| genetic evidence for host specificity in the adhesin-encoding genes hxaa of helicobacter acinonyx, hnaa of h. nemestrinae and hpaa of h. pylori. | gastric and non-gastric species of helicobacter were examined for the presence of the adhesin-encoding gene, hpaa, from the human-associated gastric helicobacter h. pylori (hp), and for adhesin subunit protein hpaa. amplification of a 375-bp internal dna fragment of hpaa by pcr demonstrated the presence of the gene in hp and in two closely related gastric helicobacters, h. nemestrinae (hn) and h. acinonyx (hx), but not in the more distantly related h. felis (hf) and h. mustelae (hm). the non-gas ... | 1995 | 7557486 |
| treatment of gastritis in cheetahs (acinonyx jubatus). | three cheetahs (acinonyx jubatus) had a clinical history of chronic spiral bacteria-associated gastritis and three cheetahs had no clinical history of gastritis. gastric biopsies were obtained from all six cheetahs prior to treatment for gastritis and 3 wk and 1 yr posttreatment. the cheetahs were treated with tetracycline hydrochloride 500 mg p.o. q.i.d., metronidazole 250 mg p.o. q.i.d., and bismuth subsalicylate 300 mg p.o. q.i.d. each drug was administered concurrently for 7 days. following ... | 1997 | 9365937 |
| helicobacter pylori porcdab and oordabc genes encode distinct pyruvate:flavodoxin and 2-oxoglutarate:acceptor oxidoreductases which mediate electron transport to nadp. | helicobacter pylori, a major cause of human gastric disease, is a microaerophilic bacterium that contains neither pyruvate nor 2-oxoglutarate dehydrogenase activity. previous studies (n. j. hughes, p. a. chalk, c. l. clayton, and d. j. kelly, j. bacteriol. 177:3953-3959, 1995) have indicated that the major routes for the generation of acetyl coenzyme a (acetyl-coa) and succinyl-coa are via pyruvate:flavodoxin oxidoreductase (por) and 2-oxoglutarate:acceptor oxidoreductase (oor), respectively. th ... | 1998 | 9495749 |
| identification of a novel enteric helicobacter species in a kitten with severe diarrhea. | a previously undescribed helicobacter sp. was recovered from a cat with severe diarrhea. based upon the absence of any other identifiable cause of diarrhea, this helicobacter may be involved in the development of the disease signs. the organism could not be cultured but was described on the basis of 16s rrna gene sequence analysis and morphology and appeared to be a new species, with helicobacter canis being the most genetically similar species. the presence of a diarrhea-inducing helicobacter i ... | 1998 | 9542907 |
| "flexispira rappini" bacteremia in a child with pneumonia. | we describe a case of "flexispira rappini" bacteremia from a 9-year-old girl who presented with a 5-day history of fever, productive cough, and malaise. a chest x-ray result was compatible with right middle lobe pneumonia. blood culture grew a gram-negative spiral fusiform bacterium 2 days after the inoculation. biochemical tests showed the organism to be catalase negative, oxidase positive, sodium hippurate hydrolysis negative, and urea hydrolysis negative. 16s rrna gene sequencing identified t ... | 1998 | 9620399 |
| characterization of an acidic-ph-inducible stress protein (hsp70), a putative sulfatide binding adhesin, from helicobacter pylori. | the in vitro glycolipid binding specificity of the gastric pathogen helicobacter pylori is altered to include sulfated glycolipids (sulfatides) following brief exposure of the organism to acid ph typical of the stomach. this change is prevented by anti-hsp70 antibodies, suggesting that hsp70 may be a stress-induced surface adhesin, mediating sulfatide recognition. to facilitate investigation of the role of hsp70 in attachment, we have cloned and sequenced the h. pylori hsp70 gene (dnak). the hsp ... | 1998 | 9712748 |
| helicobacter acinonyx sp. nov., isolated from cheetahs with gastritis. | four strains of a novel helicobacter species were isolated from the stomachs of cheetahs (acinonyx jubilatus) with gastritis. these isolates were phenotypically similar to helicobacter pylori. the isolates were gram-negative, spiral bacteria which grew under microaerophilic conditions at 37 degrees c, but not at 25 or 42 degrees c, and produced urease, catalase, oxidase, alkaline phosphatase, and gamma-glutamyl transpeptidase. the isolates did not ferment glucose, mannitol, inositol, sorbitol, r ... | 1993 | 8379970 |
| healthy cats are commonly colonized with "helicobacter heilmannii" that is associated with minimal gastritis. | gastric helicobacter infection in healthy pet cats is not well characterized. we performed endoscopy with gastric biopsy on 15 healthy pet cats that were rigorously screened to exclude underlying or concurrent diseases that might affect helicobacter colonization. gastric mucosa biopsy specimens were examined by histology, culture, and pcr for the presence of helicobacter infection and by histology for the presence of gastritis. of 15 cats, all but 1 had gastric helicobacter-like organisms (ghlos ... | 1999 | 9854088 |
| novel intestinal helicobacter species isolated from cotton-top tamarins (saguinus oedipus) with chronic colitis. | a disease similar to ulcerative colitis in humans has been identified in cotton-top tamarins (ctts) in captivity. the clinical signs include weight loss, diarrhea, and rectal bleeding with the pathological features and biochemical abnormalities of ulcerative colitis. approximately 25 to 40% of these animals develop colon cancer after 2 to 5 years of captivity. an infectious etiology has been proposed; however, no microbial agent to date has been identified. helicobacter spp. have been associated ... | 1999 | 9854080 |
| characterization of a culturable "gastrospirillum hominis" (helicobacter heilmannii) strain isolated from human gastric mucosa. | spiral organisms were isolated from an antral gastric mucosal biopsy specimen from a dyspeptic patient with gastritis. only corkscrew-shaped organisms resembling "gastrospirillum hominis" ("helicobacter heilmannii") but no helicobacter pylori-like organisms were seen in histological sections. h. pylori was not cultured from specimens from this patient. on the basis of biochemical reactions, morphology, ultrastructure, and 16s dna sequencing, the isolated "g. hominis" was shown to be a true helic ... | 1999 | 10074528 |
| serological discrimination of dogs infected with gastric helicobacter spp. and uninfected dogs. | characterization of the humoral immune responses of people to helicobacter pylori infection has facilitated the investigation of the host response to bacterial virulence factors and the development of sensitive and specific diagnostic tests. dogs are commonly infected with gastric helicobacter spp., but the presence of multiple helicobacter spp. and possible coinfection in individual dogs have complicated serological evaluation. evaluation of the antigenic homology of helicobacter spp. revealed ... | 1999 | 10203471 |
| isolation and identification of helicobacter spp. from canine and feline gastric mucosa. | it is known that virtually all healthy adult dogs and cats harbor spiral helicobacters in their gastric mucosa. three species, helicobacter felis, helicobacter bizzozeronii, and helicobacter salomonis have been isolated in vitro from the gastric mucosa of these animals. the aims of this study were to evaluate the efficacy of an isolation method for canine and feline gastric helicobacters that has been developed at the university of helsinki; to estimate the prevalence and distribution of these t ... | 1998 | 9758832 |
| chronic gastritis in tigers associated with helicobacter acinonyx. | helicobacter pylori-like organisms (hplos) were isolated from the gastric mucosa of two sumatran tigers and identified by polymerase chain reaction analysis as helicobacter acinonyx. at histological examination, both tigers revealed a chronic gastritis associated with hplos as demonstrated by immunolabelling and electron microscopy. this is the first isolation of h. acinonyx from tigers, in which, as previously reported in cheetahs, it may be a cause of gastritis. | 1998 | 9717128 |
| systemic candidiasis in a cheetah (acinonyx jubatus). | systemic candidiasis, with involvement of the spleen, liver, kidneys, and lymph nodes, was diagnosed in a geriatric captive cheetah (acinonyx jubatus). the animal had a long clinical history of intermittent chronic gastritis associated with helicobacter acinonyx and chronic renal failure, both of which were repeatedly treated with broad-spectrum antimicrobial therapy. following euthanasia, a postmortem examination showed numerous microabscesses and granulomas composed of degenerate eosinophils a ... | 1998 | 10065861 |
| comparison of iron uptake in different helicobacter species. | comparison of iron uptake of four helicobacter species (helicobacter pylori, helicobacter felis, helicobacter acinonyx, and helicobacter mustelae), associated with various degrees of gastritis in their respective host, with five other species which colonize the intestinal tract of various animals (helicobacter fennelliae, helicobacter cinaedi, helicobacter muridarum, helicobacter bilis, and helicobacter hepaticus), demonstrated that the iron acquisition system differed according to the ecologica ... | 1999 | 10540911 |
| helicobacter felis infection is associated with lymphoid follicular hyperplasia and mild gastritis but normal gastric secretory function in cats. | the relationship of helicobacter felis, a bacterium observed in the stomachs of cats, to gastric disease is unclear. the objective of this study was to determine if h. felis infection alters gastric histopathology, proinflammatory cytokine expression, and secretory function and evokes a humoral immune response in cats. five specific-pathogen-free (spf) helicobacter-free cats were studied before and for 1 year after oral inoculation with h. felis (atcc 49179). four spf h. felis-uninfected cats se ... | 2000 | 10639446 |
| helicobacter mesocricetorum sp. nov., a novel helicobacter isolated from the feces of syrian hamsters. | a spiral-shaped bacterium with bipolar, single, nonsheathed flagella was isolated from the feces of syrian hamsters. the bacterium grew as a thin spreading film at 37 degrees c under microaerobic conditions, did not hydrolyze urea, was positive for catalase and alkaline phosphatase, reduced nitrate to nitrite, did not hydrolyze hippurate, and was sensitive to nalidixic acid but resistant to cephalothin. sequence analysis of the 16s rrna gene and biochemical and phenotypic criteria indicate that ... | 2000 | 10790105 |
| misidentifying helicobacters: the helicobacter cinaedi example. | whole-cell protein electrophoresis and biochemical examination by means of a panel of 64 tests were used to identify 14 putative helicobacters to the species level. the results were confirmed by means of dna-dna hybridization experiments and were used to discuss misidentification of helicobacters based on 16s rrna gene sequence data. the data indicated that comparison of near-complete 16s ribosomal dna sequences does not always provide conclusive evidence for species level identification and may ... | 2000 | 10834986 |
| comh, a novel gene essential for natural transformation of helicobacter pylori. | helicobacter pylori is naturally competent for transformation, but the dna uptake system of this bacterium is only partially characterized, and nothing is known about the regulation of competence in h. pylori. to identify other components involved in transformation or competence regulation in this species, we screened a mutant library for competence-deficient mutants. this resulted in the identification of a novel, helicobacter-specific competence gene (comh) whose function is essential for tran ... | 2000 | 10869072 |
| slaughter pigs are commonly infected by closely related but distinct gastric ulcerative lesion-inducing gastrospirilla. | an association between (unculturable) gastrospirillum-like organisms (glo) and ulcerative lesions in the pars oesophagea in stomachs of swine has been claimed. in dogs glo detected by microscopy may represent several helicobacter species or subspecies. therefore we investigated which helicobacter spp. are present in stomachs of swine and their possible association with ulcerative lesions of the pars oesophagea. the presence of helicobacter spp. in the antrum and pars oesophagea in 122 stomachs o ... | 2000 | 10878060 |
| helicobacter acinonychis eradication leading to the resolution of gastric lesions in tigers. | | 2000 | 10975334 |
| a probable new helicobacter species isolated from a patient with bacteremia. | a probable new helicobacter species was isolated from the blood of a 14-month-old aboriginal child who presented with vomiting, diarrhea, fever, and dry cough. the most similar 16s rrna gene sequence was that of helicobacter fennelliae ccug 18820(t) but the new sequence differed from it by at least 32 base substitutions and by the presence of a large (353-nucleotide) intervening sequence. | 2000 | 11015417 |
| emergence of diverse helicobacter species in the pathogenesis of gastric and enterohepatic diseases. | since helicobacter pylori was first cultivated from human gastric biopsy specimens in 1982, it has become apparent that many related species can often be found colonizing the mucosal surfaces of humans and other animals. these other helicobacter species can be broadly grouped according to whether they colonize the gastric or enterohepatic niche. gastric helicobacter species are widely distributed in mammalian hosts and are often nearly universally prevalent. in many cases they cause an inflammat ... | 2001 | 11148003 |
| evaluation of a group-specific 16s ribosomal dna-based pcr for detection of helicobacter bizzozeronii, helicobacter felis, and helicobacter salomonis in fresh and paraffin-embedded gastric biopsy specimens. | a new specific and sensitive 16s ribosomal dna-based pcr assay was developed. the assay targets a 78-bp dna fragment unique to helicobacter bizzozeronii, helicobacter felis, and helicobacter salomonis and can be used with freshly frozen and formalin-fixed paraffin-embedded gastric biopsy specimens. | 2001 | 11230459 |
| specific detection and prevalence of helicobacter heilmannii-like organisms in the human gastric mucosa by fluorescent in situ hybridization and partial 16s ribosomal dna sequencing. | gastric infection with helicobacter heilmannii (previously known as gastrospirillum hominis) is invariably linked with the presence of chronic gastritis and the risk of developing low-grade mucosa-associated lymphoid tissue lymphoma in humans. in contrast to helicobacter pylori, various h. heilmannii species colonize the stomachs of domestic animals, which might be a reservoir for transmission to humans (zoonosis). to identify the number and prevalence of different h. heilmanni types in humans, ... | 2001 | 11283079 |
| coinfection of enteric helicobacter spp. and campylobacter spp. in cats. | during a 6-year period, 64 of 227 commercially reared cats had microaerobic bacteria isolated from their feces. all the isolates were initially identified as campylobacter-like organisms based on biochemical and phenotypic characteristics. dna extractions from 51 of these isolates were subjected to pcr using primers specific for helicobacter spp. and campylobacter spp. of the isolates, 92% (47 of 51 isolates) were positive for campylobacter spp., 41% (21 of 51 isolates) were positive for helicob ... | 2001 | 11376052 |
| interspecies transfer of antibiotic resistance between helicobacter pylori and helicobacter acinonychis. | | 2001 | 11583009 |
| helicobacter typhlonius sp. nov., a novel murine urease-negative helicobacter species. | over the past decade, several helicobacter species have been isolated from rodents. with the advent of pcr for the diagnosis of infectious agents, it has become clear that several previously uncharacterized helicobacter species also colonize rodents. in this report, we describe a novel urease-negative helicobacter, helicobacter typhlonius sp. nov., which was isolated from colonies of laboratory mice independently by two laboratories. infection of immunodeficient mice by this bacterium resulted i ... | 2001 | 11682508 |
| helicobacter cetorum sp. nov., a urease-positive helicobacter species isolated from dolphins and whales. | a novel helicobacter with the proposed name helicobacter cetorum, sp. nov. (type strain mit 99-5656; genbank accession number af 292378), was cultured from the main stomach of two wild, stranded atlantic white-sided dolphins (lagenorhynchus acutus) and from the feces of three captive cetaceans (a pacific white-sided dolphin [lagenorhynchus obliquidens]; an atlantic bottlenose dolphin [tursiops truncatus]; and a beluga whale [delphinapterus leucas]). the infected captive cetaceans were either sub ... | 2002 | 12454148 |
| helicobacter pylori mutants defective in ruvc holliday junction resolvase display reduced macrophage survival and spontaneous clearance from the murine gastric mucosa. | homologous recombination contributes to the extraordinary genetic diversity of helicobacter pylori and may be critical for surface antigen expression and adaptation to environmental challenges within the stomach. we generated isogenic, nonpolar h. pylori ruvc mutants to investigate the function of ruvc, a holliday junction endonuclease that resolves recombinant joints into nicked duplex products. inactivation of ruvc reduced the frequency of homologous recombination of h. pylori between 17- and ... | 2003 | 12654822 |
| helicobacter acinonychis: genetic and rodent infection studies of a helicobacter pylori-like gastric pathogen of cheetahs and other big cats. | insights into bacterium-host interactions and genome evolution can emerge from comparisons among related species. here we studied helicobacter acinonychis (formerly h. acinonyx), a species closely related to the human gastric pathogen helicobacter pylori. two groups of strains were identified by randomly amplified polymorphic dna fingerprinting and gene sequencing: one group from six cheetahs in a u.s. zoo and two lions in a european circus, and the other group from a tiger and a lion-tiger hybr ... | 2004 | 14702304 |
| multiplex pcr assay for differentiation of helicobacter felis, h. bizzozeronii, and h. salomonis. | helicobacter felis, helicobacter bizzozeronii, and helicobacter salomonis are frequently found in the gastric mucous membrane of dogs and cats. these large spiral organisms are phylogenetically highly related to each other. their fastidious nature makes it difficult to cultivate them in vitro, hampering traditional identification methods. we describe here a multiplex pcr test based on the trna intergenic spacers and on the urease gene, combined with capillary electrophoresis, that allows discrim ... | 2004 | 15004062 |
| comparison of helicobacter spp. in cheetahs (acinonyx jubatus) with and without gastritis. | chronic gastritis causes significant morbidity and mortality in captive cheetahs but is rare in wild cheetahs despite colonization by abundant spiral bacteria. this research aimed to identify the helicobacter species that were associated with gastritis in captive cheetahs but are apparently commensal in wild cheetahs. helicobacter species were characterized by pcr amplification and sequencing of the 16s rrna, urease, and caga genes and by transmission electron microscopy of frozen or formalin-fi ... | 2005 | 15634976 |
| discordant 16s and 23s rrna gene phylogenies for the genus helicobacter: implications for phylogenetic inference and systematics. | analysis of 16s rrna gene sequences has become the primary method for determining prokaryotic phylogeny. phylogeny is currently the basis for prokaryotic systematics. therefore, the validity of 16s rrna gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. discrepancies between 16s rrna gene analyses and dna-dna hybridization and phenotypic analyses have been noted in the genus helicobacter. to clarify these discrepancies, we sequenced the 23s rrna genes for ... | 2005 | 16109952 |
| gain and loss of multiple genes during the evolution of helicobacter pylori. | sequence diversity and gene content distinguish most isolates of helicobacter pylori. even greater sequence differences differentiate distinct populations of h. pylori from different continents, but it was not clear whether these populations also differ in gene content. to address this question, we tested 56 globally representative strains of h. pylori and four strains of helicobacter acinonychis with whole genome microarrays. of the weighted average of 1,531 genes present in the two sequenced g ... | 2005 | 16217547 |
| who ate whom? adaptive helicobacter genomic changes that accompanied a host jump from early humans to large felines. | helicobacter pylori infection of humans is so old that its population genetic structure reflects that of ancient human migrations. a closely related species, helicobacter acinonychis, is specific for large felines, including cheetahs, lions, and tigers, whereas hosts more closely related to humans harbor more distantly related helicobacter species. this observation suggests a jump between host species. but who ate whom and when did it happen? in order to resolve this question, we determined the ... | 2006 | 16789826 |
| pathogenesis of helicobacter pylori infection. | helicobacter pylori is the first formally recognized bacterial carcinogen and is one of the most successful human pathogens, as over half of the world's population is colonized with this gram-negative bacterium. unless treated, colonization usually persists lifelong. h. pylori infection represents a key factor in the etiology of various gastrointestinal diseases, ranging from chronic active gastritis without clinical symptoms to peptic ulceration, gastric adenocarcinoma, and gastric mucosa-assoc ... | 2006 | 16847081 |
| conjugative transfer of chromosomally encoded antibiotic resistance from helicobacter pylori to campylobacter jejuni. | many strains of helicobacter pylori are naturally competent for transformation and able to transfer chromosomal dna among different isolates using a conjugation-like mechanism. in this study, we sought to determine whether h. pylori can transfer dna into campylobacter jejuni, a closely related species of the campylobacterales group. to monitor the transfer, a chromosomally encoded streptomycin resistance cassette prearranged by a specific mutation in the rpsl gene of h. pylori was used. mating o ... | 2007 | 17135441 |
| conjugative transfer of chromosomally encoded antibiotic resistance from helicobacter pylori to campylobacter jejuni. | many strains of helicobacter pylori are naturally competent for transformation and able to transfer chromosomal dna among different isolates using a conjugation-like mechanism. in this study, we sought to determine whether h. pylori can transfer dna into campylobacter jejuni, a closely related species of the campylobacterales group. to monitor the transfer, a chromosomally encoded streptomycin resistance cassette prearranged by a specific mutation in the rpsl gene of h. pylori was used. mating o ... | 2007 | 17135441 |
| rapid detection, by pcr and reverse hybridization, of mutations in the helicobacter pylori 23s rrna gene, associated with macrolide resistance. | a pcr-based reverse hybridization system (research prototype kit inno-lipa for h. pylori resistance) was developed and evaluated for simultaneous detection of 23s ribosomal dna point mutations, associated with macrolide resistance in helicobacter pylori. fifty-seven h. pylori strains (51 natural, 6 laboratory-derived artificial, 52 resistant, and 5 susceptible strains) were tested by pcr-lipa (detecting mutations a2115-->g, g2141-->a, a2142-->g, a2142-->c, a2143-->g, a2143-->c, and a2143-->t), d ... | 1999 | 10390244 |
| plasmids and rickettsial evolution: insight from rickettsia felis. | the genome sequence of rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities that have confounded the categorization of r. felis as either typhus group (tg) or spotted fever group (sfg) rickettsiae. most intriguing was the first report from rickettsiae of a conjugative plasmid (prf) that contains 68 putative open reading frames, several of which are predicted to enc ... | 2007 | 17342200 |
| development and application of a novel peptide nucleic acid probe for the specific detection of helicobacter pylori in gastric biopsy specimens. | in this work, a fluorescence in situ hybridization (fish) method for the rapid detection of helicobacter pylori using a novel peptide nucleic acid (pna) probe is reported. laboratory testing with several different bacterial species, including other helicobacter spp., has shown that this probe is highly specific for h. pylori strains. in addition, the pna fish method has been successfully adapted for detection of the pathogen in paraffin-embedded gastric biopsy specimens. | 2007 | 17609326 |
| helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic sel1-like genes. | geographic partitioning is postulated to foster divergence of helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. h. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. sequenced h. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that ... | 2007 | 17696605 |
| sharcgs, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. | the latest revolution in the dna sequencing field has been brought about by the development of automated sequencers that are capable of generating giga base pair data sets quickly and at low cost. applications of such technologies seem to be limited to resequencing and transcript discovery, due to the shortness of the generated reads. in order to extend the fields of application to de novo sequencing, we developed the sharcgs algorithm to assemble short-read (25-40-mer) data with high accuracy a ... | 2007 | 17908823 |
| the complete genome sequence and analysis of the epsilonproteobacterium arcobacter butzleri. | arcobacter butzleri is a member of the epsilon subdivision of the proteobacteria and a close taxonomic relative of established pathogens, such as campylobacter jejuni and helicobacter pylori. here we present the complete genome sequence of the human clinical isolate, a. butzleri strain rm4018. | 2007 | 18159241 |
| the human gastric pathogen helicobacter pylori has a potential acetone carboxylase that enhances its ability to colonize mice. | helicobacter pylori colonizes the human stomach and is the etiological agent of peptic ulcer disease. all three h. pylori strains that have been sequenced to date contain a potential operon whose products share homology with the subunits of acetone carboxylase (encoded by acxabc) from xanthobacter autotrophicus strain py2 and rhodobacter capsulatus strain b10. acetone carboxylase catalyzes the conversion of acetone to acetoacetate. genes upstream of the putative acxabc operon encode enzymes that ... | 2008 | 18215283 |
| de novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. | novel high-throughput dna sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. however, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. this study focuses on the illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. we ... | 2008 | 18332092 |
| evaluation of 16s rrna gene-based pcr assays for genus-level identification of helicobacter species. | the inclusivity, exclusivity, and detection limit of six 16s rrna gene-based helicobacter genus-specific pcr assays were examined. five out of six assays were 100% inclusive, but the tests varied considerably in their exclusivity (9.1 to 95.5%). the clinical detection limit varied between 10(3) and 1 viable bacterial cell per reaction mixture. | 2008 | 18337392 |
| substantial biases in ultra-short read data sets from high-throughput dna sequencing. | novel sequencing technologies permit the rapid production of large sequence data sets. these technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. we generated and analyzed two illumina 1g ultra-short read data sets, i.e. 2.8 million 27mer reads from a beta vulgaris genomic clone and 12.3 million 36mers from the helicobacter acinonychis genome. we found that error rates range from 0.3% at the beginn ... | 2008 | 18660515 |
| role of the helicobacter hepaticus flagellar sigma factor flia in gene regulation and murine colonization. | the enterohepatic helicobacter species helicobacter hepaticus colonizes the murine intestinal and hepatobiliary tract and is associated with chronic intestinal inflammation, gall stone formation, hepatitis, and hepatocellular carcinoma. thus far, the role of h. hepaticus motility and flagella in intestinal colonization is unknown. in other, closely related bacteria, late flagellar genes are mainly regulated by the sigma factor flia (sigma(28)). we investigated the function of the h. hepaticus fl ... | 2008 | 18689480 |
| the helicobacter pylori hpyaxii restriction-modification system limits exogenous dna uptake by targeting gtac sites but shows asymmetric conservation of the dna methyltransferase and restriction endonuclease components. | the naturally competent organism helicobacter pylori encodes a large number of restriction-modification (r-m) systems that consist of a restriction endonuclease and a dna methyltransferase. r-m systems are not only believed to limit dna exchange among bacteria but may also have other cellular functions. we report a previously uncharacterized h. pylori type ii r-m system, m.hpyaxii/r.hpyaxii. we show that this system targets gtac sites, which are rare in the h. pylori chromosome but numerous in r ... | 2008 | 18978016 |
| de novo assembly using low-coverage short read sequence data from the rice pathogen pseudomonas syringae pv. oryzae. | we developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. by combining data generated from 454 life sciences (roche) and illumina (formerly known as solexa sequencing) sequencing platforms, we reliably assembled genomes into large scaffolds at a fraction of the traditional cost and without use of a reference sequence. we applied this method to two isolates of the phytopathogenic bacteria pseudomonas syringae. seque ... | 2009 | 19015323 |
| structural analysis of the dna-binding domain of the helicobacter pylori response regulator arsr. | the helicobacter pylori arss-arsr two-component signal transduction system, comprised of a sensor histidine kinase (arss) and a response regulator (arsr), allows the bacteria to regulate gene expression in response to acidic ph. we expressed and purified the full-length arsr protein and the dna-binding domain of arsr (arsr-dbd), and we analyzed the tertiary structure of the arsr-dbd using solution nuclear magnetic resonance (nmr) methods. both the full-length arsr and the arsr-dbd behaved as mon ... | 2009 | 19117956 |
| failure to detect helicobacter pylori dna in drinking and environmental water in dhaka, bangladesh, using highly sensitive real-time pcr assays. | the main transmission pathway of helicobacter pylori has not been determined, but several reports have described detection of h. pylori dna in drinking and environmental water, suggesting that h. pylori may be waterborne. to address this possibility, we developed, tested, and optimized two complementary h. pylori-specific real-time pcr assays for quantification of h. pylori dna in water. the minimum detection level of the assays including collection procedures and dna extraction was shown to be ... | 2009 | 19304824 |
| pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus campylobacter. | an open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. the genus campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for eight species. we estimate the campylobacter core genome at 647 genes, with 92.5% of the nonrecombinant core gen ... | 2009 | 19304960 |
| a commensal helicobacter sp. of the rodent intestinal flora activates tlr2 and nod1 responses in epithelial cells. | helicobacter spp. represent a proportionately small but significant component of the normal intestinal microflora of animal hosts. several of these intestinal helicobacter spp. are known to induce colitis in mouse models, yet the mechanisms by which these bacteria induce intestinal inflammation are poorly understood. to address this question, we performed in vitro co-culture experiments with mouse and human epithelial cell lines stimulated with a selection of helicobacter spp., including known p ... | 2009 | 19401779 |
| detection of atypical cultivable canine gastric helicobacter strain and its biochemical and morphological characters in naturally infected dogs. | helicobacter-like organisms are frequently found in canine stomachs, but the relationship between such organisms and gastric pathology has not been established. however, some such organisms have zoonotic importance. the aims of this study were to evaluate the morphological and biochemical characteristics of cultivable canine gastric helicobacter-like organisms (ghlos) in pets and stray dogs and their prevalence in these two groups of dogs. specimens were taken by gastroscopy from 30 clinically h ... | 2010 | 19486497 |
| prediction of type iii secretion signals in genomes of gram-negative bacteria. | pathogenic bacteria infecting both animals as well as plants use various mechanisms to transport virulence factors across their cell membranes and channel these proteins into the infected host cell. the type iii secretion system represents such a mechanism. proteins transported via this pathway ("effector proteins") have to be distinguished from all other proteins that are not exported from the bacterial cell. although a special targeting signal at the n-terminal end of effector proteins has bee ... | 2009 | 19526054 |
| impact of chromatin structures on dna processing for genomic analyses. | chromatin has an impact on recombination, repair, replication, and evolution of dna. here we report that chromatin structure also affects laboratory dna manipulation in ways that distort the results of chromatin immunoprecipitation (chip) experiments. we initially discovered this effect at the saccharomyces cerevisiae hmr locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. using input samples from chip-seq studies, we detected a similar bias through ... | 2009 | 19693276 |
| the dif/xer recombination systems in proteobacteria. | in e. coli, 10 to 15% of growing bacteria produce dimeric chromosomes during dna replication. these dimers are resolved by xerc and xerd, two tyrosine recombinases that target the 28-nucleotide motif (dif) associated with the chromosome's replication terminus. in streptococci and lactococci, an alternative system is composed of a unique, xer-like recombinase (xers) genetically linked to a dif-like motif (dif(sl)) located at the replication terminus. preliminary observations have suggested that t ... | 2009 | 19727445 |
| recurrent bacteremia caused by a "flexispira"-like organism in a patient with x-linked (bruton's) agammaglobulinemia. | helicobacter spp., except for helicobacter cinaedi, have only rarely been reported in cases of septicemia. a patient with x-linked (bruton's) agammaglobulinemia was found to have persistent sepsis with a helicobacter-like organism despite multiple courses of antibiotics. his periods of sepsis were associated with leg swelling thought to be consistent with cellulitis. the organism was fastidious and required a microaerophilic environment containing h(2) for growth. optimal growth was observed at ... | 1999 | 10405381 |
| evaluation of a new test, genotype helicodr, for molecular detection of antibiotic resistance in helicobacter pylori. | the eradication rate of helicobacter pylori by standard therapy is decreasing due to antibiotic resistance, mainly to clarithromycin. our aim was to provide a new molecular test to guide the treatment of new and relapsed cases. we first studied 126 h. pylori strains for phenotypic (mic) and genotypic resistance to clarithromycin (rrl mutation) and levofloxacin (gyra mutation) and then developed a dna strip genotyping test on the basis of the correlation results and literature data. clinical stra ... | 2009 | 19759218 |
| functional analysis of the helicobacter pylori flagellar switch proteins. | helicobacter pylori uses flagellum-mediated chemotaxis to promote infection. bacterial flagella change rotational direction by changing the state of the flagellar motor via a subcomplex referred to as the switch. intriguingly, the h. pylori genome encodes four switch complex proteins, flim, flin, fliy, and flig, instead of the more typical three of escherichia coli or bacillus subtilis. our goal was to examine whether and how all four switch proteins participate in flagellation. previous work de ... | 2009 | 19767432 |
| an uncommon helicobacter isolate from blood: evidence of a group of helicobacter spp. pathogenic in aids patients. | an unusual helicobacter sp. was isolated from the blood of a human immunodeficiency virus (hiv)-infected patient. this organism had spiral morphology, with single amphitrichous flagella, and was negative for hippurate hydrolysis, production of urease, and reduction of nitrate. 16s rrna gene sequence analysis verified that the isolate was a species of helicobacter, most closely related to an undescribed helicobacter-like isolate from vancouver, british columbia, canada, and to helicobacter westme ... | 1999 | 10405434 |
| examination of genome homogeneity in prokaryotes using genomic signatures. | dna word frequencies, normalized for genomic at content, are remarkably stable within prokaryotic genomes and are therefore said to reflect a "genomic signature." the genomic signatures can be used to phylogenetically classify organisms from arbitrary sampled dna. genomic signatures can also be used to search for horizontally transferred dna or dna regions subjected to special selection forces. thus, the stability of the genomic signature can be used as a measure of genomic homogeneity. the fact ... | 2009 | 19956556 |
| the helicobacter pylori groes cochaperonin hspa functions as a specialized nickel chaperone and sequestration protein through its unique c-terminal extension. | the transition metal nickel plays a central role in the human gastric pathogen helicobacter pylori because it is required for two enzymes indispensable for colonization, the nickel metalloenzyme urease and [nife] hydrogenase. to sustain nickel availability for these metalloenzymes while providing protection from the metal's harmful effects, h. pylori is equipped with several specific nickel-binding proteins. among these, h. pylori possesses a particular chaperone, hspa, that is a homolog of the ... | 2010 | 20061471 |
| in helicobacter pylori, luxs is a key enzyme in cysteine provision through a reverse transsulfuration pathway. | in many bacteria, luxs functions as a quorum-sensing molecule synthase. however, it also has a second, more central metabolic function in the activated methyl cycle (amc), which generates the s-adenosylmethionine required by methyltransferases and recycles the product via methionine. helicobacter pylori lacks an enzyme catalyzing homocysteine-to-methionine conversion, rendering the amc incomplete and thus making any metabolic role of h. pylori luxs (luxs(hp)) unclear. interestingly, luxs(hp) is ... | 2010 | 20061483 |
| expression and display of urea of helicobacter acinonychis on the surface of bacillus subtilis spores. | the bacterial endospore (spore) has recently been proposed as a new surface display system. antigens and enzymes have been successfully exposed on the surface layers of the bacillus subtilis spore, but only in a few cases the efficiency of expression and the effective surface display and have been determined. we used this heterologous expression system to produce the a subunit of the urease of the animal pathogen helicobater acinonychis. ureases are multi-subunit enzymes with a central role in t ... | 2010 | 20082702 |
| simple sequence repeats in helicobacter canadensis and their role in phase variable expression and c-terminal sequence switching. | helicobacter canadensis is an emerging human pathogen and zoonotic agent. the genome of h. canadensis was sequenced previously and determined to contain 29 annotated coding regions associated with homopolymeric tracts. | 2010 | 20105305 |
| geographic distribution of methyltransferases of helicobacter pylori: evidence of human host population isolation and migration. | helicobacter pylori colonizes the human stomach and is associated with gastritis, peptic ulcer, and gastric cancer. this ubiquitous association between h. pylori and humans is thought to be present since the origin of modern humans. the h. pylori genome encodes for an exceptional number of restriction and modifications (r-m) systems. to evaluate if r-m systems are an adequate tool to determine the geographic distribution of h. pylori strains, we typed 221 strains from africa, america, asia, and ... | 2009 | 19737407 |
| comparative genomics and proteomics of helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen. | helicobacter mustelae causes gastritis, ulcers and gastric cancer in ferrets and other mustelids. h. mustelae remains the only helicobacter other than h. pylori that causes gastric ulceration and cancer in its natural host. to improve understanding of h. mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the h. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome. | 2010 | 20219135 |
| coupled amino acid deamidase-transport systems essential for helicobacter pylori colonization. | in addition to their classical roles as carbon or nitrogen sources, amino acids can be used for bacterial virulence, colonization, or stress resistance. we found that original deamidase-transport systems impact colonization by helicobacter pylori, a human pathogen associated with gastric pathologies, including adenocarcinoma. we demonstrated that l-asparaginase (hp-ansb) and gamma-glutamyltranspeptidase (hp-gammagt) are highly active periplasmic deamidases in h. pylori, producing ammonia and asp ... | 2010 | 20368342 |
| whole genome assembly of a natto production strain bacillus subtilis natto from very short read data. | bacillus subtilis natto is closely related to the laboratory standard strain b. subtilis marburg 168, and functions as a starter for the production of the traditional japanese food "natto" made from soybeans. although re-sequencing whole genomes of several laboratory domesticated b. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, b. subtilis natto, from very short read data is more challe ... | 2010 | 20398357 |
| identification of helicobacter spp. in bile and gallbladder tissue of patients with symptomatic gallbladder disease. | this experimental study was designed to determine if helicobacter spp. contribute to benign gallbladder disease using polymerase chain reaction (pcr) methods. | 2010 | 20495657 |
| sequencing, annotation, and comparative genome analysis of the gerbil-adapted helicobacter pylori strain b8. | the mongolian gerbils are a good model to mimic the helicobacter pylori-associated pathogenesis of the human stomach. in the current study the gerbil-adapted strain b8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain b128. | 2010 | 20507619 |
| from array-based hybridization of helicobacter pylori isolates to the complete genome sequence of an isolate associated with malt lymphoma. | helicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. to determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach. | 2010 | 20537153 |
| an abc transporter and a tonb ortholog contribute to helicobacter mustelae nickel and cobalt acquisition. | the genomes of helicobacter species colonizing the mammalian gastric mucosa (like helicobacter pylori) contain a large number of genes annotated as iron acquisition genes but only few nickel acquisition genes, which contrasts with the central position of nickel in the urease-mediated acid resistance of these gastric pathogens. in this study we have investigated the predicted iron and nickel acquisition systems of the ferret pathogen helicobacter mustelae. the expression of the outer membrane pro ... | 2010 | 20643857 |
| mutagenesis of conserved amino acids of helicobacter pylori fur reveals residues important for function. | the ferric uptake regulator (fur) of the medically important pathogen helicobacter pylori is unique in that it has been shown to function as a repressor both in the presence of an fe2+ cofactor and in its apo (non-fe2+-bound) form. however, virtually nothing is known concerning the amino acid residues that are important for fur functioning. therefore, mutations in six conserved amino acid residues of h. pylori fur were constructed and analyzed for their impact on both iron-bound and apo repressi ... | 2010 | 20644138 |
| molecular phylogeny and functional genomics of beta-galactoside alpha2,6-sialyltransferases that explain ubiquitous expression of st6gal1 gene in amniotes. | sialyltransferases are key enzymes in the biosynthesis of sialoglycoconjugates that catalyze the transfer of sialic residue from its activated form to an oligosaccharidic acceptor. β-galactoside α2,6-sialyltransferases st6gal i and st6gal ii are the two unique members of the st6gal family described in higher vertebrates. the availability of genome sequences enabled the identification of more distantly related invertebrates' st6gal gene sequences and allowed us to propose a scenario of their evol ... | 2010 | 20855889 |
| molecular evolution of the helicobacter pylori vacuolating toxin gene vaca. | helicobacter pylori is a genetically diverse organism that is adapted for colonization of the human stomach. all strains contain a gene encoding a secreted, pore-forming toxin known as vaca. genetic variation at this locus could be under strong selection as h. pylori adapts to the host immune response, colonizes new human hosts, or inhabits different host environments. here, we analyze the molecular evolution of vaca. phylogenetic reconstructions indicate the subdivision of vaca sequences into t ... | 2010 | 20870762 |
| nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomics. | the ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. here we evaluate the microbial biota in healthy mule deer (odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cdna libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node rna enriched for polyadenylated rna and sequenced using ... | 2010 | 20976145 |
| quake: quality-aware detection and correction of sequencing errors. | we introduce quake, a program to detect and correct errors in dna sequencing reads. using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, quake achieves the highest accuracy on realistically simulated reads. we further demonstrate substantial improvements in de novo assembly and snp detection after using quake. quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from ... | 2010 | 21114842 |
| vitamin b(6) is required for full motility and virulence in helicobacter pylori. | despite recent advances in our understanding of how helicobacter pylori causes disease, the factors that allow this pathogen to persist in the stomach have not yet been fully characterized. to identify new virulence factors in h. pylori, we generated low-infectivity variants of a mouse-colonizing h. pylori strain using the classical technique of in vitro attenuation. the resulting variants and their highly infectious progenitor bacteria were then analyzed by global gene expression profiling. the ... | 2010 | 21151756 |
| horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. | gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. while there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. we analyzed closely related prokaryote strains or species with small genomes (helicobacter, neisseria, stre ... | 2011 | 21298028 |
| change is good: variations in common biological mechanisms in the epsilonproteobacterial genera campylobacter and helicobacter. | microbial evolution and subsequent species diversification enable bacterial organisms to perform common biological processes by a variety of means. the epsilonproteobacteria are a diverse class of prokaryotes that thrive in diverse habitats. many of these environmental niches are labeled as extreme, whereas other niches include various sites within human, animal, and insect hosts. some epsilonproteobacteria, such as campylobacter jejuni and helicobacter pylori, are common pathogens of humans tha ... | 2011 | 21372321 |
| new implications on genomic adaptation derived from the helicobacter pylori genome comparison. | helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. it evolved with its particular characteristics for biological adaptation. because several h. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium. | 2011 | 21387011 |
| a study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (chargaff's second parity rule). | chargaff's rule of intra-strand parity (isp) between complementary mono/oligonucleotides in chromosomes is well established in the scientific literature. although a large numbers of papers have been published citing works and discussions on isp in the genomic era, scientists are yet to find all the factors responsible for such a universal phenomenon in the chromosomes. in the present work, we have tried to address the issue from a new perspective, which is a parallel feature to isp. the composit ... | 2009 | 19861381 |
| comparing de novo genome assembly: the long and short of it. | recent advances in dna sequencing technology and their focal role in genome wide association studies (gwas) have rekindled a growing interest in the whole-genome sequence assembly (wgsa) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. and yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. no commonly accepted and standardized method for comparison exists yet. even worse ... | 2011 | 21559467 |
| iron-containing urease in a pathogenic bacterium. | helicobacter mustelae, a gastric pathogen of ferrets, synthesizes a distinct iron-dependent urease in addition to its archetypical nickel-containing enzyme. the iron-urease is oxygen-labile, with the inactive protein exhibiting a methemerythrin-like electronic spectrum. significantly, incubation of the oxidized protein with dithionite under anaerobic conditions leads to restoration of activity and bleaching of the spectrum. structural analysis of the oxidized species reveals a dinuclear iron met ... | 2011 | 21788478 |
| 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 |
| 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 |
| Comparative Genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans. | ABSTRACT: | 2011 | 22039924 |
| helicobacter pylori relies primarily on the purine salvage pathway for purine nucleotide biosynthesis. | helicobacter pylori is a chronic colonizer of the gastric epithelium and plays a major role in the development of gastritis, peptic ulcer disease, and gastric cancer. in its co-evolution with humans, a streamlining of the h. pylori genome has resulted in a significant reduction in metabolic pathways, one being purine nucleotide biosynthesis. bioinformatic analysis revealed that h. pylori lacks the enzymatic machinery for de novo production of inosine monophosphate (imp), the first purine nucleot ... | 2011 | 22194455 |
| 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 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| xer recombinase and genome integrity in helicobacter pylori, a pathogen without topoisomerase iv. | in the model organism e. coli, recombination mediated by the related xerc and xerd recombinases complexed with the ftsk translocase at specialized dif sites, resolves dimeric chromosomes into free monomers to allow efficient chromosome segregation at cell division. computational genome analysis of helicobacter pylori, a slow growing gastric pathogen, identified just one chromosomal xer gene (xerh) and its cognate dif site (difh). here we show that recombination between directly repeated difh sit ... | 2012 | 22511919 |
| transmission of the pabi family of restriction dna glycosylase genes: mobility and long-term inheritance. | r.pabi is an exceptional restriction enzyme that functions as a dna glycosylase. the enzyme excises an unmethylated base from its recognition sequence to generate apurinic/apyrimidinic (ap) sites, and also displays ap lyase activity, cleaving the dna backbone at the ap site to generate the 3'-phospho alpha, beta-unsaturated aldehyde end in addition to the 5'-phosphate end. the resulting ends are difficult to religate with dna ligase. the enzyme was originally isolated in pyrococcus, a hypertherm ... | 2015 | 26481899 |
| 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 |
| evidence for type iii restriction and modification systems in mycoplasma pulmonis. | mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type iii restriction and modification (r-m) enzymes. transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of r-m activity. genomic data indicate that the cassette was acquired by horizontal gene transfer and possibly located on a mobile element. | 2007 | 17209015 |
| 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 |