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PubMed1988

[Etiologic structure of bacterial dysentery in the USSR in 1983-1985].

The etiological structure of dysentery in the USSR in 1983-1985 is characterized. Sonne dysentery was found to prevail in the territories with adequate water supply, while dysentery caused by Shigella flexneri prevailed at the territories with unsatisfactory water supply. S. dysenteriae and S. boydii were found to play a limited role in the etiology of dysentery. In the presence of global pandemic, an increase in the isolation rate of S. dysenteriae I in the USSR is observed. The data on the biochemical structure of S. sonnei are presented.

Dysentery, Bacillary↗
PubMedDate not supplied

Analysis of the tertiary structure of bacterial RNase P RNA.

The ubiquitous occurrence of ribonuclease P (RNase P) as a ribonucleoprotein and the catalytic properties of bacterial RNase P RNAs indicate that RNA fulfills an ancient and important role in the function of this enzyme. This review focuses on efforts to determine the structure of the bacterial RNase P RNA ribozyme. Phylogenetic comparative analysis of a library of bacterial RNase P RNA sequences has resulted in a well-developed secondary structure model and allowed identification of some elements of tertiary structure. The native structure has been redesigned by circular permutation to facilitate intra- and inter-molecular crosslinking experiments in order to gain further structural information. The crosslinking constraints, together with the constraints provided by comparative analyses, have been incorporated into a first-order model of the structure of of the ribozyme-substrate complex. The developing structural perspective allows the design of self-cleaving pre-tRNA-RNase P RNA conjugates which are useful tools for additional structure-probing experiments.

Bacteria↗
PubMed1999

Impact of an urban effluent on the bacterial community structure in the Arga River (Spain), with special reference to culturable gram-negative rods.

The Arga River is an interesting system in which to study the impact of urban effluent pollution because it receives a single effluent in the form of wastewater discharge from the city of Pamplona. To analyze the extent of this discharge, total bacteria, culturable heterotrophic bacteria, and Gram-negative heterotrophic bacteria were enumerated and 409 isolates of the latter were identified. One sampling station was located upstream from the inflow, while five were located up to 30 km downstream. Bacterial counts increased drastically downstream from the wastewater inflow. Total bacterial numbers decreased along the 30 km downstream, the last station attaining similar values to those recorded upstream from the discharge. However, culturable heterotrophic and Gram-negative heterotrophic bacteria levels generally remained significantly higher within the 30 km zone investigated. Among the 409 isolates identified, Aeromonas spp. were the most frequent both upstream and downstream from the discharge. In contrast, although strains belonging to different genera of Enterobacteriaceae were found in all stations, their occurrence was significantly higher just downstream from the polluted discharge. Acinetobacter spp., which were never found upstream, were detected in all stations below the discharge. Our results clearly show that the bacterial community structure changes definitively downstream from the discharge and that Aeromonas were common throughout the sampling zone. Thus they cannot be considered good indicators of pollution in this setting compared to some genera of Enterobacteriaceae or some species of Acinetobacter, the distribution of which correlated better with the distance from the wastewater discharge.

Acinetobacter↗
PubMed1993

Bacterial porins: structure and function.

Within the class of integral membrane proteins, the bacterial porins display a remarkable resistance to denaturants and proteases. This stability is probably crucial for the formation of highly ordered, three-dimensional crystals. Structural analysis of these crystals has been possible in atomic detail. This analysis has revealed interesting features, such as the aromatic girdles, and has helped to explain several observations, including the porins' ability to discriminate between polar and non-polar solutes. Recent research has thus improved our understanding of the porins in a qualitative fashion.

Animals↗
PubMed2004

Stratification of activity and bacterial community structure in biofilms grown on membranes transferring oxygen.

Previous studies have shown that membrane-aerated biofilm (MAB) reactors can simultaneously remove carbonaceous and nitrogenous pollutants from wastewater in a single reactor. Oxygen is provided to MABs through gas-permeable membranes such that the region nearest the membrane is rich in oxygen but low in organic carbon, whereas the outer region of the biofilm is void of oxygen but rich in organic carbon. In this study, MABs were grown under similar conditions but at two different fluid velocities (2 and 14 cm s(-1)) across the biofilm. MABs were analyzed for changes in biomass density, respiratory activity, and bacterial community structure as functions of biofilm depth. Biomass density was generally highest near the membrane and declined with distance from the membrane. Respiratory activity exhibited a hump-shaped profile, with the highest activity occurring in the middle of the biofilm. Community analysis by PCR cloning and PCR-denaturing gradient gel electrophoresis of 16S rRNA genes demonstrated substantial stratification of the community structure across the biofilm. Population profiles were also generated by competitive quantitative PCR of gene fragments specific for ammonia-oxidizing bacteria (AOB) (amoA) and denitrifying bacteria (nirK and nirS). At a flow velocity of 14 cm s(-1), AOB were found only near the membrane, whereas denitrifying bacteria proliferated in the anoxic outer regions of the biofilm. In contrast, at a flow velocity of 2 cm s(-1), AOB were either not detected or detected at a concentration near the detection limit. This study suggests that, under the appropriate conditions, both AOB and denitrifying bacteria can coexist within an MAB.

Bacteria↗
PubMed2006

Fermentative hydrogen production and bacterial community structure in high-rate anaerobic bioreactors containing silicone-immobilized and self-flocculated sludge.

A novel continuously stirred anaerobic bioreactor (CSABR) seeded with silicone-immobilized sludge was developed for high-rate fermentative H2 production using sucrose as the limiting substrate. The CSABR system was operated at a hydraulic retention time (HRT) of 0.5-6 h and an influent sucrose concentration of 10-40 g COD/L. With a high feeding sucrose concentration (i.e., 30-40 g COD/L) and a short HRT (0.5 h), the CSABR reactor produced H2 more efficiently with the highest volumetric rate (VH2) of 15 L/h/L (i.e., 14.7 mol/d/L) and an optimal yield of ca. 3.5 mol H2/mol sucrose. The maximum VH2 value obtained from this work is much higher than any other VH2 values ever documented. Formation of self-flocculated granular sludge occurred during operation at a short HRT. The granule formation is thought to play a pivotal role in the dramatic enhancement of H2 production rate, because it led to more efficient biomass retention. A high biomass concentration of up to 35.4 g VSS/L was achieved even though the reactor was operated at an extremely low HRT (i.e., 0.5 h). In addition to gaining high biomass concentrations, formation of granular sludge also triggered a transition in bacterial community structure, resulting in a nearly twofold increase in the specific H2 production rate. According to denatured-gradient-gel-electrophoresis analysis, operations at a progressively decreasing HRT resulted in a decrease in bacterial population diversity. The culture with the best H2 production performance (at HRT = 0.5 h and sucrose concentration = 30 g COD/L) was eventually dominated by a presumably excellent H2-producing bacterial species identified as Clostridium pasteurianum.

Acetic Acid↗
PubMed2005

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops.

BACKGROUND: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. RESULTS: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. CONCLUSION: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

Agrobacterium tumefaciens↗
PubMed1997

Structure of bacterial luciferase beta 2 homodimer: implications for flavin binding.

The crystal structure of the beta 2 homodimer of Vibrio harveyi luciferase has been determined to 2.5 A resolution by molecular replacement. Crystals were grown serendipitously using the alpha beta form of the enzyme. The subunits of the homodimer share considerable structural homology to the beta subunit of the alpha beta luciferase heterodimer. The four C-terminal residues that are disordered in the alpha beta structure are fully resolved in our structure. Four peptide bonds have been flipped relative to their orientations in the beta subunit of the alpha beta structure. The dimer interface of the homodimer is smaller than the interface of the heterodimer in terms of buried surface area and number of hydrogen bonds and salt links. Inspection of the subunits of our structure suggests that FMNH2 cannot bind to the beta 2 enzyme at the site that has been proposed for the alpha beta enzyme. However, we do uncover a potential FMNH2 binding pocket in the dimer interface, and we model FMN into this site. This proposed flavin binding motif is consistent with several lines of biochemical and structural evidence and leads to several conclusions. First, only one FMNH2 binds per homodimer. Second, we predict that reduced FAD and riboflavin should be poor substrates for beta 2. Third, the reduced activity of beta 2 compared to alpha beta is due to solvent exposure of the isoalloxazine ring in the beta 2 active site. Finally, we raise the question of whether our proposed flavin binding site could also be the binding site for flavin in the alpha beta enzyme.

Binding Sites↗
PubMed2004

Three-dimensional dual-morphotype species modeling of activated sludge flocs.

An individual-based model, originally developed for a biofilm system, was adapted to simulate three-dimensional formation of activated sludge flocs. The model was extended to two different bacterial morphotypes (floc-forming and filamentous bacteria), allowing spatial development of the floc according to the bacterial morphology, diffusion, reaction, and growth processes. The model needed also extension with a process for attachment of individual cells. Despite being in an early stage of development, the model is already a tool that enables us to obtain useful information about the microfloc environment. The model indicates that filamentous bacterial morphology and substrate microgradients are important aspects in the formation of bacterial structures. In mass transport-limited regimes filamentous bacterial structures prevail, whereas in growth-limited regimes irregular shaped flocs with fingerlike structures are dominant. These modeling results suggest that activated sludge flocs and biofilms might be different manifestations of the same phenomena. The model results support the hypothesis that floc-macrogradients can be the most important parameter for development of bulking sludge. The model suggests that attachment has a very strong effect on floc structure, leading to enhancement of the effect of substrate microgradients.

Bacteria, Aerobic↗
PubMed1987

Activation of human serum complement by bacterial lipopolysaccharides: structural requirements for antibody independent activation of the classical and alternative pathways.

A variety of bacterial lipopolysaccharide (LPS) preparations with highly defined primary polysaccharide chemical structure and/or aggregate macromolecular composition have been employed to examine the molecular requirements for activation of the classical and alternative pathways of human serum complement. Evidence is presented for two independent modes of polysaccharide dependent activation of the APC by LPS. One mechanism is dependent upon specific O-antigen polysaccharides and the second is defined by a specific L-glycero-D-mannoheptose/glucose region of the core oligosaccharide. LPS O-antigen polysaccharide but not core oligosaccharide determinants can convert sheep erythrocytes to cells capable of initiating the APC. The data presented provide convincing evidence that the tertiary assembly of individual LPS subunits into an aggregate macromolecule is a critical determinant in the expression of APC activity by LPS. The results of these studies provide strong evidence that CPC activation by LPS is restricted to the Re-chemotype and isolated lipid A. LPS isolated from other R-chemotypes as well as native wild type LPS preparations do not activate the CPC, in spite of the fact that the former LPS preparations contain more lipid A than polysaccharide on a percentage by wt basis. The presence of core polysaccharide L-glycero-D-mannoheptose, which provides a critical recognition role for activation of the APC, appears to negatively regulate CPC activation in a similar inverse relationship. In addition, the presence of polysaccharide containing LPS subunits in synthetic mixed LPS micellar aggregates can also restrict CPC activation by Re LPS subunits, most probably by steric hindrance at the LPS macromolecular surface. Our data are consistent with the hypothesis that activation of either pathway of human serum complement by a given LPS preparation is a mutually exclusive event dictated by the presence or absence of L-glycero-D-mannoheptose.

Complement Activation↗
PubMed1988

Mathematical modelling of intercellular regulation causing the formation of spatial structures in bacterial colonies.

Bacterial colonies may grow forming stable spatial, particularly circular, structures. For instance, motile bacteria Proteus vulgaris or Escherichia coli grown on agar under certain conditions may form concentric rings with the centre in the inoculation point (Rüss-Münzer, 1935, Bact. Parasit Kde (Abt 1) 7, 214; Budriené, 1985, Dokl. Acad. Nauk SSR, 283, 470). A similar picture can be observed in a different situation, i.e. when a lawn of non-motile Salmonella typhimurium bacteria is cultivated on a solid agar with the locally introduced substrate (Hoppensteadt & Jäger, 1980, Lecture Notes in Biomath. 38, 68). This paper describes a mechanism of bacterial interactions through a hypothetical mediator released by the organisms. A mathematical model has been built. Its analysis has shown that the selected laws of secretion and reception of the mediator can adequately account for the formation of circular structures in the case of both motile and non-motile bacteria.

Animals↗
PubMed2003

Bacterial community structure and function in a metal-working fluid.

The diversity of bacterial populations colonizing spatially and temporally separated samples of the same metal-working fluid (MWF) formulation was investigated. Analyses were performed with a view to improve strategies for bioaugmentation of waste MWF in bioreactor systems and prevention of in-use MWF biodeterioration in engineering workshops. Significantly, complementary phenotypic, genotypic and in situ methods revealed that the bacterial communities in operationally exhausted MWFs had low diversity and were similar in species composition from different locations and uses. Of the 179 bacterial isolates studied, only 11 genera and 15 species were identified using fatty acid methyl ester (FAME) analysis, with culture independent analyses by 16S rDNA denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization being congruent with these FAME data. In order to gain some insight into functional role of detected populations, we correlated the MWF chemical composition and potential pollution load with bacterial abundance and community composition detected within samples.

Bacteria↗
PubMed2005

Assessing terminal restriction fragment length polymorphism suitability for the description of bacterial community structure and dynamics in hydrocarbon-polluted marine environments.

The distribution of bacterial communities terminal restriction fragment length polymorphism (T-RFLP) fingerprint patterns was evaluated at three proximal hydrocarbon-contaminated sites located within the harbour of Messina. In order to analyse the short-term variability of the individual terminal restriction fragment (T-RF) patterns, water samples were collected at the three sites on three occasions within 3 months (T(0), T(90) and T(91)). Four sample sizes, from 50 to 1000 ml for each collected sample, were analysed separately (36 total analysed samples) to evaluate the relationship between the sample size and the bacterial diversity estimates. The dominant T-RF groups mostly belonged to signatures of putative hydrocarbon-degrading bacteria, as revealed by the virtual analysis of the obtained bands. In order to test whether significant differences were occurring between the analysed samples, the Kruskal-Wallis non-parametric test was applied to the T-RF data set. Neither significant influence of the sample size nor short spatial variability within the three sampled sites was detected for each sampling time. On the contrary, significant temporal changes in the diversity of the bacterial communities were observed. These results were confirmed by the non-metric multidimensional scales (nMDS) analysis of the whole set of samples, which indicated three main groups corresponding to the three different sampling times. In summary, the T-RFLP technique, although a polymerase chain reaction-based method, proved to be a suitable technique for monitoring polluted marine environments, typically characterized by low diversity and high relative abundances of a few dominant groups.

Bacteria↗
PubMed1991

[Bacterial enterotoxins: structure, mode of action].

The enterotoxins are macro-proteins, produced by enterotoxic bacterial strains acting in the human or animal intestine during digestive infections. In most cases, they induce diarrhoea (associated or not with tissue damage). These molecules differ in their structure and mechanism of action. Some of them (cholera toxin, Escherichia coli LT) activate a cyclase system (adenylate or guanylate cyclase), inducing water and electrolyte flux in the gut. Conversely, others (toxins A and B, Clostridium difficile; Clostridium perfringens enterotoxin; verotoxin), provoke diarrhoea, intestinal damage associated with inflammatory response acting on cellular functions (protein synthesis, permeability to small molecules). Most enterotoxins act via membrane receptors which they specifically recognize on the surface of the enterocyte.

Animals↗
PubMed1998

The diverse and dynamic structure of bacterial genomes.

Bacterial genome sizes, which range from 500 to 10,000 kbp, are within the current scope of operation of large-scale nucleotide sequence determination facilities. To date, 8 complete bacterial genomes have been sequenced, and at least 40 more will be completed in the near future. Such projects give wonderfully detailed information concerning the structure of the organism's genes and the overall organization of the sequenced genomes. It will be very important to put this incredible wealth of detail into a larger biological picture: How does this information apply to the genomes of related genera, related species, or even other individuals from the same species? Recent advances in pulsed-field gel electrophoretic technology have facilitated the construction of complete and accurate physical maps of bacterial chromosomes, and the many maps constructed in the past decade have revealed unexpected and substantial differences in genome size and organization even among closely related bacteria. This review focuses on this recently appreciated plasticity in structure of bacterial genomes, and diversity in genome size, replicon geometry, and chromosome number are discussed at inter- and intraspecies levels.

Bacteria↗