Publications

role of hrpa in biofilm formation of neisseria meningitidis and regulation of the hrpbas transcripts.	two-partner secretion systems of gram-negative organisms are utilized in adherence, invasion, and biofilm formation. the hrpab proteins of neisseria meningitidis are members of a two-partner secretion system, and hrpa is established as being important to adherence and intracellular escape. this study set out to determine the expression pattern of members of the hrpbas putative operon and to find a functional role for the hrpa protein. the upregulation of these genes was found in situations of an ...	2009	19289515
constitutive and regulated expression vectors to construct polyphosphate deficient bacteria.	inorganic polyphosphate (polyp), a polymer of tens or hundreds of phosphate residues linked by atp-like bonds, is found in all organisms and performs a wide variety of functions. polyp is synthesized in bacterial cells by the actions of polyphosphate kinases (ppk1 and ppk2) and degraded by an exopolyphosphatase (ppx). bacterial cells with polyp deficiencies are impaired in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence. knockout ...	2009	19323822
genomic evidence for the evolution of streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens.	the continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. streptococcus equi subspecies equi (s. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen streptococcus equi subspecies zooepidemicus (s. zooepidemicus). these pathogens share approximately 80% genome sequence identity with the important human pathogen streptococ ...	2009	19325880
identification of a novel lipopolysaccharide core biosynthesis gene cluster in bordetella pertussis, and influence of core structure and lipid a glucosamine substitution on endotoxic activity.	lipopolysaccharide (lps), also known as endotoxin, is one of the main constituents of the gram-negative bacterial outer membrane. whereas the lipid a portion of lps is generally considered the main determinant for endotoxic activity, the oligosaccharide moiety plays an important role in immune evasion and the interaction with professional antigen-presenting cells. here we describe a novel four-gene cluster involved in the biosynthesis of the bordetella pertussis core oligosaccharide. by insertio ...	2009	19364841
genomic analysis of the adenylate cyclase-hemolysin c-terminal region of bordetella pertussis, bordetella parapertussis and bordetella bronchiseptica.	adenylate cyclase-hemolysin plays an important role in the virulence of bordetella pertussis, bordetella parapertussis and bordetella bronchiseptica species. its c-terminal region carries protective epitopes and receptor binding site for human cells. genomic analyses of this region indicate no polymorphism in b. pertussis and b. parapertussis regions, but substantial variability in b. bronchiseptica that might be linked to the various niches of this species.	2009	19379809
expression levels of immune markers in actinobacillus pleuropneumoniae infected pigs and their relation to breed and clinical symptoms.	in pigs little is known about the role of innate immune defence in bacterial infections of the respiratory tract, despite their major role in pig production. in the present study we characterized and compared in vitro and in vivo activation of immune markers of different pig breeds 7 days before, and 4 and 21 days after an experimental aerosol infection with actinobacillus (a.) pleuropneumoniae.	2009	19383119
immunogenicity of recombinant protective antigen and efficacy against intranasal challenge with bordetella bronchiseptica.	bordetella bronchiseptica is a gram-negative respiratory pathogen that causes substantial disease in a variety of animals. filamentous hemagglutinin (fha) and pertactin are important attachment factors and protective immunogens, which serve as protective antigens in several animal models of infection with b. bronchiseptica. here, we showed the efficacy of subcutaneous immunization of mice with a recombinant protein rf1p2, which consisted of the important immunodominant protective type i domain ( ...	2009	18852008
post-assembly modification of bordetella bronchiseptica o polysaccharide by a novel periplasmic enzyme encoded by wbme.	bordetella bronchiseptica is a pathogen of humans and animals that colonizes the respiratory tract. it produces a lipopolysaccharide o antigen that contains a homopolymer of 2,3-dideoxy-2,3-diacetamido-l-galacturonic acid (l-galnac3naca). some of these sugars are found in the uronamide form (l-galnac3nacan), and there is no discernible pattern in the distribution of amides along the chain. a b. bronchiseptica wbme mutant expresses an o polysaccharide unusually rich in uronamides. the wbme protei ...	2009	19015265
purification of legiobactin and importance of this siderophore in lung infection by legionella pneumophila.	when cultured in a low-iron medium, legionella pneumophila secretes a siderophore (legiobactin) that is both reactive in the chrome azurol s (cas) assay and capable of stimulating the growth of iron-starved legionellae. using anion-exchange high-pressure liquid chromatography (hplc), we purified legiobactin from culture supernatants of a virulent strain of l. pneumophila. in the process, we detected the ferrated form of legiobactin as well as other cas-reactive substances. purified legiobactin h ...	2009	19398549
making the cut: central roles of intramembrane proteolysis in pathogenic microorganisms.	proteolysis in cellular membranes to liberate effector domains from their transmembrane anchors is a well-studied regulatory mechanism in animal biology and disease. by contrast, the function of intramembrane proteases in unicellular organisms has received little attention. recent progress has now established that intramembrane proteases execute pivotal roles in a range of pathogens, from regulating mycobacterium tuberculosis envelope composition, cholera toxin production, bacterial adherence an ...	2009	19421188
antibody-mediated immunity to the obligate intracellular bacterial pathogen coxiella burnetii is fc receptor- and complement-independent.	the obligate intracellular bacterial pathogen coxiella burnetii causes the zoonosis q fever. the intracellular niche of c. burnetii has led to the assumption that cell-mediated immunity is the most important immune component for protection against this pathogen. however, passive immunization with immune serum can protect naïve animals from challenge with virulent c. burnetii, indicating a role for antibody (ab) in protection. the mechanism of this ab-mediated protection is unknown. therefore, we ...	2009	19426498
bordetella bronchiseptica aroa mutant as a live vaccine vehicle for heterologous porcine circovirus type 2 major capsid protein expression.	porcine circovirus type 2 (pcv2) infections cause important respiratory diseases in the pig industry and are associated with many bacterial, mycoplasmal, and viral complications. in this study, a heterologous pcv2 major capsid protein (mcp) was expressed in the bordetella bronchiseptica aroa mutant strain (bbs-mcp) and used as a live vaccine vehicle. mice and pigs were immunized with live bbs-mcp via the intranasal route. the antibodies against mcp were induced successfully in the serum as deter ...	2009	19428194
constraint-based network model of pathogen-immune system interactions.	pathogenic bacteria such as bordetella bronchiseptica modulate host immune responses to enable their establishment and persistence; however, the immune response is generally successful in clearing these bacteria. here, we model the dynamic outcome of the interplay between host immune components and b. bronchiseptica virulence factors. the model extends our previously published interaction network of b. bronchiseptica and includes the existing experimental information on the relative timing of il ...	2009	18952547
genomic and genetic analyses of diversity and plant interactions of pseudomonas fluorescens.	pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. the genome sequences of strains sbw25 and pf0-1 were determined and compared to each other and with p. fluorescens pf-5. a functional genomic in vivo expression technology (ivet) screen provided insight into genes used by p. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity with ...	2009	19432983
new yeast recombineering tools for bacteria.	recombineering with saccharomyces cerevisiae is a powerful methodology that can be used to clone multiple unmarked pieces of dna to generate complex constructs with high efficiency. here, we introduce two new tools that utilize the native recombination enzymes of s. cerevisiae to facilitate the manipulation of dna. first, yeast recombineering was used to make directed nested deletions in a bacteria-yeast shuttle plasmid using only one or two single stranded oligomers, thus obviating the need for ...	2009	19477196
comparative genomic characterization of francisella tularensis strains belonging to low and high virulence subspecies.	tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. it is caused by infection by a gram-negative bacterium, francisella tularensis. in order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different francisella subspecies (subsp.): the f. tularensis sub ...	2009	19478886
the piglet as a model for b cell and immune system development.	the ability to identify factors responsible for disease in all species depends on the ability to separate those factors which are environmental from those that are intrinsic. this is particularly important for studies on the development of the adaptive immune response of neonates. studies on laboratory rodents or primates have been ambiguous because neither the effect of environmental nor maternal factors on the newborn can be controlled in mammals that: (i) transmit potential maternal immunoreg ...	2009	19056129
vibriobactin antibodies: a vaccine strategy.	a new target strategy in the development of bacterial vaccines, the induction of antibodies to microbial outer membrane ferrisiderophore complexes, is explored. a vibriobactin (vib) analogue, with a thiol tether, 1-(2,3-dihydroxybenzoyl)-5,9-bis[[(4s,5r)-2-(2,3-dihydroxyphenyl)-4,5-dihydro-5-methyl-4-oxazolyl]carbonyl]-14-(3-mercaptopropanoyl)-1,5,9,14-tetraazatetradecane, was synthesized and linked to ovalbumin (ova) and bovine serum albumin (bsa). the antigenicity of the vib microbial iron che ...	2009	19492834
the piglet as a model for b cell and immune system development.	the ability to identify factors responsible for disease in all species depends on the ability to separate those factors which are environmental from those that are intrinsic. this is particularly important for studies on the development of the adaptive immune response of neonates. studies on laboratory rodents or primates have been ambiguous because neither the effect of environmental nor maternal factors on the newborn can be controlled in mammals that: (i) transmit potential maternal immunoreg ...	2009	19056129
the effect of the nonionic block copolymer pluronic p85 on gene expression in mouse muscle and antigen-presenting cells.	dna vaccines can be greatly improved by polymer agents that simultaneously increase transgene expression and activate immunity. we describe here pluronic p85 (p85), a triblock copolymer of ethylene oxide (eo) and propylene oxide (po) eo(26)-po(40)-eo(26). using a mouse model we demonstrate that co-administration of a bacterial plasmid dna with p85 in a skeletal muscle greatly increases gene expression in the injection site and distant organs, especially the draining lymph nodes and spleen. the r ...	2009	19064283
the effect of the nonionic block copolymer pluronic p85 on gene expression in mouse muscle and antigen-presenting cells.	dna vaccines can be greatly improved by polymer agents that simultaneously increase transgene expression and activate immunity. we describe here pluronic p85 (p85), a triblock copolymer of ethylene oxide (eo) and propylene oxide (po) eo(26)-po(40)-eo(26). using a mouse model we demonstrate that co-administration of a bacterial plasmid dna with p85 in a skeletal muscle greatly increases gene expression in the injection site and distant organs, especially the draining lymph nodes and spleen. the r ...	2009	19064283
relapsing peritonitis caused by bordetella bronchiseptica in continuous ambulatory peritoneal dialysis patient: a case report.	bordetella (b) bronchiseptica is a common veterinary pathogen, but has rarely been implicated in human infections. most patients with b. bronchiseptica infections are compromised clinically such as in patients with a malignancy, aids, malnutrition, or chronic renal failure. we experienced a case of relapsing peritonitis caused by b. bronchiseptica associated with continuous ambulatory peritoneal dialysis (capd). a 56-yr-old male, treated with capd due to end stage renal disease (esrd), was admit ...	2009	19194556
th17 cells at the crossroads of innate and adaptive immunity against infectious diseases at the mucosa.	t helper type 17 (th17) cells are a distinct lineage of t cells that produce the effector molecules il-17, il-17f, il-21, and il-22. although the role of th17 cells in autoimmunity is well documented, there is growing evidence that the th17 lineage and other interleukin (il)-17-producing cells are critical for host defense against bacterial, fungal, and viral infections at mucosal surfaces. here we summarize recent progress in our understanding of the function of il-17-producing cells as a bridg ...	2009	19587639
role of the type iii secretion system in a hypervirulent lineage of bordetella bronchiseptica.	despite the fact that closely related bacteria can cause different levels of disease, the genetic changes that cause some isolates to be more pathogenic than others are generally not well understood. we use a combination of approaches to determine which factors contribute to the increased virulence of a bordetella bronchiseptica lineage. a strain isolated from a host with b. bronchiseptica-induced disease, strain 1289, was 60-fold more virulent in mice than one isolated from an asymptomatically ...	2009	19596779
contribution of bordetella bronchiseptica filamentous hemagglutinin and pertactin to respiratory disease in swine.	bordetella bronchiseptica is pervasive in swine populations and plays multiple roles in respiratory disease. most studies addressing virulence factors of b. bronchiseptica are based on isolates derived from hosts other than pigs. two well-studied virulence factors implicated in the adhesion process are filamentous hemagglutinin (fha) and pertactin (prn). we hypothesized that both fha and prn would serve critical roles in the adhesion process and be necessary for colonization of the swine respira ...	2009	19237531
safety and efficacy of neonatal vaccination.	newborns have an immature immune system that renders them at high risk for infection while simultaneously reducing responses to most vaccines, thereby posing challenges in protecting this vulnerable population. nevertheless, certain vaccines, such as bcg and hepatitis b vaccine, do demonstrate safety and some efficacy at birth, providing proof of principal that certain antigen-adjuvant combinations are able to elicit protective neonatal responses. moreover, birth is a major point of healthcare c ...	2009	19089811
role of neutrophils in response to bordetella pertussis infection in mice.	pertussis is an acute respiratory disease caused by the bacterium bordetella pertussis, for which humans are the only known reservoir. during infection, b. pertussis releases several toxins, including pertussis toxin (pt) and adenylate cyclase toxin (act), which have both been shown to play roles in promoting bacterial growth during early infection in a mouse model. furthermore, in vitro and in vivo studies suggest that pt and act affect neutrophil chemotaxis and/or function, thereby altering th ...	2009	19103765
role of neutrophils in response to bordetella pertussis infection in mice.	pertussis is an acute respiratory disease caused by the bacterium bordetella pertussis, for which humans are the only known reservoir. during infection, b. pertussis releases several toxins, including pertussis toxin (pt) and adenylate cyclase toxin (act), which have both been shown to play roles in promoting bacterial growth during early infection in a mouse model. furthermore, in vitro and in vivo studies suggest that pt and act affect neutrophil chemotaxis and/or function, thereby altering th ...	2009	19103765
the pgaabcd locus of acinetobacter baumannii encodes the production of poly-beta-1-6-n-acetylglucosamine, which is critical for biofilm formation.	we found that acinetobacter baumannii contains a pgaabcd locus that encodes proteins that synthesize cell-associated poly-beta-(1-6)-n-acetylglucosamine (pnag). both a mutant with an in-frame deletion of the pga locus (s1deltapga) and a transcomplemented strain (s1deltapga-c) of a. baumannii were constructed, and the pnag production by these strains was compared using an immunoblot assay. deleting the pga locus resulted in an a. baumannii strain without pnag, and transcomplementation of the s1de ...	2009	19633088
rapid real-time pcr assays for detection of klebsiella pneumoniae with the rmpa or maga genes associated with the hypermucoviscosity phenotype: screening of nonhuman primates.	the relationship of mucoviscosity-associated (maga) and/or regulator of mucoid phenotype (rmpa) genes to the klebsiella pneumoniae hypermucoviscosity (hmv) phenotype has been reported. we previously demonstrated that rmpa+ k. pneumoniae can cause serious disease in african green monkeys and isolated rmpa+ and maga+ hmv k. pneumoniae from other species of non-human primates. to rapidly screen african green monkeys/non-human primates for these infections, we developed three real-time pcr assays. t ...	2009	19644019
the bordetella type iii secretion system effector btea contains a conserved n-terminal motif that guides bacterial virulence factors to lipid rafts.	the bordetella type iii secretion system (t3ss) effector protein btea is necessary and sufficient for rapid cytotoxicity in a wide range of mammalian cells. we show that btea is highly conserved and functionally interchangeable between bordetella bronchiseptica, bordetella pertussis and bordetella parapertussis. the identification of btea sequences required for cytotoxicity allowed the construction of non-cytotoxic mutants for localization studies. btea derivatives were targeted to lipid rafts a ...	2009	19650828
klebsiella pneumoniae triggers a cytotoxic effect on airway epithelial cells.	klebsiella pneumoniae is a capsulated gram negative bacterial pathogen and a frequent cause of nosocomial infections. despite its clinical relevance, little is known about the features of the interaction between k. pneumoniae and lung epithelial cells on a cellular level, neither about the role of capsule polysaccharide, one of its best characterised virulence factors, in this interaction.	2009	19650888
microbial contaminations of laboratory mice and rats in taiwan from 2004 to 2007.	limited data are available on the pathogen status of contemporary rodent colonies in taiwan. here we summarized the rodent pathogen diagnostic records of the taiwan national laboratory animal center during a 4-y period that representing approximately 10% of the rodent colonies in taiwan. demand for pathogen diagnostic service increased continuously from 2004 to 2007, with a 20% increase each year. in 2007, more than 20% of the mouse colonies were positive for mouse parvovirus, mouse hepatitis vi ...	2009	19653946
immunodominance in mouse and human cd4+ t-cell responses specific for the bordetella pertussis virulence factor p.69 pertactin.	p.69 pertactin (p.69 prn), an adhesion molecule from the causative agent of pertussis, bordetella pertussis, is present in cellular and most acellular vaccines that are currently used worldwide. although both humoral immunity and cellular immunity directed against p.69 prn have been implicated in protective immune mechanisms, the identities of cd4(+) t-cell epitopes on the p.69 prn protein remain unknown. here, a single i-a(d)-restricted b. pertussis conserved cd4(+) t-cell epitope at the n term ...	2009	19015250
bordetella bsp22 forms a filamentous type iii secretion system tip complex and is immunoprotective in vitro and in vivo.	type iii secretion system (t3ss) tip complexes serve as adaptors that bridge the t3ss needle and the pore-forming translocation apparatus. in this report we demonstrate that bsp22, the most abundantly secreted substrate of the bordetella t3ss, self-polymerizes to form the bordetella bronchiseptica tip complex. bsp22 is required for both t3ss-mediated cytotoxicity against eukaryotic cells and haemoglobin release from erythrocytes. bacterial two-hybrid analysis and protein pull-down assays demonst ...	2009	19040642
shifting the genomic gold standard for the prokaryotic species definition.	dna-dna hybridization (ddh) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. it has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. however, now, in the era of genomics, ddh appears to be an outdated method for classification that needs to be substituted. the average nucleotide identi ...	2009	19855009
enantioselective protonation.	enantioselective protonation is a common process in biosynthetic sequences. the decarboxylase and esterase enzymes that effect this valuable transformation are able to control both the steric environment around the proton acceptor (typically an enolate) and the proton donor (typically a thiol). recently, several chemical methods to achieve enantioselective protonation have been developed by exploiting various means of enantiocontrol in different mechanisms. these laboratory transformations have ...	2009	20428461
mechanisms of neutrophil accumulation in the lungs against bacteria.	bacterial lung diseases are a major cause of morbidity and mortality both in immunocompromised and in immunocompetent individuals. neutrophil accumulation, a pathological hallmark of bacterial diseases, is critical to host defense, but may also cause acute lung injury/acute respiratory distress syndrome. toll-like receptors, nucleotide-binding oligomerization domain (nod)-like receptors, transcription factors, cytokines, and chemokines play essential roles in neutrophil sequestration in the lung ...	2009	19738160
mechanisms of neutrophil accumulation in the lungs against bacteria.	bacterial lung diseases are a major cause of morbidity and mortality both in immunocompromised and in immunocompetent individuals. neutrophil accumulation, a pathological hallmark of bacterial diseases, is critical to host defense, but may also cause acute lung injury/acute respiratory distress syndrome. toll-like receptors, nucleotide-binding oligomerization domain (nod)-like receptors, transcription factors, cytokines, and chemokines play essential roles in neutrophil sequestration in the lung ...	2009	19738160
dissecting the bacterial type vi secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?	the availability of hundreds of bacterial genomes allowed a comparative genomic study of the type vi secretion system (t6ss), recently discovered as being involved in pathogenesis. by combining comparative and phylogenetic approaches using more than 500 prokaryotic genomes, we characterized the global t6ss genetic structure in terms of conservation, evolution and genomic organization.	2009	19284603
the roles of antimicrobial peptides in innate host defense.	antimicrobial peptides (amps) are multi-functional peptides whose fundamental biological role in vivo has been proposed to be the elimination of pathogenic microorganisms, including gram-positive and -negative bacteria, fungi, and viruses. genes encoding these peptides are expressed in a variety of cells in the host, including circulating phagocytic cells and mucosal epithelial cells, demonstrating a wide range of utility in the innate immune system. expression of these genes is tightly regulate ...	2009	19601838
spontaneous pathology of the common marmoset (callithrix jacchus) and tamarins (saguinus oedipus, saguinus mystax).	marmosets and tamarins are increasingly used in research, but their pathology remains poorly defined compared with old world primates.	2009	19522731
precarious balance: th17 cells in host defense.	lineage-specific responses from the effector t-cell repertoire form a critical component of adaptive immunity. the recent identification of th17 cells-a third, distinct lineage of helper t cells-collapses the long-accepted paradigm in which th1 and th2 cells distinctly mediate cellular and humoral immunity, respectively. in this minireview, we discuss the involvement of the th17 lineage during infection by extracellular bacteria, intracellular bacteria, and fungi. emerging trends suggest that th ...	2009	19901061
the vitamin d connection to pediatric infections and immune function.	over the past 20 y, a resurgence in vitamin d deficiency and nutritional rickets has been reported throughout the world, including the united states. inadequate serum vitamin d concentrations have also been associated with complications from other health problems, including tuberculosis, cancer (prostate, breast, and colon), multiple sclerosis, and diabetes. these findings support the concept of vitamin d possessing important pleiotropic actions outside of calcium homeostasis and bone metabolism ...	2009	19190532
il-17 and anti-bacterial immunity: protection versus tissue damage.	il-17 can impact health in a variety of ways. it is protective for some pathogens but it is also associated with tissue damaging inflammation. by examining the role of il-17 in a variety of bacterial infections the mechanisms by which this cytokine mediates both protection and damage can be dissected. a key element in understanding the role of this cytokine is determining where and when it is acting. dissecting its essential protective role from its immunopathologic role will allow for improved ...	2009	19283706
precarious balance: th17 cells in host defense.	lineage-specific responses from the effector t-cell repertoire form a critical component of adaptive immunity. the recent identification of th17 cells-a third, distinct lineage of helper t cells-collapses the long-accepted paradigm in which th1 and th2 cells distinctly mediate cellular and humoral immunity, respectively. in this minireview, we discuss the involvement of the th17 lineage during infection by extracellular bacteria, intracellular bacteria, and fungi. emerging trends suggest that th ...	2009	19901061
bioshock: biotechnology and bioterrorism.	in the recent past, the threat of a global bioterrorist attack has increased dramatically. in addition to the already existing microorganisms and techniques, the recent explosion in biotechnology has considerably added to the arsenal of the bioterrorist. molecular technologies are now available which can be used by committed bioterrorist groups to manipulate and modify microorganisms so as to make them increasingly infectious, virulent or treatment resistant for causing maximum casualties. infec ...	2009	27408292
performance of transport and selective media for swine bordetella bronchiseptica recovery and it comparison to polymerase chain reaction detection.	three comparative assays were performed seeking to improve the sensitivity of the diagnosis of bordetella bronchiseptica infection analyzing swine nasal swabs. an initial assay compared the recovery of b. bronchiseptica from swabs simultaneously inoculated with b. bronchiseptica and some interfering bacteria, immersed into three transport formulations (amies with charcoal, trypticase soy broth and phosphate buffer according to soerensen supplemented with 5% of bovine fetal serum) and submitted t ...	2009	24031390
neutrophil recruitment to the lungs during bacterial pneumonia.		2008	19015252
boolean network simulations for life scientists.	modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. within the theoretical models boolean networks occupy an increasing role as they are eminently suited at mapping biological observations and hypotheses into a mathematical formalism. the conceptual underpinnings of boolean modeling are very accessible even without a background in quantitative sciences, yet it allows life scientists to describe and explore a wide r ...	2008	19014577
a new pheromone trail-based genetic algorithm for comparative genome assembly.	gap closing is considered one of the most challenging and time-consuming tasks in bacterial genome sequencing projects, especially with the emergence of new sequencing technologies, such as pyrosequencing, which may result in large amounts of data without the benefit of large insert libraries for contig scaffolding. we propose a novel algorithm to align contigs with more than one reference genome at a time. this approach can successfully overcome the limitations of low degrees of conserved gene ...	2008	18445633
detection of mycoplasma hyopneumoniae by polymerase chain reaction in swine presenting respiratory problems.	since mycoplasma hyopneumoniae isolation in appropriate media is a difficult task and impractical for daily routine diagnostics, nested-pcr (n-pcr) techniques are currently used to improve the direct diagnostic sensitivity of swine enzootic pneumonia. in a first experiment, this paper describes a n-pcr technique optimization based on three variables: different sampling sites, sample transport media, and dna extraction methods, using eight pigs. based on the optimization results, a second experim ...	2008	24031248
pulmonary bacterial pathogens in cystic fibrosis patients and antibiotic therapy: a tool for the health workers.	cystic fibrosis is the most common and best known genetic disease involving a defect in transepithelial cl- transport by mutations in the cf gene on chromosome 7, which codes for the cystic fibrosis transmembrane conductance regulator protein (cftr). the most serious symptoms are observed in the lungs, augmenting the risk of bacterial infection. the objective of this review was to describe the bacterial pathogens colonizing patients with cystic fibrosis. a systematic search was conducted using t ...	2008	18992146
genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.	serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. while studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. current analysis is aimed at understanding the distribution and probable b ...	2008	19019219
molecular genetic basis of ribotyping.	nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. none precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rrna gene sequences. based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rrna operons, with rrna gene sequences serving solely as conserved, flank-linked tags. we also reveal that from such an infor ...	2008	18400796
assessment of gut bacteria for a paratransgenic approach to control dermolepida albohirtum larvae.	bacteria from the hindguts of dermolepida albohirtum larvae were assessed for their potential to be used in paratransgenic strategies that target scarab pests of sugarcane. bacteria isolated in pure culture from the hindguts of d. albohirtum larvae were from the proteobacteria, firmicutes, and actinobacteria phyla and matched closely with taxa from intestinal and rhizosphere environments. however, these isolates were not the most common gut-associated bacteria identified in denaturing gradient g ...	2008	18456847
systematic identification of stem-loop containing sequence families in bacterial genomes.	analysis of non-coding sequences in several bacterial genomes brought to the identification of families of repeated sequences, able to fold as secondary structures. these sequences have often been claimed to be transcribed and fulfill a functional role. a previous systematic analysis of a representative set of 40 bacterial genomes produced a large collection of sequences, potentially able to fold as stem-loop structures (sls). computational analysis of these sequences was carried out by searchin ...	2008	18201379
estimating the fraction of non-coding rnas in mammalian transcriptomes.	recent studies of mammalian transcriptomes have identified numerous rna transcripts that do not code for proteins; their identity, however, is largely unknown. here we explore an approach based on sequence randomness patterns to discern different rna classes. the relative z-score we use helps identify the known ncrna class from the genome, intergene and intron classes. this leads us to a fractional ncrna measure of putative ncrna datasets which we model as a mixture of genuine ncrnas and other t ...	2008	19812767
neutrophil recruitment to the lungs during bacterial pneumonia.		2008	19015252
white tide.		2008	25949289
white tide.		2008	25949289
the porcine lung as a potential model for cystic fibrosis.	airway disease currently causes most of the morbidity and mortality in patients with cystic fibrosis (cf). however, understanding the pathogenesis of cf lung disease and developing novel therapeutic strategies have been hampered by the limitations of current models. although the gene encoding the cystic fibrosis transmembrane conductance regulator (cftr) has been targeted in mice, cf mice fail to develop lung or pancreatic disease like that in humans. in many respects, the anatomy, biochemistry, ...	2008	18487356
concentration and emission of airborne contaminants in a laboratory animal facility housing rabbits.	characterization of animal housing conditions can determine the frequency of bedding and cage changes, which are not standardized from facility to facility. rabbits produce noticeable odors, and their excreta can scald and stain cages. our facility wanted to document measurable airborne contaminants in a laboratory rabbit room in which excreta pans were changed weekly and cages changed biweekly. contaminants included particulate, endotoxin, ammonia, carbon dioxide, and a rabbit salivary protein ...	2008	18351721
real-time pcr assays of single-nucleotide polymorphisms defining the major brucella clades.	members of the genus brucella are known worldwide as pathogens of wildlife and livestock and are the most common organisms of zoonotic infection in humans. in general, brucellae exhibit a range of host specificity in animals that has led to the identification of at least seven brucella species. the genomes of the various brucella species are highly conserved, which makes the differentiation of species highly challenging. however, we found single-nucleotide polymorphisms (snps) in housekeeping an ...	2008	18032628
prevalence of actinobacillus pleuropneumoniae, actinobacillus suis, haemophilus parasuis, pasteurella multocida, and streptococcus suis in representative ontario swine herds.	tonsillar and nasal swabs were collected from weanling pigs in 50 representative ontario swine herds and tested for the presence of 5 important bacterial upper respiratory tract pathogens. all but 1 herd (2%) tested positive for streptococcus suis by polymerase chain reaction (pcr); 48% of herds were s. suis serovar 2, 1/2 positive. in all but 2 herds there was evidence of haemophilus parasuis infection. in contrast, toxigenic strains of pasteurella multocida were detected by a p. multocida--enz ...	2008	18505187
during infection of epithelial cells salmonella enterica serovar typhimurium undergoes a time-dependent transcriptional adaptation that results in simultaneous expression of three type 3 secretion systems.	the biogenesis of the salmonella-containing vacuole within mammalian cells has been intensively studied over recent years. however, the ability of salmonella to sense and adapt to the intracellular environment of different types of host cells has received much less attention. to address this issue, we report the transcriptome of salmonella enterica serovar typhimurium sl1344 within epithelial cells and show comparisons with salmonella gene expression inside macrophages. we report that s. typhimu ...	2008	18031307
serendipitous discovery of an immunoglobulin-binding autotransporter in bordetella species.	we describe the serendipitous discovery of batb, a classical-type bordetella autotransporter (at) protein with an approximately 180-kda passenger domain that remains noncovalently associated with the outer membrane. like genes encoding all characterized protein virulence factors in bordetella species, batb transcription is positively regulated by the master virulence regulatory system bvgas. batb is predicted to share similarity with immunoglobulin a (iga) proteases, and we showed that batb bind ...	2008	18426869
agr-mediated dispersal of staphylococcus aureus biofilms.	the agr quorum-sensing system of staphylococcus aureus modulates the expression of virulence factors in response to autoinducing peptides (aips). recent studies have suggested a role for the agr system in s. aureus biofilm development, as agr mutants exhibit a high propensity to form biofilms, and cells dispersing from a biofilm have been observed displaying an active agr system. here, we report that repression of agr is necessary to form a biofilm and that reactivation of agr in established bio ...	2008	18437240
real-time pcr assays of single-nucleotide polymorphisms defining the major brucella clades.	members of the genus brucella are known worldwide as pathogens of wildlife and livestock and are the most common organisms of zoonotic infection in humans. in general, brucellae exhibit a range of host specificity in animals that has led to the identification of at least seven brucella species. the genomes of the various brucella species are highly conserved, which makes the differentiation of species highly challenging. however, we found single-nucleotide polymorphisms (snps) in housekeeping an ...	2008	18032628
escherichia coli biofilms.	escherichia coli is a predominant species among facultative anaerobic bacteria of the gastrointestinal tract. both its frequent community lifestyle and the availability of a wide array of genetic tools contributed to establish e. coli as a relevant model organism for the study of surface colonization. several key factors, including different extracellular appendages, are implicated in e. coli surface colonization and their expression and activity are finely regulated, both in space and time, to ...	2008	18453280
bordetella bronchiseptica responses to physiological reactive nitrogen and oxygen stresses.	bordetella bronchiseptica can establish prolonged airway infection consistent with a highly developed ability to evade mammalian host immune responses. upon initial interaction with the host upper respiratory tract mucosa, b. bronchiseptica are subjected to antimicrobial reactive nitrogen species (rns) and reactive oxygen species (ros), effector molecules of the innate immune system. however, the responses of b. bronchiseptica to redox species at physiologically relevant concentrations (nm-micro ...	2008	18462394
[expression of prn gene of bordetella bronchiseptica and development of a recombinant protein-based indirect elisa for antibodies detection].	we developed an indirect elisa method for detecting bordetella bronchiseptica (bb) pertactin antibodies based on the recombinant pertactin protein expressed in escherichia coli (de3) strain.	2008	18479059
[protecting mice from fatal bordetella bronchiseptica infection by immunization with recombinant pertactin antigens].	we evaluated the efficacy of the recombinant pertactin (prn)-specific active or passive immunization against bordetella bronchiseptica (bb) in an aerosol challenge model established by using balb/c mice.	2008	18479060
inter- and intraserotypic variation in the streptococcus pyogenes rgg regulon.	human isolates of streptococcus pyogenes, a gram-positive bacterium, are characterized by significant genetic and phenotypic variation. the rgg locus, also known as ropb, is a global transcriptional regulator of genes associated with metabolism, stress responses, and virulence in s. pyogenes strain nz131 (serotype m49). to assess the breadth of the rgg regulon, the rgg gene was inactivated in three additional strains representing serotypes m1 (strains sf370 and mgas5005) and m49 (strain cs101). ...	2008	18479433
demonstration of is711 transposition in brucella ovis and brucella pinnipedialis.	the brucella genome contains an insertion sequence (is) element called is711 or is6501, which is specific to the genus. the copy number of is711 varies in the genome of the different brucella species, ranging from 7 in b. abortus, b. melitensis and b. suis to more than 30 in b. ovis and in brucella strains isolated from marine mammals. at present, there is no experimental evidence of transposition of is711, but the occurrence of this element with a high copy number in some species, and the isola ...	2008	18218072
photorhabdus luminescens genes induced upon insect infection.	photorhabdus luminescens is a gram-negative luminescent enterobacterium and a symbiote to soil nematodes belonging to the species heterorhabditis bacteriophora. p.luminescens is simultaneously highly pathogenic to insects. this bacterium exhibits a complex life cycle, including one symbiotic stage characterized by colonization of the upper nematode gut, and a pathogenic stage, characterized by release from the nematode into the hemocoel of insect larvae, resulting in rapid insect death caused by ...	2008	18489737
authors' reply to 'misidentification of bordetella bronchiseptica as bordetella pertussis using a newly described rt-pcr targeting the pertactin gene'.		2008	18287309
burkholderia thailandensis as a model system for the study of the virulence-associated type iii secretion system of burkholderia pseudomallei.	burkholderia pseudomallei is a bacterial pathogen that causes a broad spectrum of clinical symptoms collectively known as melioidosis. since it can be acquired by inhalation and is difficult to eradicate due to its resistance to a wide group of antibiotics and capacity for latency, work with b. pseudomallei requires a biosafety level 3 (bsl-3) containment facility. the bsa (burkholderia secretion apparatus)-encoded type iii secretion system (ttss) has been shown to be required for its full virul ...	2008	18779342
detection of respiratory pathogens in air samples from acutely infected pigs.	pathogens causing significant respiratory disease in growing pigs include porcine reproductive and respiratory syndrome virus, porcine circovirus 2, swine influenza virus, porcine respiratory coronavirus, mycoplasma hyopneumoniae, and bordetella bronchiseptica. the objective of this research was to characterize the respiratory excretion of these pathogens by acutely infected pigs. pigs were inoculated under experimental conditions with 1 pathogen. samples were collected from the upper respirator ...	2008	18783027
bordetella pertussis isolates in finland: serotype and fimbrial expression.	bordetella pertussis causes whooping cough or pertussis in humans. it produces several virulence factors, of which the fimbriae are considered adhesins and elicit immune responses in the host. b. pertussis has three distinct serotypes fim2, fim3 or fim2,3. generally, b. pertussis fim2 strains predominate in unvaccinated populations, whereas fim3 strains are often isolated in vaccinated populations. in finland, pertussis vaccination was introduced in 1952. the whole-cell vaccine contained two str ...	2008	18816412
the missing link: bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic bordetellae.	bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus bordetella. phylogenetically, it connects the pathogenic bordetellae and environmental bacteria of the genera achromobacter and alcaligenes, which are opportunistic pathogens. b. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. recently, clinical isolates asso ...	2008	18826580
screening, cloning, expression, and purification of an acidic arylmalonate decarboxylase from enterobacter cloacae ku1313.	we have already isolated, purified, and characterized arylmalonate decarboxylases (amdase; ec. 4.1.1.76) from alcaligenes bronchisepticus ku1201 and achromobacter sp. ku1311. these are unique enzymes that give optically pure alpha-arylpropionates from the corresponding alpha-aryl-alpha-methylmalonates. recently, we have further screened novel amdase producers from soil samples under acidic conditions and succeeded in isolating enterobacter cloacae ku1313. the gene encoding the enzyme was cloned ...	2008	18283449
diversity of incp-9 plasmids of pseudomonas.	incp-9 plasmids are important vehicles for degradation and resistance genes that contribute to the adaptability of pseudomonas species in a variety of natural habitats. the three completely sequenced incp-9 plasmids, pww0, pdtg1 and nah7, show extensive homology in replication, partitioning and transfer loci (an approximately 25 kb region) and to a lesser extent in the remaining backbone segments. we used pcr, dna sequencing, hybridization and phylogenetic analyses to investigate the genetic div ...	2008	18832300
iterative reconstruction of a global metabolic model of acinetobacter baylyi adp1 using high-throughput growth phenotype and gene essentiality data.	genome-scale metabolic models are powerful tools to study global properties of metabolic networks. they provide a way to integrate various types of biological information in a single framework, providing a structured representation of available knowledge on the metabolism of the respective species.	2008	18840283
antibiograms of pathogenic bacteria isolated from laboratory rabbits in ibadan, nigeria.	antibiotic sensitivity patterns of 21 bacterial isolates from some clinically ill new zealand rabbits were evaluated against 12 commonly used antibiotics by the kirby-bauer disk-diffusion sensitivity testing method. the 21 isolates consisted of six bordetella bronchiseptica, eight pasteurella multocida, four staphylococcus aureus and three pseudomonas alcaligenes that were associated with snuffles, pneumonia, otitis media, genital infections and conjunctivitis in these groups of caged rabbits. t ...	2008	18840619
polysaccharides cellulose, poly-beta-1,6-n-acetyl-d-glucosamine, and colanic acid are required for optimal binding of escherichia coli o157:h7 strains to alfalfa sprouts and k-12 strains to plastic but not for binding to epithelial cells.	when escherichia coli o157:h7 bacteria are added to alfalfa sprouts growing in water, the bacteria bind tightly to the sprouts. in contrast, laboratory k-12 strains of e. coli do not bind to sprouts under similar conditions. the roles of e. coli o157:h7 lipopolysaccharide (lps), capsular polysaccharide, and exopolysaccharides in binding to sprouts were examined. an lps mutant had no effect on the binding of the pathogenic strain. cellulose synthase mutants showed a significant reduction in bindi ...	2008	18310435
a retrospective study of canine persistent nasal disease: 80 cases (1998-2003).	persistent canine nasal disease is a common complaint in small animal practice; however, an etiologic diagnosis can be difficult to establish. the aim of this retrospective study was to determine the percentage of cases for which the etiology was determined in our hospital population. medical records from 80 dogs met the criteria of inclusion in the study. nonspecific rhinitis was identified in 23.7% of cases. other diagnoses were neoplasia (15.0%), fungal infection (nasal aspergillosis) (8.7%), ...	2008	18320982
identification of bordetella spp. in respiratory specimens from individuals with cystic fibrosis.	bordetella spp. are not normally included when considering the opportunistic bacterial species that are typically involved in respiratory tract infections in individuals with cystic fibrosis (cf). by using a combination of bacterial genotyping and 16s rdna sequencing, bordetella spp. were identified in cultures obtained from 43 individuals with cf. most (n = 23) patients were infected with bordetella bronchiseptica/parapertussis; five were infected with bordetella hinzii, four with bordetella pe ...	2008	18325036
comparison of serological and real-time pcr assays to diagnose bordetella pertussis infection in 2007.	bacterial culture for diagnosing pertussis infection has high specificity but poor sensitivity and is slow. highly sensitive real-time pcr assays and single-serum pertussis serology have been developed to overcome these limitations, but there are few data available on the relative sensitivities and specificities of such assays for pertussis diagnosis. using data on 195 participants (>or=7 years old) from an epidemiological study, we assessed the sensitivity, specificity, and performance (youden ...	2008	18367565
norepinephrine mediates acquisition of transferrin-iron in bordetella bronchiseptica.	previous research demonstrated that the sympathoadrenal catecholamine norepinephrine could promote the growth of bordetella bronchiseptica in iron-restricted medium containing serum. in this study, norepinephrine was demonstrated to stimulate growth of this organism in the presence of partially iron-saturated transferrin but not lactoferrin. although norepinephrine is known to induce transcription of the bordetella bfea enterobactin catechol xenosiderophore receptor gene, neither a bfea mutant n ...	2008	18390651
helicobacter hepaticus infection promotes colon tumorigenesis in the balb/c-rag2(-/-) apc(min/+) mouse.	adenomatous polyposis coli (apc) mutations are linked to human and mouse colorectal cancers. the apc multiple intestinal neoplasia (min) mouse mutation causes adenomas to develop throughout the small and large intestines. the balb-min (c.b6-apc(min/+)) congenic strain was generated by backcrossing into balb/c the apc(min) allele from c57bl/6j-apc(min/+) mice. balb-min mice have a low tumor multiplicity (27.4 small intestine tumors/mouse) and a relatively long life span (>1 year) that makes them ...	2008	18411292
glucosamine found as a substituent of both phosphate groups in bordetella lipid a backbones: role of a bvgas-activated arnt ortholog.	endotoxins are amphipathic lipopolysaccharides (lpss), major constituents of the outer membrane of gram-negative bacteria. they consist of a lipid region, covalently linked to a core oligosaccharide, to which may be linked a repetitive glycosidic chain carrying antigenic determinants. most of the biological activities of endotoxins have been associated with the lipid moiety of the molecule: unique to gram-negative bacteria, lps is a ligand of the mammalian tlr4-md2-cd14 pathogen recognition rece ...	2008	18424515
transmission of avian influenza virus (h3n2) to dogs.	in south korea, where avian influenza virus subtypes h3n2, h5n1, h6n1, and h9n2 circulate or have been detected, 3 genetically similar canine influenza virus (h3n2) strains of avian origin (a/canine/korea/01/2007, a/canine/korea/02/2007, and a/canine/korea/03/2007) were isolated from dogs exhibiting severe respiratory disease. to determine whether the novel canine influenza virus of avian origin was transmitted among dogs, we experimentally infected beagles with this influenza virus (h3n2) isola ...	2008	18439355
comparative genomics and an insect model rapidly identify novel virulence genes of burkholderia mallei.	burkholderia pseudomallei and its host-adapted deletion clone burkholderia mallei cause the potentially fatal human diseases melioidosis and glanders, respectively. the antibiotic resistance profile and ability to infect via aerosol of these organisms and the absence of protective vaccines have led to their classification as major biothreats and select agents. although documented infections by these bacteria date back over 100 years, relatively little is known about their virulence and pathogeni ...	2008	18223084
application of intact cell-based nfat-beta-lactamase reporter assay for pasteurella multocida toxin-mediated activation of calcium signaling pathway.	pasteurella multocida toxin (pmt) stimulates and subsequently uncouples phospholipase c beta1 (plcbeta1) signal transduction through its selective action on the alpha subunit of the gq-protein. here, we describe the application of an nfat-beta-lactamase reporter assay as a functional readout for pmt-induced activation of the gq-protein-coupled plcbeta1-ip(3)-ca(2+) signaling pathway. use of the nfat-beta-lactamase reporter assay with a cell-permeable fluorogenic substrate provides high sensitivi ...	2008	18190943
application of intact cell-based nfat-beta-lactamase reporter assay for pasteurella multocida toxin-mediated activation of calcium signaling pathway.	pasteurella multocida toxin (pmt) stimulates and subsequently uncouples phospholipase c beta1 (plcbeta1) signal transduction through its selective action on the alpha subunit of the gq-protein. here, we describe the application of an nfat-beta-lactamase reporter assay as a functional readout for pmt-induced activation of the gq-protein-coupled plcbeta1-ip(3)-ca(2+) signaling pathway. use of the nfat-beta-lactamase reporter assay with a cell-permeable fluorogenic substrate provides high sensitivi ...	2008	18190943
a temperature-regulated campylobacter jejuni gluconate dehydrogenase is involved in respiration-dependent energy conservation and chicken colonization.	campylobacter jejuni is a gastrointestinal pathogen of humans but can asymptomatically colonize the avian gut. c. jejuni therefore grows at both 37 degrees c and 42 degrees c, the internal temperatures of humans and birds respectively. microarray and proteomic studies on temperature regulation in c. jejuni strain 81-176 revealed the upregulation at 42 degrees c of two proteins, cj0414 and cj0415, orthologous to gluconate dehydrogenase (gadh) from pectobacterium cypripedii. 81-176 demonstrated ga ...	2008	18284594
alveolar macrophages are indispensable for controlling influenza viruses in lungs of pigs.	alveolar macrophages constitutively reside in the respiratory tracts of pigs and humans. an in vivo role of alveolar macrophages in defending against influenza viruses in mice infected with a reassorted influenza virus, 1918 ha/na:tx/91, was reported, but there has been no report on an in vivo role of alveolar macrophages in a natural host such as a pig using currently circulating human influenza virus. here we show that in vivo depletion of alveolar macrophages in pigs by dichloromethylene diph ...	2008	18287245
structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane.	the outer membranes of gram-negative bacteria are replete with integral membrane proteins that exhibit antiparallel beta-barrel structures, but very few of these proteins function as enzymes. in escherichia coli, only three beta-barrel enzymes are known to exist in the outer membrane; these are the phospholipase ompla, the protease ompt, and the phospholipidcolon, two colonslipid a palmitoyltransferase pagp, all of which have been characterized at the structural level. structural details have al ...	2008	17880914
associations between pathogens in healthy pigs and pigs with pneumonia.	the aim of this study was to evaluate the associations between different pathogens in the development of pneumonia and bronchopneumonia in pigs. samples of bronchoalveolar lavage fluid from 100 pigs showing no clinical signs and 239 pigs with clinical signs of respiratory disease were examined for mycoplasma hyopneumoniae, mycoplasma hyorhinis, us-type porcine respiratory and reproductive syndrome virus (prrsv), eu-type prrsv, porcine circovirus type 2 (pcv-2), influenza virus type a, alpha-haem ...	2008	18310558