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PubMed1992

Intergeneric natural plasmid transformation between E. coli and a marine Vibrio species.

Natural transformation is the mechanism of procaryotic gene transfer that involves the uptake and expression of genetic information encoded in extracellular DNA. This process has been regarded as a mechanism to transfer genes (primarily chromosomal markers) between closely related strains or species. Here we demonstrate the cell-contact-dependent transfer of a non-conjugative plasmid from a laboratory E. coli strain to a marine Vibrio species, the first report of intergeneric natural plasmid transformation involving a marine bacterium. The nucleic acid synthesis inhibitors nalidixic acid and rifampicin inhibited the ability of the E. coli to function as a donor. However, dead cells also served as efficient donors. There was an obligate requirement for cell contact. No transfer occurred in the presence of DNase I, when donors and recipients were separated by a 0.2-micron filter, or when spent medium alone was used as a source of transforming DNA. These results indicate that contact-mediated intergeneric plasmid exchange can occur in the absence of detectable viable donor cells and that small non-conjugative plasmids can be spread through heterogeneous microbial communities by a process previously not recognized, natural plasmid transformation. These findings are important in the assessment of genetic risk to the environment, particularly from wastewater treatment systems and the use of genetically engineered organisms in the environment.

Bacterial Adhesion↗
PubMed1993

Expression and analysis of two gyrB genes from the novobiocin producer, Streptomyces sphaeroides.

A novobiocin producer, Streptomyces sphaeroides, contains two genes, designated gyrBS and gyrBR, that encode novobiocin-sensitive and -resistant DNA gyrase B proteins, respectively. The cloning of gyrBR was reported earlier; here, we describe the cloning of gyrBS. Both genes have been sequenced (the deduced products of gyrBS and gyrBR have M(r) values of 87.6K and 86.5K, respectively) and their transcripts have been mapped. Downstream of gyrBS, and co-transcribed with it, is the sole gyrA gene (encoding DNA gyrase A protein). By constructing hybrid gyrB genes, using fragments of gyrBS and gyrBR, a specific portion of the N-terminal domain of the gyrase B protein (corresponding to amino acid residues 134-256 of Escherichia coli gyrase B) has been implicated in the binding of novobiocin.

Amino Acid Sequence↗
PubMedDate not supplied

[Database on natural and transgenic luminous microorganisms: "BiolumBase"].

The database "BiolumBase" is designed for the selection and systematization of available world information on microorganisms containing bioluminescent systems; it includes two sections: "natural" and "transgenic" luminous microorganisms. At present, logic schemes of divisions, classification of the objects, presentation of characteristics, and the inputs of relative information, as well as the necessary program modules including links to the database, are developed. The database is constructed on the basis of published data and our own experimental results; the subsequent linkage of the database to the Internet is envisaged. Users will be able to obtain not only the catalogues of strains but also information concerning the properties and functions of the known species of luminous bacteria, the structure, regulatory mechanisms, and application of bioluminescent systems and genetically engineered constructions with lux genes, as well as to find references and to search strains by using any set of attributes. The database will provide information that is of interest for the development of microbial ecology and biotechnology, in particular, for the prediction of biological hazard from the application of transgenic strains.

Bacteria↗
PubMed1995

Heavy metal toxicity testing in environmental samples.

The toxicity of heavy metals in the environment depends on a number of physicochemical and biological factors. The complexity of these relationships has encouraged the use of bioassays for direct measurement of the [table: see text] impact of toxic metals on selected test species. Fish and daphnid bioassays are well accepted by the scientific and regulatory communities, but their length (48 h or more) and the considerable time and effort needed to culture the test organisms make their application to sample screening problematical. Microbial and biochemical assays based on the inhibition of bioluminescence, enzyme activity, enzyme biosynthesis, growth, respiration, and heat production are typically faster and less expensive than the traditional and fish bioassays. Some of these tests approach or equal the sensitivity of daphnids to heavy metals. Since the soil acts as a sink for airborne and waste-applied metals, the uptake of metals by plants and the associated toxic impacts are important. Growth inhibition, enzyme induction, and production of stress proteins have been considered as toxicity end points. Enzymatic tests have been developed that are specific for heavy metal toxicity. Such tests can facilitate toxicity reduction evaluations. Detection of individual metals in the environment may eventually be possible using biosensors consisting of genetically engineered microorganisms. Direct solid-phase tests for soil, sediment, or sludge toxicity, using bacterial bioluminescence or enzyme activity as end points, have been developed. Such tests may complement traditional solid-phase toxicity tests using nematodes or earthworms as indicator organisms. Based on the work reviewed, we draw the following conclusions: 1. The Microtox assay is sensitive to mercury but would fail to detect the toxicity of certain metals, such as cadmium. Among all the microbial assays reviewed, the bioassay based on growth inhibition of the alga Selenastrum capricornutum appears to give the lowest EC50s, similar to those seen for daphnid bioassays. 2. Biosensors, using genetically engineered microorganisms, offer an elegant means of detecting the presence of specific heavy metals in environmental samples. However, at the present time, they are not designed for assessing heavy metal toxicity. 3. The use of bioassays specific for heavy metal toxicity can be useful for directly assessing the bioavailability of these toxicants in environmental samples, thus avoiding the need for fractionation.+4

Animals↗
PubMed2004

Modeling the synergistic effect of high pressure and heat on inactivation kinetics of Listeria innocua: a preliminary study.

The survival curves of Listeria innocua CDW47 by high hydrostatic pressure were obtained at four pressure levels (138, 207, 276, 345 MPa) and four temperatures (25, 35, 45, 50 degrees C) in peptone solution. Tailing was observed in the survival curves. Elevated temperatures and pressures substantially promoted the inactivation of L. innocua. A linear and two non-linear (Weibull and log-logistic) models were fitted to these data and the goodness of fit of these models were compared. Regression coefficients (R2), root mean square (RMSE), accuracy factor (Af) values and residual plots suggested that linear model, although it produced good fits for some pressure-temperature combinations, was not as appropriate as non-linear models to represent the data. The residual and correlation plots strongly suggested that among the non linear models studied the log-logistic model produced better fit to the data than the Weibull model. Such pressure-temperature inactivation models form the engineering basis for design, evaluation and optimization of high hydrostatic pressure processes as a new preservation technique.

Colony Count, Microbial↗
PubMed2005

Highly sensitive and selective amperometric microbial biosensor for direct determination of p-nitrophenyl-substituted organophosphate nerve agents.

We report herein a whole cell-based amperometric biosensor for highly selective, highly sensitive, direct, single-step, rapid, and cost-effective determination of organophosphate pesticides with a p-nitrophenyl substituent. The biosensor was comprised of a p-nitrophenol degrader, Pseudomonas putida JS444, genetically engineered to express organophosphorus hydrolase (OPH) on the cell surface immobilized on the carbon paste electrode. Surface-expressed OPH catalyzed hydrolysis of the p-nitrophenyl substituent organophosphorus pesticides such as paraoxon, parathion, and methyl parathion to release p-nitrophenol, which was subsequently degraded by the enzymatic machinery of P. putida JS444. The electrooxidization current of the intermediates was measured and correlated to the concentration of organophosphates. The best sensitivity and response time were obtained using a sensor constructed with 0.086 mg dry weight of cells operating at 600 mV applied potential (vs Ag/AgCl reference) in 50 mM citrate--phosphate pH 7.5 buffer with 50 microM CoCl2 at room temperature. Under optimum operating conditions the biosensor measured as low as 0.28 ppb of paraoxon, 0.26 ppb of methyl parathion, and 0.29 ppb parathion. These detection limits are comparable to cholinesterase inhibition-based biosensors. Unlike the inhibition-based format, this biosensor manifests a selective response to organophosphate pesticides with a p-nitrophenyl substituent only, has a simplified single-step protocol with short response time, and can be used for repetitive/multiple and on-line analysis. The service life of the microbial amperometric biosensor was 5 days when stored in the operating buffer at 4 degrees C. The new biosensor offers great promise for rapid environmental monitoring of OP pesticides with nitrophenyl substituent.

Aryldialkylphosphatase↗
PubMed1991

Survival and catabolic activity of natural and genetically engineered bacteria in a laboratory-scale activated-sludge unit.

The survival of selected naturally occurring and genetically engineered bacteria in a fully functional laboratory-scale activated-sludge unit (ASU) was investigated. The effect of the presence of 3-chlorobenzoate (3CB) on the survival of Pseudomonas putida UWC1, with or without a chimeric plasmid, pD10, which encodes 3CB catabolism, was determined. P. putida UWC1(pD10) did not enhance 3CB breakdown in the ASU, even following inoculation at a high concentration (3 x 10(8) CFU/ml). The emergence of a natural, 3CB-degrading population appeared to have a detrimental effect on the survival of strain UWC1 in the ASU. The fate of two 3CB-utilizing bacteria, derived from activated-sludge microflora, was studied in experiments in which these strains were inoculated into the ASU. Both strains, AS2, an unmanipulated natural isolate which flocculated readily in liquid media, and P. putida ASR2.8, a transconjugant containing the recombinant plasmid pD10, survived for long periods in the ASU and enhanced 3CB breakdown at 15 degrees C. The results reported in this paper illustrate the importance of choosing strains which are well adapted to environmental conditions if the use of microbial inoculants for the breakdown of target pollutants is to be successful.

Biodegradation, Environmental↗
PubMed2002

Bulk chemicals from biotechnology: the case of 1,3-propanediol production and the new trends.

The need for a sustainable resource supply, the rapid advances in plant biotechnology and microbial genetics and the strategic shift of major chemical companies into the area of life sciences are some of the driving forces for renewed interest in producing bulk chemicals from renewable resources by biological processes. The microbial production of 1,3-propanediol as briefly reviewed in this article and compared with the competing chemical processes demonstrates the promise and constraints of bioprocesses for bulk chemicals. The new concept of biorefinery and biocommodity engineering and future research needs in this area are also outlined.

Bacteria↗
PubMed2000

Enrichment of Geobacter Species in Response to Stimulation of Fe(III) Reduction in Sandy Aquifer Sediments.

Engineered stimulation of Fe(III) has been proposed as a strategy to enhance the immobilization of radioactive and toxic metals in metal-contaminated subsurface environments. Therefore, laboratory and field studies were conducted to determine which microbial populations would respond to stimulation of Fe(III) reduction in the sediments of sandy aquifers. In laboratory studies, the addition of either various organic electron donors or electron shuttle compounds stimulated Fe(III) reduction and resulted in Geobacter sequences becoming important constituents of the Bacterial 16S rDNA sequences that could be detected with PCR amplification and denaturing gradient gel electrophoresis (DGGE). Quantification of Geobacteraceae sequences with a PCR most-probable-number technique indicated that the extent to which numbers of Geobacter increased was related to the degree of stimulation of Fe(III) reduction. Geothrix species were also enriched in some instances, but were orders of magnitude less numerous than Geobacter species. Shewanella species were not detected, even when organic compounds known to be electron donors for Shewanella species were used to stimulate Fe(III) reduction in the sediments. Geobacter species were also enriched in two field experiments in which Fe(III) reduction was stimulated with the addition of benzoate or aromatic hydrocarbons. The apparent growth of Geobacter species concurrent with increased Fe(III) reduction suggests that Geobacter species were responsible for much of the Fe(III) reduction in all of the stimulation approaches evaluated in three geographically distinct aquifers. Therefore, strategies for subsurface remediation that involve enhancing the activity of indigenous Fe(III)-reducing populations in aquifers should consider the physiological properties of Geobacter species in their treatment design.

Journal Article↗
PubMed2006

Estimation of biomass concentrations in fermentation processes for recombinant protein production.

Online biomass estimation for bioprocess supervision and control purposes is addressed. As the biomass concentration cannot be measured online during the production to sufficient accuracy, indirect measurement techniques are required. Here we compare several possibilities for the concrete case of recombinant protein production with genetically modified Escherichia coli bacteria and perform a ranking. At normal process operation, the best estimates can be obtained with artificial neural networks (ANNs). When they cannot be employed, statistical correlation techniques can be used such as multivariate regression techniques. Simple model-based techniques, e.g., those based on the Luedeking/Piret-type are not as accurate as the ANN approach; however, they are very robust. Techniques based on principal component analysis can be used to recognize abnormal cultivation behavior. For the cases investigated, a complete ranking list of the methods is given in terms of the root-mean-square error of the estimates. All techniques examined are in line with the recommendations expressed in the process analytical technology (PAT)-initiative of the FDA.

Algorithms↗
PubMedDate not supplied

Modeling the temperature kinetics of aerobic solid-state biodegradation.

This study evaluated three models of microbial temperature kinetics using CO2 respiration data from aerobic solid-state biodegradation experiments. The models included those of Andrews and Kambhu/Haug, Ratkowsky et al., and the Cardinal Temperature Model with Inflection (CTMI) of Rosso et al. A parameter estimation routine implemented the Complex-Box search method for each model on 48 data sets collected during the composting of synthetic food waste or sewage-sludge (biosolids) mixed with maple wood chips at different oxygen concentrations and extents of decomposition. Each of the three nonlinear temperature kinetic functions proved capable of modeling a wide range of experimental data sets. However, the models differed widely in the consistency of their parameters. Parameters in the CTMI model were more stable over the course of the degradation process, and that variability which did arise was directly related to changes in the microbial process. Additional benefits of the CTMI model include the ease of parameter determinations, which can be approximated directly from laboratory experiments or full-scale system analysis, and the direct value of its parameters in engineering design and process control under a wide range of biodegradation conditions.

Bacteria, Aerobic↗
PubMed2000

A gene containment strategy based on a restriction-modification system.

Engineering barriers to the spread of specific genes are of great interest both to increase the predictability of recombinant microorganisms used for environmental applications and to study the role of gene transfer in the adaptation of microbial communities to changing environments. We report here a new gene containment circuit based on a toxin-antidote pair that targets the cell DNA, i.e. the type II EcoRI restriction-modification system. The set-up involved linkage of the ecoRIR lethal gene encoding the EcoRI endonuclease (toxin) to the contained character in a plasmid and chromosomal insertion of the ecoRIM gene encoding the cognate EcoRI methylase (antidote) that protects the target DNA from restriction. Transfer of the contained character to a recipient cell lacking the antidote caused EcoRI-mediated chromosomal breaks, leading to cell death, thereby preventing gene spread. Using transformation and conjugation as mechanisms of DNA transfer and different environmentally relevant bacteria as recipients, we have shown that the potentially universal EcoRI-based containment system decreases gene transfer frequencies by more than four orders of magnitude. Analyses of the survivors escaping killing revealed a number of possible inactivation mechanisms.

Base Sequence↗
PubMed1996

Field inversion gel electrophoretic analysis of Legionella pneumophila strains associated with nosocomial legionellosis in children.

Two nosocomial cases of Legionnaires' disease occurred in children. Legionella pneumophila serogroup 1 was isolated from both patients and 30 of 39 plumbing system sites in the hospital. The patient and hospital environmental isolates yielded identical field inversion gel electrophoretic patterns which differed from patterns observed with epidemiologically unrelated strains.

Child↗
PubMed1999

Introducing optimal experimental design in predictive modeling: a motivating example.

Predictive microbiology emerges more and more as a rational quantitative framework for predicting and understanding microbial evolution in food products. During the mathematical modeling of microbial growth and/or inactivation, great, but not always efficient, effort is spent on the determination of the model parameters from experimental data. In order to optimize experimental conditions with respect to parameter estimation, experimental design has been extensively studied since the 1980s in the field of bioreactor engineering. The so-called methodology of optimal experimental design established in this research area enabled the reliable estimation of model parameters from data collected in well-designed fed-batch reactor experiments. In this paper, we introduce the optimal experimental design methodology for parameter estimation in the field of predictive microbiology. This study points out that optimal design of dynamic input signals is necessary to maximize the information content contained within the resulting experimental data. It is shown that from few dynamic experiments, more pertinent information can be extracted than from the classical static experiments. By introducing optimal experimental design into the field of predictive microbiology, a new promising frame for maximization of the information content of experimental data with respect to parameter estimation is provided. As a case study, the design of an optimal temperature profile for estimation of the parameters D(ref) and z of an Arrhenius-type model for the maximum inactivation rate kmax as a function of the temperature, T, was considered. Microbial inactivation by heating is described using the model of Geeraerd et al. (1999). The need for dynamic temperature profiles in experiments aimed at the simultaneous estimation of the model parameters from measurements of the microbial population density is clearly illustrated by analytical elaboration of the mathematical expressions involved on the one hand, and by numerical simulations on the other.

Bacteria↗
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↗