Cell Immunol, 2002 Feb, 215(2), 195 - 206 Role of MAP kinase activation in Nramp1 mRNA stability in RAW264.7 macrophages expressing Nramp1(Gly169); Lafuse WP et al.; Nramp1 (natural resistance-associated macrophage protein 1) is a phagosomal iron transport molecule . In addition to its anti-microbial activity, Nramp1 exerts a wide range of pleiotropic effects, including increased stability of Nramp1 mRNA and a variety of other mRNA species . Previously, we showed that the increased stability of Nramp1 mRNA is regulated by an oxidant-generated signaling pathway that requires PKC . In the current study, we show that inhibition of ERK1,2 and p38 MAP kinase activities decreases Nramp1 mRNA stability in Mycobacterium avium infected RAW264.7 cells expressing Nramp1(Gly169) but not in RAW264.7-Nramp1(Asp169) cells . Phosphorylation of ERK1,2 and p38 MAP kinases, which could be inhibited by the anti-oxidant BHA and a protein kinase C inhibitor, was higher in M . avium infected RAW264.7-Nramp1(Gly169) cells than in RAW26.47-Nramp1(Asp169) cells . These results suggest that generation of oxidants by Nramp1 iron transport activates MAP kinase signaling cascades that result in stabilization of Nramp1 mRNA. Appl Environ Microbiol, 2002 Sep, 68(9), 4604 - 12 Construction and characterization of a proU-gfp transcriptional fusion that measures water availability in a microbial habitat; Axtell CA et al.; We constructed and characterized a transcriptional fusion that measures the availability of water to a bacterial cell . This fusion between the proU promoter from Escherichia coli and the reporter gene gfp was introduced into strains of E . coli, Pantoea agglomerans, and Pseudomonas syringae . The proU-gfp fusion in these bacterial biosensor strains responded in a quantitative manner to water deprivation caused by the presence of NaCl, Na(2)SO(4), KCl, or polyethylene glycol (molecular weight, 8000) . The fusion was induced to a detectable level by NaCl concentrations of as low as 10 mM in all three bacterial species . Water deprivation induced proU-gfp expression in both planktonic and surface-associated cells; however, it induced a higher level of expression in the surface-associated cells . Following the introduction of P . agglomerans biosensor cells onto bean leaves, the cells detected a significant decrease in water availability within only 5 min . After 30 min, the populations were exposed, on average, to a water potential equivalent to that imposed by approximately 55 mM NaCl . These results demonstrate the effectiveness of a proU-gfp-based biosensor for evaluating water availability on leaves . Furthermore, the inducibility of proU-gfp in multiple bacterial species illustrates the potential for tailoring proU-gfp-based biosensors to specific habitats. Appl Environ Microbiol, 2002 Sep, 68(9), 4593 - 603 Microscopic examination of distribution and phenotypic properties of phylogenetically diverse Chloroflexaceae-related bacteria in hot spring microbial mats; Nubel U et al.; We investigated the diversity, distribution, and phenotypes of uncultivated Chloroflexaceae-related bacteria in photosynthetic microbial mats of an alkaline hot spring (Mushroom Spring, Yellowstone National Park) . By applying a directed PCR approach, molecular cloning, and sequence analysis of 16S rRNA genes, an unexpectedly large phylogenetic diversity among these bacteria was detected . Oligonucleotide probes were designed to target 16S rRNAs from organisms affiliated with the genus Chloroflexus or with the type C cluster, a group of previously discovered Chloroflexaceae relatives of this mat community . The application of peroxidase-labeled probes in conjunction with tyramide signal amplification enabled the identification of these organisms within the microbial mats by fluorescence in situ hybridization (FISH) and the investigation of their morphology, abundance, and small-scale distribution . FISH was combined with oxygen microelectrode measurements, microscope spectrometry, and microautoradiography to examine their microenvironment, pigmentation, and carbon source usage . Abundant type C-related, filamentous bacteria were found to flourish within the cyanobacterium-dominated, highly oxygenated top layers and to predominate numerically in deeper orange-colored zones of the investigated microbial mats, correlating with the distribution of bacteriochlorophyll a . Chloroflexus sp . filaments were rare at 60 degrees C but were more abundant at 70 degrees C, where they were confined to the upper millimeter of the mat . Both type C organisms and Chloroflexus spp . were observed to assimilate radiolabeled acetate under in situ conditions. Appl Environ Microbiol, 2002 Sep, 68(9), 4486 - 94 Quantitative tracing, by Taq nuclease assays, of a synechococcus ecotype in a highly diversified natural population; Becker S et al.; Quantitative Taq nuclease assays (TNAs) (TaqMan PCR), nested PCR in combination with denaturing gradient gel electrophoresis (DGGE), and epifluorescence microscopy were used to analyze the autotrophic picoplankton (APP) of Lake Constance . Microscopic analysis revealed dominance of phycoerythrin (PE)-rich Synechococcus spp . in the pelagic zone of this lake . Cells passing a 3- micro m-pore-size filter were collected during the growth period of the years 1999 and 2000 . The diversity of PE-rich Synechococcus spp . was examined using DGGE to analyze GC-clamped amplicons of a noncoding section of the 16S-23S intergenic spacer in the ribosomal operon . In both years, genotypes represented by three closely related PE-rich Synechococcus strains of our culture collection dominated the population, while other isolates were traced sporadically or were not detected in their original habitat by this method . For TNAs, primer-probe combinations for two taxonomic levels were used, one to quantify genomes of all known Synechococcus-type cyanobacteria in the APP of Lake Constance and one to enumerate genomes of a single ecotype represented by the PE-rich isolate Synechococcus sp . strain BO 8807 . During the growth period, genome numbers of known Synechococcus spp . varied by 2 orders of magnitude (2.9 x 10(3) to 3.1 x 10(5) genomes per ml) . The ecotype Synechococcus sp . strain BO 8807 was detected in every sample at concentrations between 1.6 x 10(1) and 1.3 x 10(4) genomes per ml, contributing 0.02 to 5.7% of the quantified cyanobacterial picoplankton . Although the quantitative approach taken in this study has disclosed several shortcomings in the sampling and detection methods, this study demonstrated for the first time the extensive internal dynamics that lie beneath the seemingly arbitrary variations of a population of microbial photoautotrophs in the pelagic habitat. Appl Environ Microbiol, 2002 Sep, 68(9), 4480 - 5 Soil-atmosphere CO exchanges and microbial biogeochemistry of CO transformations in a Brazilian agricultural ecosystem; King GM et al.; Although anthropogenic land use has major impacts on the exchange of soil and atmosphere gas in general, relatively little is known about its impacts on carbon monoxide . We compared soil-atmosphere CO exchanges as a function of land use, crop type, and tillage treatment on an experimental farm in Parana, Brazil, that is representative of regionally important agricultural ecosystems . Our results showed that cultivated soils consumed CO at rates between 3 and 6 mg of CO m(-2) day(-1), with no statistically significant effect of tillage method or crop . However, CO exchange for a pasture soil was near zero, and an unmanaged woodlot emitted CO at a rate of 9 mg of CO m(-2) day(-1) . Neither nitrite, aluminum sulfate, nor methyl fluoride additions affected CO consumption by tilled or untilled soils from soybean plots, indicating that CO oxidation did not depend on ammonia oxidizers and that CO oxidation patterns differed in part from patterns reported for forest soils . The apparent K(m) for CO uptake, 5 to 11 ppm, was similar to values reported for temperate forest soils; V(max) values, approximately 1 micro g of CO g (dry weight)(-1) h(-1), were comparable for woodlot and cultivated soils in spite of the fact that the latter consumed CO under ambient conditions . Short-term (24-h) exposure to elevated levels of CO (10% CO) partially inhibited uptake at lower concentrations (i.e., 100 ppm), suggesting that the sensitivity to CO of microbial populations that are active in situ differs from that of known carboxydotrophs . Soil-free soybean and corn roots consumed CO when they were incubated with 100-ppm concentrations and produced CO when they were incubated with ambient concentrations . These results document for the first time a role for cultivated plant roots in the dynamics of CO in an agricultural ecosystem. Appl Environ Microbiol, 2002 Sep, 68(9), 4425 - 30 Environmental factors that control microbial perchlorate reduction; Chaudhuri SK et al.; As part of a study to elucidate the environmental parameters that control microbial perchlorate respiration, we investigated the reduction of perchlorate by the dissimilatory perchlorate reducer Dechlorosoma suillum under a diverse set of environmental conditions . Our results demonstrated that perchlorate reduction by D . suillum only occurred under anaerobic conditions in the presence of perchlorate and was dependent on the presence of molybdenum . Perchlorate reduction was dependent on the presence of the enzyme chlorite dismutase, which was induced during metabolism of perchlorate . Anaerobic conditions alone were not enough to induce expression of this enzyme . Dissolved oxygen concentrations less than 2 mg liter(-1) were enough to inhibit perchlorate reduction by D . suillum . Similarly to oxygen, nitrate also regulated chlorite dismutase expression and repressed perchlorate reduction by D . suillum . Perchlorate-grown cultures of D . suillum preferentially reduced nitrate in media with equimolar amounts of perchlorate and nitrate . In contrast, an extended (40 h) lag phase was observed if a similar nitrate-perchlorate medium was inoculated with a nitrate-grown culture . Perchlorate reduction commenced only when nitrate was completely removed in either of these experiments . In contrast to D . suillum, nitrate had no inhibitory effects on perchlorate reduction by the perchlorate reducer Dechloromonas agitata strain CKB . Nitrate was reduced to nitrite concomitant with perchlorate reduction to chloride . These studies demonstrate that microbial respiration of perchlorate is significantly affected by environmental conditions and perchlorate reduction is directly dependent on bioavailable molybdenum and the presence or absence of competing electron acceptors . A microbial treatment strategy can achieve and maintain perchlorate concentrations below the recommended regulatory level, but only in environments in which the variables described above can be controlled. J Chem Ecol, 2002 Jul, 28(7), 1411 - 28 A lectin-like wheat gene responds systemically to attempted feeding by avirulent first-instar Hessian fly larvae; Williams CE et al.; Through gene-for-gene interactions, wheat plants respond to specific biotypes of Hessian fly upon the initiation of first-instar larval feeding . Leaves of plants containing the H9 resistance gene responded to avirulent biotype L . larvae with rapid changes in the levels of several mRNA transcripts and initiation of an incompatible interaction . A low-copy gene, Hfr-1 (Hessian fly-response gene 1), responded with increased mRNA levels for two days before returning to preinfestation levels by day five . Hfr-1 mRNA was constitutively expressed in uninfested control plants as well as in plants infested with virulent larvae . The cDNA sequence was similar to a maize gene encoding a beta-glucosidase aggregating factor (BGAF), to jacalin-like mannose-binding lectins, and to several plant genes that respond to microbial infections . The potential roles of Hfr-1 in defending wheat against Hessian fly damage are discussed. Gastroenterology, 2002 Sep, 123(3), 679 - 88 Mutations in NOD2 are associated with fibrostenosing disease in patients with Crohn's disease; Abreu MT et al.; BACKGROUND & AIMS: The clinical manifestations of Crohn's disease (CD) are diverse, ranging from fibrostenosing small-bowel disease to colon-predominant inflammation . These distinctions may represent genetic, immunologic, and microbial heterogeneity . NOD2 gene mutations in CD have been described recently and may alter innate immune responses . We hypothesized that NOD2 mutations may be associated with distinct phenotypic expressions of CD . METHODS: Two cohorts of consecutively identified patients referred to an inflammatory bowel disease center (n = 142 collected between 1993 and 1996; n = 59 collected between 1999 and 2001) were genotyped for 3 single nucleotide variants of NOD2-R675W, G881R, and 3020insC-and phenotyped for disease behavior, disease location, and serum immune markers . RESULTS: Univariate analysis showed that CD-associated NOD2 variants were significantly associated with fibrostenosing disease in each cohort (P = 0.049 and P = 0.002, respectively) . When both cohorts were analyzed together, the association between NOD2 variants and fibrostenosing disease was more significant (P = 0.001) . These relationships were observed in both Jews and non-Jews . Forty-six percent of patients with fibrostenosing disease carried at least 1 of these alleles, compared with only 23.5% of patients without fibrostenosing disease (odds ratio, 2.8; 95% confidence interval, 1.6-5.2) . Multivariate and conditioning analyses showed a primary association between NOD2 allelic variants and fibrostenosing disease, but not with small-bowel disease . CONCLUSIONS: In this description of a genotype/phenotype correlation in CD patients and NOD2 variants, data suggest that variation in this gene contributes to the occurrence of fibrostenotic CD of the small bowel. Nature, 2002 Aug 29, 418(6901), 988 - 94 Dendritic cell maturation triggers retrograde MHC class II transport from lysosomes to the plasma membrane; Chow A et al.; Central to the initiation of immune responses is recognition of peptide antigen by T lymphocytes . The cell biology of dendritic cells makes them ideally suited for the essential process of antigen presentation . Their life cycle includes several stages characterized by distinct functions and mechanisms of regulation . Immature dendritic cells synthesize large amounts of major histocompatibility complex class II molecules (MHC II), but the alpha beta-dimers are targeted to late endosomes and lysosomes (often referred to as MHC class II compartments) where they reside unproductively with internalized antigens . After exposure to microbial products or inflammatory mediators, endocytosis is downregulated, the expression of co-stimulatory molecules is enhanced, and newly formed immunogenic MHC II-peptide complexes are transported to the cell surface . That these MHC II molecules reach the surface is surprising, as the lysosomes comprise the terminal degradative compartment of the endocytic pathway from which exogenous components generally cannot be recovered intact . Here we have visualized this pathway in live dendritic cells by video microscopy, using cells expressing MHC II tagged with green fluorescent protein (GFP) . We show that on stimulation, dendritic cells generate tubules from lysosomal compartments that go on to fuse directly with the plasma membrane. Acta Crystallogr D Biol Crystallogr, 2002 Sep, 58(Pt 9), 1470 - 3 Epub 2002 Aug 23. Crystallization and preliminary X-ray analysis of an R-2-hydroxypropyl-coenzyme M dehydrogenase; Nocek B et al.; The R-2-hydroxypropyl-coenzyme M (2-mercaptoethanesulfonate) dehydrogenase is a key enzyme in the microbial conversion of propylene to the central metabolite acetoacetate . This enzyme is an interesting member of the NAD(P)H-dependent short-chain dehydrogenase/reductase (SDR) family of enzymes, being one of a pair of homologous dehydrogenases that act in concert in a single pathway to convert the R- and S-enantiomers of hydroxypropyl-coenzyme M to the achiral ketopropyl-coenzyme M product . Crystallization trials have revealed that the highest diffraction quality crystals (better than 2.0 A resolution) could be achieved when the reaction substrates were added to the enzyme in a stoichiometric excess prior to crystallization. EMBO J, 2002 Sep 2, 21(17), 4641 - 53 Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities; Steiner T et al.; Microbial transcription modulator NusG interacts with RNA polymerase and termination factor rho, displaying striking functional homology to eukaryotic Spt5 . The protein is also a translational regulator . We have determined crystal structures of Aquifex aeolicus NusG showing a modular design: an N-terminal RNP-like domain, a C-terminal element with a KOW sequence motif and a species-specific immunoglobulin-like fold . The structures reveal bona fide nucleic acid binding sites, and nucleic acid binding activities can be detected for NusG from three organisms and for the KOW element alone . A conserved KOW domain is defined as a new class of nucleic acid binding folds . This module is a close structural homolog of tudor protein-protein interaction motifs . Putative protein binding sites for the RNP and KOW domains can be deduced, which differ from the areas implicated in nucleic acid interactions . The results strongly argue that both protein and nucleic acid contacts are important for NusG's functions and that the factor can act as an adaptor mediating indirect protein-nucleic acid associations. Biochem Soc Trans, 2002 Aug, 30(4), 724 - 6 Relationship between intestinal iron-transporter expression, hepatic hepcidin levels and the control of iron absorption; Anderson GJ et al.; Hepcidin is an anti-microbial peptide predicted to be involved in the regulation of intestinal iron absorption . We have examined the relationship between the expression of hepcidin in the liver and the expression of the iron-transport molecules divalent-metal transporter 1, duodenal cytochrome b, hephaestin and Ireg1 in the duodenum of rats switched from an iron-replete to an iron-deficient diet or treated to induce an acute phase response . In each case, elevated hepcidin expression correlated with reduced iron absorption and depressed levels of iron-transport molecules . These data are consistent with hepcidin playing a role as a negative regulator of intestinal iron absorption. Biochem Soc Trans, 2002 Aug, 30(4), 691 - 6 Microbial siderophore-mediated transport; Winkelmann G; Microbial iron chelates, called siderophores, are synthesized by bacteria and fungi in response to low iron availability in the environment . The present review summarizes structural details of siderophore ligands with respect to their transport properties . This presentation is largely centred on the occurrence and function of siderophores in the various bacterial and fungal genera. Biochem Soc Trans, 2002 Aug, 30(4), 512 - 6 Formatting antibody fragments to mediate specific therapeutic functions; Weir AN et al.; Monoclonal antibodies are increasingly being used as therapeutic agents in a wide range of indications, including oncology, inflammation and infectious disease . In most cases the basis of the therapeutic function is the high degree of specificity and affinity the antibody-based drug has for its target antigen . However, the mechanism of action (MOA), the way the drug takes advantage of this specificity to mediate a therapeutic effect, varies considerably from drug to drug . Three basic potential categories of MOAs exist: antagonists, agonists and specific delivery mechanisms to target an active function to a particular cell type . The latter functions include selective cell killing, based on Fc-mediated events, recruitment of effector cells, and drug or radioisotope delivery . The majority of these mechanisms are not necessarily optimally mediated by an IgG structure; clearly, in the case of antibody-dependent cellular cytotoxicity or complement-mediated lysis, Fc is required . However, Fab fragments (the fragment comprising one antigen-binding arm of the Y-shaped IgG molecule) can be formatted to mediate most mechanisms and have the advantage that valency and half-life can be controlled to simplify the drug and address only the mechanism required . Moreover, Fab fragments can be produced in microbial expression systems which address manufacturing issues such as scale of supply and cost of goods. Environ Health Perspect, 2002 Aug, 110 Suppl 4, 557 - 60 Asthma in the United States: burden and current theories; Redd SC; Asthma has emerged as a major public health problem in the United States over the past 20 years . Currently, nearly 15 million Americans have asthma, including almost 5 million children . The number of asthma cases has more than doubled since 1980 . Approximately 5,500 persons die from asthma each year, and rates have increased over the past 20 years . Rates of death, hospitalization, and emergency department visits are 2-3 times higher among African Americans than among white Americans . The costs of asthma have also increased to 12.7 billion dollars in 1998 . Both lifestyle and environmental hypotheses have been invoked to explain the increase in asthma prevalence . Several studies have examined the relationship of obesity and asthma and found associations suggesting that obesity predisposes to the development of asthma . Some studies have found that day care attendance and having older siblings protect against the development of asthma . This observation has led investigators to hypothesize that increased exposure to microbial agents might protect against asthma (the hygiene hypothesis) . Environmental exposures found to predispose to asthma include house dust mite allergen and environmental tobacco smoke . Although current knowledge does not permit definitive conclusions about the causes of asthma onset, better adherence to current recommendations for medical therapy and environmental management of asthma would reduce the burden of this disease. Fish Shellfish Immunol, 2002 May, 12(5), 399 - 420 The complement system in teleosts; Holland MC et al.; Complement, an important component of the innate immune system, is comprised of about 35 individual proteins . In mammals, activation of complement results in the generation of activated protein fragments that play a role in microbial killing, phagocytosis, inflammatory reactions, immune complex clearance, and antibody production . Fish appear to possess activation pathways similar to those in mammals, and the fish complement proteins identified thus far show many homologies to their mammalian counterparts . Because information about complement proteins, regulatory proteins, and complement receptors in fish is far from complete, it is unclear whether all the complement functions that have been identified in mammals also occur in fish . However, it has been clearly demonstrated that fish complement can lyse foreign cells and opsonise foreign organisms for destruction by phagocytes . There are also indications that complement fragments participate in inflammatory reactions . Fish possess multiple isoforms of several complement proteins, such as C3 and factor B . It has been hypothesised that the function of this diversity in complement proteins serves to expand their innate immune recognition capacity and response . Understanding the functions of complement in fish and the roles the individual proteins, including the various isoforms, play in host defence, is important not only for understanding the evolution of this system but also for the development of new strategies in fish health management. Soil Biol Biochem, 2001 Jun, 33(7-8), 1059 - 66 Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP); Garland JL et al.; The relative effectiveness of average-well-color-development-normalized single-point absorbance readings (AWCD) vs the kinetic parameters mu(m), lambda, A, and integral (AREA) of the modified Gompertz equation fit to the color development curve resulting from reduction of a redox sensitive dye from microbial respiration of 95 separate sole carbon sources in microplate wells was compared for a dilution series of rhizosphere samples from hydroponically grown wheat and potato ranging in inoculum densities of 1 x 10(4)-4 x 10(6) cells ml-1 . Patterns generated with each parameter were analyzed using principal component analysis (PCA) and discriminant function analysis (DFA) to test relative resolving power . Samples of equivalent cell density (undiluted samples) were correctly classified by rhizosphere type for all parameters based on DFA analysis of the first five PC scores . Analysis of undiluted and 1:4 diluted samples resulted in misclassification of at least two of the wheat samples for all parameters except the AWCD normalized (0.50 abs . units) data, and analysis of undiluted, 1:4, and 1:16 diluted samples resulted in misclassification for all parameter types . Ordination of samples along the first principal component (PC) was correlated to inoculum density in analyses performed on all of the kinetic parameters, but no such influence was seen for AWCD-derived results . The carbon sources responsible for classification differed among the variable types with the exception of AREA and A, which were strongly correlated . These results indicate that the use of kinetic parameters for pattern analysis in CLPP may provide some additional information, but only if the influence of inoculum density is carefully considered . c2001 Elsevier Science Ltd . All rights reserved. Arch Environ Health, 2002 Mar-Apr, 57(2), 155 - 61 Relationships between indoor environments and nasal inflammation in nursing personnel; Smedbold HT et al.; In this study, the authors sought to address the relationships between measured indoor environmental factors and nasal patency (i.e., minimum cross-sectional area) and volume and markers of nasal inflammation in nasal lavage fluid . Clinical data were obtained for 115 females who worked at 36 geriatric nursing departments . The indoor climates in the nursing departments were characterized by high room temperatures (median = 23 degrees C), low relative air humidities (median = 24%), and high air exchange rates indicated by low carbon dioxide levels (median = 570 ppm) . Evidence of microbial amplification was observed in the ventilation unit in 3 of the departments . Decreased nasal patency was observed relative to microbial amplification in the ventilation units (minimum cross-sectional area 1 = 0.80 cm2 vs . 0.64 cm2, p = .003, minimum cross-sectional area 2 = 0.80 cm2 vs . 0.67 cm2, p = .02) and in relation to elevated indoor temperature (volume 1 = 3.46 cm3 vs . 3.22 cm3, p = .03) . The authors concluded that the indoor environment may have affected the nasal mucosa of nursing personnel, thus causing nasal mucosal swelling . The results support the view that fungal contamination of air-supply ducts may be a source of microbial pollution, which can affect the nasal mucosa. J Bacteriol, 2002 Sep, 184(18), 5151 - 7 barS1, a gene for biosynthesis of a gamma-butyrolactone autoregulator, a microbial signaling molecule eliciting antibiotic production in Streptomyces species; Shikura N et al.; From Streptomyces virginiae, in which production of streptogramin antibiotic virginiamycin M(1) and S is tightly regulated by a low-molecular-weight Streptomyces hormone called virginiae butanolide (VB), which is a member of the gamma-butyrolactone autoregulators, the hormone biosynthetic gene (barS1) was cloned and characterized by heterologous expression in Escherichia coli and by gene disruption in S . virginiae . The barS1 gene (a 774-bp open reading frame encoding a 257-amino-acid protein {M(r), 27,095}) is situated in the 10-kb regulator island surrounding the VB-specific receptor gene, barA . The deduced BarS1 protein is weakly homologous to beta-ketoacyl-acyl carrier protein/coenzyme A reductase and belongs to the superfamily of short-chain alcohol dehydrogenase . The function of the BarS1 protein in VB biosynthesis was confirmed by BarS1-dependent in vitro conversion of 6-dehydro-VB-A to VB-A, the last catalytic step in VB biosynthesis . Of the four possible enantiomeric products from racemic 6-dehydro-VB-A as a substrate, only the natural enantiomer of (2R,3R,6S)-VB-A was produced by the purified recombinant BarS1 (rBarS1), indicating that rBarS1 is the stereospecific reductase recognizing (3R)-isomer as a substrate and reducing it stereospecifically to the (6S) product . In the DeltabarS1 mutant created by homologous recombination, the production of VB as well as the production of virginiamycin was lost . The production of virginiamycin by the DeltabarS1 mutant was fully recovered by the external addition of VB to the culture, which indicates that the barS1 gene is essential in the biosynthesis of the autoregulator VBs in S . virginiae and that the failure of virginiamycin production was a result of the loss of VB production. Immunol Rev, 2002 Jul, 185, 54 - 68 Travels along the viral-immunobiology highway; Oldstone MB; Michael Oldstone began his biomedical research career over three decades ago, showing contrary to established scientific dogma, the host was not tolerant but made a specific antiviral immune response during persistent virus infections . Further, the immune response to the virus actually caused tissue damage and disease, the first observation that several manifestations ordinarily accompanying infections were due to the host's antiviral immune response . These observations made originally with lymphocytic choriomeningitis virus (LCMV) and murine retroviruses were extended to other microbial infections including those in humans . Buildings on this work, he showed that antibodies to virus could recognize similar amino acid sequences or motifs found in host/cell proteins and cause disease . This cross-reactivity, referred to as molecular mimicry, has and is now been extensively studied by many laboratories . Another mechanism by which persistent virus infection produced disease was uncovered by cocumenting that viruses could alter the differentiation or "luxury" function of cells with causing cell destruction, thereby altering homeostasis . Finally, Oldstone was one of the first to show that viruses caused immunosuppression, abrogated immunologic surveillance resulting in viral persistence, work carried out long before HIV was discovered . He has also defined host-cell receptors for several viruses . In recent studies, host-cell receptor used by LCMV strains or variants that cause persistence have been identified . This led to observations that a single amino acid on the viral glycoprotein provides the infectious agent a selective ability ot displace extra-cellular matrix molecule, bind to and infect dendritic cells leading to their inability to act as antigen presenting cells thereby aborting the host's ability to generate the antiviral immune response required to clean the infection. Scand J Gastroenterol, 2002 Jul, 37(7), 812 - 7 Gliadin is a good substrate of several transglutaminases: possible implication in the pathogenesis of coeliac disease; Skovbjerg H et al.; BACKGROUND: Deamidation of distinct glutamines in HLA-DQ2 restricted gliadin epitopes, considered critical in the pathogenesis of coeliac disease (CD), can be mediated by tissue transglutaminase (tTG) . To elucidate the possible role of other transglutaminases in CD we investigated whether different mammalian, microbial and vegetable transglutaminases can use gliadin as substrate . METHODS: Studies in which small amounts of transglutaminase have been measured have led to our modifying a microtitre plate assay . We used proteolytically digested gliadin as solid phase substrate and Europium-labelled streptavidine to quantify the biotinylated product covalently linked by the enzyme to the plate . RESULTS: The modified assay is ultrasensitive and quantitative, measuring guinea pig liver transglutaminase concentrations between 0.5 and 50 ng/well . The specific activities of the enzymes (counts/min/mg) against gliadin and N,N-dimethylcasein, respectively, are: tTG 9800/4900, Factor XIII 97330/55620, epidermal transglutaminase 47650/50770, streptoverticillium transglutaminase 4290/2200, phytophora cactorum transglutaminase 6910/4110 . For the first time, we have detected transglutaminase activity in bean sprouts, spinach leaves and green peas, which are commonly used Vegetables . CONCLUSION: Gliadin is a good substrate for endogenous, microbial and plant transglutaminases . An interesting altemative is that gliadins are deamidated by microbial or food transglutaminases in the intestinal lumen . The assay described provides an ultrasensitive method for measuring small amounts of transglutaminase and is considered a helpful tool in further studies of the possible role of transglutaminases in the pathogenesis of CD. Laryngorhinootologie, 2002 Aug, 81(8), 580 - 5 {Identification of CD11c+ myeloid dentritic cells in adenoids and in nasal mucosa of patients with and without allergies}; Tuma E et al.; BACKGROUND: Dendritic cells form a link between innate and acquired immunity . They are capable to detect pathogens based on the recognition of pathogen-associated microbial molecules and trigger the appropriate type of immune responses . In humans, three major subsets of dendritic cells can be distinguished, Langerhans cells of the skin, myeloid DC (MDC) and plasmacytoid DC (PDC) . It was reported that PDC infiltrate nasal mucosa in allergen-induced rhinitis . Information about the role of MDC in nasal mucosa and the corresponding mucosa-associated lymphoid tissue, the nasopharyngeal adenoids, is limited . PATIENTS AND METHODS:: Here we examined the presence of MDC in adenoids and in nasal mucosa of healthy individuals (n = 9) and in patients with allergic rhinitis . MDC were detected by flow cytometry by positive staining for MHC II and CD11c and the lack of lineage markers . Dead cells were excluded from analysis . RESULTS: In adenoids, 0.4 % of all cells were MDC . Considerable numbers of MDC could also be detected in nasal mucosa . No difference was found between healthy individuals and patients with allergies (0.3 % vs . 0.45 % MDC; p = 0.12) . Interestingly, MDC were absent in patients who received treatment with glucocorticoids, while very high numbers of MDC were found in patients who recently had upper respiratory tract infections . CONCLUSION: Our results demonstrate for the first time the presence of MDC in nasal mucosa . MDC numbers were similar in healthy individuals and in patients with allergy . This study forms the basis for examining the role of MDC in the pathogenesis of allergic rhinitis, and for the modulation of MDC functional activity with microbial molecules such as CpG oligonucleotides. Proc Natl Acad Sci U S A, 2002 Sep 17, 99(19), 12021 - 4 Epub 2002 Aug 20. Optimizing grain yields reduces CH4 emissions from rice paddy fields; Denier Van Der Gon HA et al.; Microbial production in anoxic wetland rice soils is a major source of atmospheric CH4 the most important non-CO2 greenhouse gas . Much higher CH4 emissions from well managed irrigated rice fields in the wet than in the dry season could not be explained by seasonal differences in temperature . We hypothesized that high CH4 emissions in the wet season are caused by low grain to biomass ratios . In a screenhouse experiment, removing spikelets to reduce the plants' capacity to store photosynthetically fixed C in grains increased CH4 emissions, presumably via extra C inputs to the soil . Unfavorable conditions for spikelet formation in the wet season may similarly explain high methane emissions . The observed relationship between reduced grain filling and CH4 emission provides opportunities to mitigate CH4 emissions by optimizing rice productivity. Water Sci Technol, 2002, 45(10), 255 - 60 Early warning of disturbances in a laboratory-scale MSW biogas process; Hansson M et al.; The use of near-infrared spectroscopy (NIR) to monitorthe dynamics of a biogas process was evaluated using multivariate data analysis . The digester was a completely stirred 8 I tank reactor fed with the organic fraction of source-sorted MSW . Intermittently the digester was overloaded with feed . Before and after overload on-line monitoring of NIR spectra and off-line analysis in the liquid and the gas phase of traditional chemical variables and microbial biomass, determined as total concentration of phospholipid fatty acids (PLFA and PLEL), were done . The dynamics that occurred due to overloading could be followed using principal component analysis of the obtained NIR-spectra . In addition, the response to changes in the digester fluid was reproducible and could be detected within five minutes, which can be considered as real-time monitoring . Selected wavelengths in the region 800-2,000 nm were used to make a PLS1 -regression with propionate . The regression resulted in a good correlation for propionate (R= 0.94 and RMSEP of 0.21 g/l in the range of 0.3-3 g/l) . The results indicate the possibility to develop an early warning biogas control system based on near-infrared spectroscopy monitoring of propionate. Water Sci Technol, 2002, 45(10), 127 - 32 Characterization of soluble microbial products (SMP) in effluents from anaerobic reactors; Aquino SF et al.; The residual COD from anaerobic treatment processes is usually too high to comply with legislative discharge levels . It has been shown that in well operated systems the majority of the effluent COD originates from soluble microbial products (SMP) produced by the system itself, hence the characteristics of these compounds become important when assessing post-treatment systems to remove the residual COD . The molecular weight (MW) distribution and the identification of SMP in the effluents from three different anaerobic reactors will be presented . It has been found that the bulk of SMP lies in the low MW range, though compounds with MW as high as 300 kDa were also present in all anaerobic effluents . Preliminary results on the identification of such compounds using GC/MS surprisingly revealed the presence of long chain alkenes (C12-C24) and alkanes (C12-C16), as well as some aromatic compounds . These compounds that likely come from cell lysis and endogenous decay may not be easily biodegradable, hence their presence in the effluent is likely to cause the residual COD. Water Sci Technol, 2002, 45(10), 1 - 8 Anaerobic digestion: concepts, limits and perspectives; Schink B; Anaerobic degradation processes are faced with limitations with respect to reaction energetics and reaction kinetics . The small amount of energy available in methanogenic degradation of complex organic compounds allows in most cases only the conservation of minimum amounts of energy in the lowest range of energy exploitable by biochemical reactions for ATP-synthesis . This limit has to be defined in the range of 1/3-1/4 of an ATP unit, or 15-20 kJ per mol reaction . Such small amounts of energy are exploited efficiently by syntrophic microbial communities co-operating e.g . in fatty acid conversion to methane and CO2 . Methanogens also set the stage for efficient conversion of sugars or amino acids, and channel electron fluxes to the utmost efficiency . Kinetic limitations are set by the inertness of certain compounds, e.g . hydrocarbons, to react in the absence of a strong oxidant . New reactions have been found recently which activate such compounds, e.g . aromatic hydrocarbons such as toluene, xylenes, naphthalene, methane, or ammonia . Refined techniques for analysis of microbial activities in ill defined natural environments such as digestive tracts of small invertebrates or polluted aquifers have shown an amazing capacity for anaerobic or oxygen-limited degradation processes that are still to be exploited . Thus, anaerobic digestion is still a matter of fast increasing knowledge, both on the side of basic research as well as on the side of application in treatment of soil, waste materials, or in understanding complex living communities. Environ Sci Technol, 2002 Aug 1, 36(15), 3270 - 4 Carbon isotope fractionation during permanganate oxidation of chlorinated ethylenes (cDCE, TCE, PCE); Poulson SR et al.; Permanganate oxidation of chlorinated ethylenes is an attractive technique to effect remediation of these important groundwater contaminants . Stable carbon isotope fractionation associated with permanganate oxidation of trichloroethylene (TCE), tetrachloroethylene (PCE), and cis-1,2-dichloroethylene (cDCE) has been measured, to study the possibility of applying stable carbon isotope analysis as a technique to assess the efficacy of remediation implemented by permanganate oxidation . Average carbon isotope fractionation factors of alphaTCE = 0.9786, alphaPCE = 0.9830, and alphacDCE = 0.9789 were obtained, although the fractionation factor for PCE may be interpreted to change from a value of 0.9779-0.9871 during the course of the reaction . The fractionation factors for all three compounds are quite similar, in contrast to the variation of fractionation factors vs degree of chlorination observed for other degradative processes, such as microbial dechlorination . This may be due to a common rate-determining step for permanganate oxidation of all three compounds studied . The large fractionation factors and the relative lack of dependence of the fractionation factors upon other environmental factors (e.g . oxidation rate, presence of multiple contaminants, incomplete oxidation, presence of chloride in solution) indicate that monitoring delta13C values of chlorinated ethylenes during oxidation with permanganate may be a sensitive, and potentially quantitative, technique to investigate the extent of degradation. Biotechniques, 2002 Aug, 33(2), 392 - 3, 395-6, 398 passim Yeast "knockout-and-rescue" system for identification of eIF4E-family members possessing eIF4E-activity; Joshi B et al.; Evidence from several laboratories and sequencing projects has revealed that many eukaryotes contain multiple proteins related in sequence to the human mRNA-cap binding translation initiation factor 4E (eIF4E-1) . Although some have been shown to bind cap-analogues, whether all eIF4E-family members function as translation initiation factors is unclear Furthermore, the existence of proteins related to eIF4E complicates the identification of the translation factor by sequence-based approaches . Methods to assess the functionality of eIF4E are limited . The most informative, single assay to identify proteins with eIF4E-activity is that of rescue of the lethal disruption of the single Saccharomyces cerevisiae eIF4E gene . We have developed a simplified yeast eIF4E "knockout-and-rescue" system, the characteristics of which are (i) a haploid system that obviates the needfor a "plasmid shuffle", (ii) a simple G418-based selection for yeast lacking a chromosomal eIF4E gene, and (iii) a glucose-based selection to deplete the strain of a human eIF4E-1 substitute and to assess the eIF4E-activity of an untested elF4E-family member In this form, the yeast eIF4E knockout-and-rescue system becomes a tool available to any laboratory experienced in the selection of microbial strains with antibiotics and standard media for the identification and isolation of cDNAs encoding proteins with eIF4E-activity. Genetica, 2002 May, 115(1), 1 - 12 Genome deterioration: loss of repeated sequences and accumulation of junk DNA; Frank AC et al.; A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle . Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages . In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites . In extreme cases, such as in the 650 kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated . We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences . Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences . This process may lead to temporary increases in the genomic content of pseudogenes and 'junk' DNA . We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria. Kekkaku, 2002 Jul, 77(7), 499 - 502 {Diagnosis of pulmonary tuberculosis in connection with the guideline for community-acquired pneumonia}; Ito K; The decision when to make chest X-ray examination is important for early diagnosis of pulmonary tuberculosis and community-acquired pneumonia as well . And for early diagnosis of pulmonary tuberculosis, differential diagnosis with community-acquired pneumonia is important . For this reasons, guideline for the diagnosis and treatment of community-acquired pneumonia should include when to make chest X-ray examination, and how to exclude the possibility of pulmonary tuberculosis . For example, empiric choice of anti-microbial for apparent pneumonia should be an agent without anti-tuberculosis effect . Clinical evaluation of the effect of anti-microbial should be done carefully, because pulmonary tuberculosis can be clinically improved spontaneously . In the guideline for the diagnosis and treatment of community-acquired pneumonia could include the above-mentioned views on early diagnosis of pulmonary tuberculosis, the guideline could be much more helpful for the tuberculosis program. J Biol Chem, 2002 Oct 25, 277(43), 40687 - 96 Epub 2002 Aug 16. A role for protein phosphatase-2A in p38 mitogen-activated protein kinase-mediated regulation of the c-Jun NH(2)-terminal kinase pathway in human neutrophils; Avdi NJ et al.; Human neutrophil accumulation in inflammatory foci is essential for the effective control of microbial infections . Although exposure of neutrophils to cytokines such as tumor necrosis factor-alpha (TNFalpha), generated at sites of inflammation, leads to activation of MAPK pathways, mechanisms responsible for the fine regulation of specific MAPK modules remain unknown . We have previously demonstrated activation of a TNFalpha-mediated JNK pathway module, leading to apoptosis in adherent human neutrophils (Avdi, N . J., Nick, J . A., Whitlock, B . B., Billstrom, M . A., Henson, P . M., Johnson, G . L., and Worthen, G . S . (2001) J . Biol . Chem . 276, 2189-2199) . Herein, evidence is presented linking regulation of the JNK pathway to p38 MAPK and the Ser/Thr protein phosphatase-2A (PP2A) . Inhibition of p38 MAPK by SB 203580 and M 39 resulted in significant augmentation of TNFalpha-induced JNK and MKK4 (but not MKK7 or MEKK1) activation, whereas prior exposure to a p38-activating agent (platelet-activating factor) diminished the TNFalpha-induced JNK response . TNFalpha-induced apoptosis was also greatly enhanced upon p38 inhibition . Studies with a reconstituted cell-free system indicated the absence of a direct inhibitory effect of p38 MAPK on the JNK module . Neutrophil exposure to the Ser/Thr phosphatase inhibitors okadaic acid and calyculin A induced JNK activation . Increased phosphatase activity following TNFalpha stimulation was shown to be PP2A-associated and p38-dependent . Furthermore, PP2A-induced dephosphorylation of MKK4 resulted in its inactivation . Thus, in neutrophils, p38 MAPK, through a PP2A-mediated mechanism, regulates the JNK pathway, thus determining the extent and nature of subsequent responses such as apoptosis. Genome Biol . 2002 Jul 29;3(8):REVIEWS3011 . Epub 2002 Jul 29. Toll-like receptors: a family of pattern-recognition receptors in mammals; Armant MA et al.; The innate immune system uses a variety of germline-encoded pattern-recognition receptors that recognize conserved microbial structures or pathogen-associated molecular patterns, such as those that occur in the bacterial cell-wall components peptidoglycan and lipopolysaccharide . Recent studies have highlighted the importance of Toll-like receptors (TLRs) as a family of pattern-recognition receptors in mammals that can discriminate between chemically diverse classes of microbial products . First identified on the basis of sequence similarity with the Drosophila protein Toll, TLRs are members of an ancient superfamily of proteins, which includes related proteins in invertebrates and plants . TLRs activate innate immune defense reactions, such as the release of inflammatory cytokines, but increasing evidence supports an additional critical role for TLRs in orchestrating the development of adaptive immune responses . The sequence similarity between the intracellular domains of the TLRs and the mammalian interleukin-1 and interleukin-18 cytokine receptors reflects the use of a common intracellular signal-transduction cascade triggered by these receptor classes . But more recent findings have demonstrated that there are in fact TLR-specific signaling pathways and cellular responses . Thus, TLRs function as sentinels of the mammalian immune system that can discriminate between diverse pathogen-associated molecular patterns and then elicit pathogen-specific cellular immune responses. Genome Biol . 2002 Jun 26;3(7):REVIEWS1020 . Epub 2002 Jun 26. Principles of microbial alchemy: insights from the Streptomyces coelicolor genome sequence; Thompson CJ et al.; The world's most creative producers of natural pharmaceutical compounds are soil-dwelling bacteria classified as Streptomyces . The availability of the recently completed Streptomyces coelicolor genome sequence provides a link between the folklore of antibiotics and other bioactive compounds to underlying biochemical, molecular genetic and evolutionary principles. J Endod, 2002 Aug, 28(8), 613 - 8 Course of infection and case outcome in individuals diagnosed with microbial colonies morphologically consistent with Actinomyces species; Rush JR et al.; Actinomycosis is considered to be a rare disease in the oral region . A retrospective study of files of the University of Nebraska Medical Center College of Dentistry, Department of Pathology, revealed 30 cases in which Actinomyces species were detected from the years 1982 to 2001 (28,490 specimens) . Biopsy submission forms and patient records were reviewed in each of these cases with particular attention to clinical impression, subsequent treatment, and case outcome . Classic treatment for actinomycosis involves the excision of the affected area as well as long-term antibiotics . Our study indicates that antibiotics may not be necessary in treatment of the localized dental presentation of actinomycosis. Curr Drug Targets, 2002 Oct, 3(5), 387 - 99 Computational function assignment for potential drug targets: from single genes to cellular systems; Nagl SB; Biomedical science is currently undergoing an epoch-marking transition from its classical phase to the post-genome era . The outstanding success of world-wide genome sequencing efforts, evidenced by the recent publication of the draft of the human genome, together with the completion of several genomes of eukaryotic model organisms and the availability of microbial genome sequences, is opening up data sources of unprecedented scale for drug discovery . Furthermore, the elucidation of genome expression states through transcriptomic and proteomic techniques is playing a crucial role in the characterisation of disease at the molecular level . At the same time, our still very limited knowledge of the biological functions of genes and proteins at different levels of cellular organisation is preventing full exploitation of the available data . This review will discuss current computational techniques for function prediction based on the sequence-structure-function paradigm . Newly emerging approaches aimed at gaining an expanded understanding of function through integration of data from various sources and modelling of complex cellular systems will also be highlighted. Hum Perf Extrem Environ, 1999 Oct, 4(2), 56 - 9 Critical path plan for food and nutrition research required for planetary exploration missions; Vodovotz Y et al.; In preparation for future planetary exploration, NASA-Johnson Space Center has developed a critical path plan for food and nutrition research needs . The plan highlights the risk factors pertaining to food and nutrition associated with exposure to the space flight environment as well as the possible consequences if no corrective measures are implemented . Included in the plan are the initiating events such as microgravity, remote environment and mission duration, which obviously impact the risk factors . The plan includes points of intervention where mitigating factors can be implemented to avoid outcomes such as malnutrition and unsafe foods . Physiological changes induced by lack of gravity, as well as increased exposure to radiation, may alter nutrient bio-availability, and/or nutrient requirements . An inadequate food system, whether due to technical limitations or nutritional shortcomings, can result in serious consequences . Additionally, microbial and chemical food contamination or psychological factors such as depression may lead to insufficient food intake . Critical questions define areas where further research is required to eliminate or ameliorate the risk from each of those factors . These questions delineate priorities for NASA food and nutrition research for planetary exploration missions. Ying Yong Sheng Tai Xue Bao, 2002 May, 13(5), 629 - 31 {Application of continuous-flow culture in microecological research}; Cao Y; The application of continuous-flow culture in microbial ecology and its advances were reviewed . Continuous-flow culture can be used to build in vitro models simulating ecosystems composed of normal bacteria such as human or animals intestinal and buccal bacteria, to examine the interactions between normal bacteria and pathogens, to investigate the physiological and biochemical traits of bacteria and their metabolic products, and to develop microecological preparations. Lett Appl Microbiol, 2002, 35(3), 190 - 4 Influence of co-substrates on structure of microbial aggregates in long-chain fatty acid-fed anaerobic digesters; Kuang Y et al.; AIMS: The purpose of this study was to investigate the influence of co-substrates, such as glucose and cysteine, on the structure of microbial aggregates in anaerobic digesters treating oleate, a long-chain fatty acid (LCFA) . METHODS AND RESULTS: Transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM) were used to examine the structure of microbial aggregates . Fluorescence in situ hybridization (FISH) techniques were also used to characterize and localize the different trophic groups present in the aggregates . Oleate was found to inhibit the methanogenic activity and formation of granular biomass in digesters . The addition of co-substrates, such as glucose and cysteine either singly or in combination, increased the methanogenic activity and formation of granular biomass . Glucose was more effective than cysteine in reducing the inhibition by oleate on the methanogenic bacteria and in enhancing the formation of granules . CONCLUSIONS: The addition of nutrient substrate, such as glucose and cysteine could decrease the toxicity of LCFA on anaerobic granulation . SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that the addition of other substrates might decrease the toxicity of LCFA on the granulation of biomass in anaerobic digesters and enhance methanogenic activity . A combination of TEM, CLSM and FISH techniques provides a better tool for visualizing microbial aggregates and for differentiating and localizing different microbial groups within these aggregates. J Contam Hydrol, 2002 Aug, 57(3-4), 147 - 59 Sequential anaerobic-aerobic treatment of an aquifer contaminated by halogenated organics: field results; Beeman RE et al.; In situ, sequential, anaerobic to aerobic treatment of groundwater removed perchloroethene (PCE, 1.1 microM) and benzene (0.8 microM) from a contaminated aquifer . Neither aerobic nor anaerobic treatment alone successfully degraded both the chlorinated and non-chlorinated organic contaminants in the aquifer . After the sequential treatment, PCE, trichloroethene (TCE), vinyl chloride (VC), chloroethane (CA), and benzene were not detectable in groundwater . Desorption of residual aquifer contaminants was tested by halting the groundwater recirculation and analyzing the groundwater after 3 and 7 weeks . No desorption of the chlorinated contaminants or daughter products was observed in the treated portion of the aquifer . Sequential anaerobic to aerobic treatment was successful in remediating the groundwater at this test site and may have broad applications at other contaminated sites . Over the 4-year course of the project, the predominant microbial environment of the test site varied from aerobic to sulfate-reducing, to methanogenic, and back to aerobic conditions . Metabolically active microbial populations developed under all conditions, demonstrating the diversity and robustness of natural microbial flora in the aquifer. J AOAC Int, 2002 Jul-Aug, 85(4), 906 - 10 DNA microarray technology used for studying foodborne pathogens and microbial habitats: minireview; Al-Khaldi SF et al.; Microarray analysis is an emerging technology that has the potential to become a leading trend in bacterial identification in food and feed improvement . The technology uses fluorescent-labeled probes amplified from bacterial samples that are then hybridized to thousands of DNA sequences immobilized on chemically modified glass slides . The whole gene or open reading frame(s) is represented by a polymerase chain reaction fragment of double-strand DNA, approximately 1000 base pair (bp) or 20-70 bp single-strand oligonucleotides . The technology can be used to identity bacteria and to study gene expression in complex microbial populations, such as those found in food and gastrointestinal tracts . Data generated by microarray analysis can be potentially used to improve the safety of our food supply as well as ensure the efficiency of animal feed conversion to human food, e.g., in meat and milk production by ruminants . This minireview addresses the use of microarray technology in bacterial identification and gene expression in different microbial systems and in habitats containing mixed populations of bacteria. Curr Opin Plant Biol, 2002 Aug, 5(4), 325 - 31 Cross talk between signaling pathways in pathogen defense; Kunkel BN et al.; Plant defense in response to microbial attack is regulated through a complex network of signaling pathways that involve three signaling molecules: salicylic acid (SA), jasmonic acid (JA) and ethylene . The SA and JA signaling pathways are mutually antagonistic . This regulatory cross talk may have evolved to allow plants to fine-tune the induction of their defenses in response to different plant pathogens. Genome Res, 2002 Aug, 12(8), 1221 - 30 Computational identification of operons in microbial genomes; Zheng Y et al.; By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes . The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways . We applied this algorithm to 42 microbial genomes to identify putative operon structures . The predicted operons from Escherichia coli were compared with a selected metabolism-related operon dataset from the RegulonDB database, yielding a prediction sensitivity (89%) and specificity (87%) relative to this dataset . Several examples of detected operons are given and analyzed . Modular gene cluster transfer and operon fusion are observed . A further use of predicted operon data to assign function to putative genes was suggested and, as an example, a previous putative gene (MJ1604) from Methanococcus jannaschii is now annotated as a phosphofructokinase, which was regarded previously as a missing enzyme in this organism . GC content changes in the operon region and nonoperon region were examined . The results reveal a clear GC content transition at the boundaries of putative operons . We looked further into the conservation of operons across genomes . A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution. Blood, 2002 Sep 1, 100(5), 1734 - 41 Developmental kinetics and lifespan of dendritic cells in mouse lymphoid organs; Kamath AT et al.; The labeling kinetics of 5 dendritic cell (DC) subtypes within the lymphoid organs of healthy laboratory mice during continuous administration of bromodeoxyuridine (BrdU) was determined to investigate developmental relationships and determine turnover rates . Individual DC subtypes behaved as products of separate developmental streams, at least as far back as their dividing precursors . The rate of labeling varied with the lymphoid organ and the DC subtype . Labeling was faster overall in spleen and mesenteric lymph nodes (LNs) and slower in thymus and skin-draining LNs . The CD8(+) DC subtype displayed the most rapid turnover, with a uniformly short (3-day) lifespan in spleen but with distinct short-lived and longer-lived subgroups in thymus . All the skin-derived DCs in LNs showed delayed and slow BrdU labeling, indicating a long overall lifespan; however, this was shown to reflect a long residence time in skin rather than a long-duration presenting antigen in the draining LN . Epidermal-derived Langerhans DCs displayed longer BrdU labeling lag and slower overall turnover than the dermal-derived DCs, and the movement of fluorescent Langerhans DC from skin to LN was slower than that of dermal DCs following skin painting with a fluorescent dye . However, once they arrived in lymphoid organs, all DCs present in healthy, uninfected mice displayed a rapid turnover, and this turnover was even faster after antigenic or microbial product stimulation. J Environ Qual, 2002 Jul-Aug, 31(4), 1406 - 8 Differences in microbial biomass, organic carbon, and dye sorption between flow and no-flow regions of unsaturated soil; Gaston LA et al.; Transport models in which the liquid phase is partitioned between conducting and nonconducting regions allow the possibility that degradation and sorption are different in these regions . However, there is little information on biological or chemical differences between conducting and nonconducting regions of the soil matrix . Previous work by the authors on Br transport through unsaturated, intact soil cores of Dundee silty clay loam (fine-silty, mixed, active, thermic Typic Endoaqualf) indicated non-equilibrium conditions that could be well-described by a two-region model . Fitted parameters indicated little solute transfer between flow regions, suggesting that dye movement in unsaturated soil might delineate conducting and nonconducting regions of this soil . Steady-state, unsaturated flow was established in intact cores (10 by 30 cm) of the Dundee soil, then Br and erioglaucine dye were displaced through these cores . The soil cores were then sectioned into 5-cm segments and stained soil was separated from unstained soil . Microbial biomass C, organic C, and dye sorption K(D) (= g(sorbed) kg(-1)soil/g L(-1)) values for stained and unstained soil were determined . Stained soil had higher microbial biomass C but generally lower organic C and lower affinity for dye sorption than unstained soil from the same depth increment . Fraction of immobile water, dispersion, and mass transfer between conducting and nonconducting regions were consistent with previous results. J Environ Qual, 2002 Jul-Aug, 31(4), 1146 - 56 Selenium stable isotope ratios in California agricultural drainage water management systems; Herbel MJ et al.; Selenium stable isotope ratios are known to shift in predictable ways during various microbial, chemical, and biological processes, and can be used to better understand Se cycling in contaminated environments . In this study we used Se stable isotopes to discern the mechanisms controlling the transformation of oxidized, aqueous forms of Se to reduced, insoluble forms in sediments of Se-affected environments . We measured 80Se/76Se in surface waters, shallow ground waters, evaporites, digested plants and sediments, and sequential extracts from several sites where agricultural drainage water is processed in the San Joaquin Valley of California . Selenium isotope analyses of samples obtained from the Tulare Lake Drainage District flow-through wetland reveal small isotopic contrasts (mean difference 0.7%) between surface water and reduced Se species in the underlying sediments . Selenium in aquatic macrophytes was very similar isotopically to the NaOH and Na2SO3 sediment extracts designed to recover soluble organic Se and Se(0), respectively . For the integrated on-farm drainage management sites, evaporite salts were slightly (approximately 0.6%) enriched in the heavier isotope relative to the inferred parent waters, whereas surface soils were slightly (approximately 1.4%) depleted . Bacterial or chemical reduction of Se(VI) or Se(IV) may be occurring at these sites, but the small isotopic contrasts suggest that other, less isotopically fractionating mechanisms are responsible for accumulation of reduced forms in the sediments . These findings provide evidence that Se assimilation by plants and algae followed by deposition and mineralization is the dominant transformation pathway responsible for accumulation of reduced forms of Se in the wetland sediments. J Environ Qual, 2002 Jul-Aug, 31(4), 1124 - 8 Fate of dimethyldiselenide in soil; Zhang Y et al.; Volatilization of dimethyldiselenide (DMDSe) is one of the most important processes for removing selenium (Se) from Se-contaminated environments . However, the fate of DMDSe in soil is not known . In this study, we monitored the changes of DMDSe in the head space of soil samples spiked with known amounts of DMDSe gas, and fractionated and speciated the resulting Se forms in soil . Dimethyldiselenide was highly dissolved in water in a closed air-water system and was highly sorbed onto soil in a closed air-soil system . Chemical and biological transformations of DMDSe in soil converted a large amount of DMDSe to nonvolatile Se compounds . Elemental Se {Se(0)} and nonvolatile organic Se were the major forms of Se transformed from spiked DMDSe . Microbial conversion of DMDSe to dimethylselenide (DMSe) in soil increased the production of DMSe . Calculation of the mass recovery showed that about 85 to 93% of the added DMDSe was recovered as Se(0), organic Se, organic material Se (OM-Se), Se(IV), and volatile organic Se in the head space in the non-autoclaved soils and 50 to 70% of the added DMDSe was recovered in the autoclaved soils . These results indicate that DMDSe is not a stable form of Se, and it may be one of the important precursors of DMSe in the soil environment. J Environ Qual, 2002 Jul-Aug, 31(4), 1095 - 105 Influence of flow rate on transport of bacteriophage in shale saprolite; McKay LD et al.; The objective of this study was to investigate the influence of flow rate on transport and retention of bacteriophage tracers in a fractured shale saprolite, which is a highly weathered, fine-grained subsoil that retains much of the fabric of the parent bedrock . Synthetic ground water containing PRD-1, MS-2, and bromide was passed through a saturated column of undisturbed shale saprolite at rates ranging from 0.0075 to 0.96 m d ' . First arrival of the bacteriophage tracers in effluent samples in each of the experiments occurred within 0.01 to 0.04 pore volumes (PV) of the start of injection, indicating that bacteriophage were advectively transported mainly through fractures or macropores . Bacteriophage transport velocities, based on first arrival in the effluent, were very similar to fracture flow velocities calculated using the cubic law for flow in a fractured material . For MS-2, maximum concentration and mass of tracer recovered both increased steadily as flow rate increased . For PRD-1, these values initially increased, but were nearly constant at flow rates above 0.039 m d(-1), indicating that approximately 50% of the observed losses were independent of flow rate . Evaluation of the data indicates that physical straining and electrostatic or hydrophobic attachment to fracture or macropore walls were the dominant retention processes . Inactivation and gravitational settling playing secondary roles, except at the slowest flow rates . The study suggests that microbial contamination from sources such as septic fields and sewage ponds may pose a threat to the quality of ground water and surface water in areas with saprolitic subsoils. Philos Trans R Soc Lond B Biol Sci, 2002 Jul 29, 357(1423), 863 - 9 Survival mechanisms in Antarctic lakes; Laybourn-Parry J; In Antarctic lakes, organisms are confronted by continuous low temperatures as well as a poor light climate and nutrient limitation . Such extreme environments support truncated food webs with no fish, few metazoans and a dominance of microbial plankton . The key to success lies in entering the short Antarctic summer with actively growing populations . In many cases, the most successful organisms continue to function throughout the year . The few crustacean zooplankton remain active in the winter months, surviving on endogenous energy reserves and, in some cases, continuing development . Among the Protozoa, mixotrophy is an important nutritional strategy . In the extreme lakes of the McMurdo Dry Valleys, planktonic cryptophytes are forced to sustain a mixotrophic strategy and cannot survive by photosynthesis alone . The dependence on ingesting bacteria varies seasonally and with depth in the water column . In the Vestfold Hills, Pyramimonas, which dominates the plankton of some of the saline lakes, also resorts to mixotrophy, but does become entirely photosynthetic at mid-summer . Mixotrophic ciliates are also common and the entirely photosynthetic ciliate Mesodinium rubrum has a widespread distribution in the saline lakes of the Vestfold Hills, where it attains high concentrations . Bacteria continue to grow all year, showing cycles that appear to be related to the availability of dissolved organic carbon . In saline lakes, bacteria experience sub-zero temperatures for long periods of the year and have developed biochemical adaptations that include anti-freeze proteins, changes in the concentrations of polyunsaturated fatty acids in their membranes and suites of low-temperature enzymes. Artif Life, 2002, 8(2), 123 - 53 The simulated emergence of distributed environmental control in evolving microcosms; Downing KL; This work continues investigation into Gaia theory {Lovelock, (1995) The ages of Gaia, Oxford University Press} from an artificial life perspective {Downing, (2000) in Proceedings of the 7th International Conference on Artificial Life, (pp . 90-99) MIT Press}, with the aim of assessing the general compatibility of emergent distributed environmental control with conventional natural selection . Our earlier system, GUILD {Downing and Zvirinsky, (1999) Artificial Life, 5, 291-318}, displayed emergent regulation of the chemical environment by a population of metabolizing agents, but the chemical model underlying those results was trivial, essentially admitting all possible reactions at a single energy cost . The new model, METAMIC, utilizes abstract chemistries that are both (a) constrained to a small set of legal reactions, and (b) grounded in basic fundamental relationships between energy, entropy, and biomass synthesis/breakdown . To explore the general phenomena of emergent homeostasis, we generate 100 different chemistries and use each as the basis for several METAMIC runs, as part of a Gaia hunt . This search discovers 20 chemistries that support microbial populations capable of regulating a physical environmental factor within their growth-optimal range, despite the extra metabolic cost . Case studies from the Gaia hunt illustrate a few simple mechanisms by which real biota might exploit the underlying chemistry to achieve some control over their physical environment . Although these results shed little light on the question of Gaia on Earth, they support the possibility of emergent environmental control at the microcosmic level. Eur J Gastroenterol Hepatol, 2002 Jul, 14(7), 757 - 65 Role of mucins in inflammatory bowel disease: important lessons from experimental models; Einerhand AW et al.; Inflammatory bowel disease (IBD) is characterized by a chronically inflamed mucosa of the gastrointestinal tract, caused by an underlying immune imbalance and triggered by luminal substances, including bacteria . Mucus forms a gel layer covering the gastrointestinal tract, acting as a semi-permeable barrier between the lumen and the epithelium . Mucins, the building blocks of the mucus gel, determine the thickness and properties of mucus . In IBD in humans, alterations in both membrane-bound and secretory mucins have been described involving genetic mutations in mucin genes, changes in mucin mRNA and protein levels, degree of glycosylation, sulphation, and degradation of mucins . As mucins are strategically positioned between the vulnerable mucosa and the bacterial contents of the bowel, changes in mucin structure and/or quantity probably influence their protective functions and therefore constitute possible aetiological factors in the pathogenesis of IBD . This hypothesis, however, is difficult to prove in humans . Animal models for IBD permit detailed analysis of those aspects of mucins necessary for protection against disease . These models revealed pertinent data as for how changes in mucins, in particular in MUC2, imposed by immunological or microbial factors, may contribute to the development and/or perpetuation of chronic IBD, and shed some light on possible strategies to counteract disease. Science, 2002 Aug 9, 297(5583), 1013 - 5 Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane; Michaelis W et al.; Massive microbial mats covering up to 4-meter-high carbonate buildups prosper at methane seeps in anoxic waters of the northwestern Black Sea shelf . Strong 13C depletions indicate an incorporation of methane carbon into carbonates, bulk biomass, and specific lipids . The mats mainly consist of densely aggregated archaea (phylogenetic ANME-1 cluster) and sulfate-reducing bacteria (Desulfosarcina/Desulfococcus group) . If incubated in vitro, these mats perform anaerobic oxidation of methane coupled to sulfate reduction . Obviously, anaerobic microbial consortia can generate both carbonate precipitation and substantial biomass accumulation, which has implications for our understanding of carbon cycling during earlier periods of Earth's history. J Bacteriol, 2002 Sep, 184(17), 4925 - 9 The membrane-bound alpha-glucuronidase from Pseudomonas cellulosa hydrolyzes 4-O-methyl-D-glucuronoxylooligosaccharides but not 4-O-methyl-D-glucuronoxylan; Nagy T et al.; The microbial degradation of xylan is a key biological process . Hardwood 4-O-methyl-D-glucuronoxylans are extensively decorated with 4-O-methyl-D-glucuronic acid, which is cleaved from the polysaccharides by alpha-glucuronidases . In this report we describe the primary structures of the alpha-glucuronidase from Cellvibrio mixtus (C . mixtus GlcA67A) and the alpha-glucuronidase from Pseudomonas cellulosa (P . cellulosa GlcA67A) and characterize P . cellulosa GlcA67A . The primary structures of C . mixtus GlcA67A and P . cellulosa GlcA67A, which are 76% identical, exhibit similarities with alpha-glucuronidases in glycoside hydrolase family 67 . The membrane-associated pseudomonad alpha-glucuronidase released 4-O-methyl-D-glucuronic acid from 4-O-methyl-D-glucuronoxylooligosaccharides but not from 4-O-methyl-D-glucuronoxylan . We propose that the role of the glucuronidase, in combination with cell-associated xylanases, is to hydrolyze decorated xylooligosaccharides, generated by extracellular hemicellulases, to xylose and 4-O-methyl-D-glucuronic acid, enabling the pseudomonad to preferentially utilize the sugars derived from these polymers. Phytochemistry, 2002 Sep, 61(2), 107 - 14 Transcription factors controlling plant secondary metabolism: what regulates the regulators? Vom Endt D, Kijne JW, Memelink J. Plants produce secondary metabolites, among others, to protect themselves against microbial and herbivore attack or UV irradiation . Certain metabolite classes also function in beneficial interactions with other organisms . For example, anthocyanin pigments and terpenoid essential oils have key roles in attraction of flower pollinators . Secondary metabolites also have direct uses for man . Flavonoids and terpenoids for example have health-promoting activities as food ingredients, and several alkaloids have pharmacological activities . Controlled transcription of biosynthetic genes is one major mechanism regulating secondary metabolite production in plant cells . Several transcription factors involved in the regulation of metabolic pathway genes have been isolated and studied . There are indications that transcription factor activity itself is regulated by internal or external signals leading to controlled responses . The aim of this review is to discuss the regulation of transcription factors involved in secondary metabolism in plants at gene and protein levels, using phenylpropanoid and terpenoid indole alkaloid pathways as two well-studied examples. Nutr Neurosci, 2002 Sep, 5(4), 243 - 50 Dietary prenatal lipids affect myelin gene expression in postnatal undernourished rats; Salvati S et al.; The effects on myelin gene expression of prenatal diets with a different lipid content and fatty acid composition were investigated in undernourished pups . Three groups of rats were fed ad libitum during gestation diets containing either 10% of margarine or 10% of microbial lipids or a standard diet containing 3.5% of lipids . After birth, all groups were switched to a reduced intake (60%) of the standard diet . A control group received ad libitum, the standard diet during pregnancy and throughout lactation . At birth no difference in body and brain weight was observed among the groups and the only significant difference in the brain fatty acid composition was the presence of odd-chain fatty acids in the group fed microbial lipids . Milk was removed from the stomach of pups at 1, 5 and 9 days of lactation for fatty acid analysis . During undernourishment, the monoenoic fatty acid and polyenoic fatty acid percentage was always higher and lower, respectively, in the groups fed 10% than in the group fed 3.5% of lipids during pregnancy . The expression of myelin genes at 11 days of undernutrition was determined in different brain regions by Northern analysis . In the standard group, the proteolipid protein and myelin oligodendrocyte glycoprotein transcripts were well detected only in the medulla whereas in groups fed 10% of lipids the transcripts were also visible in the cerebellum . These data suggest that the high lipid content of the prenatal diet independently from its fatty acid composition affects the myelin gene expression decreasing myelin susceptibility to postnatal undernutrition. Nature, 2002 Aug 8, 418(6898), 630 - 3 Cultivation of the ubiquitous SAR11 marine bacterioplankton clade; Rappe MS et al.; The alpha-proteobacterial lineage that contains SAR11 and related ribosomal RNA gene clones was among the first groups of organisms to be identified when cultivation-independent approaches based on rRNA gene cloning and sequencing were applied to survey microbial diversity in natural ecosystems . This group accounts for 26% of all ribosomal RNA genes that have been identified in sea water and has been found in nearly every pelagic marine bacterioplankton community studied by these methods . The SAR11 clade represents a pervasive problem in microbiology: despite its ubiquity, it has defied cultivation efforts . Genetic evidence suggests that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study . Here we report the isolation of representatives of the SAR11 clade . Eighteen cultures were initially obtained by means of high-throughput procedures for isolating cell cultures through the dilution of natural microbial communities into very low nutrient media . Eleven of these cultures have been successfully passaged and cryopreserved for future study . The volume of these cells, about 0.01 micro m(3), places them among the smallest free-living cells in culture. Nature, 2002 Aug 8, 418(6898), 627 - 30 Reassessing the evidence for the earliest traces of life; van Zuilen MA et al.; The isotopic composition of graphite is commonly used as a biomarker in the oldest (>3.5 Gyr ago) highly metamorphosed terrestrial rocks . Earlier studies on isotopic characteristics of graphite occurring in rocks of the approximately 3.8-Gyr-old Isua supracrustal belt (ISB) in southern West Greenland have suggested the presence of a vast microbial ecosystem in the early Archean . This interpretation, however, has to be approached with extreme care . Here we show that graphite occurs abundantly in secondary carbonate veins in the ISB that are formed at depth in the crust by injection of hot fluids reacting with older crustal rocks (metasomatism) . During these reactions, graphite forms from the disproportionation of Fe(II)-bearing carbonates at high temperature . These metasomatic rocks, which clearly lack biological relevance, were earlier thought to be of sedimentary origin and their graphite association provided the basis for inferences about early life . The new observations thus call for a reassessment of previously presented evidence for ancient traces of life in the highly metamorphosed Early Archaean rock record. Theor Popul Biol, 2002 Jun, 61(4), 449 - 60 Gene transfer in bacteria: speciation without species? Lawrence JG. Although Bacteria and Archaea reproduce by binary fission, exchange of genes among lineages has shaped the diversity of their populations and the diversification of their lineages . Gene exchange can occur by two distinct routes, each differentially impacting the recipient genome . First, homologous recombination mediates the exchange of DNA between closely related individuals (those whose sequences are sufficient similarly to allow efficient integration) . As a result, homologous recombination mediates the dispersal of advantageous alleles that may rise to high frequency among genetically related individuals via periodic selection events . Second, lateral gene transfer can introduce novel DNA into a genome from completely unrelated lineages via illegitimate recombination . Gene exchange by this route serves to distribute genes throughout distantly related clades and therefore may confer complex abilities--not otherwise found among closely related lineages--onto the recipient organisms . These two mechanisms of gene exchange play complementary roles in the diversification of microbial populations into independent, ecologically distinct lineages . Although the delineation of microbial "species" then becomes difficult--if not impossible--to achieve, a cogent process of speciation can be predicted . J Agric Food Chem, 2002 Aug 14, 50(17), 4867 - 74 Effects of pig slurry application on soils and soil humic acids; Plaza C et al.; The effect of three annually consecutive additions of pig slurry at two rates (90 and 150 m3 x ha(-1) x year(-1) on soils and soil humic acids (HAs) was investigated in a field experiment under semiarid conditions . Soils and pig slurries were analyzed by standard methods . The HAs were isolated from soils and pig slurry by a conventional procedure based on alkaline extraction, acidic precipitation to pH 1, purification by repeated alkaline dissolutions and acidic precipitations, water washing, dialysis, and final freeze-drying . The HAs obtained were analyzed for elemental (C, H, N, S, and O) and acidic functional group (carboxylic and phenolic) composition, and by UV-vis, FT-IR, fluorescence, and ESR spectroscopies . With respect to the control soil, the pig slurry amended soils had greater pH and electrical conductivity, slightly larger total N content, and smaller values of C/N ratio . A decrease of total organic C was observed only in soils amended for 2 and 3 years at the higher slurry rate . With respect to control soil HA, pig slurry HA was characterized by larger contents of S- and N-containing groups, smaller acidic functional group and organic free radical contents, a prevalent aliphatic character, extended molecular heterogeneity, and smaller aromatic polycondensation and humification degrees . Amendment with pig slurry HA determines a number of modifications in soil HAs, including increase of C, S, and COOH contents, C/N ratios, and aliphaticity and decrease of extraction yields and N, O, phenolic OH, and organic free radical contents . These effects are generally more evident after the first year of slurry application and tend to disappear with increasing number of treatments . Most probably, over the years the slightly humified slurry HA is mineralized through extended microbial oxidation, whereas only the most recalcitrant components, such as S-containing, phenolic, and aliphatic structures, are partially accumulated by incorporation into soil HA. Clin Oral Investig, 2002 Jun, 6(2), 75 - 8 Contamination of interdental brushes by periodontopathogens; Papaioannou W et al.; Experimental studies have shown that intraoral transmission of bacteria can occur . Of course, the question arises as to how this transmission may happen . In this study, the contamination of interdental brushes by periodontopathogens is examined and compared to the microbial load of the periodontal pockets . In ten untreated chronic periodontitis patients, four interdental sites were professionally brushed with one interdental brush per patient . Subsequently, samples from the depths of the pockets (of the specific interdental sites) were obtained with paper-points . The interdental brush samples and the samples of the subgingival plaque, obtained by the pooled paper-points, were processed for dark-field microscopy examination as well as anaerobic culturing . The results showed that, although significant differences could be found between the brushes and paper-points with direct microscopy, the culturing did not uncover many differences . On the contrary, the detection frequencies of specific bacterial species were almost the same between the two . The total anaerobic colony-forming units (CFU), P . gingivalis, F . nucleatum, and E . corrodens found on the brushes showed a significant correlation with the subgingival plaque samples (P<0.005) . These results suggest that, in untreated situations, interdental brushes are contaminated relatively easily by putative periodontopathogens in numbers comparable to their presence in periodontal pockets . This contamination could be a factor in the intraoral spread of bacteria. J Immunol, 2002 Aug 15, 169(4), 1993 - 2002 Development and compartmentalization of the porcine TCR delta repertoire at mucosal and extraintestinal sites: the pig as a model for analyzing the effects of age and microbial factors; Holtmeier W et al.; gammadelta T cells are an important component of the mucosal immune system . Previously, we have shown that the TCR delta repertoire in human intestine is polyclonal at birth and becomes increasingly restricted with age . In this study, we expand those studies to the pig which allows more extensive experiments including several organs . Tissues from different mucosal sites like the stomach, duodenum, ileum, Peyer's patches, jejunum, and colon, and also extraintestinal sites like the lung, spleen, thymus and mesenteric lymph nodes, were obtained from conventionally reared pigs aged 2 wk to 5.5 years . In addition, tissues were also obtained from 10-wk-old specified pathogen- and germ-free pigs . TCRDV1-DV5 transcripts were amplified by RT-PCR after which complementarity-determining region 3 spectratyping was performed . Individual bands were excised from the gels and directly sequenced . The intestinal TCR delta repertoire showed increasing restriction with age and was highly oligoclonal in the adult 2- to 5.5-year-old pigs . In old pigs, we observed a striking compartmentalization . Different TCR delta repertoires were present between the lungs and the intestinal mucosa but also within different parts of the gastrointestinal tract . However, occasionally we observed identical TCR delta transcripts in the intestine and the lungs and shared clones could be detected also along the entire gastrointestinal tract . Thus, subsets of gammadelta T cells are likely to transport immunological information between different compartments of the immune system . Furthermore, these data support the hypothesis that in each mucosal site, different Ags are responsible for selecting and maintaining the gammadelta TCR over time. J Gastroenterol Hepatol, 2002 Aug, 17(8), 849 - 53 Fusobacterium varium localized in the colonic mucosa of patients with ulcerative colitis stimulates species-specific antibody; Ohkusa T et al.; BACKGROUND: Microbial agents are a possible cause of ulcerative colitis . We have previously reported evidence of bacteria invading the colonic mucosa of patients with ulcerative colitis . We have isolated bacteria from inflamed colonic mucosa, examined the localization of the species in the mucosa, and assayed for serum antibodies to the bacteria . METHODS: Cohorts of 31 per group were enrolled from patients with active ulcerative colitis, Crohn's disease, ischemic colitis, and colon adenomas . A group of 31 healthy controls were also studied . The presence of bacteria in biopsies of patients with ulcerative colitis was analyzed by both isolation and immunohistochemistry . Sera from patients were tested for bacterial antibodies using both Western blots and enzyme-linked immunosorbent assay (ELISA) . RESULTS: Only sera from patients with ulcerative colitis gave specific reactions with Fusobacterium varium in Western blot assays . The detection rate of specific bands was higher for patients with ulcerative colitis (61%) than for subjects with either Crohn's disease (13%) or healthy controls (29%) (P < 0.001 and P = 0.021, respectively) . The ELISA showed that the mean optical densities with extracts of F . varium as antigen were significantly higher for ulcerative colitis patients than for subjects with either Crohn's disease or healthy controls (P < 0.001) . Immunohistochemical detection of F . varium in colonic mucosa was significantly higher in patients with ulcerative colitis (84%) than for subjects with either Crohn's disease (16%) or other controls (3-13%) (P < 0.001) . CONCLUSIONS: Fusobacterium varium bacteria were present in a significant number of patients with active ulcerative colitis, and should be tested in therapeutic trials in order to confirm the causal relationship between F . varium and ulcerative colitis. Biochem J, 2002 Nov 15, 368(Pt 1), 171 - 82 Role of proline, cysteine and a disulphide bridge in the structure and activity of the anti-microbial peptide gaegurin 5; Park SH et al.; Gaegurin 5 (GGN5) is a cationic 24-residue anti-microbial peptide isolated from the skin of a Korean frog, Rana rugosa . It contains a central proline residue and an intra-residue disulphide bridge in its C-terminus, which are common to the anti-microbial peptides found in Ranidae . We determined the solution structure of GGN5 bound to SDS micelles for the first time and investigated the role of proline, cysteine and a disulphide bridge on the structure and activity of GGN5 . GGN5 adopts an amphipathic alpha-helical structure spanning residues 3-20 kinked around Pro-14, which allows the hydrophobic residues to reside in the concave helical region, and a disulphide-bridged loop-like conformation in its C-terminus . By replacement of proline with alanine (PAGGN5), a straight and rigid helix was formed in the central region and was more stable than the kinked helix . Reduction of a disulphide bridge in the C-terminus (GGN5SH) maintained the loosely ordered loop-like conformation, while the replacement of two cysteines with serines (CSGGN5) caused the C-terminal conformation to be completely disordered . The magnitude of anti-microbial activity of the peptides was closely related to their helical stability in the order PAGGN5>GGN5>GGN5SH>CSGGN5, suggesting that the helical stability of the peptides is important for anti-microbial activity . On the other hand, the significant increase of haemolytic activity of PAGGN5 implies that a helical kink of GGN5 could be involved in the selectivity of target cells . The location of GGN5 and PAGGN5, analysed using paramagnetic probes, was mainly at the surface of SDS micelles, although the location of the N-terminal region was slightly different between them. FEBS Lett, 2002 Aug 14, 525(1-3), 48 - 52 4-isoavenaciolide covalently binds and inhibits VHR, a dual-specificity phosphatase; Ueda K et al.; A potent inhibitor of a dual-specificity protein phosphatase, VHR (vaccinia H1 related), was isolated during a screening of microbial metabolites . This inhibitor was identified as 4-isoavenaciolide (4-iA), and was determined to irreversibly inhibit VHR phosphatase activity with a 50% inhibitory concentration of 1.2 microM . Detailed tandem mass spectrometry analyses of proteolysed fragments revealed that two molecules of 4-iA bound a molecule of VHR at the two different fragments: one containing the catalytic domain and the other containing the alpha6 helix positioned surface domain . As 4-iA possesses a reactive exo-methylene moiety, it is possible that 4-iA inhibits VHR through the direct binding to the cysteine residue in the catalytic site (Cys124) . Furthermore, 4-iA inhibited dual-specificity protein phosphatases and tyrosine phosphatases, but did not inhibit serine/threonine phosphatases . These results suggest that 4-iA is a cysteine-targeting inhibitor of protein phosphatases with a common HCX5RS/T motif in the catalytic site. Curr Opin Struct Biol, 2002 Aug, 12(4), 540 - 6 Sensory rhodopsin II: functional insights from structure; Spudich JL et al.; Atomic resolution structures of a sensory rhodopsin phototaxis receptor in haloarchaea (the first sensory member of the widespread microbial rhodopsin family) have yielded insights into the interaction face with its membrane-embedded transducer and into the mechanism of spectral tuning . Spectral differences between sensory rhodopsin and the light-driven proton pump bacteriorhodopsin depend largely upon the repositioning of a conserved arginine residue in the chromophore-binding pocket . Information derived from the structures, combined with biophysical and biochemical analysis, has established a model for receptor activation and signal relay, in which light-induced helix tilting in the receptor is transmitted to the transducer by lateral transmembrane helix-helix interactions. J Ind Microbiol Biotechnol, 2002 Aug, 29(2), 83 - 92 Planktonic nitrate-reducing bacteria and sulfate-reducing bacteria in some western Canadian oil field waters; Eckford RE et al.; Oil fields that use water flooding to enhance oil recovery may become sour because of the production of H(2)S from the reduction of sulfate by sulfate-reducing bacteria (SRB) . The addition of nitrate to produced waters can stimulate the activities of nitrate-reducing bacteria (NRB) and control sulfide production . Many previous studies have focused on chemolithotrophic bacteria that can use thiosulfate or sulfide as energy sources while reducing nitrate . Little attention has been given to heterotrophic NRB in oil field waters . Three different media were used in this study to enumerate various types of planktonic NRB present in waters from five oil fields in western Canada . The numbers of planktonic SRB and bacteria capable of growth under aerobic conditions were also determined . In general, microbial numbers in the produced waters were very low (<10 ml x (-1)) in samples taken near or at wellheads . However, the numbers increased in the aboveground facilities . No thiosulfate-oxidizing NRB were detected in the oil field waters, but other types of NRB were detected in 16 of 18 produced water samples . The numbers of heterotrophic NRB were equal to or greater than the number of sulfide-oxidizing, chemolithotrophic NRB in 12 of 15 samples . These results showed that each of the oil fields contained NRB, which might be stimulated by nitrate amendment to control H(2)S production by SRB. Afr J Health Sci, 1995 Feb, 2(1), 236 - 241 Maize flour contaminated with toxigenic fungi and mycotoxins in Kenya . Muriuki GK, Siboe GM. The majority of the Kenyan human population may be exposed to regular doses of a wide spectrum of highly toxic, carcinogenic, immunosuppressive, mutagenic, and hepatotoxic mycotoxins through the consumption of maizemeal . Maizemeal is consumed in Kenya at the rate of about 0.4kg/person/day, therefore, even the lowest amount of toxins consumed can cause significant effects as some are cumulative . Maize is also a major component in livestock and poultry feed, and the therefore regular indirect human exposure through the consumption of animal products that contain mycotoxin residues could be common . Due to these suspected risks, it is imperative to establish whether consumers in Kenya are actually exposed to dangerous mycotoxins in maize products hence this survey . Forty samples of flour packed in 90kg bags, 58 samples of "Ugali" brand (milled and packed by the Milling Corporation of Kenya Ltd), and 74 samples of "Jogoo" brand ( Unga Maize Millers) were collected from the Nairobi area . The samples were analysed for resident mycoflora, and some mycotoxins associated with key fungal species . Important fungal species isolated from the flour included Aspergillus flavus, A . sulphureus, Fusarium moniliforme, Penicillium stoloniferum, and P . cyclopium . All the three brands of flour were contaminated with Aflatoxins B1 and B2 (0.4-20 ug/kg), Ochratoxin A(50-1,500 ug/kg), and Zearalenone (2,500 - 5,000 ug/kg) . Ochratoxin A was the most prevalent mycotoxin . These data provide a warning that the mycotoxin contamination problem in maizemeal is critical and consumers' health is at risk . Therefore, rigorous countrywide monitoring of mycotoxins in this staple food should be pursued . If possible, maize products should be subjected to stiff microbial quality control from the farm gate to the market shelf. Adv Mar Biol, 2002, 43, 171 - 276 Ecology of southern ocean pack ice; Brierley AS et al.; Around Antarctica the annual five-fold growth and decay of sea ice is the most prominent physical process and has a profound impact on marine life there . In winter the pack ice canopy extends to cover almost 20 million square kilometres--some 8% of the southern hemisphere and an area larger than the Antarctic continent itself (13.2 million square kilometres)--and is one of the largest, most dynamic ecosystems on earth . Biological activity is associated with all physical components of the sea-ice system: the sea-ice surface; the internal sea-ice matrix and brine channel system; the underside of sea ice and the waters in the vicinity of sea ice that are modified by the presence of sea ice . Microbial and microalgal communities proliferate on and within sea ice and are grazed by a wide range of proto- and macrozooplankton that inhabit the sea ice in large concentrations . Grazing organisms also exploit biogenic material released from the sea ice at ice break-up or melt . Although rates of primary production in the underlying water column are often low because of shading by sea-ice cover, sea ice itself forms a substratum that provides standing stocks of bacteria, algae and grazers significantly higher than those in ice-free areas . Decay of sea ice in summer releases particulate and dissolved organic matter to the water column, playing a major role in biogeochemical cycling as well as seeding water column phytoplankton blooms . Numerous zooplankton species graze sea-ice algae, benefiting additionally because the overlying sea-ice ceiling provides a refuge from surface predators . Sea ice is an important nursery habitat for Antarctic krill, the pivotal species in the Southern Ocean marine ecosystem . Some deep-water fish migrate to shallow depths beneath sea ice to exploit the elevated concentrations of some zooplankton there . The increased secondary production associated with pack ice and the sea-ice edge is exploited by many higher predators, with seals, seabirds and whales aggregating there . As a result, much of the Southern Ocean pelagic whaling was concentrated at the edge of the marginal ice zone . The extent and duration of sea ice fluctuate periodically under the influence of global climatic phenomena including the El Nino Southern Oscillation . Life cycles of some associated species may reflect this periodicity . With evidence for climatic warming in some regions of Antarctica, there is concern that ecosystem change may be induced by changes in sea-ice extent . The relative abundance of krill and salps appears to change interannually with sea-ice extent, and in warm years, when salps proliferate, krill are scarce and dependent predators suffer severely . Further research on the Southern Ocean sea-ice system is required, not only to further our basic understanding of the ecology, but also to provide ecosystem managers with the information necessary for the development of strategies in response to short- and medium-term environmental changes in Antarctica . Technological advances are delivering new sampling platforms such as autonomous underwater vehicles that are improving vastly our ability to sample the Antarctic under sea-ice environment . Data from such platforms will enhance greatly our understanding of the globally important Southern Ocean sea-ice ecosystem. Microb Ecol, 2002 Oct, 44(3), 208 - 16 Epub 2002 Aug 06. Effect of oxygen concentration on photosynthesis and respiration in two hypersaline microbial mats; Grotzschel S et al.; The effects of oxygen concentration on photosynthesis and respiration in two hypersaline cyanobacterial mats were investigated . Experiments were carried out on mats from Eilat, Israel, with moderate photosynthetic activity, and mats from Mallorca, Spain, with high photosynthetic activity . The oxygen concentration in the overlying water above the mats was increased stepwise from 0% to 100% O2 . Subsequent changes in oxygen concentration, gross photosynthetic rates, and pH values inside the mats were measured with microelectrodes . According to published reports on the regulation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the key enzyme in the CO2-fixation pathway of phototrophs, we expected photosynthetic activity to decrease with increasing oxygen concentration . Gross photosynthetic and total respiration rates in both mats were highest when the O2 concentration was at 0% in the overlying water . Net oxygen production rates under these conditions were the same as under air saturation (21% O2), while gross photosynthetic and respiration rates were lowest at air saturation . In both mats, gross photosynthetic and respiration rates increased upon gradually increasing the oxygen concentration in the overlying water from 21% to 100% . These results contradict the expectation that photosynthesis decreases with increasing oxygen concentration . Increased photosynthetic rates at oxygen concentrations above 21% were probably caused by enhanced oxidation of organic matter and concomitant CO2 production due to the increased oxygen availability . The cause of the high respiration rates at 0% O2 in the overlying water was presumably the enhanced excretion of photosynthetic products during increased photosynthesis . We conclude that the effect of the O2/CO2 concentration ratio on the activity of Rubisco as demonstrated in vitro on enzyme extracts cannot be extrapolated to the situation in intact microbial mats, because the close coupling of the activity of primary producers and heterotrophic bacteria plays a major role in this ecosystem. Environ Microbiol, 2002 Aug, 4(8), 451 - 64 Isolation of small-subunit rRNA for stable isotopic characterization; MacGregor BJ et al.; Small-subunit ribosomal RNA (SSU rRNA) has several characteristics making it a good candidate biomarker compound: it is found in bacteria, archaea and eukaryotes; it is quickly degraded extracellularly, hence SSU rRNA extracted from a sample probably derives from the currently active population; it includes both conserved and variable regions, allowing the design of capture probes at various levels of phylogenetic discrimination; and rRNA sequences from uncultured species can be classified by comparison with the large and growing public database . Here we present a method for isolation of specific classes of rRNAs from mixtures of total RNA, employing biotin-labelled oligonucleotide probes and streptavidin-coated paramagnetic beads . We also show that the stable carbon isotope composition of Escherichia coli total RNA and SSU rRNA reflects that of the growth substrate for cells grown on LB, M9 glucose and M9 acetate media . SSU rRNA is therefore a promising biomarker for following the flow of carbon, and potentially nitrogen, in natural microbial populations . Some possible applications are discussed. J Vet Diagn Invest, 2002 Jul, 14(4), 288 - 94 Evaluation of microbial culture techniques for the isolation of Pythium insidiosum from equine tissues; Grooters AM et al.; The purpose of this study was to evaluate the effects of sample handling, storage, and culture techniques on the isolation of Pythium insidiosum from infected equine tissues . Tissue and kunker samples obtained immediately posteuthanasia from a horse with subcutaneous pythiosis were used to assess the effects of sample type (kunkers vs . tissues), media type (selective vs . nonselective), storage technique, and storage time on P . insidiosum isolation rate . Overall, isolation rates were higher from fresh kunkers (94.6%) and stored kunkers (76.4%) than from fresh tissues (8.3%) or stored tissues (4.6%) . Isolation of P . insidiosum also occurred more often on antibiotic-containing media than on nonselective media for both fresh and stored samples . For samples that were stored for 1-3 days prior to culture, P . insidiosum isolation rates were highest for the following techniques: kunkers stored at room temperature and plated on selective media (100%), kunkers stored at 4 C and then plated on either nonselective (91.7%) or selective (95.8%) media, kunkers stored on cold packs and then plated on either nonselective (93.8%) or selective (100%) media, kunkers stored in ampicillin solution and plated on selective media (100%), and kunkers stored in ampicillin/gentocin solution and plated on selective media (87.5%) . For samples stored for 4-5 days, P . insidiosum isolation rates were highest for kunkers stored at 4 C and then plated on either nonselective (81.3%) or selective (87.5%) media, kunkers stored in ampicillin solution and then plated on selective media (87.5%), and kunkers stored in ampicillin/gentocin solution and plated on selective media (87.5%) . Results of this study suggest that optimal isolation rates of P . insidiosum from infected equine tissues are achieved by culturing fresh kunkers on selective media . For samples that cannot be processed immediately, acceptable handling techniques include storage at room temperature for up to 3 days, refrigeration for up to 5 days, shipping on cold packs, and storage in antibiotic solution, each combined with subsequent inoculation on selective media. Hum Reprod, 2002 Aug, 17(8), 1938 - 41 Chlamydia trachomatis in subfertile women undergoing uterine instrumentation: an alternative to direct microbial testing or prophylactic antibiotic treatment; Witkin SS et al.; Chlamydia trachomatis is the major cause of tubal occlusion, and is also associated with IVF failure and spontaneous abortion . These infections are asymptomatic in most individuals and can persist in the genital tract for long periods of time in a form resistant to immune destruction . A significant percentage of couples seeking treatment for infertility might, therefore, harbour C . trachomatis in their genital tract . An unresolved question is what to do about this possible chlamydial persistence . Cervical, endometrial and semen samples can be tested for C . trachomatis and only positive individuals treated . Alternatively, all couples undergoing infertility treatment can receive prophylactic antibiotics . We advocate a third option, to screen and treat only individuals who are positive for systemic and/or local anti-chlamydial antibody production . Detection of species-specific C . trachomatis antibodies in peripheral blood will determine which individuals have been exposed to this organism and who, therefore, may be at risk for harbouring persistent forms . Identification of IgA antibodies in genital tract secretions may be an even better indicator of the presence of C . trachomatis in the genital tract . Circulating antibodies to the chlamydial 60kDa heat shock protein (hsp60) is a specific indicator of tubal occlusion and, furthermore, correlates with the continued presence of this micro-organism in the genital tract of non-human primates . Screening for both cervical IgA antibodies to C . trachomatis and serum IgG anti-chlamydial hsp60 appears to provide the best indication as to which women may be harbouring C . trachomatis. BMC Microbiol . 2002 Jul 31;2(1):22. Measurement of microbial activity in soil by colorimetric observation of in situ dye reduction: an approach to detection of extraterrestrial life; Crawford R et al.; BACKGROUND: Detecting microbial life in extraterrestrial locations is a goal of space exploration because of ecological and health concerns about possible contamination of other planets with earthly organisms, and vice versa . Previously we suggested a method for life detection based on the fact that living entities require a continual input of energy accessed through coupled oxidations and reductions (an electron transport chain) . We demonstrated using earthly soils that the identification of extracted components of electron transport chains is useful for remote detection of a chemical signature of life . The instrument package developed used supercritical carbon dioxide for soil extraction, followed by chromatography or electrophoresis to separate extracted compounds, with final detection by voltammetry and tandem mass-spectrometry . RESULTS: Here we used Earth-derived soils to develop a related life detection system based on direct observation of a biological redox signature . We measured the ability of soil microbial communities to reduce artificial electron acceptors . Living organisms in pure culture and those naturally found in soil were shown to reduce 2,3-dichlorophenol indophenol (DCIP) and the tetrazolium dye 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt (XTT) . Uninoculated or sterilized controls did not reduce the dyes . A soil from Antarctica that was de