Microorganism

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 bacteria and in eukaryotes; Stortchevoi A et al.; Initiator tRNAs are used exclusively for initiation of protein synthesis and not for elongation . We show that both Escherichia coli and eukaryotic initiator tRNAs have negative determinants, at the same positions, that block their activity in elongation . The primary negative determinant in E . coli initiator tRNA is the C1xA72 mismatch at the end of the acceptor stem . The primary negative determinant in eukaryotic initiator tRNAs is located in the TPsiC stem, whereas a secondary negative determinant is the A1:U72 base pair at the end of the acceptor stem . Here we show that E . coli initiator tRNA also has a secondary negative determinant for elongation and that it is the U50.G64 wobble base pair, located at the same position in the TPsiC stem as the primary negative determinant in eukaryotic initiator tRNAs . Mutation of the U50.G64 wobble base pair to C50:G64 or U50:A64 base pairs increases the in vivo amber suppressor activity of initiator tRNA mutants that have changes in the acceptor stem and in the anticodon sequence necessary for amber suppressor activity . Binding assays of the mutant aminoacyl-tRNAs carrying the C50 and A64 changes to the elongation factor EF-Tu.GTP show marginally higher affinity of the C50 and A64 mutant tRNAs and increased stability of the EF-Tu.GTP . aminoacyl-tRNA ternary complexes . Other results show a large effect of the amino acid attached to a tRNA, glutamine versus methionine, on the binding affinity toward EF-Tu.GTP and on the stability of the EF-Tu.GTP.aminoacyl-tRNA ternary complex.

Water Sci Technol, 2003, 47(3), 143 - 6
A detection method for Legionella spp in (cooling) water: fluorescent in situ hybridisation (FISH) on whole bacteria; Declerck P et al.; Although traditional culture methods are appropriate for detection of Legionella species, such culture takes several days . Rapid detection (< 24 h) of individual Legionella is possible using fluorescent in situ hybridisation (FISH) on whole bacteria . Water samples were filtered and the concentrated bacteria were immediately detected (without culture) with a fluorescence microscope following appropriate labelling . The detection level was very high and quantification was possible . For the detection of all Legionella spp . the probe LEG705 was used, complementary to a 16S rRNA sequence conserved in all Legionella spp . For specific detection of L . pneumophila the probe LEGPNE1 was used . This probe is designed against a variable domain of the 16S rRNA sequence from L . pneumophila . CY3 and FLUOS labels were tested and CY3 showed clearly detectable bacteria with minimum background staining . This FISH technique is very sensitive, fast, reliable and individual bacteria are easily detected.

Shock, 2003 Mar, 19(3), 263 - 7
Hepatic killing but not clearance of systemically circulating bacteria is dependent upon peripheral leukocytes via Mac-1 (CD11b/CD18); Brengman ML et al.; The hepatic reticuloendothelial system (RES) is the primary mechanism for removing circulating bacteria from the systemic circulation . While Kupffer cells are important for this process, leukocytes appear to play a significant role as well . Hepatic leukocyte accumulation following ischemia/reperfusion or cytokine stimulation is well documented, but its contribution to phagocytic killing by the hepatic RES is not fully understood . We evaluated the role of leukocytes in general, and leukocyte-endothelial adhesion in particular, in hepatic RES function . This was done by inducing confirmed leukopenia with cyclophosphamide or by blocking leukocyte-endothelial adhesion molecules with specific blocking antibodies . Hepatic phagocytic clearance (HPC) and hepatic phagocytic killing (HKE) of systemically intravenously injected E . coli were assayed and quantitated by a validated dual isotope label technique . HPC among the various experimental groups and respective controls varied only slightly, with no statistically significant differences observed . Leukopenia or CD11b blockade each significantly decreased the HKE relative to the controls . Antibody blockade of certain other adhesion molecules had no significant effect on HKE (or HPC) . The role of leukocytes in killing systemically circulating bacteria is an integral component of hepatic RES function . This capability of the leukocyte appears to be dependent, in part, on the adhesion molecule, Mac-1.

Biofizika, 2003 Jan-Feb, 48(1), 40 - 8
{Two-level heterogenous energy migration . Modeling and application to purple bacteria}; Borisov AIu et al.; The dynamics of migration of electronic excitations and the efficiency of their trapping in two-dimensional ensembles of molecules were analyzed . Molecules were characterized using the following parameters: the width of long-wavelength bands, the values of extinction and rate constant of deactivation of electronic excitations, critical distances of migration close to those of dye molecules, in particular, bacteriochlorophyll a and purple bacteria . A comparative analysis of two-dimensional models of energy migration made it possible to chose a model with an optimum light-harvesting on traps from the largest numbers of light-absorbing molecules . It was shown that in ensembles of molecules having different spectral characteristics (spectral shifts between the short- and long-wavelength fractions of the molecules are hear 800 cm-1) the efficiency of excitation trapping is approximately 90 and 80% for the number of light-harvesting molecules per one trap 210 and 580, respectively.

Clin Infect Dis, 2003 Mar 15, 36(6), 783 - 5 Epub 2003 Mar 04.
The role of clonality in the global spread of fluoroquinolone-resistant bacteria; Klugman KP; The molecular epidemiology of fluoroquinolone resistance in a number of bacterial pathogens suggests that the persistence and spread of resistance is associated with a small number of highly successful bacterial clones . The recent description of fluoroquinolone-resistant strains among global clones of pneumococci raises the likelihood that the percentage of pneumococci resistant to fluoroquinolones will increase as this class of agent is increasingly used for the management of respiratory tract infection in adults . Although these clones remain fluoroquinolone susceptible in children, their widespread distribution argues against the extension of fluoroquinolone use to the management of respiratory tract infection in children.

J Clin Microbiol, 2003 Mar, 41(3), 1304 - 6
Isolation of sulfate-reducing bacteria from human thoracoabdominal pus; Loubinoux J et al.; To evaluate the prevalence of sulfate-reducing bacteria in septic processes, we searched for these bacteria by culture in 100 consecutive abdominal and pleural pus specimens . Twelve isolates were obtained from abdominal samples and were identified by a multiplex PCR as Desulfovibrio piger (formerly Desulfomonas pigra) (seven strains), Desulfovibrio fairfieldensis (four strains), and Desulfovibrio desulfuricans (one strain).

Indian J Exp Biol, 2002 Feb, 40(2), 223 - 6
Assessment of performance of UV sterilizer for room air bacteria; Joshi PV; Paper presents a technique for performance of UV sterilizer for room air bacteria . Patterns of decay of room air bacteria concentration during sterilization and build-up there after as a function of time is studied . Decay process seems to follow exponential pattern . Half-lives during decay are estimated . For single sterilizer unit with a dose of 16 W the decay half-life is around 8.6 min . For the dose of 32 W (2 sterilizers), half-life is estimated to be 6.18 min . The removal rates of room air bacteria due to sterilizer are compared with the natural decay of aerosols at steady state . The importance of decay half-life in the assessment has been stated . The bacteria concentration buildup process after putting off the sterilizers seems to be sigmoidal in nature . The buildup half-life is estimated to be around 53 min for present experimental conditions.

Appl Environ Microbiol, 2003 Mar, 69(3), 1687 - 94
Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease; Brinig MM et al.; Members of the uncultivated bacterial division TM7 have been detected in the human mouth, but little information is available regarding their prevalence and diversity at this site . Human subgingival plaque samples from healthy sites and sites exhibiting various stages of periodontal disease were analyzed for the presence of TM7 bacteria . TM7 ribosomal DNA (rDNA) was found in 96% of the samples, and it accounted for approximately 0.3%, on average, of all bacterial rDNA in the samples as determined by real-time quantitative PCR . Two new phylotypes of this division were identified, and members of the division were found to exhibit filamentous morphology by fluorescence in situ hybridization . The abundance of TM7 rDNA relative to total bacterial rDNA was higher in sites with mild periodontitis (0.54% +/- 0.1%) than in either healthy sites (0.21% +/- 0.05%, P < 0.01) or sites with severe periodontitis (0.29% +/- 0.06%, P < 0.05) . One division subgroup, the I025 phylotype, was detected in 1 of 18 healthy samples and 38 of 58 disease samples . These data suggest that this phylotype, and the TM7 bacterial division in general, may play a role in the multifactorial process leading to periodontitis.

Appl Environ Microbiol, 2003 Mar, 69(3), 1397 - 407
Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes; Peplies J et al.; The usability of the DNA microarray format for the specific detection of bacteria based on their 16S rRNA genes was systematically evaluated with a model system composed of six environmental strains and 20 oligonucleotide probes . Parameters such as secondary structures of the target molecules and steric hindrance were investigated to better understand the mechanisms underlying a microarray hybridization reaction, with focus on their influence on the specificity of hybridization . With adequate hybridization conditions, false-positive signals could be almost completely prevented, resulting in clear data interpretation . Among 199 potential nonspecific hybridization events, only 1 false-positive signal was observed, whereas false-negative results were more common (17 of 41) . Subsequent parameter analysis revealed that this was mainly an effect of reduced accessibility of probe binding sites caused by the secondary structures of the target molecules . False-negative results could be prevented and the overall signal intensities could be adjusted by introducing a new optimization strategy called directed application of capture oligonucleotides . The small number of false-positive signals in our data set is discussed, and a general optimization approach is suggested . Our results show that, compared to standard hybridization formats such as fluorescence in situ hybridization, a large number of oligonucleotide probes with different characteristics can be applied in parallel in a highly specific way without extensive experimental effort.

Can J Microbiol, 2002 Dec, 48(12), 1099 - 103
Activity of sulfate-reducing bacteria in human periodontal pocket; Boopathy R et al.; Samples of subgingival dental tissues were examined for the presence of sulfate-reducing bacteria (SRB) . Using enrichment cultures, SRBs were detected in 9 of 17 individuals . A pure culture of SRB was obtained from one sample collected from a patient with type IV periodontal disease . The characterization of this isolate showed that it belongs to the genus Desulfovibrio . The isolate used pyruvate, lactate, glucose, fructose, and ethanol as the sole source of carbon . However, the isolate was unable to use acetate and methanol as a carbon source, indicating it as an incomplete oxidizer unable to carry out the terminal oxidation of substrates . Apart from using sulfate as electron acceptor, the isolate also used thiosulfate and nitrate as an electron acceptor . It has the ability to use a variety of nitrogen sources, including ammonium chloride, nitrate, and glutamate . The optimum growth temperature of the isolate was 37 degrees C and the optimum pH for growth was 6.8 . The SRB isolate contained the electron carrier desulfoviridin . The numbers of SRB in the mouth are assumed to be limited by sulfate . Potential sources of sulfate in the subgingival area include free sulfate in pocket fluid and glycosaminoglycans and sulfur-containing amino acids from periodontal tissues.

J Microbiol Methods, 2003 Apr, 53(1), 131 - 5
Rapid differentiation between short-chain-length and medium-chain-length polyhydroxyalkanoate-accumulating bacteria with spectrofluorometry; Wu HA et al.; An approach for rapid differentiation between short-chain-length (scl) and medium-chain-length (mcl) polyhydroxyalkanoate (PHA) producers was developed . Polyhydroxyalkanoate-accumulated bacterial cells stained with Nile red were suspended in water and subjected to fluorescence spectroscopy at a fixed excitation wavelength of 488 nm . The scl-PHA-accumulated bacteria revealed a maximum emission wavelength at 590 nm, and for mcl-PHA producers were seen at a wavelength of 575 nm . Combining Nile red staining and fluorescence spectroscopy, the accumulated PHA granules could be rapidly differentiated into scl-PHA and mcl-PHA from the intact cells.

Microbiol Res, 2003, 158(1), 1 - 6
Genetic material in the early evolution of bacteria; Trevors JT; DNA and RNA are nucleic acids that cells and viruses use to produce copies of themselves . However, there is an immense paucity of knowledge on how these nucleic acids originated and changed as early bacteria became capable of growth and cell division . One possibility is that parallel evolution of the genetic code and protein synthesis was required for assembly of the first cells capable of growth and division . It is also possible that DNA-RNA duplices were intermediate genetic material in the early assembly of the first cells . These ideas will be discussed as well as other aspects of the assembly of the first cells on the Earth.

Environ Int, 2003 Apr, 29(1), 45 - 50
Inactivation of coliform bacteria in Black Sea waters due to solar radiation; Yukselen MA et al.; The effects of solar radiation and temperature on bacterial die-off rates in Black Sea coastal waters using total coliform as the indicator organism were studied . Coliform die-off experiments were carried out in seawater samples collected along the coastline . The experiments were conducted in beakers filled with seawater that were kept at constant temperatures and exposed to solar radiation . The membrane filter technique was used for the coliform analysis . Temperature ranging between 9 and 26 degrees C and solar radiation between 20 and 60 cal/cm(2) h were tested . Experiments in the dark were also conducted to isolate the effect of solar radiation from the other factors and, furthermore, to determine the effect of temperature on bacterial die-off . The solar radiation was found to be the most significant factor affecting the mortality of coliform bacteria .

Trends Microbiol, 2003 Feb, 11(2), 74 - 9
Converting bacteria to organelles: evolution of mitochondrial protein sorting; Herrmann JM; During the evolution of mitochondria from free-living alpha-proteobacteria, many bacterial genes were transferred into the nuclear genome of eukaryotic cells . This required the development of both targeting signals on the respective polypeptides and protein translocation machineries (translocases) in the mitochondrial membranes . Most components of these translocases have no obvious homologies to bacterial proteins or proteins found in other organelles . Membrane integration of many inner membrane proteins, however, apparently occurs via a conserved sorting pathway whose components and characteristics resemble protein translocation in bacteria . Consistent with this, the topogenic signals of these mitochondrial inner membrane proteins mimic those of bacterial proteins . The requirement for post-translational transport to their final destination has placed considerable constraints on the evolution of mitochondrial protein sequences.

J Anim Sci, 2003 Jan, 81(1), 285 - 93
Role of ovarian progesterone and potential role of prostaglandin F2alpha and prostaglandin E2 in modulating the uterine response to infectious bacteria in postpartum ewes; Lewis GS; In sheep and cattle, the postpartum uterus is resistant to bacterial challenge until after corpora lutea develop . A 2 x 2 factorial arrangement of treatments was used to determine whether prostaglandins may mediate the effects of progesterone in transforming the postpartum uterus from resistant to susceptible . On d 14 postpartum, ewes (n = 6/group) were ovariectomized or sham ovariectomized, and the vena cava was catheterized for daily collection of uteroovarian-enriched blood . From d 15 to 20, ewes received twice daily intramuscular injections of progesterone in sesame oil or plain sesame oil . On d 20, each uterus received 75 x 10(7) cfu of Arcanobacterium pyogenes and 35 x 10(7) cfu of Escherichia coli . Uteri were collected on d 25 and examined for signs of infection . For each blood sample, unstimulated and mitogen-stimulated lymphocyte proliferation was measured as {3H}thymidine incorporation, smears were prepared for differential white blood cell (WBC) counts, and progesterone, prostaglandin F2alpha, (PGF2alpha), and prostaglandin E2 (PGE2) were quantified . All 12 progesterone-treated, but only two of the 12 oil-treated, ewes developed uterine infections (P < 0.001) . Progesterone treatment increased (P < 0.001; 3.1 vs 1.5 ng/mL) and ovariectomy decreased (P < 0.001; 3.7 vs 0.9 ng/mL) vena caval progesterone . Progesterone treatment reduced (P < 0.01) PGF2alpha, (303.9 vs 801.3 pg/mL), and PGF2alpha was greater (P < 0.05) before than after inoculation (626.4 vs 478.8 pg/mL) . The PGE2 concentration was greater in progesterone-treated, ovary-intact ewes than in ewes in the other groups (ovariectomy x progesterone treatment; P < 0.01) . Ovariectomy increased (P < 0.005; 4.4 vs 2.9 pmol) and progesterone treatment decreased (P < 0.05; 3.2 vs 4.1 pmol) concanavalin A-stimulated lymphocyte proliferation . Ovariectomy increased lipopolysaccharides-stimulated proliferation (P < 0.05; 2.4 vs 1.9 pmol) . For neutrophils per 100 WBC, the ovariectomy x progesterone and progesterone x period interactions were significant (P < 0.01) . The ovariectomy x progesterone interaction was significant (P < 0.01) for lymphocytes per 100 WBC . Ovariectomy decreased monocytes (P < 0.001; 10 vs 13) and increased eosinophils (P < 0.001; 10 vs 5) per 100 WBC . Progesterone makes the postpartum uterus in ewes susceptible to infection, but ovariectomy allows ewes to remain resistant; uterine prostaglandins may mediate this change . This model creates opportunities to determine the mechanisms responsible for the shift from resistance to susceptible.

J Basic Microbiol, 2003, 43(1), 8 - 17
Screening for soluble methane monooxygenase in methanotrophic bacteria using combined molecular and biochemical methods for hydroxylase detection; Grosse S et al.; Three well known methanotrophic bacteria (Methylosinus trichosporium OB3b, Methylocystis sp . WI 14, and Methylocystis sp . GB 25) and three newly isolated methanotrophic bacteria (Methylocystis sp . WI 11, Methylocystis sp . X, and FI-9) were screened for sMMO considering the existence of hydroxylase (component A) genes as well as its gene expression . For these purposes monoclonal antibodies that specifically recognize each subunit of the hydroxylase of Methylocystis sp . WI 14 (alpha-subunit {9E5/F2}, beta-subunit {4E2/G11}, gamma-subunit {10G3/D7}) were produced . PCR amplification using well known primers showed that the hydroxylase encoding genes appear to be only present in M . trichosporium OB3b, Methylocystis sp . WI 11 and WI 14, and in the isolate FI-9 . Western and ELISA analysis using the monoclonal antibodies revealed that all subunits of hydroxylase were present . However, in FI-9, only the alpha-subunit of the hydroxylase might be expressed . Surprisingly, in Methylocystis sp . GB 25, where no sMMO activity and no amplification with sMMO specific primers was obtained, the antibody 4E2/G11 recognized a protein band with exactly the same molecular mass as the beta-subunit of the hydroxylase . Methylocystis sp . X showed no positive reaction in any of the tests . In combination with the detection methods currently used, the described antibodies provide a powerful tool for detecting even partially expressed hydroxylase genes.

Philos Trans R Soc Lond B Biol Sci, 2003 Jan 29, 358(1429), 5 - 17; discussion 517-8
Genomes at the interface between bacteria and organelles; Douglas AE et al.; The topic of the transition of the genome of a free-living bacterial organism to that of an organelle is addressed by considering three cases . Two of these are relatively clear-cut as involving respectively organisms (cyanobacteria) and organelles (plastids) . Cyanobacteria are usually free-living but some are involved in symbioses with a range of eukaryotes in which the cyanobacterial partner contributes photosynthesis, nitrogen fixation, or both of these . In several of these symbioses the cyanobacterium is vertically transmitted, and in a few instances, sufficient unsuccessful attempts have been made to culture the cyanobiont independently for the association to be considered obligate for the cyanobacterium . Plastids clearly had a cyanobacterial ancestor but cannot grow independently of the host eukaryote . Plastid genomes have at most 15% of the number of genes encoded by the cyanobacterium with the smallest number of genes; more genes than are retained in the plastid genome have been transferred to the eukaryote nuclear genome, while the rest of the cyanobacterial genes have been lost . Even the most cyanobacteria-like plastids, for example the "cyanelles" of glaucocystophyte algae, are functionally and genetically very similar to other plastids and give little help in indicating intermediates in the evolution of plastids . The third case considered is the vertically transmitted intracellular bacterial symbionts of insects where the symbiosis is usually obligate for both partners . The number of genes encoded by the genomes of these obligate symbionts is intermediate between that of organelles and that of free-living bacteria, and the genomes of the insect symbionts also show rapid rates of sequence evolution and AT (adenine, thymine) bias . Genetically and functionally, these insect symbionts show considerable similarity to organelles.

Med Microbiol Immunol (Berl), 2003 Feb, 192(1), 57 - 60 Epub 2003 Jan 30.
Immunopathogenesis of Onchocerca volvulus keratitis (river blindness): a novel role for endosymbiotic Wolbachia bacteria; Pearlman E; River blindness is thought to occur as a result of the host response to degenerating microfilariae in the eye . Utilizing a murine model of corneal inflammation (keratitis) to investigate the immune and inflammatory responses associated with river blindness, we recently demonstrated an important role for endotoxin-like products from endosymbiotic bacteria and for activation of Toll-like receptor 4 (TLR4) . These observations have led to a new understanding of the pathogenesis of this disease

Naturwissenschaften, 2003 Feb, 90(2), 72 - 5 Epub 2003 Jan 09.
Symbiotic bacteria in hornet pupal silk; Ishay JS et al.; The silk weave spun by hornet larvae before undergoing pupal metamorphosis is composed of fibers and sheets, both containing symbiotic bacteria . The bacteria are secreted from the silk gland and are glued to the secreted silk, which is made up of amino-acid polymers . In the dark, it possesses at first an electric current amounting to several hundred nanoamperes (nA) (i.e., a thermoelectric property), and a high electric capacitance of up to several milliFarads (mF) . This electrical charge is used gradually by the developing pupa . The symbiotic bacteria penetrate through slits in the coat of the silk fibers to the core or into pockets in the sheets, where they gradually digest parts of the silk weave, thereby nullifying its mechanical properties and facilitating in due time the egress of the imago from the puparium.

Environ Microbiol, 2003 Mar, 5(3), 143 - 51
Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment; Toro N; Self-splicing group II introns are present in the organelles of lower eukaryotes, plants and Bacteria and have been found recently in Archaea . It is generally accepted that group II introns originated in bacteria before spreading to mitochondria and chloroplasts . These introns are thought to be related to the progenitors of spliceosomal introns . Group II introns are also mobile genetic elements . In bacteria, they appear to spread using either other mobile genetic elements or low-expression regions as target sites . Bacteria and Archaea genome sequence annotations have revealed the diversity of group II intron classes and that they are involved in vertical and horizontal inheritance.

Indian J Exp Biol, 2002 Sep, 40(9), 1043 - 9
A novel strategy of oxygen restriction by some diazotrophic enteric bacteria; Kannan V et al.; Protection of nitrogenase against oxygen inactivation in diazotrophs involves numerous strategies . Glutathione is known to play an important role in scavenging oxyradicals in many living systems . The involvement of glutathione (reduced) (GSH), glutathione peroxidase (GPX) and glutathione reductase (GR) in the protection of nitrogenase in free living diazotrophs is reported here for the first time . Reduced glutathione content and the activity of glutathione peroxidase and glutathione reductase increased with increase in oxygen concentration under nitrogen fixing conditions but decreased under anaerobic and nitrogenase repressed conditions . This correlation is used to postulate a protecting role for GSH-GPX-GR system against oxygen inactivation of nitrogenase.

FEMS Microbiol Rev, 2003 Jan, 26(5), 533 - 54
Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives; Giraldo R; Although DNA replication is the universal process for the transmission of genetic information in all living organisms, until very recently evidence was lacking for a related structure and function in the proteins (initiators) that trigger replication in the three 'Life Domains' (Bacteria, Archaea and Eukarya) . In this article new data concerning the presence of common features in the initiators of chromosomal replication in bacteria, archaea and eukaryotes are reviewed . Initiators are discussed in the light of: (i) The structure and function of their conserved ATPases Associated with various cellular Activities (AAA+) and winged-helix domains . (ii) The nature of the macromolecular assemblies that they constitute at the replication origins . (iii) Their possible phylogenetic relationship, attempting to sketch the essentials of a hypothetical DNA replication initiator in the micro-organism proposed to be the ancestor of all living cells.

Syst Appl Microbiol, 2002 Dec, 25(4), 584 - 91
Cellulose-degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil; Wirth S et al.; In a previous study, culturable carboxymethyl-cellulose (CMC) decomposing soil bacteria isolated from different sampling positions across an agricultural encatchment have been classified into 31 pattern groups by digestion of amplified 16S rDNA using a single restriction enzyme (Ulrich and Wirth: Microb . Ecol . 37, 238-247, 1999) . In order to reveal relationships between phylogenetic diversity and phenotypic functions, a further differentiation of two selected site-specific pattern groups (I and H) was performed, resulting in a sub-classification of four and three ARDRA groups, respectively . Based on sequencing a representative isolate of each ARDRA group, the isolates were assigned to the genus Streptomyces . The ARDRA groups were dispersed across various clades of the genus with a direct affiliation to species known for cellulolytic activity in one group, only . The isolates differed in potentials to degrade colloidal, native or highly crystalline cellulose derivatives . Out of 39 isolates, 11 were capable of degrading all substrates, 17 were restricted to degrade CMC only, and 11 were active decomposers of exclusively both CMC and colloidal cellulose . In most cases, the genetic classification of the isolates corresponded with groupings based on cellulose degrading capabilities . Thus, isolates of four ARDRA groups were restricted to the degradation of CMC, while two further isolates which efficiently degraded all cellulose derivatives formed two separate ARDRA groups . The major ARDRA group, however; displayed a high variability of degradation capabilities . The study of additional phenotypic features revealed a broad potential to decompose a set of various carbon substrates, which matched the phylogenetic classification in several cases.

Trends Biochem Sci, 2003 Feb, 28(2), 62 - 6
Non-homologous end-joining: bacteria join the chromosome breakdance; Wilson TE et al.; The repair of DNA double-strand breaks by non-homologous end-joining (NHEJ) has long been thought to be restricted to eukaryotes . However, recent papers document the existence of operons encoding functional NHEJ complexes in some bacteria . These findings provide new evolutionary insights into the core biochemistry of this repair pathway, and suggest that one function driving the selection of NHEJ in bacteria, and perhaps eukaryotes, relates to prolonged periods of mitotic exit.

J Environ Health, 2003 Jan-Feb, 65(6), 18 - 20, 31
The recovery of bacteria from the handpiece of a high school telephone; Yalowitz M et al.; The purpose of the experiment reported in this paper was to study the bacteria on the public telephones at Montgomery Blair High School in Silver Spring, Maryland, to determine if there is a risk of infection to students who use the phones . Five phone handpieces from around the school--from four public phones and the principal's phone--were swabbed twice, at 7 a.m . and at 3 p.m., on November 6,2000 . Three sites on each handpiece were swabbed: the mouthpiece, the handle, and the earpiece . The swabs were streaked onto media supportive of aerobic-bacteria growth and incubated at 5 percent carbon dioxide for 24 and 48 hours at 37 degrees C . The plates were studied for quantitative and qualitative data . Microscopic examination of Gram-stain preparations and, in some cases, biochemical identification were performed on the bacterial isolates . Results showed an increase in the number of bacteria from morning to afternoon in specimens from 10 of the 15 observations (67 percent) . Eight of these 10 observations found more than threefold increases in the number of bacteria . In the afternoon, more types of bacteria were found in eight of the 15 specimens . Only one specimen had decreases in the number and types of bacteria from morning to afternoon . None of the bacteria that were found, however, were known pathogens . The authors conclude that even though more bacteria were recovered from phones in the afternoon than in the morning, their study did not show a serious health risk to students who used the public telephones on the day of the experiment.

Mol Biol Evol, 1998 Nov, 15(11), 1514 - 23
Accelerated evolutionary rate in sulfur-oxidizing endosymbiotic bacteria associated with the mode of symbiont transmission; Peek AS et al.; The nearly neutral theory of molecular evolution predicts that the rate of nucleotide substitution should accelerate in small populations at sites under low selective constraint . We examined these predictions with respect to the relative population sizes for three bacterial life histories within chemolithoautotrophic sulfur-oxidizing bacteria: (1) free-living bacteria, (2) environmentally captured symbionts, and (3) maternally transmitted symbionts . Both relative rates of nucleotide substitution and relative ratios of loop, stem, and domain substitutions from 1,165 nt of the small-subunit 16S rDNA were consistent with expectations of the nearly neutral theory . Relative to free-living sulfur-oxidizing autotrophic bacteria, the maternally transmitted symbionts have faster substitution rates overall and also in low-constraint domains of 16S rDNA . Nucleotide substitition rates also differ between loop and stem positions . All of these findings are consistent with the predictions that these symbionts have relatively small effective population sizes . In contrast, the rates of nucleotide substitution in environmentally captured symbionts are slower, particularly in high-constraint domains, than in free-living bacteria.

Wei Sheng Yan Jiu, 2002 Oct, 31(5), 361 - 3
{Study on tetrazolium salt colorimetric assay for growth and survival of bacteria}; Zhang J et al.; To establish a tetrazolium salt(MTT) colorimetric assay for bacteria growth and survival, living or boiling killed bacteria S . aureus and E . coli were incubated with MTT in microdilution plate for 36-37 degrees C at different time . DMSO was added as formazan dissolvent and the mixtures were measured for optical density(A) or absorbence at 510 nm wave length . Living bacteria were incubated with different amount of MTT for different time . The formazan were dissolved with different amount of DMSO and the A value were measured at different wave length . The results showed that yellow MTT could be reduced into blue formazan by living bacteria S . aureus and E . coli and the A value was directly proportional to concentration of the bacteria . A values of bacteria decreased with increasing of boiling time . To some extents, absorbence of living bacteria was direct proportion to MTT concentration and incubation time in the range of 0-2 hours . DMSO was good dissolvent for bacteria formazan and the highest absorbence could be reached in wave length range of 510-530 nm . It was suggested that MTT colorimetric assay could be used for measurement of bacteria growth and survival, and its optimal parameters were as follows: MTT concentration is 0.3 mg/ml . MTT incubation time was 2 hours . DMSO amount as dissoventis was 2-fold volume of bacteria suspension . Measurement wave length was 510-530 nm.

Eur J Pharmacol, 2003 Feb 7, 461(1), 63 - 71
Role of bacteria and inducible nitric oxide synthase activity in the systemic inflammatory microvascular response provoked by indomethacin in the rat; Evans SM et al.; The role of bacteria and nitric oxide (NO), formed by the inducible isoform of NO synthase (iNOS), in a widespread systemic inflammatory microvascular response that follows indomethacin administration, has been investigated in the rat . Subcutaneous administration of indomethacin (10 mg kg(-1)) daily for 2 days produced an increase in microvascular leakage of radiolabelled albumin accompanied by expression of iNOS activity in the lung, liver, spleen and kidney, as well as in the jejunum, caecum, colon and ileum . Pretreatment with dexamethasone (1 mg kg(-1) day(-1), s.c.) reduced indomethacin-provoked microvascular leakage and the expression of iNOS activity in all the tissues studied . The widespread microvascular leakage and iNOS activity was also inhibited by pretreatment with ampicillin (200 mg kg(-1) day(-1), p.o.), metronidazole (200 mg kg(-1) day(-1), p.o.) or by polymyxin B (15 mg kg(-1) day(-1), s.c.) . Administration of the highly selective iNOS inhibitor GW 273629 (3-{{2-(ethanimidoylamino)ethyl}sulphonyl}-L-alanine; five doses of 5 mg kg(-1), s.c . over 48 h) substantially inhibited the microvascular leakage in the affected organs . Such findings suggest the involvement of indigenous gut bacteria, lipopolysaccharide and iNOS expression following indomethacin-induced enteropathy in this widespread systemic inflammatory microvascular response.

Arch Microbiol, 2003 Jan-Feb, 179(2), 135 - 44 Epub 2003 Jan 16.
Growth of sulfate-reducing bacteria and methanogenic archaea with methylated sulfur compounds: a commentary on the thermodynamic aspects; Scholten JC et al.; Methylated sulfur compounds such as dimethylsulfoniopropionate, dimethylsulfide, methanethiol, and other methylated sulfur compounds can act as sources of carbon and energy for the growth under anoxic conditions of a number of sulfate-reducing bacteria and methanogenic archaea . We summarise the range of degradative reactions that do or might occur in such organisms, and present thermodynamic data for these processes . These data enable estimates of the feasibility of the reactions as growth-supporting systems, and of the possible maximum growth yields of the bacteria and archaea catalysing them . We compare our new estimates with the few data that are currently available from the literature, and show that some published growth-yield assessments need reevaluation.

Arch Microbiol, 2003 Jan-Feb, 179(2), 108 - 15 Epub 2003 Jan 14.
A comparative study of bchG from green photosynthetic bacteria; Garcia-Gil LJ et al.; The gene bchG, coding for bacteriochlorophyll a synthase from a variety of green sulfur bacteria and the filamentous anoxygenic phototrophic bacteria, Chloroflexus aurantiacus, Chloronema sp., and Roseiflexus castenholzii HL08, was partially sequenced and compared . The deduced amino acid consensus sequences for green sulfur bacteria and green filamentous anoxygenic phototrophic bacteria were found to belong to the UbiA enzyme family of polyprenyltransferases with the most similar sequences being those of photosynthetic organisms . All deduced amino acid sequences showed a highly conserved region, which includes the motif DRXXD, characteristic of polyprenyltransferases, which was extended to DREVDAINEP for green sulfur bacteria . Neighbor-joining analysis of a protein similitude matrix displayed a relatively high distance between green sulfur bacteria and the other groups . Sequences from green sulfur bacteria were more closely related to those of purple bacteria than to those of filamentous anoxygenic phototrophic bacteria . In addition, internal grouping within green sulfur bacteria was congruent regarding taxonomic features including cell shape, presence of gas vacuoles and NaCl requirement . In addition to bchlG, another gene encoding for a second chlorophyll synthetase, previously tentatively identified as chlG, was also found in Chlorobium tepidum, showing the highest similarities with polyprenyltransferases from chlorophyll- a-containing organisms.

Gene, 2003 Jan 16, 303, 139 - 45
Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas; Gueguen Y et al.; An expressed sequence tag program was undertaken to isolate genes involved in defense mechanisms of the Pacific oyster, Crassostrea gigas . Putative function could be assigned to 54% of the 1142 sequenced cDNAs . We built a public database where all EST information are accessible through numerous search profiles . Based on sequence similarities we identified 20 genes that may be implicated in immune function . We investigated the expression of four of these genes during bacterial challenge of oysters . Three of them were induced in response to challenge lending support to their involvement in oyster immunity . Moreover, four other genes were highly homologous to components of the NF-kappa B signaling pathway which is involved in innate immune response in Drosophila and mammals . Altogether, our results open a new way to investigate the immune response in mollusks.

Genetica, 2002 Nov, 116(2-3), 359 - 70
Sexual isolation and speciation in bacteria; Cohan FM; Like organisms from all other walks of life, bacteria are capable of sexual recombination . However, unlike most plants and animals, bacteria recombine only rarely, and when they do they are extremely promiscuous in their choice of sexual partners . There may be no absolute constraints on the evolutionary distances that can be traversed through recombination in the bacterial world, but interspecies recombination is reduced by a variety of factors, including ecological isolation, behavioral isolation, obstacles to DNA entry, restriction endonuclease activity, resistance to integration of divergent DNA sequences, reversal of recombination by mismatch repair, and functional incompatibility of recombined segments . Typically, individual bacterial species are genetically variable for most of these factors . Therefore, natural selection can modulate levels of sexual isolation, to increase the transfer of genes useful to the recipient while minimizing the transfer of harmful genes . Interspecies recombination is optimized when recombination involves short segments that are just long enough to transfer an adaptation, without co-transferring potentially harmful DNA flanking the adaptation . Natural selection has apparently acted to reduce sexual isolation between bacterial species . Evolution of sexual isolation is not a milestone toward speciation in bacteria, since bacterial recombination is too rare to oppose adaptive divergence between incipient species . Ironically, recombination between incipient bacterial species may actually foster the speciation process, by prohibiting one incipient species from out-competing the other to extinction . Interspecific recombination may also foster speciation by introducing novel gene loci from divergent species, allowing invasion of new niches.

J Dent, 2002 Sep-Nov, 30(7-8), 359 - 63
A method for the detection and quantification of bacteria in human carious dentine using fluorescent in situ hybridisation; Banerjee A et al.; OBJECTIVES: Previous studies have evaluated bacterial numbers in carious dentine using conventional culturing methods, capable of detecting only a proportion of the total bacteria present within lesions . The aim of this study was to detect and enumerate the total bacterial population present in carious human dentine by means of fluorescent in situ hybridisation . METHOD: Five freshly extracted carious molars were sequentially hand excavated under sterile conditions through four levels in the lesions . Replicate samples were probed with a rhodamine-tagged, 16S rRNA-directed probe (EUB338), specific for the bacterial domain . Two of the five original samples were examined using fluorescence microscopy and by using a systematic visual counting strategy; direct enumeration of the bacterial population in carious dentine was performed . RESULTS: In the superficial, middle and deep/excavation front zones, a mean of 7.34 x 10(6) (standard error of the mean, SEM +/- 0.44), 5.23 x 10(6) (SEM +/- 0.18), and 1.69 x 10(6) (SEM +/- 0.15) total bacteria/mg dentine were found, respectively . In the advancing front zone (beyond the conventional clinical excavation boundary) a mean of 0.34 x 10(6) (SEM +/- 0.05) total bacteria/mg dentine was recorded . CONCLUSION: A bacterial enumeration strategy was developed and detected greater numbers of bacteria through the depth of carious lesions that had been reported previously . The technique could be further developed using species-specific probes to determine the distribution, abundance and viability of all bacteria in carious dentine . This new information in turn will lead to a better understanding of the pathological process of caries and ultimately, its clinical treatment .

Clin Chem Lab Med, 2002 Dec, 40(12), 1191 - 9
The evolution of transthyretin synthesis in vertebrate liver, in primitive eukaryotes and in bacteria; Richardson SJ; Thyroid hormones are evolutionarily old signal molecules, which can partition between compartments by partitioning into lipid membranes . The role of thyroid hormone distributor proteins is to ensure that sufficient thyroid hormone remains in the bloodstream . Of particular interest is the role of transthyretin, synthesised by the liver and secreted into the blood . In this review, three hypotheses are presented, suggesting the selection pressures leading to the onset of transthyretin synthesis in the liver during evolution . A thyroid hormone distribution network would be a selection advantage over a single protein performing this function . Similarly to the situation in eutherians, hepatic transthyretin synthesis in marsupials is under negative acute phase regulation . The overall three-dimensional structure of transthyretin did not change appreciably during vertebrate evolution . The region of the primary sequence which evolved most was the N-terminal region of the subunit . The N-termini of transthyretin changed from longer and more hydrophobic in reptiles/birds, to shorter and more hydrophilic in eutherians . These changes are correlated with a change in preference from binding of triiodothyronine, to binding thyroxine . As the rest of the molecule had not changed significantly during vertebrate evolution, the gene coding for transthyretin must have evolved prior to the divergence of the vertebrates from the non-vertebrates . Five open reading frames in the genomes of C . elegans (2), S . dublin, S . pombe and E . coli were identified . The protein products are predicted to form tetramers similar to transthyretins . Two possible functions of these proteins are suggested.

Wei Sheng Wu Xue Bao, 1998 Apr, 38(2), 98 - 102
{Purification and characterization of cyclomaltodextrin glucanotransferase from alkaliphilic bacteria}; Zhang Q et al.; A cyclomaltodextrin glucanotransferase from alkaliphilic bacteria was purified to PAGE homogenous by ammonium sulfate precipitation and DEAE-cellulose DE-52 chromatography with 11.5 fold purification and 5.7% recovery . Mr estimated with concentration gradient PAGE was 151,000 . The optimum conditions for activity were pH 7.0, temperature 60 degrees C, stable in the range 6.0-9.0 and below 50 degrees C . The enzyme activity was activated by salicin and maltitol, slightly inhibited by Sn2+, Mn2+, inositol and pullulan, strongly inhibited by Ag+, Cu2+, Al3+, Fe2+, Pb2+, Hg2+ and Zn2+ . The maximum absorption was at 270 nm in ultraviolet spectrum, the maximum emission wavelenghth in the excitation spectrum was 283 nm, the maximum emission spectrum determined at 283 nm was 335 nm . The effects of some protein modification reagents on the CGTase activity have been studied . Histidine and tryptophan residues may be essential for activity, carboxyl groups might have some effects on the activity.

Environ Microbiol, 2003 Jan, 5(1), 48 - 54
Diversity of alpha-halocarboxylic acid dehalogenases in bacteria isolated from a pristine soil after enrichment and selection on the herbicide 2,2-dichloropropionic acid (Dalapon); Marchesi JR et al.; Five pure cultures of bacteria (strains DA1-5) able to degrade 2,2-dichloropropionic acid (22DCPA) were isolated for the first time from pristine bulk soil samples . From 16S rDNA analysis, it was concluded that strains DA2, DA3 and DA4 were members of the Bradyrhizobium subgroup (alpha-Proteobacteria), strain DA5 clustered in the Brucella assemblage (alpha-Proteobacteria) and strain DA1 clustered in the beta-Proteobacteria . Biochemical and molecular analysis of the dehalogenases from the isolates showed that these enzymes were quite diverse . Several dehalogenases were closely related to group I and II alpha-halocarboxylic acid dehalogenases, and partial polymerase chain reaction (PCR) products were obtained from isolates DA1, 2, 3 and 4 using degenerate dehalogenase primers . However, no PCR products were obtained from isolate DA5 using either of the group I or II alpha-halocarboxylic acid dehalogenase primers . Isolates DA2 and DA4 contained putative silent dehalogenases . The investigation highlighted the endemic nature of these genes in pristine environments and how diverse these were even from spatially close samples.

J Anim Sci, 2002 Dec, 80(12), 3347 - 52
Factors affecting conjugated linoleic acid and trans-C18:1 fatty acid production by mixed ruminal bacteria; Martin SA et al.; The objective of this study was to identify environmental factors that influence conjugated linoleic acid (CLA) and trans-C18:1 fatty acid production by mixed ruminal bacteria . Ruminal contents were collected from a 600-kg ruminally fistulated Hereford steer maintained on pasture . Mixed ruminal bacteria were obtained by differential centrifugation under anaerobic conditions and added to a basal medium that contained a commercial emulsified preparation of soybean oil and a mixture of soluble carbohydrates (cellobiose, glucose, maltose, and xylose) . Culture samples were collected from batch culture incubations at 0, 2, 4, 6, 8, 12, 24, 26, 28, 30, 32, and 48 h . Continuous culture incubations were conducted at dilution rates of 0.05 and 0.10 h(-1) with extracellular pH values of 5.5 and 6.5, and 0.5 and 1.0 g/L of mixed soluble carbohydrates . Culture samples were obtained from the culture vessel once steady-state conditions had been achieved . In batch culture, trans-C18:1 concentrations increased over time and reached a maximum at 48 h . Little CLA was produced during the first 8 h, but cis-9, trans-11 CLA concentrations remained high between 24 and 30 h . When mixed ruminal bacteria were maintained in continuous culture on 0.5 g/L of mixed soluble carbohydrates, concentrations of trans-C18:1 and cis-9, trans-11 CLA were reduced (P < 0.05) at a dilution rate of 0.05 h(-1) and an extracellular pH of 5.5 . Similar effects were also observed when 1.0 g/L of mixed soluble carbohydrates was used . When extracellular pH was lowered to 5.0, neither trans-C18:1 or CLA isomers were detected . In conclusion, our results suggest that culture pH appears to have the most influence on the production of trans-C18:1 and CLA isomers by mixed ruminal bacteria.

Infect Immun, 2003 Feb, 71(2), 850 - 6
DNA from periodontopathogenic bacteria is immunostimulatory for mouse and human immune cells; Nonnenmacher C et al.; Although bacterial DNA (bDNA) containing unmethylated CpG motifs stimulates innate immune cells through Toll-like receptor 9 (TLR-9), its precise role in the pathophysiology of diseases is still equivocal . Here we examined the immunostimulatory effects of DNA extracted from periodontopathogenic bacteria . A major role in the etiology of periodontal diseases has been attributed to Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Peptostreptococcus micros . We therefore isolated DNA from these bacteria and stimulated murine macrophages and human gingival fibroblasts (HGF) in vitro . Furthermore, HEK 293 cells transfected with human TLR-9 were also stimulated with these DNA preparations . We observed that DNA from these pathogens stimulates macrophages and gingival fibroblasts to produce tumor necrosis factor alpha and interleukin-6 in a dose-dependent manner . Methylation of the CpG motifs abolished the observed effects . Activation of HEK 293 cells expressing TLR-9 which were responsive to bDNA but not to lipopolysaccharide confirmed that immunostimulation was achieved by bDNA . In addition, the examined bDNA differed in the ability to stimulate murine macrophages, HGF, and TLR-9-transfected cells . DNA from A . actinomycetemcomitans elicited a potent cytokine response, while DNA from P . gingivalis and P . micros showed lower immunostimulatory activity . Taken together, the results strongly suggest that DNA from A . actinomycetemcomitans, P . gingivalis, and P . micros possesses immunostimulatory properties in regard to cytokine secretion by macrophages and fibroblasts . These stimulatory effects are due to unmethylated CpG motifs within bDNA and differ between distinct periodontopathogenic bacteria strains . Hence, immunostimulation by DNA from A . actinomycetemcomitans, P . gingivalis, and P . micros could contribute to the pathogenesis of periodontal diseases.

Curr Biol, 2003 Jan 8, 13(1), R28 - 30
DNA repair: bacteria join in; Hiom K; In higher organisms, a major pathway for repairing double stranded breaks in DNA is non-homologous end-joining . Now a similar pathway has been shown to operate in bacterial cells, indicating that this important repair mechanism has been conserved through evolution.

Mikrobiologiia, 2002 Nov-Dec, 71(6), 741 - 54
{Methanotrophic bacteria of acid sphagnum bogs}; Dedysh SN; Acid sphagnum bogs cover a considerable part of the territory of Russia and are an important natural source of biogenic methane, which is formed in their anaerobic layers . A considerable portion of this methane is consumed in the aerobic part of the bog profile by acidophilic methanotrophic bacteria, which comprise the methane filter of sphagnum bogs and decrease CH4 emission to the atmosphere . For a long time, these bacteria escaped isolation, which became possible only after the elucidation of the optimal conditions of their functioning in situ: pH 4.5 to 5.5; temperature, from 15 to 20 degrees C; and low salt concentration in the solution . Reproduction of these conditions and rejection of earlier used media with a high content of biogenic elements allowed methanotrophic bacteria of two new genera and species--Methylocella palustris and Methylocapsa acidophila--to be isolated from the peat of sphagnum bogs of the northern part of European Russia and West Siberia . These bacteria are well adapted to the conditions in cold, acid, oligotrophic sphagnum bogs . They grow in a pH range of 4.2-7.5 with an optimum at 5.0-5.5, prefer moderate temperatures (15-25 degrees C) and media with a low content of mineral salts (200-500 mg/l), and are capable of active nitrogen fixation . Design of fluorescently labeled 16S rRNA-targeted oligonucleotide probes for the detection of Methylocella palustris and Methylocapsa acidophila and their application to the analysis of sphagnum peat samples showed that these bacteria represent dominant populations of methanotrophs with a density of 10(5)-10(6) cells/g peat . In addition to Methylocella and Methylocapsa populations, one more abundant population of methanotrophs was revealed (10(6) cells/g peat), which were phylogenetically close to the genus Methylocystis.

Pediatr Pulmonol, 2003 Feb, 35(2), 75 - 82
Role of viruses and atypical bacteria in exacerbations of asthma in hospitalized children: a prospective study in the Nord-Pas de Calais region (France); Thumerelle C et al.; We studied the role of viruses and atypical bacteria in children hospitalized with exacerbated asthma by a prospective study of children with acute asthma admitted to the Department of Pediatrics in Lille, and to 15 hospitals in the Nord-Pas de Calais region, from October 1, 1998-June 30, 1999 . We included children aged 2-16 years with active asthma, defined as three or more recurrent episodes of reversible wheezing . The severity of asthma and of asthmatic exacerbations was recorded . Immunofluorescence assays (IFA) on nasopharyngeal secretions (NPS), serological tests, or both, were used for detection of influenza virus, respiratory syncytial virus (RSV), adenovirus, parainfluenza virus, and coronavirus . Polymerase chain reaction (PCR) assays on NPS were used for rhinovirus and enterovirus . Serological tests for Chlamydia pneumoniae and Mycoplasma pneumoniae were performed . A control group of asymptomatic asthmatic outpatients was examined for respiratory viruses (using IFA and PCR) . Eighty-two symptomatic children (mean age, 7.9 years) were examined . Viruses were detected in 38% (enterovirus, 15.8%; rhinovirus, 12%; RSV, 7.3%) . Serological tests for atypical bacteria were positive in 10% of patients (C . pneumoniae, 5%; M . pneumoniae, 5%) . Among the 27 control subjects (mean age, 7.9 years), one PCR was positive for enterovirus . There was no correlation between severity of chronic asthma or asthmatic exacerbations and the diagnosis of infection . Atypical bacterial pathogen infections were linked with prolonged asthmatic symptoms . In conclusion, we confirmed the high incidence of viral infection in acute exacerbations of asthma, especially enteroviruses or rhinoviruses . Persistent clinical features were more frequently associated with atypical bacterial infections, suggesting that these infections should be investigated and treated in cases of persistent asthmatic symptoms .

Zhongguo Zhong Yao Za Zhi, 2001 Apr, 26(4), 272 - 4
{Studies on metabolism of oxymatrine by human intestinal bacteria}; Wang ML et al.; OBJECTIVE: To study the oxymatrine metabolism induced by human intestinal bacteria and its absorbed metabolites in blood . METHOD: TLC and HPLC were used to examine oxymatrine and its metabolites, and UV, IR, NMR and MS were used to confirm the chemical structures of the metabolites . RESULT: Oxymatrine was transformed into matrine by human intestinal bacteria metabolism in vitro . Rats were given orally oxymatrine 100 mg.kg-1 and were decapitated 3 hours after administration, and their blood was taken to examine serum metabolites by TLC and HPLC, which revealed that oxymatrine and matrine were absorbed into blood . CONCLUSION: Oxymatrine will be transformed into matrine when it is given orally and both of the alkaloids can be absorbed to blood.

Zh Mikrobiol Epidemiol Immunobiol, 2002 Sep-Oct, (5), 92 - 7
{Common stressor proteins in bacteria}; Basnak'ian IA; Research data on common stressor proteins of bacteria obtained during recent 10 years are updated and analyzed . Bacteria of one and the same species were shown to give similar response to the action of different stressors; the main stressor proteins of different bacteria appeared to be homologous; bacteria have cross protection from different stressors . In addition, some common stressor proteins of bacteria were found to be homologous with human antigens that is of great importance for immunobiotechnology.

Proc Natl Acad Sci U S A, 2003 Jan 7, 100(1), 110 - 2 Epub 2002 Dec 23.
Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction; Miao J et al.; We report the first experimental recording, to our knowledge, of the diffraction pattern from intact Escherichia coli bacteria using coherent x-rays with a wavelength of 2 A . By using the oversampling phasing method, a real space image at a resolution of 30 nm was directly reconstructed from the diffraction pattern . An R factor used for characterizing the quality of the reconstruction was in the range of 5%, which demonstrated the reliability of the reconstruction process . The distribution of proteins inside the bacteria labeled with manganese oxide has been identified and this distribution confirmed by fluorescence microscopy images . Compared with lens-based microscopy, this diffraction-based imaging approach can examine thicker samples, such as whole cultured cells, in three dimensions with resolution limited only by radiation damage . Looking forward, the successful recording and reconstruction of diffraction patterns from biological samples reported here represent an important step toward the potential of imaging single biomolecules at near-atomic resolution by combining single-particle diffraction with x-ray free electron lasers.

Proc Natl Acad Sci U S A, 2003 Jan 21, 100(2), 478 - 83 Epub 2003 Jan 06.
Visualization of coupled protein folding and binding in bacteria and purification of the heterodimeric complex; Wang H et al.; During overexpression of recombinant proteins in Escherichia coli, misfolded proteins often aggregate and form inclusion bodies . If an aggregation-prone recombinant protein is fused upstream (as an N-terminal fusion) to GFP, aggregation of the recombinant protein domain also leads to misfolding of the downstream GFP domain, resulting in a decrease or loss of fluorescence . We investigated whether the GFP domain could fold correctly if aggregation of the upstream protein domain was prevented in vivo by a coupled protein folding and binding interaction . Such interaction has been previously shown to occur between the E . coli integration host factors alpha and beta, and between the domains of the general transcriptional coactivator cAMP response element binding protein (CREB)-binding protein and the activator for thyroid hormone and retinoid receptors . In this study, fusion of integration host factor beta or the CREB-binding protein domain upstream to GFP resulted in aggregation of the fusion protein . Coexpression of their respective partners, on the other hand, allowed soluble expression of the fusion protein and a dramatic increase in fluorescence . The study demonstrated that coupled protein folding and binding could be correlated to GFP fluorescence . A modified miniintein containing an affinity tag was inserted between the upstream protein domain and GFP to allow rapid purification and identification of the heterodimeric complex . The GFP coexpression fusion system may be used to identify novel protein-protein interactions that involve coupled folding and binding or protein partners that can solubilize aggregation-prone recombinant proteins.

Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi, 1998 Mar, 12(1), 74 - 6
{Early diagnosis of nasopharyngeal carcinoma using recombinant antigens expressed in bacteria}; Wan Z et al.; An enzyme-linked immunosorbent assay(ELISA) was developed by using recombinant purified early antigens, EA-D and EA-R to detect IgA antibodies in sera from nasopharyngeal carcinoma(NPC) patients . 30 sera from NPC patients and 49 sera from normal persons were detected by the developed ELISA . The serum positive rate and antibody titer were compared with immunoenzymatic method(IE) on slide with Raji cells mears . ELISA is more sensitive and specific . The serum positive rate of NPC patients was increased from 70% by IE to 100% by ELISA and 77% of the serum antibody titer reached > or = 1:200 . The results show that the expressed recombinant p138 and p54 antigens are effective for detection of EA/IgA antibody in sera from NPC patients and ELISA will be a sensitive, specific and convenient method for early diagnosis of NPC.

Appl Environ Microbiol, 2003 Jan, 69(1), 659 - 62
Effect of associated bacteria on the growth and toxicity of Alexandrium catenella; Uribe P et al.; Saprophytic bacteria in cultures of the marine dinoflagellate Alexandrium catenella were removed to assess their effect on growth and paralytic shellfish poisoning toxin production of this dinoflagellate . The actual axenic status was demonstrated by the lack of observable bacteria both immediately after treatment and following extended incubation in the absence of antibiotics . Bacteria were measured by counting CFU and also by epifluorescence microscopy and PCR amplification of bacterial 16S-23S spacer ribosomal DNA to detect noncultivable bacteria . Removal of bacteria did not have any effect on the growth of the dinoflagellate except for the inhibition of A . catenella disintegration after reaching the stationary phase . Toxicity was determined in dinoflagellate cell extracts by different methods: high-performance liquid chromatography (HPLC); an electrophysiological test called the Electrotest, which measures the inhibition of saxitoxin-sensitive Na(+) channels expressed in a cell line; and a mouse bioassay, which measures the toxic effect on the whole mammal neuromuscular system . A lower toxicity of the dinoflagellates in axenic culture was observed by these three methods, though the difference was significant only by the mouse bioassay and HPLC methods . Altogether the results indicate that axenic cultures of A . catenella are able to produce toxin, though the total toxicity is probably diminished to about one-fifth of that in nonaxenic cultures.

Toxicology, 2002 Dec 27, 181-182, 255 - 60
Genetically-engineered bacteria expressing human enzymes and their use in the study of mutagens and mutagenesis; Josephy PD; Expression of human enzymes in bacterial cells has made possible the development of a new generation of mutagenicity assays . Metabolic activation takes place within the internal milieu of the target cell, so that no membrane barrier is interposed between the reactive metabolite and the DNA target . This technology has been extended to all major classes of enzymes of xenobiotic biotransformation, including P450 . Expression of sequence variants of mutagen-bioactivation enzymes provides a new tool for studying their structure and function.

J Gastrointest Surg, 2002 Nov-Dec, 6(6), 891 - 903; discussion 903-4
Pathogenesis of pigment gallstones in Western societies: the central role of bacteria; Stewart L et al.; Bacteria are traditionally accorded a greater role in pigment gallstone formation in Eastern populations . Stone color is thought to predict the presence of bacteria; that is, black stones (Western predominant) are supposedly sterile and brown stones (Eastern predominant) contain bacteria . We previously reported that, regardless of appearance, most pigment gallstones contain bacteria . This study examined, in a large Western population (370 patients), the incidence, appearance, and chemical composition of pigment stones, and the characteristics of gallstone bacteria . One hundred eighty-six pigment stones were obtained aseptically . Bacteria were detected by means of scanning electron microscopy and gallstone culture . Chemical composition was determined by infrared spectroscopy . Bacteria were tested for slime and beta-glucuronidase production . Seventy-three percent of pigment stones contained bacteria . Choledocholithiasis was associated with gallstone bacteria . Ca-bilirubinate was present in all pigment stones . Ca-palmitate was characteristic of infected stones, and more than 75% Ca-carbonate was characteristic of sterile stones . Neither chemical composition nor stone appearance predicted the presence of bacteria . Ninety-five percent and 67% of infected pigment stones contained bacteria that produced slime and beta-glucuronidase, respectively . Most pigment stones contained bacteria that produced beta-glucuronidase, slime, and phospholipase, factors that facilitate stone formation . Thus bacteria have a major role in Western pigment gallstone formation . Furthermore, gallstone color did not predict composition or bacterial presence.

J Gen Appl Microbiol, 1997 Apr, 43(2), 109 - 114
Effects of salinomycin and vitamin B(6) on the in vitro synthesis of lysine from the stereoisomers of 2,6-diaminopimelic acid by mixed rumen protozoa, bacteria, and their mixture; El-Waziry AM; An in vitro study was conducted to examine the effects of salinomycin (SL) and vitamin B(6) (pyridoxine hydrochloride) (B(6)) on the production of lysine from the three stereoisomers of 2,6-diaminopimelic acid (DAP-SI) by mixed rumen protozoa (P), mixed rumen bacteria (B), and their mixture (PB) . P, B, and PB were isolated from the rumen of goats given a concentrate mixture and lucerne cubes, separately incubated for 12 h with and without DAP-SI (5 mM) as a substrate and SL (5 &mgr;g/ml) and/or B(6) (10 &mgr;g/ml) as additives . In P suspensions, SL and B(6) reduced the amount of DAP-SI by 2.1 times (p<0.001, where p is probability) and 19.9% (p<0.05), respectively, and also increased the production of lysine by 2.4 times (p<0.001) and 26.8% (p <0.05), respectively, during 12 h incubation . In B suspensions, the reductions of DAP-SI with a single addition of SL or B(6) were 8.5% (p<0.001) and 2.7%, respectively, and lysine production increased by 54.3 and 32.9% (p<0.001), respectively, during 12 h incubation . In PB suspensions, the reductions of DAP-SI were 21.9 and 11.7% (p<0.001) with a single addition of SL or B(6), respectively, and the production of lysine increased by 81.4 and 39.4% (p<0.001), respectively, during 12 h incubation . When SL and B(6) were added together to the P, B, and PB suspensions, lysine production further increased by 12.3, 21.3, and 12.4% more than the cases of adding SL only during 12 h incubation, respectively . SL and B(6) were demonstrated to enhance the production of lysine from DAP-SI by mixed rumen protozoa, mixed rumen bacteria and their mixture in this study.

J Gen Appl Microbiol, 1997 Apr, 43(2), 89 - 95
Phylogenetic relationships of the helical-shaped bacteria in the alpha Proteobacteria inferred from 16S rDNA sequences; Kawasaki H et al.; 16S ribosomal RNA gene sequences from seven strains of Aquaspirillum peregrinum, Aqu . itersonii, Aqu . polymorphum, and Oceanospirillum pusillum were compared with homologous sequences from other members of helical-shaped bacteria . The bootstrapped neighbor-joining tree, inferred from 887 aligned sites, placed the spirillum taxa assigned to Aquaspirillum, Oceanospirillum, Azospirillum, Magnetospirillum, Rhodospirillum, and Rhodocista of the Proteobacteria in seven clusters of alpha Proteobacteria separately from other shapes of bacteria . Aqu . peregrinum and Aqu . itersonii grouped together in 88% bootstrap support . They were more related to Rhodospirillum rubrum and Rsp . photometricum than Aqu . polymorphum . Aqu . polymorphum was close to Magnetospirillum gryphiswaldense, Mag . magnetotacticum, Rsp . fulvum, and Rsp . molischianum, and more close to Mag . gryphiswaldense . Oce . pusillum was not related to other spirillum taxa and was placed in a separate branch . Rhodocista was very closely related to Azospirillum . Photosynthesis and magnetotaxis, as phenotypic characters, were not important in the classification of helical bacteria.

Biofizika, 2002 Nov-Dec, 47(6), 1059 - 63
{Conflict: induction-inhibition of transgene bacteria luminescence in studying expression of lux-genes}; Lesniak DV et al.; The relationship between the induction of the luminescent operon of lux-genes fused with the naphthalene and salicylate degradation genes and the inhibition of light emission caused by these compounds was studied . The quantitative correlations between these processes manifest themselves in the fact that light intensity linearly increased in a narrow concentration range of the inductor and then decreased due to the inhibition of the luminescence reaction itself, which is not related to the regulation of expression of lux-genes.

In Vivo, 2002 Nov-Dec, 16(6), 551 - 6
Bacteria-related spontaneous and therapeutic remission of human malignancies; Nagorsen D et al.; The development of specific immunotherapeutic approaches to cancer treatment is making progress . However, a crucial clinical break-through in cancer vaccination is still missing . Spontaneous clinical remissions of malignancies are a rare phenomenon . The mechanisms are not clear but there are remissions described in correlation with bacterial infections . The use of bacteria or bacterial components might be a promising path for non-specific immunotherapy of tumors and might be a helpful adjuvant for specific immunotherapy . Here, we briefly review spontaneous remissions of various malignancies in humans, the impact of bacterial infection on tumor regression and the utilization of bacterial components in clinical trials.

J Vet Med B Infect Dis Vet Public Health, 2002 Nov, 49(9), 415 - 8
Identification of acid fast bacteria from caseous lesions in cattle in Sudan; Sulieman MS et al.; One-hundred-and-twenty caseous lesions collected from slaughtered cattle at selected slaughterhouses in Sudan were processed for the detection of acid-fast bacteria (AFB) . Sixty-four of the 120 samples showed AFB on microscopic examination after staining with the Ziehl-Neelsen method . Accordingly, it was estimated that 64 (53.3%) of the 120 caseous (purulent) lesions among the samples were due to AFB whereas 56 (46.7%) were due to other causes . Growth on Lowenstein-Jensen slants was obtained in 54 of the 120 samples . The isolated AFB were tentatively identified using microscopic and cultural characteristics . Confirmation of the phenotypic clusters was achieved by analysing the mycolic acids contents and PCR-amplification of the IS6110 insertion sequences . The above two methods have allowed the identification of Mycobacterium bovis and M . farcinogenes, the major AFB isolated from cattle in Sudan . The remaining AFB, which were negative for the above two tests, were further identified by sequencing the 16S rRNA gene . The above strategy thus allowed the identification of the isolated strains as follows: 25 (46%) M . bovis; 21 (39.9%) M . farcinogenes; 4 (7.4%) M . tuberculosis; 1 (1.9%) M . avium; 1 (1.9%) Nocardia sp., 2 (3.7%) unidentified AFB . The isolation of M . farcinogenes and M . tuberculosis, from pulmonary lymph nodes represented important findings.

Zhonghua Fu Chan Ke Za Zhi, 2002 Oct, 37(10), 588 - 90
{Relationship between vaginal sialidase bacteria vaginosis and chorioammionitis}; Zhang X et al.; OBJECTIVE: To study the relationship among vaginal sialidase, bacterial vaginosis (BV), chorioammionitis and subsequent adverse outcome of pregnancy . METHODS: Vaginal sialidase was measured by colorimetry in samples of vaginal discharges from 80 pregnant women with BV (study group) and 60 normal pregnant women at same gestation weeks (control group) . Color turning blue means positive of sialidase activity, and no color changing means negative . The diagnosis of chorioammionitis was based on pathological examination . RESULTS: Ninety six dot three percent, 3.3% exhibited sialidase activities in study group and control group, respectively . There were significant differences between these two groups (P < 0.001) . By measuring vaginal sialidase activity, the sensitivity, specificity, positive and negative predictive value in diagnosing BV were 96.3%, 96.7%, 97.5% and 95.1%, respectively . Chorioammionitis, premature rupture of membranes, premature delivery and puerperal infection in sialidase positive group were significantly higher than the negative group . Sensitivity, specialty of sialidase activity for chorioammionitis were 87.5%, 50.0%, respectively . CONCLUSION: Vaginal sialidase activity has strong relation with bacterial vaginosis . Measuring vaginal sialidase activity is a fast, easy, and useful method to diagnose bacterial vaginosis . It also has relation with chorioammionitis and subsequent adverse outcome of pregnancy.

J Contam Hydrol, 2002 Dec, 59(3-4), 267 - 89
Contaminant transport in dual-porosity media with dissolved organic matter and bacteria present as mobile colloids; Kim SB et al.; In riverbank filtration, contaminant transport is affected by colloidal particles such as dissolved organic matter (DOM) and bacterial particles . In addition, the subsurface heterogeneity influences the behavior of contaminant transport in riverbank filtration . A mathematical model is developed to describe the contaminant transport in dual-porosity media in the presence of DOM and bacteria as mobile colloids . In the model development, a porous medium is divided into the mobile and immobile regions to consider the presence of ineffective micropores in physically heterogeneous riverbanks . We assume that the contaminant transport in the mobile region is controlled by the advection and dispersion while the contaminant transport in the immobile region occurs due to the molecular diffusion . The contaminant transfer between the mobile and immobile regions takes place by diffusive mass transfer . The mobile region is conceptualized as a four-phase system: two mobile colloidal phases, an aqueous phase, and a solid matrix . The complete set of governing equations is solved numerically with a fully implicit finite difference method . The model results show that in riverbank filtration, the contaminant can migrate further than expected due to the presence of DOM and bacteria . In addition, the contaminant mobility increases further in the presence of the immobile region in aquifers . A sensitivity analysis shows that in dual-porosity media, earlier breakthrough of the contaminant takes place as the volumetric fraction of the mobile region decreases . It is also demonstrated that as the contaminant mass transfer rate coefficient between the mobile and immobile regions increases, the contaminant concentration gradient between the two regions reverses at earlier pore volumes . The contaminant mass transfer coefficient between the mobile and immobile regions mainly controls the tailing effect of the contaminant breakthrough . The contaminant breakthrough curves are sensitive to changes in contaminant adsorption and desorption rate coefficients on DOM and bacteria . In situations where the contaminant is released in the presence of DOM and bacteria in dual-porosity media, the early breakthrough and tailing occur due to the colloidal facilitation and presence of immobile regions.

J Gen Appl Microbiol, 2001 Aug, 47(4), 161 - 180
Aerobic anoxygenic photosynthetic bacteria with zinc-bacteriochlorophyll; Hiraishi A et al.; Naturally occurring chlorophyllous pigments, which function as the cofactor in the early photochemical reaction of photosynthesis, have been proven beyond question to be magnesium-complexed porphyrin derivatives . Phototrophic organisms that use (bacterio)chlorophylls ({B}Chls) containing metals other than Mg were unknown for a long time . This common knowledge of natural photosynthesis has recently been modified by the striking finding that a novel purple pigment, zinc-chelated-BChl (Zn-BChl) a, is present as the major and functional pigment in species of the genus Acidiphilium . Acidiphilium species are obligately acidophilic chemoorganotrophic bacteria that grow and produce photopigments only under aerobic conditions . Although the mechanism of photosynthesis with Zn-BChl a in Acidiphilium species is similar to that seen in common purple bacteria, some characteristic photosynthetic features of the acidophilic bacteria are also found . The discovery of natural photosynthesis with Zn-BChl has not only provided a new insight into our understanding of bacterial photosynthesis but also raised some interesting questions to be clarified . The major questions are why the acidophilic bacteria have selected Zn-BChl for their photosynthesis and how they synthesize Zn-BChl and express photosynthetic activity with it in their natural habitats . In this article we review the current knowledge of the biology of Acidiphilium as aerobic photosynthetic bacteria with Zn-BChl a and discuss the interesting topics noted above.

J Gen Appl Microbiol, 2000 Jun, 46(3), 119 - 125
Activity and properties of fumarate reductase in ruminal bacteria; Asanuma N et al.; Fumarate-reducing bacteria were sought from the main ruminal bacteria . Fibrobacter succinogenes, Selenomonas ruminantium subsp . ruminantium, Selenomonas ruminantium subsp . lactilytica, and Veillonella parvula reduced fumarate by using H(2) as an electron donor . Ruminococcus albus, Prevotella ruminicola, and Anaerovibrio lipolytica consumed fumarate, although they did not oxidize H(2) . Of these bacteria, V . parvula, two strains of Selenomonas, and F . succinogenes had a high capacity to reduce fumarate . In all the fumarate-reducing bacteria examined, fumarate reductase existed in the membrane fraction . Based on the activity per cell mass and the affinity of fumarate reductase to fumarate, these bacteria were divided into two groups, which corresponded to the capacity to use H(2): A group of bacteria with higher activity and affinity were able to use H(2) as an electron donor for fumarate reduction . The bacteria in this group should gain an advantage over the bacteria in another group in fumarate reduction in the rumen . Cellulose digestion by R . albus was improved by fumarate reduction by S . lactilytica as a result of an increased growth of R . albus, which may have been caused by the fact that S . lactilytica immediately consumed H(2) produced by R . albus . Thus fumarate reduction may play an important role in keeping a low partial pressure of H(2) in the rumen.

Cell Mol Life Sci, 2002 Oct, 59(10), 1607 - 16
Protein folding and degradation in bacteria: to degrade or not to degrade? That is the question; Dougan DA et al.; In Escherichia coli protein quality control is carried out by a protein network, comprising chaperones and proteases . Central to this network are two protein families, the AAA+ and the Hsp70 family . The major Hsp70 chaperone . DnaK, efficiently prevents protein aggregation and supports the refolding of damaged proteins . In a special case, DnaK, together with the assistance of the AAA+ protein ClpB, can also refold aggregated proteins . Other Hsp70 systems have more specialized functions in the cell, for instance HscA appears to be involved in the assembly of Fe/S proteins . In contrast to ClpB, many AAA+ proteins associate with a peptidase to form proteolytic machines which remove irreversibly damaged proteins from the cellular pool . The AAA+ component of these proteolytic machines drives protein degradation . They are required not only for recognition of the substrate but also for substrate unfolding and translocation into the proteolytic chamber . In many cases, specific adaptor proteins modify the substrate binding properties of AAA+ proteins . While chaperones and proteases do not appear to directly cooperate with each other, both systems appear to be necessary for proper functioning of the cell and can, at least in part, substitute for one another.

Science, 2002 Dec 6, 298(5600), 1980 - 4
Regulation of oceanic silicon and carbon preservation by temperature control on bacteria; Bidle KD et al.; We demonstrated in laboratory experiments that temperature control of marine bacteria action on diatoms strongly influences the coupling of biogenic silica and organic carbon preservation . Low temperature intensified the selective regeneration of organic matter by marine bacteria as the silicon:carbon preservation ratio gradually increased from approximately 1 at 33 degrees C to approximately 6 at -1.8 degrees C . Temperature control of bacteria-mediated selective preservation of silicon versus carbon should help to interpret and model the variable coupling of silicon and carbon sinking fluxes and the spatial patterns of opal accumulation in oceanic systems with different temperature regimes.

Mol Phylogenet Evol, 2003 Jan, 26(1), 82 - 8
Phylogenetic analysis of Blattabacterium, endosymbiotic bacteria from the wood roach, Cryptocercus (Blattodea: Cryptocercidae), including a description of three new species; Clark JW et al.; Members of the cockroach genus Cryptocercus are wood-feeding, subsocial insects that live in temperate forests of the Nearctic and Palaearctic . At present, nine species are recognized: Cryptocercus relictus and Cryptocercus kyebangensis in eastern Asia and Russia, Cryptocercus primarius and Cryptocercus matilei in southwestern China, Cryptocercus clevelandi in the western USA, and Cryptocercus darwini, Cryptocercus garciai, Cryptocercus punctulatus, and Cryptocercus wrighti in the eastern USA . Like all extant cockroaches, Cryptocercus harbor endosymbiotic bacteria, Blattabacterium, in their fat bodies . The endosymbionts in all cockroaches have been considered a single species, Blattabacterium cuenoti, since their discovery about a century ago . However, a recent analysis of DNA sequences from representatives of four cockroach families has indicated that there is considerable DNA sequence divergence among B . cuenoti from different host species . As a part of our studies on the evolution of Cryptocercus, we examined DNA sequence divergence among B . cuenoti from six of the nine known Cryptocercus species . Specifically, we sequenced approximately 2,400 bp of the 16S rRNA and 23S rRNA genes of B . cuenoti from six species of Cryptocercus . We found that B . cuenoti in Cryptocercus has differentiated into multiple monophyletic lineages distinguishable by DNA sequence of rRNA genes and host association . Our sequence divergence estimates were consistent with those reported for other, congeneric bacterial species . We propose the recognition of three new species of Blattabacterium within Cryptocercus species as follows: Blattabacterium relictus sp . nov . in C . relictus, Blattabacterium clevelandi sp . nov . in C . clevelandi, and Blattabacterium punctulatus sp . nov . in C . darwini, C . garciai, C . punctulatus, and C . wrighti.

J Endod, 2002 Nov, 28(11), 779 - 83
The effectiveness of increased apical enlargement in reducing intracanal bacteria; Card SJ et al.; It has been suggested that the apical portion of a root canal is not adequately disinfected by typical instrumentation regimens . The purpose of this study was to determine whether instrumentation to sizes larger than typically used would more effectively remove culturable bacteria from the canal . Forty patients with clinical and radiographic evidence of apical periodontitis were recruited from the endodontic clinic . Mandibular cuspids (n = 2), bicuspids (n = 11), and molars (mesial roots) (n = 27) were selected for the study . Bacterial sampling was performed upon access and after each of two consecutive instrumentations . The first instrumentation utilized 1% NaOCI and 0.04 taper ProFile rotary files . The cuspid and bicuspid canals were instrumented to a #8 size and the molar canals to a #7 size . The second instrumentation utilized LightSpeed files and 1% NaOCl irrigation for further enlargement of the apical third . Typically, molars were instrumented to size 60 and cuspid/bicuspid canals to size 80 . Our findings show that 100% of the cuspid/bicuspid canals and 81.5% of the molar canals were rendered bacteria-free after the first instrumentation sizes . The molar results improved to 89% after the second instrumentation . Of the (59.3%) molar mesial canals without a clinically detectable communication, 93% were rendered bacteria-free with the first instrumentation . Using a Wilcoxon rank sum test, statistically significant differences (p < 0.0001) were found between the initial sample and the samples after the first and second instrumentations . The differences between the samples that followed the two instrumentation regimens were not significant (p = 0.0617) . It is concluded that simple root canal systems (without multiple canal communications) may be rendered bacteria-free when preparation of this type is utilized.

Microbes Infect, 2002 Oct, 4(12), 1259 - 64
Neutrophil elastase-mediated killing of bacteria: lessons from targeted mutagenesis; Belaaouaj A; Engineering of mice deficient in neutrophil elastase (NE) has allowed us to demonstrate the role of this protease in host defense against bacteria and to begin to understand its killing mechanism . Strategies to inhibit NE because of its involvement in tissue-destructive diseases should be reconsidered, while preserving its beneficial properties.

J Biol Chem, 2003 Feb 7, 278(6), 3921 - 8 Epub 2002 Dec 02.
Chimeric photosynthetic reaction center complex of purple bacteria composed of the core subunits of Rubrivivax gelatinosus and the cytochrome subunit of Blastochloris viridis; Maki H et al.; A gene coding for the photosynthetic reaction center-bound cytochrome subunit, pufC, of Blastochloris viridis, which belongs to the alpha-purple bacteria, was introduced into Rubrivivax gelatinosus, which belongs to the beta-purple bacteria . The cytochrome subunit of B . viridis was synthesized in the R . gelatinosus cells, in which the native pufC gene was knocked out, and formed a chimeric reaction center (RC) complex together with other subunits of R . gelatinosus . The transformant was able to grow photosynthetically . Rapid photo-oxidization of the hemes in the cytochrome subunit was observed in the membrane of the transformant . The soluble electron carrier, cytochrome c(2), isolated from B . viridis was a good electron donor to the chimeric RC . The redox midpoint potentials and the redox difference spectra of four hemes in the cytochrome subunit of the chimeric RC were almost identical with those in the B . viridis RC . The cytochrome subunit of B . viridis seems to retain its structure and function in the R . gelatinosus cell . The chimeric RC and its mutagenesis system should be useful for further studies about the cytochrome subunit of B . viridis.

Cell, 2002 Nov 27, 111(5), 611 - 3
The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria; Dreyfus M et al.; In eukaryotes, poly(A) tails usually act as stabilizers of intact mRNAs, whereas in E . coli they serve to accelerate the destruction of fragments . The mechanisms underlying these contrasting effects of the same RNA modification are discussed.

Anal Chem, 2002 Nov 15, 74(22), 5807 - 13
Automated postprocessing of electrospray LC/MS data for profiling protein expression in bacteria; Williams TL et al.; We describe an integrated approach for automating protein analysis of bacterial cell extracts . The method uses electrospray LC/MS to generate chromatographic profiles of proteins present in an extract, along with a software program that automates the data analysis . The software program, Retana, automates the sequential summing, centroiding, and deconvolution of multiply charged proteins present in consecutive scans of the LC/MS analysis . This procedure generates a concise, single spectrum of proteins present in the extract, along with their retention time and relative abundance . A comparison of the method with "whole cell" MALDI analysis demonstrates improved mass resolution and mass accuracy, along with the appearance of a greater number of proteins . Additionally, it is possible to compare protein expression among strains of bacteria by normalizing the relative abundance of similar proteins in each analysis.

Biochim Biophys Acta, 2002 Dec 2, 1556(2-3), 247 - 53
Rhodopseudomonas acidophila strain 10050 contains photosynthetic LH2 antenna complexes that are not enriched with phosphatidylglycerol, and the phospholipids have a fatty acyl composition that is unusual for purple non-sulfur bacteria; Russell NJ et al.; The phospholipid composition of Rhodopseudomonas acidophila strain 10050 grown aerobically or anaerobically in the light was determined . The major phospholipids present in the aerobic cells were phosphatidylethanolamine (PE; 54%), phosphatidylglycerol (PG; 24%) and cardiolipin (diphosphatidylglycerol, DPG) (14%), together with phosphatidylcholine (PC; 5%) . On moving the cells to anaerobic photosynthetic growth in the light PE remained the major phospholipid (37-49%), but there was a major change in the proportion of PC, which increased to 31-33%, and corresponding reductions in the contents of PG to 11-16% and DPG to 4-5% . The fatty acid composition of the phospholipids was unusual, compared with other purple non-sulfur photosynthetic bacteria, in that it contained 16:0 (29%), 17:1 (20%) and 19:1 (9%) plus several mainly unsaturated 2-OH fatty acids (9% total) as major components, when grown aerobically in the dark . In contrast when grown photosynthetically under anaerobic conditions there was <2% 17:1 or 19:1 present, while the amounts of 16:1 and 18:1 increased, and 16:0 decreased . The phospholipid composition of the purified light-harvesting complex 2 (LH2) complex was PE (43%), PC (42%) and DPG (15%) . Unexpectedly, there was no PG associated with the purified LH2 . These findings contrast with previous studies on several other photosynthetic bacteria, which had shown an increase in PG upon photosynthetic growth {Biochem . J . 181 (1979) 339} . The prior hypothesis that phosphatidylglycerol has some specific role to play in the function of light-harvesting complexes cannot be true for Rps . acidophila . It is suggested that specific integral membrane proteins may strongly influence the phospholipid content of the host membranes into which they are inserted.

J Microbiol Methods, 2003 Feb, 52(2), 245 - 50
A simple method for DNA extraction from marine bacteria that produce extracellular materials; Lee YK et al.; We present a simple method for extracting DNA from the marine bacteria Hahella chejuensis, a Streptomyces sp., and a Cytophaga sp . Previously, DNA purification from these strains was hindered by the presence of extracellular materials . In our extraction method, the marine bacteria are lysed by freezing and grinding in liquid nitrogen, and treated with SDS . The extracted DNA is purified using a phenol/chloroform mixture, and precipitated in isopropanol . The extracted DNA is of high quality and suitable for molecular analyses, such as PCR, restriction enzyme digestion, genomic DNA blot hybridization, and genomic DNA library construction . We used this method to extract genomic DNA from several other marine bacteria . Our method is a reproducible, simple, and rapid technique for routine DNA extractions from marine bacteria . Furthermore, the low cost of this method makes it attractive for large-scale studies .

Curr Opin Microbiol, 2002 Dec, 5(6), 596 - 601
Aging in bacteria; Nystrom T; Analysis of senescent Escherichia coli cells reveals a link between protein oxidation and the fidelity of the translational apparatus . This model system has also provided a mechanistic molecular explanation for a trade-off between reproduction and survival activities, which may inspire proponents of the disposable soma theory and antagonistic pleiotropy hypothesis of aging.

Curr Opin Microbiol, 2002 Dec, 5(6), 548 - 52
Dynamic proteins in bacteria; Lutkenhaus J; Growth of the bacterial cell involves proteins that assemble into dynamic localized structures that are required for cellular morphogenesis and division . During the past year, the continued application of fluorescence microscopy has led to the discovery of novel actin-like filaments involved in cell shape and plasmid DNA segregation, and to new insights into the regulation and dynamics of the Z-ring . Studies on the Min proteins, which rapidly oscillate between the cell poles to spatially regulate Z-ring assembly, has led to a biochemical basis for the oscillation and a suggestion that MinD assembles into dynamic filaments . These studies further demonstrate that the eukaryotic cytoskeleton had its origins in bacteria.

Biol Chem, 2002 Oct, 383(10), 1565 - 72
YidC, a newly defined evolutionarily conserved protein, mediates membrane protein assembly in bacteria; Chen M et al.; Membranes contain proteins that catalyze a variety of reactions, which lead to the selective permeability of the membrane . For membrane proteins to function as receptors, transporters, channels, and ATPases, they must be targeted to their correct membrane and inserted into the lipid bilayer . Recently, a new membrane component called YidC was discovered that mediates the insertion of proteins into membranes in bacteria . YidC homologs also exist in mitochondria and chloroplasts . Depletion of YidC from the cell interferes with the insertion of membrane proteins that insert both dependent and independent of the SecYEG/SecDFYajC machinery . YidC directly interacts with membrane proteins during the membrane protein insertion process and assists in the folding of the hydrophobic regions into the membrane bilayer . The chloroplast and bacterial YidC homologs are truly functional homologs because the chloroplast homolog Alb3 functionally complements the bacterial YidC depletion strain . The role of YidC in the membrane insertion pathway will be reviewed.

Appl Environ Microbiol, 2002 Dec, 68(12), 6202 - 9
Response of ants to a deterrent factor(s) produced by the symbiotic bacteria of entomopathogenic nematodes; Zhou X et al.; The production of an ant-deterrent factor(s) (ADF) by Xenorhabdus nematophila and Photorhabdus luminescens, the symbiotic bacteria of the nematodes Steinernema carpocapsae and Heterorhabditis bacteriophora, respectively, was examined . In addition to an in vivo assay in which bacteria were tested for their ability to produce ADF within insect cadavers (M.E . Baur, H . K . Kaya, and D . R . Strong, Biol . Control 12:231-236, 1998), an in vitro microtiter dish assay was developed to monitor ADF activity produced by bacteria grown in cultures . Using these methods, we show that ADF activity is present in the supernatants of bacterial cultures, is filterable, heat stable, and acid sensitive, and passes through a 10-kDa-pore-size membrane . Thus, ADF appears to be comprised of a small, extracellular, and possibly nonproteinaceous compound(s) . The amount of ADF repellency detected depends on the ant species being tested, the sucrose concentration (in vitro assays), and the strain, form, and age of the ADF-producing bacteria . These findings demonstrate that the symbiotic bacteria of some species of entomopathogenic nematodes produce a compound(s) that deters scavengers such as ants and thus could protect nematodes from being eaten during reproduction within insect cadavers.

Mikrobiologiia, 2002 Sep-Oct, 71(5), 681 - 9
{Utilization of methane and carbon dioxide by symbiotrophic bacteria in gills of Mytilidae (Bathymodiolus) from the Rainbow and Logachev hydrothermal fields on the Mid-Atlantic Ridge}; Pimenov NV et al.; Bivalve mollusks Bathymodiolus asoricus and Bathymodiolus puteoserpentis collected from the Rainbow and Logachev hydrothermal fields during dives of Mir 1 and Mir 2 deep-sea manned submersibles were studied . Rates of methane oxidation and carbon dioxide assimilation in mussel gill tissue were determined by radiolabel analysis . During oxidation of 14Ch4, radiocarbon was detected in significant quantities not only in carbon dioxide but also in dissolved organic matter, most notably 14C-formate and 14C-acetate, occurring in a 2:1 ratio . Activities of hexulose-phosphate synthase, phosphoribulokinase, and ribulose 1,5-bisphosphate carboxylase were shown in the soluble fraction of gill tissue cells . At the same time, no activity of hydroxypyruvate reductase--the key enzyme of the serine pathway of C1-assimilation--was detected . The results of PCR amplification using genetic probes for membrane-bound methane monooxygenase (pmoA) and methanol dehydrogenase (mxaF) attest to the presence of the genes of these enzymes in the total DNA extracted from gill samples . However, no appropriate PCR responses were obtained with the mmoX primer system, which is a marker for soluble methane monooxygenase . All samples studied showed amplification with primers for the genera Methylobacter and Methylosphaera . At the same time, no genes specific to the genera Methylomonas, Methylococcus, Methylomicrobium, or Methylosinus and Methylocystis were detected . Electron microscopic examinations revealed the presence of two groups of endosymbiotic bacteria in the mussel gill tissue . The first group was represented by large cells possessing a complex system of cytoplasmic membranes, typical of methanotrophs of morphotype I . The other type of endosymbionts, having much smaller cells and lacking intracellular membrane structures, is likely to be constituted by sulfur bacteria.

Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 413 - 34
Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria; Jurgens K et al.; Predation is a major mortality factor of planktonic bacteria and an important shaping force for the phenotypic and taxonomic structure of bacterial communities . In this paper we: (1) summarise current knowledge on bacterial phenotypic properties which affect their vulnerability towards grazers, and (2) review experimental evidence demonstrating that this phenotypic heterogeneity results in shifts of bacterial community composition during enhanced protist grazing pressure . Size-structured interactions are especially important in planktonic systems and bacterial cell size influences the mortality rate and the type of grazer to which bacteria are most susceptible . When protists are the major bacterivores, both very small and large bacterial cells gain some size refuge . Recent studies have revealed that also various non-morphological traits such as motility, physicochemical surface characters and toxicity affect bacterial vulnerability and protist feeding success . These properties are effective at different stages during the feeding process of interception feeding flagellates (encounter, capture, ingestion, digestion) . Grazing-resistant bacteria in natural communities can account for a substantial portion of the total bacterial biomass at least in more productive aquatic systems . In field and laboratory experiments it has been demonstrated that increased protozoan grazing results in shifts in the phenotypic and genotypic composition of the bacterial assemblage . The importance of this shaping force for the bacterial community structure depends, however, on the overall food web structure, especially on the composition of the metazooplankton . Whereas the structuring impact of bacterial grazers is well documented, relatively little is known about how grazing-mediated changes in bacterial communities influence microbially mediated processes and biogeochemically important transformations.

Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 3 - 13
Defences against oxidative stress during starvation in bacteria; McDougald D et al.; It now seems clear that starvation adaptation is important for cells to initiate long-term survival under conditions of not only nutrient depletion but to develop resistance to other stresses, most notably oxidative stress . Clearly, oxidative stress is a condition likely to be perceived by many bacteria, for example, in the form of reactive oxygen species derived from metabolic processes or from near-UV exposure . We have found evidence for a large degree of overlap in the cell's use of global regulators to deal with both starvation and oxidative stress . Both SpoT and AI-2 signalling pathways are important regulators of starvation and stress adaptation as well as the alternative sigma factor, RpoE . We also present evidence that suggests that AI-2 signalling can mediate starvation adaptation at the molecular level by increasing the stability of the mRNAs so that cells are prepared for rapid response to nutrient addition . Moreover, such extracellular signals mediate intraspecies communication to enable enhanced survival and stress resistance of neighbouring bacterial cells . It is likely that bacteria rely on a suite of effects between cells and on transcription, translation and post-translationalprocesses, mediated by global regulators and signalling molecules, to meet their needs for growth and survival.

Proc Natl Acad Sci U S A, 2002 Dec 10, 99(25), 16243 - 8 Epub 2002 Nov 22.
The membrane protein FeoB contains an intramolecular G protein essential for Fe(II) uptake in bacteria; Marlovits TC et al.; G proteins are critical for the regulation of membrane protein function and signal transduction . Nevertheless, coupling between G proteins and membrane proteins with multiple membrane-spanning domains has so far been observed only in higher organisms . Here we show that the polytopic membrane protein FeoB, which is essential for Fe(II) uptake in bacteria, contains a guanine-nucleotide-specific nucleotide binding site . We identify the G4-motif, NXXD, responsible for guanine nucleotide specificity, and show that GTP hydrolysis occurs very slowly . In contrast to typical G proteins, the association and dissociation of GDP were found to be faster than for GTP, suggesting that in the absence of additional factors, FeoB's G protein domain may exist mostly in the GTP-bound form . Furthermore, the binding of GTP is required for efficient Fe(II) uptake through the FeoB-dependent system . Notably, even in bacteria, this covalent linkage between a G protein and a polytopic membrane protein appears, to our knowledge, to be unique . These findings raise the intriguing question whether FeoB represents a primordial archetype of G protein-regulated membrane proteins.

Genes Genet Syst, 2002 Oct, 77(5), 369 - 76
Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria supported by the newly clarified origin of functional genes; Horiike T et al.; In the previous report, we demonstrated the origin of eukaryotic cell nuclei as the symbiosis of Archaea in Bacteria by the newly developed "Homology-Hit Analysis" . In that case, we counted yeast Open Reading Frames (ORFs) showing the highest similarity to a bacterial ORF as orthologous ORFs (Orthologous ORFs were produced by speciation from a common ancestor, and have the highest similarity to each other.) by comparing whole ORFs of yeast with those of individual bacteria . However, we could not count all yeast ORFs showing the highest similarity to a bacterial ORF in functional categories of yeast . Therefore, the origin of ORFs in the functional categories of yeast could not be inferred strictly . Here, we have improved the method for detecting orthologous ORFs . In this method, we count the numbers of ORF with the highest similarity between individual yeast functional categories and individual bacteria as orthologous ORFs . By this method, it was possible to detect the correct orthologous ORFs and to infer the origins of the functional categories in eukaryotic cells . As a result, two categories, assembly of protein complexes and DNA repair were newly judged to be of Archaeal origin, while five categories, lipid (fatty-acid and isoprenoid) metabolism, protein folding and stabilization, signal transduction, organization of the plasma membrane and organization of the cytoplasm, were newly judged to be of Bacterial origin . On the other hand, the origins of two categories (meiosis and cellular import, which were determined in the previous analysis) could not be judged . It is considered that functional categories related to the nucleus have origins common to Archaea, while those related to the cytoplasm have origins common to Bacteria . From these data including the origin of plasma membrane, it was further clarified that cell nucleus originated by the symbiosis of Archaea in Bacteria.

Biomed Eng Online . 2002 Oct 16;1(1):4.
Bacteria classification using Cyranose 320 electronic nose; Dutta R et al.; BACKGROUND: An electronic nose (e-nose), the Cyrano Sciences' Cyranose 320, comprising an array of thirty-two polymer carbon black composite sensors has been used to identify six species of bacteria responsible for eye infections when present at a range of concentrations in saline solutions . Readings were taken from the headspace of the samples by manually introducing the portable e-nose system into a sterile glass containing a fixed volume of bacteria in suspension . Gathered data were a very complex mixture of different chemical compounds . METHOD: Linear Principal Component Analysis (PCA) method was able to classify four classes of bacteria out of six classes though in reality other two classes were not better evident from PCA analysis and we got 74% classification accuracy from PCA . An innovative data clustering approach was investigated for these bacteria data by combining the 3-dimensional scatter plot, Fuzzy C Means (FCM) and Self Organizing Map (SOM) network . Using these three data clustering algorithms simultaneously better 'classification' of six eye bacteria classes were represented . Then three supervised classifiers, namely Multi Layer Perceptron (MLP), Probabilistic Neural network (PNN) and Radial basis function network (RBF), were used to classify the six bacteria classes . RESULTS: A {6 x 1} SOM network gave 96% accuracy for bacteria classification which was best accuracy . A comparative evaluation of the classifiers was conducted for this application . The best results suggest that we are able to predict six classes of bacteria with up to 98% accuracy with the application of the RBF network . CONCLUSION: This type of bacteria data analysis and feature extraction is very difficult . But we can conclude that this combined use of three nonlinear methods can solve the feature extraction problem with very complex data and enhance the performance of Cyranose 320.

Naturwissenschaften, 2002 Aug, 89(8), 366 - 70 Epub 2002 Jul 12.
Is the contribution of bacteria to terrestrial carbon budget greatly underestimated?
Braissant O, Verrecchia EP, Aragno M.
Some commonly found species of soil bacteria use low molecular weight organic acids as their sole source of carbon and energy . This study shows that acids such as citrate and oxalate (produced in large amounts by fungi and plants) can rapidly be consumed by these bacteria . Two strains, Ralstonia eutropha and Xanthobacter autotrophicus, were cultured on acetate- and citrate-rich media . The resulting CO2 and/or HCO3- reacted with calcium ions to precipitate two polymorphs of calcium carbonate (CaCO3), calcite and vaterite, depending on the quantity of slime produced by the strains . This production of primary calcium carbonate crystals by oxalate- and citrate-degrading bacteria from soil organic carbon sources highlights the existence of an important and underestimated potential carbon sink.

Annu Rev Genet, 2002, 36, 47 - 73 Epub 2002 Jun 11.
Genetics of motility and chemotaxis of a fascinating group of bacteria: the spirochetes; Charon NW et al.; Spirochetes are a medically important and ecologically significant group of motile bacteria with a distinct morphology . Outermost is a membrane sheath, and within this sheath is the protoplasmic cell cylinder and subterminally attached periplasmic flagella . Here we address specific and unique aspects of their motility and chemotaxis . For spirochetes, translational motility requires asymmetrical rotation of the two internally located flagellar bundles . Consequently, they have swimming modalities that are more complex than the well-studied paradigms . In addition, coordinated flagellar rotation likely involves an efficient and novel signaling mechanism . This signal would be transmitted over the length of the cell, which in some cases is over 100-fold greater than the cell diameter . Finally, many spirochetes, including Treponema, Borrelia, and Leptospira, are highly invasive pathogens . Motility is likely to play a major role in the disease process . This review summarizes the progress in the genetics of motility and chemotaxis of spirochetes, and points to new directions for future experimentation.

J Ethnopharmacol, 2002 Dec, 83(3), 219 - 28
Evaluation of selected Sudanese medicinal plants for their in vitro activity against hemoflagellates, selected bacteria, HIV-1-RT and tyrosine kinase inhibitory, and for cytotoxicity; Ali H et al.; Ethnobotanical investigations led to the selection of 19 plant species, used traditionally in Sudan against malaria and other similar tropical diseases, for further studies . Pamianthe peruviana (Amaryllidaceae) exhibited significant activity against a chloroquine-resistant Plasmodium falciparum strain (K1) and a chloroquine-sensitive strain (NF54) with IC(50) values of 0.6 and 1.1 microg/ml, respectively . Additionally, P . peruviana showed considerable activities against Trypanosoma brucei rhodesiense (IC(50) 1.5 microg/ml) and T . cruzi (IC(50) 11.8 microg/ml) . The antiplasmodial activity of the different extracts of Salvadora persica (Salvadoraceae) against P . falciparum NF54 strain were found to be 0.6 microg/ml (stems) and 0.7 microg/ml (leaves) . Extracts of different parts of Combretum hartmannianum (Combretaceae) possessed significant activity against the chloroquine-sensitive P . falciparum strain (NF54) with IC(50) values of 0.2 microg/ml (bark), 0.4 microg/ml (stem) and 4.3 microg/ml (leaves) . Most interestingly, the extracts of the leaves of C . hartmannianum totally inhibited the enzyme HIV-1 reverse transcriptase (HIV-1 RT) at a concentration of 66 microg/ml . A comparably strong activity against p56(lck) tyrosine kinase was also seen for this extract.

FEMS Microbiol Lett, 2002 Oct 29, 216(1), 61 - 6
Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria; Taylor PM et al.; Primers were designed and successfully used to screen aromatic hydrocarbon-degrading bacteria for the presence of class II aromatic ring-hydroxylating dioxygenase (RHD) genes and to amplify novel RHD genes from DNA extracted from soil using the polymerase chain reaction . Two previously undiscovered groups of genes encoding putative class II RHDs, designated the S and T clusters, were found in RHD different soil samples . Only one of 70 RHD gene fragments amplified from these soil samples could be assigned to a cluster of previously reported RHD genes . These results suggest that distinct and potentially numerically dominant groups of as-yet unrecognized aromatic hydrocarbon-degrading bacteria exist in soils.

Arch Microbiol, 2002 Dec, 178(6), 554 - 8 Epub 2002 Sep 28.
Inducible aluminum resistance of Acidiphilium cryptum and aluminum tolerance of other acidophilic bacteria; Fischer J et al.; Aluminum ions are highly soluble in acidic environments . Toxicity of aluminum ions for heterotrophic, facultatively and obligately chemolithoautotrophic acidophilic bacteria was examined . Acidiphilium cryptum grew in glucose-mineral medium, pH 3, containing 300 mM aluminum sulfate {Al(2)(SO(4))(3)} after a lag phase of about 120 h with a doubling time of 7.6 h, as compared to 5.2 h of growth without aluminum . Precultivation with 1 mM Al(2)(SO(4))(3) and transfer to a medium with 300 mM Al(2)(SO(4))(3) reduced the lag phase from 120 to 60 h, and immediate growth was observed when A . cryptum was precultivated with 50 mM Al(2)(SO(4))(3), suggesting an aluminum-induced resistance . Aluminum resistance was not induced by Fe(3+) ions and divalent cations . Upon exposure of A . cryptum to 300 mM Al(2)(SO(4))(3), the protein profile changed significantly as determined by SDS-PAGE . When other acidophiles were cultivated with 50-200 mM aluminum sulfate, no lag phase was observed while the growth rates and the cellular yields were significantly reduced . This growth response was observed with Acidobacterium capsulatum, Acidiphilium acidophilum, Acidithiobacillus ferrooxidans, and Acidithiobacillus thiooxidans . Precultivation of these strains with aluminum ions did not alter the growth response caused by aluminum . The content of A . cryptum cultivated with 300 mM Al(2)(SO(4))(3)was 0.44 microg Al/mg cell dry weight, while that of the other strains cultivated with 50 mM Al(2)(SO(4))(3) ranged from 0.30 to 3.47 microg Al/mg cell dry weight.

Biophys J, 2002 Nov, 83(5), 2440 - 56
Spin-lattice relaxation of coupled metal-radical spin-dimers in proteins: application to Fe(2+)-cofactor (Q(A)(-.), Q(B)(-.), phi(-.)) dimers in reaction centers from photosynthetic bacteria; Calvo R et al.; The spin-lattice relaxation times (T(1)) for the reduced quinone acceptors Q(A)(-.) and Q(B)(-.), and the intermediate pheophytin acceptor phi(-.), were measured in native photosynthetic reaction centers (RC) containing a high spin Fe(2+) (S = 2) and in RCs in which Fe(2+) was replaced by diamagnetic Zn(2+) . From these data, the contribution of the Fe(2+) to the spin-lattice relaxation of the cofactors was determined . To relate the spin-lattice relaxation rate to the spin-spin interaction between the Fe(2+) and the cofactors, we developed a spin-dimer model that takes into account the zero field splitting and the rhombicity of the Fe(2+) ion . The relaxation mechanism of the spin-dimer involves a two-phonon process that couples the fast relaxing Fe(2+) spin to the cofactor spin . The process is analogous to the one proposed by R . Orbach (Proc . R . Soc . A . (Lond.) . 264:458-484) for rare earth ions . The spin-spin interactions are, in general, composed of exchange and dipolar contributions . For the spin dimers studied in this work the exchange interaction, J(o), is predominant . The values of J(o) for Q(A)(-.)Fe(2+), Q(B)(-.)Fe(2+), and phi(-.)Fe(2+) were determined to be (in kelvin) -0.58, -0.92, and -1.3 x 10(-3), respectively . The |J(o)| of the various cofactors (obtained in this work and those of others) could be fitted with the relation exp(-beta(J)d), where d is the distance between cofactor spins and beta(J) had a value of (0.66-0.86) A(-1) . The relation between J(o) and the matrix element |V(ij)|(2) involved in electron transfer rates is discussed.

Appl Environ Microbiol, 2002 Nov, 68(11), 5625 - 33
Bacteria belonging to the genus cycloclasticus play a primary role in the degradation of aromatic hydrocarbons released in a marine environment; Kasai Y et al.; To identify the bacteria that play a major role in the aerobic degradation of petroleum polynuclear aromatic hydrocarbons (PAHs) in a marine environment, bacteria were enriched from seawater by using 2-methylnaphthalene, phenanthrene, or anthracene as a carbon and energy source . We found that members of the genus Cycloclasticus became predominant in the enrichment cultures . The Cycloclasticus strains isolated in this study could grow on crude oil and degraded PAH components of crude oil, including unsubstituted and substituted naphthalenes, dibenzothiophenes, phenanthrenes, and fluorenes . To deduce the role of Cycloclasticus strains in a coastal zone oil spill, propagation of this bacterial group on oil-coated grains of gravel immersed in seawater was investigated in beach-simulating tanks that were 1 m wide by 1.5 m long by 1 m high . The tanks were two-thirds filled with gravel, and seawater was continuously introduced into the tanks; the water level was varied between 30 cm above and 30 cm below the surface of the gravel layer to simulate a 12-h tidal cycle . The number of Cycloclasticus cells associated with the grains was on the order of 10(3) cells/g of grains before crude oil was added to the tanks and increased to 3 x 10(6) cells/g of grains after crude oil was added . The number increased further after 14 days to 10(8) cells/g of grains when nitrogen and phosphorus fertilizers were added, while the number remained 3 x 10(6) cells/g of grains when no fertilizers were added . PAH degradation proceeded parallel with the growth of Cycloclasticus cells on the surfaces of the oil-polluted grains of gravel . These observations suggest that bacteria belonging to the genus Cycloclasticus play an important role in the degradation of petroleum PAHs in a marine environment.

Mol Microbiol, 2002 Oct, 46(2), 319 - 30
The GlnD and GlnK homologues of Streptomyces coelicolor A3(2) are functionally dissimilar to their nitrogen regulatory system counterparts from enteric bacteria; Hesketh A et al.; Glutamine synthetase I (GSI) enzyme activity in Streptomyces coelicolor is controlled post-translationally by the adenylyltransferase (GlnE) as in enteric bacteria . Although other homologues of the Escherichia coli Ntr system (glnK, coding for a PII family protein; and glnD, coding for an uridylyltransferase) are found in the S . coelicolor genome, the regulation of the GSI activity was found to be different . The functions of glnK and glnD were analysed by specific mutants . Surprisingly, biochemical assay and two-dimensional PAGE analysis showed that modification of GSI by GlnE occurs normally in all mutant strains, and neither GlnK nor GlnD are required for the regulation of GlnE in response to nitrogen stimuli . Analysis of the post-translational regulation of GlnK in vivo by two-dimensional PAGE and mass spectrometry indicated that it is subject to both a reversible and a non-reversible modification in a direct response to nitrogen availability . The irreversible modification was identified as removal of the first three N-terminal amino acid residues of the protein, and the reversible modification as adenylylation of the conserved tyro-sine 51 residue that is known to be uridylylated in E . coli . The glnD insertion mutant expressing only the N-terminal half of GlnD was capable of adenylylating GlnK, but was unable to perform the reverse deadenylylation reaction in response to excess ammonium . The glnD null mutant completely lacked the ability to adenylylate GlnK . This work provides the first example of a PII protein that is modified by adenylylation, and demonstrates that this reaction is performed by a homologue of GlnD, previously described only as a uridylyltransferase enzyme.

RNA, 2002 Oct, 8(10), 1189 - 232
tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features; Marck C et al.; From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs . For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies . Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription . Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist . Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya . No common features between Eukarya and Bacteria not shared with Archaea could be unveiled . Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria.

J Microbiol Methods, 2003 Jan, 52(1), 19 - 28
Direct estimate of active bacteria: CTC use and limitations; Creach V et al.; During the last 10 years, the dye 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) has been used to determine the in situ number of "active" bacteria in different ecosystems . A part of this success is due to a simple protocol, which does not require sophisticated equipment . However, it has not been established whether the method determines viable cells, e.g . those capable of growth and cell division, as opposed to cells that are active in the sense of having some detectable metabolic activity . In this study, the number of CTC-positive cells through the growth stages of Escherichia coli was estimated and compared to counts of the total number of bacteria, the culturability (CFU counts) and respiratory activity (CO(2) evolution) . There was a good correlation between the number of CTC-positive cells and the CFU count, regardless of the growth phase . However, CTC could still be reduced by a large part of the population during the first hours of stationary phase even if the bacteria were no longer releasing CO(2) . Thus, the reduction of CTC is a good estimator for cell viability, rather than cell activity . Additionally, a review of the literature showed that there is presently no standardized protocol for using CTC, which makes difficult at present the comparison of active bacterial numbers in different samples from different sites.

Curr Issues Intest Microbiol, 2002 Sep, 3(2), 39 - 48
Microencapsulation of probiotic bacteria: technology and potential applications; Kailasapathy K; In the recent past, there has been an explosion of probiotic health-based products . Many reports indicated that there is poor survival of probiotic bacteria in these products . Further, the survival of these bacteria in the human gastro-intestinal system is questionable . Providing probiotic living cells with a physical barrier against adverse environmental conditions is therefore an approach currently receiving considerable interest . The technology of micro-encapsulation of probiotic bacterial cells evolved from the immobilised cell culture technology used in the biotechnological industry . Several methods of micro-encapsulation of probiotic bacteria have been reported and include spray drying, extrusion, emulsion and phase separation . None of these reported methods however, has resulted in the large numbers of shelf-stable, viable probiotic bacterial cells necessary for use in industry for development of new probiotic products . The most commonly reported micro-encapsulation procedure is based on the calcium-alginate gel capsule formation . Kappa-carrageenan, gellan gum, gelatin and starch are also used as excipients for the micro-encapsulation of probiotic bacteria . The currently available equipment for micro-encapsulation is not able to generate large quantities of uniform sized micro or nano capsules . There is a need to design and develop equipment that will be able to generate precise and uniform micro or nano capsules in large quantities for industrial applications . The reported food vehicles for delivery of encapsulated probiotic bacteria are yoghurt, cheese, ice cream and mayonnaise . Studies need to be done on the application of micro-encapsulation of probiotic bacteria in other food systems . The number of probiotic supplements will increase in the future . More studies, however, need to be conducted on the efficacy of micro-encapsulation to deliver probiotic bacteria and their controlled or targeted release in the gastrointestinal tract.

Microb Ecol, 2002 Nov, 44(4), 327 - 35 Epub 2002 Oct 29.
Competition between picoplanktonic cyanobacteria and heterotrophic bacteria along crossed gradients of glucose and phosphate; Drakare S; A laboratory experiment was performed to test whether differences in nutrient and energy demands between picophytoplankton and heterotrophic bacteria can explain the apparent inverse biomass relationship between these organisms in lakes along gradients of organic carbon and nutrients . Growth rates and final yield of cells were analyzed in crossed gradients of glucose and phosphate . Concentrations of phosphate (10, 25, and 60 microg P L(-1)) and glucose (0, 0.3, and 3 mg C L(-1)) were used in all possible combinations giving 9 different treatments . Heterotrophic bacteria had higher maximum growth rates in all treatments and became larger than picophytoplankton in many treatments . The variance in abundance of heterotrophic bacteria between treatments could almost completely be explained by the combined effects of glucose and P . In treatments where carbon limitation slowed down the growth of heterotrophic bacteria, picophytoplankton became abundant and these organisms showed a positive response to P in combination with a negative response to glucose . The negative effect of glucose on picophytoplankton is suggested to be indirect and caused by competition with bacteria that are favored by organic C . The results suggest that competition for phosphate between phytoplankton and bacteria is not size-dependent, that heterotrophic bacteria are superior competitors for P, and that organic C produced by picophytoplankton was of minor importance for heterotrophic bacteria.

Mar Pollut Bull, 2002, 45(1-12), 290 - 4
The effect of marine colloids on the growth of photosysthetic bacteria; Zheng A et al.; Marine colloids could be an important source of nitrogen for bacteria and photoplankton . But elevated concentration of colloids may stimulate algal growth and lead to red tides in coastal waters . The effects of colloidal organic carbon (COC) concentration on the growth of photosysthetic bacteria (PSB) were investigated under different colloidal treatments in the laboratory . The PSB growth was inversely proportional to COC concentration and was restricted by high-molecular-weight (HMW) colloids (>10 KDa) in treatments with non-nutrient or just inorganic nutrient with low COC concentration ( < or = 5 microMC) . However, the PBS growth was enhanced in the presence of HMW colloids in the treatment with inorganic nutrient and high COC (127 and 255 microMC) or with both inorganic nutrient and low-molecular-weight organic matter . Both bacteria number and bacteria growth ratio increased significantly when the concentration of COC was > or = 5 microMC . Our results suggest that marine colloids can be utilized by bacteria and might regulate primary productivity in coastal waters.

J Interferon Cytokine Res, 2002 Sep, 22(9), 965 - 74
Recombinant mouse granulocyte chemotactic protein-2: production in bacteria, characterization, and systemic effects on leukocytes; Starckx S et al.; Granulocyte chemotactic protein-2 (GCP-2) is an important neutrophil chemotactic factor in the mouse that belongs to the CXC chemokine family . Although the local tissular effects of chemokines are well known, only recently has the systemic regulation of leukocytes become accepted . To study the pharmacokinetics of mouse GCP-2 and the systemic effects on leukocytes, we expressed a potent natural isoform of mouse GCP-2, GCP-2(9-78), in Escherichia coli and produced electrophoretically pure material . GCP-2(9-78) was 10-fold more potent to chemoattract neutrophils than recombinant GCP-2(5-78) . After intravenous (i.v.) injection in mice, GCP-2(9-78) persisted in the circulation with an average half-life of 42 min . When a bolus of 1 mg/kg recombinant mouse GCP-2(9-78) was injected systemically, a significant effect on circulating leukocytes was observed . After a neutropenic phase, at its height at 1 h after injection, neutrophil numbers increased to a maximum at 4 h postinjection, and a concomitant decrease in lymphocyte numbers was observed . In control mice injected with isotonic saline, changes in leukocyte numbers were less pronounced and followed a different kinetic . Whereas tissular neutrophil chemotaxis to GCP-2 is influenced by gelatinase B, the systemic effects on neutrophilia and lymphopenia were not different in gelatinase B-deficient and wild-type mice . These data reinforce the idea that chemokines, including GCP-2, influence the homeostasis of circulating leukocyte numbers.

Blood, 2002 Dec 15, 100(13), 4470 - 7 Epub 2002 Aug 01.
Induction of platelet thrombi by bacteria and antibodies; Sjobring U et al.; We have characterized 2 distinct mechanisms through which infectious agents may promote platelet adhesion and thrombus formation in flowing blood, thus contributing to the progression of disease . In one case, the process initiates when the integrin alpha(IIb)beta(3) mediates platelet arrest onto immobilized bacterial constituents that have bound plasma fibrinogen . If blood contains antibodies against the bacteria, immunoglobulin (Ig) G may cluster on the same surface and activate adherent platelets through the Fc(gamma)RIIA receptor, leading to thrombus growth . As an alternative, bacteria that cannot bind fibrinogen may attach to substrates, such as immobilized plasma proteins or components of the extracellular matrix, which also support platelet adhesion . As a result of this colocalization, IgG bound to bacteria can activate neighboring platelets and induce thrombus growth regardless of their ability to initiate platelet-surface contact . Our results demonstrate that intrinsic constituents of infectious agents and host proteins play distinct but complementary roles in recruiting platelets into thrombi, possibly contributing to complications of acute and chronic infections.

Kansenshogaku Zasshi, 2002 Sep, 76(9), 703 - 10
{Occurrence of Legionella bacteria in a variety of environmental waters--from April, 1996 to November, 2000}; Suzuki A et al.; The present paper deals with the occurrence of Legionella bacteria in a variety of man-made environmental waters, including whirlpool bathes, cooling towers and others, from April 1996 to November 2000 in the eastern part of Japan around Tokyo area . A total of 2,895 water samples were examined for the possible occurrence of Legionella, and 904 (31%) were demonstrated to be positive . Among the various water sources, Legionella were frequently detected both in whirlpool bathes and in cooling towers, of which detection rates were 48% and 46%, respectively . More precisely, occurrence of Legionella was higher in private-use whirlpool bathes than those for public-use; namely, the positive rate was 71% in bathes accommodated in private houses, 63% in company's club houses, 62% in company dormitories for employees, and 51% in old-people's homes . Occurrence of Legionella, on the other hand, was less common (< or = 30%) in bathes for public-use such as those installed in hotels and in hot spring facilities . Typing of L . pneumophila serogroups revealed that SG5 (34%) was dominant in whirlpool bath waters followed by SG3 (22%), whereas SG1 (32%) was dominantly found in cooling tower waters.

Anal Chem, 2002 Oct 1, 74(19), 4895 - 904
Bacteria sorting by field-flow fractionation . Application to whole-cell Escherichia coil vaccine strains; Reschiglian P et al.; Sorting and quantification of deactivated bacteria is an important way of quality control for whole-cell bacterial vaccines . In general, surface features of deactivated bacteria used for whole-cell bacterial vaccines affect the immunoresponse to bacteria-associated antigens . Enumeration of bacteria is also an important process development parameter for these vaccines . Field-flow fractionation (FFF) was previously applied to the separation of bacteria . For the first time, FFF is used for sorting bacteria strains of the same species on the basis of differences in bacterial membrane characteristics . Two FFF techniques, gravitational FFF (GrFFF) and asymmetrical flow FFF (AsFIFFF), are shown to be able to fractionate, distinguish, and quantify different deactivated Escherichia coli strains used for vaccines . E . coli can differ in the presence of fimbriae on the bacterial membrane . Fimbriae affect E . coli pathology and thus the use of E . coli for vaccines . GrFFF and AsFIFFF are able to fractionate fimbriated/ nonfimbriated cells in mixtures of different strains . While GrFFF is characterized by low cost and simplicity, As-FIFFF shows a higher performance in size fractionation with a high-speed separation . Coupled, on-line UV/visible turbidimetry yields the relative numbers of fractionated cells and sample recovery . Scanning electron microscopy and quasi-elastic light scattering are employed as uncorrelated techniques for size and morphology analysis of the E . coli strains.

Biotechnol Bioeng, 2002 Dec 20, 80(6), 637 - 49
Reduction kinetics of Fe(III), Co(III), U(VI), Cr(VI), and Tc(VII) in cultures of dissimilatory metal-reducing bacteria; Liu C et al.; The reduction kinetics of Fe(III)citrate, Fe(III)NTA, Co(III)EDTA-, U(VI)O(2) (2+), Cr(VI)O(4) (2-), and Tc(VII)O(4) (-) were studied in cultures of dissimilatory metal reducing bacteria (DMRB): Shewanella alga strain BrY, Shewanella putrefaciens strain CN32, Shewanella oneidensis strain MR-1, and Geobacter metallireducens strain GS-15 . Reduction rates were metal specific with the following rate trend: Fe(III)citrate > or = Fe(III)NTA > Co(III)EDTA- >> UO(2)(2+) > CrO(4)(2-) > TcO(4)(-), except for CrO(4) (2-) when H(2) was used as electron donor . The metal reduction rates were also electron donor dependent with faster rates observed for H(2) than lactate- for all Shewanella species despite higher initial lactate (10 mM) than H2 (0.48 mM) . The bioreduction of CrO(4) (2-) was anomalously slower compared to the other metals with H(2) as an electron donor relative to lactate and reduction ceased before all the CrO(4)(2-) had been reduced . Transmission electron microscopic (TEM) and energy-dispersive spectroscopic (EDS) analyses performed on selected solids at experiment termination found precipitates of reduced U and Tc in association with the outer cell membrane and in the periplasm of the bacteria . The kinetic rates of metal reduction were correlated with the precipitation of reduced metal phases and their causal relationship discussed . The experimental rate data were well described by a Monod kinetic expression with respect to the electron acceptor for all metals except CrO(4)(2-), for which the Monod model had to be modified to account for incomplete reduction . However, the Monod models became statistically over-parameterized, resulting in large uncertainties of their parameters . A first-order approximation to the Monod model also effectively described the experimental results, but the rate coefficients exhibited far less uncertainty . The more precise rate coefficients of the first-order model provided a better means than the Monod parameters, to quantitatively compare the reduction rates between metals, electron donors, and DMRB species .

Plant Mol Biol, 2002 Nov, 50(4-5), 623 - 33
Molecular cloning and functional expression in bacteria of the potassium transporters CnHAK1 and CnHAK2 of the seagrass Cymodocea nodosa; Garciadeblas B et al.; The cDNAs CnHAK1 and CnHAK2, encoding K+ transporters, were amplified from the leaves of the seagrass Cymodocea nodosa . None of these transporters suppressed the K+ deficiency of a Saccharomyces cerevisiae mutant, but both suppressed the equivalent defect of an Escherichia coli mutant . Overexpression of the transporter CnHAKI, but not CnHAK2, mediated very rapid K+ or Rb+ influxes in the E . coli mutant . The concentration dependence of these influxes demonstrated that CnHAK1 is a low-affinity K+ transporter, which does not discriminate between K+ and Rb+ . CnHAK1 expressed in E . coli worked in reverse when the external K+ concentrations were low, and we established the condition of a simple functional test of K+ loss for transporters of the Kup-HAK family . In comparison with its homologue barley transporter HvHAK2, CnHAKI was insensitive to Na+.

Electrophoresis, 2002 Sep, 23(19), 3300 - 9
Effect of bacteria growth temperature on the distribution of supercoiled DNA and its thermal stability; Adamcik J et al.; Changes in DNA supercoiling might be essential to generate the response of cellular machinery to temperature stress . The heat-induced structural transition for a topoisomer depends on the value of its specific linking difference . We detect only less negatively supercoiled DNA and an abundance of alternative irregular DNA forms at culture temperatures close to the growth limit of Escherichia coli . We show that the irregular forms are derived from regular plasmid DNAs and their population in the cells is temperature-dependent . Here, we show that it is possible to isolate and characterize individual DNA topoisomers directly from cells without a topoisomerase treatment . Temperature gradient gel electrophoresis (TGGE) and atomic force microscopy (AFM) were used to study the effect of bacteria growth temperature on the distribution of supercoiled DNA and its thermal stability.

Genome Biol . 2002 Sep 26;3(10):RESEARCH0058 . Epub 2002 Sep 26.
Asymmetric directional mutation pressures in bacteria; Lobry JR et al.; BACKGROUND: When there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand . Deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands . By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, we have been able to detect asymmetric directional mutation pressures . RESULTS: Most of the 43 chromosomes were found to be relatively enriched in G over C and T over A, and slightly depleted in G+C, in their weakly selected positions (intergenic regions and third codon positions) in the leading strand compared with the lagging strand . Deviations from A = T and G = C were highly correlated between third codon positions and intergenic regions, with a lower degree of deviation in intergenic regions, and were not correlated with overall genomic G+C content . CONCLUSIONS: During the course of bacterial chromosome evolution, the effects of asymmetric directional mutation pressures are commonly observed in weakly selected positions . The degree of deviation from equality is highly variable among species, and within species is higher in third codon positions than in intergenic regions . The orientation of these effects is almost universal and is compatible in most cases with the hypothesis of an excess of cytosine deamination in the single-stranded state during DNA replication . However, the variation in G+C content between species is influenced by factors other than asymmetric mutation pressure.

EDTNA ERCA J, 2002 Jul-Sep, 28(3), 121 - 4
The influence of bacteria in dialysis water on its endotoxin level; Trager H; The influence of bacteria in dialysis water and its endotoxin level is one of the main important issues of purified water for haemodialysis . The current methods, assessing the number of water bacteria, are insufficient; due to their large diversity, only a small fraction of them grow on our used culture agars . Bacterial cells are classified into three categories: the A cells represent cultivable cells, B cells are living though not cultivable whereas the C cells are dead cells . Methods assessing these different cell categories are discussed . Endotoxin is only released from the C-type cells and is removed by the Reverse Osmosis membranes . It is our task to ensurethat we keep the A-cell level low after the Reverse Osmosis . The purified water must not remain very long in the pipe system and the use of Permeate tanks should be avoided.

Acta Crystallogr D Biol Crystallogr, 2002 Oct, 58(Pt 10 Pt 1), 1660 - 3 Epub 2002 Sep 26.
Charge separation induces conformational changes in the photosynthetic reaction centre of purple bacteria; Fritzsch G et al.; X-ray structures of the wild-type reaction centre from Rhodobacter sphaeroides have been determined to a resolution of 1.87 A in the neutral (dark) state and to 2.06 A in the charge-separated (light-excited) state . Whereas the overall protein structures of both states are rather similar, the domain around the secondary quinone shows significant shifts . The quinone molecule itself is observed at two different positions . In the neutral state, 55% of the quinone is located distally and 45% proximally to the cytoplasmic side . After excitation by light, however, at least 90% of the quinone is found at the proximal position . Results presented by Stowell et al . (1997) are confirmed, but the quality of crystallographic data has been improved . We compare the data with the structure of the mutant RC L 209 PY that keeps the Q(B) molecule in the proximal position even in the charge-neutral state.

Prikl Biokhim Mikrobiol, 2002 Jul-Aug, 38(4), 393 - 400
{Use of methylotrophic bacteria Methylobacillus flagellatum KT for isolation of deuterated exogenous carbohydrates}; Mishina IM et al.; The cultivation conditions optimal for biosynthesis of exogenous polysaccharides by methylotrophic bacteria Methylobacillus flagellatum were evaluated . The mutant strain most active in accumulating exogenous polysaccharides was selected . Gradual adaptation of this strain to the deuterated medium containing 1 vol % CD3OD in deuterium oxide intensified biosynthesis of exogenous polysaccharides and inhibited bacterial growth (compared to the standard medium) . The monomeric composition of exogenous polysaccharides obtained during cultivation on standard and deuterated media was estimated by high-performance liquid chromatography and nuclear magnetic resonance spectroscopy . Nondeuterated exogenous polysaccharides contained only fructose, while deuterated exogenous polysaccharides included 98% fructose and 2% ribose . Paramagnetic resonance spectroscopy showed that the degree of deuterium incorporation into molecules of biosynthetic carbohydrates was 89%.

Med Hypotheses, 2002 Jun, 58(6), 558 - 60
Big bacteria pass through very small holes; Wainwright M et al.; Can normal-sized bacteria pass through small holes, and if so how? We have found that common, potentially pathogenic, bacteria (which are nominally larger than 0.2 microm) can cross a 0.2 microm nylon membrane . All of the bacteria crossed from the upper membrane surface to the solid medium below the membrane; this ability was highly repeatable and did not depend on the make of membrane used . Bacteria growing below the membrane exhibited normal size and morphology . We suggest that the ability of common bacteria to pass through small holes has important implications in relation to their role as pathogens.

Biofizika, 2002 Jul-Aug, 47(4), 663 - 72
{Mass-energy balance of the growth of phototropic purple bacteria}; Minkevich IG et al.; The principles of the theory of mass-energy balance of the growth of cellular populations are described . Based on this theory, the effect of biochemical parameters of cell metabolism on the efficiency of phototrophic growth of bacterial culture was studied . The metabolism of phototrophic bacteria was subdivided into constructive and energetic partial metabolisms . The stoichiometric coefficients describing the energetics of the two metabolism types were calculated . An equation system of the mass-energy balance for the flows of reductivity, high-energy bonds, and protons--carriers of the transmembrane electrochemical potential was derived . Equations for biomass quantum yield were obtained . The calculated yield values are in agreement with experimental data.

Biochemistry, 2002 Oct 1, 41(39), 11812 - 9
Biochemical characterization of the dissociated forms from the core antenna proteins from purple bacteria; Arluison V et al.; The core light-harvesting protein from Rhodospirillum rubrum is of particular interest for studying membrane polypeptide association, as it can be reversibly dissociated in the presence of n-octyl-beta-D-glucopyranoside (betaOG) into smaller subunit forms, which exhibit dramatically blue-shifted absorption properties (Miller et al . (1987) Biochemistry 26, 5055-5062) . During this dissociation/reassociation process, two main spectroscopic forms are observed, absorbing at 820 (B820) and 777 (B777) nm, respectively . By using polyacrylamide gel electrophoresis in the presence of betaOG, these forms were characterized from a biochemical point of view . B777 consist of a mixture of alpha or beta polypeptide chains, retaining their bound bacteriochlorophyll (BChl) molecules . The absorption properties of the BChl molecules bound to the monomeric polypeptides do not depend on the chemical nature of the polypeptides they are bound to . B820 is more complex and consist of equilibrium between alphabeta-containing oligomers and beta only containing dimers, all exhibiting very similar electronic absorption properties . Resonance Raman spectroscopy indicates that the binding site provided by the beta-only B820 to the BChl molecules is very similar to that provided by the alphabeta B820 . This, together with the observation that the alpha polypeptide alone is unable to form B820, suggests that the local organization of the BChl molecules tightly depends on BChl-protein interactions . On the other hand, our results suggest that the affinity of the beta-BChl complexes for itself and for the alpha-BChl ones are of the same order of magnitude, the formation of heterodimeric complexes being mainly driven by the inability of alpha-BChl complexes to self-associate.

Infect Control Hosp Epidemiol, 2002 Sep, 23(9), 549 - 51
Effectiveness of bacteria-controlled nursing units in preventing cross-colonization with resistant bacteria in severely burned children; Weber JM et al.; Bacteria-controlled nursing units (BCNUs) are laminar air-flow patient isolation units . The rate of cross-colonization with resistant organisms in 66 critically ill pediatric burn patients with massive open wounds and ventilators housed in BCNUs during 5 years was examined and found to be extremely low (3.2 cases per 1,000 patient-days).

Mikrobiologiia, 2002 Jul-Aug, 71(4), 500 - 8
{Study of nucleotide sequences of nifH genes in methanotrophic bacteria}; Bulygina ES et al.; Using a previously developed primer system, nifH gene fragments 450 nucleotides long were amplified, cloned, and sequenced for representatives of nitrogen-fixing methanotrophic bacteria of the genera Methylococcus, Methylocystis and Methylosinus . Fragments of nifH genes were also detected and sequenced in representatives of the genera Methylomonas and Methylobacter, which were not considered diazotrophs until recently . Phylogenetic analysis revealed remoteness of nifH genes sequences of methanotroph types I and II . At the same time, close relationship was found between nifH of type I methanotrophs and representatives of gamma-proteobacteria and between nifH genes of type II methanotrophs and representatives of alpha-proteobacteria . The results obtained in this study are in good accordance with the data of phylogenetic analysis based on 16S rRNA sequence comparison with the only exception of Methylococcus capsulatus strains, whose nifH genes proved to be closely related to nifH genes of Methylocystis and Methylosinus representatives . Our findings extend the database of primary sequences of nifH genes and allow the contribution of methanotrophs to the process of nitrogen fixation to be estimated.

Mikrobiologiia, 2002 Jul-Aug, 71(4), 445 - 51
{Dependence of the structure of malate dehydrogenase on the type of metabolism in fresh water filamentous colorless sulfur bacteria of the Beggiatoa species}; Stepanova IIu et al.; Major pathways of carbon metabolism were studied in strains D-402 and D-405 of freshwater colorless sulfur bacteria of the genus Beggiatoa grown organotrophically and mixotrophically . The bacteria were found to possess all the enzymes of the tricarboxylic acid (TCA) and glyoxylate cycles . When organotrophic growth changed to mixotrophic one, the activity of the TCA cycle enzymes decreased 2- to 3-fold, but the activity of enzymes of the glyoxylate cycle increased threefold . It follows that, in the oxidation of thiosulfate, organic compounds no longer play the leading part in the energy metabolism, and most of electrons that enter the electron transport chain (ETC) derive from inorganic sulfur compounds . A connection was established between the structure and kinetic characteristics of malate dehydrogenase--an enzyme of the TCA and glyoxylate cycles--and the type of carbon metabolism in the strains studied . Malate dehydrogenase in organotrophically grown cells of strains D-402 and D-405 is dimeric, whereas in strain D-402 grown mixotrophically it is tetrameric.

J Immunol, 2002 Oct 1, 169(7), 3854 - 62
Mycobacterium avium complex promotes recruitment of monocyte hosts for HIV-1 and bacteria; Hale-Donze H et al.; In lymphoid tissues coinfected with Mycobacterium avium complex (MAC) and HIV-1, increased viral replication has been observed . This study investigates the role of MAC in perpetuating both infections through the recruitment of monocytes as potential new hosts for bacteria and HIV-1 . Increased numbers of macrophages were present in the lymph nodes of patients with dual infection as compared with lymph nodes from HIV(+) patients with no known opportunistic pathogens . In a coculture system, monocyte-derived macrophages were treated with HIV-1 or M . avium and its constituents to further define the mechanism whereby MAC infection of macrophages initiates monocyte migration . Monocyte-derived macrophages treated with bacteria or bacterial products, but not HIV-1, induced a rapid 2- to 3-fold increase in recruitment of monocytes . Pretreatment of the monocytes with pertussis toxin inhibited the migration of these cells, indicating a G protein-linked pathway is necessary for induction of chemotaxis and thus suggesting the involvement of chemokines . Analysis of chemokine mRNA and protein levels from M . avium-treated cultures revealed MAC-induced increases in the expression of IL-8, macrophage-inflammatory protein (MIP)-1alpha, and MIP-1beta with donor-dependent changes in monocyte chemotactic protein-1 . Pyrrolidine dithiocarbamate, an antioxidant, inhibited the activation of NF-kappaB and significantly diminished the MAC-induced chemotaxis, concurrently lowering the levels of monocyte chemotactic protein-1 and MIP-1beta . These data demonstrate that MAC induces macrophage production of multiple chemotactic factors via NF-kappaB to promote monocyte migration to sites of MAC infection . In vivo, opportunistic infection may act as a recruitment mechanism in which newly arrived monocytes serve as naive hosts for both MAC and HIV-1, thus perpetuating both infections.

FEBS Lett, 2002 Sep 11, 527(1-3), 171 - 5
Tuning of the redox potential of the primary electron donor in reaction centres of purple bacteria: effects of amino acid polarity and position; Spiedel D et al.; Mutation of residues His L168 and Phe M197 in the reaction centre from Rhodobacter sphaeroides has an unusually strong effect on the mid-point redox potential (E(m)) of the pair of bacteriochlorophylls that form the primary donor of electrons, tuning E(m) over a range of nearly 250 mV . This effect is correlated to the accompanying change in the permanent dipole of the L168 or M197 residue, suggesting it is mediated by changes in charge-dipole interactions . Comparisons with mutations made at a variety of other positions show that this correlation is particular to this residue pair, perhaps reflecting their proximity to the ring I regions of the dimer bacteriochlorophylls that form the overlap region between these molecules.

Biochim Biophys Acta, 2002 Sep 10, 1555(1-3), 60 - 4
Supramolecular organisation of the photosynthetic chain in anoxygenic bacteria; Vermeglio A et al.; This minireview summarizes our present view of the supramolecular organization of the photosynthetic apparatus of Rhodobacter sphaeroides and Rhodobacter capsulatus . These two species present a close association between two reaction centers (RCs), one cytochrome (cyt) bc(1) and one cyt c . In R . sphaeroides, the RCs are only partially surrounded by LH1 complexes . This open ring of LH1 complexes is required for an efficient photoinduced cyclic electron transfer only under conditions where the quinone pool totally reduced . When the quinone pool is partially oxidized, a closed ring of LH1 complexes around the RCs does not impair the exchange of quinone molecules between the RC and the cyt bc(1) complex . To explain the efficient photochemistry of the various species which possess a RC surrounded by a closed ring of LH, it is proposed that their quinone pool is partially oxidized even under anaerobic condition.

J Immunol, 2002 Sep 15, 169(6), 3172 - 9
Caspase-9/-3 activation and apoptosis are induced in mouse macrophages upon ingestion and digestion of Escherichia coli bacteria; Hacker H et al.; A number of highly virulent, intracellular bacteria are known to induce cell death by apoptosis in infected host cells . In this work we demonstrate that phagocytosis of bacteria from the Escherichia coli laboratory strain K12 DH5alpha is a potent cell death stimulus for mouse macrophages . RAW264.7 mouse macrophages took up bacteria and digested them within 2-4 h as investigated with green fluorescent protein-expressing bacteria . No evidence of apoptosis was seen at 8 h postexposure, but at 24 h approximately 70% of macrophages displayed an apoptotic phenotype by a series of parameters . Apoptosis was blocked by inhibition of caspases or by forced expression of the apoptosis-inhibiting protein Bcl-2 . Processing of caspase-3 and caspase-9 but not caspase-8 was seen suggesting that the mitochondrial branch of the apoptotic pathway was activated . Active effector caspases could be detected in two different assays . Because the adapter molecule myeloid differentiation factor 88 (MyD88) has been implicated in apoptosis, involvement of the Toll-like receptor pathway was investigated . In RAW264.7 cells, heat-treated bacteria were taken up poorly and failed to induce significant apoptosis . However, cell activation was almost identical between live and heat-inactivated bacteria as measured by extracellular signal-regulated kinase activation, generation of free radicals, and TNF secretion . Furthermore, primary bone marrow-derived macrophages from wild-type as well as from MyD88-deficient mice underwent apoptosis upon phagocytosis of bacteria . These results show that uptake and digestion of bacteria leads to MyD88-independent apoptosis in mouse macrophages . This form of cell death might have implications for the generation of the immune response.

Water Sci Technol, 2002, 46(1-2), 139 - 44
Flow cytometric sorting and RFLP analysis of phosphate accumulating bacteria in an enhanced biological phosphorus removal system; Kawaharasaki M et al.; Phosphate accumulating organisms (PAOs) stained with 4',6-diamidino-2-phenylindol dihydrochloride (DAPI) at polyphosphate probing concentration were sorted from enhanced biological phosphorus removal (EBPR) sludge by flow cytometric sorting . All the genome DNA was extracted from the sorted bacteria and the 16S rDNA genes were cloned . Cloned 16S rDNA was PCR-amplified and analyzed by restriction fragment length polymorphism (RFLP) analysis . Eighty eight clones were analyzed and the RFLP patterns which appeared more than twice were classified into seven groups . The most dominant group (Group 1) contained four clones and accounted for 4.5% of the total clones . Four groups (from Group 2 to Group 5) contained three clones . Group 6 and 7 consisted of two clones . Sixty-eight clones gave unique RFLP patterns . By sequencing 16S rDNA in seven groups, Group 1, 2 and 5 were Rhodocyclus relatives (11%, 10/88) . Rhodocyclus relatives were suggested to be one of the bacteria responsible for EBPR in this sludge . Groups 6 and 7 were related to b- or g-Proteobacteria . Group 4 belonged to e-Proteobacteria . Group 3 was related to green nonsulfur bacteria . Considering the complex RFLP pattern and the existence of the groups not related to Rhodocyclus by sequence analysis, in this EBPR system, together with Rhodocyclus relatives, some other bacteria might also play a role as PAOs.

Extremophiles, 2002 Aug, 6(4), 333 - 40 Epub 2002 Apr 18.
Identification of thermoacidophilic bacteria and a new Alicyclobacillus genomic species isolated from acidic environments in Japan; Goto K et al.; Sixty strains of thermoacidophilic bacteria have been isolated from soil and water samples obtained from various acidic environments in Japan . An initial comparative sequence analysis of the hypervariable regions of the 16S rDNA revealed that all strains could be assigned to the Alicyclobacillus acidocaldarius- Alicyclobacillus genomic species 1 group, which could be further subdivided into three clusters (Clusters I-III) . On the basis of phenotypic characteristics, chemotaxonomic profiles, and phylogenetic data of six selected strains, five strains were identified as either A . acidocaldarius or Alicyclobacillus genomic species 1; however, one strain (MIH 332) could not be determined to belong to either of these species . 16S rDNA sequence homology values between strain MIH 332 and the reference strains of A . acidocaldarius (ATCC 27009(T)) and Alicyclobacillus genomic species 1 (DSM 11984) were 98.8% and 99.1%, respectively, which were higher than the corresponding similarity between the reference strains (98.4%) . On the other hand, DNA-DNA hybridization levels between strain MIH 332 and the reference strains were 39% and 44%, respectively, which were lower than the value between the reference strains (59% or 65%) . However, the phenotype of strain MIH 332 was also similar to those of the reference strains, and a typical phenotype could not be found for the strain, thus indicating that the strain may be a new genomic species of A . acidocaldarius, for which the name Alicyclobacillus genomic species 2 is tentatively proposed . The results of this study suggest that A . acidocaldarius and its related species are widely distributed in acidic environments in Japan, with slight regional variations in morphological and genotypic characteristics.

J Biol Chem, 2002 Nov 8, 277(45), 43262 - 70 Epub 2002 Sep 04.
Reversible unfolding of FtsZ cell division proteins from archaea and bacteria . Comparison with eukaryotic tubulin folding and assembly; Andreu JM et al.; The stability, refolding, and assembly properties of FtsZ cell division proteins from Methanococcus jannaschii and Escherichia coli have been investigated . Their guanidinium chloride unfolding has been studied by circular dichroism spectroscopy . FtsZ from E . coli and tubulin released the bound guanine nucleotide, coinciding with an initial unfolding stage at low denaturant concentrations, followed by unfolding of the apoprotein . FtsZ from M . jannaschii released its nucleotide without any detectable secondary structural change . It unfolded in an apparently two-state transition at larger denaturant concentrations . Isolated FtsZ polypeptide chains were capable of spontaneous refolding and GTP-dependent assembly . The homologous eukaryotic tubulin monomers misfold in solution, but fold within the cytosolic chaperonin CCT . Analysis of the extensive tubulin loop insertions in the FtsZ/tubulin common core and of the intermolecular contacts in model microtubules and tubulin-CCT complexes shows a loop insertion present at every element of lateral protofilament contact and at every contact of tubulin with CCT (except at loop T7) . The polymers formed by purified FtsZ have a distinct limited protofilament association in comparison with microtubules . We propose that the loop insertions of tubulin and its CCT-assisted folding coevolved with the lateral association interfaces responsible for extended two-dimensional polymerization into microtubule polymers.

J Dairy Sci, 2002 Aug, 85(8), 2015 - 22
Stimulatory and inhibitory effects of protein amino acids on growth rate and efficiency of mixed ruminal bacteria; Kajikawa H et al.; Mixed ruminal bacteria were incubated in vitro with glucose, xylose, cellobiose, and various protein amino acids replaced isonitrogenously with 25% (i.e., 25 mg of N/L) of ammonia-N, to determine the growth rate and the amount of sugar consumed in the exponential growth phase . The growth rate and efficiency (grams of bacteria per gram of sugars) increased by 46 and 15%, respectively, when a mixture of 20 amino acids was added . On the other hand, neither growth rate nor efficiency increased when any one of these amino acids was added singly, except for Glu and Gln, each of which produced significant but small improvements . The stimulatory effect of the combined amino acids on bacterial growth declined when each of Leu, Trp, Tyr, Glu, Met, Phe, and Val was removed from the original group of 20 . When a mixture of only these seven amino acids was used as a supplement, their stimulatory effects on growth rate and efficiency were only 21 and 25%, respectively, of the effects that the mixture of 20 amino acids showed . The effects increased to 76 and 72% on growth rate and efficiency, respectively, when Gly, Cys, and His were supplied in addition to the seven amino acids . The growth rate and efficiency of the ruminal bacteria were inhibited by an addition of each of Ile, Thr, Cys, Phe, Leu, Lys, or Val to ammonia-N, and the effects of the first five of these amino acids were highly significant . Isoleucine, threonine, and phenylalanine were each inhibitory even at a low concentration (1 mg of NL), while cysteine and leucine showed inhibitory effects at higher concentrations (more than 10 mg of N/L) . A higher growth rate of the ruminal bacteria when supplemented with amino acid mixtures was accompanied with a higher growth efficiency, which was attributable to a relatively smaller proportion of energy expended on maintenance according to the Pirt derivation.

Arch Pharm Res, 2002 Aug, 25(4), 528 - 33
Antithrombotic and antiallergic activities of rhaponticin from Rhei Rhizoma are activated by human intestinal bacteria; Park EK et al.; To evaluate the antithrombotic and antiallergic properties of rhaponticin extracted from Rhei Rhizoma, the in vitro and ex vivo inhibitory activities of rhaponticin and its metabolite, rhapontigenin, were measured . These compounds inhibited in vitro ADP- and collagen-induced platelet aggregation . Rhapontigenin was more potent, with IC50 values of 4 and 70 microg/ml, respectively . In ex vivo ADP- and collagen-induced rat platelet aggregation, these compounds also exhibited a potent inhibitory effect . The antiplatelet aggregation effects of rhaponticin and rhapontigenin were more potent than those of aspirin . Rhapontigenin showed significant protection from death due to pulmonary thrombosis in mice . Rhapontigenin also showed the strongest inhibitory activity against beta-hexosaminidase release induced by DNP-BSA . These compounds inhibited PCA reaction in mice . Rhapontigenin intraperitoneally administered showed the strongest inhibitory activity and significantly inhibited PCA at doses of 25 and 50 mg/kg, with inhibitory activities of 48 and 85%, respectively . The inhibitory activity of orally administered rhaponticin was stronger than that of intraperitoneally administered rhaponticin . These results suggest that rhaponticin, in the rhizome of Rhei Rhizoma, is a prodrug that has extensive antiallergic and antithrombotic properties.

J Environ Sci (China), 2002 Jul, 14(3), 339 - 44
Phytosynthetic bacteria (PSB) as a water quality improvement mechanism in saline-alkali wetland ponds; Liu FJ et al.; The efficiency of phytosynthetic bacteria (PSB) to improve the water quality in saline-alkali ponds was studied, the result showed that (1) PSB application could increase the content of DO, NO3-(-)N and effective phosphorus (EP) in ponds; (2) the changes of COD were not evident, just effective in later period after PSB application; (3) PSB application could decrease the contents of NH4-(-)N (NH3-N), NO2-(-)N; (4) PSB application could improve the structure of the effective nitrogen (EN) and EP, stimulate the growth of phytoplankton, and increase primary productivity, and finally increase the commercial profits of ponds because of the increase of EP and the decrease of EN contents; (5) the effect-exerting speed of PSB was slower, but the effect-sustaining time was longer; (6) the appropriate concentration of PSB application in saline-alkali wetland ponds was 10 x 10(-6) mg/L, one-time effective period was more than 15 days . So PSB was an efficient water quality improver in saline-alkali ponds.

Bioessays, 2002 Aug, 24(8), 700 - 7
Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions; Henkin TM et al.; Regulation of gene expression by premature termination of transcription, or transcription attenuation, is a common regulatory strategy in bacteria . Various mechanisms of regulating transcription termination have been uncovered, each can be placed in either of two broad categories of termination events . Many mechanisms involve choosing between two alternative hairpin structures in an RNA transcript, with the decision dependent on interactions between ribosome and transcript, tRNA and transcript, or protein and transcript . In other examples, modification of the transcription elongation complex is the crucial event . This article will describe and compare several of these regulatory strategies, and will cite specific examples to illustrate the different mechanisms employed .

Bioessays, 2002 Sep, 24(9), 858 - 62
Nucleotide sequence-based typing of bacteria and the impact of automation; Clarke SC; DNA-based typing methods are increasingly important for the characterisation of bacteria . They are used to monitor the epidemiology of pathogens with public health significance and also to help understand the evolution and population biology of bacteria . However, these methods require accuracy and reproducibility and are often of a high-throughput nature . Laboratory automation is therefore the key to the successful implementation of such methods . This review describes the impact of automation on DNA-based typing methods, particularly multi-locus sequence typing (MLST), and the method components that can be automated .

Arch Microbiol, 2002 Oct, 178(4), 239 - 49 Epub 2002 Jul 05.
Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria; Vorholt JA; Methylotrophic bacteria can grow on a number of substrates as energy source with only one carbon atom, such as methanol, methane, methylamine, and dichloromethane . These compounds are metabolized via the cytotoxin formaldehyde . The formaldehyde consumption pathways, especially the pathways for the oxidation of formaldehyde to CO(2) for energy metabolism, are a central and critical part of the metabolism of these aerobic bacteria . Principally, two main types of pathways for the conversion of formaldehyde to CO(2) have been described: (1) a cyclic pathway initiated by the condensation of formaldehyde with ribulose monophosphate, and (2) distinct linear pathways that involve a dye-linked formaldehyde dehydrogenase or C(1) unit conversion bound to the cofactors tetrahydrofolate (H(4)F), tetrahydromethanopterin (H(4)MPT), glutathione (GSH), or mycothiol (MySH) . The pathways involving the four cofactors have in common the following sequence of events: the spontaneous or enzyme-catalyzed condensation of formaldehyde and the respective C(1) carrier, the oxidation of the cofactor-bound C(1) unit and its conversion to formate, and the oxidation of formate to CO(2) . However, the H(4)MPT pathway is more complex and involves intermediates that were previously known solely from the energy metabolism of methanogenic archaea . The occurrence of the different formaldehyde oxidation pathways is not uniform among different methylotrophic bacteria . The pathways are in part also used by other organisms to provide C(1) units for biosynthetic reactions (e.g., H(4)F-dependent enzymes) or detoxification of formaldehyde (e.g., GSH-dependent enzymes).

Ageing Res Rev, 2002 Sep, 1(4), 693 - 703
Translational fidelity, protein oxidation, and senescence: lessons from bacteria; Nystrom T; Senescence of growth-arrested Escherichia coli cells is like mandatory aging in higher eukaryotes, accompanied by increased oxidative modifications of macromolecules . Similar to aged flies, this senescence-related oxidation targets enzymes of the Krebs cycle . Additional targets include the universal stress protein A, the Hsp70 chaperone DnaK, translation elongation factors, and histone-like proteins . However, during the early stages of stasis, protein oxidation is more general and affects a large number of proteins . Attempts to correlate this protein oxidation with a reduced activity of the antioxidant defense systems or an increased tendency of the respiratory apparatus to produce reactive oxygen species (ROS) have generated conflicting results . Instead, recent data indicate that oxidation of proteins may occur in the absence of an increased oxidative stress and is rather caused by an increased production of substrates available for oxidative attack . Misfolded and aberrant proteins appear to be such substrates and the production of aberrant polypeptides surge during the early stages of stasis due to a reduced translational fidelity . The data point to a novel mechanism involved in protein oxidation that has not been considered previously in aging research.

Proc Natl Acad Sci U S A, 2002 Dec 10, 99 Suppl 4, 16470 - 6 Epub 2002 Aug 29.
Self-perpetuating epigenetic pili switches in bacteria; Hernday A et al.; Bacteria have developed an epigenetic phase variation mechanism to control cell surface pili-adhesin complexes between heritable expression (phase ON) and nonexpression (phase OFF) states . In the pyelonephritis-associated pili (pap) system, global regulators {catabolite gene activator protein (CAP), leucine-responsive regulatory protein (Lrp), DNA adenine methylase (Dam)} and local regulators (PapI and PapB) control phase switching . Lrp binds cooperatively to three pap DNA binding sites, sites 1-3, proximal to the papBA pilin promoter in phase OFF cells, whereas Lrp is bound to sites 4-6 distal to papBA in phase ON cells . Two Dam methylation targets, GATC(prox) and GATC(dist), are located in Lrp binding sites 2 and 5, respectively . In phase OFF cells, binding of Lrp at sites 1-3 inhibits methylation of GATC(prox), forming the phase OFF DNA methylation pattern (GATC(dist) methylated, GATC(prox) nonmethylated) . Binding of Lrp at sites 1-3 blocks pap pili transcription and reduces the affinity of Lrp for sites 4-6 . Together with methylation of GATC(dist), which inhibits Lrp binding at sites 4-6, the phase OFF state is maintained . We hypothesize that transition to the phase ON state requires DNA replication to dissociate Lrp and generate a hemimethyated GATC(dist) site . PapI and methylation of GATC(prox) act together to increase the affinity of Lrp for sites 4-6 . Binding of Lrp at the distal sites protects GATC(dist) from methylation, forming the phase ON methylation pattern (GATC(dist) nonmethyated, GATC(prox) methylated) . Lrp binding at sites 4-6 together with cAMP-CAP binding 215.5 bp upstream of the papBA transcription start, is required for activation of pilin transcription . The first gene product of the papBA transcript, PapB, helps maintain the switch in the ON state by activating papI transcription, which in turn maintains Lrp binding at sites 4-6.

Biochem Soc Trans, 2002 Aug, 30(4), 768 - 70
Manganese transport and its regulation in bacteria; Bhattacharyya-Pakrasi M et al.; Regulation of manganese acquisition by bacteria occurs by both biochemical regulation of the activity of the transporters and transcriptional regulation of gene expression . Structural analysis suggests that calcium ions may regulate the function of an Mn ATP-binding cassette (ABC)-permease in Synechocystis 6803, a cyanobacterium, as well as in a number of other bacteria . The expression of genes encoding the manganese transporter in Synechocystis 6803 is regulated by a two-component signal-transduction mechanism that has not been previously observed for manganese and zinc transport in bacteria.

Int Endod J, 2001 Apr, 34(3), 216 - 20
Bacteria on the apical root surfaces of untreated teeth with periradicular lesions: a scanning electron microscopy study; Siqueira JF Jr et al.; AIM: The purpose of this study was to examine the presence of bacteria on the apical root surfaces of untreated teeth associated with chronic periradicular lesions . METHODOLOGY: Twenty-seven extracted teeth with extensive carious lesions, radiolucent lesions of varying sizes and attached periradicular lesions after extraction, were selected for study . Following fixation, lesions were removed and the apical 5-mm portion of each root was sectioned . Root tips were dehydrated, sputter-coated with gold, and then examined for the occurrence of bacteria on the apical root surfaces using a scanning electron microscope . RESULTS: Bacterial cells were usually observed close to the apical foramen, but restricted to the root canal . Morphologically, these bacteria consisted of cocci and rods . A dense bacterial aggregate composed mainly of rods was observed within the root canal and surrounding the apical foramen of one specimen . Beyond the apical foramen, other bacterial morphological types were recognized, including coaggregations of cocci and filaments, characterizing a fully developed 'corn cob' . CONCLUSIONS: Extraradicular bacteria were observed in one tooth out of 27 (4% of the cases).

Mikrobiol Z, 2002 May-Jun, 64(3), 67 - 74
{Effect of gas mixture component composition on the process of hard materials colonization by methanotrophic bacteria}; Kisten' AG et al.; A device has been proposed which allows decreasing a possibility to contaminate the inoculum of methane-using bacteria (methanotrophs) under its growing . The gas mixture composition has been investigated for the intensity of grass and polysterene colonization by two species of methanotrophs: Methylococcus capsulatus UCM B-3030, possessing hydrophilic surface and hydrophobic Methylocystis parvus UKM B-3490T . It has been shown that immobilized methanotrophic bacteria can colonize the above materials in the wide range of methane and oxygen concentrations in gas mixture . The process of hard materials colonization was most intensive when the mixture contained 17-28% of methane and 5-28% of oxygen . No essential differences have been registered under colonization of hydrophilic (glass) and hydrophobic (polysterene) materials by the both cultures.

Mikrobiol Z, 2002 Mar-Apr, 64(2), 3 - 10
{Characterization of marine bacteria Pseudoalteromonas citrea degradating fucoidan}; Nedashkovskaia OI et al.; Two strains KMM 3296 and KMM 3298, isolated from the surface of brown algae Chorda filum and Fucus evanescens thalli and strain KMM 3297, isolated from celomic fluid of holoturian Apostichopus japonicus, were identified as Pseudoalteromonas citrea on the basis of pheno-, geno- and phylotypic features . The studied bacteria were different from other bacteria of the species as to their ability to destruct sulphated polysaccharides of brown algae, fucoidans.

J Exp Med, 2002 Aug 19, 196(4), 505 - 15
Bacteria-triggered CD4(+) T regulatory cells suppress Helicobacter hepaticus-induced colitis; Kullberg MC et al.; We have previously demonstrated that interleukin (IL)-10-deficient (IL-10 knockout {KO}) but not wild-type (WT) mice develop colitis after infection with Helicobacter hepaticus . Here, we show that infected recombination activating gene (RAG) KO mice develop intestinal inflammation after reconstitution with CD4(+) T cells from IL-10 KO animals and that the cotransfer of CD4(+) T cells from H . hepaticus-infected but not uninfected WT mice prevents this colitis . The disease-protective WT CD4(+) cells are contained within the CD45RB(low) fraction and unexpectedly were found in both the CD25(+) and the CD25(-) subpopulations of these cells, their frequency being higher in the latter . The mechanism by which CD25(+) and CD25(-) CD45RB(low) CD4(+) cells block colitis involves IL-10 and not transforming growth factor (TGF)-beta, as treatment with anti-IL-10R but not anti-TGF-beta monoclonal antibody abrogated their protective effect . In vitro, CD45RB(low) CD4(+) cells from infected WT mice were shown to produce IL-10 and suppress interferon-gamma production by IL-10 KO CD4(+) cells in an H . hepaticus antigen-specific manner . Together, our data support the concept that H . hepaticus infection results in the induction in WT mice of regulatory T cells that prevent bacteria-induced colitis . The induction of such cells in response to gut flora may be a mechanism protecting normal individuals against inflammatory bowel disease.

Protein Expr Purif, 2002 Aug, 25(3), 541 - 6
Preparation of active recombinant cathepsin K expressed in bacteria as inclusion body; Hwang HS et al.; Human cathepsin K (EC 3.4.22.38) is a member of the cysteine protease family with high primary sequence homology to cathepsins S, L, and B . It has been shown that cathepsin K plays a major role in the resorption of the bone matrix by osteoclasts . Cathepsin K has a potential as a drug target for the diseases related to bone matrix metabolism such as osteoporosis . We have expressed recombinant human procathepsin K in Escherichia coli as inclusion bodies . Purified procathepsin K had size of 38kDa which is in agreement with the predicted mass of the construct . Refolding was done by rapid dilution into 50mM Tris-HCl, pH 8.0 buffer containing 5mM EDTA, 10 mM GSH, 1mM GSSG, 0.7 M L-arginine, 0.5 M NaCl, and 1% CHAPS and further dialysis against 25 mM Tris-HCl, pH 8.0 containing 0.5 M NaCl . Mature active cathepsin K was prepared from refolded procathepsin K by incubating at 40 degrees C in pH 4.0 buffers with or without pepsin or cysteine . The presence of pepsin or cysteine in autocatalysis buffer did not have effect on the degree of conversion of nascent to mature cathepsin K, but reduced the autocatalysis time slightly . Proteolytic activity was confirmed using synthetic substrate, and Western blotting identified mature cathepsin K . Active cathepsin K had type I and II collagenolytic activities which could be inhibited by E-64.

Lett Appl Microbiol, 2002, 35(3), 242 - 6
A highly selective direct method of detecting sulphate-reducing bacteria in crude oil; Tanaka Y et al.; AIMS: The aim of this work was to develop a highly selective method of detecting sulphate-reducing bacteria (SRB) in crude oil . METHODS: A pair of PCR primers was designed based on an alignment of the nucleotide sequence of the 16S rRNA genes from the Desulfovibrionaceae family . DNA extraction from crude oil was performed by the method using zirconia beads and a stool kit . RESULTS: The PCR specifically detected Desulfovibrio and Desulfomicrobium in a sediment sample . When nucleic acids extracted directly from crude oil were used for the PCR, 16S rRNA genes of Desulfovibrio and Thermodesulforhabdus norvegicus were detected . IMPACT OF STUDY: A simple direct method for detection of the SRB in crude oil using PCR was established.

Life Sci Space Res, 1975, 13, 83 - 8
Membrane damage in dehydrated bacteria and its repair; Frankenberg-Schwager M et al.; The dehydration of bacteria by vacuum exposure results in damage to the cell membrane . This membrane damage does not necessarily lead to cell death . A part of the dehydrated bacteria is capable of eliminating the membrane damage by repair processes . Repair can proceed rapidly under conditions that permit synthesizing activities . The kinetics of this repair process were studied by means of the membrane-mediated biosynthesis of the cell wall as well as by the recovery of resistance to small concentrations of lysozyme . Repair is a precondition for cell proliferation . At low temperature cells can conserve their membrane damage and the repair process can be initiated when conditions become favourable.

Trends Genet, 2002 Sep, 18(9), 437 - 40
Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria?
Henrissat B, Deleury E, Coutinho PM.
We searched 55 completely sequenced bacterial genomes for glycogen synthesis and degradation enzymes . A significant proportion of these bacteria appears to lack glycogen metabolism capability . Interestingly, these bacteria are parasitic, symbiotic or fastidious (i.e . difficult to culture outside their normal environment) . It is suggested that the lack of bacterial glycogen metabolism is a trait associated with parasitic behaviour in bacteria.

Theor Popul Biol, 2002 Jun, 61(4), 509 - 18
Transposable elements and fitness of bacteria; Martiel JL et al.; A stochastic model was designed to describe the evolution of bacterial cultures during 10,000 generations . It is based on a decreasing law for the generation of beneficial mutations as they become fixed in the genomes . Seven beneficial mutations on average were necessary to improve the relative fitness from 1.0 to 1.43 and the model was consistent with the population biology and the genetic data of 12 experimental lines . In one bacterial line, comparison between the model and the data suggests that pivotal mutations mediated by insertion sequences account for a large part of bacterial adaptation . In a more detailed analysis of one simulation, it was shown that only 0.01% of the mutations generated by a population over 10,000 generations can go to fixation as a consequence of their improved fitness . However in the model, the probability of being better fit than its parent should be set initially at ca . 10% to promote an evolution similar to the observed data .

Theor Popul Biol, 2002 Jun, 61(4), 367 - 90
Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes; Karlin S et al.; Our analysis compares bacteria, archaea, and eukaryota with respect to a wide assortment of genome and proteome properties . These properties include ribosomal protein gene distributions, chaperone protein contrasts, major variation of transcription/translation factors, gene encoding pathways of energy metabolism, and predicted protein expression levels . Significant differences within and between the three domains of life include protein lengths, information processing procedures, many metabolic and lipid biosynthesis pathways, cellular controls, and regulatory proteins . Differences among genomes are influenced by lifestyle, habitat, physiology, energy sources, and other factors .

J Mol Evol, 2002 Jul, 55(1), 24 - 36
Measuring genome divergence in bacteria: a case study using chlamydian data; Dalevi DA et al.; We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae . The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estimated to 59 +/- 6 events, including 13% inversions, 38% short inversions, and 49% transpositions . In contrast to previous findings, no examples of horizontal gene transfer subsequent to species divergence were identified, nor any evidence for an excessive number of tandem gene duplications . A statistical model was used to compare nucleotide frequencies for a set of genes uniquely present in one species to a set of orthologous genes present in both species . The two data sets were not significantly different, which is indicative of a low frequency of horizontal gene transfer events . This is based on the assumption that a foreign gene of different nucleotide content will not have become completely ameliorated, as verified by simulations of the amelioration rate at twofold and fourfold degenerate codon sites . The frequencies of nucleotide substitutions at twofold and fourfold degenerate sites, deletions, inversions, and translocations were estimated to 1.42, 0.62, 0.18, 0.01, and 0.01 per site, respectively.

J Ind Microbiol Biotechnol, 2002 Aug, 29(2), 75 - 82
Survival and nutritional requirements of three bacteria isolated from ultrapure water; McAlister MB et al.; Bacteria isolated previously from ultrapure water (UPW) systems were examined for their ability to survive in UPW, with the ultimate goal of elucidating potential carbon and energy sources for the bacteria . Two strains of Ralstonia pickettii isolated from different areas within the UPW system (pretreatment and polishing loop, and referred to as strains 3A1 and MF254A, respectively) and a strain of Bradyrhizobium sp . were compared to increase our understanding of the fundamental behavior of bacteria contaminating UPW . R . pickettii (3A1) grew significantly slower in R2A medium, with a final cell yield much lower than the isolate from the polishing loop . In addition, R . pickettii MF254A showed a broader substrate range than either strain 3A1 or Bradyrhizobium sp . In UPW, there appears to be a threshold cell concentration (approximately 10(6) colony-forming units/ml), whereby the cell numbers remain constant for a prolonged period of 6 months or more . Below this concentration, rapid proliferation is observed until the threshold concentration is attained . Preliminary experiments suggested that nitrogen gas (frequently added to UPW storage tanks) may contribute to growth of Bradyrhizobium sp . Above the threshold concentration, the strain of Ralstonia sp . isolated from the polishing loop was capable of cryptic growth with heat-killed cells in UPW . However, cryptic growth was not observed when the cells supplied as nutrients were killed using UV254 light . Furthermore, cryptic growth did not appear to contribute significantly to proliferation of Bradyrhizobium sp . or Ralstonia sp . 3A1 (isolated from the pretreatment loop) . We believe that cryptic growth may aid survival of the bacteria in UPW, but further experiments are warranted to prove this phenomenon conclusively.

J Med Dent Sci, 2000 Dec, 47(4), 233 - 41
Roles of mucosal bacteria and succinic acid in colitis caused by dextran sulfate sodium in mice; Ariake K et al.; Intestines of mice with colitis caused by dextran sulfate sodium (DSS) contain more Bacteroidaceae cells than untreated controls . We investigated the roles of intestinal bacteria and succinic acid, a by-product of Bacteroidaceae metabolism, in this model of colitis . CBA/J mice were given 3% DSS in water for 14 days . After mice were anesthetized and killed, concentrations of organic acids in stools from the cecum and colon were measured . The resected rectum and colon were washed with sterile saline; some specimens were incubated with imipenem in saline for 1 h to kill bacteria on the surfaces and others were not . Their homogenates were cultured anaerobically and aerobically . Separately, 1 mL of 20 mM succinic acid was infused into the rectum of mice, whose anal verge was glued . Animals were anesthetized and killed the next day . The rectum and colon were examined histologically . Concentrations of succinate were higher everywhere in the colon of mice with colitis than in controls . Mice with colitis had more Bacteroidaceae cells, especially B . caccae, than controls . Mice given succinate enemas had focal erosions of the mucosa and edema of the submucosa . Succinic acid, produced abundantly by members of the family Bacteroidaceae, especially B . caccae, may be the ulcerogenic agent in DSS colitis.

Plant Cell Physiol, 2002 Jul, 43(7), 802 - 9
Functional expression of two pine glutamine synthetase genes in bacteria reveals that they encode cytosolic holoenzymes with different molecular and catalytic properties; de la Torre F et al.; Two glutamine synthetase isogenes, GS1a and GS1b, isolated from pine have been functionally expressed in E . coli and the characteristics of individual gene products compared . When bacteria were grown at 37 degrees C most pine GS1 protein was found in the insoluble fraction but lowering of the expression temperature increased yield of both GS1 polypeptide and activity in the soluble fraction . High levels of functionally active GS1a (309 + or - 35 nkat mg(-1)) and GS1b (1,166 + or - 65 nkat mg(-1)) enzymes were obtained by decreasing the expression temperature to 10 degrees C . Purification and characterization of recombinant products showed that pine GS1 polypeptides are assembled in octameric GS holoenzymes showing structural and kinetic differences . The results are discussed with regard to the specific localization of GS1a and GS1b in different cell types of pine seedlings . The isoform GS1a may control the assimilation of the high levels of ammonium released in photosynthetic tissues, whereas GS1b enzyme could mitigate oscillations in glutamate availability providing a constant flux of glutamine for nitrogen transport in vascular cells.

Water Res, 2002 May, 36(10), 2533 - 40
Anaerobic biotransformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) by aquifer bacteria using hydrogen as the sole electron donor; Beller HR; RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) is a nitramine explosive that has contaminated soil and groundwater at military installations throughout the US . Although anaerobic RDX metabolism has been reported, the process is not well understood, as past studies have typically involved complex, undefined media with multiple potential electron donors and acceptors . In this study, bacteria enriched from RDX-contaminated aquifer sediments consumed RDX in a defined, bicarbonate-buffered, anaerobic medium containing hydrogen as the sole electron donor and RDX as a potential electron acceptor and sole nitrogen source . RDX was not consumed in live controls that did not contain hydrogen . Transient formation of mononitroso- and dinitroso-RDX metabolites (hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine and hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine, respectively) was documented by liquid chromatography-mass spectrometry . However, studies with 14C-labeled RDX suggested that mineralization to carbon dioxide was negligible (<2%), which is consistent with cometabolic transformation . Several lines of evidence suggest that the RDX-transforming bacteria under study were homoacetogens, including correlations between RDX consumption and acetate production . Methanogens were unlikely to be responsible for RDX metabolism, as the presence of 2-bromoethanesulfonate, an inhibitor of methanogenesis, did not appear to affect RDX metabolism . The presence of nitrate reversibly halted RDX metabolism, whereas ammonium had no discernible effect, which implies that: (i) nitrate, which commonly occurs in RDX-contaminated groundwater, may inhibit in situ RDX metabolism, and (ii) although RDX may act as both a nitrogen source and cometabolic electron sink, the latter role predominates, as RDX reduction will proceed regardless of whether or not a more favorable nitrogen source is present.

Mol Ecol, 2002 Aug, 11(8), 1275 - 83
Recent changes in phenotype and patterns of host specialization in Wolbachia bacteria; Jiggins FM et al.; Wolbachia are a genus of bacterial symbionts that are known to manipulate the reproduction of their arthropod hosts, both by distorting the host sex ratio and by inducing cytoplasmic incompatibility . Previous work has suggested that some Wolbachia clades specialize in particular host taxa, but others are diverse . Furthermore, the frequency with which related strains change in phenotype is unknown . We have examined these issues for Wolbachia bacteria from Acraea butterflies, where different interactions are known in different host species . We found that bacteria from Acraea butterflies mostly cluster together in several different clades on the bacterial phylogeny, implying specialization of particular strains on these host taxa . We also observed that bacterial strains with different phenotypic effects on their hosts commonly shared identical gene sequences at two different loci . This suggests both that the phenotypes of the strains have changed recently between sex ratio distortion and cytoplasmic incompatibility, and that host specialization is not related to the bacterial phenotype, as suggested from previous data . We also analysed published data from other arthropod taxa, and found that the Wolbachia infections of the majority of arthropod genera tend to cluster together on the bacterial phylogeny . Therefore, we conclude that Wolbachia is most likely to move horizontally between closely related hosts, perhaps because of a combination of shared vectors for transmission and physiological specialization of the bacteria on those hosts.

Mikrobiologiia, 2002 May-Jun, 71(3), 301 - 7
{Carbon and sulfur metabolism in representatives of two clusters of bacteria of the genus Leucothrix: a comparative study}; Grabovich MIu et al.; Major pathways of carbon and sulfur metabolisms were studied in representatives of two clusters of bacteria: Leucothrix thiophila (cluster I, strains 2WS, 4WS, and 6WS) and Leucothrix sp . (cluster II, strains 1WS, 3WS, and 5WS) . All strains were capable of chemoorganoheterotrophic growth, as well as of chemolithoheterotrophic growth in the presence of reduced sulfur compounds . The bacteria were found to possess a complete set of the enzymes of the tricarboxylic acid cycle and glyoxylate cycle . The hydrogenase activity in cells of cluster I strains was an order of magnitude lower than in cluster II strains and in other known heterotrophic bacteria . Cells of bacteria of both clusters exhibited high activity levels of enzymes involved in the energy metabolism of sulfur . The oxidation of sulfur compounds and the operation of the electron-transport chain were shown to be related . Cluster II bacteria more efficiently use organic compounds in their energy metabolism, whereas cluster I bacteria are characterized by more efficient utilization of reduced sulfur compounds . During sulfite oxidation, cluster I bacteria can synthesize ATP both via substrate-level phosphorylation and oxidative phosphorylation, whereas cluster II bacteria synthesize ATP only via the latter process.

J Infect Dis, 2002 Aug 1, 186(3), 423 - 7 Epub 2002 Jul 17.
Cultured human gastric explants: a model for studies of bacteria-host interaction during conditions of experimental Helicobacter pylori infection; Olfat FO et al.; The unique environment of the human stomach makes it difficult to establish representative in vitro models for Helicobacter pylori that mimic the natural infection . The in vitro explant culture (IVEC) technique is based on coculture of human gastric explants with H . pylori, where bacteria-host interaction is studied on the basis of interleukin (IL)-8 secretion of the explant tissue in response to infection . In this study, it was shown that H . pylori attachment to gastric epithelial tissue was required for induction of representative inflammatory responses, assessed here by IL-8 production . Furthermore, IL-8 production by the explant tissue in response to H . pylori infection demonstrated that the explants were adequately responsive . The IVEC technique for studies of the interplay between H . pylori and the human gastric mucosa during conditions of experimental infections in vitro could add knowledge to our understanding of the complex bacteria-host cross-talk in vivo.

Front Biosci, 2002 Aug 01, 7, d1762 - 81
The necessity of combining genomic and enzymatic data to infer metabolic function and pathways in the smallest bacteria: amino acid, purine and pyrimidine metabolism in Mollicutes; Pollack JD; Bacteria of the class Mollicutes have no cell wall . One species, Mycoplasma genitalium is the personification of the simplest form of independent cell-free life . Its small genome (580 kbp) is the smallest of any cell . Mollicutes have unique metabolic properties, perhaps because of their limited coding space and high mutability . Based on 16S rRNA analyses the Mollicutes Mycoplasma gallisepticum is thought to be the most mutable bacteria . Enzyme activities found in most Bacteria are absent from Mollicutes . The functions of apparently absent genes and enzymes can apparently be fulfilled by other genes and their expression products that have multiple capabilities . Because of these and other properties predictions of their metabolism based only on, e.g., either annotation, enzymatic assay, proteomic studies or structural analyses is problematic . To obtain a more confident appraisal of the functional capabilities of these simplest cells genomic and enzymatic data were combined to obtain a "metabolic consensus" . The consensus is represented by a biochemical circuit for central metabolism involving purine and pyrimidine interconversions and their linkages to amino acid metabolism, glycolysis and the pentose phosphate pathway in three human Mollicutes pathogens: Mycoplasma pneumoniae, Mycoplasma genitalium and Ureaplasma urealyticum.

Ned Tijdschr Geneeskd, 2002 Jun 29, 146(26), 1212 - 5
{Combatting river blindness by means of chemotherapy directed at the symbiotic Wolbachia bacteria in the causative filariae}; Kager PA; In a mouse model of river blindness it was demonstrated that Wolbachia bacteria, endosymbionts of filarial nematodes, play an important role in the inflammatory process leading to the disease and that this process depends on Toll-like receptor 4 . Wolbachia is found in many arthropods and in all filariae pathogenic for man . Treatment with doxycycline depletes female filariae of Wolbachia and renders them infertile for at least 18 months . Chemotherapy of filarial nematodes should be studied for the reduction and possibly prevention of pathology due to filariae, and for a contribution to control and eradication programmes.

Infect Immun, 2002 Aug, 70(8), 4705 - 7
Diverse bacteria are pathogens of Caenorhabditis elegans; Couillault C et al.; Practically and ethically attractive as model systems, invertebrate organisms are increasingly recognized as relevant for the study of bacterial pathogenesis . We show here that the nematode Caenorhabditis elegans is susceptible to a surprisingly broad range of bacteria and may constitute a useful model for the study of both pathogens and symbionts.

Biotechnol Bioeng, 2002 Jul 20, 79(2), 188 - 99
Catabolic enzyme levels in bacteria grown on binary and ternary substrate mixtures in continuous culture; Rudolph JM et al.; Bacteria grow on multicomponent substrates in most natural and engineered environments . To advance our ability to model bacterial growth on such substrates, axenic cultures were grown in chemostats at a low specific growth rate and a constant total energy flux on binary and ternary substrate mixtures and were assayed for key catabolic enzymes for each substrate . The substrates were benzoate, salicylate, and glucose, and the enzymes were catechol 1,2-dioxygenase, gentisate 1,2-dioxygenase, and glucose-6-phosphate dehydrogenase, respectively . The binary mixtures were salicylate with benzoate and salicylate with glucose . Measurements were also made of oxygen uptake rate by whole cells in response to each substrate . The effects of the substrate mixture on the oxygen uptake rate paralleled the effects on the measured enzymes . Catechol 1,2-dioxygenase exhibited a threshold response before synthesis occurred . Below the threshold flux of benzoate through the chemostat, either basal enzyme levels or nonspecific enzymes kept reactor concentrations too low for enzyme synthesis . Above the threshold, enzyme levels were linearly related to the fraction of the total energy flux through the chemostat due to benzoate . Gentisate 1,2-dioxygenase exhibited a linear response to the salicylate flux when mixed with benzoate, but a threshold response when mixed with glucose . Glucose-6-phosphate dehydrogenase activity increased in direct proportion to the glucose flux through the chemostat over the entire range studied . The results from two ternary mixtures were consistent with those from the binary mixtures .

Arch Microbiol, 2002 Aug, 178(2), 131 - 40 Epub 2002 May 22.
Phylogeny of green sulfur bacteria on the basis of gene sequences of 16S rRNA and of the Fenna-Matthews-Olson protein; Alexander B et al.; The phylogeny of green sulfur bacteria was studied on the basis of gene sequences of the 16S rRNA and of the Fenna-Matthews-Olson (FMO) protein . Representative and type strains (31 strains total) of most of the known species were analyzed . On the basis of fmoA gene sequences from Chlorobium tepidum ATCC 49652(T) and Chlorobium limicola DSM 249(T) available from the EMBL database, primers were constructed that allowed sequence analysis of a major part of the fmoAgene . The largely congruent phylogenetic relationship of sequences of the fmoA gene and of 16S rDNA gives considerable support to the phylogeny of green sulfur bacteria previously suggested on the basis of 16S rDNA sequences . Distinct groups of strains were recognized on the basis of 16S rDNA and FMO sequences and supported by characteristic signature amino acids of FMO . Marine strains formed clusters separate from freshwater strains . The resulting phylogenetic grouping and relationship of the green sulfur bacteria do not correlate with their current taxonomic classification.

J Periodontal Res, 2002 Jun, 37(3), 223 - 9
Simple and rapid detection of serum antibody to periodontopathic bacteria by dot blotting; Kawashima Y et al.; The aim of this study was to detect the specific immunoglobulin G antibodies against periodontopathic bacteria by dot blotting . In the procedure used, bacterial preparations were blotted on a nitrocellulose membrane . After blocking the nonspecific binding sites, the diluted serum was blotted onto the preparations . The membrane was immersed in secondary antibodies and then in substrate buffer . The colored blots were then evaluated . To test the reliability of this procedure, 20 serum samples were examined for antibody: ten for anti-Porphyromonas gingivalis antibody, and the other ten for anti-Actinobacillus actinomycetemcomitans antibody . Five samples out of each set of ten had previously been confirmed as having high enzyme-linked immunosorbant assay (ELISA) titers to the antigen, while the other five had been confirmed as having average titer levels . Both whole-cell sonic extracts and fimbriae of P . gingivalis were used as antigens in the dot blotting, in order to compare their use as antigens in assays of the patients' sera . ELISA was also used to measure anti-P . gingivalis antibody titers . For the measurement of IgG antibodies against A . actinomycetemcomitans, formalin-killed whole cells were used . Fifty serum samples were examined for IgG antibodies against A . actinomycetemcomitans by dot blotting and ELISA . With both antigens, after 4 h, coloration of blots was more clearly visible for the high-titer sera than for the average-titer sera . The intensity of coloration of the blots for P . gingivalis and A . actinomycetemcomitans showed correlation with the ELISA titers . A particularly significant correlation was shown when P . gingivalis fimbriae were used as antigen . These results suggest that this dot blot method is a simple and rapid means of detection of serum antibodies, and that it shows promise as a chair-side assay method.

Planta, 2002 Jul, 215(3), 424 - 9 Epub 2002 Apr 24.
Expression of the NH(+)(4)-transporter gene LEAMT1;2 is induced in tomato roots upon association with N(2)-fixing bacteria; Becker D et al.; Plants growing in close association with N(2)-fixing bacteria are able to overcome growth limitations in N-depleted soils . The molecular mechanism by which free-living, N(2)-fixing bacteria promote plant growth is still a matter of debate . By inoculating N-depleted tomato (Lycopersicon esculentum Mill.) plants with Azospirillum brasilense or Azoarcus sp . we could demonstrate the induction of the root NH(+)(4)-transporter gene, LEAMT1;2 (L . esculentum ammonium transporter 1;2), indicating that bacterial NH(+)(4) might be used as an N source under these conditions . Azospirillum brasilense (nif(-)) mutants, which lack the structural nifDK genes, failed to induce LEAMT1;2 expression . This suggests that root-associated N(2)-fixing bacteria do excrete NH(+)(4) to levels that can be sensed by tomato roots and is in agreement with the induction of expression of LEAMT1;2 with as low as > or = 1 microM external NH(+)(4) . While peak expression was obtained with 2-5 microM NH(+)(4), a further increase in NH(+)(4) reduced LEAMT1;2-mRNA levels in a concentration-dependent manner . The inhibition of LEAMT1;2 expression by glutamine and the glutamine synthetase blocker L-methionine sulfoximine (MSX) provided evidence for the control of LEAMT1;2 expression by cytoplasmic NH(+)(4) concentration or the plant N status . Since micromolar concentrations of NH(+)(4) strongly increased the LEAMT1;2-mRNA levels, the transported NH(+)(4) ion itself could represent a key signal in the associative interaction between higher plants and N(2)-fixing micro-organisms.

Biochimie, 2002 Apr, 84(4), 341 - 7
Hypothesis: hyperstructures regulate initiation in Escherichia coli and other bacteria; Norris V et al.; Hyperstructures or modules have been proposed to constitute a level of organisation intermediate between macromolecules and whole cells . In this model of intracellular organisation, hyperstructures compete and collaborate for existence within the membrane and cytoplasm . Those directly involved in the cell cycle include initiation, replication and division hyperstructures based on DnaA, SeqA and the 2-minute cluster, respectively . During the run-up to initiation, the mass to DNA ratio increases and, we contend, differential gene expression leads to some hyperstructures becoming more active and stable than others . This results in a drop in the diversity of hyperstructures, some of which release DnaA as they dissociate, and a DnaA-initiation hyperstructure forms . Subsequent DNA replication and cell division generate different daughter cells containing different hyperstructures . This has the advantage of increasing the phenotypic diversity of the population . In developing this model, we also invoke hyperstructures in the partitioning of origins of replication.

Biologist (London), 2002 Jun, 49(3), 113 - 7
Pods and Nods: a new look at symbiotic nitrogen fixing bacteria; Brewin NJ; How can growing a crop plant make a field more fertile? With legumes, this is precisely what happens . Working in partnership with symbiotic bacteria that can create root nodules on their chosen host, legumes can fix atmospheric nitrogen and enhance the nitrogen status of soils . How does this symbiosis develop? And how did it evolve? Bacterial and plant genomics are beginning to provide the answers.

J Invertebr Pathol, 2002 Feb, 79(2), 72 - 9
Bacteria in ovarioles of females from maleless families of ladybird beetles Adalia bipunctata L . (Coleoptera: Coccinellidae) naturally infected with Rickettsia, Wolbachia, and Spiroplasma; Sokolova MI et al.; Ovarioles were found to be infected with Spiroplasma, Wolbachia, and Rickettsia in Adalia bipunctata females with maleless progeny in different natural populations . Ooplasm was infected with few Wolbachia bacteria . In ooplasm infected by Rickettsia, bacteria were present in small foci . Spiroplasmas were found encapsulated into ooplasm from the wider intercellular spaces between epithelial and oocyte cells . The cytoplasm of follicular epithelia infected with Rickettsia was heavily destroyed, but the nucleus was intact and free from bacteria . The essential feature of follicular epithelium cells from Spiroplasma and Wolbachia infected A . bipunctata females was inclusions of three types: crystalline, filaments, and concentric myelin-like lamellae . Observations of smears prepared from ovaries of A . bipunctata from natural populations revealed a low concentration of bacteria within a microscopy field (less 10 bacteria) in more than 90% of specimens, and only a few ovaries were heavily infected . Two different ways of bacterial invasion of the oocyte are suggested: Spiroplasma-like, through the intercellular spaces in the epithelium and Rickettsia-like, through the cytoplasm of follicular epithelium cells . Bacteria were not found in germarium zones and we suggest that each follicle is infected from haemolymph . (c) 2002 Elsevier Science (USA).

Folia Microbiol (Praha), 2002, 47(3), 203 - 12
ATP-dependent proteinases in bacteria; Hlavacek O et al.; Cytoplasmic proteolysis is an indispensable process for proper function of a cell . Degradation of many intracellular proteins is initiated by ATP-dependent proteinases, which are involved in the regulation of the level of proteins with short half-lives . In addition, they remove many damaged and abnormal proteins and thus play also an important role during stress . ATP-dependent proteinases are large multi-subunit assemblies composed of proteolytic core domains and ATPase-containing regulatory domains on a single polypeptide chain or on distinct subunits, which can act as molecular chaperones . This review briefly summarizes the data about four main groups of these proteinases in bacteria (i.e . Lon, Clp family, HslUV and FtsH) and characterizes their structure, mechanism of action and properties.

Genome Biol . 2002;3(6):RESEARCH0031 . Epub 2002 May 30.
Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries; Jenkins C et al.; BACKGROUND: The planctomycetes comprise a distinct group of the domain Bacteria, forming a separate division by phylogenetic analysis . The organization of their cells into membrane-defined compartments including membrane-bounded nucleoids, their budding reproduction and complete absence of peptidoglycan distinguish them from most other Bacteria . A random sequencing approach was applied to the genomes of two planctomycete species, Gemmata obscuriglobus and Pirellula marina, to discover genes relevant to their cell biology and physiology . RESULTS: Genes with a wide variety of functions were identified in G . obscuriglobus and Pi . marina, including those of metabolism and biosynthesis, transport, regulation, translation and DNA replication, consistent with established phenotypic characters for these species . The genes sequenced were predominantly homologous to those in members of other divisions of the Bacteria, but there were also matches with nuclear genomic genes of the domain Eukarya, genes that may have appeared in the planctomycetes via horizontal gene transfer events . Significant among these matches are those with two genes atypical for Bacteria and with significant cell-biology implications - integrin alpha-V and inter-alpha-trypsin inhibitor protein - with homologs in G . obscuriglobus and Pi . marina respectively . CONCLUSIONS: The random-sequence-tag approach applied here to G . obscuriglobus and Pi . marina is the first report of gene recovery and analysis from members of the planctomycetes using genome-based methods . Gene homologs identified were predominantly similar to genes of Bacteria, but some significant best matches to genes from Eukarya suggest that lateral gene transfer events between domains may have involved this division at some time during its evolution.

Water Res, 2002 Apr, 36(8), 2091 - 7
Electron spin resonance study of copper biosorption by bacteria; Nakajima A; The biosorption of copper by bacteria was studied by using ESR spectroscopy . Among bacteria tested, Arthrobacter nicotianae has the most excellent ability to sorb copper . The biosorption of copper by Arthrobacter cells was so rapid, affected by the solution pH, and obeys the Langmuir adsorption equilibrium . The electron spin resonance (ESR) spectra of Cu(II) in bacterial cells are axial type, having a major absorption to higher field at gperpendicular and lesser absorption to lower field at gparallel with four lines . The ESR parameters showed that Cu(II) in the cells has the tetragonally distorted octahedral structure with nitrogen and oxygen as ligand atoms, which suggests that most of copper in bacterial cells combined with amino acid residues in the cell surface proteins . The variation of spectral patterns among bacteria could explain as the change of ligand circumstances caused by the pH of the cell surface.

Microb Ecol, 2002 Aug, 44(2), 137 - 43 Epub 2002 Jun 28.
Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria; Mira A et al.; Many species of bacterial endosymbionts are acquired by animal hosts before birth, through direct transmission from mothers to eggs or embryos . This vertical transmission imposes a reduction in numbers or "bottleneck," and the size of this bottleneck affects the population structure and evolution of symbiotic lineages . We have estimated the size of the transmission bottleneck in Buchnera, the bacterial symbiont of aphids, using basic light and electron microscopy techniques . By serial-sectioning whole aphid abdomens, their eggs, and embryos, we determined the following parameters: (i) The average size of a Buchnera cell is 2.9 mm in diameter . (ii) The total number of Buchnera in an Acyrthosiphon pisum embryo was around 36700 whereas a first instar nymph contained more than 119000 . (iii) The number of symbionts per bacteriocyte was around 800 in an embryo and 3200 in a first instar nymph . (iv) The total number of Buchnera transmitted to each sexual egg ranged from 850 in Nasonovia to 1800 in A . pisum to more than 8000 in Uroleucon ambrosiae . (v) The total number of secondary endosymbionts in A . pisum was 12170 for an embryo and 18360 for a first instar nymph . Secondary symbionts were arranged both extracellularly and in clusters of 2000-8000 bacteria inside bacteriocytes . These numbers are consistent with the few previous estimates of symbiont population sizes based on counts of gene copies.

Nucleic Acids Res, 2002 Jul 1, 30(13), 2987 - 94
Origin and fate of repeats in bacteria; Achaz G et al.; We investigated 53 complete bacterial chromosomes for intrachromosomal repeats . In previous studies on eukaryote chromosomes, we proposed a model for the dynamics of repeats based on the continuous genesis of tandem repeats, followed by an active process of high deletion rate, counteracted by rearrangement events that may prevent the repeats from being deleted . The present study of long repeats in the genomes of Bacteria and Archaea suggests that our model of interspersed repeats dynamics may apply to them . Thus the duplication process might be a consequence of very ancient mechanisms shared by all three domains . Moreover, we show that there is a strong negative correlation between nucleotide composition bias and the repeat density of genomes . We hypothesise that in highly biased genomes, non-duplicated small repeats arise more frequently by random effects and are used as primers for duplication mechanisms, leading to a higher density of large repeats.

Cell, 2002 May 17, 109(4), 421 - 4
Small talk . Cell-to-cell communication in bacteria; Bassler BL; In a process called quorum sensing, groups of bacteria communicate with one another to coordinate their behavior and function like a multicellular organism . A diverse array of secreted chemical signal molecules and signal detection apparatuses facilitate highly productive intra- and interspecies relationships.

Anal Sci, 2002 Jun, 18(6), 625 - 30
Bacteria-modified amperometric immunosensor for a Brucella melitensis antibody assay; Li ZZ et al.; A novel amperometric immunosensor setup is described which uses horseradish peroxidase (HRP) as a label in conjunction with a current-based Brucella sensor . The Bacteria modified immunosensor was constructed by using a biocomposite formed by dispersing graphite powder into a mixture of Brucella melitensis and silicate polymer gel . The enzyme-labeled antibody can readily diffuse toward the encapsulated antigen (Brucella melitensis), which retains its binding properties, and the association reaction is easily detected at the surface exposed to the solution . The use of an oaminophenol (o-AP) substrate and amperometric detection at -150 mV (vs . SCE) results in a relatively low detection limit of 3.5 ng/ml and a linear detection range of 3.5 ng/ml to 200 ng/ml . Based on an optimized parameter, the prepared sensor was used to detect the Brucella melitensis antibody in serum samples by using a competitive binding assay . The results demonstrate the feasibility of employing the proposed immunosensor for the detection for Brucella melitensis antibody in a clinical analysis.

Water Sci Technol, 2002, 45(9), 157 - 66
Use of simulation mass balance modeling to estimate phosphorus and bacteria dynamics in watersheds; Cassell EA et al.; Dynamic simulation technology is integrated with mass balance concepts and compartment-flux diagramming to create computer models that estimate contaminant export from watersheds over long and short-term futures under alternative simulated policies of watershed management . The Watershed Ecosystem Nutrient Dynamics (WEND) model, applied to developed watersheds with a mix of urban, agricultural, and forest land-uses, predicted phosphorus (P) export from three watersheds; a 275,000 ha dairy/urban watershed, a 77,000 ha poultry/urban watershed, and a 23,000 ha swine dominated watershed . Urban, agricultural, and forestry activities contribute to P export in different proportions . In all cases the P imports to the watershed exceed total export and P accumulates in watershed soils . Long-term future P export patterns are compared for several watershed management strategies that range from encouragement of rapid urban growth to aggressive environmental protection . The specific response of each watershed to imposed management is unique, but management strategies designed to reduce export of P over the long-term need to consider options that promote P input/output balance . Using this same approach, the Watershed Ecosystem Bacterial Dynamics (WEBD) model assesses the dynamics of bacterial populations in a small case-study watershed over an annual cycle as influenced by dairy farm management actions . WEND and WEBD models integrate the diversity of activities and stakeholders interested in the watershed and promote development of a more holistic understanding of watershed function . Model outputs are designed to assist watershed policy-makers, managers, and planners to explore potential future impacts of management/policy decisions.

Microb Pathog, 2002 May, 32(5), 239 - 48
Brucella abortus siderophore 2,3-dihydroxybenzoic acid (DHBA) facilitates intracellular survival of the bacteria; Parent MA et al.; Siderophores are low molecular weight molecules that allow bacteria to acquire iron from host cell proteins . 2,3-dihydroxybenzoic acid (DHBA) is the only known siderophore produced by the intracellular pathogen Brucella abortus . Here its role in virulence was assessed by evaluating the ability of a mutant with a disruption of the entC gene to survive and replicate in vitro in murine and bovine cells and in vivo in resistant and susceptible murine hosts . It was hypothesized that DHBA is vital for bacterial virulence by its ability to chelate intracellular iron thereby preventing generation of anti-bacterial hydroxyl radicals via the Haber-Weiss reaction, to scavenge reactive oxygen intermediates and for acquisition of iron needed for nutritional purposes . The data showed DHBA played a significant role for bacterial survival in host cells after infection including in murine macrophages cultured in the presence and absence of exogenous interferon-gamma (IFN-gamma) and in bovine trophoblasts supplemented with erythritol . In severely iron-depleted conditions, DHBA was also found to be essential for growth in murine macrophages . Despite these deficiencies, the absence of DHBA had no long-term significant effect on the number of CFU recovered in vivo from either the Brucella-resistant C57BL/6 mice or Brucella-susceptible IFN-gamma knock-out C57BL/6 mice .

Microbiology, 2002 Jun, 148(Pt 6), 1637 - 53
The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere; Tauch A et al.; Plasmid pIPO2 is a cryptic, conjugative, broad-host-range plasmid isolated from the wheat rhizosphere . It efficiently self-transfers between alpha, beta and gamma Proteobacteria and has a mobilizing/retromobilizing capacity for IncQ plasmids . The complete nucleotide sequence of pIPO2 is presented on the basis of its mini-Tn5::luxABtet-tagged derivative, pIPO2T . The pIPO2 sequence is 39815 bp long and contains at least 43 complete ORFs . Apart from a suite of ORFs with unknown function, all of the genes carried on pIPO2 are predicted to be involved in plasmid replication, maintenance and conjugative transfer . The overall organization of these genes is different from previously described plasmids, but is similar to the genetic organization seen in pSB102, a conjugative plasmid recently isolated from the bacterial community of the alfalfa rhizosphere . The putative conjugative transfer region of pIPO2 covers 23 kb and contains the genes required for DNA processing (Dtr) and mating pair formation (Mpf) . The organization of these transfer genes in pIPO2 is highly similar to the genetic organization seen in the environmental plasmid pSB102 and in pXF51 from the plant pathogen Xylella fastidiosa . Plasmids pSB102 and pXF51 have recently been proposed to form a new family of environmental broad-host-range plasmids . Here it is suggested that pIPO2 is a new member of this family . The proposed Mpf system of pIPO2 shares high amino acid sequence similarity with equivalent VirB proteins from the type IV secretion system of Brucella spp . Sequence information was used to design primers specific for the detection of pIPO2 . Environmental DNA from a range of diverse habitats was screened by PCR with these primers . Consistently positive signals for the presence of pIPO2 were obtained from a range of soil-related habitats, including the rhizospheres of young wheat plants, of field-grown oats and of grass (all gramineous plants), as well as from the rhizosphere of tomato plants . These data add to the growing evidence that plasmids carry advantageous genes with as yet undefined functions in plant-associated communities.

Int J Syst Evol Microbiol, 2002 May, 52(Pt 3), 773 - 6
Methylobacterium suomiense sp . nov . and Methylobacterium lusitanum sp . nov., aerobic, pink-pigmented, facultatively methylotrophic bacteria; Doronina NV et al.; Two aerobic, pink-pigmented, facultatively methylotrophic bacteria, strains F20T and RXM(T), are described taxonomically . On the basis of their phenotypic and genotypic properties, the isolates are proposed as novel species of the genus Methylobacterium, Methylobacterium suomiense sp . nov . (type strain F20T = VKM B-2238T = NCIMB 13778T) and Methylobacterium lusitanum sp . nov . (type strain RXMT = VKM B-2239T = NCIMB 13779T).

J Mol Biol, 2002 Apr 26, 318(2), 455 - 62
Hypothesis: a phospholipid translocase couples lateral and transverse bilayer asymmetries in dividing bacteria; Norris V et al.; Cell division in bacteria such as Escherichia coli entails changes in the radii of curvature of the invaginating cytoplasmic membrane which culminate in rearrangements of its monolayers . Division therefore risks perturbing transverse and lateral asymmetries and compromising membrane integrity . This leads us to propose that a strong selective pressure exists for a phospholipid translocator that would transfer phospholipids across the cytoplasmic membrane so as to both demarcate the division site and mediate lipid composition during division . This translocase has an affinity for phospholipids with small headgroups and unsaturated acyl chains which it translocates so as to (1) generate changes in the radius of curvature, (2) facilitate septum formation, (3) minimise bilayer disruption during fusion and (4) prevent septum formation at old or inappropriate division sites . We discuss briefly possible candidates for this translocase including ABC transporters and proteins localised to the division site . (c) 2002 Elsevier Science Ltd.

Microbes Infect, 2002 May, 4(6), 679 - 83
Correlation between oral malodor and periodontal bacteria; Nakano Y et al.; Volatile sulfur compounds (VSCs), including hydrogen sulfide, methyl mercaptan, and dimethyl sulfide, are primarily responsible for oral malodor . Recently, the mgl gene encoding L-methionine-alpha-deamino-gamma-mercaptomethane-lyase, which produces methyl mercaptan, was cloned from Porphyromonas gingivalis . This article discusses the mechanism and pathogenic role of the formation of VSCs by oral bacteria.

J Cell Sci, 2002 Jun 15, 115(Pt 12), 2603 - 11
Mediators of innate immune recognition of bacteria concentrate in lipid rafts and facilitate lipopolysaccharide-induced cell activation; Triantafilou M et al.; The plasma membrane of cells is composed of lateral heterogeneities, patches and microdomains . These membrane microdomains or lipid rafts are enriched in glycosphingolipids and cholesterol and have been implicated in cellular processes such as membrane sorting and signal transduction . In this study we investigated the importance of lipid raft formation in the innate immune recognition of bacteria using biochemical and fluorescence imaging techniques . We found that receptor molecules that are implicated in lipopolysaccharide (LPS)-cellular activation, such as CD14, heat shock protein (hsp) 70, 90, Chemokine receptor 4 (CXCR4), growth differentiation factor 5 (GDF5) and Toll-like receptor 4 (TLR4), are present in microdomains following LPS stimulation . Lipid raft integrity is essential for LPS-cellular activation, since raft-disrupting drugs, such as nystatin or MCD, inhibit LPS-induced TNF-alpha secretion . Our results suggest that the entire bacterial recognition system is based around the ligation of CD14 by bacterial components and the recruitment of multiple signalling molecules, such as hsp70, hsp90, CXCR4, GDF5 and TLR4, at the site of CD14-LPS ligation, within the lipid rafts.

Genome Res, 2002 Jun, 12(6), 962 - 8
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria; Jordan IK et al.; The "knockout-rate" prediction holds that essential genes should be more evolutionarily conserved than are nonessential genes . This is because negative (purifying) selection acting on essential genes is expected to be more stringent than that for nonessential genes, which are more functionally dispensable and/or redundant . However, a recent survey of evolutionary distances between Saccharomyces cerevisiae and Caenorhabditis elegans proteins did not reveal any difference between the rates of evolution for essential and nonessential genes . An analysis of mouse and rat orthologous genes also found that essential and nonessential genes evolved at similar rates when genes thought to evolve under directional selection were excluded from the analysis . In the present study, we combine genomic sequence data with experimental knockout data to compare the rates of evolution and the levels of selection for essential versus nonessential bacterial genes . In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales.

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