Publications

rho and rnase play a central role in fmn riboswitch regulation in corynebacterium glutamicum.	riboswitches are rna elements that regulate gene expression in response to their ligand. although these regulations are thought to be performed without any aid of other factors, recent studies suggested the participation of protein factors such as transcriptional termination factor rho and rnase in some riboswitch regulations. however, to what extent these protein factors contribute to the regulation was unclear. here, we studied the regulatory mechanism of the flavin mononucleotide (fmn) ribosw ...	2014	25477389
interleukin-6 c.-174g>c polymorphism and periodontitis in a brazilian population.	aim. periodontitis is an inflammatory disease that affects the teeth supporting structures, triggered by periodontal pathogens, and is influenced by environmental and genetic factors. genes encoding molecules related to the immune response, such as cytokine, are the main candidates for polymorphisms analysis and may be possibly associated with this pathology. a g/c promoter polymorphism on the il6 gene has been shown to affect basal il-6 levels. the aim of this study was to investigate the assoc ...	2014	25548674
diversity-generating retroelements in phage and bacterial genomes.	diversity-generating retroelements (dgrs) are dna diversification machines found in diverse bacterial and bacteriophage genomes that accelerate the evolution of ligand-receptor interactions. diversification results from a unidirectional transfer of sequence information from an invariant template repeat (tr) to a variable repeat (vr) located in a protein-encoding gene. information transfer is coupled to site-specific mutagenesis in a process called mutagenic homing, which occurs through an rna in ...	2014	26104433
next-generation models of human cardiogenesis via genome editing.	cardiogenesis is one of the earliest and most important steps during human development and is orchestrated by discrete families of heart progenitors, which build distinct regions of the fetal heart. for the past decade, a lineage map for the distinct subsets of progenitors that generate the embryonic mammalian heart has begun to lay a foundation for the development of new strategies for rebuilding the adult heart after injury, an unmet clinical need for the vast majority of patients with end-sta ...	2014	25237142
strand invasion based amplification (siba®): a novel isothermal dna amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte.	isothermal nucleic acid amplification technologies offer significant advantages over polymerase chain reaction (pcr) in that they do not require thermal cycling or sophisticated laboratory equipment. however, non-target-dependent amplification has limited the sensitivity of isothermal technologies and complex probes are usually required to distinguish between non-specific and target-dependent amplification. here, we report a novel isothermal nucleic acid amplification technology, strand invasion ...	2014	25419812
polymicrobial synergy and dysbiosis in inflammatory disease.	uncontrolled inflammation of the periodontal area may arise when complex microbial communities transition from a commensal to a pathogenic entity. communication among constituent species leads to polymicrobial synergy between metabolically compatible organisms that acquire functional specialization within the developing community. keystone pathogens, even at low abundance, elevate community virulence, and the resulting dysbiotic community targets specific aspects of host immunity to further disa ...	2014	25498392
polymicrobial synergy and dysbiosis in inflammatory disease.	uncontrolled inflammation of the periodontal area may arise when complex microbial communities transition from a commensal to a pathogenic entity. communication among constituent species leads to polymicrobial synergy between metabolically compatible organisms that acquire functional specialization within the developing community. keystone pathogens, even at low abundance, elevate community virulence, and the resulting dysbiotic community targets specific aspects of host immunity to further disa ...	2014	25498392
shifts in campylobacter species abundance may reflect general microbial community shifts in periodontitis progression.	oral campylobacter species have been found to be associated with periodontitis progression. while the etiological significance of campylobacter rectus is quite established, the association of c. gracilis, c. concisus, and c. curvus with health or disease remains contradictory.	2014	25412608
oral bacterial dna findings in pericardial fluid.	we recently reported that large amounts of oral bacterial dna can be found in thrombus aspirates of myocardial infarction patients. some case reports describe bacterial findings in pericardial fluid, mostly done with conventional culturing and a few with pcr; in purulent pericarditis, nevertheless, bacterial pcr has not been used as a diagnostic method before.	2014	25412607
the novel species streptococcus tigurinus and its association with oral infection.	streptococcus tigurinus is a novel species of viridans streptococci, shown to cause severe invasive infections such as infective endocarditis, spondylodiscitis and meningitis. s. tigurinus belongs to the streptococcus mitis group and is most closely related to streptococcus mitis, streptococcus oralis, streptococcus pneumoniae, streptococcus pseudopneumoniae and streptococcus infantis. the presence of s. tigurinus in the human oral cavity has been documented, including in patients with periodont ...	2014	25483862
the novel species streptococcus tigurinus and its association with oral infection.	streptococcus tigurinus is a novel species of viridans streptococci, shown to cause severe invasive infections such as infective endocarditis, spondylodiscitis and meningitis. s. tigurinus belongs to the streptococcus mitis group and is most closely related to streptococcus mitis, streptococcus oralis, streptococcus pneumoniae, streptococcus pseudopneumoniae and streptococcus infantis. the presence of s. tigurinus in the human oral cavity has been documented, including in patients with periodont ...	2014	25483862
host antimicrobial peptides in bacterial homeostasis and pathogenesis of disease.	innate immune responses function as a first line of host defense against the development of bacterial infection, and in some cases to preserve the sterility of privileged sites in the human host. bacteria that enter these sites must counter host responses for colonization. from the host's perspective, the innate immune system works expeditiously to minimize the bacterial threat before colonization and subsequent dysbiosis. the multifactorial nature of disease further challenges predictions of ho ...	2014	26029470
characterization of treponema denticola mutants defective in the major antigenic proteins, msp and tmpc.	treponema denticola, a gram-negative and anaerobic spirochete, is associated with advancing severity of chronic periodontitis. in this study, we confirmed that two major antigenic proteins were msp and tmpc, and examined their physiological and pathological roles using gene-deletion mutants. msp formed a large complex that localized to the outer membrane, while tmpc existed as a monomer and largely localized to the inner membrane. however, tmpc was also detected in the outer membrane fraction, b ...	2014	25401769
pre-steady-state kinetic and structural analysis of interaction of methionine γ-lyase from citrobacter freundii with inhibitors.	methionine γ-lyase (mgl) catalyzes the γ-elimination of l-methionine and its derivatives as well as the β-elimination of l-cysteine and its analogs. these reactions yield α-keto acids and thiols. the mechanism of chemical conversion of amino acids includes numerous reaction intermediates. the detailed analysis of mgl interaction with glycine, l-alanine, l-norvaline, and l-cycloserine was performed by pre-steady-state stopped-flow kinetics. the structure of side chains of the amino acids is impor ...	2014	25398880
pre-steady-state kinetic and structural analysis of interaction of methionine γ-lyase from citrobacter freundii with inhibitors.	methionine γ-lyase (mgl) catalyzes the γ-elimination of l-methionine and its derivatives as well as the β-elimination of l-cysteine and its analogs. these reactions yield α-keto acids and thiols. the mechanism of chemical conversion of amino acids includes numerous reaction intermediates. the detailed analysis of mgl interaction with glycine, l-alanine, l-norvaline, and l-cycloserine was performed by pre-steady-state stopped-flow kinetics. the structure of side chains of the amino acids is impor ...	2014	25398880
photodynamic therapy as a novel treatment for halitosis in adolescents: study protocol for a randomized controlled trial.	halitosis is a common problem that affects a large portion of the population worldwide. the origin of this condition is oral in 90% and systemic in 10% of cases. the unpleasant odor is mainly the result of volatile sulfur compounds produced by gram-negative bacteria. however, it has recently been found that anaerobic gram-positive bacteria also produce hydrogen sulfide (h2s) in the presence of amino acids, such as cysteine. light, both with and without the use of chemical agents, has been used t ...	2014	25394474
miropin, a novel bacterial serpin from the periodontopathogen tannerella forsythia, inhibits a broad range of proteases by using different peptide bonds within the reactive center loop.	all prokaryotic genes encoding putative serpins identified to date are found in environmental and commensal microorganisms, and only very few prokaryotic serpins have been investigated from a mechanistic standpoint. herein, we characterized a novel serpin (miropin) from the human pathogen tannerella forsythia, a bacterium implicated in initiation and progression of human periodontitis. in contrast to other serpins, miropin efficiently inhibited a broad range of proteases (neutrophil and pancreat ...	2014	25389290
miropin, a novel bacterial serpin from the periodontopathogen tannerella forsythia, inhibits a broad range of proteases by using different peptide bonds within the reactive center loop.	all prokaryotic genes encoding putative serpins identified to date are found in environmental and commensal microorganisms, and only very few prokaryotic serpins have been investigated from a mechanistic standpoint. herein, we characterized a novel serpin (miropin) from the human pathogen tannerella forsythia, a bacterium implicated in initiation and progression of human periodontitis. in contrast to other serpins, miropin efficiently inhibited a broad range of proteases (neutrophil and pancreat ...	2014	25389290
epithelial antimicrobial peptides: guardian of the oral cavity.	gingival epithelium provides first line of defence from the microorganisms present in dental plaque. it not only provides a mechanical barrier but also has an active immune function too. gingival epithelial cells participate in innate immunity by producing a range of antimicrobial peptides to protect the host against oral pathogens. these epithelial antimicrobial peptides (eaps) include the β-defensin family, cathelicidin (ll-37), calprotectin, and adrenomedullin. while some are constitutively e ...	2014	25435884
distinct composition of the oral indigenous microbiota in south korean and japanese adults.	a comparison of national surveys on oral health suggested that the population of south korea has a better periodontal health status than that of japan, despite their similar inherent backgrounds. here, we investigated differences in oral bacterial assemblages between individuals from those two countries. to exclude potential effects of oral health condition on the microbiota, we selected 52 korean and 88 japanese orally healthy adults (aged 40-79 years) from the participants of two cohort studie ...	2014	25384884
the oral microbiome and the immunobiology of periodontal disease and caries.	the composition of the oral microbiome differs from one intraoral site to another, reflecting in part the host response and immune capacity at each site. by focusing on two major oral infections, periodontal disease and caries, new principles of disease emerge. periodontal disease affects the soft tissues and bone that support the teeth. caries is a unique infection of the dental hard tissues. the initiation of both diseases is marked by an increase in the complexity of the microbiome. in period ...	2014	25447398
periodontal disease associates with higher brain amyloid load in normal elderly.	the accumulation of amyloid-β (aβ) plaques is a central feature of alzheimer's disease (ad). first reported in animal models, it remains uncertain if peripheral inflammatory and/or infectious conditions in humans can promote aβ brain accumulation. periodontal disease, a common chronic infection, has been previously reported to be associated with ad. thirty-eight cognitively normal, healthy, and community-residing elderly (mean age, 61 and 68% female) were examined in an alzheimer's disease resea ...	2014	25491073
periodontal disease associates with higher brain amyloid load in normal elderly.	the accumulation of amyloid-β (aβ) plaques is a central feature of alzheimer's disease (ad). first reported in animal models, it remains uncertain if peripheral inflammatory and/or infectious conditions in humans can promote aβ brain accumulation. periodontal disease, a common chronic infection, has been previously reported to be associated with ad. thirty-eight cognitively normal, healthy, and community-residing elderly (mean age, 61 and 68% female) were examined in an alzheimer's disease resea ...	2014	25491073
association between periodontal condition and subgingival microbiota in women during pregnancy: a longitudinal study.	in this study, the gingival conditions and the quantitative detection for aggregatibacter actinomycetemcomitans, fusobacterium nucleatum, porphyromonas gingivalis and prevotella intermedia in pregnant women were determined.	2014	25591021
investigate the correlation between clinical sign and symptoms and the presence of p. gingivalis, t. denticola, and t. forsythia individually or as a "red complex" by a multiplex pcr method.	the aim of this study was to investigate the correlation between endodontic clinical signs and symptoms and the presence of porphyromonas gingivalis, treponema denticola, and tannerella forsythia or their association by multiplex polymerase chain reaction assay.	2014	25506144
isolation of digital dermatitis treponemes from hoof lesions in wild north american elk (cervus elaphus) in washington state, usa.	since 2008, a large increase in the numbers of cases of lameness have been seen in wild north american elk (cervus elaphus) from washington state, usa. the most recent cases manifested as foot lesions similar both clinically and pathologically to those seen in digital dermatitis (dd) in cattle and sheep, a disease with a bacterial etiopathogenesis. to determine whether the same bacteria considered responsible for dd are associated with elk lameness, lesion samples were subjected to bacterial iso ...	2014	25355757
isolation of digital dermatitis treponemes from hoof lesions in wild north american elk (cervus elaphus) in washington state, usa.	since 2008, a large increase in the numbers of cases of lameness have been seen in wild north american elk (cervus elaphus) from washington state, usa. the most recent cases manifested as foot lesions similar both clinically and pathologically to those seen in digital dermatitis (dd) in cattle and sheep, a disease with a bacterial etiopathogenesis. to determine whether the same bacteria considered responsible for dd are associated with elk lameness, lesion samples were subjected to bacterial iso ...	2014	25355757
building carbon-carbon bonds using a biocatalytic methanol condensation cycle.	methanol is an important intermediate in the utilization of natural gas for synthesizing other feedstock chemicals. typically, chemical approaches for building c-c bonds from methanol require high temperature and pressure. biological conversion of methanol to longer carbon chain compounds is feasible; however, the natural biological pathways for methanol utilization involve carbon dioxide loss or atp expenditure. here we demonstrated a biocatalytic pathway, termed the methanol condensation cycle ...	2014	25355907
the association between the upper digestive tract microbiota by homim and oral health in a population-based study in linxian, china.	bacteria affect oral health, but few studies have systematically examined the role of bacterial communities in oral diseases. we examined this relationship in a large population-based chinese cancer screening cohort.	2014	25348940
complete genome sequence of the oral spirochete bacterium treponema putidum strain omz 758t (atcc 700334t).	the oral spirochete bacterium treponema putidum inhabits human periodontal niches. the complete genome sequence of the omz 758(t) (atcc 700334(t)) strain of this species was determined, revealing a 2,796,913-bp chromosome, with a g+c content of 37.30% and a single plasmid (ptpu1; 3,649 bp) identical to pts1 from treponema denticola.	2014	25342686
metabolic engineering of methylobacterium extorquens am1 for 1-butanol production.	butanol is a promising next generation fuel and a bulk chemical precursor. although clostridia are the primary industrial microbes for the fermentative production of 1-butanol, alternative engineered hosts have the potential to generate 1-butanol from alternative carbon feedstocks via synthetic metabolic pathways. methylobacterium extorquens am1, a facultative methylotrophic α-proteobacterium, is a model system for assessing the possibility of generating products such as 1-butanol from one-carbo ...	2014	25349627
elastase and metalloproteinase-9 concentrations in saliva in patients with chronic periodontitis.	elastase and metalloproteinase-9 (mmp-9) are two of numerous proteolytic enzymes released by neutrophilic granulocytes in the course of periodontitis. the aim of the study was to determine the concentrations of elastase and mmp-9 in saliva in patients with chronic periodontitis compared to healthy individuals. the enzyme-linked immunosorbent assay method was employed to determine the concentrations of elastase and mmp-9 in saliva in patients with chronic periodontitis and with pocket depth (pd) ...	2014	26155148
intraindividual variation in core microbiota in peri-implantitis and periodontitis.	the oral microbiota change dramatically with each part of the oral cavity, even within the same mouth. nevertheless, the microbiota associated with peri-implantitis and periodontitis have been considered the same. to improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. although the clinical symptoms of peri-implantitis were similar to those of periodontitis, ...	2014	25308100
relationship of clinical and microbiological variables in patients with type 1 diabetes mellitus and periodontitis.	the aim of the study was to analyze how metabolic control of type 1 diabetes is related to clinical and microbiological periodontal parameters.	2014	25294115
a pathogenic trace of tannerella forsythia - shedding of soluble fully active tumor necrosis factor α from the macrophage surface by karilysin.	tannerella forsythia is implicated as a pathogen causing chronic and aggressive periodontitis. however, its virulence factors, including numerous putative proteases, are mostly uncharacterized. karilysin is a newly described matrix metalloprotease-like enzyme of t. forsythia. since pathogen-derived proteases may affect the host defense system via modulation of the cytokine network, the aim of this study was to determine the influence of karilysin on tumor necrosis factor-α (tnf-α). the results s ...	2014	25175980
selective microbial genomic dna isolation using restriction endonucleases.	to improve the metagenomic analysis of complex microbiomes, we have repurposed restriction endonucleases as methyl specific dna binding proteins. as an example, we use dpni immobilized on magnetic beads. the ten minute extraction technique allows specific binding of genomes containing the dpni gm6atc motif common in the genomic dna of many bacteria including γ-proteobacteria. using synthetic genome mixtures, we demonstrate 80% recovery of escherichia coli genomic dna even when only femtogram qua ...	2014	25279840
role of porphyromonas gingivalis gingipains in multi-species biofilm formation.	periodontal diseases are polymicrobial diseases that cause the inflammatory destruction of the tooth-supporting (periodontal) tissues. their initiation is attributed to the formation of subgingival biofilms that stimulate a cascade of chronic inflammatory reactions by the affected tissue. the gram-negative anaerobes porphyromonas gingivalis, tannerella forsythia and treponema denticola are commonly found as part of the microbiota of subgingival biofilms, and they are associated with the occurren ...	2014	25270662
antimicrobial effect of ozonated water, sodium hypochlorite and chlorhexidine gluconate in primary molar root canals.	the aim was to determine the antimicrobial effect of ozonated water, ozonated water with ultrasonication, sodium hypochloride and chlorhexidine (chx) in human primary root canals contaminated by enterococcus faecalis (e. faecalis).	2014	25512726
orthodontic bracket designs and their impact on microbial profile and periodontal disease: a clinical trial.	the aim of the present study was to compare the undisturbed plaque formation on teeth bonded with preadjusted (captain ortho, libral traders, mumbai, india) and begg brackets (captain ortho, libral traders, mumbai, india) with nonbonded control sites via a de novo plaque growth over a period of 7 days.	2014	25426456
cancer-promoting effects of microbial dysbiosis.	humans depend on our commensal bacteria for nutritive, immune-modulating, and metabolic contributions to maintenance of health. however, this commensal community exists in careful balance that, if disrupted, enters dysbiosis; this has been shown to contribute to the pathogenesis of colon, gastric, esophageal, pancreatic, laryngeal, breast, and gallbladder carcinomas. this development is closely tied to host inflammation, which causes and is aggravated by microbial dysbiosis and increases vulnera ...	2014	25123079
lack of a surface layer in tannerella forsythia mutants deficient in the type ix secretion system.	tannerella forsythia, a gram-negative anaerobic bacterium, is an important pathogen in periodontal disease. this bacterium possesses genes encoding all known components of the type ix secretion system (t9ss). t. forsythia mutants deficient in genes orthologous to the t9ss-encoding genes pork, port and sov were constructed. all pork, port and sov single mutants lacked the surface layer (s-layer) and expressed less-glycosylated versions of the s-layer glycoproteins tfsa and tfsb. in addition, thes ...	2014	25023245
code blue: acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity.	actinetobacter baumannii is an important nosocomial pathogen that can cause a wide range of serious conditions including pneumonia, meningitis, necrotizing fasciitis and sepsis. it is also a major cause of wound infections in military personnel injured during the conflicts in afghanistan and iraq, leading to its popular nickname of 'iraqibacter'. contributing to its success in clinical settings is resistance to environmental stresses such as desiccation and disinfectants. moreover, in recent yea ...	2014	25052812
code blue: acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity.	actinetobacter baumannii is an important nosocomial pathogen that can cause a wide range of serious conditions including pneumonia, meningitis, necrotizing fasciitis and sepsis. it is also a major cause of wound infections in military personnel injured during the conflicts in afghanistan and iraq, leading to its popular nickname of 'iraqibacter'. contributing to its success in clinical settings is resistance to environmental stresses such as desiccation and disinfectants. moreover, in recent yea ...	2014	25052812
lack of cathelicidin processing in papillon-lefèvre syndrome patients reveals essential role of ll-37 in periodontal homeostasis.	loss-of-function point mutations in the cathepsin c gene are the underlying genetic event in patients with papillon-lefèvre syndrome (pls). pls neutrophils lack serine protease activity essential for cathelicidin ll-37 generation from hcap18 precursor.	2014	25260376
microbial signature profiles of periodontally healthy and diseased patients.	to determine microbial profiles that discriminate periodontal health from different forms of periodontal diseases.	2014	25139407
association between polycystic ovary syndrome, oral microbiota and systemic antibody responses.	polycystic ovary syndrome (pcos) is a hormonal disorder of women that not only is the leading cause of infertility but also shows a reciprocal link with oral health. this study aimed to investigate the hypothesis that the levels of putative periodontal pathogens in saliva and their antibody response in serum are elevated in pcos, compared to systemic health. a total of 125 women were included in four groups; 45 women with pcos and healthy periodontium, 35 women with pcos and gingivitis, 25 syste ...	2014	25232962
the inflammophilic character of the periodontitis-associated microbiota.	in periodontitis, dysbiotic microbial communities exhibit synergistic interactions for enhanced protection from host defenses, nutrient acquisition, and persistence in an inflammatory environment. this review discusses evidence that periodontitis-associated communities are 'inflammo-philic' (=loving or attracted to inflammation) in that they have evolved to not only endure inflammation but also to take advantage of it. in this regard, inflammation can drive the selection and enrichment of these ...	2014	24976068
expression and regulation of triggering receptor expressed on myeloid cells 1 in periodontal diseases.	periodontitis is an inflammatory infectious disease that destroys the tooth-supporting tissues. it is caused by multi-species subgingival biofilms that colonize the tooth surface. porphyromonas gingivalis, treponema denticola and tannerella forsythia (i.e. 'red complex' bacteria) are characteristic subgingival biofilm species. the triggering receptor expressed on myeloid cells 1 (trem-1) is a cell surface receptor of the immunoglobulin superfamily, with a role in the amplification of proinflamma ...	2014	24924298
definition, etiology, prevention and treatment of peri-implantitis--a review.	peri-implant inflammations represent serious diseases after dental implant treatment, which affect both the surrounding hard and soft tissue. due to prevalence rates up to 56%, peri-implantitis can lead to the loss of the implant without multilateral prevention and therapy concepts. specific continuous check-ups with evaluation and elimination of risk factors (e.g. smoking, systemic diseases and periodontitis) are effective precautions. in addition to aspects of osseointegration, type and struct ...	2014	25185675
metabolic engineering of microorganisms for the production of higher alcohols.	due to the increasing concerns about limited fossil resources and environmental problems, there has been much interest in developing biofuels from renewable biomass. ethanol is currently used as a major biofuel, as it can be easily produced by existing fermentation technology, but it is not the best biofuel due to its low energy density, high vapor pressure, hygroscopy, and incompatibility with current infrastructure. higher alcohols, including 1-propanol, 1-butanol, isobutanol, 2-methyl-1-butan ...	2014	25182323
a fast method for defb1 - 44c/g snp genotyping in brazilian patients with periodontitis.	defensins are cationic antimicrobial peptides expressed in epithelial cells. such peptides exhibit antibacterial, antifungal and antiviral properties, and are a component of the innate immune response. it has been suggested that they have a protective role in the oral cavity. this study evaluated the defb1 polymorphism in diabetic patients with or without periodontitis in comparison to healthy controls.	2014	27688368
periodontal microbiology--the lid's off the box again.		2014	25074493
newly identified pathogens associated with periodontitis: a systematic review.	there is substantial evidence supporting the role of certain oral bacteria species in the onset and progression of periodontitis. nevertheless, results of independent-culture diagnostic methods introduced about a decade ago have pointed to the existence of new periodontal pathogens. however, the data of these studies have not been evaluated together, which may generate some misunderstanding on the actual role of these microorganisms in the etiology of periodontitis. the aim of this systematic re ...	2014	25074492
the presence of cariogenic and periodontal pathogens in the oral cavity of one-year-old infants delivered pre-term with very low birthweights: a case control study.	recently, the dental literature has focused mainly on the microbial colonization of healthy full-term infants and their mothers or caretakers. however, oral microbial acquisition by premature infants has not been adequately investigated, and the correlation between pre-term birth and the presence of cariogenic and periodontal pathogens has not been determined. the aim of this study was to identify the presence and quantities of representative cariogenic and periodontal pathogens in the oral cavi ...	2014	25178742
a crispr view of development.	the crispr (clustered regularly interspaced short palindromic repeat)-cas9 (crispr-associated nuclease 9) system is poised to transform developmental biology by providing a simple, efficient method to precisely manipulate the genome of virtually any developing organism. this rna-guided nuclease (rgn)-based approach already has been effectively used to induce targeted mutations in multiple genes simultaneously, create conditional alleles, and generate endogenously tagged proteins. illustrating th ...	2014	25184674
microbial peptidyl-prolyl cis/trans isomerases (ppiases): virulence factors and potential alternative drug targets.	initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (ppiases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. intense searches revealed that ppiases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. despite the clear-cut ...	2014	25184565
a homolog of glyceraldehyde-3-phosphate dehydrogenase from riemerella anatipestifer is an extracellular protein and exhibits biological activity.	riemerella anatipestifer is the causative agent of septicemia anserum exsudativa in ducks. its pathogenesis and virulence factors are still unclear. the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (gapdh), an anchorless and multifunctional protein on the surface of several pathogenic microorganisms, is involved in virulence and adhesion. whether homologs of gapdh exist, and display similar characteristics in r. anatipestifer (ragapdh) has not been determined. in our research, the ...	2014	25183032
polybacterial human disease: the ills of social networking.	polybacterial diseases involve multiple organisms that act collectively to facilitate disease progression. although this phenomenon was highlighted early in the 20th century, recent technological advances in diagnostics have led to the appreciation that many infections are far more complex than originally believed. furthermore, it is apparent that although most treatments focus on the dominant bacterial species in an infection, other microbes, including commensals, can have a profound impact on ...	2014	24938173
l-methionase: a therapeutic enzyme to treat malignancies.	cancer is an increasing cause of mortality and morbidity throughout the world. l-methionase has potential application against many types of cancers. l-methionase is an intracellular enzyme in bacterial species, an extracellular enzyme in fungi, and absent in mammals. l-methionase producing bacterial strain(s) can be isolated by 5,5'-dithio-bis-(2-nitrobenzoic acid) as a screening dye. l-methionine plays an important role in tumour cells. these cells become methionine dependent and eventually fol ...	2014	25250324
prevalence of pseudomonas aeruginosa and acinetobacter spp. in subgingival biofilm and saliva of subjects with chronic periodontal infection.	p. aeruginosa and acinetobacter spp. are important pathogens associated with late nosocomial pneumonia in hospitalized and institutionalized individuals. the oral cavity may be a major source of these respiratory pathogens, particularly in the presence of poor oral hygiene and periodontal infection. this study investigated the prevalence of p. aeruginosa and acinetobacter spp. in subgingival biofilm and saliva of subjects with periodontal disease or health. samples were obtained from 55 periodon ...	2014	25242933
bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators.	periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. the management of chronic periodontitis (cp) relies heavily on elimination or at least control of known pathogenic consortia associated with the disease. until now, microbial plaque obtained from the subgingival (subg) sites has been the primary focus for bacterial community analysis using deep sequencing. in addition to the use of subg p ...	2014	25225610
strategies for the inhibition of gingipains for the potential treatment of periodontitis and associated systemic diseases.	gingipains are the major virulence factors of porphyromonas gingivalis, the main periodontopathogen. it is expected that inhibition of gingipain activity in vivo could prevent or slow down the progression of adult periodontitis. to date, several classes of gingipain inhibitors have been recognized. these include gingipain n-terminal prodomains, synthetic compounds, inhibitors from natural sources, antibiotics, antiseptics, antibodies, and bacteria. several synthetic compounds are potent gingipai ...	2014	25206939
identification of diversity-generating retroelements in human microbiomes.	diversity-generating retroelements (dgrs) are a unique family of retroelements that confer selective advantages to their hosts by accelerating the evolution of target genes through a specialized, error-prone, reverse transcription process. first identified in a bordetella phage (bpp-1), which mediates the phage tropism specificity by generating variability in an involved gene, dgrs were predicted to be present in a larger collection of viral and bacterial species. a minimal dgr system is compris ...	2014	25196521
subgingival air-polishing with erythritol during periodontal maintenance: randomized clinical trial of twelve months.	to evaluate repeated subgingival air-polishing in residual pockets with a new erythritol powder containing 0.3% chlorhexidine.	2014	25041441
the periodontal pathogen porphyromonas gingivalis induces expression of transposases and cell death of streptococcus mitis in a biofilm model.	oral microbial communities are extremely complex biofilms with high numbers of bacterial species interacting with each other (and the host) to maintain homeostasis of the system. disturbance in the oral microbiome homeostasis can lead to either caries or periodontitis, two of the most common human diseases. periodontitis is a polymicrobial disease caused by the coordinated action of a complex microbial community, which results in inflammation of tissues that support the teeth. it is the most com ...	2014	24866802
deep sequencing analysis reveals temporal microbiota changes associated with development of bovine digital dermatitis.	bovine digital dermatitis (dd) is a leading cause of lameness in dairy cattle throughout the world. despite 35 years of research, the definitive etiologic agent associated with the disease process is still unknown. previous studies have demonstrated that multiple bacterial species are associated with lesions, with spirochetes being the most reliably identified organism. this study details the deep sequencing-based metagenomic evaluation of 48 staged dd biopsy specimens collected during a 3-year ...	2014	24866801
proteome analysis of coinfection of epithelial cells with filifactor alocis and porphyromonas gingivalis shows modulation of pathogen and host regulatory pathways.	changes in periodontal status are associated with shifts in the composition of the bacterial community in the periodontal pocket. the relative abundances of several newly recognized microbial species, including filifactor alocis, as-yet-unculturable organisms, and other fastidious organisms have raised questions on their impact on disease development. we have previously reported that the virulence attributes of f. alocis are enhanced in coculture with porphyromonas gingivalis. we have evaluated ...	2014	24866790
maxbin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.	recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions.	2014	25136443
structural basis of pam-dependent target dna recognition by the cas9 endonuclease.	the crispr-associated protein cas9 is an rna-guided endonuclease that cleaves double-stranded dna bearing sequences complementary to a 20-nucleotide segment in the guide rna. cas9 has emerged as a versatile molecular tool for genome editing and gene expression control. rna-guided dna recognition and cleavage strictly require the presence of a protospacer adjacent motif (pam) in the target dna. here we report a crystal structure of streptococcus pyogenes cas9 in complex with a single-molecule gui ...	2014	25079318
the treponema denticola atcr lyttr domain-containing response regulator interacts with three architecturally distinct promoter elements: implications for understanding the molecular signaling mechanisms that drive the progression of periodontal disease.	treponema denticola is an oral spirochete and periopathogen that transitions from low abundance in healthy subgingival crevices to high abundance in periodontal pockets. the t. denticola response regulator atcr harbors the relatively rare, lyttr dna-binding domain. lyttr domain containing response regulators control critical transcriptional responses required for environmental adaptation. using a multi-step bioinformatics approach, 26 strong lyttr recognition motifs were identified in the genome ...	2014	24890414
leptin effects on the regenerative capacity of human periodontal cells.	obesity is increasing throughout the globe and characterized by excess adipose tissue, which represents a complex endocrine organ. adipose tissue secrets bioactive molecules called adipokines, which act at endocrine, paracrine, and autocrine levels. obesity has recently been shown to be associated with periodontitis, a disease characterized by the irreversible destruction of the tooth-supporting tissues, that is, periodontium, and also with compromised periodontal healing. although the underlyin ...	2014	25136363
accurate genome relative abundance estimation for closely related species in a metagenomic sample.	metagenomics has a great potential to discover previously unattainable information about microbial communities. an important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. most of prevalent homology-based approaches utilize solely the results of an alignment tool such as blast, limiting their estimation accuracy to high ranks of the taxonomy tree.	2014	25027647
quantitative molecular detection of putative periodontal pathogens in clinically healthy and periodontally diseased subjects.	periodontitis is a multi-microbial oral infection with high prevalence among adults. putative oral pathogens are commonly found in periodontally diseased individuals. however, these organisms can be also detected in the oral cavity of healthy subjects. this leads to the hypothesis, that alterations in the proportion of these organisms relative to the total amount of oral microorganisms, namely their abundance, rather than their simple presence might be important in the transition from health to ...	2014	25029268
infectious burden and atherosclerosis: a clinical issue.	atherosclerotic cardiovascular diseases, chronic inflammatory diseases of multifactorial etiology, are the leading cause of death worldwide. in the last decade, more infectious agents, labeled as "infectious burden", rather than any single pathogen, have been showed to contribute to the development of atherosclerosis through different mechanisms. some microorganisms, such as chlamydia pneumoniae (c. pneumoniae), human cytomegalovirus, etc. may act directly on the arterial wall contributing to en ...	2014	25032197
uncovering the molecular networks in periodontitis.	periodontitis is a complex immune-inflammatory disease that results from a preestablished infection in gingiva, mainly due to gram-negative bacteria that colonize deeper in gingival sulcus and latter periodontal pocket. host inflammatory and immune responses have both protective and destructive roles. although cytokines, prostaglandins, and proteases struggle against microbial burden, these molecules promote connective tissue loss and alveolar bone resorption, leading to several histopathologica ...	2014	24828325
beneficial effects of adiponectin on periodontal ligament cells under normal and regenerative conditions.	type 2 diabetes and obesity are increasing worldwide and linked to periodontitis, a chronic disease which is characterized by the irreversible destruction of the tooth-supporting tissues, that is, periodontium. the mechanisms underlying the association of diabetes mellitus and obesity with periodontal destruction and compromised periodontal healing are not well understood, but decreased plasma levels of adiponectin, as found in diabetic and obese individuals, might be a critical mechanistic link ...	2014	25121107
anaerobes and bacterial vaginosis in pregnancy: virulence factors contributing to vaginal colonisation.	the aetiology and pathogenesis of bacterial vaginosis (bv) is unclear but it appears to be associated with factors that disrupt the normal acidity of the vagina thus altering the equilibrium between the normal vaginal microbiota. bv has serious implications for female morbidity, including reports of pelvic inflammatory disease, adverse pregnancy outcomes, increased susceptibility to sexually transmitted infections and infertility. this paper reviewed new available information regarding possible ...	2014	25014248
intracellular localization of treponema denticola chymotrypsin-like proteinase in chronic periodontitis.	treponema denticola is an important periodontal pathogen capable of tissue invasion. its chymotrypsin-like proteinase (ctlp) can degrade a number of basement membrane components in vitro, thus suggesting a contribution to tissue invasion by the spirochete. the aim of this study was to analyze the localization of ctlp in chronic periodontitis tissues ex vivo. a polyclonal antibody specific to t. denticola cell-bound ctlp was used to detect the spirochetes in the gingival tissues of patients with ...	2014	25006362
relationship between gingival bleeding and anaerobic periodontal infection assessed by bana (n-benzoyl-dl-arginine-β-napthylamide) assay.	since periodontal diseases are primarily inflammatory in nature, the ability to detect inflammatory lesions in gingival tissue is essential for the diagnosis and monitoring of changes in gingival status. gingival bleeding has been used as a reliable and objective clinical parameter not only for the evaluation of inflammatory conditions of periodontium, but also in the detection of its activity and progression. the gingival bleeding index (loe) is based on the presence or absence of gingival blee ...	2014	25210389
oral fluid based biomarkers in periodontal disease: part 1. saliva.	traditional clinical measurements such as probing pocket depth, bleeding on probing, clinical attachment loss; plaque index and radiographs used for periodontal diagnosis are often of limited usefulness as they are indicators of previous periodontal disease rather than present disease activity. a literature search was carried out to find out all the available tests that indicate periodontal disease markers in saliva. all major databases were searched to compile the information on published repor ...	2014	25214743
serum monocyte chemoattractant protein-1 is a biomarker in patients with diabetes and periodontitis.	the role of serum monocyte chemoattractant protein-1 (mcp-1) as a biomarker of periodontitis is well documented; however, its role in diabetic patients with periodontitis is unknown.	2014	25143907
periodontal disease and subgingival microbiota as contributors for rheumatoid arthritis pathogenesis: modifiable risk factors?	since the early 1900s, the role of periodontal disease in the pathogenesis of rheumatoid arthritis has been a matter of intense research. the last decade has witnessed many advances supporting a link between periodontitis, the presence of specific bacterial species (i.e. porphyromonas gingivalis) and their effects in immune response. this review will examine available evidence on the individuals.	2014	24807405
effect of chlorhexidine chip in the treatment of chronic periodontitis.	the evaluation of clinical and specific microbiological changes associated with chlorhexidine chip in the chronic periodontitis patients.	2014	25097396
identification of a diguanylate cyclase and its role in porphyromonas gingivalis virulence.	porphyromonas gingivalis is a gram-negative obligate anaerobic bacterium and is considered a keystone pathogen in the initiation of periodontitis, one of the most widespread infectious diseases. bacterial bis-(3'-5') cyclic gmp (cyclic di-gmp [c-di-gmp]) serves as a second messenger and is involved in modulating virulence factors in numerous bacteria. however, the role of this second messenger has not been investigated in p. gingivalis, mainly due to a lack of an annotation regarding diguanylate ...	2014	24733094
intercellular communications in multispecies oral microbial communities.	the oral cavity contains more than 700 microbial species that are engaged in extensive cell-cell interactions. these interactions contribute to the formation of highly structured multispecies communities, allow them to perform physiological functions, and induce synergistic pathogenesis. co-adhesion between oral microbial species influences their colonization of oral cavity and effectuates, to a large extent, the temporal and spatial formation of highly organized polymicrobial community architec ...	2014	25071741
discovery of bovine digital dermatitis-associated treponema spp. in the dairy herd environment by a targeted deep-sequencing approach.	the bacteria associated with the infectious claw disease bovine digital dermatitis (dd) are spirochetes of the genus treponema; however, their environmental reservoir remains unknown. to our knowledge, the current study is the first report of the discovery and phylogenetic characterization of rrna gene sequences from dd-associated treponemes in the dairy herd environment. although the spread of dd appears to be facilitated by wet floors covered with slurry, no dd-associated treponemes have been ...	2014	24814794
effects of ph and lactate on hydrogen sulfide production by oral veillonella spp.	indigenous oral bacteria in the tongue coating such as veillonella have been identified as the main producers of hydrogen sulfide (h2s), one of the major components of oral malodor. however, there is little information on the physiological properties of h2s production by oral veillonella such as metabolic activity and oral environmental factors which may affect h2s production. thus, in the present study, the h2s-producing activity of growing cells, resting cells, and cell extracts of oral veillo ...	2014	24795374
common periodontal diseases of children and adolescents.	background. since 2000, studies, experiments, and clinical observations revealed high prevalence of periodontal diseases among children and adolescents. therefore, this paper was designed to provide an update for dental practitioners on epidemiology, microbiology, pathology, prevention, diagnosis, and treatment of periodontal diseases in children and adolescents. methods. this paper reviews the current literature concerning periodontal diseases in pediatric dentistry. it includes medline databas ...	2014	25053946
pathogenic microbes, the microbiome, and alzheimer's disease (ad).		2014	24982633
treatment alternatives to negotiate peri-implantitis.	peri-implant diseases are becoming a major health issue in dentistry. despite the magnitude of this problem and the potential grave consequences, commonly acceptable treatment protocols are missing. hence, the present paper reviews the literature treatment of peri-implantitis in order to explore their benefits and limitations. treatment of peri-implantitis may include surgical and nonsurgical approaches, either individually or combined. nonsurgical therapy is aimed at removing local irritants fr ...	2014	26556414
treponema denticola upregulates mmp-2 activation in periodontal ligament cells: interplay between epigenetics and periodontal infection.	periodontal pathogens initiate chronic dysregulation of inflammation and tissue homeostasis that characterize periodontal disease. to better understand oral microbe-host tissue interactions, we investigated expression and activation of mmp-2 in periodontal ligament cells following treponema denticola challenge.	2014	24973519
filifactor alocis: the newly discovered kid on the block with special talents.	infection-induced periodontal disease has been primarily focused on a small group of periodontal pathogens. a paradigm shift, based on data emerging from the oral microbiome project, now suggests the involvement of as-yet-unculturable and fastidious organisms. collectively, these studies have demonstrated that there are changes in the periodontal status associated with shifts in the composition of the bacterial community in the periodontal pocket. in addition, it is likely that the emerging new ...	2014	24898946
photodynamic therapy as novel treatment for halitosis in adolescents: a case series study.	halitosis is a common problem that affects a large portion of the population worldwide. the origin of this condition is oral in 90% of cases and systemic in 10% of cases. the foul odor is caused mainly by volatile sulfur compounds produced by gram-negative bacteria. however, it has recently been found that anaerobic gram-positive bacteria also produce hydrogen sulfide (h2s) in the presence of amino acids, such as cysteine. light with and without the combination of chemical agents has been used t ...	2014	25653814
massive parallel sequencing provides new perspectives on bacterial brain abscesses.	rapid development within the field of massive parallel sequencing (mps) is about to bring this technology within reach for diagnostic microbiology laboratories. we wanted to explore its potential for improving diagnosis and understanding of polymicrobial infections, using bacterial brain abscesses as an example. we conducted a prospective nationwide study on bacterial brain abscesses. fifty-two surgical samples were included over a 2-year period. the samples were categorized as either spontaneou ...	2014	24671797
bacteria in the adventitia of cardiovascular disease patients with and without rheumatoid arthritis.	the incidence of atherosclerosis is significantly increased in rheumatoid arthritis (ra). infection is one factor that may be involved in the pathogenesis of both diseases. the cause of ra and atherosclerosis is unknown, and infection is one of the factors that may be involved in the pathogenesis of both diseases. the aims of this study were to identify bacteria in the aortic adventitia of patients with cardiovascular disease (cvd) in the presence and absence of ra, and to determine the effect o ...	2014	24874661
auranofin and related heterometallic gold(i)-thiolates as potent inhibitors of methicillin-resistant staphylococcus aureus bacterial strains.	a series of new heterometallic gold(i) thiolates containing ferrocenyl-phoshines were synthesized. their antimicrobial properties were studied and compared to that of fda-approved drug, auranofin (ridaura), prescribed for the treatment of rheumatoid arthritis. mic in the order of one digit micromolar were found for most of the compounds against gram-positive bacteria staphylococcus aureus and ca mrsa strains us300 and us400. remarkably, auranofin inhibited s. aureus, us300 and us400 in the order ...	2014	24935090
altered oral viral ecology in association with periodontal disease.	the human oral cavity is home to a large and diverse community of viruses that have yet to be characterized in patients with periodontal disease. we recruited and sampled saliva and oral biofilm from a cohort of humans either periodontally healthy or with mild or significant periodontal disease to discern whether there are differences in viral communities that reflect their oral health status. we found communities of viruses inhabiting saliva and the subgingival and supragingival biofilms of eac ...	2014	24846382
microbial community profiling of human saliva using shotgun metagenomic sequencing.	human saliva is clinically informative of both oral and general health. since next generation shotgun sequencing (ngs) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the human microbiome project, along with a control dataset containing short ngs reads from bacterial species representative of the bacterial flora of human saliva. genius, a system designed to identify and quantify bacte ...	2014	24846174
bacteria and bacterial dna in atherosclerotic plaque and aneurysmal wall biopsies from patients with and without periodontitis.	several studies have reported an association between chronic periodontitis (cp) and cardiovascular diseases. detection of periodontopathogens, including red complex bacteria (rcb), in vascular lesions has suggested these bacteria to be involved in the pathogenesis of atherosclerosis and abdominal aortic aneurysms.	2014	25006361
prevalence of clinical periodontitis and putative periodontal pathogens among south indian pregnant women.	in view of recent understanding of the association of periodontal infections and adverse pregnancy outcomes, the present investigation was undertaken to study the periodontal infections among 390 asymptomatic pregnant women and to find an association of bacterial etiologies with the disease. prevalence of gingivitis was 38% and clinical periodontitis was 10% among the study population. subgingival plaque specimens were subjected to multiplex pcr targeting ten putative periodontopathogenic bacter ...	2014	24899898