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| Vet Microbiol, 2001 Mar 20, 79(2), 171 - 82 Effects of an experimental infection with Actinobacillus pleuropneumoniae on the interferon-alpha and interleukin-6 producing capacity of porcine peripheral blood mononuclear cells stimulated with bacteria, virus or plasmid DNA; Johansson E et al.; The effect of a bacterial infection on interferon-alpha (IFN-alpha) and interleukin-6 (IL-6) production by porcine cells was studied in specific pathogen-free (SPF) pigs, infected intranasally with Actinobacillus pleuropneumoniae serotype 2 . Three experimental groups of five pigs were used: infected non-treated pigs, infected pigs that were treated with enrofloxacin at disease onset, and non-infected, non-treated control pigs . Blood samples were collected from all pigs on the day of infection and on days 1, 4, 7, 13 and 17 post-infection . Sera were analysed for presence of antibodies to A . pleuropneumoniae and for the cytokines IL-6 and IFN-alpha . Ability to produce these cytokines was tested in vitro using whole blood cultures stimulated with inactivated virus (Aujeszky's disease virus infected porcine kidney cells (ADV/PK-15)), inactivated bacteria (A . pleuropneumoniae) or bacterial plasmid (pcDNA3) . All cytokine inducers were used neat or pre-incubated with the transfectious agent lipofectin . IL-6 appeared in the serum of all infected non-treated animals but no IFN-alpha was found in the serum of any of the experimental pigs . Accordingly, the bacteria induced a substantial IL-6 but hardly any IFN-alpha production when tested in vitro . However, following incubation with lipofectin, the inactivated bacteria as well as pcDNA3 became efficient inducers of IFN-alpha in whole blood cultures . The increased IFN-alpha production, previously recorded in vitro during the acute phase of infection with A . pleuropneumoniae, was confirmed using lipofected plasmid DNA and it was indicated that leukocytes obtained from infected but apparently cured animals also exhibited an increased production of IFN-alpha . Thus, even mild/sub-clinical bacterial infections may affect cytokine production in pigs. Appl Environ Microbiol, 2001 Mar, 67(3), 1392 - 5 Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria; Leaphart AB et al.; Primers for PCR amplification of partial (1,102 of 1,680 bp) formyltetrahydrofolate synthetase (FTHFS) gene sequences were developed and tested . Partial FTHFS sequences were successfully amplified from DNA from pure cultures of known acetogens, from other FTHFS-producing organisms, from the roots of the smooth cordgrass, Spartina alterniflora, and from fresh horse manure . The amplimers recovered were cloned, their nucleotide sequences were determined, and their translated amino acid sequences were used to construct phylogenetic trees . We found that FTHFS sequences from homoacetogens formed a monophyletic cluster that did not contain sequences from nonhomoacetogens and that FTHFS sequences appear to be informative regarding major physiological features of FTHFS-producing organisms. Appl Environ Microbiol, 2001 Mar, 67(3), 1371 - 4 Oligophilic bacteria as tools to monitor aseptic pharmaceutical production units; Nagarkar PP et al.; The bacterial loads of air, surfaces, and personnel in clean rooms are routinely monitored using a set of standard media . Bacteria that can grow on these media are a tiny fraction of the total numbers in any environment . A substantial proportion of bacteria long thought to be unculturable were recently shown to be oligophilic . Oligophile counts in clean rooms in our studies exceeded the standard plate counts by up to 2 orders of magnitude . They responded to disinfection routines in ways similar to the responses of conventional bacteria . We suggest that oligophiles are better tools than conventional bacteria for environmental monitoring in aseptic pharmaceutical production units. Appl Environ Microbiol, 2001 Mar, 67(3), 1328 - 34 Suboxic deposition of ferric iron by bacteria in opposing gradients of Fe(II) and oxygen at circumneutral pH; Sobolev D et al.; The influence of lithotrophic Fe(II)-oxidizing bacteria on patterns of ferric oxide deposition in opposing gradients of Fe(II) and O(2) was examined at submillimeter resolution by use of an O(2) microelectrode and diffusion microprobes for iron . In cultures inoculated with lithotrophic Fe(II)-oxidizing bacteria, the majority of Fe(III) deposition occurred below the depth of O(2) penetration . In contrast, Fe(III) deposition in abiotic control cultures occurred entirely within the aerobic zone . The diffusion microprobes revealed the formation of soluble or colloidal Fe(III) compounds during biological Fe(II) oxidation . The presence of mobile Fe(III) in diffusion probes from live cultures was verified by washing the probes in anoxic water, which removed ca . 70% of the Fe(III) content of probes from live cultures but did not alter the Fe(III) content of probes from abiotic controls . Measurements of the amount of Fe(III) oxide deposited in the medium versus the probes indicated that ca . 90% of the Fe(III) deposited in live cultures was formed biologically . Our findings show that bacterial Fe(II) oxidation is likely to generate reactive Fe(III) compounds that can be immediately available for use as electron acceptors for anaerobic respiration and that biological Fe(II) oxidation may thereby promote rapid microscale Fe redox cycling at aerobic-anaerobic interfaces. Mol Biochem Parasitol, 2001 Feb, 112(2), 239 - 52 A bifunctional dihydrofolate synthetase--folylpolyglutamate synthetase in Plasmodium falciparum identified by functional complementation in yeast and bacteria; Salcedo E et al.; Folate metabolism in the human malaria parasite Plasmodium falciparum is an essential activity for cell growth and replication, and the target of an important class of therapeutic agents in widespread use . However, resistance to antifolate drugs is a major health problem in the developing world . To date, only two activities in this complex pathway have been targeted by antimalarials . To more fully understand the mechanisms of antifolate resistance and to identify promising targets for new chemotherapies, we have cloned genes encoding as yet uncharacterised enzymes in this pathway . By means of complementation experiments using 1-carbon metabolism mutants of both Escherichia coli and Saccharomyces cerevisiae, we demonstrate here that one of these parasite genes encodes both dihydrofolate synthetase (DHFS) and folylpolyglutamate synthetase (FPGS) activities, which catalyse the synthesis and polyglutamation of folate derivatives, respectively . The malaria parasite is the first known example of a eukaryote encoding both DHFS and FPGS activities in a single gene . DNA sequencing of this gene in antifolate-resistant strains of P . falciparum, as well as drug-inhibition assays performed on yeast and bacteria expressing PfDHFS--FPGS, indicate that current antifolate regimes do not target this enzyme . As PfDHFS--FPGS harbours two activities critical to folate metabolism, one of which has no human counterpart, this gene product offers a novel chemotherapeutic target with the potential to deliver a powerful blockage to parasite growth. Immunol Lett, 2001 Feb 1, 76(1), 63 - 7 A clinically approved oral vaccine against pneumotropic bacteria induces the terminal maturation of CD83+ immunostimulatory dendritic cells; Zelle-Rieser C et al.; Dendritic cells (DCs) are important antigen-presenting cells of the immune system that have attracted interest as cellular adjuvants to induce immunity in clinical settings . We have investigated the effects of Broncho-Vaxom, an oral vaccine composed of lysates from eight pneumotropic bacteria, on human monocyte-derived dendritic cells (moDCs) . Broncho-Vaxom induced the terminal maturation of CD83+ moDCs . MoDCs stimulated with Broncho-Vaxom displayed a phenotype of activated DCs with high levels of major histocompatibility complex (MHC) molecules and increased levels of adhesion and co-stimulatory molecules . In addition, moDCs activated with Broncho-Vaxom exhibited enhanced T cell-stimulatory capacity in the allogeneic mixed leukocyte reaction . Broncho-Vaxom at 100 microg/ml was as potent as TNF-alpha at 1000 U/ml in activating human moDCs . Neither LPS-like activity nor bacterial DNA was found to be responsible for the maturation-inducing activity of Broncho-Vaxom, suggesting that Broncho-Vaxom contains other bacterial factors that are capable of inducing the terminal maturation of moDCs . In DC-based immunotherapy, Broncho-Vaxom could be used as a stimulus of DC maturation, which meets the standards of good manufacturing practice (GMP) . In addition, vaccination with Broncho-Vaxom-loaded moDCs may be an attractive treatment option in preventing recurrent airway infection in predisposed individuals. Indian J Exp Biol, 2000 Feb, 38(2), 160 - 6 Validity of mechanism of gene transfer in the process called conjugation in bacteria; Banerjee M et al.; We have attempted a new evaluation of the process of conjugation in bacteria, because of some basic dissimilarities observed between this and that of eukaryotes, or plants and animals . Reference donor and recipient strains, widely used to prove conjugation in bacteria, were chosen; addition of DNase during the conjugation process, led to an unexpected but highly reproducible increase in the transconjugant colony counts (TCC; ca . > or = 1 log), when compared with that of the controls without DNase . Transconjugants were also obtained when the same live donors were substituted with the UV-killed ones although the TCC was very low initially . Contrarily, donors treated with DNA-intercalating agents, e.g . acridine orange or ethidium bromide, resulted in a complete failure to produce transconjugants . There was a quantitative relationship between the DNase used on donors and levels of DNA sugars/nucleotides/DNA, which possibly resulted from interaction between the DNase and DNA being present/produced on the donor surface . This may be indicative of what may actually happen in the donor-recipient mixtures in the conjugation test proper, where the recipient DNase may activate a donor DNA production cycle . The evidences presented did not suggest that the donor DNA in the conjugation process is actually vestibuled through any intercellular conjugation passages, and is susceptible to the action of DNase or the intercalating dyes. Ultramicroscopy, 2001 Jan, 86(1-2), 121 - 8 Comparative studies of bacteria with an atomic force microscopy operating in different modes; Bolshakova AV et al.; Escherichia coli bacterial cells of two strains JM109 and K12 J62 were imaged with atomic force microscopy (AFM) in different environmental conditions . The AFM results show that the two strains have considerable difference in the surface morphology . At the same time after rehydration both strains show the loss of the topographic features and increase in lateral and vertical dimensions . Results obtained in different AFM modes (contact, tapping, MAC) were compared . Imaging in culture medium was applied for direct observation of the surface degradation effect of lysozyme . The treatment of the cells with the enzyme in the culture medium lead to the loss of surface rigidity and eventually to dramatic changes of the bacteria shape. Int J Syst Evol Microbiol, 2001 Jan, 51(Pt 1), 119 - 22 Hyphomicrobium chloromethanicum sp . nov . and Methylobacterium chloromethanicum sp . nov., chloromethane-utilizing bacteria isolated from a polluted environment; McDonald IR et al.; Two chloromethane-utilizing facultatively methylotrophic bacteria, strains CM2T and CM4T, were isolated from soil at a petrochemical factory . On the basis of their morphological, physiological and genotypical properties, strain CM2T (= VKM B-2176T = NCIMB 13687T) is proposed as a new species of the genus Hyphomicrobium, Hyphomicrobium chloromethanicum, and strain CM4T (= VKM B-2223T = NCIMB 13688T) as a new species of the genus Methylobacterium, Methylobacterium chloromethanicum. Philos Trans R Soc Lond B Biol Sci, 2001 Jan 29, 356(1405), 29 - 39 Hypermutation in bacteria and other cellular systems; Bridges BA; A temporary state of hypermutation can in principle arise through an increase in the rate of polymerase errors (which may or may not be triggered by template damage) and/or through abrogation of fidelity mechanisms such as proofreading and mismatch correction . In bacteria there are numerous examples of transient mutator states, often occurring as a consequence of stress . They may be targeted to certain regions of the DNA, for example by transcription or by recombination . The initial errors are made by various DNA polymerases which vary in their error-proneness: several are inducible and are under the control of the SOS system . There are several structurally related polymerases in mammals that have recently come to light and that have unusual properties, such as the ability to carry out 'accurate' translesion synthesis opposite sites of template damage or the possession of exceedingly high misincorporation rates . In bacteria the initial errors may be genuinely spontaneous polymerase errors or they may be triggered by damage to the template strand, for example as a result of attack by active oxidative species such as singlet oxygen . In mammalian cells, hypermutable states persisting for many generations have been shown to be induced by various agents, not all of them DNA damaging agents . A hypermutable state induced by ionizing radiation in male germ cells in the mouse results in a high rate of sequence errors in certain unstable minisatellite loci; the mechanism is unclear but believed to be associated with recombination events. Z Naturforsch {C}, 2000 Nov-Dec, 55(11-12), 965 - 70 10-Hydroxystearic acid--identified after homogenization of tissue--is derived from bacteria; Adam P et al.; 10-Hydroxystearic acid seems to be widely distributed in nature: Bacteria generate it by hydroxylation of oleic acid, but it was found also as constituent of plants, in cancer cell cultures and in mammalian tissue homogenates . Investigation of 10-hydroxystearic acid, obtained from mammalian tissue homogenates, revealed its identity with that of bacteria . Thus not 10-hydroxystearic acid is widely distributed in nature but its producers: bacteria . When biological material is processed in aqueous media, lipases are activated, these cleave membrane phospholipids . Thus liberated oleic acid is the substrate for widespread bacteria which are introduced into the media when the work up procedure is done in not sterile surrounding . The bacteria transform then oleic acid to 10R-hydroxystearic acid. Orig Life Evol Biosph, 2000 Dec, 30(6), 567 - 77 Fine structure of fossilized bacteria in Volyn kerite; Gorlenko VM et al.; Ultrathin sectioning and cryofracture of fibrous kerite, sampled from 1.8-1.75 billion year old Volyn sediments (Ukraine), revealed in bacteria-like bodies the presence of structures similar to sheath, cell wall, periplasm, cytoplasm, septum, membranes, intramembrane particles, poly-beta-hydroxybutyrate inclusions . On the strength of these data and also the fatty acid profiles of these microfossils, we concluded that fibrous kerites are biogenic formations, namely fossilized bacterial mats. Mikrobiologiia, 2000 Nov-Dec, 69(6), 753 - 63 {Organization and regulation of polyhydroxybutyrate/valerate biosynthesis in bacteria}; Trotsenko IuA et al.; Recent data on the biosynthesis of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB/V) and its regulation in bacteria are reviewed, with special emphasis on the properties and regulation of the relevant enzymes and their genes . Some conditions promoting the synthesis of PHB and PHB/V by natural, mutant, and recombinant producers are considered. Subcell Biochem, 2000, 35, 621 - 76 Reaction centres of purple bacteria; van Brederode ME et al.; The bacterial reaction centre is undoubtedly one of the most heavily studied electron transfer proteins and, as this article has tried to describe, it has made some unique contributions to our understanding of biological electron transfer and coupled protonation reactions, and has provided fascinating information in areas that concern basic properties such as protein heterogeneity and protein dynamics . Despite intensive study, much remains to be learned about how this protein catalyses the conversion of solar energy into a form that can be used by the cell . In particular, the dynamic roles played by the protein are still poorly understood . The wide range of time-scales over which the reaction centre catalyses electron transfer, and the relative ease with which electron transfer can be triggered and monitored, will ensure that the reaction centre will continue to be used as a laboratory for testing ideas about the nature of biological electron transfer for many years to come. Stud Health Technol Inform, 2000, 77, 106 - 10 Application of artificial neural network for the identification of fresh water bacteria; Giacomini M et al.; A method based on artificial neural network (ANN) for monitoring aquatic bacteria which would be useful for health care is presented . Environmental micro-organisms include a large number of taxa . Some species that normally are not pathogenic can represent a risk in certain conditions, such as old people and immuno-compromised individuals . A system based on unsupervised ANN has been set up using the fatty acid profiles of standard strains, obtained by gas-chromatography, as learning data . The Kohonen output map resulted in a powerful tool for identification of fresh isolates coming from a line of the major civil water system of Genova (Italy). J Nutr Sci Vitaminol (Tokyo), 2000 Aug, 46(4), 193 - 8 Volatile sulfur production by pig cecal bacteria in batch culture and screening inhibitors of sulfate reducing bacteria; Arakawa T et al.; We studied the effects of specific inhibitors of methanogenesis (2-bromoethane sulfonate, BES) and sulfate reduction (sodium molybdate) on volatile sulfur production in batch cultures of pig cecal bacteria . The volatile sulfur concentration in headspace gas was determined by flame-photometric detector gas chromatography . BES stimulated production of hydrogen sulfide (H2S) and methanethiol, and sodium molybdate completely inhibited the production of these volatile sulfur compounds . The results indicated that dissimilate sulfate reduction is mainly responsible for volatile sulfur production in the hindgut . Therefore the extracts of herbs, food colors, and aroma chemicals were tested for their inhibitory effects on H2S production by a dissimilatory sulfate-reducing bacteria . Desulfovibrio desulfuricans DSM642 . H2S was measured by the chromatography of the headspace gas, using a flame photometric detector . Of 306 herbal extracts tested, 69 extracts from 38 herbs inhibited H2S production at 1.0 mg/mL . Sisymbrium officinale (hedge mustard) was the most potent inhibitor . Six pigments inhibited H2S release . Erythrosine and rose bengal showed inhibitory effects at 0.01 mg/mL . Peppermint oil and 96 aroma chemicals were assayed for their effects on H2S release . Thirty-two aroma chemicals suppressed H2S production at 0.1 mg/mL, and camphene, 1-decanol, and 2-nonanone were effective at 0.01 mg/mL. J Bacteriol, 2001 Feb, 183(3), 1012 - 21 Size comparisons among integral membrane transport protein homologues in bacteria, Archaea, and Eucarya; Chung YJ et al.; Integral membrane proteins from over 20 ubiquitous families of channels, secondary carriers, and primary active transporters were analyzed for average size differences between homologues from the three domains of life: Bacteria, Archaea, and Eucarya . The results showed that while eucaryotic homologues are consistently larger than their bacterial counterparts, archaeal homologues are significantly smaller . These size differences proved to be due primarily to variations in the sizes of hydrophilic domains localized to the N termini, the C termini, or specific loops between transmembrane alpha-helical spanners, depending on the family . Within the Eucarya domain, plant homologues proved to be substantially smaller than their animal and fungal counterparts . By contrast, extracytoplasmic receptors of ABC-type uptake systems in Archaea proved to be larger on average than those of their bacterial homologues, while cytoplasmic enzymes from different organisms exhibited little or no significant size differences . These observations presumably reflect evolutionary pressure and molecular mechanisms that must have been operative since these groups of organisms diverged from each other. Med Sci Monit, 2000 Mar-Apr, 6(2), 291 - 9 Adherence of bile-isolated bacteria to the bile ducts mucosa as a pathogenic factor in the development of inflammatory lesions; Kosowski K et al.; Bacterial infection of the bile system appears to be an important factor in the formation of stones . In view of the hypothesis that strains of E . c . form an essential factor in infections of the bile ducts, an attempt has been made to determine the connection between infections of the bile ducts and the adherence of E . c . to the epithelium of the gallbladder . The research covered 148 patients operated electively for cholecystolithiasis (121), cholecystocholedocholithiasis (26) and recurrent lithiasis (1) . In bile collected from the gallbladder in the course of the operation, E . coli strains were isolated . Cholangioscopy performed in 26 patients enabled the macroscopic evaluation and grading of inflammatory lesions of bile duct mucosa . The mucosa of the gallbladder was evaluated histologically . The adherence test was performed using homologous and heterologous strains of E . c . isolated from the bile of gallstone patients . The adherence occurred most frequently in the neck of the gallbladder (71-100%) in those patients in whom an infectious process of the bile ducts mucosa was endoscopically diagnosed . The adherence of bacteria to the epithelium of the gallbladder did not depend on the type of inflammation (acute, chronic). ALTEX, 1989, 6(2), 27 - 44 {Testing the acute toxicity of chemicals using bacteria}; Hartung J; Two bacterial tests are used to screen the acute toxicity of 8 compounds which are known as pollutants in the air of stables . The procedures applied were batch-microcalorimetry (E.coli) and the Microtox(R)-test (P . phosphoreum) . It is shown that both bacterial "screening models" are suitable to evaluate the acute toxicity of the compounds tested . The test results are compared to results from other toxicity tests using higher developed organisms; additionally the comparison included compounds from the literature . It is found that the results from the different test systems are significantly correlated as far as linear correlation and as rank correlation are concerned . The range of the results supports the suggestion to apply two or more short-term tests involving different test organisms in a "test battery" . Bacterial short-term assays may not completely replace experiments involving animals but they allow an estimation of the toxic potential of substances which have not yet been tested and may thus reduce the necessary amount of experiments with animals. Environ Microbiol, 1999 Oct, 1(5), 457 - 67 Effect of temperature on sulphate reduction, growth rate and growth yield in five psychrophilic sulphate-reducing bacteria from Arctic sediments; Knoblauch C et al.; Five psychrophilic sulphate-reducing bacteria (strains ASv26, LSv21, PSv29, LSv54 and LSv514) isolated from Arctic sediments were examined for their adaptation to permanently low temperatures . All strains grew at -1.8 degrees C, the freezing point of sea water, but their optimum temperature for growth (T(opt)) were 7 degrees C (PSv29), 10 degrees C (ASv26, LSv54) and 18 degrees C (LSv21, LSv514) . Although T(opt) was considerably above the in situ temperatures of their habitats (-1.7 degrees C and 2.6 degrees C), relative growth rates were still high at 0 degrees C, accounting for 25-41% of those at T(opt) . Short-term incubations of exponentially growing cultures showed that the highest sulphate reduction rates occurred 2-9 degrees C above T(opt) . In contrast to growth and sulphate reduction rates, growth yields of strains ASv26, LSv54 and PSv29 were almost constant between -1.8 degrees C and T(opt) . For strains LSv21 and LSv514, however, growth yields were highest at the lowest temperatures, around 0 degrees C . The results indicate that psychrophilic sulphate-reducing bacteria are specially adapted to permanently low temperatures by high relative growth rates and high growth yields at in situ conditions. Environ Microbiol, 1999 Apr, 1(2), 175 - 82 A novel system for efficient gene expression and monitoring of bacteria in aquatic environments; Espinosa-Urgel M et al.; In a previous study, we reported the identification of Escherichia coli genes with increased expression in an aquatic environment . Here, we describe the use of one of these genes, gapC, as an expression system in freshwater habitats . We have identified the transcriptional start site of gapC and analysed the synthesis of the GapC protein during incubation in aquatic medium . The promoter of gapC was used to construct fusions to the reporter genes lacZ and gfp . Analysis of these fusions indicates the potential of gapC as a valuable tool for the detection of E . coli in freshwater habitats, as well as for expressing other genes in aquatic environments. Genome Biol . 2000;1(4):REVIEWS1024 . Epub 2000 Oct 10. Expression profiling in reference bacteria: dreams and reality; Danchin A et al.; Profiling of gene expression in bacteria is now being used to uncover unknown genes expressed in particular genetic backgrounds or environmental conditions . Obtaining the best possible information from the expected avalanche of such experiments will require standardization of both experimental approach and statistical analysis . The first such experiments reveal challenges, pitfalls and reasonable solutions. Infect Immun, 2001 Mar, 69(3), 1364 - 72 Interleukin-8 and intercellular adhesion molecule 1 regulation in oral epithelial cells by selected periodontal bacteria: multiple effects of Porphyromonas gingivalis via antagonistic mechanisms; Huang GT et al.; Interaction of bacteria with mucosal surfaces can modulate the production of proinflammatory cytokines and adhesion molecules produced by epithelial cells . Previously, we showed that expression of interleukin-8 (IL-8) and intercellular adhesion molecule 1 (ICAM-1) by gingival epithelial cells increases following interaction with several putative periodontal pathogens . In contrast, expression of IL-8 and ICAM-1 is reduced after Porphyromonas gingivalis ATCC 33277 challenge . In the present study, we investigated the mechanisms that govern the regulation of these two molecules in bacterially infected gingival epithelial cells . Experimental approaches included bacterial stimulation of gingival epithelial cells by either a brief challenge (1.5 to 2 h) or a continuous coculture throughout the incubation period . The kinetics of IL-8 and ICAM-1 expression following brief challenge were such that (i) secretion of IL-8 by gingival epithelial cells reached its peak 2 h following Fusobacterium nucleatum infection whereas it rapidly decreased within 2 h after P . gingivalis infection and remained decreased up to 30 h and (ii) IL-8 and ICAM-1 mRNA levels were up-regulated rapidly 2 to 4 h postinfection and then decreased to basal levels 8 to 20 h after infection with either Actinobacillus actinomycetemcomitans, F . nucleatum, or P . gingivalis . Attenuation of IL-8 secretion was facilitated by adherent P . gingivalis strains . The IL-8 secreted from epithelial cells after F . nucleatum stimulation could be down-regulated by subsequent infection with P . gingivalis or its culture supernatant . Although these results suggested that IL-8 attenuation at the protein level might be associated with P . gingivalis proteases, the Arg- and Lys-gingipain proteases did not appear to be solely responsible for IL-8 attenuation . In addition, while P . gingivalis up-regulated IL-8 mRNA expression, this effect was overridden when the bacteria were continuously cocultured with the epithelial cells . The IL-8 mRNA levels in epithelial cells following sequential challenge with P . gingivalis and F . nucleatum and vice versa were approximately identical and were lower than those following F . nucleatum challenge alone and higher than control levels or those following P . gingivalis challenge alone . Thus, together with the protease effect, P . gingivalis possesses a powerful strategy to ensure the down-regulation of IL-8 and ICAM-1. Nat Cell Biol, 2001 Feb, 3(2), 210 - 4 Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis; Horiike T et al.; The origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria was proposed on the basis of the phylogenetic topologies of genes . However, it was not possible to conclude whether or not the genes involved were authentic representative genes . Furthermore, using the BLAST and FASTA programs, the similarity of open reading frame (ORF) groups between three domains (Eukarya, Archaea and Bacteria) was estimated at one threshold . Therefore, their similarities at other thresholds could not be clarified . Here we use our newly developed 'homology-hit analysis' method, which uses multiple thresholds, to determine the origin of the nucleus . We removed mitochondria-related ORFs from yeast ORFs, and determined the number of yeast orthologous ORFs in each functional category to the ORFs in six Archaea and nine Bacteria at several thresholds (E-values) using the BLAST . Our results indicate that yeast ORFs related to the nucleus may share their origins with archaeal ORFs, whereas ORFs that are related to the cytoplasm may share their origins with bacterial ORFs . Our results thus strongly support the idea of nucleus symbiosis. Biochemistry (Mosc), 2000 Dec, 65(12), 1429 - 34 Why is electron transport in the reaction centers of purple bacteria unidirectional? Borisov AY. Although the two electron-transfer branches in the reaction centers (RC) of purple bacteria are virtually symmetric, it is well known that only one of them is functionally active (the A-branch) . The mechanisms of functional asymmetry of structurally symmetric branches of the electron transport system are analyzed in this work within the framework of the theory of bimolecular charge-transfer complexes (CTC) . CTC theory is shown to provide an explanation of this phenomenon . According to the CTC theory, the dominance of one branch is required to implement the CTC state in special bacteriochlorophyll pairs of RC, in which more than 30% of the excited electron density in the CTC is shifted toward one of the bacteriochlorophyll molecules . This causes a significant increase in the efficiency of further electron transfer to the primary quinone acceptor as compared to a system with two absolutely symmetric electron transfer branches . Specific features of dielectric asymmetry near the RC special pair are discussed . It is emphasized that a strong CTC is able to provide effective trapping of electronic excitation energy from antenna chlorophyll, which is a main function of the RC . Hypothetical stages of CTC formation in other classes of photosynthesizing bacteria during evolution are discussed. J Microbiol Methods, 2001 Mar 1, 44(2), 183 - 91 The use of a solid adsorber resin for enrichment of bacteria with toxic substrates and to identify metabolites: degradation of naphthalene, O-, and m-xylene by sulfate-reducing bacteria; Morasch B et al.; Anaerobic sulfate-reducing bacteria were enriched from contaminated aquifer samples with naphthalene, o-, and m-xylene as sole carbon and energy source in the presence of Amberlite-XAD7, a solid adsorber resin . XAD7 served as a substrate reservoir maintaining a constantly low substrate concentration in the culture medium . In equilibration experiments with XAD7, the aromatic hydrocarbons needed up to 5 days to achieve equilibrium between the water and the XAD7 phase . The equilibrium concentration was directly correlated with the amount of added substrate and XAD7 . In the enrichments presented here, XAD7 and aromatic hydrocarbons were adjusted to maintain substrate concentrations of 100 microM m-, or o-xylene, or 50 microM naphthalene . After five subsequent transfers, the three cultures were able to grow with higher substrate concentrations in the absence of XAD7 although they grew best with lower hydrocarbon concentrations . Two new xylene-degrading cultures were obtained that could not utilise toluene as carbon source . O-xylene was degraded anaerobically by a culture, which could also oxidise m-xylene but not p-xylene . Eighty-three percent of the electrons from o-xylene oxidation were recovered in the produced sulfide, indicating a complete oxidation to CO2 . Another sulfate-reducing enrichment culture oxidised m-xylene completely to CO2 but not o-, or p-xylene . A naphthalene-degrading sulfate-reducing enrichment culture oxidised naphthalene completely to CO2 . Metabolites of naphthalene degradation were recovered from the XAD7 phase and subjected to GC/MS analysis . Besides the metabolites 2-naphthoic acid and decahydro-2-naphthoic acid which were identified by the mass spectrum and coelution with chemically synthesised reference compounds, the reduced 2-naphthoic acid derivatives 5,6,7,8-tetrahydro-2-naphthoic acid and octahydro-2-naphthoic acid were tentatively identified by their mass spectra . Cultivation of bacterial cultures in the presence of XAD7 and subsequent derivatisation and extraction of metabolites directly from the solid XAD7 resin provides a new method for the isolation of sensitive bacteria and identification of metabolites. J Microbiol Methods, 2001 Mar 1, 44(2), 121 - 9 How to optimize the drop plate method for enumerating bacteria; Herigstad B et al.; The drop plate (DP) method can be used to determine the number of viable suspended bacteria in a known beaker volume . The drop plate method has some advantages over the spread plate (SP) method . Less time and effort are required to dispense the drops onto an agar plate than to spread an equivalent total sample volume into the agar . By distributing the sample in drops, colony counting can be done faster and perhaps more accurately . Even though it has been present in the laboratory for many years, the drop plate method has not been standardized . Some technicians use 10-fold dilutions, others use twofold . Some technicians plate a total volume of 0.1 ml, others plate 0.2 ml . The optimal combination of such factors would be useful to know when performing the drop plate method.This investigation was conducted to determine (i) the standard deviation of the bacterial density estimate, (ii) the cost of performing the drop plate procedure, (iii) the optimal drop plate design, and (iv) the advantages of the drop plate method in comparison to the standard spread plate method . The optimal design is the combination of factor settings that achieves the smallest standard deviation for a fixed cost . Computer simulation techniques and regression analysis were used to express the standard deviation as a function of the beaker volume, dilution factor, and volume plated . The standard deviation expression is also applicable to the spread plate method. J Biotechnol, 2001 Jan 23, 85(1), 25 - 33 Acetate as a carbon source for hydrogen production by photosynthetic bacteria; Barbosa MJ et al.; Hydrogen is a clean energy alternative to fossil fuels . Photosynthetic bacteria produce hydrogen from organic compounds by an anaerobic light-dependent electron transfer process . In the present study hydrogen production by three photosynthetic bacterial strains (Rhodopseudomonas sp., Rhodopseudomonas palustris and a non-identified strain), from four different short-chain organic acids (lactate, malate, acetate and butyrate) was investigated . The effect of light intensity on hydrogen production was also studied by supplying two different light intensities, using acetate as the electron donor . Hydrogen production rates and light efficiencies were compared . Rhodopseudomonas sp . produced the highest volume of H2 . This strain reached a maximum H2 production rate of 25 ml H2 l(-1) h(-1), under a light intensity of 680 micromol photons m(-2) s(-1), and a maximum light efficiency of 6.2% under a light intensity of 43 micromol photons m(-2) s(-1) . Furthermore, a decrease in acetate concentration from 22 to 11 mM resulted in a decrease in the hydrogen evolved from 214 to 27 ml H2 per vessel. Small Rumin, Res. . 2001 Jan, 39(1), 73 - 85 Reproductive performance of South African indigenous goats inoculated with DHP-degrading rumen bacteria and maintained on Leucaena leucocephala/grass mixture and natural pasture; Akingbade AA et al.; This study examined the reproductive performance of dihydroxy pyridone (DHP)-inoculated South African indigenous (SAIG) female goats maintained on two dietary treatments: (i) Leucaena leucocephala/grass mixture and (ii) natural pasture prior to conception, and during gestation . Leucaena leucocephala/grass mixture was nutritionally superior (crude protein and mineral elements) than the natural pasture . The average daily gain, products of pregnancy and foetal development in gravid goats raised on leucaena/grass mixture were significantly (P<0.03, P<0.009 and P<0.005, respectively) higher than those raised on natural pasture . Conception rate of goats fed natural pasture was higher than the band fed Leucaena leucocephala/grass mixture . Leucaena/grass mixture fed goats had kids that were heavier at birth than their counterparts on natural pasture . Pre-weaning kid mortality over the period of study was significantly (P<0.01) higher in the Leucaena leucocephala/grass mixture treatment . Colostrum from kidded goats fed leucaena was viscous and difficult to sample . The absence of mimosine toxicity symptoms suggests a possibility of safe use of leucaena as a feed resource to DHP-inoculated SAIG. Appl Environ Microbiol, 2001 Feb, 67(2), 1015 - 9 Nickel-resistance-based minitransposons: new tools for genetic manipulation of environmental bacteria; Taghavi S et al.; The ncc and nre nickel resistance determinants from Ralstonia eutropha-like strain 31A were used to construct mini-Tn5 transposons . Broad host expression of nickel resistance was observed for the nre minitransposons in members of the alpha, beta, and gamma subclasses of the Proteobacteria, while the ncc minitransposons expressed nickel resistance only in R . eutropha-like strains. Appl Environ Microbiol, 2001 Feb, 67(2), 972 - 6 Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR; Hermansson A et al.; Real-time PCR was used to quantify populations of ammonia-oxidizing bacteria representing the beta subdivision of the class Proteobacteria in samples of arable soil, both nitrogen fertilized and unfertilized, from Mellby, Sweden . Primers and probes targeting a 16S ribosomal DNA region of the ammonia-oxidizing bacteria were designed and used . In the fertilized soil there were approximately 6.2 x 10(7) ammonia-oxidizing bacteria per g of soil, three times more than the number of bacteria in the unfertilized soil . The lytic efficiency of bead beating in these soils was investigated by using populations of free or loosely attached bacteria, bacteria tightly bound to particles, and bacteria in nonfractionated samples . The shapes of the curves generated in these tests showed that the concentration of template DNA released at various times remained constant after 10 to 100 s of bead beating. Appl Environ Microbiol, 2001 Feb, 67(2), 814 - 20 Effects of hydrophobic and electrostatic cell surface properties of bacteria on feeding rates of heterotrophic nanoflagellates; Matz C et al.; The influence of cell surface hydrophobicity and electrostatic charge of bacteria on grazing rates of three common species of interception-feeding nanoflagellates was examined . The hydrophobicity of bacteria isolated from freshwater plankton was assessed by using two different methods (bacterial adhesion to hydrocarbon and hydrophobic interaction chromatography) . The electrostatic charge of the cell surface (measured as zeta potential) was analyzed by microelectrophoresis . Bacterial ingestion rates were determined by enumerating bacteria in food vacuoles by immunofluorescence labelling via strain-specific antibodies . Feeding rates varied about twofold for each flagellate species but showed no significant dependence on prey hydrophobicity or surface charge . Further evidence was provided by an experiment involving flagellate grazing on complex bacterial communities in a two-stage continuous culture system . The hydrophobicity values of bacteria that survived protozoan grazing were variable, but the bacteria did not tend to become more hydrophilic . We concluded that variability in bacterial cell hydrophobicity and variability in surface charge do not severely affect uptake rates of suspended bacteria or food selection by interception-feeding flagellates. Oral Microbiol Immunol, 2000 Dec, 15(6), 371 - 7 Attachment of Fusobacterium nucleatum PK1594 to mammalian cells and its coaggregation with periodontopathogenic bacteria are mediated by the same galactose-binding adhesin; Weiss EI et al.; It has been shown that Fusobacterium nucleatum PK1594 coaggregates with Prophyromonas gingivalis PK1924 through a galactose-binding adhesin . In the present study, attachment of F . nucleatum PK1594 to a variety of mammalian cells was characterized . F . nucleatum PK1594 attached to all eukaryotic cells tested, including human buccal epithelial cells, gingival and periodontal ligament fibroblasts, HeLa cells and murine lymphocytes, macrophages, and polymorphonuclear leukocytes . These attachments were (i) inhibited by galactose, lactose and N-acetylgalactosamine and (ii) inhibited by monoclonal antibody specific for the galactose-binding adhesin of F . nucleatum PK1594 . In addition, a coaggregation-defective mutant of F . nucleatum PK1594 (PK2172), which does not exhibit galactose binding activity, did not attach to the mammalian cells . Coaggregation of F . nucleatum PK1594 with P . gingivalis PK 1924 and Actinobacillus actinomycetemcomitans JP2, but not with other bacteria, showed a similar pattern with sugars, monoclonal antibody, and the adhesin-deficient mutant . The results suggest that the attachment of F . nucleatum PK1594 to mammalian cells and its coaggregation with periodontal pathogens are mediated by the same galactose-binding adhesin. Vitam Horm, 2001, 61, 157 - 71 The biosynthesis of coenzyme A in bacteria; Begley TP et al.; Coenzyme A (I) and enzyme-bound phosphopantetheine (II) function as acyl carriers and as carbonyl activating groups for Claisen reactions as well as for amide-, ester-, and thioester-forming reactions in the cell . In so doing, these cofactors play a key role in the biosynthesis and breakdown of fatty acids and in the biosynthesis of polyketides and nonribosomal peptides . Coenzyme A is biosynthesized in bacteria in nine steps . The biosynthesis begins with the decarboxylation of aspartate to give beta-alanine . Pantoic acid is formed by the hydroxymethylation of alpha-ketoisovalerate followed by reduction . These intermediates are then condensed to give pantothenic acid . Phosphorylation of pantothenic acid followed by condensation with cysteine and decarboxylation gives 4'-phosphopantetheine . Adenylation and phosphorylation of 4'-phosphopantetheine completes the biosynthesis of coenzyme A . This review will focus on the mechanistic enzymology of coenzyme A biosynthesis in bacteria. Vitam Horm, 2001, 61, 103 - 19 The biosynthesis of nicotinamide adenine dinucleotides in bacteria; Begley TP et al.; The nicotinamide adenine dinucleotides (NAD, NADH, NADP, and NADPH) are essential cofactors in all living systems and function as hydride acceptors (NAD, NADP) and hydride donors (NADH, NADPH) in biochemical redox reactions . The six-step bacterial biosynthetic pathway begins with the oxidation of aspartate to iminosuccinic acid, which is then condensed with dihydroxyacetone phosphate to give quinolinic acid . Phosphoribosylation and decarboxylation of quinolinic acid gives nicotinic acid mononucleotide . Adenylation of this mononucleotide followed by amide formation completes the biosynthesis of NAD . An additional phosphorylation gives NADP . This review focuses on the mechanistic enzymology of this pathway in bacteria. Berl Munch Tierarztl Wochenschr, 2000 Nov-Dec, 113(11-12), 423 - 30 {Coxiella burnetii infections and infections with bacteria of the genus Chlamydia in dairy cattle}; Sting R et al.; Comparative studies on the prevalence of infections caused by Coxiella burnetii (C . burnetii) and Chlamydia were carried out with 592 cattle older than 2 years and 234 cattle younger than 2 years . Of these 477 originated from 24 dairy herds with considerable fertility problems (positive herds) and 349 from 14 dairy herds without major fertility problems (control herds) . For the direct detection of these pathogens in the genitals capture ELISAs were employed, for the demonstration of antibodies the complement fixation test (CFT) . Direct detection of C . burnetii and Chlamydia single as well as mixed infection revealed significant higher values for cattle from positive herds compared with those from the control herds . Animals revealing insemination ratios of > or = 2 showed significantly more frequent excretion of Chlamydia via the genitals and antibodies against C . burnetii than cattle with an insemination ratio of < 2 . Investigations of cows which had had an abortion showed no indications of significantly more frequent C . burnetii or chlamydial infections . Inseminated but non-pregnant cows excreted significantly more C . burnetii and Chlamydia than pregnant cows . Clinical signs of endometritis were associated with an enhanced excretion of Chlamydia . Animals younger than 2 years excreted significantly more frequently C . burnetii but not Chlamydia via the genitals than animals older than 2 years . Indirect test showed results vice versa. Eur J Med Res, 2000 Dec 29, 5(12), 523 - 9 Effect of three mouthrinses, containing amine/stannous fluoride, herbal extracts or Emser salt on the growth of oral bacteria--an in vitro study; Kagermeier-Callaway AS et al.; BACKGROUND/AIMS: Clinical studies have shown the efficacy of mouthrinses in reducing plaque accumulation and inflammation of oral tissues . The aim of this in vitro study was to compare the effect of three mouthrinses: Meridol, an organic amine/ stannous fluoride solution; Parodontax, containing herbal ingredients; and an 0.8 % Emser salt solution, on the growth of oral bacteria and dental plaque . METHODS: Growth of Actinomyces viscosus T14V, Capnocytophaga ochracea 25, C . sputigena 4, Actinobacillus actinomycetemcomitans (A.a.) Y4, and pooled supragingival plaque in the presence of the various mouthrinses, applied to paper discs, was tested in an agar diffusion test . In a second series of tests, the 4 bacterial strains were exposed to the agents for about 3 min to simulate rinsing, then the agent was removed, and the bacteria were inoculated into fresh nutrient broth . After 48 h bacterial growth was measured in a spectrophotometer and compared with the controls . RESULTS: In the agar diffusion test only Meridol, the organic amine/stannous fluoride-containing solution, could inhibit bacterial growth, except for A . a . Y4 . When the bacteria where in contact with the agents for only a few minutes these results were confirmed . Neither Paradontax nor Emser salt inhibited the growth of the bacteria, and A . a . Y4 proved to be resistant to all three agents . Growth of the other three strains was inhibited by Meridol 92-99% (undiluted), 85-96% (1:5) and 83-98% (1:10) . CONCLUSIONS: We conclude that only Meridol contains ingredients capable of inhibiting the growth of oral bacteria in vitro . The efficacy of the other two mouthrinses in reducing plaque accumulation in vivo has to be explained by other mechanisms. Trends Biotechnol, 2001 Jan, 19(1), 15 - 20 Bacteria as workers in the living factory: metal-accumulating bacteria and their potential for materials science; Klaus-Joerger T et al.; Metal micro-/nano-particles with suitable chemical modification can be organized into new ceramic-metal (cermet) or organic-metal (orgmet) composites or structured materials . These materials are attracting significant attention because of their unique structures and highly optimized properties . However, the synthesis of composite materials with inhomogeneities on the nanometer or sub-micrometer scale is a continuing challenge in materials science . Many industrial physical and chemical surface-coating processes using conventional techniques are both energy and cost inefficient and require sophisticated instrumentation . In the future, biology might offer a superior option. Dis Aquat Organ, 2000 Nov 14, 43(2), 153 - 7 Use of prawn blood agar hemolysis to screen for bacteria pathogenic to cultured tiger prawns Penaeus monodon; Chang CI et al.; A newly developed prawn blood agar consisting of 1 ml of tiger prawn hemolymph in medium containing 200 ppm Rose Bengal was used to determine the hemolytic activity of 35 isolates of bacteria obtained from cultured tiger prawns Penaeus monodon and their rearing water . For comparison, the hemolytic activity of these isolates was also determined in sheep blood agar . Nine isolates (25.7% of total) showed different hemolytic reactions on prawn blood agar and sheep blood agar . From the 35 isolates, 8 with various hemolytic characteristics were selected and the relationship between the type of hemolytic activity and pathogenicity was determined and compared . Four isolates that showed hemolytic activity in prawn blood agar caused high mortality to cultured tiger prawns . By contrast, a significantly lower mortality rate was observed for tiger prawns injected with 4 isolates that did not exhibit hemolytic activity on prawn blood agar . Results further showed that mortality did not correlate with hemolytic activity determined using sheep blood agar . Prawn blood agar containing P . monodon hemocytes was faster and more accurate for determining prawn hemolytic activity of bacterial isolates. Appl Environ Microbiol, 2001 Jan, 67(1), 307 - 16 Chloromethane utilization gene cluster from Hyphomicrobium chloromethanicum strain CM2(T) and development of functional gene probes to detect halomethane-degrading bacteria; McAnulla C et al.; Hyphomicrobium chloromethanicum CM2(T), an aerobic methylotrophic member of the alpha subclass of the class proteobacteria, can grow with chloromethane as the sole carbon and energy source . H . chloromethanicum possesses an inducible enzyme system for utilization of chloromethane, in which two polypeptides (67-kDa CmuA and 35-kDa CmuB) are expressed . Previously, four genes, cmuA, cmuB, cmuC, and purU, were shown to be essential for growth of Methylobacterium chloromethanicum on chloromethane . The cmuA and cmuB genes were used as probes to identify homologs in H . chloromethanicum . A cmu gene cluster (9.5 kb) in H . chloromethanicum contained 10 open reading frames: folD (partial), pduX, orf153, orf207, orf225, cmuB, cmuC, cmuA, fmdB, and paaE (partial) . CmuA from H . chloromethanicum (67 kDa) showed high identity to CmuA from M . chloromethanicum and contains an N-terminal methyltransferase domain and a C-terminal corrinoid-binding domain . CmuB from H . chloromethanicum is related to a family of methyl transfer proteins and to the CmuB methyltransferase from M . chloromethanicum . CmuC from H . chloromethanicum shows identity to CmuC from M . chloromethanicum and is a putative methyltransferase . folD codes for a methylene-tetrahydrofolate cyclohydrolase, which may be involved in the C(1) transfer pathway for carbon assimilation and CO(2) production, and paaE codes for a putative redox active protein . Molecular analyses and some preliminary biochemical data indicated that the chloromethane utilization pathway in H . chloromethanicum is similar to the corrinoid-dependent methyl transfer system in M . chloromethanicum . PCR primers were developed for successful amplification of cmuA genes from newly isolated chloromethane utilizers and enrichment cultures. Cytogenet Cell Genet, 2000, 90(3-4), 330 - 6 Isolation and characterization of a novel human gene, NIF3L1, and its mouse ortholog, Nif3l1, highly conserved from bacteria to mammals; Tascou S et al.; We report the cloning and characterization of novel human and murine genes NIF3L1 and Nif3l1 which are strongly homologous to the yeast Ngg1-interacting factor 3 homolog . Mouse Nif3l1 and human NIF3L1 encode predicted proteins of 376 amino acids and 377 amino acids, respectively . Northern blot analysis on RNA from different postnatal murine tissues showed a ubiquitous expression pattern of mouse Nif3l1 with a transcript of approximately 1.85 kb . RT-PCR analysis on prenatal mouse RNA and embryonic stem cell RNA demonstrated expression of Nif3l1 throughout embryonic development . Additionally, expression analysis on cell lines revealed strong overexpression of Nif3l1 in the spermatogonia-derived cell line GC-1 spg and in the teratocarcinoma cell line F9 . The mouse gene was mapped to chromosome 1, region C . Human NIF3L1 consists of seven exons spanning 14.5 kb of genomic DNA and is located on chromosome 2q33 . A fusion protein consisting of the GFP (green fluorescent protein) and the ORF of human NIF3L1 showed a localization of the predicted protein in the cytoplasm . In the N-terminal and C-terminal region, mouse Nif3l1 and human NIF3L1 are strongly homologous to proteins of other species, e.g . the recently cloned Drosophila symbol=anon-35F/36F gene with 41% amino acid identity and several proteins from yeast including the yeast Ngg1-interacting factor 3 homolog with 46% amino acid identity, the hypothetical protein YGL221c and yeast Ngg1-interacting factor 3 (Nif3) with 37% amino acid identity . Other proteins from lower organisms, e.g a conserved hypothetical protein from Ureaplasma urealyticum or a hypothetical protein SCC30.09c from Streptomyces coelicolor show approximately 25-30% amino acid identity in the two flanking regions of the protein . These similarities indicate a high degree of conservation of mouse Nif3l1 and human NIF3L1 from bacteria to mammals . J Appl Microbiol, 2000 Dec, 89(6), 1038 - 47 Mixing and sulphate-reducing activity of bacteria in swelling, compacted bentonite clay under high-level radioactive waste repository conditions; Pedersen K et al.; AIM: The fate of micro-organisms in the bentonite clay surrounding high-level radioactive waste (HLW)-containing copper canisters in a future Swedish underground (500 m) repository were investigated . METHODS AND RESULTS: Laboratory experiments were designed in which the mixing of various bacterial species with swelling bentonite was studied . A clear trend of fewer cultivable bacteria at depth was seen in the clay . This trend was consistent as the incubation time was increased from 8 h to 28 weeks . Sulphate-reducing bacteria were found to be active, reducing sulphate at the lowest density studied, 1.5 g cm-3, but sulphate reduction activity ceased at higher densities . CONCLUSIONS: The number of viable micro-organisms in an HLW repository bentonite clay buffer will decrease rapidly during swelling and very few viable cells will be present at full compaction . SIGNIFICANCE AND IMPACT OF THE STUDY: Sulphate-reducing bacteria will most probably not be able to induce corrosion of HLW-containing copper canisters. J Microbiol Methods, 2000 Dec 15, 43(2), 73 - 80 DNA extraction from coral reef sediment bacteria for the polymerase chain reaction; Guthrie JN et al.; A rapid and effective method for the direct extraction of high molecular weight amplifiable DNA from two coral reef sediments was developed . DNA was amplified by the polymerase chain reaction (PCR) using 16S rDNA specific primers . The amplicons were digested with HaeIII, HinP1I and MspI and separated using polyacrylamide gel electrophoresis and silver staining . The resulting amplified ribosomal DNA restriction analysis (ARDRA) patterns were used as a fingerprint to discern differences between the coral reef sediment samples . Results indicated that ARDRA is an effective method for determining differences within the bacterial community amongst different environmental samples. Metab Eng, 2000 Oct, 2(4), 328 - 38 Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria; Jones KL et al.; Multicopy plasmids are often chosen for the expression of recombinant genes in Escherichia coli . The high copy number is generally desired for maximum gene expression; however, the metabolic burden effects that usually result from multiple plasmid copies could prove to be detrimental for maximum productivity in certain metabolic engineering applications . In this study, low-copy mini-F plasmids were compared to high-copy pMB1-based plasmids for production of two metabolites in E . coli: polyphosphate (polyP) and lycopene derived from isopentenyl diphosphate (IPP) . The stationary-phase accumulation of polyP on a per cell basis was enhanced approximately 80% when either high- or low-copy plasmids were used, from 120 micromol/g DCW without augmented polyP kinase (PPK) activity to approximately 220 micromol/g DCW . The cell density of the high-copy plasmid-containing culture at stationary phase was approximately 24% lower than the low-copy culture and 30% lower than the control culture . This difference in cell density is likely a metabolic burden effect and resulted in a lower overall product concentration for the high-copy culture (approximately 130 micromol/L culture) relative to the low-copy culture (approximately 160 micromol/L culture) . When the gene for DXP (1-deoxy-D-xylulose 5-phosphate) synthase, the first enzyme in the IPP mevalonate-independent biosynthetic pathway, was expressed from the tac promoter on multicopy and low-copy plasmids, lycopene production was enhanced two- to threefold over that found in cells expressing the chromosomal copy only . Cell growth and lycopene production decreased substantially when isopropyl beta-D-thiogalactosidase (IPTG) was added to the high-copy plasmid-containing culture, suggesting that overexpression of DXP synthase was a significant metabolic burden . In the low-copy plasmid-containing culture, no differences in cell growth or lycopene production were observed with any IPTG concentrations . When dxs was placed under the control of the arabinose-inducible promoter (P(BAD)) on the low-copy plasmid, the amount of lycopene produced was proportional to the arabinose concentration and no significant changes in cell growth resulted . These results suggest that low-copy plasmids may be useful in metabolic engineering applications, particularly when one or more of the substrates used in the recombinant pathway are required for normal cellular metabolism. J Microbiol Methods, 2001 Jan, 43(3), 213 - 22 Method for enumeration of 5-cyano-2,3-ditoyl tetrazolium chloride (CTC)-active cells and cell-specific CTC activity of benthic bacteria in riverine, estuarine and coastal sediments; Proctor LM et al.; Bacteria are the most abundant and active organisms in marine sediments and are critical for nutrient cycling and as a food source to many benthic and pelagic organisms . Bacteria are found both as free-living cells and as particle-associated cells, which can make investigations of these communities difficult . We found that common procedures for extracting bacteria from sediments leave the bacteria clay particle-associated and the clay particles clump, which reduce the reproducibility of direct counts . We optimized a sonication/surfactant method that produces a homogeneous suspension of bacterial cells against a uniform background of clay particles, which results in reproducible samples for epifluorescence microscopy . We developed a method to estimate CTC-positive cells and cell-specific CTC content in intact cores of surficial sediment communities from riverine, estuarine and coastal sites . Benthic bacterial abundances averaged 4.9x10(8) cells/g dry wt sediments in Apalachicola River, Florida sediments, 4.9-13.8x10(9) cells/g dry wt sediments in a variety of Apalachicola Bay sediments and 3.6x10(8) cells/g dry weight in shallow, anoxic Gulf of Mexico sediments . Percent CTC-positive cells ranged from low values of 9-10% CTC-positive cells in Apalachicola River and Apalachicola Bay sediments to high values of 25% CTC-positive cells in anoxic Gulf of Mexico sediments . After correction for abiotic CTC reduction and chlorophyll interference, estimates of cell-specific CTC reduction ranged from 0.15 to 0.55 fmol CTC(red)/active cell in the Apalachicola Bay sediments to 1.6 to 3.8 fmol CTC(red)/active cell in anoxic Gulf of Mexico sediments. Biochemistry (Mosc), 2000 Nov, 65(11), 1266 - 71 The widely accepted model of primary photosynthetic processes in purple bacteria must be revised; Borisov AY; Using computer simulation, it was found that, at least in case of purple bacteria, the widely accepted model for the primary photosynthetic processes (energy migration to reaction centers and its further trapping) is unable to provide a fully consistent explanation for the available experimental data . Two physical mechanisms suggested in this work are thought to be able to resolve or at least decrease the severity of this problem. Int Microbiol, 2000 Jun, 3(2), 81 - 8 How bacteria protect themselves against channel-forming colicins; Alonso G et al.; Here we review the mechanisms that bacterial cells use to protect themselves against channel-forming colicins . Four mechanisms are examined: immunity, resistance, tolerance and PacB character . Immunity confers protection to colicinogenic cells against the colicin they produce, since the colicinogenic plasmid bears the genetic determinant for such immunity protein . Resistance is provided by modifications on colicin receptors located on the outer membrane . It prevents colicin adsorption and protects against those colicins sharing a common receptor . Tolerance is achieved by changes in the translocation system . The adsorbed colicin is not translocated toward the periplasmic space . This impedes its insertion into the cell membrane as well as the formation of the transmembrane channel . Tolerance confers protection against colicins that share the same translocation system . Finally, we discuss the PacB character, that confers protection against all known channel-forming colicins . The latter property is encoded by non-colicinogenic plasmids in the H-incompatibility complex. Int Microbiol, 2000 Mar, 3(1), 3 - 8 Oxidative stress in bacteria and protein damage by reactive oxygen species; Cabiscol E et al.; The advent of O2 in the atmosphere was among the first major pollution events occurred on earth . The reaction between ferrous iron, very abundant in the reductive early atmosphere, and oxygen results in the formation of harmful superoxide and hydroxyl radicals, which affect all macromolecules (DNA, lipids and proteins) . Living organisms have to build up mechanisms to protect themselves against oxidative stress, with enzymes such as catalase and superoxide dismutase, small proteins like thioredoxin and glutaredoxin, and molecules such as glutathione . Bacterial genetic responses to oxidative stress are controlled by two major transcriptional regulators (OxyR and SoxRS) . This paper reviews major key points in the generation of reactive oxygen species in bacteria, defense mechanisms and genetic responses to oxidative stress . Special attention is paid to the oxidative damage to proteins. Int Microbiol, 1999 Dec, 2(4), 233 - 40 Light absorption by phototrophic bacteria: effects of scattering, cell concentration and size of the culture vessel; Sanchez O et al.; This article analyzes how absorption of light by suspensions of phototrophic bacteria is modulated by changes in the biomass of the culture, the size of the culture vessel and by the presence of refractile structures within the cells . Increases in biomass and culture size result in higher rates of light absorption but in the decrease of the amount of energy available per cell . The presence of refractile structures has different consequences depending on the biomass concentration . In dense cultures, the accumulation of refractile structures increases the reflection of light, and also reduces specific light absorption . In diluted cultures, however, the effect is the opposite, and refractile structures seem to increase light absorption. Ann R Coll Surg Engl, 2000 Nov, 82(6), 405 - 7 The passage of bacteria through surgical drapes; Blom A et al.; The passage of bacteria through surgical drapes is a potential cause of wound infection . Previous studies have shown that liquids and human albumin penetrate certain types of drapes . We studied the passage of bacteria through seven different types of surgical drape and an operating tray . Bacteria easily penetrated all the woven re-usable fabrics within 30 min . The disposable non-woven drapes proved to be impermeable, as did the operating tray . We recommend the use of non-woven disposable drapes or woven drapes with an impermeable operating tray in all surgical cases. FEMS Microbiol Ecol, 2000 Sep 1, 33(3), 171 - 180 Uncultured giant sulfur bacteria of the genus Achromatium; Head IM et al.; Achromatium is a genus of large unicellular sulfur bacteria . Despite being first described in the late 19th century, no Achromatium spp . have yet been isolated in culture, and for over 100 years, knowledge of their ecology, physiology and relationships to other bacteria has been scant . In recent years, the application of culture-independent techniques combined with in situ process measurements and single-cell activity measurements in sediments harbouring large Achromatium populations, has expanded our knowledge of these bacteria . Aspects of carbon and sulfur metabolism in Achromatium are now better understood, but their preferred electron acceptor(s) remain unknown . Unexpected diversity has been uncovered in Achromatium populations and it is now clear that the organism routinely described as Achromatium oxaliferum actually comprises several distinct Achromatium spp. Biofizika, 2000 Sep-Oct, 45(5), 864 - 9 {Reducing centers on the surface of Escherichia coli bacteria and their role in copper-induced plasma membrane permeability}; Lebedev VS et al.; The reducing properties of Escherichia coli and their role in the induction of nonselective cationic permeability of plasma membrane by the action of Cu2+ ions were studied . The ability of cells to reduce exogenous dithiopyridine was shown to be maximal in freshly collected culture and to decrease upon starvation or exhaustion of bacteria by dinitrophenol, in the presence of other oxidants of cell thiols in the medium, and after the disturbance of the barrier properties of membrane by tetrachloracetic acid or butanol . The alkylation of cell thiols accessible for N-ethyl maleimide completely disrupted the reducing activity of bacteria . These data are consistent with the conception that the reduction of dithiopyridine and Cu2+ ions by bacteria occurs on the thiol-containing centers of the cell surface, which are continuously reduced by the transfer of cell reducing equivalents from the inner to the outer surface of plasma membrane . The analysis of data on the effect of external oxidizing and reducing agents on the copper-induced plasmolysis of bacteria showed that the induction of membrane permeability by the action of copper can occur upon interaction with critical targets on the surface of Cu+ ions formed in the periplasmic space in the reaction of Cu2+ ions with reducing centers. Membr Cell Biol, 2000, 14(2), 173 - 80 The dipyridamole effect on the photoactive bacteriochlorophyll interaction with quinone acceptors in reaction centers of purple bacteria; Churbanova IYu et al.; The effect of Dipyridamole (10(-6)-10(-3) M) on the photomobilized electron transport in the system of quinone acceptors Q(A)-Q(B) of isolated photosynthetic reaction centers of Rhodobacter sphaeroides and on its temporary stabilization on Q(B) was studied . Depending on the type of the detergent present in the reaction center (lauryl dimethylamine oxide, Triton X-100, sodium dodecyl sulfate, and sodium cholate), dipyridamole could increase the time of the electron transfer to Q(B) . The dipyridamole effect on the efficiency of the electron stabilization on Q(B) for reaction centers with different detergents was revealed in slowing down the process of dark reduction of photoactive bacteriochlorophyll from Q(B) at initial concentrations of added dipyridamole (10(-6)-10(-5) M) with following acceleration of the process at the dipyridamole concentrations of 10(-4)-10(-3) M . The pH lowering from 6.8-7.0 to 5.9-6.0 increased the dipyridamole effect . The possibility of the dipyridamole effect on the structural-dynamic state of the reaction center complex, including its hydrogen bond system, which influences the studied parameters of functional activity, is suggested. Med Hypotheses, 2000 Dec, 55(6), 502 - 6 Single and multiple cholesterol gallstones and the influence of bacteria; Vitetta L et al.; Single and multiple cholesterol gallstones constitute at least 80% of the gallstone population observed at cholecystectomy in Western countries . While supersaturation of bile with cholesterol is necessary for gallstone growth, the kinetic determinant of crystal nucleation is perhaps the critical factor leading to the incidence of gallstones . Nucleation involves aggregation of nidus-forming materials like pigment precipitates and mucus proteins . In combination with cholesterol precipitates and crystal formation, gallstone propagation is enhanced . Bacterial species may augment the process of nucleation and gallstone growth by contributing specific enzyme activities resulting in the formation of insoluble precipitates in bile, or by acting as a nidus upon which the deposition of cholesterol crystals may initiate gallstone formation . The utilization of Raman microscopic techniques permits detailed mapping of the distribution of the gallstone components leading to identification and characterization of the site of nucleation . This, when coupled to molecular genetic tools such as PCR DNA amplification, would permit elucidation of the role of bacteria in vivo gallstone propagation mechanisms . Protein Expr Purif, 2000 Dec, 20(3), 435 - 43 Coexpression of proteins in bacteria using T7-based expression plasmids: expression of heteromeric cell-cycle and transcriptional regulatory complexes; Johnston K et al.; This report describes the development and application of a dual vector coexpression system for the overproduction of heteromeric cell cycle and transcriptional regulatory protein complexes in bacteria . To facilitate these studies we constructed a T7-based expression plasmid, pRM1 that contains an origin of replication derived from p15A, and a gene encoding kanamycin resistance . This expression vector is compatible with ColE1-derived plasmids found in the pET family of T7 expression vectors, which encode ampicillin resistance . It also has the same multiple cloning sites as the pET- derived pRSET vector, allowing easy shuttling between the two expression vectors . Cotransformation of the pRM1 and pET-derived expression vectors into an Escherichia coli strain such as BL21(DE3) results in a significant level of coexpression of heteromeric protein complexes . We demonstrate the applicability of combining the pRM1 and pET-derived vectors for the coexpression of cell cycle regulatory components, pRB/E7 and pRB/E1a, and the transcriptional regulatory complexes, SRF/SAP-1 and SRF/Elk-1 . We further use the pRB/E1a complex to demonstrate that these coexpressed complexes can be purified to homogeneity for further studies . Use of the pRM1 vector in combination with the pET-derived vectors should be generally applicable for the large-scale coexpression and purification of a wide variety of heteromeric protein complexes for biochemical, biophysical, and structural studies . J Gastrointest Surg, 2000 Sep-Oct, 4(5), 547 - 53 Pigment gallstone pathogenesis: slime production by biliary bacteria is more important than beta-glucuronidase production; Stewart L et al.; Pigment stones are thought to form as a result of deconjugation of bilirubin by bacterial beta-glucuronidase, which results in precipitation of calcium bilirubinate . Calcium bilirubinate is then aggregated into stones by an anionic glycoprotein . Slime (glycocalyx), an anionic glycoprotein produced by bacteria causing foreign body infections, has been implicated in the formation of the precipitate that blocks biliary stents . We previously showed that bacteria are present within the pigment portions of gallstones and postulated a bacterial role in pigment stone formation through beta-glucuronidase or slime production . Ninety-one biliary bacterial isolates from 61 patients and 12 control stool organisms were tested for their production of beta-glucuronidase and slime . The average slime production was 42 for biliary bacteria and 2.5 for stool bacteria (P <0.001) . Overall, 73% of biliary bacteria and 8% of stool bacteria produced slime (optical density >3) . In contrast, only 38% of biliary bacteria produced beta-glucuronidase . Eighty-two percent of all patients, 90% of patients with common bile duct (CBD) stones, 100% of patients with primary CBD stones, and 93% of patients with biliary tubes had one or more bacterial species in their stones that produced slime . By comparison, only 47% of all patients, 60% of patients with CBD stones, 62% of patients with primary CBD stones, and 50% of patients with biliary tubes had one or more bacteria that produced beta-glucuronidase . Most biliary bacteria produced slime, and slime production correlated better than beta-glucuronidase production did with stone formation and the presence of biliary tubes or stents . Patients with primary CBD stones and biliary tubes had the highest incidence of slime production . These findings suggest that bacterial slime is important in gallstone formation and the blockage of biliary tubes. Infection, 2000 Sep, 28(5), 301 - 4 Phagocytosis of periodontopathogenic bacteria by crevicular granulocytes is depressed in progressive periodontitis; Eick S et al.; BACKGROUND: The aim of this study was to examine crevicular polymorphonuclear neutrophils (PMN) of patients with rapidly progressive periodontitis (RPP) for their in vitro phagocytic activity and intracellular killing of Porphyromonas gingivalis ATCC 33277 and two strains of Actinobacillus actinomycetemcomitans (NCTC 9710 - type strain and Tanner FDC 44 - leukotoxin producing strain) . PATIENTS AND METHODS: 18 patients with RPP and nine healthy controls were included in the study . Phagocytosis and intracellular killing were assessed by fluorescence microscopy after staining with acridine orange . The percentage of phagocytosing PMN was determined.The phagocytic cells were then separated into two groups; those containing < 10 phagocytosed bacteria and those containing > 10 bacteria.The percentage of PMN containing viable bacteria was also determined . RESULTS: The leukotoxic A . actinomycetemcomitans strain was phagocytosed to a lesser degree than the corresponding type strain.The number of phagocytosing cells obtained from the RPP patients did not differ from the controls . However, in healthy subjects there were more phagocytes with more than ten ingested P . gingivalis than in RPP patients.The intracellular killing was diminished in the periodontitis group for P . gingivalis and for both A . actinomycetemcomitans strains . CONCLUSION: The PMN of patients with RPP show deficiencies in phagotcytic activity and in the intracellular killing or peridontopathogenic bacteria. Genome Inform Ser Workshop Genome Inform, 1998, 9, 13 - 21 Construction of the gyrB Database for the Identification and Classification of Bacteria; Kasai H et al.; Nucleotide sequences of small-subunit rRNA (16S rRNA) are most commonly used for the identification and characterization of bacteria and their complex communities . However, 16S rRNA evolves slowly and is often not very convenient to resolve bacterial strains at the species level . We have therefore attempted to develop a rapid and more convenient system for bacterial identification using the gyrB gene sequences . We chose the gyrB gene, because (i) it is rarely transmitted horizontally, (ii) its molecular evolution rate is higher than that of 16S rRNA, and (iii) the gene is distributed ubiquitously among bacterial species . We PCR-amplified the 1.2 kb-long gyrB segments from about 1,000 bacterial species by using degenerate primers and determined their nucleotide sequences . The resultant data have been assembled into the gyrB database accessible via WWW. Mol Microbiol, 2000 Nov, 38(3), 650 - 7 DNA-independent transport of plasmid primase protein between bacteria by the I1 conjugation system; Wilkins BM et al.; The ColIb-P9 (IncI1)-encoded conjugation system supports transfer of the plasmid T-strand plus hundreds of molecules of the Sog polypeptides determined by the plasmid primase gene . Here, we report that Sog primase is abundantly donated to the recipient cell from cells carrying a non-transferable ColIb plasmid deleted of the nic site essential for DNA export . Such DNA-independent secretion of Sog primase is typical of authentic conjugation, both in being blocked when the recipient cell specifies the entry exclusion function of ColIb and in requiring the thin I1 pilus encoded by the ColIb pil system under the mating conditions used . It is proposed that Sog polypeptides form a complex with the ColIb T-strand during conjugation and aid DNA transport through processive secretion of the proteins into the recipient cell . Functional and genetic relationships between the ColIb conjugation system and other type IV secretion pathways are discussed. Can J Microbiol, 2000 Oct, 46(10), 927 - 37 Methanogens and sulfate-reducing bacteria in oil sands fine tailings waste; Holowenko FM et al.; In the past decade, the large tailings pond (Mildred Lake Settling Basin) on the Syncrude Canada Ltd . lease near Fort McMurray, Alta., has gone methanogenic . Currently, about 60%-80% of the flux of gas across the surface of the tailings pond is methane . As well as adding to greenhouse gas emissions, the production of methane in the fine tailings zone of this and other settling basins may affect the performance of these settling basins and impact reclamation options . Enumeration studies found methanogens (10(5)-10(6) MPN/g) within the fine tailings zone of various oil sands waste settling basins . SRB were also present (10(4)-10(5) MPN/g) with elevated numbers when sulfate was available . The methanogenic population was robust, and sample storage up to 9 months at 4 degrees C did not cause the MPN values to change . Nor was the ability of the consortium to produce methane delayed or less efficient after storage . Under laboratory conditions, fine tailings samples released 0.10-0.25 mL CH4 (at STP)/mL fine tailings . The addition of sulfate inhibited methanogenesis by stimulating bacterial competition. Hautarzt, 2000 Sep, 51(9), 655 - 60 {Reduction of colonization of new mattresses with bacteria, moulds and house dust mites by complete mattress covers}; Pitten FA et al.; BACKGROUND AND OBJECTIVE: We investigated if the colonisation of new mattresses with house dust mites, bacteria, and fungi could be reduced by using synthetic mattress covers as compared to common cotton covers . PATIENTS/METHODS: 84 healthy volunteers were assigned to two groups . Group A (n = 43) received the cotton covers, group B (n = 41) the synthetic covers which were made of a polyester microfaser with a polyurethane surface layer (Pro-Tex, Germed, Schwarzenbek, Germany) . RESULTS: The mite antigen concentration after six months was significantly lower in group B . Three months after the start of the study counts of bacteria and moulds were significantly higher in group A compared to group B . CONCLUSIONS: It can be recommended that patients suffering from an allergy to mites or moulds may reduce their domestic allergen exposure by using the synthetic mattress covers tested in this study . Since cotton covers are very likely to become colonised by bacteria and moulds, they must be cleaned periodically (at least every 2nd-3d month). Transfus Med Rev, 2000 Oct, 14(4), 302 - 11 Blood group associations with parasites, bacteria, and viruses; Moulds JM et al.; Although recent investigations into the human blood groups have proceeded mainly at the molecular level, the RBC remains an exquisite model to study the expression of various genes and their related proteins . Although DNA may be informative, it may not always give meaningful information regarding protein expression on cell surfaces, which is where binding occurs . Because of their easy accessibility, RBCs will continue to be used as a major tool in the investigation of the causative agents for disease, whether they be viral, bacterial, or parasitic in nature. J Bacteriol, 2000 Nov, 182(22), 6499 - 502 Evolutionary conservation of methyl-accepting chemotaxis protein location in Bacteria and Archaea; Gestwicki JE et al.; The methyl-accepting chemotaxis proteins (MCPs) are concentrated at the cell poles in an evolutionarily diverse panel of bacteria and an archeon . In elongated cells, the MCPs are located both at the poles and at regions along the length of the cells . Together, these results suggest that MCP location is evolutionarily conserved. Acta Biochim Pol, 2000, 47(2), 451 - 7 A new look at adaptive mutations in bacteria; Janion C; This is a short survey of the adaptive mutation processes that arise in non- or slowly-dividing bacterial cells and includes: (i) bacterial models in which adaptive mutations are studied; (ii) the mutagenic lesions from which these mutations derive; (iii) the influence of DNA repair processes on the spectrum of adaptive mutations . It is proposed that in starved cells, likely as during the MFD phenomenon, lesions in tRNA suppressor genes are preferentially repaired and no suppressor tRNAs are formed as a result of adaptive mutations . Perhaps the most provocative proposal is (iv) a hypothesis that the majority of adaptive mutations are selected in a pre-apoptotic state where the cells are either mutated, selected, and survive, or they die. Membr Cell Biol, 2000, 14(1), 37 - 45 Effect of dipyridamole on the recombination kinetics between photooxidized bacteriochlorophyll and photoreduced primary quinone in reaction centres of purple bacteria; Knox PP et al.; The action of dipyridamole (DIP) on dark recombination between the photooxidized special pair bacteriochlorophyll BChl2+ and reduced primary quinone acceptor Q(A)- in the reaction centres (RCs) of the bacteria Rhodobacter sphaeroides was studied in the presence of different detergents (LDAO, Triton X-100, sodium cholate, sodium dodecyl sulfate) . DIP accelerated this reaction approximately 4-5-fold . In RCs with the extracted H-subunit, the effect of DIP was observed at lower concentrations . The possibility of modification of the RC structure-dynamic state by DIP (including changes in RC hydrogen bonds) is proposed . The modification obviously disturbs the processes of the long-life electrostatic stabilization of Q(A)-. FEMS Microbiol Ecol, 2000 Oct 1, 34(1), 57 - 62 Geostatistical analysis of the distribution of NH(4)(+) and NO(2)(-)-oxidizing bacteria and serotypes at the millimeter scale along a soil transect; Grundmann GL et al.; Soil is known to be heterogeneous for different activities at several spatial scales . Most studies have focused on macro- and meso-scales but micro-scales are rarely addressed . Hence, the spatial structure of NH(4)(+)- and NO(2)(-)-oxidizers and of various serotypes of the latter was studied along two transects of approximately 10 cm, with two micro-samples taken from each millimeter . The presence of NH(4)(+)- and NO(2)(-)-oxidizers in a micro-sample was detected using colorimetric tests for the presence or absence of NO(2)(-) in cultures of the micro-samples . Geostatistics was used to determine the range of spatial influence of the bacterial types . For both types, semi-variograms indicated a non-random spatial pattern . The spatial dependence ranged from 2 to 4 mm for NO(2)(-)- and NH(4)(+)-oxidizers respectively, and the two bacterial types were not independently spatially located . Among the six serotypes of NO(2)(-)-oxidizers, only one exhibited a spatial dependence . The existence of a spatial structure at the millimeter scale suggests that micro-scale sampling should be employed for soil studies . Therby, data on bacterial populations and activities can be referred to a spatial scale which is meaningful to these organisms. Biotechnol Bioeng, 2000 Dec 5, 70(5), 533 - 43 Ethanol utilization by sulfate-reducing bacteria: an experimental and modeling study; Nagpal S et al.; A mixed culture of sulfate-reducing bacteria containing the species Desulfovibrio desulfuricans was used to study sulfate-reduction stoichiometry and kinetics using ethanol as the carbon source . Growth yield was lower, and kinetics were slower, for ethanol compared to lactate . Ethanol was converted into acetate and no significant carbon dioxide production was observed . A mathematical model for growth of sulfate-reducing bacteria on ethanol was developed, and simulations of the growth experiments on ethanol were carried out using the model . The pH variation due to sulfate reduction, and hydrogen sulfide production and removal by nitrogen sparging, were examined . The modeling study is distinct from earlier models for systems using sulfate-reducing bacteria in that it considers growth on ethanol, and analyzes pH variations due to the product-formation reactions . Biofizika, 2000 Jul-Aug, 45(4), 648 - 53 {Effect of dipyridamole on recombination of photooxidized bacteriochlorophylla and photoreduced primary quinone in reactive centers of purple bacteria and degradation of form M412 of bacteriorhodopsin}; Zakharov NL et al.; It is shown that the addition of dipyridamole (2,6-bis(diethanolamino)-4,8-dipiperidinopyrimido{5,4d}py rim idine) (up to 10(-4) M) leads to a drastic acceleration of the dark recombination reaction between photooxidized bacteriochlorophyll and photoreduced primary quinone in reaction centers of Rhodobacter sphaeroides . The value of the acceleration is similar to that registered under cryogenic temperatures . The extent of the effect of dipyridamole derivatives depended on their structure . In wild-type bacteriorhodopsin and D96N mutant, dipyridamole slowed down the Schiff base reprotonation (the kinetics of M412 form decay was registered) . It is suggested that dipyridamole can influence the structural and dynamic state of membrane proteins by affecting the system of their hydrogen-bonds and thus modify electron and proton transport processes. FEMS Microbiol Lett, 2000 Nov 1, 192(1), 145 - 52 Localization of Legionella bacteria within ribosome-studded phagosomes is not restricted to Legionella pneumophila; Gerhardt H et al.; In this report, we investigate the intracellular fate of selected members of the genus Legionella within the monocytic cell line Mono Mac 6 cells . By means of electron microscopy and immunocytochemistry, we could show that Legionella pneumophila as well as Legionella longbeachae are able to induce ribosome-studded phagosomes which associate with the rough endoplasmic reticulum (RER), whereas Legionella micdadei remains to be located within smooth phagosomes but also shows signs of RER association . In addition, we could demonstrate a remarkable correlation between the phagosome type and the morphological phenotype of intracellular bacteria: within ribosome-studded phagosomes, bacteria generally lacked the outer coat of low electron density whereas bacteria within the smooth phagosomes still possessed this outer coat . The virulence factors responsible for inhibition of phagosome maturation and their distribution within the genus Legionella as well as the biological significance of the morphological difference of bacteria within smooth and ER-associated phagosomes remain to be investigated. Protein Expr Purif, 2000 Oct, 20(1), 37 - 44 Expression of functional soluble human alpha-globin chains of hemoglobin in bacteria; Adachi K et al.; Individual, soluble human alpha-globin chains were expressed in bacteria with exogenous heme and methionine aminopeptidase . The yields of soluble alpha chains in bacteria were comparable to those of recombinant non-alpha chains expressed under the same conditions . Molecular mass and gel-filtration properties of purified recombinant alpha chains were the same as those of authentic human alpha chains . Biochemical and biophysical properties of isolated alpha chains were identical to those of native human alpha chains as assessed by UV/vis, circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopy which contrasts with previous results of refolded precipitated alpha chains made in the presence of heme in vitro (M . T . Sanna et al., J . Biol . Chem . 272, 3478-3486, 1997) . Mixtures of purified, soluble recombinant alpha-globin and native beta-globin chains formed heterotetramers in vitro, and oxygen- and CO-binding properties as well as the heme environment of the assembled tetramers were experimentally indistinguishable from those of native human Hb A . UV/vis, CD, and NMR spectra of assembled Hb A were also the same as those of human Hb A . These results indicate that individual expressed alpha chains are stable in bacteria and fold properly in vivo and that they then can assemble with free beta chains to form hemoglobin heterotetramers in vivo as well as in vitro . Infect Immun, 2000 Nov, 68(11), 6496 - 504 Transmission electron microscopic demonstration of phagocytosis and intracellular processing of segmented filamentous bacteria by intestinal epithelial cells of the chick ileum; Yamauchi KE et al.; Segmented filamentous bacteria (SFB) are autochthonous bacteria colonizing the ileum of many young animals by attaching to intestinal epithelial cells . These nonpathogenic bacteria strongly stimulate the mucosal immune system and induce intestinal epithelial cells to express major histocompatibility complex class II molecules . We tried to discover whether SFB are phagocytized and intracellularly processed by the host cells, which is indicative of antigen processing . The middle part of the ileum was extracted from 10- and 20-day-old broiler chicks (Gallus gallus domesticus) . Samples were processed and examined by scanning and transmission electron microscopy (SEM and TEM, respectively) . In SEM, no, few, medium, and dense SFB colonization levels were classified . In TEM of cells from animals with medium or dense SFB colonization levels, we could observe extracellular particles ranging from those only indenting the cell membrane to particles found in the cytoplasmatic area beyond the terminal web . These particles had a structural similarity with SFB that were floating freely in the intestinal lumen . Furthermore, we observed unlacing of the membrane and septum surrounding the extracellular particles and their incorporation into host cytoplasmatic components, which strongly suggests that these particles are phagocytized and intracellularly processed SFB . This conclusion is supported by TEM analysis of samples with no or few SFB, in which we failed to find these characteristic morphologies . The phagocytosis process described here could be an important trigger for the stimulating effect of SFB on the mucosal immune system. FEBS Lett, 2000 Sep 1, 480(2-3), 73 - 8 Pigment-protein architecture in the light-harvesting antenna complexes of purple bacteria: does the crystal structure reflect the native pigment-protein arrangement? Leupold D, Voigt B, Beenken W, Stiel H. Structural analysis of crystallized peripheral (LH2) and core antenna complexes (LH1) of purple bacteria has revealed circular aggregates of high rotational symmetry (C8, C9 and C16, respectively) . Quantum-chemical calculations indicate that in particular the waterwheel-like arrangements of pigments should show characteristic structure-sensitive spectroscopic behavior in the near infrared absorption region . Laser-spectroscopic data obtained with non-crystallized, isolated LH2 of Rhodospirillum molischianum are in line with a highly symmetric (C8) circular aggregate, but deviations have been found for LH2 of Rhodobacter sphaeroides and Rhodopseudomonas acidophila . For both the latter, C-shaped incomplete circular aggregates (as seen only recently in electron micrographs of crystallized LH1-reaction center complexes) may be a suitable preliminary model. Gene, 2000 Sep 19, 255(2), 419 - 24 Purple acid phosphatases from bacteria: similarities to mammalian and plant enzymes; Schenk G et al.; Mammalian and plant purple acid phosphatases have similar active site structures despite low sequence identity (<20%) . Although no bacterial enzyme has been purified, a sequence database search revealed that genes that could encode potential purple acid phosphatases may be restricted to a small number of organisms (i.e . myco- and cyanobacteria) . Analysis of their deduced amino acid sequences and predicted secondary structures indicates that the cyanobacterial enzyme is similar to both the mammalian and the recently discovered low-molecular-weight plant purple acid phosphatases, while the mycobacterial enzyme is homologous to the fungal and high-molecular-weight plant purple acid phosphatases . Homology models indicate that both bacterial proteins appear to be similar to mammalian purple acid phosphatases in the immediate vicinity of the active site . It is likely that these enzymes act as Fenton-type catalysts in order to prevent damage caused by reactive oxygen species generated by invaded host cells (M . tuberculosis) or by the light-harvesting complex (Synechocystis sp.). Biophys J, 2000 Oct, 79(4), 2105 - 20 Exciton dynamics in the chlorosomal antennae of the green bacteria Chloroflexus aurantiacus and Chlorobium tepidum; Prokhorenko VI et al.; The energy transfer processes in isolated chlorosomes from green bacteria Chlorobium tepidum and Chloroflexus aurantiacus have been studied at low temperatures (1.27 K) by two-pulse photon echo and one-color transient absorption techniques with approximately 100 fs resolution . The decay of the coherence in both types of chlorosomes is characterized by four different dephasing times stretching from approximately 100 fs up to 300 ps . The fastest component reflects dephasing that is due to interaction of bacteriochlorophylls with the phonon bath, whereas the other components correspond to dephasing due to different energy transfer processes such as distribution of excitation along the rod-like aggregates, energy exchange between different rods in the chlorosome, and energy transfer to the base plate . As a basis for the interpretation of the excitation dephasing and energy transfer pathways, a superlattice-like structural model is proposed based on recent experimental data and computer modeling of the Bchl c aggregates (1994 . Photosynth . Res . 41:225-233.) This model predicts a fine structure of the Q(y) absorption band that is fully supported by the present photon echo data. Ecotoxicol Environ Saf, 2000 Oct, 47(2), 186 - 94 Comparison of four chronic toxicity tests using algae, bacteria, and invertebrates assessed with sixteen chemicals; Radix P et al.; The performances of four chronic toxicity tests, comprising the Daphnia magna 21-day (d) (crustacean), Brachionus calyciflorus 2-d (rotifer), Pseudokirchneriella subcapitata 72-h (green algae), and the Microtox chronic 22-h (bacteria) tests, were compared . Sixteen chemicals with toxicity covering 6 orders of magnitude were studied . Very high correlations were found between the NOEC/EC(10) Pseudokirchneriella 72-h, NOEC/EC(10) Brachionus 2-d, and the NOEC Daphnia 21-d tests . The toxicological response of rotifers and microalgae were within the same order of magnitude as the response of Daphnia in 80% of cases (13/16 chemicals) . The Microtox chronic test also anticipated the overall results of the Daphnia 21-d test, but the prediction was rather imprecise, compared with microalgae and rotifers . The test measuring the algal growth inhibition of P . subcapitata after 72h was the most sensitive bioassay . Toxicity on microalgae after 72h could be estimated after 5h by measuring either the direct fluorescence of either photosynthetic pigments or fluorescein diacetate in 56 and 43% of cases, respectively . The median value of the ratio between EC(10) and EC(50) was 3.75, 2, and 1.5 with the algae, the rotifers, and the bacteria, respectively . Annu Rev Microbiol, 2000, 54, 681 - 708 DNA segregation in bacteria; Gordon GS et al.; Segregation of DNA in bacterial cells is an efficient process that assures that every daughter cell receives a copy of genomic and plasmid DNA . In this review, we focus primarily on observations in recent years, including the visualization of DNA and proteins at the subcellular level, that have begun to define the events that separate DNA molecules . Unlike the process of chromosome segregation in higher cells, segregation of the bacterial chromosome is a continuous process in which chromosomes are separated as they are replicated . Essential to separation is the initial movement of sister origins to opposite ends of the cell . Subsequent replication and controlled condensation of DNA are the driving forces that move sister chromosomes toward their respective origins, which establishes the polarity required for segregation . Final steps in the resolution and separation of sister chromosomes occur at the replication terminus, which is localized at the cell center . In contrast to the chromosome, segregation of low-copy plasmids, such as Escherichia coli F, P1, and R1, is by mechanisms that resemble those used in eukaryotic cells . Each plasmid has a centromere-like site to which plasmid-specified partition proteins bind to promote segregation . Replication of plasmid DNA, which occurs at the cell center, is followed by rapid partition protein-mediated separation of sister plasmids, which become localized at distinct sites on either side of the division plane . The fundamental similarity between chromosome and plasmid segregation-placement of DNA to specific cell sites-implies an underlying cellular architecture to which both DNA and proteins refer. Appl Environ Microbiol, 2000 Oct, 66(10), 4532 - 5 Pacific Northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria; Nold SC et al.; The diversity of ammonia-oxidizing bacteria in aquatic sediments was studied by retrieving ammonia monooxygenase and methane monooxygenase gene sequences . Methanotrophs dominated freshwater sediments, while beta-proteobacterial ammonia oxidizers dominated marine sediments . These results suggest that gamma-proteobacteria such as Nitrosococcus oceani are minor members of marine sediment ammonia-oxidizing communities. Appl Environ Microbiol, 2000 Oct, 66(10), 4518 - 22 Use of combined microautoradiography and fluorescence in situ hybridization to determine carbon metabolism in mixed natural communities of uncultured bacteria from the genus Achromatium; Gray ND et al.; Combined microautoradiography and fluorescence in situ hybridization (FISH) was used to investigate carbon metabolism in uncultured bacteria from the genus Achromatium . All of the Achromatium species identified in a freshwater sediment from Rydal Water, Cumbria, United Kingdom, which were distinguishable only by FISH, assimilated both {(14)C}bicarbonate and {(14)C}acetate . This extends previous findings that Achromatium spp . present at another location could only utilize organic carbon sources . Achromatium spp., therefore, probably exhibit a range of physiologies, i.e., facultative chemolithoautotrophy, mixotrophy, and chemoorganoheterotrophy, similar to other large sulfur bacteria (e.g., Beggiatoa spp.). Mikrobiologiia, 2000 Jul-Aug, 69(4), 483 - 7 {Destruction of chlorinated derivatives of phenol: ortho-chlorophenol, para-chlorophenol, and 2,4-dichlorophenoxyacetic acid by bacteria communities in anaerobic sludge}; Berestovskaia IuIu et al.; The bacterial community of anaerobic sludge could degrade ortho-chlorophenol, para-chlorophenol, and 2,4-dichlorophenoxyacetic acid at concentrations as high as 100 mg/l . The time needed for the degradation of a given chlorinated phenol derivative increased 1.5- to 2-fold upon a twofold increase in its concentration (from 50 to 100 mg/l) . The duration of the adaptation period depended on the compound studied and on its concentration . The degradation of 2,4-dichlorophenoxyacetic acid proceeded via 2,4-dichlorophenol and p-chlorophenol as intermediates; the degradation of o-chlorophenol occurred with the formation of phenol . The dynamics of p-chlorophenol degradation and chloride ion accumulation were studied. Biochem Biophys Res Commun, 2000 Sep 16, 276(1), 64 - 70 ppGpp-dependent leuO expression in bacteria under stress; Fang M et al.; Despite the known potential transcription regulatory role of leuO gene product, LeuO, the condition when leuO expresses during bacterial growth cycle remains unclear . Mechanistically, leuO expression was shown to be part of promoter relay mechanism, however, the factor(s) responsible for the regulation of leuO expression is not known . Combining Northern and Western results, we demonstrate in the present communication that leuO expression is normally low and enhanced when bacteria are in transition from exponential growth to stationary phase . The stationary phase-associated leuO expression is ppGpp dependent and rpoS (varsigma(s) factor) independent . Biotechnol Bioeng, 2000 Nov 20, 70(4), 464 - 6 High density cultivation of two strains of iron-oxidizing bacteria through reduction of ferric iron by intermittent electrolysis; Matsumoto N et al.; Electrolytic cultivation was applied to Leptospirillum ferrooxidans strains P3A and CF27, which use ferrous iron to respire aerobically . Ferrous iron was supplied to the bacteria by intermittent electrolytic reduction of ferric iron as electron shuttle using an electrode . The yield of L . ferrooxidans and strain CF27 reached 20- and 50-fold, respectively, higher density than were achievable yields without electrolysis . The time required to obtain high density depended not on the growth ratio, but rather on the original growth rate of each strain . Proc Natl Acad Sci U S A, 2000 Oct 10, 97(21), 11397 - 402 Genes identified by an expression screen of the vector mosquito Anopheles gambiae display differential molecular immune response to malaria parasites and bacteria; Oduol F et al.; We performed a gene expression screen of the entire transcriptome of the major African malaria vector Anopheles gambiae for immune response genes in adult female mosquitoes, which is the developmental stage infected by malaria parasites . Mosquitoes were immune-stimulated for subtractive cloning by treatment with bacterial lipopolysaccharide, a potent and general elicitor of the innate immune response, and by injury . The screen yielded a highly enriched cDNA library in which more than half of the clones were immune responsive . In this paper, we describe 23 immune-regulated genes, including putative protease inhibitors, serine proteases, regulatory molecules, and a number of genes without known relatives . A molecule related to the protease inhibitor alpha-2-macroglobulin responded strongly to malaria parasite infection, but displayed little or no response to bacteria, whereas other genes exhibited the inverse pattern . These results indicate that the insect immune system discriminates between molecular signals specific to infection with bacteria and malaria parasites. Biochim Biophys Acta, 2000 Aug 15, 1459(2-3), 370 - 82 Biogenesis of iron-sulfur proteins in eukaryotes: a novel task of mitochondria that is inherited from bacteria; Muhlenhoff U et al.; Fe/S clusters are co-factors of numerous proteins with important functions in metabolism, electron transport and regulation of gene expression . Presumably, Fe/S proteins have occurred early in evolution and are present in cells of virtually all species . Biosynthesis of these proteins is a complex process involving numerous components . In mitochondria, this process is accomplished by the so-called ISC (iron-sulfur cluster assembly) machinery which is derived from the bacterial ancestor of the organelles and is conserved from lower to higher eukaryotes . The mitochondrial ISC machinery is responsible for biogenesis iron-sulfur proteins both within and outside the organelle . Maturation of the latter proteins involves the ABC transporter Atm1p which presumably exports iron-sulfur clusters from the organelle . This review summarizes recent developments in our understanding of the biogenesis of iron-sulfur proteins both within bacteria and eukaryotes. Proc Natl Acad Sci U S A, 2000 Sep 26, 97(20), 10808 - 13 Femtosecond dynamics of the forbidden carotenoid S1 state in light-harvesting complexes of purple bacteria observed after two-photon excitation; Walla PJ et al.; Time-resolved excited-state absorption intensities after direct two-photon excitation of the carotenoid S(1) state are reported for light-harvesting complexes of purple bacteria . Direct excitation of the carotenoid S(1) state enables the measurement of subsequent dynamics on a fs time scale without interference from higher excited states, such as the optically allowed S(2) state or the recently discovered dark state situated between S(1) and S(2) . The lifetimes of the carotenoid S(1) states in the B800-B850 complex and B800-B820 complex of Rhodopseudomonas acidophila are 7+/-0.5 ps and 6+/-0.5 ps, respectively, and in the light-harvesting complex 2 of Rhodobacter sphaeroides approximately 1.9+/-0.5 ps . These results explain the differences in the carotenoid to bacteriochlorophyll energy transfer efficiency after S(2) excitation . In Rps . acidophila the carotenoid S(1) to bacteriochlorophyll energy transfer is found to be quite inefficient (phi(ET1) <28%) whereas in Rb . sphaeroides this energy transfer is very efficient (phi(ET1) approximately 80%) . The results are rationalized by calculations of the ensemble averaged time constants . We find that the Car S(1) --> B800 electronic energy transfer (EET) pathway ( approximately 85%) dominates over Car S(1) --> B850 EET ( approximately 15%) in Rb . sphaeroides, whereas in Rps . acidophila the Car S(1) --> B850 EET ( approximately 60%) is more efficient than the Car S(1) --> B800 EET ( approximately 40%) . The individual electronic couplings for the Car S(1) --> BChl energy transfer are estimated to be approximately 5-26 cm(-1) . A major contribution to the difference between the energy transfer efficiencies can be explained by different Car S(1) energy gaps in the two species. Ukr Biokhim Zh, 2000 Mar-Apr, 72(2), 72 - 6 {Effect of thallium of ATP-ase activity and transmembrane potential in bacteria}; Gruzina TG et al.; Effect of thallium (TlNO3) on the ATPase activity and transmembrane potential (Dj) of bacteria with different levels of resistance to this metal has been studied . The hypothesis has been made that the resistance biochemical mechanism is based on the energy transformation systems in the cell. Nihon Hansenbyo Gakkai Zasshi, 2000 Jul, 69(2), 83 - 6 {Protective immunity against intracellular parasitic bacteria}; Mitsuyama M; Facultative intracellular bacteria are resistant to the killing mechanism inside macrophages by virtue of various escape mechanisms . Activation of macrophages by cytokines is the key event to overcome of bacterial escape in macrophages of the infected host . Generation of TH1 type of antigen-specific T cell is the essentially required for the macrophage activation . This short review summarizes the escape mechanism of activated macrophages and the mechanisms involved in the generation of TH1 cells. Microb Ecol, 2000 Jul, 40(1), 57 - 63 Substrate Concentration and Plasmid Transfer Frequency between Bacteria in a Model Rhizosphere; Pearce DA et al.; The influence of substrate concentration on plasmid transfer frequency in the rhizosphere was investigated using a physical model employing a hollow fiber membrane instead of a real root . The absolute number of transconjugants produced increased with increasing substrate (glucose) concentration, but the plasmid transfer frequency decreased exponentially with increasing substrate concentration from 4.4 x 10(-3) at 90 microg ml(-1) glucose to 1.35 x 10(-5) at 3600 microg ml(-1) glucose . These results were found to be heavily dependant on donor to recipient ratio and distribution of strains, but independent of initial donor and recipient inoculum density and regime . These observations also show that plasmid transfer frequency is reduced at high substrate concentrations, which suggests that plasmid transfer is either stimulated when growth limiting nutrient is scarce or inhibited when it is abundant. Proc Natl Acad Sci U S A, 2000 Sep 12, 97(19), 10465 - 70 Mutators and sex in bacteria: conflict between adaptive strategies; Tenaillon O et al.; Bacterial mutation rates can increase and produce genetic novelty, as shown by in vitro and in silico experiments . Despite the cost due to a heavy deleterious mutation load, mutator alleles, which increase the mutation rate, can spread in asexual populations during adaptation because they remain associated with the rare favorable mutations they generate . This indirect selection for a genetic system generating diversity (second-order selection) is expected to be highly sensitive to changes in the dynamics of adaptation . Here we show by a simulation approach that even rare genetic exchanges, such as bacterial conjugation or transformation, can dramatically reduce the selection of mutators . Moreover, drift or competition between the processes of mutation and recombination in the course of adaptation reveal how second-order selection is unable to optimize the rate of generation of novelty. Br J Nutr, 2000 Sep, 84(3), 369 - 76 Composition of bacteria harvested from the liquid and solid fractions of the rumen of sheep as influenced by feed intake; Rodriguez CA et al.; A study was conducted to determine the effect of the feed intake on the chemical composition of bacteria associated with the solid (solid-associated bacteria; SAB) and liquid (liquid-associated bacteria; LAB) fractions of rumen digesta, the digestive passage kinetics and their relationships . Whole rumen contents were sampled after a period of continuous infusion of 15NH3 from four ruminally-cannulated wethers provided successively with a hay-concentrate diet (2 : 1 w/w on a DM basis) at two rates of feed intake: 40 and 80 g DM/kg body weight 0.75 . SAB had a higher content of organic matter and total lipids (P < 0.001) and a similar N content as compared with LAB . The concentration of purines and 15N was lower (P = 0.011 and P < 0.001 respectively) in SAB than LAB, whereas the opposite was observed for the concentration of amino acids (mg/g DM; P = 0.031) . An increase in feed intake produced an increase in the N (P = 0.034) and purine (P = 0.066) concentrations in bacteria and a decrease (P = 0.033) in their amino acid concentrations . Significant increases of rumen outflow rates of liquid and particles were also observed with increased feed intake . Rates of rumen outflow showed positive and negative linear relationships (P < 0.001) with the purine : N ratio and the proportion of amino acid on total N of bacteria respectively . SAB contained significantly higher proportions of leucine, isoleucine, lysine and phenylalanine and lower proportions of alanine, methionine and valine than LAB . The increase in feed intake also induced significant changes in the amino acid profile of bacteria, increasing arginine and methionine and decreasing alanine and glycine proportions . Results show that the outflow rate of rumen contents is a major factor in determining the proportion of nucleic acids and protein in rumen bacteria and explains some of the differences observed between LAB and SAB. J Mol Biol, 2000 Aug 25, 301(4), 893 - 904 Highly efficient selection of phage antibodies mediated by display of antigen as Lpp-OmpA' fusions on live bacteria; Benhar I et al.; Delayed infectivity panning (DIP) is a novel approach for the in vivo isolation of interacting protein pairs . DIP combines phage display and cell surface display of polypeptides as follows: an antigen is displayed in many copies on the surface of F(+) Escherichia coli cells by fusing it to a Lpp-OmpA' hybrid . To prevent premature, non-specific infection by phage, the cells are rendered functionally F(-) by growth at 16 degrees C . The antigen-displaying cells are used to capture antibody-displaying phage by virtue of the antibody-antigen interaction . Following removal of unbound phage, infection of the cells by bound phage is initiated by raising the temperature to 37 degrees C that facilitates F pilus expression . The phage then dissociate from the antigen and infect the bacteria through the F pilus . Using specific scFv antibodies and the human ErbB2 proto-oncogene and IL2-Ralpha chain as model antibody-antigen pairs, we demonstrate enrichment of those phage that display a specific antibody over phage that display an irrelevant antibody of over 1,000,000 in a single DIP cycle . We further show the successful isolation of anti-toxin, anti-receptor, anti-enzyme and anti-peptide antibodies from several immune phage libraries, a shuffled library and a large synthetic human library . The effectiveness of DIP makes it suitable for the isolation of rare clones present in large libraries.Since DIP can be applied for most of the phage libraries already existing, it could be a powerful tool for the rapid isolation and characterization of binders in numerous protein-protein interactions . Nature, 2000 Aug 17, 406(6797), 768 - 74 Pathogenic strategies of enteric bacteria; Donnenberg MS; Enteric bacteria use a limited array of macromolecular systems to implement diverse pathogenic strategies . The cellular targets of several enteric virulence factors have recently been identified . The themes that have emerged from these studies include the exploitation of molecules that regulate the actin cytoskeleton and the activation of apoptotic pathways to serve the pathogen. Dig Dis Sci, 2000 Jul, 45(7), 1472 - 9 Involvement of luminal bacteria, heat shock protein 60, macrophages and gammadelta T cells in dextran sulfate sodium-induced colitis in rats; Leung FW et al.; The in vivo immunological events in dextran sulfate sodium (DSS) -induced colitis were evaluated . Rats were fed water (control) or 5% DSS . Colonic sections were assessed by light microscopy, Gram stain, immunohistochemistry, and electron microscopy . A progressive decline in number and increase in fragmentation of bacteria in the colonic lumen was observed over time . Luminal bacteria were the first to show heat shock protein 60 (HSP60) staining (day 3) . Macrophages in close proximity to these bacteria were next to show such staining (day 6), and finally the damaged epithelial cells when colitis became severe (day 15) . Ultrastructural assessment showed cell-cell contact interactions between macrophages and dendritic gammadelta T cells . An increase in the number of gammadelta T cells and ED1-positive macrophages in the affected colonic tissue over time was documented . These results suggest colonic bacteria, host macrophages, and gammadelta T cells play specific roles in the immunological reactions in DSS-induced colitis, possibly via an HSP60-mediated mechanism. J Virol, 2000 Sep, 74(18), 8452 - 9 Analysis of Mason-Pfizer monkey virus Gag domains required for capsid assembly in bacteria: role of the N-terminal proline residue of CA in directing particle shape; Rumlova-Klikova M et al.; Mason-Pfizer monkey virus (M-PMV) preassembles immature capsids in the cytoplasm prior to transporting them to the plasma membrane . Expression of the M-PMV Gag precursor in bacteria results in the assembly of capsids indistinguishable from those assembled in mammalian cells . We have used this system to investigate the structural requirements for the assembly of Gag precursors into procapsids . A series of C- and N-terminal deletion mutants progressively lacking each of the mature Gag domains (matrix protein {MA}-pp24/16-p12-capsid protein {CA}-nucleocapsid protein {NC}-p4) were constructed and expressed in bacteria . The results demonstrate that both the CA and the NC domains are necessary for the assembly of macromolecular arrays (sheets) but that amino acid residues at the N terminus of CA define the assembly of spherical capsids . The role of these N-terminal domains is not based on a specific amino acid sequence, since both MA-CA-NC and p12-CA-NC polyproteins efficiently assemble into capsids . Residues N terminal of CA appear to prevent a conformational change in which the N-terminal proline plays a key role, since the expression of a CA-NC protein lacking this proline results in the assembly of spherical capsids in place of the sheets assembled by the CA-NC protein. Nature, 2000 Aug 10, 406(6796), 637 - 41 YidC mediates membrane protein insertion in bacteria; Samuelson JC et al.; The basic machinery for the translocation of proteins into or across membranes is remarkably conserved from Escherichia coli to humans . In eukaryotes, proteins are inserted into the endoplasmic reticulum using the signal recognition particle (SRP) and the SRP receptor, as well as the integral membrane Sec61 trimeric complex (composed of alpha, beta and gamma subunits) . In bacteria, most proteins are inserted by a related pathway that includes the SRP homologue Ffh, the SRP receptor FtsY, and the SecYEG trimeric complex, where Y and E are related to the Sec61 alpha and gamma subunits, respectively . Proteins in bacteria that exhibit no dependence on the Sec translocase were previously thought to insert into the membrane directly without the aid of a protein machinery . Here we show that membrane insertion of two Sec-independent proteins requires YidC . YidC is essential for E . coli viability and homologues are present in mitochondria and chloroplasts . Depletion of YidC also interferes with insertion of Sec-dependent membrane proteins, but it has only a minor effect on the export of secretory proteins . These results provide evidence for an additional component of the translocation machinery that is specialized for the integration of membrane proteins. J Appl Microbiol, 2000 Jul, 89(1), 185 - 90 Production of rhodanese by bacteria present in bio-oxidation plants used to recover gold from arsenopyrite concentrates; Gardner MN et al.; Considerably larger quantities of cyanide are required to solubilize gold following the bio-oxidation of gold-bearing ores compared with oxidation by physical-chemical processes . A possible cause of this excessive cyanide consumption is the presence of the enzyme rhodanese . Rhodanese activities were determined for the bacteria most commonly encountered in bio-oxidation tanks . Activities of between 6.4 and 8.2 micromol SCN min(-1) mg protein(-1) were obtained for crude enzyme extracts of Thiobacillus ferrooxidans, Thiobacillus thiooxidans and Thiobacillus caldus, but no rhodanese activity was detected in Leptospirillum ferrooxidans . Rhodanese activities 2-2.5-fold higher were found in the total mixed cell mass from a bio-oxidation plant . T . ferrooxidans synthesized rhodanese irrespective of whether it was grown on iron or sulphur . With a PCR-based detection technique, only L . ferrooxidans and T . caldus cells were detected in the bio-oxidation tanks . As no rhodanese activity was associated with L . ferrooxidans, it was concluded that T . caldus was responsible for all of the rhodanese activity . Production of rhodanese by T . caldus in batch culture was growth phase-dependent and highest during early stationary phase . Although the sulphur-oxidizing bacteria were clearly able to convert cyanide to thiocyanate, it is unlikely that this rhodanese activity is responsible for the excessive cyanide wastage at the high pH values associated with the gold solubilization process. RNA, 2000 Aug, 6(8), 1079 - 90 Emerging features of mRNA decay in bacteria; Steege DA; The problem of mRNA decay in E . coli has recently seen exciting progress, with the discoveries that key degradation enzymes are associated together in a high molecular weight degradosome and that polyadenylation promotes decay . Recent advances make it clear that mRNA decay in bacteria is far more interesting enzymatically than might have been predicted . In-depth study of specific mRNAs has revealed multiple pathways for degradation . Which pathway a given mRNA follows appears to depend in large part on the location of the initiating endonucleolytic cleavage within the mRNA . During the steps of mRNA decay, stable RNA structures pose formidable barriers to the 3' --> 5' exonucleases . However, polyadenylation is now emerging as a process that plays an important role in maintaining the momentum of exonucleolytic degradation by adding single-stranded extensions to the 3' ends of mRNAs and their decay intermediates, thereby facilitating further exonuclease digestion. J Mol Microbiol Biotechnol, 1999 Aug, 1(1), 87 - 92 Pressure response in deep-sea piezophilic bacteria; Kato C et al.; Several piezophilic bacteria have been isolated from deep-sea environments under high hydrostatic pressure . Taxonomic studies of the isolates showed that the piezophilic bacteria are not widely distributed in terms of taxonomic positions, and all were assigned to particular branches of the Proteobacteria gamma-subgroup . A pressure-regulated operon from piezophilic bacteria of the genus Shewanella, S . benthica and S . violacea, was cloned and sequenced, and downstream of this operon another pressure regulated operon, cydD-C, was found . The cydD gene was found to be essential for the bacterial growth under high-pressure conditions, and the product of this gene was found to play a role in their respiratory system . Results obtained later indicated that the respiratory system in piezophilic bacteria may be important for survival in a high-pressure environment, and more studies focusing on other components of the respiratory chain have been conducted . These studies suggested that piezophilic bacteria are capable of changing their respiratory system in response to pressure conditions, and a proposed respiratory chain model has been suggested in this regard. J Mol Microbiol Biotechnol, 1999 Aug, 1(1), 79 - 86 Formation of magnetosomes in magnetotactic bacteria; Schuler D; The ability of magnetotactic bacteria to orient and migrate along geomagnetic field lines is based on intracellular magnetic structures, the magnetosomes, which comprise nano-sized, membrane bound crystals of magnetic iron minerals . The formation of magnetosomes is achieved by a biological mechanism that controls the accumulation of iron and the biomineralization of magnetic crystals with a characteristic size and morphology within membrane vesicles . This paper focuses on the current knowledge about magnetotactic bacteria and will outline aspects of the physiology and molecular biology of magnetosome formation . The biotechnological potential of the biomineralization process is discussed. FEBS Lett, 2000 Aug 11, 479(1-2), 1 - 5 The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases; Friedrich T et al.; The proton-pumping NADH:ubiquinone oxidoreductase, also called complex I, is the first of the respiratory complexes providing the proton motive force which is essential for energy consuming processes like the synthesis of ATP . Homologues of this complex exist in bacteria, archaea, in mitochondria of eukaryotes and in chloroplasts of plants . The bacterial and mitochondrial complexes function as NADH dehydrogenase, while the archaeal complex works as F420H2 dehydrogenase . The electron donor of the cyanobacterial and plastidal complex is not yet known . Despite the different electron input sites, 11 polypeptides constitute the structural framework for proton translocation and quinone binding in the complex of all three domains of life . Six of them are also present in a family of membrane-bound multisubunit {NiFe} hydrogenases . It is discussed that they build a module for electron transfer coupled to proton translocation. J Mol Microbiol Biotechnol, 2000 Apr, 2(2), 145 - 77 Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction; Sekowska A et al.; Living organisms are composed of macromolecules made of hydrogen, carbon, nitrogen, oxygen, phosphorus and sulfur . Much work has been devoted to the metabolism of the first five elements, but much remains to be understood about sulfur metabolism . We review here the situation in Escherichia coli and related bacteria, where more than one hundred genes involved in sulfur metabolism have already been discovered in this organism . Examination of the genome suggests that many more will be found, especially genes involved in regulation, scavenging of sulfur containing molecules and synthesis of coenzymes or prosthetic groups . Furthermore, the involvement of methionine as the universal start of proteins as well as that of its derivative S-adenosylmethionine in a vast variety of cell processes argue in favour of a major importance of sulfur metabolism in all organisms. Vox Sang, 2000, 78 Suppl 2, 239 - 42 Transmission of parasites and bacteria by blood components; Dodd RY; BACKGROUND AND OBJECTIVES: Although most attention has been paid to viral infections as a complication of transfusion, some parasitic infections are readily transmissible and generate a heavy burden of disease, particularly in the developing world . Additionally, bacterial infection as a result of transfusion is the most frequent serious outcome of transfusion in the developed world . MATERIALS AND METHODS: Review of current literature and ongoing research studies . RESULTS: Malaria and Chagas' disease continue to be a serious problem in endemic areas, but are also of concern as a result of their introduction into other regions . Means to control or detect bacterial contamination, particularly of platelet concentrates, are needed, but no simple, effective approach is available . CONCLUSION: Continued development and implementation of tests and of inactivation procedures will result in the eventual control of transfusion-transmitted parasitic and bacterial disease. Vox Sang, 2000, 78 Suppl 2, 205 - 10 Inactivation of viruses, bacteria, protozoa and leukocytes in platelet and red cell concentrates; Corash L; Substantial increments in the safety of blood transfusion have been achieved through continued improvements in donor testing, yet residual concern about the safety of blood components persists . To further reduce the risk of transfusion-associated infection, additional measures, such as nucleic acid testing for selected pathogens, are being introduced . Transfusion of cellular components has been implicated in transmission of viral, bacterial, and protozoan diseases {1} . While it is commonly recognized that hepatitis B virus (HBV), hepatitis C virus (HCV), cytomegalovirus (CMV), and the retroviruses, such as human immunodeficiency virus (HIV) and the human lymphotrophic viruses (HTLV) can be transmitted through cellular components, other pathogens are emerging as potentially significant transfusion-associated infectious agents . For example, transmission of protozoan infections due to trypanosomes {2-4} and babesia have been reported {5} . In addition to viral and protozoal infectious agents, bacterial contamination of platelet and red cell concentrates continues to be reported {6, 7}; and may be an under reported transfusion complication {8} . More importantly, new infectious agents may periodically enter the donor population before they can be definitively identified and tested for to maintain consistent safety of the blood supply . The paradigm for this possibility is the HIV pandemic, which erupted in 1979 . During the past decade a number of methods to inactivate infectious pathogens have been developed and have entered the advanced clinical trial phase. Microbiology, 2000 Aug, 146 ( Pt 8), 2019 - 25 Rapid detection of polyhydroxyalkanoate-accumulating bacteria isolated from the environment by colony PCR; Sheu DS et al.; Colony PCR and semi-nested PCR techniques were employed for screening polyhydroxyalkanoate (PHA) producers isolated from the environment . Three degenerate primers were designed based on multiple sequence alignment results and were used as PCR primers to detect PHA synthase genes . Optimized colony PCR conditions were achieved by adding 3% DMSO combined with 1 M betaine to the reaction mixture . The sensitivity limit of the colony PCR was 1x 10(5) viable cells for Ralstonia eutropha . Nineteen PHA-positive bacteria were used to evaluate this PCR protocol; fifteen of the nineteen could be detected by colony PCR, and the other four could be detected by applying semi-nested PCR detection following colony PCR . In a preliminary screening project, 38 PHA-positive strains were isolated from environmental samples by applying the PCR protocol, and their phenotype was further confirmed by Nile blue A staining assay . By combining the colony PCR and semi-nested PCR techniques, a rapid, reliable and highly accurate detection method has been developed for detecting PHA producers . This protocol is suitable for screening large numbers of environmental isolates . The PHA accumulation ability of well-separated colonies isolated from environmental samples can be directly validated by PCR with no further culturing or chromosomal DNA extraction procedures . In addition to its application to the screening of wild-type isolates, the individual PCR-amplified product is also suitable as a specific probe for PHA operon cloning . The results suggest that the application of this PCR protocol for rapid detection of PHA producers from the environment is plausible. Biochim Biophys Acta, 2000 Jul 31, 1467(1), 73 - 84 Requirement of the hinge domain for dimerization of Ca2+-ATPase large cytoplasmic portion expressed in bacteria; Carvalho-Alves PC et al.; The large cytoplasmic domain of rabbit sarcoplasmic reticulum Ca2+-ATPase was overexpressed in Escherichia coli as a 48 kDa fusion protein, designated p48, containing an N-terminal hexa-His tag . Purification conditions were optimized, thus conferring long-term stability to p48 . Circular dichroism spectroscopy and the pattern of limited trypsinolysis confirmed the proper folding of the domain . p48 retained 0.5 +/- 0.1 mol of high affinity 2',3'-O-(2,4,6-trinitrophenyl)adenosine-5'-triphosphate (TNP-ATP) binding sites per mol of polypeptide chain with an apparent dissociation constant of about 8 microM . Size-exclusion FPLC using protein concentrations in the range 0.03 5 mg/ml showed that p48 was essentially monodisperse with apparent molecular mass and Stokes radius (Rs) values compatible with a dimer (100 kDa and 40 A, respectively) . Analysis of p48 by small-angle X-ray scattering provided an independent second proof for a dimeric p48 particle with a radius of gyration (Rg) of 39 A, suggesting that the dimer was not spherical (Rs/Rg = 1.026) . When digested by proteinase K, p48 was converted to a 30 kDa fragment, designated p30, which was very resistant to further proteolysis . p30 retained high affinity TNP-ATP binding (Kd = 8 microM) and eluted as a monomer (35 kDa) in size-exclusion FPLC . As opposed to p48, the p30 fragment did not react with monoclonal antibody A52 {Clarke et al., J . Biol . Chem . 264 (1989) 11246-11251} which recognizes region E657-R672 located upstream of the hinge domain of the Ca2+-ATPase . These results indicate a requirement of the hinge domain (670-728) region for self-association of the p48 large hydrophilic domain as a dimer . We propose that this behavior points to a possible role of the hinge domain in dimerization of sarcoplasmic reticulum Ca2+-ATPase in the native membrane. Appl Environ Microbiol, 2000 Aug, 66(8), 3592 - 602 Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments; Ravenschlag K et al.; The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes . The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group . This group accounted for up to 73% of the SRB detected and up to 70% of the SRB rRNA detected . The predominance was shown to be a common feature for different stations along the coast of Svalbard . In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera . While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group . A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54 . 8% of the total SRB detected . A comparison of the two methods used for quantification showed that FISH and rRNA slot blot hybridization gave comparable results . Furthermore, a combination of the two methods allowed us to calculate specific cellular rRNA contents with respect to localization in the sediment profile . The rRNA contents of Desulfosarcina-Desulfococcus cells were highest in the first 5 mm of the sediment (0.9 and 1.4 fg, respectively) and decreased steeply with depth, indicating that maximal metabolic activity occurred close to the surface . Based on SRB cell numbers, cellular sulfate reduction rates were calculated . The rates were highest in the surface layer (0.14 fmol cell(-1) day(-1)), decreased by a factor of 3 within the first 2 cm, and were relatively constant in deeper layers. Appl Environ Microbiol, 2000 Aug, 66(8), 3230 - 3 Metabolic activity of permafrost bacteria below the freezing point; Rivkina EM et al.; Metabolic activity was measured in the laboratory at temperatures between 5 and -20 degrees C on the basis of incorporation of (14)C-labeled acetate into lipids by samples of a natural population of bacteria from Siberian permafrost (permanently frozen soil) . Incorporation followed a sigmoidal pattern similar to growth curves . At all temperatures, the log phase was followed, within 200 to 350 days, by a stationary phase, which was monitored until the 550th day of activity . The minimum doubling times ranged from 1 day (5 degrees C) to 20 days (-10 degrees C) to ca . 160 days (-20 degrees C) . The curves reached the stationary phase at different levels, depending on the incubation temperature . We suggest that the stationary phase, which is generally considered to be reached when the availability of nutrients becomes limiting, was brought on under our conditions by the formation of diffusion barriers in the thin layers of unfrozen water known to be present in permafrost soils, the thickness of which depends on temperature. Mikrobiologiia, 2000 May-Jun, 69(3), 407 - 9 {Characteristics of hemagglutination reaction in methanotrophic bacteria}; Kurdish IK et al.; The reaction of hemagglutination with trypsin-treated rabbit erythrocytes was used to reveal lectins on the cell surface of methanotrophic bacteria and in their culture liquids . By this method, no lectins were detected on the cell surface of Methylococcus capsulatus IMV B-3001 and Methylomonas rubra IMV B-3075 or in the culture liquid of any of the species studied . With intact cells of Methylocystis parvus IMV B-3491, the positive hemagglutination reaction observed was nonspecific and most probably occurred due to the high cell surface hydrophobicity characteristic of this species. Mikrobiologiia, 2000 May-Jun, 69(3), 370 - 6 {Screening of marine bacteria for fucoidan hydrolases}; Bakunina IIu et al.; Twenty-five strains of epiphytic marine bacteria isolated from the brown algae Fucus evanescens and Chorda filum and fifty-three bacteria isolated from the sea cucumber Apostichopus japonicus were screened for fucoidanases using fucoidans prepared from the brown algae F . evanescens, Laminaria cichorioides, and L . japonica . Eighteen bacterial epiphytes and thirty-eight bacterial isolates from the sea cucumber were found to contain fucoidanases, which were able to hydrolyze either all of the fucoidans studied or some of them . Bacteria of the genera Cytophaga and Alteromonas/Pseudoalteromonas exhibited the highest fucoidanase activities, which, however, did not exceed the activity of fucoidanases from the already known sources. FEMS Microbiol Lett, 2000 Aug 1, 189(1), 67 - 72 Characterization of methanotrophic bacteria on the basis of intact phospholipid profiles; Fang J et al.; The intact phospholipid profiles (IPPs) of seven species of methanotrophs from all three physiological groups, type I, II and X, were determined using liquid chromatography/electrospray ionization/mass spectrometry . In these methanotrophs, two major classes of phospholipids were found, phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) as well as its derivatives phosphatidylmethylethanolamine (PME) and phosphatidyldimethylethanolamine (PDME) . Specifically, the type I methanotrophs, Methylomonas methanica, Methylomonas rubra and Methylomicrobium album BG8 were characterized by PE and PG phospholipids with predominantly C16:1 fatty acids . The type II methanotrophs, Methylosinus trichosporium OB3b and CSC1 were characterized by phospholipids of PG, PME and PDME with predominantly C18:1 fatty acids . Methylococcus capsulatus Bath, a representative of type X methanotrophs, contained mostly PE (89% of the total phospholipids) . Finally, the IPPs of a recently isolated acidophilic methanotroph, Methylocella palustris, showed it had a preponderance of PME phospholipids with 18:1 fatty acids (94% of total) . Principal component analysis showed these methanotrophs could be clearly distinguished based on phospholipid profiles . Results from this study suggest that IPP can be very useful in bacterial chemotaxonomy. Arch Immunol Ther Exp (Warsz), 2000, 48(3), 177 - 82 Current status and future perspectives of DNA vaccine delivery by attenuated intracellular bacteria; Dietrich G; Vaccination by intradermal or intramuscular injection of antigen-encoding plasmid-DNA elicits strong cellular and humoral immune responses . Professional antigen presenting cells (APC) seem to induce these responses, making it, therefore, desirable to deliver the plasmid molecules directly to these cells . The exploitation of attenuated intracellular bacteria as DNA delivery vehicles makes the direct targeting of DNA vaccine vectors to professional APC feasible. Adv Microb Physiol, 2000, 43, 165 - 224 Redundancy of aerobic respiratory chains in bacteria? Routes, reasons and regulation; Poole RK et al.; Bacteria are the most remarkable organisms in the biosphere, surviving and growing in environments that support no other life forms . Underlying this ability is a flexible metabolism controlled by a multitude of environmental sensors and regulators of gene expression . It is not surprising, therefore, that bacterial respiration is complex and highly adaptable: virtually all bacteria have multiple, branched pathways for electron transfer from numerous low-potential reductants to several terminal electron acceptors . Such pathways, particularly those involved in anaerobic respiration, may involve periplasmic components, but the respiratory apparatus is largely membrane-bound and organized such that electron flow is coupled to proton (or sodium ion) transport, generating a protonmotive force . It has long been supposed that the multiplicity of pathways serves to provide flexibility in the face of environmental stresses, but the existence of apparently redundant pathways for electrons to a single acceptor, say dioxygen, is harder to explain . Clues have come from studying the expression of oxidases in response to growth conditions, the phenotypes of mutants lacking one or more oxidases, and biochemical characterization of individual oxidases . Terminal oxidases that share the essential properties of substrate (cytochrome c or quinol) oxidation, dioxygen reduction and, in some cases, proton translocation, differ in subunit architecture and complement of redox centres . Perhaps more significantly, they differ in their affinities for oxidant and reductant, mode of regulation, and inhibitor sensitivity; these differences to some extent rationalize the presence of multiple oxidases . However, intriguing requirements for particular functions in certain physiological functions remain unexplained . For example, a large body of evidence demonstrates that cytochrome bd is essential for growth and survival under certain conditions . In this review, the physiological basis of the many phenotypes of Cyd-mutants is explored, particularly the requirement for this oxidase in diazotrophy, growth at low protonmotive force, survival in the stationary phase, and resistance to oxidative stress and Fe(III) chelators. Trends Ecol Evol, 2000 Aug, 15(8), 321 - 326 Lifestyle evolution in symbiotic bacteria: insights from genomics; Moran NA et al.; Bacteria that live only in eukaryotic cells and tissues, including chronic pathogens and mutualistic bacteriocyte associates, often possess a distinctive set of genomic traits, including reduced genome size, biased nucleotide base composition and fast polypeptide evolution . These phylogenetically diverse bacteria have lost certain functional categories of genes, including DNA repair genes, which affect mutational patterns . However, pathogens and mutualistic symbionts retain loci that underlie their unique interaction types, such as genes enabling nutrient provisioning by mutualistic bacteria-inhabiting animals . Recent genomic studies suggest that many of these bacteria are irreversibly specialized, precluding shifts between pathogenesis and mutualism. Microbiology, 2000 Jul, 146 ( Pt 7), 1693 - 705 Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria; Daly K et al.; PCR primer sets for the 16S rRNA gene of six phylogenetic groups of sulfate-reducing bacteria (SRB) were designed . Their application in conjunction with group-specific internal oligonucleotide probes was used to detect SRB DNA in samples of landfill leachate . Six generic/suprageneric groups could be differentiated: DESULFOTOMACULUM:; DESULFOBULBUS:; DESULFOBACTERIUM:; DESULFOBACTER:; DESULFOCOCCUS:-DESULFONEMA:-DESULFOSARCINA:; DESULFOVIBRIO:-DESULFOMICROBIUM: The predicted specificities of the PCR primer and oligonucleotide probe combinations were confirmed with DNA from reference strains . In all cases, the PCR primers and probes were specific, the only exception being that the Desulfococcus-Desulfonema-Desulfosarcina (group 5) PCR primers were able to amplify DNA from DESULFOBACTERIUM: (group 3) reference strains but these groups could nevertheless be differentiated with the internal oligonucleotide probes . The proliferation of SRB in landfill sites interferes with methanogenesis and waste stabilization, but relatively little is known about the composition of SRB populations in this environment . DNA was extracted from samples of landfill leachate from several municipal waste landfill sites and used as template in PCR reactions with SRB group-specific primer sets . Group-specific oligonucleotide probes were then used to confirm that the PCR products obtained contained the target SRB 16S rDNA . Both 'direct' and 'nested' PCR protocols were used to amplify SRB 16S rDNA from landfill leachates . Three of the six SRB groups could be detected using the 'direct' PCR approach (DESULFOTOMACULUM:, DESULFOBACTER: and Desulfococcus-Desulfonema-Desulfosarcina) . When 'nested' PCR was applied, an additional two groups could be detected (DESULFOBULBUS: and DESULFOVIBRIO:-DESULFOMICROBIUM:) . Only DESULFOBACTERIUM: could not be detected in any leachate samples using either direct or nested PCR . The SRB-specific 16S rDNA primers and probes described here can be applied to investigations of SRB molecular ecology in general, and can be further developed for examining SRB population composition in relation to landfill site performance. J Biol Chem, 2000 Sep 1, 275(35), 26986 - 93 CLIC-1 functions as a chloride channel when expressed and purified from bacteria; Tulk BM et al.; CLIC-1 is a member of a family of proteins related to the bovine intracellular chloride channel p64 which has been proposed to function as a chloride channel . We expressed CLIC-1 as a glutathione S-transferase fusion protein in bacteria . The fusion protein was purified by glutathione affinity, and CLIC-1 was released from its fusion partner by digestion with thrombin . After further purification, CLIC-1 was reconstituted into phospholipid vesicles by detergent dialysis . Chloride permeability of reconstituted vesicles was assessed using a valinomycin dependent chloride efflux assay, demonstrating increased vesicular chloride permeability with CLIC-1 compared with control . CLIC-1-dependent chloride permeability was inhibited by indanyloxyacetic acid-94 with an apparent IC(50) of 8.6 micrometer . The single channel properties of CLIC-1 were determined using the planar lipid bilayer technique . We found that CLIC-1 forms a voltage-dependent, Cl-selective channel with a rectifying current-voltage relationship and single channel conductances of 161 +/- 7.9 and 67.5 +/- 6.9 picosiemens in symmetric 300 and 150 mm KCl, respectively . The anion selectivity of this activity is Br approximately Cl > I . The open probability of CLIC-1 channels in planar bilayers was decreased by indanyloxyacetic acid-94 with an apparent IC(50) of 86 micrometer at 50 mV . These data convincingly demonstrate that CLIC-1 is capable of forming a novel, chloride-selective channel in the absence of other subunits or proteins. Mikrobiol Z, 2000 Mar-Apr, 62(2), 3 - 10 {The properties of Pragia fontium bacteria isolated on the territories of Ukraine and the Czech Republic}; Pokhyl SI; The results are presented of the study of the properties (morphological, tinctorial, cultural, biochemical) and primary DNA structure of 28 Pragia fontium strains, 18 of which were isolated in the territory of Ukraine and 10 in the territory of Czechia . The scheme of differentiation of genera Pragia, Budvicia and Leminorella is presented . The GC (guanine + cysteine) content of DNA is 47 +/- 1.5 mol.% . The levels of DNA relatedness of P . fontium strains and the type strain (CNCTC Eb11/82) varied from 84 to 95% . The levels of DNA relatedness of P . fontium and Escherichia coli K-12 strain is 3 to 5%. Izv Akad Nauk Ser Biol, 2000 May-Jun, (3), 382 - 6 {Effect of various organic compounds on the growth and hydrocarbon production by sulfur-reducing bacteria}; Bagaeva TV et al.; The effects of lactate, pyruvate and ethanol on growth and formation of extracellular hydrocarbons by Desulfovibrio desulfuricans 1799 cultivated in H2 + CO2 atmosphere were studied . It was shown that sulfate reducing bacteria grow and produce hydrocarbons on all studied carbon and energy sources . Substitution of lactate in the medium for pyruvate or ethanol decreased only insignificantly the amount of synthesized hydrocarbons with concomitant increase in the content of isoform. Biophys J, 2000 Jul, 79(1), 14 - 25 Quinone-dependent delayed fluorescence from the reaction center of photosynthetic bacteria; Turzo K et al.; Millisecond delayed fluorescence from the isolated reaction center of photosynthetic bacteria Rhodobacter sphaeroides was measured after single saturating flash excitation and was explained by thermal repopulation of the excited bacteriochlorophyll dimer from lower lying charge separated states . Three exponential components (fastest, fast, and slow) were found with lifetimes of 1.5, 102, and 865 ms and quantum yields of 6.4 x 10(-9), 2.2 x 10(-9), and 2.6 x 10(-9) (pH 8.0), respectively . While the two latter phases could be related to transient absorption changes, the fastest one could not . The fastest component, dominating when the primary quinone was prereduced, might be due to a small fraction of long-lived triplet states of the radical pair and/or the dimer . The fast phase observed in the absence of the secondary quinone, was sensitive to pH, temperature, and the chemical nature of the primary quinone . The standard free energy of the primary stable charge pair relative to that of the excited dimer was -910 +/- 20 meV at pH 8 and with native ubiquinone, and it showed characteristic changes upon pH and quinone replacement . The interaction energy ( approximately 50 meV) between the cluster of the protonatable groups around GluL212 and the primary semiquinone provides evidence for functional linkage between the two quinone binding pockets . An empirical relationship was found between the in situ free energy of the primary quinone and the rate of charge recombination, with practical importance in the estimation of the free energy levels from the easily available lifetime of the charge recombination . The ratio of the slow and fast components could be used to determine the pH dependence of the free energy level of the secondary stable charge pair relative to that of the excited dimer. Int Dent J, 1999 Aug, 49(4), 231 - 9 The influence of oral bacteria on the surfaces of resin-based dental restorative materials--an in vitro study; Willershausen B et al.; Three tooth-coloured, resin-based restorative materials (Charisma, Dyract, and Pertac) were exposed to typical oral bacteria (S . mutans, S . oralis and A . naeslundii) over a period of up to 35 days . The three strains of bacteria all colonised the resin-based materials within a few hours and formed thick bacterial films . Determination of the bacterial glucose consumption and lactate production during the incubation period showed no difference from the controls which contained no resin samples . Following the experimental exposure, the materials were examined by scanning electron microscopy (SEM) for possible surface damage and roughness was measured in a perthometer . Little damage to the resin-based composite material surfaces (Charisma, Pertac) could be observed, whereas the polyacid-modified composite material (Dyract) showed greater damage . There was a significant difference in the resin surface roughness after exposure to S . mutans and to A . naeslundii . The study clearly showed that the bacteria used strongly adhered to the resin-based restorative materials . As a consequence of bacterial colonisation and/or poor oral hygiene, damage to the restorative materials might develop . This suggests the need for dentists to evaluate personal oral hygiene, along with general indications and economic factors, in selecting materials for restorations, since the known anti-bacterial properties of amalgam are considerable. FEMS Microbiol Ecol, 2000 Jun 1, 32(3), 215 - 223 Behavior of sulfate reducing bacteria under oligotrophic conditions and oxygen stress in particle-free systems related to drinking water; Bade K et al.; The response of sulfate reducing bacteria (SRB) to oxygen stress under oligotrophic conditions in particle-free systems was studied in (i) sterile Berlin drinking water; (ii) mineral medium; and (iii) in coculture experiments with aerobic bacteria . Using a polyphasic approach including anaerobic cultivation, fluorescent in situ hybridization (FISH) and digital image analysis, the behavior of the strains zt3l and zt10e, isolated from Berlin groundwater and affiliated to the family Desulfovibrionaceae, was compared to the type strains Desulfomicrobium baculatum and Desulfovibrio desulfuricans . Anaerobic deep agar dilution series were performed for the determination of cell culturability . FISH and subsequent digital image analysis of probe-conferred fluorescence intensities were used for the assessment of metabolic activity . For the in situ identification of both isolates in coculture tests, two strain-specific oligonucleotides were developed and evaluated . The total cell counts of stressed SRB in drinking water decreased during the course of the assay dependent on the strain . Both environmental isolates could be cultured for a longer period than cells of D . baculatum and D . desulfuricans, respectively . The FISH intensities showed a strain-specific behavior . When exposed to simultaneous oxygen stress and carbon limitation in mineral medium, total cell counts of all four strains remained constant throughout a period of 72 days . The rate of culturability differed between the investigated strains . The decrease of metabolic activity as assessed by FISH was a strain-specific property . Exposure of SRB to oxygen stress and carbon starvation in coculture experiments with Aquabacterium commune resulted in strain dependent prolonged culturability and a delayed decrease of the metabolic activity compared to pure culture tests for all strains tested . Total cell counts of SRB were constant throughout the whole experiment. Crit Rev Toxicol, 2000 May, 30(3), 287 - 306 Heterologous expression of xenobiotic mammalian-metabolizing enzymes in mutagenicity tester bacteria: an update and practical considerations; Kranendonk M et al.; There is an increasing need for metabolic competent cell systems for the mechanistic studies of biotransformation of xenobiotics in toxicology in general and in genotoxicology in particular . These cell systems combine the heterologous expression of a particular mammalian biotransformation enzyme with a specific target/ end point by which a functional analysis of the expressed gene product in the (geno)toxicity of chemicals can be performed . cDNAs of an increasing number of mammalian biotransformation enzymes is being cloned . The construction of specific expression vectors permits their heterologous expression in laboratory bacteria, such as Escherichia coli strains . This development does not only allow biochemical and enzymatic studies of (pure) enzyme preparations but also facilitates the engineering of metabolically competent mutagenicity tester bacteria, thereby providing new tools for genotoxicity testing and for studying of the roles of biotransformation in chemical carcinogenesis . In this review, we describe an update as well as an evaluation of enzymes expressed in mutagenicity tester bacteria . Four types of biotransformation enzymes are now expressed in these bacteria, namely, GSTs, CYPs, NATs, and STs . The expression of these enzymes in the tester bacteria and their subsequent application in mutagenicity assays demonstrates that heterologous expression in this type of bacteria has a number implications for the functionality of the biotransformation enzymes as well as for the functioning of the tester bacteria in mutagenicity detection . We also describe here a number of practical considerations in this regard. Ann Pharm Fr, 2000 May, 58(3), 157 - 64 {Measures for controlling the transmission of hospital bacteria}; Le Turdu F et al.; Three elemental steps need to be taken in order to control and prevent multiresistant bacteria spreading: screening for BMR carriage - signalling - isolation precautions Biochemistry, 2000 Jun 20, 39(24), 7212 - 20 Electron transfer in reaction center core complexes from the green sulfur bacteria Prosthecochloris aestuarii and Chlorobium tepidum; Schmidt KA et al.; Electron transfer in reaction center core (RCC) complexes from the green sulfur bacteria Prosthecochloris aestuarii and Chlorobium tepidum was studied by measuring flash-induced absorbance changes . The first preparation contained approximately three iron-sulfur centers, indicating that the three putative electron acceptors F(X), F(A), and F(B) were present; the Chl . tepidum complex contained on the average only one . In the RCC complex of Ptc . aestuarii at 277 K essentially all of the oxidized primary donor (P840(+)) created by a flash was rereduced in several seconds by N-methylphenazonium methosulfate . In RCC complexes of Chl . tepidum two decay components, one of 0.7 ms and a smaller one of about 2 s, with identical absorbance difference spectra were observed . The fast component might be due to a back reaction of P840(+) with a reduced electron acceptor, in agreement with the notion that the terminal electron acceptors, F(A) and F(B), were lost in most of the Chl . tepidum complexes . In both complexes the terminal electron acceptor (F(A) or F(B)) could be reduced by dithionite, yielding a back reaction of 170 ms with P840(+) . At 10 K in the RCC complexes of both species P840(+) was rereduced in 40 ms, presumably by a back reaction with F(X)(-) . In addition, a 350 micros component occurred that can be ascribed to decay of the triplet of P840, formed in part of the complexes . For P840(+) rereduction a pronounced temperature dependence was observed, indicating that electron transfer is blocked after F(X) at temperatures below 200 K. J Clin Microbiol, 2000 Jun, 38(6), 2362 - 5 Quantitative real-time PCR for Porphyromonas gingivalis and total bacteria; Lyons SR et al.; Accurate quantitation of the number of cells of individual bacterial species in dental plaque samples is needed for understanding the bacterial etiology of periodontitis . Real-time PCR offers a sensitive, efficient, and reliable approach to quantitation . Using the TaqMan system we were able to determine both the amount of Porphyromonas gingivalis and the total number of bacterial cells present in plaque samples . Using species-specific primers and a fluorescent probe, detection of DNA from serial dilutions of P . gingivalis cells was linear over a large range of DNA concentrations (correlation coefficient = 0.96) . No difference was observed between P . gingivalis DNA alone and the same DNA mixed with DNA isolated from dental plaque, indicating that P . gingivalis levels can be determined accurately from clinical samples . The total number of cells of all bacterial species was determined using universal primers and a fluorescent probe . Standard curves using four different bacterial species gave similar results (correlation coefficient = 0.86) . Levels of both P . gingivalis and total bacteria were determined from a series of human plaque samples . High levels of P . gingivalis were observed in several of the samples from subjects with periodontitis and none of those from healthy subjects . Real-time quantitative PCR provided a sensitive and reliable method for quantitating P . gingivalis . In addition, it allowed the determination of the total number of bacterial cells present in a complex sample so that the percentage of P . gingivalis cells could be determined. Protein Expr Purif, 2000 Jun, 19(1), 148 - 57 Folding and structural characterization of highly disulfide-bonded beetle antifreeze protein produced in bacteria; Liou YC et al.; The hyperactive antifreeze protein from the beetle, Tenebrio molitor, is an 8.5-kDa, threonine-rich protein containing 16 Cys residues, all of which are involved in disulfide bonds . When produced by Escherichia coli, the protein accumulated in the supernatant in an inactive, unfolded state . Its correct folding required days or weeks of oxidation at 22 or 4 degrees C, respectively, and its purification included the removal of imperfectly folded forms by reversed-phase HPLC . NMR spectroscopy was used to assess the degree of folding of each preparation . One-dimensional (1)H and two-dimensional (1)H total correlation spectroscopy spectra were particularly helpful in establishing the characteristics of the fully folded antifreeze in comparison to less well-folded forms . The recombinant antifreeze had no free -SH groups and was rapidly and completely inactivated by 10 mM DTT . It had a thermal hysteresis activity of 2.5 degrees C at a concentration of 1 mg/ml, whereas fish antifreeze proteins typically show a thermal hysteresis of approximately 1.0 degrees C at 10-20 mg/ml . The circular dichroism spectra of the beetle antifreeze had a superficial resemblance to those of alpha-helical proteins, but deconvolution of the spectra indicated the absence of alpha-helix and the presence of beta-structure and coil . NMR analysis and secondary structure predictions agree with the CD data and are consistent with a beta-helix model proposed for the antifreeze on the basis of its 12-amino-acid repeating structure and presumptive disulfide bond arrangement . Protein Expr Purif, 2000 Jun, 19(1), 91 - 8 Functional human insulin-degrading enzyme can be expressed in bacteria; Chesneau V et al.; Insulin-degrading enzyme (IDE) has been shown to degrade a number of biologically important peptides, including insulin and the amyloid-beta protein implicated in Alzheimer's disease . However, lack of a facile method to generate purified enzyme and related mutants has made it difficult to study the precise role of IDE in the clearance of these peptides . Therefore, we determined whether recombinant wild-type and mutant human IDEs can be overexpressed as functional enzymes in bacteria . Three vectors carrying cDNAs encoding N-terminally polyhistidine-tagged recombinant IDEs were constructed, and the proteins expressed in Escherichia coli were purified by metal affinity chromatography (final yield approximately 8 mg per liter of culture) . The recombinant IDEs, like the endogenous mammalian enzyme, migrate with 110-kDa apparent molecular masses in SDS-polyacrylamide gels and as a approximately 200-kDa species in gel filtration . Further analysis by native PAGE indicates that IDE can form multimers of different complexities . The wild-type recombinant endopeptidase degrades insulin with an efficiency similar to that of the enzyme purified from mammalian tissues . Purified IDEs are stable at 4 degrees C for at least 1 month . Purified recombinant protein was used to raise specific polyclonal antibodies that can immunoprecipitate native mammalian IDE . Thus, the procedure described allows the rapid production of large amounts of purified IDE and demonstrates that IDE can be produced in an active form in the absence of other potential interacting mammalian proteins . Appl Environ Microbiol, 2000 Jun, 66(6), 2589 - 98 Functional exoenzymes as indicators of metabolically active bacteria in 124,000-year-Old sapropel layers of the eastern Mediterranean Sea; Coolen MJ et al.; Hydrolytic exoenzymes as indicators of metabolically active bacteria were investigated in four consecutive sapropel layers collected from bathyal sediments of the eastern Mediterranean Sea . For comparison, the organic carbon-poor layers between the sapropels, sediment from the anoxic Urania basin, and sediments of intertidal mud flats of the German Wadden Sea were also analyzed . The sapropel layers contained up to 1.5 . 10(8) bacterial cells cm(-3), whereas cell numbers in the intermediate layers were lower by a factor of 10 . In sapropels, the determination of exoenzyme activity with fluorescently labeled substrate analogues was impaired by the strong adsorption of up to 97% of the enzymatically liberated fluorophores (4-methylumbelliferone {MUF} and 7-amino-4-methylcoumarin {MCA}) to the sediment particles . Because all established methods for the extraction of adsorbed fluorophores proved to be inadequate for sapropel sediments, we introduce a correction method which is based on the measurement of equilibrium adsorption isotherms for both compounds . Using this new approach, high activities of aminopeptidase and alkaline phosphatase were detected even in a 124,000-year-old sapropel layer, whereas the activity of beta-glucosidase was low in all layers . So far, it had been assumed that the organic matter which constitutes the sapropels is highly refractory . The high potential activities of bacterial exoenzymes indicate that bacteria in Mediterranean sapropels are metabolically active and utilize part of the subfossil kerogen . Since a high adsorption capacity was determined not only for the low-molecular-weight compounds MUF and MCA but also for DNA, the extraordinarily strong adsorption of structurally different substrates to the sapropel matrix appears to be the major reason for the long-term preservation of biodegradable carbon in this environment. Appl Environ Microbiol, 2000 Jun, 66(6), 2430 - 7 Sulfate-reducing bacteria methylate mercury at variable rates in pure culture and in marine sediments; King JK et al.; Differences in methylmercury (CH(3)Hg) production normalized to the sulfate reduction rate (SRR) in various species of sulfate-reducing bacteria (SRB) were quantified in pure cultures and in marine sediment slurries in order to determine if SRB strains which differ phylogenetically methylate mercury (Hg) at similar rates . Cultures representing five genera of the SRB (Desulfovibrio desulfuricans, Desulfobulbus propionicus, Desulfococcus multivorans, Desulfobacter sp . strain BG-8, and Desulfobacterium sp . strain BG-33) were grown in a strictly anoxic, minimal medium that received a dose of inorganic Hg 120 h after inoculation . The mercury methylation rates (MMR) normalized per cell were up to 3 orders of magnitude higher in pure cultures of members of SRB groups capable of acetate utilization (e.g., the family Desulfobacteriaceae) than in pure cultures of members of groups that are not able to use acetate (e.g., the family Desulfovibrionaceae) . Little or no Hg methylation was observed in cultures of Desulfobacterium or Desulfovibrio strains in the absence of sulfate, indicating that Hg methylation was coupled to respiration in these strains . Mercury methylation, sulfate reduction, and the identities of sulfate-reducing bacteria in marine sediment slurries were also studied . Sulfate-reducing consortia were identified by using group-specific oligonucleotide probes that targeted the 16S rRNA molecule . Acetate-amended slurries, which were dominated by members of the Desulfobacterium and Desulfobacter groups, exhibited a pronounced ability to methylate Hg when the MMR were normalized to the SRR, while lactate-amended and control slurries had normalized MMR that were not statistically different . Collectively, the results of pure-culture and amended-sediment experiments suggest that members of the family Desulfobacteriaceae have a greater potential to methylate Hg than members of the family Desulfovibrionaceae have when the MMR are normalized to the SRR . Hg methylation potential may be related to genetic composition and/or carbon metabolism in the SRB . Furthermore, we found that in marine sediments that are rich in organic matter and dissolved sulfide rapid CH(3)Hg accumulation is coupled to rapid sulfate reduction . The observations described above have broad implications for understanding the control of CH(3)Hg formation and for developing remediation strategies for Hg-contaminated sediments. Biosci Biotechnol Biochem, 2000 Apr, 64(4), 757 - 60 Genetic characteristics of cellulose-forming acetic acid bacteria identified phenotypically as Gluconacetobacter xylinus; Tanaka M et al.; Gluconacetobacter xylinus (=Acetobacter xylinum) shows variety in acid formation from sugars and sugar-alcohols . Toyosaki et al . proposed new subspecies of G . xylinus (=Acetobacter xylinum) subsp . sucrofermentans in point of acid formation from sucrose and a homology index of 58.2% with the type strain of G . xylinus subsp . xylinus in DNA-DNA hybridization experiments . We tried DNA-DNA hybridization to clarify relationship between acid formation from sugars and classification of G . xylinus . The G + C contents of G . xylinus showed 60.1-62.4 mol% with a range of 2.3 mol% . When type strains of G . xylinus subsp . xylinus, G . xylinus subsp . sucrofermentans, and IFO 3288 forming acid from sucrose, were used as probes, the DNAs from three strains showed 67-100%, 64-89%, and 60-100% similarity to those from sixteen strains including bacteria that form acid from sucrose or not . These results show that homology indexes do not reflect differences of acid formation from sucrose . As a results, the species G . xylinus was proved to be genetically homogeneous. J Food Prot, 2000 May, 63(5), 665 - 7 Evaluation of dry sheet medium culture plate (Compactdry TC) method for determining numbers of bacteria in food samples; Mizuochi S et al.; The Compactdry, a ready-to-use and self-diffusible dry medium sheet culture system, has been developed by the Nissui Pharmaceutical Co . Ltd . for enumerating bacteria in food . The Compactdry consists of special spread sheet with culture medium that is the same as standard method nutrients, a cold water-soluble gelling agent, and a unique plastic dish . The procedure for bacterial examination in a sample solution (1 ml) is to just inoculate a test solution into the center of the self-diffusible medium and incubate at 35 degrees C for 48 h . The Compactdry TC (CTC) for the enumeration of total aerobic bacteria from 97 food samples was compared with the standard plate count (SPC) method and 3M Petrifilm aerobic count plates (PAC) . The correlation coefficients between the CTC and SPC method, the CTC and PAC, and the PAC and SPC method were 0.97, 0.99, and 0.97, respectively . The Compactdry system is useful for the enumeration of total aerobic bacteria in food and may be a possible suitable alternative to the conventional pour-plate or the Petrifilm plate methods. Br J Biomed Sci, 1999, 56(3), 182 - 7 Oxoid CO2 Gen atmosphere generation system for growth of capnophilic bacteria: an evaluation; Turner A et al.; The Oxoid CO2 Gen system is compared with BBL GasPak and a carbon dioxide (CO2) incubator to evaluate its ability to support and enhance the growth of capnophilic bacteria . Clinical samples (n = 109) from various anatomical sites and 23 spiked samples are evaluated . The criteria used to compare the systems include amount of growth, colony size, colony morphology and haemolysis . Isolation rates, amounts of growth and morphology were similar in each system, but colony diameter was significantly larger in the jar-based systems . Significantly larger colonies grew in CO2 Gen than in BBL GasPak . alpha-Haemolytic zones were significantly larger in jar-based systems than in the CO2 incubator, and significantly larger in CO2 Gen than in BBL GasPak . beta-haemolytic zones were significantly larger in CO2 Gen than in the CO2 incubator . The CO2 Gen system appears to be an excellent alternative to established methods for generating an environment for capnophilic incubation. Photochem Photobiol, 2000 May, 71(5), 567 - 73 The effects of epimerization at the 3(1)-position of bacteriochlorophylls c on their aggregation in chlorosomes of green sulfur bacteria . Control of the ratio of 3(1) epimers by light intensity; Ishii T et al.; R- and S-epimerization at the 3(1) position of bacteriochlorophyll (BChl) c and the formation of rod-like aggregates in chlorosomes of green sulfur bacteria were markedly affected in Chlorobium (Cb.) tepidum and Cb . limicola by cultivation under various light intensities (photon fluence rate) . The stronger the light, the higher the ratio of the S-epimer to the R-epimer for each homolog of BChl c in the bacteria . S{P,E} BChl cF and S{I,E} BChl cF were found to be the major S-epimers in Cb . tepidum and Cb . limicola, respectively . R{P,E} BChl cF decreased markedly compared to R{E,E} BChl cF in Cb . tepidum, whereas no observable change in the ratio of R{P,E}/R{E,E} was detected for Cb . limicola . With increase in light intensity the Qy absorption maximum of the bacteria shifted to shorter wavelengths . In vitro spectroscopic studies of the aggregates showed a marked difference in the formation of aggregates from R- and S-epimers of BChl c; the S-epimers formed aggregates much more slowly than did the R-epimers . These results suggest that the ratio of the epimers of BChl c might significantly affect the aggregation of BChl in the chlorosome . We propose different roles for the R- and S-epimers in chlorosomes of Cb . limicola and Cb . tepidum. Microbes Infect, 2000 Apr, 2(4), 359 - 65 Immunocytochemistry of the AfaE adhesin and AfaD invasin produced by pathogenic Escherichia coli strains during interaction of the bacteria with HeLa cells by high-resolution scanning electron microscopy; Gounon P et al.; We used a recent scanning electron microscope equipped with field emission gun and highly sensitive detectors to develop a fast and simple protocol for double immunogold staining using 10- and 15-nm gold particles . We used this approach to analyse the afimbrial adhesive sheath produced by pathogenic Escherichia coli interacting with the surface of epithelial cells . We demonstrated that AfaE adhesin and AfaD invasin were exposed at the bacterial surface during the interaction . This method could be easily and widely extended to the study of the early invasion process of many bacterial and viral pathogens, by immunocytochemical probing. FEMS Microbiol Ecol, 2000 Apr 1, 32(2), 167 - 175 Quantitative analysis of ammonia oxidising bacteria using competitive PCR; Phillips CJ et al.; Culture-based methods for enumeration, such as most probable number (MPN) methodologies, have proved inefficient due to difficulties in the isolation and cultivation of ammonia oxidising bacteria in the laboratory . Biases are associated with the isolation of bacteria in selective media and organisms cultivated in the laboratory may not be truly representative of those in the environment . In this study, we developed a competitive PCR (cPCR)-based method based on the amplification of 16S rRNA genes specific for the beta-subgroup proteobacterial ammonia oxidising bacteria for enumeration of these organisms . Populations in both agricultural soils and estuarine sediments were quantified by traditional MPN and by cPCR . The numbers of ammonia oxidisers for both sample types were significantly underestimated by conventional MPN and were 1-3 orders of magnitude lower than those obtained by cPCR . Higher numbers of ammonia oxidisers found in fertilised plots in agricultural soils by the cPCR technique were not observed in MPN estimates . It was necessary to construct a separate standard curve for each sample type as differences in DNA extraction, quantity and purity had a significant bearing on the ease of PCR of both competitor and target DNA. J Exp Med, 2000 May 15, 191(10), 1807 - 12 Innate recognition of bacteria in human milk is mediated by a milk-derived highly expressed pattern recognition receptor, soluble CD14; Labeta MO et al.; Little is known about innate immunity to bacteria after birth in the hitherto sterile fetal intestine . Breast-feeding has long been associated with a lower incidence of gastrointestinal infections and inflammatory and allergic diseases . We found in human breast milk a 48-kD polypeptide, which we confirmed by mass spectrometry and sequencing to be a soluble form of the bacterial pattern recognition receptor CD14 (sCD14) . Milk sCD14 (m-sCD14) concentrations were up to 20-fold higher than serum sCD14 from nonpregnant, pregnant, or lactating women . In contrast, lipopolysaccharide (LPS)-binding protein was at very low levels . Mammary epithelial cells produced 48-kD sCD14 . m-sCD14 mediated activation by LPS and whole bacteria of CD14 negative cells, including intestinal epithelial cells, resulting in release of innate immune response molecules . m-sCD14 was undetectable in the infant formulas and commercial (cows') milk tested, although it was present in bovine colostrum . These findings indicate a sentinel role for sCD14 in human milk during bacterial colonization of the gut, and suggest that m-sCD14 may be involved in modulating local innate and adaptive immune responses, thus controlling homeostasis in the neonatal intestine. Mikrobiologiia, 2000 Jan-Feb, 69(1), 120 - 6 {Initial stages of interaction of Azospirillum brasilense bacteria with wheat germ roots: adsorption, deformation of root hairs}; Egorenkova IV et al.; The initial stages of colonization of wheat roots by cells of Azospirillum brasilense strains 75 and 80 isolated from soils of the Saratov oblast were studied . The adsorption of azospirilla on root hairs of soft spring wheats rapidly increased in the first hours of incubation, going then to a plateau phase . Within the first 15 h of incubation, exponential-phase cells were adsorbed more intensively than stationary-phase cells . Conversely, stationary-phase cells were adsorbed more intensively than exponential-phase cells, if the period of azospirilla incubation with the wheat roots was extended . As the time of incubation increased, the attachment of azospirilla to the wheat roots became stronger . The effect of cell attachment to root hairs was strain-dependent; the number of adsorbed cells of a given strain of azospirilla was greater in the case of host wheat cultivars . The deformation of wheat root hairs was affected by the polysaccharide-containing complexes isolated from the capsular material of azospirilla . The suggestion is made that common receptor systems are involved in the adsorption of azospirilla on roots and in root hair deformation. Subcell Biochem, 2000, 33, 541 - 57 DNA vaccine delivery by attenuated intracellular bacteria; Dietrich G et al.; Vaccination by intramuscular or intradermal injection of antigen-encoding DNA is a promising new approach leading to strong cellular and humoral immune responses . Since bone-marrow derived antigen presenting cells (APC) seem to induce these immune responses after migration to the spleen, it is desirable to deliver DNA vaccines directly to splenic APC . Recently, attenuated intracellular bacteria have been exploited for the introduction of DNA vaccine vectors into different cell types in vitro as well as in vivo and offer an attractive alternative to the direct inoculation of naked plasmid DNA. Rinsho Byori, 2000 Jan, Suppl 111, 64 - 8 {Detection methods for drug-resistant bacteria in routine examination--ESBL}; Okamoto R; Extended-spectrum beta-lactamases(ESBLs) confer resistance to cefotaxime, ceftazidime, aztreonam, extended-spectrum penicillins, and structurally related beta-lactams in clinical isolates of K . pneumoniae and E . coli . Some ESBLs, however, show a lower level of resistance and these isolates may not reach NCCLS breakpoints for resistance . Optimal methods for confirmation of ESBL-producing isolates are described. J Microbiol Methods, 2000 May, 40(3), 265 - 74 Fluorescent labelling of intracellular bacteria in living host cells; Boleti H et al.; The fluorescent reagent, CellTracker, labels metabolically-active cells and was used here to label Chlamydia in vivo during their exponential phase of growth in infected cells . HeLa cells infected with C . psittaci were labelled with the CellTracker reagents between 15 and 48 h post-infection . The fluorescent label accumulated in the host-cell membrane compartment (inclusion) within which Chlamydia reside and replicate, and was also incorporated by the bacteria . Labelling with the CellTracker affected neither the growth nor the differentiation of the chlamydiae, and labelled chlamydiae isolated from infected cells were infectious . Our results demonstrate that the CellTracker could become a valuable tool for in vivo labelling of obligate intracellular parasites for which no genetic tools exist. FEBS Lett, 2000 May 4, 473(1), 63 - 6 Adenylylsulfate reductases from archaea and bacteria are 1:1 alphabeta-heterodimeric iron-sulfur flavoenzymes--high similarity of molecular properties emphasizes their central role in sulfur metabolism; Fritz G et al.; Highly active adenylylsulfate (APS) reductase was isolated under N(2)/H(2) from sulfate-reducing and sulfide-oxidizing bacteria and archaea . It was a 1:1 alphabeta-heterodimer of molecular mass approximately 95 kDa, and two subunits (alpha approximately 75, beta approximately 20 kDa) . The specific activity was 11-14 micromol (min mg)(-1); cofactor analysis revealed 0.96+/-0.05 FAD, 7.5+/-0.1 Fe and 7.9+/-0.25 S(2-) . The photochemically reduced enzyme had a multiline EPR spectrum resulting from two interacting {4Fe-4S} centers . The properties of the different APS reductases were remarkably similar, although the enzyme is involved in different metabolic pathways and was isolated from phylogenetically far separated organisms . A structural model is proposed, with FAD bound to the alpha-subunit, and two {4Fe-4S} centers located in close proximity on the beta-subunit. Klin Khir, 1999, (12), 40 - 2 {The role of the intestines in the pathogenesis of acute pancreatitis: oxygen extraction and bacteria translocation in rats}; Krivoruchko IA et al.; In experiment on 40 male rats of the Wistar line there was investigated the oxygen extraction (O2) and the bacteria translocation in 30 min, 2, 6, 12 and 24 hours after the stimulating operation (control group) and simulation of the ductal-hypertensive form of an acute experimental pancreatitis (AEP)--the main group . The data obtained witness the general extraction of O2 raising by 222% (P < 0.001) at average and lowering of its intestinal extraction in 30 min and 2 hours (by 33 and 31% at average, P < 0.05) and its raising in 24 hours by 138% (P < 0.001) at average also . These disorders had correlated with velocity of the intestinal E . coli reproduction and with the bacteria translocation on the way intestine-->mesenterial lymph nodes in 6 hours after the disease occurrence with preservation of the lymph nodes and the liver barrier function in the AEP duration over 24 hours . The data obtained had permitted to substantiate the necessity of the remedial measures complex application, directed on the frequency of purulent complications lowering. Dev Biol Stand, 2000, 102, 115 - 23 Inactivation of viruses, bacteria, protozoa and leukocytes in platelet and red cell concentrates; Corash L; Despite the increased safety of blood achieved through continued improvements in donor testing, concern remains about the safety of blood components . Transfusion of cellular components has been implicated in transmission of viral, bacterial, and protozoan diseases {1} . While it is commonly recognized that hepatitis B virus, hepatitis C virus, cytomegalovirus, and the retroviruses, such as human immunodeficiency virus and the human lymphotrophic viruses can be transmitted through cellular components, other pathogens are emerging as potentially significant transfusion-associated infectious agents . For example, transmission of protozoan infections due to trypanosomes {2-4} and babesia {5} have been reported . In addition to viral and protozoal infectious agents, bacterial contamination of platelet and red cell concentrates continues to be reported {6, 7} and may be an under-reported transfusion complication {8} . More importantly, new infectious agents, such as HIV, may periodically enter the donor population before they can be identified . During the past decade a number of methods to inactivate infectious pathogens in blood components have been investigated . This technology is now in the clinical trial phase. Int J Food Microbiol, 2000 Apr 10, 55(1-3), 11 - 8 Survival of bacteria during oxygen limitation; Potter L et al.; Regulatory mechanisms that enable bacteria associated with food, drinks and the human body to adapt to changes in the availability of oxygen are reviewed . Excess oxygen induces two adaptive responses to oxidative stress . Five or more control circuits enable enteric bacteria to generate energy and grow well in anaerobic environments . Two sets of enzymes catalyse both nitrate and nitrite reduction, and dual two-component regulatory systems sense and respond to the available nitrate and nitrite in the environment . The periplasmic nitrate reductase enables bacteria to scavenge low concentrations of nitrate: similar systems are found in food-borne and other pathogens. J Physiol Paris, 2000 Mar-Apr, 94(2), 157 - 8 Probiotic bacteria and intestinal health: new methods of investigation; Vilpponen-Salmela T et al.; This paper highlights some new methods in the probiotic research based on the use of colonic biopsies and molecular biological techniques for strain identification. EMBO J, 2000 May 2, 19(9), 2127 - 36 Late events of translation initiation in bacteria: a kinetic analysis; Tomsic J et al.; Binding of the 50S ribosomal subunit to the 30S initiation complex and the subsequent transition from the initiation to the elongation phase up to the synthesis of the first peptide bond represent crucial steps in the translation pathway . The reactions that characterize these transitions were analyzed by quench-flow and fluorescence stopped-flow kinetic techniques . IF2-dependent GTP hydrolysis was fast (30/s) followed by slow P(i) release from the complex (1.5/s) . The latter step was rate limiting for subsequent A-site binding of EF-Tu small middle dotGTP small middle dotPhe-tRNA(Phe) ternary complex . Most of the elemental rate constants of A-site binding were similar to those measured on poly(U), with the notable exception of the formation of the first peptide bond which occurred at a rate of 0.2/s . Omission of GTP or its replacement with GDP had no effect, indicating that neither the adjustment of fMet-tRNA(fMet) in the P site nor the release of IF2 from the ribosome required GTP hydrolysis. Appl Environ Microbiol, 2000 May, 66(5), 2166 - 74 Molecular ecological analysis of the succession and diversity of sulfate-reducing bacteria in the mouse gastrointestinal tract; Deplancke B et al.; Intestinal sulfate-reducing bacteria (SRB) growth and resultant hydrogen sulfide production may damage the gastrointestinal epithelium and thereby contribute to chronic intestinal disorders . However, the ecology and phylogenetic diversity of intestinal dissimilatory SRB populations are poorly understood, and endogenous or exogenous sources of available sulfate are not well defined . The succession of intestinal SRB was therefore compared in inbred C57BL/6J mice using a PCR-based metabolic molecular ecology (MME) approach that targets a conserved region of subunit A of the adenosine-5'-phosphosulfate (APS) reductase gene . The APS reductase-based MME strategy revealed intestinal SRB in the stomach and small intestine of 1-, 4-, and 7-day-old mice and throughout the gastrointestinal tract of 14-, 21-, 30-, 60-, and 90-day-old mice . Phylogenetic analysis of APS reductase amplicons obtained from the stomach, middle small intestine, and cecum of neonatal mice revealed that Desulfotomaculum spp . may be a predominant SRB group in the neonatal mouse intestine . Dot blot hybridizations with SRB-specific 16S ribosomal DNA (rDNA) probes demonstrated SRB colonization of the cecum and colon pre- and postweaning and colonization of the stomach and small intestine of mature mice only . The 16S rDNA hybridization data further demonstrated that SRB populations were most numerous in intestinal regions harboring sulfomucin-containing goblet cells, regardless of age . Reverse transcriptase PCR analysis demonstrated APS reductase mRNA expression in all intestinal segments of 30-day-old mice, including the stomach . These results demonstrate for the first time widespread colonization of the mouse intestine by dissimilatory SRB and evidence of spatial-specific SRB populations and sulfomucin patterns along the gastrointestinal tract. Appl Environ Microbiol, 2000 May, 66(5), 1834 - 43 Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers; Bastiaens L et al.; Two different procedures were compared to isolate polycyclic aromatic hydrocarbon (PAH)-utilizing bacteria from PAH-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which PAHs were supplied as crystals and (ii) a new method in which PAH degraders were enriched on and recovered from hydrophobic membranes containing sorbed PAHs . Both techniques were successful, but selected from the same source different bacterial strains able to grow on PAHs as the sole source of carbon and energy . The liquid enrichment mainly selected for Sphingomonas spp., whereas the membrane method exclusively led to the selection of Mycobacterium spp . Furthermore, in separate membrane enrichment set-ups with different membrane types, three repetitive extragenic palindromic PCR-related Mycobacterium strains were recovered . The new Mycobacterium isolates were strongly hydrophobic and displayed the capacity to adhere strongly to different surfaces . One strain, Mycobacterium sp . LB501T, displayed an unusual combination of high adhesion efficiency and an extremely high negative charge . This strain may represent a new bacterial species as suggested by 16S rRNA gene sequence analysis . These results indicate that the provision of hydrophobic sorbents containing sorbed PAHs in the enrichment procedure discriminated in favor of certain bacterial characteristics . The new isolation method is appropriate to select for adherent PAH-degrading bacteria, which might be useful to biodegrade sorbed PAHs in soils and sludge. J Biol Chem, 2000 Jun 30, 275(26), 19735 - 41 Regulation of high affinity nickel uptake in bacteria . Ni2+-Dependent interaction of NikR with wild-type and mutant operator sites; Chivers PT et al.; Escherichia coli actively imports nickel via the ATP-dependent NikABCDE permease . NikR, a protein of the ribbon-helix-helix family of transcription factors, represses expression of the nikABCDE operon in the presence of excessive concentrations of intracellular nickel . Here, the NikR operator site is identified within the nikABCDE promoter by footprinting and mutational analyses . The operator consists of two dyad-symmetric 5'-GTATGA-3' recognition sequences separated by 16 base pairs . Mutations in the GTATGA sequences reduce NikR binding affinity in vitro and reduce repression of a P(nik)-lacZ fusion in vivo . Moreover, NikR is shown to be a direct sensor of nickel ions . Strong operator binding requires the continual presence of 20-50 micrometer nickel, indicating the presence of a low affinity nickel-binding site, and NikR dimers also contain two high affinity nickel-binding sites . In addition to both GTATGA sites and nickel, high affinity operator binding also requires the C-terminal domain of NikR. Rapid Commun Mass Spectrom, 2000, 14(8), 669 - 72 Effects of ion mode and matrix additives in the identification of bacteria by intact cell mass spectrometry; Evason DJ et al.; Protocols for the identification of bacterial cells by intact cell matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (ICM-TOFMS) are presented . A mass range of 500 to 10,000 m/z is used . The use of formic acid and the crown ether 1, 4, 7, 10, 13, 16-hexaoxacyclooctadecane (18-crown-6) is described . Crown ether is useful for removing metal ion adducts, which degrade spectral purity, and formic acid promotes positive ions, improves spectral signal, and, hence, increases identification certainty. Can J Microbiol, 2000 Apr, 46(4), 387 - 90 Effects of non-ionic surfactants on the uptake and hydrolysis of fluoresceindiacetate by alkane-oxidizing bacteria; Bruheim P et al.; Biological effects of non-ionic surfactants on alkane-oxidizing bacteria were studied by assessing their influence on the uptake of prefluorochrome fluoresceindiacetate (FDA) and its intracellular hydrolysis to fluorescein . Both decreasing and increasing rates of hydrolysis as a consequence of the presence of surfactants were observed . The surfactants influenced the uptake of FDA, but not its intracellular hydrolysis . The effects of the surfactants on the uptake rate depended strongly on the structure and physico-chemical properties of the surfactants . There was no qualitative or significant quantitative difference in surfactant susceptibility between induced (alkane grown) and non-induced bacteria (acetate grown), even though the induced cells possess greater cell surface hydrophobicity. FEMS Microbiol Ecol, 2000 Apr 1, 32(1), 53 - 59 Characterization of 3-chlorobenzoate degrading aerobic bacteria isolated under various environmental conditions; Krooneman J et al.; The rates of bacterial growth in nature are often restricted by low concentrations of oxygen or carbon substrates . In the present study the metabolic properties of 24 isolates that had been isolated using various concentrations of 3-chlorobenzoate, benzoate and oxygen as well as using continuous culture at high and low growth rates were determined to investigate the effects of these parameters on the metabolism of monoaromatic compounds . Bacteria were enriched from different sampling sites and subsequently isolated . In batch culture this was done both under low oxygen (2% O(2)) and air-saturated concentrations . Chemostat enrichments were performed under either oxygen or 3-chlorobenzoate limiting conditions . Bacteria metabolizing aromatics with gentisate or protocatechuate as intermediates (gp bacteria) as well as bacteria metabolizing aromatic compounds via catechols (cat bacteria) were isolated from batch cultures when either benzoate or 3CBA were used as C sources, regardless of the enrichment conditions applied . In contrast, enrichments performed in chemostats at low dilution rates resulted in gp-type organisms only, whereas at high dilution rates cat-type organisms were enriched, irrespective of the oxygen and 3-chlorobenzoate concentration used during enrichment . It is noteworthy that the gp-type of bacteria possessed relatively low micro(max) values on 3CBA and benzoate along with relatively high substrate and oxygen affinities for these compounds . This is in contrast with cat-type of bacteria, which seemed to be characterized by high maximum specific growth rates on the aromatic substrates and relatively high apparent half saturation constants . In contrast, bacteria degrading chlorobenzoate via gentisate or protocatechuate may possibly be better adapted to conditions leading to growth at reduced rates such as low oxygen and low substrate concentrations. J Exp Med, 2000 Apr 17, 191(8), 1429 - 36 Inflammatory responses induced by the filarial nematode Brugia malayi are mediated by lipopolysaccharide-like activity from endosymbiotic Wolbachia bacteria; Taylor MJ et al.; The pathogenesis of filarial disease is characterized by acute and chronic inflammation . Inflammatory responses are thought to be generated by either the parasite, the immune response, or opportunistic infection . We show that soluble extracts of the human filarial parasite Brugia malayi can induce potent inflammatory responses, including tumor necrosis factor (TNF)-alpha, interleukin (IL)-1beta, and nitric oxide (NO) from macrophages . The active component is heat stable, reacts positively in the Limulus amebocyte lysate assay, and can be inhibited by polymyxin B . TNF-alpha, IL-1beta, and NO responses were not induced in macrophages from lipopolysaccharide (LPS)-nonresponsive C3H/HeJ mice . The production of TNF-alpha after chemotherapy of microfilariae was also only detected in LPS-responsive C3H/HeN mice, suggesting that signaling through the Toll-like receptor 4 (TLR4) is necessary for these responses . We also show that CD14 is required for optimal TNF-alpha responses at low concentrations . Together, these results suggest that extracts of B . malayi contain bacterial LPS . Extracts from the rodent filaria, Acanthocheilonema viteae, which is not infected with the endosymbiotic Wolbachia bacteria found in the majority of filarial parasites, failed to induce any inflammatory responses from macrophages, suggesting that the source of bacterial LPS in extracts of B . malayi is the Wolbachia endosymbiont . Wolbachia extracts derived from a mosquito cell line induced similar LPS-dependent TNF-alpha and NO responses from C3H/HeN macrophages, which were eliminated after tetracycline treatment of the bacteria . Thus, Wolbachia LPS may be one of the major mediators of inflammatory pathogenesis in filarial nematode disease. Lancet, 2000 Apr 8, 355(9211), 1242 - 3 Endosymbiotic bacteria in worms as targets for a novel chemotherapy in filariasis; Hoerauf A et al.; Endosymbiotic bacteria living in plasmodia or worm parasites are required for the homoeostasis of their host and should be excellent targets for chemotherapy of certain parasitic diseases . We show that targeting of Wolbachia spp bacteria in Onchocerca volvulus filariae by doxycycline leads to sterility of adult worms to an extent not seen with drugs used against onchocerciasis, a leading cause of blindness in African countries. J Bacteriol, 2000 May, 182(9), 2393 - 401 Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria; van Embden JD et al.; The direct repeat region in Mycobacterium tuberculosis complex strains is composed of multiple direct variant repeats (DVRs), each of which is composed of a 36-bp direct repeat (DR) plus a nonrepetitive spacer sequence of similar size . It has been shown previously that clinical isolates show extensive polymorphism in the DR region by the variable presence of DVRs, and this polymorphism has been used in the epidemiology of tuberculosis . In an attempt to better understand the evolutionary scenario leading to polymorphic DR loci and to improve strain differentiation by spoligotyping, we characterized and compared the DNA sequences of the complete DR region and its flanking DNA of M . tuberculosis complex strains . We identified 94 different spacer sequences among 26 M . tuberculosis complex strains . No sequence homology was found between any of these spacers and M . tuberculosis DNA outside of the DR region or with any other known bacterial sequence . Although strains differed extensively in the presence or absence of DVRs, the order of the spacers in the DR locus was found to be well conserved . The data strongly suggest that the polymorphism in clinical isolates is the result of successive deletions of single discrete DVRs or of multiple contiguous DVRs from a primordial DR region containing many more DVRs than seen in present day isolates and that virtually no scrambling of DVRs took place during evolution . Because the majority of the novel spacer sequences identified in this study were confined to isolates of the rare Mycobacterium canettii taxon, the use of the novel spacers in spoligotyping led only to a slight improvement of strain differentiation by spoligotyping. Int J Syst Evol Microbiol, 2000 Mar, 50 Pt 2, 459 - 69 Hyphomonas adhaerens sp . nov., Hyphomonas johnsonii sp . nov . and Hyphomonas rosenbergii sp . nov., marine budding and prosthecate bacteria; Weiner RM et al.; Three strains of prosthecate, budding bacteria, MHS-2T, MHS-3T and VP6T, were isolated from marine habitats including the open ocean (the pelagic zone), the offshore region (the neritic zone) and the hydrothermal vent region . A polyphasic approach including 16S rDNA sequencing, phenotypic analyses, serology, fatty acid analyses, membrane protein profiles and DNA-DNA hybridizations was used to place these strains in the genus Hyphomonas, a taxon of the alpha-Proteobacteria . The results of these analyses also showed that strains MHS-3T, MHS-2T and VP6T each represent a new species of Hyphomonas . The names Hyphomonas adhaerens (type strain MHS-3T, ATCC 43965T), Hyphomonas johnsonii (type strain MHS-2T, ATCC 43964T) and Hyphomonas rosenbergii (type strain VP6T, ATCC 43869T) are proposed for the new species . With these additions, Hyphomonas now contains eight species. Biotechnol Prog, 2000 Mar-Apr, 16(2), 133 - 45 Optimization of tryptophan production in bacteria . Design of a strategy for genetic manipulation of the tryptophan operon for tryptophan flux maximization; Marin-Sanguino A et al.; In the present work we have applied the indirect optimization method (Torres, N . V . et al . Biotechnol . Bioeng . 1996, 49, 247-258) to the maximization of tryptophan biosynthesis in Escherichia coli . The optimization procedure is applied to an updated model of this biochemical system (Xiu, Z-L et al., J . Biotechnol . 1997, 58, 125-140) and thus extended to a problem that includes the processes of transcription and translation . The model representation used by these authors is first translated into the corresponding S-system version . Then, to guarantee cell viability, we impose a set of constraints on some variable and parameter values, all of which are able to be modulated by available techniques . Our results show that it is possible to attain a stable and robust steady state with a rate of tryptophan production increased more than 4 times . This is achieved by changing four key parameters related to the efflux of tryptophan, the growth rate, the inhibition constant, and the tryptophan repressor level . Moreover, it is demonstrated that we can reach this optimum state in a sequential manner, each step leading us to a better situation in relation to the previous one . Thus, only by doubling the tryptophan excretion we can triplicate the rate of tryptophan production . A further, although lesser, improvement can be attained by increasing 4-fold the rate of growth and subsequently by weakening the inhibitory feedback interaction of tryptophan on the enzymes leading to its synthesis . Finally, a significant jump in the rate of production can be obtained if the level of the trp operon could be decreased . When a second approach was considered, in which the growth rate is kept constant in the optimized profile, we found out that by modulation of the parameters it is possible to increase more than 2-fold the rate of tryptophan production. Vet Clin North Am Equine Pract, 2000 Apr, 16(1), 29 - 47, v-iv Equine immunity to bacteria; Giguere S et al.; The remarkable ability of the horse and other animals to prevent infection by most bacterial pathogens encountered is the result of a complex set of distinct but overlapping defense mechanisms . This article summarizes the current state of knowledge on innate and adaptive immunity to bacterial pathogens and reviews various ways in which some bacteria have evolved in order to evade components of the host response. Genetika, 2000 Feb, 36(2), 191 - 4 {Distribution of cytoplasmically inherited bacteria Spiroplasma causing female bias in the Eurasian populations of Adalia bipunctata}; Zakharov IA et al.; Two-spot ladybirds Adalia bipunctata were collected from the populations of Western and Eastern Europe and Central Asia . The agent killing males at the early embryonic stage in these populations was identified as bacteria of the genus Spiroplasma . Bacteria found in A . bipunctata proved to be phylogenetically related to Spiroplasma ixodetis (typical line Y-32) found in tick Ixodes pacificus but not to Spiroplasma causing the death of male embryos in Drosophila. Microbiology, 2000 Mar, 146 ( Pt 3), 709 - 18 Occurrence of natural dixenic associations between the symbiont Photorhabdus luminescens and bacteria related to Ochrobactrum spp . in tropical entomopathogenic Heterorhabditis spp . (Nematoda, Rhabditida); Babic I et al.; Bacteria naturally associated with the symbiont Photorhabdus luminescens subsp . akhurstii were isolated from the entomopathogenic nematode Heterorhabditis indica . Bacterial isolates distinct from P . luminescens subsp . akhurstii were obtained from 33% of the samples . Fourteen bacterial isolates, from nematodes collected from three different Caribbean islands, were characterized by conventional phenotypic tests, restriction fragment length polymorphism and sequence analyses of PCR-amplified 16S rRNA genes (16S rDNAs) . Isolates were grouped into three genotypes, each one being associated with one Caribbean island . Phenotypic characteristics and 16S rDNA analysis showed that the Photorhabdus-associated bacteria were closely related to Ochrobactrum anthropi for the group from Guadeloupe, and to Ochrobactrum intermedium for the two groups from the Dominican Republic and Puerto Rico . No pathogenicity of the Ochrobactrum spp . to the insects Galleria mellonella and Spodoptera littoralis (Lepidoptera) was detected . Since Ochrobactrum spp . are considered as human opportunist pathogens, the mass production of entomopathogenic nematodes for biological control requires strict vigilance. Biol Chem, 2000 Feb, 381(2), 89 - 93 The twin-arginine translocation system: a novel means of transporting folded proteins in chloroplasts and bacteria; Robinson C; Protein translocases have been characterised in several membrane systems and the translocation mechanisms have been shown to differ in critical respects . Nevertheless, the majority were believed to transport proteins only in a largely unfolded state, and this widespread characteristic was viewed as a likely evolutionary effort to minimise the diameter of translocation pore required . Within the last few years, however, studies on the chloroplast thylakoid membrane have revealed a novel class of protein translocase which possesses the apparently unique ability to transport fully-folded proteins across a tightly sealed energy-transducing membrane . A related system, (the twin-arginine translocation, or Tat system) has now been characterised in the Escherichia coli plasma membrane and considerations of its substrate specificity again point to its involvement in the transport of folded proteins . The emerging data suggest a critical involvement in many membranes for the biogenesis of two types of globular protein: those that are obliged to fold prior to translocation, and those that fold too tightly or rapidly for other types of protein translocase to handle. Curr Opin Microbiol, 2000 Apr, 3(2), 149 - 53 Transcription termination control in bacteria; Henkin TM; Transcription termination is a dynamic process and is subject to control at a number of levels . New information about the molecular mechanisms of transcription elongation and termination, as well as new insights into protein-RNA interactions, are providing a framework for increased understanding of the molecular details of transcription termination control. Appl Environ Microbiol, 2000 Apr, 66(4), 1617 - 21 Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria; Dojka MA et al.; Culture-independent molecular phylogenetic methods were used to explore the breadth of diversity and environmental distribution of members of the division-level "candidate" phylogenetic group WS6, recently discovered in a contaminated aquifer and with no cultivated representatives . A broad diversity of WS6-affiliated sequences were cloned from 7 of 12 environments investigated: mainly from anaerobic sediment environments . The number of sequences representing the WS6 candidate division was increased from 3 to 60 in this study . The extent of phylogenetic divergence (sequence difference) in this candidate division was found to be among the largest of any known bacterial division . This indicates that organisms representing the WS6 phylogenetic division offer a broad diversity of undiscovered biochemical and metabolic novelty . These results provide a framework for the further study of these evidently important kinds of organisms and tools, the sequences, with which to do so. Appl Environ Microbiol, 2000 Apr, 66(4), 1468 - 73 Interspecific variability in sensitivity to UV radiation and subsequent recovery in selected isolates of marine bacteria; Arrieta JM et al.; The interspecific variability in the sensitivity of marine bacterial isolates to UV-B (295- to 320-nm) radiation and their ability to recover from previous UV-B stress were examined . Isolates originating from different microenvironments of the northern Adriatic Sea were transferred to aged seawater and exposed to artificial UV-B radiation for 4 h and subsequently to different radiation regimens excluding UV-B to determine the recovery from UV-B stress . Bacterial activity was assessed by thymidine and leucine incorporation measurements prior to and immediately after the exposure to UV-B and after the subsequent exposure to the different radiation regimens . Large interspecific differences among the 11 bacterial isolates were found in the sensitivity to UV-B, ranging from 21 to 92% inhibition of leucine incorporation compared to the bacterial activity measured in dark controls and from 14 to 84% for thymidine incorporation . Interspecific differences in the recovery from the UV stress were also large . An inverse relation was detectable between the ability to recover under dark conditions and the recovery under photosynthetic active radiation (400 to 700 nm) . The observed large interspecific differences in the sensitivity to UV-B radiation and even more so in the subsequent recovery from UV-B stress are not related to the prevailing radiation conditions of the microhabitats from which the bacterial isolates originate . Based on our investigations on the 11 marine isolates, we conclude that there are large interspecific differences in the sensitivity to UV-B radiation and even larger differences in the mechanisms of recovery from previous UV stress . This might lead to UV-mediated shifts in the bacterioplankton community composition in marine surface waters. Appl Environ Microbiol, 2000 Apr, 66(4), 1429 - 34 The function of cytoplasmic flavin reductases in the reduction of azo dyes by bacteria; Russ R et al.; A flavin reductase, which is naturally part of the ribonucleotide reductase complex of Escherichia coli, acted in cell extracts of recombinant E . coli strains under aerobic and anaerobic conditions as an "azo reductase." The transfer of the recombinant plasmid, which resulted in the constitutive expression of high levels of activity of the flavin reductase, increased the reduction rate for different industrially relevant sulfonated azo dyes in vitro almost 100-fold . The flavin reductase gene (fre) was transferred to Sphingomonas sp . strain BN6, a bacterial strain able to degrade naphthalenesulfonates under aerobic conditions . The flavin reductase was also synthesized in significant amounts in the Sphingomonas strain . The reduction rates for the sulfonated azo compound amaranth were compared for whole cells and cell extracts from both recombinant strains, E . coli, and wild-type Sphingomonas sp . strain BN6 . The whole cells showed less than 2% of the specific activities found with cell extracts . These results suggested that the cytoplasmic anaerobic "azo reductases," which have been described repeatedly in in vitro systems, are presumably flavin reductases and that in vivo they have insignificant importance in the reduction of sulfonated azo compounds. J Microbiol Methods, 2000 Mar, 40(1), 105 - 10 Use of gel electrophoresis for the study of enzymatic activities of cold-adapted bacteria; Berchet V et al.; Glutamate dehydrogenase (GDH) and lactate dehydrogenase (LDH) activity of 13 cold-adapted strains, isolated from cold soils and showing GDH and/or LDH activity in spectrophotometric assays, were revealed by the use of electrophoresis on a nondenaturing acrylamide gel (zymogram) . Psychrophilic strains were grown at 4 degrees C and 10 degrees C and the psychrotolerant strains at 4 degrees, 20 degrees and 28 degrees C . Incubation with the specific substrate and staining were done at 4, 28 or 37 degrees C . In the most cold-adapted strains, LDH and GDH production was high at 4 degrees C . In psychrotrophic strains, enzyme production and activity were greater at 20 or 28 degrees C than at lower temperatures . LDH remained active up to 37 degrees C while GDH activity was more thermolabile . GDH activity was NAD-dependent in some psychrophilic strains . In other strains, it was dependent on NAD(P) only or on both NAD and NAD(P) . Two bands were seen for GDH or LDH activity in some strains . This method, which does not require a dialysis step, can be used to study the influence of temperature on enzyme production and activity, and the co-factor dependence . It detects phenotypic differences between isozymes, providing data for systematics. Lett Appl Microbiol, 2000 Jan, 30(1), 90 - 4 Phagocytosis of mycobacteria by U937 cells: a rapid method for monitoring uptake and separating phagocytosed and free bacteria by magnetic beads; Whyte J et al.; A human-derived monocytic cell line (U937) was induced to phagocytose Mycobacterium phlei by the addition of phorbol myristate acetate (PMA) to the culture medium for 50-60 h . Cells not treated with PMA were unable to phagocytose M . phlei . Magnetic beads enabled a rapid and highly efficient separation of phagocytosed and free bacteria to be achieved, an approach which is particularly useful if colony plating is used to enumerate bacterial survival within phagocytic cells . Fluorescence-activated cell sorting (FACS) analysis showed that 98% of U937 cells contained viable bacteria after 3 h. Biol Pharm Bull, 2000 Mar, 23(3), 298 - 304 Pharmacokinetics of ginsenoside deglycosylated by intestinal bacteria and its transformation to biologically active fatty acid esters; Hasegawa H et al.; Ginsenosides are deglycosylated by intestinal bacteria to active forms after oral administration . The present study demonstrated the pharmacodynamics of 20-O-beta-D-glucopyranosyl-20(S)-protopanaxadiol (M1), an intestinal bacterial metabolite of ginsenosides, and the in vitro and in vivo antitumor activities of M1-metabolites in comparison with M1 using C57BL/6 mice and Wistar rats . M1 was selectively accumulated into the liver soon after its intravenous administration to mice, and mostly excreted as bile; however, some M1 was transformed to fatty acid ester (EM1) in the liver . EM1 was isolated from rats in a recovery dose of approximately 24 mol% . Structural analysis indicated that EM1 comprised a family of fatty acid mono-esters of M1 . Because EM1 was not excreted as bile as M1 was, it was accumulated in the liver longer than M1 . Although the cytotoxicity of M1 against B16-F10 melanoma cells was attenuated by fatty acid esterification, EM1 inhibited tumor growth more than M1 in vivo . These results suggest that the fatty acid M1 esters may be the real active principles of ginsenosides in the body. J Endod, 1999 Dec, 25(12), 795 - 9 Inflammatory cytokine production and specific antibody responses to lipopolysaccharide from endodontopathic black-pigmented bacteria in patients with multilesional periapical periodontitis; Matsushita K et al.; We examined the induction of the cytokines interleukin (IL)-1 beta, IL-6, and IL-8 by lipopolysaccharides (LPSs) from several species of possible endodontopathic black-pigmented bacteria . Studies were conducted in human whole blood cultures from six patients (two from each group) with differing numbers of periapical periodontitis lesions (i.e . patients with radiographically clear periapical lesions in 10 or more teeth (high-lesion group, n = 4), in one or two teeth (low-lesion group, n = 6), and six healthy volunteers with no periapical lesions (no lesion group)) . LPS from Prevotella intermedia ATCC 25611, Porphyromonas gingivalis 381, and Prophyromonas endodontalis ATCC 27067 induced a higher IL-8 response in the subjects of the high-lesion group, compared with the subjects of the other two groups . To ascertain the degree of sensitization by test bacteria, we examined the reactivities of antibodies in serum and saliva from the subjects to different bacterial species . LPS from P . gingivalis reacted strongly with sera from the high-lesion group . Thus, LPS from black-pigmented bacteria may be involved in multilesional periapical periodontitis by inducing particular cytokines and/or humoral immune responses. Can Vet J, 2000 Feb, 41(2), 105 - 16 Bacteria and fungi of marine mammals: a review; Higgins R; A list of the different bacterial and fungal agents isolated from marine mammals in different parts of the world is presented . Importance is given to some of the most recently identified bacterial agents, including Actinobacillus delphinicola, A . scotiae, and Brucella spp . A list, in alphabetical order, of bacteria recovered from different tissues or organs from marine mammals is presented for the integumentary, respiratory, digestive, genitourinary, and reticuloendothelial systems . Infectious bacterial agents associated with abscesses and with cases of septicemia are also listed . Information about the different fungal agents recovered from marine mammals is summarized . A section covering some of the zoonotic infectious agents recovered from marine mammals is included. Stud Health Technol Inform, 1999, 68, 650 - 3 An integration system to rapidly identify aquatic bacteria; Giacomini M et al.; An identification system for aquatic bacteria which would be useful for aspects ranging from pollution monitoring to health care, is described . It contains relevant information concerning the nature, taxonomy and activity of aquatic bacteria and allows to identify fresh isolates by means of their chemotaxonomic profiles . The system is simple and user friendly, so that it can be used by people not familiar with computers and has a modular interface that allows an easy interaction with laboratory instruments . The system is also connected with artificial neural network based programs to identify strains starting from the considered chemotaxonomic features. J Nutr, 2000 Feb, 130(2S Suppl), 415S - 416S Probiotic bacteria: today and tomorrow; Klaenhammer TR; This paper provides an overview of the key issues raised during this symposium . Probiotic cultures have been associated historically with cultured milks and dairy products, from which there is substantial evidence for positive effects on human health and general well-being. J Nutr, 2000 Feb, 130(2S Suppl), 384S - 390S Considerations for use of probiotic bacteria to modulate human health; Sanders ME; Oral consumption of probiotic bacteria has the potential to support the health of American consumers . This paper will discuss the rationale of the probiotic theory, several health targets for probiotic bacteria, probiotic products in the U.S . and, finally, issues pertaining to communication about probiotic products to the consumer. J Nutr, 2000 Feb, 130(2S Suppl), 305S - 309S Long-chain acyl-CoA-dependent regulation of gene expression in bacteria, yeast and mammals; Black PN et al.; Fatty acyl-CoA thioesters are essential intermediates in lipid metabolism . For many years there have been numerous conflicting reports concerning the possibility that these compounds also serve regulatory functions . In this review, we examine the evidence that long-chain acyl-CoA is a regulatory signal that modulates gene expression . In the bacteria Escherichia coli, long-chain fatty acyl-CoA bind directly to the transcription factor FadR . Acyl-CoA binding renders the protein incapable of binding DNA, thus preventing transcription activation and repression of many genes and operons . In the yeast Saccharomyces cerevisiae, genes encoding peroxisomal proteins are activated in response to exogenously supplied fatty acids . In contrast, growth of yeast cells in media containing exogenous fatty acids results in repression of a number of genes, including that encoding the delta9-fatty acid desaturase (OLE1) . Both repression and activation are dependent upon the function of either of the acyl-CoA synthetases Faa1p or Faa4p . In mammals, purified hepatocyte nuclear transcription factor 4alpha (HNF-4alpha) like E . coli FadR, binds long chain acyl-CoA directly . Coexpression of HNF-4alpha and acyl-CoA synthetase increases the activation of transcription of a fatty acid-responsive promoter, whereas coexpression with thioesterase decreases the fatty acid-mediated response . Conflicting data exist in support of the notion that fatty acyl-CoA are natural ligands for peroxisomal proliferator-activated receptor alpha (PPARalpha). Genome Res, 2000 Mar, 10(3), 379 - 85 HOBACGEN: database system for comparative genomics in bacteria; Perriere G et al.; We present here HOBACGEN, a database system devoted to comparative genomics in bacteria . HOBACGEN contains all available protein genes from bacteria, archaea, and yeast, taken from SWISS-PROT/TrEMBL and classified into families . It also includes multiple alignments and phylogenetic trees built from these families . The database is organized under a client/server architecture with a client written in Java, which may run on any platform . This client integrates a graphical interface allowing users to select families according to various criteria and notably to select homologs common to a given set of taxa . This interface also allows users to visualize multiple alignments and trees associated to families . In tree displays, protein gene names are colored according to the taxonomy of the corresponding organisms . Users may access all information associated to sequences and multiple alignments by clicking on genes . This graphic tool thus gives a rapid and simple access to all data required to interpret homology relationships between genes and distinguish orthologs from paralogs . Instructions for installation of the client or the server are available at fr/databases/hobacgen.html. FEMS Microbiol Rev, 2000 Apr, 24(2), 193 - 219 Characterisation of bacteria by matrix-assisted laser desorption/ionisation and electrospray mass spectrometry; van Baar BL; Chemical analysis for the characterisation of micro-organisms is rapidly evolving, after the recent advent of new ionisation methods in mass spectrometry (MS): electrospray (ES) and matrix-assisted laser desorption/ionisation (MALDI) . These methods allow quick characterisation of micro-organisms, either directly or after minimum sample preparation . This review provides a brief introduction to ES and MALDI MS and a discussion of micro-organism characterisation capabilities . Some attention is devoted to the analysis of mixtures of proteins, lipids and other compounds, to the combination of polymerase chain reaction technology and MS, and to the analysis of whole bacteria and their lysates . The review of results produced hitherto is concluded with an outlook on future developments. Biochemistry (Mosc), 2000 Feb, 65(2), 149 - 59 Methods of isolation of reaction center preparations from photosynthetic purple bacteria; Zakharova NI et al.; Various modern methods of isolation of functionally active membrane complexes of the reaction centers (RC) from photosynthetic purple bacteria are reviewed . Special attention is given to the methods of RC isolation from bacteria which are widely used in experimental practice . The analysis includes the main steps of RC isolation, evaluation of purity of the resultant preparation, and characterization of its functional activity . Besides description of conventional methods of RC isolation based on ion-exchange chromatography and hydroxyapatite chromatography, some other methods such as affinity chromatography and high-performance chromatography at high and fine pressure are also considered. J Microbiol Methods, 2000 Apr, 40(2), 125 - 34 Widefield deconvolution epifluorescence microscopy combined with fluorescence in situ hybridization reveals the spatial arrangement of bacteria in sponge tissue; Manz W et al.; Widefield deconvolution epifluorescence microscopy (WDEM) combined with fluorescence in situ hybridization (FISH) was performed to identify and characterize single bacterial cells within sections of the mediterranean sponge Chondrosia reniformis . Sponges were embedded in paraffin wax or plastic prior to the preparation of thin sections, in situ hybridization and microscopy . Serial digital images generated by widefield epifluorescence microscopy were visualized using an exhaustive photon reassignment deconvolution algorithm and three-dimensional rendering software . Computer processing of series of images taken at different focal planes with the deconvolution technique provided deblurred three-dimensional images with high optical resolution on a submicron scale . Results from the deconvolution enhanced widefield microscopy were compared with conventional epifluorescent microscopical images . By the application of the deconvolution algorithm on digital image data obtained with widefield epifluorescence microscopy after FISH, the occurrence and spatial arrangement of Desulfovibrionaceae closely associated with micropores of Chondrosia reniformis could be visualized. J Magn Reson, 2000 Mar, 143(1), 24 - 9 Diffusion-weighted imaging of bacteria colonies in the STRAFI plane; Carlton KJ et al.; Imaging colonies of bacteria in water suspension using NMR requires that the water inside the bacteria can be differentiated from the surrounding water . This is commonly carried out by using diffusion-weighted pulsed field gradient techniques . However, it is also possible to use the diffusion sensitivity inherent in stray field imaging (STRAFI) . In STRAFI, the subject to be imaged is normally moved along the axis of a superconducting magnet so that it passes through the sensitive slice . However, by moving the sample in the transverse direction and by using a long copper strip in place of a surface induction coil, a diffusion-weighted one-dimensional projection profile can be obtained across the sensitive slice . Profiles from a water phantom and from a bacteria suspension show convincing discrimination between intracellular and extracellular water . Biochim Biophys Acta, 2000 Feb 24, 1457(1-2), 1 - 17 Escape probability and trapping mechanism in purple bacteria: revisited; Bernhardt K et al.; Despite intensive research for decades, the trapping mechanism in the core complex of purple bacteria is still under discussion . In this article, it is attempted to derive a conceptionally simple model that is consistent with all basic experimental observations and that allows definite conclusions on the trapping mechanism . Some experimental data reported in the literature are conflicting or incomplete . Therefore we repeated two already published experiments like the time-resolved fluorescence decay in LH1-only purple bacteria Rhodospirillum rubrum and Rhodopseudomonas viridis chromatophores with open and closed (Q(A)(-)) reaction centers . Furthermore, we measured fluorescence excitation spectra for both species under the two redox-conditions . These data, all measured at room temperature, were analyzed by a target analysis based on a three-state model (antenna, primary donor, and radical pair) . All states were allowed to react reversibly and their decay channels were taken into consideration . This leads to seven rate constants to be determined . It turns out that a unique set of numerical values of these rate constants can be found, when further experimental constraints are met simultaneously, i.e . the ratio of the fluorescence yields in the open and closed (Q(A)(-)) states F(m)/F(o) approximately 2 and the P(+)H(-)-recombination kinetics of 3-6 ns . The model allows to define and to quantify escape probabilities and the transfer equilibrium . We conclude that trapping in LH1-only purple bacteria is largely transfer-to-the-trap-limited . Furthermore, the model predicts properties of the reaction center (RC) in its native LH1-environment . Within the framework of our model, the predicted P(+)H(-)-recombination kinetics are nearly indistinguishable for a hypothetically isolated RC and an antenna-RC complex, which is in contrast to published experimental data for physically isolated RCs . Therefore RC preparations may display modified kinetic properties. Gene, 2000 Feb 22, 244(1-2), 151 - 61 The stachydrine catabolism region in Sinorhizobium meliloti encodes a multi-enzyme complex similar to the xenobiotic degrading systems in other bacteria; Burnet MW et al.; Stachydrine (proline betaine) can be used by Sinorhizobium meliloti as a source of carbon and nitrogen . Catabolism depends on an initial N-demethylation, after which the resultant N-methyl proline enters general metabolism . Deletion and insertion mutagenesis demonstrated that the information necessary for catabolism is carried on the symbiotic plasmid (pSym) distal to nodD2 and the nod-nif cluster . Sequencing of an 8.5kb fragment spanning this region revealed four open reading frames with functional homology to known proteins, including a putative monooxygenase and a putative NADPH-FMN-reductase, which were shown by insertional and frame-shift mutagenesis to be necessary for stachydrine catabolism . Other open reading frames, encoding a putative flavoprotein and a repressor, were judged not to be required for stachydrine catabolism, since they were not included in a fragment capable of complementing a deletion of the entire stc region . Sequence and mutagenesis data suggest that stachydrine is demethylated by an iron-sulfur monooxygenase of the Rieske type with a requirement for a specific reductase . The stc catabolic cluster, therefore, resembles xenobiotic degradation in other bacteria and recalls rhizopine catabolism in S . meliloti . Stachydrine appears to have multiple roles in osmoprotection, nutrition and nodulation . Genes involved in stachydrine catabolism are also necessary for carnitine degradation; thus, they could be important in the catabolism of a variety of root exudates and mediate other relationships. Bioessays, 2000 Mar, 22(3), 235 - 44 Degradation of mRNA in bacteria: emergence of ubiquitous features; Regnier P et al.; The amount of a messenger RNA available for protein synthesis depends on the efficiency of its transcription and stability . The mechanisms of degradation that determine the stability of mRNAs in bacteria have been investigated extensively during the last decade and have begun to be better understood . Several endo- and exoribonucleases involved in the mRNA metabolism have been characterized as well as structural features of mRNA which account for its stability have been determined . The most important recent developments have been the discovery that the degradosome-a multiprotein complex containing an endoribonuclease (RNase E), an exoribonuclease (polynucleotide phosphorylase), and a DEAD box helicase (RhlB)-has a central role in mRNA degradation and that oligo(A) tails synthesized by poly(A) polymerase facilitate the degradation of mRNAs and RNA fragments . Moreover, the phosphorylation status and the base pairing of 5' extremities, together with 3' secondary structures of transcriptional terminators, contribute to the stability of primary transcripts . Degradation of mRNAs can follow several independent pathways . Interestingly, poly(A) tails and multienzyme complexes also control the stability and the degradation of eukaryotic mRNAs . These discoveries have led to the development of refined models of mRNA degradation . Curr Opin Microbiol, 2000 Feb, 3(1), 73 - 8 Effector proteins of phytopathogenic bacteria: bifunctional signals in virulence and host recognition; Kjemtrup S et al.; Phytopathogenic bacteria deliver effectors of disease into plant hosts via a Type III secretion system . These Type III effectors have genetically determined roles in virulence . They also are among the components recognized by the putative receptors of the plant innate immune system . Recent breakthroughs include localization of some of these Type III effectors to specific host cell compartments, and the first dissection of pathogenicity islands that carry them. Biochem Biophys Res Commun, 2000 Feb 16, 268(2), 535 - 40 Genome-wide detection of unknown subtle mutations in bacteria by combination of MutS and RDA; Gotoh K et al.; We propose a procedure for detecting unknown, subtle DNA changes throughout the entire bacterial genome by a combination of MutS and RDA . Current techniques detect subtle mutations after PCR amplification of the target regions, so the mutation detection is done between amplified PCR fragments . In this paper, genome-wide subtle mutation scanning in bacteria was performed by combining the MutS and RDA techniques . Our strategy for cloning a small mutation region is composed of two steps: an enrichment of fragments containing subtle mutations using MutS, followed by an RDA subtraction procedure for further enrichment . We successfully identified small mutations such as a four-base insertion, a two-base insertion, and transition mutations in bacteria . Genes Dev, 2000 Feb 1, 14(3), 339 - 48 Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria; Tan Q et al.; We have identified a mutant in RPB3, the third-largest subunit of yeast RNA polymerase II, that is defective in activator-dependent transcription, but not defective in activator-independent, basal transcription . The mutant contains two amino-acid substitutions, C92R and A159G, that are both required for pronounced defects in activator-dependent transcription . Synthetic enhancement of phenotypes of C92R and A159G, and of several other pairs of substitutions, is consistent with a functional relationship between residues 92-95 and 159-161 . Homology modeling of RPB3 on the basis of the crystallographic structure of alphaNTD indicates that residues 92-95 and 159-162 are likely to be adjacent within the structure of RPB3 . In addition, homology modeling indicates that the location of residues 159-162 within RPB3 corresponds to the location of an activation target within alphaNTD (the target of activating region 2 of catabolite activator protein, an activation target involved in a protein-protein interaction that facilitates isomerization of the RNA polymerase promoter closed complex to the RNA polymerase promoter open complex) . The apparent finding of a conserved surface required for activation in eukaryotes and bacteria raises the possibility of conserved mechanisms of activation in eukaryotes and bacteria. Res Microbiol, 1999 Nov-Dec, 150(9-10), 665 - 74 Large genomic sequence repetitions in bacteria: lessons from rRNA operons and Rhs elements; Hill CW; The rrn operons and Rhs elements provide starkly contrasting examples of the evolution and interaction of large sequence repetitions in bacteria . Genomic sequencing of different species as well as comparative sequencing of independent isolates is providing provocative insights into previously obscure issues. J Infect Dis, 2000 Feb, 181(2), 671 - 80 Rapid neutrophil response controls fast-replicating intracellular bacteria but not slow-replicating Mycobacterium tuberculosis; Seiler P et al.; Being one of the first cells to invade the site of infection, neutrophils play an important role in the control of various bacterial and viral infections . In the present work, the contribution of neutrophils to the control of infection with different intracellular bacteria was investigated . Mice were treated with the neutrophil-depleting monoclonal antibody RB6-8C5, and the time course of infection in treated and untreated mice was compared by using intracellular bacterial species and strains varying in virulence and replication rate . The results indicate that neutrophils are crucial for the control of fast-replicating intracellular bacteria, whereas early neutrophil effector mechanisms are dispensable for the control of the slow-replicating Mycobacterium tuberculosis. Appl Environ Microbiol, 2000 Feb, 66(2), 820 - 4 In situ analysis of sulfate-reducing bacteria related to Desulfocapsa thiozymogenes in the chemocline of meromictic Lake Cadagno (Switzerland); Tonolla M et al.; Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) retrieved two clusters of sequences resembling sulfate-reducing bacteria within the family Desulfovibrionaceae . In situ hybridization showed that, similar to sulfate-reducing bacteria of the family Desulfobacteriaceae, bacteria of one cluster with similarity values to the closest cultured relatives of between 92.6 and 93.1% resembled free cells or cells loosely attached to other cells or debris . Bacteria of the second cluster closely related to Desulfocapsa thiozymogenes DSM7269 with similarity values between 97 . 9 and 98.4% were generally associated with aggregates of different small-celled phototrophic sulfur bacteria, suggesting a potential interaction between the two groups of bacteria. Biochemistry, 2000 Feb 8, 39(5), 1091 - 9 Exchanging cofactors in the core antennae from purple bacteria: structure and properties of Zn-bacteriopheophytin-containing LH1; Lapouge K et al.; The core light-harvesting LH1 complex of Rhodospirillum rubrum consists of an assembly of membrane-spanning alpha and beta polypeptides, each of which binds one bacteriochlorophyll (BChl) a molecule . In this work, we describe a technique that allows the replacement of the natural, Mg BChl a cofactors present in this protein by Zn-bacteriopheophytin (Zn-Bpheo) . This technique makes use of the well-characterized, reversible dissociation of LH1 induced by the detergent beta-octylglucoside . Incubation of partially dissociated LH1 with exogeneous pigments induces an equilibrium between the protein-bound BChl and the exogeneous pigment . This results in the binding of chemically modified pigments to LH1, in amounts which depend on the pigment composition and concentration of the exchange buffer . This method can yield information on the relative affinities of the LH1 protein-binding sites for the different pigments BChl and Zn-Bpheo and can also be used to obtain fully reassociated LH1 proteins, with a variable content of modified pigment, which may be precisely monitored . Absorption and FT-Raman spectroscopy indicate that this exchange procedure leads to LH1 proteins containing modified pigments, but retaining a binding site structure identical to that of native LH1 . Furthermore, examination of the binding curves suggests that there are two distinguishable binding sites, probably corresponding to the two polypeptides, with very different properties . One of these two binding sites shows a marked preference for Zn-Bpheo over BChl, while the other binding site appears to prefer BChl. Anaesthesia, 2000 Feb, 55(2), 173 - 6 The effect of facial hair and sex on the dispersal of bacteria below a masked subject; McLure HA et al.; Surgical face masks prevent the dispersal of bacteria from the upper airway to surfaces immediately in front of and below the face during talking . However, mask wiggling has been reported to increase dermabrasion and bacterial contamination of surfaces immediately below the face . Facial hair and recent shaving may alter the quantity of particles shed by dermabrasion when the mask is wiggled . We investigated the effect of mask wiggling in 10 bearded and 10 clean-shaven male subjects, and 10 female subjects . Wiggling the mask significantly increased the degree of bacterial shedding onto agar plates 15 cm below the lips in bearded males (p = 0.03) and females (p = 0.03), but not in clean-shaven males . At rest without mask wiggling the bearded subjects shed significantly more bacteria than clean-shaven males (p = 0.01) or females (p = 0.001) . To reduce the risks of contamination of the sterile field when face masks are worn females and bearded males should avoid wiggling the face mask . Bearded males may also consider removing their beards. Arch Microbiol, 2000 Jan, 173(1), 49 - 57 Two new arsenate/sulfate-reducing bacteria: mechanisms of arsenate reduction; Macy JM et al.; Two sulfate-reducing bacteria, which also reduce arsenate, were isolated; both organisms oxidized lactate incompletely to acetate . When using lactate as the electron donor, one of these organisms, Desulfomicrobium strain Ben-RB, rapidly reduced (doubling time = 8 h) 5.1 mM arsenate at the same time it reduced sulfate (9.6 mM) . Sulfate reduction was not inhibited by the presence of arsenate . Arsenate could act as the terminal electron acceptor in minimal medium (doubling time = 9 h) in the absence of sulfate . Arsenate was reduced by a membrane-bound enzyme that is either a c-type cytochrome or is associated with such a cytochrome; benzyl-viologen-dependent arsenate reductase activity was greater in cells grown with arsenate/sulfate than in cells grown with sulfate only . The second organism, Desulfovibrio strain Ben-RA, also grew (doubling time = 8 h) while reducing arsenate (3.1 mM) and sulfate (8.3 mM) concomitantly . No evidence was found, however, that this organism is able to grow using arsenate as the terminal electron acceptor . Instead, it appears that arsenate reduction by the Desulfovibrio strain Ben-RA is catalyzed by an arsenate reductase that is encoded by a chromosomally-borne gene shown to be homologous to the arsC gene of the Escherichia coli plasmid, R773 ars system. J Biomed Sci, 2000 Jan-Feb, 7(1), 42 - 50 Receptor-mediated endocytosis as a selection force to enrich bacteria expressing rhodostomin on their surface; Chang HH et al.; Previously, we developed a TraT display system to express snake venom rhodostomin (RHO), a disintegrin, on the external surface of Escherichia coli {J Biomed Sci 6:64-70;1999} . To show a new potential use of the TraT display system, we employed a biotin labeling technique coupled with SDS-PAGE and flow cytometry analyses to further demonstrate and confirm the expression of TraT-RHO on the E . coli surface . We also showed that the expression of TraT-RHO on the cell surface not only facilitated the bacteria adhesion to BHK-21 cells but also induced bacterial internalization into BHK-21 cells . This feature allowed us to enrich the TraT-RHO expression bacteria about 10,000-fold starting with a mixture of TraT-RHO bacteria with beta-galactosidase-positive bacteria in a ratio of 10(2):10(7) through four cycles of BHK-21 cell endocytosis and replating of engulfed bacteria on agar plates . We therefore suggest that the TraT display system can be applied to select out bacteria expressing a specific peptide sequence from a large population of display library through the process of receptor-mediated endocytosis and reamplification cycles . J Gen Virol, 2000 Jan, 81(Pt 1), 267 - 72 Virus-like particles assemble in plants and bacteria expressing the coat protein gene of Indian peanut clump virus; Bragard C et al.; cDNA copies of the coat protein (CP) gene of Indian peanut clump virus (IPCV)-H were introduced into cells of Nicotiana benthamiana or Escherichia coli by transformation with vectors based on pROKII or pET respectively . In both plant and bacterial cells, IPCV CP was expressed and assembled to form virus-like particles (VLP) . In plant extracts, the smallest preponderant particle length was about 50 nm . Other abundant lengths were about 85 and about 120 nm . The commonest VLP length in bacterial extracts was about 30 nm . Many of the longer VLP appeared to comprise aggregates of shorter particles . The lengths of the supposed 'monomer' VLP corresponded approximately to those expected for encapsidated CP gene transcript RNA . Immunocapture RT-PCR, using primers designed to amplify the CP gene, confirmed that the VLP contained RNA encoding IPCV-H CP . The results show that encapsidation does not require the presence of the 5'-terminal untranslated sequence of the virus RNA and suggest that if there is an 'origin of assembly' motif or sequence, it lies within the CP gene . When transgenic plants expressing IPCV-H CP were inoculated with IPCV-L, a strain that is serologically distinct from IPCV-H, the virus particles that accumulated contained both types of CP. FEMS Microbiol Ecol, 2000 Feb 1, 31(2), 107 - 115 A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints; Ranjard L et al.; The short term impact of 50 microM Hg(II) on soil bacterial community structure was evaluated in different microenvironments of a silt loam soil in order to determine the contribution of bacteria located in these microenvironments to the overall bacterial response to mercury spiking . Microenvironments and associated bacteria, designated as bacterial pools, were obtained by successive soil washes to separate the outer fraction, containing loosely associated bacteria, and the inner fraction, containing bacteria retained into aggregates, followed by a physical fractionation of the inner fraction to separate aggregates according to their size (size fractions) . Indirect enumerations of viable heterotrophic (VH) and resistant (Hg(R)) bacteria were performed before and 30 days after mercury spiking . A ribosomal intergenic spacer analysis (RISA), combined with multivariate analysis, was used to compare modifications at the community level in the unfractionated soil and in the microenvironments . The spatial heterogeneity of the mercury impact was revealed by a higher increase of Hg(R) numbers in the outer fraction and in the coarse size fractions . Furthermore, shifts in RISA patterns of total community DNA indicated changes in the composition of the dominant bacterial populations in response to Hg(II) stress in the outer and in the clay size fractions . The heterogeneity of metal impact on indigenous bacteria, observed at a microscale level, is related to both the physical and chemical characteristics of the soil microenvironments governing mercury bioavailability and to the bacterial composition present before spiking. Res Commun Mol Pathol Pharmacol, 1999, 104(2), 205 - 18 Involvement of apoptosis in activation-induced cell death of bacteria-reactive human CD45RO+ T cells; Kodera M et al.; Although the identity of the T cells that protect against bacteria in humans remains unknown, it is clear that patients with bacterial infection have reduced numbers of T cells in their blood . Here we have determined whether this T cell loss is a consequence of bacterial antigen-mediated activation-induced cell death (AICD) . By flowcytometric analysis, less than 0.3% of freshly isolated T cells from healthy volunteers and patients with severe pneumonia were identified as apoptotic . However, during culture the rate of apoptosis in peripheral blood T cells from patients was 3.0 +/- 0.9%; and increased further in the presence of anti-CD3 (7.4 +/- 2.1%) and decreased when IL-2 was added (4.4 +/- 1.3%) . In contrast, no changes were observed in healthy volunteers on addition of anti-CD3 . Further, anti-CD3 significantly increased the susceptibility to apoptosis of CD45RO+ T cells, but not CD45RA+ T cells from patients, and the percentage of CD45RO+ T cells in patients was significantly higher than that in healthy volunteers . Flowcytometric analysis revealed the expression level of Fas to be higher in the patients than healthy volunteers . Collectively, these findings demonstrated that bacteria-reactive T cells were more susceptible to AICD and that Fas-FasL pathways of apoptosis were involved . AICD of CD45RO+ T cells, therefore, provides an explanation for the loss of bacteria-reactive T cells during bacterial infection. Nat Biotechnol, 2000 Jan, 18(1), 75 - 80 Exploiting recombination in single bacteria to make large phage antibody libraries; Sblattero D et al.; The creation of large phage antibody libraries has become an important goal in selecting antibodies against any antigen . Here we describe a method for making libraries so large that the complete diversity cannot be accessed using traditional phage technology . This involves the creation of a primary phage scFv library in a phagemid vector containing two nonhomologous lox sites . Contrary to the current dogma, we found that infecting Cre recombinase-expressing bacteria by such a primary library at a high multiplicity of infection results in the entry of many different phagemid into the cell . Exchange of Vh and Vl genes between such phagemids creates many new V h/Vl combinations, all of which are functional . On the basis of the observed recombination, the library is calculated to have a diversity of 3x1011 . A library created using this method was validated by the selection of high affinity antibodies against a large number of different protein antigens. Res Microbiol, 2000 Nov, 151(9), 711 - 20 Genetic systems for analyzing protein-protein interactions in bacteria; Ladant D et al.; Analysis of protein-protein interactions has been revolutionized by the yeast two-hybrid system introduced by Fields and coworkers . In recent years, similar genetic assays have been developed in bacteria . We describe here several of these systems and highlight some potential applications of these technologies. Nucleic Acids Res, 2001 Jan 1, 29(1), 344 - 5 ICB database: the gyrB database for identification and classification of bacteria; Watanabe K et al.; The Identification and Classification of Bacteria (ICB) database contains currently available information about the DNA gyrase subunit B (gyrB) gene in bacteria . The database is designed to provide the scientific community with a reference point for using gyrB as an evolutionary and taxonomic marker . Nucleic and amino acid sequence data are currently available for over 850 strains, along with alignments at several different taxonomic levels and an exhaustive review of primer selection and background information. Genetics, 2000 Jan, 154(1), 49 - 59 Some features of the mutability of bacteria during nonlethal selection; Godoy VG et al.; We describe the mutability of the Trp(-) chromosomal +1 frameshift mutation trpE7999 during nonlethal selection, finding that the appearance of Trp(+) revertants behaves similarly to that of episomal Lac(+) revertants . In addition, we show that a feature of the Lac(+) and Trp(+) mutability is the accumulation of Trp(+) and Lac(+) revertants with additional unselected mutations, most of which are not due to heritable mutators . The cells undergoing nonlethal selection apparently experience an epigenetic change resulting in a subset of bacteria with elevated mutability that often remain hypermutable for the duration of selection . The epigenetic change provoked by nonlethal selection appears to be mediated by a unique function provided by the F'128 episome. Biochemistry, 1999 Nov 30, 38(48), 15827 - 39 Physicochemical aspects of the movement of the rieske iron sulfur protein during quinol oxidation by the bc(1) complex from mitochondria and photosynthetic bacteria; Crofts AR et al.; Crystallographic structures for the mitochondrial ubihydroquinone:cytochrome c oxidoreductase (bc(1) complex) from different sources, and with different inhibitors in cocrystals, have revealed that the extrinsic domain of the iron sulfur subunit is not fixed {Zhang, Z., Huang, L., Shulmeister, V . M., Chi, Y.-I., Kim, K . K., Hung, L.-W., Crofts, A . R., Berry, E . A., and Kim, S.-H . (1998) Nature (London), 392, 677-684}, but moves between reaction domains on cytochrome c(1) and cytochrome b subunits . We have suggested that the movement is necessary for quinol oxidation at the Q(o) site of the complex . In this paper, we show that the electron-transfer reactions of the high-potential chain of the complex, including oxidation of the iron sulfur protein by cytochrome c(1) and the reactions by which oxidizing equivalents become available at the Q(o) site, are rapid compared to the rate-determining step . Activation energies of partial reactions that contribute to movement of the iron sulfur protein have been measured and shown to be lower than the high activation barrier associated with quinol oxidation . We conclude that the movement is not the source of the activation barrier . We estimate the occupancies of different positions for the iron sulfur protein from the crystallographic electron densities and discuss the parameters determining the binding of the iron sulfur protein in different configurations . The low activation barrier is consistent with a movement between these locations through a constrained diffusion . Apart from ligation in enzyme-substrate or inhibitor complexes, the binding forces in the native structure are likely to be < = RT, suggesting that the mobile head can explore the reaction interfaces through stochastic processes within the time scale indicated by kinetic measurements. Kansenshogaku Zasshi, 1999 Nov, 73(11), 1140 - 4 {Study on the verotoxin-producing Escherichia coli--isolation of the bacteria from deer dung}; Fukuyama M et al.; To identify the source and route of verotoxin-producing Escherichia coli (VTEC) infection in humans, we tried to isolate VTEC from fresh deer dung collected from free-range animals in two parks during the period from August 1997 to January 1998 . The results are presented below . 1) VTEC were isolated from 21 of 200 deer dung samples (10.5%), consisting of 15 of 100 samples (15.0%) collected in park A and 6 of 100 samples (6.0%) collected in park B, suggesting that the incidence of VTEC isolation differs depending on location . 2) With respect to typing of verotoxin, the 21 isolated VTEC strains consisted of 10 strains (47.6%) as VT1 producer, 5 strains (23.8%) as VT2 producer, and 6 strains (28.6%) as double producer of both types . 3) With respect to serogroup of the isolated VTEC strains, 2 strains belonged to O128:H2.1 strain each belonged to the O8:H10, O128:H12, and O169:HUT groups . The remaining 16 strains failed to be identified as particular serotypes . Regarding local distribution of the serotype, in park A, 1 strain each belonged to the O128:H2, O8:H10, and O169:HUT groups . The remaining 12 strains did not clearly show particular serotypes . In park B, 2 strains belonged to O128:H2, and 4 strains failed to show particular serotypes . The remaining 1 strains showed autoagglutination . In conclusion, we isolated VTEC strains from deer that showed types of toxin and serogroups identical to those of human VTEC . Therefore, VTEC found in deer dung could well be a source of VTEC-infectious diseases in humans. Mikrobiologiia, 1999 Sep-Oct, 68(5), 632 - 46 {Horizontal gene transfer in bacteria: laboratory simulation, natural populations, genomic data}; Prozorov AA; Various aspects of horizontal gene transfer among bacteria are considered: modeling of this phenomenon in microcosms and natural environments; influence of gene migration on the composition of natural bacterial populations; peculiarities of bacterial chromosome evolution. FEMS Microbiol Lett, 2000 Jan 15, 182(2), 291 - 6 Stress induced phosphate solubilization in bacteria isolated from alkaline soils; Nautiyal CS et al.; Phosphate solubilizing bacteria NBRI0603, NBRI2601, NBRI3246 and NBRI4003 were isolated from the rhizosphere of chickpea and alkaline soils . All four strains demonstrated diverse levels of phosphate solubilization activity under in vitro conditions in the presence of various carbon and nitrogen sources . Acid production may have contributed to phosphate solubilization, but was not the only reason for phosphate release into the medium . Among the four strains, NBRI2601 was the most efficient strain in terms of its capability to solubilize phosphorus in the presence of 10% salt, pH 12, or 45 degrees C . The strains showed varied levels of phosphate solubilization when the effects of different sources of nitrogen were examined during growth . The presence of low levels of Ca(2+) and EDTA in the medium enhanced phosphate solubilization. FEMS Microbiol Ecol, 2000 Jan 1, 31(1), 29 - 38 Fluorescent oligonucleotide rDNA probes for specific detection of methane oxidising bacteria; Bourne DG et al.; Oligonucleotide probes targeting the 16S rRNA of distinct phylogenetic groups of methanotrophs were designed for the in situ detection of these organisms . A probe, MG-64, detected specifically type I methanotrophs, while probes MA-221 and MA-621, detected type II methanotrophs in whole cell hybridisations . A probe Mc1029 was also designed which targeted only organisms from the Methylococcus genus after whole cell hybridisations . All probes were labelled with the fluorochrome Cy3 and optimum conditions for hybridisation were determined . Non-specific target sites of the type I (MG-64) and type II (MA-621) probes to non-methanotrophic organisms are highlighted . The probes are however used in studying enrichment cultures and environments where selective pressure favours the growth of methanotrophs over other organisms . The application of these probes was demonstrated in the detection of type I methanotrophs with the MG-64 probe in an enrichment culture from an estuarine sample demonstrating methane oxidation . The detection of type I methanotrophs was confirmed by a 16S rDNA molecular analysis of the estuarine enrichment culture which demonstrated that the most abundant bacterial clone type in the 16S rDNA library was most closely related to Methylobacter sp . strain BB5.1, a type I methanotroph also isolated from an estuarine environment. Arch Biochem Biophys, 2000 Jan 1, 373(1), 1 - 6 Iron and oxidative stress in bacteria; Touati D; The appearance of oxygen on earth led to two major problems: the production of potentially deleterious reactive oxygen species and a drastic decrease in iron availability . In addition, iron, in its reduced form, potentiates oxygen toxicity by converting, via the Fenton reaction, the less reactive hydrogen peroxide to the more reactive oxygen species, hydroxyl radical and ferryl iron . Conversely superoxide, by releasing iron from iron-containing molecules, favors the Fenton reaction . It has been assumed that the strict regulation of iron assimilation prevents an excess of free intracellular iron that could lead to oxidative stress . Studies in bacteria supporting that view are reviewed . While genetic studies correlate oxidative stress with increase of intracellular free iron, there are only few and sometimes contradictory studies on direct measurements of free intracellular metal . Despite this weakness, the strict regulation of iron metabolism, and its coupling with regulation of defenses against oxidative stress, as well as the role played by iron in regulatory protein in sensing redox change, appear as essential factors for life in the presence of oxygen . J Hum Hypertens, 1999 Dec, 13(12), 845 - 8 Manipulating large genomic clones via in vivo recombination in bacteria; Payne CM et al.; Transgenesis is proving to be a powerful technique in studying the molecular genetics of hypertension . The ability to target specific mutations resulting in either loss of function, by gene deletion, the insertion of reporter sequences, or the subtle change of function by nucleotide replacement, can facilitate the understanding of gene function and its role in the manifestation of diseases . However an inherent problem associated with transgenic studies is the lack of consistent expression observed between independent lines of animals which have integrated the same transgene, a phenomenon known as 'position effect' . Small transgenes are almost invariably subject to position effect due to the absence of essential regulatory elements required to maintain an open chromatin structure . This phenomenon may be overcome if larger transgenes, isolated using vectors such as yeast artifical chromosomes (YACs), bacterial artificial chromosomes (BACs) or P1-based vectors, are used . Studies using such transgenes have reported levels of expression which are consistent between lines and dependent upon the number of copies integrated . The introduction of modifications into these large genomic clones is not practical by traditional restriction endonuclease strategies and so is dependent upon in vivo recombination to maintain structural integrity . Here we demonstrate the modification of a 100 Kb P1 clone spanning the renin locus using the BAC targeting strategy described by Yang et al (Nat Biotechnol 1997; 15: 859-865). Methods, 2000 Jan, 20(1), 18 - 34 Allele-specific suppression as a tool to study protein-protein interactions in bacteria; Manson MD; Suppression analysis is well suited to study the interactions of gene products . It offers the advantage of simplicity for any organism for which a convenient genetic system has been developed, which holds for a wide spectrum of bacteria and an ever-increasing number of unicellular as well as complex eukaryotes . No other method provides as much information about the functional relationships of biological macromolecules . The intrinsic value of suppression analysis is enhanced by advances in genomics and in biophysical techniques for investigating the properties of nucleic acids and proteins, such as X-ray crystallography, liquid and solid-state nuclear magnetic resonance, electron spin labeling, and isothermal calorimetry . These approaches confirm and complement whatever is revealed by genetics . Despite these sterling qualities, suppression analysis has its dangers, less in execution than in conceptualization of experiments and interpretation of data . A consistent nomenclature is essential for a uniform and widespread understanding of the results . Familiarity with the genetic background and idiosyncracies of the organism studied is critical in avoiding extraneous phenomena that can affect the outcome . Finally, it is imperative not to underestimate potentially bizarre and improbable consequences that can transpire when rigorous genetic selection is maintained for an appreciable length of time . The article begins with a somewhat pedagogical discussion of genetic terminology . It then moves on to the necessary precautions to observe while planning and conducting suppression analysis . The remainder of the article considers different manifestations of suppression: bypass suppression; gradients of suppression; suppression by relaxed specificity; allele-specific "suppression at a distance"; and true conformational suppression . The treatment is not exhaustive, but representative examples have been gleaned from the recent bacterial literature . Biochim Biophys Acta, 2000 Jan 3, 1476(1), 85 - 92 A sequential electron transfer from hydrogenases to cytochromes in sulfate-reducing bacteria; Aubert C et al.; A central step in the energy metabolism of sulfate-reducing bacteria is the oxidation of molecular hydrogen, catalyzed by a periplasmic hydrogenase . The resulting electrons are then transferred to various electron transport chains and used for cytoplasmic sulfate reduction . The complex formation between {NiFeSe} hydrogenase and the soluble periplasmic polyheme cytochromes from Desulfomicrobium norvegicum was characterized by cross-linking experiments, BIAcore and kinetics analysis . Analysis of electron transfer between {NiFeSe} hydrogenase and octaheme cytochrome c(3) (M(r) 26 inverted question mark omitted inverted question mark000) pointed out that this cytochrome is reduced faster in the presence of catalytic amounts of tetraheme cytochrome c(3) (M(r) 13 inverted question mark omitted inverted question mark000) isolated from the same organism . The activation of the hydrogenase-dependent reduction of polyheme cytochromes by cytochrome c(3) (M(r) 13 inverted question mark omitted inverted question mark000), which is now described in both Desulfovibrio and Desulfomicrobium, is proposed as a general mechanism . During this process, cytochrome c(3) (M(r) 13 inverted question mark omitted inverted question mark000) would act as an electron shuttle in between hydrogenase and the polyheme cytochromes and its conductivity appears to be an important factor. Zentralbl Veterinarmed A, 1999 Nov, 46(9), 533 - 43 Experimental actinomycosis caused by Actinomyces-like bacteria in mice and a sow; Murakami S et al.; The present experiment was performed to test the pathogenicity of Actinomyces-like bacteria in experimental animals and swine . Two rough (R) strains of Actinomyces-like bacteria isolated from a site of arthritis and from the tonsil in pigs were used as inocula . To investigate their susceptibility to Actinomyces-like bacteria, BALB/c, SS and ddY mice and guinea-pigs were inoculated intraperitoneally with the strains of Actinomyces-like bacteria . The ddY mice were used for the long-term observation of Actinomyces-like bacteria lesions and the mammary tissue of a sow was inoculated with Actinomyces-like bacteria isolated from swine tonsil . Macroscopic observation revealed many abscesses on the surfaces of the abdominal and/or thoracic organs in the mice, but not on those of the guinea-pigs . The sow developed firm nodules at the inoculation site in the mammary glands . Histopathologically, the lesions in the mice were characterized as actinomycotic abscesses in the early stage and as pus-forming granuloma (PFG) in the advanced stage; the lesions were accompanied by crystalloid particles . Actinomyces-like bacteria induced granulomatous mastitis in the sow, and the lesion was characterized as PFG . The characteristic actinomycotic lesions in swine mammary glands were reproduced by experimental infection. Protein Expr Purif, 1999 Dec, 17(3), 392 - 400 Expression of a recombinant Toxoplasma gondii ROP2 fragment as a fusion protein in bacteria circumvents insolubility and proteolytic degradation; Jacquet A et al.; A 268-amino-acid-residue carboxy-terminal antigenic fragment of the Toxoplasma gondii rhoptry protein ROP2 (recROP2(t), residues 196-464) was expressed in Escherichia coli . This recombinant fragment was produced at low concentration and in a highly insoluble form . By contrast, the level of recROP2(t) production was drastically greater when the same coding sequence was fused to the C-terminus of thioredoxin (TRX) or to the maltose-binding protein (MBP) gene . While both fusion proteins were found to be mainly insoluble, solubilization could be achieved without significant degradation . MBP was more efficient than TRX in increasing the recovery of soluble protein with more than 10% of total MBP-recROP2(t) being readily expressed in a soluble form . Moreover, the insoluble form of MBP-recROP2(t) could be correctly refolded with a recovery of more than 80% . Both forms of MBP-recROP2(t) were purified to homogeneity by amylose chromatography . In contrast, the refolding of TRX-recROP2(t) promoted aggregation of the protein, which was prevented by the use of zwitterionic detergent during the one-step purification by gel filtration . Subsequent proteolytic cleavages of purified TRX-recROP2(t) and of MBP-recROP2(t) led respectively to the complete degradation or to the truncation of the recROP2(t) moiety . However, recROP2(t), despite the presence of the fusion partners, adopted a suitable conformation recognized by human serum-derived antibodies from T . gondii-seropositive individuals . Finally, both fusion proteins were able to induce specific humoral and cell-mediated immune response to the ROP2 fragment . Such fusions could represent an alternative to study the immunogenicity of T . gondii proteins which are difficult to produce because of insolubility and degradation . J Clin Periodontol, 1999 Dec, 26(12), 814 - 21 The prevalence of BANA-hydrolyzing periodontopathic bacteria in smokers; Kazor C et al.; Smoking has been identified as a risk factor for development of periodontal disease and a strong indicator for treatment failure in periodontal patients . This study examined 172 patients categorized as current smokers (n=55), previous smokers (n=38) or individuals that had never smoked (n=79) . A total of 670 interproximal plaques collected with a wooden toothpick were analyzed for hydrolysis of the synthetic trypsin substrate benzoyl-DL-arginine naphthylamide (BANA) . About 95% of the BANA hydrolysis by plaque is due to the presence of one or more of the periodontopathogens, P . gingivalis, T . denticola or B . forsythus . Gingival health was measured using the papillary bleeding score (PBS) . Current smokers had less gingival bleeding than previous smokers or those who had never smoked (20% versus 41% and 25%, respectively) . Plaque removed from non-bleeding sites in current smokers were 11x more likely to have a positive BANA reaction when compared to plaque removed from non-bleeding sites in individuals who never smoked . A significant positive relationship exists between smoking and colonization by the BANA periodontopathogens . Smoking may select for these periodontopathic species in the plaque and may be one reason why smoking is a risk factor in periodontal disease development. Am J Pathol, 1999 Dec, 155(6), 2145 - 52 Interleukin-1 and tumor necrosis factor receptor signaling is not required for bacteria-induced osteoclastogenesis and bone loss but is essential for protecting the host from a mixed anaerobic infection; Chen CP et al.; Bacterial infection causes significant morbidity, mediated in part by the up-regulation of inflammatory cytokines . Cytokine induction is thought to stimulate osteolysis in conditions such as periodontal disease and otitis media . To establish the relative importance of interleukin-1 (IL-1) and tumor necrosis factor (TNF) in mediating the response to a mixed anaerobic infection, we used an in vivo model in which the dental pulp was inoculated with six anaerobic pathogens, in mice with functional deletions of receptors to IL-1 (IL-1RI(-/-)), TNF (TNFRp55(-/-)-p75(-/-)), or both (TNFRp55(-/-)-IL-1RI(-/-)) . Polymorphonuclear and mononuclear phagocyte recruitment occurred to the greatest extent in TNFRp55(-/-)-IL-1RI(-/-) mice, and to a lesser extent in IL-1RI(-/-) or TNFRp55(-/-)-p75(-/-) mice, and the least in wild-type mice, demonstrating that recruitment of these phagocytes is not dependent on IL-1 or TNF receptor signaling . A similar pattern was observed for bacterial penetration into host tissue . Because it had recently been reported that TNF played a critical role in mediating lipopolysaccharide-induced bone loss, we anticipated that mice with targeted deletions of TNFRp55(-/-) would have reduced osteoclastogenesis . Surprisingly, osteolytic lesion formation was greatest in animals lacking TNF and/or IL-1 receptors . These results indicate that IL-1 or TNF receptor signaling is not required for bacteria-induced osteoclastogenesis and bone loss, but does play a critical role in protecting the host against mixed anaerobic infections. Zhonghua Min Guo Wei Sheng Wu Ji Mian Yi Xue Za Zhi, 1996 Nov, 29(4), 232 - 9 {The development of shrimp blood agar for testing the hemolysis of shrimp's haemocyte by bacteria}; Chang CI et al.; A new plating medium, shrimp blood agar, was developed by using the haemolymph of shrimp plus 200 ppm rose bengal as the substrate . The colorless shrimp haemocytes were dyed by rose bengal to red . On the present agar, the hemolytic bacteria strain may show a clear zone surrounding the bacterial colony . The result on hemolysis of 45 bacteria representing 12 genera isolated from aquaculture environments against shrimp blood agar and sheep blood agar was also evaluated . There are 11 strains with different results . The study showed that, with the aim of screening the hemolytic bacteria to shrimp, shrimp blood agar might reveal a relatively quick and accurate results than that of sheep blood agar. Biochem J, 1999 Dec 15, 344 Pt 3, 633 - 42 Polyamine transport in bacteria and yeast; Igarashi K et al.; The polyamine content of cells is regulated by biosynthesis, degradation and transport . In Escherichia coli, the genes for three different polyamine transport systems have been cloned and characterized . Two uptake systems (putrescine-specific and spermidine-preferential) were ABC transporters, each consisting of a periplasmic substrate-binding protein, two transmembrane proteins and a membrane-associated ATPase . The crystal structures of the substrate-binding proteins (PotD and PotF) have been solved . They consist of two domains with an alternating beta-alpha-beta topology, similar to other periplasmic binding proteins . The polyamine-binding site is in a cleft between the two domains, as determined by crystallography and site-directed mutagenesis . Polyamines are mainly recognized by aspartic acid and glutamic acid residues, which interact with the NH(2)- (or NH-) groups, and by tryptophan and tyrosine residues that have hydrophobic interactions with the methylene groups of polyamines . The precursor of one of the substrate binding proteins, PotD, negatively regulates transcription of the operon for the spermidine-preferential uptake system, thus providing another level of regulation of cellular polyamines . The third transport system, catalysed by PotE, mediates both uptake and excretion of putrescine . Uptake of putrescine is dependent on membrane potential, whereas excretion involves an exchange reaction between putrescine and ornithine . In Saccharomyces cerevisiae, the gene for a polyamine transport protein (TPO1) was identified . The properties of this protein are similar to those of PotE, and TPO1 is located on the vacuolar membrane. Biochim Biophys Acta, 1999 Dec 6, 1473(1), 108 - 22 Physiological aspects of chitin catabolism in marine bacteria; Keyhani NO et al.; Chitin, a carbohydrate polymer composed of alternating beta-1, 4-linked N-acetylglucosamine residues is the second most abundant organic compound in nature . In the aquatic biosphere alone, it is estimated that more than 10(11) metric tons of chitin are produced annually . If this enormous quantity of insoluble carbon and nitrogen was not converted to biologically useful material, the oceans would be depleted of these elements in a matter of decades . In fact, marine sediments contain only traces of chitin, and the turnover of the polysaccharide is attributed primarily to marine bacteria, but the overall process involves many steps, most of which remain to be elucidated . Marine bacteria possess complex signal transduction systems for: (1) finding chitin, (2) adhering to chitinaceous substrata, (3) degrading the chitin to oligosaccharides, (4) transporting the oligosaccharides to the cytoplasm, and (5) catabolizing the transport products to fructose-6-P, acetate and NH(3) . The proteins and enzymes are located extracellularly, in the cell envelope, the periplasmic space, the inner membrane and the cytoplasm . In addition to these levels of complexity, the various components of these systems appear to be carefully coordinated by intricate regulatory mechanisms. Mikrobiologiia, 1999 Jul-Aug, 68(4), 547 - 56 {Diversity of bacteria at various depths in the southern part of lake Baikal as detected by 16S rRNA sequencing}; Denisova LIa et al.; Phylogenetic analysis of the bacterial community inhabiting the water of Lake Baikal was performed on the basis of 16S rRNA sequencing . The composition of the bacterial community was shown to vary significantly with depth . Cyanobacteria were dominant species at the surface of the lake . At a moderate depth (400 m), actinomycete relatives were most abundant . At a great depth and near the bottom, the community was composed mainly of proteobacteria and cyanobacteria (the latter are probably brought from the surface layers by vertical near-shore water fluxes) . Most of the bacterial 16S rRNA sequences detected exhibited low similarity to those known and formed separate clusters in the phylogenetic tree, which may indicate the endemic nature of the corresponding bacteria. Biotechniques, 1999 Nov, 27(5), 966 - 70, 972 RT-PCR: characterization of long multi-gene operons and multiple transcript gene clusters in bacteria; Gupta A; Reverse transcription (RT)-PCR is a valuable tool widely used for analysis of gene expression . In bacteria, RT-PCR is helpful beyond standard protocols of northern blot RNA/DNA hybridization (to identify transcripts) and primer extension (to locate their start points), as these methods have been difficult with transcripts that are low in abundance or unstable, similar to long multi-gene operons . In this report, RT-PCR is adapted to analyze transcripts that form long multi-gene operons--where they start and where they stop . The transcripts can also be semiquantitated to follow the expression of genes under different growth conditions . Examples using RT-PCR are presented with two different multi-gene systems for metal cation resistance to silver and mercury ions . The silver resistance system {9 open reading frames (ORFs); 12.5 kb} is shown by RT-PCR to synthesize three nonoverlapping messenger RNAs that are transcribed divergently . In the mercury resistance system (8 ORFs; 6.3 kb), all the genes are transcribed in the same orientation, and two promoter sites produce overlapping transcripts . For RT-PCR, reverse transcriptase enzyme is used to synthesize first-strand cDNA that is used as a template for PCR amplification of single-gene products, from the beginning, middle or end of long multi-gene, multi-transcript gene clusters. Ecotoxicol Environ Saf, 1999 Oct, 44(2), 182 - 9 Usefulness of the sensitivity-resistance index to estimate the toxicity of copper on bacteria in copper-contaminated soils; Kunito T et al.; Examination was made of the fluctuations of numbers of the total bacteria and copper (Cu)-resistant bacteria with soluble/exchangeable Cu (Ex-Cu) fraction in three types of soils spiked with Cu at four concentrations . Drastic increase in Cu-resistant bacteria was observed in three soils spiked with 20 mmol Cu kg(-1) after 2 weeks of incubation, indicating the strong selection of individuals originally resistant to Cu . Adaptation and proliferation of bacteria were also observed in the soil environment under the long-term exposure to extremely high concentration of Cu (800 mg kg(-1) soil of Ex-Cu), deriving from the development of Cu resistance . These bacterial fluctuations and the toxic effects of Cu depended on soil types, due to the chemical forms in which Cu occurs . It was also found that the ratio of Cu-resistant bacterial number to total bacteria was significantly correlated with the amount of Ex-Cu in the soils . This sensitivity-resistance index seems to be useful for evaluating the toxic effects of Cu on the soil bacterial community . Whereas the toxicity of Cu depended on the soil properties, they also changed with time . This phenomenon can be explained by the decrease in the most labile Cu phase, Ex-Cu, with time in the soils. FEMS Microbiol Lett, 1999 Nov 15, 180(2), 317 - 24 Genes involved in hydrogen and sulfur metabolism in phototrophic sulfur bacteria; Dahl C et al.; The dsr genes and the hydSL operon are present as separate entities in phototrophic sulfur oxidizers of the genera Allochromatium, Marichromatium, Thiocapsa and Thiocystis and are organized similarly as in Allochromatium vinosum and Thiocapsa roseopersicina, respectively . The dsrA gene, encoding the alpha subunit of 'reverse' siroheme sulfite reductase, is also present in two species of green sulfur bacteria pointing to an important and universal role of this enzyme and probably other proteins encoded in the dsr locus in the oxidation of stored sulfur by phototrophic bacteria . The hupSL genes are uniformly present in the members of the Chromatiaceae family tested . The two genes between hydS and hydL encode a membrane-bound b-type cytochrome and a soluble iron-sulfur protein, respectively, resembling subunits of heterodisulfide reductase from methanogenic archaea . These genes are similar but not identical to dsrM and dsrK, indicating that the derived proteins have distinct functions, the former in hydrogen metabolism and the latter in oxidative sulfur metabolism. Nucleic Acids Res, 1999 Dec 1, 27(23), 4570 - 6 Drunken-cell footprints: nuclease treatment of ethanol-permeabilized bacteria reveals an initiation-like nucleoprotein complex in stationary phase replication origins; Cassler MR et al.; The nucleoprotein complex formed on oriC, the Escherichia coli replication origin, is dynamic . During the cell cycle, high levels of the initiator DnaA and a bending protein, IHF, bind to oriC at the time of initiation of DNA replication, while binding of Fis, another bending protein, is reduced . In order to probe the structure of nucleoprotein complexes at oriC in more detail, we have developed an in situ footprinting method, termed drunken-cell footprinting, that allows enzymatic DNA modifying reagents access to intracellular nucleoprotein complexes in E.coli, after a brief exposure to ethanol . With this method, we observed in situ binding of Fis to oriC in exponentially growing cells, and binding of IHF to oriC in stationary cells, using DNase I and Bst NI endonuclease, respectively . Increased binding of DnaA to oriC in stationary phase was also noted . Because binding of DnaA and IHF results in unwinding of oriC in vitro, P1 endonuclease was used to probe for intracellular unwinding of oriC . P1 cleavage sites, localized within the 13mer unwinding region of oriC ', were dramatically enhanced in stationary phase on wild-type origins, but not on mutant versions of oriC unable to unwind . These observations suggest that most oriC copies become unwound during stationary phase, forming an initiation-like nucleoprotein complex. C R Acad Sci III, 1999 Sep, 322(9), 779 - 84 Does storage affect epifluorescence microscopic counts of total bacteria in freshwater samples? Garabetian F, Petit M, Lavandier P. Preservation with formalin and storage at 4 degrees C of freshwater samples, associated with sonication before counting, proved to be efficient for a few days of storage (no differences with the initial cell count within 7 d of storage); after 8 months, 95% of the initial count was preserved . This procedure always gave higher counts than those obtained from the freezing technique of filter storage at -18 degrees C after sample filtration. Appl Environ Microbiol, 1999 Nov, 65(11), 5100 - 6 Substrate uptake by uncultured bacteria from the genus Achromatium determined by microautoradiography; Gray ND et al.; Microautoradiography was used to investigate substrate uptake by natural communities of uncultured bacteria from the genus Achromatium . Studies of the uptake of (14)C-labelled substrates demonstrated that Achromatium cells from freshwater sediments were able to assimilate (14)C from bicarbonate, acetate, and protein hydrolysate; however, (14)C-labelled glucose was not assimilated . The pattern of substrate uptake by Achromatium spp . was therefore similar to those of a number of other freshwater and marine sulfur-oxidizing bacteria . Different patterns of radiolabelled bicarbonate uptake were noted for Achromatium communities from different geographical locations and indicated that one community (Rydal Water) possessed autotrophic potential, while the other (Hell Kettles) did not . Furthermore, the patterns of organic substrate uptake within a single population suggested that physiological diversity existed in natural communities of Achromatium . These observations are consistent with and may relate to the phylogenetic diversity observed in Achromatium communities . Incubation of Achromatium-bearing sediment cores from Rydal Water with (35)S-labelled sulfate in the presence and absence of sodium molybdate demonstrated that this bacterial population was capable of oxidizing sulfide to intracellular elemental sulfur . This finding supported the role of Achromatium in the oxidative component of a tightly coupled sulfur cycle in Rydal Water sediment . The oxidation of sulfide to sulfur and ultimately to sulfate by Achromatium cells from Rydal Water sediment is consistent with an ability to conserve energy from sulfide oxidation. J Invertebr Pathol, 1999 Nov, 74(3), 275 - 80 Bacteria, granulocytomas, and trematode metacercariae in the digestive gland of Mytilus edulis: seasonal and interpopulation variation; Svardh L; During the period October 1983-September 1984, mussels were sampled at monthly intervals from three populations in Denmark . The mussels were prepared for histopathological studies and 20 individuals were randomly chosen from each month and each population for a study of the prevalence and variation of the histological changes . The aim of the study was to test the hypothesis that the prevalence of parasites, bacteria, and granulocytoma differs among blue mussel populations during a year, due to the reproductive cycle and the environment . The only bacterial infection found was Chlamydia sp . and this was rare . Neither sex, month, nor population was an important determinant of the prevalence of bacteria . Metacercariae of the trematode Renicola roscovita had a prevalence of almost 54% in a population from Lilla Baelt but only 4% in a population from Isefjorden . A statistically significant interaction between month and population indicated that the prevalence varied over months but the pattern of variation was different among populations . No other parasites were found . The prevalence of granulocytomas within populations was positively correlated with the degree of anthropogenic contamination of the localities, which might suggest a functional connection . Neither month nor sex had a significant effect . Pediatr Nurs, 1999 Mar-Apr, 25(2), 151 - 5 Are ball pits the playground for potentially harmful bacteria? Davis SG, Corbitt AM, Everton VM, Grano CA, Kiefner PA, Wilson AS, Gray M. Ball pits, enclosed play areas with padded floors and pits of small plastic balls, have become popular features for children at fast food restaurants . This pilot study sought to identify and confirm bacterial organisms that place children at a potential health risk in three play pits within fast food restaurants . Data for this descriptive study were randomly collected from restaurants offering play pits with multicolored, round, hollow, plastic balls within urban communities of the Tidewater region of Virginia . Specimens were collected from entrances into the ball pits as well as various areas of the bottom lining to incur a representative sample . Results indicated an increased level of normal flora as well as nonhuman flora, demonstrating that bacteria are present within the ball pits . The results question the safety of these play pits for both health care providers and parents . Nurses play a vital role in public awareness through health education . Disinfection protocol and proper handwashing are the keys to making ball pit play areas safe for children. Curr Biol, 1999 Oct 7, 9(19), R720 - 4 Who chaperones nascent chains in bacteria? Pfanner N. The physiological roles of the molecular chaperones trigger factor and DnaK in de novo protein folding have been unclear, but two new studies have shown that they perform essential, yet partially redundant, functions in chaperoning nascent protein chains in bacteria. Eur J Pediatr Surg, 1999 Aug, 9(4), 210 - 3 Surgical stress, bacteria, and mucosal immune function; Alverdy JC et al.; Bacteria share a benign coexistence with host mucosal surfaces in the gastrointestinal tract during periods of health . Both host epithelial defense function and bacterial virulence phenotypes are significantly affected by stress . Via discreet and specific sensory input signals to bacteria, the molecular machinery of otherwise commensal strains of bacteria can shift the phenotypes of residential colonizers to more virulent and invasive strains . This occurs at a time when the host may be relatively immunosuppressed by the injury . This adaptive response demonstrates the duplicitous nature of bacteria residing on mucosal surfaces whose ability to shift their virulence characteristics may play an important role in infectious-related morbidity following surgical stress. An Acad Bras Cienc, 1999, 71(3 Pt 2), 515 - 20 Adaptation of the differential display RT-PCR technique to isolate sugarcane genes induced by plant association with endophytic nitrogen-fixing bacteria; Vargas C et al.; Differential Display RT-PCR is a powerful technique that has been used to isolate differentially expressed genes . This technique was first described by Liang & Pardee, in 1992 . Afterwards, several modifications were introduced in the original version, including a simplification described by Sokolov & Prockop, in 1994 . In this work, we describe an adaptation of the Sokolov & Prockop technique, in order to isolate sugarcane genes induced by plant association with endophytic nitrogen-fixing bacteria . Several modifications were introduced: the use of oligo-dT primer in the first strand cDNA synthesis, replicates of the PCR reactions, analysis of the amplified fragments on silver stained polyacrilamide gel and confirmation of cloning the differentially amplified selected band prior to its molecular characterisation . The methodology established was successfully used to identify a large number of differentially amplified sugarcane cDNAs . So far, one of these cDNAs was already isolated and characterized. J Surg Res, 1999 Nov, 87(1), 85 - 9 Confirmation of translocated gastrointestinal bacteria in a neonatal model; Moy J et al.; PURPOSE: The hypothesis that enteric bacteria translocate from the gastrointestinal (GI) tract to extraintestinal sites has been extensively studied . However, definitive evidence that spontaneous bacterial translocation and dissemination from the GI tract to extraintestinal sites occur in a neonatal model has been lacking . The aim of this study was to confirm this phenomenon by tracking enterally administered, plasmid-labeled bacteria to extraintestinal sites . MATERIALS AND METHODS: Escherichia coli 07:K1 (E . coli K1) with and without a nontransferable, ampicillin resistance plasmid (pGEM-7) were used in this study . Newborn New Zealand white rabbit pups were separated into three treatment groups: transformed E . coli K1 (E . coli K1 + pGEM-7, n = 20), nontransformed E . coli K1 (n = 12), and control pups (no bacteria, n = 7) . Pups were enterally fed 10% Formulac solution supplemented with a suspension of bacteria respective to their group . After the pups fed twice daily for 2 days, representative tissue specimens from the small bowel (SB), mesenteric lymph nodes (MLNs), spleen (SPL), and liver (LIV) were aseptically harvested and tested for culture growth in ampicillin-supplemented medium . RESULTS: Positive growths of plasmid-induced ampicillin-resistant bacteria were detected in tissue specimens harvested from rabbits fed transformed E . coli K1, but were not detected in the other groups . CONCLUSION: This experiment demonstrated conclusively that transformed E . coli K1 fed to healthy rabbit pups spontaneously translocated from the intestinal lumen and subsequently disseminated to the mesenteric lymph nodes, spleen, and liver . Plant Mol Biol, 1999 Aug, 40(6), 997 - 1008 Dimerisation of maize glutathione transferases in recombinant bacteria; Dixon DP et al.; Two cDNAs encoding novel type III maize (Zea mays) GST subunits, ZmGST VI and ZmGST VII, have been cloned in addition to the previously described ZmGST V . Together with the type I GSTs ZmGST I and ZmGST III, these subunits were expressed in Escherichia coli, both individually and in tandem combinations using a customised pET vector . The GST dimers formed were then characterised . When type I GSTs were co-expressed only the respective homodimers were formed rather than the ZmGST I-III heterodimer . The failure to form this heterodimer, together with the negligible herbicide-detoxifying activity associated with recombinant ZmGST III-III, suggests that the identity of herbicide-detoxifying isoenzymes described in maize as being composed of ZmGST III subunits requires re-evaluation . In contrast, co-expression of the type III GSTs ZmGST V and ZmGST VI resulted in the formation of ZmGST V-V, ZmGST VI-VI and ZmGST V-VI dimers in the ratio 1:1:2 as predicted for random subunit association . ZmGST V-VI had kinetic characteristics intermediate between those of the two homodimers, indicating that the subunits were catalytically independent of one another . Co-expression of ZmGST V and ZmGST VII resulted in the formation of ZmGST V-VII and this isoenzyme was subsequently identified in maize plants . Attempts to dimerise type I GST subunits with type III GST subunits proved unsuccessful . These results demonstrate the utility of co-expressing recombinant GSTs to explore the potential of subunit-subunit associations and to help unravel the complexity of homodimeric and heterodimeric GSTs in plants. Mutat Res, 1999 Oct 19, 429(2), 159 - 68 Visual quantification of DNA double-strand breaks in bacteria; Singh NP et al.; In this paper, we describe a method for the visualization of double-strand breaks in a single electrostretched Escherichia coli DNA molecule . We also provide evidence that electrostretched or migrated DNA under neutral microgel electrophoresis conditions is made up of individual chromosomes . Using the neutral microgel electrophoresis technique, DNA migration (stretching) was measured and the number of DNA double-strand breaks were counted following exposure of E . coli cells to 0, 12.5, 25, 50, or 100 rad of X-rays . The use of an intense fluorescent dye, YOYO and custom-made slides have helped us in visualizing individual bacterial DNA molecules . Bacterial DNA appears similar in structure compared to electrostretched DNA from human lymphocytes . We were able to detect changes in DNA migration (stretching) induced by an X-ray dose as low as 12.5 rad and an increase in the number of DNA breaks induced by a dose as low as 25 rad . The extent of DNA migration and number of breaks were directly correlated to X-ray dosage. FEMS Microbiol Lett, 1999 Oct 15, 179(2), 317 - 25 Fluorescence-based detection of lacZ reporter gene expression in intact and viable bacteria including Mycobacterium species; Rowland B et al.; A variety of fluorescein di-beta-D-galactopyranoside (FDG)-based substrates were evaluated for measuring beta-galactosidase expression in bacteria . One substrate, 5-acetylamino-FDG (C2FDG), performed well in all bacteria tested, including the slow growing mycobacterium, Mycobacterium bovis BCG . The sensitivity of C2FDG in intact, viable BCG was similar to that of o-nitrophenyl-beta-D-galactopyranoside in cell lysates when used to measure lacZ reporter gene activity . C2FDG was approximately 70-fold more sensitive than green fluorescent protein (GFP) in BCG when assayed in a fluorescence plate reader, and comparable to GFP when measured by flow cytometry . These assays provide an important new alternative for the rapid measurement of reporter gene expression in viable bacteria. Luminescence, 1999 Sep-Oct, 14(5), 267 - 70 Transfer of xenobiotics through cell membranes of luminous bacteria; Medvedeva SE; The influence of some chemical substances on luminous bacteria was studied to elucidate the interrelation between the xenobiotics action on bacterial luminescence and cell ultrastructure . Such substances as quinones, phenols, chlorides of heavy metals (in concentrations of substances inhibiting luminescence by 50%) resulted in damaging effects upon bacteria: a lot of cells had damage of membranes due to changes in their permeability . It was found that the high concentration of EDTA and toluene decreased the luminescence and caused the condensation of DNA-fibrils and the cell damage after long-term and short-term action . The low concentration of EDTA and toluene did not decrease the bacterial luminescence; the noticeable damage of cell membranes did not take place during short-term treatment . However, the long action of these substances changed the membrane permeability resulting in increased sensitivity of bacterial luminescence to some toxic substances . Biochemistry, 1999 Sep 7, 38(36), 11788 - 95 Structures of the O-specific polysaccharides from Yokenella regensburgei (Koserella trabulsii) strains PCM 2476, 2477, 2478, and 2494: high-resolution magic-angle spinning NMR investigation of the O-specific polysaccharides in native lipopolysaccharides and directly on the surface of living bacteria; Jachymek W et al.; The structures of the carbohydrate O-specific side-chain moiety of the lipopolysaccharides (LPS) of Yokenella regensburgei, strains PCM 2476, 2477, 2478, and 2494, have been investigated by (1)H and (13)C NMR, fast atom bombardment tandem mass spectrometry (FAB-MSMS), matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, methylation analysis, partial acid hydrolysis, and immunological methods . It was concluded that the O-specific polysaccharides of strains 2476, 2477, 2478, and 2494 are composed of the same basic trisaccharide repeating unit having the structure -->3)-alpha-D-FucpNAc-(1-->2)-L-alpha-D-Hepp-(1-->3)-6-deoxy -alpha-L- Talp-(1-->, in which L-alpha-D-Hepp is L-glycero-alpha-D-manno-heptopyranose . The detailed analysis revealed, however, differences in O-acetylation patterns of the 6-deoxy-L-talose residue, with 2- and 4-O-acetyl disubstituted -->3)-6-deoxy-alpha-L-Talp-(1--> in strain PCM 2476 and a 2-O-acetylated residue in strains 2477, 2478, and 2494 . These structures represent novel, trisaccharide repeating units of bacterial O-antigens that are characteristic and unique to the Y . regensburgeispecies . By use of the high-resolution magic-angle spinning (HR-MAS) technique, (1)H NMR spectra of the O-polysaccharides directly in isolated LPS were obtained . This allowed for almost full assignment and structural determination of the polysaccharide . By this technique the O-polysaccharide components were also observed in their original form directly on the surface of living bacterial cells. Trends Biotechnol, 1999 Nov, 17(11), 452 - 60 Gene-expression tools for the metabolic engineering of bacteria; Keasling JD; Recent advances in metabolic engineering have led to new methods for the synthesis of novel molecules, improved production of existing compounds and improved degradation of recalcitrant environmental contaminants . Increasing the flux through an existing pathway and introducing a new pathway into a host organism demand coordinated expression of the genes that encode the enzymes, tight control over gene expression and consistent expression in all cells . Although several gene-expression tools have been developed for the overproduction of proteins, they may not be ideal for pathway redirection . Metabolic engineering requires certain characteristics of gene-expression tools, and some new tools meet these needs. Parasitol Today, 1999 Nov, 15(11), 437 - 42 Wolbachia bacteria of filarial nematodes; Taylor MJ et al.; The finding that the intracellular bacteria of filarial nematodes are related to the Wolbachia symbionts of arthropods has generated great interest . Here, Mark Taylor and Achim Hoerauf review recent studies by several groups on the structure, distribution and phylogeny of these endosymbionts, and discuss the potential role for these bacteria in filarial disease and as a target for chemotherapy. Appl Environ Microbiol, 1999 Oct, 65(10), 4611 - 7 Sulfonates as terminal electron acceptors for growth of sulfite-reducing bacteria (Desulfitobacterium spp.) and sulfate-reducing bacteria: effects of inhibitors of sulfidogenesis; Lie TJ et al.; This study demonstrates the ability of Desulfitobacterium spp . to utilize aliphatic sulfonates as terminal electron acceptors (TEA) for growth . Isethionate (2-hydroxyethanesulfonate) reduction by Desulfitobacterium hafniense resulted in acetate as well as sulfide accumulation in accordance with the expectation that the carbon portion of isethionate was oxidized to acetate and the sulfur was reduced to sulfide . The presence of a polypeptide, approximately 97 kDa, was evident in isethionate-grown cells of Desulfitobacterium hafniense, Desulfitobacterium sp . strain PCE 1, and the two sulfate-reducing bacteria (SRB)-Desulfovibrio desulfuricans IC1 (T . J . Lie, J . R . Leadbetter, and E . R . Leadbetter, Geomicrobiol . J . 15:135-149, 1998) and Desulfomicrobium norvegicum; this polypeptide was not detected when these bacteria were grown on TEA other than isethionate, suggesting involvement in its metabolism . The sulfate analogs molybdate and tungstate, effective in inhibiting sulfate reduction by SRB, were examined for their effects on sulfonate reduction . Molybdate effectively inhibited sulfonate reduction by strain IC1 and selectively inhibited isethionate (but not cysteate) reduction by Desulfitobacterium dehalogenans and Desulfitobacterium sp . strain PCE 1 . Desulfitobacterium hafniense, however, grew with both isethionate and cysteate in the presence of molybdate . In contrast, tungstate only partially inhibited sulfonate reduction by both SRB and Desulfitobacterium spp . Similarly, another inhibitor of sulfate reduction, 1,8-dihydroxyanthraquinone, effectively inhibited sulfate reduction by SRB but only partially inhibited sulfonate reduction by both SRB and Desulfitobacterium hafniense. Appl Environ Microbiol, 1999 Oct, 65(10), 4475 - 83 Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in natural planktonic bacteria; Gasol JM et al.; Total bacterial abundances estimated with different epifluorescence microscopy methods (4',6-diamidino-2-phenylindole {DAPI}, SYBR Green, and Live/Dead) and with flow cytometry (Syto13) showed good correspondence throughout two microcosm experiments with coastal Mediterranean water . In the Syto13-stained samples we could differentiate bacteria with apparent high DNA (HDNA) content and bacteria with apparent low DNA (LDNA) content . HDNA bacteria, "live" bacteria (determined as such with the Molecular Probes Live/Dead BacLight bacterial viability kit), and nucleoid-containing bacteria (NuCC) comprised similar fractions of the total bacterial community . Similarly, LDNA bacteria and "dead" bacteria (determined with the kit) comprised a similar fraction of the total bacterial community in one of the experiments . The rates of change of each type of bacteria during the microcosm experiments were also positively correlated between methods . In various experiments where predator pressure on bacteria had been reduced, we detected growth of the HDNA bacteria without concomitant growth of the LDNA bacteria, such that the percentage contribution of HDNA bacteria to total bacterial numbers (%HDNA) increased . This indicates that the HDNA bacteria are the dynamic members of the bacterial assemblage . Given how quickly and easily the numbers of HDNA and LDNA bacteria can be obtained, and given the similarity to the numbers of "live" cells and NuCC, the %HDNA is suggested as a reference value for the percentage of actively growing bacteria in marine planktonic environments. Appl Environ Microbiol, 1999 Oct, 65(10), 4393 - 8 Ferric iron reduction by bacteria associated with the roots of freshwater and marine macrophytes; King GM et al.; In vitro assays of washed, excised roots revealed maximum potential ferric iron reduction rates of >100 micromol g (dry weight)(-1) day(-1) for three freshwater macrophytes and rates between 15 and 83 micromol (dry weight)(-1) day(-1) for two marine species . The rates varied with root morphology but not consistently (fine root activity exceeded smooth root activity in some but not all cases) . Sodium molybdate added at final concentrations of 0.2 to 20 mM did not inhibit iron reduction by roots of marine macrophytes (Spartina alterniflora and Zostera marina) . Roots of a freshwater macrophyte, Sparganium eurycarpum, that were incubated with an analog of humic acid precursors, anthroquinone disulfate (AQDS), reduced freshly precipitated iron oxyhydroxide contained in dialysis bags that excluded solutes with molecular weights of >1,000; no reduction occurred in the absence of AQDS . Bacterial enrichment cultures and isolates from freshwater and marine roots used a variety of carbon and energy sources (e.g., acetate, ethanol, succinate, toluene, and yeast extract) and ferric oxyhydroxide, ferric citrate, uranate, and AQDS as terminal electron acceptors . The temperature optima for a freshwater isolate and a marine isolate were equivalent (approximately 32 degrees C) . However, iron reduction by the freshwater isolate decreased with increasing salinity, while reduction by the marine isolate displayed a relatively broad optimum salinity between 20 and 35 ppt . Our results suggest that by participating in an active iron cycle and perhaps by reducing humic acids, iron reducers in the rhizoplane of aquatic macrophytes limit organic availability to other heterotrophs (including methanogens) in the rhizosphere and bulk sediments. Prog Nucleic Acid Res Mol Biol, 1999, 63, 311 - 66 Recombinational DNA repair in bacteria and the RecA protein; Cox MM; In bacteria, the major function of homologous genetic recombination is recombinational DNA repair . This is not a process reserved only for rare double-strand breaks caused by ionizing radiation, nor is it limited to situations in which the SOS response has been induced . Recombinational DNA repair in bacteria is closely tied to the cellular replication systems, and it functions to repair damage at stalled replication forks, Studies with a variety of rec mutants, carried out under normal aerobic growth conditions, consistently suggest that at least 10-30% of all replication forks originating at the bacterial origin of replication are halted by DNA damage and must undergo recombinational DNA repair . The actual frequency may be much higher . Recombinational DNA repair is both the most complex and the least understood of bacterial DNA repair processes . When replication forks encounter a DNA lesion or strand break, repair is mediated by an adaptable set of pathways encompassing most of the enzymes involved in DNA metabolism . There are five separate enzymatic processes involved in these repair events: (1) The replication fork assembled at OriC stalls and/or collapses when encountering DNA damage . (2) Recombination enzymes provide a complementary strand for a lesion isolated in a single-strand gap, or reconstruct a branched DNA at the site of a double-strand break . (3) The phi X174-type primosome (or repair primosome) functions in the origin-independent reassembly of the replication fork . (4) The XerCD site-specific recombination system resolves the dimeric chromosomes that are the inevitable by-product of frequent recombination associated with recombinational DNA repair . (5) DNA excision repair and other repair systems eliminate lesions left behind in double-stranded DNA . The RecA protein plays a central role in the recombination phase of the process . Among its many activities, RecA protein is a motor protein, coupling the hydrolysis of ATP to the movement of DNA branches. C R Acad Sci III, 1999 Aug, 322(8), 687 - 93 Atomic force microscopy imaging of dried or living bacteria; Robichon D et al.; Atomic force microscopy (AFM) was used to obtain micrographs of dried bacteria in air, and of living ones in their culture medium . Images of dried bacteria were very similar to images obtained elsewhere by the much more complicated cryoetching preparation technique for transmission electron microscopy . Living bacteria were immobilized on a poly-L-lysine film, and directly observed in their culture medium at a resolution unattainable by any other technique applicable to living material . The images were similar to those obtained in scanning electron microscopy where the specimen must be fixed, dried and coated with conductive material, and as a result, no longer viable. Ecotoxicol Environ Saf, 1999 Sep, 44(1), 100 - 4 A new mass screening method for methylmercury poisoning using mercury-volatilizing bacteria from Minamata Bay; Nakamura K et al.; A simplified mass screening method for methylmercury exposure was developed using methylmercury-volatilizing bacteria from Minamata Bay . Some bacteria can transform methylmercury into mercury vapor . Most mercury in the hair is methylmercury, which is readily extracted with HCl solution . Black spots are formed on X-ray film due to the reduction of Ag(+) emulsion with mercury vapor produced by methylmercury-volatilizing bacteria . By exploiting these characteristics, a screening method was developed, whereby the fur of rats injected with methylmercury chloride formed clear black spots on X-ray film, whereas the fur of rats injected with saline did not . Subsequently, 50 human hair samples were examined using this mass screening method . The method identified people who had high mercury concentration, over 20 microg/g . A few thousand hair samples may be screened in a day using this method because it is rapid, simple, and economical . This method, therefore, enables screening of persons with methylmercury poisoning in mercury-polluted areas . Ann Rheum Dis, 1999 Oct, 58(10), 598 - 610 HLA-B27 associated spondyloarthropathy, an autoimmune disease based on crossreactivity between bacteria and HLA-B27? Ringrose JH. Most autoimmune diseases are associated with certain HLA types . Therefore, spondyloarthropathies (SpA) strongly associated with HLA-B27, are also often classified as autoimmune diseases . This study questions whether SpA indeed fulfils the criteria of an autoimmune disease . The Medline database was searched for all reports between 1966 and April 1998 on the presence of autoimmune reactivity in SpA patients . This search yielded 45 articles on this subject . Only eight articles study T cell reactivity . Twelve reports were found on the assessment of antibodies crossreacting between bacteria and HLA-B27 . In the 45 studies demonstrating autoimmune reactions in SpA patients proper controls matched for HLA-B27, sex and age were nearly always lacking . Therefore, it is concluded that the frequency of increased autoreactivity in sera from patients and controls is not significantly different, and that this lack of autoreactivity does not justify classification of SpA as an autoimmune disease . As crossreactive antibodies against bacteria and HLA-B27 were equally present in sera from patients and controls, the pathogenetic significance of molecular mimicry between various bacteria and HLA-B27 is questionable . Furthermore, the regions of the B27 molecule that are supposed to be crossreactive with bacteria, differ in one or more amino acids among the distinct B27 subtypes . Although these differences strongly influence the binding of antibodies to the B27 molecule, there was no relation between the degree of crossreactivity of certain subtypes and the association of these subtypes with SpA . In conclusion, there is no evident proof that SpA is an autoimmune disease attributable to crossreactivity between bacteria and HLA-B27. Folia Microbiol (Praha), 1999, 44(1), 50 - 4 Chromium-tolerant bacteria isolated from industrial effluents and their use in detoxication of hexavalent chromium; Shakoori AR et al.; Three bacterial strains were isolated from effluents of leather (CMBL Cr13, CMBL Cr14) and steel (CMBL Cr15) industries for their possible use in chromium(VI) detoxication of industrial waste . CMBL Cr13 was found to tolerate chromium(VI) up to a concentration of 45 g/L in the medium, while CMBL Cr14 and CMBL Cr15 could tolerate up to 40 g/L . These bacteria were also checked for resistance to other metals . They resisted a lead concentration of 1 g/L and cadmium concentration of 550 mg/L in the medium . They showed optimum growth at pH 7.3-7.5 at a temperature of 35-37 degrees C . CrVI-reducing ability of the three strains ranged from 70 to 80% after 3 d of incubation . The possible use of these bacteria in environmental cleanup is discussed. Anal Chem, 1999 Sep 1, 71(17), 3894 - 900 Rapid profiling of induced proteins in bacteria using MALDI-TOF mass spectrometric detection of nonporous RP HPLC-separated whole cell lysates; Wall DB et al.; A method for rapid profiling of water-soluble proteins from whole cell lysates has been developed using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOFMS) following separation by reversed-phase high-performance liquid chromatography (RP HPLC) . Rapid separation of proteins from cell lysates was achieved using columns packed with C18 nonporous (NP) silica beads . Using this method, the whole cell lysate water-soluble proteins of E . coli were separated in under 15 min . A method using two columns in series at different temperatures was used in order to provide high loadability without loss of separation efficiency . The nonporous packing in the columns provided for high recovery . Eluting fractions were collected and analyzed by MALDI-TOFMS to determine the molecular weights and peptide maps of the proteins . These methods provided for the rapid screening and identification of proteins from E . coli where the response of E . coli to L-arabinose induction was studied . In this work, it is demonstrated that NP RP HPLC with MALDI-TOFMS detection may serve as a rapid means of detecting and identifying changes in bacterial protein expression due to external stimuli. Curr Microbiol, 1999 Nov, 39(5), 270 - 3 Effect of growth pH on the phospholipid contents of the membranes from alkaliphilic bacteria Enomoto K, Koyama N. An aerobic alkaliphile YN-2000 and a facultatively anaerobic alkaliphile BL77/1 are able to grow over the wide pH range of 7-10.5 . Net surface charges on the membranes from YN-2000 and BL77/1 were negative above pH 4, and the amounts were significantly increased when the bacteria were cultured at pH 10 as compared with those cultured at pH 7.5 . Phospholipid contents of the membranes from both bacteria grown at pH 10 were much higher than those from the bacteria grown at pH 7.5 . Phospholipids of the membranes from YN-2000 and BL77/1 were composed mainly of cardiolipin (CL), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG) . It is suggested that the increases by growth at pH 10 of negative charges on the membranes from the bacteria result mainly from the increases of acidic phospholipids such as CL and PG . Increases of phospholipid contents and/or negative charges on the membranes seem to contribute to the adaptation of YN-2000 and BL77/1 to an alkaline environment . com/link/service/journals/00284/bibs/39n5p270.html</HEA Bioorg Med Chem, 1999 Aug, 7(8), 1549 - 58 Bacteria targeted by human natural antibodies using alpha-Gal conjugated receptor-specific glycopolymers; Li J et al.; Synthesis of polymerizable beta-lactosyl, Galalpha1-->3Gal and alpha-mannosyl acrylamide derivatives with either a hydrophobic aromatic spacer or a hydrophilic biocompatible oligoethoxyl spacer was accomplished . Radical terpolymerizations of beta-lactosyl monomer . alpha-mannosyl monomer, and acrylamide were conducted in aqueous media with ammonium persulfate and N,N,N',N'-tetramethylethylenediamine as initiators . The resulting water soluble glycopolymers were further transformed efficiently by a recombinant alpha1-->3 galactosyltransferase to afford mediators bearing Galalpha1-->3Gal termini as xenoactive antigens and alpha-mannosyl termini as specific ligands for bacterial cells . The binding of the resulting multivalent glycopolymer to bacteria was tested by its ability to inhibit agglutination of yeast to E . coli . The binding of human natural anti-Gal antibodies to the alpha-Gal containing glycopolymers and a monovalent alpha-Gal-Man glycoconjugate was demonstrated by an ELISA inhibition assay. Appl Environ Microbiol, 1999 Sep, 65(9), 4230 - 3 Community size and metabolic rates of psychrophilic sulfate-reducing bacteria in Arctic marine sediments; Knoblauch C et al.; The numbers of sulfate reducers in two Arctic sediments with in situ temperatures of 2.6 and -1.7 degrees C were determined . Most-probable-number counts were higher at 10 degrees C than at 20 degrees C, indicating the predominance of a psychrophilic community . Mean specific sulfate reduction rates of 19 isolated psychrophiles were compared to corresponding rates of 9 marine, mesophilic sulfate-reducing bacteria . The results indicate that, as a physiological adaptation to the permanently cold Arctic environment, psychrophilic sulfate reducers have considerably higher specific metabolic rates than their mesophilic counterparts at similarly low temperatures. Appl Environ Microbiol, 1999 Sep, 65(9), 4223 - 6 Isolation of nitrogen-fixing bacteria containing molybdenum-independent nitrogenases from natural environments; Loveless TM et al.; Seven diazotrophs that grow well under Mo-deficient, N(2)-fixing conditions were isolated from a variety of environments . These isolates fall in the gamma subdivision of the class Proteobacteria and have genes that encode the Mo nitrogenase (nitrogenase 1) and the V nitrogenase (nitrogenase 2) . Four of the isolates also harbor genes that encode the iron-only nitrogenase (nitrogenase 3). Appl Environ Microbiol, 1999 Sep, 65(9), 3810 - 9 Transformation of sulfur compounds by an abundant lineage of marine bacteria in the alpha-subclass of the class Proteobacteria; Gonzalez JM et al.; Members of a group of marine bacteria that is numerically important in coastal seawater and sediments were characterized with respect to their ability to transform organic and inorganic sulfur compounds . Fifteen strains representing the Roseobacter group (a phylogenetic cluster of marine bacteria in the alpha-subclass of the class Proteobacteria) were isolated from seawater, primarily from the southeastern United States . Although more than one-half of the isolates were obtained without any selection for sulfur metabolism, all of the isolates were able to degrade the sulfur-containing osmolyte dimethyl sulfoniopropionate (DMSP) with production of dimethyl sulfide (DMS) . Five isolates also degraded DMSP with production of methanethiol, indicating that both cleavage and demethylation pathways for DMSP occurred in the same organism, which is unusual . Five isolates were able to reduce dimethyl sulfoxide to DMS, and several isolates also degraded DMS and methanethiol . Sulfite oxygenase activity and methanesulfonic acid oxygenase activity were also present in some of the isolates . The ability to incorporate the reduced sulfur in DMSP and methanethiol into cellular material was studied with one of the isolates . A group-specific 16S rRNA probe indicated that the relative abundance of uncultured bacteria in the Roseobacter group increased in seawater enriched with DMSP or DMS . Because this group typically accounts for >10% of the 16S ribosomal DNA pool in coastal seawater and sediments of the southern United States, clues about its potential biogeochemical role are of particular interest . Studies of culturable representatives suggested that the group could mediate a number of steps in the cycling of both organic and inorganic forms of sulfur in marine environments. Microsc Res Tech, 1999 Aug 15-Sep 1, 46(4-5), 319 - 24 Imaging faces of shadowed magnetite (Fe(3)O(4)) crystals from magnetotactic bacteria with energy-filtering transmission electron microscopy; Lins U et al.; We used energy-filtering transmission electron microscopy to image magnetite crystals isolated from uncultured magnetotactic bacteria . These magnetite crystals were shadowed in high vacuum with platinum at 45 degrees . The shadowed crystals were observed in a Zeiss (Thornwood, NY) CEM902 transmission electron microscope . Imaging shadowed crystals with inelastically scattered electrons provided information of the decoration pattern of small platinum particles over crystal surfaces, and thus information on surface characteristics of crystals . Results were comparable to those obtained from scanning electron microscopy using a field emitter gun . Electron energy loss spectra of the crystals as well as of the supporting film were recorded to evaluate variations of image contrast with energy losses . Results indicated that the contrast is attenuated with inelastic imaging and that the effect of contrast tuning caused a contrast inversion at a given point between 100 and 150 eV . We believe this approach can be useful for studying multilayered materials by transmission electron microscopy . Copyright 1999 Wiley-Liss, Inc.
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