Publications

TitleAbstractYear(sorted ascending)
Filter
PMID
Filter
bactobolin resistance is conferred by mutations in the l2 ribosomal protein.burkholderia thailandensis produces a family of polyketide-peptide molecules called bactobolins, some of which are potent antibiotics. we found that growth of b. thailandensis at 30°c versus that at 37°c resulted in increased production of bactobolins. we purified the three most abundant bactobolins and determined their activities against a battery of bacteria and mouse fibroblasts. two of the three compounds showed strong activities against both bacteria and fibroblasts. the third analog was mu ...201223249812
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
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
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
ralstonia pickettii sepsis in a hemodialysis patient from bulgaria. 201222846135
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
pvc-piping promotes growth of ralstonia pickettii in dialysis water treatment facilities.biofilms forming inside dialysis water treatment systems are one of the main sources of microbiological contamination. among the bacteria found in biofilms, ralstonia pickettii is frequently encountered in dialysis water treatment systems and has been shown to develop extreme oligotrophic talents. in austria, r. pickettii was exclusively detected in high numbers in dialysis water treatment facilities equipped with chlorinated polyvinyl chloride (pvc-c) piping. in this laboratory study it was sho ...201323985526
opportunistic bacteria in dental unit waterlines: assessment and characteristics.the study aimed to determine qualitative and quantitative contamination of dental unit reservoir water with aerobic and facultative anaerobic bacteria, with regards to health risk to dental staff and patients.201323642121
the antibiotic susceptibility of water-based bacteria ralstonia pickettii and ralstonia insidiosa.ralstonia pickettii and ralstonia insidiosa are waterborne bacteria that can survive and grow in various water sources, and that are emerging pathogens in hospital settings. not much is known about the antibiotic resistance of these bacteria. previous reports of antimicrobial susceptibility have been largely limited to a few clinical strains with no accounting for genotypic or phenotypic diversity or that these species could vary from the set breakpoints. etests and disc diffusion tests were car ...201323579396
widespread occurrence of the tfd-ii genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pdb1 and p712.variovorax sp. strain db1 and pseudomonas pickettii strain 712 are 2,4-dicholorophenoxy-acetic acid (2,4-d)-degrading bacteria, which were isolated from agricultural soils in republic of korea and usa, respectively. each strain harbors a 2,4-d degradative plasmid and is able to utilize 2,4-d as the sole source of carbon for its growth. the 2,4-d degradative plasmid pdb1 of strain db1 consisted of a 65,269-bp circular molecule with a g+c content of 66.23% and had 68 orfs. the 2,4-d degradative pl ...201323376020
the regulatory mechanism of 2,4,6-trichlorophenol catabolic operon expression by hadr in ralstonia pickettii dtp0602.ralstonia pickettii dtp0602 utilizes 2,4,6-trichlorophenol (2,4,6-tcp) as its sole source of carbon. the expression of catabolic pathway genes (hada, hadb and hadc) for 2,4,6-tcp has been reported to be regulated by the lysr-type transcriptional regulator (lttr) hadr. generally, coinducers are recognized as being important for the function of lttrs, and alteration of the lttr-protection sequence and the degree of dna bending are characteristic of lttrs with or without a recognized coinducer. in ...201323347957
sequence-based discovery of bradyrhizobium enterica in cord colitis syndrome.immunosuppression is associated with a variety of idiopathic clinical syndromes that may have infectious causes. it has been hypothesized that the cord colitis syndrome, a complication of umbilical-cord hematopoietic stem-cell transplantation, is infectious in origin.201323924002
detection of extended spectrum β-lactamase in pseudomonas spp. isolated from two tertiary care hospitals in bangladesh.extended spectrum ß-lactamases (esbls) represent a major group of lactamases responsible for resistance, mostly produced by gram-negative bacteria, to newer generations of ß-lactam drugs currently being identified in large numbers worldwide. the present study was undertaken to see the frequency of esbl producing pseudomonas spp. isolated from six hundred clinical specimens (wound, pus, aural, urine, sputum, throat and other swabs) collected over a period of three years from two tertiary care hos ...201323289861
identification and characterization of a periplasmic aminoacyl-phosphatidylglycerol hydrolase responsible for pseudomonas aeruginosa lipid homeostasis.specific aminoacylation of the phospholipid phosphatidylglycerol (pg) with alanine (or with lysine) was shown to render various organisms less susceptible to antimicrobial agents and environmental stresses. in this study, we make use of the opportunistic pathogen pseudomonas aeruginosa to decode orf pa0919-dependent lipid homeostasis. analysis of the polar lipid content of the deletion mutant δpa0919 indicated significantly enlarged levels of alanyl-pg. the resulting phenotype manifested an incr ...201323792962
novel extracellular phb depolymerase from streptomyces ascomycinicus: phb copolymers degradation in acidic conditions.the ascomycin-producer strain streptomyces ascomycinicus has been proven to be an extracellular poly(r)-3-hydroxybutyrate (phb) degrader. the fkbu gene, encoding a phb depolymerase (phaz sa ), has been cloned in e. coli and rhodococcus sp. t104 strains for gene expression. gram-positive host rhodococcus sp. t104 was able to produce and secrete to the extracellular medium an active protein form. phaz sa was purified by two hydrophobic interaction chromatographic steps, and afterwards was biochemi ...201323951224
hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities.microbial reduction of toxic hexavalent chromium (cr(vi)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. however, higher [cr(vi)] may impose stress on syntrophic communities and impact community structure and function. the study objectives were to understand the impacts of cr(vi) concentrations on community structure and on the cr(vi)-reduction potential of groundwater communities at hanford, wa. steady state continuous flow bioreactors were used to gro ...201324376771
the pathochip, a functional gene array for assessing pathogenic properties of diverse microbial communities.pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. as many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. to assess pathogenic potential in diverse habitats, we developed a functional gene array, the pathochip, constructed with key virulence genes related to major virulence factors, such as adherence, colonizat ...201323765101
filamentous phages of ralstonia solanacearum: double-edged swords for pathogenic bacteria.some phages from genus inovirus use host or bacteriophage-encoded site-specific integrases or recombinases establish a prophage state. during integration or excision, a superinfective form can be produced. the three states (free, prophage, and superinfective) of such phages exert different effects on host bacterial phenotypes. in ralstonia solanacearum, the causative agent of bacterial wilt disease of crops, the bacterial virulence can be positively or negatively affected by filamentous phages, ...201324204365
emergence of unusual nonfermenting gram-negative nosocomial pathogens in a saudi hospital.this study aimed to determine the frequency of isolation and prevalence of drug resistance in nonfermenting gram-negative bacilli (nfgnb) other than pseudomonas aeruginosa and predisposing factors for the acquisition of nosocomial infections caused by these emerging pathogens in a saudi tertiary care hospital. a total of 125 nonduplicating nfgnb nosocomial strains were isolated, of these, 68 (54.4%) were acinetobacter baumannii, 26 (20.8%) stenotrophomonas maltophilia, 14 (11.2%) alcaligenes fae ...201324270139
characterization of the survival ability of cupriavidus metallidurans and ralstonia pickettii from space-related environments.four cupriavidus metallidurans and eight ralstonia pickettii isolates from the space industry and the international space station (iss) were characterized in detail. nine of the 12 isolates were able to form a biofilm on plastics and all were resistant to several antibiotics. r. pickettii isolates from the surface of the mars orbiter prior to flight were 2.5 times more resistant to uv-c(254nm) radiation compared to the r. pickettii type strain. all isolates showed moderate to high tolerance agai ...201323212653
marine viruses, a genetic reservoir revealed by targeted viromics.metagenomics has opened new windows on investigating viral diversity and functions. viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. we have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsdna-enriched libraries from discrete viral populations from a 1-ml water sample. using this approach on an ...201324304671
marine viruses, a genetic reservoir revealed by targeted viromics.metagenomics has opened new windows on investigating viral diversity and functions. viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. we have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsdna-enriched libraries from discrete viral populations from a 1-ml water sample. using this approach on an ...201324304671
identification of silent prosthetic joint infection: preliminary report of a prospective controlled study.we will test the hypothesis that ultrasound supported by polymerase chain reaction (pcr) could improve bacterial identification in non-infected prosthetic joint loosening. the aim was to detect bacterial species in non-infected prosthetic joint loosening using ultrasound and 16s rrna gene sequencing.201323775450
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
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
detection of bacillus anthracis dna in complex soil and air samples using next-generation sequencing.bacillus anthracis is the potentially lethal etiologic agent of anthrax disease, and is a significant concern in the realm of biodefense. one of the cornerstones of an effective biodefense strategy is the ability to detect infectious agents with a high degree of sensitivity and specificity in the context of a complex sample background. the nature of the b. anthracis genome, however, renders specific detection difficult, due to close homology with b. cereus and b. thuringiensis. we therefore elec ...201324039948
epidemiology of bacteremia caused by uncommon non-fermentative gram-negative bacteria.prevalence of bacteremia caused by non-fermentative gram-negative bacteria (nfgnb) has been increasing over the past decade. although many studies have already investigated epidemiology of nfgnb bacteremia, most focused only on common nfgnb including pseudomonas aeruginosa (pa) and acinetobacter baumannii (ab). knowledge of uncommon nfgnb bacteremia is very limited. our study aimed to investigate epidemiology and identify factors associated with uncommon nfgnb bacteremia.201323566113
effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle.antimicrobial growth promoters (agps) are antimicrobial agents administered to livestock in feed for prolonged periods to enhance feed efficiency. beef cattle are primarily finished in confined feeding operations in canada and the usa, and the administration of agps such as chlortetracycline and sulfamethazine (aureo s-700 g) is the standard. the impacts of agps on the intestinal microbiota of beef cattle are currently uncertain; it is documented that agps administered to beef cattle pass throug ...201323578222
microscopic, chemical, and molecular-biological investigation of the decayed medieval stained window glasses of two catalonian churches.we investigated the decayed historical church window glasses of two catalonian churches, both under mediterranean climate. glass surfaces were studied by scanning electron microscopy (sem), energy dispersive spectrometry (eds), and x-ray diffraction (xrd). their chemical composition was determined by wavelength-dispersive spectrometry (wds) microprobe analysis. the biodiversity was investigated by molecular methods: dna extraction from glass, amplification by pcr targeting the16s rrna and its re ...201324092957
rapid 16s rrna next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. we therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. we have combined a semiconductor deep sequencing protocol that produces reads spanning 16s ribosomal rna gene variable regions ...201323734239
structures of protein-protein complexes involved in electron transfer.electron transfer reactions are essential for life because they underpin oxidative phosphorylation and photosynthesis, processes leading to the generation of atp, and are involved in many reactions of intermediary metabolism. key to these roles is the formation of transient inter-protein electron transfer complexes. the structural basis for the control of specificity between partner proteins is lacking because these weak transient complexes have remained largely intractable for crystallographic ...201323535590
complexity, temporal stability, and clinical correlates of airway bacterial community composition in primary ciliary dyskinesia.primary ciliary dyskinesia (pcd) is a genetic disease characterized by abnormalities in ciliary function, leading to compromised airway clearance and chronic bacterial infection of the upper and lower airways. the compositions of these infections and the relationships between their characteristics and disease presentation are poorly defined. we describe here the first systematic culture-independent evaluation of lower airway bacteriology in pcd. thirty-three airway samples (26 from sputum, 7 fro ...201324068019
prevent infection linked to the dialysis water in a hemodialysis center in fez city (morocco).water treatment systems are a critical variable in dialysis therapy. rigorous control of hemodialysis water quality is particularly important in order to guarantee a better quality of life of the hemodialysis patients. the objective of the study was to evaluate the chemical, microbiological quality and antimicrobial resistance of bacteria isolated from water and dialysate in a public hd center.201324839530
the use of platensimycin and platencin to fight antibiotic resistance.infectious diseases are known as one of the most life-threatening disabilities worldwide. approximately 13 million deaths related to infectious diseases are reported each year. the only way to combat infectious diseases is by chemotherapy using antimicrobial agents and antibiotics. however, due to uncontrolled and unnecessary use of antibiotics in particular, surviving bacteria have evolved resistance against several antibiotics. emergence of multidrug resistance in bacteria over the past severa ...201324082790
evaluation of a new lipase from staphylococcus sp. for detergent additive capability.lipases are the enzymes of choice for laundry detergent industries owing to their triglyceride removing ability from the soiled fabric which eventually reduces the usage of phosphate-based chemical cleansers in the detergent formulation. in the present study, a partially purified bacterial lipase from staphylococcus arlettae jpbw-1 isolated from the rock salt mine has been assessed for its triglyceride removing ability by developing a presoak solution so as to use lipase as an additive in laundr ...201324106703
copper enhanced monooxygenase activity and ft-ir spectroscopic characterisation of biotransformation products in trichloroethylene degrading bacterium: stenotrophomonas maltophilia pm102.stenotrophomonas maltophilia pm102 (ncbi genbank acc. no. jq797560) is capable of growth on trichloroethylene as the sole carbon source. in this paper, we report the purification and characterisation of oxygenase present in the pm102 isolate. enzyme activity was found to be induced 10.3-fold in presence of 0.7 mm copper with a further increment to 14.96-fold in presence of 0.05 mm nadh. optimum temperature for oxygenase activity was recorded at 36°c. the reported enzyme was found to have enhance ...201324083236
structure and evolution of chlorate reduction composite transposons.the genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. a newly isolated chlorate-reducing bacterium (shewanella algae acdc) and three previously isolated strains (ideonella dechloratans, pseudomonas sp. strain pk, and dechloromarinus chlorophilus nss) were genome sequenced and compared to published sequences (alicycliphilus denitrificans bc plasmid palide01 and pseudomonas chloritidismutans aw-1). de novo assembly of genomes failed t ...201323919996
hydroquinone: environmental pollution, toxicity, and microbial answers.hydroquinone is a major benzene metabolite, which is a well-known haematotoxic and carcinogenic agent associated with malignancy in occupational environments. human exposure to hydroquinone can occur by dietary, occupational, and environmental sources. in the environment, hydroquinone showed increased toxicity for aquatic organisms, being less harmful for bacteria and fungi. recent pieces of evidence showed that hydroquinone is able to enhance carcinogenic risk by generating dna damage and also ...201323936816
monoclonal antibody-based immunofluorescence microscopy for the rapid identification of burkholderia pseudomallei in clinical specimens.the diagnosis of melioidosis depends on the culture of burkholderia pseudomallei, which takes at least 48 hours. we used a polyclonal-fitc-based immunofluorescence microscopic assay (pab-ifa) on clinical samples to provide a rapid presumptive diagnosis. this has limitations including photobleaching and batch-to-batch variability. this study evaluated an ifa based on a monoclonal antibody specific to b. pseudomallei (mab-ifa) and alexa fluor 488. a diagnostic evaluation was performed on a prospec ...201323716405
key role for efflux in the preservative susceptibility and adaptive resistance of burkholderia cepacia complex bacteria.bacteria from the burkholderia cepacia complex (bcc) are encountered as industrial contaminants, and little is known about the species involved or their mechanisms of preservative resistance. multilocus sequence typing (mlst) revealed that multiple bcc species may cause contamination, with b. lata (n = 17) and b. cenocepacia (n = 11) dominant within the collection examined. at the strain level, 11 of the 31 industrial sequence types identified had also been recovered from either natural environm ...201323587949
microbial biosensors: engineered microorganisms as the sensing machinery.whole-cell biosensors are a good alternative to enzyme-based biosensors since they offer the benefits of low cost and improved stability. in recent years, live cells have been employed as biosensors for a wide range of targets. in this review, we will focus on the use of microorganisms that are genetically modified with the desirable outputs in order to improve the biosensor performance. different methodologies based on genetic/protein engineering and synthetic biology to construct microorganism ...201323648649
multilaboratory study of the biomic automated well-reading instrument versus microscan walkaway for reading microscan antimicrobial susceptibility and identification panels.this study compared the biomic automated well reader results to the microscan walkaway results for reading microscan antimicrobial susceptibility and identification panels at four different sites. routine fresh clinical isolates and quality control (qc) organisms were tested at each study site. a total of 46,176 microscan panel drug-organism combinations were read. the biomic category agreement for 3,117 gram-negative bacteria was 98.4%, with 1.4% minor and 0.2% major discrepancies. the biomic c ...201323486713
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
the microbiome of the middle meatus in healthy adults.rhinitis and rhinosinusitis are multifactorial disease processes in which bacteria may play a role either in infection or stimulation of the inflammatory process. rhinosinusitis has been historically studied with culture-based techniques, which have implicated several common pathogens in disease states. more recently, the nih human microbiome project has examined the microbiome at a number of accessible body sites, and demonstrated differences among healthy and diseased patients. recent dna-base ...201324386477
stability of a lipase extracted from seeds of pachira aquatica in commercial detergents and application tests in poultry wastewater pretreatment and fat particle hydrolysis.a protein extract containing a plant lipase from oleaginous seeds of pachira aquatica was tested using soybean oil, wastewater from a poultry processing plant, and beef fat particles as substrate. the hydrolysis experiments were carried out at a temperature of 40°c, an incubation time of 90 minutes, and ph 8.0-9.0. the enzyme had the best stability at ph 9.0 and showed good stability in the alkaline range. it was found that p. aquatica lipase was stable in the presence of some commercial laundry ...201324455209
scleral buckle infections: microbiological spectrum and antimicrobial susceptibility.the purpose of the present study was to evaluate the microbiological spectrum and antimicrobial susceptibility in patients with scleral buckle infection. medical records of all the patients diagnosed as buckle infection at l. v. prasad eye institute between july 1992 and june 2012 were reviewed in this non-comparative, consecutive, retrospective case series.201324330530
antibiotic susceptibility of staphylococci isolates from patients with chronic conjunctivitis: including associated factors and clinical evaluation.to determine species of staphylococci in chronic conjunctivitis, their antibiotic susceptibility pattern, patient treatments, clinical course, and clinical conditions.201323944906
complete genome sequence of ralstonia pickettii dtp0602, a 2,4,6-trichlorophenol degrader.ralstonia pickettii strain dtp0602 utilizes 2,4,6-trichlorophenol as its sole carbon and energy source. here, we report the complete genome sequence of strain dtp0602, which comprises three chromosomes and no plasmids. we also found that the two had gene clusters responsible for the degradation of 2,4,6-trichlorophenol are located on the 2.9-mb chromosome 2.201324179121
ascitic microbiota composition is correlated with clinical severity in cirrhosis with portal hypertension.identification of pathogenic bacteria in ascites correlates with poor clinical outcomes. ascites samples are commonly reported culture-negative, even where frank infection is indicated. culture-independent methods have previously reported bacterial dna in ascites, however, whether this represents viable bacterial populations has not been determined. we report the first application of 16s rrna gene pyrosequencing and quantitative pcr in conjunction with propidium monoazide sample treatment to cha ...201324086392
insights into the cross-immunity mechanism within effector families of bacteria type vi secretion system from the structure of sttae4-ectai4 complex.the gram-negative bacteria type vi secretion system (t6ss) has been found to play an important role in interbacterial competition, biofilm formation and many other virulence-related processes. the bacteria harboring t6ss inject the effectors into their recipient's cytoplasm or periplasm to kill them and meanwhile, to avoid inhibiting itself, the cognate immunity proteins were produced to acts as the effector inhibitor. tae4 (type vi amidase effector 4) and tai4 (type vi amidase immunity 4) are n ...201324023903
the rpos sigma factor negatively regulates production of iaa and siderophore in a biocontrol rhizobacterium, pseudomonas chlororaphis o6.the stationary-phase sigma factor, rpos, influences the expression of factors important in survival of pseudomonas chlororaphis o6 in the rhizosphere. a partial proteomic profile of a rpos mutant in p. chlororaphis o6 was conducted to identify proteins under rpos regulation. five of 14 differentially regulated proteins had unknown roles. changes in levels of proteins in p. chlororaphis o6 rpos mutant were associated with iron metabolism, and protection against oxidative stress. the p. chlororaph ...201325288959
prokaryotic phylogenies inferred from whole-genome sequence and annotation data.phylogenetic trees are used to represent the evolutionary relationship among various groups of species. in this paper, a novel method for inferring prokaryotic phylogenies using multiple genomic information is proposed. the method is called cgcphy and based on the distance matrix of orthologous gene clusters between whole-genome pairs. cgcphy comprises four main steps. first, orthologous genes are determined by sequence similarity, genomic function, and genomic structure information. second, gen ...201324073404
microbial biofilms and breast tissue expanders.we previously developed and validated a vortexing-sonication technique for detection of biofilm bacteria on the surface of explanted prosthetic joints. herein, we evaluated this technique for diagnosis of infected breast tissue expanders and used it to assess colonization of breast tissue expanders. from april 2008 to december 2011, we studied 328 breast tissue expanders at mayo clinic, rochester, mn, usa. of seven clinically infected breast tissue expanders, six (85.7%) had positive cultures, o ...201323956974
intraclonal genome diversity of pseudomonas aeruginosa clones cha and tb.adaptation of pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. in order to detect the impact of colonized habitats on p. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (cf) isolate cha and two temporally and geographically unrelated clonal variants. the outcome was compared with the intraclonal genome diversity between three m ...201323799896
biochemical diversity of carboxyl esterases and lipases from lake arreo (spain): a metagenomic approach.the esterases and lipases from the α/β hydrolase superfamily exhibit an enormous sequence diversity, fold plasticity, and activities. here, we present the comprehensive sequence and biochemical analyses of seven distinct esterases and lipases from the metagenome of lake arreo, an evaporite karstic lake in spain (42°46'n, 2°59'w; altitude, 655 m). together with oligonucleotide usage patterns and blastp analysis, our study of esterases/lipases mined from lake arreo suggests that its sediment conta ...201323542620
beta-lactamase induction and cell wall metabolism in gram-negative bacteria.production of beta-lactamases, the enzymes that degrade beta-lactam antibiotics, is the most widespread and threatening mechanism of antibiotic resistance. in the past, extensive research has focused on the structure, function, and ecology of beta-lactamases while limited efforts were placed on the regulatory mechanisms of beta-lactamases. recently, increasing evidence demonstrate a direct link between beta-lactamase induction and cell wall metabolism in gram-negative bacteria. specifically, exp ...201323734147
quantitative detection of borrelia burgdorferi sensu lato in erythema migrans skin lesions using internally controlled duplex real time pcr.b. burgdorferi sensu stricto, b. afzelii, b. garinii and b. bavariensis are the principal species which account for lyme borreliosis (lb) globally. we have developed an internally controlled duplex quantitative real time pcr assay targeting the borrelia 16s rrna and the human rnasep genes. this assay is well-suited for laboratory confirmation of suspected cases of lb and will be used to assess the efficacy of a vaccine against lb in clinical trials. the assay is highly specific, successfully det ...201323696863
artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the red sea.the multiple displacement amplification (mda) protocol is reported to introduce different artifacts into dna samples with impurities. in this study, we report an artifactual effect of mda with sediment dna samples from a deep-sea brine basin in the red sea. in the metagenomes, we showed the presence of abundant artifactual 454 pyrosequencing reads over sizes of 50 to 220 bp. gene fragments translocated from neighboring gene regions were identified in these reads. occasionally, the translocation ...201323646288
studying the microbiology of the indoor environment.the majority of people in the developed world spend more than 90% of their lives indoors. here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health.201323514020
a laboratory of extremophiles: iceland coordination action for research activities on life in extreme environments (carex) field campaign.existence of life in extreme environments has been known for a long time, and their habitants have been investigated by different scientific disciplines for decades. however, reports of multidisciplinary research are uncommon. in this paper, we report an interdisciplinary three-day field campaign conducted in the framework of the coordination action for research activities on life in extreme environments (carex) fp7eu program, with participation of experts in the fields of life and earth science ...201325371340
the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation.full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ...201324084083
the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation.full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ...201324084083
functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...201324062736
broad-spectrum biosensor capable of detecting and identifying diverse bacterial and candida species in blood.we describe an assay which uses broad-spectrum, conserved-site pcr paired with mass spectrometry analysis of amplicons (pcr/electrospray ionization-mass spectrometry [esi-ms]) to detect and identify diverse bacterial and candida species in uncultured specimens. the performance of the assay was characterized using whole-blood samples spiked with low titers of 64 bacterial species and 6 candida species representing the breadth of coverage of the assay. the assay had an average limit of detection o ...201323761152
identification of bacterial protein o-oligosaccharyltransferases and their glycoprotein substrates.o-glycosylation of proteins in neisseria meningitidis is catalyzed by pgll, which belongs to a protein family including waal o-antigen ligases. we developed two hidden markov models that identify 31 novel candidate pgll homologs in diverse bacterial species, and describe several conserved sequence and structural features. most of these genes are adjacent to possible novel target proteins for glycosylation. we show that in the general glycosylation system of n. meningitidis, efficient glycosylati ...201323658772
real-time comparative evaluation of biomerieux vitek ms versus bruker microflex ms, two matrix-assisted laser desorption-ionization time-of-flight mass spectrometry systems, for identification of clinically significant bacteria.matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (maldi-tof ms) recently became available for the identification of bacteria in routine diagnostic laboratories. it is rapid and cost-effective and likely to replace phenotypic identification. this study was undertaken to compare two maldi-tof ms-based, bruker microflex ms (bms) and vitek ms (vms) systems, for identification (id) of clinically significant bacterial isolates. clinically relevant broad diversity of bacteri ...201425433488
a brief review: the z-curve theory and its application in genome analysis.in theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. in the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. the z-curve theory is a geometrical approach to genome analysis. the z-curve is a three-dimensional curve that represents a given dna sequence in the sense that each can be uniquely reconst ...201424822026
f-/cl- selectivity in clcf-type f-/h+ antiporters.many bacterial species protect themselves against environmental f(-) toxicity by exporting this anion from the cytoplasm via clc(f) f(-)/h(+) antiporters, a subclass of clc superfamily anion transporters. strong f(-) over cl(-) selectivity is biologically essential for these membrane proteins because cl(-) is orders of magnitude more abundant in the biosphere than f(-). sequence comparisons reveal differences between clc(f)s and canonical cl(-)-transporting clcs within regions that, in the canon ...201425070431
polymicrobial bacteremia involving comamonas testosteroni.comamonas spp. are uncommon isolates in microbiology laboratories and have been rarely observed as an infectious agent in clinical practice. they have widespread environmental distribution and have been isolated from water, soil, and plants as well as from some hospital devices such as intravenous catheters and water contained in humidifier reservoirs used in respiratory treatment. the genus comamonas originally contained the following species: acidovorans, testosteroni, kerstersii, terrigena, d ...201425614744
draft genome assembly of ralstonia pickettii type strain k-288 (atcc 27853).we present the genome assembly of ralstonia pickettii k-288 (atcc 27511), consisting of 27 contigs placed into a single scaffold. this 4.76-mbp genome has 64.0% g+c content and 4,425 coding sequences. because this is the type strain, inclusion of its data set among other ralstonia genomes should provide a historical genomic perspective.201425258272
structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system.productive biomolecular recognition requires exquisite control of affinity and specificity. accordingly, nature has devised many strategies to achieve proper binding interactions. bacterial multicomponent monooxygenases provide a fascinating example, where a diiron hydroxylase must reversibly interact with both ferredoxin and catalytic effector in order to achieve electron transfer and o2 activation during catalysis. because these two accessory proteins have distinct structures, and because the ...201425248368
mercaptosuccinate dioxygenase, a cysteine dioxygenase homologue, from variovorax paradoxus strain b4 is the key enzyme of mercaptosuccinate degradation.the versatile thiol mercaptosuccinate has a wide range of applications, e.g. in quantum dot research or in bioimaging. its metabolism is investigated in variovorax paradoxus strain b4, which can utilize this compound as the sole source of carbon and sulfur. proteomic studies of strain b4 resulted in the identification of a putative mercaptosuccinate dioxygenase, a cysteine dioxygenase homologue, possibly representing the key enzyme in the degradation of mercaptosuccinate. therefore, the putative ...201425228698
draft genome sequences of ralstonia pickettii strains ssh4 and cw2, isolated from space equipment.ralstonia pickettii ssh4 and cw2 were isolated from space equipment. here, we report their draft genome sequences with the aim of gaining insight into their potential to adapt to these environments.201425189592
microbial communities of three sympatric australian stingless bee species.bacterial symbionts of insects have received increasing attention due to their prominent role in nutrient acquisition and defense. in social bees, symbiotic bacteria can maintain colony homeostasis and fitness, and the loss or alteration of the bacterial community may be associated with the ongoing bee decline observed worldwide. however, analyses of microbiota associated with bees have been largely confined to the social honeybees (apis mellifera) and bumblebees (bombus spec.), revealing--among ...201425148082
microbial monitoring of crewed habitats in space-current status and future perspectives.previous space research conducted during short-term flight experiments and long-term environmental monitoring on board orbiting space stations suggests that the relationship between humans and microbes is altered in the crewed habitat in space. both human physiology and microbial communities adapt to spaceflight. microbial monitoring is critical to crew safety in long-duration space habitation and the sustained operation of life support systems on space transit vehicles, space stations, and surf ...201425130885
improved multiple displacement amplification (imda) and ultraclean reagents.next-generation sequencing sample preparation requires nanogram to microgram quantities of dna; however, many relevant samples are comprised of only a few cells. genomic analysis of these samples requires a whole genome amplification method that is unbiased and free of exogenous dna contamination. to address these challenges we have developed protocols for the production of dna-free consumables including reagents and have improved upon multiple displacement amplification (imda).201424906487
rpsu-based discrimination within the genus burkholderia.sequencing of the gene rpsu reliably delineates saprophytic burkholderia (b.) thailandensis from highly pathogenic b. mallei and b. pseudomallei. we analyzed the suitability of this technique for the delineation of the b. pseudomallei complex from other burkholderia species. both newly recorded and previously deposited sequences of well-characterized or reference strains (n = 84) of azoarcus spp., b. ambifaria, b. anthina, b. caledonica, b. caribensis, b. caryophylli, b. cenocepacia, b. cepacia, ...201424883196
first evidence for the presence of iron oxidizing zetaproteobacteria at the levantine continental margins.during the 2010-2011 e/v nautilus exploration of the levantine basin's sediments at the depth of 300-1300 m, densely patched orange-yellow flocculent mats were observed at various locations along the continental margin of israel. cores from the mat and the control locations were collected by remotely operated vehicle system (rov) operated by the e/v nautilus team. microscopic observation and phylogenetic analysis of microbial 16s and 23s rrna gene sequences indicated the presence of zetaproteoba ...201424614177
mentha piperita in nephrotoxicity--a possible intervention to ameliorate renal derangements associated with gentamicin.free radical generation has a strong role in the pathogenesis of renal damage associated with the use of gentamicin. therefore, the present study was carried out to evaluate the renoprotective effect of mentha piperita against gentamicin induced nephrotoxicity.201424741187
microbial biofilms on needleless connectors for central venous catheters: comparison of standard and silver-coated devices collected from patients in an acute care hospital.microorganisms may colonize needleless connectors (ncs) on intravascular catheters, forming biofilms and predisposing patients to catheter-associated infection (cai). standard and silver-coated ncs were collected from catheterized intensive care unit patients to characterize biofilm formation using culture-dependent and culture-independent methods and to investigate the associations between nc usage and biofilm characteristics. viable microorganisms were detected by plate counts from 46% of stan ...201424371233
draft genome sequence of ralstonia pickettii au12-08, isolated from an intravascular catheter in australia.ralstonia pickettii is a nonfermenting gram-negative bacillus that creates a significant problem in clinical settings, as it is a widespread cause of nosocomial infections. here, we report the draft genome sequence of r. pickettii au12-08, isolated from an intravascular catheter tip.201424503988
directly sampling the lung of a young child with cystic fibrosis reveals diverse microbiota.the airways of people with cystic fibrosis (cf) are chronically infected with a variety of bacterial species. although routine culture methods are usually used to diagnose these infections, culture-independent, dna-based methods have identified many bacterial species in cf respiratory secretions that are not routinely cultured. many prior culture-independent studies focused either on microbiota in explanted cf lungs, reflecting end-stage disease, or those in oropharyngeal swabs, which likely sam ...201425072206
cationic synthetic peptides: assessment of their antimicrobial potency in liquid preserved boar semen.various semen extender formulas are in use to maintain sperm longevity and quality whilst acting against bacterial contamination in liquid sperm preservation. aminoglycosides are commonly supplemented to aid in the control of bacteria. as bacterial resistance is increasing worldwide, antimicrobial peptides (amps) received lively interest as alternatives to overcome multi-drug resistant bacteria. we investigated, whether synthetic cationic amps might be a suitable alternative for conventional ant ...201425148109
isolation, identification and characterization of burkholderia pseudomallei from soil of coastal region of india.melioidosis is an emerging infectious disease caused by a free living soil dwelling gram-negative bacterium burkholderia pseudomallei. the disease is endemic to most parts of southeast asia and northern australia and the organism has been isolated from moist soil and water. in india clinical cases are recently reported from the states of tamilnadu, kerala, karnataka, maharashtra, orissa, assam, west bengal, pondicherry and tripura. this study is aimed to confirm the prevalence of this important ...201425187882
persistence of microbial communities including pseudomonas aeruginosa in a hospital environment: a potential health hazard.the persistence of microbial communities and how they change in indoor environments is of immense interest to public health. moreover, hospital acquired infections are significant contributors to morbidity and mortality. evidence suggests that, in hospital environments agent transfer between surfaces causes healthcare associated infections in humans, and that surfaces are an important transmission route and may act as a reservoir for some of the pathogens.this study aimed to evaluate the diversi ...201424885173
performance of mass spectrometric identification of bacteria and yeasts routinely isolated in a clinical microbiology laboratory using maldi-tof ms.matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) is an emerging technology newly applied to identifying bacterial and yeast strains. the aim of this study was to evaluate the clinical performance of the vitek(®) ms system in the identification of bacteria and yeast strains routinely isolated from clinical samples.201424822114
the crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein cae31940 from proteobacterium bordetella bronchiseptica rb50, and evolutionary insight into the nmt1/thi5 family.we report a 2.0 å structure of the cae31940 protein, a proteobacterial nmt1/thi5-like domain-containing protein. we also discuss the primary and tertiary structure similarity with its homologs. the highly conserved fggxmp motif was identified in cae31940, which corresponds to the gcccx motif located in the vicinity of the active center characteristic for thi5-like proteins found in yeast. this suggests that the fggxmp motif may be a unique hallmark of proteobacterial nmt1/thi5-like proteins.201424908050
microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs.the ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or co2, coupled to the oxidation of inorganic or organic compounds. a broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. the physiological groups reviewed here comprise iron-, manganese-, and ...201425225493
ralstonia spp.: emerging global opportunistic pathogens.the bacterial genus ralstonia (gram-negative non-fermenters) is becoming more prevalent in cases of infection with three bacterial species, ralstonia pickettii, ralstonia insidiosa and ralstonia mannitolilytica, making up all cases reported (in the literature) to date. these organisms are prevalent in many different types of water supplies (including hospital water supplies), being well adapted to survive in low-nutrient conditions. they have been shown to cause infections, sometimes serious, su ...201424057141
non-fermentative gram-negative bacteria in hospital tap water and water used for haemodialysis and bronchoscope flushing: prevalence and distribution of antibiotic resistant strains.this study provides a detailed description of the distribution of non-fermentative gram-negative bacteria (nfgnb) collected in water sources (tap water and water used for haemodialysis and bronchoscope flushing) from different wards of a tertiary care hospital. the aim is to identify risk practices for patients or to alert clinicians to the possible contamination of environment and medical devices. the resistance profile of nfgnb environmental isolates has shown that more than half (55.56%) of t ...201425173861
saturation mutagenesis of bradyrhizobium sp. btai1 toluene 4-monooxygenase at alpha-subunit residues proline 101, proline 103, and histidine 214 for regiospecific oxidation of aromatics.a novel toluene monooxygenase (tmo) six-gene cluster from bradyrhizobium sp. btai1 having an overall 35, 36, and 38 % protein similarity with toluene o-xylene monooxygenase (tomo) of pseudomonas sp. ox1, toluene 4-monooxygenase (t4mo) of pseudomonas mendocina kr1, and toluene-para-monooxygenase (tpmo) of ralstonia pickettii pko1, respectively, was cloned and expressed in escherichia coli tg1, and its potential activity was investigated for aromatic hydroxylation and trichloroethylene (tce) degra ...201425016343
combination of photoreactor and packed bed bioreactor for the removal of ethyl violet from wastewater.an efficient treatment system that combines a photoreactor and packed bed bioreactor (pbr) was developed and evaluated for treating ethyl violet (ev)-containing wastewater. initial experiments demonstrated that the optimal operating parameters for the photoreactor in treating ev-containing wastewater were 2h reaction time, ph of 7, and 2 min liquid retention time. under these conditions, the photocatalytic reaction achieved a 61% ev removal efficiency and resulted in a significant bod/cod increa ...201425259784
detection of qnrvc and rmtb genes from a multidrug-resistant ralstonia pickettii wound infection isolate in cambodia. 201424888871
emergence of vim-2 metallo-beta-lactamase producing ralstonia pickettii clinical isolate in india.a multidrug-resistant clinical isolate of ralstonia pickettii from a woman was analysed. modified hodge test was positive for carbapenemase production. conjugation experiment revealed the presence of conjugative plasmid of >140 kb size typed as incn type. this is the first report of emergence blavim-2 in r. pickettii in india.201424713914
effects of mutation at position 285 of ralstonia pickettii t1 poly[(r)-3-hydroxybutyrate] depolymerase on its activities.asn at position 285 (n285) in the catalytic domain of poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 most likely participates in the cleavage of ester bonds as revealed by our previous evolutionary engineering study using the error-prone polymerase chain reaction (pcr) method. to exhaustively examine the effects of mutations at that position, we conducted site-directed saturation mutagenesis at that position and the resultant mutant enzymes (n285x) were evaluated in p ...201424676749
[outbreak with ralstonia pickettii caused by contaminated magnesium vials].in february 2013, 5 patients in an intensive care unit (icu) were found to have positive blood cultures with ralstonia pickettii within one week. because all patients got intravenous therapy, improper work of a staff member was suspected. some days later, a 6th patient was found with a positive blood culture of ralstonia pickettii in another department of the hospital.201424496893
transcriptional repression of the poly(3-hydroxybutyrate) depolymerase in ralstonia pickettii t1 by a tetr-like gene.ralstonia pickettii t1 secretes a poly(3-hydroxybutyrate) (phb) depolymerase (phaz) and a 3-hydroxybutyrate (3hb)-oligomer hydrolase, and extracellularly degrades phb to produce 3hb. however, it is not clear how the expression of phaz is regulated. in this study, the mechanism by which phaz expression is controlled in r. pickettii t1 was examined using a mutant made by the random insertion of a transposon, tn5. the mutant produced a larger amount of phaz than the wild type in nutrient broth or a ...201424146107
genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses.the achromobacter is a genus in the family alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. the ability to detect and correctly identify achromobacter species, particularly a. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (cf), as well as for nosocomial and other opportunistic infections. traditiona ...201425474264
metagenomic analysis of the airborne environment in urban spaces.the organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. to examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. whole metagenome sequencing was applied to dna extracted from air filters obtained during periods from each of the four seasons. the composition of bacteria, plants, fun ...201425351142
metagenomic analysis of the airborne environment in urban spaces.the organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. to examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. whole metagenome sequencing was applied to dna extracted from air filters obtained during periods from each of the four seasons. the composition of bacteria, plants, fun ...201425351142
Refresh
firstprev
12345678
nextlast
Displaying items 601 - 700 of 787