bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-scaling and mesoscopic structures
Authors: Salje E. K. H.
Published: February 2010

Multi-scaling and the systematic investigation of mesoscopic structures represent a field of fruitful cooperation in physics, chemistry, mineralogy and life sciences. The increasing miniaturization of devices as well as the emphasis of recent research on microstructures with length scales of a few nanometres lead to paradigm changes that may impact not only on our scientific understanding of fine-grained structures but also on the way we will develop device materials in the future. Here the role of interfaces becomes more important, and developments in areas such as ‘domain boundary engineering’ are evidence of this scientific evolution. In addition, nano-porous materials are particularly important in geology and in the development of artificial bones and ultra-light metals. Some of these developments are reviewed in this paper.
Flavobacterium sinopsychrotolerans sp. nov., isolated from a glacier
Authors: Xu Mingshuang , Xin Yuhua , Tian Jiesheng , Dong Kun , Yu Yong , Zhang Jianli , Liu Hongcan , Zhou Yuguang
Published: January 2010

An aerobic, Gram-negative, yellow-pigmented bacterial strain, designated 0533T, was isolated from frozen soil from the China No. 1 glacier. Phylogenetic analysis of the 16S rRNA gene sequence demonstrated that strain 0533Twas a member of the genusFlavobacteriumand exhibited 97.1–98.7 % 16S rRNA sequence similarity with its nearest phylogenetic neighbours. Strain 0533Texhibited phenotypic and chemotaxonomic characteristics common to the genusFlavobacterium: menaquinone-6 (MK-6) was the predominant quinone and iso-C15 : 0, C17 : 1ω6c, anteiso-C15 : 0, iso-C15 : 03-OH, C15 : 1ω6c, iso-C16 : 03-OH, summed feature 3 (comprising C16 : 1ω7cand/or C16 : 1ω6c), iso-C15 : 1G and iso-C17 : 03-OH were the major fatty acids (>5 %). The DNA G+C content was 32.5 mol%. On the basis of phenotypic and genotypic data, a novel species,Flavobacterium sinopsychrotoleranssp. nov., is proposed. The type strain is 0533T(=CGMCC 1.8704T=JCM 16398T).
Nocardiopsis nikkonensis sp. nov., isolated from a compost sample
Authors: Yamamura Hideki , Ohkubo Shin-ya , Ishida Yuumi , Otoguro Misa , Tamura Tomohiko , Hayakawa Masayuki
Published: January 2010

An actinomycete strain, designated YU1183-22T, was isolated from a compost sample collected in Nikko, Japan. The isolate formed white aerial mycelium with relatively long aerial hyphae showing chains of arthrospores. Strain YU1183-22T grew with 0–10 % (w/v) NaCl, at pH 6–11 and at 10–37 °C (optimum 30 °C). Strain YU1183-22T contained meso-diaminopimelic acid and no diagnostic sugars. The predominant menaquinones were MK-10(H10) and MK-10(H8). The polar lipids were phosphatidylcholine and phosphatidylglycerol. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0 and tuberculostearic acid. The G+C content of the DNA was 72.3 mol%. Chemotaxonomic and morphological characterization clearly demonstrated that strain YU1183-22T belonged to the genus Nocardiopsis. Phylogenetic analysis using 16S rRNA gene sequences showed that the isolate was closely related to Nocardiopsis salina YIM 90010T (98.0 % 16S rRNA gene sequence similarity), Nocardiopsis xinjiangensis YIM 90004T (97.9 %) and Nocardiopsis kunsanensis HA-9T (97.3 %). However, DNA–DNA relatedness as well as physiological and biochemical analyses showed that strain YU1183-22T could be differentiated from its closest phylogenetic relatives. It is proposed that this strain be classified as a representative of a novel species of the genus Nocardiopsis, with the name Nocardiopsis nikkonensis sp. nov. The type strain is YU1183-22T (=NBRC 102170T =KCTC 19666T).
Terribacillus aidingensis sp. nov., a moderately halophilic bacterium
Authors: Liu Wenyan , Jiang Linlin , Guo Chunjing , Yang Su Sheng
Published: January 2010

Three Gram-positive, moderately halophilic bacteria, designated YI7-61T, IA7 and DB2, were isolated from sediments of Aiding salt lake in the Xinjiang region of China. Cells of the strains were rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Colonies were pale yellow in colour. The strains grew optimally at 30–37 °C, pH 6–7 and 3–7 % (w/v) NaCl. The diamino acid in the murein wasmeso-diaminopimelic acid and the major quinone system was MK-7. The major cellular fatty acids were anteiso-C15 : 0and anteiso-C17 : 0. The DNA G+C content was 44.6–45.0 mol%. 16S rRNA gene sequence analysis revealed that strains YI7-61T, IA7 and DB2 were closely related to members of the genusTerribacillusand showed 96.8–97.6, 96.4–97.2 and 95.4–95.5 % 16S rRNA gene sequence similarity withTerribacillus halophilus002-051T,Terribacillus saccharophilusRB589 andTerribacillus goriensisCL-GR16T, respectively. DNA–DNA relatedness among the isolates was 88–92 % and strain YI7-61Tshared 24, 18 and 18 % DNA–DNA relatedness withT. halophilusJCM 21760T,T. saccharophilusJCM 21759TandT. goriensisDSM 18252T, respectively. On the basis of phenotypic and phylogenetic distinctiveness, the three isolates should be placed in the genusTerribacillusas representatives of a novel species, for which the nameTerribacillus aidingensissp. nov. is proposed. The type strain is YI7-61T(=CGMCC 1.8913T=NBRC 105790T).
Ekhidna lutea gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from the South East Pacific Ocean
Authors: Alain Karine , Tindall Brian J. , Catala Philippe , Intertaglia Laurent , Lebaron Philippe
Published: January 2010

A novel aerobic, heterotrophic bacterium, designated BiosLi39T, was isolated from the South East Pacific Ocean. Cells were Gram-negative gliding rods forming yellow colonies on marine agar. The isolate was oxidase-, catalase- and alkaline phosphatase-positive andβ-galactosidase-negative. Strain BiosLi39Tgrew at 20-37 °C (optimum 30 °C), at pH 7.0–9.0 (optimum pH 8.0) and with 20–60 g NaCl l−1(optimum 30–50 g NaCl l−1). The fatty acids (>1 %) comprised iso-C14 : 0, iso-C15 : 1G, iso-C15 : 0, anteiso-C15 : 0, C15 : 1G, C15 : 0, iso-C15 : 02-OH, iso-C16 : 1G, iso-C16 : 0, iso-C16 : 03-OH, iso-C16 : 02-OH, iso-C17 : 03-OH, C17 : 02-OH and three unidentified components with equivalent chain lengths of 17.87, 18.10 and 18.71. A significant proportion of the hydroxylated fatty acids are amide-linked. The lipid pattern indicated the presence of phosphatidylethanolamine, two unidentified aminolipids and three unidentified polar lipids. The strain contained menaquinone 7 as the sole respiratory lipoquinone and did not produce flexirubin-type pigments. The G+C content of the genomic DNA was 37.2 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain BiosLi39Twas distantly related to all of the representatives of the phylumBacteroidetes. Its closest relative wasMarinoscillum furvescensIFO 15994T, with which it shared 92.5 % 16S rRNA gene sequence similarity. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, we propose a novel genus and species,Ekhidnagen. nov., sp. nov., with type strain BiosLi39T(=DSM 19307T=CIP 109600T=OOB 398T).
Rhodanobacter soli sp. nov., isolated from soil of a ginseng field
Authors: Bui Thi Phuong Nam , Kim Yeon-Ju , Kim Hobin , Yang Deok-Chun
Published: January 2010

Strain DCY45Twas isolated from soil of a ginseng field in Pocheon Province, Korea. Strain DCY45Twas Gram-negative, oxidase- and catalase-positive, motile and rod-shaped and produced yellow pigments on R2A agar. The organism grew optimally at 30 °C and at pH 7.0. The G+C content of the genomic DNA was 65.4 mol%. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C17 : 1ω9c, iso-C16 : 0and iso-C15 : 0. Phylogenetic analysis based on the 16S rRNA gene sequence was used to determine the taxonomic position of strain DCY45T, which is most closely related to species of the genusRhodanobacter, with similarity levels of 96.0–98.4 %; DNA–DNA relatedness with related strains was lower than 60 %. Strain DCY45Tdiffered significantly from related type strains in phenotypic characteristics. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY45Trepresents a novel species of the genusRhodanobacter, for which the nameRhodanobacter solisp. nov. is proposed. The type strain is DCY45T(=KCTC 22620T=JCM 16126T).
Bacillus oceanisediminis sp. nov., isolated from marine sediment
Authors: Zhang Jianli , Wang Jiewei , Fang Caiyuan , Song Fei , Xin Yuhua , Qu Lei , Ding Kai
Published: January 2010

A Gram-stain-positive, spore-forming, rod-shaped and aerobic bacterium was isolated from a sediment sample from the South Sea in China. The isolate, designated H2T, grew at 4–45 °C (optimum 37 °C) and pH 6–10 (optimum pH 7.0). The cell-wall peptidoglycan containedmeso-diaminopimelic acid. The major isoprenoid quinone was MK-7 and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminophospholipid. The major fatty acid was iso-C15 : 0. The genomic DNA G+C content of strain H2Twas 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a monophyletic clade withBacillus firmusIAM 12464T. DNA–DNA relatedness between the isolate andB. firmusATCC 14575Twas low (27.5 %). Strain H2Talso had a phenotypic profile that readily distinguished it from its closest phylogenetic neighbours. It is evident from the combination of genotypic and phenotypic data that the organism should be classified in a novel species of the genusBacillus, for which the nameBacillus oceanisediminissp. nov. is proposed. The type strain is H2T(=CGMCC 1.10115T=JCM 16506T).
Serinicoccus profundi sp. nov., an actinomycete isolated from deep-sea sediment, and emended description of the genus Serinicoccus
Authors: Xiao Jing , Luo Yingxue , Xie Shujie , Xu Jun
Published: January 2010

A Gram-reaction-positive bacterial strain of the genus Serinicoccus, designated MCCC 1A05965T, was isolated from a deep-sea (5368 m) sediment of the Indian Ocean. Comparison of 16S rRNA gene sequences revealed that the isolate shared 97.6 % sequence similarity with Serinicoccus marinus JC1078T, the type strain of the only described species of the genus Serinicoccus. The DNA–DNA relatedness between these two strains was 46.2 % (standard deviation 1.86 %). The cell wall contained alanine, glycine, serine, l-ornithine and glutamic acid, which corresponds to the description of the genus Serinicoccus. The acyl type of the glycan chain of the peptidoglycan was glycolyl. Other characteristics of strain MCCC 1A05965T were consistent with those of the genus Serinicoccus. Cells were coccoid, moderately halophilic, oxidase-negative, catalase-positive and non-spore-forming. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were iso-C15 : 0 (34.7 %) and iso-C16 : 0 (17.0 %). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glycolipid. The DNA G+C content was 72 mol%. Strain MCCC 1A05965T (=0714S6-1T =DSM 21363T =CGMCC 4.5582T) is assigned as the type strain of a novel species, for which the name Serinicoccus profundi sp. nov. is proposed.
Brevibacterium salitolerans sp. nov., an actinobacterium isolated from salt-lake sediment
Authors: Guan Tong-Wei , Zhao Ke , Xiao Jing , Liu Ying , Xia Zhan-Feng , Zhang Xiao-Ping , Zhang Li-Li
Published: January 2010

A novel bacterium, designated TRM 415T, belonging to the genus Brevibacterium, was isolated from a sediment sample from a salt lake in Xinjiang province, China. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 415T was phylogenetically most closely related to Brevibacterium album YIM 90718T (98.4 % sequence similarity) and had low similarity (<95.5 %) to other species of the genus Brevibacterium; however, DNA–DNA hybridization studies between strain TRM 415T and B. album YIM 90718T showed only 41.3 % relatedness. Strain TRM 415T possessed meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, MK-8(H2) as the major menaquinone and polar lipids including phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content was 69 mol%. Based on the evidence from this polyphasic study, strain TRM 415T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium salitolerans sp. nov. is proposed. The type strain is TRM 415T (=JCM 15900T =CCTCC AB 208328T =KCTC 19616T).
hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes
Authors: Sakamoto Mitsuo , Suzuki Natsuko , Benno Yoshimi
Published: January 2010

hsp60gene sequences were determined for members of the genusBacteroidesand sequence similarities were compared with those obtained for the 16S rRNA gene. Among the 29Bacteroidestype strains, the mean sequence similarity of thehsp60gene (84.5 %) was significantly less than that of the 16S rRNA gene (90.7 %), indicating a high discriminatory power of thehsp60gene. Species of the genusBacteroideswere differentiated well byhsp60gene sequence analysis, except forBacteroides pyogenesJCM 6294T,Bacteroides suisJCM 6292TandBacteroides tectusJCM 10003T. Thehsp60gene sequence analysis and the levels of DNA–DNA relatedness observed demonstrated that these three type strains are a single species. Consequently,B. suisandB. tectusare heterotypic synonyms ofB. pyogenes. This study suggests that thehsp60gene is an alternative phylogenetic marker for the classification of species of the genusBacteroides.
Ornithinibacillus contaminans sp. nov., an endospore-forming species
Authors: Kämpfer P. , Falsen E. , Lodders N. , Langer S. , Busse H.-J. , Schumann P.
Published: January 2010

A Gram-stain-positive, endospore-forming rod, designated CCUG 53201T, was isolated from a human blood sample of a 75-year-old woman. 16S rRNA gene sequence-based phylogenetic analysis showed that strain CCUG 53201T clustered with the type strains of species of the genus Ornithinibacillus. Strain CCUG 53201T was most closely related to Ornithinibacillus bavariensis WSBC 24001T and Ornithinibacillus californiensis DSM 16628T (97.9 and 98.7 % 16S rRNA gene sequence similarity, respectively). Strain CCUG 53201T contained a peptidoglycan of type A4β
l-Orn–d-Asp. The quinone system was composed of the menaquinone MK-7 and small amounts of MK-6. The polar lipid profile of strain CCUG 53201T consisted of major amounts of diphosphatidylglycerol and an unidentified phospholipid, moderate amounts of phosphatidylglycerol and another two unidentified phospholipids and minor amounts of several other components. The fatty acid profile comprised mainly anteiso- and iso-branched fatty acids and was in accordance with those of members of the genus Ornithinibacillus. The polyamine pattern exhibited the major compounds spermidine and spermine. The results of physiological and biochemical tests and DNA–DNA hybridization allowed the phenotypic and genotypic differentiation of strain CCUG 53201T from its closest phylogenetic neighbours. We propose a novel species with the name Ornithinibacillus contaminans sp. nov., with type strain CCUG 53201T (=DSM 22953T).
Arcicella aurantiaca sp. nov., isolated from stream water
Authors: Sheu Shih-Yi , Yang Cho-Song , Chen Ming-Hui , Arun A. B. , Young Chiu-Chung , Chen Wen-Ming
Published: January 2010

A bacterial strain designated TNR-18T was isolated from stream water in southern Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-18T were Gram-stain-negative, strictly aerobic, non-motile and vibrioid, and the strain formed orange colonies. Growth occurred at 10–30 °C, with 0–0.2 % NaCl and at pH 6.0–10.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TNR-18T belonged to the genus Arcicella; its closest neighbours were Arcicella rosea TW5T and Arcicella aquatica NO-502T, with respective sequence similarities of 97.9 and 97.8 %. Predominant cellular fatty acids (>10 %) were summed feature 3 (C16 : 1
ω7c/C16 : 1
ω6c; 37.7 %), C16 : 1
ω5c (13.0 %) and iso-C15 : 0 (11.1 %). The major respiratory quinone was MK-7. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized polar lipids. The DNA G+C content was 39.9 mol%. On the basis of the phylogenetic and phenotypic data, strain TNR-18T should be classified as representing a novel species, for which the name Arcicella aurantiaca sp. nov. is proposed. The type strain is TNR-18T (=LMG 25207T =BCRC 17969T).
Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment
Authors: Tian Shi-Ping , Wang Yong-Xia , Hu Bin , Zhang Xiao-Xia , Xiao Wei , Chen Yun , Lai Yong-Hong , Wen Meng-Liang , Cui Xiao-Long
Published: January 2010

A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1
ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c; 10.7 %) and C17 : 1
ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).
Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs
Authors: Pankratov Timofey A. , Dedysh Svetlana N.
Published: January 2010

Five strains of strictly aerobic, heterotrophic bacteria that form pink–red colonies and are capable of hydrolysing pectin, xylan, laminarin, lichenan and starch were isolated from acidic Sphagnum peat bogs and were designated OB1010T, LCBR1, TPB6011T, TPB6028T and TPO1014T. Cells of these isolates were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance. Old cultures contained spherical bodies of varying sizes, which represent starvation forms. Cells of all five strains were acidophilic and psychrotolerant, capable of growth at pH 3.0–7.5 (optimum pH 3.8–4.5) and at 2–33 °C (optimum 15–22 °C). The major fatty acids were iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH). The major menaquinone detected was MK-8. The pigments were carotenoids. The genomic DNA G+C contents were 57.3–59.3 mol%. The five isolates were found to be members of subdivision 1 of the phylum Acidobacteria and displayed 95.3–98.9 % 16S rRNA gene sequence similarity to each other. The closest described relatives to strains OB1010T, LCBR1, TPB6011T, TPB6028T, and TPO1014T were members of the genera Terriglobus (94.6–95.8 % 16S rRNA gene sequence similarity) and Edaphobacter (94.2–95.4 %). Based on differences in cell morphology, phenotypic characteristics and hydrolytic capabilities, we propose a novel genus, Granulicella gen. nov., containing four novel species, Granulicella paludicola sp. nov. with type strain OB1010T (=DSM 22464T =LMG 25275T) and strain LCBR1, Granulicella pectinivorans sp. nov. with type strain TPB6011T (=VKM B-2509T =DSM 21001T), Granulicella rosea sp. nov. with type strain TPO1014T (=DSM 18704T =ATCC BAA-1396T) and Granulicella aggregans sp. nov. with type strain TPB6028T (=LMG 25274T =VKM B-2571T).
Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans
Authors: Hahn Martin W. , Kasalický Vojtěch , Jezbera Jan , Brandt Ulrike , Šimek Karel
Published: January 2010

A chemo-organotrophic, aerobic, non-motile strain, MWH-BRAZ-DAM2DT, isolated from a freshwater pond in Brazil, was characterized phenotypically, phylogenetically and chemotaxonomically. Phylogenetic analysis of 16S rRNA gene sequences indicated affiliation of the strain with the genus Limnohabitans (Comamonadaceae, Betaproteobacteria). 16S rRNA gene sequence similarities between the isolate and Limnohabitans
curvus MWH-C5T, representing the type species of the genus, and the type strains of Limnohabitans parvus and Limnohabitans planktonicus were 98.2, 96.5 and 97.0 %, respectively. DNA–DNA reassociation analyses with DNA of the type strains of all three previously described Limnohabitans species revealed similarity values in the range 26.2–44.6 %. The predominant fatty acids of the isolate were C16 : 1
ω7c/ω6c, C16 : 0, C12 : 0 and C8 : 0 3-OH, the major quinone was ubiquinone Q-8 and the DNA G+C content was 55.8 mol%. The isolate could be discriminated from the type strains of the three Limnohabitans species by several phenotypic traits including differences in the utilization of several carbon sources. Based on the phylogeny of the isolate and its differences from the three most closely related species, the isolate represents a novel species for which the name Limnohabitans australis sp. nov. is proposed. The type strain is MWH-BRAZ-DAM2DT (=DSM 21646T=CCUG 56719T).
Purification of Proteins by Chromatofocusing
Authors: Mohammad Jamil
Published: February 2010

INTRODUCTION

This protocol describes purification of proteins by chromatofocusing, a technique that separates proteins on the basis of differences in their isoelectric point (pI). The equipment required for chromatofocusing includes a chromatography column, pump, sample valve, UV monitor, pH monitor, and fraction collector. Commercially available liquid chromatography systems or high performance liquid chromatography (HPLC) systems can be used for chromatofocusing experiments. Precise pH control is essential for correct interpretation of chromatofocusing results. With a pH monitor connected to a flowthrough pH electrode, it is easy and convenient to monitor the elution pH values for chromatofocusing. Continuous monitoring of the pH profile throughout an experiment often helps explain the UV peak profiles more fully.
Chromatofocusing
Authors: Mohammad Jamil
Published: February 2010

INTRODUCTION

Chromatofocusing separates proteins on the basis of differences in their isoelectric point (pI). The stationary phase (matrix) is usually a weak anion exchanger in which the functional groups are amines, for example, a polybuffer exchanger (PBE 118 and PBE 94) or Mono P column. The eluent is a buffer containing a large number of buffering species that together give a uniform buffering capacity over a broad pH range.
S-Glycoprotein-Like Protein Regulates Defense Responses in Nicotiana Plants against Ralstonia solanacearum
Authors: Maimbo Milimo , Ohnishi Kouhei , Hikichi Yasufumi , Yoshioka Hirofumi , Kiba Akinori
Published: January 2010

RsRGA4 (for Ralstonia solanacearum-responsive gene A4) encodes a polypeptide similar to S-locus glycoprotein (SGP) from Brassica rapa and SGP-like proteins from Ipomoea trifida and Medicago truncatula. Therefore, we designated RsRGA4 as NtSGLP (for Nicotiana tabacum SGP-like protein) and NbSGLP (its Nicotiana benthamiana ortholog). NbSGLP is expressed in root, leaf, petal, gynoecium, and stamen. Expression of NbSGLP was strongly induced by inoculation with an avirulent strain of R. solanacearum (Rs8107) and slightly enhanced by inoculation with virulent R. solanacearum (RsOE1-1). Expression of NbSGLP was induced by inoculation with an hrpY-deficient mutant of RsOE1-1 and Rs8107. Expression was also induced by aminocyclopropane carboxylic acid and salicylic acid. Virus-induced gene silencing of NbSGLP enhanced the growth of Rs8107. Growth of RsOE1-1 and appearance of wilt symptoms were also accelerated in silenced plants. Expression of PR-1a and EREBP was reduced, and markers for basal defense, such as callose deposition and reduced vascular flow, were compromised in NbSGLP-silenced plants. Moreover, growth of Pseudomonas cichorii, Pseudomonas syringae pv tabaci, and P. syringae pv mellea was also enhanced in the silenced plants. On the other hand, silencing of NbSGLP did not interfere with the appearance of the hypersensitive response. NbSGLP was secreted in a signal peptide-dependent manner. Agrobacterium tumefaciens-mediated expression of NbSGLP induced PR-1a and EREBP expression, callose deposition, and reduced vascular flow. NbSGLP-induced callose deposition and reduced vascular flow were not observed in salicylic acid-deficient N. benthamiana NahG plants. Taken together, SGLP might have a role in the induction of basal defense in Nicotiana plants.
Tricarboxylic Acid Cycle Activity Regulates Tomato Root Growth via Effects on Secondary Cell Wall Production
Authors: van der Merwe Margaretha J. , Osorio Sonia , Araújo Wagner L. , Balbo Ilse , Nunes-Nesi Adriano , Maximova Eugenia , Carrari Fernando , Bunik Victoria I. , Persson Staffan , Fernie Alisdair R.
Published: January 2010

Transgenic tomato (Solanum lycopersicum ‘Moneymaker’) plants independently expressing fragments of various genes encoding enzymes of the tricarboxylic acid cycle in antisense orientation have previously been characterized as exhibiting altered root growth. In this study, we evaluate the rates of respiration of roots from these lines in addition to determining their total dry weight accumulation. Given that these features were highly correlated, we decided to carry out an evaluation of the cell wall composition in the transformants that revealed a substantial reduction in cellulose. Since the bulk of cellulose is associated with the secondary cell walls in roots, we reasoned that the transformants most likely were deficient in secondary wall cellulose production. Consistent with these findings, cross-sections of the root collar (approximately 15 mm from the junction between root and stem) displayed reduced lignified secondary cell walls for the transformants. In contrast, cell and cell wall patterning displayed no differences in elongating cells close to the root tip. To further characterize the modified cell wall metabolism, we performed feeding experiments in which we incubated excised root tips in [U-14C]glucose in the presence or absence of phosphonate inhibitors of the reaction catalyzed by 2-oxoglutarate dehydrogenase. Taken together, the combined results suggest that restriction of root respiration leads to a deficit in secondary cell wall synthesis. These data are discussed in the context of current models of biomass partitioning and plant growth.
Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression
Authors: Hajduch Martin , Hearne Leonard B. , Miernyk Jan A. , Casteel Jill E. , Joshi Trupti , Agrawal Ganesh K. , Song Zhao , Zhou Mingyi , Xu Dong , Thelen Jay J.
Published: January 2010

Previous systems analyses in plants have focused on a single developmental stage or time point, although it is often important to additionally consider time-index changes. During seed development a cascade of events occurs within a relatively brief time scale. We have collected protein and transcript expression data from five sequential stages of Arabidopsis (Arabidopsis thaliana) seed development encompassing the period of reserve polymer accumulation. Protein expression profiling employed two-dimensional gel electrophoresis coupled with tandem mass spectrometry, while transcript profiling used oligonucleotide microarrays. Analyses in biological triplicate yielded robust expression information for 523 proteins and 22,746 genes across the five developmental stages, and established 319 protein/transcript pairs for subsequent pattern analysis. General linear modeling was used to evaluate the protein/transcript expression patterns. Overall, application of this statistical assessment technique showed concurrence for a slight majority (56%) of expression pairs. Many specific examples of discordant protein/transcript expression patterns were detected, suggesting that this approach will be useful in revealing examples of posttranscriptional regulation.
BLADE-ON-PETIOLE1 Coordinates Organ Determinacy and Axial Polarity inArabidopsisby Directly Activating ASYMMETRIC LEAVES2
Authors: Jun Ji Hyung , Ha Chan Man , Fletcher Jennifer C.
Published: January 2010

Continuous organ formation is a hallmark of plant development that requires organ-specific gene activity to establish determinacy and axial patterning, yet the molecular mechanisms that coordinate these events remain poorly understood. Here, we show that the organ-specific BTB-POZ domain proteins BLADE-ON-PETIOLE1 (BOP1) and BOP2 function as transcriptional activators during Arabidopsis thaliana leaf formation. We identify as a direct target of BOP1 induction the ASYMMETRIC LEAVES2 (AS2) gene, which promotes leaf cell fate specification and adaxial polarity. We find that BOP1 associates with the AS2 promoter and that BOP1 and BOP2 are required for AS2 activation specifically in the proximal, adaxial region of the leaf, demonstrating a role for the BOP proteins as proximal-distal as well as adaxial-abaxial patterning determinants. Furthermore, repression of BOP1 and BOP2 expression by the indeterminacy-promoting KNOX gene SHOOTMERISTEMLESS is critical to establish a functional embryonic shoot apical meristem. Our data indicate that direct activation of AS2 transcription by BOP1 and BOP2 is vital for generating the conditions for KNOX repression at the leaf base and may represent a conserved mechanism for coordinating leaf morphogenesis with patterning along the adaxial-abaxial and the proximal-distal axes.
The γ -Tubulin Complex Protein GCP4 Is Required for Organizing Functional Microtubule Arrays inArabidopsis thaliana
Authors: Kong Zhaosheng , Hotta Takashi , Lee Yuh-Ru Julie , Horio Tetsuya , Liu Bo
Published: January 2010

Microtubule (MT) nucleation and organization depend on the evolutionarily conserved protein γ -tubulin, which forms a complex with GCP2-GCP6 (GCP for γ -Tubulin Complex Protein). To date, it is still unclear how GCP4-GCP6 (the non-core GCPs) may be involved in acentrosomal MT nucleation in plant cells. We found that GCP4 was associated with γ -tubulin in vivo in Arabidopsis thaliana. When GCP4 expression was repressed by an artificial microRNA, transgenic plants exhibited phenotypes of dwarfism and reduced organ size. In mitotic cells, it was observed that the γ -tubulin signal associated with the mitotic spindle, and the phragmoplast was depleted when GCP4 was downregulated. Consequently, MTs failed to converge at unified spindle poles, and the bipolar phragmoplast MT array frequently had discrete bundles with extended minus ends, resulting in failed cytokinesis as reflected by cell wall stubs in leaf epidermal cells. In addition, cortical MTs in swollen guard cells and pavement cells of the leaf epidermis became hyperparallel and bundled, which was likely caused by frequent MT nucleation with shallow angles on the wall of extant MTs. Therefore, our results support the notion that GCP4 is an indispensable component for the function of γ -tubulin in MT nucleation and organization in plant cells.
The ABORTED MICROSPORES Regulatory Network Is Required for Postmeiotic Male Reproductive Development in Arabidopsis thaliana
Authors: Xu Jie , Yang Caiyun , Yuan Zheng , Zhang Dasheng , Gondwe Martha Y. , Ding Zhiwen , Liang Wanqi , Zhang Dabing , Wilson Zoe A.
Published: January 2010

The Arabidopsis thaliana ABORTED MICROSPORES (AMS) gene encodes a basic helix-loop-helix (bHLH) transcription factor that is required for tapetal cell development and postmeiotic microspore formation. However, the regulatory role of AMS in anther and pollen development has not been fully defined. Here, we show by microarray analysis that the expression of 549 anther-expressed genes was altered in ams buds and that these genes are associated with tapetal function and pollen wall formation. We demonstrate that AMS has the ability to bind in vitro to DNA containing a 6-bp consensus motif, CANNTG. Moreover, 13 genes involved in transportation of lipids, oligopeptides, and ions, fatty acid synthesis and metabolism, flavonol accumulation, substrate oxidation, methyl-modification, and pectin dynamics were identified as direct targets of AMS by chromatin immunoprecipitation. The functional importance of the AMS regulatory pathway was further demonstrated by analysis of an insertional mutant of one of these downstream AMS targets, an ABC transporter, White-Brown Complex homolog, which fails to undergo pollen development and is male sterile. Yeast two-hybrid screens and pull-down assays revealed that AMS has the ability to interact with two bHLH proteins (AtbHLH089 and AtbHLH091) and the ATA20 protein. These results provide insight into the regulatory role of the AMS network during anther development.
Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes
Authors: Mathews Sarah
Published: January 2010

A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red–induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful.
Buying behaviour of consumers for food products in an emerging economy
Authors: Ali Jabir , Kapoor Sanjeev , Moorthy Janakiraman
Published: January 2010

Purpose

The purpose of this paper is to develop a marketing strategy for a modern food/grocery market based on consumer preferences and behaviour.

Design/methodology/approach

A total of 101 households having sufficient purchasing power were personally surveyed with a structured questionnaire. These households are spread across the well‐developed Gomtinagar area of Lucknow city. Simple statistical analysis such as descriptive statistical analysis, frequency distribution, cross tabulation, analysis of variance, and factor analysis to assess the consumers' preferences for food and grocery products and market attributes were carried out.

Findings

The preferences of the consumers clearly indicate their priority for cleanliness/freshness of food products followed by price, quality, variety, packaging, and non‐seasonal availability. The consumers' preference of marketplace largely depends on the convenience in purchasing at the marketplace along with the availability of additional services, attraction for children, basic amenities and affordability. Results suggest that most of the food and grocery items are purchased in loose form from the nearby outlets. Fruits and vegetables are mostly purchased daily or twice a week due to their perishable nature, whereas grocery items are less frequently purchased.

Research limitations/implications

This paper analyses the buying behaviour of the consumers under survey with respect to food and grocery items. These consumers are in a relatively advantageous position in terms of purchasing power and awareness of health and nutrition.

Practical implications

The results may help the food processors and outlet owners to understand a diversified set of preferences for products and market attributes, so that they can make better decisions in the emerging organized food and grocery retail environment.

Originality/value

The topic is relatively less researched in emerging markets especially where organized retail is still in its early stages.
Evaluation of food purchasing behaviour of consumers from supermarkets
Authors: Sanlier Nevin , Seren Karakus Suzan
Published: January 2010

Purpose

This study was conducted with the aim of determining the food purchasing behaviour of consumers from supermarkets.

Design/methodology/approach

A total of 430 consumers, 194 males and 236 females, with an average age of 29.96 ±10.99 were included in this study, and was conducted to find out the criteria which consumers took into account while purchasing food.

Findings

A significant relationship was determined between the scores the consumers received from nutrition, the reliability and all of the shopping criteria, and their level of education (p < 0.05) between the percentage of income spared for nutrition (p < 0.01) and between the cost (p < 0.05) and the total scores received from all of the shopping criteria (p < 0.01). It was also determined that women paid more attention to the nutrition and reliability criteria than men did (p < 0.05).

Research limitations/implications

The research is restricted in so far as it only considers consumers in the big city and as it is an exploratory study the research is limited in so far as the number of participants is only 430. Further research needs to include other big and small cities.

Practical implications

The study has concluded that consumers need effective and versatile education in the subjects of label reading and buying the right kind of food for their budgets. It is revealed that consumer education is essential in the process from cradle to grave in creating the awareness of consumers to buy food.

Originality/value

The paper is useful to both practitioners and academics in the fields of relationship consumer and marketing. Informing and training consumers will help increase the awareness of consumers and make them behave more rationally in their shopping. It will lead the studies to be carried out in the future to activate the control of the consumers on their shopping, instead of losing the control of consumers.
How “green” are small wineries? Western Australia's case
Authors: Duarte Alonso Abel
Published: January 2010

Purpose

In the wake of growing concerns about environmental issues in rural areas, some studies present environmental stewardship as a positive way for food producing businesses to benefit from consumer groups receptive to environmentally friendly growing practices. However, very little is reported on how winery operators, including those of small wineries, go about addressing environmental sustainability. The present exploratory study seeks to broaden the understanding of this area from a group of small winery operators from emerging Western Australian wine regions.

Design/methodology/approach

A qualitative approach in the form of face‐to‐face and telephone interviews among 42 participating wineries was chosen for this exploratory study.

Findings

While participants' comments suggest they are currently involved in different ways to be environmentally sustainable, the study also identifies environmental threats affecting some winery operators severely. Such issues include latent water concerns and government agencies' action in the form of forest fires near vineyards that can cause great losses to winery entrepreneurs.

Research limitations/implications

Despite several useful insights identified in this study, with an excess of over 200 small wineries in Western Australia, the limited number of participating businesses may not allow for making generalisations about the state's or nation's wine industry.

Practical implications

Some of the issues identified in this study illustrate that it is not only up to wineries to follow environmentally friendly initiatives. Moreover, such issues need to be addressed to guarantee support for the industry in areas where climatic issues or human action pose potential threats.

Originality/value

The study examines environmental sustainability from small winery operators' perspective, a dimension that to date has been under researched, particularly in Western Australia.
Traceability as part of competitive strategy in the fruit supply chain
Authors: Canavari Maurizio , Centonze Roberta , Hingley Martin , Spadoni Roberta
Published: January 2010

Purpose

The paper aims to focus on traceability as part of information management in the fruit supply chains of Emilia‐Romagna, Italy. A review of the rules in use for traceability distinguishes between baseline traceability and traceability plus (T+), which encompasses many further embedded value attributes.

Design/methodology/approach

The paper takes the form of a qualitative study involving in‐depth interviews with key informants in the Italian fresh produce chain.

Findings

Findings are discussed in terms of different themes including identification of three distinct types of supply chains and the impact upon them and categorisation of traceability systems across the different chains. Identified are the impact of information systems management; purchasing management; product management transaction costs; and co‐ordination issues.

Research limitations/implications

The study's findings are based on Italian fresh produce traceability context only.

Practical implications

Elements of competitive strategy are considered in the analysis of fruit supply chains of Emilia‐Romagna, to demonstrate that not only strategic, but also operative choices determine the way a single firm or supply network manages traceability and information issues. Applications of such elements to buyer and seller selection as well as to competing retailers of the fruit supply chain, verify the hypothesis.

Originality/value

The paper adds to the body of knowledge surrounding prior studies on the development of traceability systems and develops further the analysis of legal and value‐adding dimensions of traceability.
Implementing traceability: practical challenges at a mineral water bottling plant
Authors: Mari Karlsen Kine , Olsen Petter , Anne‐Marie Donnelly Kathryn
Published: January 2010

Purpose

The purpose of this study is to examine where product, process and traceability information is systematically lost at a mineral water bottling plant. It aims to highlight areas where traceability could be improved and to suggest changes that could be made to improve traceability. It also aims to examine the implications of these changes for the current system.

Design/methodology/approach

Process mapping was carried out at a mineral water bottling plant to investigate the flow of material and information. The results were analyzed to identify the critical traceability points (CTPs) in the production process where information is lost.

Findings

One of the CTPs at the mineral water bottling plant was the lack of a link between product, process and traceability information for the screw caps.

Research limitations/implications

This is a study of an individual case, which limits the generalizations that can be made.

Practical implications

Procedures need to be established at the mineral water bottling plant in order to achieve traceability. All the information about the resources used in production could be linked to a “best before” date on each mineral water bottle.

Originality/value

The authors have found few similar case studies in the published literature. This case study can be of value to other research institutes and industries where the focus is on traceability. It could also be of interest to researchers working with information technology systems, ontology/metadata schemes, cost/benefits analyses and the impacts of traceability. The implications of traceability highlighted in this paper can be of use to regulatory authorities in their decision making processes.
Food fraud – a current issue but an old problem
Authors: Shears Peter
Published: January 2010

Purpose

The purpose of this paper is to address the topic of food fraud which has been so widely and variously reported over recent months and years. Its purposes are to set current experience into an historical context and to illustrate the tension between the science of deception and the science of detection.

Design/methodology/approach

This is a desk study of published literature and historical documentation, together with interviews with those professionally concerned with detection and enforcement.

Findings

The piece concludes that with all the scientific developments and analytical techniques that seem so mind‐bendingly sophisticated, there remains the basic problem of a lack of resources.

Practical implications

It is asserted that more is owed to the memories and the reputations of those who pioneered the effort to combat food fraud. Without a considerable increase in the resources made available for the appliance of the science currently available and that being developed, the battle will never be fully engaged, yet alone won.

Originality/value

This review is unique in that it seeks to take a long view of current concern, and even scandal, showing that the situation is not new and lessons should have been learned from past experience.
Effective global leadership requires a global mindset
Authors: Cohen Stephen L.
Published: January 2010

Purpose

The purpose of the paper is to conduct a global literature review and develop a viewpoint on the most critical success factors required to develop a global leadership mindset.

Design/methodology/approach

The paper takes the form of a global literature review and the author's viewpoint.

Findings

Global leadership development must be driven by an organization's global business strategy. Having “global” experiences at work does not guarantee effective global leadership. The acquisition of a true global mindset enables leadership effectiveness in a global capacity. As cultural and business complexity increase so does the demand for a global mindset, almost exponentially given the intersect of this complex environment.

Practical implications

Methods for global leadership development include examination, education, experience and exposure.

Originality/value

The paper provides a fresh perspective.
Role of HR in the new world of sustainability
Authors: Rimanoczy Isabel , Pearson Tony
Published: January 2010

Purpose

The purpose of the paper is to assess the strategic role that the human resource department (HRD) can play in the development and implementation of an organization's sustainability program.

Design/methodology/approach

The paper reviews the environmental and social challenges that give rise to sustainability efforts, and outlines areas of potential benefit to an organization of the efforts.

Findings

The article posits that such programs require change in organizational culture, which in turn demands new leadership competencies, behaviors and mindsets. It instances the action reflection learning (ARL) learning methodology and its project‐based programs as proven means for developing those competencies through collaborative teamwork and specific learning goals.

Originality/value

The paper proposes that HRD is uniquely positioned to support the organization's sustainability goals of profit, people and planet, while retaining its competitive advantage.