) . Thus, a graph of e versus Y will show a positive slope between e and Y unless the model is a perfect predictor (i.e., R2 is equal to 1.0) . Significant slopes linking e to Y have been erroneously interpreted as evidence of biased models in the NRC (2001) . Conversely, the slope of e regressed on Y is expected to be zero under the assumption of an unbiased model . Therefore, residuals should be regressed against Y and not Y . When Y, as opposed to Y, was used to assess biases in the prediction of flows to the duodenum of microbial N, nonammonia-nonmicrobial N and nonammonia N in NRC (2001), mean biases became nonsignificant and linear biases over the range of predicted values are of the same magnitude or smaller than the standard errors of measurements reported in literature . Thus, although N flow predictions from NRC (2001) may not be precise, they appear to have insignificant and inconsequential biases.

J Dairy Sci, 2003 Jan, 86(1), 43 - 51
The impact of fortification with conjugated linoleic acid (CLA) on the quality of fluid milk; Campbell W et al.; The effects of added conjugated linoleic acid (CLA) on the sensory, chemical, and physical characteristics of 2% total fat (wt/wt) fluid milk were studied . Milks with 2% (wt/wt) total fat (2% CLA, 1% CLA 1% milkfat, 2% milkfat) were made by the addition of cream or CLA triglyceride oil into skim milk followed by HTST pasteurization and homogenization . The effects of adding vitamin E (200 ppm) and rosemary extract (0.1% wt/wt based on fat content) were investigated to prevent lipid oxidation . HTST pasteurization resulted in a significant decrease of the cis-9/trans-11 isomer and other minor CLA isomers . The cis-9/trans-11 isomer concentration remained stable through 2 wk of refrigerated storage . A significant loss of both the cis-9/trans-11 and the cis-10/trans-12 isomers occurred after 3 wk of refrigerated storage . The loss was attributed to lipase activity from excessive microbial growth . No differences were found in hexanal or other common indicators of lipid oxidation between milks with or without added CLA (P > 0.05) . Descriptive sensory analysis revealed that milks with 1 or 2% CLA exhibited low intensities of a "grassy/vegetable oil" flavor, not present in control milks . The antioxidant treatments were deemed to be ineffective, under the storage conditions of this study, and did not produce significant differences from the control samples (P > 0.05) . CLA-Fortified milk had significantly lower L* and b* values compared with 2% milkfat milk . No significant differences existed in viscosity . Consumer acceptability scores (n = 100) were lower (P < 0.05) for CLA-fortified milks compared to control milks, but the addition of chocolate flavor increased acceptability (P < 0.05).

J Dairy Sci, 2003 Jan, 86(1), 1 - 42
Invited review: production and digestion of supplemented dairy cows on pasture; Bargo F et al.; Literature with data from dairy cows on pasture was reviewed to evaluate the effects of supplementation on intake, milk production and composition, and ruminal and postruminal digestion . Low dry matter intake (DMI) of pasture has been identified as a major factor limiting milk production by high producing dairy cows . Pasture DMI in grazing cows is a function of grazing time, biting rate, and bite mass . Concentrate supplementation did not affect biting rate (58 bites/min) or bite mass (0.47 g of DM/bite) but reduced grazing time 12 min/d per kilogram of concentrate compared with unsupplemented cows (574 min/d) . Substitution rate, or the reduction in pasture DMI per kilogram of concentrate, is a factor which may explain the variation in milk response to supplementation . A negative relationship exists between substitution rate and milk response; the lower the substitution rate the higher the milk response to supplements . Milk production increases linearly as the amount of concentrate increases from 1.2 to 10 kg DM/d, with an overall milk response of 1 kg milk/kg concentrate . Compared with pasture-only diets, increasing the amount of concentrate supplementation up to 10 kg DM/d increased total DMI 24%, milk production 22%, and milk protein percentage 4%, but reduced milk fat percentage 6% . Compared with dry ground corn, supplementation with nonforage fiber sources or processed corn did not affect total DMI, milk production, or milk composition . Replacing ruminal degradable protein sources with ruminal undegradable protein sources in concentrates did not consistently affect milk production or composition . Forage supplementation did not affect production when substitution rate was high . Fat supplementation increased milk production by 6%, without affecting milk fat and protein content . Increasing concentrate from 1.1 to 10 kg DM/d reduced ruminal pH 0.08 and NH3-N concentration 6.59 mg/dl, compared with pasture-only diets . Replacing dry corn by high moisture corn, steam-flaked or steam-rolled corn, barley, or fiber-based concentrates reduced ruminal NH3-N concentration 4.36 mg/dl . Supplementation did not affect in situ pasture digestion, except for a reduction in rate of degradation when high amounts of concentrate were supplemented . Supplementation with energy concentrates reduced digestibility of neutral detergent fiber and intake of N but did not affect digestibility of organic matter or flow of microbial N.

Chem Commun (Camb), 2003 Feb 7, (3), 297 - 307
Enzymology of acyl chain macrocyclization in natural product biosynthesis; Kohli RM et al.; Polyketides and nonribosomal peptides constitute a large and diverse set of natural products with biological activity in microbial survival and pathogenesis, as well as broad pharmacological utility as antineoplastics, antibiotics or immunosupressants . These molecules are biosynthesized by the ordered condensation of monomer building blocks, acyl-CoAs or amino acids, leading to construction of linear acyl chains . Many of these natural products are constrained to their bioactive conformations by macrocyclization whereby, in one of the terminal steps of biosynthesis, parts of the molecule distant in the constructed linear acyl chain are covalently linked to one another . Typically, macrocyclization is catalyzed by a thioesterase domain at the C-terminal end of the biosynthetic assembly line, although alternative strategies are known . The enzymology of these macrocyclization catalysts, their structure, mechanism, and catalytic versatility, is the subject of this review . The diversity of macrocyclic structures accessed by enzyme catalyzed cyclization of linear acyl chains as well as their inherent substrate tolerance suggests their potential utility in reprogramming natural product biosynthesis pathways or accessing novel macrocyclic structures.

Pediatrics, 2003 Mar, 111(3), 653 - 9
Addressing parents' concerns: do vaccines cause allergic or autoimmune diseases?
Offit PA, Hackett CJ.
Anecdotal case reports and uncontrolled observational studies in the medical literature claim that vaccines cause chronic diseases such as asthma, multiple sclerosis, chronic arthritis, and diabetes . Several biological mechanisms have been proposed to explain how vaccines might cause allergic or autoimmune diseases . For example, allergic diseases might be caused by prevention of early childhood infections (the "hygiene hypothesis"), causing a prolongation of immunoglobulin E-promoting T-helper cell type 2-type responses . However, vaccines do not prevent most common childhood infections, and large well-controlled epidemiologic studies do not support the hypothesis that vaccines cause allergies . Autoimmune diseases might occur after immunization because proteins on microbial pathogens are similar to human proteins ("molecular mimicry") and could induce immune responses that damage human cells . However, wild-type viruses and bacteria are much better adapted to growth in humans than vaccines and much more likely to stimulate potentially damaging self-reactive lymphocytes . Consistent with critical differences between natural infection and immunization, well-controlled epidemiologic studies do not support the hypothesis that vaccines cause autoimmunity . Flaws in proposed biological mechanisms that explain how vaccines might cause chronic diseases are consistent with the findings of many well-controlled large epidemiologic studies that fail to show a causal relationship.

Arch Microbiol, 2003 Mar, 179(3), 174 - 83 Epub 2003 Feb 12.
A new purple sulfur bacterium isolated from a littoral microbial mat, Thiorhodococcus drewsii sp . nov; Zaar A et al.; A new strain of purple sulfur bacterium was isolated from a marine microbial mat sampled in Great Sippewissett Salt Marsh at the Atlantic coast (Woods Hole, Mass., USA) . Single cells of strain AZ1 were coccus-shaped, highly motile by means of a single flagellum, and did not contain gas vesicles . Intracellular membranes were of the vesicular type . However, additional concentric membrane structures were present . The photosynthetic pigments were bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series, with rhodopin as the dominant carotenoid . Hydrogen sulfide (up to 11 mM), sulfur, thiosulfate, and molecular hydrogen were used as electron donors during anaerobic phototrophic growth . During growth on sulfide, elemental sulfur globules were transiently stored inside the cells . Strain AZ1 is much more versatile than most other Chromatiaceae with respect to electron donor and organic substrates . In the presence of CO(2), it is capable of assimilating C(1)-C(5) fatty acids, alcohols, and intermediates of the tricarboxylic acid cycle . Strain AZ1 could also grow photoorganotrophically with acetate as the sole photosynthetic electron donor . Chemotrophic growth in the dark under microoxic conditions was not detected . Optimum growth occurred at pH 6.5-6.7, 30-35 degrees C, > or =50 micro mol quanta m(-2) s(-1), and 2.4-2.6% NaCl . The DNA base composition was 64.5 mol% G+C . Comparative sequence analysis of the 16S rRNA gene confirmed that the isolate is a member of the family Chromatiaceae . Sequence similarity to the most closely related species, Thiorhodococcus minor DSMZ 11518(T), was 97.8%; however, the value for DNA-DNA hybridization between both strains was only 20% . Because of the low genetic similarity and since strain AZ1 physiologically differs considerably from all other members of the Chromatiaceae, including Trc . minor, the new isolate is described as a new species of the genus Thiorhodococcus, Thiorhodococcus drewsii sp . nov.

J Microbiol Methods, 2003 Apr, 53(1), 57 - 65
Spectral imaging detection and counting of microbial cells in marine sediment; Sunamura M et al.; Semiautomated detection and counting techniques for microbial cells in soil and marine sediment using microscopic-spectral-imaging analysis were developed . Microbial cells in microscopic fields were selectively detected from other fluorescent particles by their fluorescent spectrum, based on the spectral shift between the conjunction and nonconjunction of DNA fluorochrome (SYBR Green II) with nucleic acids . Using this technique, microbial cells could be easily detected in soil and 30-cm deep sediment samples from Tokyo Bay, both of which contain particles other than microbial cells . Total cell density was semiautomatically estimated at 1-6 x 10(9) cells cm(-3) of sediment sampled at different depths in Tokyo Bay, which corresponded to 65-106% (mean 88%) of visual direct counting . This technique may be useful for detecting microbial cells in soil and sediment samples from the deeper subsurface environment.

J Asian Nat Prod Res, 2003 Mar, 5(1), 57 - 61
A new biologically active flavone glycoside from the seeds of Cassia fistula (Linn.); Yadava RN et al.; A new bioactive flavone glycoside 1 {mp 252-254 degrees C, C28H32O16, {M}+ 624 (EIMS)} was isolated from the acetone soluble fraction of the defatted seeds of Cassia fistula (Linn.) . It was characterized as a new bioactive flavone glycoside 5,3',4'-tri-hydroxy-6-methoxy-7-O-alpha-L-rhamnopyranosyl-(1 --> 2)-O-beta-D-galactopyranoside by several colour reactions, spectral analysis and chemical degradations . Compound 1 showed anti-microbial activity.

Vestn Ross Akad Med Nauk, 2003, (1), 49 - 53
{Studies of changes in human intestinal micro-biocenosis in health and in disease}; Nesvizhkii IuV; The paper contains the generalized many-year research conducted by staff of the chair for microbiology (including virology and immunology) aimed at describing the universal principles related with forming an inter-individual diversity of gastric-and-intestinal micro-biocenosis . The research demonstrated a high dependence of qualitative and quantitative parameters of the analyzed biotope on various-genesis factors . It was established that the nature of violations in the gastric-and-intestinal micro-biocenosis is not dependent on peculiarities of an influencing pathogenetic factor, and its difference is related only with quantitative and qualitative (specific) changes in the microbial composition . The marked feature makes it possible to regard the gastric-and-intestinal micro-biocenosis as a non-specific indicator of the condition of a macro-organism and that of the environmental quality.

Sci STKE . 2003 Feb 25;2003(171):re3.
The interleukin-1 receptor/Toll-like receptor superfamily: signal transduction during inflammation and host defense; Dunne A et al.; The signal transduction pathways activated by the proinflammatory cytokine interleukin-1 (IL-1) have been the focus of much attention because of the important role that IL-1 plays in inflammatory diseases . A number of proteins have been described that participate in the post-receptor activation of the transcription factor nuclear factor kappaB (NF-kappaB), and stress-activated protein kinases such as p38 mitogen-activated protein kinase (MAPK) . It has also emerged that the type I IL-1 receptor (IL-1RI) is a member of an expanding receptor superfamily . These related receptors all have sequence similarity in their cytosolic regions . The family includes the Drosophila melanogaster protein Toll, the IL-18 receptor (IL-18R), and 10 Toll-like receptors (TLRs), TLR-1 to TLR-10, which bind to microbial products, activating host defense responses . Because of the similarity of IL-1RI to Toll, the conserved sequence in the cytosolic region of these proteins has been termed the Toll-IL-1 receptor (TIR) domain . The same proteins activated during signaling by IL-1RI also participate in signaling by other receptors with TIR domains . The receptor superfamily is evolutionarily conserved; members also occur in plants and insects, where they also function in host defense . The signaling proteins that are activated are also conserved across species . Differences are, however, starting to emerge in signaling pathways activated by different receptors . This receptor superfamily, therefore, represents an ancient signaling system that is a critical determinant of the innate immune and inflammatory responses.

Biol Reprod, 2003 Jul, 69(1), 294 - 300 Epub 2003 Feb 19.
EP2 splicing variants in rhesus monkey (Macaca mulatta) epididymis; Frohlich O et al.; The expression pattern of EP2 variants was examined in the rhesus monkey (Macaca mulatta) . Using reverse transcriptase-polymerase chain reaction and rapid amplification of complementary cDNA protocols, 11 message variants were identified in rhesus epididymis, only three of which (EP2B, EP2C, and EP2E) have previously been reported . The most abundant variant found in human, EP2A, was not found in rhesus . Seven of the eight new rhesus EP2 variants (EP2J-EP2Q) use previously unidentified 5'-splicing sites in exon 3, and four variants use three previously unidentified exons whose counterparts are present in the human EP2 gene . Overall, 3 of the 11 variants, EP2C, EP2E, and EP2Q, code for beta-defensin-like peptides whose probable physiological role is to protect the male reproductive tract against microbial invasions . Because of the complex splicing pattern that causes some downstream exons to be read in any of the three reading frames, the N-termini of the other eight EP2 peptide variants consist of a partial beta-defensin motif with three cysteines, followed by amino acid sequences that have no recognizable homology to known proteins.

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