bluuebunny/crossref_metadata_2025 huggingface dataset:
structureViz: linking Cytoscape and UCSF Chimera
Authors: Morris John H. , Huang Conrad C. , Babbitt Patricia C. , Ferrin Thomas E.
Published: July 2007

Summary: structureViz is a Cytoscape plug-in that links the visualization of biological networks provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera. When combined with Cytoscape and Chimera, structureViz provides the first tool that links these two critical aspects of computational analysis in a straightforward manner. structureViz includes commands to open structures in Chimera and align them using Chimera's sequence-structure analysis tools. When a structure is opened, structureViz provides an alternative interface to Chimera: the Cytoscape Molecular Structure Navigator. This interface uses a tree-based paradigm to allow users to select and affect the display of models, chains and residues, mostly through the use of context menus.

Contact:  scooter@cgl.ucsf.edu
Age, growth, and condition of European eel (Anguilla anguilla) from six lakes in the River Havel system (Germany)
Authors: Simon Janek
Published: July 2007

Simon, J. 2007. Age, growth, and condition of European eel (Anguilla anguilla) from six lakes in the River Havel system (Germany). – ICES Journal of Marine Science, 64: 1414–1422. A total of 199 female yellow European eels (Anguilla anguilla), 21.6–66.2 cm long and 3–14 years old, was collected by electro-fishing from six lakes in the River Havel system (Germany) in spring 2001. The condition and the growth rate, estimated by otolith increments, varied between eels within single lakes and between lakes. Fulton's condition factor ranged from 0.10 to 0.24 and the gross energy content varied between 4.3 and 15.3 MJ kg−1. There were no significant differences in mean condition factor (0.16–0.18) or gross energy content (6.5–9.3 MJ kg−1) between lakes. Fastest growth was in Lake Blankensee (mean 5.3 cm year−1), and the slowest in Lake Sacrow (mean 4.0 cm year−1). For all lakes combined, the overall mean annual increment was estimated to be 4.5 cm year−1. The biggest annual increment on the otoliths was generally laid down during the first and second years in fresh water, when the growth rate was 6.1–8.5 cm year−1. Then, in the subsequent 12 years, the annual increment remained almost constant or decreased slightly (with lake-dependent values of between 1.6 and 6.8 cm year−1). In the River Havel system, the time between stocking of the lakes with glass eels and the recapture of eels at 45 cm body length was 7–10 years. The physiologically possible maximum length (L∞ values) of eels lay in the range 50–130 cm. In comparison with previous investigations (between the 1950s and the 1970s), the only difference observed was a trend towards slower growth.
Identification of 118 Arabidopsis Transcription Factor and 30 Ubiquitin-Ligase Genes Responding to Chitin, a Plant-Defense Elicitor
Authors: Libault Marc , Wan Jinrong , Czechowski Tomasz , Udvardi Michael , Stacey Gary
Published: July 2007

Chitin, found in the cell walls of true fungi and the exoskeleton of insects and nematodes, is a well-established elicitor of plant defense responses. In this study, we analyzed the expression patterns of Arabidopsis thaliana transcription factor (TF) and ubiquitin-ligase genes in response to purified chitooctaose at different treatment times (15, 30, 60, 90, and 120 min after treatment), using both quantitative polymerase chain reaction and the Affymetrix Arabidopsis whole-genome array. A total of 118 TF genes and 30 ubiquitin-ligase genes were responsive to the chitin treatment. Among these genes, members from the following four TF families were overrepresented: APETALA2/ethylene-reponsive element binding proteins (27), C2H2 zinc finger proteins (14), MYB domain-containing proteins (11), and WRKY domain transcription factors (14). Transcript variants from a few of these genes were found to respond differentially to chitin, suggesting transcript-specific regulation of these TF genes.
A Novel Nuclear Protein Interacts With the Symbiotic DMI3 Calcium- and Calmodulin-Dependent Protein Kinase of Medicago truncatula
Authors: Messinese Elsa , Mun Jeong-Hwan , Yeun Li Huey , Jayaraman Dhileepkumar , Rougé Pierre , Barre Annick , Lougnon Géraldine , Schornack Sebastian , Bono Jean-Jacques , Cook Douglas R. , Ané Jean-Michel
Published: July 2007

Many higher plants establish symbiotic relationships with arbuscular mycorrhizal (AM) fungi that improve their ability to acquire nutrients from the soil. In addition to establishing AM symbiosis, legumes also enter into a nitrogen-fixing symbiosis with bacteria known as rhizobia that results in the formation of root nodules. Several genes involved in the perception and transduction of bacterial symbiotic signals named “Nod factors” have been cloned recently in model legumes through forward genetic approaches. Among them, DMI3(Doesn't Make Infections 3) is a calcium- and calmodulin-dependent kinase required for the establishment of both nodulation and AM symbiosis. We have identified, by a yeast two-hybrid system, a novel protein interacting with DMI3 named IPD3 (Interacting Protein of DMI3). IPD3 is predicted to interact with DMI3 through a C-terminal coiled-coil domain. Chimeric IPD3∷GFP is localized to the nucleus of transformed Medicago truncatula root cells, in which split yellow fluorescent protein assays suggest that IPD3 and DMI3 physically interact in Nicotiana benthamiana. Like DMI3, IPD3 is extremely well conserved among the angiosperms and is absent from Arabidopsis. Despite this high level of conservation, none of the homologous proteins have a demonstrated biological or biochemical function. This work provides the first evidence of the involvement of IPD3 in a nuclear interaction with DMI3.
All Five Host-Range Variants ofXanthomonas citriCarry OnepthAHomolog With 17.5 Repeats That Determines Pathogenicity on Citrus, but None Determine Host-Range Variation
Authors: Al-Saadi Abdulwahid , Reddy Joseph D. , Duan Yong P. , Brunings Asha M. , Yuan Qiaoping , Gabriel Dean W.
Published: July 2007

Citrus canker disease is caused by five groups of Xanthomonas citri strains that are distinguished primarily by host range: three from Asia (A, A*, and Aw) and two that form a phylogenetically distinct clade and originated in South America (B and C). Every X. citri strain carries multiple DNA fragments that hybridize with pthA, which is essential for the pathogenicity of wide-host-range X. citri group A strain 3213. DNA fragments that hybridized with pthA were cloned from a representative strain from all five groups. Each strain carried one and only one pthA homolog that functionally complemented a knockout mutation of pthA in 3213. Every complementing homolog was of identical size to pthA and carried 17.5 nearly identical, direct tandem repeats, including three new genes from narrow-host-range groups C (pthC), Aw(pthAW), and A* (pthA*). Every noncomplementing paralog was of a different size; one of these was sequenced from group A* (pthA*-2) and was found to have an intact promoter and full-length reading frame but with 15.5 repeats. None of the complementing homologs nor any of the noncomplementing paralogs conferred avirulence to 3213 on grapefruit or suppressed avirulence of a group A* strain on grapefruit. A knockout mutation of pthC in a group C strain resulted in loss of pathogenicity on lime, but the strain was unaffected in ability to elicit an HR on grapefruit. This pthC-mutant was fully complemented by pthA, pthB, or pthC. Analysis of the predicted amino-acid sequences of all functional pthA homologs and nonfunctional paralogs indicated that the specific sequence of the 17th repeat may be essential for pathogenicity of X. citri on citrus.
The Phytotoxin Coronatine Contributes to Pathogen Fitness and Is Required for Suppression of Salicylic Acid Accumulation in Tomato Inoculated with Pseudomonas syringae pv. tomato DC3000
Authors: Uppalapati Srinivasa Rao , Ishiga Yasuhiro , Wangdi Tamding , Kunkel Barbara N. , Anand Ajith , Mysore Kirankumar S. , Bender Carol L.
Published: July 2007

The roles of the phytotoxin coronatine (COR) and salicylic acid (SA)-mediated defenses in the interaction of Pseudomonas syringae pv. tomato DC3000 and tomato (Solanum lycopersicum) were investigated. Unlike findings reported for Arabidopsis thaliana, DC3000 mutants impaired for production of COR or one of its components, coronafacic acid (CFA) or coronamic acid (CMA), induced distinctly different disease lesion phenotypes in tomato. Tomato plants inoculated with the CFA- CMA- mutant DB29 showed elevated transcript levels of SlICS, which encodes isochorismate synthase, an enzyme involved in SA biosynthesis in S. lycopersicum. Furthermore, expression of genes encoding SA-mediated defense proteins were elevated in DB29-inoculated plants compared with plants inoculated with DC3000, suggesting that COR suppresses SlICS-mediated SA responses. Sequence analysis of SlICS revealed that it encodes a protein that is 55 and 59.6% identical to the A. thaliana ICS-encoded proteins AtICS1 and AtICS2, respectively. Tomato plants silenced for SlICS were hypersusceptible to DC3000 and accumulated lower levels of SA after infection with DC3000 compared with inoculated wild-type tomato plants. Unlike what has been shown for A. thaliana, the COR- mutant DB29 was impaired for persistence in SlICS-silenced tomato plants; thus, COR has additional roles in virulence that are SA independent and important in the latter stages of disease development. In summary, the infection assays, metabolic profiling, and gene expression results described in this study indicate that the intact COR molecule is required for both suppression of SA-mediated defense responses and full disease symptom development in tomato.
Differential Effects of Combined N Sources on Early Steps of the Nod Factor–Dependent Transduction Pathway in Lotus japonicus
Authors: Barbulova Ani , Rogato Alessandra , D'Apuzzo Enrica , Omrane Selim , Chiurazzi Maurizio
Published: July 2007

The development of nitrogen-fixing nodules in legumes is induced by perception of lipochitin-oligosaccharide signals secreted by a bacterial symbiont. Nitrogen (N) starvation is a prerequisite for the formation, development, and function of root nodules, and high levels of combined N in the form of nitrate or ammonium can completely abolish nodule formation. We distinguished between nitrate and ammonium inhibitory effects by identifying when and where these combined N sources interfere with the Nod-factor-induced pathway. Furthermore, we present a small-scale analysis of the expression profile, under different N conditions, of recently identified genes involved in the Nod-factor-induced pathway. In the presence of high levels of nitrate or ammonium, the NIN gene fails to be induced 24 h after the addition of Nod factor compared with plants grown under N-free conditions. This induction is restored in the hypernodulating nitrate-tolerant har1-3 mutant only in the presence of 10 and 20 mM KNO3. These results were confirmed in Lotus plants inoculated with Mesorhizobium loti. NIN plays a key role in the nodule organogenesis program and its downregulation may represent a crucial event in the nitrate-dependent pathway leading to the inhibition of nodule organogenesis.
Comparative Expression Profiling ofNicotiana benthamianaLeaves Systemically Infected with Three Fruit Tree Viruses
Authors: Dardick Christopher
Published: July 2007

Plant viruses cause a wide array of disease symptoms and cytopathic effects. Although some of these changes are virus specific, many appear to be common even among diverse viruses. Currently, little is known about the underlying molecular determinants. To identify gene expression changes that are concomitant with virus symptoms, we performed comparative expression profiling experiments on Nicotiana benthamiana leaves infected with one of three different fruit tree viruses that produce distinct symptoms: Plum pox potyvirus (PPV; leaf distortion and mosaic), Tomato ringspot nepovirus (ToRSV; tissue necrosis and general chlorosis), and Prunus necrotic ringspot ilarvirus (PNRSV; subtle chlorotic mottling). The numbers of statistically significant genes identified were consistent with the severity of the observed symptoms: 1,082 (ToRSV), 744 (PPV), and 89 (PNRSV). In all, 56% of the gene expression changes found in PPV-infected leaves also were altered by ToRSV, 87% of which changed in the same direction. Both PPV- and ToRSV-infected leaves showed widespread repression of genes associated with plastid functions. PPV uniquely induced the expression of large numbers of cytosolic ribosomal genes whereas ToRSV repressed the expression of plastidic ribosomal genes. How these and other observed expression changes might be associated with symptom development are discussed.
Paraferrimonas sedimenticola gen. nov., sp. nov., a marine bacterium of the family Ferrimonadaceae
Authors: Khan Shams Tabrez , Harayama Shigeaki
Published: July 2007

Three strains (Mok-106T, Mok-142 and Mok-143) were isolated from marine sediment samples collected from the coast of Okinawa Island, Japan. On the basis of 16S rRNA gene sequence comparisons, the isolates were affiliated with the family Ferrimonadaceae; Shewanella denitrificans and Ferrimonas balearica were the closest relatives, having sequence similarities of 93.7 and 93.0 %, respectively. The novel isolates shared high levels of 16S rRNA gene sequence similarity with each other (98.7–99.3 %) and the results of DNA–DNA hybridization indicated that the three strains belong to the same species. The cells were rod-shaped, motile by means of single polar flagellum and formed colonies that produced a rose-coloured pigment within 6 days incubation at 25 °C. The isolates grew in the presence of 0.5–4.0 % (w/v) NaCl and at 15–40 °C. The major fatty acids were iso-13 : 0, iso-15 : 0, 16 : 0, 18 : 1ω7c and summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH). Menaquinone-6, menaquinone-7 and ubiquinone-8 were the major quinones and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 50–51 mol%. Phylogenetic and phenotypic analyses of these isolates suggested that they belong to a novel genus and species of the family Ferrimonadaceae, for which the name Paraferrimonas sedimenticola gen. nov., sp. nov. is proposed. The type strain is Mok-106T (=NBRC 101628T=CIP 109284T).
Skermanella aerolata sp. nov., isolated from air, and emended description of the genus Skermanella
Authors: Weon Hang-Yeon , Kim Byung-Yong , Hong Seung-Beom , Joa Jae-Ho , Nam Sang-Sik , Lee Ki Hwan , Kwon Soon-Wo
Published: July 2007

A light-pink-coloured bacterium, designated strain 5416T-32T, was isolated from an air sample in Korea. Cells of the strain were strictly aerobic, Gram-negative, motile (single polar or subpolar flagellum) and rod-shaped. Optimal growth occurred at 25–30 °C and at pH 6.0–7.0. The major quinones were Q-10 and Q-8. The major fatty acids were C18 : 1
ω7c (53.8 %) and C16 : 0 (15.9 %). The G+C content of the genomic DNA was 65.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 5416T-32T was most closely related to Skermanella parooensis, with a similarity of 96.2 %, but relatively low sequence similarities (<92 %) were found with respect to other species with validly published names held in GenBank. Phenotypic and genotypic analyses indicated that strain 5416T-32T could not be assigned to any recognized species. Therefore strain 5416T-32T represents a novel species of the genus Skermanella, for which the name Skermanella aerolata sp. nov. is proposed. The type strain is 5416T-32T (=KACC 11604T=DSM 18479T).
Acetobacter senegalensis sp. nov., a thermotolerant acetic acid bacterium isolated in Senegal (sub-Saharan Africa) from mango fruit (Mangifera indica L.)
Authors: Ndoye Bassirou , Cleenwerck Ilse , Engelbeen Katrien , Dubois-Dauphin Robin , Guiro Amadou Tidiane , Van Trappen Stefanie , Willems Anne , Thonart Phillipe
Published: July 2007

A thermotolerant acetic acid bacterium, designated strain CWBI-B418T, isolated in Senegal from mango fruit (Mangifera indica), was characterized in detail by means of genotypic and phenotypic methods. The novel strain was strictly aerobic and exhibited optimal growth on YGM medium at 35 °C. Cells were Gram-negative, motile and coccoid. The strain was assigned to the genusAcetobacteron the basis of 16S rRNA gene sequence analysis. DNA–DNA hybridization experiments with its phylogenetically closest relatives showed that strain CWBI-B418Trepresented a novelAcetobactergenospecies. The DNA G+C content of strain CWBI-B418Twas 56.0 mol%. Phenotypic characteristics enabling the differentiation of strain CWBI-B418Tfrom phylogenetically relatedAcetobacterspecies were: production of 2-keto-d-gluconic acid fromd-glucose, but not 5-keto-d-gluconic acid, production of catalase but not oxidase, growth on yeast extract with 30 %d-glucose, growth with ammonium as sole nitrogen source with ethanol as carbon source, utilization of glycerol and ethanol but not maltose or methanol as carbon sources, and growth in the presence of 10 % ethanol. Based on the genotypic and phenotypic data presented, strain CWBI-B418Tclearly represents a novelAcetobacterspecies, for which the nameAcetobacter senegalensissp. nov. is proposed. The type strain is CWBI-B418T(=LMG 23690T=DSM 18889T).
Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis
Authors: Hoshino Yasutaka , Watanabe Kayo , Iida Soji , Suzuki Shin-ichi , Kudo Takuji , Kogure Takahisa , Yazawa Katsukiyo , Ishikawa Jun , Kroppenstedt Reiner M. , Mikami Yuzuru
Published: July 2007

Two bacterial strains isolated from different hospitals in Japan were subjected to a polyphasic analysis. Strains IFM 0406 and IFM 0706T, producers of novel terpenoid antibiotics, were found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with their classification in the genus Nocardia, except for the presence of MK-8(H4) as one of the predominant menaquinones in addition to the major menaquinone MK-8(H4ω-cyc). The 16S rRNA gene sequence similarity of strains IFM 0406 and IFM 0706T was 99.9 %, and the closest members of Nocardia to these strains were the type strains of Nocardia nova and Nocardia mexicana, showing similarity of 97.5 and 97.1 %, respectively. Based on their characteristic phenotypic and phylogenetic properties, a novel species of the genus Nocardia, Nocardia terpenica sp. nov. is proposed for the two strains. The type strain is IFM 0706T (=JCM 13033T=DSM 44935T=NBRC 100888T).
Solirubrobacter soli sp. nov., isolated from soil of a ginseng field
Authors: Kim Myung Kyum , Na Ju-Ryun , Lee Tae-Hoo , Im Wan-Taek , Soung Nak-Kyun , Yang Deok-Chun
Published: July 2007

A Gram-positive, non-spore-forming, rod-shaped and non-motile bacterium, strain Gsoil 355T, was isolated from soil of a ginseng field in South Korea. In phylogenetic analyses based on 16S rRNA gene sequences, strain Gsoil 355T showed the highest levels of sequence similarity with respect to Solirubrobacter pauli B33D1T (97.4 %), Conexibacter woesei DSM 14684T (94.2 %) and Patulibacter minatonensis KV-614T (91.8 %). The strain possesses menaquinone MK-7(H4) and contains C16 : 0 and C18 : 0
ω9c as the predominant fatty acids. The DNA G+C content is 71.5 mol%. On the basis of genotypic and phenotypic characteristics, strain Gsoil 355T represents a novel species of the genus Solirubrobacter, for which the name Solirubrobacter soli sp. nov. is proposed. The type strain is Gsoil 355T (=KCTC 12628T=LMG 23485T).
Curtobacterium ammoniigenes sp. nov., an ammonia-producing bacterium isolated from plants inhabiting acidic swamps in actual acid sulfate soil areas of Vietnam
Authors: Aizawa Tomoko , Ve Nguyen Bao , Kimoto Ken-ichiro , Iwabuchi Noriyuki , Sumida Hiroaki , Hasegawa Isao , Sasaki Satohiko , Tamura Tomohiko , Kudo Takuji , Suzuki Ken-ichiro , Nakajima Mutsuyasu , Sunairi Michio
Published: July 2007

The ammonia-producing bacteria B55T, CA73, SA69 and SA72 were isolated from the waterweedsLudwigia adscendens(B55T) andEleocharis dulcis(CA73, SA69 and SA72) grown in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Vietnam. The isolates were Gram-positive, irregular rod-shaped, non-spore-forming bacteria. On the basis of 16S rRNA gene sequence similarity, strain B55Twas shown to belong to the genusCurtobacteriumof the classActinobacteria. Chemotaxonomic data (MK-9 as major isoprenoid quinone,d-ornithine as cell-wall diamino acid, acetyl as the acyl type of peptidoglycan) supported the affiliation of all four strains to this genus. Although their 16S rRNA gene sequence similarity was 99 % to species with validly published names within the genus, they formed a group that was distinct in the phylogenetic tree, and DNA–DNA relatedness values to these established species were less than 10 %. The results of physiological and biochemical tests and major fatty acids (cyclohexyl-C17 : 0, anteiso-C17 : 0and cyclohexyl-C19 : 0) allowed phenotypic differentiation of these strains from the species ofCurtobacteriumwith validly published names. Therefore, strains B55T, CA73, SA69 and SA72 represent a novel species, for which the nameCurtobacterium ammoniigenessp. nov. is proposed. The type strain is B55T(=NBRC 101786T=VTCC D6-11T=JCM 14609T).
Thermoanaerobacter sulfurigignens sp. nov., an anaerobic thermophilic bacterium that reduces 1 M thiosulfate to elemental sulfur and tolerates 90 mM sulfite
Authors: Lee Yong-Jin , Dashti Mona , Prange Alexander , Rainey Fred A. , Rohde Manfred , Whitman William B. , Wiegel Juergen
Published: July 2007

Two anaerobic thermophilic bacteria, designated strains JW/SL824 and JW/SL-NZ826T, were isolated from an acidic volcanic steam outlet on White Island, New Zealand. Cells were rod-shaped, spore-forming, motile and Gram-stain negative, but contained Gram-type positive cell wall. Strain JW/SL-NZ826T utilized various carbohydrates including xylose and glucose. The fermentation end products produced from glucose in the absence of thiosulfate were lactate, ethanol, acetate, CO2 and H2. The temperature range for growth was 34–72 °C, with an optimum at 63–67 °C. The pH60 °C range for growth was 4.0–8.0, with an optimum at 5.0–6.5. The doubling time of strain JW/SL-NZ826T under optimal growth conditions was 2.4 h. The DNA G+C content was 34–35 mol% (HPLC). The two strains reduced up to 1 M thiosulfate to elemental sulfur without sulfide formation, which is a trend typically observed among species belonging to the genus Thermoanaerobacterium. Sulfur globules containing short and long sulfur chains but no S8-ring sulfur were produced inside and outside the cells. Up to 90 mM sulfite was tolerated. This tolerance is assumed to be an adaptation to the geochemistry of the environment of White Island. The 16S rRNA gene sequence analysis, however, indicated that the two strains belonged to the genus Thermoanaerobacter, with similarities in the range 95.6–92.7 %. Therefore, strains JW/SL-NZ824 and JW/SL-NZ826T represent a novel taxon, for which the name Thermoanaerobacter sulfurigignens sp. nov. is proposed, with strain JW/SL-NZ826T (=ATCC 700320T=DSM 17917T) as the type strain. Based on this and previous studies, an emended description of the genus Thermoanaerobacter is given.
Reclassification of Bacillus axarquiensis Ruiz-García et al. 2005 and Bacillus malacitensis Ruiz-García et al. 2005 as later heterotypic synonyms of Bacillus mojavensis Roberts et al. 1994
Authors: Wang Li-Ting , Lee Fwu-Ling , Tai Chun-Ju , Yokota Akira , Kuo Hsiao-Ping
Published: July 2007

The Bacillus subtilis group encompasses the taxa Bacillus subtilis subsp. subtilis, B. licheniformis, B. amyloliquefaciens, B. atrophaeus, B. mojavensis, B. vallismortis, B. subtilis subsp. spizizenii, B. sonorensis, B. velezensis, B. axarquiensis and B. malacitensis. In this study, the taxonomic relatedness between the species B. axarquiensis, B. malacitensis and B. mojavensis was investigated. Sequence analysis of the 16S rRNA gene and the gene for DNA gyrase subunit B (gyrB) confirmed the very high similarities between these three type strains and a reference strain of B. mojavensis (>99 and >97 %, respectively). DNA–DNA hybridization experiments revealed high relatedness values between the type strains of B. axarquiensis, B. malacitensis and B. mojavensis and between these strains and a reference strain of B. mojavensis (83–98 %). Based on these molecular taxonomic data and the lack of phenotypic distinctive characteristics, Bacillus axarquiensis and Bacillus malacitensis should be reclassified as later heterotypic synonyms of Bacillus mojavensis.
Nocardia coubleae sp. nov., isolated from oil-contaminated Kuwaiti soil
Authors: Rodríguez-Nava Verónica , Khan Z. U. , Pötter Gabriele , Kroppenstedt Reiner M. , Boiron Patrick , Laurent Frédéric
Published: July 2007

Two bacterial isolates from Kuwaiti soil contaminated by crude oil were analysed by using a polyphasic taxonomic approach. The isolates, designated OFN N11 and OFN N12T, were shown to have molecular, chemical and morphological properties typical of members of the genus Nocardia. Based on a multigenic approach that included 16S rRNA, hsp65 and sod gene sequencing, these novel isolates formed a monophyletic clade within the genus Nocardia. The closest species was Nocardia ignorata (with 99.4 %, 99.5 %, 98.6 % gene sequence similarity to the 16S rRNA, hsp65 and sod genes, respectively). The novel isolates could be distinguished phenotypically from the type strains of recognized species of the genus Nocardia. The novel isolates were not related to the type strain of N. ignorata in DNA–DNA hybridization experiments (26 % relatedness). On the basis of these genotypic and phenotypic data, the two isolates appear to represent a novel species, for which the name Nocardia coubleae sp. nov. is proposed. The type strain is OFN N12T (=DSM 44960T=CIP 108996T).
Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan
Authors: Asker Dalal , Beppu Teruhiko , Ueda Kenji
Published: July 2007

A yellow-pigmented, Gram-negative, motile, strictly aerobic, pleomorphic bacterium (strain TDMA-16T) was isolated from a freshwater sample collected at Misasa (Tottori, Japan). Strain TDMA-16Twas slightly tolerant to gamma-ray irradiation and produced carotenoids, including zeaxanthin, nostoxanthin and an unknown carotenoid, effectively [1.7 mg (g dry cells)−1]. The DNA G+C content of strain TDMA-16Twas 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain TDMA-16Tin a distinct lineage in the familySphingomonadaceae; sequence data showed that strain TDMA-16Twas most closely related toSphingomonas maliIFO 15500T(95.1 %),Sphingomonas aquatilisJSS7T(95.0 %),Sphingomonas pruniIFO 15498T(94.9 %),Sphingomonas melonisDSM 14444T(94.9 %) andSphingomonas asaccharolyticaIFO 15499T(94.5 %). The major fatty acids of strain TDMA-16Twere C17 : 1ω6c(34.5 %) and C18 : 1ω7c(29.3 %). The presence of Q-10 as the main ubiquinone, theSphingomonadaceae-specific sphingoglycolipid in the polar lipid profile and 2-hydroxy fatty acids, plus the absence of 3-hydroxy fatty acids, supported identification of this strain as a member of the genusSphingomonas sensu stricto. Phylogenetic distinctiveness and unique phenotypic characteristics differentiated strain TDMA-16Tfrom closely relatedSphingomonasspecies. The results of polyphasic taxonomic analyses suggest that strain TDMA-16Trepresents a novelSphingomonasspecies, for which the nameSphingomonas jaspsisp. nov. is proposed. The type strain is strain TDMA-16T(=NBRC 102120T=DSM 18422T=CCUG 53607T).
Marinobacterium litorale sp. nov. in the order Oceanospirillales
Authors: Kim Hana , Choo Yoe-Jin , Song Jaeho , Lee Jung-Sook , Lee Keun Chul , Cho Jang-Cheon
Published: July 2007

A bacterial strain named IMCC1877Twas obtained from surface seawater collected near the coast of Deokjeok island (Yellow Sea), using a standard dilution-plating method. The strain was Gram-negative, chemoheterotrophic and facultatively anaerobic, requiring NaCl, and cells were motile rods with a single polar flagellum. Colonies on marine agar were very small (average diameter 0.1 mm). Based on 16S rRNA gene sequences, the most closely related species to strain IMCC1877TwasMarinobacterium stanieri(93.7 % sequence similarity to the type strain). Phylogenetic analyses based on 16S rRNA gene sequences showed that this marine isolate belonged to the orderOceanospirillalesand formed an independent phyletic line within the clade forming the genusMarinobacterium. The DNA G+C content of the strain was 60.7 mol% and the predominant constituents of the cellular fatty acids were C18 : 1ω7c(36.6 %), C16 : 1ω7cand/or iso-C15 : 02-OH (26.7 %) and C16 : 0(24.3 %). Based on the taxonomic data, only a distant relationship could be established between strain IMCC1877Tand otherMarinobacteriumspecies; the strain therefore represents a novel species of the genusMarinobacterium, for which the nameMarinobacterium litoralesp. nov. is proposed. The type strain is IMCC1877T(=KCTC 12756T=LMG 23872T).
Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine
Authors: Carlsohn Marc René , Groth Ingrid , Tan Geok Yuan Annie , Schütze Barbara , Saluz Hans-Peter , Munder Thomas , Yang Jun , Wink Joachim , Goodfellow Michael
Published: July 2007

Three actinomycetes isolated from the surfaces of rocks in a medieval slate mine were examined in a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics of the isolates were typical of strains of the genusAmycolatopsis. The isolates had identical 16S rRNA gene sequences and formed a distinct phyletic line towards the periphery of theAmycolatopsis mediterraneiclade, being most closely related toAmycolatopsis rifamycinica. The organisms shared a wide range of genotypic and phenotypic markers that distinguished them from their closest phylogenetic neighbours. On the basis of these results, a novel species,Amycolatopsis saalfeldensissp. nov., is proposed. The type strain is HKI 0457T(=DSM 44993T=NRRL B-24474T).
Streptomyces emeiensis sp. nov., a novel streptomycete from soil in China
Authors: Sun Wei , Huang Ying , Zhang Yue-Qin , Liu Zhi-Heng
Published: July 2007

An actinomycete, strain 4776T, was isolated from soil collected from Emei Mountain in Sichuan Province, China. The taxonomic status of this strain was established using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of streptomycetes. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence indicated that the novel isolate belongs to the genus Streptomyces and consistently falls into a clade together with Streptomyces prasinopilosus DSM 40098T, Streptomyces prasinus JCM 4603T, Streptomyces bambergiensis DSM 40590T, Streptomyces hirsutus DSM 40095T and Streptomyces cyanoalbus DSM 40198T. However, DNA–DNA relatedness and phenotypic data distinguished strain 4776T from these phylogenetically related type strains. It is therefore concluded that strain 4776T (=CGMCC 4.3504T=DSM 41884T) represents a novel species of the genus Streptomyces, for which the name Streptomyces emeienseis sp. nov. is proposed.
Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil
Authors: Weon Hang-Yeon , Song Myung-Hee , Son Jung-A , Kim Byung-Yong , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: July 2007

Two bacterial strains, R2A1-13T and R2A45-3T, were isolated from greenhouse soils in Korea. The cells of both strains were Gram-negative, aerobic and rod-shaped. 16S rRNA gene sequence analysis placed the isolates in the genus Flavobacterium within the family Flavobacteriaceae. Strain R2A1-13T was found to be related to Flavobacterium columnare IAM 14301T, Flavobacterium saliperosum CGMCC1.3801T and Flavobacterium croceum EMB47T, with sequence similarities of 96.8, 95.0 and 94.6 %, respectively. Strain R2A45-3T was found to be related to F. croceum EMB47T and Flavobacterium aquatile ATCC 11947T, with sequence similarities of 94.7 and 94.6 %, respectively. Both strains contained iso-C15 : 0 and iso-C16 : 0 as the main fatty acids and contained a menaquinone with six isoprene units (MK-6) as the major isoprenoid quinone. The G+C contents of the DNA from strains R2A1-13T and R2A45-3T were 34 and 38 mol%, respectively. A polyphasic taxonomic study revealed that these strains belong to two novel species within the genus Flavobacterium, for which the names Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov. are proposed. The type strains of F. terrae sp. nov. and F. cucumis sp. nov. are R2A1-13T (=KACC 11731T=DSM 18829T) and R2A45-3T (=KACC 11732T=DSM 18830T), respectively.
Piscibacillus salipiscarius gen. nov., sp. nov., a moderately halophilic bacterium from fermented fish (pla-ra) in Thailand
Authors: Tanasupawat Somboon , Namwong Sirilak , Kudo Takuji , Itoh Takashi
Published: July 2007

A Gram-positive, spore-forming and moderately halophilic bacterium was isolated from fermented fish (pla-ra) in Thailand. Cells of the isolate, RBU1-1T, were strictly aerobic, motile rods and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Menaquinone with seven isoprene units (MK-7) was the predominant quinone. This isolate grew at 15–48 °C, pH 5–9 and in 2–30 % NaCl (optimally 10–20 %). The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Polar lipid analysis revealed the presence of phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 36.7 mol%. 16S rRNA gene sequence analysis revealed that strain RBU1-1T was a member of the family Bacillaceae, and belonged to a cluster with Filobacillus and Tenuibacillus; strain RBU1-1T showed 16S rRNA gene sequence similarities of 96.0–96.9 % to members of these two genera. Strain RBU1-1T could also be differentiated from members of the genera Filobacillus and Tenuibacillus based on certain phenotypic characteristics such as cell-wall composition, mode of flagellation and growth pH range. Therefore, strain RBU1-1T is considered to represent a novel species in a new genus in the family Bacillaceae, for which the name Piscibacillus salipiscarius gen. nov., sp. nov. is proposed. The type strain of Piscibacillus salipiscarius is RBU1-1T (=JCM 13188T=PCU 270T=TISTR 1571T).
Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales
Authors: Lee Kiyoung , Choo Yoe-Jin , Giovannoni Stephen J. , Cho Jang-Cheon
Published: July 2007

A Gram-negative, chemoheterotrophic, strictly aerobic, alkaliphilic, rod-shaped marine bacterium, designated HTCC2654T, was isolated from the western Sargasso Sea by using a dilution-to-extinction culturing method. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HTCC2654T belonged to the Roseobacter clade of the order Rhodobacterales. The 16S rRNA gene sequence similarity of the strain with respect to other members of the Roseobacter clade ranged from 90.4 to 95.1 %. In the phylogenetic analyses, the strain formed an independent phyletic line and could not be assigned to any other known genera of the Rhodobacterales. The DNA G+C content of strain HTCC2654T was 61.7 mol% by HPLC and 64.1 mol% from genome sequences. The predominant constituents of the cellular fatty acids were C16 : 0 2-OH (27.3 %), 11-methyl C18 : 1
ω7c (19.6 %) and C18 : 1
ω7c (17.3 %), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine, which served to differentiate the strain from other members of the Roseobacter clade. On the basis of the taxonomic data obtained in this study, strain HTCC2654T represents a novel genus and species, for which the name Maritimibacter alkaliphilus gen. nov., sp. nov. is proposed. The type strain is HTCC2654T (=KCCM 42376T=NBRC 102057T).
Description of Azospira restricta sp. nov., a nitrogen-fixing bacterium isolated from groundwater
Authors: Bae Hee-Sung , Rash Brian A. , Rainey Fred A. , Nobre M. Fernanda , Tiago Igor , da Costa Milton S. , Moe William M.
Published: July 2007

A novel, Gram-negative bacterial strain, SUA2T, isolated from groundwater, was characterized using a polyphasic approach. Cells are Gram-negative, non-spore-forming, straight to curved rods with a single polar flagellum. Strain SUA2T is oxidase- and catalase-positive and is able to fix nitrogen. Poly-β-hydroxybutyrate storage granules are produced. Dominant fatty acids when grown in R2A and VM ethanol media for 72 h at 37 °C are C16 : 0, C16 : 1
ω7c, C17 : 0 cyclo, C10 : 0 3-OH, C18 : 1
ω7c, C12 : 0 and C15 : 0. DNA G+C content is 67.9 mol%. Phenotypic and phylogenetic data indicate that strain SUA2T is related to, but clearly differentiated from Azospira oryzae. Strain SUA2T is thus proposed as a novel species of the genus Azospira with the name Azospira restricta sp. nov. The description of the genus Azospira is emended to include the characteristics of this novel species. The type strain of Azospira restricta is SUA2T (=NRRL B-41660T=DSM 18626T=LMG 23819T).
Salirhabdus euzebyi gen. nov., sp. nov., a Gram-positive, halotolerant bacterium isolated from a sea salt evaporation pond
Authors: Albuquerque Luciana , Tiago Igor , Rainey Fred A. , Taborda Marco , Nobre M. Fernanda , Veríssimo António , da Costa Milton S.
Published: July 2007

A low-G+C, Gram-positive bacterium, designated CVS-14T, was recovered from a sea salt evaporation pond on the island of Sal in the Cape Verde Archipelago. This organism was catalase- and oxidase-positive. Cells were motile, spore-forming aerobic rods, with an optimum growth temperature of about 35–40 °C and optimum pH between 7.0 and 8.5. Optimal growth occurred in media containing 4–6 % (w/v) NaCl, although the organism was able to grow in medium without added NaCl and in medium containing 16 % NaCl. The cell-wall peptidoglycan was of A1γ type and the major respiratory quinone was menaquinone 7 (MK-7). Major fatty acids were iso-15 : 0, anteiso-15 : 0, iso-17 : 0 and anteiso-17 : 0. The DNA G+C content was 37.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain CVS-14T formed a distinct new branch within the radiation of the moderately halophilic bacilli group, forming a separate lineage from species of the genera Salinibacillus, Paucisalibacillus, Oceanobacillus, Lentibacillus and Virgibacillus. Strain CVS-14T showed 16S rRNA gene pairwise similarity values of ~95 % with species of the genus Salinibacillus. On the basis of morphological, physiological, chemotaxonomic and phylogenetic characteristics, strain CVS-14T is considered to represent a novel species in a new genus, for which the name Salirhabdus euzebyi gen. nov., sp. nov. is proposed. The type strain is CVS-14T (=LMG 22839T=CIP 108577T).
Rubritalea squalenifaciens sp. nov., a squalene-producing marine bacterium belonging to subdivision 1 of the phylum ‘Verrucomicrobia’
Authors: Kasai Hiroaki , Katsuta Atsuko , Sekiguchi Hiroshi , Matsuda Satoru , Adachi Kyoko , Shindo Kazutoshi , Yoon Jaewoo , Yokota Akira , Shizuri Yoshikazu
Published: July 2007

A taxonomic study was carried out to clarify the status of a Gram-negative, heterotrophic mesophile that was isolated from the marine sponge Halichondria okadai. The strain, designated HOact23T, was a non-motile, rod-shaped (0.44–0.53×0.65–0.79 μm) bacterium. The strain produced squalene and a red–pink carotenoid pigment. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. The G+C content of the genomic DNA was 52.4 mol%. The major fatty acids were iso-C14 : 0 (43.1 %), iso-C16 : 0 (20.6 %) and anteiso-C15 : 0 (18.1 %), and the major isoprenoid quinone was MK-9 (90.8 %). Based on 16S rRNA gene sequence data, the strain formed a distinct group within subdivision 1 in the phylum ‘Verrucomicrobia’. It showed a range of phenotypic properties that distinguished it from its closest relative, Rubritalea marina Pol012T (94.3 % 16S rRNA gene sequence similarity). On the basis of polyphasic taxonomic evidence, it was concluded that strain HOact23T should be classified within a novel species in the genus Rubritalea. The name proposed for the taxon is Rubritalea squalenifaciens sp. nov., with the type strain HOact23T (=MBIC08254T=DSM 18772T).
Thiohalomonas denitrificans gen. nov., sp. nov. and Thiohalomonas nitratireducens sp. nov., novel obligately chemolithoautotrophic, moderately halophilic, thiodenitrifying Gammaproteobacteria from hypersaline habitats
Authors: Sorokin Dimitry Yu. , Tourova Tatjana P. , Braker Gesche , Muyzer Gerard
Published: July 2007

A novel group of moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing Gammaproteobacteria was found in sediments of various inland hypersaline lakes and a solar saltern. These bacteria were enriched and isolated with thiosulfate as electron donor and nitrate as electron acceptor at 2 M NaCl. Ten isolates (HLD strains) were long non-motile rods. They grew anaerobically as complete denitrifiers, and aerobically under micro-oxic conditions. Sulfate was the final product of thiosulfate and sulfide oxidation, and nitrite and N2O were intermediates of nitrate reduction to N2. The HLD strains grew optimally at pH 7.3–7.8, and at NaCl concentrations of 1.5–2.0 M. On the basis of phenotypic and genetic analysis, the moderately halophilic, thiodenitrifying isolates are proposed to be assigned to a new genus and species, Thiohalomonas denitrificans gen. nov., sp. nov. The type strain is HLD 2T (=DSM 15841T=UNIQEM U222T ). A single strain, HRhD 3spT, with vibrio-shaped cells, was obtained from a co-culture capable of complete denitrification of nitrate in the presence of either thiocyanate or thiosulfate as electron donor. It grew anaerobically with thiosulfate, reducing nitrate to nitrite, or under micro-oxic conditions at 1.0–2.5 M NaCl with an optimum at 1.0 M. Strain HRhD 3spT was genetically related to the HLD strains at the level of a separate species and is described as Thiohalomonas nitratireducens sp. nov. The type strain is HRhD 3spT (=DSM 16925T=UNIQEM U248T).
Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster
Authors: Zhan Ming , Yamaza Haruyoshi , Sun Yu , Sinclair Jason , Li Huai , Zou Sige
Published: July 2007

Temporal and tissue-specific alterations in gene expression have profound effects on aging of multicellular organisms. However, much remains unknown about the patterns of molecular changes in different tissues and how different tissues interact with each other during aging. Previous genomic studies on invertebrate aging mostly utilized the whole body or body parts and limited age-points, and failed to address tissue-specific aging. Here we measured genome-wide expression profiles of aging in Drosophila melanogaster for seven tissues representing nervous, muscular, digestive, renal, reproductive, and storage systems at six adult ages. In each tissue, we identified hundreds of age-related genes exhibiting significant changes of transcript levels with age. The age-related genes showed clear tissue-specific patterns: <10% of them in each tissue were in common with any other tissue; <20% of the biological processes enriched with the age-related genes were in common between any two tissues. A significant portion of the age-related genes were those involved in physiological functions regulated by the corresponding tissue. Nevertheless, we identified some overlaps of the age-related functional groups among tissues, suggesting certain common molecular mechanisms that regulate aging in different tissues. This study is one of the first that defined global, temporal, and spatial changes associated with aging from multiple tissues at multiple ages, showing that different tissues age in different patterns in an organism. The spatial and temporal transcriptome data presented in this study provide a basis and a valuable resource for further genetic and genomic investigation of tissue-specific regulation of aging.
Calling cards for DNA-binding proteins
Authors: Wang Haoyi , Johnston Mark , Mitra Robi David
Published: July 2007

Identifying genomic targets of transcription factors is fundamental for understanding transcriptional regulatory networks. Current technology enables identification of all targets of a single transcription factor, but there is no realistic way to achieve the converse: identification of all proteins that bind to a promoter of interest. We have developed a method that promises to fill this void. It employs the yeast retrotransposon Ty5, whose integrase interacts with the Sir4 protein. A DNA-binding protein fused to Sir4 directs insertion of Ty5 into the genome near where it binds; the Ty5 becomes a “calling card” the DNA-binding protein leaves behind in the genome. We constructed customized calling cards for seven transcription factors of yeast by including in each Ty5 a unique DNA sequence that serves as a “molecular bar code.” Ty5 transposition was induced in a population of yeast cells, each expressing a different transcription factor–Sir4 fusion and its matched, bar-coded Ty5, and the calling cards deposited into selected regions of the genome were identified, revealing the transcription factors that visited that region of the genome. In each region we analyzed, we found calling cards for only the proteins known to bind there: In the GAL1–10 promoter we found only calling cards for Gal4; in the HIS4 promoter we found only Gcn4 calling cards; in the PHO5 promoter we found only Pho4 and Pho2 calling cards. We discuss how Ty5 calling cards might be implemented for mapping all targets of all transcription factors in a single experiment.
Memory trace stabilization leads to large-scale changes in the retrieval network: A functional MRI study on associative memory
Authors: Takashima Atsuko , Nieuwenhuis Ingrid L.C. , Rijpkema Mark , Petersson Karl Magnus , Jensen Ole , Fernández Guillén
Published: July 2007

Spaced learning with time to consolidate leads to more stabile memory traces. However, little is known about the neural correlates of trace stabilization, especially in humans. The present fMRI study contrasted retrieval activity of two well-learned sets of face-location associations, one learned in a massed style and tested on the day of learning (i.e., labile condition) and another learned in a spaced scheme over the course of one week (i.e., stabilized condition). Both sets of associations were retrieved equally well, but the retrieval of stabilized association was faster and accompanied by large-scale changes in the network supporting retrieval. Cued recall of stabilized as compared with labile associations was accompanied by increased activity in the precuneus, the ventromedial prefrontal cortex, the bilateral temporal pole, and left temporo–parietal junction. Conversely, memory representational areas such as the fusiform gyrus for faces and the posterior parietal cortex for locations did not change their activity with stabilization. The changes in activation in the precuneus, which also showed increased connectivity with the fusiform area, are likely to be related to the spatial nature of our task. The activation increase in the ventromedial prefrontal cortex, on the other hand, might reflect a general function in stabilized memory retrieval. This area might succeed the hippocampus in linking distributed neocortical representations.