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At least 1,603 records · Page 89Linked to original sources
PubMed2002

Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a correlation between host responses and HsdS components of type I restriction-modification systems.

Helicobacter pylori infects the stomachs of half of all humans. It has a relatively benign relationship with most hosts but produces severe pathology, including gastric cancer, in others. Identifying the relative contributions of host, microbial, and environmental factors to the outcome of infection has been challenging. Here we describe one approach for identifying microbial genes that affect the magnitude of host responses to infection. Single colony purified H. pylori isolates were obtained from 25 cases and 71 controls in a Swedish case-control study of gastric cancer. Strains were first phenotyped based on their ability to produce adhesins that recognize two classes of human gastric epithelial receptors. Thirteen binding strains and two non-binding controls were then subjected to whole genome genotyping using H. pylori DNA microarrays. A cohort of "variable" genes was identified based on a microarray-determined call of "absent" in at least one member of the strain panel. Each strain was subsequently introduced into two types of germ-free transgenic mice, each programmed to express a different host factor postulated to pose increased risk for development of severe pathology. Expression of biomarkers of host defense was quantitated 4 weeks after inoculation, and the magnitude of the response correlated with bacterial genotype. The proportion of genes encoding HsdS homologs (specificity subunit of hetero-oligomeric type I restriction-modification systems) was significantly higher in the pool of 18 variable genes whose presence directly correlated with a robust host response than their proportion in the remaining 352 members of the variable gene pool. This suggests that the functions of these HsdS homologs may include control of expression of microbial determinants that affect the extent of gastric responses to this potentially virulent pathogen.

Animals↗
PubMed2001

Relevance of microbial extracellular polymeric substances (EPSs)--Part I: Structural and ecological aspects.

Extracellular polymeric substances are the construction materials for microbial aggregates such as biofilms, flocs ("planktonic biofilms") and sludge. Their major components are not only polysaccharides but also proteins and in some cases lipids, with minor contents of nucleic acids and other biopolymers. In the EPS, biofilm organisms can establish stable arrangements and function multicellularly as synergistic microconsortia. The matrix facilitates the retention of exoenzymes, cellular debris and genetic material; it can be considered as a microbial recycling yard. Gradients can develop due to the physiological activity and the fact that diffusive mass transport prevails over convective transport in the matrix. Biofilm cells tolerate higher concentrations of many biocides. The EPS matrix sequesters nutrients from the water phase. In photosynthetic communities, EPS molecules can function as light transmitters and provide photons to organisms located deeper in a microbial mat. The EPS matrix is a dynamic system, constructed by the organisms and responding to environmental changes. It enables the cells to function in a manner similar to multicellular organisms.

Biofilms↗
PubMed1978

The penetration of antibiotics into bacterial cells: significance to antimicrobial action.

The penetration of antibiotics into the microbial cell is reviewed from the standpoint of the structure and function of the several types of membranes which constitute permeability barriers to the passage of hydrophilic molecules. It is clear that little is actually known about the mechanisms by which the majority of antibiotics gain access to their site of action within the target cell. Sufficient evidece is at hand to indicate that resistance to several groups of antibiotics is determined by changes in the permeability of the cell membranes, the genes for which are often carried on R-plasmids. The importance of studies to determine the precise mechanisms by which each type of antibiotic permeates the membrane of the bacterial cell is stressed by a discussion of several approaches to enhancing antibiotic permeation through manipulation of either the drug or the target cell based on knowledge of the uptake mechanisms.

Aminoglycosides↗
PubMed2004

Toward large-scale modeling of the microbial cell for computer simulation.

In the post-genomic era, the large-scale, systematic, and functional analysis of all cellular components using transcriptomics, proteomics, and metabolomics, together with bioinformatics for the analysis of the massive amount of data generated by these "omics" methods are the focus of intensive research activities. As a consequence of these developments, systems biology, whose goal is to comprehend the organism as a complex system arising from interactions between its multiple elements, becomes a more tangible objective. Mathematical modeling of microorganisms and subsequent computer simulations are effective tools for systems biology, which will lead to a better understanding of the microbial cell and will have immense ramifications for biological, medical, environmental sciences, and the pharmaceutical industry. In this review, we describe various types of mathematical models (structured, unstructured, static, dynamic, etc.), of microorganisms that have been in use for a while, and others that are emerging. Several biochemical/cellular simulation platforms to manipulate such models are summarized and the E-Cell system developed in our laboratory is introduced. Finally, our strategy for building a "whole cell metabolism model", including the experimental approach, is presented.

Biotechnology↗
PubMed1999

Bacterial function and community structure in reactors treating biopolymers and surfactants at mesophilic and thermophilic temperatures.

Microbial communities capable of degrading biopolymers and surfactants typically found in graywater were selected in continuous-flow bioreactors operated at 30, 44, 53, or 62 degrees C. The effect of temperature upon microbial activity and community composition was determined. Microbial respiration of the organic components of the medium (including linear alkylbenzene sulfonate) was detected in samples from each reactor. The microbial community in each reactor was adapted to the operating temperature. Nucleic acid-based analyses of community composition showed that distinct consortia were present at each temperature. Community complexity was inversely related to temperature. The specific maintenance rate was twofold higher at 62 degrees C than at the lower temperatures. Under starvation conditions, microbes in the 62 degrees C system lost membrane integrity 30- to 100-fold faster than microbes at lower temperatures.

Journal Article↗
PubMed1992

Treatment of patients with chronic granulomatous disease with recombinant human interferon-gamma does not improve neutrophil oxidative metabolism, cytochrome b558 content or levels of four anti-microbial proteins.

Recombinant interferon-gamma (rIFN-gamma) has been described to enhance phagocyte functions in vitro and in vivo in several patients with chronic granulomatous disease (CGD). To demonstrate the clinical usefulness of this treatment, 128 patients were treated in a randomized, double-blind multi-centre study with a placebo preparation or with rIFN-gamma. We analysed parameters of neutrophil oxidative and non-oxidative metabolism in 16 patients enrolled in this study. No enhanced superoxide-release was observed in patients treated with rIFN-gamma compared to placebo-treated patients. Phagocyte cytochrome b558 content also remained unchanged. Levels of four non-oxidative antimicrobial proteins (cathepsin G, azurocidine, p29b, lactoferrin) rose, fell, or remained unchanged, irrespective of treatment with rIFN-gamma or placebo.

Blood Proteins↗
PubMedDate not supplied

[Properties of urease immobilized on the functional organic silica surface].

The paper deals with kinetics of the urea hydrolysis by microbial-origin urease dissolved and immobilized on the organic silica surface. It is shown that hydrolysis kinetics for soluble urease is described by the Michaelis-Menten equation until the concentration of urea reaches 1 M. Two fractions differing in the Michaelis constant are revealed for silochrome immobilized urease. The rate of urea hydrolysis by native and immobilized urease was studied depending on the pH value in presence of the substrate in the 1 M and 5 mM concentration. The hydrolysis rate of 1 M urea in the buffer-free solution by silochrome-immobilized urease is practically independent of pH within 4.5-6.5. Application of a 2.5 mM phosphate-citrate buffer as a solvent causes an increase in the hydrolysis rate within this pH range. For a soluble urease the 1 M urea hydrolysis rate dependence on pH is ordinary at pH 5.8-6.0. If the substrate concentration is 5 mM, the pH-dependences for the rate of the urea hydrolysis by silochrome- and aerosil-immobilized urease are close and at pH above 6.0 coincide with those for a soluble enzyme. The found differences in the properties of soluble and immobilized ureases are explained by the substrate and reaction products diffusion.

Enzymes, Immobilized↗
PubMed1980

Psychosexual functioning in symptomatic and asymptomatic women with and without signs of vaginitis.

Women with symptoms of vaginitis, but no microbial etiology for their condition (the experimental group) were compared to women with symptoms and abnormal findings on examination, women with no symptoms and abnormal findings on examination, and women with no symptoms and normal findings on examination. Comparison was on a variety of measures of personality, marital satisfaction, and sexual function. All women were found to have normal personality structure as measured by the Minnesota Multiphasic Personality Inventory (MMPI). However, the experimental group differed from the others in their objective sexual function, subjective level of enjoyment, and the extent to which they were affected by their vaginal symptoms.

Adolescent↗
PubMed2005

Denitrification on poly-beta-hydroxybutyrate in microbial granular sludge sequencing batch reactor.

Microbial granules were successfully cultivated in an alternating aerobic-anaerobic sequencing batch reactor (SBR) for removing organic carbon and nitrogen. It was found that almost all input ammonium was converted to nitrite and nitrate in the aerobic phase, while the efficiency of denitrification was highly related to the availability of external carbon source in the anaerobic phase. Complete denitrification was achieved with sufficient supply of external carbon, while only partial denitrification was observed with no addition of external carbon. Results showed that in the absence of external carbon source, pre-accumulated poly-beta-hydroxybutyric acid (PHB) in microbial granules could be utilized for cell maintenance and denitrification. With supply of external carbon but no addition of nitrate, PHB accumulation accounted for the main mechanism of the organic removal. Under balanced growth conditions (with organic carbon and nitrogen supply), external organic carbon was consumed simultaneously for denitrification, PHB storage as well as for cell functions. It was revealed that the potential role of PHB for denitrification by microbial granules was very limited, i.e. less than 28 mg nitrate-nitrogen l(-1) was found to be denitrified with internally accumulated PHB. This study for the first time shows the limiting capacity of PHB as reducing power for denitrification by microbial granules.

Bacteria, Aerobic↗
PubMed1994

Lipid matrix-based subunit vaccines: a structure-function approach to oral and parenteral immunization.

Immunization is today the most effective defense mechanism against microbial infections. Although highly effective vaccines are currently available for a number of infectious diseases, vaccine formulations can still be improved in a number of important areas. The ability to induce antigen-specific humoral and cell-mediated immunity is crucial to the development of effective prophylactic and therapeutic vaccines for HIV and other pathogens. The approach of our laboratory has been to design and test simple, highly defined antigen-lipid complexes that would stimulate antibody and cell-mediated immune responses in the absence of any nonspecific immunological activators such as Freund's adjuvant, lipopolysaccharide (LPS), or alum. These studies have provided insight into the relationships between the properties of an immunogen and the induction of the desired immune responses. We have previously utilized this approach to define the minimal structures required for the induction of antibody responses. Our more recent studies have focused on defining the parameters involved in the induction of cell-mediated and mucosal immune responses. Toward this end we have developed a new type of subunit vaccine that is effective when given orally or intramuscularly, and elucidated structure-function relationships in peptide vaccines that affect induction of CD8+ cell responses.

AIDS Vaccines↗
PubMed2006

In vivo and in vitro regulation of type I IFN synthesis by synergistic effects of CD40 and type II IFN.

During cognate interaction with CD40 ligand (CD154)-expressing T cells, Ag-presenting accessory cells are activated for increased cytokine synthetic and costimulatory function. We examined whether CD40 modulates in vivo innate immune function over time, hypothesizing that distinct cytokine responses evolve to delayed microbial exposure. C3H/HeN mice pretreated with activating anti-CD40 Ab (FGK45) produced 10-fold more serum IFN-gamma and IL-12 p70 to delayed, but not synchronous, challenge with LPS. A novel finding was that LPS-induced IFN-alpha increased by 20-fold in mice pretreated for 24 h, but not 6 h or less, with anti-CD40. Anti-CD40-pretreated C57BL/6 RAG-2(-/-) mice similarly increased IFN-alpha responses to delayed LPS challenge, confirming mediation by innate immunity. Type I IFNR- and IFN-gamma-deficient mice treated with anti-CD40 failed to expand serum IFN-alpha responses to LPS challenge. Combined pretreatment with anti-CD40 and anti-IFN-gamma mAb showed that IFN-gamma produced after anti-CD40 pretreatment, but before LPS challenge, was necessary for IFN-alpha synthetic enhancement. Anti-CD40 also increased polyinosinic-polycytidylic acid (poly(I:C))-inducible IFN-alpha by 5-fold in an IFN-gamma-dependent fashion, but did not significantly increase IFN-alpha production to CpG or Pam(3)Cys challenges. Poly(IC)-stimulated splenocytes from anti-CD40-pretreated mice produced 4-fold more IFN-alpha than controls and production associated with CD11c(+) cells. Finally, rIFN-gamma and anti-CD40 combined synergistically to increase poly(IC)-inducible IFN-alpha synthetic capacity in bone marrow dendritic cells. We conclude that innate immune production of IFN-alpha is cooperatively regulated by CD40 and IFN-gamma acting on dendritic cells, suggesting a unique mechanism by which innate immune function evolves in response to specific adaptive immune signals.

Adjuvants, Immunologic↗
PubMed2025

Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter.

The in vivo continuous evolution system OrthoRep (orthogonal replication) is a powerful strategy for rapid enzyme evolution in Saccharomyces cerevisiae that diversifies genes at a rate exceeding the endogenous genome mutagenesis rate by several orders of magnitude. However, it is difficult to neofunctionalize genes using OrthoRep partly because of the way selection pressures are applied. Here we combine OrthoRep with optogenetics in a selection strategy we call OptoRep, which allows fine-tuning of selection pressure with light. With this capability, we evolved a truncated form of the endogenous monocarboxylate transporter JEN1 (JEN1t) into a de novo mevalonate importer. We demonstrate the functionality of the evolved JEN1t (JEN1tY180C/G) in the production of farnesene, a renewable aviation biofuel, from mevalonate fed to fermentation media or produced by microbial consortia. This study shows that the light-induced complementation of OptoRep may improve the ability to evolve functions not currently accessible for selection, while its fine tunability of selection pressure may allow the continuous evolution of genes whose desired function has a restrictive range between providing effective selection and cellular viability.

Saccharomyces cerevisiae↗
PubMed2004

Hepatic expansion of a virus-specific regulatory CD8(+) T cell population in chronic hepatitis C virus infection.

Regulatory T (T(R)) cells consist of phenotypically and functionally distinct CD4(+) and CD8(+) T cell subsets engaged both in maintaining self-tolerance and in preventing anti-non-self effector responses (microbial, tumor, transplant, and so on) that may be harmful to the host. Here we propose that the proinflammatory function of virus-specific memory effector CCR7(-)CD8(+) T cells, which are massively recruited in the liver, are inefficient (in terms of IFN-gamma production) in patients with chronic hepatitis C virus (HCV) infection because of the concomitant presence of virus-specific CCR7(-)CD8(+) T(R) cells producing considerable amounts of IL-10. These CD8(+) T(R) cells are antigen specific, as they can be stimulated by HCV epitopes and suppress T cell responses that are in turn restored by the addition of neutralizing anti-IL-10. This study provides for the first time to our knowledge direct evidence of the existence of virus-specific CD8(+) T(R) cells that infiltrate the livers of patients with chronic HCV infection, identifies IL-10 as a soluble inhibitory factor mediating suppression, and suggests that these cells play a pivotal role in controlling hepatic effector CD8(+) T cell responses.

Adult↗
PubMed2000

Comparative analyses in aquatic microbial ecology: how far do they go?

Methodological developments in recent years have led to an increase in empirical databases on the abundance and functions of aquatic microbes, now allowing synthesis studies. Most of these studies have adopted a comparative approach, such that comparative analyses are now available for most aspects of aquatic microbial food webs (more than 50 papers published in the last 15 years). Some of these analyses apparently yield conflicting results, introducing confusion and unnecessary disputes in the field. We briefly review the comparative analyses so far produced and we highlight generalities, show that some of the perceived discrepancies largely derive from partial analyses of a general underlying trend and formulate predictions based on these general trends that provide new avenues for research.

Journal Article↗
PubMed1982

Macrophage activation and effector mechanisms against microbes.

The term activation is used to designate biochemical and functional changes that are induced in macrophages by a variety of stimuli, including interaction with microbial products, synthetic substances, immunoglobulins of different classes, and factors released by lymphocytes. The changes observed comprise an increased capacity to destroy intracellular microorganisms and non-microbial target cells as well as the stimulation of biochemical pathways leading to the release of enzymes and the generation of various toxic compounds. Activation may thus be viewed as a process aimed at recalling those metabolic functions that are necessary for killing, when phagocytosis has failed to evoke them. The increased microbicidal capacity of activated macrophages is linked to the production of oxygen intermediates, as illustrated by the study of macrophage toxicity for certain intracellular protozoan parasites. Scavengers of oxygen metabolites inhibit parasite killing in macrophages; on the contrary, agents that stimulate the production or utilization of such intermediates enhance the microbicidal effect of phagocytes. Several mechanisms enable microorganisms to survive within macrophages. In some instances, intracellular survival appears to depend on the capacity of microorganisms to be endocytized without awakening the host cell oxidative machinery. In addition, the endowment of microorganisms in endogenous enzymatic scavengers of oxygen metabolites may play a role in promoting intracellular survival. These and other mechanisms, such as the property to avoid the harmful effects of lysosomal constituents by inhibiting phagosome-lysosome fusion, or by releasing agents that block the lysosomal enzymatic machinery, may explain why certain microbes are able to survive within activated macrophages.

Animals↗
PubMed2003

T cell-dendritic cell interaction in vivo: random encounters favor development of long-lasting ties.

Understanding the complexity of the functional communication between cells composing the immune system is central to improving our capacity to manipulate it and conceive better strategies to combat microbial pathogens. So far, these studies have been based on immunohistochemistry of fixed tissues and in vitro attempts to reproduce functional connections between cells. The application of two-photon laser microscopy to the observation of viable immune cells in their natural environment where foreign antigens are carried to trigger an immune response opens a new era for these studies. They reveal exceptional properties of the locomotion of T cells that facilitate encounters with dendritic cells and the receipt of information that promotes T cell survival, death, or initiation of immune responses. These studies also complement in vitro observations addressing the importance of time of stimulation in determining T cell fates.

Cell Communication↗
PubMed1989

Determination of microbial genome sizes by two-dimensional denaturing gradient gel electrophoresis.

In two-dimensional denaturing gradient gel electrophoresis, DNA is digested with a restriction endonuclease and the resulting DNA fragments are separated as a function of size by conventional agarose gel electrophoresis. Following this first dimension electrophoresis, the fragment distribution is placed at the top of a denaturing gradient slab gel and electrophoresis is carried out parallel to the gradient direction. This second dimension separation is a complex function of the base sequence of each fragment. Analysis of the DNA fragment distribution as a function of fragment size allows the DNA size to be calculated. This method has been applied to calculate three microbial genome sizes: Mycoplasma capricolum, 724 kb; Acholeplasma laidlawii, 1646 kb; and Hemophilus influenzae, 1833 kb.

Acholeplasma↗
PubMed2005

Microbial reduction of selenate and nitrate: common themes and variations.

A number of biochemically distinct systems have been characterized for the microbial reduction of the oxyanions, selenate (SeO(4)(2-)) and nitrate (NO(3)(-)). Two classes of molybdenum-dependent nitrate reductase catalyse the respiratory-linked reduction of nitrate (NO(3)(-)) to nitrite (NO(2)(-)). The main respiratory nitrate reductase (NAR) is membrane-anchored, with its active site facing the cytoplasmic compartment. The other enzyme (NAP) is water-soluble and located in the periplasm. In recent years, our understanding of each of these enzyme systems has increased significantly. The crystal structures of both NAR and NAP have now been solved and they provide new insight into the structure, function and evolution of these respiratory complexes. In contrast, our understanding of microbial selenate (SeO(4)(2-)) reduction and respiration is at an early stage; however, similarities to the nitrate reductase systems are emerging. This review will consider some of the common themes and variations between the different classes of nitrate and selenate reductases.

Amino Acid Sequence↗