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At least 667 records · Page 37Linked to original sources
PubMed2006

MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications.

Knowledge of toxins, virulence factors and antibiotic resistance genes is essential for bio-defense applications aimed at identifying 'functional' signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and antibiotic resistance genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.

Bacterial Proteins↗
PubMed1997

Microbial aldolases and transketolases: new biocatalytic approaches to simple and complex sugars.

Enzymes have become exceedingly valuable tools in organic synthesis as the reactions they catalyze generally proceed under mild conditions and in high stereo- and regioselectivity. Advances in microbiology and genetic engineering have greatly increased the availability of various enzymes. One of the most useful applications of enzyme-catalyzed chemical transformations is in the synthesis of water-soluble, polyfunctional organic molecules such as carbohydrates. As the pivotal roles that carbohydrates play in biological processes become more evident, access to these compounds becomes increasingly important. This review gives a brief overview of the use of aldolases and transketolases in the synthesis of sugars, sugar analogs, and related compounds.

Bacteria↗
PubMed1967

Ecological patterns of micro-organisms in desert soils.

The Atacama Desert's hardy aerobic microbial populations have been found to occupy ecological niches substantially different from those occupied by aerobic micro-organisms in the California and Valley of 10 000 Smokes deserts. Two specialized groups of microflora, the actinomycetes and micro-aerophiles, appear to be abundant in some portions of the Atacama Desert, though many of the bacterial and mold types and species common in the California deserts are absent. The factors defining the ecological niches and relationships of microbial populations in these soils are largely unknown. In several respects, moreover, micro-environments in these soils are similar to some of those expected on Mars. For the purpose of establishing the engineering constraints on the design of life detection instruments and their sampling and processing components, the nature and diversity of species of micro-organisms prevalent in the soils of extremely dry climates of the earth have not been adequately investigated. Useful ecological information about these soils will include an estimate of the likely lower limit in numbers or mass of viable aggregates in the autochthonous populations and the survivability of these populations under mechanical processing and isolated storage. Knowledge of the artificial niches, growth media for example, which members of these populations accept, will be useful in designing life detection instruments themselves. The range of practical designs for soil sampling devices will be determined by the nature of the particles and surfaces, and their depths, on which various physiological groups or largest populations of micro-organisms reside in the extremely dry deserts of the earth. The results of several exploratory experiments are used to provide some understanding of the environment and the ecological patterns of micro-organisms in soils of the earth's driest deserts.

Actinomycetales↗
PubMed2002

Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD(+)-dependent formate dehydrogenase.

Metabolic engineering studies have generally focused on manipulating enzyme levels through either the amplification, addition, or deletion of a particular pathway. However, with cofactor-dependent production systems, once the enzyme levels are no longer limiting, cofactor availability and the ratio of the reduced to oxidized form of the cofactor can become limiting. Under these situations, cofactor manipulation may become crucial in order to further increase system productivity. Although it is generally known that cofactors play a major role in the production of different fermentation products, their role has not been thoroughly and systematically studied. However, cofactor manipulations can potentially become a powerful tool for metabolic engineering. Nicotinamide adenine dinucleotide (NAD) functions as a cofactor in over 300 oxidation-reduction reactions and regulates various enzymes and genetic processes. The NADH/NAD+ cofactor pair plays a major role in microbial catabolism, in which a carbon source, such as glucose, is oxidized using NAD+ producing reducing equivalents in the form of NADH. It is crucially important for continued cell growth that NADH be oxidized to NAD+ and a redox balance be achieved. Under aerobic growth, oxygen is used as the final electron acceptor. While under anaerobic growth, and in the absence of an alternate oxidizing agent, the regeneration of NAD+ is achieved through fermentation by using NADH to reduce metabolic intermediates. Therefore, an increase in the availability of NADH is expected to have an effect on the metabolic distribution. This paper investigates a genetic means of manipulating the availability of intracellular NADH in vivo by regenerating NADH through the heterologous expression of an NAD(+)-dependent formate dehydrogenase. More specifically, it explores the effect on the metabolic patterns in Escherichia coli under anaerobic and aerobic conditions of substituting the native cofactor-independent formate dehydrogenase (FDH) by and NAD(+)-dependent FDH from Candida boidinii. The over-expression of the NAD(+)-dependent FDH doubled the maximum yield of NADH from 2 to 4 mol NADH/mol glucose consumed, increased the final cell density, and provoked a significant change in the final metabolite concentration pattern both anaerobically and aerobically. Under anaerobic conditions, the production of more reduced metabolites was favored, as evidenced by a dramatic increase in the ethanol-to-acetate ratio. Even more interesting is the observation that during aerobic growth, the increased availability of NADH induced a shift to fermentation even in the presence of oxygen by stimulating pathways that are normally inactive under these conditions.

Aerobiosis↗
PubMed2003

Optimization of biochemical systems by linear programming and general mass action model representations.

A new method is proposed for the optimization of biochemical systems. The method, based on the separation of the stoichiometric and kinetic aspects of the system, follows the general approach used in the previously presented indirect optimization method (IOM) developed within biochemical systems theory. It is called GMA-IOM because it makes use of the generalized mass action (GMA) as the model system representation form. The GMA representation avoids flux aggregation and thus prevents possible stoichiometric errors. The optimization of a system is used to illustrate and compare the features, advantages and shortcomings of both versions of the IOM method as a general strategy for designing improved microbial strains of biotechnological interest. Special attention has been paid to practical problems for the actual implementation of the new proposed strategy, such as the total protein content of the engineered strain or the deviation from the original steady state and its influence on cell viability.

Biochemical Phenomena↗
PubMedDate not supplied

Microbial polysaccharides of applied interest: ongoing research activities in Europe.

After an introductory note on the main reasons underlying the interest in microbial polysaccharides as subjects of fundamental structural/physicochemical investigations, as well as of applied studies, and after a brief historical account, a survey is offered of ongoing research activities in Europe in the broad field of carbohydrate polymers of microbial origin. Attention is drawn to glycopolymers of actual or potential industrial relevance.

Bacteria↗
PubMed2006

Rac GTPase signaling through the PP5 protein phosphatase.

We have investigated the Rac-dependent mechanism of KCNH2 channel stimulation by thyroid hormone in a rat pituitary cell line, GH(4)C(1), with the patch-clamp technique. Here we present physiological evidence for the protein serine/threonine phosphatase, PP5, as an effector of Rac GTPase signaling. We also propose and test a specific molecular mechanism for PP5 stimulation by Rac-GTP. Inhibition of PP5 with the microbial toxin, okadaic acid, blocked channel stimulation by thyroid hormone and by Rac, but signaling was restored by expression of a toxin-insensitive mutant of PP5, Y451A, which we engineered. PP5 is unique among protein phosphatases in that it contains an N-terminal regulatory domain with three tetratricopeptide repeats (TPR) that inhibit its activity. Expression of the TPR domain coupled to GFP blocked channel stimulation by the thyroid hormone. We also show that the published structures of the PP5 TPR domain and the TPR domain of p67, the Rac-binding subunit of NADPH oxidase, superimpose over 92 alpha carbons. Mutation of the PP5 TPR domain at two predicted contact points with Rac-GTP prevents the TPR domain from functioning as a dominant negative and blocks the ability of Y451A to rescue signaling in the presence of okadaic acid. PP5 stimulation by Rac provides a unique molecular mechanism for the antagonism of Rho-dependent signaling through protein kinases in many cellular processes, including metastasis, immune cell chemotaxis, and neuronal development.

Amino Acid Sequence↗
PubMed2006

Quantifying the roles of immigration and chance in shaping prokaryote community structure.

Naturally occurring populations of bacteria and archaea are vital to life on the earth and are of enormous practical significance in medicine, engineering and agriculture. However, the rules governing the formation of such communities are still poorly understood, and there is a need for a usable mathematical description of this process. Typically, microbial community structure is thought to be shaped mainly by deterministic factors such as competition and niche differentiation. Here we show, for a wide range of prokaryotic communities, that the relative abundance and frequency with which different taxa are observed in samples can be explained by a neutral community model (NCM). The NCM, which is a stochastic, birth-death immigration process, does not explicitly represent the deterministic factors and therefore cannot be a complete or literal description of community assembly. However, its success suggests that chance and immigration are important forces in shaping the patterns seen in prokaryotic communities.

Archaea↗
PubMedDate not supplied

Beneficial reuse and sustainability: the fate of organic compounds in land-applied waste.

Land application systems, also referred to as beneficial reuse systems, are engineered systems that have defined and permitted application areas based on site and waste characteristics to determine the land area size requirement. These terrestrial systems have orders of magnitude greater microbial capability and residence time to achieve decomposition and assimilation compared with aquatic systems. In this paper we focus on current information and information needs related to terrestrial fate pathways in land treatment systems. Attention is given to conventional organic chemicals as well as new estrogenic and pharmaceutical chemicals of commerce. Specific terrestrial fate pathways addressed include: decomposition, bound residue formation, leaching, runoff, and crop uptake. Molecular decomposition and formation of bound residues provide the basis for the design and regulation of land treatment systems. These mechanisms allow for assimilation of wastes and nondegradation of the environment and accomplish the goal of sustainable land use. Bound residues that are biologically produced are relatively immobile, degrade at rates similar to natural soil materials, and should present a significantly reduced risk to the environment as opposed to parent contaminants. With regard to leaching and runoff pathways, no comprehensive summary or mathematical model of organic chemical migration from land treatment systems has been developed. For the crop uptake pathway, a critical need exists to develop information for nonagricultural chemicals and to address full-scale performance and monitoring at more land application sites. The limited technology choices for treatment of biosolids, liquids, and other wastes implies that acceptance of some risks and occurrence of some benefits will continue to characterize land application practices that contribute directly to the goal of beneficial reuse and sustainability.

Agriculture↗
PubMed2005

Toward a live microbial microbicide for HIV: commensal bacteria secreting an HIV fusion inhibitor peptide.

Most HIV transmission occurs on the mucosal surfaces of the gastrointestinal and cervicovaginal tracts, both of which are normally coated by a biofilm of nonpathogenic commensal bacteria. We propose to genetically engineer such naturally occurring bacteria to protect against HIV infection by secreting antiviral peptides. Here we describe the development and characterization of Nissle 1917, a highly colonizing probiotic strain of Escherichia coli, secreting HIV-gp41-hemolysin A hybrid peptides that block HIV fusion and entry into target cells. By using an appropriate combination of cis- and transacting secretory and regulatory signals, micromolar secretion levels of the anti-HIV peptides were achieved. The genetically engineered Nissle 1917 were capable of colonizing mice for periods of weeks to months, predominantly in the colon and cecum, with lower concentrations of bacteria present in the rectum, vagina, and small intestine. Histological and immunocytochemical examination of the colon revealed bacterial growth and peptide secretion throughout the luminal mucosa and in association with epithelial surfaces. The use of genetically engineered live microbes as anti-HIV microbicides has important potential advantages in economy, efficacy, and durability.

Animals↗
PubMedDate not supplied

Bacterial polyesters: biosynthesis, biodegradable plastics and biotechnology.

The discovery and chemical identification, in the 1920s, of the aliphatic polyester: poly(3-hydroxybutyrate), PHB, as a granular component in bacterial cells proceeded without any of the controversies which marked the recognition of macromolecules by Staudinger. Some thirty years after its discovery, PHB was recognized as the prototypical biodegradable thermoplastic to solve the waste disposal challenge. The development effort led by Imperial Chemical Industries Ltd., encouraged interdisciplinary research from genetic engineering and biotechnology to the study of enzymes involved in biosynthesis and biodegradation. From the simple PHB homopolyester discovered by Maurice Lemoigne in the mid-twenties, a family of over 100 different aliphatic polyesters of the same general structure has been discovered. Depending on bacterial species and substrates, these high molecular weight stereoregular polyesters have emerged as a new family of natural polymers ranking with nucleic acids, polyamides, polyisoprenoids, polyphenols, polyphosphates, and polysaccharides. In this historical review, the chemical, biochemical and microbial highlights are linked to personalities and locations involved with the events covering a discovery timespan of 75 years.

3-Hydroxybutyric Acid↗
PubMed2026

Meta-analysis of growth and inactivation kinetics of Legionella.

Quantitative risk assessments intended to inform evidence-based water management plans and public health targets for Legionella in engineered water systems are constrained by fragmented and heterogeneous growth and inactivation kinetics. We conducted a meta-analysis of 25 growth and 39 thermal- and chemical-inactivation studies, fitting microbial persistence models to harmonize parameters. Nonlinear models outperformed first-order formulations, indicating that lag phases and resistant or protected subpopulations are central to Legionella persistence. Random forest analysis identified environmental and methodological drivers of variability based on 226 growth rates and reduction times for thermal (209) and chemical (135) inactivation. Growth was primarily governed by temperature, nutrient availability, and compatible Legionella-host pairings; thermal inactivation by quantification method, temperature, and turbidity; and chemical inactivation by inoculum size, disinfectant type, concentration, and host-associations. Accordingly, temperature-dependent growth parameters and exposure metrics for heat, free-chlorine, and monochloramine, expressed as TT (Temperature×time) and CT (Concentration×time), were derived as condition-specific inputs for predictive models. Growth optima around 37-40 °C, together with lag-time estimates, indicate that hot-water temperature setbacks and energy-saving practices may favor Legionella proliferation under repeated or prolonged lukewarm exposure. Culture- and viability-based TT differences highlight the need to consider viable‑but-non-culturable persistence in monitoring programs. CT comparisons suggest monochloramine may be advantageous because of its lower apparent sensitivity to host-associated protection. Although limited by restricted experimental conditions, the findings show that predictive models should account for microbial ecology, water matrix effects, and quantification endpoints. Future kinetic studies should prioritize realistic multi-host systems, strain pre-adaptation, complementary viability measurements, and standardized protocols and reporting to ensure reproducibility and enable robust system-level predictive modeling.

Legionella↗
PubMed1999

Biodesulfurization.

Microbial sulfur-specific transformations have been identified that selectively desulfurize organic sulfur compounds in fossil fuels. Recent discoveries related to biodesulfurization mechanisms may lead to commercial applications of biodesulfurization through engineering recombinant strains for over-expression of biodesulfurization genes, removal of end product repression, and/or by combining relevant industrial and environmental traits with improvements in bioprocess design.

Bacteria↗
PubMed2004

Engineering aspects of a mixed methanotrophic culture in a membrane-aerated biofilm reactor.

Methanotrophic biodegradation using the membrane-aerated biofilm reactor (MABR) is a technology offering several advantages over both conventional biofilm reactors and suspended-cell processes. In this study the oxidation efficiency of a methanotrophic biofilm in a 1.5 litre MABR was investigated. Measurements of oxygen and methane uptake rates together with biofilm thickness were taken for developing biofilms. It was found that the specific rate of metabolic activity of the biofilm was unusually high as determined by the methane and oxygen uptake rates. Microbial activity stratification was evident and the location of stratified layers of oxygen consuming components of the consortium could be manipulated via the intra-membrane oxygen pressure.

Biofilms↗
PubMedDate not supplied

Engineered bioretention for removal of nitrate from stormwater runoff.

A bioretention unit is a simple, plant- and soil-based, low-impact treatment and infiltration facility for treating stormwater runoff in developed areas. Nitrate, however, is not attenuated in conventional bioretention facilities. Thus, this study systematically evaluated a reengineered concept of bioretention for nitrate removal via microbial denitrification, which incorporates a continuously submerged anoxic zone with an overdrain. Experimental studies were performed in four phases. In the first two phases, column studies demonstrated that, overall, newspaper is the best solid-phase electron-donor substrate for denitrification out of the set studied (alfalfa, leaf mulch compost, newspaper, sawdust, wheat straw, wood chips, and elemental sulfur) based on superior nitrate removal and effluent water quality. The nitrate loading and hydraulic loading studies in the second phase provided design information. In the third phase, system viability after 30- and 84-day dormant periods was evaluated in column studies, demonstrating that newspaper-supported biological denitrification should be effective under conditions of intermittent loadings. Finally, in the fourth phase, pilot-scale bioretention studies demonstrated the effectiveness of the proposed design, showing nitrate plus nitrite mass removals of up to 80%. These results indicate that engineered bioretention for the removal of nitrogen from stormwater runoff has the potential for successful application as an urban stormwater treatment practice.

Biodegradation, Environmental↗
PubMed2000

Genetics and molecular physiology of the yeast Kluyveromyces lactis.

With the recent development of powerful molecular genetic tools, Kluyveromyces lactis has become an excellent alternative yeast model organism for studying the relationships between genetics and physiology. In particular, comparative yeast research has been providing insights into the strikingly different physiological strategies that are reflected by dominance of respiration over fermentation in K. lactis versus Saccharomyces cerevisiae. Other than S. cerevisiae, whose physiology is exceptionally affected by the so-called glucose effect, K. lactis is adapted to aerobiosis and its respiratory system does not underlie glucose repression. As a consequence, K. lactis has been successfully established in biomass-directed industrial applications and large-scale expression of biotechnically relevant gene products. In addition, K. lactis maintains species-specific phenomena such as the "DNA-killer system, " analyses of which are promising to extend our knowledge about microbial competition and the fundamentals of plasmid biology.

Aerobiosis↗
PubMed2005

Marine enzymes.

Marine enzyme biotechnology can offer novel biocatalysts with properties like high salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and ease in large-scale cultivation. This review deals with the research and development work done on the occurrence, molecular biology, and bioprocessing of marine enzymes during the last decade. Exotic locations have been accessed for the search of novel enzymes. Scientists have isolated proteases and carbohydrases from deep sea hydrothermal vents. Cold active metabolic enzymes from psychrophilic marine microorganisms have received considerable research attention. Marine symbiont microorganisms growing in association with animals and plants were shown to produce enzymes of commercial interest. Microorganisms isolated from sediment and seawater have been the most widely studied, proteases, carbohydrases, and peroxidases being noteworthy. Enzymes from marine animals and plants were primarily studied for their metabolic roles, though proteases and peroxidases have found industrial applications. Novel techniques in molecular biology applied to assess the diversity of chitinases, nitrate, nitrite, ammonia-metabolizing, and pollutant-degrading enzymes are discussed. Genes encoding chitinases, proteases, and carbohydrases from microbial and animal sources have been cloned and characterized. Research on the bioprocessing of marine-derived enzymes, however, has been scanty, focusing mainly on the application of solid-state fermentation to the production of enzymes from microbial sources.

Animals↗
PubMed1994

Construction of multipurpose gene cartridges based on a novel synthetic promoter for high-level gene expression in gram-negative bacteria.

A series of gene cartridges containing a novel synthetic promoter (Psyn) was constructed. The Psyn sequence is based on the consensus of a number of naturally occurring promoters and displays strong activity in Escherichia coli and Rhizobium leguminosarum. In a direct comparison, Psyn proved to be about twice as strong as the tac promoter in E. coli, while the difference in Rhizobium was about tenfold. A small Psyn cartridge was constructed by adding a Shine-Dalgarno sequence, an ATG codon, and a removable lac operator, whose excision can convert the regulated cartridge into a constitutively expressed unit. A second cassette was obtained by the addition of a lacIq gene in order to provide autonomous regulation also in hosts lacking lacI functions, such as R. leguminosarum. A promoterless lacZ gene was inserted to monitor the activity. This gene can be either replaced with genes of interest, or used for gene fusions by means of conveniently positioned restriction sites. A third cassette was generated by adding a mercury-resistance determinant as a selectable marker, suitable for monitoring tagged bacteria released into environments. In such cases, where a non-antibiotic-resistant marker is preferable, the use of mercury chloride adds the advantage of inhibiting fungal growth when plating soil suspensions. The presence of the second marker, lacZ driven by the strong Psyn, facilitates the selection. Furthermore, the Psyn fragment can be used as a specific probe for the detection of released bacteria engineered with any of the above constructs.

Base Sequence↗