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