bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial localization and structure-based phosphate activation mechanism of Glutaminase C with implications for cancer metabolism
Authors: Cassago Alexandre , Ferreira Amanda P. S. , Ferreira Igor M. , Fornezari Camila , Gomes Emerson R. M. , Greene Kai Su , Pereira Humberto M. , Garratt Richard C. , Dias Sandra M. G. , Ambrosio Andre L. B.
Published: January 2012

Glutamine is an essential nutrient for cancer cell proliferation, especially in the context of citric acid cycle anaplerosis. In this manuscript we present results that collectively demonstrate that, of the three major mammalian glutaminases identified to date, the lesser studied splice variant of the gene
gls
, known as Glutaminase C (GAC), is important for tumor metabolism. We show that, although levels of both the kidney-type isoforms are elevated in tumor vs. normal tissues, GAC is distinctly mitochondrial. GAC is also most responsive to the activator inorganic phosphate, the content of which is supposedly higher in mitochondria subject to hypoxia. Analysis of X-ray crystal structures of GAC in different bound states suggests a mechanism that introduces the tetramerization-induced lifting of a “gating loop” as essential for the phosphate-dependent activation process. Surprisingly, phosphate binds inside the catalytic pocket rather than at the oligomerization interface. Phosphate also mediates substrate entry by competing with glutamate. A greater tendency to oligomerize differentiates GAC from its alternatively spliced isoform and the cycling of phosphate in and out of the active site distinguishes it from the liver-type isozyme, which is known to be less dependent on this ion.
Drosophila
RNA polymerase III repressor Maf1 controls body size and developmental timing by modulating tRNA
i
Met
synthesis and systemic insulin signaling
Authors: Rideout Elizabeth J. , Marshall Lynne , Grewal Savraj S.
Published: January 2012

The target-of-rapamycin pathway couples nutrient availability with tissue and organismal growth in metazoans. The key effectors underlying this growth are, however, unclear. Here we show that Maf1, a repressor of RNA polymerase III-dependent tRNA transcription, is an important mediator of nutrient-dependent growth in
Drosophila
. We find nutrients promote tRNA synthesis during larval development by inhibiting Maf1. Genetic inhibition of Maf1 accelerates development and increases body size. These phenotypes are due to a non–cell-autonomous effect of Maf1 inhibition in the fat body, the main larval endocrine organ. Inhibiting Maf1 in the fat body increases growth by promoting the expression of brain-derived insulin-like peptides and consequently enhanced systemic insulin signaling. Remarkably, the effects of Maf1 inhibition are reproduced in flies carrying one extra copy of the initiator methionine tRNA, tRNA
i
Met
. These findings suggest the stimulation of tRNA
i
Met
synthesis via inhibition of dMaf1 is limiting for nutrition-dependent growth during development.
Policy Risk in the Canadian Dairy Industry
Authors: Nogueira Lia , Barichello Richard R. , Baylis Kathy , Chouinard Hayley H.
Published: January 2012

Canadian dairy farmers purchase a marketing quota through the Provincial Marketing Boards to sell milk in Canada. That quota captures rents created by regulations and is subject to policy risk. We define policy risk as the farmers' expectation that quota rents will decline or disappear over time. We calculate the effect of perceived policy risk to determine whether the Uruguay Round Agreement affected the amount of protection given to farmers. Calculated policy risk ranged from 14‐29%. Policy risk increased in the years leading up to the Uruguay Round Agreement, but decreased after the WTO was established and remains at a historic low.
Lack of Indinavir Effects on Methadone Disposition Despite Inhibition of Hepatic and Intestinal Cytochrome P4503A (CYP3A)
Authors: Kharasch Evan D. , Bedynek Pamela Sheffels , Hoffer Christine , Walker Alysa , Whittington Dale
Published: January 2012

Background

Methadone disposition and pharmacodynamics are highly susceptible to interactions with antiretroviral drugs. Methadone clearance and drug interactions have been attributed to cytochrome P4503A4 (CYP3A4), but actual mechanisms are unknown. Drug interactions can be clinically and mechanistically informative. This investigation assessed effects of the protease inhibitor indinavir on methadone pharmacokinetics and pharmacodynamics, hepatic and intestinal CYP3A4/5 activity (using alfentanil), and intestinal transporter activity (using fexofenadine).

Methods

Twelve healthy volunteers underwent a sequential crossover. On three consecutive days they received oral alfentanil plus fexofenadine, intravenous alfentanil, and intravenous plus oral (deuterium-labeled) methadone. This was repeated after 2 weeks of indinavir. Plasma and urine analytes were measured by mass spectrometry. Opioid effects were measured by miosis.

Results

Indinavir significantly inhibited hepatic and first-pass CYP3A activity. Intravenous alfentanil systemic clearance and hepatic extraction were reduced to 40-50% of control, apparent oral clearance to 30% of control, and intestinal extraction decreased by half, indicating 50% and 70% inhibition of hepatic and first-pass CYP3A activity. Indinavir increased fexofenadine area under the plasma concentration-time curve 3-fold, suggesting significant P-glycoprotein inhibition. Indinavir had no significant effects on methadone plasma concentrations, methadone N-demethylation, systemic or apparent oral clearance, renal clearance, hepatic extraction or clearance, or bioavailability. Methadone plasma concentration-effect relationships were unaffected by indinavir.

Conclusions

Despite significant inhibition of hepatic and intestinal CYP3A activity, indinavir had no effect on methadone N-demethylation and clearance, suggesting little or no role for CYP3A in clinical disposition of single-dose methadone. Inhibition of gastrointestinal transporter activity had no influence of methadone bioavailability.
Impaired Nociception and Peripheral Opioid Antinociception in Mice Lacking Both Kinin B1 and B2 Receptors
Authors: Cayla Cecile , Labuz Dominika , Machelska Halina , Bader Michael , Schäfer Michael , Stein Christoph
Published: January 2012

Background

Kinins (e.g., bradykinin) acting through the constitutively expressed B2 and the injury-induced B1 receptors are involved in pain and hyperalgesia, as previously shown by use of receptor-selective antagonists and single-receptor knockout models. Because the overall contribution of kinins to painful processes remains unclear, the aim of this study was to analyze pain-related behaviors of mice unable to respond to kinins because of a lack of both B1 and B2 receptors.

Methods

In knockout mice lacking both B1 and B2 receptors and in wild-type mice (n = 8-21 per group) the authors assessed nociceptive thresholds to mechanical and heat stimuli (von Frey and Hargreaves tests, respectively) in healthy animals and after induction of inflammatory and neuropathic pain, acid-induced visceral nociception, and modulation of nociceptive responses by peripherally administered opioid agonists.

Results

In knockout mice lacking both B1 and B2 receptors baseline nociceptive responses to heat were unaltered, nocifensive responses to bradykinin were abolished, acute acetic acid-induced visceral nociception was reduced by approximately 70% (mean difference: 19.5 writhes/30 min) and heat hypersensitivity in carrageenan-induced paw inflammation was decreased 48 h after injection (mean difference 2.88 s), hypersensitivities in chronic complete Freund's adjuvant-induced paw inflammation or after chronic constriction injury of the sciatic nerve were unchanged, and peripheral μ- and δ-opioid-induced analgesia after chronic constriction injury was reduced by 30-35% (mean differences: μ-agonist: 0.495 g, δ-agonist: 0.555 g).

Conclusions

These data suggest that kinins are important for nociception associated with acute short-lasting inflammation but are less essential in chronic stages of pain. The results also highlight a new protective function of kinins via interactions with the opioid system.
Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant
Authors: Srinivasan Sathiyaraj , Park Giho , Yang Hyejin , Hwang Supyong , Bae Yoonjung , Jung Yong-An , Kim Myung Kyum , Lee Myungjin
Published: January 2012

A Gram-stain-positive, strictly aerobic, short-rod-shaped, non-motile strain (designated MJ32T) was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ32T. Strain MJ32T showed highest 16S rRNA gene sequence similarity to

Gordonia hirsuta

DSM 44140T (98.1 %) and

Gordonia hydrophobica

DSM 44015T (97.0 %); levels of sequence similarity to the type strains of other recognized

Gordonia

species were less than 97.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ32T belonged to the clade formed by members of the genus

Gordonia

in the family

Gordoniaceae

. The G+C content of the genomic DNA of strain MJ32T was 69.2 mol%. Chemotaxonomically, strain MJ32T showed features typical of the genus

Gordonia

. The predominant respiratory quinone was MK-9(H2), the mycolic acids present had C56–C60 carbon atoms, and the major fatty acids were C16 : 0 (34.6 %), tuberculostearic acid (21.8 %), C16 : 1ω7c (19.5 %) and C18 : 1ω9c (12.7 %). The peptidoglycan type was based on meso-2,6-diaminopimelic acid as the diagnostic diamino acid with glycolated sugars. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ32T is considered to represent a novel species of the genus

Gordonia

, for which the name Gordonia caeni sp. nov. is proposed. The type strain is MJ32T ( = KCTC 19771T = JCM 16923T).
Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov.
Authors: Gutierrez Tony , Green David H. , Whitman William B. , Nichols Peter D. , Semple Kirk T. , Aitken Michael D.
Published: January 2012

A strictly aerobic, halotolerant, Gram-stain-negative, rod-shaped bacterium, designated strain DG1253T, was isolated from a laboratory culture of the marine dinoflagellate Lingulodinium polyedrum (CCAP 1121/2). The strain was able to degrade two- and three-ring polycyclic aromatic hydrocarbons. It exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain DG1253T was Q-8. The fatty acid profile was dominated by C18 : 1ω7c. The mean DNA G+C content of strain DG1253T was 63.6±0.25 mol%. 16S rRNA gene sequence analysis placed this organism within the order

Xanthomonadales

of the class

Gammaproteobacteria

. Its closest relatives included representatives of the

Hydrocarboniphaga

–

Nevskia

–

Sinobacter

clade (≤89.9 % 16S rRNA gene sequence similarity) in the family

Sinobacteraceae

. On the basis of distinct phenotypic and genotypic characteristics, strain DG1253T is considered to represent a novel species of a new genus in the class

Gammaproteobacteria

, for which the name Algiphilus aromaticivorans gen. nov., sp. nov. is proposed. The type strain of the type species, Algiphilus aromaticivorans, is DG1253T ( = ATCC BAA-2243T = DSM 24793T). In addition, a new family, Algiphilaceae fam. nov., is proposed to accommodate the genus Algiphilus.
Rhodanobacter caeni sp. nov., isolated from sludge from a sewage disposal plant
Authors: Woo Sung-Geun , Srinivasan Sathiyaraj , Kim Myung Kyum , Lee Myungjin
Published: January 2012

Two Gram-reaction-negative, motile bacteria, designated strains MJ01T and MJ14, were isolated from sludge collected from the Daejeon sewage disposal plant in South Korea. The taxonomic positions of both strains were determined using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strains MJ01T and MJ14 appeared indistinguishable and to be most closely related to members of the genus

Rhodanobacter

in the family

Xanthomonadaceae

of the

Gammaproteobacteria

(96.4–98.8 % sequence similarity). Strain MJ01T exhibited a relatively high level of DNA–DNA relatedness with strain MJ14 (89.3 %) but relatively low DNA–DNA relatedness values with established species in the genus

Rhodanobacter

(<60 %). The genomic DNA G+C contents of strains MJ01T and MJ14 were 65.3 and 64.8 mol%, respectively. The major respiratory quinone of both novel strains was the ubiquinone Q-8. The major fatty acids of both strains were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c, and the polar lipid profiles of the two strains contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and minor amounts of unidentified aminophospholipids and phospholipids. Based on the phenotypic, genotypic and phylogenetic evidence, strains MJ01T and MJ14 represent a single novel species in the genus

Rhodanobacter

, for which the name Rhodanobacter caeni sp. nov. is proposed. The type strain is MJ01T ( = KCTC 22449T = JCM 16242T), with MJ14 ( = KCTC 22460 = JCM 16243) as a reference strain.
Lachnoanaerobaculum gen. nov., a new genus in the

Lachnospiraceae

: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of

Eubacterium saburreum

(Prévot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.
Authors: Hedberg Maria E. , Moore Edward R. B. , Svensson-Stadler Liselott , Hörstedt Per , Baranov Vladimir , Hernell Olle , Wai Sun Nyunt , Hammarström Sten , Hammarström Marie-Louise
Published: January 2012

Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3 : 22T and N1T) are described. Strain CD3 : 22T was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1T from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H2S, NH3, butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98 % sequence similarity) between the two isolates, as well as the type strain of

Eubacterium saburreum

and four other

Lachnospiraceae

bacterium-/

E. saburreum

-like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family

Lachnospiraceae

. While

Eubacterium

species are reported to be non-spore-forming, reanalysis of

E. saburreum

CCUG 28089T confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3 : 22T and N1T represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family

Lachnospiraceae

[within the order

Clostridiales

, class

Clostridia

, phylum

Firmicutes

]. Strain CD3 : 22T ( = CCUG 58757T  = DSM 23576T) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1T ( = CCUG 60305T = DSM 24553T) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover,

Eubacterium saburreum

is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089T  = ATCC 33271T  = CIP 105341T  = DSM 3986T  = JCM 11021T  = VPI 11763T).
Mucilaginibacter litoreus sp. nov., isolated from marine sand
Authors: Yoon Jung-Hoon , Kang So-Jung , Park Sooyeon , Oh Tae-Kwang
Published: January 2012

A Gram-staining-negative, non-spore-forming, facultatively anaerobic, non-flagellated, non-gliding, rod-shaped bacterium, designated strain BR-18T, was isolated from marine sand collected on the western coast of South Korea. The taxonomic position of the novel strain was determined using a polyphasic approach. Strain BR-18T grew optimally at 25 °C, at pH 6.5–7.0 and in the absence of NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, the novel strain fell within a clade comprising members of the genus

Mucilaginibacter

and appeared most closely related to

Mucilaginibacter lutimaris

BR-3T (96.6 % sequence similarity) and

Mucilaginibacter rigui

WPCB133T (95.9 %). The novel strain showed lower levels of 16S rRNA gene sequence similarity with the type strains of other members of the genus

Mucilaginibacter

(93.4–95.5 %) and those of other species included in the phylogenetic analyses (<91.6 %). Strain BR-18T contained MK-7 as its predominant menaquinone, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C15 : 0 as its major fatty acids, phosphatidylethanolamine and an unidentified aminophospholipid as its major polar lipids, and sphingolipids. The genomic DNA G+C content of the novel strain was 42.4 mol%. Based on the phylogenetic and phenotypic data, strain BR-18T represents a novel species of the genus

Mucilaginibacter

, for which the name Mucilaginibacter litoreus sp. nov. is proposed. The type strain is BR-18T ( = KCTC 23697T  = CCUG 61484T).
Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite
Authors: Schumann Peter , Zhang De-Chao , Redzic Mersiha , Margesin Rosa
Published: January 2012

A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25T, was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1–15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25T belonged to the family

Microbacteriaceae

and showed highest 16S rRNA gene sequence similarity with

Klugiella xanthotipulae

44C3T (97.0 %). However, strain Cr8-25T could be differentiated from the type strain of

K. xanthotipulae

on the level of genomospecies by a DNA–DNA relatedness value of only 37.2 %. Strain Cr8-25T contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25T were C15 : 0 anteiso (64.6 %) and iso-C16 : 0 (22.5 %) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA–DNA relatedness data, strain Cr8-25T represents a novel species of a new genus in the family

Microbacteriaceae

, for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25T ( = DSM 23737T = LMG 26215T).
Arthrobacter cupressi sp. nov., an actinomycete isolated from the rhizosphere soil of Cupressus sempervirens
Authors: Zhang Jian , Ma Yuchao , Yu Huimin
Published: January 2012

An actinobacterial strain, designated D48T, was isolated from the rhizosphere soil of a cypress tree collected from Mianyang in Sichuan province, China. The strain was Gram-stain-positive, catalase-positive, oxidase-negative and non-motile, with lysine as the peptidoglycan diagnostic diamino acid and acetyl as the peptidoglycan acyl type. The predominant menaquinone was MK-9(H2); small amounts of MK-7(H2), MK-10(H2) and MK-6 were also present. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The isolate underwent a rod–coccus morphological cycle, had a high DNA G+C content, was aerobic and grew between 12 and 37 °C (optimum, 28 °C). On the basis of the phenotypic and chemotaxonomic analyses, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, the isolate represents a novel species of the genus

Arthrobacter

, for which the name Arthrobacter cupressi sp. nov. is proposed. The type strain is D48T ( = DSM 24664T = CGMCC 1.10783T).
Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii
Authors: Lee Jina , Whon Tae Woong , Shin Na-Ri , Roh Seong Woon , Kim Jandi , Park Seong-Kyu , Kim Min-Soo , Shin Kee-Sun , Lee Jung-Sook , Lee Keun Chul , Kim Young-Ok , Bae Jin-Woo
Published: January 2012

A slightly halophilic, Gram-negative, strictly aerobic, non-motile rod, designated TW15T, was isolated from an ark clam in South Korea. Growth occurred at 10–37 °C, with 1–5 % (w/v) NaCl and at pH 7.0–10.0. Optimal growth occurred at 25–30 °C, with 2 % (w/v) NaCl and at pH 8.0. Strain TW15T exhibited both oxidase and catalase activities. The major fatty acids of strain TW15T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The polar lipids of strain TW15T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and five unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TW15T was most closely related to

Ruegeria lacuscaerulensis

DSM 11314T (98.0 % 16S rRNA gene sequence similarity). DNA–DNA relatedness with closely related strains was <52±3 %. The DNA G+C content was 55.7 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain TW15T represents a novel species of the genus

Ruegeria

, for which the name Ruegeria conchae sp. nov. is proposed. The type strain is TW15T ( = KACC 15115T  = JCM 17315T).
Actibacterium mucosum gen. nov., sp. nov., a marine alphaproteobacterium from Mediterranean seawater
Authors: Lucena Teresa , Ruvira María A. , Garay Esperanza , Macián M. Carmen , Arahal David R. , Pujalte María J.
Published: January 2012

Strain R46T, a marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. It is an aerobic chemo-organotrophic, mesophilic and slightly halophilic organism, with complex ionic requirements. Phylogenetic analyses based on the 16S rRNA and gyrB gene sequences showed that strain R46T formed a separate branch within the family

Rhodobacteraceae

, bearing similarities below 94.7 and 80.3 %, respectively, to any other recognized species. It contained Q10 as the predominant isoprenoid quinone and C18 : 1ω7c/C18 : 1ω6c as the major cellular fatty acid. Phosphatidylglycerol was the only identified polar lipid, although other lipids were also detected. The DNA G+C content of the genomic DNA was 61.3 mol%. On the basis of extensive phenotypic and phylogenetic comparative analysis, it is concluded that the strain represents a novel genus and species, for which the name Actibacterium mucosum gen. nov., sp. nov. is proposed. The type strain of the type species is Actibacterium mucosum R46T ( = CECT 7668T = KCTC 23349T).
Mesorhizobium muleiense sp. nov., nodulating with Cicer arietinum L.
Authors: Zhang Jun Jie , Liu Tian Yan , Chen Wen Feng , Wang En Tao , Sui Xin Hua , Zhang Xiao Xia , Li Yán , Li Yàn , Chen Wen Xin
Published: January 2012

Three chickpea rhizobial strains (CCBAU 83963T, CCBAU 83939 and CCBAU 83908), which were identified previously as representing a distinctive genospecies, were further studied here and compared taxonomically with related species in the genusMesorhizobium. Results from SDS-PAGE of whole-cell soluble proteins revealed differences from closely related recognized species of the genusMesorhizobium. Levels of DNA–DNA relatedness were 15.28–50.97 % between strain CCBAU 83963Tand the type strains of recognizedMesorhizobiumspecies (except forMesorhizobium thiogangeticum). Strain CCBAU 83963Tcontained fatty acids characteristic of members of the genusMesorhizobium, but it possessed high concentrations of C19 : 0cyclo ω8cand iso-C17 : 0. Strain CCBAU 83963Thad phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids, and an ornithine-containing lipid, phosphatidyl-N-dimethylethanolamine and cardiolipin as minor components. Nodulation tests demonstrated the distinct symbiotic character of strain CCBAU 83963T; onlyCicer arietinum, its host plant, could be invaded to form effective nitrogen-fixing nodules. The narrow spectrum of utilization of sole carbon sources, lower resistance to antibiotics, and NaCl, pH and temperature growth ranges differentiated these novel rhizobia from recognized species of the genusMesorhizobium. Based on the data presented, the three novel rhizobial strains are considered to represent a novel species of the genusMesorhizobium, for which the nameMesorhizobium muleiensesp. nov. is proposed. The type strain is CCBAU 83963T( = HAMBI 3264T = CGMCC 1.11022T).
Candida adriatica sp. nov. and Candida molendinolei sp. nov., two yeast species isolated from olive oil and its by-products
Authors: Čadež Neža , Raspor Peter , Turchetti Benedetta , Cardinali Gianluigi , Ciafardini Gino , Veneziani Gianluca , Péter Gábor
Published: January 2012

Thirteen strains isolated from virgin olive oil or its by-products in several Mediterranean countries were found to be phenotypically and genetically divergent from currently recognized yeast species. Sequence analysis of the large subunit (LSU) rDNA D1/D2 domain and internal transcribed spacer regions/5.8S rDNA revealed that the strains represented two novel species described as Candida adriatica sp. nov. (type strain ZIM 2334T = CBS 12504T = NCAIM Y.02001T) and Candida molendinolei sp. nov. (type strain DBVPG 5508T = CBS 12508T = NCAIM Y.02000T). Phylogenetic analysis based on concatenated sequences of the small subunit rRNA gene, the D1/D2 region of the LSU rDNA and the translation elongation factor-1α gene suggested that C. adriatica sp. nov. and C. molendinolei sp. nov. should be placed within the Lindnera and Nakazawaea clades, respectively.
Reclassification and emended description of

Caulobacter leidyi

as Sphingomonas leidyi comb. nov., and emendation of the genus

Sphingomonas
Authors: Chen Hong , Jogler Mareike , Rohde Manfred , Klenk Hans-Peter , Busse Hans-Jürgen , Tindall Brian J. , Spröer Cathrin , Overmann Jörg
Published: January 2012

‘

Caulobacter leidyi

’ DSM 4733T has been shown to be affiliated with the family

Sphingomonadaceae

instead of the

Caulobacteraceae

, and due to its poor characterization has been omitted from the current edition of Bergey’s Manual of Systematic Bacteriology and removed to limbo. We isolated a novel sphingoglycolipid-containing dimorphic prosthecate bacterium, designated strain 247, from a pre-alpine freshwater lake. Strain 247 and ‘

Caulobacter leidyi

’ DSM 4733T were characterized in detail. The rod-shaped cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive, and formed a stalk or polar flagellum. Both strains grew optimally at 28–30 °C, and pH 6.0–8.0. The major fatty acids were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. C14 : 0 2-OH represents the major 2-hydroxy fatty acid. Q-10 was the major respiratory quinone and the major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, three glycolipids, two phosphoaminolipids and two unidentified sphingoglycolipids. The major polyamine was sym-homospermidine. The G+C content of genomic DNA of strains 247 and DSM 4733T was 67.6 mol% and 67.0 mol%, respectively. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization, strains DSM 4733T and 247 were phylogenetically closely related (99.6 % 16S rRNA gene sequence similarity, 82.9 % DNA–DNA hybridization value) and affiliated to the genus

Sphingomonas

. The closest recognized species was

Sphingomonas aquatilis

DSM 15581T (98.1 % sequence similarity). In addition, the presence of cystine arylamidase, absence of β-galactosidase, and the inability to utilize l-arabinose, galactose and sucrose distinguished strains DSM 4733T and 247 from most other members of the family

Sphingomonadaceae

. So far, the dimorphic life cycle that involves a prosthecate and a flagellated stage is unique for strains DSM 4733T and 247 among all members of the family

Sphingomonadaceae

. Therefore,

Caulobacter leidyi

is reclassified as Sphingomonas leidyi, with the type strain DSM 4733T ( = ATCC 15260T = CIP 106443T = VKM B-1368T) and strain 247 (DSM 25078 = LMG 26658) as an additional strain of this species.
Arabidopsis ETR1 and ERS1 Differentially Repress the Ethylene Response in Combination with Other Ethylene Receptor Genes
Authors: Liu Qian , Wen Chi-Kuang
Published: January 2012

The ethylene response is negatively regulated by a family of five ethylene receptor genes in Arabidopsis (Arabidopsis thaliana). The five members of the ethylene receptor family can physically interact and form complexes, which implies that cooperativity for signaling may exist among the receptors. The ethylene receptor gene mutations etr1-1  (  C65Y  )(for ethylene response1-1), ers1-1  (  I62P  ) (for ethylene response sensor1-1), and ers1C65Y are dominant, and each confers ethylene insensitivity. In this study, the repression of the ethylene response by these dominant mutant receptor genes was examined in receptor-defective mutants to investigate the functional significance of receptor cooperativity in ethylene signaling. We showed that etr1-1  (  C65Y  ), but not ers1-1  (  I62P  ), substantially repressed various ethylene responses independent of other receptor genes. In contrast, wild-type receptor genes differentially supported the repression of ethylene responses by ers1-1  (  I62P  ); ETR1 and ETHYLENE INSENSITIVE4 (EIN4) supported ers1-1  (  I62P  ) functions to a greater extent than did ERS2, ETR2, and ERS1. The lack of both ETR1 and EIN4 almost abolished the repression of ethylene responses by ers1C65Y, which implied that ETR1 and EIN4 have synergistic effects on ers1C65Y functions. Our data indicated that a dominant ethylene-insensitive receptor differentially repressed ethylene responses when coupled with a wild-type ethylene receptor, which supported the hypothesis that the formation of a variety of receptor complexes may facilitate differential receptor signal output, by which ethylene responses can be repressed to different extents. We hypothesize that plants can respond to a broad ethylene concentration range and exhibit tissue-specific ethylene responsiveness with differential cooperation of the multiple ethylene receptors.
Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean
Authors: Du Jianchang , Tian Zhixi , Sui Yi , Zhao Meixia , Song Qijian , Cannon Steven B. , Cregan Perry , Ma Jianxin
Published: January 2012

The evolutionary forces that govern the divergence and retention of duplicated genes in polyploids are poorly understood. In this study, we first investigated the rates of nonsynonymous substitution (Ka) and the rates of synonymous substitution (Ks) for a nearly complete set of genes in the paleopolyploid soybean (Glycine max) by comparing the orthologs between soybean and its progenitor species Glycine soja and then compared the patterns of gene divergence and expression between pericentromeric regions and chromosomal arms in different gene categories. Our results reveal strong associations between duplication status and Ka and gene expression levels and overall low Ks and low levels of gene expression in pericentromeric regions. It is theorized that deleterious mutations can easily accumulate in recombination-suppressed regions, because of Hill-Robertson effects. Intriguingly, the genes in pericentromeric regions—the cold spots for meiotic recombination in soybean—showed significantly lower Ka and higher levels of expression than their homoeologs in chromosomal arms. This asymmetric evolution of two members of individual whole genome duplication (WGD)-derived gene pairs, echoing the biased accumulation of singletons in pericentromeric regions, suggests that distinct genomic features between the two distinct chromatin types are important determinants shaping the patterns of divergence and retention of WGD-derived genes.
Valproate in acute mania: is our practice evidence based?
Authors: Vasudev Kamini , Mead Anna , Macritchie Karine , Young Allan H.
Published: January 2012

Purpose

This audit was conducted on acute psychiatric in‐patient wards with the aim of establishing if valproate prescribing in acute mania followed evidence‐based guidelines with particular emphasis on formulations used and whether accelerated valproate dosing was employed.

Design/methodology/approach

Case notes from 43 (42 percent male) patients admitted with mania and subsequently discharged on valproate were reviewed. Valproate formulation, weight measurement (necessary for dose‐calculation in accelerated dosing), initial valproate dose and increments, serum valproate monitoring and other prescribed psychotropic agents were noted.

Findings

Most (95 percent) patients received sodium valproate (epilim chrono/generic), the remaining received valproate semi‐sodium (depakote). All but one patient received antipsychotic medication in combination. Weight was recorded in only four (9 percent) patients. The mean valproate daily dose after the first week was 1,027 mg (sd=408). It took 29 (sd=42) days to reach the maximum daily dose (1,426 mg sd=467) from valproate initiation. Serum levels were monitored in 34 (79 percent) cases, but the mean period between valproate initiation to the first serum level test was 38 (sd=47) days. A significant positive correlation was found between days taken to reach maximum dose and hospital stay (Spearman's rho=0.41, n=43, p=0.006, two‐tailed).

Practical implications

Accelerated valproate dosing was not common practice, which may have resulted in suboptimal efficacy, probably leading to combination treatment.

Originality/value

This study highlights the need for adequate initial dosing and dose increments when treating manic patients and suggests current practice is not evidence‐based. Local prescribing policy and national guidelines' influence on practice are discussed.
The two‐week rule for suspected colorectal cancer
Authors: Ndukwe Nenna , Borowski David W. , Lee Angela , Orr Anne , Dexter‐Smith Sarah , Agarwal Anil K.
Published: January 2012

Purpose

There has been considerable interest in the “two‐week rule” referral pathway efficacy for patients with suspected colorectal cancer. This study aims to explore the psychological impact on these patients.

Design/methodology/approach

Consecutive patients referred for urgent investigations under the “two‐week rule” were invited to take part in semi‐structured interviews using interpretative phenomenological analysis (IPA). Interviews were audio‐taped, transcribed verbatim and analysed using investigator triangulation to enhance data trustworthiness.

Findings

Ten out of 23 (43.5 per cent) patients consented to interviews; none were diagnosed with cancer. Four super‐ordinate themes were explored, referring to the “making sense of the threat to health”, impact on self, impact on others, reflections on the “two‐week rule” referral, and its investigative process. Participants reported their anxiety, fear, vulnerability and coping mechanisms, but also raised concerns about the communication received during the “two‐week rule” referral process. Female participants preferred a female endoscopist.

Originality/value

This study is the first of its kind exploring the psychological effects of the “two‐week rule” process for colorectal cancer, highlighting potential areas for improvement in patient information, and satisfaction with the referral process.
The effect of bidding success in construction bidding
Authors: Lan Oo Bee , Lo Hing‐Po , Teck‐Heng Lim Benson
Published: January 2012

Purpose

Winning a bid will carry implications for capacity level of a construction firm. This paper aims to examine the impact of a winning bid on contractors' bid pricing strategies.

Design/methodology/approach

In identifying the specific types of bidding trends before and after a winning bid, the variations in bids are expressed as a function of time relative to winning bid – the “event” of interest in this study – using a piecewise mixed effects model. The bids analysed comprised series of bids with a winning bid in between, recorded from Hong Kong building contractors.

Findings

The results show that there is a relationship between bid price and bidding success. The bidders in general bid low for time periods before a winning bid and they are less competitive in time periods after a winning bid. However, by considering the individual bidders' characteristics that relate to differences in bidding competitiveness, it is shown that there is remarkable heterogeneity among the bidders in bid pricing decision for pre‐ and post‐winning periods. Nevertheless, the statistically significant bidding trends before and after a winning bid strengthen the notion that systematic changes in bidding behaviour over time do occur in reality in response to changes in firm capacity level.

Originality/value

This empirical investigation provides strong evidence on the systematic changes in bidding behaviour over time in response to changes in firm capacity level, supporting the need to incorporate firm capacity level in the future development of a suitable theoretical framework on construction bidding.
Capacity building of construction industries in Sub‐Saharan developing countries
Authors: Kululanga Grant
Published: January 2012

Purpose

The need for capacity building of construction industries in developing countries cannot be over‐emphasised in order to ensure quality of services and products as well as the application of innovative ways for delivering construction services. Accordingly, using systems institutional paradigm approach as a conceptual premise, this paper aims to make the case for a fundamental turnaround for construction developmental approach in developing countries, that identify levels which should be considered as instrumental for capacity building of the construction industry in the Sub‐Saharan region, for example Malawi.

Design/methodology/approach

To ascertain a quad‐level framework which should be considered essential for capacity building of the construction industry, a questionnaire survey was employed. Data were elicited from prominent heads of sections from five stakeholders of the construction industry that operated in Malawi on the constructs for capacity building of a construction industry. Sixty completed questionnaires were received with a response rate of 90 per cent to the designed sample size.

Findings

The quad‐level framework for capacity development of a construction industry for developing countries was validated by an overall level of 77 per cent of agreement from key and prominent heads of sections of the five stakeholders of the construction industry. The rankings of the variables for capacity building for each level of the framework have provided the key foci and orientations of the industry for one of the Southern African countries of the Sub‐Saharan region.

Research limitations/implications

The study forms the basis for further research; future research could be directed towards other developing countries to further enrich the industry on the dynamics of capacity building of construction industries in developing countries.

Originality/value

This paper is the first to critically examine the antecedents and invoke a quad‐level framework for capacity development of construction industries.
Human resource practices of contractors that lead to job satisfaction of professional staff
Authors: Lim Lewis J.W. , Ling Florence Y.Y.
Published: January 2012

Purpose

The aim of this research is to investigate the effect of contractors' human resource (HR) practices on job satisfaction of their professional staff. The specific objectives are to: determine the effectiveness of contractors' HR practices; find out the level of job satisfaction that professional staff who work for contractors have; and study the relationship between HR practices and job satisfaction.

Design/methodology/approach

The research method was based on survey and a structured questionnaire, which was specially designed for the study, was the data collection instrument. Data were collected via e‐mail surveys and face to face interviews. The sampling frame comprised randomly chosen professionals who work for building contractors in Singapore.

Findings

Results showed that contractors' professionals are significantly satisfied with many of their firms' HR practices. The study found that these professionals have significant job satisfaction in terms of career opportunities, nature of their jobs and overall working environment. The results also show that many of the HR practices are significantly correlated with job satisfaction.

Research limitations/implications

The main limitation of the research is the relatively small sample size and low response rate. In addition, respondents' indication of their satisfaction level is contextualized to professional staff working in Singapore in a specific market condition, thereby limiting generalization of the results. The implication is that the findings would be more relevant to construction firms in Singapore at the time when the industry is just emerging from a recession.

Practical implications

It is recommended that contractors make an effort to understand what their professional staff want in HRM so as to efficiently channel their resources to create job satisfaction through appropriate HR practices. The study uncovered HR practices that employees are unsatisfied with. These include dissatisfaction with quantum of rewards, and firms' methods of dealing with employees' feedback and resolving conflicts. The practical implication of the findings is that contractors should improve on these practices so that their employees would not be more dissatisfied.

Originality/value

The originality of the study is that some HR practices that lead to job satisfaction of construction companies' professionals have been uncovered. The results could inform construction firms on what HR practices they may adopt to engender higher job satisfaction among their professional employees.
Grand theories as barriers to using IC concepts
Authors: Dumay John C.
Published: January 2012

Purpose

The purpose of this paper is to answer the question “What are the barriers to the use of IC concepts?” by discussing and critiquing two contemporary grand theories about IC, being market‐to‐book ratios as a representation of IC and that disclosing IC leads to greater profitability.

Design/methodology/approach

The paper reviews contemporary IC literature and explores reasons why these grand theories of IC hinder its adoption.

Findings

The research finds that these grand theories mislead because they cannot be proven empirically. Therefore, managers should attempt to better understand the possible causal relationships between their people, processes and stakeholders (human, structural and relational capital) rather than adopting someone else's mousetrap.

Practical implications

In order to improve the use of IC concepts they should be examined as differentiation theories of practice that take into account the agent (people) as a unit of analysis, the actual practice of IC and the resultant changes within an organisation, rather than trying to achieve the impossible generalisations of IC grand theories. Researchers need to conduct more critical and performative research into IC rather than ostensive research.

Originality/value

Allows academics and practitioners to understand the barriers to implementing IC in organisations, potentially allowing for the development of better engineered IC practices rather than the development of additional IC models.
Linking knowledge processes with firm performance: organizational culture
Authors: Nold Herbert A.
Published: January 2012

Purpose

The purpose of this paper is to report the results of a matched sample comparison group study of elements of organizational culture that enable knowledge processes to drive superior firm performance.

Design/methodology/approach

A matched sample comparison group approach was used to compare firm performance among matched pairs of public companies. Companies demonstrating high levels of trust (benchmark group) were matched with firms of similar size in the same industries demonstrating lower levels of trust (control group).

Findings

The benchmark group generated significantly superior value, operating performance, and had higher average annual growth rates than matching firms in the control group. Firms with higher relative levels of trust embedded in the organizational culture are more likely to outperform similar firms with lower levels of trust.

Research limitations/implications

The findings are based on surveys and financial performance of companies with securities traded on stock exchanges in the USA and may not represent other organizational forms, other geographic, economic, or cultural environments.

Practical implications

This study begins to identify a link between knowledge management, organizational learning, and knowledge creation (collectively knowledge processes) with firm performance.

Social implications

Identifying elements of organizational culture that link knowledge processes with firm performance is essential to developing a leadership model that reinforces enabling cultural attributes.

Originality/value

Many researchers have identified a lack of empirical research linking knowledge processes with firm performance. This study begins to fill the research gap with evidence that elements of organizational culture, specifically trust, enable firms to convert knowledge and learning initiatives into tangible performance recognized by financial markets.
Intellectual capital disclosure commitment: myth or reality?
Authors: Branswijck Deborah , Everaert Patricia
Published: January 2012

Purpose

The purpose of this paper is to compare intellectual capital disclosure in the prospectus of an initial public offering (IPO) with the intellectual capital disclosure in the subsequent annual report. The first objective was to investigate whether companies make a commitment toward intellectual capital disclosure. The second objective was to investigate whether companies report more on intellectual capital in the prospectus.

Design/methodology/approach

This study investigated the prospectus and annual report using a sample of 55 firms that applied for an initial listing in Belgium and The Netherlands from 2005‐2009. A coding framework of 86 items was used to perform the content analysis.

Findings

The existence of intellectual capital disclosure commitment was confirmed. Moreover, the results demonstrated that companies report more extensively on intellectual capital in their prospectus in comparison to their annual reports.

Originality/value

This paper documents the first study to provide empirical evidence on the existence of intellectual capital disclosure commitment. Therefore, it offers a new path for future intellectual capital disclosure research.