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a comparison of computational methods for identifying virulence factors.bacterial pathogens continue to threaten public health worldwide today. identification of bacterial virulence factors can help to find novel drug/vaccine targets against pathogenicity. it can also help to reveal the mechanisms of the related diseases at the molecular level. with the explosive growth in protein sequences generated in the postgenomic age, it is highly desired to develop computational methods for rapidly and effectively identifying virulence factors according to their sequence info ...201222880014
diversity in the protein n-glycosylation pathways within the campylobacter genus.the foodborne bacterial pathogen, campylobacter jejuni, possesses an n-linked protein glycosylation (pgl) pathway involved in adding conserved heptasaccharides to asparagine-containing motifs of >60 proteins, and releasing the same glycan into its periplasm as free oligosaccharides. in this study, comparative genomics of all 30 fully sequenced campylobacter taxa revealed conserved pgl gene clusters in all but one species. structural, phylogenetic and immunological studies showed that the n-glyco ...201222859570
multifunctional role of dextran sulfate sodium for in vivo modeling of intestinal diseases.inflammatory bowel diseases (ibds) are chronic, relapsing disorders that affect the gastrointestinal tract of millions of people and continue to increase in incidence each year. while several factors have been associated with development of ibds, the exact etiology is unknown. research using animal models of ibds is beginning to provide insights into how the different factors contribute to disease development. oral administration of dextran sulfate sodium (dss) to mice induces a reproducible exp ...201222853702
clinical approach to the diagnostic evaluation of hereditary and acquired neuromuscular diseases.for diagnostic evaluation of a neuromuscular disease, the clinician must be able to obtain a relevant patient and family history and perform focused general, musculoskeletal, neurologic, and functional physical examinations to direct further diagnostic evaluations. laboratory studies for hereditary neuromuscular diseases include the relevant molecular genetic studies. the electromyogram and nerve-conduction studies remain an extension of the physical examination, and help to guide further diagno ...201222938875
luminal hypertonicity and acidity modulate colorectal afferents and induce persistent visceral hypersensitivity.carbohydrate malabsorption such as in lactose intolerance or enteric infection causes symptoms that include abdominal pain. because this digestive disorder increases intracolonic osmolarity and acidity by accumulation of undigested carbohydrates and fermented products, we tested whether these two factors (hypertonicity and acidity) would modulate colorectal afferents in association with colorectal nociception and hypersensitivity. in mouse colorectum-pelvic nerve preparations in vitro, afferent ...201222859365
role of lipid rafts and flagellin in invasion of colonic epithelial cells by shiga-toxigenic escherichia coli o113:h21.shiga-toxigenic escherichia coli (stec) o113:h21 strains that lack the locus of enterocyte effacement (lee) efficiently invade eukaryotic cells in vitro, unlike lee-positive o157:h7 strains. we used a flic deletion mutant of the o113:h21 stec strain 98nk2 (98nk2δflic) to show that invasion of colonic epithelial (hct-8) cells is heavily dependent on production of flagellin, even though adherence to the cells was actually enhanced in the mutant. flagellin binds and signals through toll-like recept ...201222689816
localization of aggregatibacter actinomycetemcomitans cytolethal distending toxin subunits during intoxication of live cells.the cytolethal distending toxin (cdt), produced by some clinically important gram-negative bacterial species, is related to the family of ab-type toxins. three heterologous proteins (cdta, cdtb, and cdtc) and a genotoxin mode of action distinguish the cdt from others in this toxin class. crystal structures of several species-specific cdts have provided a basis for predicting subunit interactions and functions. in addition, empirical studies have yielded significant insights into the in vivo inte ...201222645284
legionella pneumophila pathogenesis in the galleria mellonella infection model.legionella pneumophila is a facultative intracellular human pathogen and the etiological agent of severe pneumonia known as legionnaires' disease. its virulence depends on protein secretion systems, in particular, the dot/icm type iv secretion system (t4ss), which is essential to establish a replication-permissive vacuole in macrophages. the analysis of the role of these systems and their substrates for pathogenesis requires easy-to-use models which approximate human infection. we examined the e ...201222645286
campylobacter jejuni-mediated induction of cc and cxc chemokines and chemokine receptors in human dendritic cells.campylobacter jejuni is a leading worldwide bacterial cause of human diarrheal disease. although the specific molecular mechanisms of c. jejuni pathogenesis have not been characterized in detail, host inflammatory responses are thought to be major contributing factors to the resulting typical acute colitis. the intestinal mucosal chemokine response is particularly important in the initial stages of bacterium-induced gut inflammation. chemokines attract blood phagocytes and lymphocytes to the sit ...201222689814
pediatric renal inflammatory myofibroblastic tumours: a case report and review of the etiology and management options.inflammatory myofibroblastic tumours (imts) have been described in lung, bladder, spleen, breast, pancreas, liver, colon, spermatic cord, prostate, peripheral nerves, orbit and kidney. traditionally believed as having a reactive pathogenesis, imts are now viewed more as a neoplasm. this report describes a case of a renal imt in a 14-year-old girl with spina bifida associated neurogenic bladder and a history of recurrent urinary tract infections. this represents a unique case as pediatric renal i ...201223093568
amixicile, a novel inhibitor of pyruvate: ferredoxin oxidoreductase, shows efficacy against clostridium difficile in a mouse infection model.clostridium difficile infection (cdi) is a serious diarrheal disease that often develops following prior antibiotic usage. one of the major problems with current therapies (oral vancomycin and metronidazole) is the high rate of recurrence. nitazoxanide (ntz), an inhibitor of pyruvate:ferredoxin oxidoreductase (pfor) in anaerobic bacteria, parasites, helicobacter pylori, and campylobacter jejuni, also shows clinical efficacy against cdi. from a library of ∼250 analogues of ntz, we identified lead ...201222585229
automated detection of toxigenic clostridium difficile in clinical samples: isothermal tcdb amplification coupled to array-based detection.clostridium difficile can carry a genetically variable pathogenicity locus (paloc), which encodes clostridial toxins a and b. in hospitals and in the community at large, this organism is increasingly identified as a pathogen. to develop a diagnostic test that combines the strengths of immunoassays (cost) and dna amplification assays (sensitivity/specificity), we targeted a genetically stable paloc region, amplifying tcdb sequences and detecting them by hybridization capture. the assay employs a ...201222675134
fdhtu-modulated formate dehydrogenase expression and electron donor availability enhance recovery of campylobacter jejuni following host cell infection.campylobacter jejuni is a food-borne bacterial pathogen that colonizes the intestinal tract and causes severe gastroenteritis. interaction with host epithelial cells is thought to enhance severity of disease, and the ability of c. jejuni to modulate its metabolism in different in vivo and environmental niches contributes to its success as a pathogen. a c. jejuni operon comprising two genes that we designated fdht (cjj81176_1492) and fdhu (cjj81176_1493) is conserved in many bacterial species. de ...201222636777
selenium-dependent biogenesis of formate dehydrogenase in campylobacter jejuni is controlled by the fdhtu accessory genes.the food-borne bacterial pathogen campylobacter jejuni efficiently utilizes organic acids such as lactate and formate for energy production. formate is rapidly metabolized via the activity of the multisubunit formate dehydrogenase (fdh) enzyme, of which the fdha subunit is predicted to contain a selenocysteine (sec) amino acid. in this study we investigated the function of the cj1500 and cj1501 genes of c. jejuni, demonstrate that they are involved in selenium-controlled production of fdh, and p ...201222609917
avian resistance to campylobacter jejuni colonization is associated with an intestinal immunogene expression signature identified by mrna sequencing.campylobacter jejuni is the most common cause of human bacterial gastroenteritis and is associated with several post-infectious manifestations, including onset of the autoimmune neuropathy guillain-barré syndrome, causing significant morbidity and mortality. poorly-cooked chicken meat is the most frequent source of infection as c. jejuni colonizes the avian intestine in a commensal relationship. however, not all chickens are equally colonized and resistance seems to be genetically determined. we ...201222870198
association of campylobacter jejuni metabolic traits with multilocus sequence types.in this study, we describe the association of three campylobacter jejuni metabolism-related traits, γ-glutamyl-transpeptidase (ggt), fucose permease (fucp), and secreted l-asparaginase [ansb(s)], with multilocus sequence types (sts). a total of 710 c. jejuni isolates with known sts were selected and originated from humans, poultry, bovines, and the environment. among these isolates, we found 31.1% to produce ggt and 49.3% and 30.3% to be positive for ansb(s) and fucp, respectively. the combinati ...201222660710
seasonal diversity of planktonic protists in southwestern alberta rivers over a 1-year period as revealed by terminal restriction fragment length polymorphism and 18s rrna gene library analyses.the temporal dynamics of planktonic protists in river water have received limited attention despite their ecological significance and recent studies linking phagotrophic protists to the persistence of human-pathogenic bacteria. using molecular-based techniques targeting the 18s rrna gene, we studied the seasonal diversity of planktonic protists in southwestern alberta rivers (oldman river basin) over a 1-year period. nonmetric multidimensional scaling analysis of terminal restriction fragment le ...201222685143
arcobacter in lake erie beach waters: an emerging gastrointestinal pathogen linked with human-associated fecal contamination.the genus arcobacter has been associated with human illness and fecal contamination by humans and animals. to better characterize the health risk posed by this emerging waterborne pathogen, we investigated the occurrence of arcobacter spp. in lake erie beach waters. during the summer of 2010, water samples were collected 35 times from the euclid, villa angela, and headlands (east and west) beaches, located along ohio's lake erie coast. after sample concentration, arcobacter was quantified by rea ...201222660704
antimicrobial activities of fidaxomicin.fidaxomicin is bactericidal against clostridium difficile. the combined results of 8 in vitro studies of 1323 c. difficile isolates showed the minimum inhibitory concentration (mic) range of fidaxomicin to be ≤ 0.001-1 μg/ml, with a maximum mic for inhibition of 90% of organisms (mic(90)) of 0.5 μg/ml. isolates from 2 phase iii clinical trials demonstrated that fidaxomicin mics of baseline isolates did not predict clinical cure, failure, or recurrence of c. difficile infections. no resistance to ...201222752863
zinc competition among the intestinal microbiota.bioavailable levels of trace metals, such as iron and zinc, for bacterial growth in nature are sufficiently low that most microbes have evolved high-affinity binding and transport systems. the microbe campylobacter jejuni lives in the gastrointestinal tract of chickens, the principal source of human infection. a high-affinity abc transporter for zinc uptake is required for campylobacter survival in chicken intestines in the presence of a normal microbiota but not when chickens are raised with a ...201222851657
sialoadhesin promotes rapid proinflammatory and type i ifn responses to a sialylated pathogen, campylobacter jejuni.sialoadhesin (sn) is a macrophage (mφ)-restricted receptor that recognizes sialylated ligands on host cells and pathogens. although sn is thought to be important in cellular interactions of mφs with cells of the immune system, the functional consequences of pathogen engagement by sn are unclear. as a model system, we have investigated the role of sn in mφ interactions with heat-killed campylobacter jejuni expressing a gd1a-like, sialylated glycan. compared to sn-expressing bone marrow-derived ma ...201222851711
inhibition of listeria monocytogenes atcc 19115 on ham steak by tea bioactive compounds incorporated into chitosan-coated plastic films.the consumer demands for better quality and safety of food products have given rise to the development and implementation of edible films. the use of antimicrobial films can be a promising tool for controlling l. monocytogenes on ready to eat products. the aim of this study was to develop effective antimicrobial films incorporating bioactive compounds from green and black teas into chitosan, for controlling l. monocytogenes atcc 19115 on vacuum-packaged ham steak. the effectiveness of these anti ...201222839307
guillain-barre syndrome associated with norovirus infection.the authors describe a case of guillain-barre syndrome after the diarrhoeal infection due to norovirus. many infections have been described most notably campylobacter jejuni. to our knowledge a connection to norovirus has not been described in the world literature. the authors speculate on why this may be so.201222736780
interaction effects between sender and receiver processes in indirect transmission of campylobacter jejuni between broilers.infectious diseases in plants, animals and humans are often transmitted indirectly between hosts (or between groups of hosts), i.e. via some route through the environment instead of via direct contacts between these hosts. here we study indirect transmission experimentally, using transmission of campylobacter jejuni (c. jejuni) between spatially separated broilers as a model system. we distinguish three stages in the process of indirect transmission; (1) an infectious "sender" excretes the agent ...201222831274
examination of nanoparticle inactivation of campylobacter jejuni biofilms using infrared and raman spectroscopies.to investigate inactivation effect and mechanism of zinc oxide nanoparticles (zno nps) activity against campylobacter jejuni biofilms.201222734855
genomic and proteomic characterization of sumu, a mu-like bacteriophage infecting haemophilus parasuis.haemophilus parasuis, the causative agent of glässer's disease, is prevalent in swine herds and clinical signs associated with this disease are meningitis, polyserositis, polyarthritis, and bacterial pneumonia. six to eight week old pigs in segregated early weaning herds are particularly susceptible to the disease. insufficient colostral antibody at weaning or the mixing of pigs with heterologous virulent h. parasuis strains from other farm sources in the nursery or grower-finisher stage are con ...201222823751
exploiting the nephrotoxic effects of venom from the sea anemone, phyllodiscus semoni, to create a hemolytic uremic syndrome model in the rat.in the natural world, there are many creatures with venoms that have interesting and varied activities. although the sea anemone, a member of the phylum coelenterata, has venom that it uses to capture and immobilise small fishes and shrimp and for protection from predators, most sea anemones are harmless to man. however, a few species are highly toxic; some have venoms containing neurotoxins, recently suggested as potential immune-modulators for therapeutic application in immune diseases. phyllo ...201222851928
mucosal reactive oxygen species decrease virulence by disrupting campylobacter jejuni phosphotyrosine signaling.reactive oxygen species (ros) play key roles in mucosal defense, yet how they are induced and the consequences for pathogens are unclear. we report that ros generated by epithelial nadph oxidases (nox1/duox2) during campylobacter jejuni infection impair bacterial capsule formation and virulence by altering bacterial signal transduction. upon c. jejuni invasion, ros released from the intestinal mucosa inhibit the bacterial phosphotyrosine network that is regulated by the outer-membrane tyrosine k ...201222817987
diarrhea outbreak during u.s. military training in el salvador.infectious diarrhea remains a major risk to deployed military units worldwide in addition to their impact on travelers and populations living in the developing world. this report describes an outbreak of diarrheal illness in the u.s. military's 130(th) maneuver enhancement brigade deployed in san vicente, el salvador during a training and humanitarian assistance mission. an outbreak investigation team from u.s. naval medical research unit-six conducted an epidemiologic survey and environmental a ...201222815747
planktonic aggregates of staphylococcus aureus protect against common antibiotics.bacterial cells are mostly studied during planktonic growth although in their natural habitats they are often found in communities such as biofilms with dramatically different physiological properties. we have examined another type of community namely cellular aggregates observed in strains of the human pathogen staphylococcus aureus. by laser-diffraction particle-size analysis (lda) we show, for strains forming visible aggregates, that the aggregation starts already in the early exponential gro ...201222815921
viscosity dictates metabolic activity of vibrio ruber.little is known about metabolic activity of bacteria, when viscosity of their environment changes. in this work, bacterial metabolic activity in media with viscosity ranging from 0.8 to 29.4 mpas was studied. viscosities up to 2.4 mpas did not affect metabolic activity of vibrio ruber. on the other hand, at 29.4 mpas respiration rate and total dehydrogenase activity increased 8 and 4-fold, respectively. the activity of glucose-6-phosphate dehydrogenase (gpd) increased up to 13-fold at higher vis ...201222826705
structural heterogeneity of terminal glycans in campylobacter jejuni lipooligosaccharides.lipooligosaccharides of the gastrointestinal pathogen campylobacter jejuni are regarded as a major virulence factor and are implicated in the production of cross-reactive antibodies against host gangliosides, which leads to the development of autoimmune neuropathies such as guillain-barré and fisher syndromes. c. jejuni strains are known to produce diverse los structures encoded by more than 19 types of los biosynthesis clusters. this study demonstrates that the final c. jejuni los structure can ...201222815868
recent advances in small bowel diseases: part i.as is the case in all parts of gastroenterology and hepatology, there have been many advances in our knowledge and understanding of small intestinal diseases. over 1000 publications were reviewed for 2008 and 2009, and the important advances in basic science as well as clinical applications were considered. in part i of this editorial review, seven topics are considered: intestinal development; proliferation and repair; intestinal permeability; microbiotica, infectious diarrhea and probiotics; d ...201222807604
phylogenetic position of aquificales based on the whole genome sequences of six aquificales species.species belonging to the order aquificales are believed to be an early branching lineage within the bacteria. however, the branching order of this group in single-gene phylogenetic trees is highly variable; for example, it has also been proposed that the aquificales should be grouped with ε-proteobacteria. to investigate the phylogenetic position of aquificales at the whole-genome level, here we reconstructed the phylogenetic trees of 18 bacteria including six aquificales species based on the co ...201222844640
glycerol monolaurate antibacterial activity in broth and biofilm cultures.glycerol monolaurate (gml) is an antimicrobial agent that has potent activity against gram-positive bacteria. this study examines gml antibacterial activity in comparison to lauric acid, in broth cultures compared to biofilm cultures, and against a wide range of gram-positive, gram-negative, and non-gram staining bacteria.201222808139
campylobacter jejuni induces acute enterocolitis in gnotobiotic il-10-/- mice via toll-like-receptor-2 and -4 signaling.campylobacter jejuni is a leading cause of foodborne bacterial enterocolitis worldwide. investigation of immunopathology is hampered by a lack of suitable vertebrate models. we have recently shown that gnotobiotic mice as well as conventional il-10(-/-) animals are susceptible to c. jejuni infection and develop intestinal immune responses. however, clinical symptoms of c. jejuni infection were rather subtle and did not reflect acute bloody diarrhea seen in human campylobacteriosis.201222808254
glycopp: a webserver for prediction of n- and o-glycosites in prokaryotic protein sequences.glycosylation is one of the most abundant post-translational modifications (ptms) required for various structure/function modulations of proteins in a living cell. although elucidated recently in prokaryotes, this type of ptm is present across all three domains of life. in prokaryotes, two types of protein glycan linkages are more widespread namely, n- linked, where a glycan moiety is attached to the amide group of asn, and o- linked, where a glycan moiety is attached to the hydroxyl group of se ...201222808107
gene expression analysis of toll-like receptor pathways in heterophils from genetic chicken lines that differ in their susceptibility to salmonella enteritidis.previously conducted studies using two chicken lines (a and b) show that line a birds have increased resistance to a number of bacterial and protozoan challenges and that heterophils isolated from line a birds are functionally more responsive. furthermore, when stimulated with toll-like receptor (tlr) agonists, heterophils from line a expressed a totally different cytokine and chemokine mrna expression pattern than heterophils from line b. a large-scale gene expression profile using an agilent 4 ...201222783275
noncanonical notch signaling modulates cytokine responses of dendritic cells to inflammatory stimuli.dendritic cell (dc)-derived cytokines play a key role in specifying adaptive immune responses tailored to the type of pathogen encountered and the local tissue environment. however, little is known about how dcs perceive the local environment. we investigated whether endogenous notch signaling could affect dc responses to pathogenic stimuli. we demonstrate that concurrent notch and tlr stimulation results in a unique cytokine profile in mouse bone-marrow derived dcs characterized by enhanced il- ...201222753939
modification of the campylobacter jejuni n-linked glycan by eptc protein-mediated addition of phosphoethanolamine.campylobacter jejuni is the major worldwide cause of bacterial gastroenteritis. c. jejuni possesses an extensive repertoire of carbohydrate structures that decorate both protein and non-protein surface-exposed structures. an n-linked glycosylation system encoded by the pgl gene cluster mediates the synthesis of a rigidly conserved heptasaccharide that is attached to protein substrates or released as free oligosaccharide in the periplasm. removal of n-glycosylation results in reduced virulence an ...201222761430
infection as a cause of type 1 diabetes?it is the current opinion that pathogens, such as viruses, are contributing to the development of type 1 diabetes (t1d) in susceptible individuals. this opinion is based on epidemiological associations, direct isolation of pathogens from the islets of langerhans, as well as a large amount of data from various experimental animal models. human enteroviruses have dominated the literature associated with the etiology of t1d. however, virus infections have also been reported to protect from autoimmu ...201222504578
chemoenzymatic synthesis of an isoprenoid phosphate tool for the analysis of complex bacterial oligosaccharide biosynthesis.undecaprenyl pyrophosphate synthase (upps) is a key enzyme that catalyzes the production of bactoprenols, which act as membrane anchors for the assembly of complex bacterial oligosaccharides. one of the major hurdles in understanding the assembly of oligosaccharide assembly is a lack of chemical tools to study this process, since bactoprenols and the resulting isoprenoid-linked oligosaccharides lack handles or chromophores for use in pathway analysis. here we describe the isolation of a new upps ...201222925763
cj1136 is required for lipooligosaccharide biosynthesis, hyperinvasion, and chick colonization by campylobacter jejuni.campylobacter jejuni is a major cause of bacterial food-borne enteritis worldwide, and invasion into intestinal epithelial cells is an important virulence mechanism. recently we reported the identification of hyperinvasive c. jejuni strains and created a number of transposon mutants of one of these strains, some of which exhibited reduced invasion into int-407 and caco-2 cells. in one such mutant the transposon had inserted into a homologue of cj1136, which encodes a putative galactosyltransfera ...201222508861
comparison of medium, temperature, and length of incubation for detection of vancomycin-resistant enterococcus.campylobacter (campy; bd diagnostics, sparks, md), spectra vre (remel, lenexa, ks), and bile-esculin-azide-vancomycin (beav; remel) agars were compared for their ability to detect vancomycin-resistant enterococci (vre) in 750 stool specimens. the media were compared at 24 h and 48 h of incubation at 35°c and 42°c. when incubated for 24 h at 35°c, campy was the most sensitive (97.8%) and specific (99.9%) but was comparable to spectra, which has a sensitivity of 95.6% and a specificity of 99.1%, w ...201222535989
reactive oxygen species in the signaling and adaptation of multicellular microbial communities.one of the universal traits of microorganisms is their ability to form multicellular structures, the cells of which differentiate and communicate via various signaling molecules. reactive oxygen species (ros), and hydrogen peroxide in particular, have recently become well-established signaling molecules in higher eukaryotes, but still little is known about the regulatory functions of ros in microbial structures. here we summarize current knowledge on the possible roles of ros during the developm ...201222829965
complete genome sequence of helicobacter cinaedi strain pagu611, isolated in a case of human bacteremia.we report the complete genome sequence of helicobacter cinaedi strain pagu611, isolated in a case of human bacteremia. the pagu611 genome comprises a 2,078,348-bp chromosome and a 23,054-bp plasmid. the chromosome contains a unique genomic island, encoding a type vi secretion system and clustered regularly interspaced short palindromic repeat (crispr) loci.201222740670
assessment of public health events through international health regulations, united states, 2007-2011.under the current international health regulations, 194 states parties are obligated to report potential public health emergencies of international concern to the world health organization (who) within 72 hours of becoming aware of an event. during july 2007-december 2011, who assessed and posted on a secure web portal 222 events from 105 states parties, including 24 events from the united states. twelve us events involved human influenza caused by a new virus subtype, including the first report ...201222709566
variation of chemosensory receptor content of campylobacter jejuni strains and modulation of receptor gene expression under different in vivo and in vitro growth conditions.chemotaxis is crucial for the colonisation/infection of hosts with campylobacter jejuni. central to chemotaxis are the group a chemotaxis genes that are responsible for sensing the external environment. the distribution of group a chemoreceptor genes, as found in the c. jejuni sequenced strains, tlp1-4, 7, 10 and 11 were determined in 33 clinical human and avian isolates.201222747654
aglr is required for addition of the final mannose residue of the n-linked glycan decorating the haloferax volcanii s-layer glycoprotein.recent studies of haloferax volcanii have begun to elucidate the steps of n-glycosylation in archaea, where this universal post-translational modification remains poorly described. in hfx. volcanii, a series of agl proteins catalyzes the assembly and attachment of a n-linked pentasaccharide to the s-layer glycoprotein. although roles have been assigned to the majority of agl proteins, others await description. in the following, the contribution of aglr to n-glycosylation was addressed.201222750201
ataxia, ophthalmoplegia, and areflexia: what would you think?we present here a case of carcinomatous meningitis presenting as miller fisher syndrome (mfs). there are four further cases described in the literature with evidence of tumour invasion within the central nervous system (cns) shown either in cerebrospinal fluid examination or on histology. there are further five cases described in which an association between cancer and a miller fisher phenotype has been shown. some of these have identified antiganglioside antibodies in the serum and, in one case ...201222934206
differential glycosylation of polar and lateral flagellins in aeromonas hydrophila ah-3.polar and lateral flagellin proteins from aeromonas hydrophila strain ah-3 (serotype o34) were found to be glycosylated with different carbohydrate moieties. the lateral flagellin was modified at three sites in o-linkage, with a single monosaccharide of 376 da, which we show to be a pseudaminic acid derivative. the polar flagellin was modified with a heterogeneous glycan, comprised of a heptasaccharide, linked through the same 376-da sugar to the protein backbone, also in o-linkage. in-frame del ...201222733809
towards a pathogenic escherichia coli detection platform using multiplex sybr®green real-time pcr methods and high resolution melting analysis.escherichia coli is a group of bacteria which has raised a lot of safety concerns in recent years. five major intestinal pathogenic groups have been recognized amongst which the verocytotoxin or shiga-toxin (stx1 and/or stx2) producing e. coli (vtec or stec respectively) have received a lot of attention recently. indeed, due to the high number of outbreaks related to vtec strains, the european food safety authority (efsa) has requested the monitoring of the "top-five" serogroups (o26, o103, o111 ...201222761753
entamoeba moshkovskii is associated with diarrhea in infants and causes diarrhea and colitis in mice.entamoeba moshkovskii is prevalent in developing countries and morphologically indistinguishable from pathogenic entamoeba histolytica and nonpathogenic entamoeba dispar. it is not known if e. moshkovskii is pathogenic.201222723640
multilocus sequence typing as a replacement for serotyping in salmonella enterica.salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. we used multilocus sequence typing (mlst) to assign 4,257 isolates from 554 serovars to 1092 sequence types (sts). the majority of the isolates and many sts were grouped into 138 genetically closely related clusters called eburstgroups (ebgs). many ebgs correspond to a serovar, for example most typhimurium are in ebg1 and most enteritidis are in ebg4, but many ebgs co ...201222737074
trif mobilizes unique primary defense against gram-negative bacteria in intestinal interface.the gastrointestinal tract is the largest mucosal surface in our body. it houses diverse microorganisms that collectively form the commensal microbial community. the security of this community is kept by host-microbial interactions and is violated by foreign pathogens that induce local as well as systemic pathology. in most cases, gastrointestinal infections are caused by gram-negative enteropathogens, which trigger host immune responses through the tlr4 signaling pathways. although trif is one ...201222713267
network compression as a quality measure for protein interaction networks.with the advent of large-scale protein interaction studies, there is much debate about data quality. can different noise levels in the measurements be assessed by analyzing network structure? because proteomic regulation is inherently co-operative, modular and redundant, it is inherently compressible when represented as a network. here we propose that network compression can be used to compare false positive and false negative noise levels in protein interaction networks. we validate this hypoth ...201222719828
autoimmunity, dendritic cells and relevance for parkinson's disease.innate and adaptive immune responses in neurodegenerative diseases have become recently a focus of research and discussions. parkinson's disease (pd) is a neurodegenerative disorder without known etiopathogenesis. the past decade has generated evidence for an involvement of the immune system in pd pathogenesis. both inflammatory and autoimmune mechanisms have been recognized and studies have emphasized the role of activated microglia and t-cell infiltration. in this short review, we focus on den ...201222699458
autoimmunity, dendritic cells and relevance for parkinson's disease.innate and adaptive immune responses in neurodegenerative diseases have become recently a focus of research and discussions. parkinson's disease (pd) is a neurodegenerative disorder without known etiopathogenesis. the past decade has generated evidence for an involvement of the immune system in pd pathogenesis. both inflammatory and autoimmune mechanisms have been recognized and studies have emphasized the role of activated microglia and t-cell infiltration. in this short review, we focus on den ...201222699458
16s rrna gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease.canine idiopathic inflammatory bowel disease (ibd) is believed to be caused by a complex interaction of genetic, immunologic, and microbial factors. while mucosa-associated bacteria have been implicated in the pathogenesis of canine ibd, detailed studies investigating the enteric microbiota using deep sequencing techniques are lacking. the objective of this study was to evaluate mucosa-adherent microbiota in the duodenum of dogs with spontaneous idiopathic ibd using 16 s rrna gene pyrosequencing ...201222720094
indomethacin-induced translocation of bacteria across enteric epithelia is reactive oxygen species-dependent and reduced by vitamin c.the enteric epithelium must absorb nutrients and water and act as a barrier to the entry of luminal material into the body; this barrier function is a key component of innate immunity. nonsteroidal anti-inflammatory drug (nsaid)-induced enteropathy occurs via inhibition of prostaglandin synthesis and perturbed epithelial mitochondrial activity. here, the direct effect of nsaids [indomethacin, piroxicam (cyclooxygenase 1 and 2 inhibitors), and sc-560 (a cyclooxygenase 1 inhibitor)] on the barrier ...201222700821
serum sickness following rabbit anti-thymocyte globulin for acute vascular renal allograft rejection.a simultaneous pancreas-kidney transplant recipient developed serum sickness manifesting with severe upper limb allodynia, arthralgia and myalgia 17 days following rabbit anti-thymocyte globulin (ratg) infusion for biopsy-proven vascular rejection. rapid resolution of symptoms followed treatment with high-dose glucocorticoids. ratg is increasingly favoured over equine atg in solid-organ transplantation, and although ratg has a superior safety profile, it is important to maintain a high index of ...201225874092
structure, function and diversity of the healthy human microbiome.studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. accordingly, to characterize the ecology of human-associated microbial communities, the human microbiome project has analysed the largest cohort and set of distinct, clinically relevant body hab ...201222699609
the structural biology of enzymes involved in natural product glycosylation.the glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. in many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering va ...201222688446
phage-mediated acquisition of a type iii secreted effector protein boosts growth of salmonella by nitrate respiration.information on how emerging pathogens can invade and persist and spread within host populations remains sparse. in the 1980s, a multidrug-resistant salmonella enterica serotype typhimurium clone lysogenized by a bacteriophage carrying the sope virulence gene caused an epidemic among cattle and humans in europe. here we show that phage-mediated horizontal transfer of the sope gene enhances the production of host-derived nitrate, an energetically highly valuable electron acceptor, in a mouse colit ...201222691391
structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-trna synthetase.leucyl-trna synthetase (leurs) produces error-free leucyl-trna(leu) by coordinating translocation of the 3' end of (mis-)charged trnas from its synthetic site to a separate proofreading site for editing. here we report cocrystal structures of the escherichia coli leurs-trna(leu) complex in the aminoacylation or editing conformations, showing that translocation involves correlated rotations of four flexibly linked leurs domains. this pivots the trna to guide its charged 3' end from the closed ami ...201222683997
acinetobacter calcoaceticus-baumannii complex strains induce caspase-dependent and caspase-independent death of human epithelial cells.we investigated interactions of human isolates of acinetobacter calcoaceticus-baumannii complex strains with epithelial cells. the results showed that bacterial contact with the cells as well as adhesion and invasion were required for induction of cytotoxicity. the infected cells revealed hallmarks of apoptosis characterized by cell shrinking, condensed chromatin, and internucleosomal fragmentation of nuclear dna. the highest apoptotic index was observed for 4 of 10 a. calcoaceticus and 4 of 7 a ...201222684803
genomering: alignment visualization based on supergenome coordinates.the number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. such visualizations typically are either realized in a linear fa ...201222689781
antimicrobial-resistant bacteria: an unrecognized work-related risk in food animal production.the occupations involved in food animal production have long been recognized to carry significant health risks for workers, with special attention to injuries. however, risk of pathogen exposure in these occupations has been less extensively considered. pathogens are a food safety issue and are known to be present throughout the food animal production chain. workers employed at farms and slaughterhouses are at risk of pathogen exposure and bacterial infections. the industrialization of animal fa ...201222993711
identification of a general o-linked protein glycosylation system in acinetobacter baumannii and its role in virulence and biofilm formation.acinetobacter baumannii is an emerging cause of nosocomial infections. the isolation of strains resistant to multiple antibiotics is increasing at alarming rates. although a. baumannii is considered as one of the more threatening "superbugs" for our healthcare system, little is known about the factors contributing to its pathogenesis. in this work we show that a. baumannii atcc 17978 possesses an o-glycosylation system responsible for the glycosylation of multiple proteins. 2d-dige and mass spec ...201222685409
microbiota, disease, and back to health: a metastable journey.alterations in the composition of the commensal microbiota have been observed in many complex diseases. understanding the basis for these changes, how they relate to disease risk or activity, and the mechanisms by which the symbiotic state of colonization resistance and host homeostasis is restored is critical for future therapies aimed at manipulating the microbiota.201222674557
multiple post-translational modifications affect heterologous protein synthesis.post-translational modifications (ptms) are required for proper folding of many proteins. the low capacity for ptms hinders the production of heterologous proteins in the widely used prokaryotic systems of protein synthesis. until now, a systematic and comprehensive study concerning the specific effects of individual ptms on heterologous protein synthesis has not been presented. to address this issue, we expressed 1488 human proteins and their domains in a bacterial cell-free system, and we exam ...201222674579
beneficial effect of bupleurum polysaccharides on autoimmune-prone mrl-lpr mice.systemic lupus erythematosus (sle) is a chronic systemic autoimmune disease leading to inflammatory tissue damage in multiple organs. the crude polysaccharides (bps) isolated from the roots of bupleurum smithii var. parvifolium have anticomplementary activity and immunomodulatory functions on macrophages. to study its potential benefit on sle, we examined effects of bps on mrl-lpr mice, which have similar disease features to human sle. mrl-lpr mice were treated orally with bps 15, 30, or 60 mg k ...201222701502
investigation of antibacterial, acid and bile tolerance properties of lactobacilli isolated from koozeh cheese.lactobacillus strains are a major part of the probiotics, microflora of the intestine and of fermented dairy products, and are found in a variety of environments. the aim of this study was to find out the ability of bile and acid tolerance and antibacterial properties of the twenty eight isolates of three group lactobacilli namely lactobacillus plantarum, lactobacillus casei and lactobacillus delbruki. for this purpose twenty eight different lactobacillus strains that isolated from koozeh cheese ...201225610566
clinical importance and representation of toxigenic and non-toxigenic clostridium difficile cultivated from stool samples of hospitalized patients.the aim of this study was to fortify the clinical importance and representation of toxigenic and non-toxigenic clostridium difficile isolated from stool samples of hospitalized patients. this survey included 80 hospitalized patients with diarrhea and positive findings of clostridium difficile in stool samples, and 100 hospitalized patients with formed stool as a control group. bacteriological examination of a stool samples was conducted using standard microbiological methods. stool sample were i ...201224031820
activity of disinfectants against foodborne pathogens in suspension and adhered to stainless steel surfaces.the purpose of this study was to investigate and compare the efficacy of various disinfectants on planktonic cells and biofilm cells of listeria monocytogenes, staphylococcus aureus and escherichia coli. numbers of viable biofilm cells decreased after treatment with all tested disinfectants (iodine, biguanide, quaternary ammonium compounds, peracetic acid and sodium hypochlorite). sodium hypochlorite was the most effective disinfectant against biofilm cells, while biguanide was the least effecti ...201224031935
oxygen limitation favors the production of protein with antimicrobial activity in pseudoalteromonas sp.this study examined the effect of dissolved oxygen concentration on the production of biomass and metabolites with antimicrobial activity of pseudoalteromonas sp cultured at 0, 150, 250, or 450 revolutions per minute (rev. min(-1)). dissolved oxygen (d.o) was monitored during the fermentation process, biomass was quantified by dry weight, and antimicrobial activity was assessed using the disk diffusion method. the bacterium pseudoalteromonas reached similar concentration of biomass under all exp ...201224031945
identification of a putative glycosyltransferase responsible for the transfer of pseudaminic acid onto the polar flagellin of aeromonas caviae sch3n.motility in aeromonas caviae, in a liquid environment (in broth culture), is mediated by a single polar flagellum encoded by the fla genes. the polar flagellum filament of a. caviae is composed of two flagellin subunits, flaa and flab, which undergo o-linked glycosylation with six to eight pseudaminic acid glycans linked to serine and threonine residues in their central region. the flm genetic locus in a. caviae is required for flagellin glycosylation and the addition of pseudaminic acid (pse) o ...201222950021
the alternative translational profile that underlies the immune-evasive state of persistence in chlamydiaceae exploits differential tryptophan contents of the protein repertoire.one form of immune evasion is a developmental state called "persistence" whereby chlamydial pathogens respond to the host-mediated withdrawal of l-tryptophan (trp). a sophisticated survival mode of reversible quiescence is implemented. a mechanism has evolved which suppresses gene products necessary for rapid pathogen proliferation but allows expression of gene products that underlie the morphological and developmental characteristics of persistence. this switch from one translational profile to ...201222688818
alterations in the porcine colon microbiota induced by the gastrointestinal nematode trichuris suis.helminth parasites ensure their survival by regulating host immunity through mechanisms that dampen inflammation. these properties have recently been exploited therapeutically to treat human diseases. the biocomplexity of the intestinal lumen suggests that interactions between the parasite and the intestinal microbiota would also influence inflammation. in this study, we characterized the microbiota in the porcine proximal colon in response to trichuris suis (whipworm) infection using 16s rrna g ...201222493085
development and evaluation of a quantitative pcr assay targeting sandhill crane (grus canadensis) fecal pollution.while the microbial water quality in the platte river is seasonally impacted by excreta from migrating cranes, there are no methods available to study crane fecal contamination. here we characterized microbial populations in crane feces using phylogenetic analysis of 16s rrna gene fecal clone libraries. using these sequences, a novel crane quantitative pcr (crane1) assay was developed, and its applicability as a microbial source tracking (mst) assay was evaluated by determining its host specific ...201222492437
zoonotic agents in small ruminants kept on city farms in southern germany.sheep and goats are popular examples of livestock kept on city farms. in these settings, close contacts between humans and animals frequently occur. although it is widely accepted that small ruminants can carry numerous zoonotic agents, it is unknown which of these agents actually occur in sheep and goats on city farms in germany. we sampled feces and nasal liquid of 48 animals (28 goats, 20 sheep) distributed in 7 city farms and on one activity playground in southern germany. we found that 100% ...201222447607
rational design and directed evolution of a bacterial-type glutaminyl-trna synthetase precursor.protein biosynthesis requires aminoacyl-transfer rna (trna) synthetases to provide aminoacyl-trna substrates for the ribosome. most bacteria and all archaea lack a glutaminyl-trna synthetase (glnrs); instead, gln-trna(gln) is produced via an indirect pathway: a glutamyl-trna synthetase (glurs) first attaches glutamate (glu) to trna(gln), and an amidotransferase converts glu-trna(gln) to gln-trna(gln). the human pathogen helicobacter pylori encodes two glurs enzymes, with glurs2 specifically amin ...201222661575
experimental evolution of legionella pneumophila in mouse macrophages leads to strains with altered determinants of environmental survival.the gram-negative bacterium, legionella pneumophila, is a protozoan parasite and accidental intracellular pathogen of humans. we propose a model in which cycling through multiple protozoan hosts in the environment holds l. pneumophila in a state of evolutionary stasis as a broad host-range pathogen. using an experimental evolution approach, we tested this hypothesis by restricting l. pneumophila to growth within mouse macrophages for hundreds of generations. whole-genome resequencing and high-th ...201222693450
simulation of molecular data under diverse evolutionary scenarios. 201222693434
risk of inflammatory bowel disease following a diagnosis of irritable bowel syndrome.irritable bowel syndrome (ibs) and inflammatory bowel disease (ibd) symptoms often overlap. in some ibs cases there are subtle inflammatory changes similar to the immune-mediated pathophysiology of ibd, and the risk of both increases after infectious gastroenteritis (ige).201222639930
two plant bacteria, s. meliloti and ca. liberibacter asiaticus, share functional znuabc homologues that encode for a high affinity zinc uptake system.the znu system, encoded for by znuabc, can be found in multiple genera of bacteria and has been shown to be responsible for the import of zinc under low zinc conditions. although this high-affinity uptake system is known to be important for both growth and/or pathogenesis in bacteria, it has not been functionally characterized in a plant-associated bacterium. a single homologue of this system has been identified in the plant endosymbiont, sinorhizobium meliloti, while two homologous systems were ...201222655039
fine specificity and cross-reactions of monoclonal antibodies to group b streptococcal capsular polysaccharide type iii.group b streptococcus (gbs) is a major cause of neonatal sepsis and meningitis. despite aggressive campaigns using antenatal prophylactic antibiotic therapy, infections continue. developing an effective maternal vaccine is a public health priority. antibody (ab) to the capsular polysaccharide (cps) is considered the dominant "protective" immune mediator. here we study the fine specificity and potential host reactivity of a panel of well-characterized murine monoclonal abs against the type iii cp ...201222634296
quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.the theoretical description of the forces that shape ecological communities focuses around two classes of models. in niche theory, deterministic interactions between species, individuals, and the environment are considered the dominant factor, whereas in neutral theory, stochastic forces, such as demographic noise, speciation, and immigration, are dominant. species abundance distributions predicted by the two classes of theory are difficult to distinguish empirically, making it problematic to de ...201222615407
why do bacteria use so many enzymes to scavenge hydrogen peroxide?hydrogen peroxide (h(2)o(2)) is continuously formed by the autoxidation of redox enzymes in aerobic cells, and it also enters from the environment, where it can be generated both by chemical processes and by the deliberate actions of competing organisms. because h(2)o(2) is acutely toxic, bacteria elaborate scavenging enzymes to keep its intracellular concentration at nanomolar levels. mutants that lack such enzymes grow poorly, suffer from high rates of mutagenesis, or even die. in order to und ...201222609271
the incidence and risk of celiac disease in a healthy us adult population.celiac disease (cd) is an increasingly common disease that may affect as many as 1% of the north american population. recent population-based data suggest a substantial increase in the prevalence of cd over the last several decades. several factors are hypothesized as possible disease triggers including intercurrent illnesses, such as gastroenteritis, surgeries, and trauma. we used the active duty us military, a unique healthy worker population with essentially complete medical diagnostic coding ...201222584218
lipopolysaccharides: from erinyes to charites.following the discovery of endotoxins by richard pfeiffer, such bacterial product was associated to many severe disorders produced by an overwhelming inflammatory response and often resulting in endotoxic shock and multiple organ failure. however, recent clinical and basic sciences investigations claimed some beneficial roles of typical as well as atypical endotoxins. the aim of this paper is to focus on recent data supporting a beneficial activity of both typical and atypical endotoxins. such n ...201222665953
exoribonucleases as modulators of virulence in pathogenic bacteria. 201222919656
age of the association between helicobacter pylori and man.when modern humans left africa ca. 60,000 years ago (60 kya), they were already infected with helicobacter pylori, and these bacteria have subsequently diversified in parallel with their human hosts. but how long were humans infected by h. pylori prior to the out-of-africa event? did this co-evolution predate the emergence of modern humans, spanning the species divide? to answer these questions, we investigated the diversity of h. pylori in africa, where both humans and h. pylori originated. thr ...201222589724
genes important for catalase activity in enterococcus faecalis.little in general is known about how heme proteins are assembled from their constituents in cells. the gram-positive bacterium enterococcus faecalis cannot synthesize heme and does not depend on it for growth. however, when supplied with heme in the growth medium the cells can synthesize two heme proteins; catalase (kata) and cytochrome bd (cydab). to identify novel factors important for catalase biogenesis libraries of e. faecalis gene insertion mutants were generated using two different types ...201222590595
chemo-enzymatic modification of poly-n-acetyllactosamine (lacnac) oligomers and n,n-diacetyllactosamine (lacdinac) based on galactose oxidase treatment.the importance of glycans in biological systems is highlighted by their various functions in physiological and pathological processes. many glycan epitopes on glycoproteins and glycolipids are based on n-acetyllactosamine units (lacnac; galβ1,4glcnac) and often present on extended poly-lacnac glycans ([galβ1,4glcnac](n)). poly-lacnac itself has been identified as a binding motif of galectins, an important class of lectins with functions in immune response and tumorigenesis. therefore, the synthe ...201223015818
prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.despite the current wealth of sequencing data, one-third of all biochemically characterized metabolic enzymes lack a corresponding gene or protein sequence, and as such can be considered orphan enzymes. they represent a major gap between our molecular and biochemical knowledge, and consequently are not amenable to modern systemic analyses. as 555 of these orphan enzymes have metabolic pathway neighbours, we developed a global framework that utilizes the pathway and (meta)genomic neighbour inform ...201222569339
bone marrow involvement in a patient with alpha heavychain disease: response to tetracycline treatment.a 28-year-old man from east mediterranean area admitted with abdominal pain, weight loss and diarrhea. barium x-ray studies showed segmentation, dilatation of bowel loops, mucosal folds thickening and delayed intestinal transit. histological examination of biopsy specimens revealed villous atrophy and plasmacytic infiltration limited to mucosa and submucosa. computed tomography showed multiple lymphadenopathy in the abdomen. serum protein electropheresis and immunoelectropheresis indicated eleva ...201222708049
high adherence is necessary to realize health gains from water quality interventions.safe drinking water is critical for health. household water treatment (hwt) has been recommended for improving access to potable water where existing sources are unsafe. reports of low adherence to hwt may limit the usefulness of this approach, however.201222586491
the predominance of type i oligosaccharides is a feature specific to human breast milk.human milk and colostrum contain ∼12-13 g/l and ∼22-24 g/l of oligosaccharides, respectively. the chemical structures of >100 human milk oligosaccharides (hmo) have been characterized to date. we determined the concentrations of 10 neutral and 9 acidic colostrum hmo collected during the first 3 d of lactation by using reverse phase hplc after derivatization with 2-aminopyridine or 1-methyl-3-phenyl-5-pyrazolon. the predominant oligosaccharides were fuc(α1-2)gal(β1-4glc (2'-fl), fuc(α1-2)gal(β1-3 ...201222585927
profiles of human milk oligosaccharides and production of some human milk oligosaccharides in transgenic animals.during the decade of the 1990s and the first years of the current century, our group embarked on a project to study and synthesize human milk oligosaccharides. this report describes 2 unexpected collateral observations from that endeavor. the first observation was the detection and confirmation of 2 rare neutral human milk oligosaccharides profiles that were uncovered while assessing oligosaccharide content in hundreds of samples of human milk. one of these lacked fucosylated structures altogeth ...201222585925
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