Publications

hprk regulates succinate-mediated catabolite repression in the gram-negative symbiont sinorhizobium meliloti.	the hprk kinase/phosphatase is a common component of the phosphotransferase system (pts) of gram-positive bacteria and regulates catabolite repression through phosphorylation/dephosphorylation of its substrate, the pts protein hpr, at a conserved serine residue. phosphorylation of hpr by hprk also affects additional phosphorylation of hpr by the pts enzyme ei at a conserved histidine residue. sinorhizobium meliloti can live as symbionts inside legume root nodules or as free-living organisms and ...	2009	18931135
monitoring of leptospirosis seroprevalence in a colony of captive collared peccaries (tayassu tajacu) from the peruvian amazon.	leptospirosis, an endemic zoonoses, is maintained in the environment by several wildlife species in the peruvian amazon. in order to evaluate the possible role of collared peccaries (cp) in the maintenance this disease, two serological surveys of leptospirosis were performed and zootechnical parameters were monitored in a captive cp colony in an interval of 27 months. total seroprevalence changed from 100% (n=27) to 86.4% (n=22), with reactions to a diversity of serogroups of zoonotic importance ...	2009	19000627
disease threats to the endangered iberian lynx (lynx pardinus).	the iberian lynx, (lynx pardinus), is the most endangered felid in the world. to determine whether sympatric carnivores are reservoirs of pathogens posing a disease risk for the lynx, evidence of exposure to 17 viral, bacterial and protozoan agents was investigated in 176 carnivores comprising 26 free-living lynx, 53 domestic cats, 28 dogs, 33 red foxes (vulpes vulpes), 24 egyptian mongooses (herpestes ichneumon), 10 common genets (genetta genetta) and 2 eurasian badgers (meles meles) in the are ...	2009	18555712
investigation of carbon metabolism in "dehalococcoides ethenogenes" strain 195 by use of isotopomer and transcriptomic analyses.	members of the genus "dehalococcoides" are the only known microorganisms that can completely dechlorinate tetrachloroethene and trichloroethene to the innocuous end product, ethene. this study examines the central metabolism in "dehalococcoides ethenogenes" strain 195 via (13)c-labeled tracer experiments. supported by the genome annotation and the transcript profile, isotopomer analysis of key metabolites clarifies ambiguities in the genome annotation and identifies an unusual biosynthetic pathw ...	2009	19525347
human leptospirosis cases and the prevalence of rats harbouring leptospira interrogans in urban areas of tokyo, japan.	thirteen patients with leptospirosis were identified, as confirmed by laboratory analysis during the last 5 years in our laboratory, who came from urban areas of tokyo, japan. all of the patients came into contact with rats before the onset of illness. seventeen per cent of norway rats captured in the inner cities of tokyo carried leptospires in their kidneys. most of these rat isolates were leptospira interrogans serovar copenhageni/icterohaemorrhagiae. antibodies against these serovars and the ...	2009	19528143
distribution of the leptospiral immunoglobulin-like (lig) genes in pathogenic leptospira species and application of ligb to typing leptospiral isolates.	the family of leptospiral immunoglobulin-like (lig) genes comprises liga, ligb and ligc. this study used pcr to demonstrate the presence of lig genes among serovars from a collection of leptospiral strains and clinical isolates. whilst liga and ligc appeared to be present in a limited number of pathogenic serovars, the ligb gene was distributed ubiquitously among all pathogenic strains. none of the lig genes were detected among intermediate or saprophytic leptospira species. it was also shown th ...	2009	19528180
a newly identified protein of leptospira interrogans mediates binding to laminin.	pathogenic leptospira is the aetiological agent of leptospirosis, a life-threatening disease that affects populations worldwide. the search for novel antigens that could be relevant in host-pathogen interactions is being pursued. these antigens have the potential to elicit several activities, including adhesion. this study focused on a hypothetical predicted lipoprotein of leptospira, encoded by the gene lic12895, thought to mediate attachment to extracellular matrix (ecm) components. the gene w ...	2009	19541787
leptospira interrogans stably infects zebrafish embryos, altering phagocyte behavior and homing to specific tissues.	leptospirosis is an extremely widespread zoonotic infection with outcomes ranging from subclinical infection to fatal weil's syndrome. despite the global impact of the disease, key aspects of its pathogenesis remain unclear. to examine in detail the earliest steps in the host response to leptospires, we used fluorescently labelled leptospira interrogans serovar copenhageni to infect 30 hour post fertilization zebrafish embryos by either the caudal vein or hindbrain ventricle. these embryos have ...	2009	19547748
case of fulminant leptospirosis in a renal transplant patient.	we present a case of fulminant leptospirosis that was acquired in the suburban area by a 48-year-old male renal transplant recipient. he developed acute renal and hepatic failure with profound jaundice. spirochetes were identified on liver biopsy. weil's disease was suspected, and the diagnosis was further supported by a positive serum leptospira interrogans icterohaemorrhagiae antibody titer. unfortunately, he suffered from recurrent lower gastrointestinal bleeding, had a prolonged hospital cou ...	2009	19558375
a comprehensive approach to identification of surface-exposed, outer membrane-spanning proteins of leptospira interrogans.	leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes belonging to the genus leptospira. the leptospiral life cycle involves transmission via fresh water and colonization of the renal tubules of their reservoir hosts or infection of accidental hosts, including humans. bacterial outer membrane proteins (omps), particularly those with surface-exposed regions, play crucial roles in virulence mechanisms of pathogens and the adaptation to various environmental condi ...	2009	19562037
run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting bartonella grahamii.	the genus bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. we report the 2,341,328 bp genome sequence of bartonella grahamii, one of the most prevalent bartonella species in wild rodents. comparative genomics revealed that rodent-associated bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. many of these gene clusters are loc ...	2009	19578403
fibronectin binds to and induces conformational change in a disordered region of leptospiral immunoglobulin-like protein b.	leptospira interrogans is a pathogenic spirochete that causes disease in both humans and animals. ligb (leptospiral immunoglobulin-like protein b) contributes to the binding of leptospira to extracellular matrix proteins such as fibronectin (fn), fibrinogen, laminin, and collagen. a high affinity fn-binding region of ligb has been recently localized to ligbcen2, which contains the partial eleventh and full twelfth immunoglobulin-like repeats (ligbcen2r) and 47 amino acids of the non-repeat regio ...	2009	19581300
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 ...	2009	19581392
functional analysis of the helicobacter pylori flagellar switch proteins.	helicobacter pylori uses flagellum-mediated chemotaxis to promote infection. bacterial flagella change rotational direction by changing the state of the flagellar motor via a subcomplex referred to as the switch. intriguingly, the h. pylori genome encodes four switch complex proteins, flim, flin, fliy, and flig, instead of the more typical three of escherichia coli or bacillus subtilis. our goal was to examine whether and how all four switch proteins participate in flagellation. previous work de ...	2009	19767432
molecular characterization of the pl40 protein in leptospira interrogans.	leptospirosis is a widespread zoonotic disease caused by pathogenic leptospires. the identification of outer membrane proteins (omps) conserved among pathogenic leptospires, which are exposed on the leptospiral surface and expressed during mammalian infection, has become a major focus of leptospirosis research. pl40, a 40 kda protein coded by the la3744 gene in leptospira interrogans, was found to be unique to leptospira. triton x-114 fractionation and flow cytometry analyses indicate that pl40 ...	2009	19767845
molecular analysis of leptospira spp. isolated from humans by restriction fragment length polymorphism, real-time pcr and pulsed-field gel electrophoresis.	a total of 17 leptospira clinical strains isolated from humans in croatia were serologically and genetically analysed. for serovar identification, the microscopic agglutination test (mat) and pulsed-field gel electrophoresis (pfge) were used. to identify isolates on genomic species level, pcr-based restriction fragment length polymorphism (rflp) and real-time pcr were performed. mat revealed the following serogroup affinities: grippotyphosa (seven isolates), icterohaemorrhagiae (eight isolates) ...	2009	19780841
increase in seroprevalence of canine leptospirosis and its risk factors, ontario 1998-2006.	canine leptospirosis has been described as having re-emerged in north america around the mid-1990s, with a change in the epidemiology of the infecting serovars responsible for the disease emergence. a retrospective case-control study was conducted to examine the re-emergence of seroprevalent cases of canine leptospirosis in ontario using serology submission records from 1406 dogs from january 1, 1998 to december 31, 2006. the data collected [results of the microscopic agglutination test (mat), v ...	2009	19794888
protein typing of major outer membrane lipoproteins from chinese pathogenic leptospira spp. and characterization of their immunogenicity.	leptospirosis, caused by different leptospira species, is one of the most widespread zoonotic infections worldwide. here we expressed three major leptospiral lipoproteins and examined their immunogenicity. all the pathogenic leptospira strains tested possess the lipl21, lipl32 and lipl41 genes, but the latter two can be further divided into different gene types (lipl32-1, lipl32-2, lipl41-1, lipl41-2). microscopic agglutination test revealed that rlipls antisera had extensive cross-immunoaggluti ...	2009	19796723
nationwide survey of leptospira antibodies in dogs in japan: results from microscopic agglutination test and enzyme-linked immunosorbent assay.	leptospirosis is an infectious disease caused by leptospira interrogans sensu lato and is common in both humans and animals. in the present study, serum samples were collected from 801 dogs across all 47 prefectures in japan, and evaluated with a microscopic agglutination test (mat), using 5 major l. interrogans serovars (icterohaemorrhagiae, canicola, autumnalis, hebdomadis, and australis) as antigens, and an enzyme-linked immunosorbent assay (elisa) using recombinant ompl1 protein as the antig ...	2009	19801899
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 ...	2009	19805539
cryo-electron tomography elucidates the molecular architecture of treponema pallidum, the syphilis spirochete.	cryo-electron tomography (cet) was used to examine the native cellular organization of treponema pallidum, the syphilis spirochete. t. pallidum cells appeared to form flat waves, did not contain an outer coat and, except for bulges over the basal bodies and widening in the vicinity of flagellar filaments, displayed a uniform periplasmic space. although the outer membrane (om) generally was smooth in contour, om extrusions and blebs frequently were observed, highlighting the structure's fluidity ...	2009	19820083
[identification of immunoreactive antigens of leptospira interrogans].	a batch of 28 llama (lama gama) sera from jujuy province in argentina was studied in order to identify immune reactive antigens to leptospira interrogans. different antigenic preparations from the bacterium were used to study the immune reactivity by the microagglutination (mat), elisa and western immunoblot tests. a control pool of positive bovine sera was used. all the llama sera were negative to mat as well as to elisa. two of the llama sera and the positive bovine sera pool rendered positive ...	2009	19831309
visual proteomics of the human pathogen leptospira interrogans.	systems biology conceptualizes biological systems as dynamic networks of interacting elements, whereby functionally important properties are thought to emerge from the structure of such networks. owing to the ubiquitous role of complexes of interacting proteins in biological systems, their subunit composition and temporal and spatial arrangement within the cell are of particular interest. 'visual proteomics' attempts to localize individual macromolecular complexes inside of intact cells by templ ...	2009	19838170
destruction of spirochete borrelia burgdorferi round-body propagules (rbs) by the antibiotic tigecycline.	persistence of tissue spirochetes of borrelia burgdorferi as helices and round bodies (rbs) explains many erythema-lyme disease symptoms. spirochete rbs (reproductive propagules also called coccoid bodies, globular bodies, spherical bodies, granules, cysts, l-forms, sphaeroplasts, or vesicles) are induced by environmental conditions unfavorable for growth. viable, they grow, move and reversibly convert into motile helices. reversible pleiomorphy was recorded in at least six spirochete genera (>1 ...	2009	19843691
serological and genetic analysis of leptospirosis in patients with acute febrile illness in kandy, sri lanka.	leptospirosis has emerged as an important infectious disease in sri lanka and little information is available on circulating leptospiral species and serogroups in this country. therefore, we studied circulating leptospiral species and serogroups in patients with acute febrile illness using polymerase chain reaction and the microscopic agglutination test, respectively. anti-leptospiral antibodies were detected in 26 of 107 serum samples studied (24.3%). the predominant reacting serogroups were se ...	2009	19934544
evolutionary implication of outer membrane lipoprotein-encoding genes ompl1, upl32 and lipl41 of pathogenic leptospira species.	leptospirosis is recognized as the most widespread zoonosis with a global distribution. in this study, the antigenic variation in leptospira interrogans and leptospira borgpetersenii isolated from human urine and field rat kidney was preliminarily confirmed by microscopic agglutination test using monoclonal antibodies, and was further subjected to amplification and identification of outer membrane lipoproteins with structural gene variation. sequence similarity analysis revealed that these prote ...	2009	19944382
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 ...	2009	19946135
a pair of ligation-independent escherichia coli expression vectors for rapid addition of a polyhistidine affinity tag to the n- or c-termini of recombinant proteins.	6x his tag is one of the most widely used affinity fusion tags that facilitates detection and purification of recombinant proteins. however, the location of this tag within a particular type of protein may influence the expression, solubility, and bioactivity of the protein, and the optimal location needs to be determined experimentally. to provide a tool for rapid generation of 6x his tags at the n- or c-terminus of any recombinant protein, we have constructed a pair of escherichia coli express ...	2009	19949695
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 ...	2009	19956677
epidemic dynamics at the human-animal interface.	few infectious diseases are entirely human-specific: most human pathogens also circulate in animals or else originated in nonhuman hosts. influenza, plague, and trypanosomiasis are classic examples of zoonotic infections that transmit from animals to humans. the multihost ecology of zoonoses leads to complex dynamics, and analytical tools, such as mathematical modeling, are vital to the development of effective control policies and research agendas. much attention has focused on modeling pathoge ...	2009	19965751
comparative transcriptional and translational analysis of leptospiral outer membrane protein expression in response to temperature.	leptospirosis is a global zoonosis affecting millions of people annually. transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry. past studies found that various leptospiral outer membrane proteins are differentially expressed at different temperatures. however, our microarray studies highlighted a divergence between protein abundance and transcript levels for some proteins. given the abundance of ...	2009	19997626
inactivation of the fliy gene encoding a flagellar motor switch protein attenuates mobility and virulence of leptospira interrogans strain lai.	pathogenic leptospira species cause leptospirosis, a zoonotic disease of global importance. the spirochete displays active rotative mobility which may contribute to invasion and diffusion of the pathogen in hosts. fliy is a flagellar motor switch protein that controls flagellar motor direction in other microbes, but its role in leptospira, and paricularly in pathogenicity remains unknown.	2009	20003186
risk factors associated with the seroprevalence of leptospirosis, amongst at-risk groups in and around tanga city, tanzania.	the epidemiological status of human leptospirosis in tanzania has not been well defined because of a general lack of awareness of the disease and difficulties in its diagnosis. a cross-sectional seroprevalence study, using the microscopic agglutination test with a threshold titre of 1 : 160, was therefore conducted, among various occupational groups from tanga city, in november 2005. of the 199 subjects investigated, 30 (15.1%) were found to have antibodies that reacted with antigens from at lea ...	2009	20030995
cytopathic effect in bhk 21 (c13) cells inoculated with leptospira interrogans serovar pomona isolated from a porcine abortion.		2009	20085192
bilateral facial palsy associated with leptospirosis.	leptospirosis is a zoonosis of worldwide occurrence caused by the spirochete leptospira interrogans. it is an acute feverish disease with a broad clinical spectrum and follows a characteristic biphasic course. bilateral facial palsy is a rare clinical condition and the differential diagnosis of its causes is extensive. the objective of this exploratory study, presented as a case report, is to describe the occurrence of bilateral facial palsy as an unusual manifestation of leptospirosis. this sug ...	2009	20232000
averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization.	the reference-free averaging of three-dimensional electron microscopy (3d-em) reconstructions with empty regions in fourier space represents a pressing problem in electron tomography and single-particle analysis. we present a maximum likelihood algorithm for the simultaneous alignment and classification of subtomograms or random conical tilt (rct) reconstructions, where the fourier components in the missing data regions are treated as hidden variables. the behavior of this algorithm was explored ...	2009	20004160
unifying vertical and nonvertical evolution: a stochastic arg-based framework.	evolutionary biologists have introduced numerous statistical approaches to explore nonvertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of markov-dependent gene trees. these tree collections allow for inference of nonvertical evolution, but only indirectly, making findings difficult to interpret and models difficult to generalize. an alternative approach to explore nonvertical evolution relies on phylogenetic networks. these networ ...	2009	20525618
unifying vertical and nonvertical evolution: a stochastic arg-based framework.	evolutionary biologists have introduced numerous statistical approaches to explore nonvertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of markov-dependent gene trees. these tree collections allow for inference of nonvertical evolution, but only indirectly, making findings difficult to interpret and models difficult to generalize. an alternative approach to explore nonvertical evolution relies on phylogenetic networks. these networ ...	2009	20525618
comparing cellular proteomes by mass spectrometry.	mass spectrometry and cryo-electron tomography together enable the determination of the absolute and relative abundances of proteins and their localization, laying the groundwork for comprehensive systems analyses of cells.	2009	19886975
sphingomyelin metabolism at the plasma membrane: implications for bioactive sphingolipids.	the plasma membrane (pm) is a major resource for production of bioactive lipids and contains a large proportion of the cellular sphingomyelin (sm) content. consequently, the regulation of sm levels at the pm by enzymes such as sphingomyelinase (smase) and sm synthase 2 (sms2) can have profound effects - both on biophysical properties of the membrane, but also on cellular signaling. over the past 20 years, there has been considerable research into the physiological and cellular functions associat ...	2009	19857494
sphingomyelin metabolism at the plasma membrane: implications for bioactive sphingolipids.	the plasma membrane (pm) is a major resource for production of bioactive lipids and contains a large proportion of the cellular sphingomyelin (sm) content. consequently, the regulation of sm levels at the pm by enzymes such as sphingomyelinase (smase) and sm synthase 2 (sms2) can have profound effects - both on biophysical properties of the membrane, but also on cellular signaling. over the past 20 years, there has been considerable research into the physiological and cellular functions associat ...	2009	19857494
molecular basis of substrate promiscuity for the sam-dependent o-methyltransferase ncsb1, involved in the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin.	the small molecule component of chromoprotein enediyne antitumor antibiotics is biosynthesized through a convergent route, incorporating amino acid, polyketide, and carbohydrate building blocks around a central enediyne hydrocarbon core. the naphthoic acid moiety of the enediyne neocarzinostatin plays key roles in the biological activity of the natural product by interacting with both the carrier protein and duplex dna at the site of action. we have previously described the in vitro characteriza ...	2009	19702337
absolute abundance for the masses.		2009	19741640
testing and validation of high density resequencing microarray for broad range biothreat agents detection.	rapid and effective detection and identification of emerging microbiological threats and potential biowarfare agents is very challenging when using traditional culture-based methods. contemporary molecular techniques, relying upon reverse transcription and/or polymerase chain reaction (rt-pcr/pcr) provide a rapid and effective alternative, however, such assays are generally designed and optimized to detect only a limited number of targets, and seldom are capable of differentiation among variants ...	2009	19668365
a hidden reservoir of integrative elements is the major source of recently acquired foreign genes and orfans in archaeal and bacterial genomes.	archaeal and bacterial genomes contain a number of genes of foreign origin that arose from recent horizontal gene transfer, but the role of integrative elements (ies), such as viruses, plasmids, and transposable elements, in this process has not been extensively quantified. moreover, it is not known whether ies play an important role in the origin of orfans (open reading frames without matches in current sequence databases), whose proportion remains stable despite the growing number of complete ...	2009	19531232
therapeutic targeting of toll-like receptors for infectious and inflammatory diseases and cancer.	since first being described in the fruit fly drosophila melanogaster, toll-like receptors (tlrs) have proven to be of great interest to immunologists and investigators interested in the molecular basis to inflammation. they recognize pathogen-derived factors and also products of inflamed tissue, and trigger signaling pathways that lead to activation of transcription factors such as nuclear factor-kappab and the interferon regulatory factors. these in turn lead to induction of immune and inflamma ...	2009	19474110
overview of toll-like receptors in the cns.	mammalian toll-like receptors (tlrs) were first identified in 1997 based on their homology with drosophila toll, which mediates innate immunity in the fly. over the past eight years, the number of manuscripts describing tlr expression and function in the central nervous system (cns) has been increasing steadily and expanding beyond their traditional roles in infectious diseases to neurodegenerative disorders and injury. interest in the field serves as the impetus for this volume in the current t ...	2009	19688325
novel pharmacologic approaches to the management of sepsis: targeting the host inflammatory response.	sepsis is currently the 10(th) leading cause of death overall and accounts for significant healthcare expenditures in the developed world. there are now more deaths attributable to sepsis than coronary artery disease, stroke, or cancer, and it is widely believed that the incidence of sepsis and sepsis-related mortality will continue to rise. based on these sobering statistics, there is great interest in identifying novel treatments for managing critically ill children and adults with sepsis. unf ...	2009	19519586
retrospective evaluation of idiopathic hematuria and associated pathology in grant's gazelles (gazella granti): 10 cases.	ten cases of hematuria in grant's gazelle (gazella granti) (two male and eight female) from five institutions were examined and the clinicopathologic data summarized. five gazelles died spontaneously and five were euthanized. all gazelles had marked hematuria without pyuria. mean age at the onset of clinical signs and time of euthanasia or death was 5.0 +/- 1.4 yr and 8.2 +/- 3.7 yr, respectively. the severity of clinical signs with hematuria ranged from episodes of chronic intermittent hematuri ...	2009	20063809
experimental leptospirosis in capybaras (hydrochaeris hydrochaeris) infected with leptospira interrogans serovar pomona.	capybara (hydrochaeris hydrochaeris), the largest rodent in the world, is widely distributed in south america. these animals live in areas with abundant water, which makes them a potential reservoir for leptospira. the objective of this study was to investigate seroconversion, leptospiremia, and leptospiruria in capybaras experimentally infected with a virulent strain of leptospira interrogans serovar pomona. seven capybaras were used: one control and six infected. agglutinins against serovar po ...	2009	20063819
the farmer who didn't need a wheel barrow.	we report the difficulties encountered in diagnosing leptospirosis in an 85-year-old man who presented with non-specific signs and symptoms. initially, a wide haematologic and oncologic work-up without significant results was performed, as symptoms of several organ dysfunctions emerged and the clinical course showed a rapid deterioration. after several days without a definite diagnosis, the infection was finally detected after reviewing all results and considering the patient's profession as a f ...	2009	21687022
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 ...	2009	19923485
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 ...	2009	19923485
lateral transfer of genes and gene fragments in prokaryotes.	lateral genetic transfer (lgt) involves the movement of genetic material from one lineage into another and its subsequent incorporation into the new host genome via genetic recombination. studies in individual taxa have indicated lateral origins for stretches of dna of greatly varying length, from a few nucleotides to chromosome size. here we analyze 1,462 sets of single-copy, putatively orthologous genes from 144 fully sequenced prokaryote genomes, asking to what extent complete genes and fragm ...	2009	20333212
a flood of microbial genomes-do we need more?		2009	19513110
small intestinal intussusception in five dogs with acute renal failure and suspected leptospirosis (l. australis).	this case series describes 5 dogs with small intestinal intussusception and acute kidney injury due to infection with leptospira interrogans serovar australis.	2009	25164636
[application of multiple-locus variable number tandem repeat analysis (mlva) on molecular typing of leptospira interrogans].		2010	22997605
abundant oligonucleotides common to most bacteria.	bacteria show a bias in their genomic oligonucleotide composition far beyond that dictated by g+c content. patterns of over- and underrepresented oligonucleotides carry a phylogenetic signal and are thus diagnostic for individual species. patterns of short oligomers have been investigated by multiple groups in large numbers of bacteria genomes. however, global distributions of the most highly overrepresented mid-sized oligomers have not been assessed across all prokaryotes to date. we surveyed o ...	2010	20352124
a bacterial ortholog of class ii lysyl-trna synthetase activates lysine.	aminoacyl-trna synthetases produce aminoacyl-trnas, essential substrates for accurate protein synthesis. beyond their central role in translation some of these enzymes or their orthologs are recruited for alternative functions, not always related to their primary cellular role. we investigate here the enzymatic properties of genx (also called poxa and yjea), an ortholog of bacterial class ii lysyl-trna synthetase. genx is present in most gram-negative bacteria and is homologous to the catalytic ...	2010	20580719
leptospirosis induced pulmonary alveolar hemorrhage.	leptospirosis, a zoonosis with protean manifestations caused by the spirochete leptospira interrogans, occurs worldwide. we report a case of leptospirosis presenting as pulmonary alveolar hemorrhage in a young immunocompetent male. this organism should be considered as an important infectious cause of pulmonary alveolar hemorrhage in the appropriate epidemiological setting.	2010	21932486
infectious causes of stillbirth: a clinical perspective.	untreated infection may cause stillbirth by several mechanisms, including direct fetal infection, placental damage, and severe maternal illness. many bacteria, viruses, and protozoa have been associated with stillbirth. in developed countries, up to 24% of stillbirths have been attributed to infection, although with increased availability of sophisticated diagnostics and rigorous screening, it appears likely that higher numbers may actually be associated with infection. in developed countries, a ...	2010	20661048
complement control protein factor h: the good, the bad, and the inadequate.	the complement system is an essential component of the innate immune system that participates in elimination of pathogens and altered host cells and comprises an essential link between the innate and adaptive immune system. soluble and membrane-bound complement regulators protect cells and tissues from unintended complement-mediated injury. complement factor h is a soluble complement regulator essential for controlling the alternative pathway in blood and on cell surfaces. normal recognition of ...	2010	20580090
the expression and functions of toll-like receptors in atherosclerosis.	inflammation drives atherosclerosis. both immune and resident vascular cell types are involved in the development of atherosclerotic lesions. the phenotype and function of these cells are key in determining the development of lesions. toll-like receptors are the most characterised innate immune receptors and are responsible for the recognition of exogenous conserved motifs on pathogens, and, potentially, some endogenous molecules. both endogenous and exogenous tlr agonists may be present in athe ...	2010	20652007
infection-related stillbirths.	infection is an important cause of stillbirths worldwide: in low-income and middle-income countries, 50% of stillbirths or more are probably caused by infection. by contrast, in high-income countries only 10-25% of stillbirths are caused by infection. syphilis, where prevalent, causes most infectious stillbirths, and is the infection most amenable to screening and treatment. ascending bacterial infection is a common cause of stillbirths, but prevention has proven elusive. many viral infections c ...	2010	20223514
identification and characterization of ompa-like proteins as novel vaccine candidates for leptospirosis.	leptospira is an important infectious gram-negative bacterium causing leptospirosis in mammals. outer membrane proteins (omps) are key molecules in the interface between the cell and its environment. a group of putative leptospiral outer membrane proteins with an ompa-like domain, comprising lp0056, lp0222, lp3615, lp3685, lp4337 and lbp328, were identified by bioinformatic methods and expressed as gst-tag fusion proteins. all these recombinant proteins were screened for immune-protective potent ...	2010	20064477
of guinea pigs and men--an unusual case of jaundice.	a 21-year-old male presented at the emergency room with jaundice, itching, dry cough, malaise and weight loss of 10 kg during the preceding four weeks. eighteen months earlier, the patient had suffered an automobile accident leading to polytrauma. serological markers for viral or other causes of hepatitis were absent. for suspected secondary sclerosing cholangitis, ultrasound and ercp were performed but failed to reveal pathological findings. a liver biopsy showed cholestatic liver disease witho ...	2010	20072994
leptospira wolffii, a potential new pathogenic leptospira species detected in human, sheep and dog.	leptospirosis is the most common zoonotic disease, which is transmitted to humans through contaminated water or direct exposure to the urine of infected animals. in this study, the presence and prevalence of leptospira species in the infected samples of human (n=369) and sheep (n=75) sera and also dogs' urine (n=150), collected from four provinces of iran, were investigated by using nested-pcr/rflp assay followed by sequencing analysis. nested-pcr assay detected that 98/369 (26.5%) human, 13/75 ...	2010	20074666
differential cytokine gene expression according to outcome in a hamster model of leptospirosis.	parameters predicting the evolution of leptospirosis would be useful for clinicians, as well as to better understand severe leptospirosis, but are scarce and rarely validated. because severe leptospirosis includes septic shock, similarities with predictors evidenced for sepsis and septic shock were studied in a hamster model.	2010	20076757
virtual screening for potential inhibitors of homology modeled leptospira interrogans murd ligase.	the life-threatening infections caused by leptospira serovars remain a global challenge since long time. prevention of infection by controlling environmental factors being difficult to practice in developing countries, there is a need for designing potent anti-leptospirosis drugs. atp-dependent murd involved in biosynthesis of peptidoglycan was identified as common drug target among pathogenic leptospira serovars through subtractive genomic approach. peptidoglycan biosynthesis pathway being uniq ...	2010	21566738
in silico identification of common putative drug targets in leptospira interrogans.	infectious diseases are the leading causes of death worldwide. hence, there is a need to develop new antimicrobial agents. traditional method of drug discovery is time consuming and yields a few drug targets with little intracellular information for guiding target selection. thus, focus in drug development has been shifted to computational comparative genomics for identifying novel drug targets. leptospirosis is a worldwide zoonosis of global concern caused by leptospira interrogans. availabilit ...	2010	21572503
overoxidation of 2-cys peroxiredoxin in prokaryotes: cyanobacterial 2-cys peroxiredoxins sensitive to oxidative stress.	in eukaryotic organisms, hydrogen peroxide has a dual effect; it is potentially toxic for the cell but also has an important signaling activity. according to the previously proposed floodgate hypothesis, the signaling activity of hydrogen peroxide in eukaryotes requires a transient increase in its concentration, which is due to the inactivation by overoxidation of 2-cys peroxiredoxin (2-cys prx). sensitivity to overoxidation depends on the structural gglg and yf motifs present in eukaryotic 2-cy ...	2010	20736168
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 ...	2010	20737013
diversity and abundance of zoonotic pathogens and indicators in manures of feedlot cattle in australia.	the occurrence of 10 pathogens and three fecal indicators was assessed by quantitative pcr in manures of australian feedlot cattle. most samples tested positive for one or more pathogens. for the dominant pathogens campylobacter jejuni, listeria monocytogenes, giardia spp., cryptosporidium spp., and eaea-positive escherichia coli, 10² to 10⁷ genome copies g⁻¹ (dry weight) manure were recovered.	2010	20802080
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 ...	2010	20805337
mutations affecting leptospira interrogans lipopolysaccharide attenuate virulence.	leptospira interrogans is the causative agent of leptospirosis. lipopolysaccharide (lps) is the major outer membrane component of l. interrogans. it is the dominant antigen recognized during infection and the basis for serological classification. the structure of lps and its role in pathogenesis are unknown. we describe two defined mutants of l. interrogans serovar manilae with transposon insertions in the lps locus. mutant m895 was disrupted in gene la1641 encoding a protein with no known homol ...	2010	20807198
enhanced determination of streptococcus pneumoniae serotypes associated with invasive disease in laos by using a real-time polymerase chain reaction serotyping assay with cerebrospinal fluid.	a prospective hospital-based study was undertaken to define the incidence of invasive pneumococcal disease (ipd) and circulating serotypes in laos. of 10,799 patients with hemocultures and 353 patients with cerebrospinal fluid samples, 0.21% and 5.4%, respectively, were positive for streptococcus pneumoniae, giving a total of 35 ipd patients. we developed a real-time polymerase chain reaction to detect serotypes represented in the 13-valent pneumococcal vaccine. a blinded evaluation comparing se ...	2010	20810803
an emerging pulmonary haemorrhagic syndrome in dogs: similar to the human leptospiral pulmonary haemorrhagic syndrome?	severe pulmonary haemorrhage is a rare necropsy finding in dogs but the leptospiral pulmonary haemorrhagic syndrome (lphs) is a well recognized disease in humans. here we report a pulmonary haemorrhagic syndrome in dogs that closely resembles the human disease. all 15 dogs had massive, pulmonary haemorrhage affecting all lung lobes while haemorrhage in other organs was minimal. histologically, pulmonary lesions were characterized by acute, alveolar haemorrhage without identifiable vascular lesio ...	2010	21274452
[biological risk prevention in agriculture and animal breeding: immunization strategies].	vaccine preventable diseases are, so far, a main focus of public health programmes all over the world since people still die in consequence of dyphteria or tetanus. biological risk is widely represented in agriculture and animal breeding, due to environmental characteristics and to injury typology. moreover, aged people and migrants represent a significant part of the workforce. these two groups are, for instance, more exposed to clostridium tetani infection because not fully immunized. among in ...	2010	21438285
unifying themes in microbial associations with animal and plant hosts described using the gene ontology.	microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. effective comparisons among these symbioses, ho ...	2010	21119014
exploring the spatial and temporal organization of a cell's proteome.	to increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. these levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and spatial distribution in the cell. emerging new experimental technologies are greatly i ...	2010	21094684
exploring the spatial and temporal organization of a cell's proteome.	to increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. these levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and spatial distribution in the cell. emerging new experimental technologies are greatly i ...	2010	21094684
leptospirosis presenting in a woman with fulminant hepatic failure from wilson's disease: a case report.	we report an unusual case of wilson's disease that was revealed by presentation of leptospirosis. the prompt detection of this potentially life-threatening disease highlights the importance of careful investigation. to the best of our knowledge, this is the first reported case of leptospirosis involving the development of fulminant liver failure due to wilson's disease.	2010	20698945
differences in clinical manifestations of imported versus autochthonous leptospirosis in austria and germany.	leptospirosis, a zoonosis occurring worldwide, has a broad spectrum of clinical manifestations. recently, various countries observed an increase of severe anicteric cases. in austria and germany, growing numbers of imported cases are notified in addition to autochthonous infections. the aim of this study was to assess whether imported and autochthonous cases differ in clinical manifestations and outcome. we retrospectively analyzed 24 imported and 35 autochthonous cases treated in six infectious ...	2010	20682876
nuclear receptors and inflammation control: molecular mechanisms and pathophysiological relevance.	tissue inflammation is a tightly regulated process that normally serves to recruit the immune system to sites of infection and injury and to facilitate tissue repair processes. when an inflammatory state is excessive or prolonged, local and systemic damage to host tissues can result in loss of normal physiological functions. here, we briefly review recent studies that advance our understanding of signaling pathways involved in initiation of inflammatory responses at the level of transcription an ...	2010	20631355
intergenic transposable elements are not randomly distributed in bacteria.	insertion sequences (iss) are mobile genetic elements in bacterial genomes. in general, intergenic is elements are probably less deleterious for their hosts than intragenic iss, simply because they have a lower likelihood of disrupting native genes. however, since promoters, shine-dalgarno sequences, and transcription factor binding sites are intergenic and upstream of genes, i hypothesized that not all neighboring gene orientations (ngos) are selectively equivalent for is insertion. to test thi ...	2010	20697140
toll-like receptor agonists: are they good adjuvants?	therapeutic immunization leading to cancer regression remains a significant challenge. successful immunization requires activation of adaptive immunity, including tumor specific cd4 t cells and cd8 t cells. generally, the activation of t cells is compromised in patients with cancer because of immune suppression, loss of tumor antigen expression, and dysfunction of antigen-presenting cells. antigen-presenting cells such as dendritic cells (dcs) are key for the induction of adaptive antitumor immu ...	2010	20693851
save the tree of life or get lost in the woods.	the wealth of prokaryotic genomic data available has revealed that the histories of many genes are inconsistent, leading some to question the value of the tree of life hypothesis. it has been argued that a tree-like representation requires suppressing too much information, and that a more pluralistic approach is necessary for understanding prokaryotic evolution. we argue that trees may still be a useful representation for evolutionary histories in light of new data.	2010	20594329
host-microbe interactions in the developing zebrafish.	the amenability of the zebrafish to in vivo imaging and genetic analysis has fueled expanded use of this vertebrate model to investigate the molecular and cellular foundations of host-microbe relationships. study of microbial encounters in zebrafish hosts has concentrated on developing embryonic and larval stages, when the advantages of the zebrafish model are maximized. a comprehensive understanding of these host-microbe interactions requires appreciation of the developmental context into which ...	2010	20153622
a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ...	2010	20141328
the path to next generation biofuels: successes and challenges in the era of synthetic biology.	volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for con ...	2010	20089184
leptospirosis diagnosed by molecular dna detection on skin biopsy.	leptospirosis is one of the most common anthropozoonoses in the world. humans are accidental hosts who get infected through damaged skin or conjunctiva from environmental sources such as soil and water contaminated by urine or tissues from infected animals. we report the case of a young man for whom the diagnosis was obtained by polymerase chain reaction (pcr) detection from a skin biopsy.	2010	22242069
tlr cross-talk mechanism of hemorrhagic shock-primed pulmonary neutrophil infiltration.	hemorrhage resulted from severe trauma renders patients susceptible to the development of acute lung injury (ali). the accumulation of polymorphonuclear neutrophils (pmn) in the lung is a critical event in the development of ali. pmn migration is a result of a cascade of cellular events, in which pmn, endothelial cells (ec), and macrophages (mϕ) act in concert. recent studies explored interrelated novel findings indicating that toll-like receptors (tlrs) cross-talk mechanisms occurring in pmn, e ...	2010	20072711
early identification of leptospirosis-associated pulmonary hemorrhage syndrome by use of a validated prediction model.	to identify prediction factors for the development of leptospirosis-associated pulmonary hemorrhage syndrome (lphs).	2010	20026189
early identification of leptospirosis-associated pulmonary hemorrhage syndrome by use of a validated prediction model.	to identify prediction factors for the development of leptospirosis-associated pulmonary hemorrhage syndrome (lphs).	2010	20026189
identification of immunodominant b- and t-cell combined epitopes in outer membrane lipoproteins lipl32 and lipl21 of leptospira interrogans.	leptospirosis is a serious infectious disease caused by pathogenic leptospira. b- and t-cell-mediated immune responses contribute to the mechanisms of leptospira interrogans infection and immune intervention. lipl32 and lipl21 are the conserved outer membrane lipoproteins of l. interrogans and are considered vaccine candidates. in this study, we identified b- and t-cell combined epitopes within lipl32 and lipl21 to further develop a novel vaccine. by using a computer prediction algorithm, two b- ...	2010	20237196
altered linkage of hydroxyacyl chains in lipid a of campylobacter jejuni reduces tlr4 activation and antimicrobial resistance.	modification of the lipid a moiety of bacterial lipopolysaccharide influences cell wall properties, endotoxic activity, and bacterial resistance to antimicrobial peptides. known modifications are variation in the number or length of acyl chains and/or attached phosphoryl groups. here we identified two genes (gnna and gnnb) in the major foodborne pathogen campylobacter jejuni that enable the synthesis of a glcn3n precursor udp 2-acetamido-3-amino-2,3-dideoxy-alpha-d-glucopyranose (udp-glcnac3n) i ...	2010	20351099
use of luminescent leptospira interrogans for enumeration in biological assays.	rapid and reliable in vitro methods for the detection of pathogenic leptospires, such as leptospira interrogans, are lacking. the present study investigated the use of luminescence to replace the existing enumeration techniques. transposon tnsc189 was modified to incorporate the luxcdabe cassette from photorhabdus luminescens and was used to construct luminescent leptospira spp. there was a linear relationship between luminescence and cell number, with the theoretical detection limit being less ...	2010	20375235
the infective causes of hepatitis and jaundice amongst hospitalised patients in vientiane, laos.	there is little information on the diverse infectious causes of jaundice and hepatitis in the asiatic tropics. serology (hepatitis a, b, c and e, leptospirosis, dengue, rickettsia), antigen tests (dengue), pcr assays (hepatitis a, c and e) and blood cultures (septicaemia) were performed on samples from 392 patients admitted with jaundice or raised transaminases (> or =x3) to mahosot hospital, vientiane, laos over 3 years. conservative definitions suggested diagnoses of dengue (8.4%), rickettsios ...	2010	20378138
characterization and serologic analysis of the treponema pallidum proteome.	treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease characterized by widespread tissue dissemination and chronic infection. in this study, we analyzed the proteome of t. pallidum by the isoelectric focusing (ief) and nonequilibrating ph gel electrophoresis (nephge) forms of two-dimensional gel electrophoresis (2dge), coupled with matrix-assisted laser desorption ionization-time of flight (maldi-tof) analysis. we determined the identity of 148 t. ...	2010	20385758
translocation of borrelia burgdorferi surface lipoprotein ospa through the outer membrane requires an unfolded conformation and can initiate at the c-terminus.	borrelia burgdorferi surface lipoproteins are essential to the pathogenesis of lyme borreliosis, but the mechanisms responsible for their localization are only beginning to emerge. we have previously demonstrated the critical nature of the amino-terminal 'tether' domain of the mature lipoprotein for sorting a fluorescent reporter to the borrelia cell surface. here, we show that individual deletion of four contiguous residues within the tether of major surface lipoprotein ospa results in its inef ...	2010	20398211