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planktonic marine luminous bacteria: species distribution in the water column.luminous bacteria were isolated from oceanic water samples taken throughout the upper 1,000 m and ranged in density from 0.4 to 30 colony-forming units per 100 ml. generally, two peaks in abundance were detected: one in the upper 100 m of the water column, which consisted primarily of beneckea spp.; and a second between 250 and 1,000 m, which consisted almost entirely of photobacterium phosphoreum. the population of p. phosphoreum remained relatively stable in abundance at one station that was v ...198016345502
distribution and identification of luminous bacteria from the sargasso sea.vibrio fischeri and lucibacterium harveyi constituted 75 of the 83 luminous bacteria isolated from sargasso sea surface waters. photobacterium leiognathi and photobacterium phosphoreum constituted the remainder of the isolates. luminescent bacteria were recovered at concentrations of 1 to 63 cells per 100 ml from water samples collected at depths of 160 to 320 m. two water samples collected at the thermocline yielded larger numbers of viable, aerobic heterotrophic and luminous bacteria. luminesc ...198016345575
species composition and barotolerance of gut microflora of deep-sea benthic macrofauna collected at various depths in the atlantic ocean.the bacterial flora of marine animals collected at depths of 570 to 2,446 m was examined for population size and generic composition, and the barotolerant characteristics of selected bacterial isolates were determined. total numbers of culturable, aerobic, heterotrophic bacteria were found to be low in animals collected at the greatest ocean depths sampled in this study. vibrio spp. were predominant in 10 of 15 samples examined, and photobacterium spp. and yeasts were the major components of the ...198016345648
identification of vibrio splendidus as a member of the planktonic luminous bacteria from the persian gulf and kuwait region with luxa probes.hybridization probes specific for the luxa genes of four groups of luminous bacteria were used to screen luminous isolates obtained from the persian gulf, near al khiran, kuwait nine of these isolates were identified as vibrio harveyi, a commonly encountered planktonic isolate, while three others showed no hybridization to any of the four probes (v. harveyi, vibrio fischeri, photobacterium phosphoreum, or photobacterium leiognathi) under high-stringency conditions. polymerase chain reaction ampl ...199316349023
spinal deformity in a sandtiger shark, carcharias taurus rafinesque: a clinical-pathological study.the present study investigated spinal deformity in a captive sandtiger shark and describes the clinical and histopathological features of the lesion. clinically, the shark presented a marked spinal curvature in the region between the pectoral girdle and cranial dorsal fin. radiographic studies revealed scoliosis and kyphosis of the vertebral column with a modification of the basic structure of five vertebrae. post-mortem examination confirmed the results of radiographic studies and histological ...200616351698
[inhibitory effects of phenolic ecotoxicants on photobacteria at various ph values].kinetic characteristics of light emission by intact cells of the photobacteria photobacterium phosphoreum and vibrio harveyi at ph 5.5, 7.0, and 8.0 were studied as well as specific features of inhibitory effects of 2,4-di- and 2,4,5-triphenoxyacetic acids (2,4-d and 2,4,5-t), pentachlorophenol (pcp), and 2,6-dimethylphenol (2,6-dmp) at the same ph values. nonstationarity of emission kinetics was observed at all the ph values studied. exponential luminescence decay in a 60-sec range was observed ...200516358753
characterization of volatile compounds in chilled cod (gadus morhua) fillets by gas chromatography and detection of quality indicators by an electronic nose.volatile compounds in cod fillets packed in styrofoam boxes were analyzed during chilled storage (0.5 degrees c) by gas chromatography (gc)-mass spectrometry and gc-olfactometry to screen potential quality indicators present in concentrations high enough for detection by an electronic nose. photobacterium phosphoreum dominated the spoilage bacteria on day 12 when the fillets were rejected by sensory analysis. ketones, mainly 3-hydroxy-2-butanone, were detected in the highest level (33%) at senso ...200516366707
oxidation of resin and fatty acids by ozone: kinetics and toxicity study.the ozonation of resin and fatty acids (rfas) found in pulp mill effluents was investigated using rapid-scan stopped-flow spectrophotometry. rfas oxidation (i.e., degradation) efficiency increased with increasing the amount of used ozone and temperature. the degradation process with respect to the acid was found to follow first-order kinetics. the ozonation of rfas was modeled as an overall second-order reaction for both reactants. the apparent overall second-order rate constants were calculated ...200616376965
bioluminescence and exogenous compounds: physico-chemical basis for bioluminescent assay.bioluminescent systems are convenient objects to study mechanisms of influence of exogenous molecules on living organisms. classification of physical and physico-chemical mechanisms of the effects of luminous bacteria photobacterium leiognathi on bioluminescent reactions is suggested. five mechanisms are discussed: (1) change of electron-excited states' population and energy transfer, (2) change of efficiency of s-t conversion in the presence of external heavy atom, (3) change of rates of couple ...200616413195
the sos-lux-toxicity-test on the international space station.for the safety of astronauts and to ensure the stability and integrity of the genome of microorganisms and plants used in bioregenerative life support systems, it is important to improve our knowledge of the combined action of (space) radiation and microgravity. the sos-lux-toxicity test, as part of the triple-lux project (accepted for flight at biolab in columbus on the international space station, (iss)), will provide an estimation of the health risk resulting from exposure of astronauts to th ...200616431084
effects of chlorine disinfection on toxicity formation in reclaimed water. 200616468000
rapid identification of marine bioluminescent bacteria by amplified 16s ribosomal rna gene restriction analysis.to rapidly identify natural isolates of marine bioluminescent bacteria, we developed amplified ribosomal dna restriction analysis (ardra) methods. ardra, which is based on the restriction patterns of 16s rrna gene digested with five enzymes (ecori, ddei, hhai, hinfi, rsai), clearly distinguished the 14 species of marine bioluminescent bacteria currently known, which belong to the genera vibrio, photobacterium, and shewanella. when we applied ardra to 129 natural isolates from two cruises in saga ...200616499620
first isolation of photobacterium damselae ssp. damselae from cultured redbanded seabream, pagrus auriga valenciennes, in spain. 200616533303
evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria.evolutionary relationships of cultivated barophilic bacteria were determined. all psychrophilic and barophilic isolates were affiliated with one of five genera of the gamma subdivision of the class proteobacteria ((gamma)-proteobacteria): shewanella, photobacterium, colwellia, moritella, and a new group containing strain cnpt3. the data indicate that the barophilic phenotype has evolved independently in different (gamma)-proteobacteria genera.199716535621
photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water.a marine bacterial strain, designated fr1311t, was isolated from a sea-water sample from ganghwa island, south korea. cells were gram-negative, facultatively anaerobic, catalase- and oxidase-positive, motile, oval or rod-shaped and halophilic (optimum sea-salt concentration for growth of 5-6 %). phylogenetic analysis of its 16s rrna gene sequence revealed that it represented a distinct line of descent within the genus photobacterium. the major fatty acids were straight-chain saturated (c(16 : 0) ...200616585687
isolation of the in vivo emitter in bacterial bioluminescence.a blue fluorescence protein has been isolated and purified from extracts of the luminous bacterium photobacterium phosphoreum. it is a single polypeptide of molecular weight 22,000 with absorption maxima at 274 and 418 nm. it is efficiently fluorescent (varphi(f) 0.45), with a fully corrected spectral maximum (476 nm) and distribution identical to the in vivo bioluminescence from this same type of bacterium. at low concentration this fluorescence shifts towards the red and becomes identical to t ...197816592497
separation and structure of the prosthetic group of the blue fluorescence protein from the bioluminescent bacterium photobacterium phosphoreum.the highly fluorescent prosthetic group of the blue fluorescence protein purified from the bioluminescent bacterium photobacterium phosphoreum has been dissociated and separated from its apoprotein by affinity chromatography on cibacron blue-sepharose. it has been identified as 6,7-dimethyl-8-(1'-d-ribityl)lumazine by several methods of characterization, all of which gave results identical to those for an authentic sample. in neutral solution, absorption maxima are at 407, 275 (shoulder), and 25 ...197916592674
acyl-acyl carrier protein as a source of fatty acids for bacterial bioluminescence.pulse-chase experiments with [(3)h]tetradecanoic acid and atp showed that the bioluminescence-related 32-kda acyltransferase from vibrio harveyi can specifically catalyze the deacylation of a (3)h-labeled 18-kda protein observed in extracts of this bacterium. the 18-kda protein has been partially purified and its physical and chemical properties strongly indicate that it is fatty acyl-acyl carrier protein (acyl-acp). both this v. harveyi [(3)h]acylprotein and [(3)h]palmitoyl-acp from escherichia ...198516593602
dual function of fish hepcidin: response to experimental iron overload and bacterial infection in sea bass (dicentrarchus labrax).the role of hepcidin in iron metabolism regulation and bacterial infection has been the focus of recent attention. however, in spite of the growing number of hepcidin genes known from different organisms, little is known about its putative dual function in fish. the aim of this study was to characterize the sea bass hepcidin gene and to study its role in iron metabolism and infection. the novel sea bass hepcidin gene was found to be organized into two introns and three exons with several copies ...200616616368
photobacterium halotolerans sp. nov., isolated from lake martel in spain.a halotolerant bacterium was isolated from a saline lake located in mallorca, spain. cells of the strain, designated macl01t, were gram-negative, rod-shaped and motile by means of polar flagella. colonies of strain macl01t were white to cream in tsa medium, turning brown after 7 days of incubation; they were blue in thiosulphate/citrate/bile salts/sucrose agar medium. a neighbour-joining phylogenetic analysis based on 16s rrna gene sequences showed that strain macl01t belongs to the genus photob ...200616627656
formation of histamine and biogenic amines in cold-smoked tuna: an investigation of psychrotolerant bacteria from samples implicated in cases of histamine fish poisoning.two outbreaks and a single case of histamine fish poisoning associated with cold-smoked tuna (cst) were reported in denmark during 2004. the bacteria most likely responsible for histamine formation in cst implicated in histamine fish poisoning was identified for the first time in this study. product characteristics and profiles of biogenic amines in the implicated products were also recorded. in the single poisoning case, psychrotolerant morganella morganii-like bacteria most likely was responsi ...200616629036
aldolase-catalyzed synthesis of beta-d-galp-(1-->9)-d-kdn: a novel acceptor for sialyltransferases.[reaction: see text] beta-d-galp-(1-->9)-d-kdn, a disaccharide component of the cell wall of streptomyces sp. mb-8, was synthesized from beta-d-galp-(1-->6)-d-manp and pyruvate using a sialic acid aldolase. the obtained kdn-containing compound was a novel acceptor for bacterial sialyltransferases. unusual alpha2,3- and alpha2,6-linked sialyltrisaccharides and a tetrasaccharide were synthesized using a one-pot two-enzyme system containing a neisseria meningitidis cmp-sialic acid synthetase and a ...200616706534
drug resistance and random amplified polymorphic dna analysis of photobacterium damselae ssp. piscicida isolates from cultured seriola (yellowtail, amberjack and kingfish) in japan.to investigate the antimicrobial susceptibility and genetic characteristics of photobacterium damselae ssp. piscicida isolates obtained from cultured seriola in japan.200616706907
highly efficient chemoenzymatic synthesis of naturally occurring and non-natural alpha-2,6-linked sialosides: a p. damsela alpha-2,6-sialyltransferase with extremely flexible donor-substrate specificity. 200616721893
infection with photobacterium damselae subspecies damselae and vibrio harveyi in snapper, pagrus auratus with bloat.to diagnose the cause of chronic, low mortality associated with bloat in tanks of snapper at an aquaculture facility.200616739527
[proteolytic activity of luminous bacteria]. 200616758880
superoxide dismutase and catalase activities in photobacterium damselae ssp. piscicida.the ability of a set of photobacterium damselae ssp. piscicida strains isolated from different fish species to produce different superoxide dismutase (sod) and catalase enzymes was determined. unlike other bacterial pathogens, p. damselae ssp. piscicida is not able to produce different isoforms of sod or catalase containing different metal cofactors when cultured under oxidative stress induced by hydrogen peroxide or methyl viologen, or under iron depleted conditions. however, iron content of th ...200616768716
effect of salt stress on pigment production of serratia rubidaea n-1: a potential indicator strain for screening quorum sensing inhibitors from marine microbes. 200616778355
molecular cloning and characterisation of sea bass (dicentrarchus labrax l.) caspase-3 gene.caspase-3 is one of the major caspases operating in apoptosis, cleaving and inactivating a number of molecules and largely contributing to the apoptotic phenotype and the dismantling of the apoptoting cell. the opening reading frame of sea bass (dicentrarchus labrax l.) caspase-3 has 281 amino acids. the complete sequence of caspase-3 shows a very close homology to the correspondent sequence from other vertebrates, in particularly with that of takifugu rubripes and oryzias latipes, with 87.7 and ...200716780952
piezophilic adaptation: a genomic point of view.two-thirds of earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology of marine species. as oceans present an average depth of 3800 m, deep-sea ecosystems represent the most common marine ecological niche. one of the key ...200616780980
larval settlement of the common australian sea urchin heliocidaris erythrogramma in response to bacteria from the surface of coralline algae.bacterial biofilms are increasingly seen as important for the successful settlement of marine invertebrate larvae. here we tested the effects of biofilms on settlement of the sea urchin heliocidaris erythrogramma. larvae settled on many surfaces including various algal species, rocks, sand and shells. settlement was reduced by autoclaving rocks and algae, and by treatment of algae with antibiotics. these results, and molecular and culture-based analyses, suggested that the bacterial community on ...200616794830
cloning and sequencing analysis of alginate lyase genes from the marine bacterium vibrio sp. o2.we isolated a new marine bacteria, which displayed alginate-depolymerizing activity in plate assays, from seawater in mihonoseki harbor, japan. analysis of the 16s ribosomal rna gene sequence of one of the isolates proved that this alginate-depolymerizing bacterium belonged to the genus vibrio and it was named vibrio sp. o2. the alginate lyase genes of vibrio sp. o2 were cloned and expressed in escherichia coli. two alginate lyase-producing clones, pvoa-a4 and pvoa-b5, were obtained. the alginat ...200616810458
biogenic amine formation and microbial spoilage in chilled garfish (belone belone belone)--effect of modified atmosphere packaging and previous frozen storage.to evaluate biogenic amine formation and microbial spoilage in fresh and thawed chilled garfish.200616834594
bioavailability and toxicity of heavy metals in the presence of natural organic matter.the effect of humic acids (ha) on the toxicity of copper, zinc and lead was investigated in this study, using the photobacterium vibrio fischeri (microtox test) as a test organism. the metal species and the complexation capacity of ha were predicted using model winhumicv for speciation modeling. the toxicities of copper and lead were generally comparable, while the toxicity of zinc was lower than the ones of the other two method. the toxicity of copper decreased with the addition of ha, while th ...200616835107
application of leaching tests for toxicity evaluation of coal fly ash.the toxic properties of coal fly ash samples obtained from various coal combustion power plants were evaluated in this work using physicochemical analyses and bioassays. physicochemical analyses showed that heavy metals present in solid samples included cr, cu, mn, ni, pb, and zn. the results of the chemical analysis of eluates deduced by the application of standard leaching tests according to en 12457-2 and toxicity characteristic leaching procedure (tclp) methods indicated that the compounds c ...200616841327
luxa gene of light organ symbionts of the bioluminescent fish acropoma japonicum (acropomatidae) and siphamia versicolor (apogonidae) forms a lineage closely related to that of photobacterium leiognathi ssp. mandapamensis.a molecular phylogenetic analysis of luxa gene sequences of light organ symbionts of the fish acropoma japonicum (acropomatidae) and siphamia versicolor (apogonidae) revealed that the sequences were related to those of photobacterium leiognathi ssp. mandapamensis, which is not known to occur as a light organ symbiont among bioluminescent p. leiognathi clades. the presence of another lux gene element, luxf, coding for nonfluorescent protein, provided additional support for the identity of the lig ...200616842343
rapid and onsite bod sensing system using luminous bacterial cells-immobilized chip.a bod monitoring system based on a bio-chip which immobilized luminous bacterium in micrometer-order holes were arrayed and fabricated by micro-machine techniques, was developed. the acrylic chip (3 cmx3 cm) comprises nine micro-holes (diameter: 700 microm or 1 mm, depth: 100 microm) arranged in a three by three array. cells of the marine luminous bacterium, photobacterium phosphoreum ifo 13896, which was grown at 15 degrees c for 15 h, were immobilized with 3% or 15% sodium alginate gel. bod st ...200716846732
[heterogeneity of the populations of marine luminescent bacteria photobacterium leiognathi under different conditions of cultivation].manifestation of pleiotropic effects in the isogenic variants of luminescent bacteria photobacterium leiognathi 54 was investigated. the decrease or increase of the expression level of bioluminescence was caused by changes in lux operon regulation. the dynamics of the bioluminescence of dark and dim variants did not differ from the dynamics of the initial luminescent variant, but dependence of the level of luminescence intensity on the exogenous autoinductor of the lux operon was revealed. the i ...200616871801
toxicity and quantitative structure-activity relationships of nitriles based on pseudokirchneriella subcapitata.this study presents the toxicity data of various nitriles to pseudokirchneriella subcapitata using a closed algal toxicity testing technique with no headspace. two different response endpoints, i.e., dissolved oxygen (do) production and algal growth rate, were used to evaluate the toxicity of nitriles. in general, the do endpoint revealed higher inhibitory effects than that from algal growth rate. furthermore, halogen-substituted nitriles were found to be extremely toxic to p. subcapitata. with ...200716875732
fluorescence and bioluminescence analysis of sequential uv-biological degradation of p-cresol in water.the photolysis and penicillium tardum h-2 degradation of p-cresol in water containing humic acids was investigated by fluorescence and bioluminescence methods. humic acids extracted from peat (the vasuygan bog, tomsk region of russia) induce the phototransformation of p-cresol. the influence of humic acids on the phototransformation of p-cresol under different irradiation conditions was investigated. comparison of the data on the krcl* (lambda = 222 nm) and xecl* (lambda = 308 nm) excilamps ligh ...200716886235
influence of storage temperature on microbial spoilage characteristics of haddock fillets (melanogrammus aeglefinus) evaluated by multivariate quality prediction.the proliferation of specific spoilage organisms (sso) and quality changes were evaluated in haddock fillets stored in styrofoam boxes at 0, 7 and 15 degrees c and under temperature fluctuations. a rapid electronic nose technique was used to monitor different classes of compounds, representing microbial metabolites that were characteristic for the onset of spoilage odors. photobacterium phosphoreum predominated among the spoilage bacteria and high levels of tvb-n were observed at sensory rejecti ...200616889858
screening and estimating of toxicity formation with photobacterium bioassay during chlorine disinfection of wastewater.reclamation and reuse of wastewater is one of the most effective ways to alleviate water shortage. disinfection plays a key role in killing the harmful pathogens in reclaimed water, while an unwanted side effect is the formation of disinfection by-products (dbps). recently, a number of researches have been conducted on the formation regularities of certain dbps. however, with current physiochemical techniques, it is impossible to detect all the dbps. in this study, photobacterium bioassay was us ...200716916574
cloning and sequencing of the histidine decarboxylase gene from photobacterium phosphoreum and its functional expression in escherichia coli.the major causative agent of scombroid poisoning is histamine formed by bacterial decarboxylation of histidine. we reported previously that histamine was exclusively formed by the psychrotrophic halophilic bacteria photobacterium phosphoreum in scombroid fish during storage at or below 10 degrees c. moreover, histamine-forming ability was affected by two histidine decarboxylases (hdcs): constitutive and inducible enzymes. in this study, the gene encoding p. phosphoreum hdc was cloned into escher ...200616924898
stability of chloramphenicol residues in shrimp subjected to heat processing treatments.the stability of chloramphenicol residues in white shrimp (penaeus indicus) subjected to cooking (100 degrees c) for 10, 20 and 30 min (c1, c2 and c3) as well as retorting (121 degrees c) for 10 and 15 min (r1 and r2) was studied by a microbial assay method using photobacterium leiognathi as the test organism. the microbial assay method was found to have a good sensitivity of 1 microg/ml the loss of chloramphenicol in shrimp subjected to cooking for 10, 20 and 30 min was 6%, 12% and 29%, respect ...200616942985
ompw and ompv are required for nacl regulation in photobacterium damsela.photobacterium damsela is a marine pathogen to both fish and human beings. the bacterium can shift between the ambient seawater and hosts, suggesting the existence of proteins rapidly responding to salt concentration. in the current study, proteomic methodologies were applied to screen the outer membrane proteins (omps) related to salt stress. ompw and ompv were determined in the response in this bacterium as ompc and ompf did in e. coli. furthermore, the two genes were overexpressed in e. coli ...200616944937
effect of bacterial interactions on the spoilage of cold-smoked salmon.cold-smoked salmon is a lightly preserved fish product in which a mixed microbial flora develops during storage and where the interactive behaviour of micro-organisms may contribute to their growth and spoilage activity. the aim of this study was to assess the effect of the bacterial interactions between the main species contaminating the cold-smoked salmon on bacterial growth, chemical and sensory changes, and spoilage. first, carnobacterium piscicola, photobacterium phosphoreum, lactobacillus ...200616949172
control of the bioluminescence starting time by inoculated cell density.in this study, we attempted to control the timing of light-emission from bioluminescent bacteria, by changed cell numbers inoculated into medium. luminous bacteria express bioluminescence when the number of cells reached a threshold. inoculated cell density had an effect on the time of bioluminescence starting. samples were prepared by varying cell density of inoculation. in the results, all the vials showed different luminescence profiles in the order of inoculated cell population.200616966816
eliminating toxic compounds by composting olive mill wastewater-straw mixtures.the present work studies the changes occurring in organic matter, phenols and biotoxicity on composting olive mill wastewater with barley straw. the total organic matter decreased, a drop of 25% was reached after the stabilization phase and 52% at the end of the maturation phase. degradation of the phenols reached 54% and 95%, respectively, after these periods. the toxicity of the water extract, evaluated by the photobacterium phosphoreum fluorescence, decreased to disappear after only 2 months ...200616973264
first molecular cloning and characterisation of caspase-9 gene in fish and its involvement in a gram negative septicaemia.caspase-9 is an initiator caspase in the apoptotic process whose function is to activate effector caspases that are downstream in the mitochondrial pathway of apoptosis. this work reports for the first time the complete sequencing and characterisation of caspase-9 in fish. a 1924bp cdna of sea bass caspase-9 was obtained, consisting of 1308bp open reading frame coding for 435 amino acids, 199bp of the 5'-utr and 417bp of the 3'-utr including a canonical polyadenilation signal 10 nucleotides upst ...200716989898
photolyase confers resistance to uv light but does not contribute to the symbiotic benefit of bioluminescence in vibrio fischeri es114.recent reports suggest that the selective advantage of bioluminescence for bacteria is mediated by light-dependent stimulation of photolyase to repair dna lesions. despite evidence for this model, photolyase mutants have not been characterized in a naturally bioluminescent bacterium, nor has this hypothesis been tested in bioluminescent bacteria under natural conditions. we have now characterized the photolyase encoded by phr in the bioluminescent bacterium vibrio fischeri es114. consistent with ...200617021211
characterization of japanese flounder (paralichthys olivaceus) nk-lysin, an antimicrobial peptide.the nk-lysin cdna of japanese flounder, paralichthys olivaceus, consists of 657bp, containing an open reading frame (orf) of 444bp, which encodes 147 amino acid residues. the amino acid sequence of japanese flounder nk-lysin has 21% identity to porcine nk-lysin and bovine nk-lysin, 23% to equine nk-lysin, and 46% to zebrafish nk-lysin-like protein. multiple alignments of japanese flounder nk-lysin and other known saposin-like proteins revealed that the six cysteine residues important for structu ...200717046282
molecular characterization, 3d modelling and expression analysis of sea bass (dicentrarchus labrax l.) interleukin-10.interleukin-10 (il-10) is a pleiotropic cytokine generally known for its relevance in the resolution of inflammation, but that also has immunostimulatory properties. here is described the isolation and characterization of the sea bass il-10 (sbil-10) cdna and gene. the sbil-10 gene encodes a 187 amino acid protein and comprises a five exon-four intron structure as other known il-10 genes. important structural residues are maintained in the sbil-10 protein, including the four cysteines responsibl ...200717049605
differential annotation of trna genes with anticodon cat in bacterial genomes.we have developed three strategies to discriminate among the three types of trna genes with anticodon cat (trna(ile), elongator trna(met) and initiator trna(fmet)) in bacterial genomes. with these strategies, we have classified the trna genes from 234 bacterial and several organellar genomes. these sequences, in an aligned or unaligned format, may be used for the identification and annotation of trna (cat) genes in other genomes. the first strategy is based on the position of the problem sequenc ...200617071718
a siderophore biosynthesis gene cluster from the fish pathogen photobacterium damselae subsp. piscicida is structurally and functionally related to the yersinia high-pathogenicity island.photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis, produces a siderophore which is distinct from that produced by p. damselae subsp. damselae. using suppression subtractive hybridization, a subsp. piscicida-specific dna region of 35 kb was identified in strain di21, and 11 genes were defined: dahp, arac1, arac2, frpa, irp8, irp2, irp1, irp3, irp4, irp9 and irp5. the sequence of the predicted proteins encoded by these genes showed significant similarity with the ...200617074903
[joint toxicity on multi-component mixtures of sds and substituted aromatic compounds].the toxicity to photobacterium phosphoreum of different mixture systems of sodium dodecyl sulfate (sds) and three substituted aromatic compounds according to equiconcentration ratio of 1 : 1, as well as individual toxicity, were determined respectively. the joint toxicity was evaluated by toxicity unit (tu), additive index (ai), similarity parameter (lambda), and mixtures toxicity index (mti). four evaluating methods were compared and the modes of joint action of different systems were analyzed ...200617111627
identification of an antibacterial protein as l-amino acid oxidase in the skin mucus of rockfish sebastes schlegeli.fish skin mucus contains a variety of antimicrobial proteins and peptides that seem to play a role in self defense. we previously reported an antibacterial protein in the skin secretion of the rockfish, sebastes schlegeli, which showed selective antibacterial activity against gram-negative bacteria. this study aimed to isolate and structurally and functionally characterize this protein. the antibacterial protein, termed ssap (s. schlegeli antibacterial protein), was purified to homogeneity by le ...200717140417
[obtaining of bacterial bioluminescent strain protobacterium phosphoreum b7071 (lux+) for the determination of zinc ion concentration].the transconjugate containing hybrid plasmid (te(r)zn(r)lux+) was obtained using the conjugation method on pseudomonasfragi t2(5) (te(r)znr) strain and bioluminescent strain protobacterium phosphoreum b7071 (lux+). the expression regulation of lux-genes on the obtained plasmid is carried out by promotor-operational area conjointly with zinc resistance genes. the cells of the obtained genetically modified bacteria have the ability to specific induced luminescence, which is a respond to zinc ions' ...200617147278
in vitro effects of singular or combined anti-oxidative vitamins and/or minerals on tilapia (oreochromis hybrids) peripheral blood monocyte-derived, anterior kidney-derived, and spleen-derived macrophages.the present study was to determine the in vitro effects of singular or combined anti-oxidative vitamins (a, c, and e) and/or minerals (se, zn, cu, mn, and fe) on the immune functions of tilapia, oreochromis hybrids, peripheral blood monocyte-derived, anterior kidney-derived, and spleen-derived macrophages. an optimal dose of vitamins and minerals increased cell viability and lysozyme activity. on the other hand, the above activities decreased at the high doses of combined vitamins (a+c+e group, ...200717169575
lateral transfer of the lux gene cluster.the lux operon is an uncommon gene cluster. to find the pathway through which the operon has been transferred, we sequenced the operon and both flanking regions in four typical luminous species. in vibrio cholerae ncimb 41, a five-gene cluster, most genes of which were highly similar to orthologues present in gram-positive bacteria, along with the lux operon, is inserted between vc1560 and vc1563, on chromosome 1. because this entire five-gene cluster is present in photorhabdus luminescens tt01, ...200717169972
computer-based qsars for predicting mixture toxicity of benzene and its derivatives.during the past decades, the quantitative structure-activity relationships (qsars) have been proven to be reliable tools when little or no empirical data are available in medicinal chemistry, biochemistry, toxicology, and environmental sciences. however, only few studies that quantitatively predict mixtures toxicity have been reported. in this study, the qasr models for the binary mixtures toxicity of 12 benzene and its derivatives, including eight non-polar-narcotic compounds and four polar nar ...200717184822
characterisation of the dominant bacterial population in modified atmosphere packaged farmed halibut (hippoglossus hippoglossus) based on 16s rdna-dgge.it is not well understood why atlantic halibut (hippoglossus hippoglossus) has longer shelf-life than most other white fish species. our approach was to examine the microbiological diversity of the spoilage microbiota during modified atmosphere (ma) packaging of farmed atlantic halibut. portions were packaged with gas mixtures of co(2):n(2) and co(2):o(2) (50%:50%) and with air as a reference. the packages were stored at 4 degrees c and samples were taken 6 times during the 23 days of storage. a ...200717189762
cloning, promoter analysis and expression in response to bacterial exposure of sea bass (dicentrarchus labrax l.) interleukin-12 p40 and p35 subunits.interleukin-12 (il-12) is a heterodimeric cytokine pivotal in resistance to microbial and viral infections. in the search for immunoregulatory genes in sea bass the genes for the two il-12 subunits p40 and p35 were cloned and sequenced. molecular characterization of these two genes was performed at both the cdna and genomic levels. sea bass il-12 p40 and p35 conserve most cysteines involved in the intra-chain disulfide bonds of human il-12 subunits as well as the important structural residues fo ...200717196658
heme, an iron supply for vibrios pathogenic for fish.one of the main mechanisms present in gram-negative bacterial pathogens to obtain iron is the utilization of free heme or heme proteins from the host tissues. vibrio anguillarum, the etiological agent of vibriosis in fish, and photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis, can acquire iron from free heme or heme-containing proteins present in the host tissues by a siderophore-independent mechanism. similarly to other animal and human pathogens, the general ...200717206385
dopamine depresses immunity in the tiger shrimp penaeus monodon.the total haemocyte count (thc), differential haemocyte count (dhc), phenoloxidase activity, respiratory bursts (release of superoxide anion), superoxide dismutase activity, phagocytic activity and clearance efficiency to the pathogen photobacterium damsela were measured when tiger shrimp penaeus monodon (13.5+/-1.5 g) were individually injected with saline or dopamine at 10(-8), 10(-7), or 10(-6)mol shrimp(-1). results showed that a transient period of immunosuppression occurred between 2 and 8 ...200717210259
toxicity assessment of contaminated sediments after dredging. 200617219312
histidine decarboxylases and their role in accumulation of histamine in tuna and dried saury.histamine-producing bacteria (hpb) such as photobacterium phosphoreum and raoultella planticola possess histidine decarboxylase (hdc), which converts histidine into histamine. histamine fish poisoning (hfp) is attributable to the ingestion of fish containing high levels of histamine produced by hpb. because freezing greatly decreases the histamine-producing ability of hpb, especially of p. phosphoreum, it has been speculated that hfp is caused by hdc itself from hpb cells autolyzing during froze ...200717220267
effect of heavy atoms in bioluminescent reactions.bioluminescent reactions of luminous organisms are excellent models for studying the effects of heavy atoms on enzymatic processes. the effects of potassium halides with halide anions of different atomic weight were compared in bioluminescent reactions of the firefly (luciola mingrelica), a marine coelenterate (obelia longissima), and a marine bacterium (photobacterium leiognathi). two mechanisms of the effects of the halides were examined-the physicochemical effect of the external heavy atom, b ...200717237922
cytochemical and ultrastructural study of anoikis and secondary necrosis in enterocytes detached in vivo.detachment-induced apoptosis of enterocytes (anoikis) has not been investigated in vivo. here we describe anoikis of fish enterocytes following detachment in a septicemia by photobacterium damselae subsp. piscicida, or following injection of its exotoxin. the in vivo study was complemented with an ex vivo time-lapse analysis using conditions duplicating the in vivo situation. linings of enterocytes detached from intestine mucosa dissociate into isolated enterocytes which undergo caspase 3-mediat ...200717245641
photobacterium lutimaris sp. nov., isolated from a tidal flat sediment in korea.a gram-negative, motile, pale-yellow-pigmented, oval-shaped bacterial strain, df-42t, was isolated from a tidal flat sediment in korea. strain df-42t grew optimally at 25-30 degrees c and in the presence of 2-3 % (w/v) nacl. it contained q-8 as the predominant ubiquinone and c(16 : 0), c(18 : 1)omega7c and summed feature 3 (c(16 : 1)omega7c and/or iso-c(15 : 0) 2-oh) as the major fatty acids. the dna g+c content was 48.3 mol%. phylogenetic trees based on 16s rrna gene sequences showed that strai ...200717267974
mechanistic evidence and efficiency of the cr(vi) reduction in water by different sources of zerovalent irons.the objective of this research was to assess the mechanism and effectiveness of the zerovalent iron (zvi) to remediate the cr(vi) contaminated water. the mechanism of cr(vi) reduction by zvi was evaluated by characterising surface properties and chemical compositions of fe and cr products using sem-eds, xrd and xps analyses. the effectiveness of zvi in cr(vi) reduction was assessed by the luminescent bacteria (photobacterium phosphoreum). the cr(vi) was reduced to cr(iii), when the reactive fe(o ...200717305140
[toxicity reduction of synthetic municipal wastewater treated by anaerobic, anoxic or aerobic reactors].bioassay with photobacterium phosphoreum was used to evaluate the toxicity of municipal wastewater. the toxicity reduction capabilities of three biological treatment processes (anaerobic reactor, anoxic reactor and aerobic reactor) treating the synthetic municipal wastewater were studied. seven compounds including toluene, p-xylene, o-xylene, indole, pyridine, cyclohexanone and benzenepropanoic acid were selected to represent the main organic toxicants in the municipal wastewater. the gc-ms anal ...200617326447
isolation and characterization of marine luminous bacteria from shallow coastal waters of taiwan.marine luminous bacteria were isolated and identified from samples in shallow coastal waters of taiwan during the relatively warm seasons.200717332902
expression, characterization and immunogenicity of a major outer membrane protein from vibrio alginolyticus.vibrio alginolyticus is one of the vibrio pathogens common to humans and marine animals. during infection and induction of the host immune response, outer membrane proteins of bacteria play an important role. in this study, an outer membrane protein gene (ompw) was cloned from v. alginolyticus and expressed in escherichia coli. the 645 bp open reading frame (orf) encodes a protein of 214 amino acid residues with a predicted molecular weight of 23.3 kda. the amino acid sequence showed a high iden ...200717342258
phylogenetic diversity and cosymbiosis in the bioluminescent symbioses of "photobacterium mandapamensis"."photobacterium mandapamensis" (proposed name) and photobacterium leiognathi are closely related, phenotypically similar marine bacteria that form bioluminescent symbioses with marine animals. despite their similarity, however, these bacteria can be distinguished phylogenetically by sequence divergence of their luminescence genes, luxcdab(f)e, by the presence (p. mandapamensis) or the absence (p. leiognathi) of luxf and, as shown here, by the sequence divergence of genes involved in the synthesi ...200717369329
on-line determination of serum bactericidal activity using recombinant luminescent bacteria.intensity of luminescence quenching in recombinant strains of escherichia coli with cloned lux-operones by human blood serum is directly proportional to the degree of bactericidal effect assessed by nephelometric and bacteriological methods. this correlation was most characteristic of e. coli with luminescence genes from photobacterium leiognathi, which substantiates its use in the development of the kinetic bioluminescent method to determine of serum bactericidal activity. the possibility of us ...200617369948
systemic macrophage and neutrophil destruction by secondary necrosis induced by a bacterial exotoxin in a gram-negative septicaemia.bacterial modulation of phagocyte cell death is an emerging theme in pathogenesis. here we describe the systemic destruction of macrophages and neutrophils by the gram-negative photobacterium damselae ssp. piscicida (phdp) in fish pasteurellosis, a deadly systemic infection. following experimental inoculation, phdp spreads by bacteraemia and colonizes the organs, producing a septicaemic infection, and secretes the apoptogenic exotoxin aip56 which is systemically disseminated. in experimental and ...200717381431
one-pot three-enzyme chemoenzymatic approach to the synthesis of sialosides containing natural and non-natural functionalities.chemoenzymatic synthesis, which combines the flexibility of chemical synthesis and the high selectivity of enzymatic synthesis, is a powerful approach to obtain complex carbohydrates. it is a preferred method for synthesizing sialic acid-containing structures, including those with diverse naturally occurring and non-natural sialic acid forms, different sialyl linkages and different glycans that link to the sialic acid. starting from n-acetylmannosamine, mannose or their chemically or enzymatical ...200617406495
molecular cloning and expression analysis of sea bass (dicentrarchus labrax l.) tumor necrosis factor-alpha (tnf-alpha).in the search for pro-inflammatory genes in sea bass a tnf-alpha gene was cloned and sequenced. the sea bass tnf-alpha (sbtnf-alpha) putative protein conserves the tnf-alpha family signature, as well as the two cysteines usually involved in the formation of a disulfide bond. the mouse tnf-alpha thr-leu cleavage sequence and a potential transmembrane domain were also found, suggesting that sbtnf-alpha exists as two forms: a approximately 28 kda membrane-bound form and a approximately 18.4 kda sol ...200717433716
characterisation of the bacterial flora of modified atmosphere packaged farmed atlantic cod (gadus morhua) by pcr-dgge of conserved 16s rrna gene regions.the present article describes the use of broad-range molecular analyses to characterise the microbial population of farmed atlantic cod (gadus morhua) packaged for the retail market. cod was filleted post rigor, packaged in air or in modified atmosphere (ma) (50% co(2):50% n(2) or 50% co(2):50% o(2)) and stored at 0 degrees c for 11 days. to determine the community profiles of the samples the variable v3-region of the bacterial 16s rrna gene were amplified by pcr, before the pcr products were se ...200717467836
an unusual case of urinary tract infection in a pregnant woman with photobacterium damsela.we describe a case of a urinary tract infection with an unusual pathogen, photobacterium damsela, in a pregnant female. this pathogen has been described as having a virulent life threatening nature, so a detailed history and prompt treatment is needed.200617485811
abatement of phenolic mixtures by catalytic wet oxidation enhanced by fenton's pretreatment: effect of h2o2 dosage and temperature.catalytic wet oxidation (cwo) of a phenolic mixture containing phenol, o-cresol and p-cresol (500mg/l on each pollutant) has been carried out using a commercial activated carbon (ac) as catalyst, placed in a continuous three-phase reactor. total pressure was 16 bar and temperature was 127 degrees c. pollutant conversion, mineralization, intermediate distribution, and toxicity were measured at the reactor outlet. under these conditions no detoxification of the inlet effluent was found even at the ...200717524556
quantitative structure-activity relationships and mixture toxicity of substituted benzaldehydes to photobacterium phosphoreum. 200717541483
filter-feeder macroinvertebrates as key players in culturable bacteria biodiversity control: a case of study with sabella spallanzanii (polychaeta: sabellidae).the present study investigates the effect of the filtering activity of sabella spallanzanii on the culturable heterotrophic bacterial community through the comparison of the bacterial diversity in transplanted polychaetes and the surrounding seawater. for isolation of culturable heterotrophic bacteria, seawater samples as well as polychaete homogenates were plated in triplicates onto bacto marine agar 2216 (difco). all the colonies grown were isolated, subcultured and identified by several morph ...200717548107
synthesis of cmp-9''-modified-sialic acids as donor substrate analogues for mammalian and bacterial sialyltransferases.cytidine-5'-monophospho-sialic acid (cmp-neu5ac) derivatives bearing a phenyl group in which the tether length between the phenyl group and the 9-position of neu5ac varied were synthesized and evaluated as substrates for sialyltransferases. in the synthesis of the compounds, a coupling reaction between methyl 5-acetamido-4,7,8-tri-o-acetyl-9-azido-3,5,9-trideoxy-beta-d-glycero-d-galacto-2-nonulopyranosonate and 2-cyanoethyl 2',3'-o,n4, triacetylcytidine-5'-yl n,n-diisopropylphosphoramidite was c ...200717572399
molecular characterization of cold adaptation based on ortholog protein sequences from vibrionaceae species.a set of 298 protein families from psychrophilic vibrio salmonicida was compiled to identify genotypic characteristics that discern it from orthologous sequences from the mesophilic vibrio/photobacterium branch of the gamma-proteobacteria (vibrionaceae family). in our comparative exploration we employed alignment based bioinformatical and statistical methods. interesting information was found in the substitution matrices, and the pattern of asymmetries in the amino acid substitution process. tog ...200717576517
vibrios of the spotted rose snapper lutjanus guttatus steindachner, 1869 from northwestern mexico.to characterize and identify vibrios present in wild and cultured juvenile snappers (lutjanus guttatus) in northwestern mexico.200717578416
[formation of aggregated structures by luminescent bacteria in the presence of carbohydrates]. 200717583227
evaluation of leaching and ecotoxicological properties of sewage sludge-fly ash mixtures.the objectives of this work were the evaluation of sewage sludge stabilization by mixing with fly ash, the examination of the physicochemical properties of the produced materials and their leachates and the assessment of their environmental impact by the evaluation of the ecotoxic characteristics. different ratios of fly ash and sewage sludge (1:1, 1:2, 1:3, 1:6, and 1:9) were mixed for 48 and 72 h. after mixing, the liquid phase of the produced materials was analyzed for total coliforms and esc ...200817583693
the bacterial flora of vacuum-packed cold-smoked salmon stored at 7 degrees c, identified by direct 16s rrna gene analysis and pure culture technique.the indigenous flora of freshly chilled cold-smoked salmon just after the vacuum packaging, and the spoilage flora after storage, in vacuum package at 7 degrees c for 19 days, were to be investigated with two different sampling strategies.200717584457
natural merodiploidy of the lux-rib operon of photobacterium leiognathi from coastal waters of honshu, japan.sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. we report here that certain strains of photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and ...200717586644
photobacterium damselae ssp. damselae associated with diseased black tiger shrimp penaeus monodon fabricius in india.to characterize and identify photobacterium damselae ssp. damselae present in black gill diseased penaeus monodon collected from east coast of india.200717594465
a bioluminescent signal system: detection of chemical toxicants in water.prototype technologies of a bioluminescent signal system (bss) based on the luminous bacterium photobacterium phosphoreum and three enzymatic bioluminescence systems have been proposed for detecting and signalling the presence of toxicants in water systems. a number of pesticides, mostly known as poisonous substances, similar in their structures and physicochemical properties, have been taken as model compounds of chemical agents. the effect of toxicants (organophosphates, derivatives of dithioc ...200717603816
toxicity change patterns and its mechanism during the degradation of nitrogen-heterocyclic compounds by o(3)/uv.many nitrogen-heterocyclic compounds (nhcs) are toxic and recalcitrant contaminants that need to be degraded by advanced oxidation processes. in this study, quinoline, isoquinoline and indole were selected to investigate their toxicity patterns during the degradation by o(3)/uv. it was found that for all the three nhcs there was some h(2)o(2) formed in the degradation process, which caused the sharp increase of toxicity to photobacterium phosphoreum. the toxicity decreasing patterns after h(2)o( ...200717604078
the diversity of bacterial communities associated with atlantic cod gadus morhua.the spatial and temporal changes in the bacterial communities associated with the atlantic cod gadus morhua were investigated using terminal restriction fragment length polymorphism (t-rflp) analysis of 16s recombinant dna (rdna). epidermal mucous was sampled from 366 cod caught in three harvest locations (baltic, icelandic, and north seas) over three seasons (spring 2002, autumn 2002, and spring 2003), and an automated method for the high-throughput processing of environmental samples was devel ...200817624487
biodegradability and ecotoxicity of amine oxide based surfactants.the aerobic and anaerobic biodegradability as well as the aquatic toxicity of two fatty amine oxides and one fatty amido amine oxide were investigated. aerobic biodegradation was evaluated using the co(2) headspace test (iso 14593) and biodegradation under anaerobic conditions was assessed employing a standardised batch test. the three amine oxide based surfactants tested were readily biodegradable under aerobic conditions but only the alkyl amido amine oxide was found to be easily biodegradable ...200717631946
molecular diversity of photobacterium damselae ssp. piscicida from cultured amberjacks (seriola spp.) in japan by pulsed-field gel electrophoresis and plasmid profiles.this study deals with a pulsed-field gel electrophoresis (pfge) for discriminating between the genetic variants of photobacterium damselae ssp. piscicida, and characterizing of japanese field isolates by pfge together with plasmid profiles and antimicrobial resistances.200717650198
evaluation of different dna-based fingerprinting methods for typing photobacterium damselae ssp. piscicida.this study evaluates the effectiveness of three different molecular techniques, repetitive extragenic palindromic pcr (rep-pcr), enterobacterial repetitive intergenic consensus sequence pcr (eric-pcr) and the random amplified polymorphic dna (rapd-pcr) for rapid typing of photobacterium damselae ssp. piscicida strains isolated from different species of marine fish and geographic areas. the results obtained by the three methods showed that rapd and eric-pcr were more discriminative for suitable r ...200717657358
purification, crystallization and preliminary crystallographic characterization of the alpha 2,6-sialyltransferase from photobacterium sp. jt-ish-224.sialyltransferases transfer sialic acid from cytidine-5-monophospho-n-acetylneuraminic acid (cmp-neuac) to the nonreducing termini of the oligosaccharyl structures of various glycoproteins and glycolipids. the newly cloned alpha2,6-sialyltransferase from photobacterium sp. jt-ish-224 (from the vibrionaceae family) is composed of two domains: an unknown n-terminal domain and a catalytic c-terminal domain which shares significant homology with the pasteurella multocida multifunctional sialyltransf ...200717671362
variation in the molecular weight of photobacterium damselae subsp. piscicida antigens when cultured under different conditions in vitro.the antigenicity of photobacterium damselae (ph. d.) subsp. piscicida, cultured in four different growth media [tryptone soya broth (tsb), glucose-rich medium (grm), iron-depleted tsb (tsb + ir(-)), and iron-depleted grm (grm + ir(-))] was compared by enzyme-linked immunosorbent assay (elisa) and western blot analysis using sera obtained from sea bass (dicentrarchus labrax) raised against live or heat-killed ph. d. subsp. piscicida. the antigenic expression of ph. d. subsp. piscicida was found t ...200717679772
characterization of the bacterial community associated with the surface and mucus layer of whiting (merlangius merlangus).the bacterial community inhabiting the mucus layer and surface of whiting was examined to determine whether the bacteria present are a reflection of the surrounding water or an indigenous bacterial flora is present. the outer mucus, mouth mucus and gut of four whiting harvested from a site in the irish sea and the surrounding water were examined by terminal restriction fragment length polymorphism (trflp) analysis of the 16s rrna gene and clone library construction. the water community was the m ...200717692096
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