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 1,063 records · Page 59Linked to original sources
PubMed1999

Selected phenolic compounds in cultivated plants: ecologic functions, health implications, and modulation by pesticides.

Phenolic compounds are widely distributed in the plant kingdom. Plant tissues may contain up to several grams per kilogram. External stimuli such as microbial infections, ultraviolet radiation, and chemical stressors induce their synthesis. The phenolic compounds resveratrol, flavonoids, and furanocoumarins have many ecologic functions and affect human health. Ecologic functions include defense against microbial pathogens and herbivorous animals. Phenolic compounds may have both beneficial and toxic effects on human health. Effects on low-density lipoproteins and aggregation of platelets are beneficial because they reduce the risk of coronary heart disease. Mutagenic, cancerogenic, and phototoxic effects are risk factors of human health. The synthesis of phenolic compounds in plants can be modulated by the application of herbicides and, to a lesser extent, insecticides and fungicides. The effects on ecosystem functioning and human health are complex and cannot be predicted with great certainty. The consequences of the combined natural and pesticide-induced modulating effects for ecologic functions and human health should be further evaluated.

Animals↗
PubMed2002

Microbial genome evolution: sources of variability.

Comparative genome analyses of close relatives have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. The genomes of free-living bacteria often carry phages and repetitive sequences that mediate genomic rearrangements in contrast to the small genomes of obligate host-associated bacteria. This suggests that genomic stability correlates with the genomic content of repeated sequences and movable genetic elements, and thereby with bacterial lifestyle. Genes with unknown functions present in a single species tend to be shorter than conserved, functional genes, indicating that the fraction of unique genes in microbial genomes has been overestimated.

Bacteria↗
PubMed1998

Simulation modeling for microbial risk assessment.

Quantitative microbial risk assessment implies an estimation of the probability and impact of adverse health outcomes due to microbial hazards. In the case of food safety, the probability of human illness is a complex function of the variability of many parameters that influence the microbial environment, from the production to the consumption of a food. The analytical integration required to estimate the probability of foodborne illness is intractable in all but the simplest of models. Monte Carlo simulation is an alternative to computing analytical solutions. In some cases, a risk assessment may be commissioned to serve a larger purpose than simply the estimation of risk. A Monte Carlo simulation can provide insights into complex processes that are invaluable, and otherwise unavailable, to those charged with the task of risk management. Using examples from a farm-to-fork model of the fate of Escherichia coli O157:H7 in ground beef hamburgers, this paper describes specifically how such goals as research prioritization, risk-based characterization of control points, and risk-based comparison of intervention strategies can be objectively achieved using Monte Carlo simulation.

Animals↗
PubMed2006

[Common problems in the analyses of microbial community by denaturing gradient gel electrophoresis (DGGE)].

Denaturing gradient gel electrophoresis (DGGE) can describe microbial communities based on partial sequences of nucleic acid and monitor uncultured bacterium and it's functional genes. It is well-established molecular tools in microbial molecular ecology that allows the study of diversity and dynamics of microbial communities. Here, common issues in the analyses of microbial community by DGGE were raised, and the feasible resolving methods were introduced in this paper. The effects of samples pretreatment and PCR amplification on DGGE analysis were evaluated. Optimization and statistical analysis of DGGE profiles were discussed. Finally, prospect of DGGE for understanding microbial communities were reviewed.

Bacteria↗
PubMed2005

Comparison of different microbial biomass and activity measurement methods in metal-contaminated soils.

The aims of this study were: (1) to compare different microbial methods of detecting the effects of heavy metals on the functioning of the soil ecosystem; and (2) to evaluate the effect of incubation on microbial biomass and microbial activity in soils that were not pre-incubated after sampling in order to determine their suitability for measuring the effects of heavy metals on the soil microbial ecosystem. The microbial biomass methods (included: biomass C, N and ninhydrin-N by fumigation-extraction (FE); substrate-induced respiration (SIR); soil ATP content and microbial activity as evolved CO2-C and arginine ammonification. All were tested in soils from the Woburn Market Garden Experiment. Due to past sludge application the soils contained, Zn, Cu or Ni at around current European Union upper limits and Cd at up to three times the limit. The amount of microbial biomass in metal-contaminated soils was about half of that found in soils from the experiment that received uncontaminated organic manure or inorganic fertilizer. The amount of biomass measured by FE and soil ATP content in incubated soils showed little change over 20 days incubation. However, SIR measurements were statistically affected over the first few days of incubation. The rates of arginine ammonification were higher in this order: farmyard manure (FYM)>inorganic fertilizer>sewage-sludge throughout the incubation. However, the evolved CO2-C rates were not significantly different among the treatments. Discriminant analysis confirmed smaller amounts of biomass in the metal-contaminated soils than in the other treatments. Linked properties, such as relationships between biomass and soil organic matter, or biomass-specific respiration rates, may provide "internal control" which may help overcome problems of establishing suitable control, or comparative measurements, when moving from experimental to natural environments.

Biodegradation, Environmental↗
PubMed2004

Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice.

Indigenous microbiota have several beneficial effects on host physiological functions; however, little is known about whether or not postnatal microbial colonization can affect the development of brain plasticity and a subsequent physiological system response. To test the idea that such microbes may affect the development of neural systems that govern the endocrine response to stress, we investigated hypothalamic-pituitary-adrenal (HPA) reaction to stress by comparing germfree (GF), specific pathogen free (SPF) and gnotobiotic mice. Plasma ACTH and corticosterone elevation in response to restraint stress was substantially higher in GF mice than in SPF mice, but not in response to stimulation with ether. Moreover, GF mice also exhibited reduced brain-derived neurotrophic factor expression levels in the cortex and hippocampus relative to SPF mice. The exaggerated HPA stress response by GF mice was reversed by reconstitution with Bifidobacterium infantis. In contrast, monoassociation with enteropathogenic Escherichia coli, but not with its mutant strain devoid of the translocated intimin receptor gene, enhanced the response to stress. Importantly, the enhanced HPA response of GF mice was partly corrected by reconstitution with SPF faeces at an early stage, but not by any reconstitution exerted at a later stage, which therefore indicates that exposure to microbes at an early developmental stage is required for the HPA system to become fully susceptible to inhibitory neural regulation. These results suggest that commensal microbiota can affect the postnatal development of the HPA stress response in mice.

Adrenocorticotropic Hormone↗
PubMed1994

The role of the blood-brain barrier in HIV infection of the central nervous system.

The blood-brain barrier (BBB) functions to regulate the entry of macromolecules, microbial pathogens, and circulating leukocytes into the central nervous system (CNS). It consists, in part, of the microvascular endothelium and associated astrocyte foot processes, found in close apposition to the abluminal side of the vascular endothelial cells (EC). During the pathogenesis of certain nervous system diseases with inflammatory components, the BBB may function to facilitate the entry of leukocytes into the CNS parenchyma. A common histologic observation in human immunodeficiency virus type-1 (HIV) encephalitis is the localization of HIV proteins to multinucleated giant cells that co-immunolabel with antibodies specific for cells of the monocyte/macrophage lineage, suggesting that HIV can enter the CNS as cell-associated virus. We previously characterized a tissue culture model of the BBB that consists of the co-culture of autologous EC and astrocytes. In this presentation, we used this model to examine the expression of adhesion molecules by both the EC and astrocyte components of this BBB model, and to characterize the interactions between HIV-infected monocytes and EC. The data presented in this review of our work demonstrates that astrocytes upregulate the expression of intercellular adhesion molecule (ICAM-1) by EC. In a parallel study, western blot analysis demonstrated that ICAM-1 is also expressed in the developing human CNS. When exposed to the proinflammatory cytokine tumor necrosis factor alpha (TNF), both EC cocultured with astrocytes and astrocytes cultured alone expressed the adhesion proteins IG9, ICAM-1, vascular cell adhesion molecule 1 (VCAM) and E-selection.(ABSTRACT TRUNCATED AT 250 WORDS)

Astrocytes↗
PubMed2006

Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough.

We have investigated the molecular phylogeny of cold-seep sediments obtained from the Nankai Trough, at depths of about 600, 2,000, and 3,300 m, and compared the microbial diversity profiles of those sediments samples. The gamma-Proteobacteria that might function as sulfide oxidizers and the symbiotically related delta-Proteobacteria which might function as sulfate reducers were identified amongst the bacteria from all depths of the sediments. However, anoxic methane oxidizing archaea (ANME) and methanogens were only found in the 600 m deep sediments. These results indicated that the cold-seep microbial sulfur circulation system could be functioning in the shallow seep sediment at a depth of 600 m and the microbial activities at these sites might be more dynamic than at other deeper cold-seep sites.

Archaea↗
PubMed2001

Region-specific transcriptional activity in the genome of Streptomyces coelicolor A3(2).

Transcriptional analysis of microbial genomes is an important component of functional genomics. Strategies such as hybridization of labeled total RNA against ordered clone libraries or differential-display approaches have already been carried out to identify expressed genes. We describe here an additional method which applies subtractive hybridization between genome-specific DNA and total RNA followed by a PCR approach to identify expressed microbial genes. With the new strategy, the expression of genes in the terminal regions of the linear Streptomyces coelicolor A3(2) chromosome and the accessory linear plasmid SCP1 was analyzed. The results indicate that the method is useful for the identification of expressed genes in actinomycetes and other microbial systems. We demonstrate for the first time that at least 24 genes in the chromosome end regions (silent regions) of S. coelicolor are actively expressed. In addition, several expressed SCP1 genes were identified, including a gene which shows high similarity to microbial dnaN genes and which seems to play a role in SCP1 maintenance.

Bacterial Proteins↗
PubMed1993

Purification and characterization of microbially expressed neomycin phosphotransferase II (NPTII) protein and its equivalence to the plant expressed protein.

The gene encoding neomycin phosphotransferase II (NPTII) has been used routinely as a selectable marker in the production of genetically engineered crops. To facilitate the safety assessment of this protein, the same coding sequence used for plant transformation was introduced into Escherichia coli to produce gram quantities of this protein. A unique, simple, rapid and efficient purification method was developed to purify thirty grams of NPTII protein. The microbially produced NPTII was shown to be chemically and functionally equivalent to the NPTII protein expressed in and purified from genetically engineered cotton seed, potato tubers and tomato fruit. Microbially produced and plant produced NPTII proteins have comparable molecular weights, immuno-reactivities, epitope structures, amino terminal amino acid sequences, biological activities and both lack glycosylation. Demonstrating the equivalence of NPTII protein from these sources establishes the validity of using the microbially produced NPTII to assess the safety of the NPTII protein produced in genetically engineered crops.

Amino Acid Sequence↗
PubMed2006

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.

Bacteria↗
PubMed2006

Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere.

The rhizosphere is the site of intense interactions between plant, bacterial, and fungal partners. In plant-bacterial interactions, signal molecules exuded by the plant affect both primary initiation and subsequent behavior of the bacteria in complex beneficial associations such as biocontrol. However, despite this general acceptance that plant-root exudates have an effect on the resident bacterial populations, very little is still known about the influence of these signals on bacterial gene expression and the roles of genes found to have altered expression in plant-microbial interactions. Analysis of the rhizospheric communities incorporating both established techniques, and recently developed "omic technologies" can now facilitate investigations into the molecular basis underpinning the establishment of beneficial plant-microbial interactomes in the rhizosphere. The understanding of these signaling processes, and the functions they regulate, is fundamental to understanding the basis of beneficial microbial-plant interactions, to overcoming existing limitations, and to designing improved strategies for the development of novel Pseudomonas biocontrol strains.

Bacterial Physiological Phenomena↗
PubMed1996

Effect of d-fenfluramine on the local immune response to the opportunistic microbial pathogen Candida albicans.

In this study the effects of systemic administration of d-fenfluramine on the local lymphocyte response to Candida albicans was evaluated. Experimental animals were challenged intradermally with Candida albicans and then administered d-fenfluramine (d-FEN 1 mg/kg per day, i.p.) or a balanced salts solution. At successive time intervals, lymphocytes were derived from the draining lymph nodes and from the dermal sites of active microbial challenge. A CD8+ lymphocytosis was observed in all animals challenged with Candida albicans. The CD8+ lymphocytosis was augmented in animals that received d-FEN. Phenotypically, lymph nodes from d-FEN treated animals showed a marked increase in CD3+ and CD8+ lymphocytes, a modest increase in the numbers of NK1.1+ cells and a decrease in Ig+ lymphocytes. Functionally, lymphocytes from the site of active microbial challenge were capable of direct growth inhibition of Candida albicans. The anti-fungal activity was augmented in the animals that received d-FEN. These results suggest that d-FEN augments the local T lymphocyte response to an important microbial pathogen by increasing the number of T lymphocytes draining the site of microbial infection and by increasing the biological activity of the lymphocytes at the site of the infection.

Animals↗
PubMed2002

Functionally distinct subsets of CD1d-restricted natural killer T cells revealed by CD1d tetramer staining.

CD1d-restricted natural killer (NK)T cells are known to potently secrete T helper (Th)1 and Th2 cytokines and to mediate cytolysis, but it is unclear how these contrasting functional activities are regulated. Using lipid antigen-loaded CD1d tetramers, we have distinguished two subsets of CD1d-restricted T cells in fresh peripheral blood that differ in cytokine production and cytotoxic activation. One subset, which was CD4(-), selectively produced the Th1 cytokines interferon gamma and tumor necrosis factor alpha, and expressed NKG2d, a marker associated with cytolysis of microbially infected and neoplastic cells. This subset up-regulated perforin after exposure to interleukin (IL)-2 or IL-12. In contrast, CD4(+) CD1d-restricted NKT cells potently produced both Th1 and Th2 cytokines, up-regulated perforin in response to stimulation by phorbol myristate acetate and ionomycin but not IL-2 or IL-12, and could be induced to express CD95L. Further, for both CD1d-restricted NKT cell subsets, we found that antigenic stimulation induced cytokine production but not perforin expression, whereas exposure to inflammatory factors enhanced perforin expression but did not stimulate cytokine production. These results show that the various activities of CD1d-restricted T cells in tumor rejection, autoimmune disease, and microbial infections could result from activation of functionally distinct subsets, and that inflammatory and antigenic stimuli may influence different effector functions.

Animals↗
PubMed2001

Prediction of microbial growth in fresh-cut vegetables treated with acidic electrolyzed water during storage under various temperature conditions.

Effects of storage temperature (1, 5, and 10 degrees C) on growth of microbial populations (total aerobic bacteria, coliform bacteria, Bacillus cereus, and psychrotrophic bacteria) on acidic electrolyzed water (AcEW)-treated fresh-cut lettuce and cabbage were determined. A modified Gompertz function was used to describe the kinetics of microbial growth. Growth data were analyzed using regression analysis to generate "best-fit" modified Gompertz equations, which were subsequently used to calculate lag time, exponential growth rate, and generation time. The data indicated that the growth kinetics of each bacterium were dependent on storage temperature, except at 1 degrees C storage. At 1 degrees C storage, no increases were observed in bacterial populations. Treatment of vegetables with AcEW produced a decrease in initial microbial populations. However, subsequent growth rates were higher than on nontreated vegetables. The recovery time required by the reduced microbial population to reach the initial (treated with tap water [TW]) population was also determined in this study, with the recovery time of the microbial population at 10 degrees C being <3 days. The benefits of reducing the initial microbial populations on fresh-cut vegetables were greatly affected by storage temperature. Results from this study could be used to predict microbial quality of fresh-cut lettuce and cabbage throughout their distribution.

Bacteria↗
PubMed1994

Function of antimicrobial proteins in insects.

We have isolated and characterized various antimicrobial proteins from the haemolymph of Sarcophaga peregrina (flesh fly) larvae. Of these the sarcotoxin I family is a group of proteins mainly active against Gram-negative bacteria whereas sapecin is active mainly against Gram-positive bacteria. In addition to its function in defence, sapecin also plays a role in insect development. Recently, we identified a hendecapeptide of the sapecin homologue sapecin B that has the same antibacterial activity as the original sapecin B. Both sarcotoxin I and sapecin are inducible proteins synthesized de novo by the fat body and/or haemocytes and secreted into the haemolymph when the insect is in the acute phase response to bacterial infection. Antifungal protein (AFP) is constitutively present in the haemolymph and is active against certain fungi but not bacteria. These various antimicrobial proteins interact with microbial membranes. Sarcotoxin I interferes with membrane functions such as ATP synthesis and amino acid transport. The fungicidal activity of AFP is enhanced synergistically by sarcotoxin I, although sarcotoxin I alone has no appreciable antifungal activity. It is clear that the flesh fly has the ability to mount a potent defence response against microbial parasites by mobilizing several antimicrobial proteins.

Amino Acid Sequence↗
PubMed1991

Modulation of bone marrow cell functions in vitro by bestatin (ubenimex).

Bestatin (ubenimex), the microbial leucil-aminopeptidase B inhibitor, has been shown previously to stimulate both interleukin-1 (IL-1) and IL-2 production and to enhance T-cell, as well as macrophage mediated immunoreaction when administered in vivo in mice. Here we show that although Bestatin has no direct growth stimulatory activity, it enhances the growth of GM-CFU populations in semisolide culture and stimulates the cell production in liquide organotypic Hematon cultures in synergy with recombinant human GM-CSF. In long term human bone marrow culture Bestatin accelerated the adipocytic differentiation among colony forming stroma cells (F-CFU). Our data provide further evidences that Bestatin may interact with the hemopoietic cell renewal system at different levels of biological organisation.

Antibiotics, Antineoplastic↗
PubMed1995

Function of the oxidative burst in hypersensitive disease resistance.

Microbial elicitors or attempted infection with an avirulent pathogen strain causes the rapid production of reactive oxygen intermediates. Recent findings indicate that H2O2 from this oxidative burst plays a central role in the orchestration of the hypersensitive response: (i) as the substrate driving the cross-linking of cell wall structural proteins to slow microbial ingress prior to the deployment of transcription-dependent defenses and to trap pathogens in cells destined to undergo hypersensitive cell death, (ii) as a local threshold trigger of this programmed death in challenged cells, and (iii) as a diffusible signal for the induction in adjacent cells of genes encoding cellular protectants such as glutathione S-transferase and glutathione peroxidase. These findings provide the basis for an integrated model for the orchestration of the localized hypersensitive resistance response to attack by an avirulent pathogen.

Journal Article↗