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biosynthesis and biodegradation of 3-hydroxypropionate-containing polyesters.3-hydroxypropionate (3hp) is an important compound in the chemical industry, and the polymerized 3hp can be used as a bioplastic. in this review, we focus on polyesters consisting of 3hp monomers, including the homopolyester poly(3-hydroxypropionate) and copolyesters poly(3-hydroxybutyrate-co-3-hydroxypropionate), poly(3-hydroxypropionate-co-3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate), poly(4-hydroxybutyrate-co-3-hydroxypropionate-co-lactate), and poly(3-hydroxybutyrate-co-3-h ...201020543057
efficacy of various chemical disinfectants on biofilms formed in spacecraft potable water system components.as the provision of potable water is critical for successful habitation of the international space station (iss), life support systems were installed in december 2008 to recycle both humidity from the atmosphere and urine to conserve available water in the station. in-flight pre-consumption testing from the dispensing needle at the potable water dispenser (pwd) indicated that bacterial concentrations exceeded the current iss specifications of 50 colony-forming units (cfu) ml(-1). subsequent inve ...201020544435
differences in quality between privately and publicly banked umbilical cord blood units: a pilot study of autologous cord blood infusion in children with acquired neurologic disorders.a pilot study was conducted to determine the safety and feasibility of intravenous administration of autologous umbilical cord blood (cb) in young children with acquired neurologic disorders. most cb units (cbus) were electively stored in private cb banks. unlike public banks, which utilize specific criteria and thresholds for banking, private banks generally store all collected cbus.201020546200
the o28 antigen gene clusters of salmonella enterica subsp. enterica serovar dakar and serovar pomona are different.a 10 kb o-antigen gene cluster was sequenced from a salmonella enterica subsp. enterica dakar o28 reference strain and from two s. pomona serogroup o28 isolates. the two s. pomona o antigen gene clusters showed only moderate identity with the s. dakar o28 gene cluster, suggesting that the o antigen oligosaccharides may contain one or more sugars conferring the o28 epitope but may otherwise be different. these novel findings are absolutely critical for the correct interpretation of molecular sero ...201020652070
biosequestration via cooperative binding of copper by ralstonia pickettii.ralstonia pickettii isolated from copper-contaminated lake sediment are adapted to high levels of copper after 100 years of selective pressure. two r. pickettii strains (12d and 12j) were selected for the studies reported herein due to their distinct differences in genomic structure, different metal resistance patterns and carriage of a filamentous phage. copper sequestration studies revealed that these strains could bind up to 27.44 (12d) and 38.19 (12j) mg copper per g dry weight of cells and ...201020662391
reversible post-translational carboxylation modulates the enzymatic activity of n-acetyl-l-ornithine transcarbamylase.n-acetyl-l-ornithine transcarbamylase (aotcase), rather than ornithine transcarbamylase (otcase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. the specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. recently, several crystal structures of aotcase from xanthomonas campestris (xc) have been determined. in these structures, an unexplained electron density at the tip of the lys302 side ...201020695527
effects of nonionic surfactant addition on populations of polycyclic aromatic hydrocarbon-degrading bacteria in a bioreactor treating contaminated soil.we studied the effects of two polyethoxylated nonionic surfactants, brij 30 and c(12)e(8), on populations of polycyclic aromatic hydrocarbon- (pah-) degrading bacteria from a bioreactor treating pah-contaminated soil. each surfactant was evaluated at doses that corresponded to aqueous-phase concentrations both above and below the critical micelle concentration (cmc) after mixing with reactor slurry. real-time quantitative pcr was used to quantify 16s rrna (rrna) gene sequences representing degra ...201020707373
sea-land transitions in isopods: pattern of symbiont distribution in two species of intertidal isopods ligia pallasii and ligia occidentalis in the eastern pacific.studies of microbial associations of intertidal isopods in the primitive genus ligia (oniscidea, isopoda) can help our understanding of the formation of symbioses during sea-land transitions, as terrestrial oniscidean isopods have previously been found to house symbionts in their hepatopancreas. ligia pallasii and ligia occidentalis co-occur in the high intertidal zone along the eastern pacific with a large zone of range overlap and both species showing patchy distributions. in 16s rrna clone li ...201020730112
oxa-134, a naturally occurring carbapenem-hydrolyzing class d beta-lactamase from acinetobacter lwoffii.acinetobacter lwoffii, a species whose natural habitat is the human skin, intrinsically possesses a chromosomal gene encoding a carbapenem-hydrolyzing class d β-lactamase, oxa-134. this species may therefore constitute a reservoir for carbapenemase genes that may spread among other acinetobacter species.201020837764
isolation and physiology of bacteria from contaminated subsurface sediments.the majority of environmental microorganisms cannot be grown by traditional techniques. here we employed, and contrasted with conventional plating, an alternative approach based on cultivation of microorganisms inside diffusion chambers incubated within natural samples, followed by subculturing in petri dishes. using this approach, we isolated microorganisms from subsurface sediments from the field research center (frc) in oak ridge, tn. the sediments were acidic and highly contaminated with ura ...201020870785
genomic analysis and relatedness of p2-like phages of the burkholderia cepacia complex.the burkholderia cepacia complex (bcc) is comprised of at least seventeen gram-negative species that cause infections in cystic fibrosis patients. because bcc bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. the purpose of our study was to sequence and characterize three novel bcc-specific phages: ks5 (vb_bcem-ks5 or vb_bmuz-atcc 17616), ks14 (vb_bcem-ks14) and kl3 (vb_bamm-kl3 or vb_bcez-cep511).201020973964
characterization of filamentous bacteriophage pe226 infecting ralstonia solanacearum strains.the aim of this study was to isolate and characterize new bacteriophages that infect a wide range of plant pathogenic ralstonia solanacearum strains.201021054700
development of real-time pcr assays for detection and quantification of bacillus cereus group species: differentiation of b. weihenstephanensis and rhizoid b. pseudomycoides isolates from milk.quantitative real-time pcr (qrt-pcr) offers an alternative method for the detection of bacterial contamination in food. this method provides the quantitation and determination of the number of gene copies. in our study, we established an rt-pcr assay using the lightcycler system to detect and quantify the bacillus cereus group species, which includes b. cereus, b. anthracis, b. thuringiensis, b. weihenstephanensis, b. mycoides, and b. pseudomycoides. a taqman assay was designed to detect a 285-b ...201021057027
development of real-time pcr assays for detection and quantification of bacillus cereus group species: differentiation of b. weihenstephanensis and rhizoid b. pseudomycoides isolates from milk.quantitative real-time pcr (qrt-pcr) offers an alternative method for the detection of bacterial contamination in food. this method provides the quantitation and determination of the number of gene copies. in our study, we established an rt-pcr assay using the lightcycler system to detect and quantify the bacillus cereus group species, which includes b. cereus, b. anthracis, b. thuringiensis, b. weihenstephanensis, b. mycoides, and b. pseudomycoides. a taqman assay was designed to detect a 285-b ...201021057027
analysis of the bacterial communities present in lungs of patients with cystic fibrosis from american and british centers.the aim of this study was to determine whether geographical differences impact the composition of bacterial communities present in the airways of cystic fibrosis (cf) patients attending cf centers in the united states or united kingdom. thirty-eight patients were matched on the basis of clinical parameters into 19 pairs comprised of one u.s. and one united kingdom patient. analysis was performed to determine what, if any, bacterial correlates could be identified. two culture-independent strategi ...201021068277
analysis of the bacterial communities present in lungs of patients with cystic fibrosis from american and british centers.the aim of this study was to determine whether geographical differences impact the composition of bacterial communities present in the airways of cystic fibrosis (cf) patients attending cf centers in the united states or united kingdom. thirty-eight patients were matched on the basis of clinical parameters into 19 pairs comprised of one u.s. and one united kingdom patient. analysis was performed to determine what, if any, bacterial correlates could be identified. two culture-independent strategi ...201021068277
aerobic degradation of mercaptosuccinate by the gram-negative bacterium variovorax paradoxus strain b4.the gram-negative bacterium variovorax paradoxus strain b4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (ms). during growth with ms this strain released significant amounts of sulfate into the medium. tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using ms as a carbon source. in six of these mutants, tn5::mob insertions were mapped in a putative gene encodin ...201021075928
aerobic degradation of mercaptosuccinate by the gram-negative bacterium variovorax paradoxus strain b4.the gram-negative bacterium variovorax paradoxus strain b4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (ms). during growth with ms this strain released significant amounts of sulfate into the medium. tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using ms as a carbon source. in six of these mutants, tn5::mob insertions were mapped in a putative gene encodin ...201021075928
first investigation of the microbiology of the deepest layer of ocean crust.the gabbroic layer comprises the majority of ocean crust. opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. during the integrated ocean drilling program expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at hole 1309d, located on the atlantis massif (30 °n, 42 °w). microbial diversity in the rocks was anal ...201021079766
enzymatic functionalization of carbon-hydrogen bonds.the development of new catalytic methods to functionalize carbon-hydrogen (c-h) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. in nature, enzymes catalyze regio- and stereoselective c-h bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. the efficiency of these enzymes relative to analogous chemical processe ...201021079862
enzymatic functionalization of carbon-hydrogen bonds.the development of new catalytic methods to functionalize carbon-hydrogen (c-h) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. in nature, enzymes catalyze regio- and stereoselective c-h bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. the efficiency of these enzymes relative to analogous chemical processe ...201021079862
ralstonia pickettii community-acquired pneumonia in cambodia. 201021144257
novel pan-genomic analysis approach in target selection for multiplex pcr identification and detection of burkholderia pseudomallei, burkholderia thailandensis, and burkholderia cepacia complex species: a proof-of-concept study.burkholderia pseudomallei, burkholderia thailandensis, and the burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. yet, they are occasionally misidentified by biochemical profiling, and even 16s rrna gene sequencing may not offer adequate discrimination between certain species groups. using the 23 b. pseudomallei, four b. thailandensis, and 16 b. cepacia complex genome sequences available, we identified gene targets specific to each of them (a tat domain protein, a 70- ...201021177905
hospital epidemiology and infection control in acute-care settings.health care-associated infections (hais) have become more common as medical care has grown more complex and patients have become more complicated. hais are associated with significant morbidity, mortality, and cost. growing rates of hais alongside evidence suggesting that active surveillance and infection control practices can prevent hais led to the development of hospital epidemiology and infection control programs. the role for infection control programs has grown and continues to grow as rat ...201121233510
rapid identification of gram-negative bacteria with and without ctx-m extended-spectrum ß-lactamase from positive blood culture bottles by pcr followed by microchip gel electrophoresis.we evaluated the usefulness of pcr analysis of the 16s-23s rrna gene internal transcribed spacer (its) and the ctx-m extended-spectrum ß-lactamase (esbl) followed by microchip gel electrophoresis (mge) for direct identification and ctx-m detection of gram-negative bacteria (gnb) from positive blood culture bottles. of 251 gnb isolated from blood cultures containing a single bacterium, 225 (90%) were correctly identified at the species level directly from positive blood culture bottles by compari ...201121289149
evolution of the oligopeptide transporter family.the oligopeptide transporter (opt) family of peptide and iron-siderophore transporters includes members from both prokaryotes and eukaryotes but with restricted distribution in the latter domain. eukaryotic members were found only in fungi and plants with a single slime mold homologue clustering with the fungal proteins. all functionally characterized eukaryotic peptide transporters segregate from the known iron-siderophore transporters on a phylogenetic tree. prokaryotic members are widespread, ...201121347612
distribution of genes encoding nucleoid-associated protein homologs in plasmids.bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...201121350637
gradually accumulating beneficial mutations to improve the thermostability of n-carbamoyl-d-amino acid amidohydrolase by step-wise evolution.to further enhance repeated batch reactions with immobilized n-carbamoyl-d-amino acid amidohydrolase (dcase), which can be used for the industrial production of d-amino acids, the stability of high soluble mutant dcase-m3 from ralstonia pickettii cgmcc1596 was improved by step-wise evolution. in our previous report, six thermostability-related sites were identified by error-prone pcr. based on the above result, an improved mutant b5 (q12l/q23l/h248q/t262a/t263s) was obtained through two rounds o ...201121360152
characterisation of the putative effector interaction site of the regulatory hbpr protein from pseudomonas azelaica by site-directed mutagenesis.bacterial transcription activators of the xylr/dmpr subfamily exert their expression control via ¤â(54)-dependent rna polymerase upon stimulation by a chemical effector, typically an aromatic compound. where the chemical effector interacts with the transcription regulator protein to achieve activation is still largely unknown. here we focus on the hbpr protein from pseudomonas azelaica, which is a member of the xylr/dmpr subfamily and responds to biaromatic effectors such as 2-hydroxybiphenyl. w ...201121379585
biodiversity and geochemistry of an extremely acidic, low-temperature subterranean environment sustained by chemolithotrophy.the geochemical dynamics and composition of microbial communities within a low-temperature (ôê+8.5-¦c), long-abandoned (>ôçâ90 years) underground pyrite mine (cae coch, located in north wales) were investigated. surface water percolating through fractures in the residual pyrite ore body that forms the roof of the mine becomes extremely acidic and iron-enriched due to microbially accelerated oxidative dissolution of the sulfide mineral. water droplets on the mine roof were found to host a very li ...201121382147
a motn mutant of ralstonia solanacearum is hypermotile and has reduced virulence.ralstonia solanacearum is a soil-borne plant pathogen that causes bacterial wilt disease on many plant species. we previously showed that swimming motility contributes to virulence of this bacterium in the early stages of host invasion and colonization. in this study we identified a new negative regulator of motility, named motn, that is located in a cluster of motility-related genes. a motn mutant was hypermotile both on 0.3% agar motility plates and in rich and minimal medium broth. however, l ...201121421761
across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage.the gc content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic gc content are observed within many bacterial phyla, including both gram negative and gram positive phyla. thus, divergent genomic gc content has evolved repeatedly in widely separated bacterial taxa. since genomic gc content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic gc content within eight different phyla or classes of bacteria. w ...201121423704
differentiating the growing nosocomial infectious threats ralstonia pickettii and ralstonia insidiosa.differentiation of the growing nosocomial infectious threats, ralstonia pickettii and ralstonia insidiosa, based on nitrate reduction, desferrioxamine susceptibility, arabinose, n-acetyl-glucosamine and phenylacetate assimilation is described. these tests can be used for preliminary identification of ralstonia pickettii and ralstonia insidiosa resulting in more accurate identification of these species.201121461848
microbiology of animal bite wound infections.the microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. bacteria may also originate from the victim's own skin or the physical environment at the time of injury. our review has focused on bite wound infections in ...201121482724
degradation of chlorobenzene by strain ralstonia pickettii l2 isolated from a biotrickling filter treating a chlorobenzene-contaminated gas stream.a ralstonia pickettii species able to degrade chlorobenzene (cb) as the sole source of carbon and energy was isolated from a biotrickling filter used for the removal of cb from waste gases. this organism, strain l2, could degrade cb as high as 220 mg/l completely. following cb consumption, stoichiometric amounts of chloride were released, and co(2) production rate up to 80.2% proved that the loss of cb was mainly via mineralization and incorporation into cell material. the haldane modification o ...201121499764
bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ...201121519847
classification of plant associated bacteria using rif, a computationally derived dna marker.a dna marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of xanthomonas, a genus that contains many important phytopathogens. this dna marker comprises a portion of the dnaa replication initiation factor (rif). unlike the rrna genes, dnaa is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of rif requires genus-specific primers. in silico analysis revealed that rif has equal or ...201121533033
emerging agents to combat complicated and resistant infections: focus on ceftobiprole.antimicrobial resistance is a global concern. over the past few years, considerable efforts and resources have been expended to detect, monitor, and understand at the basic level the many different facets of emerging and increasing resistance. development of new antimicrobial agents has been matched by the development of new mechanisms of resistance by bacteria. current antibiotics act at a variety of sites within the target bacteria, including the cross-linking enzymes in the cell wall, various ...201021694889
environmental adaptability and stress tolerance of laribacter hongkongensis: a genome-wide analysis. 201121711489
antibacterial activity of some selected medicinal plants of pakistan.screening of the ethnobotenical plants is a pre-requisite to evaluate their therapeutic potential and it can lead to the isolation of new bioactive compounds.201121718504
The structural biology of +¦-barrel membrane proteins: a summary of recent reports.The outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts all contain transmembrane +¦-barrel proteins. These +¦-barrel proteins serve essential functions in cargo transport and signaling and are also vital for membrane biogenesis. They have also been adapted to perform a diverse set of important cellular functions including acting as porins, transporters, enzymes, virulence factors and receptors. Recent structures of transmembrane +¦-barrels include that of a full length aut ...201121719274
differences in lateral gene transfer in hypersaline versus thermal environments.the role of lateral gene transfer (lgt) in the evolution of microorganisms is only beginning to be understood. while most lgt events occur between closely related individuals, inter-phylum and inter-domain lgt events are not uncommon. these distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" lgt events may have significantly impacted the evolution of microbes. one mechanism driving distant lgt events is microbial transformatio ...201121740576
surveillance of single-cell behavior in different subpopulations of ralstonia pickettii ar1 during growth and polyhydroxybutyrate production phases by flow cytometry.most bacterial strains accumulate intracellular polyhydroxybutyrate (phb) granules as an energy reservoir, in response to fluctuations in their microenvironment. flow cytometry was applied for the analysis of single cells of ralstonia pickettii ar1 in response to changes in the culture conditions. two parameters, the phb production-related fl2 and side scatter (ssc) parameters, were used to monitor, distinguish and characterize different subpopulations in the growth and phb production phases. a ...201121780145
emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism.all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ...201121823229
mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria.green sulfur bacteria (gsb) constitute a closely related group of photoautotrophic and thiotrophic bacteria with limited phenotypic variation. they typically oxidize sulfide and thiosulfate to sulfate with sulfur globules as an intermediate. based on genome sequence information from 15 strains, the distribution and phylogeny of enzymes involved in their oxidative sulfur metabolism was investigated. at least one homolog of sulfide:quinone oxidoreductase (sqr) is present in all strains. in all sul ...201121833341
lobar pneumonia caused by ralstonia pickettii in a sixty-five-year-old han chinese man: a case report.abstract:201121843320
transport genes and chemotaxis in laribacter hongkongensis: a genome-wide analysis.abstract:201121849034
Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water. Diversity in Ralstonia pickettii.Ralstonia pickettii is a nosocomial infectious agent and a significant industrial contaminant. It has been found in many different environments including clinical situations, soil and industrial High Purity Water. This study compares the phenotypic and genotypic diversity of a selection of strains of Ralstonia collected from a variety of sources.201121878094
Burkholderia species are major inhabitants of white lupin cluster roots.The formation of cluster roots by plants represents a highly efficient strategy for acquisition of sparingly available phosphate. This particular root type is characterized by a densely branched structure and high exudation of organic acids and protons, which are likely to influence the resident bacterial community. Until now, the identity of the bacterial populations living in cluster roots has not been investigated. We applied cultivation-dependent and cultivation-independent methods to charac ...201121908626
metagenomic analysis of taxa associated with lutzomyia longipalpis, vector of visceral leishmaniasis, using an unbiased high-throughput approach.leishmaniasis is one of the most diverse and complex of all vector-borne diseases worldwide. it is caused by parasites of the genus leishmania, obligate intramacrophage protists characterised by diversity and complexity. its most severe form is visceral leishmaniasis (vl), a systemic disease that is fatal if left untreated. in latin america vl is caused by leishmania infantum chagasi and transmitted by lutzomyia longipalpis. this phlebotomine sandfly is only found in the new world, from mexico t ...201121909446
identification and characterization of a novel class of extracellular poly(3-hydroxybutyrate) depolymerase from bacillus sp. strain nrrl b-14911.the catalytic, linker, and denatured poly(3-hydroxybutyrate) (dphb)-binding domains of bacterial extracellular phb depolymerases (phazs) are classified into several different types. we now report a novel class of extracellular phb depolymerase from bacillus sp. strain nrrl b-14911. its catalytic domain belongs to type 1, whereas its putative linker region neither possesses the sequence features of the three known types of linker domains nor exhibits significant amino acid sequence similarity to ...201121948827
glygly-cterm and rhombosortase: a c-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease.the rhomboid family of serine proteases occurs in all domains of life. its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. the model member glpg from escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple x-ray crystal studies, yet its relationship to endogenous substrates is not well understood. here we describe an apparent membr ...201122194940
Complete Genome Sequence of the BTEX-Degrading Bacterium Pseudoxanthomonas spadix BD-a59.Pseudoxanthomonas spadix BD-a59, able to metabolize all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds, was isolated from gasoline-contaminated sediment. Here, we report the complete 3.45-Mb genome sequence and annotation of strain BD-a59. These advance the understanding of strain BD-a59's genomic properties and pollutant metabolic versatility.201222207748
a 54-kda protein encoded by pbtoxis is required for parasporal body structural integrity in bacillus thuringiensis subsp. israelensis.strains of bacillus thuringiensis such as b. thuringiensis subsp. israelensis (onr-60a) and b. thuringiensis subsp. morrisoni (pg-14) pathogenic for mosquito larvae produce a complex parasporal body consisting of several protein endotoxins synthesized during sporulation that form an aggregate of crystalline inclusions bound together by a multilamellar fibrous matrix. most studies of these strains focus on the molecular biology of the endotoxins, and although it is known that parasporal body stru ...201122210770
biology and pathogenesis of acanthamoeba.acanthamoeba is a free-living protist pathogen, capable of causing a blinding keratitis and fatal granulomatous encephalitis. the factors that contribute to acanthamoeba infections include parasite biology, genetic diversity, environmental spread and host susceptibility, and are highlighted together with potential therapeutic and preventative measures. the use of acanthamoeba in the study of cellular differentiation mechanisms, motility and phagocytosis, bacterial pathogenesis and evolutionary p ...201222229971
metagenomic evidence for h(2) oxidation and h(2) production by serpentinite-hosted subsurface microbial communities.ultramafic rocks in the earth's mantle represent a tremendous reservoir of carbon and reducing power. upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (h(2)). in order to assess the potential for microbial h(2) utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the lost city hydrot ...201122232619
metagenomic evidence for h(2) oxidation and h(2) production by serpentinite-hosted subsurface microbial communities.ultramafic rocks in the earth's mantle represent a tremendous reservoir of carbon and reducing power. upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (h(2)). in order to assess the potential for microbial h(2) utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the lost city hydrot ...201122232619
effect of modeled reduced gravity conditions on bacterial morphology and physiology.abstract: background: bacterial phenotypes result from responses to environmental conditions under which these organisms grow; reduced gravity has been demonstrated in many studies as an environmental condition that profoundly influences microorganisms. in this study, we focused on low-shear stress, modeled reduced gravity (mrg) conditions and examined, for escherichia coli and staphlyococcus aureus, a suite of bacterial responses (including total protein concentrations, biovolume, membrane pot ...201222239851
characterisation of the burkholderia pseudomallei k96243 cps i coding region.burkholderia pseudomallei is the causative agent of melioidosis, a disease endemic to regions of southeast asia and northern australia. both humans and a range of other animal species are susceptible to melioidosis and the production of a group 3 polysaccharide capsule in b. pseudomallei is essential for virulence. this b. pseudomallei capsular polysaccharide (cps) i comprises unbranched manno-heptopyranose residues and is encoded by a 34.5 kb locus on chromosome 1. despite the importance of thi ...201222252864
architectural design influences the diversity and structure of the built environment microbiome.buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome--the community of microorganisms that live indoors--is important for understanding the relationship between building design, biodiversity and human health. in this study, we used high-throughput sequencing of the bacterial ...201222278670
phylogeny and population structure of brown rot- and moko disease-causing strains of ralstonia solanacearum phylotype ii.the ancient soilborne plant vascular pathogen ralstonia solanacearum has evolved and adapted to cause severe damage in an unusually wide range of plants. in order to better describe and understand these adaptations, strains with very similar lifestyles and host specializations are grouped into ecotypes. we used comparative genomic hybridization (cgh) to investigate three particular ecotypes in the american phylotype ii group: (i) brown rot strains from phylotypes iib-1 and iib-2, historically kn ...201222286995
carbapenem resistance in elizabethkingia meningoseptica is mediated by metallo-β-lactamase blab.elizabethkingia meningoseptica, a gram-negative rod widely distributed in the environment, is resistant to most β-lactam antibiotics. three bla genes have been identified in e. meningoseptica, coding for the extended-spectrum serine-β-lactamase cme (class d) and two unrelated wide-spectrum metallo-β-lactamases, blab (subclass b1) and gob (subclass b3). e. meningoseptica is singular in being the only reported microorganism possessing two chromosomally encoded mbl genes. real-time pcr and biochemi ...201222290979
effects of high hydrostatic pressure on bacterial growth on human ossicles explanted from cholesteatoma patients.high hydrostatic pressure (hhp) treatment can eliminate cholesteatoma cells from explanted human ossicles prior to re-insertion. we analyzed the effects of hhp treatment on the microbial flora on ossicles and on the planktonic and biofilm states of selected isolates.201222291908
infectious etiologies of acute febrile illness among patients seeking health care in south-central cambodia.the agents of human febrile illness can vary by region and country suggesting that diagnosis, treatment, and control programs need to be based on a methodical evaluation of area-specific etiologies. from december 2006 to december 2009, 9,997 individuals presenting with acute febrile illness at nine health care clinics in south-central cambodia were enrolled in a study to elucidate the etiologies. upon enrollment, respiratory specimens, whole blood, and serum were collected. testing was performed ...201222302857
analysis of the sos response of vibrio and other bacteria with multiple chromosomes.the sos response is a well-known regulatory network present in most bacteria and aimed at addressing dna damage. it has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. recently, the sos response has been shown to regulate the activity of integrases in the chromosomal superintegrons of the vibrionaceae, which encompasses a wide range of pathogenic species harboring multiple chromosomes. here we combin ...201222305460
distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.pyrroloquinoline quinone (pqq) is a small, redox active molecule that serves as a cofactor for several bacterial dehydrogenases, introducing pathways for carbon utilization that confer a growth advantage. early studies had implicated a ribosomally translated peptide as the substrate for pqq production. this study presents a sequence- and structure-based analysis of the components of the pqq operon. we find the necessary components for pqq production are present in 126 prokaryotes, most of which ...201222324760
advances in electronic-nose technologies developed for biomedical applications.the research and development of new electronic-nose applications in the biomedical field has accelerated at a phenomenal rate over the past 25 years. many innovative e-nose technologies have provided solutions and applications to a wide variety of complex biomedical and healthcare problems. the purposes of this review are to present a comprehensive analysis of past and recent biomedical research findings and developments of electronic-nose sensor technologies, and to identify current and future ...201122346620
stable carbon isotope fractionation in chlorinated ethene degradation by bacteria expressing three toluene oxygenases.one difficulty in using bioremediation at a contaminated site is demonstrating that biodegradation is actually occurring in situ. the stable isotope composition of contaminants may help with this, since they can serve as an indicator of biological activity. to use this approach it is necessary to establish how a particular biodegradation pathway affects the isotopic composition of a contaminant. this study examined bacterial strains expressing three aerobic enzymes for their effect on the (13)c/ ...201222363335
characterization of a novel copper-haem c dissimilatory nitrite reductase from ralstonia pickettii.nirs (nitrite reductases) convert nitrite into no in the denitrification process. rpnir (ralstonia pickettii nir), a new type of dissimilatory cu-containing nir with a c-terminal haem c domain from r. pickettii, has been cloned, overexpressed in escherichia coli and purified to homogeneity. the enzyme has a subunit molecular mass of 50515 da, consistent with sequence data showing homology to the well-studied two-domain cu nirs, but with an attached c-terminal haem c domain. gel filtration and co ...201222414182
evaluation of the bruker biotyper and vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for identification of nonfermenting gram-negative bacilli isolated from cultures from cystic fibrosis patients.the bruker biotyper and vitek ms matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry (ms) instruments were evaluated for the identification of nonfermenting gram-negative bacilli (nfgnb) by a blinded comparison to conventional biochemical or molecular methods. two hundred nfgnb that were recovered from cultures from cystic fibrosis patients in the university of iowa health care (uihc) microbiology laboratory between 1 january 2006 and 31 october 2010 were sen ...201222495566
structural and thermodynamic characterization of the interaction between two periplasmic treponema pallidum lipoproteins that are components of a tpr-protein-associated trap transporter (tpat).tripartite atp-independent periplasmic transporters (trap-ts) are bacterial transport systems that have been implicated in the import of small molecules into the cytoplasm. a newly discovered subfamily of trap-ts [tetratricopeptide repeat-protein associated trap transporters (tpats)] has four components. three are common to both trap-ts and tpats: the p component, a ligand-binding protein, and a transmembrane symporter apparatus comprising the m and q components (m and q are sometimes fused to f ...201222504226
regulation and evolution of malonate and propionate catabolism in proteobacteria.bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. in various bacteria, transcription of these genes is controlled by the gntr family transcription factors (tfs) matr/mdcy and/or the lysr family transcription factor mdcr. propionate is metabolized via the methylcitrate pathway, comprising enzymes encoded by the prp and acn genes. prpr, the fis family sigma 54-dependent transcription factor, is known to be a transcriptional activator of the prp genes. here, we report ...201222505679
centromere binding and evolution of chromosomal partition systems in the burkholderiales.how split genomes arise and evolve in bacteria is poorly understood. since each replicon of such genomes encodes a specific partition (par) system, the evolution of par systems could shed light on their evolution. the cystic fibrosis pathogen burkholderia cenocepacia has three chromosomes (c1, c2, and c3) and one plasmid (pbc), whose compatibility depends on strictly specific interactions of the centromere sequences (pars) with their cognate binding proteins (parb). however, the par systems of b ...201222522899
combination antimicrobial susceptibility testing of multidrug-resistant stenotrophomonas maltophilia from cystic fibrosis patients.stenotrophomonas maltophilia is increasingly being isolated from the respiratory tract of individuals with cystic fibrosis, and, because of its multidrug-resistant nature, the selection of suitable treatment regimens can be problematical. etest methodology was used to facilitate mic and antimicrobial combination testing on 80 isolates of s. maltophilia cultured from the respiratory tract of scottish individuals with cystic fibrosis between 2001 and 2010. the overall rate of susceptibility for th ...201222585220
performances of the vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology.rapid and cost-effective matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms)-based systems will replace conventional phenotypic methods for routine identification of bacteria. we report here the first evaluation of the new maldi-tof ms-based vitek ms system in a large clinical microbiology laboratory. this system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. we have te ...201222593596
fluorescence-based rapid detection of microbiological contaminants in water samples.microbiological contamination of process waters is a current issue for pharmaceutical industries. traditional methods require several days to obtain results; therefore, rapid microbiological methods are widely requested to shorten time-to-result. milliflex quantum was developed for the rapid detection and enumeration of microorganisms in filterable samples. it combines membrane filtration to universal fluorescent staining of viable microorganisms. this new alternative method was validated using ...201222623887
progressive unilateral lung collapse in cystic fibrosis--a therapeutic challenge. 201222688368
analysis of two gene clusters involved in 2,4,6-trichlorophenol degradation by ralstonia pickettii dtp0602.ralstonia pickettii dtp0602 utilizes 2,4,6-trichlorophenol (2,4,6-tcp) as sole source of carbon and energy. we have characterized hadabc which is involved in the degradation of 2,4,6-tcp. to identify the other genes involved in 2,4,6-tcp degradation, the dna sequence around hadabc was determined. a regulatory gene, hadr, homologous to the lysr-type transcriptional regulator was located upstream of hada, but no maleylacetate (ma) reductase gene was located near hadabc. an 8.4-kb dna fragment cont ...201222738955
identification of acquired antimicrobial resistance genes.identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. as the costs of whole-genome sequencing (wgs) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. thus, the current challenge is to extract the relevant information from the large amount of generated data.201222782487
a multilocus sequence typing scheme implies population structure and reveals several putative novel achromobacter species.the genus achromobacter currently is comprised of seven species, including achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (cf). to enable strain typing for global epidemiologic investigations, to clarify the taxonomy of "achromobacter-like" strains, and to elucidate the population structure of this genus, we developed a genus ...201222785192
ralstonia pickettii sepsis in a hemodialysis patient from bulgaria. 201222846135
sonication of intramedullary nails: clinically-related infection and contamination.sonication is currently considered the best procedure for microbiological diagnosis of implant-related osteoarticular infection, but studies in nail-related infections are lacking. the study aim was to evaluate implant sonication after intramedullary nail explantation, and relate it to microbiological cultures and clinical outcome.201222848337
serratia odorifera a midgut inhabitant of aedes aegypti mosquito enhances its susceptibility to dengue-2 virus.mosquito midgut plays a crucial role in its vector susceptibility and pathogen interaction. identification of the sustainable microflora of the midgut environment can therefore help in evaluating its contribution in mosquito-pathogen interaction and in turn vector competence. to understand the bacterial diversity in the midgut of aedes aegypti mosquitoes, we conducted a screening study of the gut microbes of these mosquitoes which were either collected from fields or reared in the laboratory "cu ...201222848375
investigation of the bacterial communities associated with females of lutzomyia sand fly species from south america.phlebotomine sand flies are vectors of leishmania that are acquired by the female sand fly during blood feeding on an infected mammal. leishmania parasites develop exclusively in the gut lumen during their residence in the insect before transmission to a suitable host during the next blood feed. female phlebotomine sand flies are blood feeding insects but their life style of visiting plants as well as animals, and the propensity for larvae to feed on detritus including animal faeces means that t ...201222880020
intraclonal diversity of the pseudomonas aeruginosa cystic fibrosis airway isolates tbcf10839 and tbcf121838: distinct signatures of transcriptome, proteome, metabolome, adherence and pathogenicity despite an almost identical genome sequence.microevolution of closely related pseudomonas aeruginosa was compared in the clone tb strains tbcf10839 and tbcf121838 which had been isolated from two unrelated individuals with cystic fibrosis who had acquired clone tb during a local outbreak. compared with the strain pao1 reference sequence the two clone tb genomes shared 23 155 nucleotide exchanges, 32 out-of-frame indels in the coding region and another repertoire of replacement and genomic islands such as pagi-1, pagi-2, pagi-5, lesgi-1 an ...201322882573
bacterial contamination of dental unit waterlines.safety of patients and dental personnel requires the appropriate microbiological water quality in dental units. during treatment, patients and dental workers are exposed both to direct contact with bacteria-contaminated water in the form of splatter and with contaminated water aerosol emitted during work by unit handpieces, including rotating and ultrasonic instruments. the aim of the study was to determine the qualitative and quantitative contamination of water in dental unit reservoirs with ae ...201222899458
bacterial contamination of dental unit waterlines.safety of patients and dental personnel requires the appropriate microbiological water quality in dental units. during treatment, patients and dental workers are exposed both to direct contact with bacteria-contaminated water in the form of splatter and with contaminated water aerosol emitted during work by unit handpieces, including rotating and ultrasonic instruments. the aim of the study was to determine the qualitative and quantitative contamination of water in dental unit reservoirs with ae ...201222899458
the promise of bacteriophage therapy for burkholderia cepacia complex respiratory infections.in recent times, increased attention has been given to evaluating the efficacy of phage therapy, especially in scenarios where the bacterial infectious agent of interest is highly antibiotic resistant. in this regard, phage therapy is especially applicable to infections caused by the burkholderia cepacia complex (bcc) since members of the bcc are antibiotic pan-resistant. current studies in bcc phage therapy are unique from many other avenues of phage therapy research in that the investigation i ...201122919592
the promise of bacteriophage therapy for burkholderia cepacia complex respiratory infections.in recent times, increased attention has been given to evaluating the efficacy of phage therapy, especially in scenarios where the bacterial infectious agent of interest is highly antibiotic resistant. in this regard, phage therapy is especially applicable to infections caused by the burkholderia cepacia complex (bcc) since members of the bcc are antibiotic pan-resistant. current studies in bcc phage therapy are unique from many other avenues of phage therapy research in that the investigation i ...201122919592
analysis of a comprehensive dataset of diversity generating retroelements generated by the program digref.diversity generating retroelements (dgrs) are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. they achieve hypermutation through replacement of the variable region with a strongly mutated cdna copy generated by the element-encoded reverse transcriptase. in contrast to "selfish" retroelements such as group ii introns and retrotransposons, dgrs impart an advantage to their host by increasing its adaptive potential. dgrs were discovered in a bac ...201222928525
genome sequence of ralstonia sp. strain pba, a bacterium involved in the biodegradation of 4-aminobenzenesulfonate.ralstonia sp. strain pba was isolated from textile wastewater in a coculture with hydrogenophaga sp. strain pbc. here we present the assembly and annotation of its genome, which may provide further insights into the mechanism of its interaction with strain pbc during 4-aminobenzenesulfonate degradation.201222933765
directed evolution of poly[(r)-3-hydroxybutyrate] depolymerase using cell surface display system: functional importance of asparagine at position 285.poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 (phazrpit1) consists of three functional domains to effectively degrade solid phb materials, and its catalytic domain catalyzes the ester bond cleavage of the substrate. we performed the directed evolution of phazrpit1 targeted at the catalytic domain in combination with the cell surface display method to effectively screen for mutants with improved p-nitrophenyl butyrate (pnpc4) activity. mutated phazrpit1 genes generate ...201322940802
multidrug-resistance and toxic metal tolerance of medically important bacteria isolated from an aquaculture system.the use of antimicrobials and toxic metals should be considered carefully in aquaculture and surrounding environments. we aimed to evaluate medically relevant bacteria in an aquaculture system and their susceptibility to antimicrobials and toxic metals. selective cultures for enterobacteria (ent), non-fermenting gram-negative rods (nfr) and gram-positive cocci (gpc) were obtained from water samples collected in two different year seasons. the isolated bacteria were biochemically identified and a ...201222972388
gene duplication as a mechanism of genomic adaptation to a changing environment.a subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. at this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. nevertheless, enough examples have acc ...201222977152
diversity and antibiograms of bacterial organisms isolated from samples of household drinking-water consumed by hiv-positive individuals in rural settings, south africa.diarrhoea is a hallmark of hiv infections in developing countries, and many diarrhoea-causing agents are often transmitted through water. the objective of the study was to determine the diversity and antibiotic susceptibility profiles of bacterial organisms isolated from samples of household drinking-water consumed by hiv-infected and aids patients. in the present study, household water stored for use by hiv-positive patients was tested for microbial quality, and isolated bacterial organisms wer ...201223082625
mutational robustness of 16s ribosomal rna, shown by experimental horizontal gene transfer in escherichia coli.the bacterial ribosome consists of three rrna molecules and 57 proteins and plays a crucial role in translating mrna-encoded information into proteins. because of the ribosome's structural and mechanistic complexity, it is believed that each ribosomal component coevolves to maintain its function. unlike 5s rrna, 16s and 23s rrnas appear to lack mutational robustness, because they form the structural core of the ribosome. however, using escherichia coli δ7 (null mutant of operons) as a host, we h ...201223112186
defining falciparum-malaria-attributable severe febrile illness in moderate-to-high transmission settings on the basis of plasma pfhrp2 concentration.in malaria-endemic settings, asymptomatic parasitemia complicates the diagnosis of malaria. histidine-rich protein 2 (hrp2) is produced by plasmodium falciparum, and its plasma concentration reflects the total body parasite burden. we aimed to define the malaria-attributable fraction of severe febrile illness, using the distributions of plasma p. falciparum hrp2 (pfhrp2) concentrations from parasitemic children with different clinical presentations.201223136222
defining falciparum-malaria-attributable severe febrile illness in moderate-to-high transmission settings on the basis of plasma pfhrp2 concentration.in malaria-endemic settings, asymptomatic parasitemia complicates the diagnosis of malaria. histidine-rich protein 2 (hrp2) is produced by plasmodium falciparum, and its plasma concentration reflects the total body parasite burden. we aimed to define the malaria-attributable fraction of severe febrile illness, using the distributions of plasma p. falciparum hrp2 (pfhrp2) concentrations from parasitemic children with different clinical presentations.201223136222
comparative genomic analysis and benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (btex) degradation pathways of pseudoxanthomonas spadix bd-a59.pseudoxanthomonas spadix bd-a59, isolated from gasoline-contaminated soil, has the ability to degrade all six btex (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds. the genomic features of strain bd-a59 were analyzed bioinformatically and compared with those of another fully sequenced pseudoxanthomonas strain, p. suwonensis 11-1, which was isolated from cotton waste compost. the genome of strain bd-a59 differed from that of strain 11-1 in many characteristics, including the n ...201323160122
ortholugedb: a bacterial and archaeal orthology resource for improved comparative genomic analysis.prediction of orthologs (homologous genes that diverged because of speciation) is an integral component of many comparative genomics methods. although orthologs are more likely to have similar function versus paralogs (genes that diverged because of duplication), recent studies have shown that their degree of functional conservation is variable. also, there are inherent problems with several large-scale ortholog prediction approaches. to address these issues, we previously developed ortholuge, w ...201223203876
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