Genome Res, 2003 Sep, 13(9), 2190 - 4 Epub 2003 Aug 12. A new method for rapidly generating gene-targeting vectors by engineering BACs through homologous recombination in bacteria; Cotta-de-Almeida V et al.; Generating knockout mice is still an expensive and highly time-consuming process . Target construct generation, the first labor-intensive step in this process, requires the manipulation of large fragments of DNA and numerous, and often cumbersome, cloning steps . Here we show the development of a rapid approach for generating targeting constructs that capitalizes on efficient homologous recombination between linear DNA fragments and circular plasmids in Escherichia coli ("recombineering"), the availability of bacterial artificial chromosomes (BACs), and the accessibility of the sequence of the mouse genome . Employing recombineering, we demonstrate with only 1-2 template plasmids, short homologies (40-50bp) between donor and target DNA, and one subcloning step that we can efficiently manipulate BACs in situ to generate a complicated targeting vector . This procedure avoids the need to construct or screen genomic libraries and permits the generation of most standard, conditional, or knock-in targeting vectors, often within two weeks. FEBS Lett, 2003 Aug 14, 549(1-3), 43 - 6 Amiloride inhibition of the proton-translocating NADH-quinone oxidoreductase of mammals and bacteria; Nakamaru-Ogiso E et al.; The proton-translocating NADH-quinone oxidoreductase in mitochondria (complex I) and bacteria (NDH-1) was shown to be inhibited by amiloride derivatives that are known as specific inhibitors for Na(+)/H(+) exchangers . In bovine submitochondrial particles, the effective concentrations were about the same as those for the Na(+)/H(+) exchangers, whereas in bacterial membranes the inhibitory potencies were lower . These results together with our earlier observation that the amiloride analogues prevent labeling of the ND5 subunit of complex I with a fenpyroximate analogue suggest the involvement of ND5 in H(+) (Na(+)) translocation and no direct involvement of electron carriers in H(+) (Na(+)) translocation. J Trauma, 2003 Aug, 55(2), 241 - 7; discussion 247-8 The synergistic effects of hypoxia/reoxygenation or tissue acidosis and bacteria on intestinal epithelial cell apoptosis; Baylor AE 3rd et al.; BACKGROUND: Clinical data indicate that gut perfusion deficits must be rectified within 24 hours after traumatic injury to decrease organ failure and death . Ischemia/reperfusion injury to the gut causes enterocyte apoptosis (Apo), which may contribute to intestinal barrier failure . The temporal response of enterocyte Apo to acidosis and hypoxia/reoxygenation (H/R) in vitro is unknown . The purpose of this study was to examine the effect of various time points of acidosis or H/R on enterocyte apoptosis and monolayer integrity in an in vitro model . METHODS: Caco-2 cell monolayers were made acidic (Dulbecco's modified Eagle's medium, pH 6.9) by hydrochloric acid or exposed to 95% nitrogen/5% carbon dioxide (hypoxia) and then 21% oxygen (reoxygenation) . Escherichia coli C-25 were added to the apical media in subsets . Apo and necrosis were quantified by flow cytometry . Permeability was determined by fluorescein isothiocyanate-dextran . Transepithelial electrical resistance (TEER) indexed monolayer . RESULTS: Extracellular acidosis and C-25 significantly increased apoptosis of Caco-2 cells at 18 hours (extracellular acidosis {EC} + C-25, 14.5 +/- 3.0; control, 3.8 +/- 0.8; p < 0.001 by analysis of variance) . Similarly, the H/R + C-25 group showed a significant increase in apoptosis at 12 hours (H/R + C-25 vs . control, 22.86 +/- 2.12 vs . 3.74 +/- 0.7; p < 0.001 by analysis of variance) . The permeability difference was not significant for EC + C-25 versus control at 18 hours (0.68 +/- 0.25 vs . 0.43 +/- 0.0.0.36, respectively; p > 0.05) . The H/R + C-25 group had a profound increase in permeability over control at 12 hours (10.8 +/- 0.5 vs . 2.1 +/- 0.3, respectively; p < 0.001) . The TEER was significantly lowered for EC versus control at 18 hours (458 +/- 1.5 vs . 468 +/- 8.2) and at 0, 6, and 18 hours for EC + C-25 (409 +/- 28.1, 443 +/- 16.8, and 438 +/- 8.9 vs . 455 +/- 6.5, 467 +/- 6.5, and 469 +/- 8.2, respectively) . There was no significant change in the H/R and H/R + C-25 groups . CONCLUSION: Synergism of H/R or tissue acidosis and bacteria caused increased Apo, TEER, and permeability in vitro. Microbiol Res, 2003, 158(2), 91 - 7 Screening of antagonistic bacteria for biological control of nursery wilt of black pepper (Piper nigrum); Anith KN et al.; Bacterial antagonists of Phytophthora capsici were isolated from underground shoot portions of rooted cuttings of black pepper . Initially isolates were screened by dual culture on potato dextrose agar and carrot agar . Further, a screening was done on black pepper shoots for supression of lesion caused by the pathogen . Most of the antagonists showed varying levels of antagonism in the dual culture and the shoot assay . Isolate PN-026, showing the highest suppression of lesion development in the shoot assay was found to be the most efficient antagonist in reducing Phytophthora capsici induced nursery wilt of black pepper . This screening involving the host, pathogen, and the antagonist, performed on black pepper shoot (the planting material for this vegetatively propagated crop), could be used as a rapid and reliable method for the isolation of efficient bacterial antagonists of P . capsici. Appl Environ Microbiol, 2003 Aug, 69(8), 4910 - 4 Remarkable diversity of phototrophic purple bacteria in a permanently frozen Antarctic lake; Karr EA et al.; Although anoxygenic photosynthesis is thought to play an important role in the primary productivity of permanently frozen lakes in the Antarctic dry valleys, the bacterial communities responsible for this metabolism remain uncharacterized . Here we report the composition and activity of phototrophic purple bacteria in Lake Fryxell, Antarctica, as determined by analysis of a photosynthesis-specific gene, pufM . The results revealed an extensive diversity and highly stratified distribution of purple nonsulfur bacteria in Lake Fryxell and showed which phylotypes produced pufM transcripts in situ . Enrichment cultures for purple bacteria yielded two morphotypes, each with a pufM signature identical to signatures detected by environmental screening . The isolates also contained gas vesicles, buoyancy structures previously unknown in purple nonsulfur bacteria, that may be necessary for these organisms to position themselves at specific depths within the nearly freezing water column. Res Microbiol, 2003 Jul-Aug, 154(6), 399 - 407 Oxalotrophic bacteria; Sahin N; Oxalic acid and its salts are widespread in nature, as they are produced by many species of plants, algae and fungi . The bacteria, which are capable of using oxalate as a sole carbon and energy source, are described as being "oxalotrophic" . Oxalotrophic bacteria do not constitute a homogeneous taxonomic group, but they do constitute a well-defined physiological group . A limited number of aerobic bacteria which are able to utilize oxalate as sole carbon and energy source have been completely described . Most of them are facultative methylotrophs and/or facultative hydrogen-oxidizing chemolithoautotrophs . In this review, the current status of the taxonomy and biodiversity of oxalotrophic bacteria in various environments, and aspects of their biotechnological potential, are briefly summarized. J Zoo Wildl Med, 2003 Jun, 34(2), 206 - 7 Use of blood culture as a nonlethal method for isolating bacteria from fish; Klinger R et al.; Simple nonlethal blood culture methodology, an alternative to euthanasia for diagnosing systemic bacterial infections in fish, is described . Blood was extracted from the caudal vein of 20 individuals of five fish species, incubated in brain-heart infusion broth, and then plated onto enriched blood agar . Nine of these fish were subsequently euthanized and necropsied for confirmatory tissue cultures . Five species of bacteria were isolated from the blood cultures from nine fish, and the tissue culture results in euthanized, necropsied fish agreed with the blood culture results in all cases . All the fish that were not euthanized survived for 24 hr, although two heavily parasitized fish subsequently died. Opt Lett, 2003 Jul 15, 28(14), 1233 - 5 Optical waveguide sensor for on-line monitoring of bacteria; Horvath R et al.; A grating-coupled planar optical waveguide sensor is presented for sensing of bacteria by evanescent waves . The waveguide design results in increased depth of penetration into the sample volume, which makes it suitable for detecting micrometer-sized biological objects . We tested the sensor's performance by monitoring the adhesion of Escherichia coli K12 cells to the sensor surface. Biotechnol Lett, 2003 Mar, 25(6), 479 - 83 Degradation of volatile hydrocarbons from steam-classified solid waste by a mixture of aromatic hydrocarbon-degrading bacteria; Leahy JG et al.; Steam classification is a process for treatment of solid waste that allows recovery of volatile organic compounds from the waste via steam condensate and off-gases . A mixed culture of aromatic hydrocarbon-degrading bacteria was used to degrade the contaminants in the condensate, which contained approx . 60 hydrocarbons, of which 38 were degraded within 4 d . Many of the hydrocarbons, including styrene, 1,2,4-trimethylbenzene, naphthalene, ethylbenzene, m-/p-xylene, chloroform, 1,3-dichloropropene, were completely or nearly completely degraded within one day, while trichloroethylene and 1,2,3-trichloropropane were degraded more slowly. Anal Bioanal Chem, 2003 Nov, 377(6), 964 - 72 Epub 2003 Jul 19. Optical imaging: bacteria, viruses, and mammalian cells encoding light-emitting proteins reveal the locations of primary tumors and metastases in animals; Yu YA et al.; Early detection of tumors and their metastases is crucial for the prognosis of cancer treatment . Traditionally, tumor detection is achieved by various methods, including magnetic resonance imaging and computerized tomography . With the recent cloning, cellular expression, and real-time imaging of light-emitting proteins, such as Renilla luciferase (Ruc), bacterial luciferase (Lux), firefly luciferase (Luc), green fluorescent protein (GFP), or Ruc-GFP fusion protein, significant efforts have been focused on using these marker proteins for tumor detection . It has also been demonstrated that certain bacteria, viruses, and mammalian cells (BVMC), when administered systemically, are able to gain entry and replicate selectively in tumors . In addition, many tissue/tumor specific promoters have been cloned which allow transgene expression specifically in tumor tissues . Therefore, when light-emitting protein encoded BVMC are injected systemically into rodents, tumor-specific marker gene expression is achieved and is detected in real time based on light emission . Consequently, the locations of primary tumors and previously unknown metastases in animals are revealed in vivo . In the future it will likely be feasible to use engineered light-emitting BVMC as probes for tumor detection and as gene-delivery vehicles in vivo for cancer therapy. Biodegradation, 2003 Apr, 14(2), 83 - 90 Sulphate-reducing bacteria, palladium and the reductive dehalogenation of chlorinated aromatic compounds; Baxter-Plant VS et al.; The surfaces of cells of Desulfovibrio desulfuricans, Desulfovibrio vulgaris and a new strain, Desulfovibrio sp . 'Oz-7' were used to manufacture a novel bioinorganic catalyst via the reduction of Pd(II) to Pd(0) at the cell surface using hydrogen as the electron donor . The ability of the palladium coated (palladised) cells to reductively dehalogenate chlorophenol and polychlorinated biphenyl species was demonstrated . Dried, palladised cells of D . desulfuricans, D . vulgaris and Desulfovibrio sp . 'Oz-7' were more effective bioinorganic catalysts than Pd(II) reduced chemically under H2 or commercially available finely divided Pd(0) . Differences were observed in the catalytic activity of the preparations when compared with each other . Negligible chloride release occurred from chlorophenol and polychlorinated biphenyls using biomass alone. Appl Microbiol Biotechnol, 2003 Dec, 63(3), 315 - 21 Epub 2003 Jul 12. Hydrogenases in sulfate-reducing bacteria function as chromium reductase; Chardin B et al.; The ability of sulfate-reducing bacteria (SRB) to reduce chromate VI has been studied for possible application to the decontamination of polluted environments . Metal reduction can be achieved both chemically, by H(2)S produced by the bacteria, and enzymatically, by polyhemic cytochromes c(3) . We demonstrate that, in addition to low potential polyheme c-type cytochromes, the ability to reduce chromate is widespread among {Fe}, {NiFe}, and {NiFeSe} hydrogenases isolated from SRB of the genera Desulfovibrio and Desulfomicrobium . Among them, the {Fe} hydrogenase from Desulfovibrio vulgaris strain Hildenborough reduces Cr(VI) with the highest rate . Both {Fe} and {NiFeSe} enzymes exhibit the same K(m) towards Cr(VI), suggesting that Cr(VI) reduction rates are directly correlated with hydrogen consumption rates . Electron paramagnetic resonance spectroscopy enabled us to probe the oxidation by Cr(VI) of the various metal centers in both {NiFe} and {Fe} hydrogenases . These experiments showed that Cr(VI) is reduced to paramagnetic Cr(III), and revealed inhibition of the enzyme at high Cr(VI) concentrations . The significant decrease of both hydrogenase and Cr(VI)-reductase activities in a mutant lacking {Fe} hydrogenase demonstrated the involvement of this enzyme in Cr(VI) reduction in vivo . Experiments with {3Fe-4S} ferredoxin from Desulfovibrio gigas demonstrated that the low redox {Fe-S} (non-heme iron) clusters are involved in the mechanism of metal reduction by hydrogenases. FEMS Microbiol Lett, 2003 Jul 15, 224(1), 45 - 52 Quantitative structure-activity relationship (QSAR) analysis of aromatic effector specificity in NtrC-like transcriptional activators from aromatic oxidizing bacteria; Park J et al.; A quantitative structure-activity relationship (QSAR) approach was taken to provide mechanistic insights into the interaction between the chemical structure of inducing compounds and the transcriptional activation of aromatic monooxygenase operons among the XylR/DmpR subclass of bacterial NtrC-like transcriptional regulators . Compared to XylR and DmpR, a broader spectrum of effector compounds was observed for the TbuT system from Ralstonia pickettii PKO1 . The results of QSAR analysis for TbuT suggested that a steric effect, rather than hydrophobic or electronic effects, may be the predominant factor in determining aromatic effector specificity, and the active site of the regulator may positively interact not only with the methyl moiety but also with the most electron-rich aryl side of an aromatic effector. Am J Reprod Immunol, 2003 May, 49(5), 269 - 78 Uterine response to infectious bacteria in estrous cyclic ewes; Seals RC et al.; PROBLEM: Luteal-phase uteri are susceptible to infections, and PGE2 and exogenous progesterone can down-regulate, whereas PGF2alpha can up-regulate, uterine immune functions . METHOD OF STUDY: Uteri of follicular- or luteal-phase ewes were inoculated with either saline or bacteria (Arcanobacterium pyogenes and Escherichia colt) . Vena caval blood was collected for the next 3 days, and progesterone, PGE2, and PGF2alpha were measured . The effects of 10(-7) M PGE2 (Experiment 1), 10(-7) M PGF2alpha (Experiment 2), 10(-7) M indomethacin (INDO), and diluent on proliferation of lymphocytes from the vena caval blood in response to mitogens was quantified . RESULTS: Experiment 1: Progesterone was greater (P < 0.01) in luteal than in follicular ewes (3.4 versus 0.4 ng/mL), and only luteal ewes inoculated with bacteria developed infections.Lymphocyte proliferation was least (P = 0.08) in follicular ewes (2.6 versus 4.5 pmol for follicular and luteal, respectively) . Concanavalin A (Con A)-stimulated proliferation was less (P < 0.05) for ewes inoculated with bacteria and for cells cultured with diluent (5.9 versus 3.1 pmol for saline and bacteria, respectively) or with INDO (6.6 versus 2.8 pmol for saline and bacteria, respectively) . Also, Con A-stimulated lymphocytes from ewes inoculated with bacteria tended to proliferate less (P < 0.1) when cultured with PGE2 (4.9 versus 3.7 pmol for saline and bacteria, respectively) or PGE2 + INDO (5.5 versus 3.8 pmol for saline and bacteria, respectively) . Experiment 2: Progesterone was greater (P < 0.01) in luteal than in follicular ewes (6.5 versus 1.2 ng/mL), and only luteal ewes inoculated with bacteria developed infections . Con A-stimulated lymphocyte proliferation was greater (P < 0.001) for follicular ewes (4.1 versus 3.1 pmol for follicular and luteal, respectively) . Proliferation of lymphocytes collected from follicular ewes was greater (P < 0.01) when cells were cultured with PGF2alpha (3.5 versus 2.7 pmol for follicular and luteal, respectively), but INDO did not affect unstimulated or mitogen-stimulated proliferation . CONCLUSIONS: Prostaglandin F2alpha enhanced lymphocyte proliferation, whereas bacterial inoculation and in vitro treatment with PGE2 suppressed lymphocyte proliferation . This may signify the involvement of bacterial products and prostaglandins in regulation of uterine immunity. Neural Netw, 2003 Jun-Jul, 16(5-6), 907 - 14 Multimedia authenticity protection with ICA watermarking and digital bacteria vaccination; Szu H et al.; We propose the application of independent component analysis (ICA), via unsupervised neural networks, to authenticity protection for multimedia products . We give an overview of the current state of multimedia authenticity protection, including the requirements of various multimedia applications, current approaches to the problem, and the robustness of the approaches . For watermark security, a covert independent-component watermarking signal can serve as a 'vaccination' against a dormant digital 'bacteria' protecting the multimedia data . An unauthorized removal of the watermark triggers the bacteria payload, which then degrades the quality of the unauthorized data . We argue that such digital bacteria meet all the established requirements for beneficial virus-like programs, and their payload would merely affect pirated media . We show how these new approaches contribute to a flexible, robust, and secure system for protecting the authenticity of multimedia products. Appl Environ Microbiol, 2003 Jul, 69(7), 4272 - 3 Rapid staining and enumeration of small numbers of total bacteria in water by solid-phase laser cytometry; Broadaway SC et al.; The nucleic acid stain SYBR Green I was evaluated for use with solid-phase laser cytometry to obtain total bacterial cell counts from several water sources with small bacterial numbers . Results were obtained within 30 min and exceeded or equaled counts on R2A agar plates incubated for 14 days at room temperature. Cell Mol Biol (Noisy-le-grand), 2003 Feb, 49(1), 65 - 75 Pathological interactions of bacteria and toxins with the gastrointestinal epithelial tight junctions and/or the zonula adherens: an update; Hofman P; Communication between bacteria and the gastrointestinal tight junctions (TJs) and zonula adherens is examined . Bacteial-epithelial TJs "crosstalk" can be mediated by many virulence factors, mainly secreted toxins, or can be induced by direct contact of the pathogen with epithelial membrane . Moreover, there are several mechanisms by which bacteria may act on gastrointestinal TJs . First, bacteria can act indirectely at the TJs level by inducing cell transepithelial migration . More particularly, neutrophil or dendritic cells can cross the epithelium by a paracellular pathway . Secondly, bacteria and/or toxins can trigger actin cytoskeleton reorganization (depolymerization or hyperpolymerization) . Thirdly, some enteric pathogens are susceptible to act on TJs by activation of cellular signal transduction . Finally, cleavage or modification of TJs proteins can be used by bacteria . New therapeutic strategies may result from a deeper knowledge of the cellular and molecular processes induced by bacteria at the TJ level . Moreover, studies of action of the different bacterial virulence factors on the molecules comprising the TJs and zonula adherens allow us an interesting approach on our understanding of TJ complex regulation. Water Res, 2003 Aug, 37(14), 3379 - 89 Removal of sulfate and heavy metals by sulfate reducing bacteria in short-term bench scale upflow anaerobic packed bed reactor runs; Jong T et al.; Mildly acidic metal (Cu, Zn, Ni, Fe, Al and Mg), arsenic and sulfate contaminated waters were treated, over a 14 day period at 25 degrees C, in a bench-scale upflow anaerobic packed bed reactor filled with silica sand and employing a mixed population of sulfate-reducing bacteria (SRB) . The activity of SRB increased the water pH from approximately 4.5 to 7.0, and enhanced the removal of sulfate and metals in comparison to controls not inoculated with SRB . Addition of organic substrate and sulfate at loading rates of 7.43 and 3.71 kg d(-1) m(-3), respectively, resulted in >82% reduction in sulfate concentration . The reactor removed more than 97.5% of the initial concentrations of Cu, Zn and Ni, while only >77.5% and >82% of As and Fe were removed, respectively . In contrast, Mg and Al levels remained unchanged during the whole treatment process . The removal patterns for Cu, Zn, Ni and Fe reflected the trend in their solubility for their respective metal sulfides, while As removal appeared to coincide with decreasing Cu, Zn, Ni and Fe concentrations, which suggests adsorption or concomitant precipitation with the other metal sulfides. Biosci Biotechnol Biochem, 2003 May, 67(5), 1121 - 5 Degradation of chlorinated biphenyl, dibenzofuran, and dibenzo-p-dioxin by marine bacteria that degrade biphenyl, carbazole, or dibenzofuran; Fuse H et al.; Marine bacterial strains (BP-PH, CAR-SF, and DBF-MAK) were isolated using biphenyl, carbazole (CAR), or dibenzofuran (DF) respectively as substrates for growth . Their 16S ribosomal DNA sequences showed that the species closest to strain BP-PH, strain CAR-SF, and strain DBF-MAK are Alteromonas macleodii (96.3% identity), Neptunomonas naphthovorans (93.1% identity), and Cycloclasticus pugetii (97.3% identity), respectively . The metabolites produced suggested that strain CAR-SF degrades CAR via dioxygenation in the angular position and by the meta-cleavage pathway, and that strain DBF-MAK degrades DF via both lateral and angular dioxygenation . Polychlorinated biphenyl (KC-300) and 2,3-dichlorodibenzo-p-dioxin were partially degraded by strain BP-PH and strain DBF-MAK, while 2,7-dichlorodibenzo-p-dioxin and 2,4,8-trichlorodibenzofuran remained virtually unchanged. Zhongguo Wei Zhong Bing Ji Jiu Yi Xue, 2003 Mar, 15(3), 150 - 3 {Translocation of intestinal endotoxin and bacteria induced by the apoptosis of enterocytes in scald rats after delayed resuscitation}; Zhang C et al.; OBJECTIVE: To investigate the role of enterocyte apoptosis in translocation of intestinal endotoxin and bacteria after delayed resuscitation in scalded rats . METHODS: One hundred and ten male Wistar rats were divided randomly into two groups: group A, early resuscitation, n=60; group B, delayed resuscitation, n=50 . All animals were subjected to 30% total body surface area (TBSA) full-thickness scald . In group A, saline resuscitation was begun immediately after the injury . Saline resuscitation later than 6 hours after scalding was referred as delayed resuscitation . Apoptosis of enterocytes was identified by DNA fragmentation (ap%), DNA agarose gel electrophoresis, TdT-mediated dUTP nick end labeling (TUNEL) method and electron microscope (EM) . The levels of endotoxin in portal vein and systemic circulation were determined by limulus amebocyte lysate technique . The amount of bacteria in mesenteric lymph nodes (MLN) was detected by a quantitative bacteria culture of biopsy . RESULTS: The ap% of enterocytes was increased significantly in groups A and B, peaking at 12 hours postburn . The increased ap% in the group B occurred much earlier and higher than in group A from 3 hours to 48 hours postburn (P<0.05 or P<0.01) . This was corroborated by the results observed in electrophoresis, TUNEL method and EM . The portal endotoxin was much higher in group B than in group A at the same postburn timepoints . So were the endotoxin levels in systemic circulation . A significant positive relationship existed between the portal endotoxin levels and the ap% of intestinal epithelial cells in groups A and B (group A: r=0.936, P<0.01; group B: r=0.899, P<0.05) . The frequency of bacteria translocation of MLN in group B was higher than that in group A . CONCLUSION: Significant pathologic apoptosis of enterocytes is induced by delayed resuscitation after thermal injury in rats . This may lead to a compromise of intestinal barrier . It may be one of the major causes of translocation of endotoxin and bacteria postburn. Appl Microbiol Biotechnol, 2003 Dec, 63(2), 194 - 9 Epub 2003 Jun 26. Naphthalene-utilizing and mercury-resistant bacteria isolated from an acidic environment; Dore SY et al.; Soil samples were taken from areas of low pH (2.5-3.5) surrounding an outdoor coal storage pile . These samples were added to medium with naphthalene as the sole carbon source to enrich for organisms capable of degrading polycyclic aromatic hydrocarbons (PAH) at low pH . Five such bacterial strains were isolated . Sequencing of the 16S rDNA showed them to be members of the genera Clavibacter, Arthrobacter and Acidocella . These organisms were all capable of growth with naphthalene as a sole carbon source at low pH . The genes nahAc, nahAd, phnAc, nahH, xylE or GST, which are known to be associated with PAH degradation were not detected . Isolate 10, the Acidocella strain, tolerated high levels of mercury . PCR amplification and sequencing of genes from the mer operon from isolate 10 DNA suggested that mercury is transported into the bacterial cell and subsequently detoxified since the enzymes encoded by genes in this operon are involved in these processes. Scand J Gastroenterol, 2003 Jun, 38(6), 626 - 34 Non-pathogenic bacteria modulate colonic epithelial gene expression in germ-free mice; Fukushima K et al.; BACKGROUND: We established a bacterial reconstitution model to investigate epithelial cell-luminal bacteria interaction . The aim of the study was to identify the known genes directly or indirectly modulated by non-pathologic bacterial flora in the colonic epithelia of germ-free mice . METHODS: Germ-free mice were orally given a bacterial suspension prepared from specific pathogen-free counterparts (bacterial reconstitution) . Colonic epithelial cells were isolated, then total and poly (A) RNA were extracted . We investigated differential gene expression in colonic epithelial cells among germ-free, bacteria-reconstituted, and specific pathogen-free mice by DNA microarray . Finally, differential expression was confirmed by Northern blot or quantitative RT-PCR . RESULTS: Thirty genes were initially selected as differentially expressed genes in DNA microarray analysis . We confirmed that genes associated with growth (Reg IIIbeta, Reg IIIgamma, guanylate nucleotide binding protein 2), apoptosis (Bcl-associated death promotor), cytoskeleton (tubulin alpha4, erythrocyte protein band 7.2), and immune response (lymphocyte antigen complex 6) were induced by bacterial reconstitution . In contrast, genes possibly participating in extracellular oxidant defence (selenoprotein P, metallothionein 1) and cellular metabolism (cytochrome P450, HMGCoA synthase 2, alcohol dehydrogenase 1 complex, aldehyde dehydrogenase family 1, carbonic anhydrase 1, glycoprotein galactosyltransferase alpha1,3) were down-regulated by bacterial challenge . CONCLUSION: Non-pathogenic bacteria modulated colonic gene expression in germ-free mice, suggesting that non-pathogenic bacteria possibly initiate epithelial change in genetically normal and/or abnormal hosts . The present study provides a basis for the functional study of each molecule in symbiosis with luminal bacteria in healthy and diseased colon. Trends Microbiol, 2003 Jun, 11(6), 248 - 53 Transcription regulation and environmental adaptation in bacteria; Cases I et al.; Lifestyle can be viewed as the environment surrounding an organism and the relationships that it establishes with other species . It is one of the driving forces that contribute to the final shape of bacterial genomes . To assess how these forces affect global cellular functions, we investigated the fraction of the genome devoted to transcription-related proteins, small-molecule metabolism enzymes, and transport, for 60 bacterial genomes classified by lifestyle . Larger genomes were found to harbour more transcription factors per gene than smaller ones . In addition, free-living bacteria (with a few exceptions) are clearly enriched for transcription factors, beyond the expected proportion based on their genome size . This suggests that under complex conditions, gene expression regulation and signal integration have been strongly selected for to enable rapid adaptation to environmental conditions. Oral Microbiol Immunol, 2003 Aug, 18(4), 203 - 7 Bacteria-binding plasma proteins in pellicles formed on hydroxyapatite in vitro and on teeth in vivo; Carlen A et al.; Previous studies on dental pellicle formation and bacterial adherence have focussed on saliva and its components . The tooth surface is, however, also exposed to the plasma-derived crevicular fluid . In the present study, (i) . plasma proteins in in vitro and in vivo pellicles were examined using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), immunoblotting and image analysis and (ii) . the adherence of periodontopathogenic bacteria to experimental plasma and saliva pellicles was examined using radio-labelled bacteria and liquid scintillation counting . The plasma components fibrinogen, fibronectin, albumin and IgG were incorporated from plasma in the experimental pellicle and mediated the adherence of Porphyromonas gingivalis, Fusobacterium nucleatum and Actinomyces naeslundii . These proteins were also readily detected in in vivo pellicles and were found to a higher extent in pellicles formed at the gingival part of the tooth surface than at the incisal part. Environ Microbiol, 2003 Jul, 5(7), 607 - 17 Nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide-oxidizing bacteria; Greene EA et al.; Sulphate-reducing bacteria (SRB) can be inhibited by nitrate-reducing, sulphide-oxidizing bacteria (NR-SOB), despite the fact that these two groups are interdependent in many anaerobic environments . Practical applications of this inhibition include the reduction of sulphide concentrations in oil fields by nitrate injection . The NR-SOB Thiomicrospira sp . strain CVO was found to oxidize up to 15 mM sulphide, considerably more than three other NR-SOB strains that were tested . Sulphide oxidation increased the environmental redox potential (Eh) from -400 to +100 mV and gave 0.6 nitrite per nitrate reduced . Within the genus Desulfovibrio, strains Lac3 and Lac6 were inhibited by strain CVO and nitrate for the duration of the experiment, whereas inhibition of strains Lac15 and D . vulgaris Hildenborough was transient . The latter had very high nitrite reductase (Nrf) activity . Southern blotting with D . vulgaris nrf genes as a probe indicated the absence of homologous nrf genes from strains Lac3 and Lac6 and their presence in strain Lac15 . With respect to SRB from other genera, inhibition of the known nitrite reducer Desulfobulbus propionicus by strain CVO and nitrate was transient, whereas inhibition of Desulfobacterium autotrophicum and Desulfobacter postgatei was long-lasting . The results indicate that inhibition of SRB by NR-SOB is caused by nitrite production . Nrf-containing SRB can overcome this inhibition by further reducing nitrite to ammonia, preventing a stalling of the favourable metabolic interactions between these two bacterial groups . Nrf, which is widely distributed in SRB, can thus be regarded as a resistance factor that prevents the inhibition of dissimilatory sulphate reduction by nitrite. Exp Parasitol, 2003 Jan-Feb, 103(1-2), 16 - 26 Brugia pahangi and Wolbachia: the kinetics of bacteria elimination, worm viability, and host responses following tetracycline treatment; Chirgwin SR et al.; Wolbachia spp., first reported from filariae nearly 30 years ago, have been suggested to contribute to the pathogenesis associated with human filarial infection . Tetracycline has been used to cure filariae of Wolbachia, as a novel means of chemotherapeutic treatment for both ocular and lymphatic filariasis . Tetracycline treatment of L4 or adult Brugia pahangi in vivo resulted in Wolbachia clearance . Less tetracycline was required to clear Wolbachia when treatment began at the L4 stage, compared with adults . Female worms died earlier than male worms when tetracycline was administered at the L4 stage . In all cases, Wolbachia clearance was closely associated with worm death . Worm recoveries decreased following the L4-L5 molt, suggesting tetracycline does not interrupt molting in this model system . Despite worm death and the assumed release of both bacterial- and worm-derived molecules, differences in inflammatory cell population and T cell cytokine mRNA profiles were negligible between tetracycline-treated and non-treated B . pahangi infected gerbils . These data suggest the contribution of Wolbachia to the in vivo induction of the gerbil immune response to B . pahangi may be small. ScientificWorldJournal, 2002 Jun 12, 2, 1603 - 6 Separation of membrane vesicles and cytosol from yeast, cultured cells, and bacteria in a small volume self-generated gradient in a fixed-angle rotor; Graham JM; There are many situations when it is necessary to separate rapidly and efficiently a cytosolic and a membrane vesicle fraction from yeast, cultured cells, or from bacteria . This Protocol Article describes the flotation of the vesicles through a self-generated gradient from a dense sample zone using the low-viscosity medium iodixanol . As the sample is exposed to the gmax the tendency of the proteins to sediment overcomes any diffusion in the opposite direction and are therefore completely separated from the vesicles. ScientificWorldJournal, 2002 Jun 07, 2, 1555 - 9 Separation of membrane vesicles and cytosol from cultured cells and bacteria in a preformed discontinuous gradient; Graham JM; There are many situations when it is necessary to separate rapidly and efficiently a cytosolic and a membrane vesicle fraction from either cultured cells or from bacteria . Flotation of the vesicles through a low-density barrier from a dense sample zone using the low viscosity medium iodixanol allows complete separation of these compartments . As the sample is exposed to the gmax the tendency of the proteins to sediment overcomes any diffusion in the opposite direction. J Biol Chem, 2003 Aug 22, 278(34), 31884 - 90 Epub 2003 Jun 12. The conversion of fibrinogen to fibrin at the surface of curliated Escherichia coli bacteria leads to the generation of proinflammatory fibrinopeptides; Persson K et al.; The inflammatory response to bacterial infection is the result of a complex interplay between bacterial products and host effector systems, such as the immune and complement systems . Here we show that Escherichia coli bacteria expressing fibrous surface proteins, known as curli, assemble and activate factors of the human coagulation cascade at their surface . As a result of this interaction, fibrinogen is converted to fibrin and fibrinogen-derived peptides, termed fibrinopeptides, are generated . The molecular mechanisms behind the bacteria-induced formation of fibrinopeptides were investigated and shown to be triggered by the activation of the contact system, also known as the kallikrein/kinin system or the intrinsic pathway of coagulation . Samples containing fibrinopeptides generated by the interaction between bacteria and plasma were injected into animals and the inflammatory response was monitored . We found that this treatment provoked an infiltration of white blood cells, and the induction of the proinflammatory cytokine MCP-1 at the inflamed site . Our results therefore demonstrate that activation of the coagulation system at the bacterial surface contributes to the pathophysiology of bacterial infectious diseases. Eur J Oral Sci, 2003 Jun, 111(3), 223 - 7 The effects of a triclosan/copolymer dentifrice on oral bacteria including those producing hydrogen sulfide; Sreenivasan P; A clinical procedure was developed to examine the effects of short-term and extended use of a triclosan/copolymer dentifrice and a commercial fluoride dentifrice on oral bacteria, including those producing hydrogen sulfide . Healthy adults volunteered for this double-blind, crossover design clinical study and provided saliva samples for culturing on enriched and indicator media to enumerate all salivary bacteria and those producing hydrogen sulfide (odorigenic), respectively . Subjects brushed with an assigned dentifrice for 7 d and were sampled on day 8 to assess the long-term effects on bacteria . Extended use of the triclosan/copolymer dentifrice resulted in a 49% and 66% reduction of salivary and odorigenic bacteria, respectively, compared with the fluoride dentifrice . To examine short-term effects, subjects subsequently brushed with their assigned dentifrice and were sampled at 2 h and 4 h post-brushing . At 2 h and 4 h post-brushing, the triclosan/copolymer dentifrice resulted in a 62% and 52% decrease for salivary bacteria and 79% and 72% decrease for odorigenic bacteria, respectively, vs . the fluoride dentifrice . The results indicate a significant decrease of all salivary bacteria and hydrogen sulfide-producing odorigenic bacteria following use of the triclosan/copolymer dentifrice and explain previous results on the efficacy of this dentifrice on oral malodor. J Rheumatol, 2003 Jun, 30(6), 1291 - 7 Determinants of synoviocyte clearance of arthritogenic bacteria; Inman RD et al.; OBJECTIVE: Persistence of intracellular organisms may play a critical role in the initiation and perpetuation of synovitis in reactive arthritis (ReA) . We investigated factors that may influence local clearance of arthritogenic pathogens in ReA . METHODS: We studied 11 HLA-B27 positive patients with spondyloarthropathies and contrasted these patients with 6 HLA-B27 negative control patients with rheumatoid arthritis or osteoarthritis . We employed an ex vivo system in which human synoviocytes derived from patients with ReA are cocultured with arthritogenic pathogens, and intracellular clearance is measured by quantitating colony-forming units over time . RESULTS: The clearance kinetics of the organisms bore no relationship to the HLA-B27 status of the patient . Clearance of S . typhimurium over a 10 day period was accompanied by a progressive rise in nitric oxide (NO) production, but this appeared not to be rate-limiting, since (1) clearance kinetics were comparable between high versus low NO-producing synoviocytes; and (2) L-NMMA inhibition of NO production did not alter clearance kinetics of S . typhimurium . Interferon-g (IFN-g) was observed to have a small but measurable effect on bacterial clearance . In certain patients with ReA there was a paradoxical stimulatory response to IFN-g, in which the addition of IFN-g was accompanied by an increase in intracellular bacteria . This effect was found to be attributable to IFN-g mediated suppression of NO production in these cells . This pattern was not observed in B27 negative synoviocytes . CONCLUSION: Intracellular persistence of arthritogenic organisms may contribute to the cellular basis of ReA, but the molecular basis of the bacteriocidal pathways in synoviocytes has not been fully resolved . Our findings indicate that a direct effect of HLA-B27 on these events is unlikely, but that alterations in cytokine response profiles may play a contributory role . Characterizing these mechanisms holds the promise of more specific therapeutic interventions in this disease. Curr Microbiol, 2003 Jul, 47(1), 12 - 6 Growth and activities of sulfate-reducing and methanogenic bacteria in human oral cavity; Robichaux M et al.; Viable counts and activities of sulfate-reducing bacteria (SRB) and methanogenic bacteria were determined in the oral cavities of eight volunteers . Of these, seven harbored viable SRB populations, and six harbored viable methanogenic bacterial populations . Two volunteers classified as type III periodontal patients had both SRB and methanogenic bacteria . Six separate sites were sampled: posterior tongue, anterior tongue, mid-buccal mucosa, vestibular mucosa, supragingival plaque, and subgingival plaque . The SRB was found in all areas in one volunteer, and it was mostly present in posterior tongue, anterior tongue, supragingival, and subgingival plaques in many volunteers . The methanogenic bacteria were mostly found in supragingival and subgingival plaques . The activities of sulfate reduction and methane production were determined in randomly selected isolates. J Microbiol Methods, 2003 Aug, 54(2), 281 - 4 A novel colorimetric method to quantify tannase activity of viable bacteria; Nishitani Y et al.; A novel colorimetric method to quantify tannase activity of viable tannase-producing bacterial strains was developed through application of a visual reading method that was to detect the activity qualitatively . The novel method was sensitive enough to quantify the marginal tannase activity of strains that could not be otherwise measured by conventional spectrophotometric or colorimetric methods. J Theor Biol, 2003 Jun 21, 222(4), 485 - 94 A theoretical and empirical investigation of delayed growth response in the continuous culture of bacteria; Ellermeyer S et al.; When the growth of bacteria in a chemostat is controlled by limiting the supply of a single essential nutrient, the growth rate is affected both by the concentration of this nutrient in the culture medium and by the amount of time that it takes for the chemical and physiological processes that result in the production of new biomass . Thus, although the uptake of nutrient by cells is an essentially instantaneous process, the addition of new biomass is delayed by the amount of time that it takes to metabolize the nutrient . Mathematical models that incorporate this "delayed growth response" (DGR) phenomenon have been developed and analysed . However, because they are formulated in terms of parameters that are difficult to measure directly, these models are of limited value to experimentalists . In this paper, we introduce a DGR model that is formulated in terms of measurable parameters . In addition, we provide for this model a complete set of criteria for determining persistence versus extinction of the bacterial culture in the chemostat . Specifically, we show that DGR plays a role in determining persistence versus extinction only under certain ranges of chemostat operating parameters . It is also shown, however, that DGR plays a role in determining the steady-state nutrient and bacteria concentrations in all instances of persistence . The steady state and transient behavior of solutions of our model is found to be in agreement with data that we obtained in growing Escherichia coli 23716 in a chemostat with glucose as a limiting nutrient . One of the theoretical predictions of our model that does not occur in other DGR models is that under certain conditions a large delay in growth response might actually have a positive effect on the bacteria's ability to persist. Yi Chuan Xue Bao, 2003 Feb, 30(2), 189 - 92 Comparing the base usage frequency between bacteria DNA double strand; Zhong D et al.; During the Evolution, effected by select pressure or nature mutation, the compositions of bacteria genomes is various . And many experiences prove that the genes between leading strand and lagging strand is distinctly in copy, transcription and repair . Some scholars presume that the bases distribution is difference between the two strand, to verify the guess, we using the technology of bioinformatics, compare the base usage between the DNA double strand in 17 species bacteria . The result show: 1 . there is same bases usage frequency in coding sequence between leading strand and lagging strand 2 . There also same bases usage frequency in first codon, second codon and third codon . It suggest that there is a equilibrium between the two strand by the effect of select pressure and nature mutation. Science, 2003 May 30, 300(5624), 1404 - 9 Stress-induced mutagenesis in bacteria; Bjedov I et al.; The evolutionary significance of stress-induced mutagenesis was evaluated by studying mutagenesis in aging colonies (MAC) of Escherichia coli natural isolates . A large fraction of isolates exhibited a strong MAC, and the high MAC variability reflected the diversity of selective pressures in ecological niches . MAC depends on starvation, oxygen, and RpoS and adenosine 3',5'-monophosphate regulons; thus it may be a by-product of genetic strategies for improving survival under stress . MAC could also be selected through beneficial mutations that it generates, as shown by computer modeling and the patterns of stress-inducible and constitutive mutagenesis . We suggest that irrespective of the causes of their emergence, stress-induced mutations participate in adaptive evolution. J Anim Sci, 2003 May, 81(5), 1242 - 52 Progesterone increases susceptibility of gilts to uterine infections after intrauterine inoculation with infectious bacteria; Wulster-Radcliffe MC et al.; In cattle and sheep, a progestogenated uterus is susceptible to infections, but this is not well documented for pigs . Therefore, the effects of day of the estrous cycle and progesterone on the susceptibility to uterine infections were evaluated . Gilts (n = 5 per group) were assigned to treatments in 2 x 2 factorial arrays . In Exp . 1, day of cycle and bacterial challenge were main effects . On d 0 or 8, uteri were inoculated with either 70 x 10(7) cfu of Escherichia coli and 150 x 10(7) cfu of Arcanobacterium pyogenes in PBS or with PBS . In Exp . 2, ovariectomy (OVEX) and progesterone treatment were main effects . On d 0, gilts were ovariectomized or a sham procedure was performed . After surgery, gilts received i.m . injections of progesterone (10 mg/5 mL) or 5 mL of safflower oil diluent twice daily . On d 8, gilts were inoculated with the same doses of bacteria as in Exp . 1 . In Exp . 1 and 2, vena caval blood was collected for 4 d, after which uteri were collected . Sediment and ability to culture E . coli and A . pyogenes from uterine flushings were used to diagnose infections . Differential white blood cell counts and lymphocyte response to concanavalin A (Con A) and lipopolysaccharides (LPS) were used to measure lymphocyte proliferation . Progesterone, estradiol-17beta, prostaglandin F2alpha, (PGF2alpha), and prostaglandin E2 (PGE2) were measured in vena caval blood . In Exp . 1, d-8 gilts receiving bacteria developed infections, but d-0 gilts receiving bacteria did not . Daily percentages of neutrophils and lymphocytes changed (P < 0.05) with cycle day and bacterial challenge . Basal- and Con A-stimulated lymphocyte proliferation were greater (P < 0.05) for d-0 than for d-8 gilts . Concentrations of PGF2, (P < 0.01) and PGE2 (P < 0.05) increased after bacterial challenge, regardless of stage of the estrous cycle at the time of inoculation . In Exp . 2, OVEX decreased (P < 0.001) and progesterone treatment increased (P < 0.001) progesterone concentrations, and OVEX decreased (P < 0.01) estradiol-17beta . Gilts with ovarian and/or exogenous progesterone developed infections . Daily percentages of neutrophils and lymphocytes changed in response to OVEX, and neutrophils changed (P < 0.05) in response to endogenous and exogenous progesterone . Lymphocyte proliferation in response to Con A and LPS increased (P < 0.05) with OVEX and decreased (P < 0.05) with progesterone treatment . We conclude that endogenous and exogenous progesterone reduce the ability of the uterus in gilts to resist infections. J Insect Physiol, 1999 Jan, 45(1), 1 - 6 Provision of riboflavin to the host aphid, Acyrthosiphon pisum, by endosymbiotic bacteria, Buchnera; Nakabachi A et al.; Differential cDNA display and quantitative RT-PCR suggested that the riboflavin synthase complex of the aphid endosymbiont, Buchnera, is active only when the symbiotic system is maintained and well organized in young hosts . Since this finding suggested the provision of riboflavin by Buchnera, we examined the effect of dietary riboflavin on the performance of symbiotic and aposymbiotic aphids using chemically-defined diets . Our results indicate: (1) dietary riboflavin is slightly detrimental to young, symbiotic aphids; (2) dietary riboflavin is essential to aposymbiotic aphids; (3) dietary riboflavin remarkably improves the performance of aposymbiotic aphids . These results strongly suggest that young, symbiotic aphids are provided with riboflavin by their endosymbionts, Buchnera. J Insect Physiol, 1998 Jul, 44(7-8), 629 - 635 Host cell allometry and regulation of the symbiosis between pea aphids, Acyrthosiphon pisum, and bacteria, Buchnera; Douglas AE et al.; The symbiotic bacteria Buchnera in aphids are borne in cells, called bacteriocytes, in the insect haemocoel . The number and median volume of bacteriocytes in pre-reproductive adult insects varied significantly among 14 parthenogenetic clones of the pea aphid Acyrthosiphon pisum . After logarithmic transformation of the data, the relationship of both number and median volume of bacteriocytes with aphid weight for the clones could be described by common regression lines with slopes significantly greater than zero . The allometric slope for median bacteriocyte volume was calculated as 1.06, by model I regression and 1.94 by model II regression; and the equivalent values of the allometric slope for total volume of bacteriocytes were 1.51 and 2.50, suggesting that the total volume of bacteriocytes increases disproportionately with aphid body weight . The partial correlation coefficient between the number and median volume of bacteriocytes was +0.07, with body weight held constant . It is proposed that the regulation of number and size of bacteriocytes is not linked and that bacteriocytes may not exhibit compensatory changes in size, in response to alteration in number . Experimental manipulation of the rates of bacteriocyte differentiation and division could therefore perturb the total volume of the symbiosis, on which aphid pests depend for normal growth and reproduction. Mol Genet Genomics, 2003 Jul, 269(4), 517 - 25 Epub 2003 May 24. Mutations arise independently of transcription in non-dividing bacteria; Barionovi D et al.; It has been proposed that transcription introduces a bias into the random process of mutation . Although this hypothesis is supported by experimental data for mutations arising during active bacterial growth, the role of transcription in mutagenesis in non-dividing bacteria is entirely hypothetical . In the present study, we tested the hypothesis of a possible role of transcription in a non-dividing E . coli K12 strain . In this strain (BD010), a mutated trpB allele (trpB9578), placed under stringent transcriptional control, was tested for the appearance of prototrophic revertants on synthetic medium lacking tryptophan . The number of phenotypic revertants which appeared in the absence of trp transcription was compared to that observed when the mutated gene was continuously transcribed . Our results showed that transcription of trpB is not mutagenic under conditions of tryptophan starvation, and that the frequency of TrpB+ reversion is solely a function of the duration of starvation. RNA, 2003 Jun, 9(6), 711 - 21 A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya; Kaya Y et al.; Putative pseudouridine synthase genes are members of a class consisting of four subgroups that possess characteristic amino acid sequence motifs . These genes have been found in all organisms sequenced to date . In Escherichia coli, 10 such genes have been identified, and the 10 synthase gene products have been shown to function in making all of the pseudouridines found in tRNA and ribosomal RNA except for tRNA(Glu) pseudouridine13 . In this work, a protein able to make this pseudouridine was purified by standard biochemical procedures . Amino-terminal sequencing of the isolated protein identified the synthase as YgbO . Deletion of the ygbO gene caused the loss of tRNA(Glu) pseudouridine13 and plasmid-borne restoration of the structural gene restored pseudouridine13 . Reaction of the overexpressed gene product, renamed TruD, with a tRNA(Glu) transcript made in vitro also yielded only pseudouridine13 . A search of the database detected 58 homologs of TruD spanning all three phylogenetic domains, including ancient organisms . Thus, we have identified a new wide-spread class of pseudouridine synthase with no sequence homology to the previously known four subgroups . The only completely conserved sequence motif in all 59 organisms that contained aspartate was GXKD, in motif II . This aspartate was essential for in vitro activity. Di Yi Jun Yi Da Xue Xue Bao, 2003 May, 23(5), 431 - 4 {Absorption and distribution of 5-aminosalicylic acid from its chitosan capsule degraded by colon bacteria-released enzymes in rats}; Li GF et al.; OBJECTIVE: To examine the absorption and distribution of 5-aminosalicylic acid (5-ASA) in rat colon after oral administration of its chitosan capsule . METHODS: 5-ASA in chitosan capsules (4.8 mg per 3 capsules) were administered orally in rats via a polyethylene cannula under light ether anesthesia . The rats in control group were given 1 ml 5-ASA carboxymethyl cellulose suspension (4.8 mg) . Blood samples were obtained from the rat hearts and the colon tissues sampled at a given interval to measure the concentration of 5-ASA by HPLC . RESULTS: The area under the curve (AUC(0-12)) in the serum samples of chitosan capsule group was 0.62 times that of the control group, while in the colon tissue, the AUC(0-12) of chitosan capsule group was as much as 3.62 times that of the control group . CONCLUSION: The chitosan capsule may be a useful carrier of 5-ASA for colon-specific delivery. Genetics, 2003 May, 164(1), 13 - 21 Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes; Townsend JP et al.; We examine the potential beneficial effects of the expanded access to environmental DNA offered by mutators on the adaptive potential of bacterial populations . Using parameters from published studies of recombination in E . coli, we find that the presence of mutators has the potential to greatly enhance bacterial population adaptation when compared to populations without mutators . In one specific example, for which three specific amino acid substitutions are required for adaptation to occur in a 300-amino-acid protein, we found a 3500-fold increase in the rate of adaptation . The probability of a beneficial acquisition decreased if more amino acid changes, or integration of longer DNA fragments, were required for adaptation . The model also predicts that mutators are more likely than nonmutator phenotypes to acquire genetic variability from a more diverged set of donor bacteria . Bacterial populations harboring mutators in a sequence heterogeneous environment are predicted to acquire most of their DNA conferring adaptation in the range of 13-30% divergence, whereas nonmutator phenotypes become adapted after recombining with more homogeneous sequences of 7-21% divergence . We conclude that mutators can accelerate bacterial adaptation when desired genetic variability is present within DNA fragments of up to approximately 30% divergence. World J Urol, 2003 Jun, 21(2), 100 - 4 Epub 2003 May 13. Application of real-time polymerase chain reaction technology to detect prostatic bacteria in patients with chronic prostatitis/chronic pelvic pain syndrome; Takahashi S et al.; To investigate the potential association between prostate infection and chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), we used molecular approaches described in previous reports . These methods employed standard polymerase chain (PCR) reaction assays to provide a qualitative evaluation of prostatic bacterial species . Here, we report on the detection of prostatic bacteria using a real-time PCR . Template DNAs were examined from prostatic tissue samples from patients with CP/CPPS . Two PCR primer sets were used: one that amplifies a portion of all known bacterial ribosomal DNAs (16S rDNAs) and one that is specific for Escherichia coli as opposed to related, E . coli-like bacteria . The 16S rDNA real-time PCR assay detected bacterial DNAs in eight (26%) of 31 samples from patients with CP/CPPS, including three samples (10%) that were also positive by the E . coli real-time PCR assay . These E . coli positives were quantified at approximately 10(3) cfu/ml of tissue digested . Quantification, speed and specificity make real-time PCR a promising approach for the quantitative detection and identification of prostatic bacteria from CP/CPPS patients. J Dairy Sci, 2003 Apr, 86(4), 1429 - 35 Kinetics of in sacco fiber-attachment of representative ruminal cellulolytic bacteria monitored by competitive PCR; Koike S et al.; Stems of orchardgrass hay in nylon bags were incubated in the rumens of three ruminally fistulated sheep to monitor the rate and extent of fiber attachment by the representative ruminal cellulolytic bacteria via competitive polymerase chain reaction . After incubation for 5 min, the numbers of Fibrobacter succinogenes and the two ruminococcal species attached to stems were 10(5) and 10(4)/g dry matter (DM) of stem, respectively . At 10 min, the numbers of all three species attached to stems increased 10-fold . Thereafter, attached cell numbers of the three species gradually increased and peaked at 24 h (10(9)/g DM for F . succinogenes and 10(7)/g DM for Ruminococcus flavefaciens) or 48 h (10(6)/g DM for Ruminococcus albus) . On the other hand, cell numbers of all three species in the whole digesta were constant over 24 h . Changes in the rate of in sacco neutral detergent fiber disappearance of hay stem, which showed a linear increase up to 96 h, were not synchronized with changes in cellulolytic bacterial mass . These results suggest that sufficient numbers of cells of the three cellulolytic species to move to new plant fragments are present at the start of incubation, the initial attachment to new plant matter is mostly accomplished within 10 min and then bacterial growth and fibrolytic action follow . F . succinogenes was most dominant, both in the whole rumen digesta and on the suspended hay stems, demonstrating the ecological and functional significance of this species in ruminal fiber digestion. Caries Res, 2003 May-Jun, 37(3), 206 - 11 Cultivatable bacteria in dentine after caries excavation using rose-bur or carisolv; Lager A et al.; To measure the amount of viable bacteria after excavation using conventional rose-bur or the chemo-mechanical Carisolv method, a total of 22 lesions were analyzed (one vital tooth per patient) in this open, controlled and randomized study . Two samples per lesion were taken under aseptic conditions using a rose-bur, one superficially in the caries lesion and one after completed excavation . In in vitro tests more material was collected from the hard caries free dentine as compared to the carious dentine . The samples were incubated on blood agar (aerobically and anaerobically), Rogosa (SL) agar and mitis salivarius (MS) agar . For blood agar (aerobic) both methods resulted in a significant decrease in CFU, for blood agar (anaerobic) and MS agar only the Carisolv method resulted in a significant decrease in CFU and for SL agar neither method resulted in a significant decrease in CFU . Comparing CFU before and after excavation, a considerable reduction of CFU was seen ranging from 10(1) to 10(4) . Comparing the excavation methods, there were no significant differences, except in the case of blood agar (aerobic), which showed that Carisolv excavation was more effective in reducing CFU . This study indicated that bacterial sampling collected more material from hard dentine as compared from soft . Remaining bacteria after excavation were low in both groups . The Carisolv method seemed to remove bacteria at least up to and possibly beyond the extent of conventional drilling . Proc Nutr Soc, 2003 Feb, 62(1), 73 - 80 Influences of probiotic bacteria on organic acid production by pig caecal bacteria in vitro; Sakata T et al.; The mechanism of action of probiotics is largely unknown . A potential mechanism should be to increase the production of short-chain fatty acids (SCFA), known modulators of gut functions, by the bacterial ecosystem in the large intestine . The present paper reviews our recent studies in which the capacity of probiotic bacteria to increase the production of SCFA by pig caecal bacteria was investigated using batch-culture and continuous-culture techniques . All four commercial probiotic preparations and three strains of probiotic bacteria dose-dependently accelerated the net production of SCFA, succinic acid and lactic acid without changing the acid profile, and slowed the net production of NH4 . Effects on organic acid production did not vary among different probiotic species . Neither probiotic preparations nor probiotic bacteria affected the organic acid production from glucose, gastric mucin, starch or lactose, or organic acids produced:added saccharide . Glucose abolished these effects of probiotic preparations . However, the capacity of probiotics to increase SCFA production was not modified by gastric mucin, starch or lactose . These results indicate that probiotic bacteria increase SCFA production by accelerating the breakdown of carbohydrates that are resistant to indigenous bacteria, and suggest that the concept of prebiotics in terms of SCFA production as a measure of probiotic function is arguable. Oral Surg Oral Med Oral Pathol Oral Radiol Endod, 2003 May, 95(5), 621 - 5 Effect of black-pigmented bacteria on the plasminogen-plasmin system in human pulp and osteoblastic cells; Yang SF et al.; OBJECTIVE: To date, there have been relatively few studies addressing the presence and expression of the plasminogen-plasmin system at the site of bacterial infection . The aim of the present study was to investigate the effect of black-pigmented bacteria on the expression of the plasminogen-plasmin system in human pulp and osteoblastic cells . STUDY DESIGN: The supernatants of Porphyromonas endodontalis, Porphyromonas gingivalis, and Prevotella intermedia were used to evaluate tissue-type plasminogen activator (t-PA) and type 1 plasminogen activator inhibitor (PAI-1) gene expression in human pulp and osteoblastic cells . The levels of mRNA were quantitatively measured by using reverse transcription-polymerase chain reaction . RESULTS: In this study, black-pigmented bacteria induced not only t-PA but also PAI-1 gene expression in human pulp and osteoblastic cells . In addition, the ratio of t-PA to PAI-1 was higher in human pulp and osteoblastic cells stimulated by black-pigmented bacteria than in untreated cell cultures (P <.05) . CONCLUSIONS: A fine balance exists in the expression of components of the plasminogen-plasmin system, whereby tissue homeostasis is maintained . Black-pigmented bacteria activate the activator-inhibitor system in human pulp and osteoblastic cells through unbalance regulation of t-PA and PAI-1, which might result in an uncontrolled degradation of pulpal and periapical tissues. Am J Gastroenterol, 2003 Apr, 98(4), 759 - 62 Intestinal metaplasia at the gastroesophageal junction: Barrett's, bacteria, and biomarkers; Morales CP et al.; For patients found to have intestinal metaplasia at the gastroesophageal junction, technical problems can make it difficult to distinguish short-segment Barrett's esophagus from intestinal metaplasia of the gastric cardia . Whereas the risk of malignancy for the former condition seems to be higher than that for the latter, the distinction between these conditions can have practical clinical implications . Immunostaining for cytokeratins has been proposed as a means to distinguish intestinal metaplasia of esophageal and gastric origins . We review recent data on this issue, and conclude that immunostaining for cytokeratins has no clear advantages over other biomarkers that have been proposed for identifying Barrett's esophagus (e.g., mucin histochemistry, mAb Das-1 immunoreactivity) . Presently, the importance of intestinal metaplasia at the gastroesophageal junction remains unclear, and the clinical utility of biomarkers in distinguishing short-segment Barrett's esophagus from intestinal metaplasia of the gastric cardia has not yet been established. FEMS Immunol Med Microbiol, 2003 May 25, 36(3), 175 - 80 Gastric mucosal cytokine responses in Helicobacter pylori-infected patients with gastritis and peptic ulcers . Association with inflammatory parameters and bacteria load; Holck S et al.; Helicobacter pylori is an important pathogen in gastroduodenal inflammation and ulceration . Several mechanisms have been proposed to explain its role . We studied the cytokine production patterns in situ in gastric mucosal biopsies from H . pylori-positive and H . pylori-negative patients with dyspepsia . Immunohistochemistry with monoclonal antibodies was used . The study showed enhanced expression of interleukin (IL) -8, IL-10 and interferon-gamma (IFN-gamma) in H . pylori infection and a significant association was found between these cytokines and the following parameters: bacteria load, chronic inflammation and activity . These parameters were significantly correlated with the cell markers CD19 and CD56 . The study indicates a dual effect of H . pylori on the Th1 response, i.e . a stimulation of the response verified by increased IFN-gamma and a feed-back verified by an increase of the counterinflammatory IL-10, which may dampen the inflammatory and cytotoxic effect of the Th1 response . Furthermore, the study confirms the connection between increase of IL-8 and inflammatory activity in gastric mucosa in H . pylori infection. Anal Bioanal Chem, 2003 May, 376(1), 11 - 7 Epub 2003 Mar 28. Luminescence-based whole-cell-sensing systems for cadmium and lead using genetically engineered bacteria; Shetty RS et al.; Whole-cell-based sensing systems that respond to cadmium and lead ions have been designed and developed using genetically engineered bacteria . These systems take advantage of the ability of certain bacteria to survive in environments polluted with cadmium and lead ions . The bacteria used in this investigation have been genetically engineered to produce reporter proteins in response to the toxic ions . This was achieved by modifying a strain of Escherichia colito harbor plasmids pYSC1 and pYS2/pYSG1 . In these dual-plasmid-based sensing systems, the expression of the reporters beta-galactosidase and red-shifted green fluorescent protein (rs-GFP) was controlled by CadC, the regulatory protein of the cad operon . Regulation of the expression of the reporter proteins is related to the amount of cadmium and lead ions employed to induce the bacteria . The bacterial sensing systems were found to respond to cadmium, lead, and zinc ions, and had no significant response to nickel, copper, manganese, and cobalt. Appl Environ Microbiol, 2003 May, 69(5), 2875 - 8 Protocol for rapid fluorescence in situ hybridization of bacteria in cryosections of microarthropods; Thimm T et al.; A protocol was developed to detect bacteria inhabiting microarthropods by means of small-subunit rRNA-targeted fluorescence in situ hybridization and microscopy . The protocol is based on cryosections of whole specimens . In contrast to more commonly applied paraffin-embedding techniques, the protocol is quicker and reduces the number of manipulations which might damage the microscopic material . The method allowed the study of the bacterial colonization of Folsomia candida (Collembola) and the detection of bacteria in both the gut and tissue. Curr Opin Microbiol, 2003 Apr, 6(2), 125 - 34 Motifs, modules and games in bacteria; Wolf DM et al.; Global explorations of regulatory network dynamics, organization and evolution have become tractable thanks to high-throughput sequencing and molecular measurement of bacterial physiology . From these, a nascent conceptual framework is developing, that views the principles of regulation in term of motifs, modules and games . Motifs are small, repeated, and conserved biological units ranging from molecular domains to small reaction networks . They are arranged into functional modules, genetically dissectible cellular functions such as the cell cycle, or different stress responses . The dynamical functioning of modules defines the organism's strategy to survive in a game, pitting cell against cell, and cell against environment . Placing pathway structure and dynamics into an evolutionary context begins to allow discrimination between those physical and molecular features that particularize a species to its surroundings, and those that provide core physiological function . This approach promises to generate a higher level understanding of cellular design, pathway evolution and cellular bioengineering. Curr Opin Microbiol, 2003 Apr, 6(2), 120 - 4 Regulatory roles for small RNAs in bacteria; Masse E et al.; Small RNAs can act to regulate both the synthesis of proteins, by affecting mRNA transcription, translation and stability, and the activity of specific proteins by binding to them . As a result of recent genome-wide screens, around 50 small RNAs have now been identified in Escherichia coli . These include many that require the RNA-binding protein Hfq for their activity; most of these RNAs act by pairing with their target mRNAs . Small RNAs can both positively and negatively regulate translation, can simultaneously regulate multiple mRNA targets, and can change the pattern of polarity within an operon. Annu Rev Microbiol, 2003, 57, 77 - 100 Epub 2003 May 01. How bacteria assemble flagella; Macnab RM; The bacterial flagellum is both a motor organelle and a protein export/assembly apparatus . It extends from the cytoplasm to the cell exterior . All the protein subunits of the external elements have to be exported . Export employs a type III pathway, also utilized for secretion of virulence factors . Six of the components of the export apparatus are integral membrane proteins and are believed to be located within the flagellar basal body . Three others are soluble: the ATPase that drives export, a regulator of the ATPase, and a general chaperone . Exported substrates diffuse down a narrow channel in the growing structure and assemble at the distal end, often with the help of a capping structure. Chemosphere, 2003 Jul, 52(1), 103 - 11 Specific detection of organotin compounds with a recombinant luminescent bacteria; Durand MJ et al.; Organotin compounds are widely used as biocides in marine and terrestrial environments . Several currently used techniques allow either the measurement of the chemicals or their effects on living organisms . Our current research focuses on the development of a complementary method based on a bacterial bioluminescence-based bioassay for the specific detection of organotin compounds . The performance of the bioassay was assessed . The Escherichia coli bacterial strain used in this study is specific for TBT and DBT (with Cl, Br or I as the halogen group) with the central tin atom important for light production . The assay is conducted after overnight culture of the bacterial strain, followed by 60 min of contact time with the organotin compound for significant light production . The detection limits were found to be 0.08 microM for TBT (26 microgl(-1)) and 0.0001 microM for DBT (0.03 microgl(-1)) with a linear range of one logarithm . The repeatability of the bioassay is 8% and the reproducibility for TBT and DBT was approximately 14% . Lyophilization of the strains did not significantly modify the detection limit as well as the range of detection . Applications of the bioassay to environmental samples are discussed. Microbiology, 2003 May, 149(Pt 5), 1239 - 47 Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the Gammaproteobacteria radiation; Yeates C et al.; The 23S rRNA-targeted probes GAM42a and BET42a provided equivocal results with the uncultured gammaproteobacterium 'Candidatus Competibacter phosphatis' where some cells bound GAM42a and other cells bound BET42a in fluorescence in situ hybridization (FISH) experiments . Probes GAM42a and BET42a span positions 1027-1043 in the 23S rRNA and differ from each other by one nucleotide at position 1033 . Clone libraries were prepared from PCR products spanning the 16S rRNA genes, intergenic spacer region and 23S rRNA genes from two mixed cultures enriched in 'Candidatus C . phosphatis' . With individual clone inserts, the 16S rDNA portion was used to confirm the source organism as 'Candidatus C . phosphatis' and the 23S rDNA portion was used to determine the sequence of the GAM42a/BET42a probe target region . Of the 19 clones sequenced, 8 had the GAM42a probe target (T at position 1033) and 11 had G at position 1033, the only mismatch with GAM42a . However, none of the clones had the BET42a probe target (A at 1033) . Non-canonical base-pairing between the 23S rRNA of 'Candidatus C . phosphatis' with G at position 1033 and GAM42a (G-A) or BET42a (G-T) is likely to explain the probing anomalies . A probe (GAM42_C1033) was optimized for use in FISH, targeting cells with G at position 1033, and was found to highlight not only some 'Candidatus C . phosphatis' cells, but also other bacteria . This demonstrates that there are bacteria in addition to 'Candidatus C . phosphatis' with the GAM42_C1033 probe target and not the BET42a or GAM42a probe target. J Infect Dis, 2003 May 15, 187(10), 1609 - 15 Epub 2003 Apr 23. Severe inflammation and reduced bacteria load in murine helicobacter infection caused by lack of phagocyte oxidase activity; Blanchard TG et al.; The vaccine-induced immune mechanisms that protect against Helicobacter pylori infection in the mouse model have not been identified . This study investigated the contribution of reactive oxygen and nitrogen intermediates to Helicobacter pathogenesis and immunity . Mice deficient in nicotinamide-adenine dinucleotide phosphate oxidase activity (gp91(phox-/-)), nitric oxide synthase activity (NOS2(-/-)), or both (gp91(phox-/-)/NOS2(-/-)) were infected with Helicobacter organisms and evaluated for inflammation and bacteria load . Infection of all 3 transgenic strains resulted in significantly more inflammation than found in infected C57BL/6 wild-type mice . However, only gp91(phox-/-) and gp91(phox-/-)/NOS2(-/-) mice had significantly reduced numbers of infected gastric glands . Intranasal immunization of NOS2(-/-) or gp91(phox-/-)/NOS2(-/-) mice against H . pylori resulted in protective immunity comparable to that seen in C57BL/6 control mice . Therefore, reactive oxygen species may play a role in limiting the inflammatory response associated with H . pylori infection of the gastric mucosa but may also limit the host's ability to eradicate Helicobacter organisms. Curr Opin Chem Biol, 2003 Apr, 7(2), 166 - 73 Formation of iron-sulfur clusters in bacteria: an emerging field in bioinorganic chemistry; Frazzon J et al.; Biological iron-sulfur clusters are chemically versatile inorganic structures that are attached to many proteins . These clusters are intimately involved in the functions of their partner proteins and they are required to sustain life on earth . Recent work has demonstrated that, in spite of their simple structures, the assembly and insertion of iron-sulfur clusters into their protein partners is a complex biological process . This complexity is probably related to the cellular toxicity of iron and sulfur in their free forms. Vet Microbiol, 2003 Jun 10, 93(4), 361 - 8 Leptospira in slaughtered fattening pigs in southern Vietnam: presence of the bacteria in the kidneys and association with morphological findings; Boqvist S et al.; One kidney was collected from each of 32 fattening pigs at an abattoir in southern Vietnam in 2001 in order to demonstrate infecting Leptospira serovar and to associate renal macro- and microscopic findings with the presence of renal leptospires . Leptospires were demonstrated in 22 (69%) of the investigated kidneys by immunofluorescence . Multifocal interstitial nephritis (MFIN) and gross renal lesions (white spots) were each demonstrated in 24 (75%) kidneys . Leptospira interrogans serovar bratislava was isolated from one kidney . There was no association between presence of leptospires and MFIN (P=0.19), respectively and white spots (P=0.98), respectively . These data suggest that Leptospira infection is common among fattening pigs in the study area and that these animals may be considered as an occupational human health hazard . It is also suggested that the presence of white spots is an unreliable indicator of the presence of renal leptospires. Zh Mikrobiol Epidemiol Immunobiol, 2000 Jul-Aug, (4 Suppl), 99 - 100 {Anti-lysozyme activity of bacteria of the genus Brucella}; Sheenkov NV et al.; The antilysozyme activity of 122 Brucella strains has been studied . The antilysozyme sign has been found to be widely spread among different Brucella species . The antilysozyme sign has proved to be most pronounced in B . melitensis. Arch Oral Biol, 2003 May, 48(5), 329 - 36 Estimates, from salivary analyses, of the turnover time of the oral mucosal epithelium in humans and the number of bacteria in an edentulous mouth; Dawes C; The objectives were to obtain rough estimates of the number of bacteria in an edentulous mouth and the mean turnover time of the oral mucosa and the conditions under which the salivary phase in the mouth might act as a bacterial continuous culture system . The premise was that at steady state in vivo, the rates of loss of bacteria and epithelial cells in saliva must be equal to their rates of proliferation . Drooled saliva was collected from 17 subjects and the number of epithelial cells per millilitre was determined in a Coulter Counter . The numbers of adherent bacteria per epithelial cell were counted on cells stained with Toluidine Blue . For 10 subjects, salivary bacterial counts were obtained after saliva had been diluted in Reduced Transport Fluid and grown anaerobically on Blood Agar for 5 days . From the known surface areas of the oral mucosa and individual epithelial cells and the rate of loss of epithelial cells into saliva, the surface layer of epithelial cells was calculated to be replaced every 2.7h . From the calculated number of epithelial cells lining the oral mucosa, the number of bacteria per epithelial cell, and the rate of swallowing of the bacteria in saliva, the number of bacteria in an edentulous mouth was calculated to be about 1.58 x 10(9) and the mean time between bacterial cell divisions to be 1.38h . Given a residual volume of 0.8ml and a maximal bacterial division rate of 3h(-1), the salivary phase in the mouth could act as a continuous culture system for certain fast-growing bacteria only if the maximum flow rate were <0.04ml/min. Microb Ecol, 2003 May, 45(4), 444 - 54 Epub 2003 Apr 22. Unusual rise in mercury-resistant bacteria in coastal environs; Ramaiah N et al.; A sharp rise in mercury-resistant bacteria (MRB) capable of tolerating very high concentration of Hg was observed over the last 3-4 years in the coastal environs of India . While none or negligible colony-forming units (CFU) of bacteria were counted on seawater nutrient agar with 0.5 ppm ( 2.5 microM) Hg (II) as HgCl2 until 1997, from 13 to over 75% of the CFU grew on 20 times higher, 50 microM, Hg concentrations from almost every recently examined marine sample . Although exceptionally high counts of MRB (96% of CFU) were recorded from samples collected from the polluted zones off Mumbai, the MRB capable of growth on seawater nutrient agar with 50 microM Hg were quite abundant in most samples collected from many locations with few or no pollution effects . We noticed for the first time the occurrence of aerobic heterotrophic bacterial isolates capable of growth with 250 microM Hg . Such MRB grew with higher concentrations of many other toxic xenobiotics than the Hg sensitive ones . Based on the unusually high populations of viable MRB and some simple experiments, we propose that many marine bacterial species are selected, possibly through acquisition of plasmids and/or transposable elements and modifying Hg, whose concentration, according to recent studies, is on the rise in marine habitats. Biotechniques, 2003 Apr, 34(4), 804 - 8, 810, 812-3 Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5'-nuclease PCR; Nogva HK et al.; PCR techniques have significantly improved the detection and identification of bacterial pathogens . Even so, the lack of differentiation between DNA from viable and dead cells is one of the major challenges for diagnostic DNA-based methods . Certain nucleic acid-binding dyes can selectively enter dead bacteria and subsequently be covalently linked to DNA . Ethidium monoazide (EMA) is a DNA intercalating dye that enters bacteria with damaged membranes . This dye can be covalently linked to DNA by photoactivation . Our goal was to utilize the irreversible binding of photoactivated EMA to DNA to inhibit the PCR of DNA from dead bacteria . Quantitative 5'-nuclease PCR assays were used to measure the effect of EMA . The conclusion from the experiments was that EMA covalently bound to DNA inhibited the 5'-nuclease PCR . The maximum inhibition of PCR on pure DNA cross-linked with EMA gave a signal reduction of approximately -4.5 log units relative to untreated DNA . The viable/dead differentiation with the EMA method was evaluated through comparison with BacLight staining (microscopic examination) and plate counts . The EMA and BacLight methods gave corresponding results for all bacteria and conditions tested . Furthermore, we obtained a high correlation between plate counts and the EMA results for bacteria killed with ethanol, benzalkonium chloride (disinfectant), or exposure to 70 degrees C . However, for bacteria exposed to 100 degrees C, the number of viable cells recovered by plating was lower than the detection limit with the EMA method . In conclusion, the EMA method is promising for DNA-based differentiation between viable and dead bacteria. Pest Manag Sci, 2003 Apr, 59(4), 465 - 74 Local early induced resistance of plants as the first line of defence against bacteria; Klement Z et al.; This paper is an overview of a non-specific local early induced resistance (EIR) mechanism, distinct from the incompatible-specific hypersensitive reaction (HR) . We have shown that the local induced resistance (LIR) described earlier is not a single and uniform response to pathogen infection, because an early (EIR) and a late form can be distinguished . EIR operates from 3-6 h post-inoculation (hpi) until about 20 hpi, and is inhibited by a short heat-shock or the eukaryotic protein synthesis inhibitor, cycloheximide . In contrast, LIR, which corresponds to the induced resistance forms discovered earlier, requires more time (about 24 h) and intensive illumination to develop, and is effective for a longer period . EIR develops parallel with HR and is sometimes able to prevent it when the induction time of HR is longer than the time required for the development of EIR . It seems that EIR inhibits the metabolism of bacteria and the activity of hrp genes which otherwise are required for the induction of HR . In a compatible host-pathogen relationship the effect of EIR fails to take place . The rapid development of EIR is greatly influenced by temperature and the physiological state of the plant . EIR activates the accumulation of hydrogen peroxide at the bacterial attachment, expressing new peroxidase isoenzymes in the initiated plant tissue . It seems that this is a native general local defence mechanism which can localise foreign organisms even at the penetration site. Bioelectrochemistry, 2003 Apr, 59(1-2), 113 - 9 The revision of the model of primary energy conversion in purple bacteria; Borisov AY et al.; A simulation method is suggested which enables one to check whether a model for excitation energy exchange in an ensemble of dye molecules fits available experimental data . In particular, this method may deal with photosynthetic units (PSUs) in which excitation migration in antenna chlorophylls and their substantial trapping in reaction centers (RCs) take place . Its application to the purple bacteria has proved that the model, which was generally accepted during the last 20-30 years, is in contradiction with recent experimental facts and thus requires modernization . Two physical mechanisms are discussed: femtosecond polarization of mobile hydrogen atoms near the reaction center special pair ("water latch"), and the presence of excitons delocalized over several core-bacteriochlorophylls (BChls) . Our considerations give evidence that neither of these mechanisms alone can resolve the conflict, but their cumulative action appears to be sufficient . Unfortunately, these mechanisms were as yet only partially addressed experimentally. Med Device Technol, 2003 Mar, 14(2), 8 - 11 Endotoxins and medical devices: the significance of dead bacteria; Williams D; There has been some recent speculation that endotoxins, the toxic molecules that are present in the cell wall of certain bacteria, could play a role in the development of tissue reactions to medical devices . This article discusses the basis for this speculation. Biochemistry (Mosc), 2003 Feb, 68(2), 152 - 61 Mechanisms of excitation trapping in reaction centers of purple bacteria; Borisov AY; The contradiction between two groups of experimental data, which fails to be resolved within the framework of the widely accepted model of excitation migration and trapping (at least in case of purple bacteria), is discussed in the introduction to this review . Three directions of studies intended to resolve this conflict are reviewed in the three further sections: II . Exciton models; III . Water-polarization (water-latch) mechanism of excitation trapping; IV . Quantum-mechanical models . The maximum efficiency of these models in resolving the contradiction mentioned above was assessed . The advantages and disadvantages of the mechanisms described in sections II, III, and IV are discussed in the last section of this review . It is concluded that none of these mechanisms taken alone is able to solve this problem . Therefore, the fundamental problem of the primary excitation conversion in reaction centers remains unsolved and requires additional experimental research. Redox Rep, 2002, 7(5), 320 - 3 UV radiation increases the reduced coenzyme Q ratio in marine bacteria; Dunlap WC et al.; Oxidative stress is often indicated by an oxidative shift in cellular coenzyme Q (ubiquinol/ubiquinone) redox status . However, exposing two cultures of marine bacteria to intense UVA radiation increased their relative abundance of the reduced form of coenzyme Q, presumably as an adaptive response to photo-oxidative stress . This UV-signalling pathway in marine bacteria may be useful to examine molecular processes that regulate cellular coenzyme Q redox balance. J Gen Appl Microbiol, 2003 Feb, 49(1), 37 - 49 Seasonal variation of phenol/benzoate-degrading iron-reducing bacteria in irrigated tropical paddy soils as affected by some management practices; Lu WJ et al.; The study provides the first evidence of the presence and abundance of bacterial population that coupled ferric iron reduction to aromatic compounds degradation in tropical irrigated paddy soils in the Philippines . Culturable phenol/benzoate degrading iron-reducing bacteria was enumerated by the most probable number (MPN) counts using phenol or benzoate as sole carbon source, and ferric oxide {Fe(OH)(3)} as the sole electron acceptor . Population density of phenol degrading iron-reducing bacteria (P-IRB) in irrigated paddy soil ranged from 10(2) to 10(8)g(-1) dry soil, and increased with the progressive rice growth in rice cropping seasons; the study also revealed a significant rhizosphere effect on population of P-IRB . However, high enumeration of benzoate degrading iron-reducing bacteria (B-IRB) was obtained in all the tested soil samples averaging at 1.2 x 10(6)g(-1) dry soil, and did not fluctuate significantly over the rice cropping seasons . Statistical data showed that less cropping density with aerated fallow and high nitrogen rate favored the population growth of P-IRB . However, results showed that population size of B-IRB was relatively insensitive to the effect of either seasonal or extrinsic factors tested in this study. Biochim Biophys Acta, 2003 Apr 11, 1647(1-2), 152 - 6 Is the catalytic mechanism of bacteria, plant, and mammal copper-TPQ amine oxidases identical? Pietrangeli P, Nocera S, Mondovi B, Morpurgo L. This short review is mostly concerned with the work carried out in Rome on the copper amine oxidase from bovine serum (BSAO) . The first target was the copper oxidation state and its relationship with the organic cofactor . It was found that copper is not reduced on reaction with amines under anaerobic conditions or along the catalytic cycle and that it is not within bonding distance of the quinone cofactor . The copper stability in the oxidised state was supported by BSAO ability to oxidise benzylhydrazine, a slow substrate, in the presence of N,N-diethyldithiocarbamate (DDC) and by the substantial catalytic activity of Co(2+)-substituted BSAO . Parallel work established that only one subunit of the dimeric enzyme readily binds reagents of the carbonyl group . Flexible hydrazides with a long aromatic tail were found to be highly specific inhibitors, suggesting the presence of an extended hydrophobic region at the catalytic site . A study by stopped-flow transient spectroscopy and steady state kinetics led to the formulation of a simplified, yet complete and consistent, catalytic mechanism for BSAO that was compared with that available for lentil seedling amine oxidase (LSAO) . As in other copper amine oxidases, BSAO is inactivated by H(2)O(2) produced in the catalytic reaction, while the cofactor is stabilised in its reduced state . A conserved tyrosine hydrogen-bonded to the cofactor might be oxidised. Trends Genet, 2003 Apr, 19(4), 191 - 5 Much ado about bacteria-to-vertebrate lateral gene transfer; Genereux DP et al.; When the International Human Genome Sequencing Consortium (IHGSC) published its draft of the human genome in February 2001, several genes were identified as possible bacteria-to-vertebrate transfers (BVTs) . These genes were identified by their highly significant sequence similarity to bacterial genes in BLAST searches, and by their lack of matches among non-vertebrate eukaryote genes . Many were later rejected as BVTs by several methods, including recovery of probable orthologs from the genomes of incompletely sequenced eukaryotes . Whereas the BVT issue has received considerable attention, there has been no compilation of all potential BVTs considered to date, nor any proposal of a single comprehensive method for rigorously establishing the veracity of a putative BVT . In reviewing the work to date, we list all of the proteins examined and propose systematic tests to investigate whether a vertebrate gene proposed as a BVT is indeed of bacterial origin . We use the proposed strategy to test--and reject--one of the BVTs from the original IHGSC list. Tsitologiia, 2002, 44(12), 1233 - 7 {Endosymbiotic bacteria and their relationship with chlorella in the ciliate Climacostomum virens}; Karadzhian BP et al.; Structure of cytoplasmic bacterial symbionts of chlorella-free ciliate Climacostomum virens has been investigated . It is shown that ciliates are not able to support simultaneously growth and duplication of two different symbionts--bacteria and chlorella . Cells of C . virens lost bacterial symbionts after an artificial infection with chlorella by microinjection . Competitive relationships between two endopionts are discussed. Crit Rev Immunol, 2002, 22(4), 251 - 68 Innate recognition of bacteria: engagement of multiple receptors; Triantafilou M et al.; Until recently, consensus was that the mechanism of action of the innate immune system was a simplified one . Current research findings in the field of innate recognition of bacteria suggest that it involves complex associations of receptors depending on cell type and bacterial stimuli, CD14, integrins, Toll-like receptors (TLRs), CD55, ion channels, and activation clusters containing heat shock proteins, chemokine receptor 4 and a plethora of other molecules have been shown to serve as key molecules in bacterial recognition . In this article, we review all the advances in the field and discuss the possibility that the repertoire for recognition of pathogens is defined by the combinational engagement of multiple receptors. Curr Opin Genet Dev, 2003 Apr, 13(2), 179 - 84 Regulation of gene expression by histone-like proteins in bacteria; Dorman CJ et al.; Histone-like proteins in bacteria contribute to the control of gene expression, as well as participating in other DNA transactions such as recombination and DNA replication . They have also been described, somewhat vaguely, as contributors to the organization of the bacterial nucleoid . Our view of how these proteins act in the cell is becoming clearer, particularly in the cases of Fis, H-NS and HU, three of the most intensively studied members of the group . Especially helpful have been studies of the contributions of these proteins to the regulation of specific genes such as the gal operon, and genes coding for stable RNA species, topoisomerases, and the histone-like proteins themselves . Recent advances have also been assisted by insights into the effects the histone-like proteins exert on DNA structure not only at specific promoters but throughout the genome. Chin Med J (Engl), 2003 Jan, 116(1), 129 - 33 Establishment and analysis of specific DNA patterns in 16S-23S rRNA gene spacer regions for differentiating different bacteria; Shang S et al.; OBJECTIVE: To establish the specific 16S-23S rRNA gene spacer regions in different bacteria using polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), DNA cloning and sequences analysis . METHODS: A pair of primers were selected from highly conserved sequences adjacent to the 16S-23S rRNA spacer region . Bacterial DNA from sixty-one strains of standard bacteria and corresponding clinical isolates representative of 20 genera and 26 species was amplified by PCR, and further analyzed by RFLP, DNA cloning and sequences analysis . Furthermore, all specimens were examined by bacterial culturing and PCR-RFLP analysis . The evaluation of these assays in practical clinic practice was also discussed . RESULTS: Restriction enzyme analysis revealed one, two or three bands or more observed among the 26 different standard strains . The sensitivity of PCR reached 2.5 colony-forming unit (CFU), and there was no cross reaction with human genomic DNA, fungus or virus . Fourteen species could be distinguished immediately by PCR, while another 10 species were further identified by Hinf I or Alu I digestion . The only difference between K.pneumoniae and E . durans was located at the site of the 779th nucleotide according to the sequence analysis and only XmaIII digestion could distinguish one from another . Of 42 specimens from septicemic neonates, 15 were identified as positive by blood culture at a rate of 35.7% . However, 27 specimens identified as positive by PCR, with a rate of 64.2%, a method significantly more effective than blood culture (P < 0.01) . Of 6 cerebrospinal fluid (CSF) specimens, one tested positive for S.epidermidis was also positive by PCR, two culture negative were positive by PCR and diagnosed as S.epidermidis according to the DNA pattern . One positive for C.neoformans was negative by PCR . The other two specimens were negative by both PCR and culture . CONCLUSIONS: The method of detecting bacterial 16S-23S rRNA spacer regions using PCR-RFLP techniques was specific, sensitive, rapid and accurate in providing a new technique for detecting pathogens in clinical bacterial infections. J Int Acad Periodontol, 2001 Apr, 3(2), 42 - 7 Serum phenytoin concentration and IgG antibody titre to periodontal bacteria in patients with phenytoin-induced gingival overgrowth; Yamada H et al.; Epileptic patients taking phenytoin with gingival-overgrowth and those without gingival-overgrowth were compared for daily drug dose, plasma total phenytoin concentration, plasma free-phenytoin concentration and serum IgG antibody titre against 13 periodontal bacteria . Significantly higher daily drug dose was noted in patients with gingival overgrowth (P < 0.05) when compared with those without overgrowth . In addition, both total and free forms of plasma phenytoin concentration were significantly higher in sera of patients with gingival growth than of those without overgrowth (P < 0.01) . Strong positive correlation was found between daily drug dose and serum phenytoin concentration in patients with gingival overgrowth, while weak correlation was found in patients without gingival overgrowth, suggesting a difference in drug metabolism in these two groups . However, no differences were found in serum IgG antibody titres to 13 periodontal bacteria examined between two groups . These results suggest that metabolic ability of phenytoin is one of the factors for developing gingival overgrowth, and that periodontal infection may not be a primary causative factor for gingival overgrowth but act as an additive factor which increase tissue mass for this unwanted side effect. Life Sci Space Res, 1970, 8, 53 - 8 Effect of ultraviolet on the survival of bacteria airborne in simulated Martian dust clouds; Hagen CA et al.; A chamber was constructed to create simulated Martian dust storms and thereby study the survival of airborne micro-organisms while exposed to the rigors of the Martian environment, including ultraviolet irradiation . Representative types of sporeforming and non-sporeforming bacteria present in spacecraft assembly areas and indigenous to humans were studied . It was found that daily ultraviolet irradiation of 2 to 9 X 10(7) erg cm-2 was not sufficient to sterilize the dust clouds . The soil particles protected the organisms from ultraviolet irradiation since the numbers of survivors from irradiated environments were similar to those from unirradiated environments . Pending further data of the Martian environment, the contamination and dissemination of Mars with terrestrial micro-organisms is still a distinct possibility. Mikrobiol Z, 2002 Nov-Dec, 64(6), 67 - 72 {Effect of sulfate-reducing bacteria on steel corrosion in the presence of inhibitors}; Purish LM et al.; Steel 08KP corrosion was studied as affected by inhibitors in presence of sulphate-reducing bacteria (SRB) . Organic compounds, containing functional groups with nitrogen, oxygen and sulphur atoms, were investigated as corrosion inhibitors . It is shown that the studied inhibitors may be divided into three groups as to the mechanism of protective action . It has been established that cation-active nitrogen-containing surfactants ({symbol: see text} X, {symbol: see text}-1, {symbol: see text}-1M, catapin M, {symbol: see text}-2M) are the most efficient steel corrosion inhibitors . Such inhibitors, when adsorbed on metal surface, can affect the process of hydrogen precipitation on its surface, and thus inhibit catalytic function of SRB as the depolarizer of cathode process. Hum Gene Ther, 2003 Mar 1, 14(4), 329 - 39 Hybrid yeast-bacteria cloning system used to capture and modify adenoviral and nonviral genomes; Hokanson CA et al.; Adenoviral vectors are widely used to express transgenes in vitro and in vivo . A major obstacle to the generation of adenoviral vectors is the manipulation of the large (35 kb) adenoviral genome . We developed a hybrid yeast-bacteria cloning system for the creation of novel adenoviral vectors . The adenovirus 5 (Ad5) genome was cloned into a shuttle vector that contains both yeast and bacterial elements for replication and therefore functions as both a yeast artificial plasmid (YAP) and as a plasmid artificial chromosome (PAC) . Any sequence can be introduced into any region of the adenoviral genome via the highly efficient homologous recombination in yeast and then these recombinants are rapidly amplified in bacteria . Adenoviral vectors are generated by introduction of the PAC into the appropriate complementing mammalian cell without the need for plaque purification . Vectors were constructed with deletions in the E1, E3, and/or E4 regions . We have generated more than 100 vectors with a number of different transgenes and regulatory elements . In addition, the YAP/PAC vector was used to capture a DNA fragment encompassing the human factor IX gene, demonstrating the utility of this system to clone and analyze genomic DNA . This novel cloning strategy allows the rapid and versatile construction of adenoviral vectors for gene expression and gene therapy applications. Microb Ecol, 2003 Mar, 45(3), 252 - 8 Epub 2003 Mar 28. Competition between Fe(III)-reducing and methanogenic bacteria for acetate in iron-rich freshwater sediments; Roden EE et al.; The kinetics of acetate uptake and the depth distribution of {2-14C}acetate metabolism were examined in iron-rich sediments from a beaver impoundment in northcentral Alabama . The half-saturation constant (Km) determined for acetate uptake in slurries of Fe(III)-reducing sediment (0.8 mM) was more than 10-fold lower than that measured in methanogenic slurries (12 mM) which supported comparable rates of bulk organic carbon metabolism and Vmax values for acetate uptake . The endogenous acetate concentration (Sn) was also substantially lower (1.7 mM) in Fe(III)-reducing vs methanogenic (9.0 mM) slurries . The proportion of {2-14C}acetate converted to 14CH4 increased with depth from ca 0.1 in the upper 0.5 cm to ca 0.8 below 2 cm and was inversely correlated (r2 = 0.99) to a decline in amorphous Fe(III) oxide concentration . The results of the acetate uptake kinetics experiments suggest that differences in the affinity of Fe(III)-reducing bacteria vs methanogens for acetate can account for the preferential conversion of {2-14C}acetate to 14CO2 in Fe(III) oxide-rich surface sediments, and that the downcore increase in conversion of {2-14C}acetate to 14CH4 can be attributed to progressive liberation of methanogens from competition with Fe(III) reducers as Fe(III) oxides are depleted with depth. Gene, 2003 Mar 13, 306, 27 - 35 Phylogenetic relationships of non-mitochondrial nucleotide transport proteins in bacteria and eukaryotes; Linka N et al.; Current knowledge about the nucleotide metabolism of intracellular bacteria is very limited . Here we report on the identification of nucleotide transport proteins (NTT) of two obligate endoparasites, Caedibacter caryophila and Holospora obtusa, both alpha-proteobacteria, which reside in the vegetative macronucleus of Paramecium caudatum . For comparative studies, we also identified the first nucleotide transporter in chloroplasts of a red alga, i.e . Galdieria sulphuraria, and further homologs in plant chloroplasts . Heterologous expression of the NTT proteins from C . caryophila, H . obtusa, and G . sulphuraria in Escherichia coli demonstrate that the nucleotide influx mediated by these transporters is specific for ATP and ADP . The NTT proteins of C . caryophila and H . obtusa exhibit substantial sequence identity with their counterparts in chloroplasts and intracellular bacterial pathogens of humans, but not with the nucleotide transport system of mitochondria . Comprehensive phylogenetic analyses of bacterial and chloroplast NTT proteins showed that homologs in chloroplasts from plants, and green, red, stramenopile and glaucocystophyte algae are monophyletic . In contrast, the evolutionary relationships of the bacterial counterparts appear highly complex . In the presented phylogeny, NTT proteins of C . caryophila and H . obtusa are only distantly related to one another, although these two taxa are close relatives in 16S rRNA trees . The tree topology indicates that some bacterial NTT paralogs have arisen by gene duplications and others by horizontal transfer. Mol Microbiol, 2003 Apr, 48(1), 17 - 23 Conditional senescence in bacteria: death of the immortals; Nystrom T; Like ageing insects, worms and mammals, growth-arrested Escherichia coli cells accumulate oxidatively damaged proteins . In the early stages of the E . coli stationary phase, this oxidation is caused by an increased production of aberrant proteins, which are especially susceptible to oxidative attack . This route of oxidation appears to elude the classical oxidative defence proteins . The failure of growth-arrested cells fully to combat oxidative damage may also be linked to a trade-off between proliferation activities (primarily directed by the housekeeping sigma factor, sigma70) and maintenance (primarily directed by sigmaS) . This trade-off is regulated by the alarmone ppGpp such that elevated ppGpp levels allow sigmaS, and other alternative sigma factors, to work in concert with sigma70 by shifting their relative competitiveness for RNA polymerase binding . However, even during elevated ppGpp levels and stasis, E . coli cells maintain a basal transcription of housekeeping sigma70-dependent genes, and resources are thus partly diverted from maintenance and stress defences to activities relating to proliferation . An alternative view argues for ppGpp being involved in programmed cell death upon growth arrest by regulating chromosomally located toxin-antitoxin loci . Thus, models of bacterial senescence, like those dealing with ageing in higher organisms, encompass both stochastic deterioration theories and programming theories . This review summarizes and evaluates these models. Microbes Infect, 2003 Feb, 5(2), 95 - 106 Delayed type hypersensitivity-associated disruption of splenic periarteriolar lymphatic sheaths coincides with temporary loss of IFN-gamma production and impaired eradication of bacteria in Brucella abortus-infected mice; Hort GM et al.; A major problem of infections with facultative intracellular bacteria is their chronic course . We comprehensively evaluated the host response in murine brucellosis to study mechanisms contributing to bacterial persistence in the presence of an established immune response . Evidence is presented that the decrease in eradication kinetics, reproducibly occurring 18 d after infection of mice with Brucella abortus S19, is related to a state of downregulation of defense mechanisms . This is not due to a Th1 to Th2 switch or prostaglandin-mediated suppression by macrophages but is most probably caused by a severe disruption of spleen morphology at the height of Brucella-induced delayed type hypersensitivity . This results in a profound depletion of both CD4(+) and CD8(+) T cells in periarteriolar lymphatic sheaths, a consecutive deleterious shift in the relation of permissive macrophages and protective lymphocytes and an impaired capacity of splenocytes to produce IFN-gamma in response to soluble Brucella antigen. J Biol Chem, 2003 May 16, 278(20), 17672 - 9 Epub 2003 Mar 13. Common location of determinants in initiator transfer RNAs for initiator-elongator discrimination in