Publications

identification of a new family of enzymes with potential o-acetylpeptidoglycan esterase activity in both gram-positive and gram-negative bacteria.	the metabolism of the rigid bacterial cell wall heteropolymer peptidoglycan is a dynamic process requiring continuous biosynthesis and maintenance involving the coordination of both lytic and synthetic enzymes. the o-acetylation of peptidoglycan has been proposed to provide one level of control on these activities as this modification inhibits the action of the major endogenous lytic enzymes, the lytic transglycosylases. the o-acetylation of peptidoglycan also inhibits the activity of the lysozy ...	2005	16111493
flagellin induces innate immunity in nonhost interactions that is suppressed by pseudomonas syringae effectors.	arabidopsis nonhost1 (nho1) is required for limiting the in planta growth of nonhost pseudomonas bacteria but completely ineffective against the virulent bacterium pseudomonas syringae pv. tomato dc3000. however, the molecular basis underlying this observation remains unknown. here we show that nho1 is transcriptionally activated by flagellin. the nonhost bacterium p. syringae pv. tabaci lacking flagellin is unable to induce nho1, multiplies much better than does the wild-type bacterium, and cau ...	2005	16123135
novel lectin-like bacteriocins of biocontrol strain pseudomonas fluorescens pf-5.	bacteriocin llpa, produced by pseudomonas sp. strain bw11m1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (a. h. a. parret, g. schoofs, p. proost, and r. de mot, j. bacteriol. 185:897-908, 2003). biocontrol strain pseudomonas fluorescens pf-5 contains two llpa-like genes, named llpa1(pf-5) and llpa2(pf-5). recombinant escherichia coli cells expressing llpa1(pf-5) or llpa2(pf-5) acquired bacteriocin activity and secreted a 31-kda prot ...	2005	16151105
activation of the phz operon of pseudomonas fluorescens 2-79 requires the luxr homolog phzr, n-(3-oh-hexanoyl)-l-homoserine lactone produced by the luxi homolog phzi, and a cis-acting phz box.	the phz operon of pseudomonas fluorescens 2-79, which produces phenazine-1-carboxylate, is preceded by two genes, phzr and phzi, that are homologs of quorum-sensing gene pairs of the luxr-luxi family. deleting phzr and phzi from strain 2-79 led to loss of production of the antibiotics, as well as a suite of six acyl-homoserine lactones (acyl-hsls) that includes four 3-hydroxy- derivatives and two alkanoyl-hsls. strain 2-79 accumulates n-(3-hydroxy-hexanoyl)-l-hsl to levels 20 and 30 times those ...	2005	16159785
diversity in domain architectures of ser/thr kinases and their homologues in prokaryotes.	ser/thr/tyr kinases (styks) commonly found in eukaryotes have been recently reported in many bacterial species. recent studies elucidating their cellular functions have established their roles in bacterial growth and development. however functions of a large number of bacterial styks still remain elusive. the organisation of domains in a large dataset of bacterial styks has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial styks.	2005	16171520
multiple modes of motility: a second flagellar system in escherichia coli.		2005	15687183
the flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from escherichia coli.	escherichia coli k-12 possesses two adjacent, divergent, promoterless flagellar genes, fhia-mbha, that are absent from salmonella enterica. through bioinformatics analysis, we found that these genes are remnants of an ancestral 44-gene cluster and are capable of encoding a novel flagellar system, flag-2. in enteroaggregative e. coli strain 042, there is a frameshift in lfgc that is likely to have inactivated the system in this strain. tiling path pcr studies showed that the flag-2 cluster is pre ...	2005	15687208
adaptation of the yeast ura3 selection system to gram-negative bacteria and generation of a {delta}betcde pseudomonas putida strain.	a general procedure for efficient generation of gene knockouts in gram-negative bacteria by the adaptation of the saccharomyces cerevisiae ura3 selection system is described. a pseudomonas putida strain lacking the ura3 homolog pyrf (encoding orotidine-5'-phosphate decarboxylase) was constructed, allowing the use of a plasmid-borne copy of the gene as the target of selection. the delivery vector ptec contains the pyrf gene and promoter, a conditional origin of replication (orir6k), an origin of ...	2005	15691944
effect of temperature, ph, and metals on the stability and activity of phenylalanine hydroxylase from chromobacterium violaceum.	phenylalanine hydroxylase (pah) is a non-heme iron dioxygenase catalyzing the conversion of phenylalanine to tyrosine and is present in both prokaryotic and eukaryotic organisms. a relatively simple pah is expressed by chromobacterium violaceum, a gram-negative bacterium found in tropical and subtropical regions. the effects of temperature, ph and metals on the stability and catalytic activity of chromobacterium violaceum pah were determined by steady-state kinetics, circular dichroism (cd) and ...	2005	15708798
protein domains and architectural innovation in plant-associated proteobacteria.	evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ...	2005	15715905
molecular analysis of the rebeccamycin l-amino acid oxidase from lechevalieria aerocolonigenes atcc 39243.	rebeccamycin, a member of the tryptophan-derived indolocarbazole family, is produced by lechevalieria aerocolonigenes atcc 39243. the biosynthetic pathway that specifies biosynthesis of this important metabolite is comprised of 11 genes spanning 18 kb of dna. a presumed early enzyme involved in elaboration of the rebeccamycin aglycone is encoded by rebo, located at the left-hand region of the reb gene cluster. the deduced protein product, rebo (51.9 kda), is an l-amino acid oxidase (l-aao) that ...	2005	15743957
evidence for diversifying selection at the pyoverdine locus of pseudomonas aeruginosa.	pyoverdine is the primary siderophore of the gram-negative bacterium pseudomonas aeruginosa. the pyoverdine region was recently identified as the most divergent locus alignable between strains in the p. aeruginosa genome. here we report the nucleotide sequence and analysis of more than 50 kb in the pyoverdine region from nine strains of p. aeruginosa. there are three divergent sequence types in the pyoverdine region, which correspond to the three structural types of pyoverdine. the pyoverdine ou ...	2005	15743962
bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion.	like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ...	2005	15757514
genotyping of chromobacterium violaceum isolates by reca pcr-rflp analysis.	intraspecies variation of chromobacterium violaceum was examined by comparative sequence - and by restriction fragment length polymorphism analysis of the recombinase a gene (reca-pcr-rflp). primers deduced from the known reca gene sequence of the type strain c. violaceum atcc 12472(t) allowed the specific amplification of a 1040bp reca fragment from each of the 13 c. violaceum strains investigated, whereas other closely related organisms tested negative. hindii-psti-reca rflp analysis generated ...	2005	15766789
the erwinia chrysanthemi type iii secretion system is required for multicellular behavior.	enterobacterial animal pathogens exhibit aggregative multicellular behavior, which is manifested as pellicles on the culture surface and biofilms at the surface-liquid-air interface. pellicle formation behavior requires production of extracellular polysaccharide, cellulose, and protein filaments, known as curli. protein filaments analogous to curli are formed by many protein secretion systems, including the type iii secretion system (ttss). here, we demonstrate that erwinia chrysanthemi, which d ...	2005	15629935
the bldc developmental locus of streptomyces coelicolor encodes a member of a family of small dna-binding proteins related to the dna-binding domains of the merr family.	the bldc locus, required for formation of aerial hyphae in streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids d17 and d25 of a minimal ordered library. subcloning and sequencing showed that bldc encodes a member of a previously unrecognized family of small (58- to 78-residue) dna-binding proteins, related to the dna-binding domains of the merr family of transcriptional activators. bldc family members are found in a wide range of gram-positive and gram-nega ...	2005	15629942
evidence for two flagellar stators and their role in the motility of pseudomonas aeruginosa.	pseudomonas aeruginosa is a ubiquitous bacterium capable of twitching, swimming, and swarming motility. in this study, we present evidence that p. aeruginosa has two flagellar stators, conserved in all pseudomonads as well as some other gram-negative bacteria. either stator is sufficient for swimming, but both are necessary for swarming motility under most of the conditions tested, suggesting that these two stators may have different roles in these two types of motility.	2005	15629949
preliminary evaluation of the api 20ne and rapid nf plus systems for rapid identification of burkholderia pseudomallei and b. mallei.	we evaluated the api 20ne and the rapid nf plus systems with 58 burkholderia pseudomallei and 23 b. mallei strains for identification of these agents, but neither was reliable for confirmatory identification, with only 0 to 60% strains identified accurately. a greater diversity of strains in the system databases would be beneficial.	2005	15635021
seasonal change in bacterial flora and biomass in mountain snow from the tateyama mountains, japan, analyzed by 16s rrna gene sequencing and real-time pcr.	the bacterial flora and biomass in mountain snow from the tateyama mountains, toyama prefecture, japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal dna restriction analysis followed by 16s rrna gene sequencing and dna quantification by real-time pcr. samples of surface snow collected in various months during the melting season contained a psychrophilic bacterium, cryobacterium psychrophilum, and two psychrotrophic bacteria, variovorax paradoxus and jan ...	2005	15640179
manual and automated instrumentation for identification of enterobacteriaceae and other aerobic gram-negative bacilli.	identification of gram-negative bacilli, both enteric and nonenteric, by conventional methods is not realistic for clinical microbiology laboratories performing routine cultures in today's world. the use of commercial kits, either manual or automated, to identify these organisms is a common practice. the advent of rapid or "spot" testing has eliminated the need for some commonly isolated organisms to be identified with the systems approach. commercially available systems provide more in-depth id ...	2005	15653824
identification of new secreted effectors in salmonella enterica serovar typhimurium.	a common theme in bacterial pathogenesis is the secretion of bacterial products that modify cellular functions to overcome host defenses. gram-negative bacterial pathogens use type iii secretion systems (ttsss) to inject effector proteins into host cells. the genes encoding the structural components of the type iii secretion apparatus are conserved among bacterial species and can be identified by sequence homology. in contrast, the sequences of secreted effector proteins are less conserved and a ...	2005	16177297
the type iii secretion system and cytotoxic enterotoxin alter the virulence of aeromonas hydrophila.	many gram-negative bacteria use a type iii secretion system (ttss) to deliver effector proteins into host cells. here we report the characterization of a ttss chromosomal operon from the diarrheal isolate ssu of aeromonas hydrophila. we deleted the gene encoding aeromonas outer membrane protein b (aopb), which is predicted to be involved in the formation of the ttss translocon, from wild-type (wt) a. hydrophila as well as from a previously characterized cytotoxic enterotoxin gene (act)-minus str ...	2005	16177316
the transcriptome response of neisseria gonorrhoeae to hydrogen peroxide reveals genes with previously uncharacterized roles in oxidative damage protection.	symptomatic gonococcal infection, caused by the pathogen neisseria gonorrhoeae (gc), is characterized by the influx of polymorphonuclear leukocytes (pmns) to the site of infection. although pmns possess several mechanisms of oxidative killing, intact gc can be found associated with pmns, suggesting that gonococcal defences against oxidative stress are crucial for its ability to evade killing by pmns. we used microarrays to identify genes that were differentially expressed after transient exposur ...	2005	16194237
global transcriptome analysis of shewanella oneidensis mr-1 exposed to different terminal electron acceptors.	to gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer shewanella oneidensis mr-1, global mrna patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. several groups of ...	2005	16199584
intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor.	the goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. we built metagenomic libraries with dna from soil on the floodplain of the tanana river in alaska. we extracted dna directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. to identify clones of interest, we de ...	2005	16204555
contrasting occurrence of chromobacterium violaceum in tropical drinking water springs of uganda.	occurrence of chromobacterium violaceum in six protected drinking water springs in uganda was investigated. c. violaceum showed a contrasting occurrence, which was independent of human impact as assessed by faecal pollution indicators. it was isolated from two springs (s1 and s2) that were located close to each other (3 km) but not in the rest. in s1 c. violaceum was continuously detected, in concentrations ranging from 6 to 270 cfu 100 ml(-1), while in s2 it was detected on only one sampling oc ...	2005	16209027
chromobacterium violaceum in siblings, brazil.	chromobacterium violaceum, a saprophyte bacterium found commonly in soil and water in tropical and subtropical climates, is a rare cause of severe, often fatal, human disease. we report 1 confirmed and 2 suspected cases of c. violaceum septicemia, with 2 fatalities, in siblings after recreational exposure in northeastern brazil.	2005	16229777
effective extraction of elastase from bacillus sp. fermentation broth using aqueous two-phase system.	this paper presents the evaluation of an aqueous two-phase system (atps) for extracting elastase produced by bacillus sp. el31410. the elastase and cell partition behavior in polyethylene glycol (peg)/salt systems was investigated. the suitable system for elastase extraction was peg/kh(2)po(4)-k(2)hpo(4), in which elastase is mainly partitioned into the peg-rich phase, while the cells remained in the other phase. the influence of defined system parameters (e.g. peg molecular mass, ph, nacl addit ...	2005	16252343
n-butanoyl-l-homoserine lactone (bhl) deficient pseudomonas aeruginosa isolates from an intensive care unit.	acylated homoserine lactones (ahls) are self-generated diffusible signal molecules that mediate population density dependent gene expression (quorum sensing) in a variety of gram-negative bacteria, and several virulence genes of human pathogens are known to be controlled by ahls. in this study, strains of pseudomonas aeruginosa, acinetobacter baumannii, escherichia coli and klebsiella pneumoniae, isolated from intensive care patients, were screened for ahl production by using ahl responsive indi ...	2005	16255145
a case of chromobacterium infection after car accident in korea.	chromobacterium violaceum is a gram negative straight rod, 0.8-1.2 by 2.5 to 6.0 m, which is motile by one polar flagella and one to four lateral flagella. the organism inhabits soil and water and is often found in semitropical and tropical climates. infections in humans are rare. we report a case of infection caused by strains of c. violaceum. a 38-year-old male patient was admitted to kyunghee university hospital, seoul, korea on july 28th, 2003, after a car accident. the patient had multiple ...	2005	16259070
dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.	bacterial response to nitric oxide (no) is of major importance since no is an obligatory intermediate of the nitrogen cycle. transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves fnr-like transcription factors hcpr, dnr, and nnrr; two-component systems narxl and narqp; no-responsive activator norr; and nitrite-sensitive repressor nsrr. using comparative genomics approaches, we predict dna-binding motifs for these transcriptional factors and ...	2005	16261196
polyphenol oxidase activity expression in ralstonia solanacearum.	sequencing of the genome of ralstonia solanacearum revealed several genes that putatively code for polyphenol oxidases (ppos). to study the actual expression of these genes, we looked for and detected all kinds of ppo activities, including laccase, cresolase, and catechol oxidase activities, in cellular extracts of this microorganism. the conditions for the ppo assays were optimized for the phenolic substrate, ph, and sodium dodecyl sulfate concentration used. it was demonstrated that three diff ...	2005	16269713
evidence for a functional quorum-sensing type ai-1 system in the extremophilic bacterium acidithiobacillus ferrooxidans.	acidithiobacillus ferrooxidans is one of the main acidophilic chemolithotrophic bacteria involved in the bioleaching of metal sulfide ores. the bacterium-mineral interaction requires the development of biofilms, whose formation is regulated in many microorganisms by type ai-1 quorum sensing. here, we report the existence and characterization of a functional type ai-1 quorum-sensing system in a. ferrooxidans. this microorganism produced mainly acyl-homoserine lactones (ahl) with medium and large ...	2005	16269739
ecology, inhibitory activity, and morphogenesis of a marine antagonistic bacterium belonging to the roseobacter clade.	roseobacter strain 27-4 has been isolated from a turbot larval rearing unit and is capable of reducing mortality in turbot egg yolk sac larvae. here, we demonstrate that the supernatant of roseobacter 27-4 is lethal to the larval pathogens vibrio anguillarum and vibrio splendidus in a buffer system and inhibited their growth in marine broth. liquid chromatography (lc) with both uv spectral detection and high-resolution mass spectrometry (hr-ms) identified the known antibacterial compound thiotro ...	2005	16269767
coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.	long alpha-helical coiled-coil proteins are involved in diverse organizational and regulatory processes in eukaryotic cells. they provide cables and networks in the cyto- and nucleoskeleton, molecular scaffolds that organize membrane systems and tissues, motors, levers, rotating arms, and possibly springs. mutations in long coiled-coil proteins have been implemented in a growing number of human diseases. using the coiled-coil prediction program multicoil, we have previously identified all long c ...	2005	16288662
four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction.	motivation: transmembrane chemoreceptors in escherichia coli utilize ligand-binding domains for detecting various external signals. the structure of this domain in the e.coli aspartate receptor, tar, is known and its signal transduction mechanism is under investigation. current domain models for this important sensory module are inaccurate and, therefore, cannot reveal the distribution of this domain within the current genomic landscape. results: we carried out sensitive and exhaustive psi-blast ...	2005	16306392
l-canavanine made by medicago sativa interferes with quorum sensing in sinorhizobium meliloti.	sinorhizobium meliloti is a gram-negative soil bacterium, capable of establishing a nitrogen-fixing symbiosis with its legume host, alfalfa (medicago sativa). quorum sensing plays a crucial role in this symbiosis, where it influences the nodulation process and the synthesis of the symbiotically important exopolysaccharide ii (eps ii). s. meliloti has three quorum-sensing systems (sin, tra, and mel) that use n-acyl homoserine lactones as their quorum-sensing signal molecule. increasing evidence i ...	2005	16321947
cell-cell influences on bacterial community development in aquatic biofilms.	dialysis tubing containing spent culture media, when placed in a lake, was colonized by a low diversity of bacteria, whereas abiotic controls had considerable diversity. changes were seen in the presence and absence of acylated homoserine lactones, suggesting that these molecules and other factors may influence adherent-population composition.	2005	16332906
production of acylated homoserine lactones by aeromonas and pseudomonas strains isolated from municipal activated sludge.	up to now, the production and role of n-acyl homoserine lactones (ahls) in activated sludge have been poorly understood. in this study, cross-feeding assays with the reporter strains agrobacterium tumefaciens ntl4 and chromobacterium violaceum cv026 were used to investigate ahl signal production by municipal activated sludge samples. ahl signal production was consistently detected from municipal activated sludge when different samples were incubated on nutrient media. from one municipal activate ...	2005	16333331
expression, purification, crystallization and preliminary x-ray analysis of yaeq (xac2396) from xanthomonas axonopodis pv. citri.	xanthomonas axonopodis pv. citri yaeq (xac2396) is a member of a family of bacterial proteins conserved in several gram-negative pathogens. here, the cloning, expression, purification and crystallization of the 182-residue (20.6 kda) yaeq protein are described. recombinant yaeq containing selenomethionine was crystallized in space group p2(1) and crystals diffracted to 1.9 a resolution at a synchrotron source. the unit-cell parameters are a = 39.75, b = 91.88, c = 48.03 a, beta = 108.37 degrees. ...	2005	16511077
the use of violacein to study biochemical behaviour of saccharomyces cerevisiae cells.	violacein, a biochemical compound produced by chromobacterium violaceum which has antichagasic properties, was used to study biochemical behaviour of saccharomyces cerevisiae cells. at 20 microm and 40 microm, violacein did not alter the membrane potential (deltapsi) of s. cerevisae cells, which means that the integrity of the cell membrane was maintained. on the other hand, at 60 microm and 80 microm, violacein produced significant alterations in the membrane potential. this information will be ...	2005	16435565
electron spin relaxation of copper(ii) complexes in glassy solution between 10 and 120 k.	the temperature dependence, between 10 and 120 k, of electron spin-lattice relaxation at x-band was analyzed for a series of eight pyrrolate-imine complexes and for ten other copper(ii) complexes with varying ligands and geometry including copper-containing prion octarepeat domain and s100 type proteins. the geometry of the cun4 coordination sphere for pyrrolate-imine complexes with r=h, methyl, n-butyl, diphenylmethyl, benzyl, 2-adamantyl, 1-adamantyl, and tert-butyl has been shown to range fro ...	2005	16343958
electron spin relaxation of copper(ii) complexes in glassy solution between 10 and 120 k.	the temperature dependence, between 10 and 120 k, of electron spin-lattice relaxation at x-band was analyzed for a series of eight pyrrolate-imine complexes and for ten other copper(ii) complexes with varying ligands and geometry including copper-containing prion octarepeat domain and s100 type proteins. the geometry of the cun4 coordination sphere for pyrrolate-imine complexes with r=h, methyl, n-butyl, diphenylmethyl, benzyl, 2-adamantyl, 1-adamantyl, and tert-butyl has been shown to range fro ...	2005	16343958
effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria.	soils are inhabited by many bacteria from phylogenetic groups that are poorly studied because representatives are rarely isolated in cultivation studies. part of the reason for the failure to cultivate these bacteria is the low frequency with which bacterial cells in soil form visible colonies when inoculated onto standard microbiological media, resulting in low viable counts. we investigated the effects of three factors on viable counts, assessed as numbers of cfu on solid media, and on the phy ...	2005	15691937
the marine bromotyrosine derivatives.		2005	16173400
one-component systems dominate signal transduction in prokaryotes.	two-component systems that link environmental signals to cellular responses are viewed as the primary mode of signal transduction in prokaryotes. by analyzing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer domains typical of two-component systems. one-component systems are evolutionarily older, more widely distributed among bacteria and archaea, ...	2005	15680762
gene cassettes potentially encoding fosfomycin resistance determinants.		2005	15673790
the net of life: reconstructing the microbial phylogenetic network.	it has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (hgt) events. yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. here, we present a first attempt to reconstruct such an evolutionary network, which we term the "net of life". we use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference alg ...	2005	15965028
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
the 2-hydroxycarboxylate transporter family: physiology, structure, and mechanism.	the 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. they function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate. these pathways are found in the class bacillales of the low-cg gram-positive bacteria and in the gamma subdivision of the proteobacteria. the pathways have evolved into a remarkable diversity in terms of th ...	2005	16339740
a computational method to predict genetically encoded rare amino acids in proteins.	in several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. these rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. we report a method for such recoding prediction from genomic data, using read-through similarity evaluation. a survey across a set of microbial genomes identifies almost all the known cases as well as a number of no ...	2005	16168086
a computational approach for identifying pathogenicity islands in prokaryotic genomes.	pathogenicity islands (pais), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (gis) that have been acquired by horizontal gene transfer event. up to now, computational approaches for identifying pais have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. these approaches often lead to the identification of genomic islands, rather than pais.	2005	16033657
the tyra family of aromatic-pathway dehydrogenases in phylogenetic context.	the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.	2005	15888209
comparative and evolutionary analysis of the bacterial homologous recombination systems.	homologous recombination is a housekeeping process involved in the maintenance of chromosome integrity and generation of genetic variability. although detailed biochemical studies have described the mechanism of action of its components in model organisms, there is no recent extensive assessment of this knowledge, using comparative genomics and taking advantage of available experimental data on recombination. using comparative genomics, we assessed the diversity of recombination processes among ...	2005	16132081
structural classification of bacterial response regulators: diversity of output domains and domain combinations.	chey-like phosphoacceptor (or receiver [rec]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. in this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. transcriptional regulators of the ompr, narl, and ntrc families w ...	2006	16740923
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
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
[chromobacterium violaceum peritonitis: case report and literature review].	we report a case of chromobacterium violaceum infection and we review the literature for all published cases. c. violaceum grew from a peritoneal fluid of a 47-year-old woman operated on for peritonitis following perforative gastroduodenal ulcer. she was just coming back from a 1-month-holyday in french guyana, where she might have been in contact with this micro-organism. the patient fully recovered after surgical management associated with antibiotic therapy consisting of ofloxacin plus pipera ...	2006	16829475
effects of cyanide and dissolved oxygen concentration on biological au recovery.	the number of discarded electric devices containing traces of au is currently increasing. it is desirable to recover this au because of its valuable physicochemical properties. au is usually dissolved with relatively high concentrations of cyanide, which is associated with environmental risk. chromobacterium violaceum is able to produce and detoxify small amounts of cyanide, and may thus be able to recover au from discarded electric devices. this study investigated the effects of cyanide and dis ...	2006	16567012
crystallization and preliminary x-ray diffraction analysis of an anti-h(o) lectin from lotus tetragonolobus seeds.	the seed lectin from lotus tetragonolobus (lta) has been crystallized. the best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 k. a complete structural data set was collected at 2.00 angstroms resolution using a synchrotron-radiation source. lta crystals were found to be monoclinic, belonging to space group p2(1), with unit-cell parameters a = 68.89, b = 65.83, c = 102.53 angstroms, alpha = gamma = 90, beta = 92 degrees. molec ...	2006	16820693
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
up-regulation of mdr1 and induction of doxorubicin resistance by histone deacetylase inhibitor depsipeptide (fk228) and atra in acute promyelocytic leukemia cells.	the multidrug resistance 1 (mdr1) gene product p-glycoprotein (p-gp) is frequently implicated in cross-resistance of tumors to chemotherapeutic drugs. in contrast, acute promyelocytic leukemia (apl) cells do not express mdr1 and are highly sensitive to anthracyclines. the combination of atra and the novel histone deacetylase inhibitor (hdaci) depsipeptide (fk228) induced p-gp expression and prevented growth inhibition and apoptosis in nb4 apl cells subsequently exposed to doxorubicin (dox). atra ...	2006	16223781
histone deacetylase enzymes as potential drug targets in cancer and parasitic diseases.	the elucidation of the mechanisms of transcriptional activation and repression in eukaryotic cells has shed light on the important role of acetylation-deacetylation of histones mediated by histone acetyltransferases (hats) and histone deacetylases (hdacs), respectively. another group belonging to the large family of sirtuins (silent information regulators (sirs)) has an (nicotinamide adenine dinucleotide) nad(+)-dependent hdac activity. several inhibitors of hdacs (hdis) have been shown to exert ...	2006	16883049
blast screening of chlamydial genomes to identify signature proteins that are unique for the chlamydiales, chlamydiaceae, chlamydophila and chlamydia groups of species.	chlamydiae species are of much importance from a clinical viewpoint. their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. the obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. thus, it is of importance to develop additional means for their identification and characterization.	2006	16436211
production and properties of the native chromobacterium violaceum fucose-binding lectin (cv-iil) compared to homologous lectins of pseudomonas aeruginosa (pa-iil) and ralstonia solanacearum (rs-iil).	chromobacterium violaceum is a versatile, violet pigment (violacein)-producing beta-proteobacterium, confined to tropical and subtropical regions, dwelling in soil and water, like pseudomonas aeruginosa and ralstonia solanacearum. these three bacteria are saprophytes that occasionally become aggressive opportunistic pathogens virulently attacking animals (the first two) and plants (the third). the recent availability of their genome sequences enabled identification in the c. violaceum genome of ...	2006	16436433
an investigation of chlorophenol proton affinities and their influence on the biological activity of microorganisms.	the proton affinities of 15 chlorophenols are calculated by ab initio methods. straight correlation between proton affinities and changes in the electronic structure is observed. the proton affinities decrease linearly with the electronic density gain on the chlorine atoms, as the liberation of the proton increases. to confirm the importance of the proton affinities on the toxicity of chlorophenols, calorimetric responses of these molecules and related ones where the acid proton is changed to a ...	2006	16451037
quorum sensing in yersinia enterocolitica controls swimming and swarming motility.	the yersinia enterocolitica luxi homologue yeni directs the synthesis of n-3-(oxohexanoyl)homoserine lactone (3-oxo-c6-hsl) and n-hexanoylhomoserine lactone (c6-hsl). in a y. enterocolitica yeni mutant, swimming motility is temporally delayed while swarming motility is abolished. since both swimming and swarming are flagellum dependent, we purified the flagellin protein from the parent and yeni mutant. electrophoresis revealed that in contrast to the parent strain, the yeni mutant grown for 17 h ...	2006	16452428
the genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium thiobacillus denitrificans.	the complete genome sequence of thiobacillus denitrificans atcc 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of fe(ii) and u(iv), and to ...	2006	16452431
a mobile quorum-sensing system in serratia marcescens.	quorum-sensing systems that have been widely identified in bacteria play important roles in the regulation of bacterial multicellular behavior by which bacteria sense population density to control various biological functions, including virulence. one characteristic of the luxir quorum-sensing genes is their diverse and discontinuous distribution among proteobacteria. here we report that the spnir quorum-sensing system identified in the enterobacterium serratia marcescens strain ss-1 is carried ...	2006	16452435
coexistence of burkholderia, cupriavidus, and rhizobium sp. nodule bacteria on two mimosa spp. in costa rica.	rrna gene sequencing and pcr assays indicated that 215 isolates of root nodule bacteria from two mimosa species at three sites in costa rica belonged to the genera burkholderia, cupriavidus, and rhizobium. this is the first report of cupriavidus sp. nodule symbionts for mimosa populations within their native geographic range in the neotropics. burkholderia spp. predominated among samples from mimosa pigra (86% of isolates), while there was a more even distribution of cupriavidus, burkholderia, a ...	2006	16461667
quorum quenching by an n-acyl-homoserine lactone acylase from pseudomonas aeruginosa pao1.	the virulence of the opportunistic human pathogen pseudomonas aeruginosa pao1 is controlled by an n-acyl-homoserine lactone (ahl)-dependent quorum-sensing system. during functional analysis of putative acylase genes in the p. aeruginosa pao1 genome, the pa2385 gene was found to encode an acylase that removes the fatty acid side chain from the homoserine lactone (hsl) nucleus of ahl-dependent quorum-sensing signal molecules. analysis showed that the posttranslational processing of the acylase and ...	2006	16495538
identification of a meningococcal l-glutamate abc transporter operon essential for growth in low-sodium environments.	gdhr is a meningococcal transcriptional regulator that was previously shown to positively control the expression of gdha, encoding the nadp-specific l-glutamate dehydrogenase (nadp-gdh), in response to the growth phase and/or to the carbon source. in this study we used reverse transcriptase-pcr-differential display (to identify additional gdhr-regulated genes. the results indicated that gdhr, in addition to nadp-gdh, controls the expression of a number of genes involved in glucose catabolism by ...	2006	16495545
in vitro testing for genotoxicity of violacein assessed by comet and micronucleus assays.	chromobacterium violaceum is a gram (-) bacteria found in water samples and soils from tropical and subtropical regions of the world. violacein, the major pigment produced by these bacteria, has been shown to have antibiotic, antitumoral and trypanocidal activities. in the present work, the genotoxicity of violacein was investigated in four different cell lines by using the alkaline comet assay and in vero cells using the micronucleus test. in the alkaline comet assay, violacein, when tested at ...	2006	16359912
xbase, a collection of online databases for bacterial comparative genomics.	the schema of the previously described escherischia coli database colibase has been applied to a number of other bacterial taxa, under the collective name xbase. the new databases include campydb for campylobacter, helicobacter and wolinella; pseudodb for pseudomonads; clostridb for clostridia; rhizodb for rhizobium and sinorhizobium; and mycodb, for mycobacterium, streptomyces and related organisms. the databases provide user friendly access to annotation and genome comparisons through a web-ba ...	2006	16381881
xbase, a collection of online databases for bacterial comparative genomics.	the schema of the previously described escherischia coli database colibase has been applied to a number of other bacterial taxa, under the collective name xbase. the new databases include campydb for campylobacter, helicobacter and wolinella; pseudodb for pseudomonads; clostridb for clostridia; rhizodb for rhizobium and sinorhizobium; and mycodb, for mycobacterium, streptomyces and related organisms. the databases provide user friendly access to annotation and genome comparisons through a web-ba ...	2006	16381881
specificity of acyl-homoserine lactone synthases examined by mass spectrometry.	many gram-negative bacteria produce a specific set of n-acyl-l-homoserine-lactone (ahl) signaling molecules for the purpose of quorum sensing, which is a means of regulating coordinated gene expression in a cell-density-dependent manner. ahls are produced from acylated acyl-carrier protein (acyl-acp) and s-adenosyl-l-methionine by the ahl synthase enzyme. the appearance of specific ahls is due in large part to the intrinsic specificity of the enzyme for subsets of acyl-acp substrates. structural ...	2006	16385066
quorum-sensing signal synthesis by the yersinia pestis acyl-homoserine lactone synthase yspi.	the acyl-homoserine lactone molecular species (ahls) produced by the yersinia pestis ahl synthase yspi were identified by biochemical and physical/chemical techniques. bioassays of extracts from culture supernatants of the recombinant yspi and wild-type yersinia pestis showed similar profiles of ahls. analysis by liquid chromatography-mass spectrometry revealed that the predominant ahls were n-3-oxooctanoyl-l-homoserine lactone and n-3-oxo-hexanoyl-l-homoserine lactone.	2006	16385067
development and evaluation of a real-time pcr assay targeting the type iii secretion system of burkholderia pseudomallei.	here we report on the development of a discriminatory real-time assay for the rapid identification of burkholderia pseudomallei isolates and the evaluation of this assay for sensitivity against related species and detection in spiked human blood samples. the assay targets a 115-base-pair region within orf2 of the b. pseudomallei type iii secretion system gene cluster and distinguishes b. pseudomallei from other microbial species. assay performance was evaluated with 224 geographically, temporall ...	2006	16390953
anaerobic nitrate-dependent iron(ii) bio-oxidation by a novel lithoautotrophic betaproteobacterium, strain 2002.	microbial nitrate-dependent fe(ii) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. in an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent fe(ii)-oxidizing microbial community and subsequent isolation of a nitrate-dependent ...	2006	16391108
anti-quorum sensing activity of medicinal plants in southern florida.	bacterial intercellular communication, or quorum sensing (qs), controls the pathogenesis of many medically important organisms. anti-qs compounds are known to exist in marine algae and have the ability to attenuate bacterial pathogenicity. we hypothesized that terrestrial plants traditionally used as medicines may also produce anti-qs compounds. to test this hypothesis, 50 medicinal plants from southern florida were screened for anti-qs activity using two biomonitor strains, chromobacterium viol ...	2006	16406418
[chromobacteriosis in ilhéus, bahia: epidemiologic, clinical and laboratorial investigation].	in april/2004, a group of people traveled to a farm in a town in the south of bahia and afterwards, three teenagers from the same family developed symptoms of severe septicemia and two died. the health department carried out an epidemiologic, clinical, laboratory and environmental investigation that resulted in the identification of chromobacterium violaceum, in biological material from one of them, water and soil. this is the first report of the disease in bahia state.	2006	16410927
canine adenovirus vectors for lung-directed gene transfer: efficacy, immune response, and duration of transgene expression using helper-dependent vectors.	a major hurdle to the successful clinical use of some viral vectors relates to the innate, adaptive, and memory immune responses that limit the efficiency and duration of transgene expression. some of these drawbacks may be circumvented by using vectors derived from nonhuman viruses such as canine adenovirus type 2 (cav-2). here, we evaluated the potential of cav-2 vectors for gene transfer to the respiratory tract. we found that cav-2 transduction was efficient in vivo in the mouse respiratory ...	2006	16415025
detection of chromobacterium violaceum by multiplex pcr targeting the prgi, spao, invg, and sipb genes.	based on the recently completed genomic sequence of chromobacterium violaceum american type culture collection (atcc) 12472 a multiplex pcr assay targeting the prgi, spao, invg, and sipb genes of the salmonella spi-1 homologue type-iii secretion system was developed. pcr products of 255bp (prgi), 749bp (spao), 1685bp (invg), and 1752bp (sipb) were successfully amplified simultaneously in a single reaction with all chr. violaceum strains investigated whereas other bacteria tested negative. the de ...	2006	16423655
analysis of the lateral flagellar gene system of aeromonas hydrophila ah-3.	mesophilic aeromonas strains express a polar flagellum in all culture conditions, and certain strains produce lateral flagella on semisolid media or on surfaces. although aeromonas lateral flagella have been described as a colonization factor, little is known about their organization and expression. here we characterized the complete lateral flagellar gene cluster of aeromonas hydrophila ah-3 containing 38 genes, 9 of which (lafa-u) have been reported previously. among the flgll and lafa structu ...	2006	16428388
n-acylhomoserine lactones antagonize virulence gene expression and quorum sensing in staphylococcus aureus.	many gram-negative bacteria employ n-acylhomoserine lactone (ahl)-mediated quorum sensing to control virulence. to determine whether gram-positive bacteria such as staphylococcus aureus respond to ahls, we used a growth-dependent lux reporter fusion. exposure of s. aureus to different ahls revealed that 3-oxo-substituted ahls with c10 to c14 acyl chains inhibited light output and growth in a concentration-dependent manner, while short-chain ahls had no effect. n-(3-oxododecanoyl)-l-homoserine la ...	2006	16428734
a constitutively expressed, truncated umudc operon regulates the reca-dependent dna damage induction of a gene in acinetobacter baylyi strain adp1.	in response to environmentally caused dna damage, sos genes are up-regulated due to reca-mediated relief of lexa repression. in escherichia coli, the sos umudc operon is required for dna damage checkpoint functions and for replicating damaged dna in the error-prone process called sos mutagenesis. in the model soil bacterium acinetobacter baylyi strain adp1, however, the content, regulation, and function of the umudc operon are unusual. the umuc gene is incomplete, and a remnant of an isehe3-like ...	2006	16751513
structure of the pii signal transduction protein of neisseria meningitidis at 1.85 a resolution.	the p(ii) signal transduction proteins glnb and glnk are implicated in the regulation of nitrogen assimilation in escherichia coli and other enteric bacteria. p(ii)-like proteins are widely distributed in bacteria, archaea and plants. in contrast to other bacteria, neisseria are limited to a single p(ii) protein (nmb 1995), which shows a high level of sequence identity to glnb and glnk from escherichia coli (73 and 62%, respectively). the structure of the p(ii) protein from n. meningitidis (sero ...	2006	16754965
fatal septicaemia from chromobacterium violaceum: case reports and review of the literature.	chromobacterium violaceum rarely causes infection in humans and its mechanism of pathogenicity is not well understood. human infection carries a high mortality rate with a fulminating clinical progression. a high index of suspicion is required for diagnosis, and is based on recovering the organisms from blood cultures or other appropriate specimens. we present three cases of human infection managed in a tertiary referral hospital in hong kong with a review of the literature.	2006	16760554
unusual entropy-driven affinity of chromobacterium violaceum lectin cv-iil toward fucose and mannose.	the purple pigmented bacterium chromobacterium violaceum is a dominant component of tropical soil microbiota that can cause rare but fatal septicaemia in humans. its sequenced genome provides insight into the abundant potential of this organism for biotechnological and pharmaceutical applications and allowed an orf encoding a protein that is 60% identical to the fucose binding lectin (pa-iil) from pseudomonas aeruginosa and the mannose binding lectin (rs-iil) from ralstonia solanacearum to be id ...	2006	16768446
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
rooting the tree of life by transition analyses.	despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed--the most difficult problems in phylogeny. protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution; ribosome-related and dna-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it ...	2006	16834776
identification and characterization of bacterial cysteine dioxygenases: a new route of cysteine degradation for eubacteria.	in metazoa and fungi, the catabolic dissimilation of cysteine begins with its sulfoxidation to cysteine sulfinic acid by the enzyme cysteine dioxygenase (cdo). in these organisms, cdo plays an important role in the homeostatic regulation of steady-state cysteine levels and provides important oxidized metabolites of cysteine such as sulfate and taurine. to date, there has been no experimental evidence for the presence of cdo in prokaryotes. using psi-blast searches and crystallographic informatio ...	2006	16855246
roles of the host oxidative immune response and bacterial antioxidant rubrerythrin during porphyromonas gingivalis infection.	the efficient clearance of microbes by neutrophils requires the concerted action of reactive oxygen species and microbicidal components within leukocyte secretory granules. rubrerythrin (rbr) is a nonheme iron protein that protects many air-sensitive bacteria against oxidative stress. using oxidative burst-knockout (nadph oxidase-null) mice and an rbr gene knockout bacterial strain, we investigated the interplay between the phagocytic oxidative burst of the host and the oxidative stress response ...	2006	16895445
evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella.	the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ...	2006	16923880
expression, purification, crystallization and preliminary crystallographic analysis of bipd, a component of the burkholderia pseudomallei type iii secretion system.	a construct consisting of residues 10-310 of bipd, a component of the burkholderia pseudomallei type iii secretion system (t3ss), has been overexpressed as a gst fusion, cleaved from the gst tag and purified. crystals were grown of native and selenomethionine-labelled bipd. the crystals grow in two different polymorphs from the same condition. the first polymorph belongs to space group c222, with unit-cell parameters a = 103.98, b = 122.79, c = 49.17 a, a calculated matthews coefficient of 2.4 a ...	2006	16946464
two 2[5h]-furanones as possible signaling molecules in lactobacillus helveticus.	two 2[5h]-furanones, in association with medium-chain fatty acids, were released in whey by lactobacillus helveticus exposed to oxidative and heat stresses. this species plays an important role in cheese technology, particularly for swiss-type cheeses and grana cheese. moreover, it significantly contributes to cheese ripening by means of an early autolysis and the release of enzymes during processing. experimental evidence of the involvement of the two 2[5h]-furanones, detected by a gas chromato ...	2006	16957229
mouse and human cell activation by n-dodecanoyl-dl-homoserine lactone, a chromobacterium violaceum autoinducer.	chromobacterium violaceum produces autoinducers, including homoserine lactones (hsls), for genetic regulation. among the seven hsls derived from c. violaceum we evaluated, only c(12)-hsl stimulated the production of inflammatory cytokines in mammalian monocytic cell lines through the activation of the nf-kappab signaling pathway besides their quorum-sensing role, like 3-oxo-c(12)-hsl from pseudomonas aeruginosa.	2006	16982829
mutations within the catalytic motif of dna adenine methyltransferase (dam) of aeromonas hydrophila cause the virulence of the dam-overproducing strain to revert to that of the wild-type phenotype.	in this study, we demonstrated that the methyltransferase activity associated with dam was essential for attenuation of aeromonas hydrophila virulence. we mutated aspartic acid and tyrosine residues to alanine within the conserved dppy catalytic motif of dam and transformed the pbad/damd/a, pbad/damy/a, and pbad/damahssu (with the native dam gene) recombinant plasmids into the escherichia coli gm33 (dam-deficient) strain. genomic dna (gdna) isolated from either of the e. coli gm33 strains harbor ...	2006	16988254