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At least 523 records · Page 29Linked to original sources
PubMed1998

Using molecular techniques to identify new microbial biocatalysts.

Evolution has favoured microorganisms that produce efficient enzymes with substrate-adapted biocatalytic activities. Progress in molecular techniques, especially expression cloning, molecular screening, protein engineering and in vivo and in vitro shuffling, have paved the way for greater speed and accuracy in cloning enzyme genes from microorganisms and generating versions with improved properties. Recently, two new approaches have been added: screening directly from uncultivated microorganisms and generating additional hits by database mining using bioinformatic tools.

Amino Acid Sequence↗
PubMed2003

Microbial whole-cell sensing systems of environmental pollutants.

The past decade has witnessed the development of a novel class of tools for environmental monitoring: genetically engineered microorganisms 'tailored' to respond in a dose-dependent manner to changes in environmental conditions. Recent advances in the field include the expansion of available reporter functions with multicolored fluorescent proteins, a broadening of the detected chemical effects such as the availability of nutrients and enhancement of the spectrum of reporter microorganisms to include cyanobacteria, yeast and fungi. Most importantly, the stage has been set for the incorporation of such cells into various whole-cell array formats on silicon chips, optic fibres and other configurations. The future of such multiplex detection and analysis systems seems bright.

Biosensing Techniques↗
PubMed2005

Bioprospecting in plants for engineered proteins.

For more than two decades, bioengineered plants have produced protein therapeutics for human and animal use. Almost all proteins produced by other existing systems, including antibodies, vaccines and plasma proteins, have now been manufactured in plants. Considering the limitations of microbial and mammalian reactor-based protein-production technologies and the impending bottleneck in manufacturing capacity, plants are now emerging as an attractive alternative system with which to supply the growing need for protein-based therapeutics. However, full realization of the promise of plant-derived engineered proteins requires that we confront the dual challenges of bioequivalence and product consistency, challenges that are largely related to post-translational protein modifications (PTMs) that are crucial to the structure and function of most eukaryotic proteins. Among the protein PTMs, the foremost challenge for bioactivity and acceptance by the pharmaceutical and biotechnology industries and regulatory agencies is glycosylation. Advances made in recent years that 'humanize' plant glycosylation pathways combined with the discovery of terminal sialic acids (SAs) in plants now make feasible the bioengineering in plants of glycoproteins that have mammalian-like glycosylation.

Animals↗
PubMed1996

A gene replacement strategy for engineering nisin.

A lactococcal expression system was developed which allows the exclusive production of novel nisins encoded by mutated pre-nisin (nisA) genes. This system is based on a combination of a specifically constructed host strain and vectors which facilitate the genetic manipulation of the nisA gene. The wild-type chromosomal gene is effectively replaced with a variant nisA gene, by the technique of gene replacement. The recovery of full nisin immunity was employed as a means of directly selecting strains that had acquired an intact nisA gene by the gene replacement process. With this approach the other genes required for pre-nisin maturation are not affected and any alterations to DNA sequences are restricted to only those specific mutations introduced in the nisA gene. The effectiveness of the system was demonstrated by the expression of a number of variant nisA genes leading to the successful production and characterization of nisins containing the substitutions Dha5A, Dha33A, Dha5, 33A, H27K, 130W and K12L. The enhanced yields of these engineered nisin molecules, when compared to their production in a plasmid-complementation system, underlines the improvement offered by this gene replacement strategy.

Amino Acid Sequence↗
PubMed1996

Engineering strategies for the design of plant nutrient delivery systems for use in space: approaches to countering microbiological contamination.

Microbiological contamination of crops within space-based plant growth research chambers has been postulated as a potentially significant problem. Microbial infestations; fouling of Nutrient Delivery System (NDS) fluid loops; and the formation of biofilms have been suggested as the most obvious and important manifestations of the problem. Strict sanitation and quarantine procedures will reduce, but not eliminate, microbial species introduced into plant growth systems in space habitats. Microorganisms transported into space most likely will occur as surface contaminants on spacecraft components, equipment, the crew, and plant-propagative materials. Illustrations of the potential magnitude of the microbiological contamination issue will be drawn from the literature and from documentation of laboratory and commercial field experience. Engineering strategies for limiting contamination and for the development of countermeasures will be described. Microbiological control technologies and NDS hardware will be discussed. Configurations appropriate for microgravity research facilities, as well as anticipated bio-regenerative life support system implementations, will be explored. An efficiently designed NDS, capable of adequately meeting the environmental needs of crop plants in space, is considered to be critical in both the research and operational domains. Recommended experiments, tests, and technology developments, structured to allow the development of prudent engineering solutions also will be presented.

Biofilms↗
PubMed2006

Cytosolic entry controls CD8+-T-cell potency during bacterial infection.

Interaction with host immunoreceptors during microbial infection directly impacts the magnitude of the ensuing innate immune response. How these signals affect the quality of the adaptive T-cell response remains poorly understood. Utilizing an engineered strain of the intracellular pathogen Listeria monocytogenes that infects cells but fails to escape from the phagosome, we demonstrate the induction of long-lived memory T cells that are capable of secondary expansion and effector function but are incapable of providing protective immunity. We demonstrate that microbial invasion of the cytosol is required for dendritic cell activation and integration of CD40 signaling, ultimately determining the ability of the elicited CD8+-T-cell pool to protect against lethal wild-type L. monocytogenes challenge. These results reveal a crucial role for phagosomal escape, not for delivery of antigen to the class I major histocompatibility complex pathway but for establishing the appropriate cellular context during CD8+-T-cell priming.

Animals↗
PubMed1998

Ethyl-substituted erythromycin derivatives produced by directed metabolic engineering.

A previously unknown chemical structure, 6-desmethyl-6-ethylerythromycin A (6-ethylErA), was produced through directed genetic manipulation of the erythromycin (Er)-producing organism Saccharopolyspora erythraea. In an attempt to replace the methyl side chain at the C-6 position of the Er polyketide backbone with an ethyl moiety, the methylmalonate-specific acyltransferase (AT) domain of the Er polyketide synthase was replaced with an ethylmalonate-specific AT domain from the polyketide synthase involved in the synthesis of the 16-member macrolide niddamycin. The genetically altered strain was found to produce ErA, however, and not the ethyl-substituted derivative. When the strain was provided with precursors of ethylmalonate, a small quantity of a macrolide with the mass of 6-ethylErA was produced in addition to ErA. Because substrate for the heterologous AT seemed to be limiting, crotonyl-CoA reductase, a primary metabolic enzyme involved in butyryl-CoA production in streptomycetes, was expressed in the strain. The primary macrolide produced by the reengineered strain was 6-ethylErA.

Acyl Coenzyme A↗
PubMed2002

Engineering bacterial competitiveness and persistence in the phytosphere.

Several tactics exist to improve the survival of an introduced microorganism of interest in the plant environment. One, derived from studies on the Agrobacterium-plant interaction and the role of opines in this interaction, proposes to promote growth of the inoculant in the plant environment via the establishment of a bias in the rhizosphere. It is supported by the occurrence of natural biases, such as those generated by opine-like molecules, by calestegins, or by mimosine. Opine-mediated biases have allowed several investigators to favor the growth of opine-degrading bacteria or communities under sterile or axenic environments or in microcosms mimicking near field conditions. Another way to favor a given microbe consists in impeding growth of competing microorganisms. Experiments performed using detergent or bacteriostatic agents as amendments under field or near field conditions yielded promising results. Research perspectives for engineering plant-microbe interactions also include specific engineering of predation and strategies designed to interfere with some of the signals perceived by the microbes, provided these signals control the expression of functions central to microbial fitness. In this respect, quorum-sensing signal molecules, such as N-acyl-homoserine lactones, may be valuable targets for the development of biocontrol agents and procedures.

Bacteria↗
PubMed1989

Novel method for monitoring genetically engineered microorganisms in the environment.

A method has been devised for directly detecting and monitoring genetically engineered microorganisms (GEMs) by using in vitro amplification of the target DNAs by a polymerase chain reaction and then hybridizing the DNAs with a specific oligonucleotide or DNA probe. A cloned 0.3-kilobase napier grass (Pennisetum purpureum) genomic DNA that did not hybridize to DNAs isolated from various microorganisms, soil sediments, and aquatic environments was inserted into a derivative of a 2,4-dichlorophenoxyacetic acid-degradative plasmid, pRC10, and transferred into Escherichia coli. This genetically altered microorganism, seeded into filter-sterilized lake and sewage water samples (10(4)/ml), was detected by a plate count method in decreasing numbers for 6 and 10 days of sample incubation, respectively. The new method detected the amplified unique marker (0.3-kilobase DNA) of the GEM even after 10 to 14 days of incubation. This method is highly sensitive (it requires only picogram amounts of DNA) and has an advantage over the plate count technique, which can detect only culturable microorganisms. The method may be useful for monitoring GEMs in complex environments, where discrimination between GEMs and indigenous microorganisms is either difficult or requires time-consuming tests.

Colony Count, Microbial↗
PubMed2003

Therapeutic activity of an engineered synthetic killer antiidiotypic antibody fragment against experimental mucosal and systemic candidiasis.

Peptides derived from the sequence of a single-chain, recombinant, antiidiotypic antibody (IdAb; KT-scFv) acting as a functional internal image of a microbicidal, wide-spectrum yeast killer toxin (KT) were synthesized and studied for their antimicrobial activity by using the KT-susceptible Candida albicans as model organism. A decapeptide containing the first three amino acids (SAS) of the light chain CDR1 was selected and optimized by alanine replacement of a single residue. This peptide exerted a strong candidacidal activity in vitro, with a 50% inhibitory concentration of 0.056 microM, and was therefore designated killer peptide (KP). Its activity was neutralized by laminarin, a beta1-3 glucan molecule, but not by pustulan, a beta1-6 glucan molecule. KP also competed with the binding of a KT-like monoclonal IdAb to germinating cells of the fungus. In a rat model of vaginal candidiasis, local, postchallenge administration of KP was efficacious in rapidly abating infections caused by fluconazole-susceptible or -resistant C. albicans strains. In systemic infection of BALB/c or SCID mice preinfected intravenously with a lethal fungal load, KP caused a highly significant prolongation of the median survival time, with >80% of the animals still surviving after >60 days, whereas >90% of control mice died within 3 to 5 days. KP is therefore the first engineered peptide derived from a recombinant IdAb retaining KT microbicidal activity, probably through the interaction with the beta-glucan KT receptor on target microbial cells.

Amino Acid Sequence↗
PubMed2002

Evaluating the role of microbial stress response mechanisms in causing biological treatment system upset.

It is known that microbial stress mechanisms play a significant role in short-term microbial adaptation to environmental perturbations, and activation of these mechanisms enhance a cell's chance for surviving the perturbation with minimal damage. Although the target of these mechanisms is protective at the cellular level, the effect may be disruptive at the macroscopic level in engineered bioreactor systems. In this paper, it is proposed that these mechanisms are activated in response to wastewater influent perturbations and may be a significant cause of activated sludge treatment process upset. Selected microbial stress responses are reviewed and hypotheses indicating their potential role in treatment process upset are proposed. A research approach that was previously used to identify the mechanistic cause of deflocculation during perturbation by electrophilic chemicals is summarized, and a protocol for future experiments geared toward establishing source-cause-effect relationships for a range of wastewater upset conditions is put forth. Identifying source-cause-effect relationships will provide a basis for development of new monitoring technologies and operational strategies for systems under the influence of influent chemical perturbations.

Bacteria↗
PubMed1992

The effect of amino acid deletion in subtilisin E, based on structural comparison with a microbial alkaline elastase, on its substrate specificity and catalysis.

Subtilisin from a wide variety of Bacillus species has been extensively investigated as a promising target for protein engineering. In this study, we analyzed the substrate specificity of B. subtilis subtilisin E based on the structure of a new alkaline elastase produced by the alkalophilic Bacillus strain Ya-B, which has very high elastolytic activity. Despite the high homology of the primary sequences of both enzymes (54% identical), alkaline elastase was found to lack four consecutive amino acids which, in subtilisin, have been shown by X-ray analysis to lie close to the P1 binding cleft. To examine the influence of such a deletion in subtilisin on its substrate specificity, we constructed several mutants missing four amino acids by site-directed mutagenesis. When assayed with synthetic peptides, elastin and casein as substrates, a mutant lacking Ser161-Thr162-Ser163-Thr164 showed considerably lower specific activity toward the substrates for subtilisin, and its substrate specificity approached that of alkaline elastase. The results indicate that the deletion in subtilisin E influences the catalytic efficiency as well as the P1 specificity, and that this region is, in part, responsible for the difference in specificity between the two enzymes.

Amino Acid Sequence↗
PubMed1991

Nosocomial infections from contaminated endoscopes: a flawed automated endoscope washer. An investigation using molecular epidemiology.

Approximately 1 year after purchase of one manufacturer's automated endoscope washing machine, we began to detect heavy contamination of upper gastrointestinal (UGI) endoscopes cultured after cleaning and disinfection in the washer. During the first 6 months of 1988, 77% of surveillance cultures (20-mL flush through the biopsy channel) were positive for gram-negative bacilli (median concentration, 10(5) cfu/mL), most frequently Pseudomonas aeruginosa serotype 10. During the first 19 months of use of the washer, nosocomial post-UGI endoscopy colonization or infections with P. aeruginosa increased 36%. Investigations show that endoscope contamination derives from a flaw in the design of the EW-10 washer: the detergent holding tank, inlet water hose, and air vents cannot be reliably disinfected and contain heavy biofilms that recontaminate the machine after it has been disinfected, as specified by the manufacturer, with glutaraldehyde. Only by rinsing machine-cleansed endoscopes with 70% alcohol followed by forced air drying has reliable disinfection been achieved. Since adaptation of terminal alcohol treatment and drying, post-UGI endoscopy colonization or infection by P. aeruginosa has declined threefold (p less than 0.001). Testing in other centers using the manufacturer's EW-10 or EW-20 washer has shown similar contamination. In three centers, including our own, postendoscopy infections by machine-associated type 10 P. aeruginosa have been confirmed by demonstrating concordance between isolates from contaminated machines or endoscopes and from infected patients by immunoblot of whole cell lysates and by pulsed-field electrophoresis of DraI endonuclease-digested genomic DNA. This problem reaffirms the vulnerability to microbial contamination of water-containing apparatus and equipment in patient care and points up the critical importance of engineering design to prevent contamination.

Cross Infection↗
PubMed2006

Antimicrobial barrier of an in vitro oral epithelial model.

OBJECTIVE: Oral epithelia function as a microbial barrier and are actively involved in recognizing and responding to bacteria. Our goal was to examine a tissue engineered model of buccal epithelium for its response to oral bacteria and proinflammatory cytokines and compare the tissue responses with those of a submerged monolayer cell culture. DESIGN: The tissue model was characterized for keratin and beta-defensin expression. Altered expression of beta-defensins was evaluated by RT-PCR after exposure of the apical surface to oral bacteria and after exposure to TNF-alpha in the medium. These were compared to the response in traditional submerged oral epithelial cell culture. RESULTS: The buccal model showed expression of differentiation specific keratin 13, hBD1 and hBD3 in the upper half of the tissue; hBD2 was not detected. hBD1 mRNA was constitutively expressed, while hBD2 mRNA increased 2-fold after exposure of the apical surface to three oral bacteria tested and hBD3 mRNA increased in response to the non-pathogenic bacteria tested. In contrast, hBD2 mRNA increased 3-600-fold in response to bacteria in submerged cell culture. HBD2 mRNA increased over 100-fold in response to TNF-alpha in the tissue model and 50-fold in submerged cell culture. Thus, the tissue model is capable of upregulating hBD2, however, the minimal response to bacteria suggests that the tissue has an effective antimicrobial barrier due to its morphology, differentiation, and defensin expression. CONCLUSIONS: The oral mucosal model is differentiated, expresses hBD1 and hBD3, and has an intact surface with a functional antimicrobial barrier.

Cells, Cultured↗
PubMed1994

Optical biosensor for environmental on-line monitoring of naphthalene and salicylate bioavailability with an immobilized bioluminescent catabolic reporter bacterium.

An optical whole-cell biosensor based on a genetically engineered bioluminescent catabolic reporter bacterium was developed for continuous on-line monitoring of naphthalene and salicylate bioavailability and microbial catabolic activity potential in waste streams. The bioluminescent reporter bacterium, Pseudomonas fluorescens HK44, carries a transcriptional nahG-luxCDABE fusion for naphthalene and salicylate catabolism. Exposure to either compound resulted in inducible bioluminescence. The reporter culture was immobilized onto the surface of an optical light guide by using strontium alginate. This biosensor probe was then inserted into a measurement cell which simultaneously received the waste stream solution and a maintenance medium. Exposure under defined conditions to both naphthalene and salicylate resulted in a rapid increase in bioluminescence. The magnitude of the response and the response time were concentration dependent. Good reproducibility of the response was observed during repetitive perturbations with either naphthalene or salicylate. Exposure to other compounds, such as glucose and complex nutrient medium or toluene, resulted in either minor bioluminescence increases after significantly longer response times compared with naphthalene or no response, respectively. The environmental utility of the biosensor was tested by using real pollutant mixtures. A specific bioluminescence response was obtained after exposure to either an aqueous solution saturated with JP-4 jet fuel or an aqueous leachate from a manufactured-gas plant soil, since naphthalene was present in both pollutant mixtures.

Base Sequence↗
PubMed2005

The removal of uranium from mining waste water using algal/microbial biomass.

We describe a three step process for the removal of uranium (U) from dilute waste waters. Step one involves the sequestration of U on, in, and around aquatic plants such as algae. Cell wall ligands efficiently remove U(VI) from waste water. Growing algae continuously renew the cellular surface area. Step 2 is the removal of U-algal particulates from the water column to the sediments. Step 3 involves reducing U(VI) to U(IV) and transforming the ions into stable precipitates in the sediments. The algal cells provide organic carbon and other nutrients to heterotrophic microbial consortia to maintain the low E(H), within which the U is transformed. Among the microorganisms, algae are of predominant interest for the ecological engineer because of their ability to sequester U and because some algae can live under many extreme environments, often in abundance. Algae grow in a wide spectrum of water qualities, from alkaline environments (Chara, Nitella) to acidic mine drainage waste waters (Mougeotia, Ulothrix). If they could be induced to grow in waste waters, they would provide a simple, long-term means to remove U and other radionuclides from U mining effluents. This paper reviews the literature on algal and microbial adsorption, reduction, and transformation of U in waste streams, wetlands, lakes and oceans.

Adsorption↗