bluuebunny/crossref_metadata_2025 huggingface dataset:
Pseudoclavibacter caeni sp. nov., isolated from sludge of a sewage disposal plant
Authors: Srinivasan Sathiyaraj , Kim Hyun Sook , Kim Myung Kyum , Lee Myungjin
Published: May 2011

A Gram-positive, strictly aerobic, rod-shaped, non-motile bacterial strain, designated MJ28T, was isolated from a sludge sample from the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ28T. Strain MJ28T showed highest 16S rRNA gene sequence similarity to Pseudoclavibacter soli KP02T (95.2 %). Levels of 16S rRNA gene sequence similarity to the type strains of other Pseudoclavibacter species were less than 94.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ28T belonged to the clade formed by members of the genus Pseudoclavibacter in the family Microbacteriaceae. The G+C content of the genomic DNA of strain MJ28T was 65.8 mol%. The chemotaxonomic characteristics of strain MJ28T showed features typical of the genus Pseudoclavibacter, with MK-9 as the predominant respiratory quinone, 2,4-diaminobutryic acid as the diamino acid in the peptidoglycan, and anteiso-C17 : 0 (44.6 %), anteiso-C15 : 0 (35.7 %) and C16 : 0 (9.5 %) as the major fatty acids. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ28T is considered to represent a novel species of the genus Pseudoclavibacter, for which the name Pseudoclavibacter caeni sp. nov. is proposed. The type strain is MJ28T ( = KCTC 19773T = JCM 16921T).
Myroides

phaeus sp. nov., isolated from human saliva, and emended descriptions of the genus

Myroides

and the species

Myroides profundi

Zhang et al. 2009 and

Myroides marinus

Cho et al. 2011
Authors: Yan Shulin , Zhao Naixin , Zhang Xiao-Hua
Published: May 2011

A novel bacterial strain, designated MY15T, was isolated from a saliva sample taken from a student during a teaching experiment in China. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was most closely related to

Myroides marinus

JS-08T,

Myroides odoratimimus

LMG 4029T and

Myroides profundi

D25T with 96.5 %, 96.3 % and 96.1 % gene sequence similarities, respectively, demonstrating that the novel strain belonged to the genus

Myroides

. Strain MY15T formed pale yellow colonies that turned to brown on Luria–Bertani (LB) agar and that gave off a characteristic fruity odour. Cells were Gram-staining-negative, rod-shaped and non-motile. The new isolate contained menaquinone 6 (MK-6) as the major respiratory quinone and C15 : 0 iso (51.2 %), C17 : 0 iso 3-OH (12.9 %) and C13 : 0 iso (10.5 %) as the dominant fatty acids. The G+C content of the DNA was 34.3 mol%. On the basis of this study, based on a polyphasic taxonomic approach, strain MY15T ( = DSM 23313T = LMG 25566T) represents a novel species of the genus

Myroides

, for which the name
Myroides

phaeus sp. nov. is proposed. Emended descriptions of the genus

Myroides

and of the species

M. profundi

and

M. marinus

are also given.
Sphingobium jiangsuense sp. nov., a 3-phenoxybenzoic acid-degrading bacterium isolated from a wastewater treatment system
Authors: Zhang Jun , Lang Zhi-Fei , Zheng Jin-Wei , Hang Bao-Jian , Duan Xiao-Qin , He Jian , Li Shun-Peng
Published: May 2011

A non-sporulating, non-motile, catalase- and oxidase-positive, Gram-negative, rod-shaped bacterial strain, designated BA-3T, was isolated from activated sludge of a wastewater treatment facility. The strain was able to degrade about 95 % of 100 mg 3-phenoxybenzoic acid l−1within 2 days of incubation. Growth occurred in the presence of 0–2 % (w/v) NaCl [optimum, 0.5 % (w/v) NaCl], at pH 5.5–9.0 (optimum, pH 7.0) and at 10–37 °C (optimum, 28 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BA-3Twas a member of the genusSphingobium; it showed highest gene sequence similarity toSphingobium qiguoniiX23T(98.2 %), and similarities of <97.0 % with strains of otherSphingobiumspecies. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of summed feature 8 (C18 : 1ω6cand/or C18 : 1ω7c) in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genusSphingobium. Strain BA-3Tshowed low DNA–DNA relatedness values (21.3±0.8 %) withSphingobium qiguoniiX23T. Based on phenotypic, genotypic and phylogenetic data, strain BA-3Trepresents a novel species of the genusSphingobium, for which the nameSphingobium jiangsuensesp. nov. is proposed; the type strain is BA-3T( = CCTCC AB 2010217T = KCTC 23196T = KACC 16433T).
Streptomyces panacagri sp. nov., isolated from soil of a ginseng field
Authors: Cui Yingshun , Baek Sang-Hoon , Wang Liang , Lee Hyung-Gwan , Cui Changhao , Lee Sung-Taik , Im Wan-Taek
Published: May 2011

A Gram-positive, spore-forming, aerobic actinomycete, strain Gsoil 519T, was isolated from soil of a ginseng field of Pocheon province in South Korea. The closest phylogenetic relatives were
Streptomyces marinus
Sp080513GE-26T (97.94 % 16S rRNA gene sequence similarity),
Streptomyces albiaxialis
NRRL B-24327T (97.84 %), Streptomyces albus subsp. albus DSM 40313T (97.84 %),
Streptomyces almquistii
NBRC 13015T (97.81 %),
Streptomyces gibsonii
NBRC 15415T (97.81 %),
Streptomyces rangoonensis
NBRC 13078T (97.81 %),
Streptomyces sodiiphilus
YIM 80305T (97.77 %) and
Streptomyces flocculus
NBRC 13041T (97.67 %). The G+C content of the genomic DNA was 71.8 mol%. The chemotaxonomic data [MK-9(H6) and MK-9(H8) as the major menaquinones; ll-diaminopimelic acid as a component of the cell-wall peptidoglycan; ribose, xylose, mannose and glucose as the major cell-wall sugars; and anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and C16 : 0 as the major fatty acids] supported the affiliation of strain Gsoil 519T to the genus
Streptomyces
. The physiological and biochemical characteristics and the low level of DNA–DNA relatedness differentiated the isolate genotypically and phenotypically from recognized members of the genus
Streptomyces
. The isolate, therefore, represents a novel species, for which the name Streptomyces panacagri sp. nov. is proposed, with Gsoil 519T ( = KCTC 19139T = DSM 41871T) as the type strain.
Cohnella arctica sp. nov., isolated from Arctic tundra soil
Authors: Jiang Fan , Dai Jun , Wang Yang , Xue Xiuqing , Xu Mengbo , Li Wenxin , Fang Chengxiang , Peng Fang
Published: May 2011

A psychrotolerant Gram-reaction-negative, rod-shaped and orange-pigmented bacterium, designated strain M9-62T, which was motile by means of peritrichous flagella, was isolated from tundra soil sampled near Ny-Ålesund, Svalbard Islands, Norway (78° N). Growth occurred at 4–30 °C (optimum, 25 °C) and pH 5.0–8.0 (optimum, pH 6.0–7.0). Analysis of the 16S rRNA gene sequence of strain M9-62T placed it in the genus

Cohnella

; sequence similarities of the isolate with type strains of members of related genera ranged from 92.0 to 96.3 %. Strain M9-62T contained anteiso-C15 : 0 (51.1 %), iso-C16 : 0 (7.5 %) and C16 : 0 (6.1 %) as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol as the main polar lipids. The major respiratory quinone was MK-7 and the DNA G+C content was 50.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain M9-62T is considered to represent a novel species of the genus

Cohnella

, for which the name Cohnella arctica sp. nov. is proposed; the type strain is M9-62T ( = CCTCC AB 2010228T = NRRL B-59459T).
Description of Sinomonas soli sp. nov., reclassification of Arthrobacter echigonensis and Arthrobacter albidus (Ding et al. 2009) as Sinomonas echigonensis comb. nov. and Sinomonas albida comb. nov., respectively, and emended description of the genus Sinomonas
Authors: Zhou Yu , Chen Xiaoyun , Zhang Yu , Wang Wei , Xu Junfeng
Published: May 2011

A novel actinomycete strain, designated CW 59T, was isolated from a polluted forest soil sample in Anhui Province, China. Cells were strictly aerobic, non-motile, bent rods. The strain grew optimally at 30–37 °C and pH 6.0–8.0. The major fatty acids were ai-C15 : 0 (34.7 %), i-C15 : 0 (11.6 %) and ai-C17 : 0 (14.9 %); the predominant respiratory quinone was MK-9(H2), with MK-8(H2) present as a minor component. The polar lipid composition of strain CW 59T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and phosphatidylmonomethylethanolamine (minor component). The whole-cell sugars contained galactose, mannose, ribose and glucose; the major amino acids of the cell-wall were lysine, alanine and glutamic acid. The genomic DNA G+C content was 66.9 mol%. Phylogenetic analysis showed that CW 59T belonged to the genus Sinomonas and grouped with members of the species Sinomonas atrocyanea, Sinomonas flava, Arthrobacter echigonensis and Arthrobacter albidus. 16S rRNA gene sequence similarities of CW 59T to S. atrocyanea DSM 20127T, S. flava CW 108T, A. echigonensis LC10T and A. albidus LC13T were 99.5, 99.3, 98.2 and 98.0 %, respectively. DNA–DNA hybridization of the isolate showed relatedness values of 58.3 % (DSM 20127T), 41.8 % (CW 108T), 21.6 % (LC10T) and 25.5 % (LC13T) with its four closest neighbours. The taxonomic relationships of strains LC10T and LC13T with the genus Sinomonas were further clarified by means of a direct experimental comparison; results showed that strains LC10T and LC13T showed the same major fatty acid, polar lipid, cell-wall amino acid, whole-cell sugar and respiratory quinone compositions as members of the genus Sinomonas. Based on phenotypic, chemotaxonomic and phylogenetic analysis, it is proposed that: strain CW 59T represents a novel species of the genus Sinomonas, Sinomonas soli sp. nov., with CW 59T ( = CCTCC AB 207193T = KCTC 19389T) as the type strain; and the type strains of A. echigonensis and A. albidus should be reclassified as Sinomonas echigonensis comb. nov. and Sinomonas albida comb. nov., respectively. An emended description of the genus Sinomonas is given.
Corynebacterium deserti sp. nov., isolated from desert sand
Authors: Zhou Zhengfu , Yuan Menglong , Tang Ran , Chen Ming , Lin Min , Zhang Wei
Published: May 2011

A novel coryneform bacterium, designated strain GIMN1.010T, was isolated from a sand sample collected in the desert in the west of China. Cells were Gram-stain-positive, non-spore-forming, catalase-positive, irregular rods. Comparative 16S rRNA gene sequence analysis demonstrated that strain GIMN1.010T belonged to the genus Corynebacterium and was related closely to Corynebacterium
glutamicum ATCC 13032T (98.4 % similarity). However, the level of DNA–DNA relatedness between strain GIMN1.010T and C. glutamicum ATCC 13032T was only 22.4±1.72 %, showing that strain GIMN1.010T represented a genomic species distinct from C. glutamicum. On the basis of phenotypic and phylogenetic data, strain GIMN1.010T is considered to represent a novel species of the genus Corynebacterium, for which the name Corynebacterium deserti sp. nov. is proposed. The type strain is GIMN1.010T ( = CCTCC AB 2010341T  = NRRL B-59552).
Bacillus

iranensis sp. nov., a moderate halophile from a hypersaline lake
Authors: Bagheri M. , Didari M. , Amoozegar M. A. , Schumann P. , Sánchez-Porro C. , Mehrshad M. , Ventosa A.
Published: May 2011

A Gram-positive, moderately halophilic rod, designated X5BT, was isolated from saline mud of the hypersaline lake Aran-Bidgol in Iran. Strain X5BT was a strictly aerobic, motile bacterium that produced ellipsoidal endospores at a central-subterminal position in non-swollen sporangia. The isolate grew at pH 7.0–10.0 (optimum pH 7.5), at 25–45 °C (optimum 35 °C) and with 2.5–15 % (w/v) NaCl (optimum 5–7.5 %). On the basis of 16S rRNA gene sequences, strain X5BT belonged to the genus

Bacillus

and showed highest similarity with

Bacillus persepolensis

HS136T (95.6 % 16S rRNA gene sequence similarity) and

Bacillus salarius

BH169T (95.5 %). The DNA G+C content was 42.4 mol%. The major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and two glycolipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the isoprenoid quinones were MK-7 (92 %), MK-6 (6 %) and MK-5 (2 %). On the basis of phylogenetic, chemotaxonomic and phenotypic data, a novel species of the genus

Bacillus

is proposed, with the name

Bacillus

iranensis sp. nov. The type strain is X5BT ( = IBRC 10446T  = DSM 23995T).
Description of Herbiconiux flava sp. nov. and emended description of the genus Herbiconiux
Authors: Hamada Moriyuki , Komukai Chiaki , Tamura Tomohiko , Evtushenko Lyudmila I. , Vinokurova Natalia G. , Suzuki Ken-ichiro
Published: May 2011

A non-motile and non-endospore-forming rod, strain NBRC 16403T, was isolated from the phyllosphere of a sedge (Carex sp.). 16S rRNA gene sequence analysis indicated that strain NBRC 16403T was closely related to Herbiconiux solani DSM 19813T (98.6 % 16S rRNA gene sequence similarity), Herbiconiux ginsengi wged11T (97.8 %) and Herbiconiux moechotypicola RB-62T (97.8 %). The peptidoglycan (B2γ type) contained d- and l-2,4-diaminobutyric acids, d-alanine, glycine and threo-3-hydroxyglutamic acid, which replaced glutamic acid almost completely. The predominant menaquinones were MK-10 and MK-11. The polar lipid pattern comprised diphosphatidylglycerol, phosphatidylglycerol, three glycolipids and minor amounts of other polar lipids. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0; no cyclohexyl-C17 : 0 was detected. The DNA G+C content was 71.0 mol%. The results of phylogenetic and DNA–DNA relatedness studies, along with phenotypic differences between strain NBRC 16403T and recognized members of the genus Herbiconiux, indicated that the isolate should be assigned to a novel species of the genus Herbiconiux, for which the name Herbiconiux flava sp. nov. is proposed. The type strain is NBRC 16403T ( = VKM Ac-2058T).
Blautia stercoris sp. nov., isolated from human faeces
Authors: Park Seong-Kyu , Kim Min-Soo , Roh Seong Woon , Bae Jin-Woo
Published: May 2011

Strain GAM6-1T is a novel, strictly anaerobic, non-spore-forming, Gram-stain-positive bacterium that was isolated from the faeces of a healthy individual. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GAM6-1T was most closely related to Blautia producta ATCC 27340T (95.7 % sequence similarity), in the family Lachnospiraceae. Strain GAM6-1T did not exhibit catalase or oxidase activity. The strain’s cellular fatty acids were of the straight-chain saturated and mono-unsaturated types, with C14 : 0 (24.10 %), C16 : 0 (19.09 %) and C16 : 0 dimethylacetal (14.35 %) predominant. Strain GAM6-1T was able to produce acid from various carbohydrates. Glucose fermentation produced acetic acid as the major short-chain fatty acid. The genomic DNA G+C content of strain GAM6-1T was 35.6 mol%. Based on phenotypic, genotypic and phylogenetic evidence, strain GAM6-1T ( = KCTC 5981T  = JCM 17204T) is considered to represent a novel species, for which the name Blautia stercoris sp. nov. is proposed.
Derxomyces amylogenes sp. nov., Derxomyces bambusicola sp. nov. and Derxomyces corylopsis sp. nov., three ballistoconidium-forming yeast species isolated from subtropical plant leaves
Authors: Liu Xin-Zhan , Wang Qi-Ming , Boekhout Teun , Bai Feng-Yan
Published: May 2011

Among ballistoconidium-forming yeast strains isolated from various plant leaves collected from subtropical forests in eastern and central China, four strains forming cream to yellowish coloured colonies were revealed to represent three novel Derxomyces species by conventional and molecular characterization. Phylogenetic analysis based on combined sequences of the internal transcribed spacer (ITS) and 26S rRNA gene D1/D2 domain showed that strains GT-753 and ZJJ-890T were conspecific and closely related to Derxomyces boninensis, Derxomyces mrakii and Derxomyces qinlingensis. Strain ZJJ-394T was basal to the branch formed by Derxomyces komagatae, Derxomyces
pseudoschimicola and Derxomyces schimicola with strong bootstrap support. Strain GT-475T was closely related to Derxomyces linzhiensis. The strains differed significantly from their close relatives in D1/D2 and ITS sequences and in physiological criteria. Three novel species are proposed: Derxomyces amylogenes sp. nov. (type strain ZJJ-890T = CGMCC 2.4407T = CBS 12233T), Derxomyces bambusicola sp. nov. (type strain GT-475T = CGMCC 2.4411T = CBS 12234T) and Derxomyces corylopsis sp. nov. (type strain ZJJ-394T = CGMCC 2.4409T = CBS 12259T).
Thermosyntropha tengcongensis sp. nov., a thermophilic bacterium that degrades long-chain fatty acids syntrophically
Authors: Zhang Fan , Liu Xiaoli , Dong Xiuzhu
Published: May 2011

A novel anaerobic, thermophilic, syntrophic, fatty-acid-oxidizing bacterium, strain L-60T, was isolated from a Chinese hot spring. Cells of the strain were non-motile, non-spore-forming, slightly curved rods. Growth occurred between 55 and 70 °C (optimum about 60 °C) and at pH 7.0–9.3 (optimum about pH 8.2). Crotonate was the only tested carbon source that supported the growth of the strain in pure culture. In co-culture with the thermophilic, hydrogenotrophic Methanothermobacter thermautotrophicus DSM 1053T, the isolate could oxidize saturated straight-chain fatty acids with 4–18 carbon atoms, and also unsaturated fatty acids such as oleate, syntrophically. The strain was unable to utilize sulfate, sulfite, thiosulfate, nitrate, fumarate or Fe(III) as electron acceptors. The major cellular fatty acids were C14 : 0 (35.0 %), C16 : 0 (20.3 %) and iso-C17 : 1 I/anteiso-C17 : 1 B (30.9 %). The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was affiliated to the family Syntrophomonadaceae and was most closely related to Thermosyntropha lipolytica DSM 11003T (96.7 % similarity). On the basis of phylogenetic and phenotypic evidence, it is proposed that strain L-60T represents a novel species, for which the name Thermosyntropha tengcongensis sp. nov. is proposed. The type strain is L-60T ( = CGMCC 1.5161T  = JCM 17260T).
Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex
Authors: Alexandrov Andrei , Colognori David , Steitz Joan A.
Published: May 2011

Despite the lack of an exon junction complex (EJC), Saccharomyces cerevisiae contains Fal1p, a DEAD-box helicase highly homologous to eIF4AIII. We show that yeast Fal1p is functionally orthologous to human eIF4AIII, since expression of human eIF4AIII complements both the lethal phenotype and the 18S rRNA biogenesis defect of fal1Δ(null) yeast. We further show that yeast Fal1p interacts genetically with an eIF4G-like protein, Sgd1p: One allele of sgd1 acts as a dominant extragenic suppressor of a mutation in a predicted RNA-binding residue of Fal1p, whereas another synthetically exacerbates the growth defect of this fal1 mutation. Both sgd1 mutations map to a single, short, evolutionarily conserved patch that matches key eIF4A-interacting residues of eIF4G when superimposed on the X-ray structure of the eIF4A/eIF4G complex. We demonstrate direct physical interactions between yeast Sgd1p and Fal1p, and between their human orthologs (NOM1 and eIF4AIII) in vitro and in vivo, identifying human NOM1 as a missing eIF4G-like interacting partner of eIF4AIII. Knockdown of eIF4AIII and NOM1 in human cells demonstrates that this novel conserved eIF4A/eIF4G-like complex acts in pre-rRNA processing, adding to the established functions of eIF4A/eIF4G in translation initiation and of eIF4AIII as the core component of the EJC.
A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
Authors: vonHoldt Bridgett M. , Pollinger John P. , Earl Dent A. , Knowles James C. , Boyko Adam R. , Parker Heidi , Geffen Eli , Pilot Malgorzata , Jedrzejewski Wlodzimierz , Jedrzejewska Bogumila , Sidorovich Vadim , Greco Claudia , Randi Ettore , Musiani Marco , Kays Roland , Bustamante Carlos D. , Ostrander Elaine A. , Novembre John , Wayne Robert K.
Published: May 2011

High-throughput genotyping technologies developed for model species can potentially increase the resolution of demographic history and ancestry in wild relatives. We use a SNP genotyping microarray developed for the domestic dog to assay variation in over 48K loci in wolf-like species worldwide. Despite the high mobility of these large carnivores, we find distinct hierarchical population units within gray wolves and coyotes that correspond with geographic and ecologic differences among populations. Further, we test controversial theories about the ancestry of the Great Lakes wolf and red wolf using an analysis of haplotype blocks across all 38 canid autosomes. We find that these enigmatic canids are highly admixed varieties derived from gray wolves and coyotes, respectively. This divergent genomic history suggests that they do not have a shared recent ancestry as proposed by previous researchers. Interspecific hybridization, as well as the process of evolutionary divergence, may be responsible for the observed phenotypic distinction of both forms. Such admixture complicates decisions regarding endangered species restoration and protection.
Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis
Authors: Devers Emanuel A. , Branscheid Anja , May Patrick , Krajinski Franziska
Published: May 2011

The majority of plants are able to form the arbuscular mycorrhizal (AM) symbiosis in association with AM fungi. During symbiosis development, plant cells undergo a complex reprogramming resulting in profound morphological and physiological changes. MicroRNAs (miRNAs) are important components of the regulatory network of plant cells. To unravel the impact of miRNAs and miRNA-mediated mRNA cleavage on root cell reprogramming during AM symbiosis, we carried out high-throughput (Illumina) sequencing of small RNAs and degradome tags of Medicago truncatula roots. This led to the annotation of 243 novel miRNAs. An increased accumulation of several novel and conserved miRNAs in mycorrhizal roots suggest a role of these miRNAs during AM symbiosis. The degradome analysis led to the identification of 185 root transcripts as mature miRNA and also miRNA*-mediated mRNA cleavage targets. Several of the identified miRNA targets are known to be involved in root symbioses. In summary, the increased accumulation of specific miRNAs and the miRNA-mediated cleavage of symbiosis-relevant genes indicate that miRNAs are an important part of the regulatory network leading to symbiosis development.
Tomato Root Penetration in Soil Requires a Coaction between Ethylene and Auxin Signaling
Authors: Santisree Parankusam , Nongmaithem Sapana , Vasuki Himabindu , Sreelakshmi Yellamaraju , Ivanchenko Maria G. , Sharma Rameshwar
Published: May 2011

During seed germination, emerging roots display positive gravitropism and penetrate into the soil for nutrition and anchorage. Tomato (Solanum lycopersicum) seeds germinated in the presence of 1-methylcyclopropene (1-MCP), an inhibitor of ethylene action, failed to insert roots into Soilrite and grew in the air, forming loops. Time-lapse video imaging showed that 1-MCP-grown root tips retained positive gravitropism and made contact with the surface of Soilrite but failed to penetrate into the Soilrite. Time-course studies revealed that the effect of 1-MCP was most prominent when seed imbibition and germination were carried out in the continual presence of 1-MCP. Conversely, 1-MCP was ineffective when applied postgermination after penetration of roots in the Soilrite. Furthermore, treatment with 1-MCP caused a reduction in DR5::β-glucuronidase auxin-reporter activity and modified the expression of SlIAA3 and SlIAA9 transcripts, indicating interference with auxin signaling. The reduced ethylene perception mutant, Never-ripe, displayed decreased ability for root penetration, and the enhanced polar auxin transport mutant, polycotyledon, showed a nearly normal root penetration in the presence of 1-MCP, which could be reversed by application of auxin transport inhibitors. Our results indicate that during tomato seed germination, a coaction between ethylene and auxin is required for root penetration into the soil.
Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice
Authors: Movahedi Sara , Van de Peer Yves , Vandepoele Klaas
Published: May 2011

Microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. We developed a robust framework to measure expression context conservation (ECC) and found, by analyzing 4,630 pairs of orthologous Arabidopsis and rice genes, that 77% showed conserved coexpression. Examples of nonconserved ECC categories suggested a link between regulatory evolution and environmental adaptations and included genes involved in signal transduction, response to different abiotic stresses, and hormone stimuli. To identify genomic features that influence expression evolution, we analyzed the relationship between ECC, tissue specificity, and protein evolution. Tissue-specific genes showed higher expression conservation compared with broadly expressed genes but were fast evolving at the protein level. No significant correlation was found between protein and expression evolution, implying that both modes of gene evolution are not strongly coupled in plants. By integration of cis-regulatory elements, many ECC conserved genes were significantly enriched for shared DNA motifs, hinting at the conservation of ancestral regulatory interactions in both model species. Surprisingly, for several tissue-specific genes, patterns of concerted network evolution were observed, unveiling conserved coexpression in the absence of conservation of tissue specificity. These findings demonstrate that orthologs inferred through sequence similarity in many cases do not share similar biological functions and highlight the importance of incorporating expression information when comparing genes across species.
Regulatory Subunit B′γ of Protein Phosphatase 2A Prevents Unnecessary Defense Reactions under Low Light in Arabidopsis
Authors: Trotta Andrea , Wrzaczek Michael , Scharte Judith , Tikkanen Mikko , Konert Grzegorz , Rahikainen Moona , Holmström Maija , Hiltunen Hanna-Maija , Rips Stephan , Sipari Nina , Mulo Paula , Weis Engelbert , von Schaewen Antje , Aro Eva-Mari , Kangasjärvi Saijaliisa
Published: May 2011

Light is an important environmental factor that modulates acclimation strategies and defense responses in plants. We explored the functional role of the regulatory subunit B′γ (B′γ) of protein phosphatase 2A (PP2A) in light-dependent stress responses of Arabidopsis (Arabidopsis thaliana). The predominant form of PP2A consists of catalytic subunit C, scaffold subunit A, and highly variable regulatory subunit B, which determines the substrate specificity of PP2A holoenzymes. Mutant leaves of knockdown pp2a-b′γ plants show disintegration of chloroplasts and premature yellowing conditionally under moderate light intensity. The cell-death phenotype is accompanied by the accumulation of hydrogen peroxide through a pathway that requires CONSTITUTIVE EXPRESSION OF PR GENES5 (CPR5). Moreover, the pp2a-b′γ cpr5 double mutant additionally displays growth suppression and malformed trichomes. Similar to cpr5, the pp2a-b′γ mutant shows constitutive activation of both salicylic acid- and jasmonic acid-dependent defense pathways. In contrast to cpr5, however, pp2a-b′γ leaves do not contain increased levels of salicylic acid or jasmonic acid. Rather, the constitutive defense response associates with hypomethylation of DNA and increased levels of methionine-salvage pathway components in pp2a-b′γ leaves. We suggest that the specific B′γ subunit of PP2A is functionally connected to CPR5 and operates in the basal repression of defense responses under low irradiance.
Os-GIGANTEA Confers Robust Diurnal Rhythms on the Global Transcriptome of Rice in the Field
Authors: Izawa Takeshi , Mihara Motohiro , Suzuki Yuji , Gupta Meenu , Itoh Hironori , Nagano Atsushi J. , Motoyama Ritsuko , Sawada Yuji , Yano Masahiro , Hirai Masami Yokota , Makino Amane , Nagamura Yoshiaki
Published: May 2011

The circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. Under natural field conditions, however, little is known about the significance of the circadian clock in plants. By time-course transcriptome analyses of rice (Oryza sativa) leaves, using a newly isolated rice circadian clock–related mutant carrying a null mutation in Os-GIGANTEA (Os-GI), we show here that Os-GI controlled 75% (false discovery rate = 0.05) of genes among 27,201 genes tested and was required for strong amplitudes and fine-tuning of the diurnal rhythm phases of global gene expression in the field. However, transcripts involved in primary metabolism were not greatly affected by osgi. Time-course metabolome analyses of leaves revealed no trends of change in primary metabolites in osgi plants, and net photosynthetic rates and grain yields were not affected. By contrast, some transcripts and metabolites in the phenylpropanoid metabolite pathway were consistently affected. Thus, net primary assimilation of rice was still robust in the face of such osgi mutation-related circadian clock defects in the field, unlike the case with defects caused by Arabidopsis  thaliana  toc1 and ztl mutations in the laboratory.
ArabidopsisNitrate Transporter NRT1.9 Is Important in Phloem Nitrate Transport
Authors: Wang Ya-Yun , Tsay Yi-Fang
Published: May 2011

This study of the Arabidopsis thaliana nitrate transporter NRT1.9 reveals an important function for a NRT1 family member in phloem nitrate transport. Functional analysis in Xenopus laevis oocytes showed that NRT1.9 is a low-affinity nitrate transporter. Green fluorescent protein and β-glucuronidase reporter analyses indicated that NRT1.9 is a plasma membrane transporter expressed in the companion cells of root phloem. In nrt1.9 mutants, nitrate content in root phloem exudates was decreased, and downward nitrate transport was reduced, suggesting that NRT1.9 may facilitate loading of nitrate into the root phloem and enhance downward nitrate transport in roots. Under high nitrate conditions, the nrt1.9 mutant showed enhanced root-to-shoot nitrate transport and plant growth. We conclude that phloem nitrate transport is facilitated by expression of NRT1.9 in root companion cells. In addition, enhanced root-to-shoot xylem transport of nitrate in nrt1.9 mutants points to a negative correlation between xylem and phloem nitrate transport.
TheArabidopsisC2H2 Zinc Finger INDETERMINATE DOMAIN1/ENHYDROUS Promotes the Transition to Germination by Regulating Light and Hormonal Signaling during Seed Maturation
Authors: Feurtado J. Allan , Huang Daiqing , Wicki-Stordeur Leigh , Hemstock Laura E. , Potentier Mireille S. , Tsang Edward W.T. , Cutler Adrian J.
Published: May 2011

Seed development ends with a maturation phase that imparts desiccation tolerance, nutrient reserves, and dormancy degree. Here, we report the functional analysis of an Arabidopsis thaliana C2H2 zinc finger protein INDETERMINATE DOMAIN1 (IDD1)/ENHYDROUS (ENY). Ectopic expression of IDD1/ENY (2x35S:ENY) disrupted seed development, delaying endosperm depletion and testa senescence, resulting in an abbreviated maturation program. Consequently, mature 2x35S:ENY seeds had increased endosperm-specific fatty acids, starch retention, and defective mucilage extrusion. Using RAB18 promoter ENY lines (RAB18:ENY) to confine expression to maturation, when native ENY expression increased and peaked, resulted in mature seed with lower abscisic acid (ABA) content and decreased germination sensitivity to applied ABA. Furthermore, results of far-red and red light treatments of 2x35S:ENY and RAB18:ENY germinating seeds, and of artificial microRNA knockdown lines, suggest that ENY acts to promote germination. After using RAB18:ENY seedlings to induce ENY during ABA application, key genes in gibberellin (GA) metabolism and signaling were differentially regulated in a manner suggesting negative feedback regulation. Furthermore, GA treatment resulted in a skotomorphogenic-like phenotype in light-grown 2x35S:ENY and RAB18:ENY seedlings. The physical interaction of ENY with DELLAs and an ENY-triggered accumulation of DELLA transcripts during maturation support the conclusion that ENY mediates GA effects to balance ABA-promoted maturation during late seed development.
DELLAs Regulate Chlorophyll and Carotenoid Biosynthesis to Prevent Photooxidative Damage during Seedling Deetiolation in Arabidopsis
Authors: Cheminant Soizic , Wild Michael , Bouvier Florence , Pelletier Sandra , Renou Jean-Pierre , Erhardt Mathieu , Hayes Scott , Terry Matthew J. , Genschik Pascal , Achard Patrick
Published: May 2011

In plants, light represents an important environmental signal that triggers the production of photosynthetically active chloroplasts. This developmental switch is critical for plant survival because chlorophyll precursors that accumulate in darkness can be extremely destructive when illuminated. Thus, plants have evolved mechanisms to adaptively control plastid development during the transition into light. Here, we report that the gibberellin (GA)-regulated DELLA proteins play a crucial role in the formation of functional chloroplasts during deetiolation. We show that Arabidopsis thaliana DELLAs accumulating in etiolated cotyledons derepress chlorophyll and carotenoid biosynthetic pathways in the dark by repressing the transcriptional activity of the phytochrome-interacting factor proteins. Accordingly, dark-grown GA-deficient ga1-3 mutants (that accumulate DELLAs) display a similar gene expression pattern to wild-type seedlings grown in the light. Consistent with this, ga1-3 seedlings accumulate higher amounts of protochlorophyllide (a phototoxic chlorophyll precursor) in darkness but, surprisingly, are substantially more resistant to photooxidative damage following transfer into light. This is due to the DELLA-dependent upregulation of the photoprotective enzyme protochlorophyllide oxidoreductase (POR) in the dark. Our results emphasize the role of DELLAs in regulating the levels of POR, protochlorophyllide, and carotenoids in the dark and in protecting etiolated seedlings against photooxidative damage during initial light exposure.
Diffuse scattering from the lead-based relaxor ferroelectric PbMg1/3Ta2/3O3
Authors: Cervellino Antonio , Gvasaliya S. N. , Zaharko O. , Roessli B. , Rotaru G. M. , Cowley R. A. , Lushnikov S. G. , Shaplygina T. A. , Fernandez-Diaz M. T.
Published: May 2011

The relaxor ferroelectric PbMg1/3Ta2/3O3was studied by single-crystal neutron and synchrotron X-ray diffraction, and its detailed atomic structure modelled in terms of static Pb displacements that lead to the formation of polar nanoregions. Similar to the other members of the Pb-based relaxor family like PbMg1/3Nb2/3O3or PbZn1/3Nb2/3O3the diffuse scattering in the [H00]/[0K0] scattering plane has a butterfly shape around theh00 Bragg reflections and is orthogonal to the scattering vector forhh0 peaks. In the [HH0]/[00L] plane the diffuse scattering is elongated along the 〈112〉 directions and is orthogonal to the scattering vector forhhhreflections. It is found that a model consisting of correlated Pb displacements along the 〈111〉 directions reproduces adequately the main features of the diffuse scattering in PbMg1/3Ta2/3O3when the correlation lengths between the Pb-ion displacement vectors are longest along the 〈111〉 and shortest along the 〈11{\overline 2}〉 and 〈1{\overline 1}0〉 directions.
Ultrasound‐guided interscalene blocks: understanding where to inject the local anaesthetic
Authors: Spence B. C. , Beach M. L. , Gallagher J. D. , Sites B. D.
Published: May 2011

Although ultrasound‐guided regional anaesthesia has gained in popularity, few data exist describing the optimal location(s) to inject local anaesthetic. Our objective was to compare, for interscalene blocks, the effectiveness of an injection between the middle scalene muscle and brachial plexus sheath (peri‐plexus) with an injection within the brachial plexus sheath (intra‐plexus). We enrolled 170 patients undergoing shoulder surgery with general anaesthesia and interscalene block in this randomised, controlled trial. Our primary outcome variable was loss of shoulder abduction. Block quality was also measured and defined by an evaluation of onset time, sensory and motor loss and duration. There was no difference between the two groups in block onset times or block quality. After adjusting for sex, age and volume injected, intra‐plexus blocks lasted a mean of 2.6 h (16%) longer (95% CI 0.25–5.01, p = 0.03) than peri‐plexus blocks.
Evidence for a macromolecular complex in poor prognosis CLL that contains CD38, CD49d, CD44 and MMP‐9
Authors: Buggins Andrea G. S. , Levi Ana , Gohil Satyen , Fishlock Keith , Patten Piers E. M. , Calle Yolanda , Yallop Deborah , Devereux Stephen
Published: May 2011

Progressive chronic lymphocytic leukaemia is characterized by the accumulation of neoplastic B‐cells in the tissues and correlates with the expression of prognostic biomarkers, such as CD38, CD49d and matrix metalloproteinase‐9 (MMP9), which are involved in migration and tissue invasion. In this study we investigated the physical relationship between these molecules and demonstrated that CD38, CD49d, MMP9 and CD44 were physically associated in a supramolecular cell surface complex. Our findings provide a molecular basis for the correlation between expression of these proteins and prognosis and, as the complex is not present in normal B‐cells, suggest a novel leukaemia‐specific therapeutic target.
Mild haemorheological changes induced by a moderate endurance exercise in patients with sickle cell anaemia
Authors: Balayssac‐Siransy Edwige , Connes Philippe , Tuo Nalourgo , Danho Clotaire , Diaw Mor , Sanogo Ibrahima , Hardy‐Dessources Marie‐Dominique , Samb Abdoulaye , Ballas Samir K , Bogui Pascal
Published: May 2011

The levels and duration of physical activity that can be considered as completely safe in patients with sickle cell anaemia (SCA) is unknown. The present study compared the haemorheological and haematological profile, cell density distribution and basic biochemistry between a group of 17 patients with SCA and 21 healthy subjects before and after a 20 min duration submaximal cycling exercise at the same absolute workload. Blood was sampled at rest and 3 min after the end of exercise for measurement of biological parameters. Exercise did not affect the haematocrit and blood viscosity in the two groups. Plasma viscosity was not different between the two groups at rest and similarly increased with exercise. The proportion of intermediary dense cells (with density between 1·11 and 1·12 g/ml) decreased with exercise in the SCA group resulting in an increase in the proportion of red blood cells with a density >1·12 g/ml. No change was observed in the control group. The present study suggests that mild‐moderate exercise is not very harmful for SCA patients. The haemorheological and haematological changes were very mild, except for the formation of dense cells but no clinically significant signs of medical complication were present in any of the patients.
Outcome of unrelated umbilical cord blood transplantation in 88 patients with primary immunodeficiency in Japan
Authors: Morio Tomohiro , Atsuta Yoshiko , Tomizawa Daisuke , Nagamura‐Inoue Tokiko , Kato Koji , Ariga Tadashi , Kawa Keisei , Koike Kazutoshi , Tauchi Hisamichi , Kajiwara Michiko , Hara Toshiro , Kato Shunichi ,   for the Japanese Cord Blood Bank Network
Published: May 2011

We report the results of umbilical cord blood transplantation (UCBT) performed in 88 patients with primary immunodeficiency (PID) between 1998 and 2008 in Japan; severe combined immunodeficiency (SCID, n = 40), Wiskott–Aldrich syndrome (WAS, n = 23), chronic granulomatous disease (n = 7), severe congenital neutropaenia (SCN, n = 5) and other immunodeficiencies (n = 13). Five‐year overall survival (5‐year OS) for all patients was 69% [95% confidence interval (CI), 57–78%], and was 71% and 82% for SCID and WAS, respectively. The main cause of death before day 100 was infection (17/19), while that after day 100 was graft‐versus‐host disease (GVHD) (5/7). Using multivariate analyses, pre‐transplant infection, no conditioning, ≥2 human leucocyte antigen (HLA) mismatches or diagnosis other than SCID, SCN or WAS were all associated with poor prognosis. Reduced‐intensity conditioning was associated with decreased overall mortality compared with myeloablative therapy. The cumulative incidence of grade 2–4 acute GVHD at day 100 was 28% (95% CI, 19–38%), and that of chronic GVHD at day 180 was 13% (95% CI, 7–23%). We conclude that UCBT should be considered for PID patients without an HLA‐matched sibling. The control of pre‐transplant infection and selection of HLA‐matched donors will lead to a better outcome.
EVI1‐mediated down regulation of MIR449A is essential for the survival of EVI1 positive leukaemic cells
Authors: De Weer An , Van der Meulen Joni , Rondou Pieter , Taghon Tom , Konrad Torsten A. , De Preter Katleen , Mestdagh Pieter , Van Maerken Tom , Van Roy Nadine , Jeison Marta , Yaniv Isaac , Cauwelier Barbara , Noens Lucien , Poirel Hélène‐Antoine , Vandenberghe Peter , Lambert Frédéric , De Paepe Anne , Sánchez Maria García , Odero Maria , Verhasselt Bruno , Philippé Jan , Vandesompele Joke , Wieser Rotraud , Dastugue Nicole , Van Vlierberghe Pieter , Poppe Bruce , Speleman Frank
Published: May 2011

Chromosomal rearrangements involving the MECOM (MDS1 and EVI1 complex) locus are recurrent genetic events in myeloid leukaemia and are associated with poor prognosis. In this study, we assessed the role of MECOM locus protein EVI1 in the transcriptional regulation of microRNAs (miRNAs) involved in the leukaemic phenotype. For this, we profiled expression of 366 miRNAs in 38 MECOM‐rearranged patient samples, normal bone marrow controls and MECOM (EVI1) knock down/re‐expression models. Cross‐comparison of these miRNA expression profiling data showed that MECOM rearranged leukaemias are characterized by down regulation of MIR449A. Reconstitution of MIR449A expression in MECOM‐rearranged cell line models induced apoptosis resulting in a strong decrease in cell viability. These effects might be mediated in part by MIR449A regulation of NOTCH1 and BCL2, which are shown here to be bona fide MIR449A targets. Finally, we confirmed that MIR449A repression is mediated through direct promoter occupation of the EVI1 transcriptional repressor. In conclusion, this study reveals MIR449A as a crucial direct target of the MECOM locus protein EVI1 involved in the pathogenesis of MECOM‐rearranged leukaemias and unravels NOTCH1 and BCL2 as important novel targets of MIR449A. This EVI1‐MIR449A‐NOTCH1/BCL2 regulatory axis might open new possibilities for the development of therapeutic strategies in this poor prognostic leukaemia subgroup.
Expression of MHC class I dimers and ERAP1 in an ankylosing spondylitis patient cohort
Authors: Campbell Elaine C. , Fettke Franziska , Bhat Smita , Morley Kenneth D. , Powis Simon J.
Published: May 2011

The human leucocyte antigen HLA‐B27 is strongly associated with ankylosing spondylitis, a form of seronegative inflammatory arthritis. In this study aspects related to several hypothesized mechanisms of disease pathogenesis have been investigated. Blood monocyte‐derived dendritic cells (DC) from a small patient cohort of 29 patients with ankylosing spondylitis and one with reactive arthritis, were compared with DC from 34 healthy control subjects, of whom four were found to be HLA‐B27 positive. The ability of HLA‐B27 to form heavy‐chain dimers reactive with monoclonal antibody HC10 was tested, along with the induction of endoplasmic reticulum (ER) stress, assessed by splicing xbp1 mRNA and immunoblotting of Immunoglobulin Binding Protein (BiP). Additionally, the protein expression levels of the ER resident aminopeptidase gene ERAP1 in patients with ankylosing spondylitis was also determined, following its recent identification as a novel disease‐associated gene. No significant difference was noted in the global levels of HC10‐reactive MHC class I dimers formed in either the patient or control DC populations. Stress on the ER, as determined by xbp1 mRNA splicing, was not detected but lower levels of BiP were observed in the DC from patients. Of further potential interest, in this patient cohort the expression of ERAP1 appeared to be higher in a number of patient DC samples when compared with controls, suggesting over‐expression of ERAP1 as a mechanism promoting ankylosing spondylitic pathogenesis.
Arabidopsis mutants of AtABCG22, an ABC transporter gene, increase water transpiration and drought susceptibility
Authors: Kuromori Takashi , Sugimoto Eriko , Shinozaki Kazuo
Published: May 2011

In plants, water vapour is released into the atmosphere through stomata in a process called transpiration. Abscisic acid (ABA) is a key phytohormone that facilitates stomatal closure through its action on guard cells. Recently, ATP‐binding cassette (ABC) transporter genes, AtABCG25 and AtABCG40, were shown to be involved in ABA transport and responses. However, the functions of many other AtABCG family genes are still unknown. Here, we identified another ABCG gene (AtABCG22) that is required for stomatal regulation in Arabidopsis. The atabcg22 mutant plants had lower leaf temperatures and increased water loss, implying elevated transpiration through an influence on stomatal regulation. We also found that atabcg22 plants were more suspectible to drought stress than wild‐type plants. AtABCG22 was expressed in aerial organs, mainly guard cells, in which the gene expression pattern was consistent with the mutant phenotypes. Using double mutants, we investigated the genetic relationships between the mutations. The atabcg22 mutation further increased the water loss of srk2e/ost1 mutants, which were defective in ABA signalling in guard cells. Also, the atabcg22 mutation enhanced the phenotype of nced3 mutants, which were defective in ABA biosynthesis. Accordingly, the additive roles of AtABCG22 functions in ABA signalling and ABA biosynthesis are discussed.