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At least 649 records · Page 36Linked to original sources
PubMed2006

Dual strategies for peptidoglycan discrimination by peptidoglycan recognition proteins (PGRPs).

The innate immune system constitutes the first line of defense against microorganisms in both vertebrates and invertebrates. Although much progress has been made toward identifying key receptors and understanding their role in host defense, far less is known about how these receptors recognize microbial ligands. Such studies have been severely hampered by the need to purify ligands from microbial sources and a reliance on biological assays, rather than direct binding, to monitor recognition. We used synthetic peptidoglycan (PGN) derivatives, combined with microcalorimetry, to define the binding specificities of human and insect peptidoglycan recognition proteins (PGRPs). We demonstrate that these innate immune receptors use dual strategies to distinguish between PGNs from different bacteria: one based on the composition of the PGN peptide stem and another that senses the peptide bridge crosslinking the stems. To pinpoint the site of PGRPs that mediates discrimination, we engineered structure-based variants having altered PGN-binding properties. The plasticity of the PGRP-binding site revealed by these mutants suggests an intrinsic capacity of the innate immune system to rapidly evolve specificities to meet new microbial challenges.

Animals↗
PubMed1999

Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community.

We used a culture-independent approach, namely, thermal gradient gel electrophoresis (TGGE) analysis of ribosomal sequences amplified directly from community DNA, to determine changes in the structure of the microbial community following phenol shocks in the highly complex activated sludge ecosystem. Parallel experimental model sewage plants were given shock loads of chlorinated and methylated phenols and simultaneously were inoculated (i) with a genetically engineered microorganism (GEM) able to degrade the added substituted phenols or (ii) with the nonengineered parental strain. The sludge community DNA was extracted, and 16S rDNA was amplified and analyzed by TGGE. To allow quantitative analysis of TGGE banding patterns, they were normalized to an external standard. The samples were then compared with each other for similarity by using the coefficient of Dice. The Shannon index of diversity, H, was calculated for each sludge sample, which made it possible to determine changes in community diversity. We observed a breakdown in community structure following shock loads of phenols by a decrease in the Shannon index of diversity from 1.13 to 0.22 in the noninoculated system. Inoculation with the GEM (Pseudomonas sp. strain B13 SN45RE) effectively protected the microbial community, as indicated by the maintenance of a high diversity throughout the shock load experiment (H decreased from 1.03 to only 0.82). Inoculation with the nonengineered parental strain, Pseudomonas sp. strain B13, did not protect the microbial community from being severely disturbed; H decreased from 1.22 to 0.46 for a 3-chlorophenol-4-methylphenol shock and from 1.03 to 0.70 for a 4-chlorophenol-4-methylphenol shock. The catabolic trait present in the GEM allowed for bioprotection of the activated sludge community from breakdown caused by toxic shock loading. In-depth TGGE analysis with similarity and diversity algorithms proved to be a very sensitive tool to monitor changes in the structure of the activated sludge microbial community, ranging from subtle shifts during adaptation to laboratory conditions to complete collapse following pollutant shocks.

Bacteria↗
PubMed2006

Biodegradability of imidazolium and pyridinium ionic liquids by an activated sludge microbial community.

Ionic liquids (ILs) are novel organic salts that have enormous potential for industrial use as green replacements for harmful volatile organic solvents. Varying the cationic components can alter the chemical and physical properties of ILs, including solubility, to suit a variety of industrial processes. However, to complement designer engineering, it is crucial to proactively characterize the biological impacts of new chemicals, in order to fully define them as environmentally friendly. Before introduction of ILs into the environment, we performed an analysis of the biodegradability of six ILs by activated sludge microorganisms collected from the South Bend, Indiana wastewater treatment plant. We examined biodegradability of 1-butyl, 1-hexyl and 1-octyl derivatives of 3-methyl-imidazolium and 3-methyl-pyridinium bromide compounds using the standard Organisation for Economic Cooperation and Development dissolved organic carbon Die-Away Test, changes in total dissolved nitrogen concentrations, and 1H-nuclear magnetic resonance analysis of initial and final chemical structures. Further, we examined microbial community profiles throughout the incubation period using denaturing gradient gel electrophoresis (DNA-PCR-DGGE). Our results suggest that hexyl and octyl substituted pyridinium-based ILs can be fully mineralized, but that imidazolium-based ILs are only partially mineralized. Butyl substituted ILs with either cation, were not biodegradable. Biodegradation rates also increase with longer alkyl chain length, which may be related to enhanced selection of a microbial community. Finally, DGGE analysis suggests that certain microorganisms are enriched by ILs used as a carbon source. Based on these results, we suggest that further IL design and synthesis include pyridinium cations and longer alkyl substitutions for rapid biodegradability.

Electrophoresis↗
PubMed1998

Engineering of S2 site of aqualysin I; alteration of P2 specificity by excluding P2 side chain.

Gly101, one of the conserved amino acid residues which was expected to be comprised in half-sphere-shaped S2 site small pocket of aqualysin I, a microbial thermophilic alkaline serine protease, was replaced by alanine, valine, or leucine to alterate the P2 specificity of the enzyme by excluding bulky P2 side chain of the substrate. By the mutation of G101A, the catalytic efficiencies of the enzyme for bulky amino acid residues in P2 site such as valine and leucine drastically decreased by excluding the P2 side chain. By the mutation of G101V, even the side chain of the methyl group of the alanine and the side chain of proline were excluded, while the catalytic efficiency toward glycine residue was retained. The enzyme was altered to be glycine preferable. The mutation of G101L reduced catalytic efficiencies for any substrate including glycine which is corresponding to the main chain of the peptide substrate. The strategies we have adopted in this paper are applicable to all subtilisin-related enzymes.

Alanine↗
PubMed2001

Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration.

With industrial development growing rapidly, there is a need for environmentally sustainable energy sources. Bioethanol (ethanol from biomass) is an attractive, sustainable energy source to fuel transportation. Based on the premise that fuel bioethanol can contribute to a cleaner environment and with the implementation of environmental protection laws in many countries, demand for this fuel is increasing. Efficient ethanol production processes and cheap substrates are needed. Current ethanol production processes using crops such as sugar cane and corn are well-established; however, utilization of a cheaper substrate such as lignocellulose could make bioethanol more competitive with fossil fuel. The processing and utilization of this substrate is complex, differing in many aspects from crop-based ethanol production. One important requirement is an efficient microorganism able to ferment a variety of sugars (pentoses, and hexoses) as well as to tolerate stress conditions. Through metabolic engineering, bacterial and yeast strains have been constructed which feature traits that are advantageous for ethanol production using lignocellulose sugars. After several rounds of modification/evaluation/modification, three main microbial platforms, Saccharomyces cerevisiae, Zymomonas mobilis, and Escherichia coli, have emerged and they have performed well in pilot studies. While there are ongoing efforts to further enhance their properties, improvement of the fermentation process is just one of several factors-that needs to be fully optimized and integrated to generate a competitive lignocellulose ethanol plant.

Biomass↗
PubMed2002

Recombinant protein expression for therapeutic applications.

In recent years, the number of recombinant proteins used for therapeutic applications has increased dramatically. Many of these applications involve complex glycoproteins and antibodies with relatively high production needs. These demands have driven the development of a variety of improvements in protein expression technology, particularly involving mammalian and microbial culture systems.

Animals↗
PubMed1996

Bioaugmentation as a soil bioremediation approach.

The debate over the efficacy of bioaugmentation rages on, with research continuing to demonstrate that its advantages for soil bioremediation are difficult to predict; however, when it works, the results are often very encouraging. The difficulties arise from, among others, the diversity of the microorganisms used, environmental heterogeneity, and variations in the influence of critical parameters (e.g. humidity, microbial predation and "bioavailability') which, unfortunately, are not even always identified.

Biodegradation, Environmental↗
PubMed2002

Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae.

Assessment of reproducibility of DNA-microarray analysis from published data sets is complicated by the use of different microbial strains, cultivation techniques, and analytical procedures. Because intra- and interlaboratory reproducibility is highly relevant for application of DNA-microarray analysis in functional genomics and metabolic engineering, we designed a set of experiments to specifically address this issue. Saccharomyces cerevisiae CEN.PK113-7D was grown under defined conditions in glucose-limited chemostats, followed by transcriptome analysis with Affymetrix GeneChip arrays. In each of the laboratories, three independent replicate cultures were grown aerobically as well as anaerobically. Although variations introduced by in vitro handling steps were small and unbiased, greater variation from replicate cultures underscored that, to obtain reliable information, experimental replication is essential. Under aerobic conditions, 86% of the most highly expressed yeast genes showed an average intralaboratory coefficient of variation of 0.23. This is significantly lower than previously reported for shake-flask-culture transcriptome analyses and probably reflects the strict control of growth conditions in chemostats. Using the triplicate data sets and appropriate statistical analysis, the change calls from anaerobic versus aerobic comparisons yielded an over 95% agreement between the laboratories for transcripts that changed by over 2-fold, leaving only a small fraction of genes that exhibited laboratory bias.

Aerobiosis↗
PubMed2000

Suppression of endogenous IL-10 gene expression in dendritic cells enhances antigen presentation for specific Th1 induction: potential for cellular vaccine development.

A new paradigm for designing vaccines against certain microbial pathogens, including Chlamydia trachomatis, is based on the induction of local mucosal Th1 response. IL-10 is an anti-inflammatory cytokine that exerts negative immunoregulatory influence on Th1 response. This study investigated whether biochemical modulation of endogenous IL-10 expression at the level of APCs is a practical strategy for enhancing the specific Th1 response against pathogens controlled by Th1 immunity. The results revealed that the high resistance of genetically engineered IL-10-/- (IL-10KO) mice to genital chlamydial infection is a function of the predilection of their APCs to rapidly and preferentially activate a high Th1 response. Thus, in microbiological analysis, IL-10KO mice suffered a shorter duration of infection, less microbial burden, and limited ascending infection than immunocompetent wild-type mice. Also, IL-10KO were resistant to reinfection after 8 wk of the primary infection. Cellular and molecular immunologic evaluation indicated that IL-10KO mice induced greater frequency of chlamydial-specific Th1 response following C. trachomatis infection. Moreover, IL-10KO APCs or antisense IL-10 oligonucleotide-treated wild-type APCs were potent activators of Th1 response from naive or immune T cells. Furthermore, both Ag-pulsed dendritic cells from IL-10KO mice and IL-10 antisense-treated dendritic cells from wild-type mice were efficient cellular vaccines in adoptive immunotherapeutic vaccination against genital chlamydial infection. These findings may furnish a novel immunotherapeutic strategy for boosting the Th1 response against T cell-controlled pathogens and tumors, using IL-10-deficient APCs as vaccine delivery agents.

Adjuvants, Immunologic↗
PubMed2004

Evaluation of disinfectant efficacy against biofilm and suspended bacteria in a laboratory swimming pool model.

Laboratory reactor systems designed to model specific environments enable researchers to explore environmental dynamics in a more controlled manner. This paper describes the design and operation of a reactor system built to model a swimming pool in the laboratory. The model included relevant engineering parameters such as filter loading and turn-overs per day. The water chemistry in the system's bulk water was balanced according to standard recommendations and the system was challenged with a bacterial load and synthetic bather insult, formulated to represent urine and perspiration. The laboratory model was then used to evaluate the efficacy of six chemical treatments against biofilm and planktonic bacteria. Results showed that the biofilm was able to accumulate on coupons and in the filter systems of reactors treated with either 1-3 mg/L free chlorine or 10 mg/L polyhexamethylene biguanide (PHMB). All the treatments tested resulted in at least a 4 log reduction in biofilm density when compared to the control, but shock treatments were the most effective at controlling biofilm accumulation. A once weekly shock dose of 10 mg/L free chlorine resulted in the greatest log reduction in biofilm density. The research demonstrated the importance of studying a biofilm in addition to the planktonic bacteria to assess the microbial dynamics that exist in a swimming pool model.

Bacteria↗
PubMed2000

Eradication of a resistant Pseudomonas aeruginosa strain after a cluster of infections in a hematology/oncology unit.

OBJECTIVES: This report chronicles an outbreak of a multiply resistant strain of Pseudomonas aeruginosa and the measures required to contain this outbreak. METHODS: Laboratory-based ward-liaison surveillance allowed the detection of a multiply resistant strain of P. aeruginosa infecting patients in our hematology/oncology unit. Sampling of the immediate environment was carried out. Pulsed field gel electrophoresis was used to compare the patients' organisms with those found in the environment. Extensive dismantling of the drainage system, repeated cleaning and disinfection, and a review of the departmental antibiotic policy were some of the infection control measures instigated. RESULTS: During a period of 11 months, three patients in the hematology department and two patients in the oncology department were infected with multiply resistant P. aeruginosa. There were two cases of pneumonia, one of which was fatal, and two cases of neutropenic septicaemia. Pulsed field gel electrophoresis performed on the isolates showed that the isolates from geographically separate areas could be divided into two strains that were closely related but distinct. Two genotypically identical strains were also isolated from the plumbing systems in the areas of each ward where patients had been treated. CONCLUSIONS: The potential for serious nosocomial infections with P. aeruginosa is well recognized. Eradication of the organism from the environment may require the co-ordinated efforts of clinicians, nurses, pharmacy and hospital engineers, working in collaboration with the hospital infection control team. To date, the same strains have not been isolated despite repeated surveillance over the past 18 months and therefore these measures have, in our opinion, successfully removed the potential for nosocomial infection with this resistant organism in our hospital.

Bacteremia↗
PubMed2006

High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineered Escherichia coli.

Reconstructing synthetic metabolic pathways in microbes holds great promise for the production of pharmaceuticals in large-scale fermentations. By recreating biosynthetic pathways in bacteria, complex molecules traditionally harvested from scarce natural resources can be produced in microbial cultures. Here we report on a strain of Escherichia coli containing a heterologous, nine-gene biosynthetic pathway for the production of the terpene amorpha-4,11-diene, a precursor to the anti-malarial drug artemisinin. Previous reports have underestimated the productivity of this strain due to the volatility of amorphadiene. Here we show that amorphadiene evaporates from a fermentor with a half-life of about 50 min. Using a condenser, we take advantage of this volatility by trapping the amorphadiene in the off-gas. Amorphadiene was positively identified using nuclear magnetic resonance spectroscopy and determined to be 89% pure as collected. We captured amorphadiene as it was produced in situ by employing a two-phase partitioning bioreactor with a dodecane organic phase. Using a previously characterized caryophyllene standard to calibrate amorphadiene production and capture, the concentration of amorphadiene produced was determined to be 0.5 g/L of culture medium. A standard of amorphadiene collected from the off-gas showed that the caryophyllene standard overestimated amorphadiene production by approximately 30%.

Antimalarials↗
PubMed1995

Bioremediation of organic and metal contaminants with dissimilatory metal reduction.

Dissimilatory metal reduction has the potential to be a helpful mechanism for both intrinsic and engineered bioremediation of contaminated environments. Dissimilatory Fe(III) reduction is an important intrinsic process for removing organic contaminants from aquifers contaminated with petroleum or landfill leachate. Stimulation of microbial Fe(III) reduction can enhance the degradation of organic contaminants in ground water. Dissimilatory reduction of uranium, selenium, chromium, technetium, and possibly other metals, can convert soluble metal species to insoluble forms that can readily be removed from contaminated waters or waste streams. Reduction of mercury can volatilize mercury from waters and soils. Despite its potential, there has as yet been limited applied research into the use of dissimilatory metal reduction as a bioremediation tool.

Bacteria↗
PubMed2006

Attenuation of mining-derived pollutants in the hyporheic zone: a review.

Mine water pollution is a major cause of surface- and groundwater pollution in former mining districts throughout Europe. It is a potential barrier to achieving good status water bodies, which is a requirement of the EU Water Framework Directive. In the UK, a concerted effort has been made over the last decade or so to address the scientific and practical challenges relating to the remediation of mine water pollution. However, most of this work has focused on remediation of point sources of pollution (typically arising from abandoned mines and shafts), while the behaviour of mine water at the groundwater-surface water interface (the "hyporheic zone") has received far less attention in relevant scientific and engineering literature. The extent of mine water pollution and capacity for its attenuation at the hyporheic zone has not been well quantified while, furthermore, the complex chemical and microbial processes occurring there (specifically with reference to mining-derived pollutants) have not been investigated in any depth. The absence of such data may relate, in a large part, to the difficulty in physically measuring volumes and concentrations associated with these river inputs/exports. A far greater body of literature addresses biogeochemical processes at the hyporheic zone (especially relating to manganese), albeit many such articles relate to aqueous metal dynamics in general, rather than mine water specifically. This paper presents a review of the natural attenuation processes that may limit the movement and availability of mining-derived pollutants at the groundwater-surface water (GW-SW) interface, and specifically within the hyporheic zone. A substantial part focuses on precipitation and adsorption processes at the hyporheic zone, as well as discussing the role of microbial processes in governing metal ion mobility.

Adsorption↗
PubMed2006

Chemically engineered extracts as an alternative source of bioactive natural product-like compounds.

The access to libraries of molecules with interesting biomolecular properties is a limiting step in the drug discovery process. By virtue of a long molecular evolution process, natural products are recognized as biologically validated starting points in structural space for library development. We introduce here a strategy to generate natural product-like libraries. A semisynthetic mixture of compounds was produced by diversification of a natural product extract through the chemical transformation of common chemical functionalities in natural products into chemical functionalities rarely found in nature. The resulting mixture showed antifungal activity against Candida albicans, whereas the starting extract did not show such activity. Bioguided fractionation led to the isolation of a previously undescribed active semisynthetic pyrazole. The result illustrates how biological activity can be generated by designed chemical diversification of a natural product mixture, and represents the proof of principle of an alternative strategy for producing natural product-like libraries from natural products libraries.

Antifungal Agents↗
PubMed2006

Therapeutic potential of chitosan and its derivatives in regenerative medicine.

BACKGROUND: Cell-based transplantation, tissue engineering and gene therapy are important therapeutic strategies for present and future regenerative medicine. One challenge is to present the target cells in a suitable matrix to allow the cells to survive the wound contraction, tissue repair, and remodeling in certain tissues. Recently, functional biomaterial research has been directed towards the development of improved scaffolds and new drug delivery systems for regenerative medicine. MATERIALS AND METHODS: A literature survey was performed in basic and clinic publications relevant to the therapeutic potential of chitosan and its derivatives in regenerative medicine. In this review the functional properties and potential applications of chitosan and its derivatives in regenerative medicine are presented and discussed. RESULTS: Chitosan can be obtained by alkaline deacetylation of chitin and is found to be a natural-based nontoxic, biocompatible, and biodegradable polymer with anti-microbial activity. Chitosan and its derivatives could accelerate wound healing by enhancing the functions of inflammatory cells and repairing cells. Recent studies further indicated that chitosan and its derivatives also are novel scaffold materials for tissue engineering and are-promising non-viral vectors for gene delivery. CONCLUSIONS: Regenerative medicine has entered a new era with the development of modern science and technology. The novel properties of chitosan make it a versatile biomaterial for cell therapy, tissue engineering and gene therapy. It is hoped that these diverse approaches for regenerative medicine will translate from "bench to bedside" in the future.

Animals↗
PubMed2003

Microbial starch-binding domains as a tool for targeting proteins to granules during starch biosynthesis.

Modification of starch biosynthesis pathways holds an enormous potential for tailoring granules or polymers with new functionalities. In this study, we explored the possibility of engineering artificial granule-bound proteins, which can be incorporated in the granule during biosynthesis. The starch-binding domain (SBD)-encoding region of cyclodextrin glycosyltransferase from Bacillus circulans was fused to the sequence encoding the transit peptide (amyloplast entry) of potato granule-bound starch synthase I (GBSS I). The synthetic gene was expressed in the tubers of two potato cultivars (cv. Kardal and cv. Karnico) and one amylose-free (amf) potato mutant. SBDs accumulated inside starch granules, not at the granule surface. Amylose-free granules contained 8 times more SBD (estimated at ca. 1.6% of dry weight) than the amylose-containing ones. No consistent differences in physicochemical properties between transgenic SBD starches and their corresponding controls were found, suggesting that SBD can be used as an anchor for effector proteins without having side-effects. To test this, a construct harbouring the GBSS I transit peptide, the luciferase reporter gene, a PT-linker, and the SBD (in frame), and a similar construct without the linker and the SBD, were introduced in cv. Kardal. The fusion protein accumulated in starch granules (with retainment of luciferase activity), whereas the luciferase alone did not. Our results demonstrate that SBD technology can be developed into a true platform technology, in which SBDs can be fused to a large choice of effector proteins to generate potato starches with new or improved functionalities.

Amino Acid Sequence↗