Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| effect of heavy-metal-resistant bacteria on enhanced metal uptake and translocation of the cu-tolerant plant, elsholtzia splendens. | a hydroponics trial was employed to study the effects of pseudomonas putida cz1 (cz1), a heavy-metal-resistant bacterial strain isolated from the rhizosphere of elsholtzia splendens (e. splendens), on the uptake and translocation of copper (cu) in e. splendens. significant promotion of plant growth coupled with the obvious plant-growth-promoting (pgp) characters of the bacteria suggested that cz1 would be a plant-growth-promoting rhizobacterium (pgpr) to e. splendens under cu stress condition. t ... | 2015 | 25510610 |
| simultaneous detection of major blackleg and soft rot bacterial pathogens in potato by multiplex polymerase chain reaction. | a multiplex polymerase chain reaction (pcr) assay for simultaneous, fast and reliable detection of the main soft rot and blackleg potato pathogens in europe has been developed. it utilises three pairs of primers and enables detection of three groups of pectinolytic bacteria frequently found in potato, namely: pectobacterium atrosepticum, pectobacterium carotovorum subsp. carotovorum together with pectobacterium wasabiae and dickeya spp. in a multiplex pcr assay. in studies with axenic cultures o ... | 2014 | 25506085 |
| the ethylene response factor pti5 contributes to potato aphid resistance in tomato independent of ethylene signalling. | ethylene response factors (erfs) comprise a large family of transcription factors that regulate numerous biological processes including growth, development, and response to environmental stresses. here, we report that pti5, an erf in tomato [solanum lycopersicum (linnaeus)] was transcriptionally upregulated in response to the potato aphid macrosiphum euphorbiae (thomas), and contributed to plant defences that limited the population growth of this phloem-feeding insect. virus-induced gene silenci ... | 2014 | 25504643 |
| the ethylene response factor pti5 contributes to potato aphid resistance in tomato independent of ethylene signalling. | ethylene response factors (erfs) comprise a large family of transcription factors that regulate numerous biological processes including growth, development, and response to environmental stresses. here, we report that pti5, an erf in tomato [solanum lycopersicum (linnaeus)] was transcriptionally upregulated in response to the potato aphid macrosiphum euphorbiae (thomas), and contributed to plant defences that limited the population growth of this phloem-feeding insect. virus-induced gene silenci ... | 2014 | 25504643 |
| sensor kinase pa4398 modulates swarming motility and biofilm formation in pseudomonas aeruginosa pa14. | pseudomonas aeruginosa is an opportunistic human pathogen that is able to sense and adapt to numerous environmental stimuli by the use of transcriptional regulators, including two-component regulatory systems. in this study, we demonstrate that the sensor kinase pa4398 is involved in the regulation of swarming motility and biofilm formation in p. aeruginosa pa14. apa4398 mutant strain was considerably impaired in swarming motility, while biofilm formation was increased by approximately 2-fold. t ... | 2015 | 25501476 |
| is there a common water-activity limit for the three domains of life? | archaea and bacteria constitute a majority of life systems on earth but have long been considered inferior to eukarya in terms of solute tolerance. whereas the most halophilic prokaryotes are known for an ability to multiply at saturated nacl (water activity (a(w)) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a(w). here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for halanaerobium ... | 2014 | 25500507 |
| is there a common water-activity limit for the three domains of life? | archaea and bacteria constitute a majority of life systems on earth but have long been considered inferior to eukarya in terms of solute tolerance. whereas the most halophilic prokaryotes are known for an ability to multiply at saturated nacl (water activity (a(w)) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a(w). here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for halanaerobium ... | 2014 | 25500507 |
| molecular mechanisms of the microsomal mixed function oxidases and biological and pathological implications. | the cytochrome p450 mixed function oxidase enzymes play a major role in the metabolism of important endogenous substrates as well as in the biotransformation of xenobiotics. the liver p450 system is the most active in metabolism of exogenous substrates. this review briefly describes the liver p450 (cyp) mixed function oxidase system with respect to its enzymatic components and functions. electron transfer by the nadph-p450 oxidoreductase is required for reduction of the heme of p450, necessary f ... | 2014 | 25498968 |
| molecular mechanisms of the microsomal mixed function oxidases and biological and pathological implications. | the cytochrome p450 mixed function oxidase enzymes play a major role in the metabolism of important endogenous substrates as well as in the biotransformation of xenobiotics. the liver p450 system is the most active in metabolism of exogenous substrates. this review briefly describes the liver p450 (cyp) mixed function oxidase system with respect to its enzymatic components and functions. electron transfer by the nadph-p450 oxidoreductase is required for reduction of the heme of p450, necessary f ... | 2014 | 25498968 |
| fringe-controlled biodegradation under dynamic conditions: quasi 2-d flow-through experiments and reactive-transport modeling. | biodegradation in contaminated aquifers has been shown to be most pronounced at the fringe of contaminant plumes, where mixing of contaminated water and ambient groundwater, containing dissolved electron acceptors, stimulates microbial activity. while physical mixing of contaminant and electron acceptor by transverse dispersion has been shown to be the major bottleneck for biodegradation in steady-state plumes, so far little is known on the effect of flow and transport dynamics (caused, e.g., by ... | 2015 | 25496820 |
| development of bio-based fine chemical production through synthetic bioengineering. | fine chemicals that are physiologically active, such as pharmaceuticals, cosmetics, nutritional supplements, flavoring agents as well as additives for foods, feed, and fertilizer are produced by enzymatically or through microbial fermentation. the identification of enzymes that catalyze the target reaction makes possible the enzymatic synthesis of the desired fine chemical. the genes encoding these enzymes are then introduced into suitable microbial hosts that are cultured with inexpensive, natu ... | 2014 | 25494636 |
| identification of pseudomonas fluorescens chemotaxis sensory proteins for malate, succinate, and fumarate, and their involvement in root colonization. | pseudomonas fluorescens pf0-1 exhibited chemotactic responses to l-malate, succinate, and fumarate. we constructed a plasmid library of 37 methyl-accepting chemotaxis protein (mcp) genes of p. fluorescens pf0-1. to identify a mcp for l-malate, the plasmid library was screened using the pa2652 mutant of pseudomonas aeruginosa pao1, a mutant defective in chemotaxis to l-malate. the introduction of pfl01_0728 and pfl01_3768 genes restored the ability of the pa2652 mutant to respond to l-malate. the ... | 2014 | 25491753 |
| a chromosomally encoded t7 rna polymerase-dependent gene expression system for corynebacterium glutamicum: construction and comparative evaluation at the single-cell level. | corynebacterium glutamicum has become a favourite model organism in white biotechnology. nevertheless, only few systems for the regulatable (over)expression of homologous and heterologous genes are currently available, all of which are based on the endogenous rna polymerase. in this study, we developed an isopropyl-β-d-1-thiogalactopyranosid (iptg)-inducible t7 expression system in the prophage-free strain c. glutamicum mb001. for this purpose, part of the de3 region of escherichia coli bl21(de3 ... | 2014 | 25488698 |
| a chromosomally encoded t7 rna polymerase-dependent gene expression system for corynebacterium glutamicum: construction and comparative evaluation at the single-cell level. | corynebacterium glutamicum has become a favourite model organism in white biotechnology. nevertheless, only few systems for the regulatable (over)expression of homologous and heterologous genes are currently available, all of which are based on the endogenous rna polymerase. in this study, we developed an isopropyl-β-d-1-thiogalactopyranosid (iptg)-inducible t7 expression system in the prophage-free strain c. glutamicum mb001. for this purpose, part of the de3 region of escherichia coli bl21(de3 ... | 2014 | 25488698 |
| characterization of the ability to form biofilms by plant-associated pseudomonas species. | successful colonization is the initial step for plant-bacteria interactions; therefore, the development of strategies to improve adherence to plant surfaces is critically important for environmental bacteria. biofilm formation is thought to be one such strategy for bacteria to establish stable colonization on inert and living surfaces. although biofilms play potential roles in enabling persistent bacterial colonization, little attention has been paid to biofilms formed by plant-associated bacter ... | 2015 | 25487118 |
| the ppui-rsal-ppur quorum-sensing system regulates cellular motility, pectate lyase activity, and virulence in potato opportunistic pathogen pseudomonas sp. stflb209. | pseudomonas sp. stflb209 was isolated from potato leaf as an n-acylhomoserine lactone (ahl)-producing bacterium and showed a close phylogenetic relationship with p. cichorii, a known plant pathogen. although there are no reports of potato disease caused by pseudomonads in japan, stflb209 was pathogenic to potato leaf. in this study, we reveal the complete genome sequence of stflb209, and show that the strain possesses a ppui-rsal-ppur quorum-sensing system, the sequence of which shares a high si ... | 2015 | 25485871 |
| tetracycline resistance genes in campylobacter jejuni and c. coli isolated from poultry carcasses. | campylobacter is one of the leading bacterial species causing foodborne illnesses in humans. antimicrobial agents have been extensively used for treatment of campylobacter infections; but in the recent years, both animal and human isolates of this bacterium have shown resistance to several antibiotics such as tetracycline. | 2014 | 25485062 |
| glycan moiety of flagellin in acidovorax avenae k1 prevents the recognition by rice that causes the induction of immune responses. | abstract recognition of pathogen-associated molecular patterns (pamps) such as flagellin, a main component of the bacterial flagellum, constitutes the first layer of plant immunity and is referred to as pamp-triggered immunity (pti). the rice avirulent n1141 strain of gram-negative phytopathogenic bacterium, acidovorax avenae, induces pti including h2o2 generation, while flagellin from the rice virulent k1 strain of a. avenae does not induce these immune responses. mass spectrometry analyses rev ... | 2014 | 25482815 |
| bioremediation of dyes by fungi isolated from contaminated dye effluent sites for bio-usability. | biodegradation and detoxification of dyes, malachite green, nigrosin and basic fuchsin have been carried out using two fungal isolates aspergillus niger, and phanerochaete chrysosporium, isolated from dye effluent soil. three methods were selected for biodegradation, viz. agar overlay and liquid media methods; stationary and shaking conditions at 25 °c. aspergillus niger recorded maximum decolorization of the dye basic fuchsin (81.85%) followed by nigrosin (77.47%), malachite green (72.77%) and ... | 2014 | 25477943 |
| production of humic substances through coal-solubilizing bacteria. | in this paper, the production of humic substances (hs) through the bacterial solubilization of low rank coal (lrc) was evaluated. the evaluation was carried out by 19 bacterial strains isolated in microenvironments with high contents of coal wastes. the biotransformed lrc and the hs produced were quantified in vitro in a liquid growth medium. the humic acids (ha) obtained from the most active bacterial strain were characterized via elemental composition (c, h, n, o), ir analyses, and the e4/e6 r ... | 2014 | 25477925 |
| draft genome sequence of the versatile alkane-degrading bacterium aquabacterium sp. strain nj1. | the draft genome sequence of a soil bacterium, aquabacterium sp. strain nj1, capable of utilizing both liquid and solid alkanes, was deciphered. this is the first report of an aquabacterium genome sequence. | 2014 | 25477416 |
| draft genome sequence of the nicotinate-metabolizing soil bacterium bacillus niacini dsm 2923. | bacillus niacini is a member of a small yet diverse group of bacteria able to catabolize nicotinic acid. we report here the availability of a draft genome for b. niacini, which we will use to understand the evolution of its namesake phenotype, which appears to be unique among the species in its phylogenetic neighborhood. | 2014 | 25477409 |
| site-specific fluorescence dynamics in an rna 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function. | rna thermometers control the translation of several heat shock and virulence genes by their temperature-sensitive structural transitions. changes in the structure and dynamics of minirose rna, which regulates translation in the temperature range of 20-45°c, were studied by site specifically replacing seven adenine residues with the fluorescent analog, 2-aminopurine (2-ap), one at a time. dynamic fluorescence observables of 2-ap-labeled rnas were compared in their free versus ribosome-bound state ... | 2014 | 25477380 |
| site-specific fluorescence dynamics in an rna 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function. | rna thermometers control the translation of several heat shock and virulence genes by their temperature-sensitive structural transitions. changes in the structure and dynamics of minirose rna, which regulates translation in the temperature range of 20-45°c, were studied by site specifically replacing seven adenine residues with the fluorescent analog, 2-aminopurine (2-ap), one at a time. dynamic fluorescence observables of 2-ap-labeled rnas were compared in their free versus ribosome-bound state ... | 2014 | 25477380 |
| conservation analysis of the cydx protein yields insights into small protein identification and evolution. | the reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. the 37 amino acid cydx protein in escherichia coli is a member of the cytochrome bd oxidase complex, an enzyme found throughout eubacteria. to investigate the extent of cydx conservation and prevalence and evaluate different methods of small protein homologue identification, we surveyed 1095 eubacteria species for the presence of the small protein. | 2014 | 25475368 |
| antimicrobial activities of commercial essential oils and their components against food-borne pathogens and food spoilage bacteria. | this study was undertaken to determine the in vitro antimicrobial activities of 15 commercial essential oils and their main components in order to pre-select candidates for potential application in highly perishable food preservation. the antibacterial effects against food-borne pathogenic bacteria (listeria monocytogenes, salmonella typhimurium, and enterohemorrhagic escherichia coli o157:h7) and food spoilage bacteria (brochothrix thermosphacta and pseudomonas fluorescens) were tested using pa ... | 2014 | 25473498 |
| bacteria dialog with santa rosalia: are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions? | since the landmark santa rosalia paper by hutchinson, niche theory addresses the determinants of biodiversity in terms of both environmental and biological aspects. disentangling the role of habitat filtering and interactions with other species is critical for understanding microbial ecology. macroscopic biogeography explores hypothetical ecological interactions through the analysis of species associations. these methods have started to be incorporated into microbial ecology relatively recently, ... | 2014 | 25472003 |
| de novo production of the monoterpenoid geranic acid by metabolically engineered pseudomonas putida. | production of monoterpenoids as valuable chemicals using recombinant microbes is a growing field of interest. unfortunately, antimicrobial activity of most monoterpenoids hampers a wide application of microorganisms for their production. strains of pseudomonas putida, a fast growing and metabolically versatile bacterium, often show an outstanding high tolerance towards organic solvents and other toxic compounds. therefore, pseudomonas putida constitutes an attractive alternative host in comparis ... | 2014 | 25471523 |
| the interplay between cell wall mechanical properties and the cell cycle in staphylococcus aureus. | the nanoscale mechanical properties of live staphylococcus aureus cells during different phases of growth were studied by atomic force microscopy. indentation to different depths provided access to both local cell wall mechanical properties and whole-cell properties, including a component related to cell turgor pressure. local cell wall properties were found to change in a characteristic manner throughout the division cycle. splitting of the cell into two daughter cells followed a local softenin ... | 2014 | 25468333 |
| phage therapy as an approach to prevent vibrio anguillarum infections in fish larvae production. | fish larvae in aquaculture have high mortality rates due to pathogenic bacteria, especially the vibrio species, and ineffective prophylactic strategies. vaccination is not feasible in larvae and antibiotics have reduced efficacy against multidrug resistant bacteria. a novel approach to controlling vibrio infections in aquaculture is needed. the potential of phage therapy to combat vibriosis in fish larvae production has not yet been examined. we describe the isolation and characterization of two ... | 2014 | 25464504 |
| ner enzymes maintain genome integrity and suppress homologous recombination in the absence of exogenously induced dna damage in pseudomonas putida. | in addition to its prominence in producing genetic diversity in bacterial species, homologous recombination (hr) plays a key role in dna repair and damage tolerance. the frequency of hr depends on several factors, including the efficiency of dna repair systems as hr is involved in recovery of replication forks perturbed by dna damage. nucleotide excision repair (ner) is one of the major dna repair pathways involved in repair of a broad range of dna lesions generally induced by exogenous chemical ... | 2015 | 25463394 |
| contribution of arbuscular mycorrhizal fungi and/or bacteria to enhancing plant drought tolerance under natural soil conditions: effectiveness of autochthonous or allochthonous strains. | autochthonous microorganisms [a consortium of arbuscular-mycorrhizal (am) fungi and bacillus thuringiensis (bt)] were assayed and compared to rhizophagus intraradices (ri), bacillus megaterium (bm) or pseudomonas putida (psp) and non-inoculation on trifolium repens in a natural arid soil under drought conditions. the autochthonous bacteria bt and the allochthonous bacteria psp increased nutrients and the relative water content and decreased stomatal conductance, electrolyte leakage, proline and ... | 2015 | 25462971 |
| integrated micro-biochemical approach for phytoremediation of cadmium and zinc contaminated soils. | the integrated potential of oilcake manure (om), elemental sulphur (s(0)), glomus fasciculatum and pseudomonas putida by growing helianthus annuus l for phytoremediation of cadmium and zinc contaminated soils was investigated under pot experiment. the integrated treatment (2.5 g kg(-1) om, 0.8 g kg(-1) s(0) and co-inoculation with g. fasciculatum and p. putida promoted the dry biomass of the plant. the treatment was feasible for enhanced cadmium accumulation up to 6.56 and 5.25 mg kg(-1) and zin ... | 2015 | 25450919 |
| a moonlighting function of mycobacterium smegmatis ku in zinc homeostasis? | ku protein participates in dna double-strand break repair via the nonhomologous end-joining pathway. the three-dimensional structure of eukaryotic ku reveals a central core consisting of a β-barrel domain and pillar and bridge regions that combine to form a ring-like structure that encircles dna. homologs of ku are encoded by a subset of bacterial species, and they are predicted to conserve this core domain. in addition, the bridge region of ku from some bacteria is predicted from homology model ... | 2014 | 25450225 |
| a moonlighting function of mycobacterium smegmatis ku in zinc homeostasis? | ku protein participates in dna double-strand break repair via the nonhomologous end-joining pathway. the three-dimensional structure of eukaryotic ku reveals a central core consisting of a β-barrel domain and pillar and bridge regions that combine to form a ring-like structure that encircles dna. homologs of ku are encoded by a subset of bacterial species, and they are predicted to conserve this core domain. in addition, the bridge region of ku from some bacteria is predicted from homology model ... | 2014 | 25450225 |
| a novel d-mandelate dehydrogenase used in three-enzyme cascade reaction for highly efficient synthesis of non-natural chiral amino acids. | a novel nad(+)-dependent d-mandelate dehydrogenase was identified from lactobacillus brevis (lbdmdh). after purified to homogeneity, the optimum ph and temperature for oxidation of d-mandelate were ph 10.0 and 40 °c, and the km and kcat were 1.1 mm and 355 s(-1) respectively. employing the lbdmdh together with a mandelate racemase from pseudomonas putida and a leucine dehydrogenase (esleudh) from exiguobacterium sibiricum, we established a three-step one-pot domino reaction system for preparing ... | 2015 | 25449542 |
| enhancement of protocatechuate decarboxylase activity for the effective production of muconate from lignin-related aromatic compounds. | the decarboxylation reaction of protocatechuate has been described as a bottleneck and a rate-limiting step in cis,cis-muconate (ccma) bioproduction from renewable feedstocks such as sugar. because sugars are already in high demand in the development of many bio-based products, our work focuses on improving protocatechuate decarboxylase (pdc) activity and ccma production in particular, from lignin-related aromatic compounds. we previously had transformed an escherichia coli strain using aroy, wh ... | 2014 | 25449108 |
| development of recombinant methioninase to target the general cancer-specific metabolic defect of methionine dependence: a 40-year odyssey. | all tested cancer cell types are methionine dependent in that the cells arrest and eventually die when deprived of methionine, a condition that is generally nontoxic to normal cells. methionine dependence is the only known general metabolic defect in cancer. methionine-deprived cancer cells arrest at the s/g2 phase, an unusual position for cell cycle arrest. in order to exploit the cancer-specific metabolic defect of methionine dependence, methioninases were developed. | 2015 | 25439528 |
| an intimate link: two-component signal transduction systems and metal transport systems in bacteria. | bacteria have evolved various strategies to contend with high concentrations of environmental heavy metal ions for rapid, adaptive responses to maintain cell viability. evidence gathered in the past two decades suggests that bacterial two-component signal transduction systems (tcstss) are intimately involved in monitoring cation accumulation, and can regulate the expression of related metabolic and virulence genes to elicit adaptive responses to changes in the concentration of these ions. using ... | 2014 | 25437189 |
| global genome comparative analysis reveals insights of resistome and life-style adaptation of pseudomonas putida strain t2-2 in oral cavity. | most pseudomonas putida strains are environmental microorganisms exhibiting a wide range of metabolic capability but certain strains have been reported as rare opportunistic pathogens and some emerged as multidrug resistant p. putida. this study aimed to assess the drug resistance profile of, via whole genome analysis, p. putida strain t2-2 isolated from oral cavity. at the same time, we also compared the nonenvironmental strain with environmentally isolated p. putida. in silico comparative geno ... | 2014 | 25436236 |
| zinc oxide nanoparticles for revolutionizing agriculture: synthesis and applications. | nanotechnology is the most innovative field of 21st century. extensive research is going on for commercializing nanoproducts throughout the world. due to their unique properties, nanoparticles have gained considerable importance compared to bulk counterparts. among other metal nanoparticles, zinc oxide nanoparticles are very much important due to their utilization in gas sensors, biosensors, cosmetics, drug-delivery systems, and so forth. zinc oxide nanoparticles (zno nps) also have remarkable o ... | 2014 | 25436235 |
| 1-aminocyclopropane-1-carboxylic acid (acc) in plants: more than just the precursor of ethylene! | ethylene is a simple two carbon atom molecule with profound effects on plants. there are quite a few review papers covering all aspects of ethylene biology in plants, including its biosynthesis, signaling and physiology. this is merely a logical consequence of the fascinating and pleiotropic nature of this gaseous plant hormone. its biochemical precursor, 1-aminocyclopropane-1-carboxylic acid (acc) is also a fairly simple molecule, but perhaps its role in plant biology is seriously underestimate ... | 2014 | 25426135 |
| plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. | extremely cold environments are a challenge for all organisms. they are mostly inhabited by psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the cold. such harsh environments are often highly vulnerable to the influence of external factors and may undergo frequent dynamic changes. the rapid adjustment of bacteria to changing environmental conditions is crucial for their survival. such "short-term" evolution is often enabled by plasmids-extrachromosomal rep ... | 2014 | 25426110 |
| flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks. | the prokaryotic pangenome partitions genes into core and dispensable genes. the order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. based on data from 30 species, including 425 genomes from six phyla, we grouped core genes into syntenic blocks in the context of a pangenome according to their stabili ... | 2014 | 25425232 |
| constrictor: constraint modification provides insight into design of biochemical networks. | advances in computational methods that allow for exploration of the combinatorial mutation space are needed to realize the potential of synthetic biology based strain engineering efforts. here, we present constrictor, a computational framework that uses flux balance analysis (fba) to analyze inhibitory effects of genetic mutations on the performance of biochemical networks. constrictor identifies engineering interventions by classifying the reactions in the metabolic model depending on the exten ... | 2014 | 25422896 |
| david t. gibson: from biodegradation to biocatalysis. | 2014 | 25422435 | |
| functional type 1 secretion system involved in legionella pneumophila virulence. | legionella pneumophila is a gram-negative pathogen found mainly in water, either in a free-living form or within infected protozoans, where it replicates. this bacterium can also infect humans by inhalation of contaminated aerosols, causing a severe form of pneumonia called legionellosis or legionnaires' disease. the involvement of type ii and iv secretion systems in the virulence of l. pneumophila is now well documented. despite bioinformatic studies showing that a type i secretion system (t1ss ... | 2014 | 25422301 |
| functional type 1 secretion system involved in legionella pneumophila virulence. | legionella pneumophila is a gram-negative pathogen found mainly in water, either in a free-living form or within infected protozoans, where it replicates. this bacterium can also infect humans by inhalation of contaminated aerosols, causing a severe form of pneumonia called legionellosis or legionnaires' disease. the involvement of type ii and iv secretion systems in the virulence of l. pneumophila is now well documented. despite bioinformatic studies showing that a type i secretion system (t1ss ... | 2014 | 25422301 |
| isolation of vim-2-producing pseudomonas monteilii clinical strains disseminated in a tertiary hospital in northern spain. | we describe here the occurrence of blavim-2 in 10 carbapenem-resistant pseudomonas monteilii strains isolated from different clinical samples from patients at the university hospital marqués de valdecilla in northern spain. all the blavim-2-harboring p. monteilii isolates possessed a class 1 integron, with the cassette array [inti1_blavim-2_aac(6')-ib_qaceδ1_sul1]. our results show the emergence of vim-2-producing multidrug-resistant species other than pseudomonas aeruginosa or pseudomonas putid ... | 2015 | 25421471 |
| enhanced 3-methylcatechol production by pseudomonas putida tode1 in a two-phase biotransformation system. | in this study, genetically engineered pseudomonas putida tode1 served as a biocatalyst for the bioproduction of valuable 3-methylcatechol (3mc) from toluene in an aqueous-organic two-phase system. the two-phase system was used as an approach to increase the biocatalyst efficiency. among the organic solvent tested, n-decanol offered several benefits including having the highest partitioning of 3mc, with a high 3mc yield and low cell toxicity. the effect of media supplementation with carbon/energy ... | 2014 | 25420423 |
| complete genome sequence analysis of two pseudomonas plecoglossicida phages, potential therapeutic agents. | pseudomonas plecoglossicida is a lethal pathogen of ayu (plecoglossus altivelis) in japan and is responsible for substantial economic costs to ayu culture. previously, we demonstrated the efficacy of phage therapy against p. plecoglossicida infection using two lytic phages (pppw-3 and pppw-4) (s. c. park, i. shimamura, m. fukunaga, k. mori, and t. nakai, appl environ microbiol 66:1416-1422, 2000, http://dx.doi.org/10.1128/aem.66.4.1416-1422.2000; s. c. park and t. nakai, dis aquat org 53:33-39, ... | 2015 | 25416766 |
| multi-drug resistance, inappropriate initial antibiotic therapy and mortality in gram-negative severe sepsis and septic shock: a retrospective cohort study. | the impact of in vitro resistance on initially appropriate antibiotic therapy (iaat) remains unclear. we elucidated the relationship between non-iaat and mortality, and between iaat and multi-drug resistance (mdr) in sepsis due to gram-negative bacteremia (gns). | 2014 | 25412897 |
| comparison of chromogenic media for recovery of carbapenemase-producing enterobacteriaceae (cpe) and evaluation of cpe prevalence at a tertiary care academic medical center. | we evaluated the performance characteristics of chromid carba and hardychrom carbapenemase for the detection of carbapenemase-producing enterobacteriaceae (cpe). a cpe prevalence study was conducted using chromid carba; this demonstrated that in low-prevalence settings, cpe screening agars may lack specificity, and confirmation of putative isolates is necessary. | 2014 | 25411175 |
| comparison of chromogenic media for recovery of carbapenemase-producing enterobacteriaceae (cpe) and evaluation of cpe prevalence at a tertiary care academic medical center. | we evaluated the performance characteristics of chromid carba and hardychrom carbapenemase for the detection of carbapenemase-producing enterobacteriaceae (cpe). a cpe prevalence study was conducted using chromid carba; this demonstrated that in low-prevalence settings, cpe screening agars may lack specificity, and confirmation of putative isolates is necessary. | 2014 | 25411175 |
| adsorption studies of the gram-negative bacteria onto nanostructured silicon carbide. | in this study, we demonstrated a significant adsorption of pseudomonas putida bacteria onto aggregates of nanofibers (nfsic) and nanorods (nrsic) of silicon carbide (sic) in aqueous suspensions. langmuir and freundlich isotherms were used to quantify adsorption affinities. it was found that adsorption of the bacteria strongly depended on the structure of the silicon carbide and the ph of the aqueous solution, which affected the isoelectric point of both the silicon carbide and the bacterial cell ... | 2014 | 25410802 |
| adsorption studies of the gram-negative bacteria onto nanostructured silicon carbide. | in this study, we demonstrated a significant adsorption of pseudomonas putida bacteria onto aggregates of nanofibers (nfsic) and nanorods (nrsic) of silicon carbide (sic) in aqueous suspensions. langmuir and freundlich isotherms were used to quantify adsorption affinities. it was found that adsorption of the bacteria strongly depended on the structure of the silicon carbide and the ph of the aqueous solution, which affected the isoelectric point of both the silicon carbide and the bacterial cell ... | 2014 | 25410802 |
| quantitative analysis of chemotaxis towards toluene by pseudomonas putida in a convection-free microfluidic device. | chemotaxis has been shown to be beneficial for the migration of soil-inhabiting bacteria towards industrial chemical pollutants, which they degrade. many studies have demonstrated the importance of this microbial property under various circumstances; however, few quantitative analyses have been undertaken to measure the two essential parameters that characterize the chemotaxis of bioremediation bacteria: the chemotactic sensitivity coefficient χ(0) and the chemotactic receptor constant k(c). the ... | 2015 | 25408100 |
| omics profiles used to evaluate the gene expression of exiguobacterium antarcticum b7 during cold adaptation. | exiguobacterium antarcticum strain b7 is a gram-positive psychrotrophic bacterial species isolated in antarctica. although this bacteria has been poorly studied, its genome has already been sequenced. therefore, it is an appropriate model for the study of thermal adaptation. in the present study, we analyzed the transcriptomes and proteomes of e. antarcticum b7 grown at 0°c and 37°c by solid rna-seq, ion torrent rna-seq and two-dimensional difference gel electrophoresis tandem mass spectrometry ... | 2014 | 25407400 |
| convergent bacterial microbiotas in the fungal agricultural systems of insects. | the ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating conv ... | 2014 | 25406380 |
| structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis. | catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ... | 2014 | 25406313 |
| structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis. | catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ... | 2014 | 25406313 |
| reclassification of bacteriovorax marinus as halobacteriovorax marinus gen. nov., comb. nov. and bacteriovorax litoralis as halobacteriovorax litoralis comb. nov.; description of halobacteriovoraceae fam. nov. in the class deltaproteobacteria. | the taxonomic status of saltwater bdellovibrio-like prokaryotic predators has been revised to assign species to halobacteriovorax gen. nov. a reclassification of bacteriovorax marinus as halobacteriovorax marinus comb. nov. (type strain atcc baa-682(t) = dsm 15412(t)) and bacteriovorax litoralis as halobacteriovorax litoralis comb. nov. (type strain atcc baa-684(t) = dsm 15409(t)) is proposed. this revision is necessary because a previous proposal to retain saltwater isolates as species of bacte ... | 2015 | 25406234 |
| comparative characterization of the lactimidomycin and iso-migrastatin biosynthetic machineries revealing unusual features for acyltransferase-less type i polyketide synthases and providing an opportunity to engineer new analogues. | lactimidomycin (ltm, 1) and iso-migrastatin (iso-mgs, 2) belong to the glutarimide-containing polyketide family of natural products. we previously cloned and characterized the mgs biosynthetic gene cluster from streptomyces platensis nrrl 18993. the iso-mgs biosynthetic machinery featured an acyltransferase (at)-less type i polyketide synthase (pks) and three tailoring enzymes (mgsijk). we now report cloning and characterization of the ltm biosynthetic gene cluster from streptomyces amphibiospor ... | 2014 | 25405956 |
| screening a strain of aspergillus niger and optimization of fermentation conditions for degradation of aflatoxin b₁. | aflatoxin b₁, a type of highly toxic mycotoxin produced by some species belonging to the aspergillus genus, such as aspergillus flavus and aspergillus parasiticus, is widely distributed in feed matrices. here, coumarin was used as the sole carbon source to screen microorganism strains that were isolated from types of feed ingredients. only one isolate (nd-1) was able to degrade aflatoxin b₁ after screening. nd-1 isolate, identified as a strain of aspergillus niger using phylogenetic analysis on ... | 2014 | 25401962 |
| biodegradation of variable-chain-length n-alkanes in rhodococcus opacus r7 and the involvement of an alkane hydroxylase system in the metabolism. | rhodococcus opacus r7 is a gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its versatile metabolism; indeed the strain is able to grow on naphthalene, o-xylene, and several long- and medium-chain n-alkanes. in this work we determined the degradation of n-alkanes in rhodococcus opacus r7 in presence of n-dodecane (c12), n-hexadecane (c16), n-eicosane (c20), n-tetracosane (c24) and the metabolic pathway in presence of c12. the consumption rate of c12 w ... | 2014 | 25401074 |
| subpopulation-proteomics reveal growth rate, but not cell cycling, as a major impact on protein composition in pseudomonas putida kt2440. | population heterogeneity occurring in industrial microbial bioprocesses is regarded as a putative effector causing performance loss in large scale. while the existence of subpopulations is a commonly accepted fact, their appearance and impact on process performance still remains rather unclear. during cell cycling, distinct subpopulations differing in cell division state and dna content appear which contribute individually to the efficiency of the bioprocess. to identify stressed or impaired sub ... | 2014 | 25401072 |
| genome features of pseudomonas putida ls46, a novel polyhydroxyalkanoate producer and its comparison with other p. putida strains. | a novel strain of pseudomonas putida ls46 was isolated from wastewater on the basis of its ability to synthesize medium chain-length polyhydroxyalkanoates (mcl-phas). p.putida ls46 was differentiated from other p.putida strains on the basis of cpn60 (ut). the complete genome of p.putida ls46 was sequenced and annotated. its chromosome is 5,86,2556 bp in size with gc ratio of 61.69. it is encoding 5316 genes, including 7 rrna genes and 76 trna genes. nucleotide sequence data of the complete p. pu ... | 2014 | 25401060 |
| evaluation of antibiotic effects on pseudomonas aeruginosa biofilm using raman spectroscopy and multivariate analysis. | we investigate the mode of action and classification of antibiotic agents (ceftazidime, patulin, and epigallocatechin gallate; egcg) on pseudomonas aeruginosa (p. aeruginosa) biofilm using raman spectroscopy with multivariate analysis, including support vector machine (svm) and principal component analysis (pca). this method allows for quantitative, label-free, non-invasive and rapid monitoring of biochemical changes in complex biofilm matrices with high sensitivity and specificity. in this stud ... | 2014 | 25401035 |
| bacterial bloodstream infections and antimicrobial susceptibility pattern in pediatric hematology/oncology patients after anticancer chemotherapy. | bloodstream infections in pediatric hematology and oncology represent a major problem worldwide, but this has not been studied in qatar. in this study, we investigated the burden of infection and the resistance pattern in the bacterial etiology, in the only tertiary pediatric hematology and oncology center in qatar. | 2014 | 25395866 |
| diversity of small rnas expressed in pseudomonas species. | rna sequencing (rna-seq) has revealed several hundreds of previously undetected small rnas (srnas) in all bacterial species investigated, including strains of pseudomonas aeruginosa, pseudomonas putida and pseudomonas syringae. nonetheless, only little is known about the extent of conservation of expressed srnas across strains and species. in this study, we have used rna-seq to identify srnas in p. putida dot-t1e and pseudomonas extremaustralis 14-3b. this is the first strain of p. extremaustral ... | 2015 | 25394275 |
| the complete alk sequences of rhodococcus erythropolis from lake baikal. | rhodococci are bacteria able to degrade a wide range of hydrocarbons, including the alkanes present in crude oil, due to alk genes in their genomes. | 2014 | 25392791 |
| the influence of biofilms in the biology of plasmids. | the field of plasmid biology has historically focused on bacteria growing in liquid culture. surface attached communities of bacterial biofilms have recently been understood to be the normal environment of bacteria in the natural world. thus, studies examining plasmid replication, maintenance, and transfer in biofilms are essential for a true understanding of bacterial plasmid biology. this chapter reviews the current knowledge of the interplay between bacterial biofilms and plasmids, focusing o ... | 2014 | 25392747 |
| cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics. | the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ... | 2014 | 25392417 |
| cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics. | the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ... | 2014 | 25392417 |
| seva 2.0: an update of the standard european vector architecture for de-/re-construction of bacterial functionalities. | the standard european vector architecture 2.0 database (seva-db 2.0, http://seva.cnb.csic.es) is an improved and expanded version of the platform released in 2013 (doi: 10.1093/nar/gks1119) aimed at assisting the choice of optimal genetic tools for de-constructing and re-constructing complex prokaryotic phenotypes. by adopting simple compositional rules, the seva standard facilitates combinations of functional dna segments that ease both the analysis and the engineering of diverse gram-negative ... | 2014 | 25392407 |
| seva 2.0: an update of the standard european vector architecture for de-/re-construction of bacterial functionalities. | the standard european vector architecture 2.0 database (seva-db 2.0, http://seva.cnb.csic.es) is an improved and expanded version of the platform released in 2013 (doi: 10.1093/nar/gks1119) aimed at assisting the choice of optimal genetic tools for de-constructing and re-constructing complex prokaryotic phenotypes. by adopting simple compositional rules, the seva standard facilitates combinations of functional dna segments that ease both the analysis and the engineering of diverse gram-negative ... | 2014 | 25392407 |
| new transposon tools tailored for metabolic engineering of gram-negative microbial cell factories. | re-programming microorganisms to modify their existing functions and/or to bestow bacteria with entirely new-to-nature tasks have largely relied so far on specialized molecular biology tools. such endeavors are not only relevant in the burgeoning metabolic engineering arena but also instrumental to explore the functioning of complex regulatory networks from a fundamental point of view. à la carte modification of bacterial genomes thus calls for novel tools to make genetic manipulations easier. w ... | 2014 | 25389526 |
| interplay of physical mechanisms and biofilm processes: review of microfluidic methods. | bacteria in natural and artificial environments often reside in self-organized, integrated communities known as biofilms. biofilms are highly structured entities consisting of bacterial cells embedded in a matrix of self-produced extracellular polymeric substances (eps). the eps matrix acts like a biological 'glue' enabling microbes to adhere to and colonize a wide range of surfaces. once integrated into biofilms, bacterial cells can withstand various forms of stress such as antibiotics, hydrody ... | 2015 | 25385289 |
| the c-di-gmp phosphodiesterase bifa is involved in the virulence of bacteria from the pseudomonas syringae complex. | in a recent screen for novel virulence factors involved in the interaction between pseudomonas savastanoi pv. savastanoi and the olive tree, a mutant was selected that contained a transposon insertion in a putative cyclic diguanylate (c-di-gmp) phosphodiesterase-encoding gene. this gene displayed high similarity to bifa of pseudomonas aeruginosa and pseudomonas putida. here, we examined the role of bifa in free-living and virulence-related phenotypes of two bacterial plant pathogens in the pseud ... | 2015 | 25385023 |
| proline metabolism increases katg expression and oxidative stress resistance in escherichia coli. | the oxidation of l-proline to glutamate in gram-negative bacteria is catalyzed by the proline utilization a (puta) flavoenzyme, which contains proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase domains in a single polypeptide. previous studies have suggested that aside from providing energy, proline metabolism influences oxidative stress resistance in different organisms. to explore this potential role and the mechanism, we characterized the oxidative stress resis ... | 2014 | 25384482 |
| proline metabolism increases katg expression and oxidative stress resistance in escherichia coli. | the oxidation of l-proline to glutamate in gram-negative bacteria is catalyzed by the proline utilization a (puta) flavoenzyme, which contains proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase domains in a single polypeptide. previous studies have suggested that aside from providing energy, proline metabolism influences oxidative stress resistance in different organisms. to explore this potential role and the mechanism, we characterized the oxidative stress resis ... | 2014 | 25384482 |
| pseudomonas 2.0: genetic upgrading of p. putida kt2440 as an enhanced host for heterologous gene expression. | because of its adaptability to sites polluted with toxic chemicals, the model soil bacterium pseudomonas putida is naturally endowed with a number of metabolic and stress-endurance qualities which have considerable value for hosting energy-demanding and redox reactions thereof. the growing body of knowledge on p. putida strain kt2440 has been exploited for the rational design of a derivative strain in which the genome has been heavily edited in order to construct a robust microbial cell factory. | 2014 | 25384394 |
| metagenomic insights into the rdx-degrading potential of the ovine rumen microbiome. | the manufacturing processes of royal demolition explosive (rdx), or hexahydro-1,3,5-trinitro-1,3,5-triazine, have resulted in serious water contamination. as a potential carcinogen, rdx can cause a broad range of harmful effects to humans and animals. the ovine rumen is capable of rapid degradation of nitroaromatic compounds, including rdx. while ruminal rdx-degrading bacteria have been identified, the genes and pathways responsible for rdx degradation in the rumen have yet to be characterized. ... | 2014 | 25383623 |
| high prevalence of class 1 to 3 integrons among multidrug-resistant diarrheagenic escherichia coli in southwest of iran. | horizontal transfer of integrons is one of the important factors that can contribute to the occurrence of multidrug-resistant (mdr) bacteria. this study aimed to determine the prevalence of integrons among mdr escherichia coli strains isolated from stool specimens and investigate the associations between the existence of integrons and mdr properties in the southwest of iran. | 2014 | 25379369 |
| wastewater treatment using integrated anaerobic baffled reactor and bio-rack wetland planted with phragmites sp. and typha sp. | the purpose of this study is to examine the potential use of anaerobic baffled reactor (abr) followed by bio-rack wetland planted with phragmites sp. and typha sp. for treating domestic wastewater generated by small communities (751 mg cod/l, 500 scod mg/l, 348 mg bod5/l). two parallel laboratory-scale models showed that the process planted with phragmites sp. and typha sp. are capable of removing cod by 87% & 86%, scod by 90% & 88%, bod5 by 93% & 92%, tss by 88% & 86%, tn by 79% & 77%, po4-p by ... | 2014 | 25379186 |
| a review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. | microbial cell factories (mcfs) are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. this review highlights the progress of computational models for the rational design of an mcf to produce a target bio-commodity. in particular, the rational design of an mcf involves: (i) product selection, (ii) de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial), (iii) mcf chassis selection, (iv) enzyme engineering of ... | 2014 | 25379147 |
| singlet oxygen photosensitisation by the fluorescent protein pp2fbfp l30m, a novel derivative of pseudomonas putida flavin-binding pp2fbfp. | flavin-binding fluorescent proteins (fbfps) are a class of fluorescent reporters that have been increasingly used as reporters in the study of cellular structures and dynamics. flavin's intrinsic high singlet oxygen ((1)o2) quantum yield (φδ = 0.51) provides a basis for the development of new fbfp mutants capable of photosensitising (1)o2 for mechanistic and therapeutic applications, as recently exemplified by the fbfp minisog. in the present work we report an investigation on the (1)o2 photopro ... | 2015 | 25375892 |
| novel metabolic features in acinetobacter baylyi adp1 revealed by a multiomics approach. | expansive knowledge of bacterial metabolism has been gained from genome sequencing output, but the high proportion of genes lacking a proper functional annotation in a given genome still impedes the accurate prediction of the metabolism of a cell. to access to a more global view of the functioning of the soil bacterium acinetobacter baylyi adp1, we adopted a multi 'omics' approach. application of rna-seq transcriptomics and lc/ms-based metabolomics, along with the systematic phenotyping of the c ... | 2014 | 25374488 |
| reconstruction of lactate utilization system in pseudomonas putida kt2440: a novel biocatalyst for l-2-hydroxy-carboxylate production. | as an important method for building blocks synthesis, whole cell biocatalysis is hindered by some shortcomings such as unpredictability of reactions, utilization of opportunistic pathogen, and side reactions. due to its biological and extensively studied genetic background, pseudomonas putida kt2440 is viewed as a promising host for construction of efficient biocatalysts. after analysis and reconstruction of the lactate utilization system in the p. putida strain, a novel biocatalyst that only ex ... | 2014 | 25373400 |
| supercritical carbon dioxide and its potential as a life-sustaining solvent in a planetary environment. | supercritical fluids have different properties compared to regular fluids and could play a role as life-sustaining solvents on other worlds. even on earth, some bacterial species have been shown to be tolerant to supercritical fluids. the special properties of supercritical fluids, which include various types of selectivities (e.g., stereo-, regio-, and chemo-selectivity) have recently been recognized in biotechnology and used to catalyze reactions that do not occur in water. one suitable exampl ... | 2014 | 25370376 |
| structure and functional characterization of pyruvate decarboxylase from gluconacetobacter diazotrophicus. | bacterial pyruvate decarboxylases (pdc) are rare. their role in ethanol production and in bacterially mediated ethanologenic processes has, however, ensured a continued and growing interest. pdcs from zymomonas mobilis (zmpdc), zymobacter palmae (zppdc) and sarcina ventriculi (svpdc) have been characterized and zmpdc has been produced successfully in a range of heterologous hosts. pdcs from the acetobacteraceae and their role in metabolism have not been characterized to the same extent. examples ... | 2014 | 25369873 |
| draft genome sequence analysis of a pseudomonas putida w15oct28 strain with antagonistic activity to gram-positive and pseudomonas sp. pathogens. | pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. p. putida w15oct28, isolated from a stream in brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens staphylococcus aureus, pseudomonas aeruginosa, and the plant pathogen pseudomonas syringae, an unusual characteristic for p. putida. the active compound production only occurred in media with low iron content and w ... | 2014 | 25369289 |
| enhancing stress-resistance for efficient microbial biotransformations by synthetic biology. | chemical conversions mediated by microorganisms, otherwise known as microbial biotransformations, are playing an increasingly important role within the biotechnology industry. unfortunately, the growth and production of microorganisms are often hampered by a number of stressful conditions emanating from environment fluctuations and/or metabolic imbalances such as high temperature, high salt condition, strongly acidic solution, and presence of toxic metabolites. therefore, exploring methods to im ... | 2014 | 25368869 |
| ipro54-pseknc: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. | the σ(54) promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. with the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ(54) promoters. here, a predictor called 'ipro54-pseknc' was developed. in the predictor, the samples of dna sequences were formulated by a novel feature vector called 'pseudo k-tuple nucleotide composition', w ... | 2014 | 25361964 |
| rapid identification of stenotrophomonas maltophilia by peptide nucleic acid fluorescence in situ hybridization. | the objective of this study was to develop a novel peptide nucleic acid (pna) probe for stenotrophomonas maltophilia identification by fluorescence in situ hybridization (fish). the probe was evaluated using 33 human and veterinary clinical s. maltophilia isolates and 45 reference strains representing common bacterial species in the respiratory tract. the probe displayed 100% sensitivity and 100% specificity on pure cultures and allowed detection in sputum from cystic fibrosis patients. the dete ... | 2014 | 25356348 |
| the fused anthranilate synthase from streptomyces venezuelae functions as a monomer. | recently, we showed that the fused chorismate-utilizing enzyme from the antibiotic-producing soil bacterium streptomyces venezuelae is an anthranilate synthase (designated svas), not a 2-amino-2-deoxyisochorismate (adic) synthase, as was predicted based on its amino acid sequence similarity to the phenazine biosynthetic enzyme phze (an adic synthase). here, we report the characterization of svas using steady-state kinetics, gel filtration chromatography, and laser light scattering. the recombina ... | 2014 | 25355158 |
| the fused anthranilate synthase from streptomyces venezuelae functions as a monomer. | recently, we showed that the fused chorismate-utilizing enzyme from the antibiotic-producing soil bacterium streptomyces venezuelae is an anthranilate synthase (designated svas), not a 2-amino-2-deoxyisochorismate (adic) synthase, as was predicted based on its amino acid sequence similarity to the phenazine biosynthetic enzyme phze (an adic synthase). here, we report the characterization of svas using steady-state kinetics, gel filtration chromatography, and laser light scattering. the recombina ... | 2014 | 25355158 |
| metabolic engineering of methylobacterium extorquens am1 for 1-butanol production. | butanol is a promising next generation fuel and a bulk chemical precursor. although clostridia are the primary industrial microbes for the fermentative production of 1-butanol, alternative engineered hosts have the potential to generate 1-butanol from alternative carbon feedstocks via synthetic metabolic pathways. methylobacterium extorquens am1, a facultative methylotrophic α-proteobacterium, is a model system for assessing the possibility of generating products such as 1-butanol from one-carbo ... | 2014 | 25349627 |
| cyclic di-gmp-mediated repression of swarming motility by pseudomonas aeruginosa pa14 requires the motab stator. | the second messenger cyclic diguanylate (c-di-gmp) plays a critical role in the regulation of motility. in pseudomonas aeruginosa pa14, c-di-gmp inversely controls biofilm formation and surface swarming motility, with high levels of this dinucleotide signal stimulating biofilm formation and repressing swarming. p. aeruginosa encodes two stator complexes, motab and motcd, that participate in the function of its single polar flagellum. here we show that the repression of swarming motility requires ... | 2014 | 25349157 |
| cyclic di-gmp-mediated repression of swarming motility by pseudomonas aeruginosa pa14 requires the motab stator. | the second messenger cyclic diguanylate (c-di-gmp) plays a critical role in the regulation of motility. in pseudomonas aeruginosa pa14, c-di-gmp inversely controls biofilm formation and surface swarming motility, with high levels of this dinucleotide signal stimulating biofilm formation and repressing swarming. p. aeruginosa encodes two stator complexes, motab and motcd, that participate in the function of its single polar flagellum. here we show that the repression of swarming motility requires ... | 2014 | 25349157 |