| nonpigmented chromobacterium violaceum bacteremic cellulitis after fish bite. | a case of nonpigmented chromobacterium violaceum bacteremic cellulitis after fish bite in taiwan is reported. the patient was successfully treated with ciprofloxacin and doxycycline for an extended period. chromobacterium violaceum should be listed in the differential diagnosis of patients with nonspecific cellulitis associated with marked leukocytosis and rapid progression to septicemia either with or without a distinct history of exposure to water or soil. a combination of prompt diagnosis, op ... | 2011 | 21524969 |
| functional consequences of t-stem mutations in e. coli trnathrugu in vitro and in vivo. | the binding affinities between escherichia coli ef-tu and 34 single and double base-pair changes in the t stem of e. coli trna(thr)(ugu) were compared with similar data obtained previously for several aa-trnas binding to thermus thermophilus ef-tu. with a single exception, the two proteins bound to mutations in three t-stem base pairs in a quantitatively identical manner. however, trna(thr) differs from other trnas by also using its rare a52-c62 pair as a negative specificity determinant. using ... | 2011 | 21527672 |
| a bacterial sub-family of luxr regulators that respond to plant compounds. | pseudomonas fluorescens are rhizobacteria known for their biocontrol properties; several antimicrobial functions are crucial for this process; experiments here investigate the modulation of their expression during the plant-bacterial interaction. the role of a luxr family regulator in interkingdom signalling has been investigated using genome-scale transcriptome analysis, gene promoter studies in vivo and in vitro, biocontrol assays and response to plant compounds. psor, a luxr solo or orphan re ... | 2011 | 21531826 |
| immunomodulatory and protective roles of quorum sensing signaling molecules n-acyl homoserine lactones during infection of mice with aeromonas hydrophila. | aeromonas hydrophila leads to both intestinal and extra-intestinal infections in animals and humans, and the underlying mechanisms leading to mortality are largely unknown. by using a septicemic mouse model of infection, we showed that animals challenged with a. hydrophila die because of kidney and liver damage, hypoglycemia, and thrombocytopenia. pretreatment of animals with quorum sensing-associated signaling molecules n-acyl homoserine lactones (ahls), such as butanoyl and hexanoyl homoserine ... | 2011 | 21536794 |
| pseudomonas aeruginosa biofilm inactivation: decreased cell culturability, adhesiveness to surfaces, and biofilm thickness upon high-pressure nonthermal plasma treatment. | bacterial biofilms are more resilient to standard killing methods than free-living bacteria. pseudomonas aeruginosa pao1 biofilms grown on borosilicate coupons were treated with gas-discharge plasma for various exposure times. almost 100% of the cells were inactivated after a 5-min plasma exposure. atomic force microscopy was used to image the biofilms and study their micromechanical properties. results show that the adhesiveness to borosilicate and the thickness of the pseudomonas biofilms are ... | 2010 | 21544254 |
| anaerobiosis-induced loss of cytotoxicity is due to inactivation of quorum sensing in pseudomonas aeruginosa. | pseudomonas aeruginosa, an opportunistic pathogen of clinical importance, causes chronic airway infections in patients with cystic fibrosis (cf). current literature suggests that pockets with reduced oxygen tension exist in the cf airway mucus. however, virulence features of this opportunistic pathogen under such conditions are largely unknown. cell-free supernatant of the standard laboratory p. aeruginosa strain pao1 obtained from anaerobic culture, but not aerobic culture, failed to kill a549 ... | 2011 | 21555402 |
| distribution of n-acylhomoserine lactone-producing fluorescent pseudomonads in the phyllosphere and rhizosphere of potato (solanum tuberosum l.). | four hundred and fifty nine isolates of fluorescent pseudomonads were obtained from the leaves and roots of potato plants. of these, 20 leaf isolates and 28 root isolates induced violacein production in two n-acylhomoserine lactone (ahl)-reporter strains-chromobacterium violaceum cv026 and vir24. vir24 is a new reporter strain for long n-acyl-chain-homoserine lactones, which can not be detected by cv026. thin-layer chromatography revealed that the isolates produced multiple ahl molecules. we com ... | 2009 | 21566390 |
| cellular and molecular action of the mitogenic protein-deamidating toxin from pasteurella multocida. | the mitogenic toxin from pasteurella multocida (pmt) is a member of the dermonecrotic toxin family, which includes toxins from bordetella, escherichia coli and yersinia. members of the dermonecrotic toxin family modulate g-protein targets in host cells through selective deamidation and/or transglutamination of a critical active site gln residue in the g-protein target, which results in the activation of intrinsic gtpase activity. structural and biochemical data point to the uniqueness of pmt amo ... | 2011 | 21569202 |
| crystal structure of the bifunctional trna modification enzyme mnmc from escherichia coli. | post-transcriptional modifications of bases within the transfer rnas (trna) anticodon significantly affect the decoding system. in bacteria and eukaryotes, uridines at the wobble position (u34) of some trnas are modified to 5-methyluridine derivatives (xm(5) u). these xm(5) u34-containing trnas read codons ending with a or g, whereas trnas with the unmodified u34 are able to read all four synonymous codons of a family box. in escherichia coli (e.coli), the bifunctional enzyme mnmc catalyzes the ... | 2011 | 21574198 |
| romidepsin (istodax, nsc 630176, fr901228, fk228, depsipeptide): a natural product recently approved for cutaneous t-cell lymphoma. | romidepsin (istodax), a selective inhibitor of histone deacetylases (hdacs), was approved for the treatment of cutaneous t-cell lymphoma in november 2009 by the us food and drug administration. this unique natural product was discovered from cultures of chromobacterium violaceum, a gram-negative bacterium isolated from a japanese soil sample. this bicyclic compound acts as a prodrug, its disulfide bridge being reduced by glutathione on uptake into the cell, allowing the free thiol groups to inte ... | 2011 | 21587264 |
| metabolism as a key to histone deacetylase inhibition. | there is growing interest in the epigenetic mechanisms that are dysregulated in cancer and other human pathologies. under this broad umbrella, modulators of histone deacetylase (hdac) activity have gained interest as both cancer chemopreventive and therapeutic agents. of the first generation, fda-approved hdac inhibitors to have progressed to clinical trials, vorinostat represents a "direct acting" compound with structural features suitable for docking into the hdac pocket, whereas romidepsin ca ... | 2011 | 21599534 |
| biochemical and localization analyses of putative type iii secretion translocator proteins copb and copb2 of chlamydia trachomatis reveal significant distinctions. | chlamydia spp. are among the many pathogenic gram-negative bacteria that employ a type iii secretion system to overcome host defenses and exploit available resources. significant progress has been made in elucidating contributions of t3s to the pathogenesis of these medically important, obligate intracellular parasites, yet important questions remain. chief among these is how secreted effector proteins traverse eukaryotic membranes to gain access to the host cytosol. due to a complex development ... | 2011 | 21606186 |
| identification of phenylalanine 3-hydroxylase for meta-tyrosine biosynthesis. | phenylalanine hydroxylase (pheh) is an iron(ii)-dependent enzyme that catalyzes the hydroxylation of aromatic amino acid l-phenylalanine (l-phe) to l-tyrosine (l-tyr). the enzymatic modification has been demonstrated to be highly regiospecific, forming proteinogenic para-tyr (p-tyr) exclusively. here we biochemically characterized the first example of a phenylalanine 3-hydroxylase (phe3h) that catalyzes the synthesis of meta-tyr (m-tyr) from phe. subsequent mutagenesis studies revealed that two ... | 2011 | 21615132 |
| regulation of lectin production by the human pathogens pseudomonas aeruginosa and chromobacterium violaceum: effects of choline, trehalose, and ethanol. | | 2011 | 21618111 |
| quorum sensing in chromobacterium violaceum: dna recognition and gene regulation by the cvir receptor. | the bacterial pathogen chromobacterium violaceum uses a luxir-type quorum-sensing system to detect and respond to changes in cell population density. cvii synthesizes the autoinducer c10-homoserine lactone (c10-hsl) and cvir is a cytoplasmic dna binding transcription factor that activates gene expression following binding to c10-hsl. a number of behaviors are controlled by quorum sensing in c. violaceum. however, few genes have been shown to be directly controlled by cvir, in part because the dn ... | 2011 | 21622734 |
| chronic granulomatous disease: a review of the infectious and inflammatory complications. | abstract: chronic granulomatous disease is the most commonly encountered immunodeficiency involving the phagocyte, and is characterized by repeated infections with bacterial and fungal pathogens, as well as the formation of granulomas in tissue. the disease is the result of a disorder of the nadph oxidase system, culminating in an inability of the phagocyte to generate superoxide, leading to the defective killing of pathogenic organisms. this can lead to infections with staphylococcus aureus, ps ... | 2011 | 21624140 |
| physiological traits of the symbiotic bacterium teredinibacter turnerae isolated from the mangrove shipworm neoteredo reynei. | nutrition in the teredinidae family of wood-boring mollusks is sustained by cellulolytic/nitrogen fixing symbiotic bacteria of the teredinibacter clade. the mangrove teredinidae neoteredo reynei is popularly used in the treatment of infectious diseases in the north of brazil. in the present work, the symbionts of n. reynei, which are strictly confined to the host's gills, were conclusively identified as teredinibacter turnerae. symbiont variants obtained in vitro were able to grow using casein a ... | 2009 | 21637522 |
| computational analysis suggests that virulence of chromobacterium violaceum might be linked to biofilm formation and poly-nag biosynthesis. | groups of genes that produce exopolysaccharide with a n-acetyl-d-glucosamine monomer are in the genome of several pathogenic bacteria. chromobacterium violaceum, an opportunistic pathogen, has the operon hmshfr-cv2940, whose proteins can synthesize such polysaccharide. in this work, multiple alignments among proteins from bacteria that synthesize such polysaccharide were used to verify the existence of amino acids that might be critical for pathogen activity. three-dimensional models were genera ... | 2009 | 21637531 |
| multiple loci are involved in quorum quenching of autoinducer i molecules in the nitrogen-fixing symbiont (sino-) rhizobium sp. ngr234. | rhizobium sp. ngr234 is a unique α-proteobacterium (order - rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other micro-symbiont. since we have previously described the complete genome sequence of ngr234, we now report on a genome wide functional analysis of the genes and enzymes involved in autoinducer i hydrolysis in this microbe. altogether we identified five cosmid clones that repeatedly gave a positive result in our function-based approach for the detection of aut ... | 2011 | 21642401 |
| definition of microbial diversity in aeromonas strains based on multilocus sequence typing, phenotype and presence of putative genes of virulence. | the genus aeromonas has been described as comprising several species associated with the aquatic environment that represents their principal reservoir. aeromonas is commonly isolated from diseased and healthy fish, but the involvement of such bacteria in human infection and gastroenteritis has frequently been reported. the primary challenge in establishing an unequivocal link between the aeromonas genus and pathogenesis in humans is the extremely complicated taxonomy. with the aim of clarifying ... | 2011 | 21642403 |
| folding dynamics of phenylalanine hydroxylase depends on the enzyme's metallation state: the native metal, iron, protects against aggregate intermediates. | phenylalanine hydroxylase (pah), a non-heme iron enzyme, is responsible for the phenylalanine conversion to tyrosine. its malfunction causes phenylketonuria (pku). to better understand how protein structure and folding profiles are affected by the metal cofactor, we investigated the chemical (un)folding of apo- and holo-pah from chromobacterium violaceum (cpah) using circular dichroism (cd) and analytical ultracentrifugation (auc). holo-cpah shows a two-state unfolding transition. in contrast, t ... | 2011 | 21647679 |
| extreme antimicrobial peptide and polymyxin b resistance in the genus burkholderia. | cationic antimicrobial peptides and polymyxins are a group of naturally occurring antibiotics that can also possess immunomodulatory activities. they are considered a new source of antibiotics for treating infections by bacteria that are resistant to conventional antibiotics. members of the genus burkholderia, which includes various human pathogens, are inherently resistant to antimicrobial peptides. the resistance is several orders of magnitude higher than that of other gram-negative bacteria s ... | 2011 | 21811491 |
| thiolactone modulators of quorum sensing revealed through library design and screening. | quorum sensing (qs) is a process by which bacteria use small molecules or peptidic signals to assess their local population densities. at sufficiently high density, bacteria can alter gene expression levels to regulate group behaviors involved in a range of important and diverse phenotypes, including virulence factor production, biofilm formation, root nodulation, and bioluminescence. gram-negative bacteria most commonly use n-acylated l-homoserine lactones (ahls) as their qs signals. the ahl la ... | 2011 | 21798746 |
| thailandepsins: bacterial products with potent histone deacetylase inhibitory activities and broad-spectrum antiproliferative activities. | histone deacetylase (hdac) inhibitors have emerged as a new class of anticancer drugs, with one synthetic compound, saha (vorinostat, zolinza; 1), and one natural product, fk228 (depsipeptide, romidepsin, istodax; 2), approved by fda for clinical use. our studies of fk228 biosynthesis in chromobacterium violaceum no. 968 led to the identification of a cryptic biosynthetic gene cluster in the genome of burkholderia thailandensis e264. genome mining and genetic manipulation of this gene cluster fu ... | 2011 | 21793558 |
| the antiproliferative function of violacein-like purple violet pigment (pvp) from an antarctic janthinobacterium sp. ant5-2 in uv-induced 2237 fibrosarcoma. | background in this study, we have investigated the chemotherapeutic potential of a purple violet pigment (pvp), which was isolated from a previously undescribed antarctic janthinobacterium sp. (ant5-2), against murine uv-induced 2237 fibrosarcoma and b16f10 melanoma cells. methods the 2237, b16f10, c50, and nih3t3 cells were treated with pvp at different doses and for different times, and their proliferation and viability were detected by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium br ... | 2011 | 21790550 |
| characterisation of an n-acetylmuramic acid/n-acetylglucosamine kinase of clostridium acetobutylicum. | here, we report the cloning and characterisation of a cytoplasmic kinase of clostridium acetobutylicum, named murk (for murein sugar kinase). the enzyme has a unique specificity for both amino sugars of the bacterial cell wall, n-acetylmuramic acid (murnac) and n-acetylglucosamine (glcnac), which are phosphorylated at the 6-hydroxyl group. kinetic analyses revealed k(m)values of 190 and 127 µm for murnac and glcnac, respectively, and a k(cat) value (65.0 sec(-1)) that was 1.5 fold higher for the ... | 2011 | 21784936 |
| violacein and related tryptophan metabolites produced by chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core. | violacein is a natural violet pigment produced by several gram-negative bacteria, including chromobacterium violaceum, janthinobacterium lividum, and pseudoalteromonas tunicata d2, among others. this pigment has potential medical applications as antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs. the structure of violacein consists of three units: a 5-hydroxyindole, an oxindole, and a 2-pyrrolidone. the biosynthetic origins of hydrogen, nitrogen, and carbon in the pyrrolido ... | 2011 | 21779844 |
| inhibiting effect of bioactive metabolites produced by mushroom cultivation on bacterial quorum sensing-regulated behaviors. | aims: this study aimed to search for novel quorum sensing (qs) inhibitors from mushroom and to analyze their inhibitory activity, with a view to their possible use in controlling detrimental infections. methods: the bioactive metabolites produced by mushroom cultivation were tested for their abilities to inhibit qs-regulated behavior. all mushroom strains were cultivated in potato-dextrose medium by large-scale submerged fermentation. the culture supernatant was condensed into 0.2 vol by freeze- ... | 2011 | 21778717 |
| environmental adaptability and stress tolerance of laribacter hongkongensis: a genome-wide analysis. | | 2011 | 21711489 |
| the chlamydial type iii secretion mechanism: revealing cracks in a tough nut. | present-day members of the chlamydiaceae contain parasitic bacteria that have been co-evolving with their eukaryotic hosts over hundreds of millions of years. likewise, a type iii secretion system encoded within all genomes has been refined to complement the unique obligate intracellular niche colonized so successfully by chlamydia spp. all this adaptation has occurred in the apparent absence of the horizontal gene transfer responsible for creating the wide range of diversity in other gram-negat ... | 2010 | 21738522 |
| identification of xanthomonas fragariae, xanthomonas axonopodis pv. phaseoli, and xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis. | phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. dna-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. the genus xanthomonas includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. in this work, we propose 21 new xa ... | 2011 | 21705524 |
| virulence determinants, drug resistance and mobile genetic elements of laribacter hongkongensis: a genome-wide analysis. | | 2011 | 21711902 |
| genetic diversity study of chromobacterium violaceum isolated from kolli hills by amplified ribosomal dna restriction analysis (ardra) and random amplified polymorphic dna (rapd). | aim:ôçé chromobacterium are saprophytes that cause highly fatal opportunistic infections. identification and strain differentiation were performed to identify the strain variability among the environmental samples. we have evaluated the suitability of individual and combined methods to detect the strain variations of the samples collected in different seasons. methods and results:ôçé amplified ribosomal dna restriction analysis (ardra) and random amplified polymorphic dna (rapd) profiles were ob ... | 2011 | 21726246 |
| quorum sensing and bacterial pathogenicity: from molecules to disease. | quorum sensing in prokaryotic biology refers to the ability of a bacterium to sense information from other cells in the population when they reach a critical concentration (i.e. a quorum) and communicate with them. the "language" used for this intercellular communication is based on small, self-generated signal molecules called as autoinducers. quorum sensing is thought to afford pathogenic bacteriaa mechanism to minimize host immune responses by delaying theproduction of tissue-damaging virulen ... | 2011 | 21701655 |
| general metabolism of laribacter hongkongensis: a genome-wide analysis. | | 2011 | 21711917 |
| transcription analysis of a lantibiotic gene cluster from bifidobacterium longum djo10a. | bifidobacterium longum djo10a was previously demonstrated to produce a lantibiotic, but only during growth on agar media. to evaluate the feasibility of production of this lantibiotic in broth media, a transcription analysis of the lana gene was undertaken. comparative microarray analysis of broth and agar cultures of b. longum djo10a revealed that the lantibiotic production, modification, transport/peptidase, and immunity genes were significantly upregulated in agar cultures, while the two-comp ... | 2011 | 21742926 |
| plasmid encoded antibiotics inhibit protozoan predation of escherichia coli k12. | bacterial plasmids and phages encode the synthesis of toxic molecules that inhibit protozoan predation. one such toxic molecule is violacein, a purple pigmented, anti-tumour antibiotic produced by the gram-negative soil bacterium chromobacterium violaceum. in the current experiments a range of escherichia coli k12 strains were genetically engineered to produce violacein and a number of its coloured, biosynthetic intermediates. a bactivorous predatory protozoan isolate, colpoda sp.a4, was isolate ... | 2011 | 21839110 |
| microbial survival in space shuttle crash. | a slow growing, heat resistant bacterium, identified by 16s rrna gene sequencing as microbispora sp., was recovered from the wreckage of the ill-fated space shuttle columbia (sts-107). as this organism survived disintegration of the space craft, heat of reentry, and impact, it supports the possibility of a natural mechanism for the interplanetary spread of life by meteorites. | 2006 | 21804644 |
| Sharing of quorum-sensing signals and role of interspecies communities in a bacterial plant disease. | Pathogenic bacteria interact not only with the host organism but most probably also with the resident microbial flora. In the knot disease of the olive tree (Olea europaea), the causative agent is the bacterium Pseudomonas savastanoi pv. savastanoi (Psv). Two bacterial species, namely Pantoea agglomerans and Erwinia toletana, which are not pathogenic and are olive plant epiphytes and endophytes, have been found very often to be associated with the olive knot. We identified the chemical signals t ... | 2011 | 21677694 |
| Draft genome sequence of the biocontrol bacterium Chromobacterium sp. strain C-61. | Chromobacterium sp. strain C-61 is a plant-associated bacterium with proven capacities to suppress plant diseases. Here, we report the draft genome sequence and automatic annotation of strain C-61. A comparison of this sequence to the sequenced genome of Chromobacterium violaceum ATCC 12472 indicates the novelty of C-61 and a subset of gene functions that may be related to its biocontrol activities. | 2011 | 22072653 |
| Histone deacetylase inhibitors from Burkholderia thailandensis. | Bioactivity-guided fractionation of an extract of Burkholderia thailandensis led to the isolation and identification of a new cytotoxic depsipeptide and its dimer. Both compounds potently inhibited the function of histone deacetylases 1 and 4. The monomer, spiruchostatin C (2), was tested side by side with the clinical depsipeptide FK228 (1, Istodax, romidepsin) in a murine hollow fiber assay consisting of 12 implanted tumor cell lines. Spiruchostatin C (2) showed good activity toward LOX IMVI ... | 2011 | 21967146 |
| glygly-cterm and rhombosortase: a c-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. | the rhomboid family of serine proteases occurs in all domains of life. its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. the model member glpg from escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple x-ray crystal studies, yet its relationship to endogenous substrates is not well understood. here we describe an apparent membr ... | 2011 | 22194940 |
| chromobacterium violaceum infection: a clinical review of an important but neglected infection. | increasing reported cases with chrombacterium violaceum infection has been noticed in recent decades. it is noteworthy for its difficult-to-treat entity characterized by a high frequency of sepsis, easily distantant metastasis, multidrug-resistance, and frequent relapse, and high mortality rate. | 2011 | 22036134 |
| identification of a new gene required for the biosynthesis of rhodoquinone in rhodospirillum rubrum. | rhodoquinone (rq) is a required cofactor for anaerobic respiration in rhodospirillum rubrum, and it is also found in several helminth parasites that utilize a fumarate reductase pathway. rq is an aminoquinone that is structurally similar to ubiquinone (q), a polyprenylated benzoquinone used in the aerobic respiratory chain. rq is not found in humans or other mammals, and therefore inhibition of its biosynthesis may provide a novel anti-parasitic drug target. to identify a gene specifically requi ... | 2011 | 22194448 |
| The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. | As obligate symbionts of most land plants, arbuscular mycorrhizal fungi (AMF) have a crucial role in ecosystems, but to date, in the absence of genomic data, their adaptive biology remains elusive. In addition, endobacteria are found in their cytoplasm, the role of which is unknown. In order to investigate the function of the Gram-negative Candidatus Glomeribacter gigasporarum, an endobacterium of the AMF Gigaspora margarita, we sequenced its genome, leading to an ~1.72-Mb assembly. Phylogenetic ... | 2012 | 21866182 |
| The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. | As obligate symbionts of most land plants, arbuscular mycorrhizal fungi (AMF) have a crucial role in ecosystems, but to date, in the absence of genomic data, their adaptive biology remains elusive. In addition, endobacteria are found in their cytoplasm, the role of which is unknown. In order to investigate the function of the Gram-negative Candidatus Glomeribacter gigasporarum, an endobacterium of the AMF Gigaspora margarita, we sequenced its genome, leading to an ~1.72-Mb assembly. Phylogenetic ... | 2012 | 21866182 |
| Burkholderia cenocepacia BC2L-C is a super lectin with dual specificity and proinflammatory activity. | Lectins and adhesins are involved in bacterial adhesion to host tissues and mucus during early steps of infection. We report the characterization of BC2L-C, a soluble lectin from the opportunistic pathogen Burkholderia cenocepacia, which has two distinct domains with unique specificities and biological activities. The N-terminal domain is a novel TNF-a-like fucose-binding lectin, while the C-terminal part is similar to a superfamily of calcium-dependent bacterial lectins. The C-terminal domain d ... | 2011 | 21909279 |
| efficient biostimulation of native and introduced quorum-quenching rhodococcus erythropolis populations is revealed by a combination of analytical chemistry, microbiology, and pyrosequencing. | degradation of the quorum-sensing (qs) signals known as n-acylhomoserine lactones (ahl) by soil bacteria may be useful as a beneficial trait for protecting crops, such as potato plants, against the worldwide pathogen pectobacterium. in this work, analytical chemistry and microbial and molecular approaches were combined to explore and compare biostimulation of native and introduced ahl-degrading rhodococcus erythropolis populations in the rhizosphere of potato plants cultivated in farm greenhouse ... | 2012 | 22081576 |
| [screening and identification of marine fungi against bacterial quorum sensing]. | the discovery of quorum sensing (qs) system and its critical role in bacterial virulence have revealed a new way to attack pathogenic bacterium. the pathogenecity of qs deletion mutants decreases significantly. targeting bacterial qs system is a promising therapeutic approach to control infections and anti-microbial resistance. to obtain natural qs inhibitors from marine organisms, marine fungi (69 strains) were isolated from marine mollusca, and their extracts were screened using improved qsis2 ... | 2011 | 22117517 |
| cluster k mycobacteriophages: insights into the evolutionary origins of mycobacteriophage tm4. | five newly isolated mycobacteriophages--angelica, crimd, adephagia, anaya, and pixie--have similar genomic architectures to mycobacteriophage tm4, a previously characterized phage that is widely used in mycobacterial genetics. the nucleotide sequence similarities warrant grouping these into cluster k, with subdivision into three subclusters: k1, k2, and k3. although the overall genome architectures of these phages are similar, tm4 appears to have lost at least two segments of its genome, a centr ... | 2011 | 22053209 |
| A novel property of propolis (bee glue): Anti-pathogenic activity by inhibition of N-acyl-homoserine lactone mediated signaling in bacteria. | An alternative approach to antibiotics is the development of anti-pathogenic agents to control the bacterial virulome. Such anti-pathogenic agents could target a phenomena known as quorum sensing (QS). | 2011 | 22063726 |
| a novel metagenomic short-chain dehydrogenase/reductase attenuates pseudomonas aeruginosa biofilm formation and virulence on caenorhabditis elegans. | in pseudomonas aeruginosa, the expression of a number of virulence factors, as well as biofilm formation, are controlled by quorum sensing (qs). n-acylhomoserine lactones (ahls) are an important class of signaling molecules involved in bacterial qs and in many pathogenic bacteria infection and host colonization are ahl-dependent. the ahl signaling molecules are subject to inactivation mainly by hydrolases (enzyme commission class number ec 3) (i.e. n-acyl-homoserine lactonases and n-acyl-homoser ... | 2011 | 22046268 |
| transport genes and chemotaxis in laribacter hongkongensis: a genome-wide analysis. | abstract: | 2011 | 21849034 |
| serratia infections: from military experiments to current practice. | serratia species, in particular serratia marcescens, are significant human pathogens. s. marcescens has a long and interesting taxonomic, medical experimentation, military experimentation, and human clinical infection history. the organisms in this genus, particularly s. marcescens, were long thought to be nonpathogenic. because s. marcescens was thought to be a nonpathogen and is usually red pigmented, the u.s. military conducted experiments that attempted to ascertain the spread of this organi ... | 2011 | 21976608 |
| preclinical studies on histone deacetylase inhibitors as therapeutic reagents for endometrial and ovarian cancers. | histone deacetylases (hdacs) remove acetyl groups from lysine residues of histones and the deacetylation allows for tighter electrostatic interactions between dna and histones, leading to a more compact chromatin conformation with limited access for transactivators and the suppression of transcription. hdac mrna and protein overexpression was observed in endometrial and ovarian cancers. numerous in vitro studies have shown that hdac inhibitors, through their actions on histone and nonhistone pro ... | 2011 | 22112317 |
| detection of acylated homoserine lactones produced by vibrio spp. and related species isolated from water and aquatic organisms. | aims: to assess the diversity in production of acylated homoserine lactones (ahls) among vibrio spp and related species. methods and results: a total of 106 isolates, with representatives of 28 vibrio spp and related species, were investigated for the production of ahls. for this, a rapid method for the screening of ahls was developed based on the use of bacterial biosensors using a double-layer microplate assay. at least one bacterial biosensor was activated in 20 species, agrobacterium tumef ... | 2011 | 22098208 |
| Screening & profiling of quorum sensing signal molecules in Pseudomonas aeruginosa isolates from catheterized urinary tract infection patients. | Catheter associated urinary tract infections are the second most common nosocomial infections and Pseudomonas aeruginosa is the third most common organism responsible for these infections. In this study P. aeruginosa isolates from catheterized urinary tract infection patients were screened and profiled for the presence of different type of quorum sensing (QS) signal molecules. | 2011 | 21911974 |
| probing the impact of ligand binding on the acyl-homoserine lactone-hindered transcription factor esar of pantoea stewartii subsp. stewartii. | the quorum-sensing regulator esar from pantoea stewartii subsp. stewartii is a luxr homologue that is inactivated by acyl-homoserine lactone (ahl). in the corn pathogen p. stewartii, production of exopolysaccharide (eps) is repressed by esar at low cell densities. however, at high cell densities when high concentrations of its cognate ahl signal are present, esar is inactivated and derepression of eps production occurs. thus, esar responds to ahl in a manner opposite to that of most luxr family ... | 2011 | 21949066 |
| characterization of mtfa, a novel regulatory output signal protein of the glucose-phosphotransferase system in e. coli k-12. | the glucose phosphotransferase system (pts) in escherichia coli k-12 is a complex sensory and regulatory system. in addition to its central role in glucose uptake, it informs other global regulatory networks about carbohydrate availability and the physiological status of the cell. the expression of the ptsg gene encoding the glucose pts transporter eiicb(glc) is primarily regulated via the repressor mlc, whose inactivation is glucose dependent. during transport of glucose and dephosphorylation o ... | 2011 | 22178967 |
| Biochemical characteristics and biological properties of annurca apple cider. | Abstract Our work aimed to investigate the phenolic composition and antioxidant capacity of the de-alcoholized extract of cider obtained from the Annurca apple (Malus domestica var. Annurca). The antimicrobial effect of the extract against different pathogens, including Chronobacter sakazakii, was also examined. The extract's potential anti-quorum-sensing (AQS) activity was assessed using the test microorganism Chromobacterium violaceum. Biochemical analysis of the extract using ultra-performa ... | 2011 | 21861727 |
| The NLRC4 inflammasome receptors for bacterial flagellin and type III secretion apparatus. | Inflammasomes are large cytoplasmic complexes that sense microbial infections/danger molecules and induce caspase-1 activation-dependent cytokine production and macrophage inflammatory death. The inflammasome assembled by the NOD-like receptor (NLR) protein NLRC4 responds to bacterial flagellin and a conserved type III secretion system (TTSS) rod component. How the NLRC4 inflammasome detects the two bacterial products and the molecular mechanism of NLRC4 inflammasome activation are not understoo ... | 2011 | 21918512 |
| Inhibition of marine biofouling by bacterial quorum sensing inhibitors. | Seventy eight natural products from chemical libraries containing compounds from marine organisms (sponges, algae, fungi, tunicates and cyanobacteria) and terrestrial plants, were screened for the inhibition of bacterial quorum sensing (QS) using a reporter strain Chromobacterium violaceum CV017. About half of the natural products did not show any QS inhibition. Twenty four percent of the tested compounds inhibited QS of the reporter without causing toxicity. The QS inhibitory activities of the ... | 2011 | 21882898 |
| crystal structure of qscr, a pseudomonas aeruginosa quorum sensing signal receptor. | acyl-homoserine lactone (ahl) quorum sensing controls gene expression in hundreds of proteobacteria including a number of plant and animal pathogens. generally, the ahl receptors are members of a family of related transcription factors, and although they have been targets for development of antivirulence therapeutics there is very little structural information about this class of bacterial receptors. we have determined the structure of the transcription factor, qscr, bound to n-3-oxo-dodecanoyl- ... | 2011 | 21911405 |
| Inhibition of Quorum Sensing in the Opportunistic Pathogenic Bacterium Chromobacterium violaceum by an Extract from Fruiting Bodies of Lingzhi or Reishi Medicinal Mushroom, Ganoderma lucidum (W.Curt.:Fr.) P. Karst. (Higher Basidiomycetes). | Extracts of Lingzhi or Reishi medicinal mushroom, Ganoderma lucidum, inhibited quorum sensing in Chromobacterium violaceum CV026. G. lucidum fruiting bodies were milled and extracted with ethyl acetate. The crude extract was dissolved in an appropriate concentration of methanol, sterilized by filtration through a 0.22-µm membrane filter, and added to Ch. Violaceum CV026 cultures, which were used as an indicator to monitor quorum sensing inhibition. Inhibitory activity was measured by quantifying ... | 2011 | 22181844 |
| malabaricone c from myristica cinnamomea exhibits anti-quorum sensing activity. | a methanol-soluble extract of the bark of myristica cinnamomea was found to exhibit anti-quorum sensing activity, and subsequent bioassay-guided isolation led to the identification of the active compound malabaricone c (1). compound 1 inhibited violacein production by chromobacterium violaceum cv026 when grown in the presence of a cognate signaling molecule, n-3-oxohexanoyl-homoserine lactone. furthermore, 1 inhibited the quorum sensing-regulated pyocyanin production and biofilm formation in pse ... | 2011 | 21910441 |
| Chromobacterium violaceum lymphadenitis successfully treated in a Northern Italian hospital. | Lymphadenitis can be caused by different gram positive and gram negative bacteria and non-tuberculous mycobacteria. Cervical lymphadenitis in children is thought to result from ingestion of or contact with environmental microrganisms. Chromobacterium violaceum is a common inhabitant of soil and water in tropical and sub tropical countries. In these parts of the world Chromobacterium violaceum is able to cause skin infection with diffuse pustular lesions and also multiple liver abscess with often ... | 2011 | 22143820 |
| Prevalence of Ca2+-ATPase-Mediated Carbonate Dissolution among Cyanobacterial Euendoliths. | Recent physiological work has shown that the filamentous euendolithic cyanobacterium Mastigocoleus testarum (strain BC008) is able to bore into solid carbonates using Ca(2+)-ATPases to take up Ca(2+) from the medium at the excavation front, promoting dissolution of CaCO(3) there. It is not known, however, if this is a widespread mechanism or, rather, a unique capability of this model strain. To test this, we undertook a survey of multispecies euendolithic microbial assemblages infesting natural ... | 2012 | 22038600 |
| environmental factors affecting the expression of pilab as well as the proteome and transcriptome of the grass endophyte azoarcus sp. strain bh72. | bacterial communication is involved in regulation of cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. in the nitrogen-fixing model endophyte of grasses azoarcus sp. strain bh72, known cell-cell signaling systems have not been identified; however, the pila gene encoding the structural protein of type iv pili that are essential for plant colonization appears to be regulated in a population density-dependent manner. | 2012 | 22276194 |
| the novel sigma factor-like regulator rpoq controls luminescence, chitinase activity, and motility in vibrio fischeri. | abstract vibrio fischeri, the bacterial symbiont of the hawaiian bobtail squid, euprymna scolopes, uses quorum sensing to control genes involved in bioluminescence, host colonization, and other biological processes. previous work has shown that ains/r-directed quorum sensing also regulates the expression of rpoq (vf_a1015), a gene annotated as an rpos-like sigma factor. in this study, we demonstrate using phylogenetics that rpoq is related to, but distinct from, the stationary-phase sigma factor ... | 2012 | 22233679 |
| identification of n-acyl-l-homoserine lactones produced by non-pigmented chromobacterium aquaticum cc-seya-1(t) and pigmented chromobacterium subtsugae praa4-1(t). | many members of the genus chromobacterium produce violacein, a characteristic purple pigment which is induced by small diffusible n-acyl homoserine lactones (ahl) quorum-sensing molecules. in this study, the production of ahl of the non-pigmented c. aquaticum cc-seya-1(t) and the pigmented c. subtsugae praa4-1(t) were determined by using a cv026 biosensor assay. the profile of ahl was identified from the extracts of stationary phase cultures using gas chromatography-mass spectroscopy (gc-ms) and ... | 2011 | 22558542 |
| complications of port-a-cath® in patients with sickle cell disease. | red cell exchange/transfusion is frequently used in the management of patients with medical complications related to acute severe sickle cell disease (scd). however, peripheral venous access is often difficult without central venous catheters (cvcs) in adult patients with moderate or severe scd. | 2011 | 22341844 |
| antiquorum sensing and antibiofilm potential of capparis spinosa. | emergence of antibiotic resistance among bacterial pathogens often leads to the failure of existing antibiotics to treat bacterial infections; thus, there is a need to seek alternative treatment measures. the aim of this study was to evaluate the anti-quorum sensing (anti-qs) and antibiofilm potential of capparis spinosa to prevent the onset of bacterial infections as an alternate to antibiotics. | 2011 | 22222491 |
| chromobacterium violaceum infections in 13 non-human primates. | recently, an indian-origin macaque was found dead and chromobacterium violaceum was isolated from the skin wound, and hepatic and pulmonary abscesses. | 2011 | 22211858 |
| pharmacological effects of rosa damascena. | rosa damascena mill l., known as gole mohammadi in is one of the most important species of rosaceae family flowers. r. damascena is an ornamental plant and beside perfuming effect, several pharmacological properties including anti-hiv, antibacterial, antioxidant, antitussive, hypnotic, antidiabetic, and relaxant effect on tracheal chains have been reported for this plant. this article is a comprehensive review on pharmacological effects of r. damascena. online literature searches were performed ... | 2011 | 23493250 |
| inhibition of quorum sensing mediated virulence factors production in urinary pathogen serratia marcescens ps1 by marine sponges. | the focal intent of this study was to find out an alternative strategy for the antibiotic usage against bacterial infections. the quorum sensing inhibitory (qsi) activity of marine sponges collected from palk bay, india was evaluated against acyl homoserine lactone (ahl) mediated violacein production in chromobacterium violaceum (atcc 12472), cv026 and virulence gene expressions in clinical isolate serratia marcescens ps1. out of 29 marine sponges tested, the methanol extracts of aphrocallistes ... | 2012 | 23729876 |
| assessment of anti-quorum sensing activity for some ornamental and medicinal plants native to egypt. | this study investigated the effects of some plant extracts on the bacterial communication system, expressed as quorum sensing (qs) activity. quorum sensing has a directly proportional effect on the amount of certain compounds, such as pigments, produced by the bacteria. alcohol extracts of 23 ornamental and medicinal plants were tested for anti-qs activity by the chromobacterium violaceum assay using the agar cup diffusion method. the screening revealed the anti-qs activity of six plants; namely ... | 2012 | 23641343 |
| chronic granulomatous disease. | chronic granulomatous disease (cgd) is a paradigm for nonlymphoid primary immune defects, and has guided elucidation of oxygen metabolism in the phagocyte, vasculature, and brain. it has been in the forefront of the development of antimicrobial prophylaxis before the advent of advanced hiv and before its routine use in neutropenia. it has been an attractive target for gene therapy and bone marrow transplantation for nonmalignant diseases. therefore, cgd is worthy of attention for its historical ... | 2012 | 23351990 |
| chronic granulomatous disease. | chronic granulomatous disease (cgd) is a paradigm for nonlymphoid primary immune defects, and has guided elucidation of oxygen metabolism in the phagocyte, vasculature, and brain. it has been in the forefront of the development of antimicrobial prophylaxis before the advent of advanced hiv and before its routine use in neutropenia. it has been an attractive target for gene therapy and bone marrow transplantation for nonmalignant diseases. therefore, cgd is worthy of attention for its historical ... | 2012 | 23351990 |
| chromobacterium violaceum necrotizing fasciitis: a case report and review of the literature. | necrotizing fasciitis is a severe, rapidly progressive infection of the subcutaneous tissue that causes significant destruction. it is rarely encountered in the pediatric population. we describe the case of a 14-year-old boy who was diagnosed with chromobacterium violaceum necrotizing fasciitis and subsequently found to have autosomal recessive chronic granulomatous disease. | 2012 | 23288793 |
| dissection of quorum-sensing genes in burkholderia glumae reveals non-canonical regulation and the new regulatory gene tofm for toxoflavin production. | burkholderia glumae causes bacterial panicle blight of rice and produces major virulence factors, including toxoflavin, under the control of the quorum-sensing (qs) system mediated by the luxi homolog, tofi, and the luxr homolog, tofr. in this study, a series of markerless deletion mutants of b. glumae for tofi and tofr were generated using the suicide vector system, pkksacb, for comprehensive characterization of the qs system of this pathogen. consistent with the previous studies by other resea ... | 2012 | 23284909 |
| eugenol inhibits quorum sensing at sub-inhibitory concentrations. | in bacteria, quorum sensing (qs) is a process of chemical communication involving the production, release, and subsequent detection of signaling molecules. qs regulates the production of key virulence factors in pathogens. during the screening of herbal extracts, clove extract was found to inhibit qs-controlled gene expression in pseudomonas aeruginosa qsis-lasi and chromobacterium violaceum cv026 biosensors. using a bioautographic tlc assay, preparative tlc, and hplc analysis, eugenol, the majo ... | 2012 | 23264268 |
| l-2-haloacid dehalogenase (dehl) from rhizobium sp. rc1. | l-2-haloacid dehalogenase (dehl) from rhizobium sp. rc1 is a stereospecific enzyme that acts exclusively on l-isomers of 2-chloropropionate and dichloroacetate. the amino acid sequence of this enzyme is substantially different from those of other l-specific dehalogenases produced by other organisms. dehl has not been crystallised, and hence its three-dimensional structure is unavailable. herein, we review what is known concerning dehl and tentatively identify the amino acid residues important fo ... | 2016 | 27347470 |
| 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 |
| biotechnological applications of functional metagenomics in the food and pharmaceutical industries. | microorganisms are found throughout nature, thriving in a vast range of environmental conditions. the majority of them are unculturable or difficult to culture by traditional methods. metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbia ... | 2015 | 26175729 |
| the mysterious orphans of mycoplasmataceae. | the length of a protein sequence is largely determined by its function. in certain species, it may be also affected by additional factors, such as growth temperature or acidity. in 2002, it was shown that in the bacterium escherichia coli and in the archaeon archaeoglobus fulgidus, protein sequences with no homologs were, on average, shorter than those with homologs (bmc evol biol 2:20, 2002). it is now generally accepted that in bacterial and archaeal genomes the distributions of protein length ... | 2016 | 26747447 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| different biosynthetic pathways to fosfomycin in pseudomonas syringae and streptomyces species. | fosfomycin is a wide-spectrum antibiotic that is used clinically to treat acute cystitis in the united states. the compound is produced by several strains of streptomycetes and pseudomonads. we sequenced the biosynthetic gene cluster responsible for fosfomycin production in pseudomonas syringae pb-5123. surprisingly, the biosynthetic pathway in this organism is very different from that in streptomyces fradiae and streptomyces wedmorensis. the pathways share the first and last steps, involving co ... | 2012 | 22615277 |
| transcriptional regulation of nad metabolism in bacteria: nrtr family of nudix-related regulators. | a novel family of transcription factors responsible for regulation of various aspects of nad synthesis in a broad range of bacteria was identified by comparative genomics approach. regulators of this family (here termed nrtr for nudix-related transcriptional regulators), currently annotated as adp-ribose pyrophosphatases from the nudix family, are composed of an n-terminal nudix-like effector domain and a c-terminal dna-binding hth-like domain. nrtr regulons were reconstructed in diverse bacteri ... | 2008 | 18276643 |
| two new families of the ftsz-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea. | several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the ftsz-tubulin superfamily. one of these families is limited in its spread to proteobacteria whereas the other is represented in ... | 2010 | 20459678 |
| the rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. | bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. by replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomal ... | 2015 | 25567229 |
| pharmacological inhibition of quorum sensing for the treatment of chronic bacterial infections. | traditional treatment of infectious diseases is based on compounds that aim to kill or inhibit bacterial growth. a major concern with this approach is the frequently observed development of resistance to antimicrobial compounds. the discovery of bacterial-communication systems (quorum-sensing systems), which orchestrate important temporal events during the infection process, has afforded a novel opportunity to ameliorate bacterial infection by means other than growth inhibition. compounds able t ... | 2003 | 14597754 |
| 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 |
| coverage of whole proteome by structural genomics observed through protein homology modeling database. | we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ... | 2006 | 17146617 |
| 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 |
| predicting prokaryotic ecological niches using genome sequence analysis. | automated dna sequencing technology is so rapid that analysis has become the rate-limiting step. hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. as a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. we hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that ... | 2007 | 17710143 |
| 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 |
| 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 |