Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
|---|
| leaner and meaner genomes in escherichia coli. | a 'better' escherichia coli k-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions. | 2006 | 17076878 |
| [introduction of transpozon tn9 to endogenic plasmids of erwinia carotovora during lysogenization of cells by coliphage p1]. | it has been shown that phage p1 of escherichia coli is able not only to lysogenize the cells of erwinia carotovora but also to be a source of transpozon tn9 for mutagenesis of cryptic plasmids of this important phytopathogen. since the amount of the introduction in one of plasmids pca25::tn9 is 3.8 kb, at an average, it is supposed that tn9 is inherited as a double tandem structure. a convenient method is offered for selecting bacterial clones carrying the plasmid pca25::tn9 which is based on co ... | 2006 | 17100326 |
| detection and characterization of bacteria from the potato rhizosphere degrading n-acyl-homoserine lactone. | quorum sensing plays a role in the regulation of soft rot diseases caused by the plant pathogenic bacterium pectobacterium carotovorum subsp. carotovorum. the signal molecules involved in quorum sensing in p. carotovorum subsp. carotovorum belong to the group of n-acyl homoserine lactones (ahls). in our study, we screened bacteria isolated from the potato rhizosphere for the ability to degrade ahls produced by p. carotovorum subsp. carotovorum. six isolates able to degrade ahls were selected for ... | 2006 | 17110970 |
| substrate recognition by the hetero-octameric atp phosphoribosyltransferase from lactococcus lactis. | two families of atp phosphoribosyl transferases (atp-prt) join atp and 5-phosphoribosyl-1 pyrophosphate (prpp) in the first reaction of histidine biosynthesis. these consist of a homohexameric form found in all three kingdoms and a hetero-octameric form largely restricted to bacteria. hetero-octameric atp-prts consist of four hisgs catalytic subunits related to periplasmic binding proteins and four hisz regulatory subunits that resemble histidyl-trna synthetases. to clarify the relationship betw ... | 2006 | 17154531 |
| high precision multi-genome scale reannotation of enzyme function by eficaz. | the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction. | 2006 | 17166279 |
| the complete genome sequence and comparative genome analysis of the high pathogenicity yersinia enterocolitica strain 8081. | the human enteropathogen, yersinia enterocolitica, is a significant link in the range of yersinia pathologies extending from mild gastroenteritis to bubonic plague. comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. here we report the genome of y. enterocolitica strain 8081 (serotype 0:8; biotype 1b) and extensive microarray data relating to the genetic diversity of the y. enterocolitica species. our analysis reveals that the ... | 2006 | 17173484 |
| low-abundance kutznerides from kutzneria sp. 744. | five new (5-9) and four known (1-4) kutznerides were isolated from the actinomycete kutzneria sp. 744. compounds 1-9 all consisted of a cyclohexadepsipeptide core with the general structure 2-(1-methylcyclopropyl)-d-glycine-(2s,3ar,8as)-6,7-dichloro-3a-hydroxy-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acid-3-hydroxy-d-glutamic acid-o-methyl-l-serine-l-piperazic acid-(s)-2-hydroxy-3,3-dimethylbutyric acid. compounds 5, 6, and 8 contained erythro-3-hydroxy-d-glutamic acid, whereas 7 ... | 2006 | 17190458 |
| phytotoxicity and innate immune responses induced by nep1-like proteins. | we show that oomycete-derived nep1 (for necrosis and ethylene-inducing peptide1)-like proteins (nlps) trigger a comprehensive immune response in arabidopsis thaliana, comprising posttranslational activation of mitogen-activated protein kinase activity, deposition of callose, production of nitric oxide, reactive oxygen intermediates, ethylene, and the phytoalexin camalexin, as well as cell death. transcript profiling experiments revealed that nlps trigger extensive reprogramming of the arabidopsi ... | 2006 | 17194768 |
| identification of a dna restriction-modification system in pectobacterium carotovorum strains isolated from poland. | polish isolates of pectinolytic bacteria from the species pectobacterium carotovorum were screened for the presence of a dna restriction-modification (r-m) system. | 2006 | 16430511 |
| the global regulatory proteins leta and rpos control phospholipase a, lysophospholipase a, acyltransferase, and other hydrolytic activities of legionella pneumophila jr32. | legionella pneumophila possesses a variety of secreted and cell-associated hydrolytic activities that could be involved in pathogenesis. the activities include phospholipase a, lysophospholipase a, glycerophospholipid:cholesterol acyltransferase, lipase, protease, phosphatase, rnase, and p-nitrophenylphosphorylcholine (p-nppc) hydrolase. up to now, there have been no data available on the regulation of the enzymes in l. pneumophila and no data at all concerning the regulation of bacterial phosph ... | 2006 | 16452402 |
| novel organic hydroperoxide-sensing and responding mechanisms for ohrr, a major bacterial sensor and regulator of organic hydroperoxide stress. | xanthomonas campestris pv. phaseoli ohrr belongs to a major family of multiple-cysteine-containing bacterial organic hydroperoxide sensors and transcription repressors. site-directed mutagenesis and subsequent in vivo functional analyses revealed that changing any cysteine residue to serine did not alter the ability of ohrr to bind to the p1 ohrr-ohr promoter but drastically affected the organic hydroperoxide-sensing and response mechanisms of the protein. xanthomonas ohrr requires two cysteine ... | 2006 | 16452421 |
| the genome of the novel phage rtp, with a rosette-like tail tip, is homologous to the genome of phage t1. | a new escherichia coli phage, named rtp, was isolated and shown to be closely related to phage t1. electron microscopy revealed that phage rtp has a morphologically unique tail tip consisting of four leaf-like structures arranged in a rosette, whereas phage t1 has thinner, flexible leaves that thicken toward the ends. in contrast to t1, rtp did not require fhua and tonb for infection. the 46.2-kb genome of phage rtp encodes 75 open reading frames, 47 of which are homologous to phage t1 genes. li ... | 2006 | 16452425 |
| active-site residues in the type iv prepilin peptidase homologue pibd from the archaeon sulfolobus solfataricus. | archaeal preflagellin peptidases and bacterial type iv prepilin peptidases belong to a family of aspartic acid proteases that cleave the leader peptides of precursor proteins with type iv prepilin signal sequences. the substrate repertoire of pibd from the crenarchaeon sulfolobus solfataricus is unusually diverse. in addition to flagellin, pibd cleaves three sugar-binding proteins unique to this species and a number of proteins with unknown function. here we demonstrate that pibd contains two as ... | 2006 | 16452426 |
| tetrapyrrole biosynthesis in rhodobacter capsulatus is transcriptionally regulated by the heme-binding regulatory protein, hbrl. | we demonstrate that the expression of hem genes in rhodobacter capsulatus is transcriptionally repressed in response to the exogenous addition of heme. a high-copy suppressor screen for regulators of hem gene expression resulted in the identification of an lysr-type transcriptional regulator, called hbrl, that regulates hem promoters in response to the availability of heme. hbrl is shown to activate the expression of hema and hemz in the absence of exogenous hemin and repress hemb expression in ... | 2006 | 16452440 |
| within-species flagellin polymorphism in xanthomonas campestris pv campestris and its impact on elicitation of arabidopsis flagellin sensing2-dependent defenses. | bacterial flagellins have been portrayed as a relatively invariant pathogen-associated molecular pattern. we have found within-species, within-pathovar variation for defense-eliciting activity of flagellins among xanthomonas campestris pv campestris (xcc) strains. arabidopsis thaliana flagellin sensing2 (fls2), a transmembrane leucine-rich repeat kinase, confers flagellin responsiveness. the flg22 region was the only xcc flagellin region responsible for detectable elicitation of arabidopsis defe ... | 2006 | 16461584 |
| a quorum-quenching approach to investigate the conservation of quorum-sensing-regulated functions within the burkholderia cepacia complex. | taxonomic studies of the past few years have shown that the burkholderia cepacia complex, a heterogeneous group of b. cepacia-like organisms, consists of at least nine species. b. cepacia complex strains are ubiquitously distributed in nature and have been used for biocontrol, bioremediation, and plant growth promotion purposes. at the same time, b. cepacia complex strains have emerged as important opportunistic pathogens of humans, particularly those with cystic fibrosis. all b. cepacia complex ... | 2006 | 16461713 |
| participation of a galactose-specific c-type lectin in drosophila immunity. | a galactose-specific c-type lectin has been purified from a pupal extract of drosophila melanogaster. this lectin gene, named dl1 (drosophila lectin 1), is part of a gene cluster with the other two galactose-specific c-type lectin genes, named dl2 (drosophila lectin 2) and dl3 (drosophila lectin 3). these three genes are expressed differentially in fruit fly, but show similar haemagglutinating activities. the present study characterized the biochemical and biological properties of the dl1 protei ... | 2006 | 16475980 |
| antibiotic inducibility of the mexxy multidrug efflux system of pseudomonas aeruginosa: involvement of the antibiotic-inducible pa5471 gene product. | the mexxy components of the mexxy-oprm multidrug efflux system of pseudomonas aeruginosa are encoded by a mexz repressor-regulated operon that is inducible by antibiotics that target the ribosome. mutant strains disrupted in a gene, pa5471, were shown to be compromised for drug-inducible mexxy expression and, therefore, mexxy-oprm-mediated antimicrobial resistance. the pa5471 gene was inducible by the same ribosome-targeting agents that induce mexxy expression. moreover, vector-driven expression ... | 2006 | 16484195 |
| the dcta gene of pseudomonas chlororaphis o6 is under rpon control and is required for effective root colonization and induction of systemic resistance. | transcription from the dcta gene, which encodes an organic acid transporter in the root-colonizing bacterium pseudomonas chlororaphis o6, is under complex regulatory control. promoter sequence analysis revealed an rpon binding site. the regulation of transcript accumulation by the level of ammonium ions in the growth medium confirmed rpon regulation, even in the presence of glucose. a dcta mutant colonized tobacco roots to a lesser extent than the wild-type mutant during early seedling developme ... | 2006 | 16487325 |
| identification of the central quorum sensing regulator of virulence in the enteric phytopathogen, erwinia carotovora: the virr repressor. | in the gram-negative phytopathogen, erwinia carotovora ssp. atroseptica (eca) virulence depends on the production of a n-(3-oxohexanoyl)-l-homoserine lactone (ohhl) quorum sensing (qs) signal. this work identifies the elusive 'missing link' between qs and virulence in erwinia. we have identified and characterized a novel regulator of virulence, virr, in eca and show that a virr mutation completely restores virulence factor production to an eca mutant unable to synthesize ohhl. this effect of the ... | 2006 | 16359322 |
| the lpf gene cluster for long polar fimbriae is not involved in adherence of enteropathogenic escherichia coli or virulence of citrobacter rodentium. | using the enteropathogenic escherichia coli (epec) genome sequence, we found that epec e2348/69 has an lpfabcde gene cluster homologous (about 60% identical at the protein level) to the salmonella long polar fimbria (lpf) operon. to determine whether this operon is essential for adherence, the lpfabcd(e2)(3) genes were deleted from epec strain e2348/69 by allelic exchange. analysis of the resulting epecdeltalpfabcd(e23) strain showed no change in adherence to hela cells or to human intestinal bi ... | 2006 | 16368980 |
| the genome sequence of methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and h2 for methane formation and atp synthesis. | methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. this human intestinal inhabitant can generate methane only by reduction of methanol with h2 and is dependent on acetate as a carbon source. we report here the genome sequence of m. stadtmanae, which was found to be composed of 1,767,403 bp with an average g+c content of 28% and to harbor only 1,534 protein-encoding sequences (cds). the genome lacks 37 cds present in the genomes of all other methanoge ... | 2006 | 16385054 |
| antimicrobial activity of glycosidase inhibitory protein isolated from cyphomandra betacea sendt. fruit. | broad-spectrum antimicrobial activity of an invertase inhibitory protein (iip) isolated from cyphomandra betacea ripe fruits is documented. minimal inhibitory concentration (mic) values were determined by agar macrodilution and broth microdilution assays. this iip inhibited the growth of xylophagous and phytopatogenic fungi (ganoderma applanatum, schizophyllum commune, lenzites elegans, pycnoporus sanguineous, penicillium notatum, aspergillus niger, phomopsis sojae and fusarium mango) and phytop ... | 2006 | 16406143 |
| sensitive and specific detection of xanthomonas axonopodis pv. citri by pcr using pathovar specific primers based on hrpw gene sequences. | a sensitive and specific assay was developed to detect citrus bacterial canker caused by xanthomonas axonopodis pv. citri, in leaves and fruits of citrus. primers xacf and xacr from hrpw homologous to pectate lyase, modifying the structure of pectin in plants, were used to amplify a 561 bp dna fragment. pcr technique was applied to detect the pathogen in naturally or artificially infected leaves of citrus. the pcr product was only produced from x. axonopodis pv. citri among 26 isolates of xantho ... | 2006 | 16427518 |
| a selc-associated genomic island of the extraintestinal avian pathogenic escherichia coli strain ben2908 is involved in carbohydrate uptake and virulence. | the complete nucleotide sequence and genetic organization of a new genomic island (agi-3) isolated from the extraintestinal avian pathogenic escherichia coli strain ben2908 is reported. this 49,600-bp island is inserted at the selc locus and contains putative mobile genetic elements such as a phage-related integrase gene, transposase genes, and direct repeats. agi-3 shows a mosaic structure of five modules. some of these modules are present in other e. coli strains and in other pathogenic bacter ... | 2006 | 16428402 |
| characterization of the biosynthetic pathway of glucosylglycerate in the archaeon methanococcoides burtonii. | the pathway for the synthesis of the organic solute glucosylglycerate (gg) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp) from methanococcoides burtonii. a mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgp) was found in the genome of m. burtonii (http://www.jgi.doe.gov), but an mpgs gene coding for mannosyl-3-phosphoglycerate synthase (mpgs) was absent. the gene upstream of the mpgp ... | 2006 | 16428406 |
| role of salmonella enterica serovar typhimurium two-component system prea/preb in modulating pmra-regulated gene transcription. | the pmra/pmrb two-component system encoded by the pmrcab operon regulates the modification of salmonella enterica serovar typhimurium lipopolysaccharide leading to polymyxin b resistance. pmra and phop are the only known activators of pmrcab. a transposon mutagenesis screen for additional regulators of a pmrc::mudj fusion led to the identification of a two-component system, termed prea/preb (pmrcab regulators a and b), that controls the transcription of the pmrcab operon in response to unknown s ... | 2006 | 16352830 |
| inhibition of plant-pathogenic bacteria by short synthetic cecropin a-melittin hybrid peptides. | short peptides of 11 residues were synthesized and tested against the economically important plant pathogenic bacteria erwinia amylovora, pseudomonas syringae, and xanthomonas vesicatoria and compared to the previously described peptide pep3 (wklfkkilkvl-nh(2)). the antimicrobial activity of pep3 and 22 analogues was evaluated in terms of the mic and the 50% effective dose (ed(50)) for growth. peptide cytotoxicity against human red blood cells and peptide stability toward protease degradation we ... | 2006 | 16672470 |
| wrba from escherichia coli and archaeoglobus fulgidus is an nad(p)h:quinone oxidoreductase. | wrba (tryptophan [w] repressor-binding protein) was discovered in escherichia coli, where it was proposed to play a role in regulation of the tryptophan operon; however, this has been put in question, leaving the function unknown. here we report a phylogenetic analysis of 30 sequences which indicated that wrba is the prototype of a distinct family of flavoproteins which exists in a diversity of cell types across all three domains of life and includes documented nad(p)h:quinone oxidoreductases (n ... | 2006 | 16672604 |
| direct visualization of red fluorescent lipoproteins indicates conservation of the membrane sorting rules in the family enterobacteriaceae. | chimeras created by fusing the monomeric red fluorescent protein (rfp) to a bacterial lipoprotein signal peptide (liporfps) were visualized in the cell envelope by epifluorescence microscopy. plasmolysis of the bacteria separated the inner and outer membranes, allowing the specific subcellular localization of liporfps to be determined in situ. when equipped with the canonical inner membrane lipoprotein retention signal cdsr, liporfp was located in the inner membrane in escherichia coli, whereas ... | 2006 | 16672606 |
| application of comparative phylogenomics to study the evolution of yersinia enterocolitica and to identify genetic differences relating to pathogenicity. | yersinia enterocolitica, an important cause of human gastroenteritis generally caused by the consumption of livestock, has traditionally been categorized into three groups with respect to pathogenicity, i.e., nonpathogenic (biotype 1a), low pathogenicity (biotypes 2 to 5), and highly pathogenic (biotype 1b). however, genetic differences that explain variation in pathogenesis and whether different biotypes are associated with specific nonhuman hosts are largely unknown. in this study, we applied ... | 2006 | 16672618 |
| detecting uber-operons in prokaryotic genomes. | we present a study on computational identification of uber-operons in a prokaryotic genome, each of which represents a group of operons that are evolutionarily or functionally associated through operons in other (reference) genomes. uber-operons represent a rich set of footprints of operon evolution, whose full utilization could lead to new and more powerful tools for elucidation of biological pathways and networks than what operons have provided, and a better understanding of prokaryotic genome ... | 2006 | 16682449 |
| comparative genomics reveals what makes an enterobacterial plant pathogen. | the bacterial family enterobacteriaceae contains some of the most devastating human and animal pathogens, including escherichia coli, salmonella enterica and species of yersinia and shigella. these are among the best-studied of any organisms, yet there is much to be learned about the nature and evolution of interactions with their hosts and with the wider environment. comparative and functional genomics have fundamentally improved our understanding of their modes of adaptation to different ecolo ... | 2006 | 16704357 |
| evolution of immunity and host chromosome integration site of p2-like coliphages. | the amount and distribution of variation in the genomic region containing the genes in the lytic-lysogenic genetic switch and the sequence that determines the integration site into the host chromosome were analyzed for 38 p2-like phages from escherichia coli. the genetic switch consists of two convergent mutually exclusive promoters, pe and pc, and two repressors, c and cox. the immunity repressor c blocks the early pe promoter, leading to the establishment of lysogeny. the cox repressor blocks ... | 2006 | 16707684 |
| structural and functional characterization of three polyketide synthase gene clusters in bacillus amyloliquefaciens fzb 42. | although bacterial polyketides are of considerable biomedical interest, the molecular biology of polyketide biosynthesis in bacillus spp., one of the richest bacterial sources of bioactive natural products, remains largely unexplored. here we assign for the first time complete polyketide synthase (pks) gene clusters to bacillus antibiotics. three giant modular pks systems of the trans-acyltransferase type were identified in bacillus amyloliquefaciens fzb 42. one of them, pks1, is an ortholog of ... | 2006 | 16707694 |
| altering glucosinolate profiles modulates disease resistance in plants. | plant diseases are major contributing factors for crop loss in agriculture. here, we show that arabidopsis plants with high levels of novel glucosinolates (gss) as a result of the introduction of single cyp79 genes exhibit altered disease resistance. arabidopsis expressing cyp79d2 from cassava accumulated aliphatic isopropyl and methylpropyl gs, and showed enhanced resistance against the bacterial soft-rot pathogen erwinia carotovora, whereas arabidopsis expressing the sorghum cyp79a1 or over-ex ... | 2006 | 16709192 |
| outer membrane protein genes and their small non-coding rna regulator genes in photorhabdus luminescens. | three major outer membrane protein genes of escherichia coli, ompf, ompc, and ompa respond to stress factors. transcripts from these genes are regulated by the small non-coding rnas micf, micc, and mica, respectively. here we examine photorhabdus luminescens, an organism that has a different habitat from e. coli for outer membrane protein genes and their regulatory rna genes. | 2006 | 16716220 |
| biology of pseudomonas stutzeri. | pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. the species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many ... | 2006 | 16760312 |
| [effect of exogenous plasmid r68.45 on productive and lisogenic development of temperate bacteriophage zf40 erwinia carotovora]. | the erwinia carotoerora strains bearing exogenous plasmid r68.45 have been obtained by means of transconjugation. dynamics and frequency characteristics of plasmid transfer to erwinia cells have been studied. plasmid-phage interrelations have been studied for the first time in e. carotovora. it has been established that the presence of exogenous plasmid r68.45 affects essentially the culture growth parameters and lisogenization of e. carotovora by the wild phage zf40 and its clear-mutants. the p ... | 2006 | 16786628 |
| genomic analysis of carbon source metabolism of shewanella oneidensis mr-1: predictions versus experiments. | genomic sequences have been used to find the genetic foundation for carbon source metabolism in shewanella oneidensis mr-1. annotated s. oneidensis mr-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the biocyc database (http://www.biocyc.org/) or in the primary literature. a picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for ... | 2006 | 16788168 |
| erwinia carotovora subspecies produce duplicate variants of expr, luxr homologs that activate rsma transcription but differ in their interactions with n-acylhomoserine lactone signals. | the n-acylhomoserine lactone (ahl) signaling system comprises a producing system that includes acylhomoserine synthase (ahli, a luxi homolog) and a receptor, generally a luxr homolog. ahl controls exoprotein production in erwinia carotovora and consequently the virulence for plants. in previous studies we showed that expr, a luxr homolog, is an ahl receptor and that it activates transcription of rsma, the gene encoding an rna binding protein which is a global negative regulator of exoproteins an ... | 2006 | 16788181 |
| bacteriocin-like substance inhibits potato soft rot caused by erwinia carotovora. | soft rot is a major problem encountered in potatoes during postharvest storage. the soft rot bacterium erwinia carotovora was inhibited by a novel bacteriocin-like substance (bls) produced by bacillus licheniformis p40. the bls caused a bactericidal effect on e. carotovora cells at 30 microg ml(-1). transmission electron microscopy showed that bls-treated cells presented wrinkled bacterial surfaces and shrinkage of the whole cell, indicating plasmolysis. erwinia carotovora cells treated with bls ... | 2006 | 16788721 |
| prevalence of local immune response against oral infection in a drosophila/pseudomonas infection model. | pathogens have developed multiple strategies that allow them to exploit host resources and resist the immune response. to study how drosophila flies deal with infectious diseases in a natural context, we investigated the interactions between drosophila and a newly identified entomopathogen, pseudomonas entomophila. flies orally infected with p. entomophila rapidly succumb despite the induction of both local and systemic immune responses, indicating that this bacterium has developed specific stra ... | 2006 | 16789834 |
| cooperation of two distinct expr regulators controls quorum sensing specificity and virulence in the plant pathogen erwinia carotovora. | quorum sensing, the population density-dependent regulation mediated by n-acylhomoserine lactones (ahsl), is essential for the control of virulence in the plant pathogen erwinia carotovora ssp. carotovora (ecc). in erwinia carotovora ssp. the ahsl signal with an acyl chain of either 6 or 8 carbons is generated by an ahsl synthase, the expi gene product. this work demonstrates that the ahsl receptor, expr1, of ecc strain scc3193 has strict specificity for the cognate ahsl 3-oxo-c8-hsl. we have al ... | 2006 | 16796682 |
| molecular characterization of pantoea stewartii subsp. stewartii hrpy, a conserved response regulator of the hrp type iii secretion system, and its interaction with the hrps promoter. | pantoea stewartii subsp. stewartii is a bacterial pathogen of corn. its pathogenicity depends on the translocation of effector proteins into host cells by the hrp type iii secretion system. we previously showed by genetic analysis that the hrpx sensor kinase and the hrpy response regulator are at the head of a complex cascade of regulators controlling hrp/hrc secretion and wts effector genes. this cascade also includes the hrps response regulator and the hrpl alternative sigma factor. these regu ... | 2006 | 16816181 |
| prediction of csra-regulating small rnas in bacteria and their experimental verification in vibrio fischeri. | the role of small rnas as critical components of global regulatory networks has been highlighted by several recent studies. an important class of such small rnas is represented by csrb and csrc of escherichia coli, which control the activity of the global regulator csra. given the critical role played by csra in several bacterial species, an important problem is the identification of csra-regulating small rnas. in this paper, we develop a computer program (csrna_find) designed to locate potentia ... | 2006 | 16822857 |
| herbivore-induced resistance against microbial pathogens in arabidopsis. | caterpillars of the herbivore pieris rapae stimulate the production of jasmonic acid (ja) and ethylene (et) in arabidopsis (arabidopsis thaliana) and trigger a defense response that affects insect performance on systemic tissues. to investigate the spectrum of effectiveness of p. rapae-induced resistance, we examined the level of resistance against different pathogens. although the necrotrophic fungus alternaria brassicicola is sensitive to ja-dependent defenses, herbivore-induced resistance was ... | 2006 | 16829584 |
| restraining erwinia virulence by expression of n-acyl homoserine lactonase gene pro3a-aiia in bacillus thuringiensis subsp leesis. | to widen the biological control function of a genetically modified bacillus thuringiensis subsp leesis strain bmb-005, an acyl homoserine lactonase (ahl lactonase) gene aiia transcribed by the promoter of insecticidal crystal protein coding gene cry3a, was transformed into strain bmb-005. the amount of ahl lactonase protein produced by transformant bmb821a was 2.4-fold more than that produced by bmb-005. ahl-degradation assay showed that transformant bmb821a could degrade more ahls molecules tha ... | 2006 | 16838380 |
| n-acylhomoserine lactonase producing rhodococcus spp. with different ahl-degrading activities. | n-acylhomoserine lactones (ahls) are conserved signal molecules that control diverse biological activities in quorum sensing system of gram-negative bacteria. recently, several soil bacteria were found to degrade ahls, thereby interfering with the quorum sensing system. previously, rhodococcus erythropolis w2 was reported to degrade ahls by both oxido-reductase and ahl-acylase. in the present study, two ahl-utilizing bacteria, strains ls31 and pi33, were isolated and identified as the genus rhod ... | 2006 | 16842366 |
| [functional organization of prophage and lysogeny in erwinia carotovora with participation of a temperate bacteriophage zf40]. | functional organization of a prophage of the temperate bacteriophage zf40 of erwinia carotovora subsp. carotovora which includes its immunity and inducibility as well as its effect on the host phenotype. it was established that the prophage zf40 forms several different states in e. carotovora which are distinguished by the indices of spontaneous and lysogenic induction. in contrast to other prophages, including the lambdoid ones, the prophage zf40 is capable to establish cytoplasmic overimmunity ... | 2006 | 16869142 |
| [characteristics of lysogenic induction of bacteriocins in thymine mutants of erwinia carotovora]. | peculiarities of lisogenic induction of bacteriocins in thymine-dependent mutants of erwinia carotovora subsp. carotovora have been studied. it was shown for the first time that availability of carotovoricins of two (and above) types characterized the defect polylysogeny of strains of different geographic origin. use of various methods of induction of thy--mutants or inducing agents of different nature leads to a selective accumulation of carotovoricins of certain types in the cell lysates. resu ... | 2006 | 16869143 |
| identification of drosophila gene products required for phagocytosis of candida albicans. | phagocytosis is a highly conserved aspect of innate immunity. we used drosophila melanogaster s2 cells as a model system to study the phagocytosis of candida albicans, the major fungal pathogen of humans, by screening an rnai library representing 7,216 fly genes conserved among metazoans. after rescreening the initial genes identified and eliminating certain classes of housekeeping genes, we identified 184 genes required for efficient phagocytosis of c. albicans. diverse biological processes are ... | 2006 | 16336044 |
| identification of drosophila gene products required for phagocytosis of candida albicans. | phagocytosis is a highly conserved aspect of innate immunity. we used drosophila melanogaster s2 cells as a model system to study the phagocytosis of candida albicans, the major fungal pathogen of humans, by screening an rnai library representing 7,216 fly genes conserved among metazoans. after rescreening the initial genes identified and eliminating certain classes of housekeeping genes, we identified 184 genes required for efficient phagocytosis of c. albicans. diverse biological processes are ... | 2006 | 16336044 |
| conserved and variable functions of the sigmae stress response in related genomes. | bacteria often cope with environmental stress by inducing alternative sigma (sigma) factors, which direct rna polymerase to specific promoters, thereby inducing a set of genes called a regulon to combat the stress. to understand the conserved and organism-specific functions of each sigma, it is necessary to be able to predict their promoters, so that their regulons can be followed across species. however, the variability of promoter sequences and motif spacing makes their prediction difficult. w ... | 2006 | 16336047 |
| conserved and variable functions of the sigmae stress response in related genomes. | bacteria often cope with environmental stress by inducing alternative sigma (sigma) factors, which direct rna polymerase to specific promoters, thereby inducing a set of genes called a regulon to combat the stress. to understand the conserved and organism-specific functions of each sigma, it is necessary to be able to predict their promoters, so that their regulons can be followed across species. however, the variability of promoter sequences and motif spacing makes their prediction difficult. w ... | 2006 | 16336047 |
| a methodology to detect and quantify five pathogens causing potato tuber decay using real-time quantitative polymerase chain reaction. | abstract late blight (phytophthora infestans), pink rot (phytophthora erythroseptica), leak (pythium ultimum), dry rot (fusarium sambucinum), and soft rot (erwinia carotovora subsp. carotovora and subsp. atroseptica) are particularly damaging diseases of stored potato tubers worldwide. in this study, we present a methodology to detect and quantify the causal agents of the five aforementioned diseases from whole potato tubers, using real-time quantitative-polymerase chain reaction. six primer pai ... | 2006 | 18944060 |
| caspar, a suppressor of antibacterial immunity in drosophila. | drosophila has a primitive yet highly effective innate immune system. although the infection-dependent activation mechanisms of the drosophila immune system are well understood, its inhibitory regulation remains elusive. to find novel suppressors of the immune system, we performed a genetic screening for drosophila mutants with hyperactivated immune responses and isolated a loss-of-function mutant of caspar whose product is homologous to fas-associating factor 1 in mammals. interestingly, caspar ... | 2006 | 17050695 |
| early responsive to dehydration 15, a negative regulator of abscisic acid responses in arabidopsis. | early responsive to dehydration 15 (erd15) is rapidly induced in response to various abiotic and biotic stress stimuli in arabidopsis (arabidopsis thaliana). modulation of erd15 levels by overexpression or rnai silencing altered the responsiveness of the transgenic plants to the phytohormone abscisic acid (aba). overexpression of erd15 reduced the aba sensitivity of arabidopsis manifested in decreased drought tolerance and in impaired ability of the plants to increase their freezing tolerance in ... | 2006 | 17056758 |
| purification of l-asparaginase from a bacteria erwinia carotovora and effect of a dihydropyrimidine derivative on some of its kinetic parameters. | l-asparaginase shows antileukemic activity and is generally administered in the body in combination with other anticancer drugs like pyrimidine derivatives. in the present study, l-asparaginase was purified from a bacteria erwinia carotovora and the effect of a dihydropyrimidine derivative (1-amino-6-methyl-4-phenyl-2-thioxo, 1,2,3,4-tetrahydropyrimidine-5-carboxylic acid methyl ester) was studied on the kinetic parameters km and vmax of the enzyme using l-asparagine as substrate. the enzyme had ... | 2006 | 17285805 |
| [phage system for studying the restriction-modification of erwinia carotovora]. | a model for revealing and type identifying the systems of restriction-modification of phytopathogenic bacterium ewinia carotovora with the help of two virulent polyvalent phages-fe 44 and t7 is proposed in the work. the joint use of the phages permits to identify both the limitations of phages development on the part of rm-systems of three major types, and on the part of the competing episomes. the proposed system also allows to reveal other kinds of limitations, in particular those connected wi ... | 2006 | 17243364 |
| [intragenome heterogeneity of the temperate bacteriophage zf40 erwinia carotovora]. | it has been shown that the temperate bacteriophage zf40 erwinia carotovora combines in it two kinds of intragenome heterogeneity--cyclic permutation and cohesive end structures. the latter reassociate more quickly than analogous cos-sites of the phage lambda escherichia coli. a series of clear-mutants was found after the temperature inactivation of the phage particles; they are the components of the complementation group being involved in the repressor gene. one of the mutants, zf40c(5/5), was i ... | 2006 | 17243365 |
| sigmae-dependent small rnas of salmonella respond to membrane stress by accelerating global omp mrna decay. | the bacterial envelope stress response (esr) is triggered by the accumulation of misfolded outer membrane proteins (omps) upon envelope damage or excessive omp synthesis, and is mediated by the alternative sigma factor, sigmae. activation of the ge pathway causes a rapid downregulation of major omp mrnas, which prevents further build-up of unassembled omps and liberates the translocation and folding apparatus under conditions that require envelope remodelling. the factors that facilitate the rap ... | 2006 | 17427289 |
| two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling. | quantitative proteomics is the workhorse of the modern proteomics initiative. the gel-based and mudpit approaches have facilitated vital advances in the measurement of protein expression alterations in normal and disease phenotypic states. the methodological advance in two-dimensional gel electrophoresis (2dge) has been the multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2d-dige). 2d-dige is based on direct labeling of lysine groups on proteins with cyanine ... | 2006 | 17487156 |
| asparaginase (native asnase or pegylated asnase) in the treatment of acute lymphoblastic leukemia. | the discovery of the tumor-inhibitory properties of asparaginase (asnase) began in the early 1950s with the observation that guinea pig serum-treated lymphoma-bearing mice underwent rapid and often complete regression. about 4000 cases of acute lymphoblastic leukemia (all) are diagnosed very year in the us and many more through out the world. the majority of these cases are in children and young adults, making all the most common form of malignancy in these age groups. the treatment protocols of ... | 2006 | 17717965 |
| bacterial elicitation and evasion of plant innate immunity. | recent research on plant responses to bacterial attack has identified extracellular and intracellular host receptors that recognize conserved pathogen-associated molecular patterns and more specialized virulence proteins, respectively. these findings have shed light on our understanding of the molecular mechanisms by which bacteria elicit host defences and how pathogens have evolved to evade or suppress these defences. | 2006 | 16936700 |
| identification of a gene encoding a functional reverse transcriptase within a highly variable locus in the p2-like coliphages. | the p2-like coliphages are highly similar; the structural genes show at least 96% identity. however, at two loci they have genes believed to be horizontally transferred. we show that the genetic content at the second loci, the to region, contains six completely different sequences with high at contents and with different open reading frames. the product of one of them exhibits reverse transcriptase activity and blocks infection of phage t5. | 2006 | 16452449 |
| diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-i release factor that potentially recognizes atypical mrna signals other than normal stop codons. | while all codons that specify amino acids are universally recognized by trna molecules, codons signaling termination of translation are recognized by proteins known as class-i release factors (rf). in most eukaryotes and archaea a single rf accomplishes termination at all three stop codons. in most bacteria, there are two rfs with overlapping specificity, rf1 recognizes ua(a/g) and rf2 recognizes u(a/g)a. | 2006 | 16970810 |
| messing with bacterial quorum sensing. | quorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. interestingly, eukaryotes produce quorum-sensing-interfering (qsi) compo ... | 2006 | 17158701 |
| multiple determinants influence root colonization and induction of induced systemic resistance by pseudomonas chlororaphis o6. | summary colonization of the roots of tobacco by pseudomonas chlororaphis o6 induces systemic resistance to the soft-rot pathogen, erwinia carotovora ssp. carotovara scc1. a screen of the transposon mutants of p. chlororaphis o6 showed mutants with about a fivefold reduction in ability to induce systemic resistance to the soft-rot disease. these mutations disrupted genes involved in diverse functions: a methyl-accepting chemotaxis protein, biosynthesis of purines, phospholipase c, transport of br ... | 2006 | 20507461 |
| genetic and proteomic analysis of the role of luxs in the enteric phytopathogen, erwinia carotovora. | summary erwinia carotovora is a gram-negative phytopathogen that is an important cause of soft rot disease, including stem and tuber rot in potatoes. quorum sensing is the process by which bacteria detect their population density and regulate gene expression accordingly. quorum sensing, an important example of intercellular communication, involves the production and detection of chemical signal molecules. the enzyme luxs is responsible for the production of autoinducer-2 (ai-2), a molecule that ... | 2006 | 20507426 |
| asap: a resource for annotating, curating, comparing, and disseminating genomic data. | asap is a comprehensive web-based system for community genome annotation and analysis. asap is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. new tools, such as the genome alignment program mauve, have been incorporated into asap in order to improve display and analysis of related genomes. recent improvements to the database and challenges for future development of the system are discussed. asap ... | 2006 | 16381899 |
| asap: a resource for annotating, curating, comparing, and disseminating genomic data. | asap is a comprehensive web-based system for community genome annotation and analysis. asap is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. new tools, such as the genome alignment program mauve, have been incorporated into asap in order to improve display and analysis of related genomes. recent improvements to the database and challenges for future development of the system are discussed. asap ... | 2006 | 16381899 |
| dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain. | recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ... | 2006 | 16407325 |
| how phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. | the phosphoenolpyruvate(pep):carbohydrate phosphotransferase system (pts) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. to carry out its catalytic function in sugar transport and phosphorylation, the pts uses pep as an energy source and phosphoryl donor. the phosphoryl group of pep is usually transferred via four distinct proteins (domains) to the transported sugar bo ... | 2006 | 17158705 |
| 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 |
| gata factors participate in tissue-specific immune responses in drosophila larvae. | drosophila responds to infection by producing a broad range of antimicrobial agents in the fat body and more restricted responses in tissues such as the gut, trachea, and malpighian tubules. the regulation of antimicrobial genes in larval fat depends on linked rel/nf-kappab and gata binding sites. serpent functions as the major gata transcription factor in the larval fat body. however, the transcriptional regulation of other tissue-specific responses is less well understood. here, we present evi ... | 2006 | 17032752 |
| an essential complementary role of nf-kappab pathway to microbicidal oxidants in drosophila gut immunity. | in the drosophila gut, reactive oxygen species (ros)-dependent immunity is critical to host survival. this is in contrast to the nf-kappab pathway whose physiological function in the microbe-laden epithelia has yet to be convincingly demonstrated despite playing a critical role during systemic infections. we used a novel in vivo approach to reveal the physiological role of gut nf-kappab/antimicrobial peptide (amp) system, which has been 'masked' in the presence of the dominant intestinal ros-dep ... | 2006 | 16858400 |
| stringent and relaxed recognition of orit by related systems for plasmid mobilization: implications for horizontal gene transfer. | the plasmids r1162 and psc101 have origins of conjugative transfer (orits) and corresponding relaxases that are closely related. the orits are made up of a highly conserved core, where dna is cleaved by the relaxase prior to transfer, and an inverted repeat that differs in size and sequence. we show that in each case the seven base pairs adjacent to the core and within one arm of the inverted repeat are sufficient to determine specificity. within this dna there are three at base pairs located 4 ... | 2006 | 16385040 |
| extratrain: a database of extragenic regions and transcriptional information in prokaryotic organisms. | transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. in these processes, the regulatory proteins and the regulatory dna signals located in extragenic regions are the key elements involved. as all extragenic spaces are putative regulatory regions, extratrain covers all extragenic regions of available genomes and regulatory proteins from bacteria and archaea included in the uniprot database. | 2006 | 16539733 |
| bacterial conversations: talking, listening and eavesdropping. a nerc discussion meeting held at the royal society on 7 december 2005. | 2006 | 16849274 | |
| the drosophila inhibitor of apoptosis protein diap2 functions in innate immunity and is essential to resist gram-negative bacterial infection. | the founding member of the inhibitor of apoptosis protein (iap) family was originally identified as a cell death inhibitor. however, recent evidence suggests that iaps are multifunctional signaling devices that influence diverse biological processes. to investigate the in vivo function of drosophila melanogaster iap2, we have generated diap2 null alleles. diap2 mutant animals develop normally and are fully viable, suggesting that diap2 is dispensable for proper development. however, these animal ... | 2006 | 16894030 |
| cooperative control of drosophila immune responses by the jnk and nf-kappab signaling pathways. | jun n-terminal kinase (jnk) signaling is a highly conserved pathway that controls both cytoskeletal remodeling and transcriptional regulation in response to a wide variety of signals. despite the importance of jnk in the mammalian immune response, and various suggestions of its importance in drosophila immunity, the actual contribution of jnk signaling in the drosophila immune response has been unclear. drosophila tak1 has been implicated in the nf-kappab/relish-mediated activation of antimicrob ... | 2006 | 16763552 |
| downregulation of the drosophila immune response by peptidoglycan-recognition proteins sc1 and sc2. | peptidoglycan-recognition proteins (pgrps) are evolutionarily conserved molecules that are structurally related to bacterial amidases. several drosophila pgrps have lost this enzymatic activity and serve as microbe sensors through peptidoglycan recognition. other pgrp family members, such as drosophila pgrp-sc1 or mammalian pgrp-l, have conserved the amidase function and are able to cleave peptidoglycan in vitro. however, the contribution of these amidase pgrps to host defense in vivo has remain ... | 2006 | 16518472 |
| diversity in penaeidin antimicrobial peptide form and function. | penaeidins are a diverse family of two-domain antimicrobial peptides expressed in shrimp. variation in penaeidin sequence results in functional diversity, which was discovered using synthetic reproductions of native penaeidins. an isoform of penaeidin class 3 from litopenaeus setiferus (litset pen3-4) was synthesized using native ligation and compared directly with the synthetic penaeidin class 4 known to be expressed in the same organism. new antimicrobial activity data are included in this rev ... | 2007 | 17716729 |
| diversity in penaeidin antimicrobial peptide form and function. | penaeidins are a diverse family of two-domain antimicrobial peptides expressed in shrimp. variation in penaeidin sequence results in functional diversity, which was discovered using synthetic reproductions of native penaeidins. an isoform of penaeidin class 3 from litopenaeus setiferus (litset pen3-4) was synthesized using native ligation and compared directly with the synthetic penaeidin class 4 known to be expressed in the same organism. new antimicrobial activity data are included in this rev ... | 2007 | 17716729 |
| populations of fungi and bacteria associated with samples of stored rice in korea. | stored rice was collected from rice processing complexes of national agricultural cooperative federation of 11 regions in korea to evaluate the occurrence of fungi and bacteria and to identify the predominant fungi and bacteria to the genus levels. most rice samples generally produced the higher levels of fungi and bacteria than white rice. the occurrence of fungi and bacteria varied in various locations of korea. among fungi observed, aspergillus spp. and penicillium spp. were dominant in the s ... | 2007 | 24015066 |
| small mobile sequences in bacteria display diverse structure/function motifs. | small repeat sequences in bacterial genomes, which represent non-autonomous mobile elements, have close similarities to archaeon and eukaryotic miniature inverted repeat transposable elements. these repeat elements are found in both intergenic and intragenic chromosomal regions, and contain an array of diverse motifs. these can include dna sequences containing an integration host factor binding site and a proposed dna methyltransferase recognition site, transcribed rna secondary structural motif ... | 2007 | 18086200 |
| small mobile sequences in bacteria display diverse structure/function motifs. | small repeat sequences in bacterial genomes, which represent non-autonomous mobile elements, have close similarities to archaeon and eukaryotic miniature inverted repeat transposable elements. these repeat elements are found in both intergenic and intragenic chromosomal regions, and contain an array of diverse motifs. these can include dna sequences containing an integration host factor binding site and a proposed dna methyltransferase recognition site, transcribed rna secondary structural motif ... | 2007 | 18086200 |
| biosynthesis of proline. | proline was among the last biosynthetic precursors to have its biosynthetic pathway unraveled. this review recapitulates the findings on the biosynthesis and transport of proline. glutamyl kinase (gk) catalyzes the atp-dependent phosphorylation of l-glutamic acid. purification of γ-gk from escherichia coli was facilitated by the expression of the prob and proa genes from a high-copy-number plasmid and the development of a specific coupled assay based on the nadph-dependent reduction of gp by γ-g ... | 2007 | 26443591 |
| quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time pcr on openarrays. | diagnostics and disease-management strategies require technologies to enable the simultaneous detection and quantification of a wide range of pathogenic microorganisms. most multiplex, quantitative detection methods available suffer from compromises between the level of multiplexing, throughput and accuracy of quantification. here, we demonstrate the efficacy of a novel, high-throughput, ligation-based assay for simultaneous quantitative detection of multiple plant pathogens. the ligation probes ... | 2007 | 17697351 |
| myc2 differentially modulates diverse jasmonate-dependent functions in arabidopsis. | the arabidopsis thaliana basic helix-loop-helix leu zipper transcription factor (tf) myc2/jin1 differentially regulates jasmonate (ja)-responsive pathogen defense (e.g., pdf1.2) and wound response (e.g., vsp) genes. in this study, genome-wide transcriptional profiling of wild type and mutant myc2/jin1 plants followed by functional analyses has revealed new roles for myc2 in the modulation of diverse ja functions. we found that myc2 negatively regulates trp and trp-derived secondary metabolism su ... | 2007 | 17616737 |
| arginine-to-lysine substitutions influence recombinant horseradish peroxidase stability and immobilisation effectiveness. | horseradish peroxidase (hrp) plays important roles in many biotechnological fields, including diagnostics, biosensors and biocatalysis. often, it is used in immobilised form. with conventional immobilisation techniques, the enzyme adheres in random orientation: the active site may face the solid phase rather than bulk medium, impeding substrate access and leading to sub-optimal catalytic performance. the ability to immobilise hrp in a directional manner, such that the active site would always fa ... | 2007 | 18053254 |
| drosophila calcineurin promotes induction of innate immune responses. | the sophisticated adaptive immune system of vertebrates overlies an ancient set of innate immune-response pathways, which have been genetically dissected in drosophila. although conserved regulatory pathways have been defined, calcineurin, a ca(2+)-dependent phosphatase, has not been previously implicated in drosophila immunity. calcineurin activates mammalian immune responses by activating the nuclear translocation of the vertebrate-specific transcription factors nfat1-4. in drosophila, infecti ... | 2007 | 18060786 |
| genome-wide investigation reveals pathogen-specific and shared signatures in the response of caenorhabditis elegans to infection. | there are striking similarities between the innate immune systems of invertebrates and vertebrates. caenorhabditis elegans is increasingly used as a model for the study of innate immunity. evidence is accumulating that c. elegans mounts distinct responses to different pathogens, but the true extent of this specificity is unclear. here, we employ direct comparative genomic analyses to explore the nature of the host immune response. | 2007 | 17875205 |
| non-heme fe(iv)-oxo intermediates. | high-valent non-heme iron-oxo intermediates have been proposed for decades as the key intermediates in numerous biological oxidation reactions. in the past three years, the first direct characterization of such intermediates has been provided by studies of several alphakg-dependent oxygenases that catalyze either hydroxylation or halogenation of their substrates. in each case, the fe(iv)-oxo intermediate is implicated in cleavage of the aliphatic c-h bond to initiate hydroxylation or halogenatio ... | 2007 | 17542550 |
| effective asparagine depletion with pegylated asparaginase results in improved outcomes in adult acute lymphoblastic leukemia: cancer and leukemia group b study 9511. | calgb 9511 used pegaspargase (peg-asp) in lieu of the native enzyme. the aim was to compare differences in overall survival (os) and disease-free survival (dfs) between patients who did and did not achieve asparagine depletion, defined by enzyme levels greater than 0.03 u/ml plasma for 14 consecutive days after at least 1 of 4 planned peg-asp administrations. samples were available from 85 eligible patients. on univariate analyses, the 22 patients who did not achieve asparagine depletion had inf ... | 2007 | 17264295 |
| toll and imd pathways synergistically activate an innate immune response in drosophila melanogaster. | the inducible expression of antimicrobial peptide genes in drosophila melanogaster is regulated by the conserved toll and peptidoglycan recognition protein lc/immune deficiency (pgrp-lc/imd) signaling pathways. it has been proposed that the two pathways have independent functions and mediate the specificity of innate immune responses towards different microorganisms. scattered evidence also suggests that some antimicrobial target genes can be activated by both toll and imd, albeit to different e ... | 2007 | 17438142 |
| role of lipid composition and lipid peroxidation in the sensitivity of fungal plant pathogens to aluminum chloride and sodium metabisulfite. | aluminum chloride and sodium metabisulfite have shown high efficacy at low doses in controlling postharvest pathogens on potato tubers. direct effects of these two salts included the loss of cell membrane integrity in exposed pathogens. in this work, four fungal potato pathogens were studied in order to elucidate the role of membrane lipids and lipid peroxidation in the relative sensitivity of microorganisms exposed to these salts. inhibition of mycelial growth in these fungi varied considerably ... | 2007 | 17337539 |
| an informatic pipeline for the data capture and submission of quantitative proteomic data using itraq. | proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. in order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic te ... | 2007 | 17270041 |
| 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 |