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rapid and accurate diagnosis of human intestinal spirochetosis by fluorescence in situ hybridization.human intestinal spirochetosis (his) is associated with overgrowth of the large intestine by spirochetes of the genus brachyspira. the microbiological diagnosis of his is hampered by the fastidious nature and slow growth of brachyspira spp. in clinical practice, his is diagnosed histopathologically, and a significant portion of cases may be missed. fluorescence in situ hybridization (fish) is a molecular method that allows the visualization and identification of single bacteria within tissue sec ...200919279178
the genome of bacillus subtilis bacteriophage spo1.we report the genome sequence of bacillus subtilis phage spo1. the unique genome sequence is 132,562 bp long, and dna packaged in the virion (the chromosome) has a 13,185-bp terminal redundancy, giving a total of 145,747 bp. we predict 204 protein-coding genes and 5 trna genes, and we correlate these findings with the extensive body of investigations of spo1, including studies of the functions of the 61 previously defined genes and studies of the virion structure. sixty-nine percent of the encod ...200919285085
unique structure and stability of hmuy, a novel heme-binding protein of porphyromonas gingivalis.infection, survival, and proliferation of pathogenic bacteria in humans depend on their capacity to impair host responses and acquire nutrients in a hostile environment. among such nutrients is heme, a co-factor for oxygen storage, electron transport, photosynthesis, and redox biochemistry, which is indispensable for life. porphyromonas gingivalis is the major human bacterial pathogen responsible for severe periodontitis. it recruits heme through hmuy, which sequesters heme from host carriers an ...200919424422
bypass suppression analysis maps the signalling pathway within a multidomain protein: the rsbp energy stress phosphatase 2c from bacillus subtilis.the network controlling the general stress response in bacillus subtilis requires both the rsbp phosphatase and the rsbq alpha/beta hydrolase to convey signals of energy stress. rsbp contains three domains: an n-terminal pas, a central coiled-coil and a c-terminal pp2c phosphatase. we report here a genetic analysis that established the functional interactions of the domains and their relationship to rsbq. random mutagenesis of rsbp yielded 17 independent bypass suppressors that had activity in a ...200919432806
plasminogen acquisition and activation at the surface of leptospira species lead to fibronectin degradation.pathogenic leptospira species are the etiological agents of leptospirosis, a widespread disease of human and veterinary concern. in this study, we report that leptospira species are capable of binding plasminogen (plg) in vitro. the binding to the leptospiral surface was demonstrated by indirect immunofluorescence confocal microscopy with living bacteria. the plg binding to the bacteria seems to occur via lysine residues because the ligation is inhibited by addition of the lysine analog 6-aminoc ...200919581392
borrelia burgdorferi resistance to a major skin antimicrobial peptide is independent of outer surface lipoprotein content.we hypothesize a potential role for borrelia burgdorferi ospc in innate immune evasion at the initial stage of mammalian infection. we demonstrate that b. burgdorferi is resistant to high levels (>200 microg/ml) of cathelicidin and that this antimicrobial peptide exhibits limited binding to the spirochetal outer membrane, irrespective of ospc or other abundant surface lipoproteins. we conclude that the essential role of ospc is unrelated to resistance to this component of innate immunity.200919651916
leptosome-entrapped leptospiral antigens conferred significant higher levels of protection than those entrapped with pc-liposomes in a hamster model.we prepared novel liposomes from total polar lipids of non-pathogenic leptospira biflexa serovar potac (designated leptosomes) and evaluated their vaccine delivery/adjuvant potential with novel protective antigens (lp0607, lp1118 and lp1454) of l. interrogans serovar pomona in a hamster model. the immune response induced by three individual antigens and protective efficacy were evaluated and compared to those induced by same antigens entrapped with pc-liposomes and e. coli lipid liposomes (esche ...200919729088
bioinformatics and functional analysis define four distinct groups of alkb dna-dioxygenases in bacteria.the iron(ii)- and 2-oxoglutarate (2og)-dependent dioxygenase alkb from escherichia coli (ecalkb) repairs alkylation damage in dna by direct reversal. ecalkb substrates include methylated bases, such as 1-methyladenine (m(1)a) and 3-methylcytosine (m(3)c), as well as certain bulkier lesions, for example the exocyclic adduct 1,n(6)-ethenoadenine (epsilona). ecalkb is the only bacterial alkb protein characterized to date, and we here present an extensive bioinformatics and functional analysis of ba ...200919786499
leptospira interrogans binds to human cell surface receptors including proteoglycans.leptospirosis is a global public health problem, primarily in the tropical developing world. the pathogenic mechanisms of the causative agents, several members of the genus leptospira, have been underinvestigated. the exception to this trend has been the demonstration of the binding of pathogenic leptospires to the extracellular matrix (ecm) and its components. in this work, interactions of leptospira interrogans bacteria with mammalian cells, rather than the ecm, were examined. the bacteria bou ...200919805539
evaluation of high performance liquid chromatography purified leptospiral antigen for the diagnosis of leptospirosis.leptospirosis is a re-emerging infection, and often occurs in outbreaks. early diagnosis is important for appropriate control measures and treatment. the sensitivity and specificity of the diagnostic test depends on the antigen, which is used for the detection of antibodies. in the present study, an effort was made to purify and characterize leptospiral antigens, and their performance in the laboratory was assessed. leptospira biflexa semaranga, patoc was subjected to processing by the heat extr ...200919934533
cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways.aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ...200919946135
multilocus sequence analysis for typing leptospira interrogans and leptospira kirschneri.fifty-three strains belonging to the pathogenic species leptospira interrogans and leptospira kirschneri were analyzed by multilocus sequence analysis. the species formed two distinct branches. in the l. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. genogroups and serogroups were superimposed but not strictly.201019955271
multilocus sequence analysis for typing leptospira interrogans and leptospira kirschneri.fifty-three strains belonging to the pathogenic species leptospira interrogans and leptospira kirschneri were analyzed by multilocus sequence analysis. the species formed two distinct branches. in the l. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. genogroups and serogroups were superimposed but not strictly.201019955271
evidence that two atp-dependent (lon) proteases in borrelia burgdorferi serve different functions.the canonical atp-dependent protease lon participates in an assortment of biological processes in bacteria, including the catalysis of damaged or senescent proteins and short-lived regulatory proteins. borrelia spirochetes are unusual in that they code for two putative atp-dependent lon homologs, lon-1 and lon-2. borrelia burgdorferi, the etiologic agent of lyme disease, is transmitted through the blood feeding of ixodes ticks. previous work in our laboratory reported that b. burgdorferi lon-1 i ...200919956677
use of rpsl as a counterselectable marker in borrelia burgdorferi.we have demonstrated that rpsl, encoding the s12 protein of the small ribosomal subunit, can be used as a counterselectable marker in borrelia burgdorferi, the causative agent of lyme disease. mutations in rpsl confer streptomycin resistance. streptomycin susceptibility is dominant in an rpsl merodiploid, and streptomycin selects for the loss of wild-type rpsl carried in trans. this is the first description of a counterselectable marker in b. burgdorferi.201019966024
use of rpsl as a counterselectable marker in borrelia burgdorferi.we have demonstrated that rpsl, encoding the s12 protein of the small ribosomal subunit, can be used as a counterselectable marker in borrelia burgdorferi, the causative agent of lyme disease. mutations in rpsl confer streptomycin resistance. streptomycin susceptibility is dominant in an rpsl merodiploid, and streptomycin selects for the loss of wild-type rpsl carried in trans. this is the first description of a counterselectable marker in b. burgdorferi.201019966024
a highly coordinated cell wall degradation machine governs spore morphogenesis in bacillus subtilis.how proteins catalyze morphogenesis is an outstanding question in developmental biology. in bacteria, morphogenesis is intimately linked to remodeling the cell wall exoskeleton. here, we investigate the mechanisms by which the mother cell engulfs the prospective spore during sporulation in bacillus subtilis. a membrane-anchored protein complex containing two cell wall hydrolases plays a central role in this morphological process. we demonstrate that one of the proteins (spoiip) has both amidase ...201020159959
functional characterization of lcpa, a surface-exposed protein of leptospira spp. that binds the human complement regulator c4bp.we have previously shown that pathogenic leptospiral strains are able to bind c4b binding protein (c4bp). surface-bound c4bp retains its cofactor activity, indicating that acquisition of this complement regulator may contribute to leptospiral serum resistance. in the present study, the abilities of seven recombinant putative leptospiral outer membrane proteins to interact with c4bp were evaluated. the protein encoded by lic11947 interacted with this human complement regulator in a dose-dependent ...201020404075
antibiotic resistance markers for genetic manipulations of leptospira spp.we measured the frequency of appearance of spontaneous mutants resistant to gentamicin, kanamycin, streptomycin, and spectinomycin in saprophytic and pathogenic leptospira strains. the mutations responsible for the spontaneous resistance to streptomycin and spectinomycin were identified in the rpsl and rrs genes, respectively. we also generated a gentamicin resistance cassette that allows the use of a third selectable marker in leptospires. these results may facilitate further advances in gene t ...201020511419
the complete genome sequence of the pathogenic intestinal spirochete brachyspira pilosicoli and comparison with other brachyspira genomes.the anaerobic spirochete brachyspira pilosicoli colonizes the large intestine of various species of birds and mammals, including humans. it causes "intestinal spirochetosis", a condition characterized by mild colitis, diarrhea and reduced growth. this study aimed to sequence and analyse the bacterial genome to investigate the genetic basis of its specialized ecology and virulence.201020625514
deriving enzymatic and taxonomic signatures of metagenomes from short read data.we propose a method for deriving enzymatic signatures from short read metagenomic data of unknown species. the short read data are converted to six pseudo-peptide candidates. we search for occurrences of specific peptides (sps) on the latter. sps are peptides that are indicative of enzymatic function as defined by the enzyme commission (ec) nomenclature. the number of sp hits on an ensemble of short reads is counted and then converted to estimates of numbers of enzymatic genes associated with di ...201020649951
obstacles of multiplex real-time pcr for bacterial 16s rdna: primer specifity and dna decontamination of taq polymerase.background: the detection of a broad range of bacteria by pcr is applied for the screening of blood and blood products with special attention to platelet concentrates. for practical use it is desirable that detection systems include gram-positive, gram-negative and non-gram-stainable bacteria. it is quite challenging to achieve high sensitivity along with a clear negative control with pcr reagents, because especially taq polymerase is contaminated with traces of bacterial dna. methods: bacterial ...201020737013
transcriptional response of leptospira interrogans to iron limitation and characterization of a perr homolog.leptospirosis is a globally significant zoonosis caused by leptospira spp. iron is essential for growth of most bacterial species. since iron availability is low in the host, pathogens have evolved complex iron acquisition mechanisms to survive and establish infection. in many bacteria, expression of iron uptake and storage proteins is regulated by fur. l. interrogans encodes four predicted fur homologs; we have constructed a mutation in one of these, la1857. we conducted microarray analysis to ...201020805337
risk factors for clinical leptospirosis from western jamaica.a retrospective, matched case-control study was conducted in jamaica's western regional health authority (wrha). forty-three individuals developing clinical leptospirosis between january 2005 and december 2007 (i.e., cases) were age and neighborhood matched to 89 controls. odds ratios (or) and associated 95% confidence intervals (cis) and the relative excess risk due to interaction (reri) were calculated. cases had increased odds of contact with rodents or 3.52, goats or 3.38, and being engaged ...201020810831
leptospira as an emerging pathogen: a review of its biology, pathogenesis and host immune responses.leptospirosis, the most widespread zoonosis in the world, is an emerging public health problem, particularly in large urban centers of developing countries. several pathogenic species of the genus leptospira can cause a wide range of clinical manifestations, from a mild, flu-like illness to a severe disease form characterized by multiorgan system complications leading to death. however, the mechanisms of pathogenesis of leptospira are largely unknown. this article will address the animal models ...201020860485
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
simultaneous detection and differentiation of pathogenic and nonpathogenic leptospira spp. by multiplex real-time pcr (taqman) assay.leptospirosis, caused by pathogenic leptospira, is one of the most important zoonoses in the world. several molecular techniques have been developed for detection and differentiation between pathogenic and saprophytic leptospira spp. the aim of this study was to develop a rapid and simple assay for specific detection and differentiation of pathogenic leptospira spp. by multiplex real-time pcr (taqman) assay using primers and probes targeting leptospira genus specific 16s ribosomal rna gene, the ...201021033579
expanding the genetic toolbox for leptospira species by generation of fluorescent bacteria.our knowledge of the genetics and molecular basis of the pathogenesis associated with leptospira, in comparison to those of other bacterial species, is very limited. an improved understanding of pathogenic mechanisms requires reliable genetic tools for functional genetic analysis. here, we report the expression of gfp and mrfp1 genes under the control of constitutive spirochetal promoters in both saprophytic and pathogenic leptospira strains. we were able to reliably measure the fluorescence of ...201021037299
transcriptional responses of leptospira interrogans to host innate immunity: significant changes in metabolism, oxygen tolerance, and outer membrane.leptospira interrogans is the major causative agent of leptospirosis. phagocytosis plays important roles in the innate immune responses to l. interrogans infection, and l. interrogans can evade the killing of phagocytes. however, little is known about the adaptation of l. interrogans during this process.201021049008
2010 acvim small animal consensus statement on leptospirosis: diagnosis, epidemiology, treatment, and prevention.this report offers a consensus opinion on the diagnosis, epidemiology, treatment, and prevention of leptospirosis in dogs, an important zoonosis. clinical signs of leptospirosis in dogs relate to development of renal disease, hepatic disease, uveitis, and pulmonary hemorrhage. disease may follow periods of high rainfall, and can occur in dogs roaming in proximity to water sources, farm animals, or wildlife, or dogs residing in suburban environments. diagnosis is based on acute and convalescent p ...201021155890
responses of human endothelial cells to pathogenic and non-pathogenic leptospira species.leptospirosis is a widespread zoonotic infection that primarily affects residents of tropical regions, but causes infections in animals and humans in temperate regions as well. the agents of leptospirosis comprise several members of the genus leptospira, which also includes non-pathogenic, saprophytic species. leptospirosis can vary in severity from a mild, non-specific illness to severe disease that includes multi-organ failure and widespread endothelial damage and hemorrhage. to begin to inves ...201021179504
plasmids with a chromosome-like role in rhizobia.replicon architecture in bacteria is commonly comprised of one indispensable chromosome and several dispensable plasmids. this view has been enriched by the discovery of additional chromosomes, identified mainly by localization of rrna and/or trna genes, and also by experimental demonstration of their requirement for cell growth. the genome of rhizobium etli cfn42 is constituted by one chromosome and six large plasmids, ranging in size from 184 to 642 kb. five of the six plasmids are dispensable ...201121217003
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.201121220775
immunostimulatory and antigen delivery properties of liposomes made up of total polar lipids from non-pathogenic bacteria leads to efficient induction of both innate and adaptive immune responses.novel liposomes prepared from total polar lipids of non-pathogenic bacteria, viz. leptospira biflexa serovar potac (designated leptosomes) and mycobacterium smegmatis (designated smegmosomes) were evaluated for their adjuvant effects with various antigen presenting cells (apcs), viz. murine macrophage cell line, j774a.1 and bone marrow derived dendritic cells (bmdcs). these liposomes induced strong membrane fusion as evident from resonance energy transfer (ret) assays and effectively transferred ...201121300103
the multifunctional ligb adhesin binds homeostatic proteins with potential roles in cutaneous infection by pathogenic leptospira interrogans.leptospirosis is a potentially fatal zoonotic disease in humans and animals caused by pathogenic spirochetes, such as leptospira interrogans. the mode of transmission is commonly limited to the exposure of mucous membrane or damaged skin to water contaminated by leptospires shed in the urine of carriers, such as rats. infection occurs during seasonal flooding of impoverished tropical urban habitats with large rat populations, but also during recreational activity in open water, suggesting it is ...201121347378
new implications on genomic adaptation derived from the helicobacter pylori genome comparison.helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. it evolved with its particular characteristics for biological adaptation. because several h. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium.201121387011
comparative proteogenomic analysis of the leptospira interrogans virulence-attenuated strain ipav against the pathogenic strain 56601.the virulence-attenuated leptospira interrogans serovar lai strain ipav was derived by prolonged laboratory passage from a highly virulent ancestral strain isolated in china. we studied the genetic variations of ipav that render it avirulent via comparative analysis against the pathogenic l. interrogans serovar lai strain 56601. the complete genome sequence of the ipav strain was determined and used to compare with, and then rectify and reannotate the genome sequence of strain 56601. aside from ...201121423275
prophage-stimulated toxin production in clostridium difficile nap1/027 lysogens.tcda and tcdb exotoxins are the main virulence factors of clostridium difficile, one of the most deadly nosocomial pathogens. recent data suggest that prophages can influence the regulation of toxin expression. here we present the characterization of ?cd38-2, a pac-type temperate siphoviridae phage that stimulates toxin expression when introduced as a prophage into c. difficile. host range analysis showed that ?cd38-2 was able to infect 99/207 isolates of c. difficile representing 11 different p ...201121441508
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
crystal structure of the novel paib transcriptional regulator from geobacillus stearothermophilus. 201121633969
seasonality of human leptospirosis in reunion island (indian ocean) and its association with meteorological data.leptospirosis is a disease which occurs worldwide but particularly affects tropical areas. transmission of the disease is dependent on its excretion by reservoir animals and the presence of moist environment which allows the survival of the bacteria.201121655257
heterologous expression of pathogen-specific genes liga and ligb in the saprophyte leptospira biflexa confers enhanced adhesion to cultured cells and fibronectin.in comparison to other bacterial pathogens, our knowledge of the molecular basis of the pathogenesis of leptospirosis is extremely limited. an improved understanding of leptospiral pathogenetic mechanisms requires reliable tools for functional genetic analysis. leptospiral immunoglobulin-like (lig) proteins are surface proteins found in pathogenic leptospira, but not in saprophytes. here, we describe a system for heterologous expression of the leptospira interrogans genes liga and ligb in the sa ...201121658265
frequent mutations within the genomic magnetosome island of magnetospirillum gryphiswaldense are mediated by reca.genes for magnetosome formation in magnetotactic bacteria are clustered in large genomic magnetosome islands (mai). spontaneous deletions and rearrangements were frequently observed within these regions upon metabolic stress. this instability was speculated to be due to reca-dependent homologous recombination between the numerous sequence repeats present within the mai. here, we show that a reca deficient strain of magnetospirillum gryphiswaldense (strain ik-1) no longer exhibits genetic instabi ...201121821768
characteristic features of intracellular pathogenic leptospira in infected murine macrophages.leptospira interrogans is a spirochaete responsible for a zoonotic disease known as leptospirosis. leptospires are able to penetrate the abraded skin and mucous membranes and rapidly disseminate to target organs such as the liver, lungs and kidneys. how this pathogen escape from innate immune cells and spread to target organs remains poorly understood. in this paper, the intracellular trafficking undertaken by non-pathogenic leptospira biflexa and pathogenic l.ôçâinterrogans in mouse bone marrow ...201121819516
the rela/spot homolog (rsh) superfamily: distribution and functional evolution of ppgpp synthetases and hydrolases across the tree of life.rela/spot homologue (rsh) proteins, named for their sequence similarity to the rela and spot enzymes of escherichia coli, comprise a superfamily of enzymes that synthesize and/or hydrolyze the alarmone ppgpp, activator of the "stringent" response and regulator of cellular metabolism. the classical "long" rshs rel, rela and spot with the ppgpp hydrolase, synthetase, tgs and act domain architecture have been found across diverse bacteria and plant chloroplasts, while dedicated single domain ppgpp- ...201121858139
deciphering morphological determinants of the helix-shaped leptospira.leptospira spp. are thin, highly motile, slow-growing spirochetes that can be distinguished from other bacteria on the basis of their unique helical shape. defining the mechanisms by which these bacteria generate and maintain this atypical morphology should greatly enhance our understanding of the fundamental physiology of these pathogens. in this study, we showed that peptidoglycan sacculi from leptospira spp. retain the helical shape of intact cells. interestingly, the distribution of muropept ...201121926230
calcium-binding to leptospira outer membrane antigen lipl32 is not necessary for its interaction with plasma fibronectin, collagen type iv and plasminogen.lipl32 is the most abundant outer membrane protein from pathogenic leptospira and has been shown to bind extracellular matrix (ecm) proteins as well as ca2+. recent crystal structures have been obtained for the protein in the apo and ca2+-bound forms. in this work, we produced three lipl32 mutants (d163-168a, q67a and s247a) and evaluated their ability to interact with ca2+ and with ecm glycoproteins and with human plasminogen. the d163-d168a mutant modifies aspartate residues involved in ca2+-b ...201122147698
calcium-binding to leptospira outer membrane antigen lipl32 is not necessary for its interaction with plasma fibronectin, collagen type iv and plasminogen.lipl32 is the most abundant outer membrane protein from pathogenic leptospira and has been shown to bind extracellular matrix (ecm) proteins as well as ca2+. recent crystal structures have been obtained for the protein in the apo and ca2+-bound forms. in this work, we produced three lipl32 mutants (d163-168a, q67a and s247a) and evaluated their ability to interact with ca2+ and with ecm glycoproteins and with human plasminogen. the d163-d168a mutant modifies aspartate residues involved in ca2+-b ...201122147698
a highly stable plastidic-type ferredoxin-nadp(h) reductase in the pathogenic bacterium leptospira interrogans.leptospira interrogans is a bacterium that is capable of infecting animals and humans, and its infection causes leptospirosis with a range of symptoms from flu-like to severe illness and death. despite being a bacteria, leptospira interrogans contains a plastidic class ferredoxin-nadp(h) reductase (fnr) with high catalytic efficiency, at difference from the bacterial class fnrs. these flavoenzymes catalyze the electron transfer between nadp(h) and ferredoxins or flavodoxins. the inclusion of a p ...201122039544
Monoclonal antibodies against the leptospiral immunoglobulin-like proteins A and B conserved regions.Leptospirosis is an infectious disease caused by pathogenic spirochetes of the genus Leptospira that affects humans and a wide variety of animals. Recently the genomes of Leptospira interrogans, Leptospira borgpetersenii and Leptospira biflexa species were sequenced allowing the identification of new virulence factors involved in survival and pathogenesis of bacteria. LigA and LigB are surface-exposed bacterial adhesins whose expression is correlated with the virulence of Leptospira strains. In ...201121903270
three-dimensional structures of pathogenic and saprophytic leptospira revealed by cryo-electron tomography.leptospira interrogans is the primary causative agent of the most widespread zoonotic disease, leptospirosis. an in-depth structural characterization of l. interrogans is needed to understand its biology and pathogenesis. in this study, cryo-electron tomography (cryo-et) was used to compare pathogenic and saprophytic species and examine the unique morphological features of this group of bacteria. specifically, our study revealed a structural difference between the cell envelopes of l. interrogan ...201222228733
evaluation of pathogenic serovars of leptospira interrogans in dairy cattle herds of shahrekord by pcr.leptospirosis is an important zoonotic disease caused by leptospira interrogans. leptospirosis leads to economical losses in dairy farm industry. the objective of this study was to evaluate the pathogenic serovars of leptospira interrogans in dairy cattle herds of shahrekord by pcr.201122347596
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...201124710297
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ...201424931479
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 ...201426019546
rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique.a real-time pcr assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. current real-time pcr technologies cannot accomplish this task due to severe limitations in multiplexing ability. to this end, we developed a new assay system which supports very high degrees of multiplexing. we developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelt ...200919923485
rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique.a real-time pcr assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. current real-time pcr technologies cannot accomplish this task due to severe limitations in multiplexing ability. to this end, we developed a new assay system which supports very high degrees of multiplexing. we developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelt ...200919923485
chemotactic behavior of pathogenic and nonpathogenic leptospira species.we have developed a capillary tube assay in combination with real-time pcr to quantitate the number of chemoattracted leptospira cells. we identified tween 80, glucose, sucrose, and pyruvate as attractants for leptospira cells; amino acids and vitamin b(12) were found to be nonchemotactic or weakly chemotactic. this assay has the general applicability to further our understanding of leptospiral chemotaxis.201223001652
flaa proteins in leptospira interrogans are essential for motility and virulence but are not required for formation of the flagellum sheath.spirochetes have periplasmic flagella composed of a core surrounded by a sheath. the pathogen leptospira interrogans has four flab (proposed core subunit) and two flaa (proposed sheath subunit) genes. the flaa genes are organized in a locus with flaa2 immediately upstream of flaa1. in this study, flaa1 and flaa2 mutants were constructed by transposon mutagenesis. both mutants still produced periplasmic flagella. the flaa1 mutant did not produce flaa1 but continued to produce flaa2 and retained n ...201222451522
structural and functional characterization of an orphan atp-binding cassette atpase involved in manganese utilization and tolerance in leptospira spp.pathogenic leptospira species are the etiological agents of the widespread zoonotic disease leptospirosis. most organisms, including leptospira, require divalent cations for proper growth, but because of their high reactivity, these metals are toxic at high concentrations. therefore, bacteria have acquired strategies to maintain metal homeostasis, such as metal import and efflux. by screening leptospira biflexa transposon mutants for their ability to use mn(2+), we have identified a gene encodin ...201324123817
role for cis-acting rna sequences in the temperature-dependent expression of the multiadhesive lig proteins in leptospira interrogans.the spirochete leptospira interrogans causes a systemic infection that provokes a febrile illness. the putative lipoproteins liga and ligb promote adhesion of leptospira to host proteins, interfere with coagulation, and capture complement regulators. in this study, we demonstrate that the expression level of the liga and ligb proteins was substantially higher when l. interrogans proliferated at 37°c instead of the standard culture temperature of 30°c. the rna comprising the 175-nucleotide 5' unt ...201324013626
a phylogenomic and molecular signature based approach for characterization of the phylum spirochaetes and its major clades: proposal for a taxonomic revision of the phylum.the spirochaetes species cause many important diseases including syphilis and lyme disease. except for their containing a distinctive endoflagella, no other molecular or biochemical characteristics are presently known that are specific for either all spirochaetes or its different families. we report detailed comparative and phylogenomic analyses of protein sequences from spirochaetes genomes to understand their evolutionary relationships and to identify molecular signatures for this group. these ...201323908650
b-cell-specific peptides of leptospira interrogans liga for diagnosis of patients with acute leptospirosis.leptospirosis is a reemerging infectious disease that is underdiagnosed and under-recognized due to low-sensitivity and cumbersome serological tests. rapid reliable alternative tests are needed for early diagnosis of the disease. considering the importance of the pathogenesis-associated leptospiral liga protein expressed in vivo, we have evaluated its application in the diagnosis of the acute form of leptospirosis. the c-terminal coding sequence of liga (liga-c) was cloned into pet15b and expres ...201424403522
direct measurement of helical cell motion of the spirochete leptospira.leptospira are spirochete bacteria distinguished by a short-pitch coiled body and intracellular flagella. leptospira cells swim in liquid with an asymmetric morphology of the cell body; the anterior end has a long-pitch spiral shape (s-end) and the posterior end is hook-shaped (h-end). although the s-end and the coiled cell body called the protoplasmic cylinder are thought to be responsible for propulsion together, most observations on the motion mechanism have remained qualitative. in this stud ...201424411236
control of gene expression in leptospira spp. by transcription activator-like effectors demonstrates a potential role for liga and ligb in leptospira interrogans virulence.leptospirosis is a zoonotic disease that affects ∼1 million people annually, with a mortality rate of >10%. currently, there is an absence of effective genetic manipulation tools for targeted mutagenesis in pathogenic leptospires. transcription activator-like effectors (tales) are a recently described group of repressors that modify transcriptional activity in prokaryotic and eukaryotic cells by directly binding to a targeted sequence within the host genome. to determine the applicability of tal ...201526341206
neglected bacterial zoonoses.bacterial zoonoses comprise a group of diseases in humans or animals acquired by direct contact with or by oral consumption of contaminated animal materials, or via arthropod vectors. among neglected infections, bacterial zoonoses are among the most neglected given emerging data on incidence and prevalence as causes of acute febrile illness, even in areas where recognized neglected tropical diseases occur frequently. although many other bacterial infections could also be considered in this negle ...201525964152
a replicative plasmid vector allows efficient complementation of pathogenic leptospira strains.leptospirosis, an emerging zoonotic disease, remains poorly understood because of a lack of genetic manipulation tools available for pathogenic leptospires. current genetic manipulation techniques include insertion of dna by random transposon mutagenesis and homologous recombination via suicide vectors. this study describes the construction of a shuttle vector, pmaori, that replicates within saprophytic, intermediate, and pathogenic leptospires. the shuttle vector was constructed by the insertio ...201525724960
interaction of bovine peripheral blood polymorphonuclear cells and leptospira species; innate responses in the natural bovine reservoir host.cattle are the reservoir hosts of leptospira borgpetersenii serovar hardjo, and can also be reservoir hosts of other leptospira species such as l. kirschneri, and leptospira interrogans. as a reservoir host, cattle shed leptospira, infecting other animals, including humans. previous studies with human and murine neutrophils have shown activation of neutrophil extracellular trap or net formation, and upregulation of inflammatory mediators by neutrophils in the presence of leptospira. humans, comp ...201627486445
evidence of in vivo existence of borrelia biofilm in borrelial lymphocytomas.lyme borreliosis, caused by the spirochete borrelia burgdorferi sensu lato, has grown into a major public health problem. we recently identified a novel morphological form of b. burgdorferi, called biofilm, a structure that is well known to be highly resistant to antibiotics. however, there is no evidence of the existence of borrelia biofilm in vivo; therefore, the main goal of this study was to determine the presence of borrelia biofilm in infected human skin tissues. archived skin biopsy tissu ...201627141311
structural, bioinformatic, and in vivo analyses of two treponema pallidum lipoproteins reveal a unique trap transporter.treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite atp-independent periplasmic transporter (trap-t). trap-ts typically employ a periplasmic substrate-binding protein (sbp) to deliver the cognate ligand to the transmembrane symporter. herein, we demonstrate that the genes encoding the putative trap-t components from t. pallidum, tp0957 (the sbp), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. we determined the cryst ...201222306465
motility is crucial for the infectious life cycle of borrelia burgdorferi.the lyme disease spirochete, borrelia burgdorferi, exists in a zoonotic cycle involving an arthropod tick and mammalian host. dissemination of the organism within and between these hosts depends upon the spirochete's ability to traverse through complex tissues. additionally, the spirochete outruns the host immune cells while migrating through the dermis, suggesting the importance of b. burgdorferi motility in evading host clearance. b. burgdorferi's periplasmic flagellar filaments are composed p ...201323529620
a flood of microbial genomes-do we need more? 200919513110
ankyrin domains across the tree of life.ankyrin (ank) repeats are one of the most common amino acid sequence motifs that mediate interactions between proteins of myriad sizes, shapes and functions. we assess their widespread abundance in bacteria and archaea for the first time and demonstrate in bacteria that lifestyle, rather than phylogenetic history, is a predictor of ank repeat abundance. unrelated organisms that forge facultative and obligate symbioses with eukaryotes show enrichment for ank repeats in comparison to free-living b ...201424688847
leptospira spp. strain identification by maldi tof ms is an equivalent tool to 16s rrna gene sequencing and multi locus sequence typing (mlst).in this study mass spectrometry was used for evaluating extracted leptospiral protein samples and results were compared with molecular typing methods. for this, an extraction protocol for leptospira spp. was independently established in two separate laboratories. reference spectra were created with 28 leptospiral strains, including pathogenic, non-pathogenic and intermediate strains. this set of spectra was then evaluated on the basis of measurements with well-defined, cultured leptospiral strai ...201222925589
reductive evolution and the loss of pdc/pas domains from the genus staphylococcus.the per-arnt-sim (pas) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. although pas domains and the subclass of phoq-dcus-cita (pdc) domains have a common structure, there is limited amino acid sequence similarity. to gain greater insight into the evolution of pdc/pas domains present in the bacterial kingdom and staphylococci in specific, the pdc/pas domains from the genomic sequences of 4 ...201323902280
enhanced diastereoselectivity in beta-mannopyranosylation through the use of sterically minimal propargyl ether protecting groups.[reaction: see text] 2-o-propargyl ethers are shown to be advantageous in the 4,6-o-benzylidene acetal directed beta-mannosylation reaction. the effect is most pronounced when the o3 protecting group is a bulky silyl ether or a glycosidic bond; however, even with a 3-o-benzyl ether, the use of a 2-o-propargyl ether results in a significant increase in diastereoselectivity. the beneficial effect of the propargyl ether is thought to be a combination of its minimal steric bulk, as determined by a m ...200616599600
convergent synthesis of a beta-(1-->3)-mannohexaose.an as yet unknown beta-(1-->3)-mannohexaose has been synthesized by a block route involving the coupling of two trisaccharides. comparison of three closely related attempted mannohexaose syntheses reinforces the influence of subtle matching and/or mismatching interactions on the outcome of convergent oligosaccharide synthesis.200717665957
the shape and dynamics of the leptospiraceae.most swimming bacteria produce thrust by rotating helical filaments called flagella. typically, the flagella stick out into the external fluid environment; however, in the spirochetes, a unique group that includes some highly pathogenic species of bacteria, the flagella are internalized, being incased in the periplasmic space; i.e., between the outer membrane and the cell wall. this coupling between the periplasmic flagella and the cell wall allows the flagella to serve a skeletal, as well as a ...200717434949
mosaic: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.the recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. it is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons.200819038022
genomes of model organisms: know thy tools. 200818474084
the tryptophan pathway genes of the sargasso sea metagenome: new operon structures and the prevalence of non-operon organization.the enormous database of microbial dna generated from the sargasso sea metagenome provides a unique opportunity to locate genes participating in different biosynthetic pathways and to attempt to understand the relationship and evolution of those genes. in this article, an analysis of the sargasso sea metagenome is made with respect to the seven genes of the tryptophan pathway.200818221558
leptospirosis: the "mysterious" mimic.leptospirosis is a potentially fatal bacterial disease that can display a wide array of clinical presentations thus mimicking better-known illnesses. although, leptospirosis is primarily a zoonotic disease, it frequently inflicts severe illness and death on communities around the globe. a comprehensive overview of the disease in wake of the 2006 outbreaks in india is hereby presented and discussed.200819561939
amidoligases with atp-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins.recent studies have shown that the ubiquitin system had its origins in ancient cofactor/amino acid biosynthesis pathways. preliminary studies also indicated that conjugation systems for other peptide tags on proteins, such as pupylation, have evolutionary links to cofactor/amino acid biosynthesis pathways. following up on these observations, we systematically investigated the non-ribosomal amidoligases of the atp-grasp, glutamine synthetase-like and acetyltransferase folds by classifying the kno ...200920023723
comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.the prokaryotic toxin-antitoxin systems (tas, also referred to as ta loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in various forms of stress response and management of prokaryotic population. several distinct tas of type 1, where the toxin is a protein and the antitoxin is an antisense rna, and numerous, unr ...200919493340
characterization of the genome, proteome, and structure of yersiniophage ϕr1-37.the bacteriophage vb_yecm-ϕr1-37 (ϕr1-37) is a lytic yersiniophage that can propagate naturally in different yersinia species carrying the correct lipopolysaccharide receptor. this large-tailed phage has deoxyuridine (du) instead of thymidine in its dna. in this study, we determined the genomic sequence of phage ϕr1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. t ...201222973030
leptospiral outer membrane protein microarray, a novel approach to identification of host ligand-binding proteins.leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes belonging to the genus leptospira. the leptospiral life cycle involves transmission via freshwater and colonization of the renal tubules of their reservoir hosts. infection requires adherence to cell surfaces and extracellular matrix components of host tissues. these host-pathogen interactions involve outer membrane proteins (omps) expressed on the bacterial surface. in this study, we developed an leptospira ...201222961849
automatic assignment of prokaryotic genes to functional categories using literature profiling.in the last years, there was an exponential increase in the number of publicly available genomes. once finished, most genome projects lack financial support to review annotations. a few of these gene annotations are based on a combination of bioinformatics evidence, however, in most cases, annotations are based solely on sequence similarity to a previously known gene, which was most probably annotated in the same way. as a result, a large number of predicted genes remain unassigned to any functi ...201223077617
positive regulation of leptospira interrogans kdp expression by kdpe as demonstrated with a novel β-galactosidase reporter in leptospira biflexa.leptospirosis is a potentially deadly zoonotic disease that afflicts humans and animals. leptospira interrogans, the predominant agent of leptospirosis, encounters diverse conditions as it proceeds through its life cycle, which includes stages inside and outside the host. unfortunately, the number of genetic tools available for examining the regulation of gene expression in l. interrogans is limited. consequently, little is known about the genetic circuits that control gene expression in leptosp ...201222685146
multiple leptospiral sphingomyelinases (or are there?).culture supernatants of leptospiral pathogens have long been known to haemolyse erythrocytes. this property is due, at least in part, to sphingomyelinase activity. indeed, genome sequencing reveals that pathogenic leptospira species are richly endowed with sphingomyelinase homologues: five genes have been annotated to encode sphingomyelinases in leptospira interrogans. such redundancy suggests that this class of genes is likely to benefit leptospiral pathogens in their interactions with the mamm ...201222422753
leptospire genomic diversity revealed by microarray-based comparative genomic hybridization.comparative genomic hybridization was used to compare genetic diversity of five strains of leptospira (leptospira interrogans serovars bratislava, canicola, and hebdomadis and leptospira kirschneri serovars cynopteri and grippotyphosa). the array was designed based on two available sequenced leptospira reference genomes, those of l. interrogans serovar copenhageni and l. interrogans serovar lai. a comparison of genetic contents showed that l. interrogans serovar bratislava was closest to the ref ...201222344655
vesiculation from pseudomonas aeruginosa under sos.bacterial infections can be aggravated by antibiotic treatment that induces sos response and vesiculation. this leads to a hypothesis concerning association of sos with vesiculation. to test it, we conducted multiple analyses of outer membrane vesicles (omvs) produced from the pseudomonas aeruginosa wild type in which sos is induced by ciprofloxacin and from the lexa noncleavable (lexan) strain in which sos is repressed. the levels of omv proteins, lipids, and cytotoxicity increased for both the ...201222448133
mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes.the sizes of proteins are relevant to their biochemical structure and for their biological function. the statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes.201222296664
detection of human leptospirosis as a cause of acute fever by capture elisa using a leptospira interrogans serovar copenhageni (m20) derived antigen.leptospirosis is a potentially lethal zoonosis mainly affecting low-resource tropical countries, including peru and its neighbouring countries. timely diagnosis of leptospirosis is critical but may be challenging in the regions where it is most prevalent. the serodiagnostic gold standard microagglutination test (mat) may be technically prohibitive. our objective in this study was to assess the sensitivity, specificity, and predictive value of an igm antibody capture enzyme-linked immunoassay (ma ...201324053555
responses of murine and human macrophages to leptospiral infection: a study using comparative array analysis.leptospirosis is a re-emerging tropical infectious disease caused by pathogenic leptospira spp. the different host innate immune responses are partially related to the different severities of leptospirosis. in this study, we employed transcriptomics and cytokine arrays to comparatively calculate the responses of murine peritoneal macrophages (mpms) and human peripheral blood monocytes (hbms) to leptospiral infection. we uncovered a series of different expression profiles of these two immune cell ...201324130911
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
chiral colloidal molecules and observation of the propeller effect.chiral molecules play an important role in biological and chemical processes, but physical effects due to their symmetry-breaking are generally weak. several physical chiral separation schemes which could potentially be useful, including the propeller effect, have therefore not yet been demonstrated at the molecular scale. however, it has been proposed that complex nonspherical colloidal particles could act as "colloidal molecules" in mesoscopic model systems to permit the visualization of molec ...201323883328
family of prokaryote cyclic nucleotide-modulated ion channels.cyclic nucleotide-modulated ion channels are molecular pores that mediate the passage of ions across the cell membrane in response to camp or gmp. structural insight into this class of ion channels currently comes from a related homolog, mlok1, that contains six transmembrane domains and a cytoplasmic cyclic nucleotide binding domain. however, unlike eukaryote hyperpolarization-activated cyclic nucleotide-modulated (hcn) and cyclic nucleotide-gated (cng) channels, mlok1 lacks a c-linker region, ...201424821777
periplasmic flagellar export apparatus protein, flih, is involved in post-transcriptional regulation of flab, motility and virulence of the relapsing fever spirochete borrelia hermsii.spirochetes are bacteria characterized in part by rotating periplasmic flagella that impart their helical or flat-wave morphology and motility. while most other bacteria rely on a transcriptional cascade to regulate the expression of motility genes, spirochetes employ post-transcriptional mechanism(s) that are only partially known. in the present study, we characterize a spontaneous non-motile mutant of the relapsing fever spirochete borrelia hermsii that was straight, non-motile and deficient i ...201324009690
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