bluuebunny/crossref_metadata_2025 huggingface dataset:
Up-Regulation of Transient Receptor Potential Canonical 1 (TRPC1) following Sarco(endo)plasmic Reticulum Ca2+ATPase 2 Gene Silencing Promotes Cell Survival: A Potential Role for TRPC1 in Darier's Disease
Authors: Pani Biswaranjan , Cornatzer Eric , Cornatzer William , Shin Dong-Min , Pittelkow Mark R. , Hovnanian Alain , Ambudkar Indu S. , Singh Brij B.
Published: August 2006

The mechanism(s) involved in regulation of store operated calcium entry in Darier's disease (DD) is not known. We investigated the distribution and function of transient receptor potential canonical (TRPC) in epidermal skin cells. DD patients demonstrated up-regulation of TRPC1, but not TRPC3, in the squamous layers. Ca2+influx was significantly higher in keratinocytes obtained from DD patients and showed enhanced proliferation compared with normal keratinocytes. Similar up-regulation of TRPC1 was also detected in epidermal layers of SERCA2+/−mice. HaCaT cells expressed TRPC1 in the plasma membrane. Expression of sarco(endo)plasmic reticulum Ca2+ATPase (SERCA)2 small interfering RNA (siRNA) in HaCaT cells increased TRPC1 levels and thapsigargin-stimulated Ca2+influx, which was blocked by store-operated calcium entry inhibitors. Thapsigargin-stimulated intracellular Ca2+release was decreased in DD cells. DD keratinocytes exhibited increased cell survival upon thapsigargin treatment. Alternatively, overexpression of TRPC1 or SERCA2-siRNA in HaCaT cells demonstrated resistance to thapsigargin-induced apoptosis. These effects were dependent on external Ca2+and activation of nuclear factor-κB. Isotretinoin reduced Ca2+entry in HaCaT cells and decreased survival of HaCaT and DD keratinocytes. These findings put forward a novel consequence of compromised SERCA2 function in DD wherein up-regulation of TRPC1 augments cell proliferation and restrict apoptosis. We suggest that the anti-apoptotic effect of TRPC1 could potentially contribute to abnormal keratosis in DD.
Characterization of DNA Damage in Yeast Apoptosis Induced by Hydrogen Peroxide, Acetic Acid, and Hyperosmotic Shock
Authors: Ribeiro Gabriela F. , Côrte-Real Manuela , Johansson Björn
Published: August 2006

Saccharomyces cerevisiae has been reported to die, under certain conditions, from programmed cell death with apoptotic markers. One of the most important markers is chromosomal DNA fragmentation as indicated by terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining. We found TUNEL staining in S. cerevisiae to be a consequence of both single- and double-strand DNA breaks, whereas in situ ligation specifically stained double-strand DNA breaks. Cells treated with hydrogen peroxide or acetic acid staining positively for TUNEL assay stained negatively for in situ ligation, indicating that DNA damage in both cases mainly consists of single-strand DNA breaks. Pulsed field gel electrophoresis of chromosomal DNA from cells dying from hydrogen peroxide, acetic acid, or hyperosmotic shock revealed DNA breakdown into fragments of several hundred kilobases, consistent with the higher order chromatin degradation preceding DNA laddering in apoptotic mammalian cells. DNA fragmentation was associated with death by treatment with 10 mM hydrogen peroxide but not 150 mM and was absent if cells were fixed with formaldehyde to eliminate enzyme activity before hydrogen peroxide treatment. These observations are consistent with a process that, like mammalian apoptosis, is enzyme dependent, degrades chromosomal DNA, and is activated only at low intensity of death stimuli.
Top3 Processes Recombination Intermediates and Modulates Checkpoint Activity after DNA Damage
Authors: Mankouri Hocine W. , Hickson Ian D.
Published: August 2006

Mutation of TOP3 in Saccharomyces cerevisiae causes poor growth, hyperrecombination, and a failure to fully activate DNA damage checkpoints in S phase. Here, we report that overexpression of a dominant-negative allele of TOP3, TOP3Y356F, which lacks the catalytic (decatenation) activity of Top3, causes impaired S-phase progression and the persistence of abnormal DNA structures (X-shaped DNA molecules) after exposure to methylmethanesulfonate. The impaired S-phase progression is due to a persistent checkpoint-mediated cell cycle delay and can be overridden by addition of caffeine. Hence, the catalytic activity of Top3 is not required for DNA damage checkpoint activation, but it is required for normal S-phase progression after DNA damage. We also present evidence that the checkpoint-mediated cell cycle delay and persistence of X-shaped DNA molecules resulting from overexpression of TOP3Y356Fare downstream of Rad51 function. We propose that Top3 functions in S phase to both process homologous recombination intermediates and modulate checkpoint activity.
Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales
Authors: Cavaletti Linda , Monciardini Paolo , Schumann Peter , Rohde Manfred , Bamonte Ruggiero , Busti Elena , Sosio Margherita , Donadio Stefano
Published: August 2006

Two novel Gram-positive, acidophilic bacterial strains were isolated from forest soil. According to their 16S rRNA gene sequences, these strains are related closely to each other and form a distinct cluster within the order Actinomycetales. They show the typical features of filamentous actinomycetes, with branched vegetative hyphae and production of aerial hyphae. The distinct phylogenetic positions and the combination of chemotaxonomic characteristics of these strains justify the proposal of Actinospica gen. nov. Both strains display 3-hydroxydiaminopimelic acid plus traces of meso-diaminopimelic acid, the phospholipids diphosphatidylglycerol, phosphatidylethanolamine, methylphosphatidylethanolamine and phosphatidylinositol, the predominant cellular fatty acids i-C15 : 0, i-C16 : 0 and ai-C15 : 0 and the whole-cell sugars mannose and rhamnose. They differ in the fatty acid profiles, in the quantitative ratios of the major menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) and in the occurrence of additional whole-cell sugars (arabinose and xylose in strain GE134766T and galactose in strain GE134769T). Differences in the phenotypic characteristics and in the 16S rRNA gene sequences suggest the description of two species, Actinospica robiniae gen. nov., sp. nov. (the type species) and Actinospica acidiphila sp. nov., with the type strains GE134769T (=DSM 44927T=NRRL B-24432T) and GE134766T (=DSM 44926T=NRRL B-24431T), respectively. The DNA G+C contents of strains GE134769T and GE134766T are 70.8 and 69.2 mol%, respectively. Due to the large phylogenetic distance from known actinomycete genera, it is proposed to accommodate Actinospica gen. nov. in Actinospicaceae fam. nov. In addition, Catenulisporineae subord. nov. is proposed to harbour Actinospicaceae fam. nov. and the newly proposed family Catenulisporaceae, described in the accompanying paper.
Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas
Authors: Mayilraj S. , Kroppenstedt R. M. , Suresh K. , Saini H. S.
Published: August 2006

A reddish orange bacterium, strain K07-05T, was isolated from soil during a study of the bacterial diversity of a cold desert of the Indian Himalayas and was studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusKocuria. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain K07-05Twas closely related toKocuria roseaDSM 20447TandKocuria polarisMTCC 3702T(98.1 and 97.8 % sequence similarity, respectively), whereas the sequence similarity values with respect to the otherKocuriaspecies with validly published names were between 96.4 and 94.2 %. However, the genomic relatedness, as shown by DNA–DNA hybridization, of strain K07-05TandK. polarisMTCC 3702Tis 49.5 % and that withK. roseaMTCC 2522Tis 24.0 %. The DNA G+C content of the strain is 75.3 mol%. The above data in combination with the phenotypic distinctiveness of K07-05Tclearly indicate that the strain represents a novel species, for which the nameKocuria himachalensissp. nov. is proposed. The type strain is K07-05T(=MTCC 7020T=DSM 44905T=JCM 13326T).
Aeromonas sharmana sp. nov., isolated from a warm spring
Authors: Saha P. , Chakrabarti T.
Published: August 2006

A Gram-negative, facultatively anaerobic bacterial strain designated GPTSA-6Twas isolated from a water sample collected from a warm spring in Assam, India. Preliminary analysis of the 16S rRNA gene sequence of this isolate revealed its affiliation to the familyAeromonadaceae. Detailed characterization using a polyphasic approach indicated that strain GPTSA-6Tis most closely related toAeromonas sobriabut differs significantly from existing members of the genusAeromonas. Analysis of the almost-complete (1430 nt) 16S rRNA gene sequence of this strain revealed that its closest relative (99.23 % similarity) is an uncultured bacterial clone, A-8, isolated from an algal bloom. Of the taxa with validly published names,Aeromonas sobriaATCC 43979Tshowed the highest level of sequence similarity (95.13 %) with respect to strain GPTSA-6T, followed byAeromonas molluscorum848TTandAeromonas popoffiiLMG 17541T(95.04 % similarity in both cases). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it can be concluded that strain GPTSA-6Trepresents a novel species of the genusAeromonas, for which the nameAeromonas sharmanasp. nov. is proposed. The type strain is GPTSA-6T(=MTCC 7090T=DSM 17445T).
Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter
Authors: Gallego Virginia , García Maria Teresa , Ventosa Antonio
Published: August 2006

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain AR107T) was isolated from the drinking water distribution system of Seville (Spain). A polyphasic taxonomic study of the isolate resulted in its identification as a member of the genus Pedobacter. On the basis of 16S rRNA gene sequence comparisons, strain AR107T was shown to belong to the phylum Bacteroidetes, being related to members of the genus Pedobacter. It showed 95.2 % sequence similarity with respect to the type strains of Pedobacter heparinus and Pedobacter piscium, and 94.1 % similarity with respect to the type strain of Pedobacter himalayensis. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c), which supports the affiliation of strain AR107T to the genus Pedobacter. The DNA G+C content of this strain was 38 mol%. On the basis of the phenotypic, phylogenetic and genotypic results, strain AR107T represents a novel species, for which the name Pedobacter aquatilis sp. nov. is proposed. The type strain is AR107T (=CCM 7347T=CECT 7114T=JCM 13454T).
Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces
Authors: Satomi Masataka , La Duc Myron T. , Venkateswaran Kasthuri
Published: August 2006

Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genusBacillus, the greatest sequence similarity (99.9 %) being found withBacillus pumilus. However, these isolates share a mere 91.2 %gyrBsequence similarity withBacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA–DNA hybridization showed only 54–66 % DNA relatedness between the novel isolates and strains ofB. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates fromB. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA andgyrBgene sequences, repetitive element primer-PCR fingerprinting and DNA–DNA hybridization, the 13 isolates represent a novel species of the genusBacillus, for which the nameBacillus safensissp. nov. is proposed. The type strain is FO-36bT(=ATCC BAA-1126T=NBRC 100820T).
Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains l-lysine in its cell wall
Authors: Lee Jae-Chan , Lim Jee-Min , Park Dong-Jin , Jeon Che Ok , Li Wen-Jun , Kim Chang-Jin
Published: August 2006

A halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724T, was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724T grew at salinities of 0–10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15–50 °C with an optimum of 40 °C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724T belonged to the genus Bacillus and that Bacillus aquimaris TF-12T, Bacillus marisflavi TF-11T and Bacillus vietnamensis JCM 11124T were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The peptidoglycan type was A1α, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724T represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724T (=KCTC 3913T=DSM 16464T).
Lipomyces orientalis sp. nov., a yeast species isolated from soil in Vietnam
Authors: Thanh Vu Nguyen
Published: August 2006

Five strains of the novel ascogenous yeast species Lipomyces orientalis sp. nov. were isolated from soil samples collected in Vietnam. The yeast forms asci containing one to four ascospores. The ascospores of L. orientalis have warty surfaces and differ from the characteristic striated ascospores of Lipomyces tetrasporus. Phylogenetic analyses of D1/D2 26S rDNA and ITS sequences indicate that L. orientalis and L. tetrasporus are closely related, but they differ from each other by 6 nucleotides in the D1/D2 region and 16 nucleotides in the ITS region. The type culture is strain Lip 95T (=CBS 10300T=NRRL Y-27927T).
Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng
Authors: Weon Hang-Yeon , Kim Byung-Yong , Yoo Seung-Hee , Lee Seon-Young , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: August 2006

Two novel strains, GR20-10T and GR20-13T, were isolated from soil using R2A medium. The soil sample was collected from a field in the Yeongju region of Korea that was cultivated with Korean ginseng. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains formed a cluster with several uncultured bacterial clones and with Flexibacter filiformis, Flexibacter sancti, Flexibacter japonensis, Cytophaga arvensicola and Flavobacterium ferrugineum (recently reclassified as Terrimonas ferruginea) in the phylum Bacteroidetes. The level of 16S rRNA gene sequence similarity between the two novel strains was 98.9 %. Isolates GR20-10T and GR20-13T showed the highest sequence similarities to Flexibacter japonensis IFO 16041T (91.8 and 91.9 %, respectively) and T. ferruginea ATCC 13524T (90.4 and 90.6 %, respectively). The whole-cell fatty acid profiles of the two isolates were similar and their major fatty acids were 15 : 0 iso, 17 : 0 iso 3-OH and 15 : 1 iso G. The major isoprenoid quinone of both strains was MK-7. The G+C contents of GR20-10T and GR20-13T were 45.8 and 44.3 mol%, respectively. DNA–DNA hybridization (57 % DNA–DNA hybridization value) and phenotypic data indicated that strains GR20-10T and GR20-13T each belong to a separate species. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains GR20-10T and GR20-13T represent two novel species in a novel genus in the phylum Bacteroidetes; the names Niastella koreensis gen. nov., sp. nov. (the type species; type strain GR20-10T=KACC 11465T=DSM 17620T) and Niastella yeongjuensis sp. nov. (type strain GR20-13T=KACC 11466T=DSM 17621T) are proposed.
Agrococcus lahaulensis sp. nov., isolated from a cold desert of the Indian Himalayas
Authors: Mayilraj S. , Suresh K. , Schumann P. , Kroppenstedt R. M. , Saini H. S.
Published: August 2006

The taxonomic position of a lemon-yellow-pigmented actinobacterium, strain K22-21T, isolated from a soil sample from Lahaul-Spiti Valley in the Indian Himalayas, was determined using a polyphasic approach. The strain had phenotypic and chemical properties that were consistent with its classification in the genusAgrococcus. Alignment of the 16S rRNA gene sequence of strain K22-21Twith sequences fromAgrococcus jenensisDSM 9580T,Agrococcus baldriDSM 14215TandAgrococcus citreusDSM 12453Trevealed similarities of 98.5, 96.8 and 96.6 %, respectively. However, the level of DNA–DNA relatedness between strain K22-21TandA. jenensiswas 55.1 %. The novel strain could be distinguished from type strains of the three species of the genusAgrococcususing DNA–DNA relatedness and phenotypic data. Based on these differences, strain K22-21T(=MTCC 7154T=DSM 17612T) should be classified as the type strain of a novel species ofAgrococcus, for which the nameAgrococcus lahaulensissp. nov. is proposed.
Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil
Authors: Nunes Inês , Tiago Igor , Pires Ana Luísa , da Costa Milton S. , Veríssimo António
Published: August 2006

A Gram-positive bacterium, designated B22T, was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 °C and pH 8.0–8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0–8 % NaCl. The cell wall peptidoglycan is of the A4αtype with a cross-linkage containingd-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22Tformed a new branch within the familyBacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the generaSalinibacillus,Virgibacillus,OceanobacillusandLentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22Texhibited 16S rRNA gene pairwise sequence similarity values of 94.7–94.3 % with members of the genusSalinibacillus, 95.1–92.8 % with members of the genusVirgibacillus, 94.7–93.2 % with members of the genusOceanobacillusand 93.1–92.3 % with members of the genusLentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22Trepresents a novel species in a new genus,Paucisalibacillus globulusgen. nov., sp. nov. Strain B22T(=LMG 23148T=CIP 108857T) is the type strain ofPaucisalibacillus globulus.
Brevibacterium samyangense sp. nov., an actinomycete isolated from a beach sediment
Authors: Lee Soon Dong
Published: August 2006

A novel actinomycete, strain SST-8T, was isolated from sand sediment of Samyang Beach in Jeju, Korea, and subjected to a polyphasic taxonomic study. The organism, which produced opaque, circular, yellow colonies, with a coryneform morphology, showed the following chemotaxonomic characteristics:meso-diaminopimelic acid as the diamino acid in the peptidoglycan, MK-8(H2) as the major menaquinone, phosphatidylglycerol as the only polar lipid, anteiso-C15 : 0and anteiso-C17 : 0as major fatty acids and a DNA G+C content of 70.7 mol%. The combination of morphological and chemotaxonomic features supported its classification in the genusBrevibacterium. Phylogenetic analyses, based on 16S rRNA gene sequence studies, showed that strain SST-8Tformed an intermediate branch between theBrevibacterium luteolum/Brevibacterium otitidisandBrevibacterium mcbrellneri/Brevibacterium paucivoransclusters. Sequence similarity calculations based on a neighbour-joining analysis revealed that the closest relatives of strain SST-8Twere the type strains ofB. paucivorans(96.6 %),B. luteolum(96.5 %),B. mcbrellneri(96.3 %),Brevibacterium avium(96.0 %) andB. otitidis(95.9 %). Based on a broad set of phenotypic and genetic data, it was evident that the strain represents a novel species of the genusBrevibacterium. The nameBrevibacterium samyangensesp. nov. is proposed, with SST-8T(=NRRL B-41420T=KCCM 42316T) as the type strain.
Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983
Authors: Dellaglio Franco , Vancanneyt Marc , Endo Akihito , Vandamme Peter , Felis Giovanna E. , Castioni Anna , Fujimoto Junji , Watanabe Koichi , Okada Sanae
Published: August 2006

The taxonomic status of the speciesLactobacillus durianisandLactobacillus vaccinostercusis briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1523 bp), partialrecAgene sequences (99.5 % similarity over 600 bp) and partialhsp60gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA–DNA binding level (87 %) and similar genomic DNA G+C contents (41–44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of theBacteriological Code, the nameLactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the nameLactobacillus durianisshould be considered a later heterotypic synonym.
Brooklawnia cerclae gen. nov., sp. nov., a propionate-forming bacterium isolated from chlorosolvent-contaminated groundwater
Authors: Bae Hee-Sung , Moe William M. , Yan Jun , Tiago Igor , da Costa Milton S. , Rainey Fred A.
Published: August 2006

Two novel facultatively anaerobic bacterial strains, BL-34Tand BL-35, isolated from groundwater contaminated by a mixture of chlorosolvents were characterized using a polyphasic approach. The two strains exhibited essentially identical taxonomic features except for a vitamin B12requirement by strain BL-35 for optimal growth. Phylogenetically, the isolates were affiliated with members of the familyPropionibacteriaceaeand were placed in a phylogenetic branch adjacent to, but distinct from, those of the generaPropionimicrobium,Propionibacterium,Luteococcus,PropioniferaxandTessaracoccus. The cells of the novel strains were Gram-positive, non-motile, non-spore-forming pleomorphic rods. They produced catalase but not oxidase, and nitrate reduction did not occur in peptone/yeast extract/glucose medium. Propionate and acetate were the predominant products of glucose fermentation. Fermentation occurred in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations up to at least 9.8 mM. The genomic DNA G+C content was 67.5–67.9 mol%. Menaquinone MK-9(H4) was the predominant respiratory quinone andmeso-diaminopimelic acid was present in the cell-wall peptidoglycan layer. The major cellular fatty acids were C15 : 0and anteiso-C15 : 0. On the basis of the results obtained in this study, strains BL-34Tand BL-35 should be classified within a novel taxon, for which the nameBrooklawnia cerclaegen. nov., sp. nov. is proposed. The type strain ofBrooklawnia cerclaeis BL-34T(=LMG 23248T=NRRL B-41418T). An additional strain, BL-35 (=LMG 23249=NRRL B-41419), was also characterized.
Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America
Authors: Chen Wen-Ming , James Euan K. , Coenye Tom , Chou Jui-Hsing , Barrios Edmundo , de Faria Sergio M. , Elliott Geoffrey N. , Sheu Shih-Yi , Sprent Janet I. , Vandamme Peter
Published: August 2006

Fourteen strains were isolated from nitrogen-fixing nodules on the roots of plants of the genus Mimosa growing in Taiwan, Brazil and Venezuela. On the basis of 16S rRNA gene sequence similarities, all of the strains were previously shown to be closely related to each other and to belong to the genus Burkholderia. A polyphasic approach, including DNA–DNA reassociation, whole-cell protein analysis, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains: all 14 strains were classified as representing a novel species, for which the name Burkholderia mimosarum sp. nov. is proposed. The type strain, PAS44T (=LMG 23256T =BCRC 17516T), was isolated from Mimosa pigra nodules in Taiwan.
Myroides pelagicus sp. nov., isolated from seawater in Thailand
Authors: Yoon Jaewoo , Maneerat Suppasil , Kawai Fusako , Yokota Akira
Published: August 2006

An aerobic, Gram-negative, non-motile, yellow-to-orange pigmented and rod-shaped bacterium, designated strain SM1T, was isolated from seawater in Thailand and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate shared 93–95 % sequence similarity with species of the genus Myroides. The DNA–DNA relatedness values of strain SM1T with Myroides odoratimimus JCM 7460T and Myroides odoratus JCM 7458T were below 70 %. The DNA G+C content of strain SM1T was 33.6 mol%, the major menaquinone was MK-6 and the major fatty acids were C15 : 0 iso, C17 : 1
ω9c iso and C17 : 0 iso 3-OH. Based on its phenotypic and chemotaxonomic characteristics, strain SM1T was classified as representing a novel species of the genus Myroides, for which the name Myroides pelagicus sp. nov. is proposed. The type strain is SM1T (=IAM 15337T=KCTC 12661T).
Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake
Authors: Cui Heng-Lin , Tohty Dilbr , Zhou Pei-Jin , Liu Shuang-Jiang
Published: August 2006

Halophilic archaeal strains ABH32T and AX-7T were isolated from Aibi salt lake in Xin-Jiang, China, and were subjected to taxonomic studies. The cells of both strains were rod-shaped, and growth required at least 10 % (w/v) NaCl. The cellular polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD). The isolates were different in that strain ABH32T did not require magnesium and had strong ability to assimilate sugars for growth, whereas strain AX-7T required magnesium and did not assimilate glucose, sucrose or maltose for growth. Both strain ABH32T and strain AX-7T were most closely related to members of the genera Haloterrigena and Natrinema. On the basis of phenotypic and genotypic characteristics, especially their cellular polar lipids, the two isolates were assigned to the genus Haloterrigena. Moreover, the DNA relatedness values for strains ABH32T and AX-7T with respect to members of the genus Haloterrigena were found to be well below 70 %. Thus, strains ABH32T and AX-7T represent two novel species within the genus Haloterrigena, for which the names Haloterrigena longa sp. nov. (type strain ABH32T=CGMCC 1.5334T=JCM 13562T) and Haloterrigena limicola sp. nov. (type strain AX-7T=CGMCC 1.5333T=JCM 13563T) are proposed.
Græmlin: General and robust alignment of multiple large interaction networks
Authors: Flannick Jason , Novak Antal , Srinivasan Balaji S. , McAdams Harley H. , Batzoglou Serafim
Published: August 2006

The recent proliferation of protein interaction networks has motivated research into network alignment: the cross-species comparison of conserved functional modules. Previous studies have laid the foundations for such comparisons and demonstrated their power on a select set of sparse interaction networks. Recently, however, new computational techniques have produced hundreds of predicted interaction networks with interconnection densities that push existing alignment algorithms to their limits. To find conserved functional modules in these new networks, we have developed Græmlin, the first algorithm capable of scalable multiple network alignment. Græmlin's explicit model of functional evolution allows both the generalization of existing alignment scoring schemes and the location of conserved network topologies other than protein complexes and metabolic pathways. To assess Græmlin's performance, we have developed the first quantitative benchmarks for network alignment, which allow comparisons of algorithms in terms of their ability to recapitulate the KEGG database of conserved functional modules. We find that Græmlin achieves substantial scalability gains over previous methods while improving sensitivity.
Human embryonic stem cells have a unique epigenetic signature
Authors: Bibikova Marina , Chudin Eugene , Wu Bonnie , Zhou Lixin , Garcia Eliza Wickham , Liu Ying , Shin Soojung , Plaia Todd W. , Auerbach Jonathan M. , Arking Dan E. , Gonzalez Rodolfo , Crook Jeremy , Davidson Bruce , Schulz Thomas C. , Robins Allan , Khanna Aparna , Sartipy Peter , Hyllner Johan , Vanguri Padmavathy , Savant-Bhonsale Smita , Smith Alan K. , Chakravarti Aravinda , Maitra Anirban , Rao Mahendra , Barker David L. , Loring Jeanne F. , Fan Jian-Bing
Published: August 2006

Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We compared the DNA methylation status of 1536 CpG sites (from 371 genes) in 14 independently isolated hES cell lines with five other cell types: 24 cancer cell lines, four adult stem cell populations, four lymphoblastoid cell lines, five normal human tissues, and an embryonal carcinoma cell line. We found that the DNA methylation profile clearly distinguished the hES cells from all of the other cell types. A subset of 49 CpG sites from 40 genes contributed most to the differences among cell types. Another set of 25 sites from 23 genes distinguished hES cells from normal differentiated cells and can be used as biomarkers to monitor differentiation. Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential.
High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
Authors: Peiffer Daniel A. , Le Jennie M. , Steemers Frank J. , Chang Weihua , Jenniges Tony , Garcia Francisco , Haden Kirt , Li Jiangzhen , Shaw Chad A. , Belmont John , Cheung Sau Wai , Shen Richard M. , Barker David L. , Gunderson Kevin L.
Published: August 2006

Array-CGH is a powerful tool for the detection of chromosomal aberrations. The introduction of high-density SNP genotyping technology to genomic profiling, termed SNP-CGH, represents a further advance, since simultaneous measurement of both signal intensity variations and changes in allelic composition makes it possible to detect both copy number changes and copy-neutral loss-of-heterozygosity (LOH) events. We demonstrate the utility of SNP-CGH with two Infinium whole-genome genotyping BeadChips, assaying 109,000 and 317,000 SNP loci, to detect chromosomal aberrations in samples bearing constitutional aberrations as well tumor samples at sub-100 kb effective resolution. Detected aberrations include homozygous deletions, hemizygous deletions, copy-neutral LOH, duplications, and amplifications. The statistical ability to detect common aberrations was modeled by analysis of an X chromosome titration model system, and sensitivity was modeled by titration of gDNA from a tumor cell with that of its paired normal cell line. Analysis was facilitated by using a genome browser that plots log ratios of normalized intensities and allelic ratios along the chromosomes. We developed two modes of SNP-CGH analysis, a single sample and a paired sample mode. The single sample mode computes log intensity ratios and allelic ratios by referencing to canonical genotype clusters generated from ∼120 reference samples, whereas the paired sample mode uses a paired normal reference sample from the same individual. Finally, the two analysis modes are compared and contrasted for their utility in analyzing different types of input gDNA: low input amounts, fragmented gDNA, and Phi29 whole-genome pre-amplified DNA.
The ATTEMPT cohort: a multi‐national longitudinal study of predictors, patterns and consequences of smoking cessation; introduction and evaluation of internet recruitment and data collection methods
Authors: West Robert , Gilsenan Alicia , Coste Florence , Zhou Xiaolei , Brouard Remi , Nonnemaker James , Curry Susan J. , Sullivan Sean D.
Published: August 2006

Aims  The ATTEMPT study was designed to chart the natural history of smoking cessation and associated short‐term health outcomes and effects on medical resource utilization among a cohort recruited across multiple countries. This paper describes the methods for recruitment and follow‐up, the baseline population characteristics of the enrolled population and 1‐year response rates.

Design  ATTEMPT is a multi‐national prospective cohort study that used the internet for subject recruitment and online assessments every 3 months for 2.5 years.

Setting  Subjects were recruited via e‐mail from existing internet panels [Canada (n = 208), France (n = 201), the United Kingdom (n = 200) and the United States (n = 1400].

Subjects  Panel members who were aged 35–65 years, smoked at least five cigarettes per day and at initiation stated an intention to quit smoking within the next 3 months were eligible for this study.

Measurements  Measures included: attempts to quit, smoking status, smoking history, nicotine dependence and craving, methods used to quit smoking, reasons for quitting or failing to quit smoking, short‐term health effects, health resource utilization, wellbeing, concern over weight gain, confidence in preventing weight gain, body weight and demographics. In addition, in‐home assessments of weight were undertaken by field staff for a random sample of US participants.

Findings  Country‐specific recruitment was completed within 17 days. The recruitment method produced a sample with characteristics broadly similar to those found in national surveys of smokers except for higher prevalence of obesity in the US and Canadian samples and higher educational level. At the end of 1 year the response rate was 52%, and there was little evidence of differential loss to follow‐up by key subject characteristics. Weight reported in the survey was found to correlate highly with weight measured during in‐home visits.

Conclusion  This paper demonstrates the feasibility of enrolling and following a diverse cohort of smokers for self‐reported health and behaviour measures via the internet.
Reducing substance use improves adolescents’ school attendance
Authors: Engberg John , Morral Andrew R.
Published: August 2006

Aims  Substance use initiation and frequency are associated with reduced educational attainments among adolescents. We examined if decreases in substance use substantially improve youths’ school attendance.

Design  A total of 1084 US adolescents followed quarterly for 1 year after entering substance abuse treatment.

Methods  Random and fixed effects regression models were used to differentiate the lagged effects of drug use from other time‐varying and time‐invariant covariates. Self‐reports of alcohol, marijuana, stimulants, sedatives, hallucinogens and other drug use were used to predict subsequent school attendance, after controlling for demographic and drug use history characteristics, problem indices and other covariates.

Findings  Reductions in the frequency of alcohol, stimulants and other drug use and the elimination of marijuana use were each associated independently with increased likelihoods of school attendance.

Conclusions  Because years of completed schooling is highly correlated with long‐term social and economic outcomes, the possibility that reductions in substance use may improve school attendance has significant implications for the cost‐effectiveness of substance abuse treatment and other interventions designed to reduce adolescents’ substance use.
Should substance use disorders be considered as categorical or dimensional?
Authors: Muthén Bengt
Published: August 2006

Aims  This paper discusses the representation of diagnostic criteria using categorical and dimensional statistical models. Conventional modeling using categorical or continuous latent variables in the form of latent class analysis and factor (IRT) analysis has limitations for the analysis of diagnostic criteria.

Methods  New hybrid models are discussed which provide both categorical and dimensional representations in the same model using mixture models. Conventional and new models are applied and compared using recent data for Diagnostic and Statistical Manual of Mental Disorders version IV (DSM‐IV) alcohol dependence and abuse criteria from the National Epidemiologic Survey on Alcohol and Related Conditions. Classification results from hybrid models are compared to the DSM‐IV approach of using the number of diagnostic criteria fulfilled.

Results  It is found that new hybrid mixture models are more suitable than latent class and factor (IRT) models.

Conclusion  Implications for DSM‐V are discussed in terms of reporting results using both categories and dimensions.
The neurobiology of addiction: a neuroadaptational view relevant for diagnosis
Authors: Koob George F.
Published: August 2006

Aims  The purpose of this review is to provide a synthesis of our knowledge of the neurobiological bases of addiction relevant for the diagnosis of addiction.

Methods  A heuristic framework of neuroadaptive changes within key brain neurocircuitry responsible for different stages of the addiction cycle is outlined and linked to human studies to provide important future translational links for diagnosis. 

Results  Animal studies have revealed dysregulation of specific neurochemical mechanisms (dopamine, opioid peptides) in the brain reward systems and recruitment of brain stress systems (corticotropin‐releasing factor) during the development of dependence that convey vulnerability to relapse. Animal studies have implicated the prefrontal cortex and basolateral amygdala in drug‐ and cue‐induced relapse, respectively, and the brain stress systems in stress‐induced relapse. Genetic studies suggest roles for the genes encoding the neurochemical elements involved in both the brain reward and stress systems in the vulnerability to addiction, and molecular studies have identified transduction and transcription factors that may mediate dependence‐induced reward dysregulation. Human imaging studies reveal similar neurocircuits involved in acute intoxication, chronic drug dependence and vulnerability to relapse. 

Conclusions  Major neurobiological changes in substance abuse disorders common to human and animal studies relevant for diagnosis include a compromised reward system, overactivated brain stress systems and compromised orbitofrontal/prefrontal cortex function. No biological markers of substance abuse disorders currently exist, but there are many promising neurobiological features of substance abuse disorders that will eventually aid in the specific diagnoses of substance use, misuse and dependence.
Comorbidity between substance use disorders and psychiatric conditions
Authors: Schuckit Marc A.
Published: August 2006

Aims  To review information relevant to the question of whether substance‐induced mental disorders exist and their implications.

Design and method  This paper utilized a systematic review of manuscripts published in the English language since approximately 1970 dealing with comorbid psychiatric and substance use disorders.

Findings  The results of any specific study depended on the definitions of comorbidity, the methods of operationalizing diagnostic criteria, the interview and protocol invoked several additional methodological issues. The results generally support the conclusion that substance use mental disorders exist, especially regarding stimulant or cannabinoid‐induced psychoses, substance‐induced mood disorders, as well as substance‐induced anxiety conditions.

Conclusions  The material reviewed indicates that induced disorders are prevalent enough to contribute significantly to rates of comorbidity between substance use disorders and psychiatric conditions, and that their recognition has important treatment implications. The current literature review underscores the heterogeneous nature of comorbidity.
Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38
Authors: Fang M. , Berg F. , Ducos A. , Andersson L.
Published: August 2006

Wild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10‐fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.
A dominant role for chemoattractant receptor‐homologous molecule expressed on T helper type 2 (Th2) cells (CRTH2) in mediating chemotaxis of CRTH2+ CD4+ Th2 lymphocytes in response to mast cell supernatants
Authors: Gyles Shân L. , Xue Luzheng , Townsend Elizabeth R. , Wettey Frank , Pettipher Roy
Published: August 2006

Human cultured mast cells, immunologically activated with immunoglobuin E (IgE)/anti‐IgE, released a factor(s) that promoted chemotaxis of human CRTH2+ CD4+ T helper type 2 (Th2) lymphocytes. Mast cell supernatants collected at 20 min, 1 hr, 2 hr and 4 hr after activation caused a concentration‐dependent increase in the migration of Th2 cells. The effect of submaximal dilutions of mast‐cell‐conditioned media was inhibited in a dose‐dependent manner by ramatroban (IC50 = 96 nm), a dual antagonist of both the thromboxane‐like prostanoid (TP) receptor and the chemoattractant receptor‐homologous molecule expressed on Th2 cells (CRTH2), but not by the selective TP antagonist SQ29548, implicating CRTH2 in mediating the chemotactic response of these Th2 cells. The effect of mast‐cell‐conditioned media was mimicked by prostaglandin D2 (PGD2) and this eicosanoid was detected in the conditioned media from activated mast cells in concentrations sufficient to account for the activity of the mast cell supernatants. Treatment of the mast cells with the cyclo‐oxygenase inhibitor diclofenac (10 μm) inhibited both the production of PGD2 and the CRTH2+ CD4+ Th2‐stimulatory activity, while addition of exogenous PGD2 to conditioned media from diclofenac‐treated mast cells restored the ability of the supernatants to promote chemotaxis of these Th2 cells. The degree of inhibition caused by diclofenac treatment of the mast cells was concordant with the degree of inhibition of chemotactic responses afforded by CRTH2 blockade. These data suggest that PGD2, or closely related metabolites of arachidonic acid, produced from mast cells may play a central role in the activation of CRTH2+ CD4+ Th2 lymphocytes through a CRTH2‐dependent mechanism.
Endodontics and infective endocarditis – is antimicrobial chemoprophylaxis required?
Authors: Brincat M. , Savarrio L. , Saunders W.
Published: August 2006

The purpose of this review is to evaluate the evidence implicating nonsurgical endodontic procedures in inducing infective endocarditis (IE). The literature is reviewed and findings about dental procedures that elicit bacteraemia [in particular root canal treatment (RCT)], sequelae of bacteraemia, relationship between IE and RCT and variation between antibiotic prophylaxis (AP) guidelines are highlighted. At present, there is still significant debate as to which dental procedures require chemoprophylaxis and what antibiotic regimen should be prescribed. Currently, there are insufficient primary data to know whether AP is effective or ineffective against IE. Practitioners are bound by current guidelines and medico‐legal considerations. Thus, the profession requires clear, uniform guidelines that are evidence‐based.
Parent and child reports of fruit and vegetable intakes and related family environmental factors show low levels of agreement
Authors: Tak N. I. , Te Velde S. J. , De Vries J. H. M. , Brug J.
Published: August 2006

Objective  The purpose of the present study was to determine the level of agreement between child and parent reports of 9‐ to 10‐year‐old children's consumption of fruit and vegetables and potential family–environmental determinants.

Methods  Schoolchildren and their parents completed parallel questionnaires at baseline and at follow‐up (1 year later) about usual fruit and vegetable consumption of the child, potential determinants and general demographics. Matched child–parent couples were included in the analyses (baseline = 380; follow‐up = 307). To assess the level of agreement between child and parent reports at both points in time, dependent‐sample t‐test, correlation coefficients, weighted Cohen's kappa coefficients and Bland–Altman plots including limits of agreement were used.

Results  Both at baseline and at follow‐up, the mean intake of fruit and vegetable reported by the children were significantly higher than reported by their parents, but differences were smaller at follow‐up. Correlation coefficients between child and parent reports (0.28–0.43) and weighted Cohen's kappa coefficients (0.25–0.28) were weak to moderate. Limits of agreement were wide.

Conclusion  The agreement between parent and child reports is weak to moderate and may depend on the age of the child. Fourth graders may overestimate their own intake of fruit and vegetables.