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Results for “microbial evolution”

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At least 631 records · Page 35Linked to original sources
PubMed2002

Mammalian toll-like receptors.

OBJECTIVE: To review the role of mammalian Toll-like receptors (TLRs) in host defense. DATE SOURCES: MEDLINE search and current literature. RESULTS: First, TLRs participate in the recognition of molecular patterns present on microorganisms. Second, TLRs are expressed at the interface with the environment, the site of microbial invasion. Third, activation of TLRs induces expression of costimulatory molecules and the release of cytokines that instruct the adaptive immune response. Fourth, activation of TLRs leads to direct antimicrobial effector pathways that can result in elimination of the foreign invader. CONCLUSIONS: Maintained throughout evolution, mammalian TLRs are proteins that participate in innate immunity to microbial pathogens. Insights into TLR activation pathways provide new therapeutic targets for intervention in infectious and immunologic disease.

Animals↗
PubMed2026

Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.

Though they jointly shape community responses to environmental perturbations, ecology and evolution are often examined separately, even in microorganisms where both occur over short timescales. Here we examine ecological and evolutionary responses to 33 years of nitrogen fertilization using the legume-rhizobium mutualism. Pairing a manipulative inoculation study with full-length 16S rRNA gene amplicon sequencing and structural equation modeling allows us to synthesize across biological scales: whole bacterial community, genus Rhizobium, Rhizobium ASVs, and symbiosis plasmids. Clover's preferred partner decreases in N-addition soils, limiting host growth, while a diverse and largely uncharacterized Rhizobium community increases. This ecological change is compounded by a concurrent evolutionary degradation of symbiont partner quality via changing frequencies of symbiotic plasmids. Ecological (rarer symbionts) and evolutionary (inferior symbionts) processes each accounted for roughly half of this loss of host benefit, revealing that ecology and evolution jointly shape mutualism breakdown over the short timescales typical of microbial systems.

ecology↗
PubMed1997

Marine microbial diversity: the tip of the iceberg.

New techniques for evaluating the biological diversity of naturally occurring microbial assemblages combine nucleic-acid-sequencing techniques with molecular-phylogenetic analysis. These molecular techniques avoid many of the selective biases inherent in traditional cultivation-based surveys and provide a universal criterion for identifying and relating diverse microbial species. Application of the molecular approach in marine environments has revealed the existence of unique and previously unrecognized microorganisms. These are providing fresh insight into the ecology, evolution and biotechnological potential of the largely untapped resource represented by the marine microbial world.

Biotechnology↗
PubMed1982

Somatic cell parasitism and the evolution of somatic tissue compatibility.

Selection pressures proposed to account for the convergent evolution of self/not-self recognition systems in lower organisms include defense against microbial parasites and somatic cell variants. Direct support for the existence of somatic cell parasites in natural populations has been lacking. I here report the occurrence of a somatic cell parasite in the cellular slime mold Dictyostelium mucoroides and discuss the implications of this phenomenon to the evolution of mechanisms of somatic tissue compatibility.

Animals↗
PubMedDate not supplied

Bacteriocin diversity: ecological and evolutionary perspectives.

The bacteriocin family is the most abundant and diverse group of bacterial defense systems. Bacteriocins range from the well-studied narrow spectrum, high molecular weight colicins produced by Escherichia coli and the short polypeptide lantibiotics of lactic acid bacteria to the relatively unknown halocins produced almost universally by the haolobacteria. The abundance and diversity of this potent arsenal of weapons is clear. Less clear is their evolutionary origins and the role they play in mediating microbial interactions. The goal of this review is to explore what we know about the evolution and ecology of the best-characterized family of bacteriocins, the colicins. We summarize current knowledge of how such extraordinary protein diversity arose and is maintained in microbial populations and what role these toxins play in mediating microbial population-level and community-level dynamics.

Bacteriocins↗
PubMed1984

Effective diffusivity of oxygen in microbial pellets.

In a typical submerged aerobic fermentation with microbial pellets, the effective diffusivity of oxygen in the pellets is probably the most important, yet most difficult transport property to characterize experimentally. Its values directly indicate the efficiency or deficiency of oxygen to individual cells, and thus the biological activity of the microorganisms. In the past, it was not possible to assess reliably the effective diffusivity of oxygen in pellets due to several reasons. Firstly, most oxygen electrodes available were coarse, and hence not suitable for in situ measurements. Secondly, there was a lack of methods rigorous enough to characterize the structure of the microbial pellets. A state-of-the-art review of the literature relating to the feature subject is presented. Emphasis is laid upon development and evolution of the means for quantitative characterization of the effective diffusivity of oxygen in microbial pellets.

Journal Article↗
PubMed1995

Of microbes and macrophages: entry, survival and persistence.

The macrophage is capable of fulfilling the roles of both host cell and effector cell in the immune clearance of many microbial infections. This dual capacity has led to the evolution of intriguing mechanisms whereby pathogens ensure the establishment and maintenance of intracellular infections. The strategies developed range from passive avoidance mechanisms to extremely active modulation of cell function. Recent advances have been made in our appreciation of the processes of intramacrophage parasitization from initial ligand-receptor interactions, through establishment of a stable intracellular environment, to the maintenance of a persistent infection.

Animals↗
PubMed2004

Effects of bacterial activities on the release of heavy metals from contaminated dredged sediments.

The potential impact of indigenous bacterial processes on the release of heavy metals from dredged sediment deposits was investigated. Batch re-suspension experiments were conducted in order to investigate the release of Zn, Cd, Cu and Pb from a polluted anoxic sediment submitted to oxidative perturbations. The concentrations of heavy metals, sulphate and dissolved organic carbon (DOC) were periodically recorded, and cell counts were performed to follow the evolution of several bacterial species. The specific effects of microbial processes were quantified by performing re-suspension assays on sterilised samples. Moreover, the effect of an initial acidification of the system was studied. The results showed that metal release was mainly due to oxidation of sulphide minerals contained in the sediment. Sulphur-oxidising bacteria such as Acidithiobacillus thiooxidans were identified to play a major role in the process, by enhancing the oxidation kinetic. However, the acid production resulting from these reactions was almost totally buffered by the dissolution of the calcite present in the sediment. Copper was released to a lesser extent, and a strong association with organic matter was observed. Lead was not observed in solution, because of its low solubility at neutral conditions and of its re-adsorption on the solid phase. The initial acidification of the system resulted in an faster growth of the acidophilic A. thiooxidans. A subsequent pH drop originating from microbial processes was then observed during the first stages of the experiment. As a consequence, drastic increases in metal (Zn, Cd) release were observed.

Acidithiobacillus thiooxidans↗
PubMed1999

Testing ancient RNA-protein interactions.

The past decade in molecular biology has seen remarkable advances in the study of the origin and early evolution of life. The mathematical tools for analyzing DNA and protein sequences, coupled with the availability of complete microbial genome sequences, provide insight almost as far back as the age of the nucleic acids themselves. Experimental evolution in the laboratory and especially in vitro evolution of RNA provide insight into a hypothetical world where RNA, or a close relative, may have debuted as a primary functional and informational molecule. The ability to isolate new functional RNAs from random sequences now ultimately makes the world of possible primitive chemical interactions accessible even when the molecules or reactions are no longer present in modern species. Thus we can at last form direct experimental tests of specific models for the origin of RNA-protein associations, such as those that influenced the genetic code. This marks a turning point for probing the origin and early history of life at the molecular level.

Biological Evolution↗
PubMed2003

Possibilities for the detection of microbial life on extrasolar planets.

We consider possibilities for the remote detection of microbial life on extrasolar planets. The Darwin/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes. Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms. Satellites in Earth orbit routinely monitor colonies of terrestrial algae in oceans and lakes by analysis of reflected ocean light in the visible region of the spectrum. These remote sensing techniques suggest strategies for extrasolar searches for signatures of chlorophylls and related photosynthetic compounds associated with life. However, identification of such life-related compounds on extrasolar planets would require observations through strong, interfering absorptions and scattering radiances from the remote atmospheres and landmasses. Techniques for removal of interfering radiances have been extensively developed for remote sensing from Earth orbit. Comparable techniques would have to be developed for extrasolar planet observations also, but doing so would be challenging for a remote planet. Darwin/TPF coronagraph concepts operating in the visible seem to be best suited for searches for extrasolar microbial life forms with instruments that can be projected for the 2010-2020 decades, although resolution and signal-to-noise ratio constraints severely limit detection possibilities on terrestrial-type planets. The generation of telescopes with large apertures and extremely high spatial resolutions that will follow Darwin/TPF could offer striking possibilities for the direct detection of extrasolar microbial life.

Biological Evolution↗
PubMed2003

On the nature of gene innovation: duplication patterns in microbial genomes.

Gene duplication is considered a major force in gene family expansion and gene innovation. As gene copies assume novel functions, they must avoid periods of neutrality or be deleted from the genome. Current opinions state that copies avoid neutrality through gene dosage effects. These copies are therefore selected from an early stage. This study concentrates on the flow of copies from recent duplication to gene innovation. We have studied 21 microbial genomes using amino acid divergence to describe paralog evolution in the long-term perspective. Five of these were studied in closer detail using nucleotide divergence for a shorter perspective. It was found that rates of duplication and deletion are high, with only a small fraction of duplications retained and apparently selected. This leads to a steady accumulation of paralogs, which seems to be of a similar magnitude in most of the genomes. Furthermore, it is found that genes of high expression level, as measured by their codon bias, are strongly underrepresented among the most recent duplications. Based on these and other observations, it is suggested that gene innovation is driven by amplification of weak, ancillary functions rather than strong, established functions.

DNA Transposable Elements↗
PubMed1996

The beta-ketoadipate pathway and the biology of self-identity.

The beta-ketoadipate pathway is a chromosomally encoded convergent pathway for aromatic compound degradation that is widely distributed in soil bacteria and fungi. One branch converts protocatechuate, derived from phenolic compounds including p-cresol, 4-hydroxybenzoate and numerous lignin monomers, to beta-ketoadipate. The other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates. Enzyme studies and amino acid sequence data indicate that the pathway is highly conserved in diverse bacteria, including Pseudomonas putida, Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Rhodococcus erythropolis, and many others. The catechol branch of the beta-ketoadipate pathway appears to be the evolutionary precursor for portions of the plasmid-borne ortho-pathways for chlorocatechol degradation. However, accumulating evidence points to an independent and convergent evolutionary origin for the eukaryotic beta-ketoadipate pathway. In the face of enzyme conservation, the beta-ketoadipate pathway exhibits many permutations in different bacterial groups with respect to enzyme distribution (isozymes, points of branch convergence), regulation (inducing metabolites, regulatory proteins), and gene organization. Diversity is also evident in the behavioral responses of different bacteria to beta-ketoadipate pathway-associated aromatic compounds. The presence and versatility of transport systems encoded by beta-ketoadipate pathway regulons is just beginning to be explored in various microbial groups. It appears that in the course of evolution, natural selection has caused the beta-ketoadipate pathway to assume a characteristic set of features or identity in different bacteria. Presumably such identities have been shaped to optimally serve the diverse lifestyles of bacteria.

Adipates↗
PubMed1991

Human lysosomal cathepsin G and granzyme B share a functionally conserved broad spectrum antibacterial peptide.

Human neutrophil lysosomal cathepsin G (cat G) exerts broad-spectrum antibacterial action in vitro against Gram-negative and -positive bacteria independent of its serine protease activity. We recently determined that an internal peptide of cat G (HPQYNQR), obtained after digestion of cat G with clostripain, possessed broad-spectrum antibacterial action in vitro, displaying an ED50 of 5 x 10(-5) M. In order to evaluate the structure-antibacterial properties of this peptide, synthetic variants with single alanine substitutions at each position were prepared and tested for antibacterial action. We found that alanine substitution for His-1 or Tyr-4, or certain modifications of the His-1 side chain, produced nonbactericidal peptides. A hexapeptide lacking the COOH-terminal Arg-7 but not a pentapeptide lacking both Gln-6 and Arg-7 possessed in vitro bactericidal activity. Interestingly, the cat G bactericidal peptide displays similarity to sequences within other serine proteases, notably the proposed cytotoxic granzymes present in the cytolytic granules of human and mouse cytotoxic T lymphocytes. We now report that an internal peptide of one human granzyme (granzyme B) with the sequence of HPAYNPK also displays bactericidal action in vitro. Our results suggest that an internal antibacterial domain among human serine proteases cat G and granzyme B has been functionally conserved through evolution perhaps for the purpose of host defense against microbial pathogens and targets of cytotoxic T lymphocyte killing.

Amino Acid Sequence↗
PubMed1997

The versatility of Helicobacter pylori in the adaptation to the human stomach.

A growing body of data indicates that H. pylori colonization of human is ancient, which is consistent with its high prevalence, chronicity of carriage, and generally low level of disease, which, when it occurs has only marginal or no effects on host reproductive capacity. All of these phenomena are markers for a relatively benign co-existence, which may include all of the entire spectrum of interactions from parasitism, through commensalism, to symbiosis. Recent studies suggest the emergence of "quasispecies" during prolonged colonization, and the presence of multiple strains colonizing individual hosts. Such observations suggest that concepts of competition between strains and mutualism will be important in understanding the ecology of colonization and its effects on hosts. The presence of particular pathologies in the host may in part be a function of the characteristics of the bacterial population present. At a genomic level, H. pylori appears to adapt to changing conditions by point mutation, genomic rearrangement, and horizontal gene transfer, the latter is favored by its natural competence. The ability of H. pylori to alter phenotypic properties including superficial Lewis antigen expression and secretion of proinflammatory molecules is evidence of its sensitivity to environmental signals from the host. In such a universe, disease outcomes such as ulceration or neoplasia may be considered as accidents secondary to microbial persistence.

Biological Evolution↗
PubMed1983

Effects of combinations of simulated acid rain and cadmium or zinc on microbial activity in soil.

There was little effect on the rate of CO2 evolution from glucose-supplemented soil, adjusted to pH 3.2 with a 2:1 combination of H2SO4 and fuming HNO3, and concomitant additions of 100 or 1000 ppm Cd or of 1000 or 10,000 ppm Zn (as sulfates) were no more inhibitory than in soil untreated with acid. In soil adjusted to pH 2.8, the lag in CO2 evolution was increased by 1 day, and was extended further by the concomitant addition of 10,000 but not 1000 ppm Zn or of 1000 but not 100 ppm Cd. The growth of Aspergillus niger in soil acidified to pH levels of 3.6 to 4.2 was further reduced by the addition of either 100 or 250 ppm Cd or of 1000 ppm Zn.

Air Pollutants↗