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contrasting immune responses mediate campylobacter jejuni-induced colitis and autoimmunity.campylobacter jejuni is a leading cause of foodborne enteritis that has been linked to the autoimmune neuropathy, guillain barré syndrome (gbs). c57bl/6 interleukin (il)-10(+/+) and congenic il-10(-/-) mice serve as c. jejuni colonization and colitis models, respectively, but a mouse model for gbs is lacking. we demonstrate that il-10(-/-) mice infected with a c. jejuni colitogenic human isolate had significantly upregulated type 1 and 17 but not type 2 cytokines in the colon coincident with inf ...201324220299
contrasting immune responses mediate campylobacter jejuni-induced colitis and autoimmunity.campylobacter jejuni is a leading cause of foodborne enteritis that has been linked to the autoimmune neuropathy, guillain barré syndrome (gbs). c57bl/6 interleukin (il)-10(+/+) and congenic il-10(-/-) mice serve as c. jejuni colonization and colitis models, respectively, but a mouse model for gbs is lacking. we demonstrate that il-10(-/-) mice infected with a c. jejuni colitogenic human isolate had significantly upregulated type 1 and 17 but not type 2 cytokines in the colon coincident with inf ...201324220299
in planta mutagenesis of src homology 3 domain-like fold of ndhs, a ferredoxin-binding subunit of the chloroplast nadh dehydrogenase-like complex in arabidopsis: a conserved arg-193 plays a critical role in ferredoxin binding.chloroplast nadh dehydrogenase-like (ndh) complex mediates cyclic electron transport around photosystem i and chlororespiration in angiosperms. the src homology 3 domain (sh3)-like fold protein ndhs/crr31 is an ndh subunit that is necessary for high affinity binding of ferredoxin, indicating that chloroplast ndh functions as a ferredoxin:plastoquinone oxidoreductase. however, the mechanism of the interaction between ndhs and ferredoxin is unclear. in this study, we analyzed their interaction in ...201324225949
burden of laboratory-confirmed campylobacter infections in guatemala 2008-2012: results from a facility-based surveillance system.campylobacteriosis is one of the leading causes of gastroenteritis worldwide. this study describes the epidemiology of laboratory-confirmed campylobacter diarrheal infections in two facility-based surveillance sites in guatemala.201324534336
burden of laboratory-confirmed campylobacter infections in guatemala 2008-2012: results from a facility-based surveillance system.campylobacteriosis is one of the leading causes of gastroenteritis worldwide. this study describes the epidemiology of laboratory-confirmed campylobacter diarrheal infections in two facility-based surveillance sites in guatemala.201324534336
pneumococcal meningitis in a young adult female with common variable immunodeficiency.female, 22 final diagnosis: pneumococcal meningitis symptoms: fever • headache • neck stiffness • nuchal rigidity • photophobia201324265845
the interplay between nlrs and autophagy in immunity and inflammation.since they were first described as cytosolic sensors of microbial molecules a decade ago, the nod-like receptors (nlrs) have been shown to have many different and important roles in various aspects of immune and inflammatory responses, ranging from antimicrobial mechanisms to control of adaptive responses. in this review, we focus on the interplay between nlrs and autophagy, an evolutionarily conserved mechanism that is crucial for homeostasis and has recently been shown to be involved in the pr ...201324273538
antimicrobial activity of turmeric extract and its potential use in food industry.the present study investigates the antimicrobial and preservative potentials of turmeric extracts for food industry. turmeric extracts prepared in n-hexane, water, chloroform and ethanol were applied to meals as preservatives and antibacterial agent. the samples were assessed microbiologically (total bacterial, total fungal and total coliform counts) and organoleptically (color, odor, taste) at day zero and after 15 days intervals. meals autoclaved for shorter time (5 min) and treated with combi ...201325829609
antimicrobial activity of turmeric extract and its potential use in food industry.the present study investigates the antimicrobial and preservative potentials of turmeric extracts for food industry. turmeric extracts prepared in n-hexane, water, chloroform and ethanol were applied to meals as preservatives and antibacterial agent. the samples were assessed microbiologically (total bacterial, total fungal and total coliform counts) and organoleptically (color, odor, taste) at day zero and after 15 days intervals. meals autoclaved for shorter time (5 min) and treated with combi ...201325829609
(non-)translational medicine: targeting bacterial rna.the rise and spread of antibiotic resistance is among the most severe challenges facing modern medicine. despite this fact, attempts to develop novel classes of antibiotic have been largely unsuccessful. the traditional mechanisms by which antibiotics work are subject to relatively rapid bacterial resistance via mutation, and hence have a limited period of efficacy. one promising strategy to ameliorate this problem is to shift from the use of chemical compounds targeting protein structures and p ...201324265632
discrimination of multilocus sequence typing-based campylobacter jejuni subgroups by maldi-tof mass spectrometry.campylobacter jejuni, the most common bacterial pathogen causing gastroenteritis, shows a wide genetic diversity. previously, we demonstrated by the combination of multi locus sequence typing (mlst)-based upgma-clustering and analysis of 16 genetic markers that twelve different c. jejuni subgroups can be distinguished. among these are two prominent subgroups. the first subgroup contains the majority of hyperinvasive strains and is characterized by a dimeric form of the chemotaxis-receptor tlp7(m ...201324195572
dna damage repair and bacterial pathogens. 201324244154
gastrointestinal illness among triathletes swimming in non-polluted versus polluted seawater affected by heavy rainfall, denmark, 2010-2011.recent years have seen an increase in the frequency of extreme rainfall and subsequent flooding across the world. climate change models predict that such flooding will become more common, triggering sewer overflows, potentially with increased risks to human health. in august 2010, a triathlon sports competition was held in copenhagen, denmark, shortly after an extreme rainfall. the authors took advantage of this event to investigate disease risks in two comparable cohorts of physically fit, long ...201324244306
signal transduction of helicobacter pylori during interaction with host cell protein receptors of epithelial and immune cells.helicobacter pylori infections can induce pathologies ranging from chronic gastritis, peptic ulceration to gastric cancer. bacterial isolates harbor numerous well-known adhesins, vacuolating cytotoxin vaca, protease htra, urease, peptidoglycan, and type iv secretion systems (t4ss). it appears that h. pylori targets more than 40 known host protein receptors on epithelial or immune cells. a series of t4ss components such as cagl, cagi, cagy, and caga can bind to the integrin α 5β 1 receptor. other ...201324280762
multi-omics approaches to deciphering a hypervirulent strain of campylobacter jejuni.campylobacter jejuni clone sa recently emerged as the predominant cause of sheep abortion in the united states and is also associated with foodborne gastroenteritis in humans. a distinct phenotype of this clone is its ability to induce bacteremia and abortion. to facilitate understanding the pathogenesis of this hypervirulent clone, we analyzed a clinical isolate (ia3902) of clone sa using multi-omics approaches. the genome of ia3902 contains a circular chromosome of 1,635,045 bp and a circular ...201324201373
campylobacter jejuni actively invades the amoeba acanthamoeba polyphaga and survives within non digestive vacuoles.the gram-negative bacterium campylobacter jejuni is able to enter, survive and multiply within the free living amoeba acanthamoeba polyphaga, but the molecular mechanisms behind these events are still unclear. we have studied the uptake and intracellular trafficking of viable and heat killed bacterial cells of the c. jejuni strain 81-176 in a. polyphaga. we found that viable bacteria associated with a substantially higher proportion of acanthamoeba trophozoites than heat killed bacteria. further ...201324223169
common duckweed (lemna minor) is a versatile high-throughput infection model for the burkholderia cepacia complex and other pathogenic bacteria.members of the burkholderia cepacia complex (bcc) have emerged in recent decades as problematic pulmonary pathogens of cystic fibrosis (cf) patients, with severe infections progressing to acute necrotizing pneumonia and sepsis. this study presents evidence that lemna minor (common duckweed) is useful as a plant model for the bcc infectious process, and has potential as a model system for bacterial pathogenesis in general. to investigate the relationship between bcc virulence in duckweed and gall ...201324223216
structural and biochemical characterization of a bifunctional ketoisomerase/n-acetyltransferase from shewanella denitrificans.unusual n-acetylated sugars have been observed on the o-antigens of some gram-negative bacteria and on the s-layers of both gram-positive and gram-negative bacteria. one such sugar is 3-acetamido-3,6-dideoxy-α-d-galactose or fuc3nac. the pathway for its production requires five enzymes with the first step involving the attachment of dtmp to glucose-1-phosphate. here, we report a structural and biochemical characterization of a bifunctional enzyme from shewanella denitificans thought to be involv ...201324128043
serine phosphorylation of cortactin is required for maximal host cell invasion by campylobacter jejuni.campylobacter jejuni causes acute disease characterized by severe diarrhea containing blood and leukocytes, fever, and abdominal cramping. disease caused by c. jejuni is dependent on numerous bacterial and host factors. c. jejuni invasion of the intestinal epithelial cells is seen in both clinical samples and animal models indicating that host cell invasion is, in part, necessary for disease. c. jejuni utilizes a flagellar type iii secretion system (t3ss) to deliver the campylobacter invasion an ...201324188565
a base composition analysis of natural patterns for the preprocessing of metagenome sequences.on the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. our tool uses these natural patterns to determine relatedness across sequence data. we introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. we suggest that t ...201324564274
lenvardb: database of length-variant protein domains.protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. this array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. length variations (indels) can introduce changes at structural, functional and interaction levels. lenvardb (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting f ...201324194591
lenvardb: database of length-variant protein domains.protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. this array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. length variations (indels) can introduce changes at structural, functional and interaction levels. lenvardb (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting f ...201324194591
cytotoxicity, phytochemical analysis and antioxidant activity of crude extracts from rhizomes of elephantorrhiza elephantina and pentanisia prunelloides.elephantorrhiza elephantina (ee) and pentanisia prunelloides (pp) are two medicinal plants which are widely used to remedy various ailments including diarrhoea, dysentery, inflammation, fever, rheumatism, heartburn, tuberculosis, haemorrhoids, skin diseases, perforated peptic ulcers and sore joints in southern africa (south africa, swaziland, botswana and zimbabwe). the following study was conducted to explore the in vitro cytotoxicity, antioxidant properties and phytochemical profile of the two ...201324653552
cytotoxicity, phytochemical analysis and antioxidant activity of crude extracts from rhizomes of elephantorrhiza elephantina and pentanisia prunelloides.elephantorrhiza elephantina (ee) and pentanisia prunelloides (pp) are two medicinal plants which are widely used to remedy various ailments including diarrhoea, dysentery, inflammation, fever, rheumatism, heartburn, tuberculosis, haemorrhoids, skin diseases, perforated peptic ulcers and sore joints in southern africa (south africa, swaziland, botswana and zimbabwe). the following study was conducted to explore the in vitro cytotoxicity, antioxidant properties and phytochemical profile of the two ...201324653552
effect of bacillus subtilis-based direct-fed microbials on immune status in broiler chickens raised on fresh or used litter.type of dietary direct-fed microbials (dfms) or poultry litter could directly influence the composition of gut microbiota. gut microbiota plays an important role in shaping the developing immune system and maintaining the homeostasis of the mature immune system in mammal and chickens. the present study was carried out to investigate the interaction among litter, dfms and immunity in broiler chickens exposed to a field-simulated environment. immune status of broiler chickens was assessed by serum ...201325049746
sialic acids siglec interaction: a unique strategy to circumvent innate immune response by pathogens.sialic acids (sias) are nine-carbon keto sugars primarily present on the terminal residue of cell surface glycans. sialic acid binding immunoglobulins (ig)-like lectins (siglecs) are generally expressed on various immune cells. they selectively recognize different linkage-specific sialic acids and undertake a variety of cellular functions. many pathogens either synthesize or acquire sialic acids from the host. sialylated pathogens generally use siglecs to manipulate the host immune response. the ...201324434319
clinical features of candidiasis in patients with inherited interleukin 12 receptor β1 deficiency.interleukin 12rβ1 (il-12rβ1)-deficient patients are prone to clinical disease caused by mycobacteria, salmonella, and other intramacrophagic pathogens, probably because of impaired interleukin 12-dependent interferon γ production. about 25% of patients also display mucocutaneous candidiasis, probably owing to impaired interleukin 23-dependent interleukin 17 immunity. the clinical features and outcome of candidiasis in these patients have not been described before, to our knowledge. we report her ...201324186907
clinical features of candidiasis in patients with inherited interleukin 12 receptor β1 deficiency.interleukin 12rβ1 (il-12rβ1)-deficient patients are prone to clinical disease caused by mycobacteria, salmonella, and other intramacrophagic pathogens, probably because of impaired interleukin 12-dependent interferon γ production. about 25% of patients also display mucocutaneous candidiasis, probably owing to impaired interleukin 23-dependent interleukin 17 immunity. the clinical features and outcome of candidiasis in these patients have not been described before, to our knowledge. we report her ...201324186907
increased incidence of campylobacter spp. infection and high rates among children, israel.during 1999-2010, the annual incidence of campylobacter spp. infection in israel increased from 31.04 to 90.99 cases/100,000 population, a yearly increase of 10.24%. children <2 years of age were disproportionally affected; incidence in this age group (356.12 cases/100,000 population) was >26-fold higher than for the 30-<50 age group.201324188185
the transcriptional landscape of campylobacter jejuni under iron replete and iron limited growth conditions.the genome-wide campylobacter jejuni transcriptional response under iron replete and iron limited conditions was characterized using rna-seq. we have identified 111 novel c. jejuni 5'utrs and mapped 377 co-transcribed genes into 230 transcriptional operons. in contrast to previous microarray results, the c. jejuni iron stimulon is less extensive than previously believed and consists of 77 iron activated genes and 50 iron repressed genes. as anticipated, the iron repressed genes are primarily tho ...201324223952
deciphering the contribution of human meningothelial cells to the inflammatory and antimicrobial response at the meninges.we have investigated the response of primary human meningothelial cells to neisseria meningitidis. through a transcriptome analysis, we provide a comprehensive examination of the response of meningothelial cells to bacterial infection. a wide range of chemokines are elicited which act to attract and activate the main players of innate and adaptive immunity. we showed that meningothelial cells expressed a high level of toll-like receptor 4 (tlr4), and, using a gene silencing strategy, we demonstr ...201324002066
transcriptional profiling of neisseria meningitidis interacting with human epithelial cells in a long-term in vitro colonization model.neisseria meningitidis is a commensal of humans that can colonize the nasopharyngeal epithelium for weeks to months and occasionally invades to cause life-threatening septicemia and meningitis. comparatively little is known about meningococcal gene expression during colonization beyond those first few hours. in this study, the transcriptome of adherent serogroup b n. meningitidis strain mc58 was determined at intervals during prolonged cocultivation with confluent monolayers of the human respira ...201323980104
relative contributions of lipooligosaccharide inner and outer core modifications to nontypeable haemophilus influenzae pathogenesis.nontypeable haemophilus influenzae (nthi) is a frequent commensal of the human nasopharynx that causes opportunistic infection in immunocompromised individuals. existing evidence associates lipooligosaccharide (los) with disease, but the specific and relative contributions of nthi los modifications to virulence properties of the bacterium have not been comprehensively addressed. using nthi strain 375, an isolate for which the detailed los structure has been determined, we compared systematically ...201323980106
insights into the mode of action of benzyl isothiocyanate on campylobacter jejuni.campylobacter jejuni is a widespread pathogen responsible for most of the food-borne gastrointestinal diseases in europe. the use of natural antimicrobial molecules is a promising alternative to antibiotic treatments for pathogen control in the food industry. isothiocyanates are natural antimicrobial compounds, which also display anticancer activity. several studies described the chemoprotective effect of isothiocyanates on eukaryotic cells, but the antimicrobial mechanism is still poorly unders ...201324014524
whole-genome sequencing of gentamicin-resistant campylobacter coli isolated from u.s. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes.aminoglycoside resistance in campylobacter has been routinely monitored in the united states in clinical isolates since 1996 and in retail meats since 2002. gentamicin resistance first appeared in a single human isolate of campylobacter coli in 2000 and in a single chicken meat isolate in 2007, after which it increased rapidly to account for 11.3% of human isolates and 12.5% of retail isolates in 2010. pulsed-field gel electrophoresis analysis indicated that gentamicin-resistant c. coli isolates ...201323959310
pasteurella multocida heddleston serovar 3 and 4 strains share a common lipopolysaccharide biosynthesis locus but display both inter- and intrastrain lipopolysaccharide heterogeneity.pasteurella multocida is a gram-negative multispecies pathogen and the causative agent of fowl cholera, a serious disease of poultry which can present in both acute and chronic forms. the major outer membrane component lipopolysaccharide (lps) is both an important virulence factor and a major immunogen. our previous studies determined the lps structures expressed by different p. multocida strains and revealed that a number of strains belonging to different serovars contain the same lps biosynthe ...201323974032
intestinal microbiome of poultry and its interaction with host and diet.the gastrointestinal (gi) tract of poultry is densely populated with microorganisms which closely and intensively interact with the host and ingested feed. the gut microbiome benefits the host by providing nutrients from otherwise poorly utilized dietary substrates and modulating the development and function of the digestive and immune system. in return, the host provides a permissive habitat and nutrients for bacterial colonization and growth. gut microbiome can be affected by diet, and differe ...201324256702
intestinal microbiome of poultry and its interaction with host and diet.the gastrointestinal (gi) tract of poultry is densely populated with microorganisms which closely and intensively interact with the host and ingested feed. the gut microbiome benefits the host by providing nutrients from otherwise poorly utilized dietary substrates and modulating the development and function of the digestive and immune system. in return, the host provides a permissive habitat and nutrients for bacterial colonization and growth. gut microbiome can be affected by diet, and differe ...201324256702
comprehensive analysis of prokaryotes in environmental water using dna microarray analysis and whole genome amplification.the microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. a novel dna microarray was developed as a simplified detection protocol. multiple dna probes were designed against each of the 97,927 sequences in the dna data bank of japan and mounted on a glass chip in ...201325437334
postinfectious guillain-barre syndrome in a patient with methimazole-induced agranulocytosis.both graves disease and guillain-barre syndrome (gbs) are autoimmune disorders caused by impaired self-tolerance mechanisms and triggered by interactions between genetic and environmental factors. gbs in patients who suffer from other autoimmune diseases is rarely reported, and the development of postinfectious gbs in a patient with graves disease has not been previously reported in the literature. herein, we report a patient with graves disease who developed postinfectious gbs during a course o ...201324307850
characterization of the viable but nonculturable (vbnc) state in saccharomyces cerevisiae.the viable but non culturable (vbnc) state has been thoroughly studied in bacteria. in contrast, it has received much less attention in other microorganisms. however, it has been suggested that various yeast species occurring in wine may enter in vbnc following sulfite stress.in order to provide conclusive evidences for the existence of a vbnc state in yeast, the ability of saccharomyces cerevisiae to enter into a vbnc state by applying sulfite stress was investigated. viable populations were mo ...201324204887
the abc-type efflux pump macab protects salmonella enterica serovar typhimurium from oxidative stress.multidrug efflux pumps are integral membrane proteins known to actively excrete antibiotics. the macrolide-specific pump macab, the only abc-type drug efflux pump in salmonella, has previously been linked to virulence in mice. the molecular mechanism of this link between macab and infection is unclear. we demonstrate that macab plays a role in the detoxification of reactive oxygen species (ros), compounds that salmonellae are exposed to at various stages of infection. macab is induced upon expos ...201324169575
bactofencin a, a new type of cationic bacteriocin with unusual immunity.bacteriocin production is an important probiotic trait of intestinal bacteria. in this study, we identify a new type of bacteriocin, bactofencin a, produced by a porcine intestinal isolate lactobacillus salivarius dpc6502, and assess its potency against pathogenic species including staphylococcus aureus and listeria monocytogenes. genome sequencing of the bacteriocin producer revealed bfna, which encodes the mature and highly basic (pi 10.59), 22-amino-acid defensin-like peptide. matrix-assisted ...201324169573
sandwich assay for mixed-sequence recognition of double-stranded dna: invader-based detection of targets specific to foodborne pathogens.a 96-well plate sandwich assay based on invader capture/signalling probes is used to recognize 28-mer mixed-sequence dsdna targets specific to salmonella enterica, campylobacter jejuni, escherichia coli. targets are detected down to 20-55 pm concentration with excellent binding specificity.201324036937
pathogenfinder--distinguishing friend from foe using bacterial whole genome sequence data.although the majority of bacteria are harmless or even beneficial to their host, others are highly virulent and can cause serious diseases, and even death. due to the constantly decreasing cost of high-throughput sequencing there are now many completely sequenced genomes available from both human pathogenic and innocuous strains. the data can be used to identify gene families that correlate with pathogenicity and to develop tools to predict the pathogenicity of newly sequenced strains, investiga ...201324204795
protein o-glucosylation in lactobacillus buchneri.based on the previous demonstration of surface (s-) layer protein glycosylation in lactobacillus buchneri 41021/251 and because of general advantages of lactic acid bacteria for applied research, protein glycosylation in this bacterial species was investigated in detail. the cell surface of l. buchneri cd034 is completely covered with an oblique 2d crystalline array (lattice parameters, a = 5.9 nm; b = 6.2 nm; γ ~ 77°) formed by self-assembly of the s-layer protein slpb. biochemical and mass spe ...201324162649
protein o-glucosylation in lactobacillus buchneri.based on the previous demonstration of surface (s-) layer protein glycosylation in lactobacillus buchneri 41021/251 and because of general advantages of lactic acid bacteria for applied research, protein glycosylation in this bacterial species was investigated in detail. the cell surface of l. buchneri cd034 is completely covered with an oblique 2d crystalline array (lattice parameters, a = 5.9 nm; b = 6.2 nm; γ ~ 77°) formed by self-assembly of the s-layer protein slpb. biochemical and mass spe ...201324162649
the role of the bacterial flagellum in adhesion and virulence.the bacterial flagellum is a complex apparatus assembled of more than 20 different proteins. the flagellar basal body traverses the cell wall, whereas the curved hook connects the basal body to the whip-like flagellar filament that protrudes several µm from the bacterial cell. the flagellum has traditionally been regarded only as a motility organelle, but more recently it has become evident that flagella have a number of other biological functions. the major subunit, flagellin or flic, of the fl ...201324833223
small gtpases of the ras superfamily regulate intestinal epithelial homeostasis and barrier function via common and unique mechanisms.the intestinal epithelium forms a stable barrier protecting underlying tissues from pathogens in the gut lumen. this is achieved by specialized integral membrane structures such as tight and adherens junctions that connect neighboring cells and provide stabilizing links to the cytoskeleton. junctions are constantly remodeled to respond to extracellular stimuli. assembly and disassembly of junctions is regulated by interplay of actin remodeling, endocytotic recycling of junctional proteins, and v ...201324868497
novel methods for analysing bacterial tracks reveal persistence in rhodobacter sphaeroides.tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. the trajectories obtained contain much information relating to the complex patterns of bacterial motility. however, methods for the quantitative analysis of such data are limited. most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. it is therefore necessary to segment observed tracks into swimming and reorientation phases to extract ...201324204227
critical role of a ferritin-like protein in the control of listeria monocytogenes cell envelope structure and stability under β-lactam pressure.the human pathogen listeria monocytogenes is susceptible to the β-lactam antibiotics penicillin g and ampicillin, and these are the drugs of choice for the treatment of listerial infections. however, these antibiotics exert only a bacteriostatic effect on this bacterium and consequently, l. monocytogenes is regarded as β-lactam tolerant. it is widely accepted that the phenomenon of bacterial tolerance to β-lactams is due to the lack of adequate autolysin activity, but the mechanisms of l. monocy ...201324204978
coestimation of recombination, substitution and molecular adaptation rates by approximate bayesian computation.the estimation of parameters in molecular evolution may be biased when some processes are not considered. for example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate bayesian computation (abc). we describe the implementation of a regression-based strategy for choosing s ...201324149652
coestimation of recombination, substitution and molecular adaptation rates by approximate bayesian computation.the estimation of parameters in molecular evolution may be biased when some processes are not considered. for example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate bayesian computation (abc). we describe the implementation of a regression-based strategy for choosing s ...201324149652
inference of the properties of the recombination process from whole bacterial genomes.patterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. the underlying model is sequentially markovian so that data can be simulated very efficiently, and we use approximate bayesian computation techniques to infer paramete ...201324172133
inference of the properties of the recombination process from whole bacterial genomes.patterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. the underlying model is sequentially markovian so that data can be simulated very efficiently, and we use approximate bayesian computation techniques to infer paramete ...201324172133
enzymatic basis for n-glycan sialylation: structure of rat α2,6-sialyltransferase (st6gal1) reveals conserved and unique features for glycan sialylation.glycan structures on glycoproteins and glycolipids play critical roles in biological recognition, targeting, and modulation of functions in animal systems. many classes of glycan structures are capped with terminal sialic acid residues, which contribute to biological functions by either forming or masking glycan recognition sites on the cell surface or secreted glycoconjugates. sialylated glycans are synthesized in mammals by a single conserved family of sialyltransferases that have diverse link ...201324155237
enteric bacterial invasion of intestinal epithelial cells in vitro is dramatically enhanced using a vertical diffusion chamber model.the interactions of bacterial pathogens with host cells have been investigated extensively using in vitro cell culture methods. however as such cell culture assays are performed under aerobic conditions, these in vitro models may not accurately represent the in vivo environment in which the host-pathogen interactions take place. we have developed an in vitro model of infection that permits the coculture of bacteria and host cells under different medium and gas conditions. the vertical diffusion ...201324192850
the campylobacter jejuni ciad effector protein activates map kinase signaling pathways and is required for the development of disease.enteric pathogens utilize a distinct set of proteins to modulate host cell signaling events that promote host cell invasion, induction of the inflammatory response, and intracellular survival. human infection with campylobacter jejuni, the causative agent of campylobacteriosis, is characterized by diarrhea containing blood and leukocytes. the clinical presentation of acute disease, which is consistent with cellular invasion, requires the delivery of the campylobacter invasion antigens (cia) to t ...201324144181
impact of a single phage and a phage cocktail application in broilers on reduction of campylobacter jejuni and development of resistance.campylobacteriosis is currently the most frequent foodborne zoonosis in many countries. one main source is poultry. the aim of this study was to enhance the knowledge about the potential of bacteriophages in reducing colonization of broilers with campylobacter , as there are only a few in vivo studies published. commercial broilers were inoculated with 10⁴ cfu/bird of a campylobacter jejuni field strain. groups of 88 birds each were subsequently treated with a single phage or a four-phage cockta ...201324205254
recognition of extracellular bacteria by nlrs and its role in the development of adaptive immunity.innate immune recognition of bacteria is the first requirement for mounting an effective immune response able to control infection. over the previous decade, the general paradigm was that extracellular bacteria were only sensed by cell surface-expressed toll-like receptors (tlrs), whereas cytoplasmic sensors, including members of the nod-like receptor (nlr) family, were specific to pathogens capable of breaching the host cell membrane. it has become apparent, however, that intracellular innate i ...201324155747
o-linked protein glycosylation in mycoplasma.although mycoplasmas have a paucity of glycosyltransferases and nucleotidyltransferases recognizable by bioinformatics, these bacteria are known to produce polysaccharides and glycolipids. we show here that mycoplasmas also produce glycoproteins and hence have glycomes more complex than previously realized. proteins from several species of mycoplasma reacted with a glycoprotein stain, and the murine pathogen mycoplasma arthritidis was chosen for further study. the presence of m. arthritidis glyc ...201324118505
a novel type of n-acetylglutamate synthase is involved in the first step of arginine biosynthesis in corynebacterium glutamicum.arginine biosynthesis in corynebacterium glutamicum consists of eight enzymatic steps, starting with acetylation of glutamate, catalysed by n-acetylglutamate synthase (nags). there are different kinds of known nagss, for example, "classical" arga, bifunctional argj, argo, and s-nags. however, since c. glutamicum possesses a monofunctional argj, which catalyses only the fifth step of the arginine biosynthesis pathway, glutamate must be acetylated by an as of yet unknown nags gene.201324138314
guillain-barre syndrome-like illness in association with electrical shock injury.a 19-year-old man presented 4 weeks after an electrical shock injury with gradual onset limb weakness, altered sensation in the peripheries and respiratory difficulty. there was immediate tingling of the fingers following the electrical injury that persisted. he subsequently had transient facial weakness responsive to oral steroids before the development of further limb symptoms. on admission the clinical picture and investigation findings, including neurophysiology, cerebrospinal fluid examinat ...201324136915
alternative roles for crispr/cas systems in bacterial pathogenesis. 201324146613
flow cytometry-based enrichment for cell shape mutants identifies multiple genes that influence helicobacter pylori morphology.the helical cell shape of helicobacter pylori is highly conserved and contributes to its ability to swim through and colonize the viscous gastric mucus layer. a multi-faceted peptidoglycan (pg) modification programme involving four recently characterized peptidases and two accessory proteins is essential for maintaining h. pylori's helicity. to expedite identification of additional shape-determining genes, we employed flow cytometry with fluorescence-activated cell sorting (facs) to enrich a tra ...201324112477
antimicrobial activity of the bioactive components of essential oils from pakistani spices against salmonella and other multi-drug resistant bacteria.the main objective of this study was the phytochemical characterization of four indigenous essential oils obtained from spices and their antibacterial activities against the multidrug resistant clinical and soil isolates prevalent in pakistan, and atcc reference strains.201324119438
assessment of glycan interactions of clinical and avian isolates of campylobacter jejuni.campylobacter jejuni strain 11168 was demonstrated to have a broad specificity for eukaryotic surface glycosylation using glycan array analysis. the initial screen indicated that sialic acid and mannose are important binding partners after environmental stress, while galactose and fucose structures are likely to be involved in persistent infection.201324119179
corbi: a new r package for biological network alignment and querying.in the last decade, plenty of biological networks are built from the large scale experimental data produced by the rapidly developing high-throughput techniques as well as literature and other sources. but the huge amount of network data have not been fully utilized due to the limited biological network analysis tools. as a basic and essential bioinformatics method, biological network alignment and querying have been applied in many fields such as predicting new protein-protein interactions (ppi ...201324565104
crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of n-linked protein glycosylation.oligosaccharyltransferase transfers an oligosaccharide chain to the asparagine residues in proteins. the archaeal and eubacterial oligosaccharyltransferases are single subunit membrane enzymes, referred to as "aglb" (archaeal glycosylation b) and "pglb" (protein glycosylation b), respectively. only one crystal structure of a full-length pglb has been solved. here we report the crystal structures of the full-length aglb from a hyperthermophilic archaeon, archaeoglobus fulgidus. the aglb and pglb ...201324127570
antimicrobial resistance in human and animal pathogens in zambia, democratic republic of congo, mozambique and tanzania: an urgent need of a sustainable surveillance system.a review of the published and unpublished literature on bacterial resistance in human and animals was performed. sixty-eight articles/reports from the democratic republic of congo (drc), mozambique, tanzania and zambia were reviewed. the majority of these articles were from tanzania. there is an increasing trend in the incidence of antibiotic resistance; of major concern is the increase in multidrug- resistant escherichia coli, klebsiella pneumoniae, staphylococcus aureus, vibrio cholera, non-ty ...201324119299
the fibronectin-binding motif within flpa facilitates campylobacter jejuni adherence to host cell and activation of host cell signaling.campylobacter jejuni is a gram-negative, curved and rod-shaped bacterium that causes human gastroenteritis. acute disease is associated with c. jejuni invasion of the intestinal epithelium. epithelial cells infected with c. jejuni strains containing mutations in the flpa and cadf fibronectin (fn)-binding proteins exhibit reduced invasion of host cells and a c. jejuni cadf flpa double mutant is impaired in the activation of epidermal growth factor receptor (egfr) and rho gtpase rac1. although the ...201326038437
formative research on hygiene behaviors and geophagy among infants and young children and implications of exposure to fecal bacteria.we conducted direct observation of 23 caregiver-infant pairs for 130 hours and recorded wash-related behaviors to identify pathways of fecal-oral transmission of bacteria among infants. in addition to testing fingers, food, and drinking water of infants, three infants actively ingested 11.3 ± 9.2 (mean ± sd) handfuls of soil and two ingested chicken feces 2 ± 1.4 times in 6 hours. hand washing with soap was not common and drinking water was contaminated with escherichia coli in half (12 of 22) o ...201324002485
beware of the patient with thymectomy: good's syndrome in a patient presenting with diarrhea.good's syndrome is a rare cause of immunodeficiency in adults associated with thymoma. we describe an 80-year-old female with chronic diarrhea, multiple opportunistic infections, and cytopenias. she underwent a thymectomy 5 years ago for a thymoma. laboratory tests revealed neutropenia, hypogammaglobulinaemia, complete b-cell lymphopenia, and low cd4 t cells with inverted cd4:cd8 ratio, which is consistent with good's syndrome. we recommend checking immunoglobulin levels in all patients with a h ...201326157815
mgla/sspa complex interactions are modulated by inorganic polyphosphate.the transcription factors mgla and sspa of francisella tularensis form a heterodimer complex and interact with the rna polymerase to regulate the expression of the francisella pathogenicity island (fpi) genes. these genes are essential for this pathogen's virulence and survival within host cells. our goal was to determine if an intracellular metabolite modulate these protein/protein interactions. in this study, we identified inorganic polyphosphate (polyp) as a signal molecule that promotes the ...201324116108
milk oligosaccharide sialyl(α2,3)lactose activates intestinal cd11c+ cells through tlr4.breast milk oligosaccharides shape the intestinal environment by affecting mucosal immunity and bacterial colonization. to clarify the role of milk oligosaccharide sialyl(α2,3)lactose (3sl) in intestinal physiology and disease, we investigated colitis development in il10(-/-) mice exposed to normal or 3sl-deficient milk during lactation. onset and progression of intestinal inflammation were delayed in il10(-/-) mice deficient for the α2,3 sialyltransferase 4 (st3gal4) responsible for 3sl biosynt ...201324101501
patent human infections with the whipworm, trichuris trichiura, are not associated with alterations in the faecal microbiota.the soil-transmitted helminth (sth), trichuris trichiura colonises the human large intestine where it may modify inflammatory responses, an effect possibly mediated through alterations in the intestinal microbiota. we hypothesised that patent t. trichiura infections would be associated with altered faecal microbiota and that anthelmintic treatment would induce a microbiota resembling more closely that observed in uninfected individuals.201324124574
interaction of microbes with mucus and mucins: recent developments.due to the recent rapid expansion in our understanding of the composition of the gut microflora and the consequences of altering that composition the question of how bacteria colonise mucus layers and interact with components of mucus, such as mucin, is now receiving widespread attention. using a combination of mucus secreting cells, and a novel mucin microarray platform containing purified native mucins from different sources we recently demonstrated that two gastrointestinal pathogens, helicob ...201324149677
interaction of microbes with mucus and mucins: recent developments.due to the recent rapid expansion in our understanding of the composition of the gut microflora and the consequences of altering that composition the question of how bacteria colonise mucus layers and interact with components of mucus, such as mucin, is now receiving widespread attention. using a combination of mucus secreting cells, and a novel mucin microarray platform containing purified native mucins from different sources we recently demonstrated that two gastrointestinal pathogens, helicob ...201324149677
fucosylated but not sialylated milk oligosaccharides diminish colon motor contractions.human milk oligosaccharides (hmo) are being studied by different groups exploring a broad range of potential beneficial effects to the breastfed infant. many of these effects have been attributed to a growth promotion effect on certain gut organisms such as bifidobacteria. additionally, evidence indicates that hmo are able to directly promote positive changes in gut epithelium and immune responses under certain conditions. this study utilizes a standardized ex vivo murine colon preparation to ex ...201324098451
transcriptional regulation by ferric uptake regulator (fur) in pathogenic bacteria.in the ancient anaerobic environment, ferrous iron (fe(2+)) was one of the first metal cofactors. oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (fe(3+)) and later to defend against reactive oxygen species (ros) generated by the fenton chemistry. to acquire fe(3+), bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for fe(3+). however, during infection the host restricts iron from pathogens by prod ...201324106689
purification and characterization of bacteriocin produced by lactobacillus brevis un isolated from dhulliachar: a traditional food product of north east india.a bacteriocin producing strain lactobacillus brevis un isolated from dulliachar-a salted pickle and identified by biochemical and molecular methods. l. brevis un was found to produce bacteriocin with broad spectrum activity against spoilage causing/food borne pathogens viz. l. monocytogenes, c. perfringens, s. aureus, l. mesenteroides, l. plantarum and b. cereus. bacteriocin production was optimized through classical one variable at a time method. the isolate showed maximum bacteriocin productio ...201325320420
purification and characterization of bacteriocin produced by lactobacillus brevis un isolated from dhulliachar: a traditional food product of north east india.a bacteriocin producing strain lactobacillus brevis un isolated from dulliachar-a salted pickle and identified by biochemical and molecular methods. l. brevis un was found to produce bacteriocin with broad spectrum activity against spoilage causing/food borne pathogens viz. l. monocytogenes, c. perfringens, s. aureus, l. mesenteroides, l. plantarum and b. cereus. bacteriocin production was optimized through classical one variable at a time method. the isolate showed maximum bacteriocin productio ...201325320420
gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study.elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. to this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gallstone patients as well as the gut of 38 normal individuals, examining and analyzing some 299, 217 bacterial 16s rrna gene sequences from 120 samples.201324083370
guillain barre syndrome as a manifestation of neurological melioidosis.neurological melioidosis is a very rare and very few cases have been reported from india. presentation is an extremely varied and as this disease is associated with high mortality, high index of suspicion is needed to diagnose and treat. in this context, we report a patient presenting as guillain barre syndrome evaluated as melioidosis.201324339608
the mucin muc2 limits pathogen burdens and epithelial barrier dysfunction during salmonella enterica serovar typhimurium colitis.salmonella enterica serovar typhimurium is a model organism used to explore the virulence strategies underlying salmonella pathogenesis. although intestinal mucus is the first line of defense in the intestine, its role in protection against salmonella is still unclear. the intestinal mucus layer is composed primarily of the muc2 mucin, a heavily o-glycosylated glycoprotein. the core 3-derived o-glycans of muc2 are synthesized by core 3 β1,3-n-acetylglucosaminyltransferase (c3gnt). mice lacking t ...201323876803
survey of culture, goldengate assay, universal biosensor assay, and 16s rrna gene sequencing as alternative methods of bacterial pathogen detection.cultivation-based assays combined with pcr or enzyme-linked immunosorbent assay (elisa)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. the aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in the gambia, mali, kenya, and bangladesh. the children were ide ...201323884998
increased emergence of fluoroquinolone-resistant campylobacter jejuni in biofilm. 201323896469
unique structural modifications are present in the lipopolysaccharide from colistin-resistant strains of acinetobacter baumannii.acinetobacter baumannii is a nosocomial opportunistic pathogen that can cause severe infections, including hospital-acquired pneumonia, wound infections, and sepsis. multidrug-resistant (mdr) strains are prevalent, further complicating patient treatment. due to the increase in mdr strains, the cationic antimicrobial peptide colistin has been used to treat a. baumannii infections. colistin-resistant strains of a. baumannii with alterations to the lipid a component of lipopolysaccharide (lps) have ...201323877686
clonal distribution and virulence of campylobacter jejuni isolates in blood.campylobacter jejuni bacteria are highly diverse enteropathogens. seventy-three c. jejuni isolates from blood collected in finland were analyzed by multilocus sequence typing and serum resistance. approximately half of the isolates belonged to the otherwise uncommon sequence type 677 clonal complex. isolates of this clonal complex were more resistant than other isolates to human serum.201324047729
helicobacter pylori salvages purines from extracellular host cell dna utilizing the outer membrane-associated nuclease nuct.helicobacter pylori is a bacterial pathogen that establishes life-long infections in humans, and its presence in the gastric epithelium is strongly associated with gastritis, peptic ulcer disease, and gastric cancer. having evolved in this specific gastric niche for hundreds of thousands of years, this microbe has become dependent on its human host. bioinformatic analysis reveals that h. pylori has lost several genes involved in the de novo synthesis of purine nucleotides, and without this pathw ...201323893109
nitrite reductase nirbd is induced and plays an important role during in vitro dormancy of mycobacterium tuberculosis.mycobacterium tuberculosis is one of the strongest reducers of nitrate among all mycobacteria. reduction of nitrate to nitrite, mediated by nitrate reductase (narghji) of m. tuberculosis, is induced during the dormant stage, and the enzyme has a respiratory function in the absence of oxygen. nitrite reductase (nirbd) is also functional during aerobic growth when nitrite is the sole nitrogen source. however, the role of nirbd-mediated nitrite reduction during the dormancy is not yet characterized ...201323935045
species-specificity of equine and porcine lawsonia intracellularis isolates in laboratory animals.lawsonia intracellularis infection causes proliferative enteropathy (pe) in many mammalian species, with porcine and equine proliferative enteropathy (ppe and epe) known worldwide. hamsters are a well-published animal model for ppe infection studies in pigs. there is no laboratory animal model for epe infection studies and it is not known whether there is species-specificity for equine or porcine isolates of l. intracellularis in animal models. the objective of this study was to determine whethe ...201324124268
the human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to cyanobacteria.cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to cyanobacteria, for which we propose the designation 'melainabacteria'. metabolic analysis suggests that the ancestors to both lineages were non-photosynth ...201324137540
transmigration route of campylobacter jejuni across polarized intestinal epithelial cells: paracellular, transcellular or both?intact intercellular junctions and cellular matrix contacts are crucial structural components for the formation and maintenance of epithelial barrier functions in humans to control the commensal flora and protect against intruding microbes. campylobacter jejuni is one of the most important zoonotic pathogens causing food-borne gastroenteritis and potentially more severe diseases such as reactive arthritis or guillain-barré syndrome. crossing the intestinal epithelial barrier and host cell invasi ...201324079544
changes in the symptom pattern and the densities of large-intestinal endocrine cells following campylobacter infection in irritable bowel syndrome: a case report.irritable bowel syndrome (ibs) is a common chronic functional gastrointestinal disorder. post-infectious ibs (pi-ibs) is a subset of ibs that accounts for a large proportion of ibs patients. the pi-ibs symptoms meet the rome criteria for ibs with diarrhoea (ibs-d) or ibs with mixed bowel habits (ibs-m). a low-grade inflammation has been reported to occur in pi-ibs. abnormalities in intestinal endocrine cells have been reported in both sporadic ibs and pi-ibs.201324073715
expression, crystallization and preliminary x-ray crystallographic analysis of peptide deformylase from campylobacter jejuni.campylobacter jejuni is one of the major foodborne pathogens causing human infection. peptide deformylase, a metallohydrolase, catalyzes the deformylation of n-formylated methionine in newly synthesized polypeptides in prokaryotes and some eukaryotic organelles. the deformylation process is an essential step in protein synthesis and has attracted much attention as a potential target for the development of novel antibacterial agents. here, the cloned codon-optimized def gene from c. jejuni was sy ...201324100562
archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in sulfolobus acidocaldarius.in this study, the in vitro and in vivo functions of the only two identified protein phosphatases, saci-ptp and saci-pp2a, in the crenarchaeal model organism sulfolobus acidocaldarius were investigated. biochemical characterization revealed that saci-ptp is a dual-specific phosphatase (against pser/pthr and ptyr), whereas saci-pp2a exhibited specific pser/pthr activity and inhibition by okadaic acid. deletion of saci_pp2a resulted in pronounced alterations in growth, cell shape and cell size, wh ...201324078887
comparison of rectal swabs and faeces for real-time pcr detection of enteric agents in rwandan children with gastroenteritis.molecular diagnostics have emerged as an efficient and feasible alternative for broad detection of pathogens in faeces. however, collection of stool samples is often impractical in both clinical work and in epidemiology studies. the aim of this study was to investigate the diagnostic performance of rectal swabs as compared with traditional faeces samples for detection of enteric agents by pcr.201324073740
outbreak investigation: salmonella food poisoning.an outbreak of food poisoning was reported from a military establishment on 29 may 2011 when 43 cases of food poisoning reported sick in a span of few hours.201324600149
viable but nonculturable bacteria: food safety and public health perspective.the viable but nonculturable (vbnc) state is a unique survival strategy of many bacteria in the environment in response to adverse environmental conditions. vbnc bacteria cannot be cultured on routine microbiological media, but they remain viable and retain virulence. the vbnc bacteria can be resuscitated when provided with appropriate conditions. a good number of bacteria including many human pathogens have been reported to enter the vbnc state. though there have been disputes on the existence ...201324191231
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