| recombination and dna repair in helicobacter pylori. | all organisms have pathways that repair the genome, ensuring their survival and that of their progeny. but these pathways also serve to diversify the genome, causing changes at the nucleotide, whole gene, and genome structure levels. sequencing of bacteria has revealed wide allelic diversity and differences in gene content within the same species, highlighting the importance of understanding pathways of recombination and dna repair. the human stomach pathogen helicobacter pylori is an excellent ... | 2011 | 21682641 |
| sequence divergence and conservation in genomes of helicobacter cetorum strains from a dolphin and a whale. | strains of helicobacter cetorum have been cultured from several marine mammals and have been found to be closely related in 16 s rdna sequence to the human gastric pathogen h. pylori, but their genomes were not characterized further. | 2013 | 24358262 |
| helicobacter pylori genomic microevolution during naturally occurring transmission between adults. | the human gastric pathogen helicobacter pylori is usually acquired during childhood and, in the absence of treatment, chronic infection persists through most of the host's life. however, the frequency and importance of h. pylori transmission between adults is underestimated. here we sequenced the complete genomes of h. pylori strains that were transmitted between spouses and analysed the genomic changes. similar to h. pylori from chronic infection, a significantly high proportion of the determin ... | 2013 | 24340004 |
| genome sequences of three hpafrica2 strains of helicobacter pylori. | we present the genome sequences of three hpafrica2 strains of helicobacter pylori, which are postulated to have evolved in isolation for many millennia in people of san ethnicity. although previously considered to be ancestral to helicobacter acinonychis, the hpafrica2 strains differ markedly from h. acinonychis in their gene arrangement. these data provide new insights into helicobacter evolution. | 2013 | 24072860 |
| comparison of the complete genome sequence of two closely related isolates of 'candidatus phytoplasma australiense' reveals genome plasticity. | 'candidatus phytoplasma australiense' is associated with at least nine diseases in australia and new zealand. the impact of this phytoplasma is considerable, both economically and environmentally. the genome of a nz isolate was sequenced in an effort to understand its pathogenicity and ecology. comparison with a closely related australian isolate enabled us to examine mechanisms of genomic rearrangement. | 2013 | 23915186 |
| biosynthesis of the urease metallocenter. | metalloenzymes often require elaborate metallocenter assembly systems to create functional active sites. the medically important dinuclear nickel enzyme urease provides an excellent model for studying metallocenter assembly. nickel is inserted into the urease active site in a gtp-dependent process with the assistance of ured/ureh, uree, uref, and ureg. these accessory proteins orchestrate apoprotein activation by delivering the appropriate metal, facilitating protein conformational changes, and ... | 2013 | 23539618 |
| genome sequencing reveals a phage in helicobacter pylori. | helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. genomic analysis of several strains has revealed an extensive h. pylori pan-genome, likely to grow as more genomes are sampled. here we describe the draft genome sequence (63 contigs; 26× mean coverage) of h. pylori strain b45, isolated from a patient with gastric mucosa-associa ... | 2011 | 22086490 |
| The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. | Here, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase genome harbors no extrachromosomal elements and 2,051 open reading frames are identified, covering 90.6% of the complete sequence, which represents a high coding density. Derived from the gene content, T. tenax is a representative member of the Crenarchaeota. The organism is stric ... | 2011 | 22003381 |
| synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. | comparison of the ratio of nonsynonymous to synonymous polymorphisms within species with the ratio of nonsynonymous to synonymous substitutions between species has been widely used as a supposed indicator of positive darwinian selection, with the ratio of these 2 ratios being designated as a neutrality index (ni). comparison of genome-wide polymorphism within 12 species of bacteria with divergence from an outgroup species showed substantial differences in ni among taxa. a low level of nonsynonym ... | 2008 | 18667439 |
| evolution of the selenoproteome in helicobacter pylori and epsilonproteobacteria. | by competing for the acquisition of essential nutrients, helicobacter pylori has the unique ability to persist in the human stomach, also causing nutritional insufficiencies in the host. although the h. pylori genome apparently encodes selenocysteine synthase (sela, hp1513), a key pyridoxal phosphate (plp)-dependent enzyme for the incorporation of selenium into bacterial proteins, nothing is known about the use of this essential element in protein synthesis by this pathogen. we analyzed the evol ... | 2015 | 26342139 |
| unsupervised statistical clustering of environmental shotgun sequences. | the development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. while previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed. | 2009 | 19799776 |
| genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. | the mobility of restriction-modification (rm) gene complexes and their association with genome rearrangements is a subject of active investigation. here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect rm-linked genome rearrangements. rm genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. they were flanked by direct and inverted repeats at a significantly high frequen ... | 2010 | 20071371 |
| identification and characterization of a lipopolysaccharide α,2,3-sialyltransferase from the human pathogen helicobacter bizzozeronii. | terminal sialic acid in the lipopolysaccharides (lpss) of mucosal pathogens is an important virulence factor. here we report the characterization of a helicobacter sialyltransferase involved in the biosynthesis of sialylated lps in helicobacter bizzozeronii, the only non-pylori gastric helicobacter species isolated from humans thus far. starting from the genome sequences of canine and human strains, we identified potential sialyltransferases downstream of three genes involved in the biosynthesis ... | 2012 | 22408169 |
| characterization of α2,3- and α2,6-sialyltransferases from helicobacter acinonychis. | genome sequence data were used to clone and express two sialyltransferase enzymes of the gt-42 family from helicobacter acinonychis atcc 51104, a gastric disease isolate from cheetahs. the deposited genome sequence for these genes contains a large number of tandem repeat sequences in each of them: hac1267 (rqkele)(15) and hac1268 (eekllefkni)(13). we obtained two clones with different numbers of repeat sequences for the hac1267 gene homolog and a single clone for the hac1268 gene homolog. both g ... | 2012 | 22504533 |
| outer membrane biogenesis in escherichia coli, neisseria meningitidis, and helicobacter pylori: paradigm deviations in h. pylori. | the bacterial pathogen helicobacter pylori is capable of colonizing the gastric mucosa of the human stomach using a variety of factors associated with or secreted from its outer membrane (om). lipopolysaccharide (lps) and numerous om proteins have been shown to be involved in adhesion and immune stimulation/evasion. many of these factors are essential for colonization and/or pathogenesis in a variety of animal models. despite this wide array of potential targets present on the bacterial surface, ... | 2012 | 22919621 |
| the complex methylome of the human gastric pathogen helicobacter pylori. | the genome of helicobacter pylori is remarkable for its large number of restriction-modification (r-m) systems, and strain-specific diversity in r-m systems has been suggested to limit natural transformation, the major driving force of genetic diversification in h. pylori. we have determined the comprehensive methylomes of two h. pylori strains at single base resolution, using single molecule real-time (smrt®) sequencing. for strains 26695 and j99-r3, 17 and 22 methylated sequence motifs were id ... | 2013 | 24302578 |
| the complex methylome of the human gastric pathogen helicobacter pylori. | the genome of helicobacter pylori is remarkable for its large number of restriction-modification (r-m) systems, and strain-specific diversity in r-m systems has been suggested to limit natural transformation, the major driving force of genetic diversification in h. pylori. we have determined the comprehensive methylomes of two h. pylori strains at single base resolution, using single molecule real-time (smrt®) sequencing. for strains 26695 and j99-r3, 17 and 22 methylated sequence motifs were id ... | 2013 | 24302578 |
| electron microscopic, genetic and protein expression analyses of helicobacter acinonychis strains from a bengal tiger. | colonization by helicobacter species is commonly noted in many mammals. these infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. the aim of this study was to isolate and characterize putative novel helicobacter spp. from bengal tigers in thailand. morphological investigation (gram-staining and electron microscopy) and genetic studies (16srrna, 23srrna, flagellin, urease and prophage gene analyses, rapd dna fingerprinting and ... | 2013 | 23940723 |
| innate endogenous adjuvants prime to desirable immune responses via mucosal routes. | vaccination is an effective strategy to prevent infectious or immune related diseases, which has made remarkable contribution in human history. recently increasing attentions have been paid to mucosal vaccination due to its multiple advantages over conventional ways. subunit or peptide antigens are more reasonable immunogens for mucosal vaccination than live or attenuated pathogens, however adjuvants are required to augment the immune responses. many mucosal adjuvants have been developed to prim ... | 2014 | 25503634 |
| innate endogenous adjuvants prime to desirable immune responses via mucosal routes. | vaccination is an effective strategy to prevent infectious or immune related diseases, which has made remarkable contribution in human history. recently increasing attentions have been paid to mucosal vaccination due to its multiple advantages over conventional ways. subunit or peptide antigens are more reasonable immunogens for mucosal vaccination than live or attenuated pathogens, however adjuvants are required to augment the immune responses. many mucosal adjuvants have been developed to prim ... | 2014 | 25503634 |
| a variable homopolymeric g-repeat defines small rna-mediated posttranscriptional regulation of a chemotaxis receptor in helicobacter pylori. | phase variation of hypermutable simple sequence repeats (ssrs) is a widespread and stochastic mechanism to generate phenotypic variation within a population and thereby contributes to host adaptation of bacterial pathogens. although several examples of ssrs that affect transcription or coding potential have been reported, we now show that a ssr also impacts small rna-mediated posttranscriptional regulation. based on in vitro and in vivo analyses, we demonstrate that a variable homopolymeric g-re ... | 2014 | 24474799 |
| comparative genomics and genome biology of invasive campylobacter jejuni. | campylobacter jejuni is a major pathogen in bacterial gastroenteritis worldwide and can cause bacteremia in severe cases. c. jejuni is highly structured into clonal lineages of which the st677cc lineage has been overrepresented among c. jejuni isolates derived from blood. in this study, we characterized the genomes of 31 c. jejuni blood isolates and 24 faecal isolates belonging to st677cc in order to study the genome biology related to c. jejuni invasiveness. we combined the genome analyses with ... | 2015 | 26603914 |
| comparative analysis of prophage-like elements in helicobacter sp. genomes. | prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. information on helicobacter sp. prophages remains scarce. in this study, sixteen prophages were identified and analyzed in detail. eight of them are described for the first time. based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. phylogenetic relationships of cluster a helicobacter ... | 2016 | 27169002 |
| diagnosis of genus helicobacter through a hemi-nested pcr assay of 16s rrna. | the present study aimed to establish a genus-specific pcr-based assay to detect helicobacters using 16s rrna gene as the target template. we designed the hemi-nested primers based on sequences of 16s rrna gene of 34 types of helicobacter species. the inclusivity, sensitivity, and specificity of the pcr assay using these primers were examined in three different models, comprising feces simulated samples, blab/c mice infection model and clinic patients samples. the detection sensitivity of helicob ... | 2016 | 27275113 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| gastric helicobacter spp. infection in captive neotropical brazilian feline. | ten captive neotropical brazilian feline were submitted to gastroscopic examination and samples of gastric mucosa from fundus, corpus and pyloric antrum were evaluated for the presence of helicobacter species. warthin-starry (ws) staining and pcr assay with species-specific primers and enzymatic cleavage were applied for bacterial detection and identification. histological lesions were evaluated by haematoxylin and eosin staining. all animals showed normal gross aspect of gastric mucosa. helicob ... | 2011 | 24031634 |
| optimizing hybrid assembly of next-generation sequence data from enterococcus faecium: a microbe with highly divergent genome. | sequencing of bacterial genomes became an essential approach to study pathogen virulence and the phylogenetic relationship among close related strains. bacterium enterococcus faecium emerged as an important nosocomial pathogen that were often associated with resistance to common antibiotics in hospitals. with highly divergent gene contents, it presented a challenge to the next generation sequencing (ngs) technologies featuring high-throughput and shorter read-length. this study was designed to i ... | 2012 | 23282199 |
| in silico evolutionary analysis of helicobacter pylori outer membrane phospholipase a (ompla). | in the past decade, researchers have proposed that the plda gene for outer membrane phospholipase a (ompla) is important for bacterial colonization of the human gastric ventricle. several conserved helicobacter pylori genes have distinct genotypes in different parts of the world, biogeographic patterns that can be analyzed through phylogenetic trees. the current study will shed light on the importance of the plda gene in h. pylori. in silico sequence analysis will be used to investigate whether ... | 2012 | 22974200 |
| sequencing error correction without a reference genome. | next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. identifying sequencing errors from true biological variants is a challenging task. for organisms without a reference genome this difficulty is even more challenging. | 2013 | 24350580 |
| new stable anchor protein and peptide linker suitable for successful spore surface display in b. subtilis. | in last decade spores have been successfully used as a surface display platform. various peptides or proteins were displayed this way as functional enzymes or antigens. nearly all attempts involved use of three coat proteins: cotb, cotc or cotg. increasing knowledge of the structure of the spore coat allowed us to propose the use of other proteins whose localization in the spore envelope has been determined. we also propose the application of a new linker suitable for building fusion proteins. | 2013 | 23448318 |
| mucosal adjuvant activity of il-2 presenting spores of bacillus subtilis in a murine model of helicobacter pylori vaccination. | the endospores of bacillus subtilis are now widely used as a platform for presentation of heterologous proteins and due to their safety record and high resistance to harsh environmental conditions can be considered as potential vehicles for oral vaccination. in this research we show that recombinant b. subtilis spores presenting a fragment of the helicobacter acinonychis ureb protein and expressing the ureb gene under vegetative promoter elicit a strong cellular immune response in orally immuniz ... | 2014 | 24743850 |
| a system of vectors for bacillus subtilis spore surface display. | bacterial spores have been utilized as platforms for protein display. the best studied display systems are based on bacillus subtilis spores in which several coat proteins have successfully been used as anchors for heterologous protein. increasing knowledge about spore coat structure enables selection of new anchor proteins such as cotz and cgea. here we describe a system of vectors for display of proteins on the surface of b. subtilis spores. | 2014 | 24568122 |
| evolution of helicobacter: acquisition by gastric species of two histidine-rich proteins essential for colonization. | metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. virulence of the human gastric pathogen helicobacter pylori is dependent on nickel, cofactor of two enzymes essential for in vivo colonization, urease and [nife] hydrogenase. we found that two small paralogous nickel-binding proteins with high content in histidine (hpn and hpn-2) play a central role in maintaining non-toxic intracellular ... | 2015 | 26641249 |
| dormant phages of helicobacter pylori reveal distinct populations in europe. | prophages of helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. however, their role in the diversity of h. pylori strains is unknown. we demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between european populations, and that h. pylori prophages and their host bacteria share a complex evolutionary history. by comparing the phylogenetic trees of two prophage genes (integra ... | 2015 | 26387443 |
| pathology in captive wild felids at german zoological gardens. | this retrospective study provides an overview on spontaneous diseases occurring in 38 captive wild felids submitted for necropsy by german zoological gardens between 2004 and 2013. species included 18 tigers, 8 leopards, 7 lions, 3 cheetahs and 2 cougars with an age ranging from 0.5 to 22 years. renal lesions, predominantly tubular alterations (intra-tubular concrements, tubular degeneration, necrosis, intra-tubular cellular debris, proteinaceous casts, dilated tubuli) followed by interstitial ( ... | 2015 | 26086731 |
| complete genome sequences of two helicobacter pylori strains from a canadian arctic aboriginal community. | we report here the complete genome sequences of two amerind helicobacter pylori strains from aklavik, northwest territories, canada. one strain contains extra iron-cofactored urease genes and ~140 rearrangements in its chromosome relative to other described strains (typically differing from one another by <10 rearrangements), suggesting that it represents a novel lineage of h. pylori. | 2015 | 25883278 |
| recombinant bacillus subtilis spores elicit th1/th17-polarized immune response in a murine model of helicobacter pylori vaccination. | current progress in research on vaccines against helicobacter pylori emphasizes the significance of eliciting the th1/th17-polarized immune response. such polarization can be achieved by selection of appropriate antigen and adjuvant. in this study, we wanted to check the polarization of the immune response elicited by ureb protein of helicobacter acinonychis delivered by recombinant bacillus subtilis spores upon oral immunization. b. subtilis spores presenting fragment of ureb protein and able t ... | 2015 | 25779639 |
| plant proteins are smaller because they are encoded by fewer exons than animal proteins. | protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. we found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. while eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. proteins unique to plants are ∼81aa s ... | 2016 | 27998811 |
| how old are bacterial pathogens? | only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. the global genetic diversity of helicobacter pylori, which infects human stomachs, parallels that of its human host. the time to the most recent common ancestor (tmrca) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence withi ... | 2016 | 27534956 |
| pattern recognition on read positioning in next generation sequencing. | the usefulness and the utility of the next generation sequencing (ngs) technology are based on the assumption that the dna or cdna cleavage required to generate short sequence reads is random. several previous reports suggest the existence of sequencing bias of ngs reads. to address this question in greater detail, we analyze ngs data from four organisms with different gc content, plasmodium falciparum (19.39%), arabidopsis thaliana (36.03%), homo sapiens (40.91%) and streptomyces coelicolor (72 ... | 2016 | 27299343 |
| mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids. | in the past few years, several researchers have focused their attention on nucleic acid mimics due to the increasing necessity of developing a more robust recognition of dna or rna sequences. fluorescence in situ hybridization (fish) is an example of a method where the use of these novel nucleic acid monomers might be crucial to the success of the analysis. to achieve the expected accuracy in detection, fish probes should have high binding affinity towards their complementary strands and discrim ... | 2015 | 25840566 |