bluuebunny/crossref_metadata_2025 huggingface dataset:
Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection
Authors: Garmaroudi Farshid S. , Marchant David , Si Xiaoning , Khalili Abbas , Bashashati Ali , Wong Brian W. , Tabet Aline , Ng Raymond T. , Murphy Kevin , Luo Honglin , Janes Kevin A. , McManus Bruce M.
Published: September 2010

Signal transduction networks can be perturbed biochemically, genetically, and pharmacologically to unravel their functions. But at the systems level, it is not clear how such perturbations are best implemented to extract molecular mechanisms that underlie network function. Here, we combined pairwise perturbations with multiparameter phosphorylation measurements to reveal causal mechanisms within the signaling network response of cardiomyocytes to coxsackievirus B3 (CVB3) infection. Using all possible pairs of six kinase inhibitors, we assembled a dynamic nine-protein phosphorylation signature of perturbed CVB3 infectivity. Cluster analysis of the resulting dataset showed repeatedly that paired inhibitor data were required for accurate data-driven predictions of kinase substrate links in the host network. With pairwise data, we also derived a high-confidence network based on partial correlations, which identified phospho-IκBα as a central “hub” in the measured phosphorylation signature. The reconstructed network helped to connect phospho-IκBα with an autocrine feedback circuit in host cells involving the proinflammatory cytokines, TNF and IL-1. Autocrine blockade substantially inhibited CVB3 progeny release and improved host cell viability, implicating TNF and IL-1 as cell autonomous components of CVB3-induced myocardial damage. We conclude that pairwise perturbations, when combined with network-level intracellular measurements, enrich for mechanisms that would be overlooked by single perturbants.
Inducible expression eliminates the fitness cost of vancomycin resistance in enterococci
Authors: Foucault Marie-Laure , Depardieu Florence , Courvalin Patrice , Grillot-Courvalin Catherine
Published: September 2010

Inducible vancomycin resistance in enterococci is due to a sophisticated mechanism that combines synthesis of cell wall peptidoglycan precursors with low affinity for glycopeptides and elimination of the normal target precursors. Although this dual mechanism, which involves seven genes organized in two operons, is predicted to have a high fitness cost, resistant enterococci have disseminated worldwide. We have evaluated the biological cost of VanB-type resistance due to acquisition of conjugative transposon Tn
154
9 in
Enterococcus faecium
and
Enterococcus faecalis
. Because fitness was dependent on the integration site of Tn
1549
, an isogenic set of
E. faecalis
was constructed to determine the cost of inducible or constitutive expression of resistance or of carriage of Tn
1549
. A luciferase gene was inserted in the integrase gene of the transposon to allow differential quantification of the strains in cocultures and in the digestive tract of gnotobiotic mice. Both in vitro and in vivo, carriage of inactivated or inducible Tn
1549
had no cost for the host in the absence of induction by vancomycin. In contrast, induced or constitutively resistant strains not only had reduced fitness but were severely impaired in colonization ability and dissemination among mice. These data indicate that tight regulation of resistance expression drastically reduces the biological cost associated with vancomycin resistance in
Enterococcus
spp. and accounts for the widespread dissemination of these strains. Our findings are in agreement with the observation that regulation of expression is common in horizontally acquired resistance and represents an efficient evolutionary pathway for resistance determinants to become selectively neutral.
A binary search approach to whole-genome data analysis
Authors: Brodsky Leonid , Kogan Simon , BenJacob Eshel , Nevo Eviatar
Published: September 2010

A sequence analysis-oriented binary search-like algorithm was transformed to a sensitive and accurate analysis tool for processing whole-genome data. The advantage of the algorithm over previous methods is its ability to detect the margins of both short and long genome fragments, enriched by up-regulated signals, at equal accuracy. The score of an enriched genome fragment reflects the difference between the actual concentration of up-regulated signals in the fragment and the chromosome signal baseline. The “divide-and-conquer”-type algorithm detects a series of nonintersecting fragments of various lengths with locally optimal scores. The procedure is applied to detected fragments in a nested manner by recalculating the lower-than-baseline signals in the chromosome. The algorithm was applied to simulated whole-genome data, and its sensitivity/specificity were compared with those of several alternative algorithms. The algorithm was also tested with four biological tiling array datasets comprising
Arabidopsis
(
i
) expression and (
ii
) histone 3 lysine 27 trimethylation CHIP-on-chip datasets;
Saccharomyces cerevisiae
(
iii
) spliced intron data and (
iv
) chromatin remodeling factor binding sites. The analyses’ results demonstrate the power of the algorithm in identifying both the short up-regulated fragments (such as exons and transcription factor binding sites) and the long—even moderately up-regulated zones—at their precise genome margins. The algorithm generates an accurate whole-genome landscape that could be used for cross-comparison of signals across the same genome in evolutionary and general genomic studies.
Reliability of Statistical Software
Authors: Odeh Oluwarotimi O. , Featherstone Allen M. , Bergtold Jason S.
Published: September 2010

The reliability of several statisitcal software packages was examined using the National Institute of Standards and Technology linear and nonlinear least squares datasets and models. Software tested include Excel 2007, GAMS 23.4, GAUSS 9.0, LIMDEP 8.0, Mathematica 7.0, MATLAB 7.5, R 2.10, SAS 9.1, SHAZAM 10, and Stata 10. While some of these packages have been previously examined, others, including GAMS and MATLAB, have not been extensively examined. Reliability tests indicate improvements in some of the software packages that were previously tested, but some of these packages failed reliability tests under certain conditions. The findings underscore the need to benchmark software packages to ascertain reliability before use and the importance of solving econometric problems using more than one package.
Separation Hypothesis Tests in the Agricultural Household Model
Authors: Le Kien T.
Published: September 2010

In an agricultural household model, farmers’ production decisions can be either separated or nonseparated from preferences. Since previous studies on agricultural household behavior and policy effects have shown that the model with separation yields different results than the model with nonseparation, it is important to have a test to identify the correct model. This paper provides new tests that extend current tests in two directions. First, the new tests avoid issues that current tests have to address, such as simultaneity bias and the estimation of the production function. Second, the new tests make use of more information implied from the separation hypothesis than current tests.
The Impact of Food Stamp Program Participation on Household Food Insecurity
Authors: Mykerezi Elton , Mills Bradford
Published: September 2010

This study examines the impact that participation in the Food Stamp Program has on household food insecurity using data from the Panel Survey of Income Dynamics. Two strategies are used to identify the causal effect of the program. First, endogenous treatment effect models are estimated using state‐level errors in payments of benefits as instruments. Additionally the impact of losing benefits due to a government decision on the food insecurity of program participants is examined. The paper finds that program participation lowers food insecurity by at least 18%.
Performance evaluation of harvest control rules for Pacific herring management in British Columbia, Canada
Authors: Cleary J. S. , Cox S. P. , Schweigert J. F.
Published: September 2010

Cleary, J. S., Cox, S. P., and Schweigert, J. F. 2010. Performance evaluation of harvest control rules for Pacific herring management in British Columbia, Canada. – ICES Journal of Marine Science, 67: 2005–2011. Despite application of a harvest control rule (HCR) since 1986, abundance of several Pacific herring (Clupea pallasi) stocks in British Columbia, Canada, are currently below levels considered adequate for exploitation. An alternative HCR, based on default limit and upper stock reference (USR) points at 0.4 BMSY and 0.8 BMSY, was recently developed under Canada's precautionary fisheries management policy. We simulated the Pacific herring fishery management system to examine whether (i) realized fishery performance over the past 10 years is an expected consequence of applying the existing herring HCR (with a single lower reference point) and (ii) performance could be improved by adopting the Department of Fisheries and Oceans new HCR with limit and USR points. Both HCRs successfully rebuilt stocks to sustainable levels under a high-productivity scenario, but performed poorly when stock productivity was low. The two HCRs were sensitive to stock productivity, because the effect of a target harvest rate (20%) that is independent of productivity was much larger than the effects of biomass reference-point choices. We therefore recommend further research on estimating reference points and sustainable harvest rates for Pacific herring, so that HCRs may be made more responsive to changes in productivity.
Bacillus alkalisediminis sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from sediment of extremely shallow soda ponds
Authors: Borsodi Andrea K. , Pollák Beatrix , Kéki Zsuzsa , Rusznyák Anna , Kovács Attila L. , Spröer Cathrin , Schumann Peter , Márialigeti Károly , Tóth Erika M.
Published: September 2010

Alkaliphilic strains characterized by optimal growth at pH 9.0 and 5 % (w/v) NaCl designated K1-25T and H3-93 were isolated from extremely shallow soda ponds located in Hungary. Cells of both strains were Gram-stain-positive, non-motile, straight rods and formed central, ellipsoidal endospores with swollen sporangia. The isolates were aerobic, catalase-positive, oxidase-negative and contained a peptidoglycan of type A1γ based on meso-diaminopimelic acid. In both strains, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and the major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C contents of strains K1-25T and H3-93 were 39.0 and 36.3 mol%, respectively. 16S rRNA gene sequence-based phylogenetic analysis revealed 99.2 % similarity between strains K1-25T and H3-93 and the novel isolates had the highest similarities to Bacillus akibai 1139T (97.8 and 98.3 %, respectively), Bacillus wakoensis N-1T (97.0 and 97.4 %), Bacillus okhensis Kh10-101T (97.1 and 97.4 %) and Bacillus krulwichiae AM31DT (96.9 and 97.1 %). DNA–DNA hybridization between our strains and the type strains of closely related Bacillus species was lower than 70 %. Although DNA–DNA hybridization between strains K1-25T and H3-93 was 27 %, the phenotypic and chemotaxonomic data did not support the differentiation of these two strains into separate species. Therefore, they represent genomovars of a novel species, for which the name Bacillus alkalisediminis sp. nov. is proposed. The type strain is K1-25T ( = DSM 21670T  = NCAIM B02301T).
Leifsonia psychrotolerans sp. nov., a psychrotolerant species of the family Microbacteriaceae from Livingston Island, Antarctica
Authors: Ganzert Lars , Bajerski Felizitas , Mangelsdorf Kai , Lipski André , Wagner Dirk
Published: September 2010

A cold-tolerant, yellow-pigmented, Gram-positive, motile, facultatively anaerobic bacterial strain, LI1T, was isolated from a moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St. Kliment Ohridski. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species Leifsonia kafniensis KFC-22T, Leifsonia pindariensis PON10T and Leifsonia antarctica SPC-20T, with which it showed sequence similarities of 99.0, 97.9 and 97.9 %, respectively. DNA–DNA hybridization revealed a reassociation value of 2.7 % with L. kafniensis LMG 24362T. The DNA G+C content of strain LI1T was 64.5 mol%. The growth temperature range was −6 to 28 °C, with optimum growth at 16 °C. Growth occurred in 0–5 % NaCl and at pH 4.5–9.5, with optimum growth in 1–2 % NaCl and at pH 5.5–6.5. The predominant fatty acids were anteiso-C15 : 0, C18 : 0 and iso-C15 : 0. The polar lipids were phosphatidylglycerol and diphosphatidylglycerol. Physiological and biochemical tests clearly differentiated strain LI1T from L. kafniensis. Therefore, a novel cold-tolerant species within the genus Leifsonia is proposed: Leifsonia psychrotolerans sp. nov. (type strain LI1T = DSM 22824T = NCCB 100313T).
Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil
Authors: Lee Dong Wan , Lee Soo-Young , Yoon Jung-Hoon , Lee Soon Dong
Published: September 2010

Two novel Gram-reaction-positive, rod-shaped actinobacterial strains, designated RP-B26T and RP-B30T, were isolated from rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.) which was collected from Mara Island, Republic of Korea. The colonies of the isolates were circular, smooth, convex and moderately yellow–light-yellow in colour. 16S rRNA gene sequence analysis revealed that the isolates belonged to the family Nocardioidaceae and formed two distinct sublineages within the radiation of the genus Nocardioides. 16S rRNA gene sequence similarity between the isolates was 98.2 %. The closest phylogenetic neighbours of strain RP-B26T were Nocardioides humi DCY24T and Nocardioides kongjuensis A2-4T with 97.4 and 97.0 % 16S rRNA gene sequence similarity, respectively, whereas 16S rRNA gene sequence similarities between strain RP-B30T and N. humi DCY24T and N. kongjuensis A2-4T were 96.5 and 96.0 %, respectively. Both of the isolates contained ll-diaminopimelic acid as the diagnostic diamino acid in the cell walls. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylinositol and phosphatidylglycerol. The fatty acid profiles of the isolates were characterized by the presence of saturated, unsaturated, 10-methyl and hydroxyl fatty acids, with small amounts of branched fatty acids. The DNA G+C contents of strains RP-B26T and RP-B30T were 73.0 and 71.7 mol%, respectively. Levels of DNA–DNA relatedness between the isolates were 44.9±1.5 % (thermal renaturation method) and 43.2 % (photobiotin-labelled method); the isolates showed low DNA–DNA relatedness values (<11 %) to the most closely related strain, N. humi KCTC 19265T. On the basis of the phenotypic, genotypic and DNA–DNA hybridization data presented here, the isolates are considered to represent two novel species of the genus Nocardioides, for which the names Nocardioides ultimimeridianus sp. nov. (type strain RP-B26T  = KCTC 19368T  = DSM 19768T) and Nocardioides maradonensis sp. nov. (type strain RP-B30T  = KCTC 19384T  = DSM 19769T) are proposed.
Chryseomicrobium imtechense gen. nov., sp. nov., a new member of the family Planococcaceae
Authors: Arora Pankaj Kumar , Chauhan Archana , Pant Bhawana , Korpole Suresh , Mayilraj Shanmugam , Jain Rakesh Kumar
Published: September 2010

A Gram-stain-positive, rod-shaped, yellow, non-motile, non-spore-forming, strictly aerobic bacterial strain, designated MW 10T, was isolated from seawater of the Bay of Bengal, India, and was subjected to a polyphasic taxonomic study. Analysis of the 16S rRNA gene sequence revealed that strain MW 10T showed highest similarity to the type strains of Psychrobacillus psychrodurans (96.15 %) and Psychrobacillus psychrotolerans (96.01 %) and showed less than 96 % similarity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MW 10T formed a clade separate from members of closely related genera. The morphological, physiological and chemotaxonomic characteristics of strain MW 10T differed from those of members of closely related genera. The major fatty acid in strain MW 10T was iso-C15 : 0 and the menaquinones were MK-7 (48.4 %), MK-8 (32.3 %), MK-7(H2) (13.7 %) and MK-6 (5.6 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown phospholipid, an unknown lipid and an unknown glycolipid. The cell-wall peptidoglycan type was l-Lys–d-Asp. The genomic DNA G+C content (53.4 mol%) of strain MW 10T was significantly different from those of members of closely related genera. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as our phylogenetic analysis, we conclude that strain MW 10T is a member of a novel genus and species, for which the name Chryseomicrobium imtechense gen. nov., sp. nov., is proposed. The type strain of Chryseomicrobium imtechense is MW 10T ( = MTCC 10098T  = JCM 16573T).
Peptostreptococcus russellii sp. nov., isolated from a swine-manure storage pit
Authors: Whitehead Terence R. , Cotta Michael A. , Falsen Enevold , Moore Edward , Lawson Paul A.
Published: September 2010

Using a polyphasic approach, a taxonomic study was performed on seven strains of an unknown Gram-reaction-positive, non-spore-forming, obligately anaerobic coccus-shaped bacterium, isolated from a swine-manure storage pit. Comparative 16S rRNA gene sequencing confirmed that all seven isolates were highly related to each other and formed a hitherto unknown lineage within the clostridial rRNA XI cluster of organisms. Pairwise analysis demonstrated that the novel organism was most closely related to Peptostreptococcus anaerobius CCUG 7835T and Peptostreptococcus stomatis CCUG 51858T with 16S rRNA gene sequence similarities of 95.5 and 93.0 %, respectively. The peptidoglycan type of the cell wall was determined to be A4α l-Lys–d-Asp and glucose, xylose and traces of mannose were detected as the cell–wall sugars. Based on biochemical, chemotaxonomic and phylogenetic evidence the unknown bacterium represents a new species of the genus Peptostreptococcus, for which the name Peptostreptococcus russellii sp. nov, is proposed. The type strain is RT-10BT ( = CCUG 58235T  = NRRL B-59380T  = DSM 23041T).
Pontibacillus yanchengensis sp. nov., a moderately halophilic bacterium isolated from salt field soil
Authors: Yang Yan , Zou Zhengzhong , He Minyan , Wang Gejiao
Published: September 2010

A Gram-positive-staining, aerobic, moderately halophilic bacterium, designated strain Y32T, was isolated from subsurface soil of the Sanwei salt field, Yancheng, Jiangsu province, South-east China. The cell-wall peptidoglycan type of strain Y32T was meso-diaminopimelic acid. The menaquinone was menaquinone-7 (MK-7). The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the DNA G+C content of strain Y32T was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y32T was closely related to the type strains of the genus Pontibacillus. The 16S rRNA gene sequence similarities of strain Y32T with the type strains of species of the genus Pontibacillus were 97.8 % (Pontibacillus marinus KCTC 3917T), 96.9 % (Pontibacillus chungwhensis BH030062T), 96.8 % (Pontibacillus litoralis JSM 072002T) and 96.0 % (Pontibacillus halophilus JSM 076056T). DNA–DNA relatedness between strain Y32T and P. marinus KCTC 3917T was 42 %. On the basis of phenotypic, chemotaxonomic and phylogenetic evidences, strain Y32T was found to be affiliated to the genus Pontibacillus, but was clearly differentiated from other members of this genus. Strain Y32T represents a novel member of the genus, for which the name Pontibacillus yanchengensis sp. nov. is proposed. The type strain is Y32T ( = CGMCC 1.10680T = CCTCC AB209311T = NRRL B-59408T).
Lactococcus lactis subsp. tructae subsp. nov. isolated from the intestinal mucus of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss)
Authors: Pérez Tania , Balcázar José Luis , Peix Alvaro , Valverde Angel , Velázquez Encarna , de Blas Ignacio , Ruiz-Zarzuela Imanol
Published: September 2010

The species Lactococcus lactis currently includes three subspecies; L. lactis subsp. lactis and L. lactis subsp. cremoris, isolated from milk sources, and L. lactis subsp. hordniae, isolated from the leafhopper Hordnia circellata. In this study, three strains, designated L105T, I3 and L101, were isolated from the intestinal mucus of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss). These strains were closely related to members of the species Lactococcus lactis. Strain L105T showed 99.4 % 16S rRNA gene sequence similarity to that of the type strains L. lactis subsp. lactis NCDO 604T and L. lactis subsp. hordniae NCDO 2181T and showed 99.9 % similarity to the type strain Lactococcus lactis subsp. cremoris NCDO 607T. Analysis of two housekeeping genes, rpoB and recA, confirmed the close relationship between the novel strains and L. lactis subsp. cremoris with similarities of 99.3 and 99.7 %, respectively. The three strains could, however, be differentiated from their closest relatives on the basis of several phenotypic characteristics, as was the case for L. lactis subsp. lactis and L. lactis subsp. hordniae, which were also closely related on the basis of 16S rRNA, rpoB and recA gene sequence similarities. The strains isolated in this study represent a new subspecies, for which the name Lactococcus lactis subsp. tructae subsp. nov. is proposed. The type strain is L105T ( = LMG 24662T  = DSM 21502T).
Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera
Authors: Chen Ming-Hui , Sheu Shih-Yi , Arun A. B. , Young Chiu-Chung , Chen Chaolun Allen , Wang Jih-Terng , Chen Wen-Ming
Published: September 2010

A Gram-negative, heterotrophic, marine bacterium, designated strain SW-11T, was isolated from the reef-building coral Isopora palifera in Kenting, Taiwan. Cells were rods and were motile by a single polar flagellum. The strain grew at 10–45 °C (optimum, 30–35 °C), at pH 7.0–8.0 (optimum, pH 7.5) and with 2.0–4.0 % NaCl (optimum, 2.5–3.0 %). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unknown phospholipids. Isoprenoid quinones consisted of ubiquinone 9 (78.8 %) and ubiquinone 8 (21.1 %). Major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 22.3 %), C17 : 1ω8c (13.4 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c; 13.1 %), C16 : 0 (10.3 %) and anteiso-C17 : 1ω9c (10.0 %). The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis indicated that strain SW-11T belongs to the class Gammaproteobacteria and is a member of the order Alteromonadales. Strain SW-11T shared 93.2 % 16S rRNA gene sequence similarity with Teredinibacter turnerae T7902T and 92.1 % with Saccharophagus degradans 2-40T, and can be further distinguished from these two related strains by distinct patterns of fatty acid content and differences in the polar lipid profile, the ability to utilize different compounds as carbon sources, the ability to degrade various compounds and differences in enzyme activities. The phylogenetic data and those from physiological, morphological and chemotaxonomic characterizations indicate that strain SW-11T represents a novel species and genus, for which the name Pseudoteredinibacter isoporae gen. nov., sp. nov. is proposed. The type strain of Pseudoteredinibacter isoporae is SW-11T ( = BCRC 17935T  = LMG 25246T).
Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans
Authors: Coorevits An , Logan Niall A. , Dinsdale Anna E. , Halket Gillian , Scheldeman Patsy , Heyndrickx Marc , Schumann Peter , Van Landschoot Anita , De Vos Paul
Published: September 2010

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.
Persicivirga ulvanivorans sp. nov., a marine member of the family Flavobacteriaceae that degrades ulvan from green algae
Authors: Barbeyron Tristan , Lerat Yannick , Sassi Jean-François , Le Panse Sophie , Helbert William , Collén Pi Nyvall
Published: September 2010

A rod shaped, Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, non-gliding bacterium, designated strain PLRT, was isolated from faeces of the mollusc Aplysia punctata (Mollusca, Gastropoda) that had been fed with green algae belonging to the genus Ulva. The novel strain was able to degrade ulvan, a polysaccharide extracted from green algae (Chlorophyta, Ulvophyceae). The taxonomic position of strain PLRT was investigated by using a polyphasic approach. Strain PLRT was dark orange, oxidase-positive, catalase-positive and grew optimally at 25 °C, at pH 7.5 and in the presence of 2.5 % (w/v) NaCl with an oxidative metabolism using oxygen as the electron acceptor. Nitrate could not be used as the electron acceptor. Strain PLRT had a Chargaff’s coefficient (DNA G+C content) of 35.3 mol%. Phylogenetic analysis based on the sequence of the 16S rRNA gene placed the novel strain in the family Flavobacteriaceae (phylum ‘Bacteroidetes’), within a clade comprising Stenothermobacter spongiae, Nonlabens tegetincola, Sandarakinotalea sediminis, Persicivirga xylanidelens and Persicivirga dokdonensis. The closest neighbours of strain PLRT were P. xylanidelens and P. dokdonensis, sharing 95.2 and 95.5 % 16S rRNA gene sequence similarity, respectively. Phylogenetic inference and differential phenotypic characteristics demonstrated that strain PLRT represents a novel species of the genus Persicivirga, for which the name Persicivirga ulvanivorans sp. nov. is proposed. The type strain is PLRT ( = CIP 110082T = DSM 22727T).
Mycobacterium algericum sp. nov., a novel rapidly growing species related to the Mycobacterium terrae complex and associated with goat lung lesions
Authors: Sahraoui Naima , Ballif Marie , Zelleg Samir , Yousfi Nadir , Ritter Claudia , Friedel Ute , Amstutz Beat , Yala Djamel , Boulahbal Fadila , Guetarni Djamel , Zinsstag Jakob , Keller Peter M.
Published: September 2010

A previously undescribed, rapid-growing, non-chromogenic Mycobacterium isolate from a goat lung lesion in Algeria is reported. Biochemical and molecular tools were used for its complete description and showed its affiliation to the Mycobacterium
terrae complex. 16S rRNA, rpoB and hsp65 gene sequences were unique. Phylogenetic analyses showed a close relationship with M. terrae sensu stricto and Mycobacterium
senuense. Culture and biochemical characteristics were generally similar to those of M. terrae and M. senuense. However, in contrast to M. terrae and M. senuense, the isolate was positive for urease production and had faster growth. The mycolic acid profile was distinct from those of M. terrae and M. senuense, thus further supporting the new taxonomic position of the isolate. We propose the name Mycobacterium algericum sp. nov. for this novel species. The type strain is TBE 500028/10T ( = BejaiaT = CIP 110121T = DSM 45454T).
Rhizobium herbae sp. nov. and Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China
Authors: Ren Da Wei , Wang En Tao , Chen Wen Feng , Sui Xin Hua , Zhang Xiao Xia , Liu Hong Can , Chen Wen Xin
Published: September 2010

SevenRhizobiumstrains associated with various legume species grown in different geographical regions of China were defined into four genomic groups related toRhizobium giardinii, based upon ribosomal intergenic spacer RFLP, phylogenies of 16S rRNA and housekeeping (atpD,recAandglnII) genes, and DNA relatedness. Three strains in group I were classified asR. giardinii, as they showed high gene sequence similarities (>97 %) and DNA relatedness (64.3–67.5 %) toR.giardiniiH152T. Groups II, III and IV differed from all definedRhizobiumspecies based upon the consensus of all analyses. As group II contained two strains that originated from two distinct populations, we propose this group as a novel species,Rhizobium herbaesp. nov., with strain CCBAU 83011T( = LMG 25718T = HAMBI 3117T) as the type strain.
Description of Catellibacterium caeni sp. nov., reclassification of Rhodobacter changlensis Anil Kumar et al. 2007 as Catellibacterium changlense comb. nov. and emended description of the genus Catellibacterium
Authors: Zheng Jin-Wei , Chen Yi-Guang , Zhang Jun , Ni Ying-Ying , Li Wen-Jun , He Jian , Li Shun-Peng
Published: September 2010

A novel non-sporulating, non-motile, catalase- and oxidase-positive, strictly aerobic, Gram-negative, rod-shaped bacterial strain, designated DCA-1T, was isolated from activated sludge collected from a butachlor wastewater treatment facility. The strain was able to degrade about 85 % of 100 mg butachlor l−1 within 5 days of incubation. Growth occurred in the presence of 0–6 % (w/v) NaCl [optimum, 1 % (w/v) NaCl] and at pH 5.5–9.0 (optimum, pH 7.0) and 15–35 °C (optimum, 25–30 °C). Vesicular internal membrane structures and photoheterotrophic growth were not observed. The major respiratory quinone was ubiquinone 10 (Q-10) and the major cellular fatty acids were C18 : 1ω7c and 11-methyl C18 : 1ω7c. The genomic DNA G+C content of strain DCA-1T was 62.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain DCA-1T was a member of the family Rhodobacteraceae and was related most closely to the type strain of Catellibacterium aquatile (96.5 % sequence similarity). The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data supports the suggestion that strain DCA-1T represents a novel species of the genus Catellibacterium, for which the name Catellibacterium caeni sp. nov. is proposed. The type strain is DCA-1T ( = CGMCC 1.7745T  = DSM 21823T). In addition, based on the characterization data obtained in this study, it is proposed that Rhodobacter changlensis should be reclassified as Catellibacterium changlense comb. nov. (type strain JA139T  = DSM 18774T  = CCUG 53722T  = JCM 14338T). An emended description of the genus Catellibacterium is also presented.
Five novel Wickerhamomyces- and Metschnikowia-related yeast species, Wickerhamomyces chaumierensis sp. nov., Candida pseudoflosculorum sp. nov., Candida danieliae sp. nov., Candida robnettiae sp. nov. and Candida eppingiae sp. nov., isolated from plants
Authors: Groenewald Marizeth , Robert Vincent , Smith Maudy Th
Published: September 2010

On the basis of nucleotide divergences in the D1/D2 domain of the 26S rRNA gene and the internal transcribed spacers (ITS) domain of the rRNA gene, five novel yeast species, Wickerhamomyces chaumierensis sp. nov. (CBS 8565T  = JCM 17246T), Candida pseudoflosculorum sp. nov. (CBS 8584T  = JCM 17242T), Candida danieliae sp. nov. (CBS 8533T  = JCM 17247T), Candida robnettiae sp. nov. (CBS 8580T  = JCM 17243T) and Candida eppingiae sp. nov. (CBS 8586T  = JCM 17241T), isolated from plants in Thailand and Guyana, are proposed in this study.
The phylogenetic placement of the non-phototrophic, Gram-positive thermophile ‘Thermobaculum terrenum’ and branching orders within the phylum ‘ Chloroflexi ’ inferred from gene order comparisons
Authors: Kunisawa Takashi
Published: September 2010

The phylogenetic position of an anaerobic, non-spore-forming thermophile ‘Thermobaculum terrenum’ was investigated on the basis of gene order data from completely sequenced bacterial genomes. Gene order data can be an excellent source of phylogenetic information. Shared gene arrangements are unlikely to have arisen by chance convergence. They are likely to reflect common ancestry. ‘Thermobaculum terrenum’ was found to share three gene arrangements that are present uniquely in genomes of members of the phylum ‘Chloroflexi’, indicating convincingly that ‘Thermobaculum terrenum’ is a member of this phylum. Branching orders within the phylum ‘Chloroflexi’ were inferred by identifying monophyletic groups of species, which were circumscribed by characteristic gene arrangements. The branching orders thus inferred were in good agreement with previously reported phylogenies based on single 16S rRNA gene sequences and on multiple protein sequences. The gene order comparisons revealed a close phylogenetic affinity of ‘Thermobaculum terrenum’ toSphaerobacter thermophilusandThermomicrobium roseum.
Digital Gene Expression Signatures for Maize Development
Authors: Eveland Andrea L. , Satoh-Nagasawa Namiko , Goldshmidt Alexander , Meyer Sandra , Beatty Mary , Sakai Hajime , Ware Doreen , Jackson David
Published: September 2010

Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect the determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression profiles using Illumina’s high-throughput sequencing technology and the newly assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in axillary meristem determinacy. The RA3 gene encodes a trehalose-6-phosphate phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of digital gene expression libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20- to 21-nucleotide reads with frequencies spanning 4 orders of magnitude. Unique sequence tags were anchored to 3′-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of nonredundant signature tags to the maize genome, which associated with 37,117 gene models and unannotated regions of expression. In total, 66% of genes were detected by at least nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) in functional analyses of differentially expressed maize genes. Results from this study provide a basis for the analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene.
Regulatory Network Identification by Genetical Genomics: Signaling Downstream of the Arabidopsis Receptor-Like Kinase ERECTA
Authors: Terpstra Inez R. , Snoek L. Basten , Keurentjes Joost J.B. , Peeters Anton J.M. , Van den Ackerveken Guido
Published: September 2010

Gene expression differences between individuals within a species can be largely explained by differences in genetic background. The effect of genetic variants (alleles) of genes on expression can be studied in a multifactorial way by the application of genetical genomics or expression quantitative trait locus mapping. In this paper, we present a strategy to construct regulatory networks by the application of genetical genomics in combination with transcript profiling of mutants that are disrupted in single genes. We describe the network identification downstream of the receptor-like kinase ERECTA in Arabidopsis (Arabidopsis thaliana). Extending genetical genomics on the Landsberg erecta/Cape Verde Islands (Ler/Cvi) recombinant inbred population with expression profiling of monogenic mutants enabled the identification of regulatory networks in the so far elusive ERECTA signal transduction cascade. We provide evidence that ERECTA is the causal gene for the major hotspot for transcript regulation in the Arabidopsis Ler/Cvi recombinant inbred population. We further propose additional genetic variation between Ler and Cvi in loci of the signaling pathway downstream of ERECTA and suggest candidate genes underlying these loci. Integration of publicly available microarray expression data of other monogenic mutants allowed us to link ERECTA to a downstream mitogen-activated protein kinase signaling cascade. Our study shows that microarray data of monogenic mutants can be effectively used in combination with genetical genomics data to enhance the identification of genetic regulatory networks.
Genome Structures and Halophyte-Specific Gene Expression of the Extremophile Thellungiella parvula in Comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis
Authors: Oh Dong-Ha , Dassanayake Maheshi , Haas Jeffrey S. , Kropornika Anna , Wright Chris , d’Urzo Matilde Paino , Hong Hyewon , Ali Shahjahan , Hernandez Alvaro , Lambert Georgina M. , Inan Gunsu , Galbraith David W. , Bressan Ray A. , Yun Dae-Jin , Zhu Jian-Kang , Cheeseman John M. , Bohnert Hans J.
Published: September 2010

The genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5′ untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species.
Classification in a social world: bias and trust
Authors: Mai Jens‐Erik
Published: September 2010

Purpose

The purpose of this paper is to establish pluralism as the basis for bibliographic classification theory and practice and examine the possibility of establishing trustworthy classifications.

Design/methodology/approach

The paper examines several key notions in classification and extends previous frameworks by combining an explanation‐based approach to classification with the concepts of cognitive authority and trust.

Findings

The paper presents an understanding of classification that allows designers and editors to establish trust through the principle of transparency. It demonstrates that modern classification theory and practice are tied to users' activities and domains of knowledge and that trustworthy classification systems are in close dialogue with users to handle bias responsible and establish trust.

Originality/value

The paper establishes a foundation for exploring trust and authority for classification systems.
Mental models of the bibliographic universe. Part 1: mental models of descriptions
Authors: Pisanski Jan , Žumer Maja
Published: September 2010

Purpose

The paper aims to present the results of the first two tasks of a user study looking into mental models of the bibliographic universe and especially their comparison to the Functional Requirements for Bibliographic Records (FRBR) conceptual model, which has not yet been user tested.

Design/methodology/approach

The paper employes a combination of techniques for eliciting mental models and consisted of three tasks, two of which, card sorting and concept mapping, are presented herein. Its participants were 30 individuals residing in the general area of Ljubljana, Slovenia.

Findings

Cumulative results of concept mapping show a strong resemblance to FRBR. Card sorts did not produce conclusive results. In both tasks, participants paid special attention to the original expression, indicating that a special place for it should be considered.

Research limitations/implications

The study was performed using a relatively small sample of participants living in a geographically limited space using relatively straight‐forward examples.

Practical implications

Some solid evidence is provided for adoption of FRBR as the conceptual basis for cataloguing.

Originality/value

This is the first widely published user study of FRBR, applying novel methodological approaches in the field of Library and Information Science.
Mental models of the bibliographic universe. Part 2: comparison task and conclusions
Authors: Pisanski Jan , Žumer Maja
Published: September 2010

Purpose

The paper aims to provide some insight into mental models of the bibliographic universe and how they compare with functional requirements for bibliographic records (FRBR) as a conceptual model of the bibliographic universe.

Design/methodology/approach

To get a more complete picture of the mental models, different elicitation techniques were used. The three tasks of the paper were: card‐sorting, concept mapping and comparison task. The paper deals with comparison task, which consisted of interviews and rankings, and provides a discussion of the results of the paper as a whole.

Findings

Results of the ranking part of the comparison task confirm the findings of concept mapping task. In both cases, while there are individual differences between mental models, on average they gravitate towards FRBR.

Research limitations/implications

This is a small study and it provides only a glimpse of the implications of using FRBR as a conceptual basis for cataloguing. More FRBR‐related user studies are needed, including similar studies on different groups of individuals and different types of materials, as well as practical studies of user needs and user interfaces.

Practical implications

The results of this study are the first user‐tested indication of the validity of FRBR as a conceptual basis for the future of cataloguing.

Originality/value

This is the first published paper of mental models of the bibliographic universe and uses a unique combination of mental model elicitation techniques.
The h‐index: a broad review of a new bibliometric indicator
Authors: Norris Michael , Oppenheim Charles
Published: September 2010

Purpose

This review aims to show, broadly, how the h‐index has become a subject of widespread debate, how it has spawned many variants and diverse applications since first introduced in 2005 and some of the issues in its use.

Design/methodology/approach

The review drew on a range of material published in 1990 or so sources published since 2005. From these sources, a number of themes were identified and discussed ranging from the h‐index's advantages to which citation database might be selected for its calculation.

Findings

The analysis shows how the h‐index has quickly established itself as a major subject of interest in the field of bibliometrics. Study of the index ranges from its mathematical underpinning to a range of variants perceived to address the indexes' shortcomings. The review illustrates how widely the index has been applied but also how care must be taken in its application.

Originality/value

The use of bibliometric indicators to measure research performance continues, with the h‐index as its latest addition. The use of the h‐index, its variants and many applications to which it has been put are still at the exploratory stage. The review shows the breadth and diversity of this research and the need to verify the veracity of the h‐index by more studies.
Information literacy and knowledge management at work
Authors: Toledano O'Farrill Rubén
Published: September 2010

Purpose

The purpose of this paper is to explore theoretically and empirically the concept of workplace information literacy (IL) and its connections to knowledge management (KM), and to examine the applicability of the mainstream institutional IL frameworks (American Library Association, The Australian and New Zealand Institute for IL, The Society of College, National and University Libraries, The UK Chartered Institute of Library Professionals, etc.) to the workplace environment.

Design/methodology/approach

Phenomenographic study of conceptions of effective information use of frontline staff at NHS24, which are discussed with respect to organizational characteristics of NHS Scotland and against the background of the two theoretical concepts: KM and IL.

Findings

The paper shows that the main institutional IL frameworks do not properly reflect some important ways in which information is used by participants in the study, particularly the use of people as information sources and the social sense making and interpretation of the value of information and its application in the workplace environment.

Research limitations/implications

The results from this qualitative study of a small population can be useful inasmuch as they highlight characteristics of workplace IL that may be relevant in several organizational settings, as well as presenting a critical analysis of the IL frameworks developed by librarians in regard to their applicability to workplace settings.

Practical implications

The paper highlights the importance of developing organization‐specific guidelines for IL development, endorsing views of learning and information use grounded in socio‐constructive perspectives and a consideration of context as situated practice.

Originality/value

This is an original research study conducted as part of a PhD qualification which has contributed to further the understanding of workplace IL.