| further perspective on the catalytic core and secondary structure of ribonuclease p rna. | phylogenetic comparative analyses of rnase p rna-encoding gene sequences from chlorobium limicola, chlorobium tepidum, bacteroides thetaiotaomicron, and flavobacterium yabuuchiae refine the secondary structure model of the general (eu)bacterial rnase p rna and show that a highly conserved feature of that rna is not essential. two helices, comprised of 2 base pairs each, are added to the secondary structure model and form part of a cruciform in the rna. novel sequence variations in the b. thetaio ... | 1994 | 7511814 |
| evaluation of the vitek 2 system for rapid identification of medically relevant gram-negative rods. | the new vitek 2 system (biomérieux) was evaluated at two independent sites with the identification card for gram-negative bacilli (id-gnb card). of the 845 strains tested, which represented 70 different taxa belonging to either the family enterobacteriaceae or the nonenteric bacilli, 716 (84.7%) were correctly identified at the species level. thirty-two (3.8%) additional strains were identified to the species level after the performance of simple, rapid manual tests (oxidase, hemolysis, indole r ... | 1998 | 9650942 |
| isolation and expression in escherichia coli of csla and cslb, genes coding for the chondroitin sulfate-degrading enzymes chondroitinase ac and chondroitinase b, respectively, from flavobacterium heparinum. | in medium supplemented with chondroitin sulfate, flavobacterium heparinum synthesizes and exports two chondroitinases, chondroitinase ac (chondroitin ac lyase; ec 4.2.2.5) and chondroitinase b (chondroitin b lyase; no ec number), into its periplasmic space. chondroitinase ac preferentially depolymerizes chondroitin sulfates a and c, whereas chondroitinase b degrades only dermatan sulfate (chondroitin sulfate b). the genes coding for both enzymes were isolated from f. heparinum and designated csl ... | 2000 | 10618199 |
| evaluation of autoscan-w/a and the vitek gni+ automicrobic system for identification of non-glucose-fermenting gram-negative bacilli. | the autoscan-w/a (w/a; dade behring microscan inc., west sacramento, calif.) and vitek automicrobic system (vitek ams; biomérieux vitek systems, inc., hazelwood, mo.) are both fully automated microbiology systems. we evaluated the accuracy of these two systems in identifying nonglucose-fermenting gram-negative bacilli. we used the w/a with conventional-panel neg combo type 12 and vitek gni+ identification systems. a total of 301 isolates from 25 different species were tested. of these, 299 isola ... | 2000 | 10699007 |
| a novel protein-deamidating enzyme from chryseobacterium proteolyticum sp. nov., a newly isolated bacterium from soil. | a novel protein-deamidating enzyme, which has potential for industrial applications, was purified from the culture supernatant of chryseobacterium proteolyticum strain 9670(t) isolated from rice field soil in tsukuba, japan. the deamidating activities on carboxybenzoxy (cbz)-gln-gly and caseins and protease activity were produced synchronously by the isolate. both deamidating activities were eluted as identical peaks separated from several proteases by phenyl-sepharose chromatography of the cult ... | 2000 | 10919788 |
| phylogenetic characterization and in situ detection of a cytophaga-flexibacter-bacteroides phylogroup bacterium in tuber borchii vittad. ectomycorrhizal mycelium. | mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. in this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus tuber borchii vittad. universal eubacterial primers specific for the 5' and 3' ends of the 16s rrna gene (16s rdna) were used for pcr ampli ... | 2000 | 11055961 |
| seasonal change in bacterial flora and biomass in mountain snow from the tateyama mountains, japan, analyzed by 16s rrna gene sequencing and real-time pcr. | the bacterial flora and biomass in mountain snow from the tateyama mountains, toyama prefecture, japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal dna restriction analysis followed by 16s rrna gene sequencing and dna quantification by real-time pcr. samples of surface snow collected in various months during the melting season contained a psychrophilic bacterium, cryobacterium psychrophilum, and two psychrotrophic bacteria, variovorax paradoxus and jan ... | 2005 | 15640179 |
| extrinsic allergic alveolitis (hypersensitivity pneumonitis) caused by sphingobacterium spiritivorum from the water reservoir of a steam iron. | a case of extrinsic allergic alveolitis (eaa) caused by sphingobacterium spiritivorum is described. the symptoms were associated with the use of a steam iron. the water reservoir was heavily contaminated with s. spiritivorum (10(6) cfu ml(-1)). this is the first report of s. spiritivorum as a causative agent of eaa. | 2005 | 16145174 |
| molecular characterization of membrane-associated soluble serine palmitoyltransferases from sphingobacterium multivorum and bdellovibrio stolpii. | serine palmitoyltransferase (spt) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl coenzyme a (coa) to form 3-ketodihydrosphingosine (kds). eukaryotic spts comprise tightly membrane-associated heterodimers belonging to the pyridoxal 5'-phosphate (plp)-dependent alpha-oxamine synthase family. sphingomonas paucimobilis, a sphingolipid-containing bacterium, contains an abundant water-soluble homodimeric spt of the same family (h. ... | 2007 | 17557831 |
| multiplex tandem pcr: a novel platform for rapid detection and identification of fungal pathogens from blood culture specimens. | we describe the first development and evaluation of a rapid multiplex tandem pcr (mt-pcr) assay for the detection and identification of fungi directly from blood culture specimens that have been flagged as positive. the assay uses a short-cycle multiplex amplification, followed by 12 simultaneous pcrs which target the fungal internal transcribed spacer 1 (its1) and its2 region, elongation factor 1-alpha (ef1-alpha), and beta-tubulin genes to identify 11 fungal pathogens: candida albicans, candid ... | 2008 | 18632914 |
| evaluation of an immunochromatographic assay kit for rapid identification of mycobacterium tuberculosis complex in clinical isolates. | we evaluated a new immunochromatographic assay (ica) using mouse monoclonal anti-mpt64 antibody for rapid discrimination between mycobacterium tuberculosis and nontuberculous mycobacteria in clinical isolates. a study with mycobacteria and other organisms showed excellent sensitivity (approximately equal 99%) and specificity (100%) and an appropriate detection limit (10(5) cfu/ml) when tested with m. tuberculosis h37rv. this ica can simplify the identification of m. tuberculosis in clinical labo ... | 2009 | 19052177 |
| evaluation of an immunochromatographic assay kit for rapid identification of mycobacterium tuberculosis complex in clinical isolates. | we evaluated a new immunochromatographic assay (ica) using mouse monoclonal anti-mpt64 antibody for rapid discrimination between mycobacterium tuberculosis and nontuberculous mycobacteria in clinical isolates. a study with mycobacteria and other organisms showed excellent sensitivity (approximately equal 99%) and specificity (100%) and an appropriate detection limit (10(5) cfu/ml) when tested with m. tuberculosis h37rv. this ica can simplify the identification of m. tuberculosis in clinical labo ... | 2009 | 19052177 |
| sphingobacterium respiratory tract infection in patients with cystic fibrosis. | bacteria that belong to the genus sphingobacterium are gram-negative, non-fermentative bacilli, ubiquitous in nature and rarely involved in human infections. the aims of this study were to evaluate the epidemiology of infection by sphingobacterium in a cohort of patients affected by cystic fibrosis (cf), the antibiotic susceptibility and the dna fingerprinting of the isolated strains and to analyze some clinical outcomes of the infected patients. | 2009 | 20030840 |
| species specificity, surface exposure, protein expression, immunogenicity, and participation in biofilm formation of porphyromonas gingivalis hmuy. | porphyromonas gingivalis is a major etiological agent of chronic periodontitis. the aim of this study was to examine the species specificity, surface exposure, protein expression, immunogenicity, and participation in biofilm formation of the p. gingivalis heme-binding protein hmuy. | 2010 | 20438645 |
| identification of cold-temperature-regulated genes in flavobacterium psychrophilum. | flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease (bcwd) and rainbow trout fry syndrome (rtfs). it causes disease primarily in fresh water-reared salmonids, but other fish species can also be affected. a diverse array of clinical conditions is associated with bcwd, including tail rot (peduncle disease), necrotic myositis, and cephalic osteochondritis. degradation of connective and muscular tissues by extracellular proteases is common to all of these presentatio ... | 2011 | 21216906 |
| cross-protective immunity against leptospirosis elicited by a live, attenuated lipopolysaccharide mutant. | leptospira species cause leptospirosis, a zoonotic disease found worldwide. current vaccines against leptospirosis provide protection only against closely related serovars. | 2011 | 21220775 |
| achromobacter xylosoxidans respiratory tract infection in cystic fibrosis patients. | the aims of this study were to evaluate the frequency of achromobacter xylosoxidans infection in a cohort of cystic fibrosis patients, to investigate antimicrobial sensitivity, to establish possible clonal likeness among strains, and to address the clinical impact of this infection or colonization on the general outcome of these patients. the study was undertaken between january 2004 and december 2008 on 300 patients receiving care at the regional cystic fibrosis center of the naples university ... | 2011 | 21279730 |
| 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 ... | 2011 | 21289149 |
| a novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and dna viral systems. | the use of nucleases as toxins for defense, offense or addiction of selfish elements is widely encountered across all life forms. using sensitive sequence profile analysis methods, we characterize a novel superfamily (the sukh superfamily) that unites a diverse group of proteins including smi1/knr4, pgs2, fbxo3, skip16, syd, herpesviral us22, irs1 and trs1, and their bacterial homologs. using contextual analysis we present evidence that the bacterial members of this superfamily are potential imm ... | 2011 | 21306995 |
| structural properties of 2/2 hemoglobins: the group iii protein from helicobacter hepaticus. | the e-proteobacterium helicobacter hepaticus (hh) contains a gene coding for a hemoglobin (hb). the protein belongs to the 2/2 hb lineage and is representative of group iii, a set of hbs about which little is known. an expression and purification procedure was developed for hh hb. electronic absorption and nuclear magnetic resonance (nmr) spectra were used to characterize ligation states of the ferric and ferrous protein. the pk(a) of the acid/alkaline transition of ferric hh hb was 7.3, an unus ... | 2011 | 21445851 |
| comparative fecal metagenomics unveils unique functional capacity of the swine gut. | abstract: background: uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. nonetheless, limited information on the functional diversity of the swine gut microbiome is available. results: analysis of 637, 722 pyrosequencing reads (130 megabases) generated from yorkshire pig fecal dna extracts was performed ... | 2011 | 21575148 |
| Identification and Characterization of the Rhizobium sp. Strain GIN611 Glycoside Oxidoreductase Resulting in the Deglycosylation of Ginsenosides. | Using enrichment culture, Rhizobium sp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex from Rhizobium sp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosyl ... | 2012 | 22020506 |
| ehrlichia chaffeensis tandem repeat proteins and ank200 are type 1 secretion system substrates related to the repeats-in-toxin exoprotein family. | ehrlichia chaffeensis has type 1 and 4 secretion systems (t1ss and t4ss), but the substrates have not been identified. potential substrates include secreted tandem repeat protein (trp) 47, trp120, and trp32, and the ankyrin repeat protein, ank200, that are involved in molecular host-pathogen interactions including dna binding and a network of protein-protein interactions with host targets associated with signaling, transcriptional regulation, vesicle trafficking, and apoptosis. in this study we ... | 2011 | 22919588 |
| gliding motility and por secretion system genes are widespread among members of the phylum bacteroidetes. | the phylum bacteroidetes is large and diverse, with rapid gliding motility and the ability to digest macromolecules associated with many genera and species. recently, a novel protein secretion system, the por secretion system (porss), was identified in two members of the phylum, the gliding bacterium flavobacterium johnsoniae and the nonmotile oral pathogen porphyromonas gingivalis. the components of the porss are not similar in sequence to those of other well-studied bacterial secretion systems ... | 2013 | 23123910 |
| evolution of dna ligases of nucleo-cytoplasmic large dna viruses of eukaryotes: a case of hidden complexity. | eukaryotic nucleo-cytoplasmic large dna viruses (ncldv) encode most if not all of the enzymes involved in their dna replication. it has been inferred that genes for these enzymes were already present in the last common ancestor of the ncldv. however, the details of the evolution of these genes that bear on the complexity of the putative ancestral ncldv and on the evolutionary relationships between viruses and their hosts are not well understood. | 2009 | 20021668 |
| polyketide genes in the marine sponge plakortis simplex: a new group of mono-modular type i polyketide synthases from sponge symbionts. | sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. screening of the metagenome of the marine sponge plakortis simplex led to the discovery of the swf family, a new group of mono-modular type i polyketide synthase/fatty acid synthase (pks/fas) specifically associated with sponge symbionts. two different example ... | 2013 | 24249289 |
| matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity. | sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. however, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. in the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity a ... | 2016 | 27749924 |
| molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers. | highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ... | 2014 | 26019546 |
| streptophyte phytochromes exhibit an n-terminus of cyanobacterial origin and a c-terminus of proteobacterial origin. | phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. prototypical phytochromes exhibit an n-terminal tridomain (pgp) consisting of pas, gaf and phy domains and a c-terminal histidine kinase (hk). | 2015 | 25886068 |
| phylum-wide general protein o-glycosylation system of the bacteroidetes. | the human gut symbiont bacteroides fragilis has a general protein o-glycosylation system in which numerous extracytoplasmic proteins are glycosylated at a three amino acid motif. in b. fragilis, protein glycosylation is a fundamental and essential property as mutants with protein glycosylation defects have impaired growth and are unable to competitively colonize the mammalian intestine. in this study, we analysed the phenotype of b. fragilis mutants with defective protein glycosylation and found ... | 2013 | 23551589 |
| metaphylogenomic and potential functionality of the limpet patella pellucida's gastrointestinal tract microbiome. | this study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet patella pellucida. using a modified indirect dna extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. the members of three significantly abundant phyla of proteobacteria, firmicutes and bacteroidetes were characterized through the literature and their ... | 2014 | 25334059 |
| comprehensive laboratory evaluation of a highly specific lateral flow assay for the presumptive identification of bacillus anthracis spores in suspicious white powders and environmental samples. | we conducted a comprehensive, multiphase laboratory evaluation of the anthrax biothreat alert(®) test strip, a lateral flow immunoassay (lfa) for the rapid detection of bacillus anthracis spores. the study, conducted at 2 sites, evaluated this assay for the detection of spores from the ames and sterne strains of b. anthracis, as well as those from an additional 22 strains. phylogenetic near neighbors, environmental background organisms, white powders, and environmental samples were also tested. ... | 2016 | 27661796 |
| retro-morfs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction. | many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (morfs). a well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. in this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying morf-based protein-protein interactions. the method of reverse sequ ... | 2010 | 21152297 |
| matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. | within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (ms). historically, ms was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. today, matrix-assisted laser desorption ionization-time of flight ... | 2013 | 23824373 |
| trends of antibiotic resistance in mesophilic and psychrotrophic bacterial populations during cold storage of raw milk. | psychrotrophic bacteria in raw milk are most well known for their spoilage potential and cause significant economic losses in the dairy industry. despite their ability to produce several exoenzyme types at low temperatures, psychrotrophs that dominate the microflora at the time of spoilage are generally considered benign bacteria. it was recently reported that raw milk-spoiling gram-negative-psychrotrophs frequently carried antibiotic resistance (ar) features. the present study evaluated ar to f ... | 2012 | 23724333 |
| occurrence of horizontal gene transfer of p(ib)-type atpase genes among bacteria isolated from the uranium rich deposit of domiasiat in north east india. | uranium (u) tolerant aerobic heterotrophs were isolated from the subsurface soils of one of the pre-mined u-rich deposits at domiasiat located in the north-eastern part of india. on screening of genomic dna from 62 isolates exhibiting superior u and heavy metal tolerance, 32 isolates were found to be positive for p(ib)-type atpase genes. phylogenetic incongruence and anomalous dna base compositions revealed the acquisition of p(ib)-type atpase genes by six isolates through horizontal gene transf ... | 2012 | 23133569 |
| cloning, sequencing, and in silico analysis of β-propeller phytase bacillus licheniformis strain pb-13. | β -propeller phytases (bpphy) are widely distributed in nature and play a major role in phytate-phosphorus cycling. in the present study, a bpphy gene from bacillus licheniformis strain was expressed in e. coli with a phytase activity of 1.15 u/ml and specific activity of 0.92 u/mg proteins. the expressed enzyme represented a full length orf "phypb13" of 381 amino acid residues and differs by 3 residues from the closest similar existing bpphy sequences. the phypb13 sequence was characterized in ... | 2014 | 24864215 |
| biodiversity of sphingoid bases ("sphingosines") and related amino alcohols. | "sphingosin" was first described by j. l. w. thudichum in 1884 and structurally characterized as 2s,3r,4e-2-aminooctadec-4-ene-1,3-diol in 1947 by herb carter, who also proposed the designation of "lipides derived from sphingosine as sphingolipides." this category of amino alcohols is now known to encompass hundreds of compounds that are referred to as sphingoid bases and sphingoid base-like compounds, which vary in chain length, number, position, and stereochemistry of double bonds, hydroxyl gr ... | 2008 | 18499644 |
| a novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes. | the mucosal microbiota is recognised as an important factor for our health, with many disease states linked to imbalances in the normal community structure. hence, there is considerable interest in identifying the molecular basis of human-microbe interactions. in this work we investigated the capacity of microbes to thrive on mucosal surfaces, either as mutualists, commensals or pathogens, using comparative genomics to identify co-occurring molecular traits. we identified a novel domain we named ... | 2012 | 22299034 |
| draft genome sequence of arcticibacter svalbardensis strain mn12-7t, a member of the family sphingobacteriaceae isolated from an arctic soil sample. | the 4.69-mb genome sequence of arcticibacter svalbardensis strain mn12-7(t), isolated from an arctic soil sample, is reported. | 2013 | 23846277 |
| the first korean case of sphingobacterium spiritivorum bacteremia in a patient with acute myeloid leukemia. | sphingobacterium spiritivorum has been rarely isolated from clinical specimens of immunocompromised patients, and there have been no case reports of s. spiritivorum infection in korea to our knowledge. we report a case of s. spiritivorum bacteremia in a 68-yr-old woman, who was diagnosed with acute myeloid leukemia and subsequently received chemotherapy. one day after chemotherapy ended, her body temperature increased to 38.3℃. a gram-negative bacillus was isolated in aerobic blood cultures and ... | 2013 | 23826566 |
| a novel sphingolipid-torc1 pathway critically promotes postembryonic development in caenorhabditis elegans. | regulation of animal development in response to nutritional cues is an intensely studied problem related to disease and aging. while extensive studies indicated roles of the target of rapamycin (tor) in sensing certain nutrients for controlling growth and metabolism, the roles of fatty acids and lipids in tor-involved nutrient/food responses are obscure. caenorhabditis elegans halts postembryonic growth and development shortly after hatching in response to monomethyl branched-chain fatty acid (m ... | 2013 | 23705068 |
| nasopharyngeal carriage of klebsiella pneumoniae and other gram-negative bacilli in pneumonia-prone age groups in semarang, indonesia. | gram-negative bacilli (gnb) cause many cases of pneumonia in indonesia. we investigated nasopharyngeal carriage of gnb in semarang, indonesia. klebsiella pneumoniae carriage in adults (15%) was higher than in children (7%) (p = 0.004), while that of other gnb was comparable. poor food and water hygiene are determinants of carriage of these bacteria. | 2013 | 23486716 |
| genome of the pathogen porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. | although biofilms have been shown to be reservoirs of pathogens, our knowledge of the microbial diversity in biofilms within critical areas, such as health care facilities, is limited. available methods for pathogen identification and strain typing have some inherent restrictions. in particular, culturing will yield only a fraction of the species present, pcr of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect ... | 2013 | 23564253 |
| a prospective study of the causes of febrile illness requiring hospitalization in children in cambodia. | febrile illnesses are pre-eminent contributors to morbidity and mortality among children in south-east asia but the causes are poorly understood. we determined the causes of fever in children hospitalised in siem reap province, cambodia. | 2013 | 23593267 |
| draft genome sequence of sphingobacterium sp. strain pm2-p1-29, a tetracycline-degrading tetx-expressing aerobic bacterium isolated from agricultural soil. | the genome of sphingobacterium sp. strain pm2-p1-29 was sequenced. the bacterium contains a physiologically active tet(x) gene, encoding a tetracycline-degrading monooxygenase. to our knowledge, this is the only bacterium naturally harboring tet(x) for which tetracycline degradation has been demonstrated. | 2014 | 25301646 |
| phylogenetic analysis and evolutionary origins of dna polymerase x-family members. | mammalian dna polymerase (pol) β is the founding member of a large group of dna polymerases now termed the x-family. dna polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the x-family of dna polymerases. the bacterial x-family dna polymerases, saccharomyces cerevisiae pol iv, and four mammalian x-fam ... | 2014 | 25112931 |
| four novel algal virus genomes discovered from yellowstone lake metagenomes. | phycodnaviruses are algae-infecting large dsdna viruses that are widely distributed in aquatic environments. here, partial genomic sequences of four novel algal viruses were assembled from a yellowstone lake metagenomic data set. genomic analyses revealed that three yellowstone lake phycodnaviruses (yslpvs) had genome lengths of 178,262 bp, 171,045 bp, and 171,454 bp, respectively, and were phylogenetically closely related to prasinoviruses (phycodnaviridae). the fourth (yslgv), with a genome le ... | 2015 | 26459929 |
| unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw. | based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted rws and tws (bred on wheat straw). using the metagenomes of three selected batches of two experimental systems, about 1.2 gb of sequence was generated. comparative analyses revealed an overrepresentation of predicted carbohy ... | 2015 | 26343383 |
| characterization of two-step deglycosylation via oxidation by glycoside oxidoreductase and defining their subfamily. | herein, we report a two-step deglycosylation mediated by the oxidation of glycoside which is different from traditional glycoside hydrolase (gh) mechanism. previously, we reported a novel flavin adenine dinucleotide (fad)-dependent glycoside oxidoreductase (fad-go) having deglycosylation activity. various features of the reaction of fad-go such as including mechanism and catalytic residue and substrate specificity were studied. in addition, classification of novel fad-go subfamily was attempted. ... | 2015 | 26057169 |
| whole-genome optical mapping and finished genome sequence of sphingobacterium deserti sp. nov., a new species isolated from the western desert of china. | a novel gram-negative bacterium, designated zwt, was isolated from a soil sample of the western desert of china, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. growth occurred on tgy medium at 5-42°c with an optimum of 30°c, and at ph 7.0-11.0 with an optimum of ph 9.0. the predominant cellular fatty acids were summed feature 3 (c16:1ω7c/c16:1ω6c or c16:1ω6c/c16:1ω7c) (39.22%), iso-c15:0 (27.91%), iso-c17:0 3oh (15.21%), c16:0 (4.98%), iso- ... | 2015 | 25830331 |
| draft genome sequence of pedobacter sp. strain nl19, a producer of potent antibacterial compounds. | here, we report the draft genome sequence of pedobacter sp. strain nl19. the genome has 5.99 mbp and a g+c content of 39.0%. nl19 was isolated from sludge from an abandoned uranium mine in the north of portugal, and it produces potent antibacterials against gram-positive and gram-negative bacteria. | 2015 | 25814603 |
| complete genome sequence of sphingobacterium sp. strain ml3w, isolated from wings of myotis lucifugus infected with white nose syndrome. | sphingobacterium sp. strain ml3w was isolated from the wing of a bat infected with white nose syndrome. we report the complete 5.33-mb genome sequence of sphingobacterium sp. strain ml3w, obtained using pacific biosciences technology. being the second complete sphingobacterium sequence, this will increase knowledge of the genus. | 2015 | 25614576 |
| astrovirus va1/hmo-c: an increasingly recognized neurotropic pathogen in immunocompromised patients. | an 18-month-old boy developed encephalopathy, for which extensive investigation failed to identify an etiology, 6 weeks after stem cell transplant. to exclude a potential infectious cause, we performed high-throughput rna sequencing on brain biopsy. | 2015 | 25572899 |
| evaluation of various culture media for detection of rapidly growing mycobacteria from patients with cystic fibrosis. | isolation of nontuberculous mycobacteria (ntm) from the sputum of patients with cystic fibrosis (cf) is challenging due to overgrowth by rapidly growing species that colonize the lungs of patients with cf. extended incubation on burkholderia cepacia selective agar (bcsa) has been recommended as an expedient culture method for the isolation of rapidly growing ntm in this setting. the aim of this study was to assess five selective media designed for the isolation of burkholderia cepacia complex, a ... | 2016 | 27098962 |
| sphingobacterium spiritivorum infection in a patient with end stage renal disease on haemodialysis. | sphingobacterium spiritivorum is a microorganism that is ubiquitously found in the environment. however, it is rarely isolated from human clinical specimens. there are few reports to date of sphingobacterium spiritivorum causing disease in humans. | 2016 | 27090094 |