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At least 937 records · Page 52Linked to original sources
PubMed2003

Human oral cavity as a model for the study of genome-genome interactions.

The enormous diversity of culturable bacteria within the oral microbial community coupled with experimental accessibility renders the human oral cavity a valuable model to investigate genome-genome interactions. The complex interactions of oral bacteria result in the formation of biofilms on the surfaces of the oral cavity. One mechanism thought to be important in biofilm formation is the coaggregation of bacterial partners. In this paper, we examine the role of coaggregation in oral biofilms and develop protocols to elucidate the spatial organization of bacterial species retained within oral biofilms. To explore these issues, we have employed two experimental systems: the saliva-coated flowcell and the retrievable enamel chip. From flowcell studies, we have determined that coaggregation can greatly influence the ability of an oral bacterial species to grow and be retained within the developing biofilm. To examine the spatial architecture of oral biofilms, fluorescent in situ hybridization protocols were developed that successfully target specific members of the oral microbial community. Together, these approaches provide insight into the development of oral biofilms and expand our understanding of genome-genome interactions.

Bacterial Physiological Phenomena↗
PubMed1991

The antibacterial activity of a siderophore. 2. The influence of deferoxamine alone and combined with ascorbic acid on the activity of antibiotics against Staphylococcus aureus.

The in vitro activity of deferoxamine (DFO) combined with cephalothin, gentamicin, cefotaxime, vancomycin, and fusidic acid, in the presence or absence of the reductant ascorbic acid (AA) was investigated against Staphylococcus aureus by a macrobroth dilution technique and killing curve kinetics. DFO and in particular DFO + AA lowered the MICs of cephalothin, gentamicin, cefotaxime, and fusidic acid for most of the strains and in some instances also the MICs of vancomycin. To characterize the interaction between DFO or DFO + AA and antimicrobials we applied the growth constants of logarithmic growth phase. Generally DFO acted synergistically with cephalothin, gentamicin, vancomycin, and fusidic acid, particularly in the presence of AA, and in some cases synergy was demonstrated with cefotaxime, too.

Anti-Bacterial Agents↗
PubMed1992

Microbial predation in a periodically operated chemostat: a global study of the interaction between natural and externally imposed frequencies.

Predator-prey systems in continuously operated chemostats exhibit sustained oscillations over a wide range of operating conditions. When the chemostat is operated periodically, the interaction of the natural oscillation frequency with the external forcing gives rise to a wealth of dynamic behavior patterns. Using numerical bifurcation techniques, we perform a detailed computational study of these patterns and the transitions (local and especially global) between them as the amplitude and frequency of the forcing vary. The transition from low-forcing-amplitude quasiperiodicity to entrainment of the chemostat behavior by strong forcing (involving the concerted closing of resonance horns) is analyzed. We concentrate on certain strong resonance phenomena between the two frequencies and provide an extensive atlas of computed phase portraits for our model system. Our observations corroborate recent mathematical results and case studies of periodically forced chemical oscillators. In particular, the existence and relative succession of several distinct types of global bifurcations resulting in chaotic transients and multistability are studied in detail. The location in the operating diagram of several key codimension 2 local bifurcations of periodic solutions is computed, and their interaction with an interesting feature we name "real-eigenvalues horns" is examined.

Animals↗
PubMed2005

Preincubation of pneumococci with beta-lactams alone or combined with levofloxacin prevents quinolone-induced resistance without increasing intracellular levels of levofloxacin.

Preincubation of pneumococci with sub-MIC concentrations of ceftriaxone (1/16x MIC), cefotaxime (1/8x MIC), and meropenem (1/4x MIC) alone or combined with levofloxacin (1/8x MIC) over 6 h prevents the emergence of levofloxacin-resistant mutants after 96 h of incubation but does not affect the intracellular accumulation of levofloxacin in two penicillin-resistant pneumococcal strains, suggesting a link between the mechanism of action of beta-lactams and the emergence of quinolone-induced resistance in pneumococci.

Anti-Infective Agents↗
PubMed1991

An evolutionary conserved mechanism of T cell activation by microbial toxins. Evidence for different affinities of T cell receptor-toxin interaction.

The enterotoxins produced by Staphylococcus aureus are the most potent mitogens known. They belong to a group of distantly related mitogenic toxins that differ in other biologic activities. In this study we have compared the molecular mechanisms by which these mitogens activate human T lymphocytes. We used the staphylococcal enterotoxins A to E, the staphylococcal toxic shock syndrome toxin, the streptococcal erythrogenic toxins A and C (scarlet fever toxins, erythrogenic toxins (ET)A, ETC), and the soluble mitogen produced by Mycoplasma arthritidis. We found that all these toxins can activate both CD4+ and CD8+ T cells and require MHC class II expression on accessory and target cells. However, T cells could be activated in the absence of class II molecules if the toxins ETA or SEB were co-cross-linked on beads together with anti-CD8 or anti-CD2 antibodies. Enterotoxins, toxic shock syndrome toxin and scarlet toxins stimulate a major fraction of human T cells, and show preferential, but not exclusive, stimulation of T cells carrying certain TCR V beta. In contrast, the mitogen of M. arthritidis, a pathogen for rodents stimulates only a minority of human T cells but activates a major fraction of murine T cells. Analysis of human T cell clones expressing V beta 5 or V beta 8 TCR showed that these clones responded also to those toxins that did not stimulate V beta 5+ and V beta 8+ T cells in bulk cultures. These results indicate that different TCR bind to these toxins with different affinities and that the specificity of the TCR-V beta-toxin interaction is quantitative rather than qualitative in nature. Taken together our findings suggest that these toxins use a common mechanism of T cell activation. They are functionally bivalent proteins crosslinking MHC class II molecules with variable parts of the TCR. Besides V beta, other parts of the TCR must be involved in this binding. The finding that murine T cells responded more weakly to the toxins produced by the human-pathogenic bacteria than to the Mycoplasma mitogen could indicate that the toxins have been adapted to the host's immune system in evolution.

Animals↗
PubMed2002

Bacteriophage-host interaction in the enhanced biological phosphate removing activated sludge system.

Bacteriophages were isolated from a laboratory scale enhanced biological phosphate removing (EBPR) activated sludge process, and their host range was examined. Bacterial isolates to host the bacteriophages were isolated from the EBPR activated sludge process. Bacteriophages were eluted from the EBPR activated sludge, enriched by incubation with the bacterial isolates, and then tested for plaque formation on each of the bacterial isolates. Out of 12 bacterial isolates isolated, 4 supported plaque formation. Four bacteriophages were obtained from the plaques. The host range test was conducted with the combination of the bacteriophage isolates and the bacterial isolates. Three of the bacteriophages were found to form plaques on more than one host, and one of them formed plaques on both gram +ve and gram -ve bacterial isolates. Two of the four bacteriophages failed to form plaques on their original bacterial host, indicating the existence of mutation on either both or one of the host and the bacteriophage. This study strongly suggests that bacteriophages are an active part of the activated sludge microbial ecosystem, having very complex interaction with their host bacteria.

Bacteriophages↗
PubMed2004

Residual toxicity after biodegradation: interactions among benzene, toluene, and chloroform.

A microbial enrichment originating from a pristine aquifer was found to aerobically biodegrade benzene and toluene, but not chloroform. This enrichment culture was used to study changes in pollutant toxicity as affected by biodegradative activity. Two assays for toxicity were used: (1) a 48-h acute toxicity test using the freshwater invertebrate Ceriodaphnia dubia and (2) microbial biodegradation activity as affected by the presence of mixed pollutants. At 20-ppm concentrations, toluene was significantly more toxic (99% mortality) to C. dubia than benzene (48% mortality) or chloroform (40% mortality). Also at 20-ppm concentrations, but before biodegradation, toluene was significantly more toxic (88% mortality) to C. dubia than benzene (33% mortality). After biodegradation of 98% of toluene and benzene, significant residual toxicity still remained in the bacterial supernatant: toluene-degraded supernatant caused 33% mortality in C. dubia and benzene-degraded supernatant caused 24% mortality. In the second toxicity assay, examining the effect of mixed pollutants on biodegradation activity, the presence of benzene slowed the biodegradation of toluene, but chloroform had no effect on either benzene or toluene biodegradation. Results indicate that significant toxicity remain after biodegradation and that halogenated aliphatic hydrocarbons may have little or no effect on aromatic hydrocarbon biodegradation at sites impacted by mixed pollutants.

Animals↗
PubMed2005

Identification of two new Helicobacter pylori surface proteins involved in attachment to epithelial cell lines.

Helicobacter pylori causes the development of gastritis, gastric ulcers and adenocarcinomas in humans. The establishment of infection is influenced by adherence to the gastric epithelium, and several bacterial adhesins and host cell receptors have been identified. H. pylori recognize the Lewis(b) receptor through the BabA adhesin but also readily adhere to epithelia in the absence of the Lewis(b) epitope, demonstrating the relevance of additional adhesive interactions. This study presents a novel method of identifying bacterial adhesins. Nickel beads were coated with H. pylori-derived, recombinantly expressed ORF proteins, and epithelial cells from the human stomach, intestine or urinary tract were allowed to adhere to those beads. The binding of epithelial cells to the protein-coated nickel beads was confirmed by electron microscopy or flow cytometry using antibodies directed towards the His-tags. Among the five ORFs tested, two new adhesive proteins (HP1188 and HP1430) were identified. Both were expressed on the surface of virulent H. pylori, with the HP1188 protein being most abundant. The purified HP1188 and HP1430 proteins bound more strongly to gastric than to other epithelial cell lines, suggesting that they may be involved in the colonization of the human gastric mucosa. In conclusion, this method facilitates the identification of ORFs of microbial origin involved in cellular interactions such as adherence.

Adhesins, Bacterial↗
PubMed2004

Binding and insertion of alpha-helical anti-microbial peptides in POPC bilayers studied by molecular dynamics simulations.

We have performed molecular dynamics simulations of the interactions of two alpha-helical anti-microbial peptides, magainin2 and its synthetic analog of MSI-78, with palmitoyl-oleoyl-phosphatidylcholine (POPC) lipid bilayers. We used various initial positions and orientations of the peptide with respect to the lipid bilayer, including a surface-bound state parallel to the interface, a trans-membrane state, and a partially inserted state. Our 20 ns long simulations show that both magainin2 and MSI-78 are most stable in the lipid environment, with the peptide destabilized to different extents in both aqueous and lipid/water interfacial environments. We found that there are strong specific interactions between the lysine residues of the peptides and the lipid head-group regions. MSI-78, owing to its large number of lysines, shows better binding characteristics and overall stability when compared to magainin2. We also find that both peptides destabilize the bilayer environment, as observed by the increase in lipid tail disorder and the induction of local curvature on the lipid head-groups by the peptides. From all the simulations, we conclude that the hydrogen bonding interactions between the lysines of the peptides and the oxygens of the polar lipid head-groups are the strongest and determine the overall peptide binding characteristics to the lipids.

Antimicrobial Cationic Peptides↗
PubMed1990

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↗
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↗
PubMed2001

Evolutionary engineering of industrially important microbial phenotypes.

The tremendous complexity of dynamic interactions in cellular systems often impedes practical applications of metabolic engineering that are largely based on available molecular or functional knowledge. In contrast, evolutionary engineering follows nature's 'engineering' principle by variation and selection. Thus, it is a complementary strategy that offers compelling scientific and applied advantages for strain development and process optimization, provided a desired phenotype is amenable to direct or indirect selection. In addition to simple empirical strain development by random mutation and direct selection on plates, evolutionary engineering also encompasses recombination and continuous evolution of large populations over many generations. Two distinct evolutionary engineering applications are likely to gain more relevance in the future: first, as an integral component in metabolic engineering of strains with improved phenotypes, and second, to elucidate the molecular basis of desired phenotypes for subsequent transfer to other hosts. The latter will profit from the broader availability of recently developed methodologies for global response analysis at the genetic and metabolic level. These methodologies facilitate identification of the molecular basis of evolved phenotypes. It is anticipated that, together with novel analytical techniques, bioinformatics, and computer modeling of cellular functions and activities, evolutionary engineering is likely to find its place in the metabolic engineer's toolbox for research and strain development. This review presents evolutionary engineering of whole cells as an emerging methodology that draws on the latest advances from a wide range of scientific and technical disciplines.

Biological Evolution↗
PubMed1990

Beneficial interactions between micro-organisms and roots.

Microbial activity in the rhizosphere can have positive and negative effects on plants. Some of the beneficial processes act by minimizing the negative effects or by modifying the cropping environment to enhance productivity. Processes that are considered here include the provision of nitrogen, phosphorus and iron to the plant, the biocontrol of diseases and deleterious organisms and the stabilization of soil structures. The use of genetic engineering techniques in studying these processes and generating novel strains which may enhance them is discussed, along with the possible consequences of the release of organisms into the environment.

Journal Article↗
PubMed2004

Biocorrosion: towards understanding interactions between biofilms and metals.

The term microbially influenced corrosion, or biocorrosion, refers to the accelerated deterioration of metals owing to the presence of biofilms on their surfaces. The detailed mechanisms of biocorrosion are still poorly understood. Recent investigations into biocorrosion have focused on the influence of biomineralization processes taking place on metallic surfaces and the impact of extracellular enzymes, active within the biofilm matrix, on electrochemical reactions at the biofilm-metal interface.

Biofilms↗
PubMed1995

Does variability in salivary protein concentrations influence oral microbial ecology and oral health?

Salivary protein interactions with oral microbes in vitro include aggregation, adherence, cell-killing, inhibition of metabolism, and nutrition. Such interactions might be expected to influence oral ecology. However, inconsistent results have been obtained from in vivo tests of the hypothesis that quantitative variation in salivary protein concentrations will affect oral disease prevalence. Results may have been influenced by choices made during study design, including saliva source, stimulation status, control for flow rate, and assay methods. Salivary protein concentrations also may be subject to circadian variation. Values for saliva collected at the same time of day tend to remain consistent within subjects, but events such as stress, inflammation, infection, menstruation, or pregnancy may induce short-term changes. Long-term factors such as aging, systemic disease, or medication likewise may influence salivary protein concentrations. Such sources of variation may increase the sample size needed to find statistically significant differences. Clinical studies also must consider factors such as human population variation, strain and species differences in protein-microbe interactions, protein polymorphism, and synergistic or antagonistic interaction between proteins. Salivary proteins may form heterotypic complexes with unique effects, and different proteins may exert redundant effects. Patterns of protein-microbe interaction also may differ between oral sites. Future clinical studies must take those factors into account. Promising approaches might involve meta-analysis or multi-center studies, retrospective and prospective longitudinal designs, short-term measurement of salivary protein effects, and consideration of individual variation in multiple protein effects such as aggregation, adherence, and cell-killing.

Aging↗
PubMed2003

Fungal colonization on stoneworks. Interaction fungi-powdered stone samples.

The microbial activity plays an important role in the biodegradative processes implied in stonework decay. In natural environments it is not possible to separate the damage produced by microorganisms from damage caused by physical and chemical agents. In vitro assays carried out with microbes isolated from weathered stones are required in order to understand the biological mechanisms involved in stone deterioration. We have described, as commented in the text, how fungal colonization observed on scaglia may be the result of the fine grain size of rock, whereas inhibition of growth on marble may depend on the surface characteristics of calcite grains after grinding. The extent of microbial growth clearly depends on the quantity of cations released in solution. However, fungal growth may, in turn, induce a decrease in pH, thus promoting mineral chemical attack. These observation points to selective action of fungal species in promoting weathering well evidenced by the presence of different extents of cations released in suspension from the same sample. Detailed studies are in progress in order to go into this question.

Art↗