Publications

bacterial colonization immediately after installation on oral titanium implants.	information on bacterial colonization immediately after dental implant insertion is limited.	2007	17501978
treponema denticola induces interleukin-8 and macrophage chemoattractant protein 1 production in human umbilical vein epithelial cells.	treponema denticola, a major pathogen of periodontitis, has also been detected in the lesions of atherosclerosis. the aim of this study was to investigate induction of chemokine production in human umbilical vein endothelial cells (huvecs) by t. denticola and determine whether those chemokines were degraded by a protease, dentilisin. t. denticola atcc35405 or dentilisin-deficient mutant k1 were added to huvecs and levels of interleukin-8 (il-8) and monocyte chemoattractant protein-1 (mcp-1) in t ...	2007	17533151
microbiological findings after periodontal therapy using curettes, er:yag laser, sonic, and ultrasonic scalers.	to evaluate and compare the microbiological effects of hand instruments, er:yag-laser, sonic, and ultrasonic scalers in patients with chronic periodontitis. patient perception of each treatment was documented.	2007	17555412
an actin-stabilizing peptide conjugate deduced from the major outer sheath protein of the bacterium treponema denticola.	a synthetic peptide conjugated to bovine serum albumin, p34(bsa), based on a 10-mer in the deduced amino acid sequence of the major outer sheath protein of treponema denticola, was found to stabilize actin filaments of fibroblasts. pretreatment of cells with p34(bsa) inhibited the actin disruption induced by cytochalasin d and latrunculin b. p34(bsa) was taken up by the cells and localized among actin filaments. p34(bsa) bound actin from fibroblast lysates, and cell exposure to p34(bsa) led to t ...	2007	17565753
population-based study of salivary carriage of periodontal pathogens in adults.	large, general population-based data on carriage rates of periodontal pathogens hardly exist in the current literature. the objectives of the present study were to examine the salivary detection of aggregatibacter (formerly actinobacillus) actinomycetemcomitans, campylobacter rectus, porphyromonas gingivalis, prevotella intermedia, tannerella forsythensis, and treponema denticola in a representative sample of the adult population living in southern finland and to clarify which determinants are a ...	2007	17567788
interleukin- 1 gene polymorphisms as assessed in a 10-year study of patients with early-onset periodontitis.	our 10-year study of early-onset periodontitis (eop) patients includes repeated clinical observations, microbiological characteristics and analysis of genetic polymorphism of il-1a and il-1b genes. twenty patients (age 15-26 years) were divided according to the clinical status in the 4th year into a group with mean number of teeth with bleeding on probing (bp) 9.8 and mean number of teeth with periodontal pocket (pp) 2.23, and a group with mean number of teeth with bp 5.37 and no pp. significant ...	2007	17575917
molecular architecture and divalent cation activation of tvok, a prokaryotic potassium channel.	rck (regulator of conductance of potassium) domains form a family of ligand-binding domains found in many prokaryotic k+ channels and transport proteins. although many rck domains contain an apparent nucleotide binding motif, some are known instead to bind ca2+, which can then facilitate channel opening. here we report on the molecular architecture and ligand activation properties of an rck-containing potassium channel cloned from the prokaryote thermoplasma volcanium. this channel, called tvok, ...	2007	17588939
the chymotrypsin-like protease complex of treponema denticola atcc 35405 mediates fibrinogen adherence and degradation.	treponema denticola is an anaerobic spirochete strongly associated with human periodontal disease. t. denticola bacteria interact with a range of host tissue proteins, including fibronectin, laminin, and fibrinogen. the latter localizes in the extracellular matrix where tissue damage has occurred, and interactions with fibrinogen may play a key role in t. denticola colonization of the damaged sites. t. denticola atcc 35405 showed saturable binding of fluid-phase fibrinogen to the cell surface an ...	2007	17591786
lesion formation and antibody response induced by papillomatous digital dermatitis-associated spirochetes in a murine abscess model.	papillomatous digital dermatitis (pdd), also known as hairy heel wart, is a growing cause of lameness of cows in the u.s. dairy industry. farms with pdd-afflicted cows experience economic loss due to treatment costs, decreased milk production, lower reproductive efficiency, and premature culling. while the exact cause of pdd is unknown, lesion development is associated with the presence of anaerobic spirochetes. this study was undertaken to investigate the virulence and antigenic relatedness of ...	2007	17591787
gamma-glutamyl transpeptidase has a role in the persistent colonization of the avian gut by campylobacter jejuni.	the contribution of gamma-glutamyl transpeptidase (ggt) to campylobacter jejuni virulence and colonization of the avian gut has been investigated. the presence of the ggt gene in c. jejuni strains directly correlated with the expression of ggt activity as measured by cleavage and transfer of the gamma-glutamyl moiety. inactivation of the monocistronic ggt gene in c. jejuni strain 81116 resulted in isogenic mutants with undetectable ggt activity; nevertheless, these mutants grew normally in vitro ...	2007	17600669
detection of azithromycin resistance in treponema pallidum by real-time pcr.	we describe a real-time pcr assay for the discrimination of azithromycin-resistant and -susceptible strains of treponema pallidum. this assay is rapid and allows for as many as 30 clinical specimens to be analyzed simultaneously without the need for dna sequencing.	2007	17620374
identification of 22 candidate structured rnas in bacteria using the cmfinder comparative genomics pipeline.	we applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate rna motifs. we predicted six to be riboswitches, which are mrna elements that regulate gene expression on binding a specific metabolite. in separate studies, we confirmed that two of these are novel riboswitches. three other riboswitch candidates are upstream of either a putative transporter gene in the order lactobacillales, citric acid cycle genes in burkholderiales or molybdenum co ...	2007	17621584
comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis.	molecular machinery governing bacterial chemotaxis consists of the chea-chey two-component system, an array of specialized chemoreceptors, and several auxiliary proteins. it has been studied extensively in escherichia coli and, to a significantly lesser extent, in several other microbial species. emerging evidence suggests that homologous signal transduction pathways regulate not only chemotaxis, but several other cellular functions in various bacterial species. the availability of genome sequen ...	2007	17628132
use of multiple-displacement amplification and checkerboard dna-dna hybridization to examine the microbiota of endodontic infections.	multiple-displacement amplification (mda) has been used to uniformly amplify bacterial genomes present in small samples, providing abundant targets for molecular analysis. the purpose of this investigation was to combine mda and checkerboard dna-dna hybridization to examine the microbiota of endodontic infections. sixty-six samples were collected from teeth with endodontic infections. nonamplified and amplified samples were analyzed by checkerboard dna-dna hybridization for levels and proportion ...	2007	17634304
relationship of periodontal infection to serum antibody levels to periodontopathic bacteria and inflammatory markers in periodontitis patients with coronary heart disease.	several reports have demonstrated a possible association of periodontal infections with coronary heart disease (chd) by elevated antibody titre to periodontopathic bacteria in chd patients compared with non-diseased controls. although each periodontopathic bacterium may vary in virulence for periodontitis and atherosclerosis, antibody response to multiple bacteria in chd patients has not been understood fully. therefore, serum levels of antibody to 12 periodontopathic bacteria together with othe ...	2007	17645769
minocycline hcl microspheres reduce red-complex bacteria in periodontal disease therapy.	the objective of this trial was to measure the antimicrobial effects of a minocycline hcl microsphere (mm) local drug-delivery system when used as an adjunct to scaling and root planing (srp). dna probe analysis for 40 bacteria was used to evaluate the oral bacteria of 127 subjects with moderate to advanced chronic periodontitis.	2007	17668977
length of guanosine homopolymeric repeats modulates promoter activity of subfamily ii tpr genes of treponema pallidum ssp. pallidum.	in treponema pallidum, homopolymeric guanosine repeats of varying length are present upstream of both subfamily i (tprc, d, f and i) and ii (tpre, g and j) tpr genes, a group of potential virulence factors, immediately upstream of the +1 nucleotide. to investigate the influence of these poly-g sequences on promoter activity, tpre, g, j, f and i promoter regions containing homopolymeric tracts with different numbers of gs, the ribosomal binding site and start codon were cloned in frame with the g ...	2007	17683506
human wild-type alanine:glyoxylate aminotransferase and its naturally occurring g82e variant: functional properties and physiological implications.	human hepatic peroxisomal agt (alanine:glyoxylate aminotransferase) is a plp (pyridoxal 5'-phosphate)-dependent enzyme whose deficiency causes primary hyperoxaluria type i, a rare autosomal recessive disorder. to acquire experimental evidence for the physiological function of agt, the k(eq),(overall) of the reaction, the steady-state kinetic parameters of the forward and reverse reactions, and the pre-steady-state kinetics of the half-reactions of the plp form of agt with l-alanine or glycine an ...	2007	17696873
microbiologic analysis of periodontal pockets and carotid atheromatous plaques in advanced chronic periodontitis patients.	in recent years, many researchers have focused their attention on the ability of periodontal pathogens to colonize atheromatous plaques. nevertheless, a clear correlation between the detection rates of periodontopathic bacterial dna in atheromas and in subgingival plaque samples has not been established. the aim of our study was to assess the presence of five periodontal pathogens (actinobacillus actinomycetemcomitans, prevotella intermedia, porphyromonas gingivalis, treponema denticola, and tan ...	2007	17760541
the impact of a low-frequency chlorhexidine rinsing schedule on the subgingival microbiota (the teeth clinical trial).	information on the efficacy of chlorhexidine (chx) rinsing on the subgingival microbiota is limited. this study tested if intermittent chx rinsing over 5 years had an impact on the subgingival microbiota.	2007	17760545
a comparison of sensitivities of the conventional and the real-time polymerase chain reaction methods for detection of treponema denticola in periapical abscesses.		2007	17768483
steroid 5alpha-reductase activity of treponema denticola.	previously we have shown that reference and freshly isolated treponema denticola cultures possess 5alpha-reductase (5alpha-r) and 3beta- and 17beta-hydroxysteroid dehydrogenase activity. a gene matching the 3-oxo-5alpha-steroid 4-dehydrogenase family protein (gene id: 2739284; locus tag: tde2697) has been identified in t. denticola atcc 35405. the aim of the work presented here was to optimize assay conditions and determine steroid substrate specificities for the 5alpha-r activity of t. denticol ...	2007	17803630
correlation between infections with different genotypes of human cytomegalovirus and epstein-barr virus in subgingival samples and periodontal status of patients.	accumulating evidence indicates that herpesviruses may be putative pathogens in various types of periodontal diseases. the present study was performed to examine infections with different genotypes of human cytomegalovirus (hcmv) and epstein-barr virus (ebv) in subgingival samples from a chinese population and to analyze the correlation with periodontal status. a nested pcr assay was used to identify the presence of hcmv, ebv type 1 (ebv-1), and ebv-2; and the amplicons were further analyzed by ...	2007	17804655
assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data.	comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving.	2007	18047665
quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes.	most bacterial chromosomes exhibit asymmetry of base composition with respect to leading vs. lagging strands (gc and at skews). these skews reflect mainly those in protein coding sequences, which are driven by asymmetric mutation pressures during replication and transcription (notably asymmetric cytosine deamination) plus subsequent selection for preferred structures, signals, amino acid or codons. the transcription-associated effects but not the replication-associated effects contribute to the ...	2007	17711583
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
phylogenetic distribution of translational gtpases in bacteria.	translational gtpases are a family of proteins in which gtpase activity is stimulated by the large ribosomal subunit. conserved sequence features allow members of this family to be identified.	2007	17214893
periodontal therapy alters gene expression of peripheral blood monocytes.	we investigated the effects of periodontal therapy on gene expression of peripheral blood monocytes.	2007	17716309
hydrogen production by termite gut protists: characterization of iron hydrogenases of parabasalian symbionts of the termite coptotermes formosanus.	cellulolytic flagellated protists in the guts of termites produce molecular hydrogen (h(2)) that is emitted by the termites; however, little is known about the physiology and biochemistry of h(2) production from cellulose in the gut symbiotic protists due to their formidable unculturability. in order to understand the molecular basis for h(2) production, we here identified two genes encoding proteins homologous to iron-only hydrogenases (fe hydrogenases) in pseudotrichonympha grassii, a large ce ...	2007	17766465
high content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm olavius algarvensis.	selenocysteine (sec) and pyrrolysine (pyl) are rare amino acids that are cotranslationally inserted into proteins and known as the 21st and 22nd amino acids in the genetic code. sec and pyl are encoded by uga and uag codons, respectively, which normally serve as stop signals. herein, we report on unusually large selenoproteomes and pyrroproteomes in a symbiont metagenomic dataset of a marine gutless worm, olavius algarvensis. we identified 99 selenoprotein genes that clustered into 30 families, ...	2007	17626042
small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.	the beta-grasp fold (beta-gf), prototyped by ubiquitin (ub), has been recruited for a strikingly diverse range of biochemical functions. these functions include providing a scaffold for different enzymatic active sites (e.g. nudix phosphohydrolases) and iron-sulfur clusters, rna-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. to understand the basis for the functional versatil ...	2007	17605815
mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.	selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. since a number of microbial genomes have been completely sequenced to date, it is tempting to ask whether the 23rd amino acid is left undiscovered in these genomes. recently, a computational study addressed this question and reported that no trna gene for unknown amino acid was found in genome sequences available. however, performance of the trna prediction program on an unknown trna f ...	2007	17597547
maternal oral health status and preterm low birth weight at muhimbili national hospital, tanzania: a case-control study.	the study examined the relationship between oral health status (periodontal disease and carious pulpal exposure (cpe)) and preterm low-birth-weight (ptlbw) infant deliveries among tanzanian-african mothers at muhimbili national hospital (mnh), tanzania.	2007	17594498
an in vitro biofilm model of subgingival plaque.	numerous biofilm models have been described for the study of bacteria associated with the supragingival plaque. however, there are fewer models available for the study of subgingival plaque. the purpose of this study was to develop and validate a model that closely mimicked the composition of the subgingival flora.	2007	17488440
the crisprdb database and tools to display crisprs and to generate dictionaries of spacers and repeats.	in archeae and bacteria, the repeated elements called crisprs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. short sequences called spacers are stored in-between repeated elements. in the current model, motifs comprising spacers and repeats may target an invading dna and lead to its degradation through a proposed mechanism similar to rna interference. analysis of intra-species polymorphism shows that new motifs (one spa ...	2007	17521438
oral fluid-based biomarkers of alveolar bone loss in periodontitis.	periodontal disease is a bacteria-induced chronic inflammatory disease affecting the soft and hard supporting structures encompassing the teeth. when left untreated, the ultimate outcome is alveolar bone loss and exfoliation of the involved teeth. traditional periodontal diagnostic methods include assessment of clinical parameters and radiographs. though efficient, these conventional techniques are inherently limited in that only a historical perspective, not current appraisal, of disease status ...	2007	17435132
nursing home-associated pneumonia, hospital-acquired pneumonia and ventilator-associated pneumonia: the contribution of dental biofilms and periodontal inflammation.		2007	17474932
how phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.	the phosphoenolpyruvate(pep):carbohydrate phosphotransferase system (pts) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. to carry out its catalytic function in sugar transport and phosphorylation, the pts uses pep as an energy source and phosphoryl donor. the phosphoryl group of pep is usually transferred via four distinct proteins (domains) to the transported sugar bo ...	2006	17158705
dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues.	selenocysteine (sec) is co-translationally inserted into protein in response to uga codons. it occurs in oxidoreductase active sites and often is catalytically superior to cysteine (cys). however, sec is used very selectively in proteins and organisms. the wide distribution of sec and its restricted use have not been explained.	2006	17054778
oral malodour (halitosis).		2006	16990322
periodontal disease and systemic conditions: a bidirectional relationship.	for decades, physicians and dentists have paid close attention to their own respective fields, specializing in medicine pertaining to the body and the oral cavity, respectively. however, recent findings have strongly suggested that oral health may be indicative of systemic health. currently, this gap between allopathic medicine and dental medicine is quickly closing, due to significant findings supporting the association between periodontal disease and systemic conditions such as cardiovascular ...	2006	16998613
structural classification of bacterial response regulators: diversity of output domains and domain combinations.	chey-like phosphoacceptor (or receiver [rec]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. in this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. transcriptional regulators of the ompr, narl, and ntrc families w ...	2006	16740923
clinical review: molecular mechanisms underlying the role of antithrombin in sepsis.	in disseminated intravascular coagulation (dic) there is extensive crosstalk between activation of inflammation and coagulation. endogenous anticoagulatory pathways are downregulated by inflammation, thus decreasing the natural anti-inflammatory mechanisms that these pathways possess. supportive strategies aimed at inhibiting activation of coagulation and inflammation may theoretically be justified and have been found to be beneficial in experimental and initial clinical studies. this review ass ...	2006	16542481
on the acquisition of periodontopathic bacteria by children from mothers: a randomized double-masked placebo-controlled trial in bauru, brazil.	objective: the purpose of this study was two-fold: 1) to determine the effects of mechanical and chemical modalities treatments on periodontal clinical and microbiological parameters of mothers; and 2) to determine the subsequent colonization of periodontal pathogens in tongue samples from their infants. design: a total of 168 mothers met inclusion criteria to participate in a randomized double-masked placebo-controlled clinical trial. of those, 121 mothers (and their infants) of 158 seen at bas ...	2006	22267892
the glycolytic pathway of trimastix pyriformis is an evolutionary mosaic.	glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. the glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. however, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. we have conducted an expressed sequence tag (est) survey of the anaerobic flagellate trimastix pyriformis to investigate the nature of the evolut ...	2006	17123440
comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms.	hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ...	2006	16780600
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
paths of lateral gene transfer of lysyl-aminoacyl-trna synthetases with a unique evolutionary transition stage of prokaryotes coding for class i and ii varieties by the same organisms.	while the premise that lateral gene transfer (lgt) is a dominant evolutionary force is still in considerable dispute, the case for widespread lgt in the family of aminoacyl-trna synthetases (aars) is no longer contentious. aarss are ancient enzymes, guarding the fidelity of the genetic code. they are clustered in two structurally unrelated classes. only lysine aminoacyl-trna synthetase (lysrs) is found both as a class 1 and a class 2 enzyme (lysrs1-2). remarkably, in several extant prokaryotes b ...	2006	16529662
algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.	comparison of metabolic networks is typically performed based on the organisms' enzyme contents. this approach disregards functional replacements as well as orthologies that are misannotated. direct comparison of the structure of metabolic networks can circumvent these problems.	2006	16478540
periodontitis as a risk factor of coronary heart diseases?	unstable atherosclerotic plaque is a dangerous clinical state, possibly leading to acute coronary deficiency resulting in cardiac infarction. inflammatory factor's role in creating pathological lesions in the endothelium of coronary vessels is frequently raised. this state may be caused by bacteria able to initiate clot formation in blood vessel and destabilizing atherosclerotic plaque already present. source of these pathogens are chronic inflammatory processes occurring in organism, among them ...	2006	17458056
dimerization and folding processes of treponema denticola cystalysin: the role of pyridoxal 5'-phosphate.	cystalysin, the key virulence factor in the bacterium treponema denticola responsible for periodontitis, is a homodimeric pyridoxal 5'-phosphate (plp)-c-s lyase. the dimerization process and the urea-induced unfolding equilibrium of holocystalysin were compared with those of the apo form. the presence of plp decreases approximately 4 times the monomer-dimer equilibrium dissociation constant. by using a variety of spectroscopic and analytical procedures, we demonstrated a difference in their unfo ...	2006	17115709
infection frequency of epstein-barr virus in subgingival samples from patients with different periodontal status and its correlation with clinical parameters.	to detect the infection frequencies of different genotypes of epstein-barr virus (ebv) in subgingival samples from chronic periodontitis (cp) patients, and to discuss the correlation between infection with ebv and clinical parameters.	2006	17048301
prospective study of the long term change of the oral flora after radiation therapy.	the aim of this prospective study was to evaluate the long term change in oral pathogens following radiation therapy.	2006	16341728
distribution of 10 periodontal bacteria in saliva samples from japanese children and their mothers.	we analyzed the distribution of 10 periodontal bacteria species (porphyromonas gingivalis, tannerella forsythensis, prevotella intermedia, prevotella nigrescens, campylobacter rectus, eikenella corrodens, actinobacillus actinomycetemcomitans, capnocytophaga ochracea, capnocytophaga sputigena, and treponema denticola) in children, and then compared their distribution in those children and their mothers, with special attention given to three of the species known as the red complex (p. gingivalis, ...	2006	16269128
inflammatory responses of a macrophage/epithelial cell co-culture model to mono and mixed infections with porphyromonas gingivalis, treponema denticola, and tannerella forsythia.	accumulated evidence points to porphyromonas gingivalis, treponema denticola, and tannerella forsythia as three major etiologic agents of chronic periodontitis. epithelial cells and macrophages play a major role in the host response to periodontopathogens, and the secretion of inflammatory mediators and matrix metalloproteinases (mmps) by these host cells is believed to contribute to periodontal tissue destruction. the aim of this study was to investigate the inflammatory response of a macrophag ...	2006	16153871
characterization, distribution, and expression of novel genes among eight clinical isolates of streptococcus pneumoniae.	eight low-passage-number streptococcus pneumoniae clinical isolates, each of a different serotype and a different multilocus sequence type, were obtained from pediatric participants in a pneumococcal vaccine trial. comparative genomic analyses were performed with these strains and two s. pneumoniae reference strains. individual genomic libraries were constructed for each of the eight clinical isolates, with an average insert size of approximately 1 kb. a total of 73,728 clones were picked for ar ...	2006	16368987
fusobacterium nucleatum transports noninvasive streptococcus cristatus into human epithelial cells.	analysis of human buccal epithelial cells frequently reveals an intracellular polymicrobial consortium of bacteria. although several oral bacteria have been demonstrated to invade cultured epithelial cells, several others appear unable to internalize. we hypothesized that normally noninvasive bacteria may gain entry into epithelial cells via adhesion to invasive bacteria. fusobacterium nucleatum is capable of binding to and invading oral epithelial cells. by contrast, streptococcus cristatus bin ...	2006	16369022
lipoprotein computational prediction in spirochaetal genomes.	lipoproteins are of great interest in understanding the molecular pathogenesis of spirochaetes. because spirochaete lipobox sequences exhibit more plasticity than those of other bacteria, application of existing prediction algorithms to emerging sequence data has been problematic. in this paper a novel lipoprotein prediction algorithm is described, designated splip, constructed as a hybrid of a lipobox weight matrix approach supplemented by a set of lipoprotein signal peptide rules allowing for ...	2006	16385121
relationship of periodontal bacteria and porphyromonas gingivalis fima variations with phenytoin-induced gingival overgrowth.	we investigated the relationship between phenytoin-induced gingival overgrowth (go) and the harboring of periodontal bacteria.	2006	16390469
[microbiological study on the prognosis of immediate implant and periodontal disease].	the aim of the present study was to investigate the prevalence of periodontal marker organisms and specific interleukin-1 (il-1) gene polymorphisms (which show a close association with periodontitis) and their effect on the success of immediate implant placement postextraction in the patient with periodontal disease.	2006	16395549
recovery and evolutionary analysis of complete integron gene cassette arrays from vibrio.	integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be). multiple insertion events can lead to the assembly of large integron-associated cassette arrays. the most striking examples are found in vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. besides those found in ...	2006	16417647
biological basis for syphilis.	syphilis is a chronic sexually transmitted disease caused by treponema pallidum subsp. pallidum. clinical manifestations separate the disease into stages; late stages of disease are now uncommon compared to the preantibiotic era. t. pallidum has an unusually small genome and lacks genes that encode many metabolic functions and classical virulence factors. the organism is extremely sensitive to environmental conditions and has not been continuously cultivated in vitro. nonetheless, t. pallidum is ...	2006	16418521
regulation and physiologic significance of the agmatine deiminase system of streptococcus mutans ua159.	we previously demonstrated that streptococcus mutans expresses a functional agmatine deiminase system (agds) encoded by the agmatine-inducible agubdac operon (a. r. griswold, y. y. chen, and r. a. burne, j. bacteriol. 186:1902-1904, 2004). the agds yields ammonia, co2, and atp while converting agmatine to putrescine and is proposed to augment the acid resistance properties and pathogenic potential of s. mutans. to initiate a study of agu gene regulation, the agub transcription initiation site wa ...	2006	16428386
function and evolution of plasmid-borne genes for pyrimidine biosynthesis in borrelia spp.	the thyx gene for thymidylate synthase of the lyme borreliosis (lb) agent borrelia burgdorferi is located in a 54-kb linear plasmid. in the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (rf) agent borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. the functions of the b. hermsii and b. burgdorferi thyx gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient escherichia ...	2006	16428394
the transmission of anaerobic periodontopathic organisms.	the oral microbial flora is unique, and available evidence indicates that it is passed vertically from parents to children. in this investigation, we used a chairside assay for the n-benzoyl-dl-arginine-2-naphthylamide (bana)-sensitive enzyme found in porphyromonas gingivalis, treponema denticola, and tannerella forsythensis, to determine the prevalence of these bana-positive species in young children and their caregivers. we predicted that if the bana enzyme was found in plaque samples of child ...	2006	16434739
the metabolism of cholesterol and certain hormonal steroids by treponema denticola.	the aim was to investigate whether reference cultures and fresh isolates of treponema denticola are able to 5alpha-reduce and further metabolise testosterone, 4-androstenedione, progesterone, corticosterone, cortisol or cholesterol. two reference and five freshly isolated cultures of t. denticola were incubated with either radiolabeled or unlabeled steroid substrates; in the first case products were identified by thin layer chromatography and in the latter by gas chromatography-mass spectroscopy ...	2006	16436288
supportive periodontal therapy using mechanical instrumentation or 2% minocycline gel: a 12 month randomized, controlled, single masked pilot study.	to compare the short-term performance of subgingival local delivery of 2% minocycline gel and conventional subgingival debridement in supportive periodontal therapy (spt) patients.	2006	16441740
comparison of bacterial plaque samples from titanium implant and tooth surfaces by different methods.	studies have shown similarities in the microflora between titanium implants or tooth sites when samples are taken by gingival crevicular fluid (gcf) sampling methods. the purpose of the present study was to study the microflora from curette and gcf samples using the checkerboard dna-dna hybridization method to assess the microflora of patients who had at least one oral osseo-integrated implant and who were otherwise dentate. plaque samples were taken from tooth/implant surfaces and from sulcular ...	2006	16441779
early colonization of non-submerged dental implants in patients with a history of advanced aggressive periodontitis.	the aim of the study was to evaluate the early colonization of non-submerged implants over a 6-month period in partially edentulous patients treated for advanced aggressive periodontal disease. in 22 patients treated for advanced aggressive periodontitis and in a supportive maintenance program for a period between 12 and 240 months at implant surgery, a total of 68 non-submerged dental implants were installed. patients had a plaque score below 20%, and less than 20% of the pockets around the tee ...	2006	16441780
inhibition of periodontopathogen-derived proteolytic enzymes by a high-molecular-weight fraction isolated from cranberry.	porphyromonas gingivalis, tannerella forsythia and treponema denticola are three major aetiological agents of chronic periodontitis. the strong proteolytic activities of these bacteria are critical to their survival since their energy source is obtained from peptides and amino acids derived from proteins. in addition, proteases are important factors contributing to periodontal tissue destruction by a variety of mechanisms, including direct tissue degradation and modulation of host inflammatory r ...	2006	16473919
brucella abortus synthesizes phosphatidylcholine from choline provided by the host.	the brucella cell envelope is characterized by the presence of phosphatidylcholine (pc), a common phospholipid in eukaryotes that is rare in prokaryotes. studies on the composition of brucella abortus 2308 phospholipids revealed that the synthesis of pc depends on the presence of choline in the culture medium, suggesting that the methylation biosynthetic pathway is not functional. phospholipid composition of pmta and pcs mutants indicated that in brucella, pc synthesis occurs exclusively via the ...	2006	16484204
is pre-term labour associated with periodontitis in a danish maternity ward?	to reveal differences in periodontal status and presence of subgingival bacteria in a scandinavian population of women with pre-term birth compared with women who delivered at term.	2006	16489943
modulation of human neutrophil functions in vitro by treponema denticola major outer sheath protein.	in this study of human polymorphonuclear leukocytes (pmns), pretreatment with treponema denticola major outer sheath protein (msp) inhibited formyl-methionyl-leucyl-phenylalanine (fmlp)-induced chemotaxis, phagocytosis of immunoglobulin g-coated microspheres, fmlp-stimulated calcium transients, and actin assembly. msp neither altered oxidative responses to phorbol myristate or fmlp nor induced apoptosis. msp selectively impairs chemotaxis and phagocytosis by impacting the pmn cytoskeleton.	2006	16495573
selective binding of borrelia burgdorferi ospe paralogs to factor h and serum proteins from diverse animals: possible expansion of the role of ospe in lyme disease pathogenesis.	the binding of borrelia burgdorferi ospe, ospf, and family 163 (elp) proteins to factor h/factor h-like protein 1 (fhl-1) and other serum proteins from different animals was assessed. ospe paralogs bound factor h and unidentified serum proteins from a subset of animals, while ospf and elp proteins did not. these data advance our understanding of factor h binding, the host range of the lyme spirochetes, and the expanding role of ospe in pathogenesis.	2006	16495576
anti-inflammatory activity of a high-molecular-weight cranberry fraction on macrophages stimulated by lipopolysaccharides from periodontopathogens.	periodontitis is a chronic inflammatory disease affecting oral tissues. the continuous, high production of cytokines by host cells triggered by periodontopathogens is thought to be responsible for the destruction of tooth-supporting tissues. macrophages play a critical role in this host inflammatory response to periodontopathogens. the aim of this study was to investigate the effect of non-dialyzable material prepared from cranberry juice concentrate on the pro-inflammatory cytokine response of ...	2006	16498070
description of the subgingival microbiota of periodontally untreated mexican subjects: chronic periodontitis and periodontal health.	recent studies have suggested that changes in the prevalence and/or proportion of distinct microorganisms characterize the subgingival microbial profiles of populations around the world. at present, no information is available on the subgingival microbiota of mexican subjects. the purpose of the present study was to determine the microbial composition of subgingival plaque in mexican subjects with untreated chronic periodontitis.	2006	16512761
detection of bacterial dna in atheromatous plaques by quantitative pcr.	this is the first study to analyze atheromatous plaques for the presence of bacterial dna from ten species, including periodontal species and chlamydia pneumoniae. we examined 129 samples of dna extracted from atheromas from 29 individuals for the presence of bacterial 16s rdna sequences from ten different species: porphyromonas gingivalis, actinobacillus actinomycetemcomitans (a.a.), tannerella forsythensis, eikenella corrodens, prevotella intermedia, staphylococcus aureus, staphylococcus epide ...	2006	16513386
periodontal infections and coronary heart disease: role of periodontal bacteria and importance of total pathogen burden in the coronary event and periodontal disease (corodont) study.	chronic inflammation from any source is associated with increased cardiovascular risk. periodontitis is a possible trigger of chronic inflammation. we investigated the possible association between periodontitis and coronary heart disease (chd), focusing on microbiological aspects.	2006	16534043
identification of a homozygous deletion in the ap3b1 gene causing hermansky-pudlak syndrome, type 2.	we report on the molecular etiology of an unusual clinical phenotype associating congenital neutropenia, thrombocytopenia, developmental delay, and hypopigmentation. using genetic linkage analysis and targeted gene sequencing, we defined a homozygous genomic deletion in ap3b1, the gene encoding the beta chain of the adaptor protein-3 (ap-3) complex. the mutation leads to in-frame skipping of exon 15 and thus perturbs proper assembly of the heterotetrameric ap-3 complex. consequently, trafficking ...	2006	16537806
molecular analyses of the interaction of borrelia hermsii fhba with the complement regulatory proteins factor h and factor h-like protein 1.	borrelia hermsii, the primary etiological agent of tick-borne relapsing fever in north america, binds the complement regulatory protein factor h (fh) as a means of evading opsonophagocytosis and the alternative complement pathway. the ability of fh-binding protein a (fhba) to bind fh-like protein 1 (fhl-1) has not been assessed previously. in this study, using a whole-cell absorption assay, we demonstrated that b. hermsii absorbs both fh and fhl-1 from human serum. consistent with this, affinity ...	2006	16552029
exposure of lymphocytes to high doses of actinobacillus actinomycetemcomitans cytolethal distending toxin induces rapid onset of apoptosis-mediated dna fragmentation.	we have shown previously that treatment of human lymphocytes with the actinobacillus actinomycetemcomitans cytolethal distending toxin (cdt) results in dose-dependent g2 arrest, followed 24 h later by apoptotic cell death. here we demonstrated that for jurkat cells exposed to high concentrations of cdt (>0.2 ng/ml) there was a dose-dependent increase in the level of s-phase cells and a concomitant decrease in the level of g2 cells. fluorescence-activated cell sorter analysis demonstrated that th ...	2006	16552037
topical h2 antagonist prevents periodontitis in a rabbit model.	cimetidine is a powerful h2 receptor antagonist that eliminates histamine's effects on chemotaxis, phagocytosis, and superoxide anion production by phagocytes. the purpose of this study was to analyze the clinical and histopathological changes associated with experimental periodontitis in rabbits in response to topically applied cimetidine. experimental periodontitis was induced in 21 new zealand white rabbits using porphyromonas gingivalis (10(9) cfu) topically applied three times a week for a ...	2006	16552070
the treponema denticola surface protease dentilisin degrades interleukin-1 beta (il-1 beta), il-6, and tumor necrosis factor alpha.	dentilisin is a major surface protease and virulence factor of the bacterium treponema denticola. in this study, we found that t. denticola reduced inflammatory cytokines, including interleukin-1beta (il-1beta), il-6, and tumor necrosis factor alpha, in peripheral blood mononuclear cells through degradation by dentilisin.	2006	16552080
clinical and microbiological effects of different antimicrobials on generalized aggressive periodontitis.	to evaluate and compare the effects of adjunctive metronidazole plus amoxicillin, doxycycline and metronidazole on clinical and microbiological parameters in patients with generalized aggressive periodontitis.	2006	16553634
protease-activated receptor-2 activation: a major role in the pathogenesis of porphyromonas gingivalis infection.	we have investigated the specific contribution of protease-activated receptor-2 (par(2)) to host defense during porphyromonas gingivalis infection. culture supernatants from p. gingivalis strains 33277 and w50 provoked ca(2+) mobilization in cells transfected with par(2) (par(2)-knrk) and desensitized the subsequent responses to par(2)-selective agonist. in addition, culture supernatants of p. gingivalis e8 (rgpa/rgpb double knockout) did not cause calcium response in par(2)-knrk cells, evidenci ...	2006	16565494
subgingival and tongue microbiota during early periodontitis.	periodontal infections have a microbial etiology. association of species with early disease would be useful in determining which microbes initiate periodontitis. we hypothesized that the microbiota of subgingival and tongue samples would differ between early periodontitis and health. a cross-sectional evaluation of 141 healthy and early periodontitis adults was performed with the use of oligonucleotide probes and pcr. most species differed in associations with sample sites; most subgingival spec ...	2006	16567551
relationship of serum advanced glycation end products with deterioration of periodontitis in type 2 diabetes patients.	a close relationship between diabetes and chronic periodontitis has been demonstrated. we previously found that porphyromonas gingivalis with the type ii fima gene is an infectious factor closely associated with the deterioration seen in diabetic periodontitis patients. in the present study, we examined whether other biomarkers are related to the development and deterioration of periodontitis often seen in type 2 diabetic individuals.	2006	16579698
local oxygen therapy for treating acute necrotizing periodontal disease in smokers.	the main aim of treatment for acute necrotizing periodontal disease is fast and effective reduction of anaerobic destructive microorganisms to avoid periodontal damage. the effect of adjunctive local oxygen therapy in the treatment of necrotizing periodontal disease was examined in this study.	2006	16579700
langerhans' cell histiocytosis in a 5-year-old girl: evidence of periodontal pathogens.	langerhans' cell histiocytosis (lch) is a rare disorder characterized by langerhans' cell proliferation in various organs or tissues. when periodontal tissue is involved, clinical manifestations can vary from gingival recession and pocket formation to severe alveolar bone loss. this case report describes periodontal pathogens found in the pockets of involved primary teeth.	2006	16584357
identification of oral bacteria associated with crevicular epithelial cells from chronic periodontitis lesions.	bacterial invasion of host epithelial cells plays an important role in the pathogenesis of periodontal diseases; however, the interactions between subgingival species and the gingival crevice cells are not fully understood. this study determined the prevalence of a group of oral bacterial species on or in epithelial cells derived from periodontal pockets and the gingival crevice of subjects with periodontitis. samples of epithelial cells were obtained from 120 sites with periodontal pockets > or ...	2006	16585650
the hemoglobin receptor protein of porphyromonas gingivalis inhibits receptor activator nf-kappab ligand-induced osteoclastogenesis from bone marrow macrophages.	extracellular proteinaceous factors of porphyromonas gingivalis, a periodontal pathogen, that influence receptor activator of nuclear factor-kappab (nf-kappab) ligand (rankl)-induced osteoclastogenesis from bone marrow macrophages were investigated. the culture supernatant of p. gingivalis had the ability to inhibit rankl-induced in vitro osteoclastogenesis. a major protein of the culture supernatant, hemoglobin receptor protein (hbr), suppressed rankl-induced osteoclastogenesis in a dose-depend ...	2006	16622189
inhibitory effects of macrocarpals on the biological activity of porphyromonas gingivalis and other periodontopathic bacteria.	macrocarpals, which are phloroglucinol derivatives contained in eucalyptus leaves, exhibit antimicrobial activity against a variety of bacteria including oral bacteria. this study examined effects of macrocarpals a, b, and c on periodontopathic bacteria, especially porphyromonas gingivalis.	2006	16626372
[quantitative analysis of periodontal pathogens in aggressive periodontitis patients in a japanese population].	the aim of the present study was to clarify the relationship between the relative/absolute numbers of periodontal bacteria and different types of periodontitis. fifteen patients with localized aggressive periodontitis (lagp), 25 patients with generalized aggressive periodontitis (gagp) and 28 patients with chronic periodontitis (cp) were included in this study. saliva and subgingival plaque samples were collected from all subjects for microbiological analysis. the prevalence and proportions of a ...	2006	16629473
escherichia coli acid resistance: ph-sensing, activation by chloride and autoinhibition in gadb.	escherichia coli and other enterobacteria exploit the h+ -consuming reaction catalysed by glutamate decarboxylase to survive the stomach acidity before reaching the intestine. here we show that chloride, extremely abundant in gastric secretions, is an allosteric activator producing a 10-fold increase in the decarboxylase activity at ph 5.6. cooperativity and sensitivity to chloride were lost when the n-terminal 14 residues, involved in the formation of two triple-helix bundles, were deleted by m ...	2006	16675957
prevalence of periodontopathic bacteria on the tongue dorsum of elderly people.	the aim of this study was to analyse the prevalence of oral bacteria on the dorsum of the tongue. in addition, the relationship between the number of teeth and the microflora present on the coating of the tongue in a population of 85-year-old people was assessed.	2006	16677187
whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium "roseburia inulinivorans".	"roseburia inulinivorans" is an anaerobic polysaccharide-utilizing firmicute bacterium from the human colon that was identified as a producer of butyric acid during growth on glucose, starch, or inulin. r. inulinivorans a2-194 is also able to grow on the host-derived sugar fucose, following a lag period, producing propionate and propanol as additional fermentation products. a shotgun genomic microarray was constructed and used to investigate the switch in gene expression that is involved in chan ...	2006	16740940
usefulness of real time pcr for the differentiation and quantification of 652 and jp2 actinobacillus actinomycetemcomitans genotypes in dental plaque and saliva.	the aim of our study is to describe a fast molecular method, able to distinguish and quantize the two different genotypes (652 and jp2) of an important periodontal pathogen: actinobacillus actinomycetemcomitans. the two genotypes show differences in the expression of an important pathogenic factor: the leukotoxin (ltx). in order to evidence this, we performed a real time pcr procedure on the ltx operon, able to recognize aa clinical isolates with different leukotoxic potentials.	2006	16772039
t-cell expression cloning of porphyromonas gingivalis genes coding for t helper-biased immune responses during infection.	exposure of the mouse oral cavity to porphyromonas gingivalis results in the development of gingivitis and periapical bone loss, which apparently are associated with a th1 response to bacterial antigens. we have used this infection model in conjunction with direct t-cell expression cloning to identify bacterial antigens that induce a preferential or biased t helper response during the infectious process. a p. gingivalis-specific cd4 t-cell line derived from mice at 3 weeks postchallenge was used ...	2006	16790769
omega-3 fatty acid effect on alveolar bone loss in rats.	gingival inflammation and alveolar bone resorption are hallmarks of adult periodontitis, elicited in response to oral micro-organisms such as porphyromonas gingivalis. we hypothesized that omega (omega)-3 fatty acids (fa) dietary supplementation would modulate inflammatory reactions leading to periodontal disease in infected rats. rats were fed fish oil (omega-3 fa) or corn oil (n-6 fa) diets for 22 weeks and were infected with p. gingivalis. rats on the omega-3 fa diet exhibited elevated serum ...	2006	16798867
bacterial profile and burden of periodontal infection in subjects with a diagnosis of acute coronary syndrome.	periodontitis has been identified as a potential risk factor in cardiovascular diseases. it is possible that the stimulation of host responses to oral infections may result in vascular damage and the inducement of blood clotting. the aim of this study was to assess the role of periodontal infection and bacterial burden as an explanatory variable to the activation of the inflammatory process leading to acute coronary syndrome (acs).	2006	16805672