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n-glycosylation of campylobacter jejuni surface proteins promotes bacterial fitness.campylobacter jejuni is the etiologic agent of human bacterial gastroenteritis worldwide. in contrast, despite heavy colonization, c. jejuni maintains a commensal mode of existence in chickens. the consumption of contaminated chicken products is thought to be the principal mode of c. jejuni transmission to the human population. c. jejuni harbors a system for n-linked protein glycosylation that has been well characterized and modifies more than 60 periplasmic and membrane-bound proteins. however, ...201323460522
mutations to essential orphan response regulator hp1043 of helicobacter pylori result in growth-stage regulatory defects.helicobacter pylori establishes lifelong infections of the gastric mucosa, a niche considered hostile to most microbes. while responses to gastric acidity and local inflammation are understood, little is known as to how they are integrated into homeostatic control of cell division and growth-stage gene expression. here we investigate the essential orphan response regulator hp1043, a member of the ompr/phob subfamily of transcriptional regulators that is unique to the epsilonproteobacteria and th ...201323429531
campylobacter jejuni dps protein binds dna in the presence of iron or hydrogen peroxide.iron is an essential cofactor for many enzymes; however, this metal can lead to the formation of reactive oxygen species. ferritin proteins bind and oxidize fe(2+) to fe(3+), storing this metal in a nonreactive form. in some organisms, a particular subfamily of ferritins, namely, dps proteins, have the ability to bind dna. here we show that the campylobacter jejuni dps has dna binding activity that is uniquely activated by fe(2+) or h2o2 at below neutral ph. the dps-dna binding activity correlat ...201323435977
simultaneous quantification of multiple food- and waterborne pathogens by use of microfluidic quantitative pcr.the direct quantification of multiple pathogens has been desired for diagnostic and public health purposes for a long time. in this study, we applied microfluidic quantitative pcr (qpcr) technology to the simultaneous detection and quantification of multiple food- and waterborne pathogens. in this system, multiple singleplex qpcr assays were run under identical detection conditions in nanoliter-volume chambers that are present in high densities on a chip. first, we developed 18 taqman qpcr assay ...201323435884
comparison of milk oligosaccharides between goats with and without the genetic ability to synthesize αs1-casein.milk oligosaccharides (os)-free complex carbohydrates-confer unique health benefits to the nursing neonate. though human digestive enzymes cannot degrade these sugars, they provide nourishment to specific commensal microbes and act as decoys to prevent the adhesion of pathogenic micro-organisms to gastrointestinal cells. at present, the limited quantities of human milk oligosaccharides (hmo) impede research on these molecules and their potential applications in functional food formulations. cons ...201324587592
targeted delivery of lipid antigen to macrophages via the cd169/sialoadhesin endocytic pathway induces robust invariant natural killer t cell activation.invariant natural killer t (inkt) cells induce a protective immune response triggered by foreign glycolipid antigens bound to cd1d on antigen-presenting cells (apcs). a limitation of using glycolipid antigens to stimulate immune responses in human patients has been the inability to target them to the most effective apcs. recent studies have implicated phagocytic cd169(+) macrophages as major apcs in lymph nodes for priming inkt cells in mice immunized with glycolipid antigen in particulate form. ...201323610394
a subgraph isomorphism algorithm and its application to biochemical data.graphs can represent biological networks at the molecular, protein, or species level. an important query is to find all matches of a pattern graph to a target graph. accomplishing this is inherently difficult (np-complete) and the efficiency of heuristic algorithms for the problem may depend upon the input graphs. the common aim of existing algorithms is to eliminate unsuccessful mappings as early as and as inexpensively as possible.201323815292
spatial and numerical regulation of flagellar biosynthesis in polarly flagellated bacteria.control of surface organelle number and placement is a crucial aspect of the cell biology of many gram-positive and gram-negative bacteria, yet mechanistic insights into how bacteria spatially and numerically organize organelles are lacking. many surface structures and internal complexes are spatially restricted in the bacterial cell (e.g. type iv pili, holdfasts, chemoreceptors), but perhaps none show so many distinct patterns in terms of number and localization as the flagellum. in this review ...201323600726
salmonella uses energy taxis to benefit from intestinal inflammation.chemotaxis enhances the fitness of salmonella enterica serotype typhimurium (s. typhimurium) during colitis. however, the chemotaxis receptors conferring this fitness advantage and their cognate signals generated during inflammation remain unknown. here we identify respiratory electron acceptors that are generated in the intestinal lumen as by-products of the host inflammatory response as in vivo signals for methyl-accepting chemotaxis proteins (mcps). three mcps, including trg, tsr and aer, enh ...201323637594
differential resuscitative effect of pyruvate and its analogues on vbnc (viable but non-culturable) salmonella.an environmental isolate of salmonella enteritidis (se), grown to the logarithmic phase, rapidly lost culturability by the addition of 3 mm h2o2 to cultures grown in luria-bertani (lb) medium; however, some h2o2-treated bacteria regained their culturability in m9 minimal medium, if sodium pyruvate was present at at least 0.3 mm. in addition, most pyruvate analogues, such as bromopyruvate or phenylpyruvate, did not show restoration activity similar to that of pyruvate, except in the case of α-ket ...201323595023
phylum-wide general protein o-glycosylation system of the bacteroidetes.the human gut symbiont bacteroides fragilis has a general protein o-glycosylation system in which numerous extracytoplasmic proteins are glycosylated at a three amino acid motif. in b. fragilis, protein glycosylation is a fundamental and essential property as mutants with protein glycosylation defects have impaired growth and are unable to competitively colonize the mammalian intestine. in this study, we analysed the phenotype of b. fragilis mutants with defective protein glycosylation and found ...201323551589
interpreting infective microbiota: the importance of an ecological perspective.complex microbiota are being reported increasingly across a range of chronic infections, including those of the cystic fibrosis airways. such diversity fits poorly into classical models of sterile tissue infections, which generally involve one species, and where microbe-outcome associations usually imply causality. it has been suggested that microbiota at sites of infection could represent pathogenic entities, analogous to individual species. we argue that our ability to identify causality in mi ...201323598051
variation in the complex carbohydrate biosynthesis loci of acinetobacter baumannii genomes.extracellular polysaccharides are major immunogenic components of the bacterial cell envelope. however, little is known about their biosynthesis in the genus acinetobacter, which includes a. baumannii, an important nosocomial pathogen. whether acinetobacter sp. produce a capsule or a lipopolysaccharide carrying an o antigen or both is not resolved. to explore these issues, genes involved in the synthesis of complex polysaccharides were located in 10 complete a. baumannii genome sequences, and th ...201323614028
gut microbiota, tight junction protein expression, intestinal resistance, bacterial translocation and mortality following cholestasis depend on the genetic background of the host.failure of the intestinal barrier is a characteristic feature of cholestasis. we have previously observed higher mortality in c57bl/6j compared with a/j mice following common bile duct ligation (cbdl). we hypothesized the alteration in gut barrier function following cholestasis would vary by genetic background. following one week of cbdl, jejunal teer was significantly reduced in each ligated mouse compared with their sham counterparts; moreover, jejunal teer was significantly lower in both sham ...201323652772
enteropathic spondyloarthritis: from diagnosis to treatment.enteropathic arthritis (ea) is a spondyloarthritis (spa) which occurs in patients with inflammatory bowel diseases (ibds) and other gastrointestinal diseases. diagnosis is generally established on the medical history and physical examination. it was, generally, made according to the european spondyloarthropathy study group (essg) criteria. rheumatic manifestations are the most frequent extraintestinal findings of ibd with a prevalence between 17% and 39%, and ibd is associated, less frequently, ...201323690825
bartonella henselae infection in a family experiencing neurological and neurocognitive abnormalities after woodlouse hunter spider bites.bartonella species comprise a group of zoonotic pathogens that are usually acquired by vector transmission or by animal bites or scratches.201323587343
a crispr/cas system mediates bacterial innate immune evasion and virulence.crispr/cas (clustered regularly interspaced palindromic repeats/crispr-associated) systems are a bacterial defence against invading foreign nucleic acids derived from bacteriophages or exogenous plasmids. these systems use an array of small crispr rnas (crrnas) consisting of repetitive sequences flanking unique spacers to recognize their targets, and conserved cas proteins to mediate target degradation. recent studies have suggested that these systems may have broader functions in bacterial phys ...201323584588
targeting the bacteria-host interface: strategies in anti-adhesion therapy.bacterial infections are a major cause of morbidity and mortality worldwide and are increasingly problematic to treat due to the rise in antibiotic-resistant strains. it becomes more and more challenging to develop new antimicrobials that are able to withstand the ever-increasing repertoire of bacterial resistance mechanisms. this necessitates the development of alternative approaches to prevent and treat bacterial infections. one of the first steps during bacterial infection is adhesion of the ...201323799663
optimized protocol for expression and purification of membrane-bound pglb, a bacterial oligosaccharyl transferase.asparagine-linked glycosylation (nlg) plays a significant role in a diverse range of cellular processes, including protein signaling and trafficking, the immunologic response, and immune system evasion by pathogens. a major impediment to nlg-related research is an incomplete understanding of the central enzyme in the biosynthetic pathway, the oligosaccharyl transferase (otase). characterization of the otase is critical for developing ways to inhibit, engineer, and otherwise manipulate the enzyme ...201323583934
the glove-like structure of the conserved membrane protein tatc provides insight into signal sequence recognition in twin-arginine translocation.in bacteria, two signal-sequence-dependent secretion pathways translocate proteins across the cytoplasmic membrane. although the mechanism of the ubiquitous general secretory pathway is becoming well understood, that of the twin-arginine translocation pathway, responsible for translocation of folded proteins across the bilayer, is more mysterious. tatc, the largest and most conserved of three integral membrane components, provides the initial binding site of the signal sequence prior to pore ass ...201323583035
interferon-inducible mechanism of dendritic cell-mediated hiv-1 dissemination is dependent on siglec-1/cd169.human immunodeficiency virus type 1 (hiv-1) interactions with myeloid dendritic cells (dcs) can result in virus dissemination to cd4⁺ t cells via a trans infection pathway dependent on virion incorporation of the host cell derived glycosphingolipid (gsl), gm3. the mechanism of dc-mediated trans infection is extremely efficacious and can result in infection of multiple cd4⁺ t cells as these cells make exploratory contacts on the dc surface. while it has long been appreciated that activation of dc ...201323593001
secondary membranous nephropathy associated with guillain-barré syndrome.membranous nephropathy (mn) is one of the most common causes of nephrotic syndrome (ns) in adults. it may be primary, usually mediated by igg4 anti-phospholipase a2 autoantibodies or secondary to various other conditions. guillain- barré syndrome (gbs) has been associated with mn, but a cause and effect relation has not been proven. we present a case of concurrent development of gbs and severe ns, with renal biopsy demonstrating mn. igg4 stain was negative, indicating that most likely, the mn wa ...201323626596
effect of spatial separation of pigs on spread of streptococcus suis serotype 9.the spread of an infectious agent in a population can be reduced by interfering in the infectiousness or susceptibility of individuals, and/or in their contact structure. the aim of this study was to quantify the effect of prevention of direct contact between infectious and susceptible pigs on the transmission of streptococcus suis (s. suis). in three replicate experiments, s. suis-free pigs were housed in boxes either in pairs (25 pairs) or alone (15 pigs). the distance between the boxes was ±1 ...201323593467
risk factor analysis may provide clues to diarrhea prevention in outdoor-housed rhesus macaques (macaca mulatta).seventy-five percent of rhesus macaques at national primate research centers are housed outside. annually, 15-39% of these animals experience diarrhea and require veterinary treatment for dehydration, electrolyte imbalance, or weight loss. an estimated 21-33% of these patients will die or be euthanized. many studies have explored the various infectious etiologies of non-human primate diarrhea. however, there is little published information on diarrhea incidence rates and risk factors in outdoor- ...201323568382
trypanosoma cruzi trans-sialidase initiates a program independent of the transcription factors rorγt and ahr that leads to il-17 production by activated b cells.here we identified b cells as a major source of rapid, innate-like production of interleukin 17 (il-17) in vivo in response to infection with trypanosoma cruzi. il-17(+) b cells had a plasmablast phenotype, outnumbered cells of the th17 subset of helper t cells and were required for an optimal response to this pathogen. with both mouse and human primary b cells, we found that exposure to parasite-derived trans-sialidase in vitro was sufficient to trigger modification of the cell-surface mucin cd ...201323563688
the tracrrna and cas9 families of type ii crispr-cas immunity systems.crispr-cas is a rapidly evolving rna-mediated adaptive immune system that protects bacteria and archaea against mobile genetic elements. the system relies on the activity of short mature crispr rnas (crrnas) that guide cas protein(s) to silence invading nucleic acids. a set of crispr-cas, type ii, requires a trans-activating small rna, tracrrna, for maturation of precursor crrna (pre-crrna) and interference with invading sequences. following co-processing of tracrrna and pre-crrna by rnase iii, ...201323563642
case-control study on the role of enterotoxigenic bacteroides fragilis as a cause of diarrhea among children in kolkata, india.a total of 874 fecal specimens (446 diarrheal cases and 428 controls) from diarrheal children admitted in the infectious diseases hospital, kolkata and age and sex matched asymptomatic subjects from an urban community were assessed for the prevalence of enterotoxigenic bacteroides fragilis (etbf). isolates of b. fragilis were tested for the presence of enterotoxin gene (bft) by pcr. the detection rate of etbf was 7.2% (63 of 874 specimens) that prevailed equally in diarrheal cases and controls ( ...201323577134
bacterial oncogenesis in the colon.the human colon plays host to a diverse and metabolically complex community of microorganisms. while the colonic microbiome has been suggested to contribute to the development of colorectal cancer (crc), a definitive link has not been made. the role in which the colon microflora could contribute to the initiation and/or progression of crc is explored in this review. potential mechanisms of bacterial oncogenesis are presented, along with lines of evidence derived from animal models of microbially ...201323534358
cytomegalovirus colitis in a 10 year-old girl after kidney transplantation.cytomegalovirus is an important infection in kidney transplantation. isolation of the cmv virus or detection of its proteins or nucleic acid in any body fluid or tissue specimen is defined as "cmv infection".201323724187
circovirus in tissues of dogs with vasculitis and hemorrhage.we characterized the complete genome of a novel dog circovirus (dogcv) from the liver of a dog with severe hemorrhagic gastroenteritis, vasculitis, and granulomatous lymphadenitis. dogcv was detected by pcr in fecal samples from 19/168 (11.3%) dogs with diarrhea and 14/204 (6.9%) healthy dogs and in blood from 19/409 (3.3%) of dogs with thrombocytopenia and neutropenia, fever of unknown origin, or past tick bite. co-infection with other canine pathogens was detected for 13/19 (68%) dogcv-positiv ...201323628223
xenocin export by the flagellar type iii pathway in xenorhabdus nematophila.the xenocin operon of xenorhabdus nematophila consists of xcia and ximb genes encoding a 64-kda xenocin and 42-kda immunity protein to kill competing microbes in the insect larva. the catalytic domain of xenocin has rnase activity and is responsible for its cytotoxicity. under sos conditions, xenocin is produced with immunity protein as a complex. here, we show that xenocin and immunity protein complex are exported through the flagellar type iii system of x. nematophila. secretion of xenocin com ...201323335409
multilocus sequence typing and flaa sequencing reveal the genetic stability of campylobacter jejuni enrichment during coculture with acanthamoeba polyphaga.low concentrations of campylobacter jejuni cells in environmental samples make them difficult to study with conventional culture methods. here, we show that enrichment by amoeba cocultures works well with low-concentration samples and that this method can be combined with molecular techniques without loss of genetic specificity.201323377942
modulation of porcine β-defensins 1 and 2 upon individual and combined fusarium toxin exposure in a swine jejunal epithelial cell line.defensins are small antimicrobial peptides (amps) that play an important role in the innate immune system of mammals. since the effect of mycotoxin contamination of food and feed on the secretion of intestinal amps is poorly understood, the aim of this study was to elucidate the individual and combined effects of four common fusarium toxins, deoxynivalenol (don), nivalenol (niv), zearalenone (zea), and fumonisin b1 (fb1), on the mrna expression, protein secretion, and corresponding antimicrobial ...201323354708
legionella pneumophila transcriptional response following exposure to cuo nanoparticles.copper ions are an effective antimicrobial agent used to control legionnaires' disease and pontiac fever arising from institutional drinking water systems. here, we present data on an alternative bactericidal agent, copper oxide nanoparticles (cuo-nps), and its efficacy on legionella pneumophila. in broth cultures, the cuo-nps caused growth inhibition, which appeared to be concentration and exposure time dependent. the transcriptomic response of l. pneumophila to cuo-np exposure was investigated ...201323416998
evaluation of bovine feces-associated microbial source tracking markers and their correlations with fecal indicators and zoonotic pathogens in a brisbane, australia, reservoir.this study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (baccow-ucd and cowm3) and one viral [bovine adenovirus (b-avs)] microbial source tracking (mst) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast queensland, australia. in addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal ...201323417003
contact killing of bacteria on copper is suppressed if bacterial-metal contact is prevented and is induced on iron by copper ions.bacteria are rapidly killed on copper surfaces, and copper ions released from the surface have been proposed to play a major role in the killing process. however, it has remained unclear whether contact of the bacteria with the copper surface is also an important factor. using laser interference lithography, we engineered copper surfaces which were covered with a grid of an inert polymer which prevented contact of the bacteria with the surface. using enterococcus hirae as a model organism, we sh ...201323396344
effect of micro- and nanoscale topography on the adhesion of bacterial cells to solid surfaces.attachment and biofilm formation by bacterial pathogens on surfaces in natural, industrial, and hospital settings lead to infections and illnesses and even death. minimizing bacterial attachment to surfaces using controlled topography could reduce the spreading of pathogens and, thus, the incidence of illnesses and subsequent human and financial losses. in this context, the attachment of key microorganisms, including escherichia coli, listeria innocua, and pseudomonas fluorescens, to silica and ...201323416997
recurrent acute inflammatory demyelinating polyradiculoneuropathy following r-chop treatment for non-hodgkin lymphoma.acute flaccid paralysis following chemotherapy has a wide differential diagnosis, including drug toxicity, acute inflammatory demyelinating polyradiculoneuropathy (aidp), and malignant nerve infiltration. we present a case of recurrent acute quadriparesis due to aidp following chemotherapy for non-hodgkin lymphoma, which resolved each time following administration of intravenous immunoglobulin. although many chemotherapeutic agents can cause neurologic side effects, such as peripheral neuropathy ...201323543974
ecology of subglacial lake vostok (antarctica), based on metagenomic/metatranscriptomic analyses of accretion ice.lake vostok is the largest of the nearly 400 subglacial antarctic lakes and has been continuously buried by glacial ice for 15 million years. extreme cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier) and dissolved oxygen (delivered by melting meteoric ice), in addition to limited nutrients and complete darkness, combine to produce one of the most extreme environments on earth. metagenomic/metatranscriptomic analyses of ice that accreted over a shallow embay ...201324832801
epidemiological investigation of an outbreak of hepatitis a at a residential facility for the disabled, 2011.an outbreak of hepatitis a occurred at a residential facility for the disabled in july 10, 2011. this investigation was carried out to develop a response plan, and to find the infection source of the disease.201323573370
a review of therapeutic aptamer conjugates with emphasis on new approaches.the potential to emulate or enhance antibodies with nucleic acid aptamers while lowering costs has prompted development of new aptamer-protein, sirna, drug, and nanoparticle conjugates. specific focal points of this review discuss dna aptamers covalently bound at their 3' ends to various proteins for enhanced stability and greater pharmacokinetic lifetimes in vivo. the proteins can include fc tails of igg for opsonization, and the first component of complement (c1q) to trigger complement-mediate ...201324276022
recruiting the host's immune system to target helicobacter pylori's surface glycans.due to the increased prevalence of bacterial strains that are resistant to existing antibiotics, there is an urgent need for new antibacterial strategies. bacterial glycans are an attractive target for new treatments, as they are frequently linked to pathogenesis and contain distinctive structures that are absent in humans. we set out to develop a novel targeting strategy based on surface glycans present on the gastric pathogen helicobacter pylori (hp). in this study, metabolic labeling of bacte ...201323512824
identification of an o-antigen chain length regulator, wzzp, in porphyromonas gingivalis.the periodontal pathogen porphyromonas gingivalis has two different lipopolysaccharides (lpss) designated o-lps and a-lps, which are a conventional o-antigen polysaccharide and an anionic polysaccharide that are both linked to lipid a-cores, respectively. however, the precise mechanisms of lps biosynthesis remain to be determined. in this study, we isolated a pigment-less mutant by transposon mutagenesis and identified that the transposon was inserted into the coding sequence pgn_2005, which enc ...201323509024
bacterial and viral etiology of childhood diarrhea in ouagadougou, burkina faso.diarrhea is the most frequent health problem among children in developing countries. this study investigated the bacterial and viral etiology and related clinical and epidemiological factors in children with acute diarrhea in ouagadougou, burkina faso.201323506294
thermo-regulation of genes mediating motility and plant interactions in pseudomonas syringae.pseudomonas syringae is an important phyllosphere colonist that utilizes flagellum-mediated motility both as a means to explore leaf surfaces, as well as to invade into leaf interiors, where it survives as a pathogen. we found that multiple forms of flagellum-mediated motility are thermo-suppressed, including swarming and swimming motility. suppression of swarming motility occurs between 28° and 30 °c, which coincides with the optimal growth temperature of p. syringae. both flic (encoding flagel ...201323527276
resistance-nodulation-division multidrug efflux pumps in gram-negative bacteria: role in virulence.resistance-nodulation-division (rnd) efflux pumps are one of the most important determinants of multidrug resistance (mdr) in gram-negative bacteria. with an ever increasing number of gram-negative clinical isolates exhibiting mdr phenotypes as a result of the activity of rnd pumps, it is clear that the design of novel effective clinical strategies against such pathogens must be grounded in a better understanding of these pumps, including their physiological roles. to this end, recent evidence s ...201327029297
development of a broad-range 23s rdna real-time pcr assay for the detection and quantification of pathogenic bacteria in human whole blood and plasma specimens.molecular methods are important tools in the diagnosis of bloodstream bacterial infections, in particular in patients treated with antimicrobial therapy, due to their quick turn-around time. here we describe a new broad-range real-time pcr targeting the 23s rdna gene and capable to detect as low as 10 plasmid copies per reaction of targeted bacterial 23s rdna gene. two commercially available dna extraction kits were evaluated to assess their efficiency for the extraction of plasma and whole bloo ...201323586027
diet, microbiome, and the intestinal epithelium: an essential triumvirate?the intestinal epithelium represents a critical barrier protecting the host against diverse luminal noxious agents, as well as preventing the uncontrolled uptake of bacteria that could activate an immune response in a susceptible host. the epithelial monolayer that constitutes this barrier is regulated by a meshwork of proteins that orchestrate complex biological function such as permeability, transepithelial electrical resistance, and movement of various macromolecules. because of its key role ...201323586037
the contribution of arsb to arsenic resistance in campylobacter jejuni.arsenic, a toxic metalloid, exists in the natural environment and its organic form is approved for use as a feed additive for animal production. as a major foodborne pathogen of animal origin, campylobacter is exposed to arsenic selection pressure in the food animal production environments. previous studies showed that campylobacter isolates from poultry were highly resistant to arsenic compounds and a 4-gene operon (containing arsp, arsr, arsc, and acr3) was associated with arsenic resistance i ...201323554953
iron homeostasis in the rhodobacter genus.metals are utilized for a variety of critical cellular functions and are essential for survival. however cells are faced with the conundrum of needing metals coupled with e fact that some metals, iron in particular are toxic if present in excess. maintaining metal homeostasis is therefore of critical importance to cells. in this review we have systematically analyzed sequenced genomes of three members of the rhodobacter genus, r. capsulatus sb1003, r. sphaeroides 2.4.1 and r. ferroxidans sw2 to ...201324382933
intestinal microbiota, probiotics and mental health: from metchnikoff to modern advances: part ii - contemporary contextual research.in recent years there has been a renewed interest concerning the ways in which the gastrointestinal tract - its functional integrity and microbial residents - might influence human mood (e.g. depression) and behavioral disorders. once a hotbed of scientific interest in the early 20th century, this area lay dormant for decades, in part due to its association with the controversial term 'autointoxication'. here we review contemporary findings related to intestinal permeability, small intestinal ba ...201323497633
mass spectrometry of membrane proteins: a focus on aquaporins.membrane proteins are abundant, critically important biomolecules that conduct essential functions in all cells and are the targets of a significant number of therapeutic drugs. however, the analysis of their expression, modification, protein-protein interactions, and structure by mass spectrometry has lagged behind similar studies of soluble proteins. here we review the limitations to analysis of integral membrane and membrane-associated proteins and highlight advances in sample preparation and ...201323394619
can microbiota transplantation abrogate murine colonization resistance against campylobacter jejuni?enterocolitis caused by campylobacter jejuni represents an important socioeconomic burden worldwide. the host-specific intestinal microbiota is essential for maintaining colonization resistance (cr) against c. jejuni in conventional mice. notably, cr is abrogated by shifts of the intestinal microbiota towards overgrowth with commensal e. coli during acute ileitis. thus, we investigated whether oral transplantation (tx) of ileal microbiota derived from c. jejuni susceptible mice with acute ileiti ...201324265916
diagnosis and treatment of gastrointestinal disorders in patients with primary immunodeficiency.gastrointestinal disorders such as chronic or acute diarrhea, malabsorption, abdominal pain, and inflammatory bowel diseases can indicate immune deficiency. the gastrointestinal tract is the largest lymphoid organ in the body, so it is not surprising that intestinal diseases are common among immunodeficient patients. gastroenterologists therefore must be able to diagnose and treat patients with primary immunodeficiency. immune-related gastrointestinal diseases can be classified as those that dev ...201323501398
molecular identification of giardia and cryptosporidium from dogs and cats.the aim of the present study was to diagnose the presence of giardia cysts and cryptosporidium oocysts in household animals using nested polymerase chain reaction (pcr) and sequence analysis. one hundred faecal samples obtained from 81 dogs and 19 cats were investigated. the cryptosporidium genotypes were determined by sequencing a fragment of the small subunit (ssu) rrna gene, while the giardia assemblages were determined through analysis of the glutamate dehydrogenase (gdh) locus. isolates fro ...201323477297
the microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the biscuit study.children presenting for the first time with inflammatory bowel disease (ibd) offer a unique opportunity to study aetiological agents before the confounders of treatment. microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; helicobacter and campylobacter are previously implicated in ibd pathogenesis. we set out to study these and other microaerophilic bacteria in de-novo paediatric ibd.201323554935
the multifaceted roles of antibiotics and antibiotic resistance in nature.antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. however, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. while it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed i ...201323487476
rapid pcr detection of mycoplasma hominis, ureaplasma urealyticum, and ureaplasma parvum.objective. we compared laboratory developed real-time pcr assays for detection of mycoplasma hominis and for detection and differentiation of ureaplasma urealyticum and parvum to culture using genitourinary specimens submitted for m. hominis and ureaplasma culture. methods. 283 genitourinary specimens received in the clinical bacteriology laboratory for m. hominis and ureaplasma species culture were evaluated. nucleic acids were extracted using the total nucleic acid kit on the magna pure 2.0. 5 ...201326904723
pinworm infestation mimicking crohns' disease.we here report a case of a young man who presented to his general practitioner with diarrhea. inflammatory bowel disease was suspected and a colonoscopy showed aphthous lesions suggestive of crohns' disease but biopsies revealed eggs of enterobius vermicularis. when treated for this parasite, his symptoms were alleviated and a followup colonoscopy revealed a normal colon and distal ileum. enterobius vermicularis is the most common parasite worldwide and has been attributed with many different pr ...201323555063
edge-pro: estimated degree of gene expression in prokaryotic genomes.the expression levels of bacterial genes can be measured directly using next-generation sequencing (ngs) methods, offering much greater sensitivity and accuracy than earlier, microarray-based methods. most bioinformatics software for estimating levels of gene expression from ngs data has been designed for eukaryotic genomes, with algorithms focusing particularly on detection of splicing patterns. these methods do not perform well on bacterial genomes.201323531787
biosynthetic assembly of the bacteroides fragilis capsular polysaccharide a precursor bactoprenyl diphosphate-linked acetamido-4-amino-6-deoxygalactopyranose.the sugar capsule capsular polysaccharide a (cpsa), which coats the surface of the mammalian symbiont bacteroides fragilis, is a key mediator of mammalian immune system development. in addition, this sugar polymer has shown therapeutic potential in animal models of multiple sclerosis and other autoimmune disorders. the structure of the cpsa polymer includes a rare stereoconfiguration sugar acetamido-4-amino-6-deoxygalactopyranose (aadgal) that we propose is the first sugar linked to a bactopreny ...201323458065
norovirus gastroenteritis in immunocompromised patients. 201323465122
one-pot multi-enzyme (opme) chemoenzymatic synthesis of sialyl-tn-muc1 and sialyl-t-muc1 glycopeptides containing natural or non-natural sialic acid.a series of stn-muc1 and st-muc1 glycopeptides containing naturally occurring and non-natural sialic acids have been chemoenzymatically synthesized from tn-muc1 glycopeptide using one-pot multienzyme (opme) approaches. in situ generation of the sialyltransferase donor cytidine 5'-monophosphate-sialic acid (cmp-sia) using a cmp-sialic acid synthetase in the presence of an extra amount of cytidine 5'-triphosphate (ctp) and removal of cmp from the reaction mixture by flash c18 cartridge purificatio ...201323535562
comparative genomics of defense systems in archaea and bacteria.our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative genomic analysis, followed by experimental validation. this expansion is both quantitative, including the discovery of diverse new examples of known types of defense systems, such as restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery of fundamentally new defense mechanisms, such as the crispr-cas immunity system. large-scale statistical analysis reveals that th ...201323470997
determination of the structure of the catabolic n-succinylornithine transaminase (astc) from escherichia coli.escherichia coli possesses two acyl ornithine aminotransferases, one catabolic (astc) and the other anabolic (argd), that participate in l-arginine metabolism. although only 58% identical, the enzymes have been shown to be functionally interchangeable. here we have purified astc and have obtained x-ray crystal structures of apo and holo-astc and of the enzyme complexed with its physiological substrate, succinylornithine. we compare the structures obtained in this study with those of argd from sa ...201323484010
capsaicin-sensitive vagal afferent neurons contribute to the detection of pathogenic bacterial colonization in the gut.vagal activation can reduce inflammation and disease activity in various animal models of intestinal inflammation via the cholinergic anti-inflammatory pathway. in the current model of this pathway, activation of descending vagal efferents is dependent on a signal initiated by stimulation of vagal afferents. however, little is known about how vagal afferents are activated, especially in the context of subclinical or clinical pathogenic bacterial infection. to address this question, we first dete ...201323481698
in vitro activity of neisseria meningitidis pgll o-oligosaccharyltransferase with diverse synthetic lipid donors and a udp-activated sugar.oligosaccharyltransferases (otases) are enzymes that catalyze the transfer of an oligosaccharide from a lipid carrier to an acceptor molecule, commonly a protein. otases are classified as n-otases and o-otases, depending on the nature of the glycosylation reaction. the n-otases catalyze the glycan transfer to amide groups in asparagines in a reaction named n-linked glycosylation. the o-otases are responsible for protein o-linked glycosylation, which involves the attachment of glycans to hydroxyl ...201323460642
role of antidiarrhoeal drugs as adjunctive therapies for acute diarrhoea in children.acute diarrhoea is a leading cause of child mortality in developing countries. principal pathogens include escherichia coli, rotaviruses, and noroviruses. 90% of diarrhoeal deaths are attributable to inadequate sanitation. acute diarrhoea is the second leading cause of overall childhood mortality and accounts for 18% of deaths among children under five. in 2004 an estimated 1.5 million children died from diarrhoea, with 80% of deaths occurring before the age of two. treatment goals are to preven ...201323533446
shallow breathing: bacterial life at low o(2).competition for molecular oxygen (o(2)) among respiratory microorganisms is intense because o(2) is a potent electron acceptor. this competition leads to the formation of microoxic environments wherever microorganisms congregate in aquatic, terrestrial and host-associated communities. bacteria can harvest o(2) present at low, even nanomolar, concentrations using high-affinity terminal oxidases. here, we report the results of surveys searching for high-affinity terminal oxidase genes in sequenced ...201323411864
postinfectious functional gastrointestinal disorders: a focus on epidemiology and research agendas.epidemiologic research is fundamental and complementary to our understanding of disease and development of primary, secondary, and tertiary interventions. to put the current evidence into context and identify gaps and research priorities in the areas of disease attribution, burden of disease, clinical characterization, and management of postinfectious functional gastrointestinal disorders (pi-fgds), we took a multidisciplinary approach from the domains of infectious disease, gastroenterology, ep ...201323961264
asellus aquaticus as a potential carrier of escherichia coli and other coliform bacteria into drinking water distribution systems.individuals of the water louse, asellus aquaticus, enter drinking water distribution systems in temperate parts of the world, where they establish breeding populations. we analysed populations of surface water a. aquaticus from two ponds for associated faecal indicator bacteria and assessed the risk of a. aquaticus transporting bacteria into distribution systems. concentrations of up to two e. coli and five total coliforms·ml-1 were measured in the water and 200 e. coli and >240 total coliforms· ...201323455399
antimicrobial resistance and antimicrobial use associated with laboratory-confirmed cases of campylobacter infection in two health units in ontario.a population-based study was conducted over a two-year period in the perth district (pd) and wellington-dufferin-guelph (wdg) health units in ontario to document antimicrobial resistance and antimicrobial use associated with clinical cases of laboratory-confirmed campylobacteriosis.201324421795
unique gangliosides synthesized in vitro by sialyltransferases from marine bacteria and their characterization: ganglioside synthesis by bacterial sialyltransferases.on the basis of the results outlined in our previous report, bacterial sialyltransferases (st) from marine sources were further characterized using glycosphingolipids (gsl), especially ganglio-series gsls, based on the enzymatic characteristics and kinetic parameters obtained by line weaver-burk plots. among them, ga1 and ga2 were found to be good substrates for these unique sts. thus, new gangliosides synthesized by α2-3 and α2-6sts were structurally characterized by several analytical procedur ...201323220479
predictive models for escherichia coli concentrations at inland lake beaches and relationship of model variables to pathogen detection.predictive models, based on environmental and water quality variables, have been used to improve the timeliness and accuracy of recreational water quality assessments, but their effectiveness has not been studied in inland waters. sampling at eight inland recreational lakes in ohio was done in order to investigate using predictive models for escherichia coli and to understand the links between e. coli concentrations, predictive variables, and pathogens. based upon results from 21 beach sites, mo ...201323291550
the k1 capsular polysaccharide from acinetobacter baumannii is a potential therapeutic target via passive immunization.the emergence of extremely resistant and panresistant gram-negative bacilli, such as acinetobacter baumannii, requires consideration of nonantimicrobial therapeutic approaches. the goal of this report was to evaluate the k1 capsular polysaccharide from a. baumannii as a passive immunization target. its structure was determined by a combination of mass spectrometric and nuclear magnetic resonance (nmr) techniques. molecular mimics that might raise the concern for autoimmune disease were not ident ...201323297385
the polysaccharide capsule of campylobacter jejuni modulates the host immune response.campylobacter jejuni is a major cause of bacterial diarrheal disease worldwide. the organism is characterized by a diversity of polysaccharide structures, including a polysaccharide capsule. most c. jejuni capsules are known to be decorated nonstoichiometrically with methyl phosphoramidate (meopn). the capsule of c. jejuni 81-176 has been shown to be required for serum resistance, but here we show that an encapsulated mutant lacking the meopn modification, an mpnc mutant, was equally as sensitiv ...201323250948
prokaryotic nucleotide excision repair.nucleotide excision repair (ner) has allowed bacteria to flourish in many different niches around the globe that inflict harsh environmental damage to their genetic material. ner is remarkable because of its diverse substrate repertoire, which differs greatly in chemical composition and structure. recent advances in structural biology and single-molecule studies have given great insight into the structure and function of ner components. this ensemble of proteins orchestrates faithful removal of ...201323457260
prevalence and antibiotic resistance patterns of diarrheagenic escherichia coli isolated from adolescents and adults in hamedan, western iran.pathogenic strains of escherichia coli are a common cause of acute infectious diarrhea. the aim of this study was to investigate the frequency, virulence markers and antibiotic resistance patterns of diarrheagenic e. coli (dec) isolated from adolescents and adults in hamadan, west of iran.201323466523
the poultry-associated microbiome: network analysis and farm-to-fork characterizations.microbial communities associated with agricultural animals are important for animal health, food safety, and public health. here we combine high-throughput sequencing (hts), quantitative-pcr assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple ...201323468931
symptoms and clinical course of ehec o104 infection in hospitalized patients: a prospective single center study.shiga-toxin producing o157:h7 entero haemorrhagic e. coli (stec/ehec) is one of the most common causes of haemolytic uraemic syndrome (hus) related to infectious haemorrhagic colitis. nearly all recommendations on clinical management of ehec infections refer to this strain. the 2011 outbreak in northern europe was the first to be caused by the serotype o104:h4. this ehec strain was found to carry genetic features of entero aggregative e. coli (eaec) and extended spectrum β lactamase (esbl). we r ...201323460784
the variability of the 16s rrna gene in bacterial genomes and its consequences for bacterial community analyses.16s ribosomal rna currently represents the most important target of study in bacterial ecology. its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. here we use the information from sequenced bacterial genomes to explore the variability of 16s rrna sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome an ...201323460914
mlst genotypes and antibiotic resistance of campylobacter spp. isolated from poultry in grenada.this study determined whether multilocus sequence types (mlst) of campylobacter from poultry in 2 farms in grenada, west indies, differed by farm, antimicrobial resistance and farm antibiotic use. farm a used fluoroquinolones in the water and farm b used tetracyclines. the e-test was used to determine resistance of isolates to seven antibiotics. pcr of the ipxa gene confirmed species and mlst was used to characterize 38 isolates. all isolates were either c. jejuni or c. coli. farm antibiotic use ...201323555097
pseudomonas fluorescens-like bacteria from the stomach: a microbiological and molecular study.to characterize oxidase- and urease-producing bacterial isolates, grown aerobically, that originated from antral biopsies of patients suffering from acid peptic diseases.201323466902
detection of genetic diversity in campylobacter jejuni isolated from a commercial turkey flock using flaa typing, mlst analysis and microarray assay.campylobacter is genetically highly diverse and undergoes frequent intraspecific recombination. turkeys have been identified as an important reservoir for campylobacter jejuni which is of public health significance. the assessment of the genetic diversity among campylobacter population is critical for our understanding of the epidemiology of this bacterium. the genetic profiles were different according to the molecular typing methods used. the performance of established flaa genotyping, multiloc ...201323437035
effects of lipooligosaccharide inner core truncation on bile resistance and chick colonization by campylobacter jejuni.campylobacter jejuni is the most common bacterium that causes diarrhea worldwide, and chickens are considered the main reservoir of this pathogen. this study investigated the effects of serial truncation of lipooligosaccharide (los), a major component of the outer membrane of c. jejuni, on its bile resistance and intestinal colonization ability in chickens. genes encoding manno-heptose synthetases or glycosyltransferases were inactivated to generate isogenic mutants. serial truncation of the los ...201323437265
natural hla-b*2705 protein ligands with glutamine as anchor motif: implications for hla-b27 association with spondyloarthropathy.the presentation of short viral peptide antigens by human leukocyte antigen (hla) class i molecules on cell surfaces is a key step in the activation of cytotoxic t lymphocytes, which mediate the killing of pathogen-infected cells or initiate autoimmune tissue damage. hla-b27 is a well known class i molecule that is used to study both facets of the cellular immune response. using mass spectrometry analysis of complex hla-bound peptide pools isolated from large amounts of hla-b*2705(+) cells, we i ...201323430249
cell wall elongation mode in gram-negative bacteria is determined by peptidoglycan architecture.cellular integrity and morphology of most bacteria is maintained by cell wall peptidoglycan, the target of antibiotics essential in modern healthcare. it consists of glycan strands, cross-linked by peptides, whose arrangement determines cell shape, prevents lysis due to turgor pressure and yet remains dynamic to allow insertion of new material, and hence growth. the cellular architecture and insertion pattern of peptidoglycan have remained elusive. here we determine the peptidoglycan architectur ...201323422664
the nose knows not: poor predictive value of stool sample odor for detection of clostridium difficile. 201323166192
development and validation of a novel diagnostic test for human brucellosis using a glyco-engineered antigen coupled to magnetic beads.brucellosis is a highly contagious zoonosis and still a major human health problem in endemic areas of the world. although several diagnostic tools are available, most of them are difficult to implement especially in developing countries where complex health facilities are limited. taking advantage of the identical structure and composition of the brucella spp. and yersinia enterocolitica o:9 o-polysaccharide, we explored the application of a recombinant y. enterocolitica o:9-polysaccharide-prot ...201323459192
immune evasion, immunopathology and the regulation of the immune system.costs and benefits of the immune response have attracted considerable attention in the last years among evolutionary biologists. given the cost of parasitism, natural selection should favor individuals with the most effective immune defenses. nevertheless, there exists huge variation in the expression of immune effectors among individuals. to explain this apparent paradox, it has been suggested that an over-reactive immune system might be too costly, both in terms of metabolic resources and risk ...201325436882
resistance mechanisms in campylobacter jejuni.campylobacter jejuni is a major cause of food-borne gastroenteritis worldwide. while mortality is low, morbidity imparted by post-infectious sequelae such as guillain-barré syndrome, reiter syndrome/reactive arthritis and irritable bowel syndrome is significant. in addition, the economic cost is high due to lost productivity. food animals, particularly poultry, are the main reservoirs of c. jejuni. the over-use of antibiotics in the human population and in animal husbandry has led to an increase ...201323406779
a novel synthetic receptor-based immunoassay for influenza vaccine quantification.vaccination is the most effective prophylactic method for preventing influenza. quantification of influenza vaccine antigens is critically important before the vaccine is used for human immunization. currently the vaccine antigen quantification relies on hemagglutinin content quantification, the key antigenic component, by single radial immunodiffusion (srid) assay. due to the inherent disadvantages associated with the traditional srid; i.e. low sensitivity, low throughput and need for annual re ...201323424631
increased levels of igg antibodies against human hsp60 in patients with spondyloarthritis.spondyloarthritis (spa) comprises a heterogeneous group of inflammatory diseases, with strong association to human leukocyte antigen (hla)-b27. a triggering bacterial infection has been considered as the cause of spa, and bacterial heat shock protein (hsp) seems to be a strong t cell antigen. since bacterial and human hsp60, also named hspd1, are highly homologous, cross-reactivity has been suggested in disease initiation. in this study, levels of antibodies against bacterial and human hsp60 wer ...201323424650
identification of autoantigens recognized by the 2f5 and 4e10 broadly neutralizing hiv-1 antibodies.many human monoclonal antibodies that neutralize multiple clades of hiv-1 are polyreactive and bind avidly to mammalian autoantigens. indeed, the generation of neutralizing antibodies to the 2f5 and 4e10 epitopes of hiv-1 gp41 in man may be proscribed by immune tolerance because mice expressing the v(h) and v(l) regions of 2f5 have a block in b cell development that is characteristic of central tolerance. this developmental blockade implies the presence of tolerizing autoantigens that are mimick ...201323359068
deletion of pic results in decreased virulence for a clinical isolate of shigella flexneri 2a from china.shigella is a major pathogen responsible for bacillary dysentery, a severe form of shigellosis. severity of the disease depends on the virulence of the infecting strain. shigella pathogenicity is a multi-gene phenomenon, involving the participation of genes on an unstable large virulence plasmid and chromosomal pathogenicity islands.201323391153
practicalities of using non-local or non-recent multilocus sequence typing data for source attribution in space and time of human campylobacteriosis.in this study, 1208 campylobacter jejuni and c. coli isolates from humans and 400 isolates from chicken, collected in two separate periods over 12 years in the netherlands, were typed using multilocus sequence typing (mlst). statistical evidence was found for a shift of st frequencies in human isolates over time. the human mlst data were also compared to published data from other countries to determine geographical variation. because only mlst typed data from chicken, taken from the same time po ...201323405107
rnd multidrug efflux pumps: what are they good for?multidrug efflux pumps are chromosomally encoded genetic elements capable of mediating resistance to toxic compounds in several life forms. in bacteria, these elements are involved in intrinsic and acquired resistance to antibiotics. unlike other well-known horizontally acquired antibiotic resistance determinants, genes encoding for multidrug efflux pumps belong to the core of bacterial genomes and thus have evolved over millions of years. the selective pressure stemming from the use of antibiot ...201323386844
mechanism of bacterial oligosaccharyltransferase: in vitro quantification of sequon binding and catalysis.n-linked glycosylation is an essential post-translational protein modification in the eukaryotic cell. the initial transfer of an oligosaccharide from a lipid carrier onto asparagine residues within a consensus sequon is catalyzed by oligosaccharyltransferase (ost). the first x-ray structure of a complete bacterial ost enzyme, campylobacter lari pglb, was recently determined. to understand the mechanism of pglb, we have quantified sequon binding and glycosylation turnover in vitro using purified ...201323382388
strategy for identification & characterization of bartonella henselae with conventional & molecular methods.bartonella henselae is a fastidious gram-negative bacterium usually causing self limiting infections in immunocompetent individuals but often causes potentially life threatening infection, such as bacillary angiomatosis in immunocompromised patients. both diagnosis of infections and research into molecular mechanisms of pathogenesis have been hindered by lack of appropriate and reliable diagnostic techniques. we undertook this study to standardize methods to characterize b. henselae in clinical ...201323563383
cell sorting enriches escherichia coli mutants that rely on peptidoglycan endopeptidases to suppress highly aberrant morphologies.bacterial morphology imparts physiological advantages to cells in different environments and, judging by the fidelity with which shape is passed to daughter cells, is a tightly regulated characteristic. surprisingly, only in the past 10 to 15 years has significant headway been made in identifying the mechanisms by which cells create and maintain particular shapes. one reason for this is that the relevant discoveries have relied heavily on the arduous, somewhat subjective process of manual micros ...201323243305
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