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Analysis of TLR4 polymorphic variants: new insights into TLR4/MD-2/CD14 stoichiometry, structure, and signaling.

TLR4 is the signal-transducing receptor for structurally diverse microbial molecules such as bacterial LPS, respiratory syncytial virus fusion (F) protein, and chlamydial heat shock protein 60. Previous studies associated two polymorphic mutations in the extracellular domain of TLR4 (Asp(299)Gly and Thr(399)Ile) with decreased LPS responsiveness. To analyze the molecular basis for diminished responsiveness, site-specific mutations (singly or coexpressed) were introduced into untagged and epitope (Flag)-tagged wild-type (WT) TLR4 expression vectors to permit a direct comparison of WT and mutant signal transduction. Coexpression of WT TLR4, CD14, and MD-2 expression vectors in HEK293T cells was first optimized to achieve optimal LPS-induced NF-kappaB reporter gene expression. Surprisingly, transfection of cells with MD-2 at high input levels often used in the literature suppressed LPS-induced signaling, whereas supraoptimal CD14 levels did not. Under conditions where WT and polymorphic variants were comparably expressed, significant differences in NF-kappaB activation were observed in response to LPS and two structurally unrelated TLR4 agonists, chlamydial heat shock protein 60 and RSV F protein, with the double, cosegregating mutant TLR4 exhibiting the greatest deficiency. Overexpression of Flag-tagged WT and mutant vectors at input levels resulting in agonist-independent signaling led to equivalent NF-kappaB signaling, suggesting that these mutations in TLR4 affect appropriate interaction with agonist or coreceptor. These data provide new insights into the importance of stoichiometry among the components of the TLR4/MD-2/CD14 complex. A structural model that accounts for the diminished responsiveness of mutant TLR4 polymorphisms to structurally unrelated TLR4 agonists is proposed.

Amino Acid Substitution↗

The toll-like receptor TLR4 is necessary for lipopolysaccharide-induced oligodendrocyte injury in the CNS.

The immediate or innate immune response is the first line of defense against diverse microbial pathogens and requires the expression of recently discovered toll-like receptors (TLRs). TLR4 serves as a specific receptor for lipopolysaccharide (LPS) and is localized on the surface of a subset of mammalian cells. Although innate immunity is a necessary host defense against microbial pathogens, the consequences of its activation in the CNS can be deleterious, as we show here in a developing neural model. We examined the major non-neuronal cell types in the CNS for expression of TLR4 and found that microglia expressed high levels, whereas astrocytes and oligodendrocytes expressed none. Consistent with TLR4 expression solely in microglia, we show that microglia are the only CNS glial cells that bind fluorescently tagged lipopolysaccharide. Lipopolysaccharide led to extensive oligodendrocyte death in culture only under conditions in which microglia were present. To determine whether TLR4 is necessary for lipopolysaccharide-induced oligodendrocyte death in mixed glial cultures, we studied cultures generated from mice bearing a loss-of-function mutation in the tlr4 gene. Lipopolysaccharide failed to induce oligodendrocyte death in such cultures, in contrast to the death induced in cultures from wild-type mice. Finally, stereotactic intracerebral injection of lipopolysaccharide into the developing pericallosal white matter of immature rodents resulted in loss of oligodendrocytes and hypomyelination and periventricular cysts. Our data provide a general mechanistic link between (1) lipopolysaccharide and similar microbial molecular motifs and (2) injury to oligodendrocytes and myelin as occurs in periventricular leukomalacia and multiple sclerosis.

Animals↗

Random amplified polymorphic DNA analysis and demonstration of genetic variability among bifidobacteria isolated from rats fed with raw kidney beans.

A rise in bifidobacterial numbers resembling the Escherichia coli overgrowth phenomenon was observed in the rat small intestine in a feeding experiment with kidney beans. Bifidobacterial colony counts increased from 7.6 x 10(6) to 1.7 x 10(8) cfu.g-1 of intestinal tissue in the anterior part and from less than 1 x 10(5) to 2.65 x 10(8) cfu.g-1 in posterior part of the intestine. Fifteen bifidobacterial strains were purified and further analysed. Random amplified polymorphic DNA (RAPD) assays were used to genetically differentiate bifidobacterial isolates from rat gut and compare them with type strains of 20 different species from the genus Bifidobacterium. A total of 80 arbitrary decamere primers were screened with 6 isolates, and 7 primers were chosen for the final analysis. The amplified DNA bands were scored and analysed by the unweighted pair-group method using arithmetic averages clustering. The isolates were not identical to each other nor to the screened type strains. Whereas it was possible to group 12 of the isolates into 2 separate clusters, 3 strains showed no significant relatedness to any strain. The results of the RAPD analysis indicated that there was a large degree variability among the bifidobacteria in the rat gut and demonstrated the potential applicability of such an approach in the investigation of microbial diversity in complex ecosystems.

Animal Nutritional Physiological Phenomena↗

[Unique properties of highly radioresistant bacteria].

In connection with the Chernobyl Nuclear Power Plant (ChNPP) accident and the negative ecological after-effects for biota in this zone the interest has arisen to radioresistant bacteria, as to the most dynamic model of the given ecosystem, and to mechanisms which provide resistance of bacteria to ionizing radiation. The analysis of published data has shown that the radioresistant bacteria are not interrelated taxonomically and phylogenetically. The extreme radioresistant bacteria are represented by the Deinococcus species, which form a group phylogenetically close to the line Thermus-Meiothermus. Other radioresistant bacteria are the representatives of the genera Rubrobacter, Methylobacterium, Kocuria, Bacillus and some archebacteria. Data on natural habitats, of radioresistant bacteria are not numerous. In a number of cases it is difficult to distinguish their natural habitats, as they were isolated from the samples which were previously exposed to X-ray or gamma-irradiation, or from the ecosystems with the naturally raised radioactivity. To understand the strategy of survival of radioresistant bacteria, we briefly reviewed the mechanism of action of various species of radiation on cells and macromolecules; physiological signs of the cell damage caused by radiation; mechanisms eliminating (repairing) these damages. More details on mechanisms of the DNA repair in D. radiodurans are described. The extreme resistance of D. radiodurans to the DNA damaging factors is defined by 1) repair mechanisms which fundamentally differ from those in other procaryotes; 2) ability to increase the efficiency of a standard set of the DNA repairing proteins. Literary and own data on the effect of radiation on survival of various groups of bacteria in natural ecosystems are summarized. The ecological consequences of the ChNPP accident for soil bacteria in this region were estimated. The reduction of the number of soil bacteria and recession of microbial diversity under the effect of anthropogenic radiation was shown.

Bacteria↗

Expression and isolation of antimicrobial small molecules from soil DNA libraries.

Natural products have been a critically important source of clinically relevant small molecule therapeutics. However, the discovery rate of novel structural classes of antimicrobial molecules has declined. Recently, increasing evidence has shown that the number of species cultivated from soil represents less than 1% of the total population, opening up the exciting possibility that these uncultured species may provide a large untapped pool from which novel natural products can be discovered. We have constructed and expressed in E. coli a BAC (bacterial artificial chromosome) library containing genomic fragments of DNA (5-120kb) isolated directly from soil organisms (S-DNA). Screening of the library resulted in the identification of several antimicrobial activities expressed by different recombinant clones. One clone (mg1.1) has been partially characterized and found to express several small molecules related to and including indirubin. These results show that genes involved in natural product synthesis can be cloned directly from S-DNA and expressed in a heterologous host, supporting the idea that this technology has the potential to provide novel natural products from the wealth of environmental microbial diversity and is a potentially important new tool for drug discovery.

Amino Acid Sequence↗

Anaerobic biodegradation of alkanes by enriched consortia under four different reducing conditions.

Enrichments of alkane-degrading microorganisms were established under sulfate-reducing, denitrifying, iron-reducing, and methanogenic conditions using an estuarine sediment. The sulfate-reducing and denitrifying enrichments mineralized [1-14C]hexadecane to 14CO2. Degradation was coupled to sulfate reduction and denitrification, as indicated by the ratios of hexadecane degraded to the electron acceptors reduced. Dependence of hexadecane degradation by the sulfate-reducing enrichments on sulfate reduction was also shown. The results indicate the existence of diverse microbial communities capable of alkane degradation in the sediment studied.

Alkanes↗

Effects of temperature on biodegradation characteristics of organic pollutants and microbial community in a solid phase aerobic bioreactor treating high strength organic wastewater.

The BOD removal rate and microbial community structure in a solid phase aerobic bioreactor using polyvinyl alcohol gel particles as packing material for the treatment of high strength organic wastewater were investigated at various temperatures. The BOD removal rate in the bioreactor increased when the temperature increased from 20 degrees C to 30 degrees C, 40 degrees C, and 50 degrees C, but it decreased when the temperature increased from 50 degrees C to 60 degrees C. Higher temperature enhanced the endogenous respiration of microbes in the bioreactor. The microbial community structure in the bioreactor was analyzed with quinone profile. The experimental results showed that the microbial community structure in the bioreactor was significantly affected by temperature. The dominant quinone of the microbes inhabiting the bioreactor was ubiquinone-8 at 30 degrees C, but that at 50 degrees C and 60 degrees C was menaquinone-7. It was estimated that the thermophilic Bacillus having menaquinone-7 dominated in the bioreactor at higher temperature. The microbial diversity in the bioreactor varied with temperature.

Bacillus↗

Characterization of microbial community in an activated sludge process treating domestic wastewater using quinone profiles.

The dynamics of microbial community structure of activated sludges in a small-scale domestic wastewater treatment process were examined using a novel approach of quinone profiles. The composition and content of quinones in the activated sludges were analyzed monthly over a period of one year. More than 4 types of ubiquinones and 12 types of menaquinones were observed in the activated sludges, with the dominant quinones being ubiquinone (UQ)-8, menaquinone (MK)-7, followed by UQ-10, MK-8 and MK-6. The total quinone contents in the activated sludges varied from 0.93 to 2.68 mumol per gram of particle organic carbon. The molar ratio of ubiquinones to menaquinones (UK/MK) changed from 0.38 to 0.98, indicating that anaerobic bacteria dominated the microbial community of the activated sludges examined. The ratio of UQ/MK varied similar to that of dissolved oxygen in the bulk. The microbial diversity of the activated sludges calculated from the quinone compositions was 13.4-16.8. The diversity of menaquinones was much higher than that of ubiquinones, and increased slightly with increasing temperature. The microorganisms containing menaquinones appear to be sensitive to the change in temperature than those containing ubiquinones.

Bacteria↗

Monitoring biofilm formation and activity in drinking water distribution networks under oligotrophic conditions.

In this study, the construction a model distribution system suitable for studies of attached and suspended microbial consisted of two loops connected in series with a total of 140 biofilm sampling points. The biofilm from the system was studied using 11 different microbial methods and the results were compared and discussed. The methods were used for biomass quantification (AODC, HPC and ATP determination), visualisation of structure (CLSM), activity measurement (leucine incorporation, AOC removal rate, respiration of benzoic acid, CTC and live/dead stains), and microbial diversity profiling (clone libraries and DGGE).

Adenosine Triphosphate↗

Microbial community structure of membrane fouling film in an intermittently and continuously aerated submerged membrane bioreactor treating domestic wastewater.

There was an observable difference in microbial community structure between suspended microorganisms and membrane biofouling film in intermittently and continuously aerated SMBRs. The dominant quinone type of membrane biofouling film in an intermittently aerated SMBR was ubiquinone (UQs)-8, -10 followed by menaquinone (MKs)-8(H4) and -8(H2). But that of the continuously aerated SMBR was UQs-10, -8 followed by MKs-6 and -8(H4). The experimental results also showed that the conditions of an intermittently aerated SMBR may contribute to biofouling by Pseudomonas, Moraxella, Vibrio (quinone type UQ-8), Staphylococcus warneri (quinone type MK-7), Micrococcus sp. (quinone type MK-8(H2)) and Nocardia sp. (quinone type MK-8(H4)), but biofouling in a continuously aerated SMBR may be due to Paracoccus sp. (quinone type: UQ-10) and Flavobacterium species (quinone type: MK-6). The microbial diversities in the intermittently aerated SMBR were 10.9 and 9.4 for biofouling film and suspended microorganisms, respectively. For the continuously aerated SMBR, the results were 10.4 and 10.5 for biofouling film and suspended microorganisms, respectively.

Bacteria↗

Change of microbial community structure by respiratory quinone profile at intermittently aerated membrane bioreactor.

In the present study, the microbial community structure in an intermittently aerated submerged membrane bioreactor treating domestic wastewater was observed using the respiratory quinone profiles. The effects of different time interval for the aerobic and anoxic period on microbial community structure were examined with 60/90 min (Step 1) and 90/60 min (Step 2) as anoxic/aerobic periods. There was an observable slight difference in microbial community structure between Step 1 and Step 2 in the submerged membrane bioreactor. The dominant quinone types for Step 1 at both anoxic and aerobic conditions were UQ-8 followed by UQ-10 and MK-6, but those for Step 2 were UQ-8, MK-6 and MK-10(H4). The microbial diversity of Step 1 and Step 2 based on the composition of all quinones was 10.6-11.7 and 13.3-13.0 for anoxic and aerobic conditions, respectively. The present results suggest that the introduction of intermittent aeration into the submerged membrane bioreactor has little influence on the bacterial community structure.

Air Movements↗

Studies on cultured and uncultured microbiota of wild culex quinquefasciatus mosquito midgut based on 16s ribosomal RNA gene analysis.

To describe the midgut microbial diversity and the candidate bacteria for the genetic manipulation for the generation of transgenic mosquitoes refractory to transmission of diseases, the microbiota of wild Culex quinquefasciatus mosquito midgut was studied using a conventional culture technique and analysis of a 16S ribosomal RNA (rRNA) gene sequence library. The culturable microbiota was identified as Acinetobacter junii, Ac. calcoaceticus, Aeromonas culicicola, Bacillus thuringiensis, Microbacterium oxydans, Pantoea agglomerans, Pseudomonas aeruginosa, Staphylococcus epidermidis, Stenotrophomonas maltophila and an unidentified bacterium from the host Drosophila paulistorium. The 16S rRNA gene library was composed of 46% unidentified and uncultured bacteria, 41% Acinetobacter spp., and 13% Lactococcus spp. The coverage calculated for the 150 clones was 83.3%. Thus, the probability of the next cloned sequence falling in a novel operational taxonomic unit (not yet observed) was 16.7%. The majority of the cultured isolates and the 16S rRNA gene library clones belonged to the gamma-proteobacteria class. Most of the bacteria have been previously reported to inhabit the midgut of different mosquito species. Therefore, the results of this study indicate that different mosquito species harbor common representatives of the microbiota that may be the potential candidates for genetic manipulation to control the disease transmission capabilities of the host.

Animals↗

How are gene sequence analyses modifying bacterial taxonomy? The case of Klebsiella.

Bacterial names are continually being changed in order to more adequately describe natural groups (the units of microbial diversity) and their relationships. The problems in Klebsiella taxonomy are illustrative and common to other bacterial genera. Like other bacteria, Klebsiella spp. were isolated long ago, when methods to identify and classify bacteria were limited. However, recently developed molecular approaches have led to taxonomical revisions in several cases or to sound proposals of novel species.

Bacterial Typing Techniques↗

[Ecological interpretation and related strategies for low culturability of microorganisms].

Pure culture technique has been a fundamental method since its invention in microbiology, but its isolated and monotonous environment contradicts microbial diversity and cooperation relationship in natural environment. And this contradiction directly results in the uncultivability of some microbes in media. From ecological viewpoint, the recovery barriers of natural microbes mainly include the crash of cooperation in natural environment, the great change of nutrient in new environment and the loss of native niche. The main methods and strategies on low curturability of microorganisms are culture-independent methods, enrichment culture, mixed culture, dilution culture, simulating nature culture and synthetic method, which can to some degree compensate for the traditional approach and improve the low culturability of some bacteria.

Biodiversity↗

Application of molecular nucleic acid-based techniques for the study of microbial communities in monuments and artworks.

Microorganisms play critical roles in every kind of habitat on Earth, including those constructed by humans. Thus, our cultural heritage is affected by microbial colonization. While classical microbiological methods based on culturing procedures have provided important, but limited information on the microbial diversity of natural samples, novel molecular techniques have been extremely valuable in unraveling the diversity of microbiota involved in the biodeterioration of our monuments and artworks. The knowledge gained from these approaches has allowed the design of strategies for conserving and protecting monuments for the benefit of future generations. This review describes the state-of-the-art of the application of molecular methods to the analysis of cultural assets, and provides near-future perspectives on the subject.

Bacteria↗

Impact of the nematophagous fungus Pochonia chlamydosporia on nematode and microbial populations.

The microbial and nematode populations associated with two plants (tomato and cabbage) inoculated with the nematophagous fungus, Pochonia chlamydosporia var. chlamydosporia or root knot nematode (Meloidogyne incognita), or both, were compared with those in unplanted controls. The dominant factor affecting culturable microbial populations was found to be the presence or absence of tomato plants. Generally microbial colony counts were lowest in unplanted soil, small increases were associated with cabbage and significantly greater numbers with tomato plants. Differences in microbial diversity (estimated from community profiles of carbon substrate utlisation, using Biolog) were observed between planted and unplanted soils, however, there were few differences between soils with either of the two plants. The presence of P. chlamydosporia was associated with a reduction in the numbers of plant parasitic nematodes (51%-78%) including the migratory ectoparasites, whereas free-living nematodes, culturable bacteria and bacterial populations assessed by Biolog were unaffected by the application of fungus.

Animals↗

Life's unity and flexibility: the ecological link.

The small size, ubiquity, metabolic versatility and flexibility, and genetic plasticity (horizontal transfer) of microbes allow them to tolerate and quickly adapt to unfavorable and/or changing environmental conditions. Prokaryotes are endowed with sophisticated cellular envelopes that contain molecules not found elsewhere in the biological world. Although prokaryotic cells lack the organelles that characterize their eukaryotic counterparts, their interiors are surprisingly complex. Prokaryotes sense their environment and respond as individual cells to specific environmental challenges; but prokaryotes also act cooperatively, displaying communal activities. In many microbial ecosystems, the functionally active unit is not a single species or population (clonal descendence of the same bacterium) but a consortium of two or more types of cells living in close symbiotic association. Only recently have we become aware that microbes are the basis for the functioning of the biosphere. Thus, we are at a unique time in the history of science, in which the interaction of technological advances and the exponential growth in our knowledge of the present microbial diversity will lead to significant advances not only in microbiology but also in biology and other sciences in general.

Adaptation, Physiological↗

[Methods for the study of microbial communities in fermented foods].

The importance of ecological concepts to understand the presence and growth of microorganisms in foods is presently recognized. The production of fermented foods under controlled conditions and its safety assurance depend on the knowledge and control of their microbiota. Traditional fermented foods are obtained by natural fermentations (in which no inoculum is added) and contain complex microbiotas, which are difficult to describe through the use of traditional microbiological methods. The microbial structure of these foods can be studied with different approaches. One of them consists on the typification of isolated microorganisms with methods based on DNA as RFLP, ribotyping, AFLP, ARDRA and RAPD. In order to detect non-culturable or not yet cultured microorganisms, nucleic acids are directly extracted from foods and the microbial diversity is determined from them. Examples of these techniques are the construction of 16S rDNA clone libraries and fingerprinting techniques, such as DGGE and TGGE. Recent advances on the application of these techniques on the study of fermented foods are presented.

Bacteria↗