Publications
Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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draft genome sequence of a pseudomonas sp. strain carrying blaimp-25 and blavim-2 carbapenemase genes from hospital sewage. | pseudomonas strain wchp16 recovered from hospital sewage in west china hospital, chengdu, china was found to carry two carbapenemase genes blaimp-25 and blavim-2 here, we report its 5.7-mb draft genome sequence, comprising 141 contigs and an average 59.53% g+c content. the genome contained 5,504 coding sequences and 67 trna genes. | 2016 | 27795238 |
label-free, rapid and quantitative phenotyping of stress response in e. coli via ramanome. | rapid profiling of stress-response at single-cell resolution yet in a label-free, non-disruptive and mechanism-specific manner can lead to many new applications. we propose a single-cell-level biochemical fingerprinting approach named "ramanome", which is the collection of single-cell raman spectra (scrs) from a number of cells randomly selected from an isogenic population at a given time and condition, to rapidly and quantitatively detect and characterize stress responses of cellular population ... | 2016 | 27756907 |
metabolic engineering of corynebacterium glutamicum for enhanced production of 5-aminovaleric acid. | 5-aminovaleric acid (5ava) is an important five-carbon platform chemical that can be used for the synthesis of polymers and other chemicals of industrial interest. enzymatic conversion of l-lysine to 5ava has been achieved by employing lysine 2-monooxygenase encoded by the davb gene and 5-aminovaleramidase encoded by the dava gene. additionally, a recombinant escherichia coli strain expressing the davb and dava genes has been developed for bioconversion of l-lysine to 5ava. to use glucose and xy ... | 2016 | 27717386 |
mitochondrial carriers link the catabolism of hydroxyaromatic compounds to the central metabolism in candida parapsilosis. | the pathogenic yeast candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. the orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exce ... | 2016 | 27707801 |
structure and catalytic mechanism of monodehydroascorbate reductase, mdhar, from oryza sativa l. japonica. | ascorbic acid (asa) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. the enzyme monodehydroascorbate reductase (mdhar) regenerates asa by catalysing the reduction of monodehydroascorbate, using nadh or nadph as an electron donor. the detailed recycling mechanism of mdhar remains unclear due to lack of structural information. here, we present the crystal structures of mdhar in the presence of cofactors, nicotinamide adenine dinuc ... | 2016 | 27652777 |
genome-based genetic tool development for bacillus methanolicus: theta- and rolling circle-replicating plasmids for inducible gene expression and application to methanol-based cadaverine production. | bacillus methanolicus is a thermophilic methylotroph able to overproduce amino acids from methanol, a substrate not used for human or animal nutrition. based on our previous rna-seq analysis a mannitol inducible promoter and a putative mannitol activator gene mtlr were identified. the mannitol inducible promoter was applied for controlled gene expression using fluorescent reporter proteins and a flow cytometry analysis, and improved by changing the -35 promoter region and by co-expression of the ... | 2016 | 27713731 |
disruption of pseudomonas putida by high pressure homogenization: a comparison of the predictive capacity of three process models for the efficient release of arginine deiminase. | disruption of pseudomonas putida kt2440 by high-pressure homogenization in a french press is discussed for the release of arginine deiminase (adi). the enzyme release response of the disruption process was modelled for the experimental factors of biomass concentration in the broth being disrupted, the homogenization pressure and the number of passes of the cell slurry through the homogenizer. for the same data, the response surface method (rsm), the artificial neural network (ann) and the suppor ... | 2016 | 27699703 |
structural and histone binding ability characterization of the arb2 domain of a histone deacetylase hda1 from saccharomyces cerevisiae. | hda1 is the catalytic core component of the h2b- and h3- specific histone deacetylase (hdac) complex from saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events. though the n-terminal catalytic hdac domain of hda1 is well characterized, the function of the c-terminal arb2 domain remains unknown. in this study, we determine the crystal structure of the arb2 domain from s. cerevisiae hda1 at a resolut ... | 2016 | 27665728 |
flavin-dependent redox transfers by the two-component diketocamphane monooxygenases of camphor-grown pseudomonas putida ncimb 10007. | the progressive titres of key monooxygenases and their requisite native donors of reducing power were used to assess the relative contribution of various camphor plasmid (cam plasmid)- and chromosome-coded activities to biodegradation of (rac)-camphor at successive stages throughout growth of pseudomonas putida ncimb 10007 on the bicylic monoterpenoid. a number of different flavin reductases (frs) have the potential to supply reduced flavin mononucleotide to both 2,5- and 3,6-diketocamphane mono ... | 2016 | 27754389 |
draft genome sequence of the marine rhodobacteraceae strain o3.65, cultivated from oil-polluted seawater of the deepwater horizon oil spill. | the marine alphaproteobacterium strain o3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the deepwater horizon (dwh) oil spill and belongs to the ubiquitous, diverse and ecological relevant roseobacter group within the rhodobacteraceae. here, we present a preliminary set of physiological features of strain o3.65 and a description and annotation of its draft genome sequence. based on our data we suggest potential ecological roles of th ... | 2016 | 27777651 |
cpxr activates mexab-oprm efflux pump expression and enhances antibiotic resistance in both laboratory and clinical nalb-type isolates of pseudomonas aeruginosa. | resistance-nodulation-division (rnd) efflux pumps are responsible for multidrug resistance in pseudomonas aeruginosa. in this study, we demonstrate that cpxr, previously identified as a regulator of the cell envelope stress response in escherichia coli, is directly involved in activation of expression of rnd efflux pump mexab-oprm in p. aeruginosa. a conserved cpxr binding site was identified upstream of the mexa promoter in all genome-sequenced p. aeruginosa strains. cpxr is required to enhance ... | 2016 | 27736975 |
inhibition of xanthomonas fragariae, causative agent of angular leaf spot of strawberry, through iron deprivation. | in commercial production settings, few options exist to prevent or treat angular leaf spot (als) of strawberry, a disease of economic importance and caused by the bacterial pathogen xanthomonas fragariae. in the process of isolating and identifying x. fragariae bacteria from symptomatic plants, we observed growth inhibition of x. fragariae by bacterial isolates from the same leaf macerates. identified as species of pseudomonas and rhizobium, these isolates were confirmed to suppress growth of x. ... | 2016 | 27790193 |
plant drought tolerance enhancement by trehalose production of desiccation-tolerant microorganisms. | a collection of desiccation-tolerant xeroprotectant-producing microorganisms was screened for their ability to protect plants against drought, and their role as plant growth-promoting rhizobacteria was investigated in two different crops (tomato and pepper). the most commonly described biochemical mechanisms for plant protection against drought by microorganisms including the production of phytohormones, antioxidants and xeroprotectants were analyzed. in particular, the degree of plant protectio ... | 2016 | 27746776 |
harnessing host-vector microbiome for sustainable plant disease management of phloem-limited bacteria. | plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as candidatus (ca.) phytoplasma species and several species of ca. liberibacter. recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that ... | 2016 | 27746788 |
draft genome sequences of four hospital-associated pseudomonas putida isolates. | we present here the draft genome sequences of four pseudomonas putida isolates belonging to a single clone suspected for nosocomial transmission between patients and a bronchoscope in a tertiary hospital. the four genome sequences belong to a single lineage but contain differences in their mobile genetic elements. | 2016 | 27688339 |
activation of the glutamic acid-dependent acid resistance system in escherichia coli bl21(de3) leads to increase of the fatty acid biotransformation activity. | the biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. the productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. here, we have investigated factors that influence the tolerance of escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. the metabolic and genomic responses of e. coli bl21(de3) and mg1655 grown in the presence of n-heptanoic acid ... | 2016 | 27681369 |
biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants. | the 1,4-naphthoquinones (1,4-nqs) are a diverse group of natural products found in every kingdom of life. plants, including many horticultural species, collectively synthesize hundreds of specialized 1,4-nqs with ecological roles in plant-plant (allelopathy), plant-insect and plant-microbe interactions. numerous horticultural plants producing 1,4-nqs have also served as sources of traditional medicines for hundreds of years. as a result, horticultural species have been at the forefront of many b ... | 2016 | 27688890 |
physiological response of escherichia coli o157:h7 sakai to dynamic changes in temperature and water activity as experienced during carcass chilling. | enterohemeorrhagic escherichia coli is a leading cause of foodborne illness, with the majority of cases linked to foods of bovine origin. currently, no completely effective method for controlling this pathogen during carcass processing exists. understanding how this pathogen behaves under those stress conditions experienced on the carcass during chilling in cold air could offer opportunities for development or improvement of effective decontamination processes. therefore, we studied the growth k ... | 2016 | 27615263 |
occurrence and antimicrobial susceptibility of enteric rods and pseudomonads isolated from the dental prostheses biofilm. | to determine the occurrence and the in vitro antimicrobial susceptibility of enteric rods and pseudomonads from the denture biofilm of 52 subjects at the center for dental specialties of sobral/ ceara, brazil. | 2016 | 27812616 |
identification of klebsiella pneumoniae carbapenemase-producing klebsiella oxytoca in clinical isolates in tehran hospitals, iran by chromogenic medium and molecular methods. | production of carbapenemase, especially klebsiella pneumoniae carbapenemases (kpc), is one of the antibiotic resistance mechanisms of enterobacteriaceae such as klebsiella oxytoca. this study aimed to investigate and identify kpc-producing k. oxytoca isolates using molecular and phenotypic methods. | 2016 | 27812488 |
recent advances in synthetic biosafety. | synthetically engineered organisms hold promise for a broad range of medical, environmental, and industrial applications. organisms can potentially be designed, for example, for the inexpensive and environmentally benign synthesis of pharmaceuticals and industrial chemicals, for the cleanup of environmental pollutants, and potentially even for biomedical applications such as the targeting of specific diseases or tissues. however, the use of synthetically engineered organisms comes with several r ... | 2016 | 27635235 |
interspecific bacterial interactions are reflected in multispecies biofilm spatial organization. | interspecies interactions are essential for the persistence and development of any kind of complex community, and microbial biofilms are no exception. multispecies biofilms are structured and spatially defined communities that have received much attention due to their omnipresence in natural environments. species residing in these complex bacterial communities usually interact both intra- and interspecifically. such interactions are considered to not only be fundamental in shaping overall biomas ... | 2016 | 27630624 |
engineering of tm1459 from thermotoga maritima for increased oxidative alkene cleavage activity. | oxidative cleavage of alkenes is a widely employed process allowing oxyfunctionalization to corresponding carbonyl compounds. recently, a novel biocatalytic oxidative alkene cleavage activity on styrene derivatives was identified in tm1459 from thermotoga maritima. in this work we engineered the enzyme by site-saturation mutagenesis of active site amino acids to increase its activity and to broaden its substrate scope. a high-throughput assay for the detection of the ketone products was successf ... | 2016 | 27713741 |
triclosan in water, implications for human and environmental health. | triclosan (tcs) is a broad spectrum antibacterial agent present as an active ingredient in some personal care products such as soaps, toothpastes and sterilizers. it is an endocrine disrupting compound and its increasing presence in water resources as well as in biosolid-amended soils used in farming, its potential for bioaccumulation in fatty tissues and toxicity in aquatic organisms are a cause for concern to human and environmental health. tcs has also been detected in blood, breast milk, uri ... | 2016 | 27722057 |
antibiotic resistance of diverse bacteria from aquaculture in borneo. | the administration of antimicrobials in aquaculture provides a selective pressure creating a reservoir of multiple resistant bacteria in the cultured fish and shrimps as well as the aquaculture environment. the objective of this study was to determine the extent of antibiotic resistance in aquaculture products and aquaculture's surrounding environment in sarawak, malaysian borneo. ninety-four identified bacterial isolates constituted of 17 genera were isolated from sediment, water, and cultured ... | 2016 | 27746817 |
transcriptomic analysis of the highly efficient oil-degrading bacterium acinetobacter venetianus rag-1 reveals genes important in dodecane uptake and utilization. | the hydrocarbonoclastic bacterium acinetobacter venetianus rag-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. in this study, we compare the transcriptome of the strain rag-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. comparison of the transcriptional responses of rag ... | 2016 | 27664055 |
biosynthesis of catechol melanin from glycerol employing metabolically engineered escherichia coli. | melanins comprise a chemically-diverse group of polymeric pigments whose function is related to protection against physical and chemical stress factors. these polymers have current and potential applications in the chemical, medical, electronics and materials industries. the biotechnological production of melanins offers the possibility of obtaining these pigments in pure form and relatively low cost. in this study, escherichia coli strains were engineered to evaluate the production of melanin f ... | 2016 | 27659593 |
draft genome sequence of a diazotrophic, plant growth-promoting rhizobacterium of the pseudomonas syringae complex. | we report here the draft genome sequence of pseudomonas syringae gr12-2, a nitrogen-fixing, plant growth-promoting bacterium, isolated from the rhizosphere of an arctic grass. the 6.6-mbp genome contains 5,676 protein-coding genes, including a nitrogen-fixation island similar to that in p. stutzeri. | 2016 | 27660794 |
identification and characterization of an aeromonas hydrophila oligopeptidase gene pepf negatively related to biofilm formation. | bacterial biofilms are involved in adaptation to complex environments and are responsible for persistent bacterial infections. biofilm formation is a highly complex process during which multifarious genes work together regularly. in this study, we screened the ez-tn5 transposon mutant library to identify genes involved in biofilm formation of aeromonas hydrophila. a total of 24 biofilm-associated genes were identified, the majority of which encoded proteins related to cell structure, transcripti ... | 2016 | 27713736 |
novel nad+-farnesal dehydrogenase from polygonum minus leaves. purification and characterization of enzyme in juvenile hormone iii biosynthetic pathway in plant. | juvenile hormone iii is of great concern due to negative effects on major developmental and reproductive maturation in insect pests. thus, the elucidation of enzymes involved jh iii biosynthetic pathway has become increasing important in recent years. one of the enzymes in the jh iii biosynthetic pathway that remains to be isolated and characterized is farnesal dehydrogenase, an enzyme responsible to catalyze the oxidation of farnesal into farnesoic acid. a novel nad+-farnesal dehydrogenase of p ... | 2016 | 27560927 |
toxin yafq reduces escherichia coli growth at low temperatures. | toxin/antitoxin (ta) systems reduce metabolism under stress; for example, toxin yafq of the yafq/dinj escherichia coli ta system reduces growth by cleaving transcripts with in-frame 5'-aaa-g/a-3' sites, and antitoxin dinj is a global regulator that represses its locus as well as controls levels of the stationary sigma factor rpos. here we investigated the influence on cell growth at various temperatures and found that deletion of the antitoxin gene, dinj, resulted in both reduced metabolism and ... | 2016 | 27557125 |
the diversity of mtdna rns introns among strains of ophiostoma piliferum, ophiostoma pluriannulatum and related species. | based on previous studies, it was suspected that the mitochondrial rns gene within the ophiostomatales is rich in introns. this study focused on a collection of strains representing ophiostoma piliferum, ophiostoma pluriannulatum and related species that cause blue-stain; these fungi colonize the sapwood of trees and impart a dark stain. this reduces the value of the lumber. the goal was to examine the mtdna rns intron landscape for these important blue stain fungi in order to facilitate future ... | 2016 | 27610327 |
functional genomic analyses of enterobacter, anopheles and plasmodium reciprocal interactions that impact vector competence. | malaria exerts a tremendous socioeconomic impact worldwide despite current control efforts, and novel disease transmission-blocking strategies are urgently needed. the enterobacter bacterium esp_z, which is naturally harboured in the mosquito midgut, can inhibit the development of plasmodium parasites prior to their invasion of the midgut epithelium through a mechanism that involves oxidative stress. here, a multifaceted approach is used to study the tripartite interactions between the mosquito, ... | 2016 | 27549662 |
flhf is required for swarming motility and full pathogenicity of bacillus cereus. | besides sporulation, bacillus cereus can undergo a differentiation process in which short swimmer cells become elongated and hyperflagellated swarmer cells that favor migration of the bacterial community on a surface. the functionally enigmatic flagellar protein flhf, which is the third paralog of the signal recognition particle (srp) gtpases ffh and ftsy, is required for swarming in many bacteria. previous data showed that flhf is involved in the control of the number and positioning of flagell ... | 2016 | 27807433 |
exported epoxide hydrolases modulate erythrocyte vasoactive lipids during plasmodium falciparum infection. | erythrocytes are reservoirs of important epoxide-containing lipid signaling molecules, including epoxyeicosatrienoic acids (eets). eets function as vasodilators and anti-inflammatory modulators in the bloodstream. bioactive eets are hydrolyzed to less active diols (dihydroxyeicosatrienoic acids) by epoxide hydrolases (ehs). the malaria parasite plasmodium falciparum infects host red blood cells (rbcs) and exports hundreds of proteins into the rbc compartment. in this study, we show that two para ... | 2016 | 27795395 |
an apple fruit fermentation (aff) treatment improves the composition of the rhizosphere microbial community and growth of strawberry (fragaria × ananassa duch 'benihoppe') seedlings. | plant growth can be promoted by the application of apple fruit fermentation (aff), despite unclear of the underlying mechanisms, the effects involved in aff on rhizosphere microorganisms have been hypothesized. we investigated the consequences of applying aff alone or in combination with bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of denaturing gradient gel electrophoresis (dgge) and 16s rdna were performed to determine aff effects on rhizosphere. moreove ... | 2016 | 27755580 |
determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. | protein function often depends on global, collective internal motions. however, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. we demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. with this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrom ... | 2016 | 27757419 |
investigation into the mode of phosphate activation in the 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase from pseudomonas putida f1. | the 4-hydroxy-4-methyl-2-oxoglutarate (hmg)/4-carboxy-4-hydroxy-2-oxoadipate (cha) aldolase is the last enzyme of both the gallate and protocatechuate 4,5-cleavage pathways which links aromatic catabolism to central cellular metabolism. the enzyme is a class ii, divalent metal dependent, aldolase which is activated in the presence of inorganic phosphate (pi), increasing its turnover rate >10-fold. this phosphate activation is unique for a class ii aldolase. the aldolase pyruvate methyl proton ex ... | 2016 | 27741265 |
physical forces shape group identity of swimming pseudomonas putida cells. | the often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. one commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinc ... | 2016 | 27695443 |
cloning, expression, and characterization of a peptidoglycan hydrolase from the burkholderia pseudomallei phage st79. | the lytic phage st79 of burkholderia pseudomallei can lyse a broad range of its host including antibiotic resistant isolates from within using a set of proteins, holin, lysb, lysc and endolysin, a peptidoglycan (pg) hydrolase enzyme. the phage st79 endolysin gene identified as peptidase m15a was cloned, expressed and purified to evaluate its potential to lyse pathogenic bacteria. the molecular size of the purified enzyme is approximately 18 kda and the in silico study cited here indicated the pr ... | 2016 | 27637947 |
recent advances on multi-parameter flow cytometry to characterize antimicrobial treatments. | the investigation on antimicrobial mechanisms is a challenging and crucial issue in the fields of food or clinical microbiology, as it constitutes a prerequisite to the development of new antimicrobial processes or compounds, as well as to anticipate phenomenon of microbial resistance. nowadays it is accepted that a cells population exposed to a stress can cause the appearance of different cell populations and in particular sub-lethally compromised cells which could be defined as viable but non- ... | 2016 | 27551279 |
insights into the genome sequences of an n-acyl homoserine lactone molecule producing two pseudomonas spp. isolated from the arctic. | we report for the first time the draft genome sequence of two psychrotrophic pseudomonas species, pseudomonas simiae rgcb 73 and pseudomonas brenneri rgcb 108, from the arctic that produce more than one acyl homoserine lactone molecule of varied n-acyl length. the study confirms the presence of a luxr-luxi (type) mediated quorum-sensing system in both the pseudomonas species and enables us to understand the role of quorum sensing in their survival in extremely cold environments. | 2016 | 27491995 |
from the lab to the farm: an industrial perspective of plant beneficial microorganisms. | any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. this paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. in addition, we review some of the most effective microbial product ... | 2016 | 27540383 |
fine-tuning of amino sugar homeostasis by eiia(ntr) in salmonella typhimurium. | the nitrogen-metabolic phosphotransferase system, pts(ntr), consists of the enzymes i(ntr), npr and iia(ntr) that are encoded by ptsp, ptso, and ptsn, respectively. due to the proximity of ptso and ptsn to rpon, the pts(ntr) system has been postulated to be closely related with nitrogen metabolism. to define the correlation between pts(ntr) and nitrogen metabolism, we performed ligand fishing with eiia(ntr) as a bait and revealed that d-glucosamine-6-phosphate synthase (glms) directly interacted ... | 2016 | 27628932 |
genomic, transcriptomic and proteomic analysis provide insights into the cold adaptation mechanism of the obligate psychrophilic fungus mrakia psychrophila. | mrakia psychrophila is an obligate psychrophilic fungus. the cold adaptation mechanism of psychrophilic fungi remains unknown. comparative genomics analysis indicated that m. psychrophila had a specific codon usage preference, especially for codons of gly and arg and its major facilitator superfamily (mfs) transporter gene family was expanded. transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°c, while genes involved in unfolded protein b ... | 2016 | 27633791 |
comprehensive genomic and phenotypic metal resistance profile of pseudomonas putida strain s13.1.2 isolated from a vineyard soil. | trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. as such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. a soil pseudomonas putida, strain s13.1.2 has been isolated from french vineyard soil samples, and shown to confer resistance to copper ions. further investigation revealed a high capacity to tolerate elevated c ... | 2016 | 27730570 |
molecular detection of acanthamoeba spp., naegleria fowleri and vermamoeba (hartmannella) vermiformis as vectors for legionella spp. in untreated and solar pasteurized harvested rainwater. | legionella spp. employ multiple strategies to adapt to stressful environments including the proliferation in protective biofilms and the ability to form associations with free-living amoeba (fla). the aim of the current study was to identify legionella spp., acanthamoeba spp., vermamoeba (hartmannella) vermiformis and naegleria fowleri that persist in a harvested rainwater and solar pasteurization treatment system. | 2016 | 27724947 |
highly efficient and stable novel nanobiohybrid catalyst to avert 3,4-dihydroxybenzoic acid pollutant in water. | the present study reported for the first time covalent immobilization of protocatechuate 3,4-dioxygenase (3,4-pod) onto functionalized multi-walled carbon nanotubes (f-mwcnt) for degrading the toxic 3,4-dihydroxybenzoic acid (3,4-dhba) pollutant in water. the f-mwcnts had a maximum 3,4-pod loading of 1060 μg/mg. immobilized 3,4 pod had 44% of relative structural changes to its free configurations. nevertheless, >90% of relative activity and about 50% of catalytic efficiency were retained to the ... | 2016 | 27721429 |
saccharomyces cerevisiae metabolism in ecological context. | the architecture and regulation of saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles bei ... | 2016 | 27634775 |
systems metabolic engineering of corynebacterium glutamicum for the production of the carbon-5 platform chemicals 5-aminovalerate and glutarate. | the steadily growing world population and our ever luxurious life style, along with the simultaneously decreasing fossil resources has confronted modern society with the issue and need of finding renewable routes to accommodate for our demands. shifting the production pipeline from raw oil to biomass requires efficient processes for numerous platform chemicals being produced with high yield, high titer and high productivity. | 2016 | 27618862 |
architecture of class 1, 2, and 3 integrons from gram negative bacteria recovered among fruits and vegetables. | the spread of antibiotic resistant bacteria throughout the food chain constitutes a public health concern. to understand the contribution of fresh produce in shaping antibiotic resistance bacteria and integron prevalence in the food chain, 333 antibiotic resistance gram negative isolates were collected from organic and conventionally produced fruits (pears, apples, and strawberries) and vegetables (lettuces, tomatoes, and carrots). although low levels of resistance have been detected, the bacter ... | 2016 | 27679611 |
the structure of the periplasmic sensor domain of the histidine kinase cuss shows unusual metal ion coordination at the dimeric interface. | in bacteria, two-component systems act as signaling systems to respond to environmental stimuli. two-component systems generally consist of a sensor histidine kinase and a response regulator, which work together through histidyl-aspartyl phosphorelay to result in gene regulation. one of the two-component systems in escherichia coli, cuss-cusr, is known to induce expression of cuscfba genes at increased periplasmic cu(i) and ag(i) concentrations to help maintain metal ion homeostasis. cuss is a m ... | 2016 | 27583660 |
identification of gefitinib off-targets using a structure-based systems biology approach; their validation with reverse docking and retrospective data mining. | gefitinib, an egfr tyrosine kinase inhibitor, is used as fda approved drug in breast cancer and non-small cell lung cancer treatment. however, this drug has certain side effects and complications for which the underlying molecular mechanisms are not well understood. by systems biology based in silico analysis, we identified off-targets of gefitinib that might explain side effects of this drugs. the crystal structure of egfr-gefitinib complex was used for binding pocket similarity searches on a d ... | 2016 | 27653775 |
comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide. | γ-hexachlorocyclohexane (γ-hch) is a recalcitrant man-made chlorinated pesticide. here, the complete genome sequences of four γ-hch-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-hch degrader, were compared. together with several experimental data, we showed that (i) all the four strains carry almost identical lina to line genes for the conversion of γ-hch to maleylacetate (designated "specific" lin genes), (ii) considerably different genes are ... | 2016 | 27581378 |
primary succession of nitrogen cycling microbial communities along the deglaciated forelands of tianshan mountain, china. | structural succession and its driving factors for nitrogen (n) cycling microbial communities during the early stages of soil development (0-44 years) were studied along a chronosequence in the glacial forelands of the tianshan mountain no.1 glacier in the arid and semi-arid region of central asia. we assessed the abundance and population of functional genes affiliated with n-fixation (nifh), nitrification (bacterial and archaeal amoa), and denitrification (nirk/s and nosz) in a glacier foreland ... | 2016 | 27625641 |
matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (maldi-tof ms) based microbial identifications: challenges and scopes for microbial ecologists. | matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (maldi-tof ms) based biotyping is an emerging technique for high-throughput and rapid microbial identification. due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, maldi-tof ms has started replacing existing practices prevalent in clinical diagnosis. however, applicability of maldi-tof ms in the area of micr ... | 2016 | 27625644 |
molecular and structural considerations of tf-dna binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the lysr-type transcriptional regulator family as a study model. | the goal of most programs developed to find transcription factor binding sites (tfbss) is the identification of discrete sequence motifs that are significantly over-represented in a given set of sequences where a transcription factor (tf) is expected to bind. these programs assume that the nucleotide conservation of a specific motif is indicative of a selective pressure required for the recognition of a tf for its corresponding tfbs. despite their extensive use, the accuracies reached with these ... | 2016 | 27567672 |
physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine bacillus subtilis c01 to alumina nanoparticles. | an increasing number of studies have investigated the effects of nanoparticles (nps) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against nps. whether secondary metabolism biosynthesis is a response to np stress and contributes to the adaption of bacteria to nps is unclear. here, a significant induction in the surfactin production and biofilm formation were detected by adding al2o3 nps to the b. subtilis fermentation broth. physiological ... | 2016 | 27440502 |
methane-oxidizing enzymes: an upstream problem in biological gas-to-liquids conversion. | biological conversion of natural gas to liquids (bio-gtl) represents an immense economic opportunity. in nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (mmo) and methyl coenzyme m reductase (mcr) enzymes. although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditio ... | 2016 | 27366961 |
transcriptome analysis of pseudomonas aeruginosa pao1 grown at both body and elevated temperatures. | functional genomics research can give us valuable insights into bacterial gene function. rna sequencing (rna-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. in this study, we used the rna-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen pseudomonas aeruginosa pao1 following heat shock. samples were grown at both the human body temperature (37 °c) and an arbitrarily-selected temperature of 46 °c. in this work ... | 2016 | 27547539 |
thusin, a novel two-component lantibiotic with potent antimicrobial activity against several gram-positive pathogens. | due to the rapidly increasing prevalence of multidrug-resistant bacterial strains, the need for new antimicrobial drugs to treat infections has become urgent. bacteriocins, which are antimicrobial peptides of bacterial origin, are considered potential alternatives to conventional antibiotics and have attracted widespread attention in recent years. among these bacteriocins, lantibiotics, especially two-component lantibiotics, exhibit potent antimicrobial activity against some clinically relevant ... | 2016 | 27486447 |
unknown unknowns: essential genes in quest for function. | the experimental design of a minimal synthetic genome revealed the presence of a large number of genes without ascribed function, in part because the abstract laws of life must be implemented within ad hoc material contraptions. creating a function needs recruitment of some pre-existing structure and this reveals kludges in their set-up and history. here, we show that looking for functions as an engineer would help in discovery of a significant number of those, proposed together with conceptual ... | 2016 | 27435445 |
sepsis-induced takotsubo cardiomyopathy leading to torsades de pointes. | background. takotsubo cardiomyopathy (tcm) is sudden and reversible myocardial dysfunction often attributable to physical or emotional triggers. case report. we describe a 51-year-old man presented to emergency department with sepsis from urinary tract infection (uti). he was placed on cefepime for uti and non-st-elevation myocardial infarction protocol given elevated troponins with chest pain. subsequently, patient was pulseless with torsades de pointes (tdp) and then converted to sinus rhythm ... | 2016 | 27525128 |
genetic dissection of the regulatory network associated with high c-di-gmp levels in pseudomonas putida kt2440. | most bacteria grow in nature forming multicellular structures named biofilms. the bacterial second messenger cyclic diguanosine monophosphate (c-di-gmp) is a key player in the regulation of the transition from planktonic to sessile lifestyles and this regulation is crucial in the development of biofilms. in pseudomonas putida kt2440, rup4959, a multidomain response regulator with diguanylate cyclase activity, when overexpressed causes an increment in the intracellular levels of c-di-gmp that giv ... | 2016 | 27489550 |
nitrogen regulation of the xyl genes of pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil. | the nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by pseudomonas putida. nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m-xylene in soil, the natural habitat of this bacterium. to address this issue, we have developed a test-tube-to-soil model system that ex ... | 2016 | 27561962 |
immune modulation enables a specialist insect to benefit from antibacterial withanolides in its host plant. | the development of novel plant chemical defenses and counter adaptations by herbivorous insect could continually drive speciation, producing more insect specialists than generalists. one approach to test this hypothesis is to compare closely related generalist and specialist species to reveal the associated costs and benefits of these different adaptive strategies. we use the specialized moth heliothis subflexa, which feeds exclusively on plants in the genus physalis, and its close generalist re ... | 2016 | 27561781 |
efficient reconstruction of predictive consensus metabolic network models. | understanding cellular function requires accurate, comprehensive representations of metabolism. genome-scale, constraint-based metabolic models (gsms) provide such representations, but their usability is often hampered by inconsistencies at various levels, in particular for concurrent models. commgen, our tool for consensus metabolic model generation, automatically identifies inconsistencies between concurrent models and semi-automatically resolves them, thereby contributing to consolidate knowl ... | 2016 | 27563720 |
comparative genomics and metabolic analysis reveals peculiar characteristics of rhodococcus opacus strain m213 particularly for naphthalene degradation. | the genome of rhodococcus opacus strain m213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a g+c content of 66.72%. among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (cogs); 55% of the cogs were present as paralog clusters. pulsed field gel electrophoresis (pfge) analysis of m213 revealed the presence of three different sized replicons- a circ ... | 2016 | 27532207 |
folding analysis of the most complex stevedore's protein knot. | dehi is a homodimeric haloacid dehalogenase from pseudomonas putida that contains the most complex 61 stevedore's protein knot within its folding topology. to examine how dehi attains such an intricate knotted topology we combined far-uv circular dichroism (cd), intrinsic fluorescence spectroscopy and small angle x-ray scattering (saxs) to investigate its folding mechanism. equilibrium unfolding of dehi by chemical denaturation indicated the presence of two highly populated folding intermediates ... | 2016 | 27527519 |
listeria monocytogenes dna glycosylase adlp affects flagellar motility, biofilm formation, virulence, and stress responses. | the temperature-dependent alteration of flagellar motility gene expression is critical for the foodborne pathogen listeria monocytogenes to respond to a changing environment. in this study, a genetic determinant, l. monocytogenes f2365_0220 (lmof2365_0220), encoding a putative protein that is structurally similar to the bacillus cereus alkyl base dna glycosylase (alkd), was identified. this determinant was involved in the transcriptional repression of flagellar motility genes and was named adlp ... | 2016 | 27316964 |
comparative single-cell analysis of different e. coli expression systems during microfluidic cultivation. | recombinant protein production is mostly realized with large-scale cultivations and monitored at the level of the entire population. detailed knowledge of cell-to-cell variations with respect to cellular growth and product formation is limited, even though phenotypic heterogeneity may distinctly hamper overall production yields, especially for toxic or difficult-to-express proteins. unraveling phenotypic heterogeneity is thus a key aspect in understanding and optimizing recombinant protein produ ... | 2016 | 27525986 |
bacterial dispersal promotes biodegradation in heterogeneous systems exposed to osmotic stress. | contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of ... | 2016 | 27536297 |
two distinct cardiolipin synthases operate in agrobacterium tumefaciens. | cardiolipin (cl) is a universal component of energy generating membranes. in most bacteria, it is synthesized via the condensation of two molecules phosphatidylglycerol (pg) by phospholipase d-type cardiolipin synthases (pld-type cls). in the plant pathogen and natural genetic engineer agrobacterium tumefaciens cl comprises up to 15% of all phospholipids in late stationary growth phase. a. tumefaciens harbors two genes, atu1630 (cls1) and atu2486 (cls2), coding for pld-type cls. heterologous exp ... | 2016 | 27472399 |
engineering salmonella as intracellular factory for effective killing of tumour cells. | salmonella have many desirable properties as antitumour-agent due to its ability to proliferate inside tumours and induce tumour regression. additionally, this bacterium can be genetically engineered to deliver therapeutic proteins intratumourally. the main limitation of this approach is the efficient release of therapeutic molecules from intratumoural bacteria. here we have developed an inducible autolysis system based in the lysis operon of the lambda phage that, in response to anhydrotetracyc ... | 2016 | 27464652 |
the importance of integrons for development and propagation of resistance in shigella: the case of latin america. | in latin america, the disease burden of shigellosis is found to coexist with the rapid and rampant spread of resistance to commonly used antibiotics. the molecular basis of antibiotic resistance lies within genetic elements such as plasmids, transposons, integrons, genomic islands, etc., which are found in the bacterial genome. integrons are known to acquire, exchange, and express genes within gene cassettes and it is hypothesized that they play a significant role in the transmission of multidru ... | 2016 | 27528086 |
gut microbiota profiling: metabolomics based approach to unravel compounds affecting human health. | the gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. the microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and diet ... | 2016 | 27507964 |
matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) can precisely discriminate the lineages of listeria monocytogenes and species of listeria. | the genetic lineages of listeria monocytogenes and other species of the genus listeria are correlated with pathogenesis in humans. although matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) has become a prevailing tool for rapid and reliable microbial identification, the precise discrimination of listeria species and lineages remains a crucial issue in clinical settings and for food safety. in this study, we constructed an accurate and reliable ms databa ... | 2016 | 27442502 |
analysis of plant growth-promoting effects of fluorescent pseudomonas strains isolated from mentha piperita rhizosphere and effects of their volatile organic compounds on essential oil composition. | many species or strains of the genus pseudomonas have been characterized as plant growth promoting rhizobacteria (pgpr). we used a combination of phenotypic and genotypic techniques to analyze the community of fluorescent pseudomonas strains in the rhizosphere of commercially grown mentha piperita (peppermint). biochemical techniques, amplified rdna restriction analysis (ardra), and 16s rrna gene sequence analysis revealed that the majority of the isolated native fluorescent strains were p. puti ... | 2016 | 27486441 |
metabolic pathway involved in 6-chloro-2-benzoxazolinone degradation by pigmentiphaga sp. strain dl-8 and identification of the novel metal-dependent hydrolase cbaa. | 6-chloro-2-benzoxazolinone (cdhb) is a precursor of herbicide, insecticide, and fungicide synthesis and has a broad spectrum of biological activity. pigmentiphaga sp. strain dl-8 can transform cdhb into 2-amino-5-chlorophenol (2a5cp), which it then utilizes as a carbon source for growth. the cdhb hydrolase (cbaa) was purified from strain dl-8, which can also hydrolyze 2-benzoxazolinone (boa), 5-chloro-2-boa, and benzamide. the specific activity of purified cbaa was 5,900 u · mg protein(-1) for c ... | 2016 | 27208123 |
environmental factors modulating the stability and enzymatic activity of the petrotoga mobilis esterase (pmest). | enzymes isolated from thermophilic organisms found in oil reservoirs can find applications in many fields, including the oleochemical, pharmaceutical, bioenergy, and food/dairy industries. in this study, in silico identification and recombinant production of an esterase from the extremophile bacteria petrotoga mobilis (designated pmest) were performed. then biochemical, bioinformatics and structural characterizations were undertaken using a combination of synchrotron radiation circular dichroism ... | 2016 | 27351338 |
disk carbapenemase test for the rapid detection of kpc-, ndm-, and other metallo-β-lactamase-producing gram-negative bacilli. | rapid detection of carbapenemase-producing gram-negative bacilli (gnb) is required for optimal treatment of infected patients. we developed and assessed a new disk carbapenemase test (dct). | 2016 | 27374708 |
development of a quadruplex loop-mediated isothermal amplification assay for field detection of four vibrio species associated with fish disease. | a quadruplex loop-mediated isothermal amplification (lamp) method was developed to detect four vibrio species, including vibrio ichthyoenteri, vibrio parahaemolyticus, vibrio scophthalmi, and vibrio vulnificus, simultaneously. four sets of species-specific primers were designed with different restriction sites contained in the inner primers. the quadruplex lamp method could distinguish four vibrio species via the subsequent restriction enzyme analysis. the sensitivity of the quadruplex lamp meth ... | 2016 | 27468405 |
inter-sigmulon communication through topological promoter coupling. | divergent transcription from within bacterial intergenic regions frequently involves promoters dependent on alternative σ-factors. this is the case for the non-overlapping σ(70)- and σ(54)-dependent promoters that control production of the substrate-responsive regulator and enzymes for (methyl)phenol catabolism. here, using an array of in vivo and in vitro assays, we identify transcription-driven supercoiling arising from the σ(54)-promoter as the mechanism underlying inter-promoter communicatio ... | 2016 | 27422872 |
engineering pseudomonas putida kt2440 for simultaneous degradation of carbofuran and chlorpyrifos. | currently, chlorpyrifos (cp) and carbofuran are often applied together to control major agricultural pests in many developing countries, in most cases, they are simultaneously detected in agricultural soils. some cost-effective techniques are required for the remediation of combined pollution caused by multiple pesticides. in this work, we aim at constructing a detectable recombinant microorganism with the capacity to simultaneously degrade cp and carbofuran. to achieve this purpose, cp/carbofur ... | 2016 | 27418102 |
draft genome sequence of pseudomonas putida cbf10-2, a soil isolate with bioremediation potential in agricultural and industrial environmental settings. | pseudomonas putida cbf10-2 is a microorganism isolated from farmland soil in fairchild, tx, found to degrade high-impact xenobiotics, including organophosphate insecticides, petroleum hydrocarbons, and both monocyclic and polycyclic aromatics. the versatility of cbf10-2 makes it useful for multipurpose bioremediation of contaminated sites in agricultural and industrial environments. | 2016 | 27417844 |
arabidopsis thaliana contains both ni2+ and zn2+ dependent glyoxalase i enzymes and ectopic expression of the latter contributes more towards abiotic stress tolerance in e. coli. | the glyoxalase pathway is ubiquitously found in all the organisms ranging from prokaryotes to eukaryotes. it acts as a major pathway for detoxification of methylglyoxal (mg), which deleteriously affects the biological system in stress conditions. the first important enzyme of this system is glyoxalase i (glyi). it is a metalloenzyme which requires divalent metal ions for its activity. this divalent metal ion can be either zn2+ as found in most of eukaryotes or ni2+ as seen in prokaryotes. in the ... | 2016 | 27415831 |
genomic potential of stenotrophomonas maltophilia in bioremediation with an assessment of its multifaceted role in our environment. | the gram negative bacterium stenotrophomonas is rapidly evolving as a nosocomial pathogen in immuno-compromised patients. treatment of stenotrophomonas maltophilia infections is problematic because of their increasing resistance to multiple antibiotics. this article aims to review the multi-disciplinary role of stenotrophomonas in our environment with special focus on their metabolic and genetic potential in relation to bioremediation and phytoremediation. current and emerging treatments and dia ... | 2016 | 27446008 |
the induction and identification of novel colistin resistance mutations in acinetobacter baumannii and their implications. | acinetobacter baumannii is a significant cause of opportunistic hospital acquired infection and has been identified as an important emerging infection due to its high levels of antimicrobial resistance. multidrug resistant a. baumannii has risen rapidly in vietnam, where colistin is becoming the drug of last resort for many infections. in this study we generated spontaneous colistin resistant progeny (up to >256 μg/μl) from four colistin susceptible vietnamese isolates and one susceptible refere ... | 2016 | 27329501 |
structural analysis and biological toxicity of aflatoxins b1 and b2 degradation products following detoxification by ocimum basilicum and cassia fistula aqueous extracts. | this study showed the comparison between ocimum basilicum and cassia fistula (leaves and branch) aqueous extracts for their ability to detoxify of aflatoxins b1 and b2 (afb1; 100 μg l(-1) and afb2; 50 μg l(-1)) by in vitro assays and decontamination studies. results indicated that o. basilicum leaves extract was found to be highly significant (p < 0.05) in degrading afb1 and afb2, i.e., 90.4 and 88.6%, respectively. however, o. basilicum branch, c. fistula leaves and branch extracts proved to be ... | 2016 | 27471501 |
crystal structure of sgcj, an ntf2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic c-1027. | comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. here we report the crystal structures of sgcj and its homologue ncs-orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. gene inactivation in vivo establishes that sgcj is required for c-1027 production in streptomyces globisporus. sgcj and ncs-orf16 share a common struct ... | 2016 | 27406907 |
sublethal concentrations of antibiotics cause shift to anaerobic metabolism in listeria monocytogenes and induce phenotypes linked to antibiotic tolerance. | the human pathogenic bacterium listeria monocytogenes is exposed to antibiotics both during clinical treatment and in its saprophytic lifestyle. as one of the keys to successful treatment is continued antibiotic sensitivity, the purpose of this study was to determine if exposure to sublethal antibiotic concentrations would affect the bacterial physiology and induce antibiotic tolerance. transcriptomic analyses demonstrated that each of the four antibiotics tested caused an antibiotic-specific ge ... | 2016 | 27462313 |
mcsm-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. | the ability to predict how a mutation affects ligand binding is an essential step in understanding, anticipating and improving the design of new treatments for drug resistance, and in understanding genetic diseases. here we present mcsm-lig, a structure-guided computational approach for quantifying the effects of single-point missense mutations on affinities of small molecules for proteins. mcsm-lig uses graph-based signatures to represent the wild-type environment of mutations, and small-molecu ... | 2016 | 27384129 |
control of fluxes in metabolic networks. | understanding the control of large-scale metabolic networks is central to biology and medicine. however, existing approaches either require specifying a cellular objective or can only be used for small networks. we introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. we identify the driver reactions facilitating control of ... | 2016 | 27197218 |
replisome assembly at bacterial chromosomes and iteron plasmids. | the proper initiation and occurrence of dna synthesis depends on the formation and rearrangements of nucleoprotein complexes within the origin of dna replication. in this review article, we present the current knowledge on the molecular mechanism of replication complex assembly at the origin of bacterial chromosome and plasmid replicon containing direct repeats (iterons) within the origin sequence. we describe recent findings on chromosomal and plasmid replication initiators, dnaa and rep protei ... | 2016 | 27563644 |
overexpression of transport proteins improves the production of 5-aminovalerate from l-lysine in escherichia coli. | bacterial transporters mediate the exchanges between intracellular and extracellular environments. modification of transport route could be applied to speed up the metabolic reactions and promote the production of aimed compounds. herein, lysine 2-monooxygenase (davb) and δ-aminovaleramidase (dava) were co-expressed in escherichia coli bl21(de3) to produce nylon-5 monomer 5-aminovalerate from l-lysine. then, pp2911 (4-aminobutyrate transporter in pseudomonas putida) and lysp (the lysine specific ... | 2016 | 27510748 |
modeling central metabolism and energy biosynthesis across microbial life. | automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (etc). further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. | 2016 | 27502787 |
expression of a grapevine nac transcription factor gene is induced in response to powdery mildew colonization in salicylic acid-independent manner. | tissue colonization by grape powdery mildew (pm) pathogen erysiphe necator (schw.) burr triggers a major remodeling of the transcriptome in the susceptible grapevine vitis vinifera l. while changes in the expression of many genes bear the signature of salicylic acid (sa) mediated regulation, the breadth of pm-induced changes suggests the involvement of additional regulatory networks. to explore pm-associated gene regulation mediated by other sa-independent systems, we designed a microarray exper ... | 2016 | 27488171 |
new family of biosensors for monitoring btx in aquatic and edaphic environments. | benzene, toluene, ethylbenzene and xylenes (btex) contamination is a serious threat to public health and the environment, and therefore, there is an urgent need to detect its presence in nature. the use of whole-cell reporters is an efficient, easy-to-use and low-cost approach to detect and follow contaminants outside specialized laboratories; this is especially important in oil spills that are frequent in marine environments. the aim of this study is the construction of a bioreporter system and ... | 2016 | 27484951 |
flra, flrb and flrc regulate adhesion by controlling the expression of critical virulence genes in vibrio alginolyticus. | adhesion is an important virulence trait of vibrio alginolyticus. bacterial adhesion is influenced by environmental conditions; however, the molecular mechanism underlying this effect remains unknown. the expression levels of flra, flrb and flrc were significantly downregulated in adhesion-deficient v. alginolyticus strains cultured under cu(2+), pb(2+), hg(2+) and low-ph stresses. silencing these genes led to deficiencies in adhesion, motility, flagellar assembly, biofilm formation and exopolys ... | 2016 | 27485498 |
mapping the patent landscape of synthetic biology for fine chemical production pathways. | a goal of synthetic biology bio-foundries is to innovate through an iterative design/build/test/learn pipeline. in assessing the value of new chemical production routes, the intellectual property (ip) novelty of the pathway is important. exploratory studies can be carried using knowledge of the patent/ip landscape for synthetic biology and metabolic engineering. in this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable ... | 2016 | 27489206 |