Publications

an analysis of the use of genomic dna as a universal reference in two channel dna microarrays.	dna microarray is an invaluable tool for gene expression explorations. in the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. to compare a large number of samples, the 'reference design' is widely used, in which all rna samples are hybridized to a common reference. genomic dna is an attractive candidate for use as a universal reference, especially for bacterial systems with a low percentage of non-coding sequences. ...	2005	15877823
crystallization and preliminary x-ray crystallographic analysis of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from mycobacterium tuberculosis.	the enzymes of the shikimate pathway are attractive targets for new-generation antimicrobial agents. the first step of this pathway is catalysed by 3-deoxy-d-arabino-heptulosonate-7-phosphate (dah7p) synthase and involves the condensation of phosphoenolpyruvate (pep) and erythrose 4-phosphate (e4p) to form dah7p. dah7p synthases have been classified into two apparently evolutionarily unrelated types and whereas structural data have been obtained for the type i dah7p synthases, no structural info ...	2005	16511053
a double mutation of escherichia coli2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate.	the essential enzyme 2c-methyl-d-erythritol-2,4-cyclodiphosphate (mecp) synthase, found in most eubacteria and the apicomplexan parasites, participates in isoprenoid-precursor biosynthesis and is a validated target for the development of broad-spectrum antimicrobial drugs. the structure and mechanism of the enzyme have been elucidated and the recent exciting finding that the enzyme actually binds diphosphate-containing isoprenoids at the interface formed by the three subunits that constitute the ...	2005	16511114
antibody polyspecificity and neutralization of hiv-1: a hypothesis.	hiv-1 has evolved many ways to evade protective host immune responses, thus creating a number of problems for hiv vaccine developers. in particular, durable, broadly specific neutralizing antibodies to hiv-1 have proved difficult to induce with current hiv-1 vaccine candidates. the recent observation that some broadly neutralizing anti-hiv-1 envelope monoclonal antibodies have polyspecific reactivities to host antigens have raised the hypothesis that one reason antibodies against some of the con ...	2005	16720975
lymphocytic colitis: a clue to bacterial etiology.	to find out the role of bacteria as a possible etiological factor in lymphocytic colitis.	2005	16437626
detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays.	to detect the common intestinal pathogenic bacteria quickly and accurately.	2005	16437687
epidemiology of campylobacter jejuni and campylobacter coli infections in the zenica--doboj canton, bosnia and herzegovina--a laboratory based surveillance in the 1999-2001 period.	previous studies in the zenica--doboj canton, bosnia and herzegovina, indicated some different epidemiological features of campylobacter infections and high degree of antimicrobial resistance. therefore, it was important to investigate epidemiology of campylobacter jejuni and campylobacter coli infections by demographic features and antimicrobial resistance in the 1999-2001 period. a total number of 40 (75.5%) c. jejuni and 13 (24.5%) c. coli non-repeated clinical isolates were analyzed. more th ...	2005	16417178
screening of feral pigeon (colomba livia), mallard (anas platyrhynchos) and graylag goose (anser anser) populations for campylobacter spp., salmonella spp., avian influenza virus and avian paramyxovirus.	a total of 119 fresh faecal samples were collected from graylag geese migrating northwards in april. also, cloacal swabs were taken from 100 carcasses of graylag geese shot during the hunting season in august. in addition, samples were taken from 200 feral pigeons and five mallards. the cultivation of bacteria detected campylobacter jejuni jejuni in six of the pigeons, and in one of the mallards. salmonella diarizona 14: k: z53 was detected in one graylag goose, while all pigeons and mallards we ...	2005	16398331
backbone 1h, 15n, and 13c resonance assignments and secondary-structure of conserved hypothetical protein hp0894 from helicobacter pylori.	hp0894 (swissprot/trembl id o25554) is an 88-residue conserved hypothetical protein from helicobacter pylori strain 26695 with a calculated pi of 8.5 and a molecular weight of 10.38 kda. proteins with sequence similarity to hp0894 exist in vibrio choierae, enterococcus faecalis, campylobacter jejuni, streptococcus pneumoniae, haemophilus influenzae, escherichia coli o157, etc. here we report the sequence-specific backbone resonance assignments of hp0894. about 97.5% (418/429) of the hn, n, co, c ...	2005	16404162
recovery of campylobacter jejuni in feces and semen of caged broiler breeder roosters following three routes of inoculation.	we previously reported the recovery of campylobacter (naturally colonized) from the ductus deferens of 5 of 101 broiler breeder roosters, and four of those five positive roosters had previously produced campylobacter-positive semen samples. those results prompted further evaluation to determine if inoculation route influenced the prevalence or level of campylobacter contamination of semen, the digestive tract, or reproductive organs. individually caged roosters, confirmed to be feces and semen n ...	2005	16405002
prevalence of four virulence genes in campylobacter jejuni determined by pcr and sequence analysis.	the presence of four virulence genes (racr, wlan, cgtb, virb11) in 356 campylobacter jejuni strains isolated from confirmed clinical cases was examined by pcr and sequence analysis. the investigated genes were chosen on the basis of their variation in prevalence.	2005	16392901
immunopathological investigations on bovine digital epidermitis.	paraffin-embedded fragments of bovine digital skin lesions were sectioned and stained with warthin-starry, haematoxylin and eosin, grocott's methenamine silver and immunohistochemical techniques. microorganisms observed in the silver-stained sections were classified into four major morphological groups. spirochaetes were the most prevalent organisms, but bacillary and coccoid elements were also present in most sections. immunohistochemical probing demonstrated that approximately 80 per cent, 46 ...	2005	16377788
luxs-dependent gene regulation in escherichia coli k-12 revealed by genomic expression profiling.	the bacterial quorum-sensing autoinducer 2 (ai-2) has received intense interest because the gene for its synthase, luxs, is common among a large number of bacterial species. we have identified luxs-controlled genes in escherichia coli under two different growth conditions using dna microarrays. twenty-three genes were affected by luxs deletion in the presence of glucose, and 63 genes were influenced by luxs deletion in the absence of glucose. minimal overlap among these gene sets suggests the ro ...	2005	16321939
campylobacter in food animals and humans in northern thailand.	cross-sectional, longitudinal, and case-control studies were conducted to describe the epidemiology of campylobacter in chickens, swine, dairy cows, farm workers, nonfarm residents, and children with diarrhea. samples were collected in chiang mai and lamphung provinces of northern thailand from 2000 through 2003. a total of 2,360 samples were processed. results from the cross-sectional study indicated that the prevalences of campylobacter in chickens at the farm, slaughterhouse, and market were ...	2005	16355821
evaluation of detection methods for screening meat and poultry products for the presence of foodborne pathogens.	rapid and molecular technologies such as enzyme-linked immunosorbent assay (elisa), pcr, and lateral flow immunoprecipitation can reduce the time and labor involved in screening food products for the presence of pathogens. these technologies were compared with conventional culture methodology for the detection of salmonella, campylobacter, listeria, and escherichia coli o157:h7 inoculated in raw and processed meat and poultry products. recommended protocols were modified so that the same enrichm ...	2005	16355836
chemoenzymatic synthesis of glycopeptides with pglb, a bacterial oligosaccharyl transferase from campylobacter jejuni.	the gram-negative bacterium campylobacter jejuni has a general n-linked glycosylation pathway encoded by the pgl gene cluster. one of the proteins in this cluster, pgib, is thought to be the oligosaccharyl transferase due to its significant homology to stt3p, a subunit of the yeast oligosaccharyl transferase complex. pgib has been shown to be involved in catalyzing the transfer of an undecaprenyl-linked heptasaccharide to the asparagine side chain of proteins at the asn-x-ser/thr motif. using a ...	2005	16356848
characterization of a cmeabc operon in a quinolone-resistant campylobacter coli isolate of irish origin.	in this study, a tripartite-operon-encoding efflux system together with its regulatory gene was characterized in an irish campylobacter coli isolate cit-382 showing high-level resistance to nalidixic acid and ciprofloxacin. sequence comparisons revealed significant homology between c. coli and the cmeabc operon of campylobacter jejuni. conservation of functional sequence domains and motifs were noted among c. coli and similar operons in unrelated organisms. a transcriptional regulatory gene cmer ...	2005	16359189
emergence of fluoroquinolone resistance in campylobacter jejuni in chickens exposed to enrofloxacin treatment at the inherent dosage licensed in japan.	the objective of the present study was to determine whether selection of fluoroquinolone resistance could be easily induced in campylobacter jejuni-colonized chickens by treatment with enrofloxacin of representative fluoroquinolones at the inherent dosage licensed in japan (50 ppm in drinking water for 3 days). in the case of isolates from chickens of study 1, an increase in the population of susceptible isolates appeared after the cessation of treatment and maintained throughout the experiments ...	2005	16364022
is campylobacter involved in antibiotic associated diarrhoea?	campylobacter jejuni is an important cause of acute bacterial diarrhoea. in developing countries like india, children gain immunity early during infancy. however, the incidence is higher in non-immune hosts. antibiotic use destabilizes the gut flora and can inhibit the local immune responses, thereby compromising resistance to a variety of infections. it is not yet known whether antibiotic intake can also precipitate c. jejuni enteritis as the infectious dose is low and attack rates are high. we ...	2005	16366118
[symptoms of food-borne diseases and gastroenteritis in kyushu, japan].	in this study we analyzed the symptoms of gastroenteritis or food-borne disease caused by the 10 most prevalent pathogens: norovirus, salmonella, vibrio parahaemolyticus, campylobacter jejuni, clostridium perfringens, shiga toxin-producing escherichia coli (stec), enterotoxigenic e. coli (etec), shigella sonnei/flexneri (shigella), staphylococcus aureus, and emetic-type bacillus cereus. the symptoms diarrhea, vomiting, fever, abdominal pain, and headache, and the incubation period in 646 cases i ...	2005	16366357
genomic comparison of plant pathogenic and nonpathogenic serratia marcescens strains by suppressive subtractive hybridization.	cucurbit yellow vine disease (cyvd) is caused by disease-associated serratia marcescens strains that have phenotypes significantly different from those of nonphytopathogenic strains. to identify the genetic differences responsible for pathogenicity-related phenotypes, we used a suppressive subtractive hybridization (ssh) strategy. s. marcescens strain z01-a, isolated from cyvd-affected zucchini, was used as the tester, whereas rice endophytic s. marcescens strain r02-a (irbg 502) was used as the ...	2005	16332744
signature-tagged transposon mutagenesis studies demonstrate the dynamic nature of cecal colonization of 2-week-old chickens by campylobacter jejuni.	we have constructed plasmids to be used for in vitro signature-tagged mutagenesis (stm) of campylobacter jejuni and used these to generate stm libraries in three different strains. statistical analysis of the transposon insertion sites in the c. jejuni nctc 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon int ...	2005	16332783
comparison of two target genes for detection and genotyping of giardia lamblia in human feces by pcr and pcr-restriction fragment length polymorphism.	a pcr assay targeting the tpi gene was developed to detect and to genotype giardia lamblia in human feces. our assay was specific and discriminated between g. lamblia assemblages a and b. g. lamblia cysts isolated from human feces were also analyzed with two previously described pcr-restriction fragment length polymorphism (rflp) assays, which are based on the detection of tpi or gdh genes. these rflp analyses distinguished groups i and ii within assemblage a or groups iii and iv within assembla ...	2005	16333079
noroviruses as a cause of traveler's diarrhea among students from the united states visiting mexico.	stool specimens from 124 international travelers with acute diarrhea were tested for the presence of enteropathogens. noroviruses (novs) were the second most commonly identified enteric pathogen in diarrheal stool samples (21/124, 17%), exceeded only by enterotoxigenic escherichia coli (50/106, 47%). this study indicates that nov is an underappreciated cause of traveler's diarrhea.	2005	16333110
broth microdilution susceptibility testing of campylobacter jejuni and the determination of quality control ranges for fourteen antimicrobial agents.	quality control ranges were developed for broth microdilution testing of campylobacter jejuni atcc 33560 against 14 antimicrobials. cation-adjusted mueller-hinton broth containing 2.5% laked horse blood was the preferred medium, with incubation in a microaerobic atmosphere of 10% co(2), 5% o(2), and 85% n(2) at 36 degrees c for 48 h or 42 degrees c for 24 h.	2005	16333113
isolation of dna for pcr assays from noncultivable campylobacter jejuni isolates.	isolates of campylobacter jejuni shipped internationally often arrive in a noncultivable state. we describe a pcr-based methodology whereby phylogenetic information can be recovered from noncultivable c. jejuni stored in wang's transport medium. the robustness of this methodology was initially tested using 5 previously characterized strains of c. jejuni isolated from various sources associated with poultry production. these isolates were stored in wang's transport medium before being subjected t ...	2005	16335120
alternative sigma factors and their roles in bacterial virulence.	sigma factors provide promoter recognition specificity to rna polymerase holoenzyme, contribute to dna strand separation, and then dissociate from the core enzyme following transcription initiation. as the regulon of a single sigma factor can be composed of hundreds of genes, sigma factors can provide effective mechanisms for simultaneously regulating expression of large numbers of prokaryotic genes. one newly emerging field is identification of the specific roles of alternative sigma factors in ...	2005	16339734
a truncated haemoglobin implicated in oxygen metabolism by the microaerophilic food-borne pathogen campylobacter jejuni.	of the three groups of haemoglobins identified in micro-organisms (single-domain globins, flavohaemoglobins and truncated globins), the last group is the least well understood. the function of the truncated haemoglobin (ctb) encoded by cj0465c in the microaerophilic food-borne bacterial pathogen campylobacter jejuni was investigated by constructing a ctb mutant and characterizing its phenotype. the effects of the ctb mutation on the kinetics of terminal oxidase function in c. jejuni were investi ...	2005	16339953
[pcr-restriction fragment length polymorphism assay (pcr-rflp) as an useful tool for detection of mutation in gyra gene at 86-thr position associated with fluoroquinolone resistance in campylobacter jejuni].	the aim of this study was to investigate the mutations in gyra gene at thr-86 position in fluoroquinolone resistant c. jejuni clinical isolates (2003-2005). the change of thr to ile at 86 position is associated with high-level resistance to fluoroquinolone in c. jejuni. thirty five (58%) of 65 c. jejuni strains were found to be resistant to ciprofloxacin using e-test method. pcr-rflp technique with the rsai enzyme was used for the identification of mutation in gyra gene. the primers spanning a p ...	2005	16494206
salmonella and campylobacter spp. in northern elephant seals, california.	campylobacter and salmonella spp. prevalence and antimicrobial drug sensitivity were determined in northern elephant seals that had not entered the water and seals that were stranded on the california coast. stranded seals had a higher prevalence of pathogenic bacteria, possibly from terrestrial sources, which were more likely to be resistant.	2005	16485493
genomic adaptation to acidic environment: evidence from helicobacter pylori.	the origin of new functions is fundamental in understanding evolution, and three processes known as adaptation, preadaptation, and exaptation have been proposed as possible evolutionary pathways leading to the origin of new functions. here we examine the origin of an acid resistance mechanism in the mammalian gastric pathogen helicobacter pylori, with reference to these three evolutionary pathways. the mechanism involved is that h. pylori, when exposed to the acidic environment in mammalian stom ...	2005	16475092
efficacy of electrolyzed water in the prevention and removal of fecal material attachment and its microbicidal effectiveness during simulated industrial poultry processing.	this study was undertaken to investigate the efficacy of alkaline and acidic electrolyzed (eo) water in preventing and removing fecal contaminants and killing campylobacter jejuni on poultry carcasses under simulated industrial processing conditions. new york dressed and defeathered chicken carcasses spot-inoculated with cecal material or c. jejuni were subjected to spraying treatment with alkaline eo or 10% trisodium phosphate (tsp) water or combinations of spraying and immersion treatments wit ...	2005	16463977
genomes are covered with ubiquitous 11 bp periodic patterns, the "class a flexible patterns".	the genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. this bias is present throughout a given genome, both in coding and non-coding sequences. until now this bias remained of unknown origin.	2005	16120222
the tyra family of aromatic-pathway dehydrogenases in phylogenetic context.	the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.	2005	15888209
a computational method to predict genetically encoded rare amino acids in proteins.	in several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. these rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. we report a method for such recoding prediction from genomic data, using read-through similarity evaluation. a survey across a set of microbial genomes identifies almost all the known cases as well as a number of no ...	2005	16168086
inhibition of bacterial rna polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.	we define the target, mechanism, and structural basis of inhibition of bacterial rna polymerase (rnap) by the tetramic acid antibiotic streptolydigin (stl). stl binds to a site adjacent to but not overlapping the rnap active center and stabilizes an rnap-active-center conformational state with a straight-bridge helix. the results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix rnap-active-center conformations exist and that cycling between st ...	2005	16122422
epidemiology and management of infectious diseases in international adoptees.	international adoptees represent a group of children with unique health care needs. data from published studies, along with the recent experience of the yale international adoption clinic, suggest that the risk of serious infections in adoptees is low, although infections associated with institutionalization still occur commonly. interpretation of these data must be undertaken with caution, however, since many, if not most, international adoptees are not evaluated in specialty clinics. thus, pro ...	2005	16020687
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
differentiation of regions with atypical oligonucleotide composition in bacterial genomes.	complete sequencing of bacterial genomes has become a common technique of present day microbiology. thereafter, data mining in the complete sequence is an essential step. new in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of orfs. we tested the usefulness of local oligonucleotide usage (ou) patterns to recognize and differentiate types of atypical oligonucleotide composition in dna sequences of ba ...	2005	16225667
protein length in eukaryotic and prokaryotic proteomes.	we analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. comparing eukaryotes and prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. the magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended m ...	2005	15951512
identification of genomic features using microsyntenies of domains: domain teams.	the detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). our approach adopts the technique of temporarily forgetting genes and working directly with p ...	2005	15899966
predicted highly expressed genes in archaeal genomes.	based primarily on 16s rrna sequence comparisons, life has been broadly divided into the three domains of bacteria, archaea, and eukarya. archaea is further classified into crenarchaea and euryarchaea. archaea generally thrive in extreme environments as assessed by temperature, ph, and salinity. for many prokaryotic organisms, ribosomal proteins (rp), transcription/translation factors, and chaperone genes tend to be highly expressed. a gene is predicted highly expressed (phx) if its codon usage ...	2005	15883368
among b cell non-hodgkin's lymphomas, malt lymphomas express a unique antibody repertoire with frequent rheumatoid factor reactivity.	we analyzed the structure of antigen receptors of a comprehensive panel of mature b non-hodgkin's lymphomas (b-nhls) by comparing, at the amino acid level, their immunoglobulin (ig)v(h)-cdr3s with cdr3 sequences present in genbank. follicular lymphomas, diffuse large b cell lymphomas, burkitt's lymphomas, and myelomas expressed a cdr3 repertoire comparable to that of normal b cells. mantle cell lymphomas and b cell chronic lymphocytic leukemias (b-clls) expressed clearly restricted albeit differ ...	2005	15837810
systematic association of genes to phenotypes by genome and literature mining.	one of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. so far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. we first mine the medline literature database for terms that reflect phenotypic simil ...	2005	15799710
transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in is element gene expression.	transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mrnas. individual mrna molecules within this population differ in the number of nucleotides they contain that are not specified by the template. when transcriptional slippage occurs in a coding sequence, translation of the resulting mrnas yields more than one protein product. except where the products of the resulting mrnas have distinct functions, transcription sl ...	2005	15774026
clustering the annotation space of proteins.	current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas.	2005	15703069
growth and multiplexed analysis of microorganisms on a subdivided, highly porous, inorganic chip manufactured from anopore.	a highly porous inorganic material (anopore) was shown to be an effective support for culturing and imaging a wide range of microorganisms. an inert barrier grid was printed on the rigid surface of anopore to create a "living chip" of 336 miniaturized compartments (200/cm2) with broad applications in microbial culture.	2005	16332904
evidence of a large novel gene pool associated with prokaryotic genomic islands.	microbial genes that are "novel" (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in yet-to-be-cultured microorganisms. by analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome) in 63 prokaryotic genomes, and then characterized the distrib ...	2005	16299586
enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of epsilonproteobacteria.	the carbon and energy metabolisms of a variety of cultured chemolithoautotrophic epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. all the epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rtca) cycle enzymatic activities--atp-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (rubisco) ac ...	2005	16269773
mechanism of diarrhea in microscopic colitis.	to search the pathophysiological mechanism of diarrhea based on daily stool weights, fecal electrolytes, osmotic gap and ph.	2005	16222750
guillain barré syndrome precipitated by the use of antilymphocyte globulin in the treatment of severe aplastic anaemia.	this report describes the case of a 54 year old woman with very severe aplastic anaemia who was treated with antilymphocyte globulin (alg) and developed guillain barré syndrome (gbs). no antecedent infective aetiology was identified. although there are numerous reports of autoimmune disease after treatment with alg in aplastic anaemia, and gbs after immunosuppressive treatment, there are none reporting gbs after the use of alg for severe aplastic anaemia. the occurrence of autoimmune disease aft ...	2005	16126887
posttranslational protein modification in archaea.	one of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. whereas these and other posttranslational protein modifications have been well characterized in eucarya and bact ...	2005	16148304
the prokaryotic enzyme dsbb may share key structural features with eukaryotic disulfide bond forming oxidoreductases.	three different classes of thiol-oxidoreductases that facilitate the formation of protein disulfide bonds have been identified. they are the ero1 and sox/alr family members in eukaryotic cells, and the dsbb family members in prokaryotic cells. these enzymes transfer oxidizing potential to the proteins pdi or dsba, which are responsible for directly introducing disulfide bonds into substrate proteins during oxidative protein folding in eukaryotes and prokaryotes, respectively. a comparison of the ...	2005	15930008
unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression.	a major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. in vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. the widely used gene-to-phenotype approach involves the identification of altered niche-related phen ...	2005	15944455
comparative mapping of sequence-based and structure-based protein domains.	protein domains have long been an ill-defined concept in biology. they are generally described as autonomous folding units with evolutionary and functional independence. both structure-based and sequence-based domain definitions have been widely used. but whether these types of models alone can capture all essential features of domains is still an open question.	2005	15790427
population genetics of microbial pathogens estimated from multilocus sequence typing (mlst) data.	the inference of population recombination (rho), population mutation (theta), and adaptive selection is of great interest in microbial population genetics. these parameters can be efficiently estimated using explicit statistical frameworks (evolutionary models) that describe their effect on gene sequences. within this framework, we estimated rho and theta using a coalescent approach, and adaptive (or destabilizing) selection under heterogeneous codon-based and amino acid property models in micro ...	2005	16503511
population genetics of microbial pathogens estimated from multilocus sequence typing (mlst) data.	the inference of population recombination (rho), population mutation (theta), and adaptive selection is of great interest in microbial population genetics. these parameters can be efficiently estimated using explicit statistical frameworks (evolutionary models) that describe their effect on gene sequences. within this framework, we estimated rho and theta using a coalescent approach, and adaptive (or destabilizing) selection under heterogeneous codon-based and amino acid property models in micro ...	2005	16503511
prokaryotic phylogenies inferred from protein structural domains.	the determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. in this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. the evolution of the structura ...	2005	15741510
relative predicted protein levels of functionally associated proteins are conserved across organisms.	we show that the predicted protein levels of functionally related proteins change in a coordinated fashion over many unicellular organisms. for each protein, we created a profile containing a protein abundance measure in each of a set of organisms. we show that for functionally related proteins these profiles tend to be correlated. using the codon adaptation index as a predictor of protein abundance in 48 unicellular organisms, we demonstrated this phenomenon for two types of functional relation ...	2005	15718304
neurologic aspects of infections in international travelers.	as international travel for business and pleasure becomes part of contemporary lifestyle, the clinician today is confronted with an increasing number of travelers returning ill with unfamiliar syndromes. the physician will encounter a myriad of patients with exotic infections, emerging infectious diseases, or resurgent old-world infections.	2005	15631642
will worms really cure crohn's disease?		2005	15591496
genomic and proteomic adaptations to growth at high temperature.	most positively selected mutations cause changes in metabolism, resulting in a better-adapted phenotype. but as well as acting on the information content of genes, natural selection may also act directly on nucleic acid and protein molecules. we review the evidence for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes.	2004	15461805
phase and antigenic variation in bacteria.	phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. this form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. this review provides an overview of the many bacterial proteins a ...	2004	15258095
inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.	the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ...	2004	15214963
sigi: score-based identification of genomic islands.	genomic islands can be observed in many microbial genomes. these stretches of dna have a conspicuous composition with regard to sequence or encoded functions. genomic islands are assumed to be frequently acquired via horizontal gene transfer. for the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands.	2004	15113412
prediction of rna-binding proteins from primary sequence by a support vector machine approach.	elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. computational methods have been developed for the prediction of protein-protein interactions. but insufficient attention has been paid to the prediction of protein-rna interactions, which play central roles in regulating gene expression and certain rna-mediated enzymatic processes. this work explored the use of a machine learning method, support vector machines (svm) ...	2004	14970381
bacterial sexually transmitted diseases.	common sexually transmitted bacterial organisms may affect the anorectum and perianal skin. while some of these infections are a result of contiguous spread from genital infection, most result from receptive anal intercourse. polymicrobial infection is common and there is overlap in symptoms caused by the organisms that may infect the anorectum. this article addresses the most common bacterial organisms that are sexually transmitted and affect the anorectum. it includes discussions of gonorrhea, ...	2004	20011261
recovery of cephalosporin-resistant escherichia coli and salmonella from pork, beef and chicken marketed in nova scotia.	antimicrobial use in farm animals is a potentially important contributor to the emergence of antimicrobial resistance. resistant salmonella may lead to serious human infections and resistant escherichia coli may transfer plasmid-encoded resistance genes to other pathogens.	2004	18159497
[incidence of the virulence markers iam in campylobacter jejuni and campylobacter coli strains isolated from poultry carcases].	previously found dna sequence (iam), correlated with the invasiveness of campylobacter strains, became a starting point for present investigation. main goal of this study was to isolate number of campylobacter strains from chicken carcasses, to determine their taxonomic position and to establish the presence of iam sequence in their genoms. it was found, that invasion associated marker is present in all campylobacter coli strains and in majority but not all campylobacter jejuni. this may confirm ...	2004	19097580
atp-binding cassette transporters are targets for the development of antibacterial vaccines and therapies.		2004	15557595
the prokaryotic selenoproteome.	in the genetic code, the uga codon has a dual function as it encodes selenocysteine (sec) and serves as a stop signal. however, only the translation terminator function is used in gene annotation programs, resulting in misannotation of selenoprotein genes. here, we applied two independent bioinformatics approaches to characterize a selenoprotein set in prokaryotic genomes. one method searched for selenoprotein genes by identifying rna stem-loop structures, selenocysteine insertion sequence eleme ...	2004	15105824
high-throughput computational and experimental techniques in structural genomics.	structural genomics has as its goal the provision of structural information for all possible orf sequences through a combination of experimental and computational approaches. the access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the new york structural genomics research consortium. in this report, we outline the progress of the consortium in establishing its pipeline for structural genomics, and some of the ...	2004	15489337
abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents.	since the discovery of hydrothermal vents more than 25 years ago, the calvin-bassham-benson (calvin) cycle has been considered the principal carbon fixation pathway in this microbe-based ecosystem. however, on the basis of recent molecular data of cultured free-living and noncultured episymbiotic members of the epsilon subdivision of proteobacteria and earlier carbon isotope data of primary consumers, an alternative autotrophic pathway may predominate. here, genetic and culture-based approaches ...	2004	15466576
crohn's disease and infections: a complex relationship.		2004	15520637
cpc1, a chlamydomonas central pair protein with an adenylate kinase domain.	mutations at cpc1 disrupt assembly of a central pair microtubule-associated complex and alter flagellar beat frequency in chlamydomonas. sequences of wild-type genomic clones that complement cpc1, and of corresponding cdnas, reveal the gene product to be a 205 kda protein with two predicted functional domains, a single ef hand motif near the c-terminus and an unusual centrally located adenylate kinase domain. homologs are expressed in mammals (testis and tracheal cilia) as well as ciliated lower ...	2004	15292403
reiter's syndrome--a case report and review of literature.	the occurrence of reiter's syndrome is rare and not commonly reported in nigeria. this paper reports a case of a 35 yr old male nigerian with reiter's syndrome, occurring 1-2 weeks after a bout of a dysenteric illness. the patient presented with fever, conjunctivitis, dysentery, urethritis and arthralgia. the joint pains involved the left wrist (which was swollen), the right knee and ankle joints. the patient was managed conservatively. the case is presented with a view to documenting the occurr ...	2004	15477194
a novel auxin conjugate hydrolase from wheat with substrate specificity for longer side-chain auxin amide conjugates.	this study investigates how the ilr1-like indole acetic acid (iaa) amidohydrolase family of genes has functionally evolved in the monocotyledonous species wheat (triticum aestivum). an ortholog for the arabidopsis iar3 auxin amidohydrolase gene has been isolated from wheat (taiar3). the taiar3 protein hydrolyzes negligible levels of iaa-ala and no other iaa amino acid conjugates tested, unlike its ortholog iar3. instead, taiar3 has low specificity for the ester conjugates iaa-glc and iaa-myoinos ...	2004	15299127
mlstdbnet - distributed multi-locus sequence typing (mlst) databases.	multi-locus sequence typing (mlst) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. the mlstdbnet software enables the implementation of distributed web-accessible mlst databases that can be linked widely over the internet.	2004	15230973
arrayprospector: a web resource of functional associations inferred from microarray expression data.	dna microarray experiments have provided vast amounts of data which can be used for inferring gene function. however, most methods for predicting functional associations between genes from expression data are not suited to simultaneous analysis of multiple datasets, and a comprehensive resource of coexpression-based predictions is currently lacking. here, we present an interactive web resource of gene associations predicted by applying a novel algorithm to all expression data in the stanford mic ...	2004	15215427
computational inference of scenarios for alpha-proteobacterial genome evolution.	the alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches sep ...	2004	15210995
sirtuins: sir2-related nad-dependent protein deacetylases.	silent information regulator 2 (sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (nad) and are found in organisms ranging from bacteria to humans. in eukaryotes, sirtuins regulate transcriptional repression, recombination, the cell-division cycle, microtubule organization, and cellular responses to dna-damaging agents. sirtuins have also been implicated in regulating the molecular mechanisms of aging. the sir2 catalytic domain, which is shared amon ...	2004	15128440
lymphocytic colitis: a retrospective clinical study of 199 swedish patients.	lymphocytic colitis is characterised by chronic diarrhoea and specific microscopic changes in a macroscopically normal colonic mucosa. we report clinical features and treatment outcome in a large patient cohort.	2004	15016748
specific and common alterations in host gene transcript accumulation following infection of the chestnut blight fungus by mild and severe hypoviruses.	we report the use of a cdna microarray to monitor global transcriptional responses of the chestnut blight fungus, cryphonectria parasitica, to infection by mild and severe isolates of virulence-attenuating hypoviruses that share 87 to 93% and 90 to 98% identity at the nucleotide and amino acid levels, respectively. infection by the mild hypovirus isolate chv1-euro7 resulted in differential expression of 166 of the ca. 2,200 genes represented on the microarray (90 upregulated and 76 downregulated ...	2004	15047830
management of infectious diarrhoea.		2004	14724167
need for susceptibility testing guidelines for fastidious or less-frequently isolated bacteria.		2004	14766806
automated correction of genome sequence errors.	by using information from an assembly of a genome, a new program called autoeditor significantly improves base calling accuracy over that achieved by previous algorithms. this in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery. we describe the algorithm and its application in a large set of recent genome sequencing projects. the number of erroneous base calls in these projects was reduced by 80%. in an analysis of over ...	2004	14744981
effects of trisodium phosphate and sodium chloride dipping on the microbial quality and shelf life of refrigerated tray-packaged chicken breasts.	effects of trisodium phosphate (tsp) and/or sodium chloride (nacl) dipping on microbial quality and shelf life of chicken breasts were investigated during refrigeration. chicken breasts were dipped in aqueous solution (w/v) of 10% tsp, 10% nacl, combination of tsp and nacl (7.5% + 7.5%) or distilled water (control) for 10 min, followed by tray-packaging storage at 2 degrees c. during storage, chicken breasts dipped in tsp maintained almost constant ph, while ph of control or nacl-treated samples ...	2004	17330156
physiological changes in campylobacter jejuni on entry into stationary phase.	campylobacter jejuni nctc 11168 does not exhibit the general increase in cellular stress resistance on entry into stationary phase that is seen in most other bacteria. this is consistent with the lack of global stationary phase regulatory elements in this organism, deduced from an analysis of its genome sequence. we now show that c. jejuni nctc 11168 does undergo certain changes in stationary phase, of a pattern not previously described. as cells entered stationary phase there was a change in me ...	2004	15878401
prevalence and clonal diversity of campylobacter jejuni from dairy farms and urban sources.	to investigate the role of free-living animals such as sparrows, rodents and flies as potential reservoirs of campylobacter spp on a dairy farm, and to assess the genetic diversity among campylobacter isolates from the farm and an urban source.	2004	15768139
an annotated checklist of pathogenic microorganisms associated with migratory birds.	the potential for transport and dissemination of certain pathogenic microorganisms by migratory birds is of concern. migratory birds might be involved in dispersal of microorganisms as their biological carriers, mechanical carriers, or as carriers of infected hematophagous ecto-parasites (e.g., ixodid ticks). many species of microorganisms pathogenic to homeothermic vertebrates including humans have been associated with free-living migratory birds. migratory birds of diverse species can play sig ...	2004	15650082
guillain-barre syndrome with meningoencephalitis after campylobacter jejuni infection.	a 14-year-old boy presented with progressive ascending muscle weakness, urinary retention and disturbed consciousness. initially his cerebrospinal fluid showed pleocytosis, and protein-cellular dissociation developed later. campylobacter jejuni was isolated from his stool and serum anti-ganglioside antibodies were positive. our case suggests that coexistence of meningoencephalitis at an early stage of illness does not necessarily exclude the diagnosis of guillain-barre syndrome.	2004	15602203
outbreaks of enteric infections caused by multiple pathogens associated with calves at a farm day camp.	transmission of enteric pathogens at venues where the public contacts farm animals is a growing problem, particularly among children. in 2000 and again in 2001, enteric illness outbreaks caused by multiple pathogens occurred at a farm day camp for children in minnesota.	2004	15626945
phenotypic characterisation of flagellin and flagella of urease-positive thermophilic campylobacters.	in this study, flagellin is purified biochemically from eight urease-positive thermophilic camplylobacters (uptc) isolated from river water, sea water and mussels, and purified also from two isolates of campylobacter jejuni and c. coli and fractionated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (sds-page). results showed that no flagellin components were detected in the two japanese uptc isolates (cf89-12 and cf89-14) and the two uptc nctc strains (nctc12893 and nctc12894). fl ...	2004	15649010
anion-independent iron coordination by the campylobacter jejuni ferric binding protein.	campylobacter jejuni, the leading cause of human gastroenteritis, expresses a ferric binding protein (cfbpa) that in many pathogenic bacteria functions to acquire iron as part of their virulence repertoire. recombinant cfbpa is isolated with ferric iron bound from escherichia coli. the crystal structure of cfbpa reveals unprecedented iron coordination by only five protein ligands. the histidine and one tyrosine are derived from the n-terminal domain, whereas the three remaining tyrosine ligands ...	2004	15613474
isolated abducens nerve paresis associated with high titer of anti-asialo-gm1 following campylobacter jejuni enteritis.		2004	15592739
immunoproliferative small intestinal disease associated with campylobacter jejuni.	immunoproliferative small intestinal disease (also known as alpha chain disease) is a form of lymphoma that arises in small intestinal mucosa-associated lymphoid tissue (malt) and is associated with the expression of a monotypic truncated immunoglobulin alpha heavy chain without an associated light chain. early-stage disease responds to antibiotics, suggesting a bacterial origin. we attempted to identify a causative agent.	2004	14724303
campylobacter insulaenigrae sp. nov., isolated from marine mammals.	phenotypic and phylogenetic studies were performed on four campylobacter-like organisms recovered from three seals and a porpoise. comparative 16s rrna gene sequencing studies demonstrated that the organisms represent a hitherto unknown subline within the genus campylobacter, associated with a subcluster containing campylobacter jejuni, campylobacter coli and campylobacter lari. dna-dna hybridization studies confirmed that the bacteria belonged to a single species, for which the name campylobact ...	2004	15545485
development of an extensive set of 16s rdna-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time pcr.	the microbiota of the human intestinal tract constitutes a complex ecosystem. we report the design and optimization of an extensive set of 16s rdna-targeted species- and group-specific primers for more accurate quantification of bacteria from faecal samples with real-time pcr.	2004	15546407
rubrerythrin from the hyperthermophilic archaeon pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase.	rubrerythrin was purified by multistep chromatography under anaerobic, reducing conditions from the hyperthermophilic archaeon pyrococcus furiosus. it is a homodimer with a molecular mass of 39.2 kda and contains 2.9 +/- 0.2 iron atoms per subunit. the purified protein had peroxidase activity at 85 degrees c using hydrogen peroxide with reduced p. furiosus rubredoxin as the electron donor. the specific activity was 36 micromol of rubredoxin oxidized/min/mg with apparent k(m) values of 35 and 70 ...	2004	15547260
the campylobacter jejuni dccrs two-component system is required for optimal in vivo colonization but is dispensable for in vitro growth.	a campylobacter jejuni two-component signal transduction system (tcsts), designated dccr-dccs (diminished capacity to colonize; cj1223c-cj1222c), has been found to be important for in vivo colonization but dispensable for in vitro growth. a deltadccr response regulator mutant generated using the virulent strain 81-176 background exhibited significantly reduced colonization of immunocompetent limited flora (i-lf) mice, severe combined immunodeficient limited flora (scid-lf) mice, and 1-day-old ch ...	2004	15554967