| role of the high affinity immunoglobulin e receptor in bacterial translocation and intestinal inflammation. | a role for immunoglobulin e and its high affinity receptor (fc epsilon ri) in the control of bacterial pathogenicity and intestinal inflammation has been suggested, but relevant animal models are lacking. here we compare transgenic mice expressing a humanized fc epsilon ri (hfc epsilon ri), with a cell distribution similar to that in humans, to fc epsilon ri-deficient animals. in hfc epsilon ri transgenic mice, levels of colonic interleukin 4 were higher, the composition of fecal flora was great ... | 2001 | 11136818 |
| hyper-immunoglobulin a in the hyperimmunoglobulinemia d syndrome. | the hyperimmunoglobulinemia d syndrome (hids) is an autosomal recessive disorder characterized by recurrent febrile attacks with abdominal, articular, and skin manifestations. apart from elevated immunoglobulin d (igd) levels (>100 iu/ml), there are high iga levels in the majority of cases. mutations in the gene encoding mevalonate kinase constitute the molecular defect in hids. the cause of elevated iga concentrations in hids patients remains to be elucidated. we studied the hyper-iga response ... | 2001 | 11139196 |
| srpdb (signal recognition particle database). | signal recognition particle (srp) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. the srp database (srpdb) provides compilations of srp components, ordered alphabetically and phylogenetically. alignments emphasize phylogenetically-supported base pairs in srp rna and conserved residues in the proteins. data are provided in various formats including a column arrangement for improved access and simplified computati ... | 2001 | 11125080 |
| bacterial autoinduction: looking outside the cell for new metabolic engineering targets. | recent evidence has demonstrated that cell-to-cell signaling is a fundamental activity carried out by numerous microorganisms. a number of specialized processes are reported to be regulated by density-dependent signaling molecules including antibiotic production, bioluminescence, biofilm formation, genetic competence, sporulation, swarming motility and virulence. however, a more centralized role for quorum sensing is emerging where quorum signaling pathways overlap with stress and starvation cir ... | 2002 | 12537600 |
| role of nerves in enteric infection. | peripheral and central effects of enteric infection are considered. nerves play a vital part in the immediate response to enteric infection, promoting pathogen expulsion by orchestrating intestinal secretion and propulsive motor patterns. laboratory studies indicate that therapeutic agents aimed at modulating the neural response can profoundly alter the outcome of infection. as our understanding of the role of nerves increases, exciting new targets for therapeutic intervention will emerge in bot ... | 2002 | 12427768 |
| bacterial chemotaxis toward environmental pollutants: role in bioremediation. | | 2002 | 12450797 |
| wound botulism associated with subcutaneous drug use. | | 2002 | 12411365 |
| occupational health and safety in small animal veterinary practice: part ii--parasitic zoonotic diseases. | | 2002 | 12395769 |
| acute cholecystitis. | | 2002 | 12242178 |
| unravelling an acute flaccid paralysis event. | | 2002 | 20046317 |
| dictionary-driven prokaryotic gene finding. | gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale sequencing projects. previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. in this paper, we propose a new gene identification scheme that c ... | 2002 | 12060689 |
| molecular genetics of bacteria and phages, 2001. | | 2002 | 11976284 |
| the identification of functional modules from the genomic association of genes. | by combining the pairwise interactions between proteins, as predicted by the conserved co-occurrence of their genes in operons, we obtain protein interaction networks. here we study the properties of such networks to identify functional modules: sets of proteins that together are involved in a biological process. the complete network contains 3,033 orthologous groups of proteins in 38 genomes. it consists of one giant component, containing 1,611 orthologous groups, and of 516 small disjointed cl ... | 2002 | 11983890 |
| facts and ideas from anywhere. | | 2002 | 16333443 |
| the past, present and future of genome-wide re-annotation. | annotation, the process by which structural or functional information is inferred for genes or proteins, is crucial for obtaining value from genome sequences. we define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches. | 2002 | 11864365 |
| facts and ideas from anywhere. | | 2002 | 16333418 |
| ribosomal protection proteins and their mechanism of tetracycline resistance. | | 2003 | 14638464 |
| conservation of dna curvature signals in regulatory regions of prokaryotic genes. | dna curvature plays a well-characterized role in many transcriptional regulation mechanisms. we present evidence for the conservation of curvature signals in putative regulatory regions of several archaeal and eubacterial genomes. genes with highly curved upstream regions were identified in orthologous groups, based on the annotations of the cluster of orthologous groups of proteins (cog) database. cogs possessing a significant number of genes with curvature signals were analyzed, and conserved ... | 2003 | 14627810 |
| chemical communication among bacteria. | cell-cell communication in bacteria is accomplished through the exchange of chemical signal molecules called autoinducers. this process, called quorum sensing, allows bacteria to monitor their environment for the presence of other bacteria and to respond to fluctuations in the number and/or species present by altering particular behaviors. most quorum-sensing systems are species- or group-specific, which presumably prevents confusion in mixed-species environments. however, some quorum-sensing ci ... | 2003 | 12949263 |
| the versatile bacterial type iv secretion systems. | bacteria use type iv secretion systems for two fundamental objectives related to pathogenesis--genetic exchange and the delivery of effector molecules to eukaryotic target cells. whereas gene acquisition is an important adaptive mechanism that enables pathogens to cope with a changing environment during invasion of the host, interactions between effector and host molecules can suppress defence mechanisms, facilitate intracellular growth and even induce the synthesis of nutrients that are benefic ... | 2003 | 15035043 |
| measuring disease frequency in the marshfield epidemiologic study area (mesa). | the marshfield epidemiologic study area (mesa) is a rare resource for population-based health and medical research developed at marshfield clinic research foundation. because of high population coverage and health event capture, mesa is particularly useful for determining the frequency of disease in the general population. a substantial proportion of mesa-based publications appearing in the peer reviewed literature have reported incidence or prevalence rates of disease or disease-related factors ... | 2003 | 15931320 |
| optic neuritis in anti-gq1b positive recurrent miller fisher syndrome. | | 2003 | 12928295 |
| evidence of chemolithoautotrophy in the bacterial community associated with alvinella pompejana, a hydrothermal vent polychaete. | the deep-sea polychaete alvinella pompejana colonizes tubes on the sides of black smoker chimneys along the east pacific rise. a diverse, yet phylogenetically constrained episymbiotic community is obligately associated with its dorsal surface. the morphologically and phylogenetically distinct dominant episymbionts have not yet been cultured, and there are no clearly defined roles for these bacteria in this symbiosis. a large insert fosmid library was screened for the presence of the two dominant ... | 2003 | 12957888 |
| the source of laterally transferred genes in bacterial genomes. | laterally transferred genes have often been identified on the basis of compositional features that distinguish them from ancestral genes in the genome. these genes are usually a+t-rich, arguing either that there is a bias towards acquiring genes from donor organisms having low g+c contents or that genes acquired from organisms of similar genomic base compositions go undetected in these analyses. | 2003 | 12952536 |
| rapid identification of bacteria from positive blood cultures by terminal restriction fragment length polymorphism profile analysis of the 16s rrna gene. | bacteremia results in significant morbidity and mortality, especially among patient populations that are immunocompromised. broad-spectrum antibiotics are administered to patients suspected to have bloodstream infections that are awaiting diagnosis that depends on blood culture analysis. significant delays in identification of pathogens can result, primarily due to the dependence on growth-based identification systems. to address these limitations, we took advantage of terminal restriction fragm ... | 2003 | 12904391 |
| rotavirus - a retrospective study of incidence at the hospital universiti sains malaysia (husm). | the present study, analyzes data from 1991 to 2000 for rotavirus infection among children with diarrhoea and acute gastroenteritis admitted to the hospital universiti sains malaysia (husm). the latex slide agglutination test was used for the detection of rotavirus antigens. out of 1097 stool samples tested, 207 samples or 18.8 % were found to be positive for rotavirus. the infection occurred most frequently in infants and young children from 6 months to 2 years of age. the infection was recorded ... | 2003 | 23386803 |
| microbial genome jambalaya. | | 2003 | 12702204 |
| abc of learning and teaching in medicine: written assessment. | | 2003 | 12649242 |
| intestinal epithelial responses to enteric pathogens: effects on the tight junction barrier, ion transport, and inflammation. | the effects of pathogenic organisms on host intestinal epithelial cells are vast. innumerable signalling pathways are triggered leading ultimately to drastic changes in physiological functions. here, the ways in which enteric bacterial pathogens utilise and impact on the three major physiological functions of the intestinal epithelium are discussed: alterations in the structure and function of the tight junction barrier, induction of fluid and electrolyte secretion, and activation of the inflamm ... | 2003 | 12584232 |
| detecting adverse events using information technology. | although patient safety is a major problem, most health care organizations rely on spontaneous reporting, which detects only a small minority of adverse events. as a result, problems with safety have remained hidden. chart review can detect adverse events in research settings, but it is too expensive for routine use. information technology techniques can detect some adverse events in a timely and cost-effective way, in some cases early enough to prevent patient harm. | 2003 | 12595401 |
| evolutionary history, structural features and biochemical diversity of the nlpc/p60 superfamily of enzymes. | peptidoglycan is hydrolyzed by a diverse set of enzymes during bacterial growth, development and cell division. the n1pc/p60 proteins define a family of cell-wall peptidases that are widely represented in various bacterial lineages. currently characterized members are known to hydrolyze d-gamma-glutamyl-meso-diaminopimelate or n-acetylmuramate-l-alanine linkages. | 2003 | 12620121 |
| elucidation of trna-dependent editing by a class ii trna synthetase and significance for cell viability. | editing of misactivated amino acids by class i trna synthetases is encoded by a specialized internal domain specific to class i enzymes. in contrast, little is known about editing activities of the structurally distinct class ii enzymes. here we show that the class ii alanyl-trna synthetase (alars) has a specialized internal domain that appears weakly related to an appended domain of threonyl-trna synthetase (thrrs), but is unrelated to that found in class i enzymes. editing of misactivated glyc ... | 2003 | 12554667 |
| travellers' diarrhea in children. | diarrhea is the most common medical problem affecting all travellers to developing countries. younger children are at especially high risk of acquiring travellers' diarrhea and of suffering more severe consequences. up to 50% of travellers from developed to developing countries can expect to have at least one episode of acute diarrhea during a two-week stay. episodes of travellers' diarrhea usually begin abruptly, either during travel or soon after returning home, and are generally self-limited. | 2003 | 20019926 |
| the health status of newly arrived refugee children in miami-dade county, florida. | | 2003 | 12554586 |
| 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 |
| 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 |
| deficiency of functional mannose-binding lectin is not associated with infections in patients with systemic lupus erythematosus. | infection imposes a serious burden on patients with systemic lupus erythematosus (sle). the increased infection rate in sle patients has been attributed in part to defects of immune defence. recently, the lectin pathway of complement activation has also been suggested to play a role in the occurrence of infections in sle. in previous studies, sle patients homozygous for mannose-binding lectin (mbl) variant alleles were at an increased risk of acquiring serious infections in comparison with patie ... | 2006 | 17166254 |
| an environmental signature for 323 microbial genomes based on codon adaptation indices. | codon adaptation indices (cais) represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. here, we evaluate and compare two very different methods for estimating cai values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias. | 2006 | 17156429 |
| tropical malabsorption. | malabsorption is an important clinical problem both in visitors to the tropics and in native residents of tropical countries. infections of the small intestine are the most important cause of tropical malabsorption. protozoal infections cause malabsorption in immunocompetent hosts, but do so more commonly in the setting of immune deficiency. helminth infections occasionally cause malabsorption or protein-losing enteropathy. intestinal tuberculosis, chronic pancreatitis and small-bowel bacterial ... | 2006 | 17148698 |
| genes and environment in irritable bowel syndrome: one step forward. | | 2006 | 17124153 |
| how flagellin and toll-like receptor 5 contribute to enteric infection. | | 2006 | 17118981 |
| how flagellin and toll-like receptor 5 contribute to enteric infection. | | 2006 | 17118981 |
| influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16s rrna gene-based diagnostic arrays. | dangling ends and surface-proximal tails of gene targets influence probe-target duplex formation and affect the signal intensity of probes on diagnostic microarrays. this phenomenon was evaluated using an oligonucleotide microarray containing 18-mer probes corresponding to the 16s rrna genes of 10 waterborne pathogens and a number of synthetic and pcr-amplified gene targets. signal intensities for klenow/random primer-labeled 16s rrna gene targets were dissimilar from those for 45-mer synthetic ... | 2006 | 17114322 |
| influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16s rrna gene-based diagnostic arrays. | dangling ends and surface-proximal tails of gene targets influence probe-target duplex formation and affect the signal intensity of probes on diagnostic microarrays. this phenomenon was evaluated using an oligonucleotide microarray containing 18-mer probes corresponding to the 16s rrna genes of 10 waterborne pathogens and a number of synthetic and pcr-amplified gene targets. signal intensities for klenow/random primer-labeled 16s rrna gene targets were dissimilar from those for 45-mer synthetic ... | 2006 | 17114322 |
| demyelinating diseases. | a diagnosis of demyelination carries important therapeutic and prognostic implications. in most cases the diagnosis is made clinically, and involvement of the histopathologist is largely confined to postmortem confirmation and clinicopathological correlation. however, every now and then, accurate diagnosis of the presence or cause of demyelination before death hinges on the histopathological assessment. recognition of demyelination depends on an awareness of this as a diagnostic possibility, and ... | 2006 | 17071802 |
| divergent evolution of a structural proteome: phenomenological models. | we develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. to identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. we view the network of structural similarities as a graph, called the organismal protein domain universe graph (opdug); vertices ... | 2006 | 17071665 |
| divergent evolution of a structural proteome: phenomenological models. | we develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. to identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. we view the network of structural similarities as a graph, called the organismal protein domain universe graph (opdug); vertices ... | 2006 | 17071665 |
| application of smartgene idns software to partial 16s rrna gene sequences for a diverse group of bacteria in a clinical laboratory. | laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. with the emergence of 16s rrna gene sequencing as an identification tool, we evaluated the usefulness of smartgene idns, a 16s rrna sequence database and software program for microbial identification. identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the smartgene and mic ... | 2006 | 17050811 |
| manndb - a microbial database of automated protein sequence analyses and evidence integration for protein characterization. | manndb was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. thus, we built a fully automated system for executing software tools and for storage, integration, and display of ... | 2006 | 17044936 |
| detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. | in bacteria, sigma factors and other transcriptional regulatory proteins recognize dna patterns upstream of their target genes and interact with rna polymerase to control transcription. as a consequence of evolution, dna sequences recognized by transcription factors are thought to be enriched in intergenic regions (irs) and depleted from coding regions of prokaryotic genomes. | 2006 | 17014715 |
| household pasteurization of drinking-water: the chulli water-treatment system. | a simple flow-through system has been developed which makes use of wasted heat generated in traditional clay ovens (chullis) to pasteurize surface water. a hollow aluminium coil is built into the clay chulli, and water is passed through the coil during normal cooking events. by adjusting the flow rate, effluent temperature can be maintained at approximately 70 degrees c. laboratory testing, along with over 400 field tests on chulli systems deployed in six pilot villages, showed that the treatmen ... | 2006 | 17366777 |
| graemlin: general and robust alignment of multiple large interaction networks. | the recent proliferation of protein interaction networks has motivated research into network alignment: the cross-species comparison of conserved functional modules. previous studies have laid the foundations for such comparisons and demonstrated their power on a select set of sparse interaction networks. recently, however, new computational techniques have produced hundreds of predicted interaction networks with interconnection densities that push existing alignment algorithms to their limits. ... | 2006 | 16899655 |
| rapid and accurate pyrosequencing of angiosperm plastid genomes. | plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. the past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional sanger sequencing technology. here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the genome seque ... | 2006 | 16934154 |
| publication bias in foodborne outbreaks of infectious intestinal disease and its implications for evidence-based food policy. england and wales 1992-2003. | systematic national surveillance of outbreaks of infectious intestinal disease (iid) was introduced in england and wales in 1992 to provide comprehensive information on causative organisms, sources or vehicles of infection and modes of transmission. we compared information from this system with that published in the peer-reviewed literature between 1 january 1992 and 31 january 2003 to assess the potential effect of publication bias on food-safety policy. during the study period 1763 foodborne o ... | 2006 | 16420723 |
| pyrosequencing as a rapid tool for identification of ges-type extended-spectrum beta-lactamases. | a pyrosequencing technique was used for identification of extended-spectrum beta-lactamases (esbls) of ges type. these beta-lactamases are isolated increasingly emerging in gram-negative bacteria worldwide. this rapid and reliable identification method is interesting, since ges variants, including not only expanded-spectrum cephalosporins but also carbapenems, cephamycins, and monobactams, are the only esbls that possess different hydrolysis profiles. | 2006 | 16891529 |
| an analysis of amino acid sequences surrounding archaeal glycoprotein sequons. | despite having provided the first example of a prokaryal glycoprotein, little is known of the rules governing the n-glycosylation process in archaea. as in eukarya and bacteria, archaeal n-glycosylation takes place at the asn residues of asn-x-ser/thr sequons. since not all sequons are utilized, it is clear that other factors, including the context in which a sequon exists, affect glycosylation efficiency. as yet, the contribution to n-glycosylation made by sequon-bordering residues and other re ... | 2006 | 17350928 |
| an analysis of amino acid sequences surrounding archaeal glycoprotein sequons. | despite having provided the first example of a prokaryal glycoprotein, little is known of the rules governing the n-glycosylation process in archaea. as in eukarya and bacteria, archaeal n-glycosylation takes place at the asn residues of asn-x-ser/thr sequons. since not all sequons are utilized, it is clear that other factors, including the context in which a sequon exists, affect glycosylation efficiency. as yet, the contribution to n-glycosylation made by sequon-bordering residues and other re ... | 2006 | 17350928 |
| painful peripheral neuropathies. | peripheral neuropathies are a heterogeneous group of diseases affecting peripheral nerves. the causes are multiple: hereditary, metabolic, infectious, inflammatory, toxic, traumatic. the temporal profile includes acute, subacute and chronic conditions. the majority of peripheral neuropathies cause mainly muscle weakness and sensory loss, positive sensory symptoms and sometimes pain. when pain is present, however, it is usually extremely intense and among the most disabling symptoms for the patie ... | 2006 | 18615140 |
| prevention and self-treatment of traveler's diarrhea. | of the millions who travel from the industrialized world to developing countries every year, between 20% and 50% will develop at least one episode of diarrhea, making it the most common medical ailment afflicting travelers. although usually a mild illness, traveler's diarrhea can result in significant morbidity and hardship overseas. precautions can be taken to minimize the risk of developing traveler's diarrhea, either through avoidance of potentially contaminated food or drink or through vario ... | 2006 | 16847088 |
| shield as signal: lipopolysaccharides and the evolution of immunity to gram-negative bacteria. | | 2006 | 16846256 |
| bacterial genotyping by 16s rrna mass cataloging. | it has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids. because mass spectrometry is extremely rapid and widely available such techniques offer significant advantages in some applications. a key element in favor of mass spectrometric analysis of rna fragmentation patterns is that a reference database for analysis of the results can be generated from sequence information. in co ... | 2006 | 16796754 |
| quick identification of febrile neonates with low risk for serious bacterial infection: an observational study. | to examine the possible usefulness of simple and quick criteria for identifying febrile neonates with low risk for serious bacterial infection (sbi). | 2006 | 17185424 |
| quick identification of febrile neonates with low risk for serious bacterial infection: an observational study. | to examine the possible usefulness of simple and quick criteria for identifying febrile neonates with low risk for serious bacterial infection (sbi). | 2006 | 17185424 |
| involvement of dna curvature in intergenic regions of prokaryotes. | it is known that dna curvature plays a certain role in gene regulation. the distribution of curved dna in promoter regions is evolutionarily preserved, and it is mainly determined by temperature of habitat. however, very little is known on the distribution of dna curvature in termination sites. our main objective was to comprehensively analyze distribution of curved sequences upstream and downstream to the coding genes in prokaryotic genomes. we applied curvature software to 170 complete prokary ... | 2006 | 16679450 |
| biogas: a bright idea for africa. | | 2006 | 16675412 |
| new methods for inferring population dynamics from microbial sequences. | the reduced cost of high throughput sequencing, increasing automation, and the amenability of sequence data for evolutionary analysis are making dna data (or the corresponding amino acid sequences) the molecular marker of choice for studying microbial population genetics and phylogenetics. concomitantly, due to the ever-increasing computational power, new, more accurate (and sometimes faster), sequence-based analytical approaches are being developed and applied to these new data. here we review ... | 2006 | 16627010 |
| new methods for inferring population dynamics from microbial sequences. | the reduced cost of high throughput sequencing, increasing automation, and the amenability of sequence data for evolutionary analysis are making dna data (or the corresponding amino acid sequences) the molecular marker of choice for studying microbial population genetics and phylogenetics. concomitantly, due to the ever-increasing computational power, new, more accurate (and sometimes faster), sequence-based analytical approaches are being developed and applied to these new data. here we review ... | 2006 | 16627010 |
| multiplex bead array assays: performance evaluation and comparison of sensitivity to elisa. | the measurement of soluble cytokines and other analytes in serum and plasma is becoming increasingly important in the study and management of many diseases. as a result, there is a growing demand for rapid, precise, and cost-effective measurement of such analytes in both clinical and research laboratories. multiplex bead array assays provide quantitative measurement of large numbers of analytes using an automated 96-well plate format. enzyme-linked immunosorbent assay (elisas) have long been the ... | 2006 | 16481199 |
| clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria. | efflux pump genes and proteins are present in both antibiotic-susceptible and antibiotic-resistant bacteria. pumps may be specific for one substrate or may transport a range of structurally dissimilar compounds (including antibiotics of multiple classes); such pumps can be associated with multiple drug (antibiotic) resistance (mdr). however, the clinical relevance of efflux-mediated resistance is species, drug, and infection dependent. this review focuses on chromosomally encoded pumps in bacter ... | 2006 | 16614254 |
| comparison of vertical distributions of prokaryotic assemblages in the anoxic cariaco basin and black sea by use of fluorescence in situ hybridization. | individual prokaryotic cells from two major anoxic basins, the cariaco basin and the black sea, were enumerated throughout their water columns using fluorescence in situ hybridization (fish) with the fluorochrome cy3 or horseradish peroxidase-modified oligonucleotide probes. for both basins, significant differences in total prokaryotic abundance and phylogenetic composition were observed among oxic, anoxic, and transitional (redoxcline) waters. epsilon-proteobacteria, crenarchaeota, and euryarch ... | 2006 | 16597973 |
| the neurology of enteric disease. | | 2006 | 16574728 |
| telithromycin in the treatment of acute bacterial sinusitis, acute exacerbations of chronic bronchitis, and community-acquired pneumonia. | acute bacterial sinusitis (abs), acute exacerbations of chronic bronchitis (aecb), and community-acquired pneumonia (cap) are common conditions and constitute a substantial socioeconomic burden. the ketolides are a new class of antibacterials with a targeted spectrum of antibacterial activity. in vitro, telithromycin is active against common bacterial pathogens that cause upper and lower respiratory tract infections, including some isolates that are resistant to other antibiotic classes. in 2004 ... | 2006 | 18360582 |