Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “microbial function”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources

Loss of N-glycolylneuraminic acid in humans: Mechanisms, consequences, and implications for hominid evolution.

The surface of all mammalian cells is covered with a dense and complex array of sugar chains, which are frequently terminated by members of a family of molecules called sialic acids. One particular sialic acid called N-glycolylneuraminic acid (Neu5Gc) is widely expressed on most mammalian tissues, but is not easily detectable on human cells. In fact, it provokes an immune response in adult humans. The human deficiency of Neu5Gc is explained by an inactivating mutation in the gene encoding CMP-N-acetylneuraminic acid hydroxylase, the rate-limiting enzyme in generating Neu5Gc in cells of other mammals. This deficiency also results in an excess of the precursor sialic acid N-acetylneuraminic acid (Neu5Ac) in humans. This mutation appears universal to modern humans, occurred sometime after our last common ancestor with the great apes, and happens to be one of the first known human-great ape genetic differences with an obvious biochemical readout. While the original selection mechanisms and major biological consequences of this human-specific mutation remain uncertain, several interesting clues are currently being pursued. First, there is evidence that the human condition can explain differences in susceptibility or resistance to certain microbial pathogens. Second, the functions of some endogenous receptors for sialic acids in the immune system may be altered by this difference. Third, despite the lack of any obvious alternate pathway for synthesis, Neu5Gc has been reported in human tumors and possibly in human fetal tissues, and traces have even been detected in normal human tissues. One possible explanation is that this represents accumulation of Neu5Gc from dietary sources of animal origin. Finally, a markedly reduced expression of hydroxylase in the brains of other mammals raises the possibility that the human-specific mutation of this enzyme could have played a role in human brain evolution.

Animals↗

Pattern recognition receptors: a contemporary view on liver diseases.

Pattern recognition receptors (PRRs) function as sensors of microbial danger signals enabling the vertebrate host to initiate an immune response. PRRs are present not only in immune cells but also in liver parenchymal cells and the complexity of the cell populations provide unique aspects to pathogen recognition and tissue damage in the liver. This review discusses the role of different PRRs in pathogen recognition in the liver, and focuses on the role of PRRs in hepatic inflammation, cholestasis, ischemia, repair and fibrosis. PRRs as novel therapeutic targets are evaluated.

Animals↗

Siderophores.

Siderophores, defined as low-iron-induced virtually ferric-specific ligands, are widely distributed in microbial species where they function in the sequestration and transport of iron. In Escherichia coli biosynthesis of siderophores is negatively regulated at the transcriptional level by ferrous ion in conjunction with a repressor protein, Fur (ferric uptake regulation). Siderophores are a component of the virulence armamentarium of clinical isolates of E. coli and of certain other microorganisms pathogenic to man, animals, and plants. The mechanism whereby cells accumulate sufficient iron for activation of essential enzymes while, at the same time, avoiding excess of a potentially toxic element remains one of the most challenging problems in biochemistry.

Bacteria↗

Bacterial inoculum density and probability of para-nitrophenol biodegradability test response.

This study has been carried out to establish a model linking probability of positive response in para-nitrophenol biodegradability test to controlled variables of the test (suspended solids, SS; total bacteria, AODC; cultivable bacteria, CFU; specific biodegraders, MPN). Series of dilution of 11 raw inocula (6 activated sludges, 5 river waters) were tested. They reveal very dispersed values of biomass measured as SS, AODC, and CFU and quite comparable values of specific biodegraders for each category of inoculum (river or sludge). The proposed model fits well the empirical distribution of the experimental frequency of positive results versus inoculum density for each controlled variable. The constants k of the model, representing the fraction of biodegraders for each inoculum, were tested by the likelihood ratio test and were proven to be different from one another according to the biomass descriptor and the origin of the inoculum. The probabilistic model, in the case of para-nitrophenol biodegradation, indicates that standardized official tests (closed bottle, AFNOR, Sturm, and MITI I) are seldom optimal under those conditions. It allows the determination of which inoculum concentration can lead to a high probability (e.g., 99.9%) of observing paranitrophenol biodegradation by raw inocula.

Bacteria↗

Microbial methods for assessing contaminant effects in sediments.

Contaminated sediments influence drastically the long-term toxicological and ecological properties of aquatic ecosystems. During the past three decades, scientific knowledge about sediment-water exchange processes and the deposition and distribution of pollutants in water and sediment phases has been supplemented by extensive research on the effects of sediment-associated pollutants on aquatic organisms. Basic research in microbiology, ecology, and toxicology has uncovered the crucial role of sediment microorganisms for the biodegradation of organic matter and for the cycling of nutrients, as well as the susceptibility of these processes to toxic pollution events. Microorganisms have been extensively applied in aquatic toxicology, and various microbial toxicity tests are today available that successfully couple microbial toxicity endpoints to the specificity of the sediment matrix. Sediment-associated toxicants can be brought in contact with test bacteria using sediment pore waters, elutriates, extracts, or whole-sediment material. Toxicity indication principles for microorganisms are versatile and comprise growth and biomass determinations, respiration or oxygen uptake, bacterial luminescence, the activity of a variety of enzymes, and a compendium of genotoxicity assays. The border between toxicological and ecological contaminant effect evaluations in sediments is flexible, and long-term ecological predictions should also include an assessment of pollutant degradation capacities and of key reactions in element cycling. Evaluating microbial community structure and function in environmental systems makes use of modern molecular techniques and bioindicators that could trigger a new quality in the assessment of contaminated sediments in terms of indication of subtoxic effects and early-warning requirements.

Bacteriological Techniques↗

Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles.

Network topology is a necessary fundament to understand function and properties of microbial reaction networks. A valuable method for experimental elucidation of metabolic network topology is metabolic flux ratio analysis, which quantifies the relative contribution of two or more converging pathways to a given metabolite. It is based on 13C-labeling experiments, gas chromatography-mass spectrometry analysis, and probabilistic equations that relate mass distributions in proteinogenic amino acids to pathway activity. Here, we describe the protocol for sample generation and illustrate the principles underlying the calculation of metabolic flux ratios with three examples. These principles are also implemented in the publicly available software FiatFlux, which directly calculates flux ratios from the mass spectra of amino acids.

Amino Acids↗

Visualization of the bacterial polysaccharide capsule.

The highly hydrated capsule of E. coli strains is composed of a large number of polysaccharide fibers of which the thinnest measure about 2 nm in width. The fibers may span the entire distance from the outer membrane to the outer rim of the capsule and show a propensity to associate with each other to form thicker filaments. Presence of thick filaments may also indicate a partial collapse of the capsular organization due to removal of water. The in vivo capsule represents a relatively open structure with the negatively charged polysaccharide fibers permitting the binding of large quantities of water and ions, and providing intracellular space for diffusing molecules to access the envelope membranes even in conditions of high cell density. Negative charge and steric hindrance of the polysaccharide strands protect the cells against attack by a large variety of harmful macromolecules and against infection by most bacteriophages. Two types of procedure have been most successful in maintaining the size and overall structure of the capsule: (a) the interaction of cationic molecules with the in vivo capsule, and (b) the use of antibody to stabilize capsules for subsequent dehydration and plastic embedding. A further type of potentially useful procedure, cryofixation and cryosubstitution, has shown interesting results in a number of cases. These techniques are expected to play a significant role in structural studies in the near future. The sites of export of capsular antigen have been described in earlier conventional electron microscopic studies. Data obtained from the recent technique of "on-section" labeling support the model that both the capsular antigen and the O antigen are assembled at junctions of the inner and outer membrane. It is anticipated that one will be able to discern in greater ultrastructural detail the membranes at which the antigen is translocated. Novel membrane fixation and isolation techniques will have to be established and employed in a combination of sensitive microscopic techniques and immuno- and enzyme localization methods. These developments will make it possible to explore questions pertaining to the maintenance and structural organization of microbial capsules and the functional interaction of polysaccharides with natural surfaces, man-made substances and drugs.

Antigens, Bacterial↗

Seminalplasmin: a protein with many biological properties.

Proteins present in the seminal plasma of mammals are known to influence functions associated with ejaculated spermatozoa such as motility, capacitation, acrosome reaction and fertilising ability. The proteins isolated and characterised so far influence only one of the above functions of spermatozoa. Seminalplasmin, a protein isolated from the seminal plasma of bull is exceptional in that it influences many of the above spermatozoal functions. It is also a potent antimicrobial protein and capable of lysing microbial and mammalian cells. The physiological function of seminalplasmin as nature's own antifertility agent is discussed.

Acrosome↗

Expression of human lysozyme mRNA in the mammary gland of transgenic mice.

Owing to its inherent antimicrobial effect and positive charge, the expression of human lysozyme in bovine milk could be beneficial by altering the overall microbial level and the functional and physical properties of the milk. We have used transgenic mice as model systems to evaluate the expression of human lysozyme containing fusion gene constructs in the mammary gland. Expression of human lysozyme was targeted to the mammary gland by using the 5' promoter elements of either the bovine beta (line B mice) or alpha s1 (line H mice) casein genes coupled to the cDNA for human lysozyme. Expression of human lysozyme mRNA was not found in mammary tissue from any of line B mice. Tissues were analysed from six lines of H mice and two, H6 and H5, were found to express human lysozyme mRNA in the mammary gland at 42% and 116%, respectively, of the levels of the endogenous mouse whey acidic protein gene. At peak lactation, female mice homozygous for the H5 and H6 transgene have approximately twice the amount of mRNA encoding human lysozyme as hemizygous animals. Expression levels of human lysozyme mRNA in the mammary gland at time points representing late pregnancy, early, peak and late lactation corresponded to the profile of casein gene expression. Human lysozyme mRNA expression was not observed in transgenic males, virgin females or in the kidney, liver, spleen or brain of lactating females. A very low level of expression of human lysozyme mRNA was observed in the salivary gland of line H5.

Animals↗

Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem.

Alterations in soil bacterial communities across a transect between a semi natural upland grassland and an agriculturally improved enclosure were assessed using culture-based methods and a nucleic-acid-based method, terminal restriction fragment length polymorphism (TRFLP). While plant diversity decreased across the transect towards the improved area, numbers of 16S rDNA terminal restriction fragments increased, indicating an increase in numbers of bacterial ribotypes. Bacterial numbers, microbial activity, and potential functional diversity also followed a similar trend, increasing with decreasing plant diversity. Alterations in bacterial community structure were coincident with changes in soil physicochemical properties which also changed across the transect. Increases in soil pH, nitrate, phosphorus, potassium, and calcium occurred toward the improved grassland, while organic matter and ammonium declined. The inverse relationship between floristic diversity and bacterial ribotype numbers suggests that soil physicochemical factors may be as influential in determining bacterial diversity in soils of upland grassland communities as floristic diversity.

Bacteria↗

Archaeal community structure and pathway of methane formation on rice roots.

The community structure of methanogenic Archaea on anoxically incubated rice roots was investigated by amplification, sequencing, and phylogenetic analysis of 16S rRNA and methyl-coenzyme M reductase (mcrA) genes. Both genes demonstrated the presence of Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Rice cluster I, an uncultured methanogenic lineage. The pathway of CH4 formation was determined from the 13C-isotopic signatures of the produced CH4, CO2 and acetate. Conditions and duration of incubation clearly affected the methanogenic community structure and the pathway of CH4 formation. Methane was initially produced from reduction of CO2 exclusively, resulting in accumulation of millimolar concentrations of acetate. Simultaneously, the relative abundance of the acetoclastic methanogens (Methanosarcinaceae, Methanosaetaceae), as determined by T-RFLP analysis of 16S rRNA genes, was low during the initial phase of CH4 production. Later on, however, acetate was converted to CH4 so that about 40% of the produced CH4 originated from acetate. Most striking was the observed relative increase of a population of Methanosarcina spp. (but not of Methanosaeta spp.) briefly before acetate concentrations started to decrease. Both acetoclastic methanogenesis and Methanosarcina populations were suppressed by high phosphate concentrations, as observed under application of different buffer systems. Our results demonstrate the parallel change of microbial community structure and function in a complex environment, i.e., the increase of acetoclastic Methanosarcina spp. when high acetate concentrations become available.

Acetates↗

Inhibition and stimulation effects in communities of wood decay fungi: exudates from colonized wood influence growth by other species.

The effects of exudates from uncolonized and from partly decayed beech wood on the extension rates of 16 later stage decay fungi were investigated. The partly decayed wood had been colonized by the pyrenomycete Eutypa spinosa, or the basidiomycetes Fomes fomentarius, Stereum hirsutum, and Trametes versicolor, all known as common early decay agents in European beech forests. Sterilized wood pieces were placed onto 0.5% malt agar, opposite to small agar plugs containing the test fungi. The latter showed very variable and species-specific growth responses to the various wood types. The presence of uncolonized wood stimulated extension rates in many species, whereas the four previously decayed wood types had variable stimulatory or inhibitory effects. Wood decayed by S. hirsutum resulted in reduced extension rate, delayed growth, or total inhibition in the majority of species, thus it is suggested that this species uses secondary metabolites in a defensive strategy. A single species was, however, stimulated in the presence of S. hirsutum-decayed wood. In contrast, the presence of wood decayed by F. fomentarius was stimulatory to 45% of the species. The other previously decayed wood types generally resulted in more variable responses, depending upon species. The results are discussed in an ecological context and it is suggested that the exudates from the partly decayed wood that are responsible for the reported effects may function as infochemicals, structuring microbial communities in wood.

Ecology↗

Whole-stream nitrate addition affects litter decomposition and associated fungi but not invertebrates.

We assessed the effect of whole-stream nitrate enrichment on decomposition of three substrates differing in nutrient quality (alder and oak leaves and balsa veneers) and associated fungi and invertebrates. During the 3-month nitrate enrichment of a headwater stream in central Portugal, litter was incubated in the reference site (mean NO3-N 82 microg l-1) and four enriched sites along the nitrate gradient (214-983 microg NO3-N l-1). A similar decomposition experiment was also carried out in the same sites at ambient nutrient conditions the following year (33-104 microg NO3-N l-1). Decomposition rates and sporulation of aquatic hyphomycetes associated with litter were determined in both experiments, whereas N and P content of litter, associated fungal biomass and invertebrates were followed only during the nitrate addition experiment. Nitrate enrichment stimulated decomposition of oak leaves and balsa veneers, fungal biomass accrual on alder leaves and balsa veneers and sporulation of aquatic hyphomycetes on all substrates. Nitrate concentration in stream water showed a strong asymptotic relationship (Michaelis-Menten-type saturation model) with temperature-adjusted decomposition rates and percentage initial litter mass converted into aquatic hyphomycete conidia for all substrates. Fungal communities did not differ significantly among sites but some species showed substrate preferences. Nevertheless, certain species were sensitive to nitrogen concentration in water by increasing or decreasing their sporulation rate accordingly. N and P content of litter and abundances or richness of litter-associated invertebrates were not affected by nitrate addition. It appears that microbial nitrogen demands can be met at relatively low levels of dissolved nitrate, suggesting that even minor increases in nitrogen in streams due to, e.g., anthropogenic eutrophication may lead to significant shifts in microbial dynamics and ecosystem functioning.

Alnus↗

A comparative study of secretory immunoglobulin A and immunoglobulin G in host defense in an in vitro pneumonia model.

BACKGROUND: An exaggerated inflammatory response to infections including nosocomial pneumonia may be detrimental to the host and contribute to morbidity and mortality. Both secretory immunoglobulin A (SIgA) and IgG contribute to the immune defense of respiratory surfaces. However, their relative ability to protect against invasive infections and the resultant host inflammatory response are unknown and were the basis for this study. METHODS: Calu-3 cell (a respiratory epithelial cell line) monolayers were established in a Transwell system (Costar Corp., Cambridge, MA). Escherichia coli and either polyclonal SIgA or IgG were inoculated into the apical chamber and neutrophils (polymorphonuclear neutrophils) were added to the basal chamber. PMN cytotoxic potential was indexed by %CD11b expression, superoxide anion (O(2)-) production, and % elastase release. Bacterial translocation into the basal chamber was quantitated after log transformation. Calu-3 monolayer integrity was indexed by permeability to dextran fluorescein isothiocyanate. RESULTS: The addition of E coli to Calu-3/polymorphonuclear cocultures led to increases in O(2)- generation, elastase release, and CD11b expression. These effects were diminished by the addition of SIgA but not IgG. A similar effect was noted with Calu-3 barrier function. CONCLUSIONS: SIgA may function to protect against microbial invasion of respiratory surfaces and protect against tissue injury from an exaggerated inflammatory response.

Bacterial Translocation↗

Effect of heavy metals on substrate utilization pattern, biomass, and activity of microbial communities in a reclaimed mining wasteland of red soil area.

The microbial biomass, basal respiration, and substrate utilization pattern in a copper mining wasteland of red soil area, southern China, were investigated, and indicated that soil microflora were obviously affected by heavy metals. Microbial biomass and basal respiration were negatively affected by comparatively high heavy metal levels. Two important microbial ecophysiological parameters, namely, the microbial biomass C (C(mic))/microbial biomass N (N(mic)) ratio and the metabolic quotient (qCO(2)) were significantly correlated to heavy metal stress. There was a significant decrease in the C(mic)/N(mic) ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of Biolog data for sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and functional diversity. All the results showed that soil microbiological parameters could have great potential as sensitive, effective, and liable indicators of the stresses or perturbations in soils of mining ecosystems.

Biodegradation, Environmental↗