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At least 343 records · Page 19Linked to original sources
PubMed2005

Bacteriophages--potential for application in wastewater treatment processes.

Bacteriophages are viruses that infect and lyse bacteria. Interest in the ability of phages to control bacterial populations has extended from medical applications into the fields of agriculture, aquaculture and the food industry. Here, the potential application of phage techniques in wastewater treatment systems to improve effluent and sludge emissions into the environment is discussed. Phage-mediated bacterial mortality has the potential to influence treatment performance by controlling the abundance of key functional groups. Phage treatments have the potential to control environmental wastewater process problems such as: foaming in activated sludge plants; sludge dewaterability and digestibility; pathogenic bacteria; and to reduce competition between nuisance bacteria and functionally important microbial populations. Successful application of phage therapy to wastewater treatment does though require a fuller understanding of wastewater microbial community dynamics and interactions. Strategies to counter host specificity and host cell resistance must also be developed, as should safety considerations regarding pathogen emergence through transduction.

Bacteria↗
PubMed2006

Sucrose fatty acid sulphate esters as novel vaccine adjuvant.

In search for novel adjuvants for human and veterinary vaccines, we focus on synthetic carbohydrates because microbial carbohydrates function as important alarming signals to the immune system. Mono- and disaccharides were added chemically with various functional groups and adjuvant activity and reactogenicity were determined in parallel. In our test model, we used poor immunogens to identify the most effective adjuvants and non-rodent mammals to facilitate extrapolation to humans. Disaccharides added with both fatty acid and sulphate esters and immobilized on a vehicle exerted high adjuvanticity. Chemical structure and presentation of the compound were optimized for a maximal in vivo performance. The formulation selected for human therapeutic vaccines (designated as 'CoVaccine HT') consists of a sucrose fatty acid sulphate ester immobilized on the oil droplets of a submicron emulsion of squalane-in-water. Both humoral and cell-mediated responses were enhanced in a dosedependent fashion against a wide range of antigens, e.g. inactivated viruses, bacterial subunits, recombinant proteins, virus-like particles and peptide-protein conjugates. Remarkably high booster reactions indicated strong immunological memory established by the first contact between host and antigen in presence of the adjuvant. In comparison with existing adjuvants, CoVaccine HT revealed similar or even higher adjuvanticity than mineral oil emulsions (O/W, W/O or O/W) but significantly lower reactogenicity. We concluded that CoVaccine HT is a promising adjuvant as it combines the efficacy of strong adjuvants with the safety of mild ones, is effective towards various types of antigens in large non-rodent mammals and is a chemically defined, stable, aqueous formulation.

Adjuvants, Immunologic↗
PubMed2000

Comparative analysis shows that bacterivory, not viral lysis, controls the abundance of heterotrophic prokaryotic plankton.

Empirical models derived from literature data were used to compare the factors controlling prokaryotic abundance (PN) and prokaryotic heterotrophic production (PHP) in solar salterns. These empirical relationships were generated as multiple linear regressions with PN or PHP as dependent variables, while the independent variables were chosen to reflect the likely sources of organic matter, inorganic nutrients and temperature. These variables were then measured in solar salterns and the predictions made by the general relationships were compared to actual saltern values of PN and PHP. Saltern ponds of salinity higher than 100 per thousand departed significantly from the general relationships, while the ponds of salinity lower than 100 per thousand fitted well within the range of values predicted by the general models. The most likely explanation for the discrepancy of the former was the absence of bacterivory. This hypothesis was tested with data from other very different aquatic systems: karstic lakes with anaerobic hypolimnia and two marine areas in the Mediterranean and the Southern Ocean. The anoxic regions of karstic lakes departed significantly from the predictions of the general model, while the oxic layers conformed to the predictions. As in the case of salterns, this difference could be explained by the presence of significant predation in the oxic, but not in the anoxic, layers of these lakes. Finally, two marine areas with similar predation pressure on prokaryotes but very different impacts of viral lysis were tested. In all cases, PN values conformed to the predictions, suggesting that lysis due to viruses is not the main factor controlling PN in aquatic systems, which is more likely to be determined by the balance between bacterivory and resource supply. The present work also demonstrates the usefulness of empirical comparative analyses to generate predictions and to draw inferences on the functioning of microbial communities.

Journal Article↗
PubMed2000

Microbial superantigens: from structure to function.

Superantigens are highly potent immune stimulators with a unique ability to interact simultaneously with MHC class II molecules and T cell receptors, forming a trimolecular complex that induces profound T-cell proliferation and massive cytokine production. Recent structural studies have provided a wealth of information regarding these complex interactions, and it is now emerging that, despite their common 3-D architecture, superantigens are able to crosslink MHC class II molecules and T cell receptors in a variety of ways.

Amino Acid Motifs↗
PubMed1998

In situ methods for assessment of microorganisms and their activities.

Recent technical developments in the field of molecular biology and microsensors are beginning to enable microbiologists to study the abundance, localization and activity of microorganisms in situ. The various new methods on their own bear high potential but it is the combination of studies on structure and function of microbial communities that will yield the most detailed insights in the way microorganisms operate in nature.

Bacteria↗
PubMed1999

Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products.

Terminal restriction fragment length polymorphism is a recent molecular approach that can assess subtle genetic differences between strains as well as provide insight into the structure and function of microbial communities. The technique has both high sensitivity and throughput making it ideal for comparative analyses.

Ecosystem↗
PubMed2006

Formation and characterization of chitosan membranes.

In this paper, hydrophilic polymer membranes based on macromolecular chitosan networks have been synthesized and characterized. The structure of the membrane has been altered in several ways during the formation to adjust the properties, particularly with regard to the elasticity, tensile strength, permeability, and surface structure. An alteration of the network structure was achieved by addition of flexibilizer, cross-linking with dialdehydes, symplex formation of the chitosan with the polyanion sulfoethyl cellulose, and the introduction of artificial pores on the micro- and nanometer scale into the chitosan matrix with silica particles or poly(ethylene glycol). The resulting network structures and morphologies of these unique membranes that combine the novel alteration techniques have been characterized in detail and correlated with molecular parameters of the chitosan as degree of deacetylation, molar mass, and charge density. Finally, we report on the impact of the new network structures on physical properties of the membranes, the water vapor and gas permeability and the tensile strength, to evaluate possible application of the membranes as a wet wound dressing material with microbial barrier function that actively assists the healing process of problematic wounds. Parts of the novel combined membrane alteration and formation techniques are now covered by the patent DE 102004047115.

Chitosan↗
PubMed2006

Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system.

The bacterium Vibrio cholerae, like other human pathogens that reside in environmental reservoirs, survives predation by unicellular eukaryotes. Strains of the O1 and O139 serogroups cause cholera, whereas non-O1/non-O139 strains cause human infections through poorly defined mechanisms. Using Dictyostelium discoideum as a model host, we have identified a virulence mechanism in a non-O1/non-O139 V. cholerae strain that involves extracellular translocation of proteins that lack N-terminal hydrophobic leader sequences. Accordingly, we have named these genes "VAS" genes for virulence-associated secretion, and we propose that these genes encode a prototypic "type VI" secretion system. We show that vas genes are required for cytotoxicity of V. cholerae cells toward Dictyostelium amoebae and mammalian J774 macrophages by a contact-dependent mechanism. A large number of Gram-negative bacterial pathogens carry genes homologous to vas genes and potential effector proteins secreted by this pathway (i.e., hemolysin-coregulated protein and VgrG). Mutations in vas homologs in other bacterial species have been reported to attenuate virulence in animals and cultured macrophages. Thus, the genes encoding the VAS-related, type VI secretion system likely play an important conserved function in microbial pathogenesis and represent an additional class of targets for vaccine and antimicrobial drug-based therapies.

Animals↗
PubMed2000

Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin.

The solution structure of bacteriocin AS-48, a 70-residue cyclic polypeptide from Enterococcus faecalis, consists of a globular arrangement of five alpha-helices enclosing a compact hydrophobic core. The head-to-tail union lies in the middle of helix 5, a fact that is shown to have a pronounced effect on the stability of the three-dimensional structure. Positive charges in the side chains of residues in helix 4 and in the turn linking helix 4 to helix 5 form a cluster that most probably determine its antibacterial activity by promoting pore formation in cell membranes. A similar five-helix structural motif has been found in the antimicrobial NK-lysin, an effector polypeptide of T and natural killer (NK) cells. Bacteriocin AS-48 lacks the three disulfide bridges characteristic of the saposin fold present in NK-lysin, and has no sequence homology with it. Nevertheless, the similar molecular architecture and high positive charge strongly suggest a common mechanism of antibacterial action.

Bacterial Proteins↗
PubMed1997

Catalytic mechanism of the adenylyl and guanylyl cyclases: modeling and mutational analysis.

The adenylyl and guanylyl cyclases catalyze the formation of 3', 5'-cyclic adenosine or guanosine monophosphate from the corresponding nucleoside 5'-triphosphate. The guanylyl cyclases, the mammalian adenylyl cyclases, and their microbial homologues function as pairs of homologous catalytic domains. The crystal structure of the rat type II adenylyl cyclase C2 catalytic domain was used to model by homology a mammalian adenylyl cyclase C1-C2 domain pair, a homodimeric adenylyl cyclase of Dictyostelium discoideum, a heterodimeric soluble guanylyl cyclase, and a homodimeric membrane guanylyl cyclase. Mg2+ATP or Mg2+GTP were docked into the active sites based on known stereochemical constraints on their conformation. The models are consistent with the activities of seven active-site mutants. Asp-310 and Glu-432 of type I adenylyl cyclase coordinate a Mg2+ ion. The D310S and D310A mutants have 10-fold reduced Vmax and altered [Mg2+] dependence. The NTP purine moieties bind in mostly hydrophobic pockets. Specificity is conferred by a Lys and an Asp in adenylyl cyclase, and a Glu, an Arg, and a Cys in guanylyl cyclase. The models predict that an Asp from one domain is a general base in the reaction, and that the transition state is stabilized by a conserved Asn-Arg pair on the other domain.

Adenylyl Cyclases↗
PubMed1999

The mast cell tumor necrosis factor alpha response to FimH-expressing Escherichia coli is mediated by the glycosylphosphatidylinositol-anchored molecule CD48.

Mast cells are well known for their harmful role in IgE-mediated hypersensitivity reactions, but their physiological role remains a mystery. Several recent studies have reported that mast cells play a critical role in innate immunity in mice by releasing tumor necrosis factor alpha (TNF-alpha) to recruit neutrophils to sites of enterobacterial infection. In some cases, the mast cell TNF-alpha response was triggered when these cells directly bound FimH on the surface of Escherichia coli. We have identified CD48, a glycosylphosphatidylinositol-anchored molecule, to be the complementary FimH-binding moiety in rodent mast cell membrane fractions. We showed that (i) pretreatment of mast cell membranes with antibodies to CD48 or phospholipase C inhibited binding of FimH+ E. coli, (ii) FimH+ E. coli but not a FimH- derivative bound isolated CD48 in a mannose-inhibitable manner, (iii) binding of FimH+ bacteria to Chinese hamster ovary (CHO) cells was markedly increased when these cells were transfected with CD48 cDNA, and (iv) antibodies to CD48 specifically blocked the mast cell TNF-alpha response to FimH+ E. coli. Thus, CD48 is a functionally relevant microbial receptor on mast cells that plays a role in triggering inflammation.

Adhesins, Bacterial↗
PubMed2006

Effect of methamidophos and urea application on microbial communities in soils as determined by microbial biomass and community level physiological profiles.

In this study, we evaluated the effect of the application by two agrochemicals, methamidophos (O,S-dimethyl phosphoroamidothioate) and urea, on microbial diversity in soil, using the combined approaches of soil microbial biomass analysis and community level physiological profiles (CLPPs). The results showed that both a low and a high level of methamidophos application (CS2 and CS3) and urea application (CS4) significantly decreased microbial biomass C (Cmic) by 41-83% compared with the control (CS1). The soil organic C (Corg) values of CS3 and CS4 were significantly higher and lower by 24% and 14%, respectively, than that of CS1. Similarly to Cmic, the values of Cmic/Corg of the three applied soils which decreased were lower by 31-84% than that of CS1. In contrast, the respiration activity of the three applied soils were significantly higher than the control. Agrochemical application also significantly increased the soil total of N and P (Ntol and Ptol) and decreased the Corg/Ntol and Corg/Ptol values. The CLPPs results showed that the AWCD (average well color development) of the three applied soils were significantly higher than that of CS1 during the incubation period. Substrate richness, Shannon and Simpson indices of microbial communities under chemical stresses, increased significantly. In addition, the CFU (colony-forming unit) numbers of methamidophos metabolized bacteria in CS2 and CS3 also increased significantly by 86.1% and 188.9% compared with that of CS1. The combined results suggest that agrochemicals reduce microbial biomass and enhance functional diversities of soil microbial communities; meanwhile, some species of bacteria may be enriched in soils under methamidophos stress.

Biomass↗
PubMed2002

Assembly and activation of the neutrophil NADPH oxidase in granule membranes.

Phagocyte activation is accompanied by assembly of an NADPH oxidase that reduces oxygen to form a number of reactive species. These oxygen radicals can eradicate invading microorganisms, regulate the function of other immune reactive cells, and cause damage to "innocent bystander" cells. It is generally assumed that the NADPH oxidase is activated exclusively in the plasma membrane. In neutrophils, this assumption does not fit with the subcellular localization of the membrane component of the oxidase, which is stored in granule compartments. It has now become increasingly evident that oxidants are also produced in an intracellular compartment that we identify as the specific granules. Myeloperoxidase is stored in another granule subset, the azurophil granules, and participates in the processing of the oxidative metabolites. We suggest that neutrophil activation is accompanied by fusion between azurophil and specific granules, allowing these peroxidase-dependent reactions to take place. The presented data suggest a requisite role for neutrophil oxidants complementing their function as microbial killing agents. Signaling capabilities of the oxidants, affecting for example, the state of protein phosphorylation, regulation of transcription factors, and induction of apoptosis, are discussed.

Animals↗
PubMed2025

CoverM: read alignment statistics for metagenomics.

SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results. AVAILABILITY AND IMPLEMENTATION: CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.

Metabolomics↗
PubMed1990

Gamma delta T cell receptor-bearing lymphocytes during Epstein-Barr virus infection.

Lymphocytes bearing gamma delta T cell receptors (TCR) constitute a minor subpopulation of human peripheral blood lymphocytes. Their role and function during microbial infections are largely unknown. In 10 patients with Epstein-Barr virus-induced infectious mononucleosis, the gamma delta TCR-expressing T cell population expanded during the acute phase. These cells were largely delta TCS1-, CD4-, and CD8- but expressed activation antigens such as human leukocyte antigen-DR and CD38. The convalescent phase of infectious mononucleosis was characterized by a relative persistence of gamma delta T cells. Together these data suggest a possible role of gamma delta T cells in the control of primary Epstein-Barr virus infection in humans.

Acute Disease↗
PubMed1995

M proteins of group G streptococci: mechanisms of resistance to phagocytosis.

Group G streptococci that express M protein and resist phagocytosis in human blood (virulent strains) were compared with strains of groups G and A that are readily phagocytosed (avirulent). Virulent group G streptococci were less effective (P < .05) as activators of the alternative complement pathway (ACP) than were avirulent streptococci. In immunofluorescence studies, C3 bound more avidly to avirulent than to virulent group G streptococci. Resistance of virulent group G strains to ACP opsonization and to phagocytosis was markedly diminished by removal with pepsin of the type-specific portion of the M molecule. Preincubation with fibrinogen did not diminish ACP activation or C3 binding by virulent group G and A streptococci but did exert an antiphagocytic effect. Given the similarity of M proteins of groups G and A in structure and function, other microbial constituents are likely responsible for differences in the spectra of illnesses attributable to the two serogroups.

Antigens, Bacterial↗
PubMed2003

Xylose reductase from the Basidiomycete fungus Cryptococcus flavus: purification, steady-state kinetic characterization, and detailed analysis of the substrate binding pocket using structure-activity relationships.

Xylose reductase has been purified to apparent homogeneity from cell extracts of the fungus Cryptococcus flavus grown on D-xylose as carbon source. The enzyme, the first of its kind from the phylum Basidiomycota, is a functional dimer composed of identical subunits of 35.3 kDa mass and requires NADP(H) for activity. Steady-state kinetic parameters for the reaction, D-xylose + NADPH + H(+)<--> xylitol + NADP(+), have been obtained at pH 7.0 and 25 degrees C. The catalytic efficiency for reduction of D-xylose is 150 times that for oxidation of xylitol. This and the 3-fold tighter binding of NADPH than NADP(+) indicate that the enzyme is primed for unidirectional metabolic function in microbial physiology. Kinetic analysis of enzymic reduction of aldehyde substrates differing in hydrophobic and hydrogen bonding capabilities with binary enzyme-NADPH complex has been used to characterize the substrate-binding pocket of xylose reductase. Total transition state stabilization energy derived from bonding with non-reacting sugar hydroxyls is approximately 15 kJ/mol, with a major contribution of 5-8 kJ/mol made by interactions with the C-2(R) hydroxy group. The aldehyde binding site is approximately 1.2 times more hydrophobic than n-octanol and can accommodate linear alkyl chains of <or=6 carbons. Hydrophobic interactions provide a total binding energy of approximately 10 kJ/mol. Specificity for the aldehyde substrate is achieved through large decreases in apparent K(m) ( approximately 100-fold) and smaller but significant increases in turnover number ( approximately 5-fold). We observed up to 250-fold preference of xylose reductase for reaction with pyridine carbaldehydes, 4-nitro-benzaldehyde, and alpha-oxo-aldehydes over reaction with D-xylose, perhaps reflecting a secondary role of this enzyme in detoxication metabolism of reactive endogenous aldehydes and compounds of xenobiotic origin.

Aldehyde Reductase↗