| identification of surprisingly diverse type iv pili, across a broad range of gram-positive bacteria. | in gram-negative bacteria, type iv pili (tfp) have long been known to play important roles in such diverse biological phenomena as surface adhesion, motility, and dna transfer, with significant consequences for pathogenicity. more recently it became apparent that gram-positive bacteria also express type iv pili; however, little is known about the diversity and abundance of these structures in gram-positives. computational tools for automated identification of type iv pilins are not currently ava ... | 2011 | 22216142 |
| sialic acid, periodontal pathogens and tannerella forsythia: stick around and enjoy the feast! | periodontal pathogens, like any other human commensal or pathogenic bacterium, must possess both the ability to acquire the necessary growth factors and the means to adhere to surfaces or reside and survive in their environmental niche. recent evidence has suggested that sialic acid containing host molecules may provide both of these requirements in vivo for several periodontal pathogens but most notably for the red complex organism tannerella forsythia. several other periodontal pathogens also ... | 2012 | 22230462 |
| sialic acid, periodontal pathogens and tannerella forsythia: stick around and enjoy the feast! | periodontal pathogens, like any other human commensal or pathogenic bacterium, must possess both the ability to acquire the necessary growth factors and the means to adhere to surfaces or reside and survive in their environmental niche. recent evidence has suggested that sialic acid containing host molecules may provide both of these requirements in vivo for several periodontal pathogens but most notably for the red complex organism tannerella forsythia. several other periodontal pathogens also ... | 2012 | 22230462 |
| porphyromonas endodontalis in chronic periodontitis: a clinical and microbiological cross-sectional study. | although previous studies have shown the presence of porphyromonas endodontalis in chronic periodontitis associated with periapical lesions, the occurrence of this pathogen in diseased periodontal sites without periapical lesions has been poorly investigated. | 2012 | 22232719 |
| periodontal pathogens affect the level of protease inhibitors in gingival crevicular fluid. | in periodontitis, an effective host-response is primarily related to neutrophils loaded with serine proteases, including elastase (ne) and protease 3 (pr3), the extracellular activity of which is tightly controlled by endogenous inhibitors. in vitro these inhibitors are degraded by gingipains, cysteine proteases produced by porphyromonas gingivalis. the purpose of this study was to determine the level of selected protease inhibitors in gingival crevicular fluid (gcf) in relation to periodontal i ... | 2012 | 22230465 |
| probiotics and periodontal health. | periodontitis is one of the most common chronic inflammatory diseases. the etiology is clearly bacterial and a number of putative bacterial pathogens have been associated with the disease, including aggregatibacter actinomycetemcomitans, tannerella forsythus and porphyromonas gingivalis. comparatively, little attention has been paid to the identification of health-associated and potentially beneficial bacterial species that may reside in the gingival sulcus. probiotic technology represents a bre ... | 2011 | 22514571 |
| relationship between the pathogenic representatives of periodontal pockets microbiocenosis in patients with periodontitis with varying degrees of severity. | periodontitis is a common disease that is considered to be a manifestation of the distortion of the ratio between the normal and conditionally pathogenic microflora of periodontal pockets. in this study, the ratio between the six most important periodontal pathogens and the total microflora of the periodontal pocket in healthy individuals and patients with varying severity of periodontitis was ascertained by quantitative real-time pcr. it was ascertained that the relative content ofporphyromonas ... | 2011 | 22649688 |
| microflora and periodontal disease. | periodontitis is a disease that affects and destroys the tissues that support teeth. tissue damage results from a prolonged inflammatory response to an ecological shift in the composition of subgingival biofilms. three bacterial species that constitute the red complex group, porphyromonas gingivalis, tannerella forsythia, and treponema denticola, are considered the main pathogens involved in periodontitis. | 2012 | 23814584 |
| plaque retention on elastomeric ligatures. an in vivo study. | fixed orthodontic appliances make it difficult to maintain the oral hygiene, resulting in plaque accumulation. retention of bacterial plaque, represents a risk for white spot lesions and development of periodontal disease. | 2012 | 23741603 |
| plaque retention on elastomeric ligatures. an in vivo study. | fixed orthodontic appliances make it difficult to maintain the oral hygiene, resulting in plaque accumulation. retention of bacterial plaque, represents a risk for white spot lesions and development of periodontal disease. | 2012 | 23741603 |
| evaluation of periodontal pathogens in amniotic fluid and the role of periodontal disease in pre-term birth and low birth weight. | pre-term birth and/or low birth weight (ptlbw) is a serious problem in developing countries. the absence of known risk factors in ≈ 50% of ptlbw cases has resulted in a continued search for other causes. the aim of this study was to examine the effect of periodontitis on pregnancy outcomes. | 2012 | 23638858 |
| periodontal conditions during the pregnancy associated with periodontal pathogens. | to describe the bacterial associations in the periodontal pockets of pregnant women and to correlate the presence of prevotella intermedia, tannerella forsythia (t. forsythia), treponema denticola (t. denticola), aggregatibacter actinomycetemcomitans, and porphyromona gingivalis (p. gingivalis) with periodontal parameters of severity. | 2012 | 23335585 |
| [expression of cytokines in dentogingival sulcus in patients after dental implantation and during development of peri-implantitis]. | determination of cytokine content in various areas of dentition in patients with peri-implantitis associated with parodontopathogenic bacteria species of i and ii order. | 2012 | 23297645 |
| treponema denticola associates with increased levels of mmp-8 and mmp-9 in gingival crevicular fluid. | objectives: the aim was to assess the association between the presence of site-specific subgingival micro-organisms and the levels of matrix metalloproteinases-8 and matrix metalloproteinases-9 (mmp-8 and mmp-9) in gingival crevicular fluid (gcf). materials and methods: the patient group consisted of 56 subjects with periodontitis and the control group of 43 subjects without periodontitis. gcf samples from four test sites for each subject were collected. polymerase chain reaction was used to det ... | 2012 | 23294114 |
| treponema pallidum infection in the wild baboons of east africa: distribution and genetic characterization of the strains responsible. | it has been known for decades that wild baboons are naturally infected with treponema pallidum, the bacterium that causes the diseases syphilis (subsp. pallidum), yaws (subsp. pertenue), and bejel (subsp. endemicum) in humans. recently, a form of t. pallidum infection associated with severe genital lesions has been described in wild baboons at lake manyara national park in tanzania. in this study, we investigated ten additional sites in tanzania and kenya using a combination of macroscopic obser ... | 2012 | 23284649 |
| vima mediates multiple functions that control virulence in porphyromonas gingivalis. | porphyromonas gingivalis, a black-pigmented, gram-negative anaerobe, is an important etiological agent of periodontal disease. its ability to survive in the periodontal pocket and orchestrate the microbial/host activities that can lead to disease suggest that p. gingivalis possesses a complex regulatory network involving transcriptional and post-transcriptional mechanisms. the vima (virulence modulating) gene is part of the 6.15-kb bcp-reca-vima-vime-vimf-arog locus and plays a role in oxidative ... | 2012 | 23279905 |
| vima mediates multiple functions that control virulence in porphyromonas gingivalis. | porphyromonas gingivalis, a black-pigmented, gram-negative anaerobe, is an important etiological agent of periodontal disease. its ability to survive in the periodontal pocket and orchestrate the microbial/host activities that can lead to disease suggest that p. gingivalis possesses a complex regulatory network involving transcriptional and post-transcriptional mechanisms. the vima (virulence modulating) gene is part of the 6.15-kb bcp-reca-vima-vime-vimf-arog locus and plays a role in oxidative ... | 2012 | 23279905 |
| validation of a quantitative real-time pcr assay and comparison with fluorescence microscopy and selective agar plate counting for species-specific quantification of an in vitro subgingival biofilm model. | subgingival biofilms are the prime etiological factor of periodontal disease. owing to their complex polymicrobial nature, quantification of individual bacterial species within the biofilm for research and diagnostic purposes can be methodologically challenging. the aims of this study were to establish a quantitative real-time pcr (qpcr) assay to quantify the bacteria used in our 10-species in vitro 'subgingival' biofilm model and to compare the quantitative outcome with fluorescence microscopy ... | 2012 | 23278531 |
| management of peri-implantitis. | peri-implantitis is a site-specific infectious disease that causes an inflammatory process in soft tissues, and bone loss around an osseointegrated implant in function. the etiology of the implant infection is conditioned by the status of the tissue surrounding the implant, implant design, degree of roughness, external morphology, and excessive mechanical load. the microorganisms most commonly associated with implant failure are spirochetes and mobile forms of gram-negative anaerobes, unless the ... | 2012 | 23559913 |
| role of sex steroid hormones in bacterial-host interactions. | sex steroid hormones play important physiological roles in reproductive and nonreproductive tissues, including immune cells. these hormones exert their functions by binding to either specific intracellular receptors that act as ligand-dependent transcription factors or membrane receptors that stimulate several signal transduction pathways. the elevated susceptibility of males to bacterial infections can be related to the usually lower immune responses presented in males as compared to females. t ... | 2012 | 23509808 |
| role of sex steroid hormones in bacterial-host interactions. | sex steroid hormones play important physiological roles in reproductive and nonreproductive tissues, including immune cells. these hormones exert their functions by binding to either specific intracellular receptors that act as ligand-dependent transcription factors or membrane receptors that stimulate several signal transduction pathways. the elevated susceptibility of males to bacterial infections can be related to the usually lower immune responses presented in males as compared to females. t ... | 2012 | 23509808 |
| periodontitis and systemic diseases: a literature review. | studies have revealed possible link between periodontitis and different systemic diseases. there is need to review this interesting subject. the aims are: to provide a comprehensive literature that can easily be consulted, on the subject; to draw the attention of health practitioners to the impact of oral health on the general well-being; and to emphasize the need for a deeper interaction between medical and dental training. the medline database was searched for relevant literature by combining ... | 2012 | 23493942 |
| the low incidence of diversity-generating retroelements in sequenced genomes. | the insertion of a retrotransposable element is usually associated with adverse or, at best, neutral effects on the host. diversity-generating retroelements (dgrs) are the first elements that seem to offer a direct selective advantage to their phage or prokaryote host by exact replacement of a short, defined region of a host gene with a hypermutated variant. in a previous study, we presented the software digref for identification of dgrs in genome sequences, and compiled the first comprehensive ... | 2012 | 23481467 |
| effect of antimicrobial photodynamic therapy on periodontally infected tooth sockets in rats. | the aim of the present study was to evaluate the antimicrobial effect of antimicrobial photodynamic therapy (apdt) in alveolar treatment of areas with induced periodontitis. thirty male wistar rats were subjected to ligature-induced periodontal disease (pd) in the first left inferior molars, while the right side molars did not receive ligatures. after 7 days of pd evolution, ligatures were removed from the left side, and the first left and right mandibular molars were extracted. afterwards, anim ... | 2013 | 23912780 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins. | the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ... | 2012 | 22192777 |
| bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins. | the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ... | 2012 | 22192777 |
| the unique hmuy gene sequence as a specific marker of porphyromonas gingivalis. | porphyromonas gingivalis, a major etiological agent of chronic periodontitis, acquires heme from host hemoproteins using the hmuy hemophore. the aim of this study was to develop a specific p. gingivalis marker based on a hmuy gene sequence. subgingival samples were collected from 66 patients with chronic periodontitis and 40 healthy subjects and the entire hmuy gene was analyzed in positive samples. phylogenetic analyses demonstrated that both the amino acid sequence of the hmuy protein and the ... | 2013 | 23844074 |
| pg1058 is a novel multidomain protein component of the bacterial type ix secretion system. | porphyromonas gingivalis utilises the bacteroidetes-specific type ix secretion system (t9ss) to export proteins across the outer membrane (om), including virulence factors such as the gingipains. the secreted proteins have a conserved carboxy-terminal domain essential for type ix secretion that is cleaved upon export. in p. gingivalis the t9ss substrates undergo glycosylation with anionic lipopolysaccharide (a-lps) and are attached to the om. in this study, comparative analyses of 24 bacteroidet ... | 2016 | 27711252 |
| integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. | integrons are horizontal gene transfer (hgt) systems containing elements necessary for site-specific recombination and expression of foreign dna. the overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. this report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. first, using culture-independent techniques, we explored the diversity of integrons and integron-tran ... | 2004 | 14766601 |
| electron cryotomography: a new view into microbial ultrastructure. | electron cryotomography (ect) is an emerging technology that allows thin samples such as small bacterial cells to be imaged in 3d in a nearly native state to 'molecular' (approximately 4nm) resolution. as such, ect is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. here we briefly explain ect, review its recent contributions to micr ... | 2009 | 19427259 |
| comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease. | polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. periodontitis represents a polymicrobial disease; porphyromonas gingivalis, treponema denticola and tannerella forsythia, called 'the red complex', have been recognized as the causative agents of periodontitis. although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are u ... | 2014 | 25171331 |
| comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease. | polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. periodontitis represents a polymicrobial disease; porphyromonas gingivalis, treponema denticola and tannerella forsythia, called 'the red complex', have been recognized as the causative agents of periodontitis. although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are u ... | 2014 | 25171331 |
| type i pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines. | pyridoxal 5'-phosphate (plp)-dependent enzymes of fold type i, the most studied structural class of the plp-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. these enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (pks) and nonribosomal peptides (nrps). the aim of this work is to provide a proteome-wide view of the distribution and characteristics of type i domains covalently ... | 2013 | 24148833 |
| the gain and loss of chromosomal integron systems in the treponema species. | integron systems are now recognized as important agents of bacterial evolution and are prevalent in most environments. one of the human pathogens known to harbor chromosomal integrons, the treponema spirochetes are the only clade among spirochete species found to carry integrons. with the recent release of many new treponema genomes, we were able to study the distribution of chromosomal integrons in this genus. | 2013 | 23339550 |
| nomenclature for macrolide and macrolide-lincosamide-streptogramin b resistance determinants. | | 1999 | 10582867 |
| 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 |
| inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy. | the growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. we have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underp ... | 2004 | 15214963 |
| comparative genomic analyses of the bacterial phosphotransferase system. | we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ... | 2005 | 16339738 |
| the glycolytic pathway of trimastix pyriformis is an evolutionary mosaic. | glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. the glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. however, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. we have conducted an expressed sequence tag (est) survey of the anaerobic flagellate trimastix pyriformis to investigate the nature of the evolut ... | 2006 | 17123440 |
| comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms. | hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ... | 2006 | 16780600 |
| a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins. | lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ... | 2006 | 16585737 |
| paths of lateral gene transfer of lysyl-aminoacyl-trna synthetases with a unique evolutionary transition stage of prokaryotes coding for class i and ii varieties by the same organisms. | while the premise that lateral gene transfer (lgt) is a dominant evolutionary force is still in considerable dispute, the case for widespread lgt in the family of aminoacyl-trna synthetases (aars) is no longer contentious. aarss are ancient enzymes, guarding the fidelity of the genetic code. they are clustered in two structurally unrelated classes. only lysine aminoacyl-trna synthetase (lysrs) is found both as a class 1 and a class 2 enzyme (lysrs1-2). remarkably, in several extant prokaryotes b ... | 2006 | 16529662 |
| algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. | comparison of metabolic networks is typically performed based on the organisms' enzyme contents. this approach disregards functional replacements as well as orthologies that are misannotated. direct comparison of the structure of metabolic networks can circumvent these problems. | 2006 | 16478540 |
| assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. | comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. | 2007 | 18047665 |
| quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes. | most bacterial chromosomes exhibit asymmetry of base composition with respect to leading vs. lagging strands (gc and at skews). these skews reflect mainly those in protein coding sequences, which are driven by asymmetric mutation pressures during replication and transcription (notably asymmetric cytosine deamination) plus subsequent selection for preferred structures, signals, amino acid or codons. the transcription-associated effects but not the replication-associated effects contribute to the ... | 2007 | 17711583 |
| transcriptional regulatory network discovery via multiple method integration: application to e. coli k12. | transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ... | 2007 | 17397539 |
| phylogenetic distribution of translational gtpases in bacteria. | translational gtpases are a family of proteins in which gtpase activity is stimulated by the large ribosomal subunit. conserved sequence features allow members of this family to be identified. | 2007 | 17214893 |
| minimum contradiction matrices in whole genome phylogenies. | minimum contradiction matrices are a useful complement to distance-based phylogenies. a minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix y(i) (,) (j) (n). a matrix element corresponds to the distance from a reference vertex n to the path (i, j). for an x-tree or a split network, the minimum contradiction matrix is a robinson matrix. it therefore fulfills all the inequalities defining perfect order: y(i) (,) (j) (n) >or= y(i) (,) (k) (n ... | 2008 | 19204821 |
| evolutionary primacy of sodium bioenergetics. | the f- and v-type atpases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of atp. both the f-type (found in most bacteria and eukaryotic mitochondria and chloroplasts) and v-type (found in archaea, some bacteria, and eukaryotic vacuoles) atpases can translocate either protons or sodium ions. the prevalent proton-dependent atpases are generally viewed as the primary form of the enzyme whereas the sodium-transloca ... | 2008 | 18380897 |
| rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique. | a real-time pcr assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. current real-time pcr technologies cannot accomplish this task due to severe limitations in multiplexing ability. to this end, we developed a new assay system which supports very high degrees of multiplexing. we developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelt ... | 2009 | 19923485 |
| rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique. | a real-time pcr assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. current real-time pcr technologies cannot accomplish this task due to severe limitations in multiplexing ability. to this end, we developed a new assay system which supports very high degrees of multiplexing. we developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelt ... | 2009 | 19923485 |
| target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. | to study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common tim barrel fold and catalyze a wide range of chemical reactions. here, we describe a collaboration between the enzyme specificity consortium (enspec) and the new york sgx research center for structural genomics (nysgxrc) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. using sequence- and s ... | 2009 | 19219566 |
| complement control protein factor h: the good, the bad, and the inadequate. | the complement system is an essential component of the innate immune system that participates in elimination of pathogens and altered host cells and comprises an essential link between the innate and adaptive immune system. soluble and membrane-bound complement regulators protect cells and tissues from unintended complement-mediated injury. complement factor h is a soluble complement regulator essential for controlling the alternative pathway in blood and on cell surfaces. normal recognition of ... | 2010 | 20580090 |
| electron cryotomography. | electron cryotomography (ect) is an emerging technology that allows thin samples such as macromolecular complexes and small bacterial cells to be imaged in 3-d in a nearly native state to "molecular" ( approximately 4 nm) resolution. as such, ect is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal fi laments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. this article describes the techniqu ... | 2010 | 20516135 |
| filament formation associated with spirochetal infection: a comparative approach to morgellons disease. | bovine digital dermatitis is an emerging infectious disease that causes lameness, decreased milk production, and weight loss in livestock. proliferative stages of bovine digital dermatitis demonstrate keratin filament formation in skin above the hooves in affected animals. the multifactorial etiology of digital dermatitis is not well understood, but spirochetes and other coinfecting microorganisms have been implicated in the pathogenesis of this veterinary illness. morgellons disease is an emerg ... | 2011 | 22253541 |
| molecular evolution of urea amidolyase and urea carboxylase in fungi. | urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. urea amidolyase has been found only in some fungal species among eukaryotes. it contains two major domains: the amidase and urea carboxylase domains. a shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. eukaryotic urea carboxylase has been found only in several fungal species and green algae. in order to elucid ... | 2011 | 21447149 |
| chemotactic behavior of pathogenic and nonpathogenic leptospira species. | we have developed a capillary tube assay in combination with real-time pcr to quantitate the number of chemoattracted leptospira cells. we identified tween 80, glucose, sucrose, and pyruvate as attractants for leptospira cells; amino acids and vitamin b(12) were found to be nonchemotactic or weakly chemotactic. this assay has the general applicability to further our understanding of leptospiral chemotaxis. | 2012 | 23001652 |
| characterization of biofilm formation by borrelia burgdorferi in vitro. | borrelia burgdorferi, the causative agent of lyme disease, has long been known to be capable of forming aggregates and colonies. it was recently demonstrated that borrelia burgdorferi aggregate formation dramatically changes the in vitro response to hostile environments by this pathogen. in this study, we investigated the hypothesis that these aggregates are indeed biofilms, structures whose resistance to unfavorable conditions are well documented. we studied borrelia burgdorferi for several kno ... | 2012 | 23110225 |
| whole genome sequence of treponema pallidum ssp. pallidum, strain mexico a, suggests recombination between yaws and syphilis strains. | treponema pallidum ssp. pallidum (tpa), the causative agent of syphilis, and treponema pallidum ssp. pertenue (tpe), the causative agent of yaws, are closely related spirochetes causing diseases with distinct clinical manifestations. the tpa mexico a strain was isolated in 1953 from male, with primary syphilis, living in mexico. attempts to cultivate tpa mexico a strain under in vitro conditions have revealed lower growth potential compared to other tested tpa strains. | 2012 | 23029591 |
| comparative genomics of brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity. | the anaerobic spirochaete brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. to date, the only available genome sequence of b. pilosicoli is that of strain 95/1000, a porcine isolate. in the first intra-species genome comparison within the brachyspira genus, we report the whole genome sequence of b. pilosicoli b2904, an avian isolate, the incomplete genome sequence of b. pilosicoli wesb, a human isolate, and the comparisons with b. pilosicoli 95/1000 ... | 2012 | 22947175 |
| the rickettsial ompb β-peptide of rickettsia conorii is sufficient to facilitate factor h-mediated serum resistance. | pathogenic species of the spotted fever group rickettsia are subjected to repeated exposures to the host complement system through cyclic infections of mammalian and tick hosts. the serum complement machinery is a formidable obstacle for bacteria to overcome if they endeavor to endure this endozoonotic cycle. we have previously demonstrated that that the etiologic agent of mediterranean spotted fever, rickettsia conorii, is susceptible to complement-mediated killing only in the presence of speci ... | 2012 | 22615250 |
| two chew coupling proteins are essential in a chemosensory pathway of borrelia burgdorferi. | in the model organism escherichia coli, the coupling protein chew, which bridges the chemoreceptors and histidine kinase chea, is essential for chemotaxis. unlike the situation in e. coli, borrelia burgdorferi, the causative agent of lyme disease, has three chew homologues (chew(1) , chew(2) and chew(3) ). here, a comprehensive approach is utilized to investigate the roles of the three chews in chemotaxis of b. burgdorferi. first, genetic studies indicated that both the chew(1) and chew(3) genes ... | 2012 | 22780444 |
| borrelia burgdorferi needs chemotaxis to establish infection in mammals and to accomplish its enzootic cycle. | borrelia burgdorferi, the causative agent of lyme disease, can be recovered from different organs of infected animals and patients, indicating that the spirochete is very invasive. motility and chemotaxis contribute to the invasiveness of b. burgdorferi and play important roles in the process of the disease. recent reports have shown that motility is required for establishing infection in mammals. however, the role of chemotaxis in virulence remains elusive. our previous studies showed that chea ... | 2012 | 22508862 |
| bactquant: an enhanced broad-coverage bacterial quantitative real-time pcr assay. | bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. based on our analysis of a diverse collection of 16 s rrna gene sequences, we designed a broad-coverage quantitative real-time pcr (qpcr) assay--bactquant--for quantifying 16 s rrna gene copy number and estimating bacterial load. we further utilized in silico evaluation to complement laboratory-based qpcr characte ... | 2012 | 22510143 |
| development of a modified gentamicin resistance cassette for genetic manipulation of the oral spirochete treponema denticola. | herein, we report that a modified gentamicin cassette and a pcr-based method can be used for targeted mutagenesis of the oral spirochete treponema denticola. this approach minimizes polar effects and spontaneous antibiotic resistance. therefore, it can serve as a reliable tool for genetic manipulation of t. denticola. | 2012 | 22247130 |
| structure of factor h-binding protein b (fhbb) of the periopathogen, treponema denticola: insights into progression of periodontal disease. | periodontitis is the most common disease of microbial etiology in humans. periopathogen survival is dependent upon evasion of complement-mediated destruction. treponema denticola, an important contributor to periodontitis, evades killing by the alternative complement cascade by binding factor h (fh) to its surface. bound fh is rapidly cleaved by the t. denticola protease, dentilisin. in this report, the structure of the t. denticola fh-binding protein, fhbb, was solved to 1.7 å resolution. fhbb ... | 2012 | 22371503 |
| the unique paradigm of spirochete motility and chemotaxis. | spirochete motility is enigmatic: it differs from the motility of most other bacteria in that the entire bacterium is involved in translocation in the absence of external appendages. using the lyme disease spirochete borrelia burgdorferi (bb) as a model system, we explore the current research on spirochete motility and chemotaxis. bb has periplasmic flagella (pfs) subterminally attached to each end of the protoplasmic cell cylinder, and surrounding the cell is an outer membrane. these internal h ... | 2012 | 22994496 |
| sequence, biophysical, and structural analyses of the psts lipoprotein (bb0215) from borrelia burgdorferi reveal a likely binding component of an abc-type phosphate transporter. | the lyme disease agent borrelia burgdorferi, which is transmitted via a tick vector, is dependent on its tick and mammalian hosts for a number of essential nutrients. like other bacterial diderms, it must transport these biochemicals from the extracellular milieu across two membranes, ultimately to the b. burgdorferi cytoplasm. in the current study, we established that a gene cluster comprising genes bb0215 through bb0218 is cotranscribed and is therefore an operon. sequence analysis of these pr ... | 2013 | 24318969 |
| sequence, biophysical, and structural analyses of the psts lipoprotein (bb0215) from borrelia burgdorferi reveal a likely binding component of an abc-type phosphate transporter. | the lyme disease agent borrelia burgdorferi, which is transmitted via a tick vector, is dependent on its tick and mammalian hosts for a number of essential nutrients. like other bacterial diderms, it must transport these biochemicals from the extracellular milieu across two membranes, ultimately to the b. burgdorferi cytoplasm. in the current study, we established that a gene cluster comprising genes bb0215 through bb0218 is cotranscribed and is therefore an operon. sequence analysis of these pr ... | 2013 | 24318969 |
| viscous dynamics of lyme disease and syphilis spirochetes reveal flagellar torque and drag. | the spirochetes that cause lyme disease (borrelia burgdorferi) and syphilis (treponema pallidum) swim through viscous fluids, such as blood and interstitial fluid, by undulating their bodies as traveling, planar waves. these undulations are driven by rotation of the flagella within the periplasmic space, the narrow (∼20-40 nm in width) compartment between the inner and outer membranes. we show here that the swimming speeds of b. burgdorferi and t. pallidum decrease with increases in viscosity of ... | 2013 | 24268139 |
| use of nonelectrolytes reveals the channel size and oligomeric constitution of the borrelia burgdorferi p66 porin. | in the lyme disease spirochete borrelia burgdorferi, the outer membrane protein p66 is capable of pore formation with an atypical high single-channel conductance of 11 ns in 1 m kcl, which suggested that it could have a larger diameter than 'normal' gram-negative bacterial porins. we studied the diameter of the p66 channel by analyzing its single-channel conductance in black lipid bilayers in the presence of different nonelectrolytes with known hydrodynamic radii. we calculated the filling of th ... | 2013 | 24223145 |
| nlrp3 inflammasome and host protection against bacterial infection. | the inflammasome is a multi-protein complex that induces maturation of inflammatory cytokines interleukin (il)-1β and il-18 through activation of caspase-1. several nucleotide binding oligomerization domain-like receptor family members, including nlrp3, recognize unique microbial and danger components and play a central role in inflammasome activation. the nlrp3 inflammasome is critical for maintenance of homeostasis against pathogenic infections. however, inflammasome activation acts as a doubl ... | 2013 | 24133343 |
| inactivation of cyclic di-gmp binding protein tde0214 affects the motility, biofilm formation, and virulence of treponema denticola. | as a ubiquitous second messenger, cyclic dimeric gmp (c-di-gmp) has been studied in numerous bacteria. the oral spirochete treponema denticola, a periodontal pathogen associated with human periodontitis, has a complex c-di-gmp signaling network. however, its function remains unexplored. in this report, a pilz-like c-di-gmp binding protein (tde0214) was studied to investigate the role of c-di-gmp in the spirochete. tde0214 harbors a pilz domain with two signature motifs: rxxxr and dxsxxg. biochem ... | 2013 | 23794624 |
| porphyromonas gingivalis and treponema denticola synergistic polymicrobial biofilm development. | chronic periodontitis has a polymicrobial biofilm aetiology and interactions between key bacterial species are strongly implicated as contributing to disease progression. porphyromonas gingivalis, treponema denticola and tannerella forsythia have all been implicated as playing roles in disease progression. p. gingivalis cell-surface-located protease/adhesins, the gingipains, have been suggested to be involved in its interactions with several other bacterial species. the aims of this study were t ... | 2013 | 23990979 |
| manganese and zinc regulate virulence determinants in borrelia burgdorferi. | borrelia burgdorferi, the causative agent of lyme disease, must adapt to two diverse niches, an arthropod vector and a mammalian host. rpos, an alternative sigma factor, plays a central role in spirochetal adaptation to the mammalian host by governing expression of many genes important for mammalian infection. b. burgdorferi is known to be unique in metal utilization, and little is known of the role of biologically available metals in b. burgdorferi. here, we identified two transition metal ions ... | 2013 | 23690398 |
| a phylogenomic and molecular signature based approach for characterization of the phylum spirochaetes and its major clades: proposal for a taxonomic revision of the phylum. | the spirochaetes species cause many important diseases including syphilis and lyme disease. except for their containing a distinctive endoflagella, no other molecular or biochemical characteristics are presently known that are specific for either all spirochaetes or its different families. we report detailed comparative and phylogenomic analyses of protein sequences from spirochaetes genomes to understand their evolutionary relationships and to identify molecular signatures for this group. these ... | 2013 | 23908650 |
| improved culture conditions for the growth and detection of borrelia from human serum. | in this report we present a method to cultivate borrelia spirochetes from human serum samples with high efficiency. this method incorporates improved sample collection, optimization of culture media and use of matrix protein. the method was first optimized utilizing borrelia laboratory strains, and later by demonstrating growth of borrelia from sera from fifty seropositive lyme disease patients followed by another cohort of 72 lyme disease patients, all of whom satisfied the strict cdc surveilla ... | 2013 | 23470960 |
| evidence for an abc-type riboflavin transporter system in pathogenic spirochetes. | bacterial transporter proteins are involved in the translocation of many essential nutrients and metabolites. however, many of these key bacterial transport systems remain to be identified, including those involved in the transport of riboflavin (vitamin b(2)). pathogenic spirochetes lack riboflavin biosynthetic pathways, implying reliance on obtaining riboflavin from their hosts. using structural and functional characterizations of possible ligand-binding components, we have identified an abc-t ... | 2013 | 23404400 |
| structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of treponema pallidum and treponema paraluiscuniculi strains. | this study examined the sequences of the two rrna (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of t. pallidum ssp. pallidum (tpa), five strains of t. pallidum ssp. pertenue (tpe), two strains of t. pallidum ssp. endemicum (ten), a simian fribourg-blanc strain and a rabbit t. paraluiscuniculi (tpc) strain. pcr was used to determine the type of 16s-23s ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. whe ... | 2013 | 23082031 |
| association of spirochetal infection with morgellons disease. | morgellons disease (md) is an emerging multisystem illness characterized by skin lesions with unusual filaments embedded in or projecting from epithelial tissue. filament formation results from abnormal keratin and collagen expression by epithelial-based keratinocytes and fibroblasts. recent research comparing md to bovine digital dermatitis, an animal infectious disease with similar skin features, provided clues that spirochetal infection could play an important role in the human disease as it ... | 2013 | 24715950 |
| sensitive real-time pcr detection of pathogenic leptospira spp. and a comparison of nucleic acid amplification methods for the diagnosis of leptospirosis. | bacteria of the genus leptospira, the causative agents of leptospirosis, are categorized into pathogenic and non-pathogenic species. however, the benefit of using a clinical diagnostic that is specific for pathogenic species remains unclear. in this study, we present the development of a real-time pcr (rtpcr) for the detection of pathogenic leptospira (the pathogenic rtpcr), and we perform a comparison of the pathogenic rtpcr with a published assay that detects all leptospira species [the undiff ... | 2014 | 25379890 |
| collection and characterization of samples for establishment of a serum repository for lyme disease diagnostic test development and evaluation. | serological assays and a two-tiered test algorithm are recommended for laboratory confirmation of lyme disease. in the united states, the sensitivity of two-tiered testing using commercially available serology-based assays is dependent on the stage of infection and ranges from 30% in the early localized disease stage to near 100% in late-stage disease. other variables, including subjectivity in reading western blots, compliance with two-tiered recommendations, use of different first- and second- ... | 2014 | 25122862 |
| metagenomic analysis reveals presence of treponema denticola in a tissue biopsy of the iceman. | ancient hominoid genome studies can be regarded by definition as metagenomic analyses since they represent a mixture of both hominoid and microbial sequences in an environment. here, we report the molecular detection of the oral spirochete treponema denticola in ancient human tissue biopsies of the iceman, a 5,300-year-old copper age natural ice mummy. initially, the metagenomic data of the iceman's genomic survey was screened for bacterial ribosomal rna (rrna) specific reads. through ranking th ... | 2014 | 24941044 |
| initial characterization of the flge hook high molecular weight complex of borrelia burgdorferi. | the spirochete periplasmic flagellum has many unique attributes. one unusual characteristic is the flagellar hook. this structure serves as a universal joint coupling rotation of the membrane-bound motor to the flagellar filament. the hook is comprised of about 120 flge monomers, and in most bacteria these structures readily dissociate to monomers (∼ 50 kda) when treated with heat and detergent. however, in spirochetes the flge monomers form a large mass of over 250 kda [referred to as a high mo ... | 2014 | 24859001 |
| superoxide dismutases and superoxide reductases. | | 2014 | 24684599 |
| membrane lipids in agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis. | many cellular processes critically depend on the membrane composition. in this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen agrobacterium tumefaciens. the major components of a. tumefaciens membranes are the phospholipids (pls), phosphatidylethanolamine (pe), phosphatidylglycerol, phosphatidylcholine (pc) and cardiolipin, and ornithine lipids (ols). under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipid ... | 2014 | 24723930 |
| expression of alzheimer-type neurofibrillary epitopes in primary rat cortical neurons following infection with enterococcus faecalis. | the neurofibrillary tau pathology and amyloid deposits seen in alzheimer's disease (ad) also have been seen in bacteria-infected brains. however, few studies have examined the role of these bacteria in the generation of tau pathology. one suggested link between infection and ad is edentulism, the complete loss of teeth. edentulism can result from chronic periodontal disease due to infection by enterococcus faecalis. the current study assessed the ability to generate early alzheimer-like neurofib ... | 2015 | 26834627 |
| expression of alzheimer-type neurofibrillary epitopes in primary rat cortical neurons following infection with enterococcus faecalis. | the neurofibrillary tau pathology and amyloid deposits seen in alzheimer's disease (ad) also have been seen in bacteria-infected brains. however, few studies have examined the role of these bacteria in the generation of tau pathology. one suggested link between infection and ad is edentulism, the complete loss of teeth. edentulism can result from chronic periodontal disease due to infection by enterococcus faecalis. the current study assessed the ability to generate early alzheimer-like neurofib ... | 2015 | 26834627 |
| intestinal spirochaetes (genus brachyspira) colonise wild birds in the southern atlantic region and antarctica. | the genus brachyspira contains well-known enteric pathogens of veterinary significance, suggested agents of colonic disease in humans, and one potentially zoonotic agent. there are recent studies showing that brachyspira are more widespread in the wildlife community than previously thought. there are no records of this genus in wildlife from the southern atlantic region and antarctica. our aim was therefore, to determine whether intestinal spirochaetes of genus brachyspira colonise marine and co ... | 2015 | 26584828 |
| spirochetal motility and chemotaxis in the natural enzootic cycle and development of lyme disease. | two-thirds of all bacterial genomes sequenced to-date possess an organelle for locomotion, referred to as flagella, periplasmic flagella or type iv pili. these genomes may also contain a chemotaxis-signaling system which governs flagellar rotation, thus leading a coordinated function for motility. motility and chemotaxis are often crucial for infection or disease process caused by pathogenic bacteria. although motility-associated genes are well-characterized in some organisms, the highly orchest ... | 2015 | 26519910 |
| flagellar motility of the pathogenic spirochetes. | bacterial pathogens are often classified by their toxicity and invasiveness. the invasiveness of a given bacterium is determined by how capable the bacterium is at invading a broad range of tissues in its host. of mammalian pathogens, some of the most invasive come from a group of bacteria known as the spirochetes, which cause diseases, such as syphilis, lyme disease, relapsing fever and leptospirosis. most of the spirochetes are characterized by their distinct shapes and unique motility. they a ... | 2015 | 26481969 |
| brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics. | the genus brachyspira currently encompasses seven valid species that colonize the intestines of mammals and birds. in a previous study a group of strongly haemolytic isolates from pigs and mallards was provisionally described as a new species within genus brachyspira, "b. suanatina", and enteropathogenic properties were demonstrated in a porcine challenge model. | 2015 | 26458507 |
| can oral infection be a risk factor for alzheimer's disease? | alzheimer's disease (ad) is a scourge of longevity that will drain enormous resources from public health budgets in the future. currently, there is no diagnostic biomarker and/or treatment for this most common form of dementia in humans. ad can be of early familial-onset or sporadic with a late-onset. apart from the two main hallmarks, amyloid-beta and neurofibrillary tangles, inflammation is a characteristic feature of ad neuropathology. inflammation may be caused by a local central nervous sys ... | 2015 | 26385886 |
| individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology. | for bacteria, replication mainly involves growth by binary fission. however, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. they thereby evade detection by conventional culture-based methods. such dormant cells may also be observed in laboratory cultures and in clinical microbiology. they are usually more tolerant to s ... | 2015 | 26629334 |
| digital dermatitis in dairy cows: a review of risk factors and potential sources of between-animal variation in susceptibility. | digital dermatitis (dd) is a bacterial disease that primarily affects the skin on the heels of cattle. it is a major cause of lameness in dairy cows and a significant problem for the dairy industry in many countries, causing reduced animal welfare and economic loss. a wide range of infection levels has been found on infected farms, prompting investigations into both farm level and animal level risk factors for dd occurrence. there also appears to be individual variation between animals in suscep ... | 2015 | 26479371 |
| association between periodontitis and alzheimer's disease. | alzheimer's disease (ad) is a neurodegenerative disease which significantly increases with age. its onset can be either early or late. ad is characterized by the salient inflammatory features, microglial activation, and increased levels of proinflammatory cytokines which contribute to the inflammatory status of the central nervous system (cns). whereas, periodontitis is a common oral infection associated with the gram negative anaerobic bacteria. periodontitis can be marked as a "low-grade syste ... | 2015 | 26199919 |
| complement system part ii: role in immunity. | the complement system has been considered for a long time as a simple lytic cascade, aimed to kill bacteria infecting the host organism. nowadays, this vision has changed and it is well accepted that complement is a complex innate immune surveillance system, playing a key role in host homeostasis, inflammation, and in the defense against pathogens. this review discusses recent advances in the understanding of the role of complement in physiology and pathology. it starts with a description of com ... | 2015 | 26074922 |