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At least 1,513 records · Page 84Linked to original sources
PubMed2005

Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community.

Horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. Even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. In this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced by the donor strain and that various mating conditions and isolation strategies increased the diversity of transconjugants detected. To detect transconjugants, the plasmid pB10 was marked with lacp-rfp, while rfp expression was repressed in the donors by chromosomal lacI(q). The phylogeny of 306 transconjugants obtained was determined by analysis of partial 16S rRNA gene sequences. The transconjugants belonged to 15 genera of the alpha- and gamma-Proteobacteria. The phylogenetic diversity of transconjugants obtained in separate matings with donors Pseudomonas putida SM1443, Ralstonia eutropha JMP228, and Sinorhizobium meliloti RM1021 was significantly different. For example, the transconjugants obtained after matings in sludge with S. meliloti RM1021 included eight genera that were not represented among the transconjugants obtained with the other two donors. Our results indicate that the spectrum of hosts to which a promiscuous plasmid transfers in a microbial community can be strongly influenced by the donor from which it transfers.

Conjugation, Genetic↗
PubMed2006

Food-protein enzymatic hydrolysates possess both antimicrobial and immunostimulatory activities: a "cause and effect" theory of bifunctionality.

The antimicrobial activity (the ability to activate the microbial autolytic system) and immunostimulatory activity (the ability to improve the phagocytic cell functioning) of 20 food-protein hydrolysates [five food proteins (casein, alpha-lactalbumin, beta-lactoglobulin, ovalbumin and serum albumin) hydrolyzed with four gastrointestinal proteinases (trypsin, alpha-chymotrypsin, pepsin and pancreatin)] were examined. All the food-protein hydrolysates acted antimicrobially in vitro towards all 24 microbial strains tested: autolysis of 20 naturally autolyzing strains was activated, with the autolysis activation index (K(A)) ranging from 1.04 to 22.0, while autolysis was induced to values of 2.81-56.7% in four naturally nonautolyzing strains. When given to mice per os, all the food-protein hydrolysates enhanced the phagocytosing capacity of peritoneal macrophages, with the enhancement index (K(I)) ranging from 1.02 to 1.41. A direct correlation between K(A) and K(I) was observed. We make the presumption that K(I) is a function of K(A).

Adjuvants, Immunologic↗
PubMed2004

Analysis of signal-dependent changes in the proteome of Drosophila blood cells during an immune response.

Innate immunity is based on the recognition of cell-surface molecules of infecting agents. Microbial substances, such as peptidoglycan, lipopolysaccharide, and beta-1,3-glucans, produce functional responses in Drosophila hemocytes that contribute to innate immunity. We have used two-dimensional gel electrophoresis and MS to resolve lipopolysaccharide-induced changes in the protein profile of a Drosophila hemocytic cell line. We identified 24 intracellular proteins that were up- or down-regulated, or modified, in response to immune challenge. Several proteins with predicted immune functions, including lysosomal proteases, actin-binding/remodeling proteins, as well as proteins involved in cellular responses to oxidative stress, were affected by the immune assault. Intriguingly, a number of the proteins identified in this study have recently been implicated in phagocytosis in higher vertebrates. We suggest that phagocytosis is activated in Drosophila hemocytes by the presence of microbial substances, and that this activation constitutes an evolutionarily conserved arm of innate immunity. In addition, a number of proteins involved in calcium-regulated signaling, mRNA processing, and nuclear transport were affected, consistent with a possible role in reprogramming of gene expression. In conclusion, the present proteome analysis identified many proteins previously not linked to innate immunity, demonstrating that differential protein profiling of Drosophila hemocytes is a valuable tool for identification of new players in immune-related cellular processes.

Animals↗
PubMed2025

Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.

MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA. RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems. AVAILABILITY AND IMPLEMENTATION: PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.

Phylogeny↗
PubMed1999

Carbon stable isotopes reveal complex trophic interactions in lake plankton.

The lower trophic linkages in lake plankton food webs are generally described as relatively simple, even accounting for the additional complexity of potential 'microbial looping'. Crustacean zooplankton are frequently amalgamated into one trophic functional group as grazers of autotrophic production. The carbon stable isotope ratios for separated zooplankton species, particulate organic matter (POM) and phytoplankton from a number of lakes in Finland and the UK were analysed. These revealed greater complexity in trophic interactions than would otherwise be observed if the zooplankton had been represented by a mixed sample. Grazing zooplankton were usually depleted in (13)C relative to the bulk POM on which they might feed, with (13)C deviating by up to 17 per thousand There were no consistent differences between (13)C values for copepods and cladocerans. Predatory cladocerans were generally enriched by greater than 1 per thousand compared to their putative prey. We suggest that care in separating the zooplankton species for stable isotope analysis may expose otherwise undetected sources of carbon and facilitate unravelling trophic links further up the food web. Copyright 1999 John Wiley & Sons, Ltd.

Journal Article↗
PubMed2001

Specialization and complementarity in microbial molecule recognition by human myeloid and plasmacytoid dendritic cells.

Following encounter with pathogens, dendritic cells (DC) mature and migrate from peripheral tissues to the T cell areas of secondary lymphoid organs, where they produce regulatory cytokines and prime naive T lymphocytes. We investigated in two subsets of human peripheral blood DC the expression of Toll-like receptors (TLR1 through TLR9) and the regulation of chemokine receptors and cytokine production in response to different maturation stimuli. Myeloid DC express all TLR except TLR7 and TLR9, which are selectively expressed by plasmacytoid DC. Myeloid and plasmacytoid DC respond to pathogen-associated molecular patterns according to their TLR expression. In response to the appropriate stimuli both DC types up-regulate CCR7, a receptor that drives DC migration to the T cell areas. Type I IFN was produced only by plasmacytoid DC and at early time points after stimulation. Furthermore, its production was elicited by some of the maturation stimuli tested. These results reveal a remarkable specialization and complementarity in microbial molecule recognition as well as a flexibility in effector function among myeloid and plasmacytoid DC.

Cytokines↗
PubMed2003

Statistical bioinformatic methods in microbial genome analysis.

It is probable that, increasingly, genome investigations are going to be based on statistical formalization. This review summarizes the state of art and potentiality of using statistics in microbial genome analysis. First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites. Then I describe how to use phylogenetic methods in genome analysis and methods for genome-wide scanning for positively selected amino acids. I conclude with speculations on the future course of genome statistical modeling.

Computational Biology↗
PubMed2006

Genetic engineering of taxol biosynthetic genes in Saccharomyces cerevisiae.

Baccatin III, an intermediate of Taxol biosynthesis and a useful precursor for semisynthesis of the anti-cancer drug, is produced in yew (Taxus) species by a sequence of 15 enzymatic steps from primary metabolism. Ten genes encoding enzymes of this extended pathway have been described, thereby permitting a preliminary attempt to reconstruct early steps of taxane diterpenoid (taxoid) metabolism in Saccharomyces cerevisiae as a microbial production host. Eight of these taxoid biosynthetic genes were functionally expressed in yeast from episomal vectors containing one or more gene cassettes incorporating various epitope tags to permit protein surveillance and differentiation of those pathway enzymes of similar size. All eight recombinant proteins were readily detected by immunoblotting using specific monoclonal antibodies and each expressed protein was determined to be functional by in vitro enzyme assay, although activity levels differed considerably between enzyme types. Using three plasmids carrying different promoters and selection markers, genes encoding five sequential pathway steps leading from primary isoprenoid metabolism to the intermediate taxadien-5alpha- acetoxy-10beta-ol were installed in a single yeast host. Metabolite analysis showed that yeast isoprenoid precursors could be utilized in the reconstituted pathway because products accumulated from the first two engineered pathway steps (leading to the committed intermediate taxadiene); however, a pathway restriction was encountered at the first cytochrome P450 hydroxylation step. The means of overcoming this limitation are described in the context of further development of this novel approach for production of Taxol precursors and related taxoids in yeast.

Alkaloids↗
PubMed1997

Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.

Mining the emerging abundance of microbial genome sequences for hypotheses is an exciting prospect of "functional genomics". At the forefront of this effort, we compared the predictions of the complete Escherichia coli genomic sequence with the observed gene products by assessing 381 proteins for their mature N-termini, in vivo abundances, isoelectric points, molecular masses, and cellular locations. Two-dimensional gel electrophoresis (2-DE) and Edman sequencing were combined to sequence Coomassie-stained 2-DE spots representing the abundant proteins of wild-type E. coli K-12 strains. Greater than 90% of the abundant proteins in the E. coli proteome lie in a small isoelectric point and molecular mass window of 4-7 and 10-100 kDa, respectively. We identified several highly abundant proteins, YjbJ, YjbP, YggX, HdeA, and AhpC, which would not have been predicted from the genomic sequence alone. Of the 223 uniquely identified loci, 60% of the encoded proteins are proteolytically processed. As previously reported, the initiator methionine was efficiently cleaved when the penultimate amino acid was serine or alanine. In contrast, when the penultimate amino acid was threonine, glycine, or proline, cleavage was variable, and valine did not signal cleavage. Although signal peptide cleavage sites tended to follow predicted rules, the length of the putative signal sequence was occassionally greater than the consensus. For proteins predicted to be in the cytoplasm or inner membrane, the N-terminal amino acids were highly constrained compared to proteins localized to the periplasm or outer membrane. Although cytoplasmic proteins follow the N-end rule for protein stability, proteins in the periplasm or outer membrane do not follow this rule; several have N-terminal amino acids predicted to destabilize the proteins. Surprisingly, 18% of the identified 2-DE spots represent isoforms in which protein products of the same gene have different observed pI and M(r), suggesting they are post-translationally processed. Although most of the predicted and observed values for isoelectric point and molecular mass show reasonable concordance, for several proteins the observed values significantly deviate from the expected values. Such discrepancies may represent either highly processed proteins or misinterpretations of the genomic sequence. Our data suggest that AhpC, CspC, and HdeA exist as covalent homomultimers, and that IcdA exists as at least three isoforms even under conditions in which covalent modification is not predicted. We enriched for proteins based on subcellular location and found several proteins in unexpected subcellular locations.

Amino Acid Sequence↗
PubMed2002

Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity.

The crystal structure of Bacillus stearothermophilus PhoE (originally termed YhfR), a broad specificity monomeric phosphatase with a molecular mass of approximately 24 kDa, has been solved at 2.3 A resolution in order to investigate its structure and function. PhoE, already identified as a homolog of a cofactor-dependent phosphoglycerate mutase, shares with the latter an alpha/beta/alpha sandwich structure spanning, as a structural excursion, a smaller subdomain composed of two alpha-helices and one short beta-strand. The active site contains residues from both the alpha/beta/alpha sandwich and the sub-domain. With the exception of the hydrophilic catalytic machinery conserved throughout the cofactor-dependent phosphoglycerate mutase family, the active-site cleft is strikingly hydrophobic. Docking studies with two diverse, favored substrates show that 3-phosphoglycerate may bind to the catalytic core, while alpha-napthylphosphate binding also involves the hydrophobic portion of the active-site cleft. Combining a highly favorable phospho group binding site common to these substrate binding modes and data from related enzymes, a catalytic mechanism can be proposed that involves formation of a phosphohistidine intermediate on His10 and likely acid-base behavior of Glu83. Other structural factors contributing to the broad substrate specificity of PhoE can be identified. The dynamic independence of the subdomain may enable the active-site cleft to accommodate substrates of different sizes, although similar motions are present in simulations of cofactor-dependent phosphoglycerate mutases, perhaps favoring a more general functional role. A significant number of entries in protein sequence databases, particularly from unfinished microbial genomes, are more similar to PhoE than to cofactor-dependent phosphoglycerate mutases or to fructose-2,6-bisphosphatases. This PhoE structure will therefore serve as a valuable basis for inference of structural and functional characteristics of these proteins.

Amino Acid Sequence↗
PubMed1986

How do food passage rate and assimilation differ between herbivorous lizards and nonruminant mammals?

What digestive adaptations permit herbivorous nonruminant mammals to sustain much higher metabolic rates than herbivorous lizards, despite gross similarity in digestive anatomy and physiology? We approached this question by comparing four herbivorous species eating the same diet of alfalfa pellets: two lizards (chuckwalla and desert iugana) and two mammals (desert woodrat and laboratory mouse). The mammals had longer small and large intestines, greater intestinal surface area, much higher (by an order of magnitude) food intake normalized to metabolic live mass, and much faster food passage times (a few hours instead of a few days). Among both reptiles and mammals, passage times increase with body size and are longer for herbivores than for carnivores. The herbivorous lizards, despite these much slower passage times, had slightly lower apparent digestive efficiencies than the mammals. At least for chuckwallas, this difference from mammals was not due to differences in body temperature regime. Comparisons of chuckwallas and woodrats in their assimilation of various dietary components showed that the woodrat's main advantage lay in greater assimilation of the dietary fiber fraction. Woodrats achieved greater fiber digestion despite shorter residence time, but possibly because of a larger fermentation chamber, coprophagy, and/or different conditions for microbial fermentation. We conclude with a comparative overview of digestive function in herbivorous lizards and mammals, and with a list of four major unsolved questions.

Adaptation, Biological↗
PubMed2004

Earthworm leukocyte populations specifically harbor lysosomal enzymes that may respond to bacterial challenge.

Earthworm leukocytes (coelomocytes) are responsible for innate cellular immune functions such as phagocytosis and encapsulation against parasites and pathogens. Microbial killing results from the combined action of the phagocytic process with humoral immune factors such as agglutinins (e.g., lectins), lysosomal enzymes (e.g., acid phosphatase, lysozyme), and various cytotoxic and antimicrobial molecules. There is also evidence of weak adaptive immune responses against foreign transplants. This study focused on aspects of the innate immune response. First, anti-human acid phosphatase (anti-AcP) polyclonal antibody characterized different acid hydrolase patterns in coelomocytes. Second, flow cytometry identified a strongly immunoreactive coelomocyte population. Third, ultrastructural and cytochemical analyses revealed acid phosphatase in discrete granules (lysosomes) of effector hyaline and granular coelomocytes but not in mature chloragocytes. Coelomocytes were exposed to bacteria to assess how phagocytosis influences: (a) the production of acid phosphatase using Western blot, and (b) release of acid phosphatase using ELISA from cell-free coelomic fluid. Fourth, after phagocytosis, acid phosphatase levels differed between controls and experimentals. Fifth, we found a 39-kDa molecule that reacted intensely with anti-AcP. Our results suggest that effector earthworm coelomocytes may not eliminate pathogens only by phagocytosis but also by extracellular lysis.

Acid Anhydride Hydrolases↗
PubMed1984

Infections in burn patients: a paradigm for cutaneous infection in the patient at risk.

The burn patient is in many ways the archetypical immunosuppressed host: the anatomic barriers have been breached and the host's defenses suppressed. Infection is the leading cause of death in hospitalized burn patients not having inhalation injury, being responsible for between 50 and 75 percent of the hospital deaths. Burn injury produces profound abnormalities in immunologic function. These changes are generally proportional to the degree of burn injury (surface area and depth). Cell-mediated immune function is suppressed. Anergy and depressed allograft rejection occur. Acute burn serum samples contain several factors that suppress cell-mediated immune functions. Antibody levels are usually mildly to moderately reduced. Complement, particularly the alternative complement pathway, may be massively activated and depleted, removing a critical defense mechanism against gram-negative rod infections for which preformed antibodies are absent. This depression is further exacerbated by malnutrition and infection. Fibronectin levels are also reduced. Phagocytic cell function is abnormal with burns. Neutrophil numbers may be depressed, and function is abnormal. Chemotactic responsiveness, cytoplasmic granule enzyme content, and oxygen radical generation are abnormal. Monocyte/macrophage dysfunction has similarly been demonstrated. Burn infections reflect abnormal host functions as well as changes in the hospital environment and microbial selection pressures. The burn patient is a model of cutaneous infection in the patient at risk.

Antibody Formation↗
PubMed1981

Characterization of a respiratory mutant of Escherichia coli with reduced uptake of aminoglycoside antibiotics.

A strain of Escherichia coli (NSW77) which is partially resistant to streptomycin was isolated by selecting for growth on plates supplemented with 12.5 micrograms/ml streptomycin, a concentration which completely inhibits growth of wild-type strains. The low-level resistance of the mutant appears to result from a reduced ability to accumulate streptomycin intracellularly. In addition, the mutant strain is unable to use succinate for growth because of a defective respiratory chain. Thus, membranes of the mutant strain were found to have approximately half the NADH and D-lactate oxidase activity of the parent strain. Moreover, membranes of the mutant were found to contain demethyl-menaquinone and, in place of ubiquinone, a structural analogue, 2-octaprenyl-3-methyl-6-methoxy-1,4 benzoquinone. The mutation responsible for both the Suc-phenotype and partial resistance to streptomycin was found to be located near minute 15 on the bacterial chromosome. Both the biochemical and genetic evidence suggests the the mutation in strain NSW77 resides in the ubi F gene. Another previously characterized ubi F strain was also found to have a reduced capacity to take up an aminoglycoside antibiotic (gentamicin). These results suggest that the respiratory defects in ubi F strains are responsible for the reduced capacity of such strains to accumulate aminoglycosides.

Biological Transport↗
PubMed1994

A new flow cytometric assay for the evaluation of phagocytosis and the oxidative burst in whole blood.

Phagocytes play an important role in host defence against microorganisms and different techniques are needed to evaluate their functional activities. Here we describe a rapid, simple and reliable one step procedure to measure the phagocytosis rate and oxidative burst activation of both polymorphonuclear leukocytes (PMN) and monocytes, by means of flow cytometry using only small quantities of whole blood. The two species of bacteria employed as test microorganisms, Staphylococcus aureus and Candida albicans showed a somewhat different behaviour. We found that the present method could be used as an alternative test in the diagnosis of chronic granulomatous disease (CGD). Moreover we were able to analyse, in a one step procedure, defective phagocyte functions in a group of paediatric patients suffering from recurrent microbial infections.

Bacterial Infections↗
PubMed1995

Application of a mathematical model to describe the behaviour of the Lactobacillus spp. during the ripening of a Spanish dry fermented sausage (Chorizo).

The evolution of Lactobacillus spp. during the curing process of dry fermented sausage (Chorizo), has been studied under natural climatic conditions and in a controlled drying chamber, with regulated temperature and relative humidity. In order to fully understand the development of the microorganisms in each of these two cases, it applied a mathematical model based on a modified Gompertz equation. The proposed mathematical function is easy to use and statistically appropriate. Furthermore, it allows the distinction to be made between the four phases which characterise the behaviour of these microorganisms during the curing of the sausage (a) latency from an initial threshold level; (b) exponential growth; (c) stationary state; (d) depletion to a residual level. The mathematical analysis of this function has highlighted certain differences in the behaviour of the microbial flora depending on the technological conditions to which the drying of the sausages is subjected. Under the climatically controlled conditions of the drying process, a better development of the lactobacillus spp. is observed, but conversely the final stage of the exponential growth is brought forward, the length of the stationary phase is shortened and is reached before the end of the drying period, at which point the marginal decline of the microorganisms becomes ever more reduced.

Fermentation↗
PubMed2006

Macrophage activation and nitric oxide production by water soluble components of Hericium erinaceum.

Hericium erinaceum is a medicinal and edible mushroom with anti-microbial and anti-cancer activities. To evaluate the immunoregulatory functions of H. erinaceum, we prepared water extract from H. erinaceum (WEHE) and investigated its ability to activate macrophages and to induce nitric oxide (NO) production in macrophages. Rat peritoneal macrophages stimulated with 1 to 100 mug/ml of WEHE for 24, 48, or 72 h produced NO in a time- and dose-dependent manner. Reverse transcription-polymerase chain reaction demonstrated that WEHE augmented the steady-state level of inducible NO synthase (iNOS) mRNA in both the peritoneal macrophages and a murine macrophage cell-line, RAW 264.7. Electrophoretic mobility shift assay showed that WEHE increased DNA binding activity of the transcription factor NF-kappaB, which is responsible for iNOS gene expression. Furthermore, its trans-acting activity was confirmative as determined by in vitro transfection assay using a reporter gene construct, p(NF-kappaB)(3)-CAT, whose expression is solely regulated by the activity of NF-kappaB. Concomitantly with the activation of NF-kappaB, WEHE markedly decreased intracellular IkappaBalpha level as demonstrated by Western blot assay. These results suggested that WEHE induces iNOS gene expression followed by NO production in macrophages via enhancing the activation of transcription factor, NF-kappaB.

Agaricales↗