Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “microbial engineering”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53Linked to original sources
PubMed1997

Effects of bioreactor retention time on aerobic microbial decomposition of CELSS crop residues.

The focus of resource recovery research at the KSC-CELSS Breadboard Project has been the evaluation of microbiologically mediated biodegradation of crop residues by manipulation of bioreactor process and environmental variables. We will present results from over 3 years of studies that used laboratory- and breadboard-scale (8 and 120 L working volumes, respectively) aerobic, fed-batch, continuous stirred tank reactors (CSTR) for recovery of carbon and minerals from breadboard grown wheat and white potato residues. The paper will focus on the effects of a key process variable--bioreactor retention time--on response variables indicative of bioreactor performance. The goal is to determine the shortest retention time that is feasible for processing CELSS crop residues, thereby reducing bioreactor volume and weight requirements. Pushing the lower limits of bioreactor retention times will provide useful data for engineers who need to compare biological and physicochemical components. Bioreactor retention times were manipulated to range between 0.25 and 48 days. Results indicate that increases in retention time lead to a 4-fold increase in crop residue biodegradation, as measured by both dry weight losses and CO2 production. A similar overall trend was also observed for crop residue fiber (cellulose and hemicellulose), with a noticeable jump in cellulose degradation between the 5.3 day and 10.7 day retention times. Water-soluble organic compounds (measured as soluble TOC) were appreciably reduced by more than 4-fold at all retention times tested. Results from a study of even shorter retention times (down to 0.25 days), in progress, will also be presented.

Aerobiosis↗
PubMed1996

Biochemistry and genetics of microbial xylanases.

Xylanases are classified into two major families (10 or F and 11 or G) of glycosyl hydrolases. Both use ion pair catalytic mechanisms and both retain anomeric configuration following hydrolysis. Family 10 xylanases are larger, more complex and produce smaller oligosaccharides; Family 11 xylanases are more specific for xylan. Alkaline-active and extreme-thermophilic enzymes are of particular interest. Such xylanases are being commercialized for bleaching pulps and other applications.

Binding Sites↗
PubMed1998

Intrinsic capacities of soil microflorae for gasoline degradation.

A methodology to determine the intrinsic capacities of a microflora to degrade gasoline was developed, in particular for assessing the potential of autochtonous populations of polluted and non polluted soils for natural attenuation and engineered bioremediation. A model mixture (GM23) constituted of the 23 most representative hydrocarbons of a commercial gasoline was used. The capacities of the microflorae (kinetics and extent of biodegradation) were assessed by chromatographic analysis of hydrocarbon consumption and of CO2 production. The degradation of the components of GM23 was assayed in separate incubations of each component and in the complete mixture. For the microflora of an unpolluted spruce forest soil, all hydrocarbons of GM23 except cyclohexane, 2,2,4- and 2,3,4-trimethylpentane isomers were degraded to below detection limit in 28 days. This microflora was reinforced with two mixed microbial communities selected from gasoline-polluted sites and shown to degrade cyclohexane and 2,2,4-trimethylpentane. With the reinforced microflora, complete degradation of GM23 was observed. The degradation patterns of individual components of GM23 were similar when the compounds were present individually or in the GM23 mixture, as long as the concentrations of 2-ethyltoluene and trimethylbenzene isomers were kept sufficiently low (< or = 35 mg.l-1) to remain below their inhibitory level.

Biodegradation, Environmental↗
PubMed2000

Microbial production of amino acids in Japan.

The microbial biotechnology of amino acids production which was developed and industrialized in Japan have been summarized. The amino acids include L-glutamic acid, L-lysine, L-threonine, L-aspartic acid, L-alanine, L-cysteine, L-dihydroxyphenylalanine, D-p-hydroxyphenyl-glycine, and hydroxy-L-proline.

Amino Acids↗
PubMed2003

The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems.

Evolutionary links between cytochrome P450 monooxygenases, a superfamily of extraordinarily divergent heme-thiolate proteins catalyzing a wide array of NADPH/NADH- and O(2)-dependent reactions, are becoming better understood because of availability of an increasing number of fully sequenced genomes. Among other reactions, P450s catalyze the site-specific oxidation of the precursors to macrolide antibiotics in the genus Streptomyces introducing regiochemical diversity into the macrolide ring system, thereby significantly increasing antibiotic activity. Developing effective uses for Streptomyces enzymes in biosynthetic processes and bioremediation requires identification and engineering of additional monooxygenases with activities toward a diverse array of small molecules. To elucidate the molecular basis for substrate specificity of oxidative enzymes toward macrolide antibiotics, the x-ray structure of CYP154C1 from Streptomyces coelicolor A3(2) was determined (Protein Data Bank code ). Relocation of certain common P450 secondary structure elements, along with a novel structural feature involving an additional beta-strand transforming the five-stranded beta-sheet into a six-stranded variant, creates an open cleft-shaped substrate-binding site between the two P450 domains. High sequence similarity to macrolide monooxygenases from other microbial species translates into catalytic activity of CYP154C1 toward both 12- and 14-membered ring macrolactones in vitro.

Anti-Bacterial Agents↗
PubMed1999

Imagene: an integrated computer environment for sequence annotation and analysis.

MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagene

Bacillus subtilis↗
PubMed2005

Modulation of quorum sensing in Pseudomonas aeruginosa through alteration of membrane properties.

Changes in the cellular envelope are major physiological adaptations that occur when micro-organisms encounter extreme environmental conditions. An appropriate degree of membrane fluidity is crucial for survival, and alteration of membrane lipids is an essential adaptive response. Emerging data suggest that microbial cells may recognize alterations in their membrane viscosity resulting from certain environmental changes as a trigger for adaptive cellular responses. In Pseudomonas aeruginosa, the quorum-sensing (QS) system involves a complex regulatory circuitry that coordinates the expression of genes according to a critical population density. Interestingly, it has been shown that the QS system of P. aeruginosa can also be activated by nutritional stress, independently of the cell density, and therefore may be part of a more general adaptive response to stressful environmental conditions. In order to examine the proposed link between membrane properties and stress signalling, the effects of genetically engineered alterations of the membrane phospholipid composition of P. aeruginosa PAO1 on the activation of the stringent response and the QS system were examined. The lptA gene encoding a functional homologue of PlsC, an Escherichia coli enzyme that catalyses the second step of the phospholipid biosynthesis pathway, was identified and disrupted. Inactivation of lptA altered the fatty acid profile of phospholipids and the membrane properties, resulting in decreased membrane fluidity. This resulted in a premature production of the QS signals N-butanoyl- and N-hexanoyl-homoserine lactone (C4-HSL and C6-HSL) and a repression of 2-heptyl-3-hydroxy-4-quinolone (PQS) synthesis at later growth phases. The effects on C4- and C6-HSL depended upon the expression of relA, encoding the (p)ppGpp alarmone synthase, which was increased in the lptA mutant. Together, the findings support the concept that alterations in membrane properties can act as a trigger for stress-related gene expression.

Acyltransferases↗
PubMed2000

Bioremedial potential of microbial mechanisms of metal mobilization and immobilization.

Microorganisms play important roles in the environmental fate of toxic metals and radionuclides with a multiplicity of mechanisms effecting transformations between soluble and insoluble forms. These mechanisms are integral components of natural biogeochemical cycles and are of potential for both in situ and ex situ bioremedial treatment processes for solid and liquid wastes.

Alkylation↗
PubMed1998

Perspectives in agrobiotechnology.

This review surveys the most important and promising contributions of agricultural biotechnology to the development of sustainable, environment-friendly agriculture. It deals with the recent achievements of genetic technology for the development of new transgenic microbial, plant and animal products. It also deals with the newest developments and perspectives of microbial intervention in agricultural practices, such as biofertilizers, biocontrol agents, and various microbiological products used in modern agriculture. The review surveys the outlook for a waste-free, environment-friendly sustainable agricultural practice, including waste management, recycling and bioremediation technologies. The review lists the most important marketable agrobiotechnological products, and their present and projected sales volume.

Agriculture↗
PubMedDate not supplied

Reporter gene bioassays in environmental analysis.

In parallel to the continuous development of increasingly more sophisticated physical and chemical analytical technologies for the detection of environmental pollutants, there is a progressively more urgent need also for bioassays which report not only on the presence of a chemical but also on its bioavailability and its biological effects. As a partial fulfillment of that need, there has been a rapid development of biosensors based on genetically engineered bacteria. Such microorganisms typically combine a promoter-operator, which acts as the sensing element, with reporter gene(s) coding for easily detectable proteins. These sensors have the ability to detect global parameters such as stress conditions, toxicity or DNA-damaging agents as well as specific organic and inorganic compounds. The systems described in this review, designed to detect different groups of target chemicals, vary greatly in their detection limits, specificity, response times and more. These variations reflect on their potential applicability which, for most of the constructs described, is presently rather limited. Nevertheless, present trends promise that additional improvements will make microbial biosensors an important tool for future environmental analysis.

Biological Assay↗
PubMed2006

Natural attenuation processes for remediation of arsenic contaminated soils and groundwater.

Arsenic (As) contamination presents a hazard in many countries. Natural attenuation (NA) of As-contaminated soils and groundwater may be a cost-effective in situ remedial option. It relies on the site intrinsic assimilative capacity and allows in-place cleanup. Sorption to solid phases is the principal mechanism immobilizing As in soils and removing it from groundwater. Hydroxides of iron, aluminum and manganese, clay and sulfide minerals, and natural organic matter are commonly associated with soils and aquifer sediments, and have been shown to be significant As adsorbents. The extent of sorption is influenced by As speciation and the site geochemical conditions such as pH, redox potential, and the co-occurring ions. Microbial activity may catalyze the transformation of As species, or mediate redox reactions thus influencing As mobility. Plants that are capable of hyperaccumulating As may translocate As from contaminated soils and groundwater to their tissues, providing the basis for phytoremediation. However, NA is subject to hydrological changes and may take substantial periods of time, thus requiring long-term monitoring. The current understanding of As NA processes remains limited. Sufficient site characterization is critical to the success of NA. Further research is required to develop conceptual and mathematical models to predict the fate and transport of As and to evaluate the site NA capacity. Engineering enhanced NA using environmentally benign products may be an effective alternative.

Arsenic↗
PubMed2004

A cutaneous gene therapy approach to treat infection through keratinocyte-targeted overexpression of antimicrobial peptides.

Infection represents a major associated problem in severely burned patients, as it causes skin graft failure and increases the risk of mortality. Topical and systemic antibiotic treatment is limited by the appearance of resistant bacterial strains. Antimicrobial peptides (AMPs) are gene-encoded "natural antibiotics" that form part of the innate mechanism of defense and may be active against such antibiotic-resistant microorganisms. Several microbicidal peptides are expressed in human skin under inflammatory conditions, and their function is not only limited to microbial killing but also influences tissue repair and adaptive immunity. Protein delivery through cutaneous gene therapy is a promising therapeutic tool for both skin and nonskin diseases. Here we present a gene transfer approach aimed at delivering antimicrobial peptides from keratinocytes. Adenoviral vectors encoding antimicrobial peptide genes were used to infect human keratinocytes growing either on plastic or as part of cultured skin equivalents. Inhibition of bacterial growth occurred both in conditioned media and in direct contact with AMPs gene-transduced keratinocytes. In addition, we showed cooperative effects after transfer of combinations of genes encoding for AMPs with structural differences. Combined cutaneous tissue engineering in conjunction with (microbicidal) gene therapy emerges as a tailored therapeutic approach that is useful for wound coverage and, in this case, concomitantly combating infection.

Adenoviridae↗
PubMed2002

Process engineering variables in the spray washing of meat and produce.

Recently, much attention has been focused on the safety of fruits and vegetables. Washing is a fundamental operation in the processing of produce. Aqueous spray energy can be, and often is, used to remove mineral, chemical, or biological contaminants from produce. A few advantages of spray washing over washing by dipping, soaking, or gravity rinse are increased energy directed to contaminants, reduced volume of water use and wastewater generation, and reduced water uptake by produce. The kinetic energy of the spray droplets produces the cleaning action. Increased spray pressure increases energy. If the energy is too great, produce may be physically damaged. If the energy is too little, the surface may not be cleaned. Indeed, studies on meat have shown that water pressures ranging from 1,379 to 2,070 kPa (200 to 300 psi) are effective in reducing microbial contamination, and a water flow rate of 7.5 liters/min is recommended. Water temperature >70 degrees C has been found to reduce bacterial counts in carcass tissue by 2 to 3 log CFU/cm2. These levels are likely too high for the fragile produce; hence, the main function of spray washing in produce applications will probably shift to being a delivery system for antimicrobial agents. Several other equipment, process, and product variables are relevant to the optimization of such a system. Qualities of the spray, such as droplet spectrum, droplet velocity, angle of droplet impingement, number and orientation of nozzles, spray rate, and resident time of the produce in the sprayer, also can be manipulated to adjust the amount of energy directed to the surface. There is a need to scientifically investigate the effects of these processes and equipment parameters on the removal of microbiological contaminants on meats and produce. Such empirical investigations guided by the results from fundamental studies about produce surface characteristics and the mechanism of bacterial attachment to plant tissue surfaces would allow for the efficient development of spray washers that effectively decontaminate produce.

Animals↗
PubMed2005

Statistical assessment of a laboratory method for growing biofilms.

Microbial biofilms have been grown in laboratories using a variety of different approaches. A laboratory biofilm reactor system, called the CDC biofilm reactor (CBR) system, has been devised for growing biofilms under moderate to high fluid shear stress. The reactor incorporates 24 removable biofilm growth surfaces (coupons) for sampling and analysing the biofilm. Following preliminary experiments to verify the utility of the CBR system for growing biofilms of several clinically relevant organisms, a standard operating procedure for growing a Pseudomonas aeruginosa biofilm was created. This paper presents the results of a rigorous, intra-laboratory, statistical evaluation of the repeatability and ruggedness of that procedure as well as the results of the experiments with clinically relevant organisms. For the statistical evaluations, the outcome of interest was the density (c.f.u. cm(-2)) of viable P. aeruginosa. Replicate experiments were conducted to assess the repeatability of the log density outcome. The mean P. aeruginosa log10 density was 7.1, independent of the coupon position within the reactor. The repeatability standard deviation of the log density based on one coupon per experiment was 0.59. Analysis of variance showed that the variability of the log density was 53 % attributable to within-experiment sources and 47 % attributable to between-experiments sources. The ruggedness evaluation applied response-surface design and regression analysis techniques, similar to those often used for sensitivity analyses in other fields of science and engineering. This approach provided a quantitative description of ruggedness; specifically, the amount the log density was altered by small adjustments to four key operational factors--time allowed for initial surface colonization, temperature, nutrient concentration, and fluid shear stress on the biofilm. The small size of the regression coefficient associated with each operational factor showed that the method was rugged; that is, relatively insensitive to minor perturbations of the four factors. These results demonstrate that the CBR system is a reliable experimental tool for growing a standard biofilm in the laboratory and that it can be adapted to study several different micro-organisms.

Bacteriological Techniques↗
PubMedDate not supplied

The synthesis and in vivo assembly of functional antibodies in yeast.

The yeast Saccharomyces cerevisiae can synthesize, process and secrete higher eukaryotic proteins. We have investigated the expression of immunoglobulin chains in yeast and demonstrate here the synthesis, processing and secretion of light and heavy chains, the glycosylation of heavy chain, the intracellular localization of these foreign proteins by immunofluorescence, and the detection of functional antibodies in cells co-expressing both chains. This may provide the basis of a microbial fermentation process for the production of monoclonal antibodies. The co-expression of light and heavy chains in Escherichia coli has been reported but functional antibodies were not assembled in vivo. Furthermore, only low-level assembly of these chains was found in vitro.

Antibodies, Fungal↗
PubMed2001

Evaluating the safety of microbial enzyme preparations used in food processing: update for a new century.

Microbial enzymes used in food processing are typically sold as enzyme preparations that contain not only a desired enzyme activity but also other metabolites of the production strain, as well as added materials such as preservatives and stabilizers. The added materials must be food grade and meet applicable regulatory standards. The purpose of this report is to present guidelines that can be used to evaluate the safety of the metabolites of the production strain that are also present in the enzyme preparation, including of course, but not limited to, the desired enzyme activity itself. This discussion builds on previously published decision tree mechanisms and includes consideration of new genetic modification technologies, for example, modifying the primary structure of enzymes to enhance specific properties that are commercially useful. The safety of the production strain remains the primary consideration in evaluating enzyme safety, in particular, the toxigenic potential of the production strain. Thoroughly characterized nonpathogenic, nontoxigenic microbial strains, particularly those with a history of safe use in food enzyme manufacture, are logical candidates for generating a safe strain lineage, through which improved strains may be derived via genetic modification by using either traditional/classical or rDNA strain improvement strategies. The elements needed to establish a safe strain lineage include thoroughly characterizing the host organism, determining the safety of all new DNA that has been introduced into the host organism, and ensuring that the procedure(s) that have been used to modify the host organism are appropriate for food use. Enzyme function may be changed by intentionally altering the amino acid sequence (e.g., protein engineering). It may be asked if such modifications might also affect the safety of an otherwise safe enzyme. We consider this question in light of what is known about the natural variation in enzyme structure and function and conclude that it is unlikely that changes which improve upon desired enzyme function will result in the creation of a toxic protein. It is prudent to assess such very small theoretical risks by conducting limited toxicological tests on engineered enzymes. The centerpiece of this report is a decision tree mechanism that updates previous enzyme safety evaluation mechanisms to accommodate advances in enzymology. We have concluded that separate mutagenicity testing is not needed if this decision tree is used to evaluate enzyme safety. Under the criteria of the decision tree, no new food enzyme can enter the market without critical evaluation of its safety.

Animals↗
PubMed1999

Chitinases in biological control.

The public concern over the harmful effects of chemical pesticides on the environment and human health has enhanced the search for safer, environmentally friendly control alternatives. Control of plant pests by the application of biological agents holds great promise as an alternative to the use of chemicals. It is generally recognized that biological control agents are safer and more environmentally sound than is reliance on the use of high volumes of pesticides. Due to the importance of chitinolytic enzymes in insect, nematode, and fungal growth and development, they are receiving attention in regard to their development as biopesticides or chemical defense proteins in transgenic plants and microbial biocontrol agents. In this sense, biological control of some soil-borne fungal diseases has been correlated with chitinase production. Fungi- and bacteria-producing chitinases exhibit antagonism against fungi, and inhibition of fungal growth by plant chitinases has been demonstrated. Insect pathogenic fungi have considerable potential for the biological control of insect pests. Entomopathogenic fungi apparently overcome physical barriers of the host by producing multiple extracellular enzymes including chitinolytic enzymes, which help to penetrate the cuticle and facilitate infection. In this chapter, the role of chitinases in biological control and their potential use in the improvement of biocontrol agents and crop plants by genetic engineering is analyzed in view of recent findings.

Bacterial Physiological Phenomena↗
PubMed2004

Food allergy and the gastrointestinal tract.

PURPOSE OF REVIEW: Adverse reactions to food resulting in gastrointestinal symptoms are common in the general population. Although only a minority of individuals complaining of such symptoms have immune-mediated reactions to food (food allergy), gastrointestinal food allergies do exist in both children and adults. This review provides an update on the pathogenesis and clinical management of food allergy manifesting in the gut, emphasizing recent developments in the field. RECENT FINDINGS: Recent studies have broadened our understanding of the innate gastrointestinal defense systems and the role of the gut flora for protection against allergy. These findings support the hygiene theory in which microbial challenge in early life is thought to protect against the development of allergic disease. New insights into the regulation of mast cells and eosinophils, their homing to the intestine, and their interaction with the specific immune system and the enteric nervous system have been given. In parallel, the molecular structure of major food allergens is being unraveled, and new therapies that focus largely on modulating the immune response to food antigens have been developed. SUMMARY: These new findings have important implications for the diagnosis and management of food allergies. The availability of recombinant allergens will improve methods to diagnose and treat food allergy, and genetic engineering will allow future therapies such as vaccination against food allergy. Emerging knowledge of the role of the gut flora in mucosal immunity will enhance strategies to prevent and treat food allergy using probiotics such as Lactobacillus GG. Such new approaches will extend existing options for managing food allergy and preventing anaphylaxis.

Journal Article↗