bluuebunny/crossref_metadata_2025 huggingface dataset:
Population Dynamics of Fusarium spp. and Microdochium nivale in Crops and Crop Residues of Winter Wheat
Authors: Köhl J. , de Haas B. H. , Kastelein P. , Burgers S. L. G. E. , Waalwijk C.
Published: July 2007

Naturally occurring populations of Fusarium avenaceum, F. culmorum, F. graminearum, F. poae, and Microdochium nivale were studied in two field experiments from anthesis in June 2003 until harvest in crops of winter wheat, and subsequently during 10 months after harvest until June 2004 on their residues exposed on the soil surface under field conditions. The dynamics of the different pathogens were estimated by quantifying the amount of DNA present in wheat tissues using TaqMan-polymerase chain reaction. While colonization of grain by Fusarium spp. and M. nivale was low, high amounts of DNA of F. avenaceum, F. graminearum, and F. culmorum were found in ear residues, internodes, and nodes of the mature crop. Amounts of DNA of pathogens decreased significantly during the following 10 months in residues of internodes and nodes, but not in residues of stem bases. Knowledge on population dynamics of pathogens will help to develop preventive measures aimed at reduction of inoculum sources of head blight pathogens.
Heritability of Latent Period Estimated from Wild-Type and Selected Populations of Puccinia triticina
Authors: Lehman Jeffrey S. , Shaner Gregory
Published: July 2007

Durability of partially resistant wheat cultivars to wheat leaf rust depends on the amount of genetic variation in parasitic fitness within populations of the pathogen Puccinia triticina. To assess the durability of partial resistance, selection experiments were used to explore quantitative variation in parasitic fitness of P. triticina. Fungal populations 881-WT and 882-WT were selected for shortened latent period on partially resistant cvs. CI 13277 and Sw 72469-6 for multiple generations. Fitness components were measured for wild-type and selected fungal populations. Responses to selection and selection differentials were calculated, and broad-sense, realized heritabilities for latent period were estimated for wild-type fungal populations on CI 13227 and on Sw 72469-6. Selected populations had fitness characteristics, not limited to latent period, that could provide greater fitness in nature. Generally, more cycles of selection had greater effects on fitness. In particular cases, selected populations on a partially resistant cultivar had values for latent period, uredinium area, and sporulation no different from those of a susceptible host–pathogen combination. Heritabilities of latent period of populations 881-WT and 882-WT on CI 13227 or populations 881-WT and 882-WT on Sw 72469-6 ranged from 0.65 to 0.76 and 0.17 to 0.24, respectively. Our results suggest the variation to overcome quantitative host resistance exists in extant populations of P. triticina. In addition, because more of the variation in latent period for populations of P. triticina on CI 13227 was genetic than for populations on Sw 72469-6, CI 13227 is likely to be more vulnerable to pathogen adaptation despite its exceptionally long latent period.
Staphylococcus pettenkoferi sp. nov., a novel coagulase-negative staphylococcal species isolated from human clinical specimens
Authors: Trülzsch Konrad , Grabein Béatrice , Schumann Peter , Mellmann Alexander , Antonenka Uladzimir , Heesemann Jürgen , Becker Karsten
Published: July 2007

Five coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human blood cultures in different German and Belgian medical facilities. A novel species, ‘Staphylococcus pettenkoferi’ was proposed recently to accommodate two of these strains (B3117Tand A6664), although the name was not validly published. All five strains belonged to the genusStaphylococcusbecause they were non-motile, Gram-positive, catalase-positive cocci with peptidoglycan type (A3αtypel-lys–gly2–4–l-Ser–Gly), menaquinone pattern (MK-7, MK-6 and MK-8) and major cellular fatty acids (ai-C15 : 0, ai-C17 : 0and i-C15 : 0) that corresponded to those of staphylococci. Phenotypically, the isolates most closely resembledStaphylococcus capitissubsp.capitisandStaphylococcus auricularis, but they could be distinguished from these species by physiological tests and chemotaxonomic investigations. The results of DNA–DNA hybridization, chemotaxonomic investigations and 16S rRNA gene and RNA polymerase B gene (rpoB) sequence analysis enabled strains B3117T, K6999, 229 and 230 to be differentiated genotypically and phenotypically from knownStaphylococcusspecies, indicating that these isolates are representatives of a novel species. The nameStaphylococcus pettenkoferisp. nov. is proposed for this novel species, with strain B3117T(=CIP 107711T=CCUG 51270T) as the type strain. Due to differences in the results of physiological and chemotaxonomic investigations and DNA–DNA hybridization data, strain A6664 was not included in the description of the novel species.
Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes
Authors: Kim Myung Kyum , Schubert Karin , Im Wan-Taek , Kim Kyung-Ho , Lee Sung-Taik , Overmann Jörg
Published: July 2007

Three Gram-negative, non-motile, non-spore-forming short rods (strains PB56T, PB180, PB229) were isolated from soil in South Korea. Cells were orange–red in colour. Strains PB180 and PB229 contained small amounts of bacteriochlorophylla, which was not detected in strain PB56T. However, all three isolates contained the genes for the photosynthetic type II reaction centre,pufLM. They contained Q-10 as the dominant quinone and C18 : 1as the dominant fatty acid. The highest 16S rRNA gene sequence similarities were found toSphingomonas oligophenolicaJCM 12082T(95.8 %),Sphingomonas koreensisKCTC 2882T(95.1 %),Sphingomonas maliIFO 15500T(95.1 %),Sphingomonas faeniDSM 14747T(94.8 %),Sphingomonas pruniIFO 15498T(94.7 %) andSphingomonas aquatilisKCTC 2881T(94.6 %), as well as toSphingosinicella microcystinivoransY2TandSphingosinicella xenopeptidilytica3-2W4T(95.0–95.2 %). Phylogenetic analyses supported the assignment of strains PB56T, PB180, PB229 to the genusSphingomonas. The novel isolates differ from all established species of the genusSphingomonasby their higher G+C content and the absence of straight-chain 2-hydroxy fatty acids. Based on the phylogenetic distances from species with validly published names and their phenotypic properties, the strains constitute a separate species, for which the nameSphingomonas kaistensissp. nov. is proposed. The type strain is PB56T(=KCTC 12334T=DSM 16846T).
Thermobacillus composti sp. nov., a moderately thermophilic bacterium isolated from a composting reactor
Authors: Watanabe Keiko , Nagao Norio , Yamamoto Shuich , Toda Tatsuki , Kurosawa Norio
Published: July 2007

A Gram-negative, rod-shaped, spore-forming and moderately thermophilic bacterium, strain KWC4T, was isolated from a composting reactor. Cells of strain KWC4T were 2.0–5.0 μm long and 0.5–0.7 μm in diameter. Strain KWC4T grew aerobically at 32–61 °C, with optimal growth occurring at 50 °C. It grew at pH 5.6–10.1, with optimal growth at around pH 9.0. The optimum NaCl concentration for growth was almost 0 % (w/v), but strain KWC4T was moderately halotolerant and was able to grow at NaCl concentrations up to 4.4 % (w/v). The DNA G+C content of strain KWC4T was 60.0 mol%. The major fatty acids were iso-16 : 0 (39.0 %) and anteiso-15 : 0 (33.3 %). Based on 16S rRNA gene sequence similarity data, strain KWC4T belonged to the genus Thermobacillus and was related to Thermobacillus xylanilyticus. However, strain KWC4T had a 38 bp insertion sequence located near the 3′ end of its 16S rRNA gene that was not present in T. xylanilyticus. The 16S rRNA gene sequence similarity value between strain KWC4T and T. xylanilyticus was 95.7 %. The DNA–DNA hybridization value between strain KWC4T and T. xylanilyticus strain XET was 66 %. On the basis of phenotypic and genotypic evidence, strain KWC4T (=DSM 18247T=JCM 13945T) is the type strain of a novel species, for which the name Thermobacillus composti sp. nov. is proposed.
Andreprevotia chitinilytica gen. nov., sp. nov., isolated from forest soil from Halla Mountain, Jeju Island, Korea
Authors: Weon Hang-Yeon , Kim Byung-Yong , Yoo Seung-Hee , Joa Jae-Ho , Kwon Soon-Wo , Kim Wan-Gyu
Published: July 2007

A motile, Gram-negative, rod-shaped bacterium, designated strain JS11-7T, was isolated from forest soil from Halla Mountain, Jeju Island, Korea. It grew optimally at 28 °C, pH 6–7 and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JS11-7T belongs to the family Neisseriaceae, with Silvimonas terrae as its closest relative (95.0 % similarity). It contained Q-8 as the predominant quinone and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1
ω6c), C16 : 0 and C18 : 1
ω7c as the major fatty acids. The DNA G+C content was 62 mol%. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, strain JS11-7T represents a novel genus and species, for which the name Andreprevotia chitinilytica gen. nov., sp. nov. is proposed. The type species is Andreprevotia chitinilytica and the type strain is JS11-7T (=KACC 11608T=DSM 18519T).
Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia
Authors: Li Wen-Jun , Xu Ping , Schumann Peter , Zhang Yu-Qin , Pukall Rüdiger , Xu Li-Hua , Stackebrandt Erko , Jiang Cheng-Lin
Published: July 2007

A Gram-positive, motile, short-rod-shaped strain, designated YIM 004T, was isolated from a forest-soil sample collected from Lijiang, Yunnan Province, China, and was investigated using a polyphasic taxonomic approach. The isolate contained chemotaxonomic markers that corresponded to those of its phylogenetic neighbour,Georgenia muralis, i.e. it possessed peptidoglycan type A4αwith lysine as the diagnostic cell-wall diamino acid, the predominant menaquinone was MK-8(H4) and the major fatty acid was ai-C15 : 0. The G+C content of the genomic DNA was 72.9 mol%. Strain YIM 004Texhibited a 16S rRNA gene sequence similarity of 97.3 % and a DNA–DNA relatedness value of 18 % with respect toG. muralisDSM 14418T. On the basis of the phenotypic and genotypic differences between the isolate andG. muralis, strain YIM 004Trepresents a novel species of the genusGeorgenia, for which the nameGeorgenia ruaniisp. nov. is proposed. The type strain is YIM 004T(=CCTCC AB 204065T=DSM 17458T=KCTC 19029T). In addition, an emended description of the genusGeorgeniais presented.
Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water
Authors: Kämpfer Peter , Rosselló-Mora Ramon , Hermansson Malte , Persson Frank , Huber Birgit , Falsen Enevold , Busse Hans-Jürgen
Published: July 2007

Two Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (strains CCUG 49009T and CCUG 49012), both isolated from drinking water, were characterized. On the basis of chemotaxonomic data [major ubiquinone, Q-8; predominant polyamines, putrescine and 2-hydroxyputrescine; major polar lipids, phosphatidylethanolamine, moderate amounts of diphosphatidylglycerol and phosphatidylglycerol and minor amounts of three aminolipids and phosphatidylserine; major fatty acids, C16 : 0 and summed feature 3 (C16 : 1
ω7c/C15 : 0 iso 2-OH)] and 16S rRNA gene sequence similarities, both strains clearly belong to the family Oxalobacteraceae of the Betaproteobacteria. 16S rRNA gene sequence similarities with members of the most closely related genera of this group (Herminiimonas, Massilia, Duganella, Telluria, Herbaspirillum, Janthinobacterium, Naxibacter and Paucimonas) were less than 96.5 % for both strains. The two strains also shared a relatively low 16S rRNA gene sequence similarity (96.8 %). Although phylogenetic analysis based on 16S rRNA gene sequence similarities clearly showed that the two organisms formed a separate branch, their phenotypes (including chemotaxonomic features) were hardly distinguishable and showed high similarities to those reported for the most closely related genera. On the basis of DNA–DNA hybridization results, the two strains were shown to represent separate species (sharing only 20 % DNA–DNA relatedness), but they could not be clearly differentiated phenotypically from each other. It is evident that these organisms represent a new genus, Undibacterium gen. nov., with one species, Undibacterium pigrum sp. nov. The type strain of Undibacterium pigrum is strain CCUG 49009T (=CIP 109318T). Strain CCUG 49012 (=CIP 108976) probably represents a second species of this genus, but is described here as a second genomovar of this species because of the lack of differentiating characters.
Lactobacillus ghanensis sp. nov., a motile lactic acid bacterium isolated from Ghanaian cocoa fermentations
Authors: Nielsen Dennis S. , Schillinger Ulrich , Franz Charles M. A. P. , Bresciani José , Amoa-Awua Wisdom , Holzapfel Wilhelm H. , Jakobsen Mogens
Published: July 2007

Three Gram-positive, catalase-negative, motile, rod-shaped strains, designated L486, L489T and L499, were isolated from fermenting cocoa. These organisms produced dl-lactic acid from glucose without gas formation. Ammonia was not produced from arginine. Acid was produced from amygdalin, d-cellobiose, aesculin, d-fructose, d-glucose, d-galactose, d-mannitol, d-mannose, N-acetylglucosamine, l-rhamnose, sucrose, salicin and d-trehalose. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type. A 16S rRNA gene sequence analysis revealed that the isolates belong phylogenetically to the genus Lactobacillus and are closely related to Lactobacillus nagelii, Lactobacillus vini and Lactobacillus satsumensis. Low DNA–DNA reassociation values were obtained between the isolates and the phylogenetically closest neighbours. On the basis of the genetic and phenotypic results, the isolates are considered to represent a novel species, for which the name Lactobacillus ghanensis is proposed. The type strain is L489T (=DSM 18630T=CCUG 53453T).
Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples
Authors: Huys Geert , Vancanneyt Marc , D'Haene Klaas , Falsen Enevold , Wauters Georges , Vandamme Peter
Published: July 2007

The taxonomic position of 12 isolates tentatively assigned to the genusBifidobacteriumon the basis of a limited phenotypic characterization was examined. The isolates were collected between 1978 and 2005 in Belgium, Sweden and Norway, and originated from various human clinical samples, including urine, blood, urethra, oral cavity, tonsil, and abscesses of lung and aortic valve. On the basis of band number and clustering analysis, repetitive DNA element-based PCR fingerprinting using the BOXA1R and (GTG)5primers indicated that the clinical isolates represented a taxon probably not belonging to the genusBifidobacterium. Analysis of 16S rRNA gene sequence similarities revealed that the isolates were most closely affiliated toParascardovia denticolensLMG 18312T(93.0–93.2 %),Scardovia inopinataLMG 18313T(92.9–93.1 %) and other members of theBifidobacteriaceae, indicating that the isolates belong to a novel genus within that family. This observation was further substantiated by the results of partial sequencing of the heat-shock protein 60 gene (hsp60) and determination of the DNA G+C contents (47.3–48.3 mol%). Members of the novel taxon can be phenotypically distinguished fromS. inopinata,P. denticolensandGardnerella vaginalisby the ability to grow on agar under aerobic conditions and on the basis of positive reactions for acid production froml-arabinose, raffinose, salicin andd-xylose. Unambiguous phenotypic differentiation fromAeriscardovia aeriphilaandBifidobacteriumspecies may be difficult, so phenotypic analyses should be complemented by molecular methods. The values for DNA–DNA binding among four members of the novel genus were in the range of 89–100 %, indicating that the strains should be considered as a single novel species of a novel genus, for which the nameAlloscardovia omnicolensgen. nov., sp. nov. is proposed. The type strain ofAlloscardovia omnicolensis CCUG 31649T(=LMG 23792T).
Pelagibacillus goriensis gen. nov., sp. nov., a moderately halotolerant bacterium isolated from coastal water off the east coast of Korea
Authors: Kim Yoon-Gon , Hwang Chung Yeon , Yoo Kwang Woo , Moon Hyung Tae , Yoon Jung-Hoon , Cho Byung Cheol
Published: July 2007

A Gram-positive, moderately halotolerant bacterium, designated CL-GR16T, was isolated from coastal water off the east coast of Korea. The strain was strictly aerobic, rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represented an independent lineage within Bacillus rRNA group 1, showing 93.6–94.6 % similarity with respect to the genus Ornithinibacillus, 94.0 % with respect to Paucisalibacillus, 91.0–93.5 % with respect to Virgibacillus, 93.2–93.3 % with respect to Salinibacillus and 92.8–93.2 % with respect to Oceanobacillus. The optimum temperature and pH for growth were 30 °C and pH 7.5. Strain CL-GR16T was able to grow at NaCl concentrations from 0 to 14 %, with optimum growth occurring at 0–2 % NaCl. The strain lacked oxidase. The major fatty acids were anteiso-C15 : 0 (65.6 %), anteiso-C17 : 0 (11.0 %) and iso-C15 : 0 (9.1 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The predominant menaquinone was MK-7. The G+C content of the DNA was 43 mol%. On the basis of the results of the polyphasic analysis, strain CL-GR16T represents a novel genus and species, for which the name Pelagibacillus goriensis gen. nov., sp. nov. is proposed. The type strain is strain CL-GR16T (=KCCM 42329T=DSM 18252T).
Nocardia amamiensis sp. nov., isolated from a sugar-cane field in Japan
Authors: Yamamura Hideki , Tamura Tomohiko , Sakiyama Yayoi , Harayama Shigeaki
Published: July 2007

An actinomycete, strain TT 00-78T, was isolated from soil from a sugar-cane field on Amami Island in Japan, using an SDS/yeast extract pre-treatment method, and the taxonomy was studied using a polyphasic approach. The chemotaxonomic and morphological characterizations clearly demonstrated that the strain belongs to the genus Nocardia. 16S rRNA gene sequencing studies showed that the strain was closely related to the type strains of Nocardia pneumoniae (98.6 %), Nocardia araoensis (98.1 %), Nocardia arthritidis (97.9 %) and Nocardia beijingensis (97.7 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain TT 00-78T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Therefore this strain represents a novel species of the genus Nocardia, for which the name Nocardia amamiensis sp. nov. is proposed. The type strain is TT 00-78T (=NBRC 102102T=DSM 45066T=KCTC 19208T).
Acetobacter ghanensis sp. nov., a novel acetic acid bacterium isolated from traditional heap fermentations of Ghanaian cocoa beans
Authors: Cleenwerck Ilse , Camu Nicholas , Engelbeen Katrien , De Winter Tom , Vandemeulebroecke Katrien , De Vos Paul , De Vuyst Luc
Published: July 2007

Twenty-three acetic acid bacteria, isolated from traditional heap fermentations of Ghanaian cocoa beans, were subjected to a polyphasic taxonomic study. The isolates were catalase-positive, oxidase-negative, Gram-negative rods. They oxidized ethanol to acetic acid and were unable to produce 2-ketogluconic acid, 5-ketogluconic acid and 2,5-diketogluconic acid from glucose; therefore, they were tentatively identified asAcetobacterspecies. 16S rRNA gene sequencing and phylogenetic analysis confirmed their position in the genusAcetobacter, withAcetobacter syzygiiandAcetobacter lovaniensisas their closest phylogenetic neighbours. (GTG)5-PCR fingerprinting grouped the strains in a cluster that did not contain any type strains of members of the genusAcetobacter. DNA–DNA hybridization with the type strains of all recognizedAcetobacterspecies revealed DNA–DNA relatedness values below the species level. The DNA G+C contents of three selected strains were 56.9–57.3 mol%. The novel strains had phenotypic characteristics that enabled them to be differentiated from phylogenetically relatedAcetobacterspecies, i.e. they were motile, did not produce 2-ketogluconic acid or 5-ketogluconic acid from glucose, were catalase-positive and oxidase-negative, grew on yeast extract with 30 % glucose, grew on glycerol (although weakly) but not on maltose or methanol as carbon sources, and did not grow with ammonium as sole nitrogen source and ethanol as carbon source. Based on the genotypic and phenotypic data, the isolates represent a novel species of the genusAcetobacterfor which the nameAcetobacter ghanensissp. nov. is proposed. The type strain is R-29337T(=430AT=LMG 23848T=DSM 18895T).
Rheinheimera aquimaris sp. nov., isolated from seawater of the East Sea in Korea
Authors: Yoon Jung-Hoon , Park Soon Ei , Kang So-Jung , Oh Tae-Kwang
Published: July 2007

Two Gram-negative, motile, non-spore-forming bacterial strains, SW-353Tand SW-369, were isolated from seawater from the East Sea, Korea, and their taxonomic positions were investigated by means of a polyphasic study. Strains SW-353Tand SW-369 grew optimally at 30–37 °C and pH 7.0–8.0. Strains SW-353Tand SW-369 contained Q-8 as the predominant ubiquinone and contained C16 : 0, C18 : 1ω7cand C16 : 1ω7cand/or iso-C15 : 02-OH as the major fatty acids. The DNA G+C contents were 50.1 and 50.5 mol%. Strains SW-353Tand SW-369 exhibited no differences in their 16S rRNA gene sequences and showed a mean DNA–DNA relatedness level of 91 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-353Tand SW-369 belong to the genusRheinheimera. Similarity values between the 16S rRNA gene sequences of the two isolates and the type strains of the recognizedRheinheimeraspecies were in the range 96.6–97.9 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strains SW-353Tand SW-369 differ from the recognizedRheinheimeraspecies. On the basis of phenotypic, phylogenetic and genetic data, therefore, strains SW-353Tand SW-369 represent a novel species of the genusRheinheimera, for which the nameRheinheimera aquimarissp. nov. is proposed. The type strain is SW-353T(=KCTC 12840T=JCM 14331T).
Pelotomaculum propionicicum sp. nov., an anaerobic, mesophilic, obligately syntrophic, propionate-oxidizing bacterium
Authors: Imachi Hiroyuki , Sakai Sanae , Ohashi Akiyoshi , Harada Hideki , Hanada Satoshi , Kamagata Yoichi , Sekiguchi Yuji
Published: July 2007

An anaerobic, mesophilic, syntrophic, propionate-oxidizing bacterium, strain MGPT, was isolated as a defined co-culture withMethanospirillum hungateifrom the methanogenic sludge of a mesophilic upflow anaerobic sludge blanket (UASB) reactor. The strain grew in the presence of propionate, but only in co-culture with methanogens, suggesting that it is an obligately syntrophic bacterium. The optimum temperature for growth was 37 °C, and the optimum pH was between 6.5 and 7.2. Based on comparative 16S rRNA gene sequence analysis, strain MGPTwas affiliated with subcluster Ih of ‘Desulfotomaculumcluster I’, in which it was found to be moderately related to known species of the generaPelotomaculumandCryptanaerobacter. Similar to known species of the genusPelotomaculum, strain MGPTcould degrade propionate in syntrophy, but had no ability to reduce sulfate, sulfite and thiosulfate. Further phenotypic and genetic studies supported the affiliation of the strain as a novel species in this genus, for which the namePelotomaculum propionicicumsp. nov. is proposed. The type strain is MGPT(=DSM 15578T=JCM 11929T). The strain has been deposited in the DSM and JCM culture collections as a defined co-culture withMethanospirillum hungatei.
Sphingobacterium composti sp. nov., isolated from cotton-waste composts
Authors: Yoo Seung-Hee , Weon Hang-Yeon , Jang Han-Byul , Kim Byung-Yong , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: July 2007

A Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterial strain designated 4M24Twas isolated from cotton-waste compost. Analysis of the 16S rRNA gene sequence of strain 4M24Trevealed that it is a member of the genusSphingobacterium, sharing 88.5–94.5 % sequence similarity with type strains of the genusSphingobacteriumand being most closely related toSphingobacterium daejeonenseTR6-04T(94.5 % sequence similarity) andSphingobacterium mizutaiiATCC 33299T(92.2 % similarity). The major fatty acids of strain 4M24Tgrown on trypticase soy agar medium were summed feature 3 (iso-C15 : 02-OH and/or C16 : 1ω7c; 37.5 %), iso-C15 : 0(29.5 %) and iso-C17 : 03-OH (19.7 %). The G+C content of the genomic DNA was 42.3 mol%. On the basis of phenotypic and genotypic characteristics, strain 4M24Trepresents a novel species of the genusSphingobacterium, for which the nameSphingobacterium compostisp. nov. is proposed. The type strain is 4M24T(=KACC 11313T=DSM 18850T).
Deinococcus peraridilitoris sp. nov., isolated from a coastal desert
Authors: Rainey Fred A. , Ferreira Margarida , Nobre M. Fernanda , Ray Keren , Bagaley Danielle , Earl Ashlee M. , Battista John R. , Gómez-Silva Benito , McKay Christopher P. , da Costa Milton S.
Published: July 2007

Three ionizing-radiation-resistant bacterial strains (designated KR-196, KR-198 and KR-200T) were isolated from a sample of arid soil collected from a coastal desert in Chile. The soil sample was irradiated before serial dilution plating was performed using one-tenth-strength plate count agar. Phylogenetic analysis of the 16S rRNA gene sequences showed these organisms to represent a novel species of the genus Deinococcus, having sequence similarities of 87.3–90.8 % with respect to recognized Deinococcus species. Strains KR-196, KR-198 and KR-200T were aerobic and showed optimum growth at 30 °C and pH 6.5–8.0. The major respiratory menaquinone was MK-8. The predominant fatty acids in these strains were 16 : 1ω7c, 16 : 0, 15 : 1ω6c, 17 : 0 and 18 : 0. The DNA G+C content of strain KR-200T was 63.9 mol%. Strains KR-196, KR-198 and KR-200T were found to be resistant to >10 kGy gamma radiation. On the basis of the phylogenetic, chemotaxonomic and phenotypic data, strain KR-200T represents a novel species of the genus Deinococcus, for which the name Deinococcus peraridilitoris sp. nov. is proposed. The type strain is KR-200T (=LMG 22246T=CIP 109416T).
Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community
Authors: Robert Céline , Chassard Christophe , Lawson Paul A. , Bernalier-Donadille Annick
Published: July 2007

A strictly anaerobic cellulolytic bacterium, strain CRE21T, was isolated from a human faecal sample. Cells were Gram-negative non-motile rods that were about 1.7 μm in length and 0.9 μm in width. Strain CRE21T degraded different types of cellulose and was able to grow on a variety of carbohydrates. Cellulose and sugars were mainly converted to acetate, propionate and succinate. The G+C content of the DNA was 41.1 mol%. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Bacteroides with highest sequence similarity to the type strain of Bacteroides intestinalis (98 %). DNA–DNA hybridization results revealed that strain CRE21T was distinct from B. intestinalis (40 % DNA–DNA relatedness). Strain CRE21T also showed several characteristics distinct from B. intestinalis. In particular, it exhibited different capacity to degrade polysaccharides such as cellulose. On the basis of phylogenetic analysis and the morphological, physiological and biochemical data presented in this study, strain CRE21T can be readily differentiated from recognized species of the genus Bacteroides. The name Bacteroides cellulosilyticus sp. nov. is proposed to accommodate this organism. The type strain is CRE21T (=DSM 14838T=CCUG 44979T).
Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China
Authors: Gutiérrez M. C. , Castillo A. M. , Kamekura M. , Xue Y. , Ma Y. , Cowan D. A. , Jones B. E. , Grant W. D. , Ventosa A.
Published: July 2007

Strain SH-6Twas isolated from the sediment of Lake Shangmatala, a saline lake in Inner Mongolia (China). Cells were pleomorphic. The organism was neutrophilic and required at least 2.5 M (15 %) NaCl, but not MgCl2, for growth; optimal growth occurred at 4.3 M (25 %) NaCl. The G+C content of its DNA was 63.1 mol%. 16S rRNA gene sequence analysis revealed that strain SH-6Tis a member of the familyHalobacteriaceae, but there was a low level of similarity with other members of this family. Highest sequence similarity (94.6 %) was obtained with the 16S rRNA genes of the type strains ofNatronolimnobius innermongolicusandNatronolimnobius baerhuensis. Polar lipid analyses revealed that strain SH-6Tcontains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C20C20and C20C25glycerol diethers together with the glycolipid S2-DGD-1. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain SH-6Tis thus considered to represent a novel species in a new genus within the familyHalobacteriaceae, orderHalobacteriales, for which the nameHalopiger xanaduensisgen. nov., sp. nov. is proposed. The type strain ofHalopiger xanaduensisis SH-6T(=CECT 7173T=CGMCC 1.6379T=JCM 14033T).
Nonomuraea bangladeshensis sp. nov. and Nonomuraea coxensis sp. nov.
Authors: Ara Ismet , Kudo Takuji , Matsumoto Atsuko , Takahashi Yoko , Omura Satoshi
Published: July 2007

Two novel bacterial strains were isolated from sandy soil from Cox's Bazar, Bangladesh. Strains 5-10-10T and 5-38-42T were Gram-positive, aerobic, non-motile actinomycetes that form branched substrate and aerial mycelium. On the basis of 16S rRNA gene sequence similarity studies, the novel strains were shown to belong to the genus Nonomuraea, being most closely related to Nonomuraea fastidiosa. Chemotaxonomic data supported the assignment of the novel strains as members of the genus Nonomuraea. Strain 5-10-10T contained MK-9(H4) and strain 5-38-42T contained MK-9(H6) and MK-9(H4) as the major menaquinones. Major polar lipids were phosphatidylethanolamine and hydroxyphosphatidylethanolamine. The major cellular fatty acid for strain 5-10-10T was iso-C16 : 0 (26.4 %); C16 : 0 (17.4 %) was the major cellular fatty acid for strain 5-38-42T. The results of DNA–DNA hybridization and physiological tests enabled strains 5-10-10T and 5-38-42T to be differentiated genotypically and phenotypically from each other and from the closely related species, N. fastidiosa. On the basis of these results, strains 5-10-10T and 5-38-42T represent two novel species of the genus Nonomuraea. Following an evaluation of morphological, physiological and chemotaxonomic characteristics, 16S rRNA gene sequence comparisons and DNA–DNA hybridization experiments, the new isolates are proposed as two novel species, Nonomuraea bangladeshensis sp. nov. [type strain, 5-10-10T (=MTCC 8089T=JCM 13930T)] and Nonomuraea coxensis sp. nov. [type strain, 5-38-42T (=MTCC 8090T=JCM 13931T)].
Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent
Authors: Pikuta Elena V. , Marsic Damien , Itoh Takashi , Bej Asim K. , Tang Jane , Whitman William B. , Ng Joseph D. , Garriott Owen K. , Hoover Richard B.
Published: July 2007

A hyperthermophilic, sulfur-reducing, organo-heterotrophic archaeon, strain OGL-20PT, was isolated from ‘black smoker’ chimney material from the Rainbow hydrothermal vent site on the Mid-Atlantic Ridge (36.2°N, 33.9°W). The cells of strain OGL-20PThave an irregular coccoid shape and are motile with a single flagellum. Growth was observed within a pH range of 5.0−8.5 (optimum pH 7.0), an NaCl concentration range of 1–5 % (w/v) (optimum 3 %) and a temperature range of 55–94 °C (optimum 83–85 °C). The novel isolate is strictly anaerobic and obligately dependent upon elemental sulfur as an electron acceptor, but it does not reduce sulfate, sulfite, thiosulfate, Fe(III) or nitrate. Proteolysis products (peptone, bacto-tryptone, Casamino acids and yeast extract) are utilized as substrates during sulfur reduction. Strain OGL-20PTis resistant to ampicillin, chloramphenicol, kanamycin and gentamicin, but sensitive to tetracycline and rifampicin. The G+C content of the DNA is 52.9 mol%. The 16S rRNA gene sequence analysis revealed that strain OGL-20PTis closely related toThermococcus coalescensand related species, but no significant homology by DNA–DNA hybridization was observed between those species and the new isolate. On the basis of physiological and molecular properties of the new isolate, we conclude that strain OGL-20PTrepresents a new separate species within the genusThermococcus, for which we propose the nameThermococcus thioreducenssp. nov. The type strain is OGL-20PT(=JCM 12859T=DSM 14981T=ATCC BAA-394T).
Alkalimonas collagenimarina sp. nov., a psychrotolerant, obligate alkaliphile isolated from deep-sea sediment
Authors: Kurata Atsushi , Miyazaki Masayuki , Kobayashi Tohru , Nogi Yuichi , Horikoshi Koki
Published: July 2007

A psychrotolerant, obligately alkaliphilic, collagenolytic enzyme-producing bacterium, strain AC40T, was isolated from a deep-sea sediment off Torishima Island, Japan, at a depth of 4026 m. Phylogenetic analysis of 16S rRNA gene sequences indicated that this bacterium was closely related to members of the genusAlkalimonas, with highest sequence similarity (97.9 %) toAlkalimonas delamerensis1E1T. DNA–DNA hybridization experiments of strain AC40TwithA. delamerensis1E1Trevealed a level of relatedness of less than 30 %. Cells of strain AC40Twere strictly aerobic, rod-shaped, Gram-negative and motile by means of a single polar flagellum. The organism grew over a range of temperatures from 5 to 37 °C and at initial pH values between 7.0 and 10.5. Optimal growth was observed at 33 °C and at pH 8.5–10.0. Cellular fatty acids of strain AC40Twere predominantly saturated and mono-unsaturated straight-chain components (C16 : 0and C18 : 1). The major isoprenoid quinone was Q-8. The G+C content of the DNA was 49.3 mol%. Phylogenetic characteristics, physiological properties and DNA–DNA hybridization data indicate that strain AC40Trepresents a novel species of the genusAlkalimonas, for which the nameAlkalimonas collagenimarinasp. nov. is proposed. The type strain is AC40T(=JCM 14267T=NCIMB 14266T).
Genus Megamonas should be placed in the lineage of Firmicutes; Clostridia; Clostridiales; ‘Acidaminococcaceae’; Megamonas
Authors: Morotomi Masami , Nagai Fumiko , Sakon Hiroshi
Published: July 2007

Megamonas hypermegaleis the sole species of the genusMegamonasincluded in the List of Prokaryotic Names with Standing in Nomenclature and in the databases of DDBJ, EBI/EMBL and NCBI/GenBank it is placed in the lineage ofBacteroidetes;Bacteroidetes(class); ‘Bacteroidales’;Bacteroidaceae;Megamonas. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that this species clustered with species of the family ‘Acidaminococcaceae’ but not with those of theBacteroidaceae. The genusMegamonasshould be placed in the lineage ofFirmicutes;Clostridia;Clostridiales; ‘Acidaminococcaceae’;Megamonas.
Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere
Authors: Wong Lee H. , Brettingham-Moore Kate H. , Chan Lyn , Quach Julie M. , Anderson Melissa A. , Northrop Emma L. , Hannan Ross , Saffery Richard , Shaw Margaret L. , Williams Evan , Choo K.H. Andy
Published: July 2007

The centromere is a complex structure, the components and assembly pathway of which remain inadequately defined. Here, we demonstrate that centromeric α-satellite RNA and proteins CENPC1 and INCENP accumulate in the human interphase nucleolus in an RNA polymerase I–dependent manner. The nucleolar targeting of CENPC1 and INCENP requires α-satellite RNA, as evident from the delocalization of both proteins from the nucleolus in RNase-treated cells, and the nucleolar relocalization of these proteins following α-satellite RNA replenishment in these cells. Using protein truncation and in vitro mutagenesis, we have identified the nucleolar localization sequences on CENPC1 and INCENP. We present evidence that CENPC1 is an RNA-associating protein that binds α-satellite RNA by an in vitro binding assay. Using chromatin immunoprecipitation, RNase treatment, and “RNA replenishment” experiments, we show that α-satellite RNA is a key component in the assembly of CENPC1, INCENP, and survivin (an INCENP-interacting protein) at the metaphase centromere. Our data suggest that centromere satellite RNA directly facilitates the accumulation and assembly of centromere-specific nucleoprotein components at the nucleolus and mitotic centromere, and that the sequestration of these components in the interphase nucleolus provides a regulatory mechanism for their timely release into the nucleoplasm for kinetochore assembly at the onset of mitosis.
Recombination rate estimation in the presence of hotspots
Authors: Auton Adam , McVean Gil
Published: July 2007

Fine-scale estimation of recombination rates remains a challenging problem. Experimental techniques can provide accurate estimates at fine scales but are technically challenging and cannot be applied on a genome-wide scale. An alternative source of information comes from patterns of genetic variation. Several statistical methods have been developed to estimate recombination rates from randomly sampled chromosomes. However, most such methods either make poor assumptions about recombination rate variation, or simply assume that there is no rate variation. Since the discovery of recombination hotspots, it is clear that recombination rates can vary over many orders of magnitude at the fine scale. We present a method for the estimation of recombination rates in the presence of recombination hotspots. We demonstrate that the method is able to detect and accurately quantify recombination rate heterogeneity, and is a substantial improvement over a commonly used method. We then use the method to reanalyze genetic variation data from the HLA and MS32 regions of the human genome and demonstrate that the method is able to provide accurate rate estimates and simultaneously detect hotspots.
Age-related decline of sleep-dependent consolidation
Authors: Spencer Rebecca M.C. , Gouw Arvin M. , Ivry Richard B.
Published: July 2007

Sleep-dependent memory consolidation is observed following motor skill learning: Performance improvements are greater over a 12-h period containing sleep relative to an equivalent interval without sleep. Here we examined whether older adults exhibit sleep-dependent consolidation on a sequence learning task. Participants were trained on one of two sequence learning tasks. Performance was assessed after a 12-h break that included sleep and after a 12-h break that did not include sleep. Older and younger adults showed similar degrees of initial learning. However, performance of the older adults did not improve following sleep, providing evidence that sleep-dependent consolidation is diminished with age.
The Impact of Audit Committee Existence and Audit Committee Meeting Frequency on the External Audit: Perceptions of Australian Auditors
Authors: Stewart Jenny , Munro Lois
Published: July 2007

This article examines the impact of audit committee existence, the frequency of audit committee meetings and the auditor's attendance at meetings on aspects of the external audit. Using an experimental design, we find that the audit committee, the frequency of committee meetings and the auditor's attendance at meetings are significantly associated with a reduction in perceived audit risk. The impact on audit efficiency and audit testing is perceived to be minimal. Manager and partner hours are greater when meetings are more frequent and the partner attends all meetings. The audit committee is expected to provide assistance in resolving conflicts with management and to lead to some improvement in overall audit quality. In neither case is this affected by meeting frequency or the auditor's attendance at meetings. Participants expect the existence of an audit committee to lead to an increase in audit fees, particularly when meetings are more frequent and the auditor is required to attend meetings. Reasons given for any fee increase relate to the additional preparation for and attendance at meetings.
Role of UGT1A1*6, UGT1A1*28 and ABCG2 c.421C>A polymorphisms in irinotecan‐induced neutropenia in Asian cancer patients
Authors: Jada Srinivasa Rao , Lim Robert , Wong Chiung Ing , Shu Xiaochen , Lee Soo Chin , Zhou Qingyu , Goh Boon Cher , Chowbay Balram
Published: July 2007

The objectives of the present study were (i) to study the pharmacogenetics of UGT1A1*6, UGT1A1*28 and ABCG2 c.421C>A in three distinct healthy Asian populations (Chinese, Malays and Indians), and (ii) to investigate the polygenic influence of these polymorphic variants in irinotecan‐induced neutropenia in Asian cancer patients. Pharmacokinetic and pharmacogenetic analyses were done after administration of irinotecan as a 90‐min intravenous infusion of 375 mg/m2 once every 3 weeks (n = 45). Genotypic–phenotypic correlates showed a non‐significant influence of UGT1A1*28 and ABCG2 c.421C>A polymorphisms on the pharmacokinetics of SN‐38 (P > 0.05), as well as severity of neutropenia (P > 0.05). Significantly higher exposure levels to SN‐38 (P = 0.018), lower relative extent of glucuronidation (REG; P = 0.006) and higher biliary index (BI; P = 0.003) were found in cancer patients homozygous for the UGT1A1*6 allele compared with patients harboring the reference genotype. The mean absolute neutrophil count (ANC) was 85% lower and the prevalence of grade 4 neutropenia (ANC ≤ 500/µL) was 27% in patients homozygous for UGT1A1*6 compared with the reference group. Furthermore, the presence of the UGT1A1*6 allele was associated with an approximately 3‐fold increased risk of developing severe grade 4 neutropenia compared with patients harboring the reference genotype. These exploratory findings suggest that homozygosity for UGT1A1*6 allele may be associated with altered SN‐38 disposition and may increase the risk of severe neutropenia in Asian cancer patients, particularly in the Chinese cancer patients who comprised 80% (n = 36) of the patient population in the present study. (Cancer Sci 2007; 98: 1461–1467)
CR229, a novel derivative of β‐carbolin‐1‐one, induces cell cycle arrest and apoptosis in HeLa cells via p53 activation
Authors: Kim Min Kyoung , Oh Ha Lim , Choi Bu‐Young , Lim Haeyoung , Cho Youl‐Hee , Lee Chul‐Hoon
Published: July 2007

In the course of screening for novel anticancer compounds, CR229 (6‐Bromo‐2,3,4,9‐tetrahydro‐carbolin‐1‐one), a novel derivative of β‐carbolin‐1‐one, was generated as a new scaffold candidate. For the first time, the authors demonstrate that CR229 inhibited the growth of HeLa cells by the induction of cell cycle arrest and apoptosis. Analysis of flow cytometry and western blots of HeLa cells treated with 2.5 µM CR229 revealed an appreciable cell cycle arrest in the G1, G2/M phase and apoptotic induction via thep53‐dependent pathway. Furthermore, the release of cytochromecfrom mitochondria was detected using confocal microscopy in HeLa cells treated with CR229. Accordingly, these data demonstrate that the anticancer activity of CR229 is associated with: (i) the down‐regulation of cyclins and cyclin‐dependent kinase; (ii) the induction of p53, p21, and p16; and (iii) the activation of caspase‐3. (Cancer Sci2007; 98: 1402–1407)
Pertuzumab, a novel HER dimerization inhibitor, inhibits the growth of human lung cancer cells mediated by the HER3 signaling pathway
Authors: Sakai Kazuko , Yokote Hideyuki , Murakami‐Murofushi Kimiko , Tamura Tomohide , Saijo Nagahiro , Nishio Kazuto
Published: July 2007

A humanized anti‐HER2 monoclonal antibody pertuzumab (Omnitarg, 2C4), binding to a different HER2 epitope than trastuzumab, is known as an inhibitor of heterodimerization of the HER receptors. Potent antitumor activity against HER2‐expressing breast and prostate cancer cell lines has been clarified, but this potential is not clear against lung cancers. The authors investigated the in vitro anti‐tumor activity of pertuzumab against eight non‐small cell lung cancer cells expressing various members of the HER receptors. A lung cancer 11_18 cell line expressed a large amount of HER2 and HER3, and its cell growth was stimulated by an HER3 ligand, heregulin (HRG)‐α. Pertuzumab significantly inhibited the HRG‐α‐stimulated cellular growth of the 11_18 cells. Pertuzumab blocked HRG‐α‐stimulated phosphorylation of HER3, mitogen‐activated protein kinase (MAPK), and Akt. In contrast, pertuzumab failed to block epidermal growth factor (EGF)‐stimulated phosphorylation of EGF receptor (EGFR) and MAPK. Immunoprecipitation showed that pertuzumab inhibited HRG‐α‐stimulated HER2/HER3 heterodimer formation. HRG‐α‐stimulated HER3 phosphorylation was also observed in the PC‐9 cells co‐overexpressing EGFR, HER2, and HER3, but the cell growth was neither stimulated by HRG‐α nor inhibited by pertuzumab. The present results suggest that pertuzumab is effective against HRG‐α‐dependent cell growth in lung cancer cells through inhibition of HRG‐α‐stimulated HER2/HER3 signaling. (Cancer Sci 2007; 98: 1498–1503)
Assessment of 11C‐labeled‐4‐N‐(3‐bromoanilino)‐6, 7‐dimethoxyquinazoline as a positron emission tomography agent to monitor epidermal growth factor receptor expression
Authors: Wang Hui , Yu Jinming , Yang Guoren , Song Xianrang , Sun Xiaorong , Zhao Shuqiang , Mu Dianbin
Published: July 2007

The aim of the present study was to investigate the biodistribution of 11C‐labeled‐4‐N‐(3‐bromoanilino), 6,7‐dimethoxyquinazoline (11C‐PD153035) and the relationship between accumulation of the tracer and epidermal growth factor receptor (EGFR) expression levels. Biodistribution studies of 11C‐PD153035 were performed in tumor‐bearing nude mice. The amount of radioactivity in the lungs was small while concentrations were highest in the liver and intestine. From in vitro studies, the level of 11C‐PD153035 accumulation was detected in MDA‐MB‐468, A549, and MDA‐MB‐231 cells. The uptake of 11C‐PD153035 in cells was closely correlated with the EGFR expression level of cells (r2 = 0.85; P < 0.001), and the results obtained in excised tumors were also significantly correlated (r2 = 0.63; P = 0.003). Binding in MDA‐MB‐468, A549, and MDA‐MB‐231 tumors was reduced to background level at 60 min post injection 11C‐PD153035 by pretreatment with cold PD153035. The present study showed that whether in vitro or ex vivo the uptake of 11C‐PD153035 closely correlated with EGFR expression levels. In contrast, blocking studies revealed specific binding in the three kinds of tumors. Thus 11C‐PD153035 may be used as a positron emission tomography tracer to yield useful information about tumors, particularly for lung cancer with different EGFR expression levels. (Cancer Sci 2007; 98: 1413–1416)