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At least 1,135 records · Page 63Linked to original sources
PubMed1999

Reductive dechlorination of chlorinated ethene DNAPLs by a culture enriched from contaminated groundwater.

A microbial culture enriched from a trichloroethene-contaminated groundwater aquifer reductively dechlorinated trichloroethene (TCE) and tetrachloroethene (PCE) to ethene. Initial PCE dechlorination rate studies indicated a first-order dependence with respect to substrate at low PCE concentrations, and a zero-order dependence at high concentrations. Studies of TCE and vinyl chloride (VC) dechlorination indicated a first-order dependence at all substrate concentrations. VC had little or no effect on the initial rate of TCE dechlorination. With subsaturating concentrations of chlorinated ethenes, nearly stoichiometric amounts of the toxic intermediate vinyl chloride accumulated prior to its dechlorination to ethene. In contrast, under saturating conditions, in which a dense, nonaqueous-phase liquid existed in equilibrium with the aqueous phase, the chlorinated ethene was dechlorinated to ethene, at a rapid rate, with the accumulation of relatively small amounts of chlorinated intermediates.

Biodegradation, Environmental↗
PubMed2000

Production of antifungal recombinant peptides in Escherichia coli.

Antifungal peptides derived from the human bactericidal/permeability-increasing protein (BPI) were produced in Escherichia coli as fusion proteins with human BoneD. Bacterial cultures transformed with the gene encoding the fusion protein were grown to a high cell density (OD(600)>100), and induced with L-arabinose to initiate product expression. Fusion protein accumulated into cytoplasmic inclusion bodies and recombinant peptide was released from BoneD by acid hydrolysis at an engineered aspartyl-prolyl dipeptide linker. Acid hydrolysis of purified inclusion bodies at pH <2.6 followed Arrhenius kinetics and did not require prior inclusion body solubilization in detergents or denaturants. Surprisingly, at pH <2.6 and 85 degrees C, cell lysis and aspartyl-prolyl hydrolysis with concomitant peptide release occurred simultaneously. Bacterial cultures were, therefore, adjusted to approximately pH 2.6 with HCl directly in the bioreactor and incubated at elevated temperature. Peptide, which is soluble in the aqueous acidic environment, was separated from the insoluble material and purified using column separation techniques. Recombinant peptide was separated from the hydrolyzed bioreactor culture with >76% recovery and a final peptide purity of >97%. Antifungal peptide prepared by recombinant and solid phase synthesis methods demonstrated similar activity against Candida sp. in a broth microdilution assay.

Amino Acid Sequence↗
PubMed2006

Glycosyltransferases involved in type 1 chain and Lewis antigen biosynthesis exhibit glycan and core chain specificity.

Sialyl Lewis A (SLe(a)), Lewis A (Le(a)), and Lewis B (Le(b)) have been studied in many different biological contexts, for example in microbial adhesion and cancer. Their biosynthesis is complex and involves beta1,3-galactosyltransferases (beta3Gal-Ts) and a combined action of alpha2- and/or alpha4-fucosyltransferases (Fuc-Ts). Further, O-glycans with different core structures have been identified, and the ability of beta3Gal-Ts and Fuc-Ts to use these as substrates has not been resolved. Therefore, to examine the in vivo specificity of enzymes involved in SLe(a), Le(a), and Le(b) synthesis, we have transiently transfected CHO-K1 cells with relevant human glycosyltransferases and, on secreted reporter proteins, detected the resulting Lewis antigens on N- and O-linked glycans using western blotting and Le-specific antibodies. beta3Gal-T1, -T2, and -T5 could synthesize type 1 chains on N-linked glycans, but only beta3Gal-T5 worked on O-linked glycans. The latter enzyme could use both core 2 and core 3 precursor structures. Furthermore, the specificity of FUT5 and FUT3 in Le(a) and Le(b) synthesis was different, with FUT5 fucosylating H type 1 only on core 2, but FUT3 fucosylating H type 1 much more efficient on core 3 than on core 2. Finally, FUT1 and FUT2 were both found to direct alpha2-fucosylation on type 1 chains on both N- and O-linked structures. This knowledge enables us to engineer recombinant glycoproteins with glycan- and core chain-specific Lewis antigen substitution. Such tools will be important for investigations on the fine carbohydrate specificity of Le(b)-binding lectins, such as Helicobacter pylori adhesins and DC-SIGN, and may also prove useful as therapeutics.

Animals↗
PubMed2004

Enzymatic labeling of a single chain variable fragment of an antibody with alkaline phosphatase by microbial transglutaminase.

Functional cross-linking of a single chain Fv fragment of anti-hen egg-white lysozyme antibody (scFv) and alkaline phosphatase (AP) was explored using microbial transglutaminase (MTG) from Streptomyces mobaraensis. A specific peptidyl linker for MTG was genetically fused to the N-terminus of each protein and the resultant proteins were obtained separately by bacterial expression. The recombinant peptide-tagged scFv and AP were site-specifically cross-linked by MTG through the extra peptidyl linkers in vitro, which mainly yielded the heterodimer (i.e., scFv-AP conjugate). The enzymatic cross-linking reaction had little influence on either the antigen-binding ability of the scFv moiety or the enzymatic activity of the AP moiety of the conjugate, allowing use within an enzyme-linked immunosorbent assay. The results obtained suggest that the enzymatic approach with MTG facilitates the posttranslational construction of functional fusion proteins.

Alkaline Phosphatase↗
PubMed2026

Membrane and proteome allocation constraints in Escherichia coli models during overflow metabolism.

The allocation of finite cellular resources is a fundamental principle that dictates microbial metabolic strategies and gives rise to complex phenomena, such as overflow metabolism, characterized by the production of respiro-fermentative by-products, including acetate, during rapid growth. Although proteome-constrained models have successfully predicted overflow metabolism in Escherichia coli, they often overlook the distinct biophysical and energetic costs associated with protein localization. The cellular membrane, in particular, represents a critical and constrained compartment where competition for space and synthesis machinery can create significant metabolic bottlenecks. To investigate this, we developed the membrane-associated constrained flux balance analysis (MAFBA), a scalable, genome-scale metabolic model that introduces a tunable constraint on the total protein mass allocated to the cellular membrane. Our model demonstrates that the overall and membrane-associated proteome allocation constraints interact to improve the accuracy of predicting the onset of overflow metabolism. It mechanistically reveals that at high growth rates, competition for limited membrane allocation forces a trade-off between growth-essential functions and respiratory capacity, leading to acetate production. Furthermore, MAFBA quantitatively explains the widely observed experimental phenomenon that expressing heterologous membrane proteins imposes a significantly higher metabolic burden than expressing cytosolic proteins. This study establishes membrane resource allocation as a key constraint governing bacterial physiology, acting in concert with overall proteome limitations. The resulting MAFBA framework provides a powerful and accessible tool for synthetic biology and metabolic engineering, enabling the prediction of metabolic costs associated with expressing membrane-bound proteins and guiding strain design strategies, holding promise for applications in bioproduction and metabolic engineering.

Escherichia coli↗
PubMed2006

Novel gyrase mutations in quinolone-resistant and -hypersusceptible clinical isolates of Mycobacterium tuberculosis: functional analysis of mutant enzymes.

Mutations in the DNA gyrase GyrA2GyrB2 complex are associated with resistance to quinolones in Mycobacterium tuberculosis. As fluoroquinolones are being used increasingly in the treatment of tuberculosis, we characterized several multidrug-resistant clinical isolates of M. tuberculosis carrying mutations in the genes encoding the GyrA or GyrB subunits associated with quinolone resistance or hypersusceptibility. In addition to the reported putative quinolone resistance mutations in GyrA, i.e., A90V, D94G, and D94H, we found that the GyrB N510D mutation was also associated with ofloxacin resistance. Surprisingly, several isolates bearing a novel combination of gyrA T80A and A90G changes were hypersusceptible to ofloxacin. M. tuberculosis GyrA and GyrB subunits (wild type [WT] and mutants) were overexpressed in Escherichia coli, purified to homogeneity, and used to reconstitute highly active gyrase complexes. Mutant proteins were produced similarly from engineered gyrA and gyrB alleles by mutagenesis. MICs, enzyme inhibition, and drug-induced DNA cleavage were determined for moxifloxacin, gatifloxacin, ofloxacin, levofloxacin, and enoxacin. Mutant gyrase complexes bearing GyrA A90V, D94G, and D94H and GyrB N510D were resistant to quinolone inhibition (MICs and 50% inhibitory concentrations [IC50s] at least 3.5-fold higher than the concentrations for the WT), and all, except the GyrB mutant, were less efficiently trapped as a quinolone cleavage complex. In marked contrast, gyrase complexes bearing GyrA T80A or A90G were hypersusceptible to the action of many quinolones, an effect that was reinforced for complexes bearing both mutations (MICs and IC50s up to 14-fold lower than the values for the WT). This is the first detailed enzymatic analysis of hypersusceptibility and resistance in M. tuberculosis.

Antitubercular Agents↗
PubMed2001

Molecular basis of multidrug transport by ATP-binding cassette transporters: a proposed two-cylinder engine model.

ATP-binding cassette multidrug transporters are probably present in all living cells, and are able to export a variety of structurally unrelated compounds at the expense of ATP hydrolysis. The elevated expression of these proteins in multidrug resistant cells interferes with the drug-based control of cancers and infectious pathogenic microorganisms. Multidrug transporters interact directly with the drug substrates. Insights into the structural elements in drug molecules and transport proteins that are required for this interaction are now beginning to emerge. However, much remains to be learned about the nature and number of drug binding sites in the transporters, and the mechanism(s) by which ATP hydrolysis is coupled to changes in affinity and/or accessibility of drug binding sites. This review summarizes recent advances in answering these questions for the human multidrug resistance P-glycoprotein and its prokaryotic homolog LmrA. The relevance of these findings for other ATP-binding cassette transporters will be discussed.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed2000

Introduction of chloramphenicol resistance into the modified mouse mitochondrial genome: cloning of unstable sequences by passage through yeast.

Despite increasing awareness of the importance of the mitochondrial genome in human pathology, very few attempts have been made so far toward genetic engineering of mitochondrial DNA (mtDNA). One of the reasons for this slow progress is the difficulty of cloning mtDNA in Escherichia coli, a trait in common with repetitive or palindromic sequences, and some viral sequences. We have previously made a construct containing the entire mouse mitochondrial genome and a cDNA sequence coding for human ornithine transcarbamylase in a yeast/bacterial shuttle vector, which can be stably maintained in E. coli. We wished to modify this vector for mitochondrial gene therapy by the addition of mitochondrial chloramphenicol resistance, conferred by a point mutation in the 16S rRNA gene. Attempts to modify this construct by a straightforward cloning approach in E. coli proved unsuccessful. Two successful strategies for modification of large unstable constructs in both E. coli and the yeast Saccharomyces cerevisiae are compared here.

Animals↗
PubMed2001

Liposome-mediated DNA uptake and transient expression in Thermotoga.

We report here the successful application of a PCR-based method to detect genetic transformation of Thermotoga neapolitana and Thermotoga maritima. Plasmid vectors were constructed using pRQ7, an 846-bp plasmid found in Thermotoga species strain RQ7, which replicates by a rolling circle mechanism. The vector pJY1 was constructed by placing a gene encoding a thermostable chloramphenicol acetyltransferase from Stacphylococcus aureus under the control of the tac promoter and joining this with pRQ7 in a pBluescript vector. A second vector, pJY2, was similarly constructed using a gene encoding a kanamycin nucleotidyltransferase previously engineered for thermostability. Genetic transformation of T. neapolitana and T. maritima spheroplasts was achieved using cationic liposomes. The transforming DNA was detected in cells grown in liquid cultures using polymerase chain reaction amplification of the cat or kan genes. T. neapolitana could maintain pJY1 for at least 25 generations in liquid medium containing chloramphenicol. The pJY2 vector conferred kanamycin resistance to T. maritima cells grown in liquid culture. Isolation of stable transformants on solid media after 2-3 days of incubation at 77 degrees C was not possible with either vector, probably because of the instability of both vectors and antibiotics under these conditions. However, this transformation procedure provides, for the first time, a method to introduce DNA into this hyperthermophilic bacterium for potential applications such as targeted gene disruption analyses.

Anti-Bacterial Agents↗
PubMed2025

The Elements of Life, Photosynthesis and Genomics.

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute's efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets - focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors - that are well-used and appreciated by the community. A new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true "green yeast" and as a platform for engineering algae to produce useful bioproducts.

Photosynthesis↗
PubMed2004

Assessment of the role of antibiotics and enterococcal virulence factors in a mouse model of extraintestinal translocation.

OBJECTIVE: To study the relative contribution of antibiotics and bacterial virulence factors in the process of translocation of Enterococcus faecalis from the gut to extraintestinal organs. DESIGN: Prospective controlled animal study. SETTING: Animal experimental laboratory at a university medical center. SUBJECTS: Fifty-two female Balb/c mice. INTERVENTIONS: We developed a mouse model to study the translocation of Enterococcus faecalis from the intestinal tract. Balb/c mice received sterile drinking water or antibiotic combinations to deplete their indigenous intestinal microflora. The animals subsequently were fed genetically engineered enterococci expressing different combinations of the putative enterococcal virulence factors aggregation substance and binding substance. Animals were killed, and their livers, spleens, and mesenteric lymph nodes were aseptically removed and cultured along with fecal samples for enumeration of bacteria. MEASUREMENTS AND MAIN RESULTS: All animals were colonized with the test strains at 2-6 x 109 colony forming units/g of feces; in the antibiotic-treated animals, feces were free from anaerobes and Enterobacteriaceae. In animals fed the identical bacterial mutant, the colony counts in mesenteric lymph nodes were significantly lower in mice not treated with antibiotics than in those treated with antibiotics (p =.016). Multigroup analysis of variance revealed no significant differences of the translocation frequencies for the different mutant strains; however, the differences were statistically significant for all groups receiving antibiotics vs. the group not receiving antibiotics (p <.05-.01). There was a trend (although not statistically significant) for a higher proportion of positive cultures from either spleen or liver in mice that had enterococci recovered from their mesenteric lymph nodes (28%) relative to those that did not have enterococci isolated from the lymph nodes (12%; rate ratio 2.39, p =.30 by logistic regression analysis). CONCLUSIONS: Oral antibiotics can select for extraintestinal translocation of Enterococcus faecalis, and neither aggregation substance nor binding substance seems to be required for this process. The experiments encourage further exploration of host and microbial factors contributing to translocation and may provide a better understanding of the pathogenesis of enterococcal infections in patients in intensive care units.

Animals↗
PubMed2006

Interleukin-17A: a T-cell-derived growth factor for murine and human mesenchymal stem cells.

Interleukin-17A (IL-17A) is a proinflammatory cytokine expressed in activated T-cells. It is required for microbial host defense and is a potent stimulator of granulopoiesis. In a dose-dependent fashion, IL-17A expanded human mesenchymal stem cells (MSCs) and induced the proliferation of mature stroma cells in bone marrow-derived stroma cultures. Recombinant human interleukin-17A (rhIL-17A) nearly doubled colony-forming unit-fibroblast (CFU-f) frequency and almost tripled the surface area covered by stroma. In a murine transplant model, in vivo murine (m)IL-17A expression enhanced CFU-f by 2.5-fold. Enrichment of the graft with CD4(+) T-cell resulted in a 7.5-fold increase in CFU-f in normal C57BL/6, but only threefold in IL-17Ra(-/-) mice on day 14 post-transplant. In this transplant model, in vivo blockade of IL-17A in C57BL/6 mice resembled the phenotype of IL-17Ra(-/-) mice. Approximately half of the T-cell-mediated effect on MSC recovery following radiation-conditioned transplantation was attributed to the IL-17A/IL-17Ra pathway. Pluripotent MSCs have the potential of regenerating various tissues, and mature stroma cells are critical elements of the hematopoietic microenvironment (HME). The HME is pivotal for formation and maintenance of functional blood cells. As a newly identified stroma cell growth factor, IL-17A might have potential applications for novel treatment approaches involving MSCs, such as tissue graft engineering.

Animals↗
PubMed2006

Current status of technical protein refolding.

The expression of heterologous proteins in microbial hosts frequently leads to the formation of insoluble aggregates. To fully exploit the production capacity of the cells, efficient strategies for further processing have to be developed. While in lab scale matrix assisted refolding techniques, especially of histidine-tagged proteins have become very popular, in production scale refolding by dilution is still predominant due to its simplicity. However scaling up dilution processes leads to large volumes and low protein concentration. This is a heavy burden both for liquid handling and for subsequent downstream processing steps. Process development aims to operate at uniform, reproducible conditions, to reduce costs to a minimum and to guarantee the required quality of the product. The general refolding kinetics, exploration of appropriate refolding conditions are reviewed. The major refolding operations such as dilution, matrix assisted refolding, pressure driven refolding or continuous refolding applications are discussed in view of industrial applicability.

Algorithms↗
PubMed2000

A high yielding mutant of mycobacteriophage L1 and its application as a diagnostic tool.

L1 is a lysogenic phage of mycobacteria, which along with L5 and D29 constitute a closely linked family of homoimmune mycobacteriophages. These phages can be potentially used for genetic engineering of mycobacteria and diagnosis of mycobacterial infection. The effectiveness of such phage based systems depends on the efficiency with which they infect and grow within target cells. While working with phage L1c1ts which is a temperature sensitive mutant of phage L1, we observed that high yielding phage stocks were generated by repeated passage through the host, Mycobacterium smegmatis. A plaque purified mutant L1-P2, obtained from one such high yielding stock, when analyzed further was found to infect host cells with increased efficiency. The DNA obtained from L1-P2 was examined by restriction digestion, and it was observed that spontaneous loss of DNA fragment from the right arm, which encodes early regulatory factors, had occurred. It has been further demonstrated that the high yielding property of the mutant phage could be utilized to increase the sensitivity of mycobacteriophage-based detection systems.

Adsorption↗
PubMed2005

Microbial diversity in biofilms from corroding heating systems.

Culture-independent investigations of the bacterial diversity and activity in district heating systems with and without corrosion did not make it possible to relate one group of microorganisms with the observed corrosion. Fluorescence in situ hybridization by oligonucleotide probes revealed the dominance of beta-proteobacteria, sulphate reducing prokaryotes and alpha-proteobacteria. Analysis of a clone library from one Danish heating (DH) system showed that the most sequences formed two clusters within the alpha-proteobacteria affiliated to the families Rhizobiaceae and Acetobacteraceae and two clusters within the beta-proteobacteria belonging to the family Comamonadaceae. Functional groups were determined by microautoradiography showing aerobic and anaerobic bacteria (sulphate reducing and methanogenic bacteria). The corrosion study showed that pitting corrosion rates were five to ten times higher than the general corrosion rates, suggesting the presence of biocorrosion. The results indicate that several bacterial groups could be involved in corrosion of DH system piping including sulphate reducing prokaryotes, Acidovorax (within the beta-proteobacteria), methanogenic bacteria and others.

Bacteria↗
PubMed1990

Optimized vectors and selection for transformation of Neurospora crassa and Aspergillus nidulans to bleomycin and phleomycin resistance.

To provide a dominant selectable marker for transformation of Neurospora crassa strains lacking specific auxotrophic mutations, we have engineered the bleomycin (Bm) resistance-encoding gene (ble) from the bacterial transposon Tn5 for expression in N. crassa. The coding region of the ble gene was fused to the promoter and terminator regions of the N. crassa am gene. In some vectors, multiple cloning sites were placed flanking the ble gene to provide a versatile ble cassette. When introduced into N. crassa, the hybrid ble gene conferred resistance to greater than 15 micrograms Bm/ml. Under optimal conditions, the levels of Bm required (2.5 micrograms/ml) make even large-scale transformation experiments very economical. Aspergillus nidulans could also be efficiently transformed to Bm resistance using the N. crassa ble gene fusion. Since the ble gene functions in both N. crassa and A. nidulans, the gene should be useful as a transformation marker for the many other filamentous fungi which are sensitive to Bm.

Aspergillus nidulans↗
PubMed1996

Why don't ruminal bacteria digest cellulose faster?

The bacteria Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus generally are regarded as the predominant cellulolytic microbes in the rumen. Comparison of available data from the literature reveals that these bacteria are the most actively cellulolytic of all mesophilic organisms described to date from any habitat. In light of numerous proposals to improve microbial cellulose digestion in ruminants, it is instructive to examine the characteristics of these species that contribute to their superior cellulolytic capabilities and to identify the factors that prevent them from digesting cellulose even more rapidly. As a group, these species have extreme nutritional specialization. They are able to utilize cellulose (or in some cases xylan) and its hydrolytic products as their nearly sole energy sources for growth. Moreover, each species apparently has evolved to similar maximum rates of cellulose digestion (first-order rate constants of 0.05 to 0.08 h-1). Active cellulose digestion involves adherence of cells to the fibers via a glycoprotein glycocalyx, which protects cells from protozoal grazing and cellulolytic enzymes from degradation by ruminal proteases while it retains-at least temporarily-the cellodextrin products for use by the cellulolytic bacteria. These properties result in different ecological roles for the adherent and nonadherent populations of each species, but overall provide an enormous selective advantage to these cellulolytic bacteria in the ruminal environment. However, major constraints to cellulose digestion are caused by cell-wall structure of the plant (matrix interactions among wall biopolymers and low substrate surface area) and by limited penetration of the nonmotile cellulolytic microbes into the cell lumen. Because of these constraints and the highly adapted nature of cellulose digestion by the predominant cellulolytic bacteria in the rumen, transfer of cellulolytic capabilities to noncellulolytic ruminal bacteria (e.g., by genetic engineering) that display other desirable properties offers limited opportunities to improve ruminal digestion of cellulose.

Animals↗
PubMed1996

Modified entry and syncytium formation by herpes simplex virus type 1 mutants selected for resistance to heparin inhibition.

Herpes simplex virus type 1 (HSV-1) mutants were selected by passage of HSV-1 (KOS) in HEp-2 cells such that binding and penetration occurred in the presence of heparin. Analysis of selected uncloned virus pools revealed that approximately 95% of virus formed syncytia and greater than 58% were gC-negative. Plaque-purified gC-negative syncytial mutants were more resistant than HSV-1 (KOS) to heparin inhibition, as was an engineered nonsyncytial recombinant deleted for gC, delta gC6. Thus, absence of gC was sufficient to explain the enrichment for gC-negative mutants. The syncytial phenotype of most mutants mapped to a mutation in gK. Transfer of this mutation to HSV-1 (KOS) resulted in a recombinant that induced fusion of Vero cells but not HEp-2 cells and was more sensitive to heparin inhibition of entry, revealing a previously undescribed phenotype of mutations in gK. Engineered gC-negative virus containing the gK syncytial mutation induced fusion of both cell lines and was as resistant to heparin inhibition as was delta gC6. Because deletion of gC reduces infectivity of HSV-1 in the absence of heparin, mutations in gC combined with the syncytial mutation could have provided a selective advantage. Thus, absence of gC reduced heparin inhibition of binding and penetration while the combination of the gC and gK mutations enhanced spread through the HEp-2 cell monolayer by cell fusion. Because extreme selective pressure was required to favor these mutations and such mutations are rare in clinical isolates, the wild-type forms of gC and gK must provide for optimal viral replication and propagation in cell culture as well as in vivo, despite the view that gC is dispensable in cultured cells.

Amino Acid Sequence↗