Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| 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 |
| signature proteins that are distinctive of alpha proteobacteria. | the alpha (alpha) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16s rrna trees, with no known molecular characteristic that is unique to this group. the genomes of three alpha-proteobacteria, rickettsia prowazekii (rp), caulobacter crescentus (cc) and bartonella quintana (bq), were analyzed in order to search for proteins that are unique to this group. | 2005 | 15960851 |
| predictive value of clinical and microbiological parameters for the treatment outcome of scaling and root planing. | to compare the clinical and microbiological outcome of non-surgical periodontal therapy after 6 months with data obtained after hygienic phase or 6 weeks after completion of non-surgical therapy, in order to evaluate the value of clinical and microbiological parameters to predict treatment success. | 2005 | 15966873 |
| association between coinfection of porphyromonas gingivalis, actinobacillus actinomycetemcomitans and treponema denticola and periodontal tissue destruction in chronic periodontitis. | the association between the infection of porphyromonas gingivalis, actinobacillus actinomycetemcomitans and treponema denticola in chronic periodontitis (cp) and the severity of periodontal disease remains to be elucidated. the aim of this study was to investigate the subgingival infection frequencies of three periodontopathic bacteria in chinese cp patients and to evaluate the correlations between infection by these bacteria and periodontal destruction. | 2005 | 15978192 |
| the bioinformatics resource for oral pathogens. | complete genomic sequences of several oral pathogens have been deciphered and multiple sources of independently annotated data are available for the same genomes. different gene identification schemes and functional annotation methods used in these databases present a challenge for cross-referencing and the efficient use of the data. the bioinformatics resource for oral pathogens (brop) aims to integrate bioinformatics data from multiple sources for easy comparison, analysis and data-mining thro ... | 2005 | 15980574 |
| periodontal disease and coronary heart disease: a reappraisal of the exposure. | results from studies relating periodontal disease to cardiovascular disease have been mixed. residual confounding by smoking and use of clinical measures of periodontal disease rather than measures of infection have been 2 major criticisms. the aims of this study were to investigate relationships between prevalent coronary heart disease (chd) and 2 exposures, (1) clinical periodontal disease and (2) igg antibodies to 17 oral organisms, and to evaluate the role of smoking in these relationships. | 2005 | 15983248 |
| the salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects. | the purpose of the present investigation was to determine if the salivary counts of 40 common oral bacteria in subjects with an oral squamous cell carcinoma (oscc) lesion would differ from those found in cancer-free (oscc-free) controls. | 2005 | 15987522 |
| a leptospira interrogans enzyme with similarity to yeast ste14p that methylates the 1-phosphate group of lipid a. | distinct from other spirochetes, cells of leptospira interrogans contain orthologues of all the escherichia coli lpx genes required for lipid a biosynthesis, but they synthesize a modified form of lipopolysaccharide that supposedly activates toll-like receptor 2 (tlr2) instead of tlr4. the recent determination of the l. interrogans lipid a structure revealed an unprecedented o-methylation of its 1-phosphate group (que-gewirth, n. l. s., ribeiro, a. a., kalb, s. r., cotter, r. j., bulach, d. m., ... | 2005 | 15994324 |
| prevalence of putative periodontopathogens in subgingival dental plaques from gingivitis lesions in korean orthodontic patients. | the objective of this study was to detect and compare the presence of periodontopathogens in the subgingival plaques of gingivitis lesions in adults who wore fixed orthodontic appliances, as opposed to adults who did not wear any orthodontic appliances. thirty-six individuals participated in this study. nineteen of these subjects did not wear any orthodontic appliances, and these subjects comprised the control group. the other 17 individuals had been wearing fixed orthodontic appliances for at l ... | 2005 | 15995644 |
| uncultivated phylotypes and newly named species associated with primary and persistent endodontic infections. | endodontic infections have been traditionally studied by culture methods, but recent reports showing that over 50% of the oral microbiota is still uncultivable (b. j. paster et al., j. bacteriol. 183:3770-3783, 2001) raise the possibility that many endodontic pathogens remain unknown. this study intended to investigate the prevalence of several uncultivated oral phylotypes, as well as newly named species in primary or persistent endodontic infections associated with chronic periradicular disease ... | 2005 | 16000454 |
| oral bacteria in the occluded arteries of patients with buerger disease. | recent studies have suggested that infectious organisms play a role in vascular diseases. in this study, to explore a possible link between oral infection and buerger disease, we investigated whether oral (periodontal) bacteria were present in occluded arteries removed from patients with characteristic buerger disease. | 2005 | 16012459 |
| origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. | we report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (aeps). this analysis greatly expands the range of diversity of the aeps and reveals the unique active site shared by all members of this superfamily. in particular, it is shown that eukaryotic nucleo-cytoplasmic large dna viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode aeps of a distinct family, which also includ ... | 2005 | 16027112 |
| selective capture of salmonella enterica serovar typhi genes expressed in macrophages that are absent from the salmonella enterica serovar typhimurium genome. | thirty-six salmonella enterica serovar typhi-specific genes, absent from the salmonella enterica serovar typhimurium genome, that were expressed in human macrophages were identified by selective capture of transcribed sequences. these genes are located on 15 unique loci of the serovar typhi genome, including salmonella pathogenicity islands (spi-7, spi-8, and spi-10) and bacteriophages (st15, st18, and st35). | 2005 | 16041043 |
| the leptospira interrogans lexa gene is not autoregulated. | footprinting and mutagenesis experiments demonstrated that leptospira interrogans lexa binds the palindrome tttgn(5)caaa found in the reca promoter but not in the lexa promoter. in silico analysis revealed that none of the other canonical sos genes is under direct control of lexa, making the leptospiral lexa gene the first described which is not autoregulated. | 2005 | 16077133 |
| identification of candidate periodontal pathogens and beneficial species by quantitative 16s clonal analysis. | most studies of the bacterial etiology of periodontitis have used either culture-based or targeted dna approaches, and so it is likely that pathogens remain undiscovered. the purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. samples from subjects with periodontitis and controls were analyzed using ribosomal 16s cloning and sequencing. several genera, ma ... | 2005 | 16081935 |
| synergistic biofilm formation by treponema denticola and porphyromonas gingivalis. | biofilm formation is an important step in the etiology of periodontal diseases. in this study, in vitro biofilm formation by treponema denticola and porphyromonas gingivalis 381 displayed synergistic effects. confocal microscopy demonstrated that p. gingivalis attaches to the substratum first as a primary colonizer followed by coaggregation with t. denticola to form a mixed biofilm. the t. denticola flagella mutant as well as the cytoplasmic filament mutant were shown to be essential for biofilm ... | 2005 | 16085371 |
| detection of bacteria in endodontic samples by polymerase chain reaction assays and association with defined clinical signs in italian patients. | the presence of selected bacteria (enterococcus faecalis, porphyromonas gingivalis, prevotella intermedia, tannerella forsythensis, treponema denticola) in infected root canals was studied using polymerase chain reaction (pcr) assays, and the association of bacteria with clinical signs of endodontic disease was assessed. the null hypothesis, that no difference could be observed between clinical signs of apical periodontitis and a specific bacterial strain, was tested. | 2005 | 16101964 |
| impact of smoking on the clinical, microbiological and immunological parameters of adult patients with periodontitis. | the aim of the current study was to assess the impact of smoking on the clinical indices, the humoral immune response and the detection frequency of putative periodontal pathogens in patients with periodontitis cross-sectionally and following therapy. | 2005 | 16104962 |
| identification of genes of vsh-1, a prophage-like gene transfer agent of brachyspira hyodysenteriae. | vsh-1 is a mitomycin c-inducible prophage of the anaerobic spirochete brachyspira hyodysenteriae. purified vsh-1 virions are noninfectious, contain random 7.5-kb fragments of the bacterial genome, and mediate generalized transduction of b. hyodysenteriae cells. in order to identify and sequence genes of this novel gene transfer agent (gta), proteins associated either with vsh-1 capsids or with tails were purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. the n-terminal amino ... | 2005 | 16109929 |
| gene organization and transcriptional analysis of the tprj, tpri, tprg, and tprf loci in treponema pallidum strains nichols and sea 81-4. | the tpr gene family of treponema pallidum subsp. pallidum, the causative agent of syphilis, has recently become the focus of intensive investigation. tprf and tpri sequences are highly conserved among different isolates and are the targets of strong humoral and cellular immune responses of the host, and immunization with a recombinant peptide from the amino terminus of these antigens has been shown to alter significantly lesion development following homologous challenge. this indicates that thes ... | 2005 | 16109950 |
| horizontally acquired genes for purine salvage in borrelia spp. causing relapsing fever. | unlike borrelia burgdorferi, the relapsing fever agent borrelia hermsii and the related borrelia miyamotoi had pura and purb genes of the purine salvage pathway. these were located among the rrna genes. phylogenetic analysis indicated that these genes had a different evolutionary history than those of orthologs in other spirochetes. | 2005 | 16113341 |
| discrimination of streptococcus pneumoniae from viridans group streptococci by genomic subtractive hybridization. | two oligonucleotide primer sets for the discrimination of streptococcus pneumoniae from "pneumococcus-like" oral streptococcal isolates by pcr were developed. genomic subtractive hybridization was performed to search for differences between streptococcus pneumoniae strain wu2 and the most closely related oral streptococcus, streptococcus mitis strain 903. we identified 19 clones that contained s. pneumoniae-specific nucleotide fragments that were absent from the chromosomal dna of typical labora ... | 2005 | 16145102 |
| amylomaltase of pyrobaculum aerophilum im2 produces thermoreversible starch gels. | amylomaltases are 4-alpha-glucanotransferases (ec 2.4.1.25) of glycoside hydrolase family 77 that transfer alpha-1,4-linked glucans to another acceptor, which can be the 4-oh group of an alpha-1,4-linked glucan or glucose. the amylomaltase-encoding gene (pae1209) from the hyperthermophilic archaeon pyrobaculum aerophilum im2 was cloned and expressed in escherichia coli, and the gene product (pyamase) was characterized. pyamase displays optimal activity at ph 6.7 and 95 degrees c and is the most ... | 2005 | 16151092 |
| the 2-hydroxycarboxylate transporter family: physiology, structure, and mechanism. | the 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. they function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate. these pathways are found in the class bacillales of the low-cg gram-positive bacteria and in the gamma subdivision of the proteobacteria. the pathways have evolved into a remarkable diversity in terms of th ... | 2005 | 16339740 |
| a computational method to predict genetically encoded rare amino acids in proteins. | in several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. these rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. we report a method for such recoding prediction from genomic data, using read-through similarity evaluation. a survey across a set of microbial genomes identifies almost all the known cases as well as a number of no ... | 2005 | 16168086 |
| statistical analyses of complex denaturing gradient gel electrophoresis profiles. | studies using molecular techniques have demonstrated that a culture-based approach can severely underestimate the bacterial diversity in most environments. one of the molecular techniques that has been applied in microbial ecology is denaturing gradient gel electrophoresis (dgge). the purpose of this study was to investigate differences in the microbiota of plaque, using a number of analysis techniques, from children without gingivitis (n = 30) and from those with gingivitis (n = 30). extracted ... | 2005 | 16081938 |
| evolution of selenium utilization traits. | the essential trace element selenium is used in a wide variety of biological processes. selenocysteine (sec), the 21st amino acid, is co-translationally incorporated into a restricted set of proteins. it is encoded by an uga codon with the help of trnasec (selc), sec-specific elongation factor (selb) and a cis-acting mrna structure (secis element). in addition, sec synthase (sela) and selenophosphate synthetase (seld) are involved in the biosynthesis of sec on the trnasec. selenium is also found ... | 2005 | 16086848 |
| diagnostic biomarkers for oral and periodontal diseases. | this article provides an overview of periodontal disease diagnosis that uses clinical parameters and biomarkers of the disease process.this article discusses the use of biomarkers of disease that can be identified at the tissue, cellular, and molecular levels and that are measurable in oral fluids such as saliva and gingival crevicular fluid. biomarkers identified from these biologic fluids include microbial, host response, and connective tissue-related molecules that can target specific pathway ... | 2005 | 15978241 |
| antimicrobial peptides in the oral environment: expression and function in health and disease. | the oral cavity is a unique environment in which antimicrobial peptides play a key role in maintaining health and may have future therapeutic applications. present evidence suggests that alpha-defensins, beta-defensins, ll-37, histatin, and other antimicrobial peptides and proteins have distinct but overlapping roles in maintaining oral health and preventing bacterial, fungal, and viral adherence and infection. the expression of the inducible hbd-2 in normal oral epithelium, in contrast to other ... | 2005 | 16053246 |
| 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 |
| comparative genomic analyses of the bacterial phosphotransferase system. | we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ... | 2005 | 16339738 |
| biofilms 2003: emerging themes and challenges in studies of surface-associated microbial life. | 2004 | 15231774 | |
| 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 |
| the prokaryotic selenoproteome. | in the genetic code, the uga codon has a dual function as it encodes selenocysteine (sec) and serves as a stop signal. however, only the translation terminator function is used in gene annotation programs, resulting in misannotation of selenoprotein genes. here, we applied two independent bioinformatics approaches to characterize a selenoprotein set in prokaryotic genomes. one method searched for selenoprotein genes by identifying rna stem-loop structures, selenocysteine insertion sequence eleme ... | 2004 | 15105824 |
| effect of systemic matrix metalloproteinase inhibition on periodontal wound repair: a proof of concept trial. | the adjunctive use of matrix metalloproteinase (mmp) inhibitors with scaling and root planing (srp) promotes new attachment in patients with periodontal disease. this pilot study was designed to examine aspects of the biological response brought about by the mmp inhibitor low dose doxycycline (ldd) combined with access flap surgery (afs) on the modulation of periodontal wound repair in patients with severe chronic periodontitis. | 2004 | 15088883 |
| 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 |
| integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. | integrons are horizontal gene transfer (hgt) systems containing elements necessary for site-specific recombination and expression of foreign dna. the overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. this report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. first, using culture-independent techniques, we explored the diversity of integrons and integron-tran ... | 2004 | 14766601 |
| 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 |
| 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 |
| a cdp-choline pathway for phosphatidylcholine biosynthesis in treponema denticola. | the genomes of treponema denticola and treponema pallidum contain a gene, licca, which is predicted to encode a fusion protein containing choline kinase and ctp:phosphocholine cytidylyltransferase activities. because both organisms have been reported to contain phosphatidylcholine, this raises the possibility that they use a cdp-choline pathway for the biosynthesis of phosphatidylcholine. this report shows that phosphatidylcholine is a major phospholipid in t. denticola, accounting for 35-40% of ... | 2004 | 14756787 |
| physical and enzymological interaction of bacillus subtilis proteins required for de novo pyridoxal 5'-phosphate biosynthesis. | bacillus subtilis synthesizes pyridoxal 5'-phosphate, the active form of vitamin b(6), by a poorly characterized pathway involving the yaad and yaae genes. the pdxs (yaad) mutant was confirmed to be a strict b(6) auxotroph, but the pdxt (yaae) mutant turned out to be a conditional auxotroph depending on the availability of ammonium in the growth medium. the pdxs and pdxt proteins copurified during affinity chromatography and apparently form a complex that has glutaminase activity. pdxs and pdxt ... | 2004 | 14762015 |
| genome size of human oral treponema species by pulsed-field gel electrophoresis. | the genome sizes of seven strains of oral treponemes were determined using pulsed-field gel electrophoresis (pfge). these strains represent members from six of the currently known cultivable oral treponeme groups. the pfge fragments were digitally recorded and then quantitated using gimp v 1.2, an image manipulation program. the results show that the six oral treponeme genomes are comparable in size, ranging from approximately 2.2 to 2.5 mbp. the genome sizes of these strains are 20-25% smaller ... | 2004 | 14871355 |
| human beta-defensins 2 and 3 demonstrate strain-selective activity against oral microorganisms. | human beta-defensins 2 and 3 (hbd-2 and hbd-3) are inducible peptides present at sites of infection in the oral cavity. a few studies have reported broad-spectrum antimicrobial activity for both peptides. however, no comprehensive study has thoroughly investigated their potential against oral pathogens. the purpose of this study was to test the effectiveness of hbd-2 and hbd-3 against a collection of oral organisms (actinobacillus actinomycetemcomitans, fusobacterium nucleatum, porphyromonas gin ... | 2004 | 15004048 |
| correlation between detection rates of periodontopathic bacterial dna in coronary stenotic artery plaque [corrected] and in dental plaque samples. | utilizing pcr, the 16s rrna detection rates for porphyromonas gingivalis, actinobacillus actinomycetemcomitans, bacteroides forsythus, treponema denticola, and campylobacter rectus in samples of stenotic coronary artery plaques were determined to be 21.6, 23.3, 5.9, 23.5, and 15.7%, respectively. the detection rates for p. gingivalis and c. rectus correlated with their presence in subgingival plaque. | 2004 | 15004106 |
| description of treponema azotonutricium sp. nov. and treponema primitia sp. nov., the first spirochetes isolated from termite guts. | long after their original discovery, termite gut spirochetes were recently isolated in pure culture for the first time. they revealed metabolic capabilities hitherto unknown in the spirochaetes division of the bacteria, i.e., h(2) plus co(2) acetogenesis (j. r. leadbetter, t. m. schmidt, j. r. graber, and j. a. breznak, science 283:686-689, 1999) and dinitrogen fixation (t. g. lilburn, k. s. kim, n. e. ostrom, k. r. byzek, j. r. leadbetter, and j. a. breznak, science 292:2495-2498, 2001). howeve ... | 2004 | 15006748 |
| quadrant root planing versus same-day full-mouth root planing. | the aim of this study was to determine whether same-day full-mouth scaling and root planing (fm-srp) and quadrant scaling and root planing (q-srp) resulted in variations in the systemic humoral immune response dynamics (antibody titres and avidity) during active treatment and 3 and 6 months post-therapy. | 2004 | 15016017 |
| debridement and local application of tetracycline-loaded fibres in the management of persistent periodontitis: results after 12 months. | the aim of our study was to evaluate the clinical, radiological and microbiological response to the local delivery of tetracycline (te) of sites with persistent periodontal lesions. | 2004 | 15016019 |
| quadrant root planing versus same-day full-mouth root planing. ii. microbiological findings. | the aim of this study was to test the hypothesis that over a period of 6 months, same-day full-mouth scaling and root planing (fm-srp) resulted in greater reductions in the detection frequency of five putative periodontal pathogens compared with quadrant scaling and root planing (q-srp) in chronic periodontitis patients. | 2004 | 15016040 |
| a 43-kda protein of treponema denticola is essential for dentilisin activity. | a protease of treponema denticola, dentilisin, is thought to be part of a complex with 43- and 38-kda proteins. a sequence encoding a 43-kda protein was located in the 3' region of the prca gene upstream of the dentilisin gene (prtp). the 43-kda protein was apparently generated from digestion of prca. to clarify the function of the protein, we constructed a mutant of the 43-kda protein following homologous recombination. the mutant lacked detectable dentilisin activity. immunoblot analysis demon ... | 2004 | 15033237 |
| a methylated phosphate group and four amide-linked acyl chains in leptospira interrogans lipid a. the membrane anchor of an unusual lipopolysaccharide that activates tlr2. | leptospira interrogans differs from other spirochetes in that it contains homologs of all the escherichia coli lpx genes required for the biosynthesis of the lipid a anchor of lipopolysaccharide (lps). lps from l. interrogans cells is unusual in that it activates tlr2 rather than tlr4. the structure of l. interrogans lipid a has now been determined by a combination of matrix-assisted laser desorption ionization time-of-flight mass spectrometry, nmr spectroscopy, and biochemical studies. lipid a ... | 2004 | 15044492 |
| the major outer sheath protein of treponema denticola inhibits the binding step of collagen phagocytosis in fibroblasts. | bacterial infections contribfute to the chronicity of connective tissue lesions in part by perturbing extracellular matrix remodelling processes. we examined a novel mechanism by which the major outer sheath protein (msp) of the spirochaete treponema denticola disrupts matrix remodelling mediated by intracellular digestion of collagen. the initial collagen-binding step of phagocytosis was examined in human gingival fibroblasts and rat-2 fibroblasts. cells were pretreated with msp or vehicle, and ... | 2004 | 15056218 |
| expression of treponema denticola oligopeptidase b in escherichia coli. | treponema denticola is a small anaerobic spirochete often isolated from periodontal lesions and closely associated with periodontal diseases. this bacterium possesses a particular arginine peptidase activity (previously called "bana-peptidase" or "trypsin-like enzyme") that is common to the three cultivable bacterial species most highly associated with severe periodontal disease. we recently reported the identification of the opdb locus that encodes the bana-peptidase activity of t. denticola th ... | 2004 | 15060736 |
| comparison of the genome of the oral pathogen treponema denticola with other spirochete genomes. | we present the complete 2,843,201-bp genome sequence of treponema denticola (atcc 35405) an oral spirochete associated with periodontal disease. analysis of the t. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. comparisons with previously sequenced spirochete genomes revealed specific f ... | 2004 | 15064399 |