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At least 685 records · Page 38Linked to original sources
PubMed2004

Genomics for the ecological toolbox.

Genomics technologies have expanded the types of question that can be addressed in human genetics and health and in fields such as ecology. Genome-scale approaches provide ways to examine physiological changes that occur when a pathogen invades a host, the response of an organism to a change in its environment, and the way in which changes in the microbial community affect ecosystem function. Here, we examine successful applications of genomics to ecological science to date and describe ways that classic ecological research disciplines might benefit from genomic approaches. We also address some of the challenges of using this methodology, and discuss how ecological researchers embracing these approaches enhance its effectiveness in applications such as gene hunting and gene expression analysis.

Journal Article↗
PubMed2004

Does Toll-like receptor 3 play a biological role in virus infections?

The Toll-like receptor (TLR) family functions to recognize conserved microbial and viral structures with the purpose of activating signal pathways to instigate immune responses against infections by these organisms. For example, in vitro studies reveal that the TLR3 ligand is a double-stranded RNA (dsRNA), a product of viral infections. From this observation, it has been proposed that TLR3 is likely an important first signal for virus infections. We approached this issue by investigating the role of TLR3 in four different infectious viral models (lymphocytic choriomeningitis virus (LCMV), vesicular stomatitis virus (VSV), murine cytomegalovirus (MCMV), and reovirus) and in TLR3 genetically deficient ((-/-)) mice. Our results indicate that TLR3 is not universally required for the generation of effective antiviral responses because the absence of TLR3 does not alter either viral pathogenesis or impair host's generation of adaptive antiviral responses to these viruses.

Animals↗
PubMed2001

The effect of TBT on the structure of a marine sediment comunity--a Boxcosm study.

The effect of tri-n-butyl tin (TBT) on an intact marine sediment community after five months exposure was investigated. Changes in the structure of macro- and meiofauna communities were determined, as well as the functional diversity of the microbial community using BIOLOG microplates for Gram negative bacteria. Development of tolerance in the microbial community was investigated using Pollution Induced Community Tolerance (PICT) experiments with fluxes of nutrients as effect indicators. TBT affected the structure and recruitment of the macro- and meiofauna at nominal additions of 30-137 micromol TBT/m2 sediment. Number of species, diversity, biomass and community similarity was reduced at these concentrations compared to control. Species that molt seemed to be the most tolerant since they were predominant in boxes that had received the highest TBT addition and echinoderms were the most sensitive species. Renewed addition of TBT in PICT experiments with sediment from each boxcosm showed that TBT had an effect on individual nutrient fluxes from all sediments. Analyses of the flux patterns revealed a memory of previous TBT exposure, either due to induced tolerance or other community conditioning.

Adaptation, Physiological↗
PubMed2002

Bacterial genomics: the use of DNA microarrays and bacterial artificial chromosomes.

Immense amounts of genetic information are contained within microbial genomes. As the number of completely sequenced microbial genomes is increasing, functional and comparative genomic techniques will be employed for sequence analysis and gene characterization. Sequence comparison and expression profiling by DNA microarrays can determine phylogenetic relationships and identify genes while bacterial artificial chromosomes (BACs) allow the study of entire biochemical pathways and permit the expression of bacterial genes in a foreign host.

Anti-Bacterial Agents↗
PubMed2003

Bioindication of air pollution effects near a copper smelter in Brazil using mango trees and soil microbiological properties.

A field study near the copper smelter of a large industrial complex examined air pollution effects on vegetation and soil parameters in Camaçari (northeast Brazil). Close to the smelter, soil pH-value was lower and total acidity as well as organic carbon contents were higher compared with a site far from the source and two reference sites. The acidification of top soil particularly and the drastically enhanced plant-available copper concentrations were caused by atmospheric deposition. High sulphur and copper deposition significantly reduced microbial biomass and altered functional diversity of soil microorganisms (arylsulphatase and xylanase). Large accumulations of sulphur, arsenic and copper were detected in mango leaves (Mangifera indica) growing downwind from the smelter suggesting potential food chain-mediated risk.

Air Pollutants↗
PubMed2003

Increase of atmospheric CO2: response patterns of a simple terrestrial man-made ecosystem.

Simple models of terrestrial ecosystems with a limited number of components are an efficient tool to study the main laws of functioning of populations, including microbial ones, and their communities, as components of natural ecosystems, under variable environmental conditions. Among other factors are the increase of carbon dioxide in the atmosphere and limitation of plants' growth by biogenic elements. The main types of ecosystems' responses to changes in environmental conditions (a change in CO2 concentration) have been demonstrated in a "plants-rhizospheric microorganisms-artificial soil" simple experimental system. The mathematical model of interactions between plants and microorganisms under normal and elevated atmospheric CO2 and limitation by nutrients (nitrogen and phosphorus) yielded a qualitative agreement between calculated and experimental values of limiting substances concentrations and release rates of exudates.

Atmosphere↗
PubMed2004

Synthesis of gramicidin S and its analogues via an on-resin macrolactamization assisted by a predisposed conformation of the linear precursors.

A simple and efficient preparation of gramicidin S and its analogues is described. It involves solid-phase peptide synthesis and on-resin macrolactamization without side chain protection, affording cyclic products in high yield and high purity. The high specificity of the cyclization reaction was shown to originate in the formation of a pre-organized conformation of the linear biosynthetic precursor of gramicidin S. This facile method will provide convenient access to the analogues of the natural product for functional optimization to counter microbial resistance.

Alanine↗
PubMed2003

Virulence factors of Porphyromonas gingivalis are modified by polyphenol oxidase and asparaginase.

Porphyromonas gingivalis is a well-adapted pathogen of the periodontal pocket distinguished by its wide array of proteolytic activities and its ability to adhere to multiple substrata in the oral cavity. Microbial proteins with binding functions (such as adhesins and enzymes) very often contain critical tyrosine residues, supported by one or more asparagines in the binding cleft. This study investigates the reduction in adhesiveness and in proteolytic activity after treating P. gingivalis with the tyrosine- and asparagine-targeting enzymes polyphenol oxidase (PPO) and asparaginase (ASG). Cysteine protease activity was reduced by pretreatment with both enzymes, while the trypsin-like activity was affected only by PPO. Adhesion to buccal epithelial cells, laminin and fibronectin as well as hemagglutination was reduced by one or both of the enzymes. PPO, but not ASG, reduced the coaggregation of P. gingivalis with Actinomyces naeslundii. Treatment with these enzymes might provide an alternative to traditional antimicrobial strategies.

Actinomyces↗
PubMed1999

The therapeutic prescription for the organ transplant recipient: the linkage of immunosuppression and antimicrobial strategies.

Infection and rejection, the two major barriers to successful organ transplantation, are closely linked, with immunosuppressive therapy being central to the pathogenesis of both. After almost two decades when azathioprine and prednisone, supplemented by antilymphocyte antibody therapy, were the cornerstones of post-transplant immunosuppressive programs, there has been a major increase in the therapeutic armamentarium available to treat rejection: cyclosporine, tacrolimus, mycophenolate mofetil, rapamycin, and antibodies directed against the interleukin-2 receptor. These agents are potent inhibitors of microbial specific T cell function, thus potentiating opportunistic infection with herpes group viruses, fungal and mycobacterial species, Strongyloides stercoralis, and a variety of intracellular pathogens. The mechanisms by which each of these drugs exerts its effects are an important determinant of the antimicrobial strategies that will be necessary to combat infection. Indeed, strategies to limit these infections are being linked to the nature of the immunosuppressive therapy required in a particular patient. Thus, the therapeutic prescription for the transplant patient is said to have two components: an immunosuppressive component to prevent and treat rejection, and an antimicrobial one to make it safe. In addition to using antimicrobial agents therapeutically, in the transplant patient prevention is stressed in which antibiotics are deployed prophylactically or preemptively.

Anti-Infective Agents↗
PubMed1995

Sequence specificity and transcriptional activation in the binding of lactoferrin to DNA.

Lactoferrin, an iron-binding glycoprotein found in high concentrations in human milk and other epithelial secretions and in the secondary (specific) granules of neutrophils, is thought to be responsible for primary defence against microbial infection, mainly as a result of lactoferrin sequestration of iron required for microbial growth. Many other functions have been attributed to lactoferrin, including immunomodulation and cell growth regulation (reviewed in ref. 4). Some of these functions appear to be at least in part independent of the iron-binding activity of lactoferrin. It also has been consistently observed that lactoferrin interacts avidly with nucleic acids. Lactoferrin enhancement of the activity of natural killer and lymphokine-activated killer cells in vitro is inhibited by RNA and DNA. Lactoferrin taken up by K562 human myelogenous leukaemia cells appears in the nucleus where it is bound to DNA. We report here that binding of lactoferrin to DNA occurs under stringent conditions with distinct sequence specificity, and that interaction between lactoferrin and these sequences intracellularly leads to transcriptional activation.

Amino Acid Sequence↗
PubMed1971

Microbial oxidation of amines. Partial purification of a mixed-function secondary-amine oxidase system from Pseudomonas aminovorans that contains an enzymically active cytochrome-P-420-type haemoprotein.

1. Crude extracts of Pseudomonas aminovorans grown on methylamine, di-methylamine, trimethylamine or trimethylamine N-oxide contain an enzyme or enzyme system catalysing the NADH- or NADPH- and oxygen-dependent oxidation of dimethylamine to methylamine and formaldehyde. 2. The enzyme has been partially purified about five-fold. It is unstable, but can be stabilized by addition of 5% (v/v) ethanol. 3. The partially purified enzyme will utilize either NADH (K(m) 6.5mum) or NADPH (K(m) 13.2mum): The following secondary amines have been shown to be substrates: dimethylamine, ethylmethylamine, diethylamine, methyl-n-propylamine, ethyl-n-propylamine, n-butylmethylamine and N-methylethanolamine. The K(m) values and comparative reaction rates for each substrate have been determined. Where the alkyl groups are different, the aldehyde products are derived from both groups. 4. The enzyme system has a pH optimum of 6.8 and is inhibited by mercurials, thiol compounds, cyanide and carbon monoxide. 5. The partially purified preparation had a spectral maximum at 412nm with shoulders at 427 and 550nm. Reduction with dithionite or NAD(P)H bleached the 412nm peak, and the shoulder at 427nm became a peak. Additional peaks appeared at 550 and 580-588nm. Reduction of a preparation bubbled with carbon monoxide enhanced and sharpened the Soret peak and caused it to shift to 422nm. 6. Analysis of the preparation showed the presence of flavin, acid-extractable iron and non-acid-extractable iron in the proportion 1.1:1.9:1. On reduction with dithionite or NADPH the preparation showed an electron-paramagnetic-resonance signal at around g=1.946.

Amines↗
PubMed2001

Functional and structural response of a cellulose-degrading methanogenic microbial community to multiple aeration stress at two different temperatures.

Two cellulose-fermenting methanogenic enrichment cultures originating from rice soil, one at 15 degrees C with Methanosaeta and the other at 30 degrees C with Methanosarcina as the dominant acetoclastic methanogen, both degraded cellulose anaerobically via propionate, acetate and H2 to CH4. The degradation was a two-stage process, with CH4 production mainly from H2/CO2 and accumulation of acetate and propionate during the first, and methanogenic consumption of acetate during the second stage. Aeration stress of 12, 24, 36 and 76 h duration was applied to these microbial communities during both stages of cellulose degradation. The longer the aeration stress, the stronger the inhibition of CH4 production at both 30 degrees C and 15 degrees C. The 72 h stressed culture at 30 degrees C did not fully recover. Aeration stress at 30 degrees C exerted a more pronounced effect, but lasted for a shorter time than that at 15 degrees C. The aeration stress was especially effective during the second stage of fermentation, when consumption of acetate (and to a lesser extent propionate) was also increasingly inhibited as the duration of the stress increased. The patterns of CH4 production and metabolite accumulation were consistent with changes observed in the methanogenic archaeal community structure. Fluorescence in situ hybridization showed that the total microbial community at the beginning consisted of about 4% and 10% archaea, which increased to about 50% and 30% during the second stage of cellulose degradation at 30 degrees C and 15 degrees C respectively. Methanosarcina and Methanosaeta species became the dominant archaea at 30 degrees C and 15 degrees C respectively. The first round of aeration stress mainly reduced the non-Methanosarcina archaea (30 degrees C) and the non-Methanosaeta archaea (15 degrees C). Aeration stress also retarded the growth of Methanosarcina and Methanosaeta at 30 degrees C and 15 degrees C respectively. The longer the stress, the lower was the percentage of Methanosarcina cells to total microbial cells after the first stress at 30 degrees C. A later aeration stress decreased the population of Methanosarcina (at 30 degrees C) in relation to the duration of stress, so that non-Methanosarcina archaea became dominant. Hence, aeration stress affected the acetotrophic methanogens more than the hydrogenotrophic ones, thus explaining the metabolism of the intermediates of cellulose degradation under the different incubation conditions.

Air↗
PubMed2002

Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities.

The effect that culture methods have on the diversity of degradative microbial communities is not well understood. We compared conventional batch enrichment with a biofilm culture method for the isolation of polycyclic aromatic hydrocarbon (PAH)-degrading microbial communities from a PAH-contaminated soil. The two methods were assessed by comparing: (i) the diversity of culturable bacteria; (ii) the diversity of PAH-catabolic genes in isolated bacteria; (iii) the inter- and intraspecific diversity of active PAH-catabolic gene classes; (iv) the diversity of bacteria present in 16S rRNA gene libraries generated from RNA extracted from the two communities and soil; and (v) the estimated diversity of active bacteria in the soil and culture systems. Single-strand conformation polymorphism analysis showed that the biofilm culture yielded 36 bacterial and two fungal species compared with 12 bacterial species from the enrichment culture. Application of accumulation and non-parametric estimators to clone libraries generated from 16S rRNA confirmed that the biofilm community contained greater diversity. Sequencing of clones showed that only species from the Proteobacteria were active in the enrichment culture, and that these species were expressing an identical nahAc-like naphthalene dioxygenase. 16S rRNA clones generated from the biofilm community indicated that species from the Cytophaga/Flavobacterium, high G+C bacteria and Proteobacteria were active at the time of sampling, expressing cndA-, nahAc- and phnAc-like naphthalene dioxygenases. The diversity of active species in the biofilm culture system closely matched that in the PAH-contaminated source soil. The results of this study showed that biofilm culture methods are more appropriate for the study of community-level interactions in PAH-degrading microbial communities. The study also indicated that cultivation of microbial communities on solid media might be the primary source of bias in the recovery of diverse species.

Base Sequence↗
PubMed2004

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.

MOTIVATION: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics. RESULTS: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl.

Chromosome Mapping↗
PubMed2003

The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining.

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.

Biodegradation, Environmental↗