Publications

genetic and molecular characterization of a dental pathogen using genome-wide approaches.	actinobacillus actinomycetemcomitans causes periodontitis, a costly chronic infection that affects a large number of patients. the pathogenesis of this dental infection is a multifactorial process that results in a serious degenerative disease of the periodontium. although significant progress has been achieved after the identification of this gram-negative bacterium as the etiological agent of this infection, much remains to be done to understand in detail the bacterial factors and host-pathoge ...	2003	15126217
prolinks: a database of protein functional linkages derived from coevolution.	the advent of whole-genome sequencing has led to methods that infer protein function and linkages. we have combined four such algorithms (phylogenetic profile, rosetta stone, gene neighbor and gene cluster) in a single database--prolinks--that spans 83 organisms and includes 10 million high-confidence links. the proteome navigator tool allows users to browse predicted linkage networks interactively, providing accompanying annotation from public databases. the prolinks database and the proteome n ...	2004	15128449
quantitative microbiological study of subgingival plaque by real-time pcr shows correlation between levels of tannerella forsythensis and fusobacterium spp.	a taqman-based real-time pcr assay was established to quantify the periodontopathic bacteria tannerella forsythensis and fusobacterium spp. with this assay, the prevalence and proportion of these bacteria in clinical specimens were evaluated. our preliminary results suggest a positive colocalization of t. forsythensis and fusobacterium spp. in periodontal pockets.	2004	15131205
changes in oral microbial profiles after periodontal treatment as determined by molecular analysis of 16s rrna genes.	terminal rflp (t-rflp) analysis was used to investigate changes in the oral microbiota in saliva and subgingival plaque samples from one patient with aggressive periodontitis (subject a) and two patients with chronic periodontitis (subjects b and c) before and 3 months after periodontal treatment. substantial changes in the t-rflp patterns of subgingival plaque samples of subjects b and c were noted after 3 months of improved oral hygiene and full-mouth supra- and subgingival scaling and root pl ...	2004	15150339
induction of de novo subcortical actin filament assembly by treponema denticola major outer sheath protein.	treponema denticola and its major outer sheath protein (msp) induce actin reorganization in fibroblasts. we adapted a barbed-end labeling/imaging assay to monitor msp-induced subcortical actin filament assembly in neutrophils and fibroblasts. msp, at an actin-reorganizing concentration, inhibited migration of these dissimilar cell types, whose cytoskeletal functions in locomotion and phagocytosis are crucial for immunity and healing of peripheral infections.	2004	15155678
genomic diversity of burkholderia pseudomallei clinical isolates: subtractive hybridization reveals a burkholderia mallei-specific prophage in b. pseudomallei 1026b.	burkholderia pseudomallei is the etiologic agent of the disease melioidosis and is a category b biological threat agent. the genomic sequence of b. pseudomallei k96243 was recently determined, but little is known about the overall genetic diversity of this species. suppression subtractive hybridization was employed to assess the genetic variability between two distinct clinical isolates of b. pseudomallei, 1026b and k96243. numerous mobile genetic elements, including a temperate bacteriophage de ...	2004	15175308
diversity in chemotaxis mechanisms among the bacteria and archaea.	the study of chemotaxis describes the cellular processes that control the movement of organisms toward favorable environments. in bacteria and archaea, motility is controlled by a two-component system involving a histidine kinase that senses the environment and a response regulator, a very common type of signal transduction in prokaryotes. most insights into the processes involved have come from studies of escherichia coli over the last three decades. however, in the last 10 years, with the sequ ...	2004	15187186
the role of bacterial antizyme: from an inhibitory protein to atoc transcriptional regulator.	this review considers the role of bacterial antizyme in the regulation of polyamine biosynthesis and gives new perspectives on the involvement of antizyme in other significant cellular mechanisms. antizyme is a protein molecule induced by the end product of the enzymic reaction that it inhibits, in a non-competitive manner. the bacterial ornithine decarboxylase is regulated by nucleotides, phosphorylation and antizyme. the inhibition of ornithine decarboxylase by antizyme can be relieved to diff ...	2004	15200682
site-directed mutagenesis provides insight into racemization and transamination of alanine catalyzed by treponema denticola cystalysin.	in addition to alpha, beta-elimination of l-cysteine, treponema denticola cystalysin catalyzes the racemization of both enantiomers of alanine accompanied by an overall transamination. lys-238 and tyr-123 or a water molecule located on the si and re face of the cofactor, respectively, have been proposed to act as the acid/base catalysts in the proton abstraction/donation at calpha/c4' of the external aldimine. in this investigation, two site-directed mutants, k238a and y123f, have been character ...	2004	15210695
subgingival microbiota of chilean patients with chronic periodontitis.	an association between race/ethnicity and the composition of the subgingival microbiota has been found in chronic periodontitis. a study was undertaken to determine the characteristics of the subgingival microbiota of chronic periodontitis in chileans residing in santiago.	2004	15212354
inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.	the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ...	2004	15214963
in vitro activities of iodonium salts against oral and dental anaerobes.	the comparative in vitro activities of 11 iodonium salt compounds, 0.12% chlorhexidine, and four antimicrobial agents against 322 anaerobic and fastidious potential dental and periodontal bacterial pathogens were studied. iodonium salts 3, 4, 5, 9, and 10 had in vitro activities comparable to that of chlorhexidine against most isolates. these compounds may be suitable for incorporation into an oral mouthwash.	2004	15215147
biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life.		2004	15231774
evidence that the algi/algj gene cassette, required for o acetylation of pseudomonas aeruginosa alginate, evolved by lateral gene transfer.	pseudomonas aeruginosa strains, isolated from chronically infected patients with cystic fibrosis, produce the o-acetylated extracellular polysaccharide, alginate, giving these strains a mucoid phenotype. o acetylation of alginate plays an important role in the ability of mucoid p. aeruginosa to form biofilms and to resist complement-mediated phagocytosis. the o-acetylation process is complex, requiring a protein with seven transmembrane domains (algi), a type ii membrane protein (algj), and a pe ...	2004	15231808
novel hairpin-shaped primer assay to study the association of the -44 single-nucleotide polymorphism of the defb1 gene with early-onset periodontal disease.	a powerful, cost-effective new method for studying single-nucleotide polymorphisms (snps) is described. this method is based on the use of hairpin-shaped primers (hp), which give a sensitive and specific pcr amplification of each specific allele, without the use of costly fluorophore-labeled probes and any post-pcr manipulation. the amplification is monitored in real-time using sybr green i dye and takes only 2 h to yield results. the hp assay has a simple design and utilizes a conventional real ...	2004	15242954
molecular analysis of the microflora associated with dental caries.	molecular techniques have revealed many novel, presumed unculturable, taxa in oral infections. the aim of this study was to characterize the bacterial community of the middle and advancing front of carious dental lesions by cultural and molecular analyses. samples were collected with a hand excavator from five teeth with carious lesions involving dentine. samples were cultured on blood agar and rogosa agar incubated in air plus 5% co(2) and on fastidious anaerobe agar anaerobically. dna was also ...	2004	15243054
frequent and preferential infection of treponema denticola, streptococcus mitis, and streptococcus anginosus in esophageal cancers.	multiple cancers frequently occur in the upper digestive tract. one possible explanation is that specific bacterial infection stimulates the normal epithelium to initiate inflammation and/or promotes carcinogenesis. this study was undertaken to determine which bacterial species is predominantly associated with esophageal cancer. we examined the bacterial diversity in this type of cancer and in the saliva from healthy people by using a culture-independent molecular method. here we report the pref ...	2004	15245592
genetic analysis of treponema denticola atcc 35405 biofilm formation.	treponema denticola is a major aetiological organism implicated in periodontal disease. the interaction of t. denticola with other oral bacteria, in particular porphyromonas gingivalis, in biofilm formation is thought to be an important step in the onset of periodontal disease. the interaction between t. denticola and p. gingivalis has been examined using a panel of t. denticola mutants and their effects on mixed biofilm formation tested in a static biofilm model. t. denticola atcc 35405 did not ...	2004	15256581
where does bacterial replication start? rules for predicting the oric region.	three methods, based on dna asymmetry, the distribution of dnaa boxes and dnaa gene location, were applied to identify the putative replication origins in 120 chromosomes. the chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. dna asymmetry is the most universal method of putative oric identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. the three meth ...	2004	15258248
multiple functions of the leucine-rich repeat protein lrra of treponema denticola.	the gene lrra, encoding a leucine-rich repeat protein, lrra, that contains eight consensus tandem repeats of 23 amino acid residues, has been identified in treponema denticola atcc 35405. a leucine-rich repeat is a generally useful protein-binding motif, and proteins containing this repeat are typically involved in protein-protein interactions. southern blot analysis demonstrated that t. denticola atcc 35405 expresses the lrra gene, but the gene was not identified in t. denticola atcc 33520. in ...	2004	15271922
treponema putidum sp. nov., a medium-sized proteolytic spirochaete isolated from lesions of human periodontitis and acute necrotizing ulcerative gingivitis.	so far, little phenotypic heterogeneity has been detected in cultured oral treponemes with trypsin-like proteolytic activity, and all have been assigned to the species treponema denticola. however, comparisons of protein patterns and antigen expression in our collection of proteolytic oral treponemes occasionally identified isolates with a unique phenotype; e.g. strain omz 830 (=atcc 700768), which qualified as a 'pathogen-related oral spirochaete' due to the presence of a approximately 37 kda p ...	2004	15280279
implant therapy following liver transplantation: clinical and microbiological results after 10 years.	the number of immunocompromised patients is increasing as a consequence of successful organ transplantation. placing dental implants in these patients has been questioned because of their increased risk for infections. the 10-year follow-up data of a 71-year-old liver transplant recipient with long-term immunosuppressive therapy is reported. six months after liver transplantation, two interforaminal implants were inserted in the edentulous mandible, and an overdenture using non-rigid telescopic ...	2004	15295960
real-time taqman pcr for quantifying oral bacteria during biofilm formation.	a taqman pcr was developed for quantifying early colonizer microorganisms in dental biofilms. to design species-specific primers and taqman probes, genomic subtractive hybridization was used. this quantitative assay in combination with subtractive hybridization may be of value in the study of microbial ecosystems consisting of related species that are involved in the formation and etiology of biofilms.	2004	15297540
microbiological shifts in intra- and extraoral habitats following mechanical periodontal therapy.	the aim of the present study was to analyze the intra- and extraoral colonization dynamics of periodontal pathogens following supra- and subgingival debridement.	2004	15312101
development of a novel chloramphenicol resistance expression plasmid used for genetic complementation of a flig deletion mutant in treponema denticola.	a new expression plasmid containing the fla operon promoter and a staphylococcal chloramphenicol resistance gene, was constructed to help assess the role of flig in treponema denticola motility. deletion of flig resulted in a nonmotile mutant with a markedly decreased number of flagellar filaments. wild-type flig genes from t. denticola and from treponema pallidum were cloned into this expression plasmid. in both cases, the gene restored the ability of the mutant to gyrate its cell ends and enab ...	2004	15322052
treponema species associated with abscesses of endodontic origin.	spirochetes have been frequently observed in abscesses of endodontic origin, but they have rarely been identified. this study sought to investigate the prevalence of eight oral treponemes in acute periradicular abscesses using a species-specific nested polymerase chain reaction assay. purulent exudate was collected by aspiration from 19 cases diagnosed as acute periradicular abscesses and dna extracted from the samples was initially amplified using universal 16s rdna primers. a second round of a ...	2004	15327648
selected endodontic pathogens in the apical third of infected root canals: a molecular investigation.	bacteria located at the apical portion of the root canals are conceivably in a strategic position to induce damage to the periradicular tissues and resulting inflammatory diseases. this study sought to investigate the prevalence of 11 selected putative endodontic pathogens in the apical third of infected root canals associated with periradicular lesions. the apical root portion of 23 extracted teeth with carious pulpal exposures and attached periradicular lesions was sectioned, and the root cana ...	2004	15329567
in search of rnase p rna from microbial genomes.	a simple procedure has been developed to quickly retrieve and validate the dna sequence encoding the rna subunit of ribonuclease p (rnase p rna) from microbial genomes. rnase p rna sequences were identified from 94% of bacterial and archaeal complete genomes where previously no rnase p rna was annotated. a sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative rnase p rna in terms of conserved primary features an ...	2004	15337843
contribution of periodontal pathogens on tongue dorsa analyzed with real-time pcr to oral malodor.	oral malodor is considered to originate primarily from tongue microbiota populations. however, the relationship between oral malodor and tongue microbiota remains unclear. in this study, tongue periodontal pathogens were analyzed via real-time pcr, and the association between oral malodor and tongue periodontal pathogens, including porphyromonas gingivalis, tannerella forsythia, prevotella intermedia, prevotella nigrescens and treponema denticola, was examined. the subject population consisted o ...	2004	15380777
outer membrane proteins of pathogenic spirochetes.	pathogenic spirochetes are the causative agents of several important diseases including syphilis, lyme disease, leptospirosis, swine dysentery, periodontal disease and some forms of relapsing fever. spirochetal bacteria possess two membranes and the proteins present in the outer membrane are at the site of interaction with host tissue and the immune system. this review describes the current knowledge in the field of spirochetal outer membrane protein (omp) biology. what is known concerning bioge ...	2004	15449605
clinical and microbiological effects of topical subgingival application of hyaluronic acid gel adjunctive to scaling and root planing in the treatment of chronic periodontitis.	hyaluronic acid (ha) has shown anti-inflammatory effects in gingivitis therapy. the potential benefits of local subgingival application of ha adjunctive to scaling and root planing (srp) were evaluated in this study.	2004	15455740
treponema pallidum fibronectin-binding proteins.	putative adhesins were predicted by computer analysis of the treponema pallidum genome. two treponemal proteins, tp0155 and tp0483, demonstrated specific attachment to fibronectin, blocked bacterial adherence to fibronectin-coated slides, and supported attachment of fibronectin-producing mammalian cells. these results suggest tp0155 and tp0483 are fibronectin-binding proteins mediating t. pallidum-host interactions.	2004	15466055
genome-wide transposon mutagenesis of borrelia burgdorferi for identification of phenotypic mutants.	the spirochete borrelia burgdorferi is the causative agent of lyme disease, the leading vector-borne illness in the united states. many of the genetic factors affecting spirochete morphology and physiology are unknown due to the limited genetic tools available and the large number of open reading frames with unknown functions. by adapting a mariner transposon to function in b. burgdorferi, we have developed a random mutagenesis system that tags the mutated locus for rapid identification. transpo ...	2004	15466540
comparative genomics of the ftsk-hera superfamily of pumping atpases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.	recently, it has been shown that a predicted p-loop atpase (the hera or mlaa protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a bidirectional helicase activity and forms hexameric rings similar to those described for the trwb atpase. in this study, the ftsk-hera superfamily of p-loop atpases, in which the hera clade comprises one of the major branches, is analyzed in detail. we show that, in addition to the ftsk and hera clades, this ...	2004	15466593
need for procedural details in detection of periodontopathic bacterial dna in the atheromatous plaque by pcr.		2004	15472382
subgingival microbiota of chronic periodontitis subjects from different geographic locations.	most clinical studies assume that the subgingival microbiota is similar from one geographic location to another. the purpose of the present investigation was to examine the composition of the subgingival microbiota in chronic periodontitis subjects from four countries.	2004	15491316
the distribution of periodontopathic bacteria among japanese children and their parents.	it is not well known how periodontopathic bacteria colonize in the oral cavity during childhood. the purpose of this study was to investigate the distribution of periodontopathic bacteria in oral cavities of children and their parents and the relationship between the bacterial findings and clinical parameters.	2004	15491344
detection frequency of periodontitis-associated bacteria by polymerase chain reaction in subgingival and supragingival plaque of periodontitis and healthy subjects.	the aim of this study was to compare the detection frequencies of 25 bacterial species in subgingival and supragingival plaque of 18 untreated periodontitis subjects and 12 periodontally healthy subjects. genomic dna was extracted from subgingival and supragingival plaque samples, and bacterial detection was performed by polymerase chain reaction of the 16s rrna genes. fourteen bacteria showed no relationship with periodontitis, and 11 of these 14 species were frequently detected (> or =50%) in ...	2004	15491463
resistance to human beta-defensins is common among oral treponemes.	oral treponemes are implicated in the pathogenesis of periodontal disease. we have previously shown that treponema denticola atcc type strains and strain gm-1 are resistant to killing by human beta-defensins (hbetad)-1 and -2. we hypothesize that resistance to beta-defensins is a common feature of oral treponemes, which allows colonization and persistence in the oral cavity. in this study, we tested additional isolates of t. denticola, as well as six other species of treponemes, for resistance t ...	2004	15491467
extracellular secretion of the borrelia burgdorferi oms28 porin and bgp, a glycosaminoglycan binding protein.	borrelia burgdorferi, the lyme disease pathogen, cycles between its ixodes tick vector and vertebrate hosts, adapting to vastly different biochemical environments. spirochete gene expression as a function of temperature, ph, growth phase, and host milieu is well studied, and recent work suggests that regulatory networks are involved. here, we examine the release of borrelia burgdorferi strain b31 proteins into conditioned medium. spirochetes intrinsically radiolabeled at concentrations ranging f ...	2004	15501754
intra-familial distribution of nine putative periodontopathogens in dental plaque samples analyzed by pcr.	it is of great importance to understand the distribution of periodontopathogens within family members when considering the risk of periodontitis in children. the purpose of this study was to investigate the distribution of periodontopathogens among family members. we used the polymerase chain reaction method to test 4,8, and 7 probands with healthy gingiva, gingivitis, and periodontitis, respectively, and their 60 immediate family members. plaque samples were collected from all erupted teeth sit ...	2004	15508747
an unusual integron in treponema denticola.		2004	15528643
the microbiological case for adjunctive therapy for periodontitis.	that chronic periodontitis is an infectious disease is now firmly established, and the primary role of porphyromonas gingivalis, tannerella forsythensis and treponema denticola is generally accepted. treatment by mechanical means such as scaling and root planing or surgery generally results in significant clinical improvement but may not arrest the progress or recurrence of disease. several studies have shown that the probability of achieving lasting stability as measured by the arrest of progre ...	2004	15536782
identification of early microbial colonizers in human dental biofilm.	to elucidate the first colonizers within in vivo dental biofilm and to establish potential population shifts that occur during the early phases of biofilm formation.	2004	15546422
comparative analysis of the borrelia garinii genome.	three members of the genus borrelia (b.burgdorferi, b.garinii, b.afzelii) cause tick-borne borreliosis. depending on the borrelia species involved, the borreliosis differs in its clinical symptoms. comparative genomics opens up a way to elucidate the underlying differences in borrelia species. we analysed a low redundancy whole-genome shotgun (wgs) assembly of a b.garinii strain isolated from a patient with neuroborreliosis in comparison to the b.burgdorferi genome. this analysis reveals that mo ...	2004	15547252
rubrerythrin from the hyperthermophilic archaeon pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase.	rubrerythrin was purified by multistep chromatography under anaerobic, reducing conditions from the hyperthermophilic archaeon pyrococcus furiosus. it is a homodimer with a molecular mass of 39.2 kda and contains 2.9 +/- 0.2 iron atoms per subunit. the purified protein had peroxidase activity at 85 degrees c using hydrogen peroxide with reduced p. furiosus rubredoxin as the electron donor. the specific activity was 36 micromol of rubredoxin oxidized/min/mg with apparent k(m) values of 35 and 70 ...	2004	15547260
herpesviruses, the missing link between gingivitis and periodontitis?	herpesviruses appear to assume a major etiopathogenic role in various types of destructive periodontal disease. human cytomegalovirus (hcmv), epstein-barr virus (ebv) and hcmv-ebv co-infection are closely associated with disease-active periodontitis in juveniles and adults, with acute necrotizing ulcerative gingivitis in children, and with periodontal abscesses. in particular, hcmv reactivation in periodontitis lesions seems to be linked to advancing disease. hcmv infects periodontal monocytes/m ...	2004	15553977
evolutionary relationships of fusobacterium nucleatum based on phylogenetic analysis and comparative genomics.	the phylogenetic position and evolutionary relationships of fusobacteria remain uncertain. especially intriguing is their relatedness to low g+c gram positive bacteria (firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. taking advantage of the recent completion of the fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of fusobacterium genes by phylogenetic analysis and comparative genomics tools.	2004	15566569
role of a nosx homolog in streptococcus gordonii in aerobic growth and biofilm formation.	oral streptococci such as streptococcus gordonii are facultative anaerobes that initiate biofilm formation on tooth surfaces. an isolated s. gordonii::tn917-lac biofilm-defective mutant contained a transposon insertion in an open reading frame (orf) encoding a homolog of nosx of ralstonia eutropha, a putative maturation factor of nitrous oxide reductase. located downstream are two genes, qor1 and qor2, predicted to encode two putative nadph quinone oxidoreductases. these three genes are cotransc ...	2004	15576767
culture-independent identification of periodontitis-associated porphyromonas and tannerella populations by targeted molecular analysis.	periodontitis is the commonest bacterial disease of humans and is the major cause of adult tooth loss. about half of the oral microflora is unculturable; and 16s rrna pcr, cloning, and sequencing techniques have demonstrated the high level of species richness of the oral microflora. in the present study, a pcr primer set specific for the genera porphyromonas and tannerella was designed and used to analyze the bacterial populations in subgingival plaque samples from inflamed shallow and deep site ...	2004	15583276
molecular detection of treponema denticola and porphyromonas gingivalis in carotid and aortic atheromatous plaques by fish: report of two cases.	treponema denticola and porphyromonas gingivalis have been identified in atheromatous plaques of two patients suffering from atherosclerosis by pcr and fluorescence in situ hybridization (fish). the use of the fish technique suggested that these periodontopathic micro-organisms might be metabolically active within the wall of arteries, under the atherosclerotic lesion.	2005	15591262
enzyme adaptation to alkaline ph: atomic resolution (1.08 a) structure of phosphoserine aminotransferase from bacillus alcalophilus.	the crystal structure of the vitamin b(6)-dependent enzyme phosphoserine aminotransferase from the obligatory alkaliphile bacillus alcalophilus has been determined at 1.08 a resolution. the model was refined to an r-factor of 11.7% (r(free) = 13.9%). the enzyme displays a narrow ph optimum of enzymatic activity at ph 9.0. the final structure was compared to the previously reported structure of the mesophilic phosphoserine aminotransferase from escherichia coli and to that of phosphoserine aminot ...	2005	15608117
upregulation of intercellular adhesion molecule 1 and proinflammatory cytokines by the major surface proteins of treponema maltophilum and treponema lecithinolyticum, the phylogenetic group iv oral spirochetes associated with periodontitis and endodontic infections.	treponema maltophilum and treponema lecithinolyticum belong to the group iv oral spirochetes and are associated with endodontic infections, as well as periodontitis. recently, the genes encoding the major surface proteins (msps) of these bacteria (mspa and msptl, respectively) were cloned and sequenced. the amino acid sequences of these proteins showed significant similarity. in this study we analyzed the functional role of these homologous proteins in human monocytic thp-1 cells and primary cul ...	2005	15618163
the cytolethal distending toxin induces receptor activator of nf-kappab ligand expression in human gingival fibroblasts and periodontal ligament cells.	actinobacillus actinomycetemcomitans is associated with localized aggressive periodontitis, a disease characterized by rapid loss of the alveolar bone surrounding the teeth. receptor activator of nf-kappab ligand (rankl) and osteoprotegerin (opg) are two molecules that regulate osteoclast formation and bone resorption. rankl induces osteoclast differentiation and activation, whereas opg blocks this process by acting as a decoy receptor for rankl. the purpose of this study was to investigate the ...	2005	15618171
biochemical characterization of phosphoryl transfer involving hpr of the phosphoenolpyruvate-dependent phosphotransferase system in treponema denticola, an organism that lacks pts permeases.	treponema pallidum and treponema denticola encode within their genomes homologues of energy coupling and regulatory proteins of the phosphoenolpyruvate:sugar phosphotransferase system (pts) but no recognizable homologues of pts permeases. these homologues include (1) enzyme i, (2) hpr, (3) two iia(ntr)-like proteins, and (4) hpr(ser) kinase/phosphorylase (hprk). because the enzyme i-encoding gene in t. pallidum is an inactive pseudogene and because all other pts genes in both t. pallidum and t. ...	2005	15641785
clinical effects of scaling and root planing on untreated teeth.	the aim of this report is to examine whether scaling and root planing (srp) in one area of the mouth may affect periodontal improvement in untreated areas in the same patient, possibly through systemic effects of treatment.	2005	15642054
nature of the genome of the saprophytic spirochete spirochaeta aurantia and its ribosomal rna operons.	using restriction endonucleases drai, asei, and i-ceui in conjunction with pulsed-field gel electrophoresis, we have shown that spirochaeta aurantia m1 possesses a circular 3.98-mb genome. this is the second largest spirochete chromosome yet analyzed. the observation that the latter enzyme cuts in 3 places suggests the presence of 3 copies of the large subunit (23s) rrna gene (rrl), which was confirmed by southern hybridizations. the complete sequence of 2 of the ribosomal rna operons was determ ...	2004	15644914
detection of dna from periodontal pathogenic bacteria in biofilm obtained from waterlines in dental units.	direct person-to-person transmission of periodontal bacteria through saliva has recently been widely reported and dental units have been demonstrated to retract saliva from patients under treatment and to release it into the mouths of subjects undergoing the next operation. in this study the presence of a group of periodontal pathogenic bacteria inside waterlines in dental units was investigated using polymerase chain reaction (pcr) based methods. briefly, 18 dental units of three different manu ...	2004	15646054
characterization of the roka and hexa broad-substrate-specificity hexokinases from bacteroides fragilis and their role in hexose and n-acetylglucosamine utilization.	bacteroides fragilis, a human gastrointestinal commensal and an opportunistic pathogen, utilizes simple and complex sugars and polysaccharides for growth in the large intestine and at sites of infection. because b. fragilis lacks transport-linked sugar phosphorylation systems, cytoplasmic kinase(s) was expected to be required for the phosphorylation of hexoses and hexosamines. we have now identified two hexose kinases that are important for growth of b. fragilis on glucose, mannose, and other su ...	2005	15659667
fusobacterium nucleatum increases collagenase 3 production and migration of epithelial cells.	fusobacterium nucleatum is closely associated with human periodontal diseases and may also be a causative agent in other infections, such as pericarditis, septic arthritis, and abscesses of tonsils and liver. initiation and outcome of infective diseases depend critically on the host cell signaling system altered by the microbe. production of proteinases by infected cells is an important factor in pericellular tissue destruction and cell migration. we studied binding of f. nucleatum to human epit ...	2005	15664960
mutagenesis of a novel gene in the prca-prtp protease locus affects expression of treponema denticola membrane complexes.	a novel gene was identified in the treponema denticola prca-prtp protease operon. strains with mutations in either the prca-prtp or the msp region showed altered expression of a product(s) of the other locus. together, these results provide information on the assembly of outer membrane complexes involved in t. denticola interaction with host cells and tissue.	2005	15664975
clinical and microbiological effect of scaling and root planing in smoker and non-smoker chronic and aggressive periodontitis patients.	to compare the effects of scaling and root planing (srp) on clinical and microbiological parameters at selected sites in smoker and non-smoker chronic and generalized aggressive periodontitis patients.	2005	15691352
periodontal microbiota and carotid intima-media thickness: the oral infections and vascular disease epidemiology study (invest).	chronic infections, including periodontal infections, may predispose to cardiovascular disease. we investigated the relationship between periodontal microbiota and subclinical atherosclerosis.	2005	15699278
protein domains and architectural innovation in plant-associated proteobacteria.	evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ...	2005	15715905
transcriptome of treponema pallidum: gene expression profile during experimental rabbit infection.	rna transcript levels in the syphilis spirochete treponema pallidum subsp. pallidum (nichols) isolated from experimentally infected rabbits were determined by the use of dna microarray technology. this characterization of the t. pallidum transcriptome during experimental infection provides further insight into the importance of gene expression levels for the survival and pathogenesis of this bacterium.	2005	15716460
impact of sample storage on detection of periodontal bacteria.	information on the impact of sample storage prior to analysis by dna methods is limited. the aim of this study was to investigate the effect of subgingival sample storage on bacterial detection and enumeration.	2005	15720575
identification of a new borrelia species among small mammals in areas of northern spain where lyme disease is endemic.	the role of small mammals as reservoir hosts for borrelia burgdorferi was investigated in several areas where lyme disease is endemic in northern spain. a low rate of infestation by ixodes ricinus nymphs was found in the small mammal populations studied that correlated with the near-absence of b. burgdorferi sensu lato in 184 animals tested and with the lack of transmission of b. burgdorferi sensu lato to i. ricinus larvae that fed on them. in contrast, questing ticks collected at the same time ...	2005	15746336
quantitative detection of volatile sulfur compound- producing microorganisms in oral specimens using real-time pcr.	it is well-known that some periodontopathic bacteria, especially porphyromonas gingivalis, fusobacterium nucleatum, tannerella forsythia (formerly bacteroides forsythus or tan. forsythensis), and treponema denticola, actively produce volatile sulfur compounds (vscs), such as h2s and ch3sh. we previously reported a qualitative relationship between periodontopathic bacteria and vscs; however, a quantitative analysis of periodontopathic bacteria in oral specimens is required for further characteriz ...	2005	15752104
halitosis and periodontal disease in subjects with mental disabilities.	the aim of this study was to investigate the relationship between halitosis, presence of n-benzoyl-dl-arginine-2-naphthylamide (bana) positive activity (indicative of treponema denticola, porphyromonas gingivalis, tannerella forsythensis) and periodontal conditions in subjects with mental disabilities.	2005	15752108
mechanisms of porphyromonas gingivalis-induced monocyte chemoattractant protein-1 expression in endothelial cells.	monocyte chemoattractant protein-1 (mcp-1) is expressed in vascular endothelial cells of inflamed gingival tissues and plays an important role in periodontal pathogenesis. endothelial cells produce high levels of mcp-1 in response to porphyromonas gingivalis, an important periodontal pathogen. the present study investigated the mechanisms involved in mcp-1 production by human umbilical vein endothelial cells (huvec) following infection with p. gingivalis. in contrast to p. gingivalis, bacteroide ...	2005	15780578
the thermophilic, homohexameric aminopeptidase of borrelia burgdorferi is a member of the m29 family of metallopeptidases.	proteases are implicated in several aspects of the physiology of microorganisms, as well as in host-pathogen interactions. aminopeptidases are also emerging as novel drug targets in infectious agents. in this study, we have characterized an aminopeptidase from the spirochete borrelia burgdorferi, the causative agent of lyme disease. the aminopeptidolytic activity was identified in cell extracts from b. burgdorferi by using the substrate leucine-7-amido-4-methylcoumarin. a protein displaying this ...	2005	15784569
phototargeting oral black-pigmented bacteria.	we have found that broadband light (380 to 520 nm) rapidly and selectively kills oral black-pigmented bacteria (bpb) in pure cultures and in dental plaque samples obtained from human subjects with chronic periodontitis. we hypothesize that this killing effect is a result of light excitation of their endogenous porphyrins. cultures of prevotella intermedia and p. nigrescens were killed by 4.2 j/cm2, whereas p. melaninogenica required 21 j/cm2. exposure to light with a fluence of 42 j/cm2 produced ...	2005	15793117
crystal structure of the flagellar rotor protein flin from thermotoga maritima.	flin is a component of the bacterial flagellum that is present at levels of more than 100 copies and forms the bulk of the c ring, a drum-shaped structure at the inner end of the basal body. flin interacts with flig and flim to form the rotor-mounted switch complex that controls clockwise-counterclockwise switching of the motor. in addition to its functions in motor rotation and switching, flin is thought to have a role in the export of proteins that form the exterior structures of the flagellum ...	2005	15805535
scaling and root planing, systemic metronidazole and professional plaque removal in the treatment of chronic periodontitis in a brazilian population ii--microbiological results.	the current investigation evaluated changes in levels and proportions of 39 bacterial species in subgingival plaque samples after scaling and root planing (srp) alone or in combination with systemic metronidazole and/or professional cleaning in subjects with chronic periodontitis.	2005	15811059
effective antiprotease-antibiotic treatment of experimental anthrax.	inhalation anthrax is characterized by a systemic spread of the challenge agent, bacillus anthracis. it causes severe damage, including multiple hemorrhagic lesions, to host tissues and organs. it is widely believed that anthrax lethal toxin secreted by proliferating bacteria is a major cause of death, however, the pathology of intoxication in experimental animals is drastically different from that found during the infectious process. in order to close a gap between our understanding of anthrax ...	2005	15819985
folding pathway of the pyridoxal 5'-phosphate c-s lyase maly from escherichia coli.	maly from escherichia coli is a bifunctional dimeric plp (pyridoxal 5'-phosphate) enzyme acting as a beta-cystathionase and as a repressor of the maltose system. the spectroscopic and molecular properties of the holoenzyme, in the untreated and nabh4-treated forms, and of the apoenzyme have been elucidated. a systematic study of the urea-induced unfolding of maly has been monitored by gel filtration, cross-linking, ans (8-anilino-1-naphthalenesulphonic acid) binding and by visible, near- and far ...	2005	15823094
differences in prevalence of selected bacterial species in primary endodontic infections from two distinct geographic locations.	this study intended to compare the prevalence of 7 putative endodontic pathogens in samples of primary endodontic infections taken from patients of 2 distant geographic locations.	2005	15829891
non-surgical periodontal therapy with adjunctive topical doxycycline: a double-masked, randomized, controlled multicenter study. ii. microbiological results.	topical application of active substances offers an additional option in periodontal therapy. the aim of this study was to examine the influence of the administration of a novel, biodegradable 14% doxycycline gel on microbiological findings, in connection with scaling and root planing.	2005	15830639
dna probe identification of bacteria colonizing internal surfaces of the implant-abutment interface: a preliminary study.	currently, there is limited knowledge concerning the specific genus and species of bacteria that may colonize internal surfaces of the implant-abutment interface (iai) of two-stage dental implants. the purpose of this study was to use dna probe analysis to identify those periodontopathic bacteria that may inhabit the internal surfaces and healing abutment screw-threads of the iai of dental implants in situ.	2005	15830645
synthesis of autoinducer 2 by the lyme disease spirochete, borrelia burgdorferi.	defining the metabolic capabilities and regulatory mechanisms controlling gene expression is a valuable step in understanding the pathogenic properties of infectious agents such as borrelia burgdorferi. the present studies demonstrated that b. burgdorferi encodes functional pfs and luxs enzymes for the breakdown of toxic products of methylation reactions. consistent with those observations, b. burgdorferi was shown to synthesize the end product 4,5-dihydroxy-2,3-pentanedione (dpd) during laborat ...	2005	15838035
severe periodontitis in a 5-year-old girl with hyperimmunoglobulin e syndrome.	the hyperimmunoglobulin e syndrome (hies) is a multisystem disorder that affects the: (1) dentition; (2) skeleton; (3) connective tissues; and (4) immune system. little is known about periodontal manifestations of the syndrome. the purpose of this report was to describe a 5-year-old girl with suspected autosomal-recessive hies syndrome who revealed profusely bleeding and painful gingiva and generalized aggressive periodontitis. a polymerase chain reaction (pcr)-based microbiological examination ...	2005	15839398
high production of methyl mercaptan by l-methionine-alpha-deamino-gamma-mercaptomethane lyase from treponema denticola.	methyl mercaptan is derived from l-methionine by the action of l-methionine-alpha-deamino-gamma-mercaptomethane lyase (metase) and is a major component of oral malodor. this compound is highly toxic and is thought to play an important role in periodontal disease. we found that treponema denticola, a member of the subgingival biofilm at periodontal disease sites, produced a large amount of methyl mercaptan even at low concentration of l-methionine. metase activity in a cell-free extract from t. d ...	2005	15845368
binding properties and adhesion-mediating regions of the major sheath protein of treponema denticola atcc 35405.	there is growing evidence that a number of oral treponema species, in particular treponema denticola, are associated with the progression of human periodontal disease. the major sheath (or surface) protein (msp) of t. denticola is implicated in adhesion of bacteria to host cells and tissue proteins and is likely to be an important virulence factor. however, the binding regions of the msp are not known. we have purified from escherichia coli recombinant msp (rmsp) polypeptides corresponding to th ...	2005	15845495
a monoclonal antibody that conveys in vitro killing and partial protection in experimental syphilis binds a phosphorylcholine surface epitope of treponema pallidum.	immunization with purified treponema pallidum outer membrane vesicles (omv) has previously resulted in high-titer complement-dependent serum bactericidal activity. in this study, omv immunization resulted in the isolation of a monoclonal antibody, m131, with complement-dependent killing activity. passive immunization of rabbits with m131 administered intravenously conferred significant immunity demonstrated by the failure of syphilitic lesions to appear at 29% of intradermal challenge sites (7/2 ...	2005	15845516
a novel class of dual-family immunophilins.	immunophilins are protein chaperones with peptidylprolyl isomerase activity that belong to one of two large families, the cyclosporin-binding cyclophilins (cyps) and the fk506-binding proteins (fkbps). each family displays characteristic and conserved sequence features that differ between the two families. we report a novel group of dual-family immunophilins that contain both cyp and fkbp domains for which we propose the name fcbp (fk506- and cyclosporin-binding protein). the fcbp of toxoplasma ...	2005	15845546
porphyromonas gingivalis, treponema denticola, and tannerella forsythia: the "red complex", a prototype polybacterial pathogenic consortium in periodontitis.		2005	15853938
molecular analysis of human oral microbiota.	the application of molecular, mainly 16s ribosomal rna (rrna)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the human oral cavity. in this mini-review, we describe the impact of these culture-independent approaches on our knowledge of the ecology of the human oral cavity and provide directions for future studies that should emphasize the role of specific strains, specie ...	2005	15853975
detection of actinobacillus actinomycetemcomitans but not bacteria of the red complex in aortic aneurysms by multiplex polymerase chain reaction.	aortic aneurysms affect an increasing number of elderly patients and cause considerable morbidity and mortality. the understanding of the mechanisms involved in the pathogenesis of aortic aneurysms is unclear and little is known about the role of microorganisms in the development of the condition. the aim of the present study was to examine aortic aneurysm samples for the presence of four putative periodontal pathogens: actinobacillus actinomycetemcomitans, treponema denticola, tannerella forsyt ...	2005	15857100
loop-mediated isothermal amplification method for rapid detection of the periodontopathic bacteria porphyromonas gingivalis, tannerella forsythia, and treponema denticola.	loop-mediated isothermal amplification (lamp), a novel nucleic acid amplification method, was developed for the rapid detection of the major periodontal pathogens porphyromonas gingivalis, tannerella forsythia, and treponema denticola. the lamp method amplifies dna with high specificity, efficiency, and rapidity under isothermal conditions using a set of four specially designed primers and a dna polymerase with strand displacement activity. in this study, we initially designed the primers for la ...	2005	15872275
proportional distribution of the red complex and its individual pathogens after sample storage using the checkerboard dna-dna hybridization technique.	information on the impact of sample storage prior to analysis by dna methods is limited.	2005	15882222
clinical and microbiological evaluation of the effectiveness of the nd:yap laser for the initial treatment of adult periodontitis. a randomized controlled study.	enhancement of the results obtained by scaling and planing is most often sought by using antimicrobial therapies. laser beams have been shown to be bactericidal and could possibly target pathogens more effectively and with fewer compliance problems than antiseptic solutions.	2005	15882229
strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.	the x-ray susceptibility of the lysine-pyridoxal-5'-phosphate schiff base in bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 k to 1.3 a resolution, complemented by on-line spectroscopic studies. x-rays induce deprotonation of the internal aldimine, changes in the schiff base conformation, displacement of the cofactor molecule, and disruption of the schiff base linkage between pyridoxal-5'-phosphate and the lys residue. analy ...	2005	15883191
prostaglandin e(2) is a main mediator in receptor activator of nuclear factor-kappab ligand-dependent osteoclastogenesis induced by porphyromonas gingivalis, treponema denticola, and treponema socranskii.	periodontitis is an inflammatory disease that often leads to destruction of alveolar bone; a number of bacteria in subgingival plaque are associated with bone destruction in periodontitis. to understand the mechanism of how periodontopathogens induce osteoclastogenesis, we determined which mediators are involved in the osteoclastogenesis.	2005	15898943
debridement and local application of tetracycline in the management of persistent periodontitis. clinical and microbiological results after 12 months.	the purpose of this study was to evaluate the clinical and microbiological efficacy of local delivery of tetracycline in persistent periodontal lesions after topical therapy.	2005	15902062
immunological evaluation and cellular location analysis of the tpri antigen of treponema pallidum subsp. pallidum.	the tpri antigen of treponema pallidum subsp. pallidum is a putative virulence factor predicted to be located in the outer membrane of the syphilis spirochete. in this study, we analyzed the immune response against tpri and its subunits in sera collected both from rabbits experimentally infected with the nichols strain and from patients with syphilis, showing a different pattern of reactivity toward the antigen in these two groups of samples. the protective ability of recombinant tpri and its hy ...	2005	15908421
protein-protein interactions in the chemotaxis signalling pathway of treponema denticola.	motile bacteria employ sophisticated chemotaxis signal transduction systems to transform environmental cues into corresponding behavioural responses. the proteins involved in this signalling pathway have been extensively studied on a molecular level in various model organisms, including enterobacteria and bacillus subtilis, and specific protein-protein interactions have been identified. the chemotaxis operon of spirochaetes encodes a novel chemotaxis protein, chex, in addition to homologues to t ...	2005	15941989
microarrays complement culture methods for identification of bacteria in endodontic infections.	the aim of this study was to investigate the microbial composition of necrotic root canals using culture methods and microarray technology. twenty uniradicular teeth with radiographic evidence of periapical bone loss and with no previous endodontic treatment were selected for this study. for molecular diagnosis a dna chip with 20 different species-specific, 16s-rdna-directed catcher probes was used. the microorganisms most frequently detected by the dna chip were: micromonas micros, fusobacteriu ...	2005	15943771
the tetr family of transcriptional repressors.	we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ...	2005	15944459
a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts.	analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.	2005	15955239
use of the genomic subtractive hybridization technique to develop a real-time pcr assay for quantitative detection of prevotella spp. in oral biofilm samples.	genomic subtractive hybridization was used to design prevotella nigrescens-specific primers and taqman probes. based on this technique, a taqman real-time pcr assay was developed for quantifying four oral black-pigmented prevotella species. the combination of real-time pcr and genomic subtractive hybridization is useful for preparing species-specific primer-probe sets for closely related species.	2005	15956428