Publications

release factor 2 frameshifting sites in different bacteria.	the mrna encoding escherichia coli polypeptide chain release factor 2 (rf2) has two partially overlapping reading frames. synthesis of rf2 involves ribosomes shifting to the +1 reading frame at the end of the first open reading frame (orf). frameshifting serves an autoregulatory function. the rf2 gene sequences from the 86 additional bacterial species now available have been analyzed. thirty percent of them have a single orf and their expression does not require frameshifting. in the approximate ...	2002	11897659
clinical and microbiological studies of periodontal disease in sjögren syndrome patients.	little is known about the periodontal status of patients with sjögren's syndrome (ss), a chronic inflammatory autoimmune disease characterized by xerophthalmia and xerostomia. the aim of the present study was to evaluate whether the periodontal status of ss patients, in terms of clinical and microbiological parameters, differs from systemically healthy age- and gender-matched controls.	2002	11908470
periodontopathic bacterial infection in childhood.	little information is available on periodontopathic bacterial infection in childhood. we assessed the prevalence by age of 10 putative periodontopathic microorganisms in periodontally healthy children using a polymerase chain reaction (pcr) assay.	2002	11846195
inhibition of proteolytic, serpinolytic, and progelatinase-b activation activities of periodontopathogens by doxycycline and the non-antimicrobial chemically modified tetracycline derivatives.	tetracyclines, particularly doxycycline (doxy), and their non-antimicrobial chemically-modified derivatives (cmts) inhibit the activities of human matrix metalloproteinases (mmps), and reduce the severity and progression of periodontal disease in animal models and humans. in this study, the effects of doxy and cmt-1, -3, and -5 on proteolytic, serpinolytic, and progelatinase-b activation activities of potent periodontopathogens were studied.	2002	11846203
role of glutathione metabolism of treponema denticola in bacterial growth and virulence expression.	hydrogen sulfide (h(2)s) is a major metabolic end product detected in deep periodontal pockets that is produced by resident periodontopathic microbiota associated with the progression of periodontitis. treponema denticola, a member of the subgingival biofilm at disease sites, produces cystalysin, an enzyme that catabolizes cysteine, releasing h(2)s. the metabolic pathway leading to h(2)s formation in periodontal pockets has not been determined. we used a variety of thiol compounds as substrates ...	2002	11854190
bac library of t. pallidum dna in e. coli.	treponema pallidum subspecies pallidum (nichols) chromosomal dna was used to construct a large insert bacterial artificial chromosome (bac) library in escherichia coli dh10b using the pbelobac11 cloning vector; 678 individual insert termini of 339 bac clones (13.9 x coverage) were sequenced and the cloned chromosomal region in each clone was determined by comparison to the genomic sequence. a single 15.6-kb region of the t. pallidum chromosome was missing in the bac library, between bp 248727 an ...	2002	11875041
23s rrna point mutation associated with erythromycin resistance in treponema denticola.	mechanisms and occurrence of macrolide resistance in the periodontal pathogen treponema denticola have received little attention. in this study, erythromycin resistance due to mutations in the genes encoding t. denticola 23s rrna was investigated. the t. denticola genome was shown to contain two copies of 23s rdna. 23s rrna genes of nine erythromycin-resistant isolates derived from t. denticola were amplified and sequences were analyzed. all the erythromycin-resistant strains had at least one a- ...	2002	11886748
treponema denticola is resistant to human beta-defensins.	spirochetes, including treponema denticola, are implicated in the pathogenesis of periodontal disease. because t. denticola lacks lipopolysaccharides that serve as targets for human beta-defensin (h beta d) binding, we postulated that t. denticola would resist killing by h beta d. we showed that t. denticola is resistant to h beta d-1 and -2. protease inhibitors did not enhance killing of t. denticola by h beta d-2, suggesting that degradation of h beta d-2 by treponemal proteases is not a major ...	2002	12065549
cleavage of treponema denticola prca polypeptide to yield protease complex-associated proteins prca1 and prca2 is dependent on prtp.	analysis of potential virulence factors of oral spirochetes focuses on surface and secreted proteins. the treponema denticola chymotrypsin-like protease (ctlp) is implicated in degradation of host cell molecules and contributes to tissue invasion. the ctlp complex, composed of the 72-kda prtp protein and two auxiliary proteins with molecular masses of approximately 40 and 30 kda, is also involved in localization and oligomerization of the t. denticola major surface protein (msp). the larger auxi ...	2002	12081957
spectroscopic and kinetic analyses reveal the pyridoxal 5'-phosphate binding mode and the catalytic features of treponema denticola cystalysin.	to obtain insight into the functional properties of treponema denticola cystalysin, we have analyzed the ph- and ligand-induced spectral transitions, the ph dependence of the kinetic parameters, and the substrate specificity of the purified enzyme. the absorption spectrum of cystalysin has maxima at 418 and 320 nm. the 320 nm band increases at high ph, while the 418 nm band decreases; the apparent pk(spec) of this spectral transition is about 8.4. cystalysin emitted fluorescence at 367 and 504 n ...	2002	12119031
functional annotation of class i lysyl-trna synthetase phylogeny indicates a limited role for gene transfer.	functional and comparative genomic studies have previously shown that the essential protein lysyl-trna synthetase (lysrs) exists in two unrelated forms. most prokaryotes and all eukaryotes contain a class ii lysrs, whereas most archaea and a few bacteria contain a less common class i lysrs. in bacteria the class i lysrs is only found in the alpha-proteobacteria and a scattering of other groups, including the spirochetes, while the class i protein is by far the most common form of lysrs in archae ...	2002	12142429
microbial profile on metallic and ceramic bracket materials.	the placement of orthodontic appliances creates a favorable environment for the accumulation of a microbiota and food residues, which, in time, may cause caries or exacerbate any pre-existing periodontal disease. the purpose of the present study was to compare the total bacterial counts present on metallic and ceramic orthodontic brackets in order to clarify which bracket type has a higher plaque retaining capacity and to determine the levels of streptococcus mutans and lactobacillus spp on both ...	2002	12169034
microbiological findings and host response in patients with peri-implantitis.	the aim of the present study was to characterise microbiota and inflammatory host response around implants and teeth in patients with peri-implantitis. we included 17 partly edentulous patients with a total of 98 implants, of which 45 showed marginal bone loss of more than three fixture threads after the first year of loading. nineteen subjects with stable marginal tissue conditions served as controls. oral hygiene, gingival inflammation, and probing pocket depth were evaluated clinically at tee ...	2002	12175371
microbiological, immunological and genetic factors in family members with periodontitis as a manifestation of systemic disease, associated with hematological disorders.	the microflora, immunological profiles of host defence functions, and human leukocyte antigen (hla) findings are reported for a mother, son and daughter who were diagnosed as having 'periodontitis as a manifestation of systemic diseases, associated with hematological disorders'. examinations were made of the bacterial flora from the periodontal pocket, neutrophil chemotaxis, neutrophil phagocytosis, and the genotypes (dqb1) and serotypes (dr locus) of hla class ii antigens. phenotypic analyses o ...	2002	12200976
pcr-based identification of bacteria associated with endodontic infections.	pcr primers that target the bacterial 16s rrna genes (or the tuf gene for the genus enterococcus) were used to identify 10 putative bacterial pathogens in root canals with necrotic pulp. in addition, the associations of these microorganisms with symptoms and a history of diabetes mellitus were investigated. microbial samples from the root canals of 24 teeth with necrotic pulp were included in the study. pcr with universal bacterial primers identified bacterial dna in 22 specimens; the remaining ...	2002	12202557
detection and quantification of oral treponemes in subgingival plaque by real-time pcr.	oral treponemes have been associated with periodontal diseases. we developed a highly sensitive and specific method to detect and quantify cultivable oral treponemes (treponema denticola, treponema vincentii, and treponema medium) in 50 subgingival plaque samples from 13 healthy subjects as well as 37 patients with periodontal diseases using real-time pcr assays with specific primers and a taqman probe for each 16s rrna sequence. the specificity for each assay was examined by using dna specimens ...	2002	12202575
communication among oral bacteria.	human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. as each bacterial cell attaches, it forms a new surface to which other cells can adhere. adherence and community development are spatiotemporal; such order requires communication. the discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. direct- ...	2002	12209001
clinical and microbiological analysis of periodontally diseased sites after renal transplant.	this study compared the clinical and microbiological status of periodontally diseased sites in 42 patients who had a renal transplant and were undergoing immunosuppressive therapy (21 taking azathioprin and corticosteroids [az-c] and 21 taking cyclosporin-a [cy-a] with those of 21 systemically healthy matched controls. probing pocket depth (ppd), bleeding on probing (bop) and gingival hyperplasia (gh) were measured at 339 sites. subgingival plaque samples were analyzed for the presence of porphy ...	2002	12240891
salivary iga subclasses and bacteria-reactive iga in patients with aggressive periodontitis.	the local salivary immunoglobulin a (iga) response in patients with aggressive periodontitis to oral microorganisms and its role for the pathogenesis has not been determined. this study investigated the hypothesis that aggressive periodontitis patients have impaired oral secretory immunity. our test group was made-up of 19 aggressive periodontitis patients and 19 age- and gender-matched periodontally healthy controls. total iga, iga subclass 1, iga subclass 2 and iga reactive to actinobacillus a ...	2002	12366855
transmission of periodontal disease-associated bacteria from teeth to osseointegrated implant regions.	the presence of periodontopathic bacteria is a risk factor for peri-implantitis. the present study examined colonization by periodontopathic bacteria and their transmission from periodontal pockets to osseointegrated implant sulcus.	2002	12381070
elimination of channel-forming activity by insertional inactivation of the p13 gene in borrelia burgdorferi.	p13 is a chromosomally encoded 13-kda integral outer membrane protein of the lyme disease agent, borrelia burgdorferi. the aim of this study was to investigate the function of the p13 protein. here, we inactivated the p13 gene by targeted mutagenesis and investigated the porin activities of outer membrane proteins by using lipid bilayer experiments. channel-forming activity was lost in the p13 mutant compared to wild-type b. burgdorferi, indicating that p13 may function as a porin. we purified n ...	2002	12446631
construction and analysis of hemin binding protein mutants in the oral pathogen treponema denticola.	treponema denticola, a periodontal pathogen, can use hemin as its sole iron source. the organism synthesizes two low-iron-induced outer-membrane hemin-binding proteins, hbpa and hbpb. to characterize genetically the function of these two novel proteins, standard recombinant dna procedures and electroporation were used to construct t. denticola strains in which the genomic copies of either hbpa or both hbpa and hbpb were interrupted with an erythromycin resistance cassette. northern blot and rt-p ...	2002	12455704
evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers.	lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltd) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by suda). the scattere ...	2002	12455964
comparison of 16s rdna-based pcr and checkerboard dna-dna hybridisation for detection of selected endodontic pathogens.	molecular methods have been used recently to investigate the bacteria encountered in human endodontic infections. the aim of the present study was to compare the ability of a 16s rdna-based pcr assay and checkerboard dna-dna hybridisation in detecting actinobacillus actinomycetemcomitans, bacteroides forsythus, peptostreptococcus micros, porphyromonas endodontalis, por. gingivalis and treponema denticola directly from clinical samples. specimens were obtained from 50 cases of endodontic infectio ...	2002	12466407
elucidation of structure-function relationships in the protein subunit of bacterial rnase p using a genetic complementation approach.	rnase p is a ribonucleoprotein involved in trna biosynthesis in all living organisms. bacterial rnase p is comprised of a catalytic rna subunit and a lone protein cofactor which plays a supporting, albeit essential, role in the trna processing reaction in vivo. in this study, we have searched various databases to identify homologs of the protein subunit of rnase p from diverse bacteria and used an alignment of their primary sequences to determine the most highly conserved residues, and thereby e ...	2002	12466529
treponema denticola may stimulate both epithelial proliferation and apoptosis through map kinase signal pathways.	mitogen-activated protein kinases (map kinases) play a key role in the regulation of cell survival and death. effects of treponema denticola atcc 35405 on erk, p38 and jnk map kinases, and cell behavior was studied using non-keratinizing periodontal ligament epithelial cells (ple) in vitro. compared to chinese hamster ovary cells, human cervix adenocarcinoma cells, human osteosacroma cells and human gingival fibroblasts, ple cells were much more resistant to t. denticola-induced reduction in cel ...	2002	12472839
the relationship of oral malodor in patients with or without periodontal disease.	halitosis has been correlated with the concentration of volatile sulfur compounds (vsc) produced in the oral cavity by metabolic activity of bacteria colonizing the periodontal area and the dorsum of the tongue. the aim of this study was to determine whether there is some relationship between the presence of n-benzoyl-dl-arginine-2-napthylamide (bana)-positive species treponema denticola, porphyromonas gingivalis, and bacteroides forsythus and clinical and oral malodor parameters.	2002	12479639
correlations between bacterial levels in autologous subgingival plaque and saliva of adult sudanese.	the aim of this study was to assess levels of oral bacteria and their correlations in paired samples of saliva and subgingival plaque in a population of adult sudanese. whole saliva and pooled subgingival plaque samples from six probing sites of one tooth in each jaw were obtained from 56 sudanese adults (mean age 35.2+/-8.9 years). levels of 24 oral bacteria in the autologous saliva and pooled plaque sample of each subject were assessed by dna probes and checkerboard dna-dna hybridization. ther ...	2002	12483235
transient state kinetic investigation of 5-aminolevulinate synthase reaction mechanism.	5-aminolevulinate synthase (alas), a pyridoxal 5'-phosphate-dependent enzyme, catalyzes the first, and regulatory, step of the heme biosynthetic pathway in nonplant eukaryotes and some bacteria. 5-aminolevulinate synthase is a dimeric protein having an ordered kinetic mechanism with glycine binding before succinyl-coa and with aminolevulinate release after coa and carbon dioxide. rapid scanning stopped-flow absorption spectrophotometry in conjunction with multiple turnover chemical quenched-flow ...	2002	12191993
the effect of apically repositioned flap surgery on clinical parameters and the composition of the subgingival microbiota: 12-month data.	the purpose of this investigation was to examine the clinical and microbiologic effects of apically repositioned flap surgery. eighteen patients with chronic periodontitis received initial preparation (ip) including scaling and root planing, followed at 3 months by apically repositioned flap surgery at sites with pocket depth > 4 mm. subjects were monitored clinically and microbiologically at baseline, 3 months after ip, and at 3, 6, 9, and 12 months postsurgery. clinical assessments of plaque a ...	2002	12186343
a genomic overview of pyridoxal-phosphate-dependent enzymes.	enzymes that use the cofactor pyridoxal phosphate (plp) constitute a ubiquitous class of biocatalysts. here, we analyse their variety and genomic distribution as an example of the current opportunities and challenges for the study of protein families. in many free-living prokaryotes, almost 1.5% of all genes code for plp-dependent enzymes, but in higher eukaryotes the percentage is substantially lower, consistent with these catalysts being involved mainly in basic metabolism. assigning the funct ...	2003	12949584
bugging the bugs. genomics and proteomics may provide new ways of making the lives of bacteria more miserable.		2003	12671675
tmrdb (tmrna database).	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the bioinformatics research center, aarhus, denmark (http://www.bioinf.au.dk/tmrdb/). the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ...	2003	12520048
on the evolution of structure in aminoacyl-trna synthetases.	the aminoacyl-trna synthetases are one of the major protein components in the translation machinery. these essential proteins are found in all forms of life and are responsible for charging their cognate trnas with the correct amino acid. the evolution of the trna synthetases is of fundamental importance with respect to the nature of the biological cell and the transition from an rna world to the modern world dominated by protein-enzymes. we present a structure-based phylogeny of the aminoacyl-t ...	2003	14665676
ancient origin of the tryptophan operon and the dynamics of evolutionary change.	the seven conserved enzymatic domains required for tryptophan (trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. a comparative bioinformatics evaluation of the conservation and organization of the genes of trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and oper ...	2003	12966138
common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea.	transmembrane receptors in microorganisms, such as sensory histidine kinases and methyl-accepting chemotaxis proteins, are molecular devices for monitoring environmental changes. we report here that sensory domain sharing is widespread among different classes of transmembrane receptors. we have identified two novel conserved extracellular sensory domains, named chase2 and chase3, that are found in at least four classes of transmembrane receptors: histidine kinases, adenylate cyclases, predicted ...	2003	12486065
induction of osteoclastogenesis and matrix metalloproteinase expression by the lipooligosaccharide of treponema denticola.	alveolar bone destruction is a characteristic feature of periodontitis. treponema denticola is known to be involved in periodontitis. to elucidate the role of t. denticola in alveolar bone destruction in periodontitis, the effects of lipooligosaccharide (los) from t. denticola on osteoclast formation and on expression of osteoclast differentiation factor (odf) and osteoprotegerin (opg) mrnas were examined in a coculture system by using mouse calvaria and bone marrow cells. in addition, the effec ...	2003	12496170
role for recombinant gamma-glutamyltransferase from treponema denticola in glutathione metabolism.	volatile sulfur compounds, including hydrogen sulfide (h(2)s), have been implicated in the development of periodontal disease. glutathione is an important thiol source for h(2)s production in periodontal pockets. our recent studies have delineated a pathway of glutathione metabolism in treponema denticola that releases h(2)s. in this pathway, gamma-glutamyltransferase (ggt) has been proposed to catalyze the first step of glutathione degradation. we have cloned the gene of ggt from t. denticola, ...	2003	12496183
treponema denticola cystalysin exhibits significant alanine racemase activity accompanied by transamination: mechanistic implications.	to obtain information on the reaction specificity of cystalysin from the spirochaete bacterium treponema denticola, the interaction with l- and d-alanine has been investigated. binding of both alanine enantiomers leads to the appearance of an external aldimine absorbing at 429 nm and of a band absorbing at 498 nm, indicative of a quinonoid species. racemization and transamination reactions were observed to occur with both alanine isomers as substrates. the steady-state kinetic parameters for rac ...	2003	12519070
recombination activity of a distinctive integron-gene cassette system associated with pseudomonas stutzeri populations in soil.	class 1 integrons have strongly influenced the evolution of multiple antibiotic resistance. diverse integrons have recently been detected directly in a range of natural environments. in order to characterize the properties of these environmental integrons, we sought to isolate organisms containing integrons from soils, which resulted in the isolation of pseudomonas stutzeri strain q. further isolation efforts targeted at this species resulted in recovery of two other strains (p and bam). 16s rrn ...	2003	12533467
oral treponemes and their outer membrane extracts activate human gingival epithelial cells through toll-like receptor 2.	oral treponemes are considered to be important in the development and progression of periodontal diseases. we investigated the mechanisms of recognition and activation of human gingival epithelial cells (hgec) with the oral treponemes treponema denticola, treponema vincentii, and treponema medium and their outer membrane extracts (omes). t. vincentii and t. medium but not t. denticola produced interleukin 8 (il-8) in an hgec culture. further, all three treponemes induced il-8 mrna expression and ...	2003	12540550
epithelial cell surface sites involved in the polyvalent adherence of porphyromonas gingivalis: a convincing role for neuraminic acid and glucuronic acid.	we investigated the target structures of the epithelial cells responsible for the attachment of porphyromonas gingivalis by immunocytofluorimetry, enzyme-linked immunosorbent assay, and confocal microscopy. integrins (beta1, beta3, and alphav) and e-cadherin played no significant role. carbohydrates (such as alpha-d-methylglucoside, l-fucose, d- and l-mannose, n-acetylglucosamine, and n-acetylgalactosamine) had little inhibitory effect on bacterial binding. enzymatic treatments of the epithelial ...	2003	12540582
diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients.	the primary purpose of the present study was to compare the microbial profiles of the tongue dorsa of healthy subjects and subjects with halitosis by using culture-independent molecular methods. our overall goal was to determine the bacterial diversity on the surface of the tongue dorsum as part of our ongoing efforts to identify all cultivable and not-yet-cultivated species of the oral cavity. tongue dorsum scrapings were analyzed from healthy subjects with no complaints of halitosis and subjec ...	2003	12574246
development of a 5' fluorogenic nuclease-based real-time pcr assay for quantitative detection of actinobacillus actinomycetemcomitans and porphyromonas gingivalis.	a 5' nuclease taqman pcr was developed for the quantitative detection of the periodontopathic bacteria actinobacillus actinomycetemcomitans and porphyromonas gingivalis. the relative numbers of bacteria were measured by the comparative threshold cycle method. this simplified method is a way of obtaining the relative quantities of these organisms from specimens and of monitoring the effect of therapy.	2003	12574302
periodontopathogens in the saliva and subgingival dental plaque of a group of mothers.	the aim of this study was to assess the periodontal condition and the presence of putative periodontal pathogens in 30 brazilian mothers, aging 21-40 years (28.4 4.49 years), and in their children, aging 5-6 years, since mothers can be a source of pathogens and, thus, influence their children's bacteriological and clinical condition. besides assessing the plaque index (pi), gingival index (gi) and pocket probing depth (pd), the survey analyzed four subgingival dental plaque samples from mother ...	2003	12612769
excision and integration of cassettes by an integron integrase of nitrosomonas europaea.	we found in the environmental strain nitrosomonas europaea a chromosomal integron-like structure with an integrase gene, inti(neu). we have tested the capacity of the intineu integrase to excise and integrate several resistance gene cassettes. the results allow us to consider intineu a new functional integron integrase.	2003	12618471
helicobacter pylori and campylobacter rectus share a common antigen.	aim: the aim of this study was to investigate the presence of antigens with immunological cross-reactivity in periodontopathogenic bacteria and helicobacter pylori, the pathogen associated with gastritis and peptic ulcers in human. materials and methods/results: among the putative periodontopathogens tested (actinobacillus actinomycetemcomitans, campylobacter rectus, fusobacterium nucleatum, porphyromonas gingivalis, prevotella intermedia and treponema denticola), cross-reactive bands were only ...	2003	12654095
amended biochemical characteristics and phylogenetic position of treponema medium.	umemoto et al. (1997, int j syst bacteriol 47, pp. 67-72) proposed spirochete strain g7201, isolated from the periodontal pocket of an adult patient, as a new species, treponema medium. they deposited this strain in the american type culture collection (atcc) as type strain atcc 700293t. recently, atcc suggested that there is a discrepancy between the previous report and the results obtained by atcc in biochemical tests on t. medium atcc 700293t. in this study, we re-examined and verified the bi ...	2003	12654104
antibiotic resistance in bacteria isolated from subgingival plaque in a norwegian population with refractory marginal periodontitis.	the prevalence of beta-lactamase-producing bacteria in subgingival plaque from patients with refractory periodontitis in norway was assessed by the chromogenic nitrocefin method. beta-lactamase activity was detected in 68% of the patients. enzyme-producing strains belonged predominantly to the genus prevotella; others were staphylococci, enteric gram-negative rods, and bacillus spp.	2003	12654689
oral treponemes in primary root canal infections as detected by nested pcr.	to investigate the prevalences of four treponema species in primary root canal infections using a nested pcr assay.	2003	12656510
herpesviral-bacterial interactions in aggressive periodontitis.	human cytomegalovirus, epstein-barr virus and herpesvirus co-infections occur with significantly higher frequency in actively progressing than in stable periodontitis sites of adolescents and young adults. also, periodontal presence of cytomegalovirus and epstein-barr virus is associated with increased occurrence of subgingival porphyromonas gingivalis, bacteroides forsythus, dialister pneumosintes, prevotella intermedia, prevotella nigrescens, treponema denticola and actinobacillus actinomycete ...	2003	12716334
involvement of conserved asparagine and arginine residues from the n-terminal region in the catalytic mechanism of rat liver and trypanosoma cruzi tyrosine aminotransferases.	rat liver and trypanosoma cruzi tyrosine aminotransferases (tats) share over 40% sequence identity, but differ in their substrate specificities. to explore the molecular features related to these differences, comparative mutagenesis studies were conducted on full length t. cruzi tat and n-terminally truncated rat tat recombinant enzymes. the functionality of arg315 and arg417 in rat tat was investigated for comparison with the conserved arg292 and arg386 in aspartate and bacterial aromatic amino ...	2003	12717026
genetic relatedness and phenotypic characteristics of treponema associated with human periodontal tissues and ruminant foot disease.	treponema have been implicated recently in the pathogenesis of digital dermatitis (dd) and contagious ovine digital dermatitis (codd) that are infectious diseases of bovine and ovine foot tissues, respectively. previous analyses of treponemal 16s rdna sequences, pcr-amplified directly from dd or codd lesions, have suggested relatedness of animal treponema to some human oral treponema species isolated from periodontal tissues. in this study a range of adhesion and virulence-related properties of ...	2003	12724370
accidentally induced periodontitis in primary dentition: longitudinal examinations of periodontal bacteria and clinical conditions.	periodontitis is very rare in the primary dentition although it can be accidentally induced in young children. the purpose of this study was to describe a case of periodontitis in a 4-year-old child, which was accidentally induced by insertion of small plastic tubes into the dental cervix of the primary incisors during play, and to discuss the clinical, radiographic, and microbiological findings. removal of the plastic tubes resulted in resolution of the periodontal condition. prevotella nigresc ...	2003	12752919
inhibitory effect of procyanidin oligomer from elm cortex on the matrix metalloproteinases and proteases of periodontopathogens.	the purpose of this study was to evaluate a partially purified extract (elm extract) from the ulmi cortex (ulmi macrocarpa hance) and its active ingredient, a mix of procyanidin oligomers (3 to 12 flavan-3-ol monomers, an average molecular weight of 1,518 with an average polymerization degree of 5.3) for a possible inhibitory effect against proteases.	2003	12753366
periodontal pathogens in subgingival plaque of hiv-positive subjects with chronic periodontitis.	many putative periodontal pathogens associated with periodontal disease in human immunodeficiency virus (hiv)-infected patients also occur in non-hiv-infected individuals. this study examined the prevalence of eight periodontal pathogens in hiv-positive and hiv-negative patients with chronic periodontitis using the 16s rna polymerase chain reaction technique. the results showed a significant prevalence of porphyromonas gingivalis and treponema denticola among hiv-negative patients compared to hi ...	2003	12753474
enzymatic degradation of collagen-guided tissue regeneration membranes by periodontal bacteria.	bacterial infection in the vicinity of guided tissue regeneration barrier membranes was shown to have a negative effect on the clinical outcomes of this increasingly used technique. several oral and specifically periodontal bacteria were shown to adhere to such membranes in vivo and in vitro with a higher affinity to membranes constructed from collagen. the present study examined the role of periodontal bacteria and their enzymes in the degradation of commercially used collagen membranes. degrad ...	2003	12755775
subgingival microbiota levels and their associations with periodontal status at the sampled sites in an adult sudanese population using miswak or toothbrush regularly.	little information is available on the effect of miswak use on gingival microbiota. we assessed levels of 28 oral bacteria in subgingival plaque of adult sudanese miswak (n = 38) and toothbrush users (n = 36) age range 20-53 years (mean 34.6 years) to study associations between these bacteria, oral hygiene method, and periodontal status at the sampled sites. a pooled subgingival plaque sample from 6 probing sites of 1 selected tooth in each jaw was obtained from each subject. whole genomic dna p ...	2003	12790510
characterization of treponema phagedenis-like spirochetes isolated from papillomatous digital dermatitis lesions in dairy cattle.	four spirochete strains were isolated from papillomatous digital dermatitis (pdd) lesions in iowa dairy cattle and compared with two previously described spirochete strains isolated from dairy cattle in california. these six strains shared an identical 16s ribosomal dna sequence that was 98% similar to treponema phagedenis and 99% similar to the uncultivated pdd spirochete sequence ddlk-4. the whole-cell protein profiles resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of th ...	2003	12791876
five-year maintenance follow-up of early-onset periodontitis patients.	the purpose of this study was to evaluate the clinical and microbiological status of patients with early-onset or aggressive periodontitis (eop) who had received supportive periodontal care (spc) every 3-6 months for a period of 5 years, following active periodontal treatment.	2003	12795796
pcr methodology as a valuable tool for identification of endodontic pathogens.	this paper reviews the principles of polymerase chain reaction (pcr) methodology, its application in identification of endodontic pathogens and the perspectives regarding the knowledge to be reached with the use of this highly sensitive, specific and accurate methodology as a microbial identification test.	2003	12799118
genome analysis of f. nucleatum sub spp vincentii and its comparison with the genome of f. nucleatum atcc 25586.	we present the draft genome sequence and its analysis for fusobacterium nucleatum sub spp. vincentii (fnv), and compare that genome with f. nucleatum atcc 25586 (fn). a total of 441 fnv open reading frames (orfs) with no orthologs in fn have been identified. of these, 118 orfs have no known function and are unique to fnv, whereas 323 orfs have functional orthologs in other organisms. in addition to the excretion of butyrate, h2s and ammonia-like fn, fnv has the additional capability to excrete l ...	2003	12799352
the benzoyl-dl arginine-naphthylamide (bana) test and polymerase chain reaction measurement of pathogenic bacteria can assess the severity of periodontal disease.	the benzoyl-dl arginine-naphthylamide (bana) test for detecting digesting peptidase and polymerase chain reaction (pcr) measurement of pathogenic bacteria were performed in 15 patients with periodontal disease. the number of porphyromonas gingivalis, bacteroides forsythus and treponema denticola, which are the most potent accelerators of alveolar bone resorption, were determined. attachment loss and the bana test showed significant close correlations with the number of pathogenic bacteria as wel ...	2003	12854883
effect of inactivation of the arg- and/or lys-gingipain gene on selected virulence and physiological properties of porphyromonas gingivalis.	proteolytic enzymes produced by porphyromonas gingivalis are thought to play critical roles in the pathogenesis of periodontitis. the aim of this study was to investigate the effect of gingipain cysteine proteinase gene inactivation on selected pathological and physiological functions of p. gingivalis. our results showed that arg- and lys-gingipain activities are critical components for the efficient growth of p. gingivalis in human serum. however, when the serum was supplemented with peptides p ...	2003	12874356
positive and negative bacterial associations involving dialister pneumosintes in primary endodontic infections.	dialister pneumosintes is an anaerobic gram-negative rod that has been recently implicated as a candidate endodontic pathogen. in this study, samples taken from abscessed teeth and infected root canals associated with asymptomatic or symptomatic periradicular lesions were examined for the occurrence of bacterial associations involving d. pneumosintes. dna was extracted from the samples, and the presence of d. pneumosintes and 16 other bacterial species was determined by means of species-specific ...	2003	12877258
lysine 238 is an essential residue for alpha,beta-elimination catalyzed by treponema denticola cystalysin.	treponema denticola cystalysin is a pyridoxal 5'-phosphate (plp) enzyme that catalyzes the alpha,beta-elimination of l-cysteine to pyruvate, ammonia, and h2s. similar to other plp enzymes, an active site lys residue (lys-238) forms an internal schiff base with plp. the mechanistic role of this residue has been studied by an analysis of the mutant enzymes in which lys-238 has been replaced by ala (k238a) and arg (k238r). both apomutants reconstituted with plp bind noncovalently approximately 50% ...	2003	12882978
regulation of the vitamin b12 metabolism and transport in bacteria by a conserved rna structural element.	cobalamin in the form of adenosylcobalamin (ado-cbl) is known to repress expression of genes for vitamin b(12) biosynthesis and be transported by a posttranscriptional regulatory mechanism, which involves direct binding of ado-cbl to 5'untranslated gene regions (5'utr). using comparative analysis of genes and regulatory regions, we identified a highly conserved rna structure, the b12-element, which is widely distributed in 5'utrs of vitamin b(12)-related genes in eubacteria. multiple alignment o ...	2003	12923257
complete genome sequence of the oral pathogenic bacterium porphyromonas gingivalis strain w83.	the complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium porphyromonas gingivalis strain w83, a major contributor to periodontal disease, was determined. whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the cytophaga-flavobacteria-bacteroides (cfb) phylum and the green-sulfur bacteria. within the cfb phyla, the genomes most similar to that of p. gingivalis are those of bacteroides thetaiotaom ...	2003	12949112
analysis of genes of tetrahydrofolate-dependent metabolism from cultivated spirochaetes and the gut community of the termite zootermopsis angusticollis.	the hindguts of wood-feeding termites are the sites of intense, co2-reductive acetogenesis. this activity profoundly influences host nutrition and methane emissions. homoacetogens previously isolated from diverse termites comprised novel taxa belonging to two distinct bacterial phyla, firmicutes and spirochates. little else is known about either the diversity or abundance of homoacetogenic species present in any given termite or the genetic details underlying co2-reductive acetogenesis by spiroc ...	2003	12949177
development of a 5' nuclease-based real-time pcr assay for quantitative detection of cariogenic dental pathogens streptococcus mutans and streptococcus sobrinus.	a 5' nuclease taqman pcr assay was developed for the quantitative detection of the major cariogenic bacteria streptococcus mutans and streptococcus sobrinus. the absolute and relative numbers of bacteria were measured by this method. this assay will be useful for quantifying these organisms in oral specimens and for analyzing biofilm formation.	2003	12958287
control of enzyme iiscr and sucrose-6-phosphate hydrolase activities in streptococcus mutans by transcriptional repressor scrr binding to the cis-active determinants of the scr regulon.	in streptococcus mutans, enzyme ii(scr) and sucrose-6-phosphate hydrolase are two important enzymes in the transport and metabolism of dietary sucrose. the scr regulon of s. mutans is composed of three genes, scra and scrb, which code for enzyme ii(scr) and sucrose-6-phosphate hydrolase, respectively, and scrr, which codes for a galr-laci-type transcription regulator. it was previously shown that expression of both scra and scrb is similarly induced by sucrose. mutation in the scrr gene resulted ...	2003	13129950
role for periodontitis in the progression of lipid deposition in an animal model.	epidemiologic studies have implicated periodontitis as a risk factor for the development of cardiovascular disease. however, no prospective studies investigating this potential relationship have been carried out. age- and sex-matched new zealand white rabbits were maintained on a diet consisting of 0.5% fat for 13 weeks to induce the accumulation of lipid deposits in the aorta as a model for atherogenesis. one-half of the animals received silk ligatures around their mandibular premolars followed ...	2003	14500522
antibody responses elicited against the treponema pallidum repeat proteins differ during infection with different isolates of treponema pallidum subsp. pallidum.	variation in the expression of the different tpr proteins in the syphilis spirochete, treponema pallidum subsp. pallidum, may have important implications in its ability to evade host immune detection and cause persistent infection. in the present study we examined the pattern of antibody responsiveness to different tpr members during infection with three isolates of t. pallidum. there was variability in the specificities and temporal patterns of reactivity of the antibodies elicited against the ...	2003	14500529
[distribution of 3 kinds of periodontal pathogens in subgingival plaques of patients with chronic periodontitis].	to observe the prevalence of porphyromonas gingivalis(pg), treponema denticola(td) and bacterides forsythus(bf) subgingivally in diseased sites of chronic periodontitis (cp) patients.	2003	14513585
binding of porphyromonas gingivalis fimbriae to treponema denticola dentilisin.	treponema denticola has been reported to coaggregate with porphyromonas gingivalis and localize closely together in matured subgingival plaque. in this study of the interaction of t. denticola with p. gingivalis, the p. gingivalis fimbria-binding protein of t. denticola was identified by two-dimensional electrophoresis followed by a ligand overlay assay with p. gingivalis fimbriae, and was determined to be dentilisin, a chymotrypsin-like proteinase of t. denticola. the binding was further demons ...	2003	14553921
sequence diversity of treponema pallidum subsp. pallidum tprk in human syphilis lesions and rabbit-propagated isolates.	the tprk gene of treponema pallidum subsp. pallidum, the causative agent of venereal syphilis, belongs to a 12-member gene family and encodes a protein with a predicted cleavable signal sequence and predicted transmembrane domains. except for the nichols type strain, all rabbit-propagated isolates of t. pallidum examined thus far are comprised of mixed populations of organisms with heterogeneous tprk sequences. we show that tprk sequences in treponemes obtained directly from syphilis patients ar ...	2003	14563860
clinical and microbiological evaluation of the periodontal status of children with unilateral complete cleft lip and palate.	to compare periodontal conditions in children with and without cleft.design: clinical examinations and microbiological analysis of 57 selected children, including 30 with unilateral complete cleft lip and palate (experimental group) and 27 without clefts (control group).	2003	14577819
role of dentilisin in treponema denticola epithelial cell layer penetration.	treponema denticola is an oral anaerobic spirochete implicated in periodontal diseases. the chymotrypsin-like protease, dentilisin (prtp), has been suggested to be an important virulence factor of t. denticola. in this study, we examined the role of dentilisin in t. denticola epithelial monolayer penetration by comparing the wild type and prtp mutant. wild-type t. denticola can disrupt transepithelial resistance (ter) and substantially penetrate the hep-2 cell layer. the prtp mutant altered the ...	2003	14596901
oriented adhesion of escherichia coli to polystyrene particles.	the adhesion of nonflagellated escherichia coli strain k-12 to polystyrene (ps) latex spheres or glass capillaries has been observed by using several techniques. attention was focused on the orientation of the rod-shaped bacteria as they adhered to the surfaces in 100 mm phosphate-buffered saline. data show that ps particles adhered to the ends of the bacteria more than 90% of the time. moreover, the ps particles adhered to one end only, never to both. similarly, for experiments with bacteria ad ...	2003	14602608
two paralogous families of a two-gene subtilisin operon are widely distributed in oral treponemes.	certain oral treponemes express a highly proteolytic phenotype and have been associated with periodontal diseases. the periodontal pathogen treponema denticola produces dentilisin, a serine protease of the subtilisin family. the two-gene operon prca-prtp is required for expression of active dentilisin (prtp), a putative lipoprotein attached to the treponeme's outer membrane or sheath. the purpose of this study was to examine the diversity and structure of treponemal subtilisin-like proteases in ...	2003	14617650
treponema denticola cystalysin catalyzes beta-desulfination of l-cysteine sulfinic acid and beta-decarboxylation of l-aspartate and oxalacetate.	pyridoxal 5'-phosphate-dependent cystalysin from treponema denticola catalyzes the beta-displacement of the beta-substituent from both l-aspartate and l-cysteine sulfinic acid. the steady-state kinetic parameters for beta-desulfination of l-cysteine sulfinic acid, k(cat) and k(m), are 89+/-7 s(-1) and 49+/-9 mm, respectively, whereas those for beta-decarboxylation of l-aspartate are 0.8+/-0.1 s(-1) and 280+/-70 mm. moreover, cystalysin in the pyridoxamine 5'-phosphate form has also been found to ...	2003	14623084
the effects of extracts from periodontopathic bacteria on human periodontal fibroblasts stimulated with mineralization supplements.	bacterial effects on in vitro mineralization of human periodontal fibroblasts (hpf) have not yet been examined in great detail. in our study, we investigated the effects of soluble extracts of the periodontopathic bacteria porphyromonas gingivalis, bacteroides forsythus and, treponema denticola on cell proliferation, mineralization, as well as on osteoblastic markers present in hpf cultured in vitro, such as alkaline phosphatase (alp) activity and collagen content. periodontal fibroblasts stimul ...	2003	14650577
prevalence of periodontopathic bacteria in aggressive periodontitis patients in a japanese population.	actinobacillus actinomycetemcomitans is considered a major etiologic agent of aggressive periodontitis. other periodontopathic bacteria such as porphyromonas gingivalis are also suspected of participating in aggressive periodontitis, although the evidence is controversial. the aim of the present study was to investigate the prevalence of periodontopathic bacteria and to clarify the microbiological features of aggressive periodontitis in japanese patients.	2003	14653392
mixed infections with porphyromonas gingivalis and treponema denticola cause excessive inflammatory responses in a mouse pneumonia model compared with monoinfections.	periodontopathic anaerobes such as porphyromonas gingivalis are frequently found in aspiration pneumonia and lung abscesses. however, defense mechanisms and responses to these bacterial infections in the lung in vivo remain poorly understood. the coexistence of p. gingivalis with treponema denticola has been found at higher levels and proportions in periodontally diseased sites. we hypothesized that mixed infections with p. gingivalis and t. denticola can cause severe respiratory disease. in the ...	2003	14670448
effects of a mixed infection with porphyromonas gingivalis and treponema denticola on abscess formation and immune responses in mice.	porphyromonas gingivalis and treponema denticola have been found together in lesions of human periodontitis. we examined the ability of a mixed infection by both bacteria to synergistically form abscesses and disturb immune responses in mice. absorbance of an invasive p. gingivalis 16-1 strain grown in tryptic soy broth and t. denticola atcc 33520 strain grown in tygvs medium were adjusted. balb/c mice were injected with 200 microliters of the cell suspension at a site on the lateral dorsal area ...	2003	14694829
occurrence of periodontal bacteria in healthy children: a 2-year longitudinal study.	to examine the occurrence of specific periodontal bacteria in children and adolescents.	2003	14986909
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
relationship between periodontal pocket sulfide levels and subgingival species.	many species implicated in the pathogenesis of periodontal disease produce volatile sulfur compounds (vsc). this investigation examined the relationship between levels of sulfide and subgingival bacterial species in the same periodontal pockets.	2003	14761124
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
the influence of tobacco smoking on the onset of periodontitis in young persons.	abstract : this paper reviews the evidence for cigarette smoking as a risk factor for the development of severe destructive periodontal disease in young adults. a high prevalence of cigarette smoking has been identified among young individuals with aggressive periodontitis and tobacco usage increases the risk of periodontal destruction most significantly in young populations. the effect appears to be dose related and is independent of levels of plaque accumulation. young smokers have more alveol ...	2004	19570272
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