bluuebunny/crossref_metadata_2025 huggingface dataset:
Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin
Authors: Lin Ying-Wu , Yeung Natasha , Gao Yi-Gui , Miner Kyle D. , Tian Shiliang , Robinson Howard , Lu Yi
Published: April 2010

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative Fe
B
site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by ∼110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu has a different role in redox tuning. More importantly, introducing the second Glu resulted in a ∼100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the Fe
B
site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.
Insights into protein folding mechanisms from large scale analysis of mutational effects
Authors: Naganathan Athi N. , Muñoz Victor
Published: April 2010

Protein folding mechanisms are probed experimentally using single-point mutant perturbations. The relative effects on the folding (
ϕ
-values) and unfolding (1 - 
ϕ
) rates are used to infer the detailed structure of the transition-state ensemble (TSE). Here we analyze kinetic data on > 800 mutations carried out for 24 proteins with simple kinetic behavior. We find two surprising results: (
i
) all mutant effects are described by the equation:

. Therefore all data are consistent with a single
ϕ
-value (0.24) with accuracy comparable to experimental precision, suggesting that the structural information in conventional
ϕ
-values is low. (
ii
)
ϕ
-values change with stability, increasing in mean value and spread from native to unfolding conditions, and thus cannot be interpreted without proper normalization. We eliminate stability effects calculating the
ϕ
-values at the mutant denaturation midpoints; i.e., conditions of zero stability (
ϕ
0
). We then show that the intrinsic variability is
ϕ
0
 = 0.36 ± 0.11, being somewhat larger for β-sheet-rich proteins than for α-helical proteins. Importantly, we discover that
ϕ
0
-values are proportional to how many of the residues surrounding the mutated site are local in sequence. High
ϕ
0
-values correspond to protein surface sites, which have few nonlocal neighbors, whereas core residues with many tertiary interactions produce the lowest
ϕ
0
-values. These results suggest a general mechanism in which the TSE at zero stability is a broad conformational ensemble stabilized by local interactions and without specific tertiary interactions, reconciling
ϕ
-values with many other empirical observations.
Loss of lipid synthesis as an evolutionary consequence of a parasitic lifestyle
Authors: Visser Bertanne , Le Lann Cécile , den Blanken Frank J. , Harvey Jeffrey A. , van Alphen Jacques J. M. , Ellers Jacintha
Published: April 2010

Evolutionary loss of traits can result from negative selection on a specific phenotype, or if the trait is selectively neutral, because the phenotype associated with the trait has become redundant. Even essential traits may be lost, however, if the resulting phenotypic deficiencies can be compensated for by the environment or a symbiotic partner. Here we demonstrate that loss of an essential me-tabolic trait in parasitic wasps has evolved through environmental compensation. We tested 24 species for the ability to synthesize lipids de novo and collected additional data from the literature. We found the majority of adult parasitoid species to be incapable of synthesizing lipids, and phylogenetic analyses showed that the evolution of lack of lipogenesis is concurrent with that of parasitism in insects. Exploitive host manipulation, in which the host is forced to synthesize lipids to the benefit of the parasitoid, presumably facilitates loss of lipogenesis through environmental compensation. Lipogenesis re-evolved in a small number of parasitoid species, particularly host generalists. The wide range of host species in which generalists are able to develop may impede effective host manipulation and could have resulted in regaining of lipogenic ability in generalist parasitoids. As trait loss through environmental compensation is unnoticed at the phenotypic level, it may be more common than currently anticipated, especially in species involved in intricate symbiotic relationships with other species.
Noncommutative topology and the world’s simplest index theorem
Authors: van Erp Erik
Published: April 2010

In this article we outline an approach to index theory on the basis of methods of noncommutative topology. We start with an explicit index theorem for second-order differential operators on 3-manifolds that are Fredholm but not elliptic. This low-brow index formula is expressed in terms of winding numbers. We then proceed to show how it is derived as a special case of an index theorem for hypoelliptic operators on contact manifolds. Finally, we discuss the noncommutative topology that is employed in the proof of this theorem. The article is intended to illustrate that noncommutative topology can be a powerful tool for proving results in classical analysis and geometry.
Resistive g-modes in a reversed-field pinch plasma
Authors: Zuin M. , Spagnolo S. , Paccagnella R. , Martines E. , Cavazzana R. , Serianni G. , Spolaore M. , Vianello N.
Published: April 2010

The first direct experimental evidence of high frequency, high toroidal mode number magnetic fluctuations due to unstable resistive interchange modes (g-modes) resonant in the edge region of a RFX-mod reversed-field pinch device is presented. Experimental characterization of time and space periodicities of the modes is provided by means of highly resolved in-vessel edge and insertable magnetic diagnostics. Although the saturated energy spectrum of the measured modes is expected to be highly nonlinear, it is found that the spectral mode properties are in good agreement with the predictions of a simple linear resistive magnetohydrodynamic stability analysis. Also a simple quasi-linear saturation model is proposed to explain the observed mode amplitudes.
Cross section of the d + 3He → α + p reaction of relevance for fusion plasma applications
Authors: Nocente M. , Gorini G. , Källne J. , Tardocchi M.
Published: April 2010

The cross section of the d + 3He → α + p fusion reaction has been determined with regard to its systematic variation with energy (E
CM) based on the available experimental data. Information is provided on the angular distribution dσ/dΩ(θp, E) at energies up to E
CM = 8.0 MeV and the total cross section σ(E
CM) for the range E
CM = 3.0–8.0 MeV. The relevance of the presented results for fusion plasmas heated with RF heating of 3He minority in D and DT plasmas is discussed.
Transport simulation of ELM pacing by pellet injection in tokamak plasmas
Authors: Kim Ki Min , Na Yong-Su , Hong Sang Hee , Lang P.T. , Alper B.
Published: April 2010

This paper deals mainly with the numerical simulation on edge localized mode (ELM) pacing by pellet injection that is useful for fuelling and control of plasma profiles to achieve enhanced tokamak operations. The fuelling and pellet-induced ELMs are simulated with a 1.5-dimensional core transport code, which includes a neutral gas shielding model and a grad-B drift model for pellet deposition in H-mode tokamak plasmas. Fuelling and ELM pacing experiments by pellet injections at JET are introduced as a current experimental approach. For the description of ELM triggering by pellet injection based on ideal ballooning mode criteria, three possible models are suggested and discussed on their ELM characteristics, respectively: (i) the density enhanced ELMs in the post-pellet phase, (ii) the modification of the surface averaged pressure profiles in a transport time scale and (iii) the local increase in the pressure (density and/or temperature) gradients perturbed by pellets. Among them, the pellet-induced density perturbation model is adopted, in practice, to carry out an ELM pacing simulation in preparation for future experiments in KSTAR. The numerical simulation shows that the artificially induced ELM by pellets releases the reduced energy bursts, compared with spontaneous ELMs. The energy loss per burst by the pellet-induced ELM turns out to be much smaller than that by the spontaneous ELM as the pellet injection frequency becomes higher in ELM pacing. Based on the simulation results showing good agreement with the general ELM characteristics observed in pellet pacing experiments, the ELM pacing by pellet injection is very promising for mitigating the ELM energy bursts to the divertor by controlling the injection frequency.
Comment on ‘Plasma current spikes due to internal reconnection during tokamak disruptions’
Authors: Izzo V.A. , Parks P.B.
Published: April 2010

In tokamak disruptions, a brief increase in the total plasma current—an I
p spike—frequently precedes the current quench. The I
p spike is commonly attributed to an internal reconnection event that lowers the internal inductance. Plasma current spikes seen in four fixed-boundary MHD disruption simulations support this explanation and are discussed in terms of the evolution of poloidal flux and poloidal magnetic energy.
CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs
Authors: van Houte Bart P.P. , Binsl Thomas W. , Hettling Hannes , Heringa Jaap
Published: April 2010

Summary: CGHnormaliter is a package for normalization of array comparative genomic hybridization (aCGH) data. It uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). CGHnormaliter is integrated in the Bioconductor environment allowing a smooth link to visualization tools and further data analysis.

Availability and Implementation: The CGHnormaliter package is implemented in R and under GPL 3.0 license available at Bioconductor: http://www.bioconductor.org

Contact:  heringa@few.vu.nl
FABIA: factor analysis for bicluster acquisition
Authors: Hochreiter Sepp , Bodenhofer Ulrich , Heusel Martin , Mayr Andreas , Mitterecker Andreas , Kasim Adetayo , Khamiakova Tatsiana , Van Sanden Suzy , Lin Dan , Talloen Willem , Bijnens Luc , Göhlmann Hinrich W. H. , Shkedy Ziv , Clevert Djork-Arné
Published: April 2010

Motivation: Biclustering of transcriptomic data groups genes and samples simultaneously. It is emerging as a standard tool for extracting knowledge from gene expression measurements. We propose a novel generative approach for biclustering called ‘FABIA: Factor Analysis for Bicluster Acquisition’. FABIA is based on a multiplicative model, which accounts for linear dependencies between gene expression and conditions, and also captures heavy-tailed distributions as observed in real-world transcriptomic data. The generative framework allows to utilize well-founded model selection methods and to apply Bayesian techniques.

Results: On 100 simulated datasets with known true, artificially implanted biclusters, FABIA clearly outperformed all 11 competitors. On these datasets, FABIA was able to separate spurious biclusters from true biclusters by ranking biclusters according to their information content. FABIA was tested on three microarray datasets with known subclusters, where it was two times the best and once the second best method among the compared biclustering approaches.

Availability: FABIA is available as an R package on Bioconductor (http://www.bioconductor.org). All datasets, results and software are available at http://www.bioinf.jku.at/software/fabia/fabia.html

Contact:  hochreit@bioinf.jku.at

Supplementary information:  Supplementary data are available at Bioinformatics online.
Efficacy and safety of angiotensin receptor blockade are not modified by aspirin in patients with chronic heart failure: a cohort study from the Candesartan in Heart failure – Assessment of Reduction in Mortality and morbidity (CHARM) programme
Authors: Chang Su Min , Granger Christopher B. , Johansson Peter A. , Kosolcharoen Peter , McMurray John J.V. , Michelson Eric L. , Murray David R. , Olofsson Bertil , Pfeffer Marc A. , Solomon Scott D. , Swedberg Karl , Yusuf Salim , Dunlap Mark E. ,   for the CHARM Investigators
Published: April 2010

Aims

It is unknown whether there is an interaction between aspirin and angiotensin receptor blockers on outcomes in patients with heart failure (HF).

Methods and results

The efficacy and safety of candesartan vs. placebo was assessed in 7599 patients with symptomatic HF and reduced or preserved left ventricular ejection fraction enrolled in the CHARM programme according to baseline aspirin use. Patients were randomized to candesartan or matching placebo and were followed for a median of 38 months. Aspirin was used in 4246 (55.9%) of patients at baseline. When compared with placebo, candesartan use was associated with lower event rates for cardiovascular (CV) death or HF hospitalization (primary outcome) in both the aspirin group (28 vs. 31.9%, HR 0.81, 95% CI 0.72–0.90) and non‐aspirin group (33 vs. 38%, HR 0.81, 95% CI 0.72–0.91). Baseline aspirin use did not modify the effectiveness of candesartan in reducing the risk of CV death or HF hospitalization in CHARM overall (P = 0.64) or in the CHARM individual trials. In addition, there was no significant interaction between aspirin therapy and candesartan in terms of discontinuation of study drug due to adverse reactions (P = 0.72).

Conclusion

There appears to be no significant modification of the benefit of candesartan on CV mortality and morbidity outcomes or safety by concomitant use of aspirin in patients with chronic HF.
An alternative approach on the existence of affine realizations for HJM term structure models
Authors: Tappe Stefan
Published: April 2010

We propose an alternative approach on the existence of affine realizations for Heath, Jarrow and Morton interest rate models. It is applicable to a wide class of models, and simultaneously it is conceptually rather comprehensible. We also supplement some known existence results for particular volatility structures and provide further insights into the geometry of term structure models.
Mycoplasma mucosicanis sp. nov., isolated from the mucosa of dogs
Authors: Spergser Joachim , Langer Stefan , Muck Simone , Macher Kathrin , Szostak Michael , Rosengarten Renate , Busse Hans-Jürgen
Published: April 2010

Fourteen Mycoplasma strains were isolated from the oral cavity and genital tract of asymptomatic dogs. Isolates had been preliminarily identified by conventional serological testing as Mycoplasma bovigenitalium, but in 16S–23S rRNA intergenic spacer PCR-RFLP assays the isolates exhibited an RFLP pattern distinct from M. bovigenitalium PG11T. Analysis of the 16S rRNA gene placed a representative of the isolates (strain 1642T) in the M. bovigenitalium subcluster of the Mycoplasma bovis cluster of mycoplasmas, with the highest sequence similarities to Mycoplasma californicum ST-6T (96.4 %), M. bovigenitalium PG11T (96.3 %) and Mycoplasma phocirhinis 852T (96.2 %). 16S rRNA gene sequence similarities almost equidistant from three recognized species and results obtained by sequence analysis of the 16S–23S rRNA intergenic spacer region, polar lipid profiles and serological reactions indicated that this organism represents a novel species of the genus Mycoplasma for which the name Mycoplasma mucosicanis sp. nov. is proposed, with strain 1642T ( = ATCC BAA-1895T  = DSM 22457T) as the type strain.
Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil
Authors: Ara Ismet , Tsetseg Baljinova , Daram Damdinsuren , Suto Manabu , Ando Katsuhiko
Published: April 2010

Two actinomycetes, designated MN08-A0270T and MN08-A0297T, were isolated from soil from the area around Khuvsgul Lake, Khuvsgul province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, branched substrate hyphae and, similar to closely related species of the genus Pseudonocardia, produced zigzag-shaped aerial hyphae by acropetal budding and blastospores. A comparative analysis of 16S rRNA gene sequences indicated that strains MN08-A0270T and MN08-A0297T formed two distinct clades within the genus Pseudonocardia and were respectively most closely related to Pseudonocardia yunnanensis NBRC 15681T (97.3 % similarity) and Pseudonocardia thermophila IMSNU 20112T (97.1 %). Chemotaxonomic characteristics, including cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Pseudonocardia. Strains MN08-A0270T and MN08-A0297T could be differentiated from each other and from closely related species of the genus Pseudonocardia by physiological and biochemical characteristics, predominant fatty acids, menaquinones and whole-cell sugar components. Combined with the results of a broad range of phenotypic tests and DNA–DNA hybridization data and phylogenetic analysis, these results support the conclusion that these strains represent two novel species of the genus Pseudonocardia, for which we propose the names Pseudonocardia mongoliensis sp. nov. (type strain MN08-A0270T  = NBRC 105885T  = VTCC D9-25T) and Pseudonocardia khuvsgulensis sp. nov. (type strain MN08-A0297T  = NBRC 105886T  = VTCC D9-26T).
Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella
Authors: Lee Se Hee , Shim Jae Kuk , Kim Jeong Myeong , Choi Hyung-Kyoon , Jeon Che Ok
Published: April 2010

A Gram-staining-negative, strictly aerobic bacterium, designated strain SD10T, was isolated from a tidal flat of the Yellow Sea, South Korea. Cells were non-spore-forming rods that showed catalase- and oxidase-positive reactions. Growth of strain SD10T was observed at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 6.5–8.5) and in the presence of 1–10 % (w/v) NaCl. Strain SD10T contained ubiquinone-10 (Q-10) as a major isoprenoid quinone and C18 : 1ω7c (39.3 %), C16 : 0 (20.2 %), C17 : 0 (8.9 %) and C17 : 1ω6c (8.1 %) as major fatty acids. The cellular polar lipids were identified as phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 55.2 mol%. Based on 16S rRNA gene sequence similarities, the strain was most closely related to Henriciella marina Iso4T and Maribaculum marinum P38T, with similarities of 97.8 and 97.0 %, respectively. The DNA–DNA relatedness between strain SD10T and H. marina Iso4T was 12.0±3.2 %. A phylogenetic analysis based on 16S rRNA gene sequences showed that M. marinum P38T and H. marina Iso4T formed a monophyletic cluster and that their 16S rRNA gene sequence similarity was 98.1 %. DNA–DNA hybridization between H. marina Iso4T and M. marinum LMG 24711T was 22.9±2.7 %, indicating that the two strains belong to separate species. On the basis of chemotaxonomic data and molecular properties, we propose that strain SD10T represents a novel species of the genus Henriciella, for which the name Henriciella litoralis sp. nov. is proposed. The type strain is SD10T ( = KACC 13700T  = DSM 22014T). In addition, we propose to transfer Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. (type strain P38T  = CCTCC AB 208227T  = LMG 24711T  = MCCC 1A01086T), and we present an emended description of the genus Henriciella.
Spiroplasma eriocheiris sp. nov., associated with mortality in the Chinese mitten crab, Eriocheir sinensis
Authors: Wang Wen , Gu Wei , Gasparich Gail E. , Bi Keran , Ou Jiangtao , Meng Qingguo , Liang Tingming , Feng Qi , Zhang Jianqiong , Zhang Ying
Published: April 2010

A motile bacterium, designated strain TDA-040725-5T, was isolated from the haemolymph of a Chinese mitten crab, Eriocheir sinensis, with tremor disease. Based on 16S rRNA gene sequence analysis, the strain was phylogenetically distinct from other spiroplasmas but was closely related to Spiroplasma mirum ATCC 29335T. Cells of strain TDA-040725-5T were variable in length and shape, helical and motile, as determined by phase-contrast light microscopy. Examination by electron microscopy revealed wall-less cells delimited by a single membrane. The strain grew in M1D or R-2 liquid media at 20–40 °C, with optimum growth at 30 °C. Doubling time at the optimal temperature was 24 h. The strain catabolized glucose and hydrolysed arginine but did not hydrolyse urea. The DNA G+C content was 29.7±1 mol%. The genome size was ~1.4–1.6 Mbp. Serological analysis, performed using the deformation test, did not reveal any reciprocal titres ≥320, indicating that strain TDA-040725-5T had minimal cross-reactivity to strains of recognized species of the genus Spiroplasma. Based on this evidence, strain TDA-040725-5T ( = CCTCC M 207170T  = DSM 21848T) represents a novel species of the genus Spiroplasma, for which the name Spiroplasma eriocheiris sp. nov. is proposed, belonging to the novel Spiroplasma serological group XLIII.
Desulfosoma caldarium gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a terrestrial hot spring
Authors: Baena Sandra , Perdomo Natalia , Carvajal Catalina , Díaz Carolina , Patel Bharat K. C.
Published: April 2010

A thermophilic, sulfate-reducing bacterium, designated strain USBA-053T, was isolated from a terrestrial hot spring located at a height of 2500 m in the Colombian Andes (5° 45′ 33.29″ N 73° 6′ 49.89″ W), Colombia. Cells of strain USBA-053T were oval- to rod-shaped, Gram-negative and motile by means of a single polar flagellum. The strain grew autotrophically with H2 as the electron donor and heterotrophically on formate, propionate, butyrate, valerate, isovalerate, lactate, pyruvate, ethanol, glycerol, serine and hexadecanoic acid in the presence of sulfate as the terminal electron acceptor. The main end products from lactate degradation, in the presence of sulfate, were acetate, CO2 and H2S. Strain USBA-053T fermented pyruvate in the absence of sulfate and grew optimally at 57 °C (growth temperature ranged from 50 °C to 62 °C) and pH 6.8 (growth pH ranged from 5.7 to 7.7). The novel strain was slightly halophilic and grew in NaCl concentrations ranging from 5 to 30 g l−1, with an optimum at 25 g l−1 NaCl. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not elemental sulfur, nitrate or nitrite. The G+C content of the genomic DNA was 56±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA-053T was a member of the class Deltaproteobacteria, with Desulfacinum hydrothermale MT-96T as the closest relative (93 % gene sequence similarity). On the basis of physiological characteristics and phylogenetic analysis, it is suggested that strain USBA-053T represents a new genus and novel species for which the name Desulfosoma caldarium gen. nov., sp. nov. is proposed. The type strain of the type species is USBA-053T ( = KCTC 5670T = DSM 22027T).
Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater
Authors: Park Seong Chan , Baik Keun Sik , Choe Han Na , Lim Chae Hong , Kim Ho Jun , Ka Jong-Ok , Seong Chi Nam
Published: April 2010

Two non-motile, orange- or yellow-pigmented bacteria, designated strains KYW48T and KYW147T, were isolated from seawater collected from the South Sea, Republic of Korea. Cells of both strains were Gram-reaction-negative, aerobic and catalase- and oxidase-positive. The major fatty acids of strain KYW48T were C18 : 1ω7c (35.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) (22.7 %), C17 : 1ω6c (19.8 %), C14 : 0 2-OH (7.4 %) and C16 : 0 (5.9 %), and those of strain KYW147T were C18 : 1ω7c (36.0 %), summed feature 3 (18.3 %), C16 : 0 (14.7 %), 11-methyl C18 : 1ω7c (10.7 %), C16 : 0 2-OH (9.1 %) and C18 : 1ω9c (8.0 %). The predominant isoprenoid quinone of both strains was ubiquinone 10 (Q-10). The DNA G+C contents of strains KYW48T and KYW147T were 63.8 and 67.2 mol%, respectively. A phylogenetic tree based on 16S rRNA gene sequences showed that strains KYW48T and KYW147T were grouped with the members of the family Erythrobacteraceae and formed a distinct clade with the members of the genus Altererythrobacter (<95.7 % sequence similarity). On the basis of the evidence presented in this study, the novel species Altererythrobacter namhicola sp. nov. (type strain KYW48T  = KCTC 22736T  = JCM 16345T) and Altererythrobacter aestuarii sp. nov. (type strain KYW147T  = KCTC 22735T  = JCM 16339T) are proposed.
Cohaesibacter marisflavi sp. nov., isolated from sediment of a seawater pond used for sea cucumber culture, and emended description of the genus Cohaesibacter
Authors: Qu Lingyun , Lai Qiliang , Zhu Fengling , Hong Xuguang , Sun Xiuqin , Shao Zongze
Published: April 2010

A Gram-negative, catalase-negative, oxidase-positive, rod-shaped bacterium, strain DQHS21T, was isolated from sediment of a seawater pond used for sea cucumber culture at Jimo in Qingdao province on the east coast of China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DQHS21T belonged to the genus Cohaesibacter, sharing the highest sequence similarity (96.1 %) with Cohaesibacter gelatinilyticus CL-GR15T, while the similarity to other strains was below 93.0 %. The cellular fatty acids consisted mainly of C18 : 1ω7c (60.7 %), C18 : 0 (17.8 %), C16 : 0 (8.5 %) and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 6.0 %), which together accounted for 93 % of the total fatty acids. Ubiquinone 10 was the major quinone. The G+C content of the chromosomal DNA of strain DQHS21T was 55.2 mol%. The combined genotypic and phenotypic data showed that strain DQHS21T represents a novel species of the genus Cohaesibacter, for which the name Cohaesibacter marisflavi sp. nov. is proposed, with the type strain DQHS21T ( = CGMCC 1.9157T  = NCCB 100300T).
Paenibacillus puldeungensis sp. nov., isolated from a grassy sandbank
Authors: Traiwan Jitsopin , Park Mi-Hak , Kim Wonyong
Published: April 2010

The taxonomic position of a Gram-stain-positive, rod-shaped, endospore-forming, facultatively anaerobic bacterial strain, CAU 9324T, isolated from a grassy sandbank was investigated by using a polyphasic approach. Strain CAU 9324T grew optimally at 30 °C and pH 6.0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major isoprenoid quinone was menaquinone-7 (MK-7). The polar lipid profile consisted of diphosphatidylglycerol as the major component. The predominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content of strain CAU 9324T was 48.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain belonged to the genus Paenibacillus, showing <96.4 % similarity to the type strains of all recognized Paenibacillus species. On the basis of phenotypic, chemotaxonomic and genotypic data, strain CAU 9324T was considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus puldeungensis sp. nov. is proposed. The type strain is CAU 9324T (=KCTC 13718T =CCUG 59189T).
Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree
Authors: Kaewkla Onuma , Franco Christopher M. M.
Published: April 2010

A novel strain, designated EUM 374T, was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374T grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095T and Pseudonocardia spinosispora LM 141T, respectively, and 93–96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374T from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374T ( = DSM 45351T  = ACM 5285T).
Citreicella marina sp. nov., isolated from deep-sea sediment
Authors: Lai Qiliang , Fu Yuanyuan , Wang Jianning , Chen Shuangxi , Zhong Huanzi , Sun Fengqin , Shao Zongze
Published: April 2010

A taxonomic study was carried out on a novel strain, designated CK-I3-6T, which was isolated from deep-sea sediment of the south-west Indian Ocean Ridge. Cells were Gram-reaction-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at 4–38 °C and in 1–12 % (w/v) NaCl. Cells were able to degrade gelatin and oxidize thiosulfate but did not reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CK-I3-6T belonged to the genus Citreicella with a sequence similarity of 97.3 % to Citreicella thiooxidans CHLG 1T, while similarities with other taxa were <95.7 %. DNA–DNA hybridization showed that strain CK-I3-6T and C. thiooxidans CHLG 1T showed a low DNA–DNA relatedness (48±3 %). The principal fatty acids were C16 : 0 (7.8 %), C18 : 1ω7c (66.6 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 6.3 %) and C19 : 0ω8c cyclo (10.0 %). The chromosomal DNA G+C content was 67.5 mol%. On the basis of the combined genotypic and phenotypic data, strain CK-I3-6T represents a novel species of the genus Citreicella, for which the name Citreicella marina sp. nov. is proposed. The type strain is CK-I3-6T ( = CCTCC AB 209064T  = LMG 25230T  = MCCC 1A03060T).
Actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a Thai jasmine rice plant
Authors: Indananda Chantra , Thamchaipenet Arinthip , Matsumoto Atsuko , Inahashi Yuki , Duangmal Kannika , Takahashi Yoko
Published: April 2010

The novel strain GMKU 370T was isolated from roots of a Thai jasmine rice plant (Oryza sativa L. ‘KDML 105’) collected from Pathum Thani Rice Research Center, Pathum Thani province, Thailand. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GMKU 370T formed a distinct clade within the genus Actinoallomurus. Strain GMKU 370T contained meso-diaminopimelic acid and lysine in the cell-wall peptidoglycan and galactose and madurose as whole-cell sugars. No mycolic acids were detected. The predominant menaquinones were MK-9(H6) and MK-9(H8). The polar phospholipids consisted of phosphatidylglycerol and phosphatidylinositol. These chemical properties reveal that strain GMKU 370T belongs to the genus Actinoallomurus. Strain GMKU 370T is distinct from the phylogenetically closely related type strains Actinoallomurus iriomotensis NBRC 103685T and Actinoallomurus coprocola NBRC 103688T (99.20 % 16S rRNA gene sequence similarity to both) in terms of differences in phenotypic characteristics and DNA–DNA relatedness (51 and 17 %, respectively). It is proposed that strain GMKU 370T represents a novel species of the genus Actinoallomurus, for which the name Actinoallomurus oryzae sp. nov. is proposed. The type strain is GMKU 370T ( = BCC 31373T  = NBRC 105246T).
Lindnera rhizosphaerae sp. nov., a yeast species isolated from rhizospheric soil
Authors: Mestre M. Cecilia , Rosa Carlos A. , Fontenla Sonia B.
Published: April 2010

Two strains of a novel yeast species were isolated from ectomycorrhizal Nothofagus pumilio rhizospheric soil in a native forest of Patagonia, Argentina. Analysis of the D1/D2 large-subunit rRNA gene sequences indicated that the novel species belongs to the recently described genus Lindnera. The name Lindnera rhizosphaerae sp. nov. is proposed to accommodate these isolates, and the type strain is CRUB 1796T ( = CBS 11400T  = JCM 16499T).
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
Authors: Shoemaker Robert , Deng Jie , Wang Wei , Zhang Kun
Published: April 2010

In diploid mammalian genomes, parental alleles can exhibit different methylation patterns (allele-specific DNA methylation, ASM), which have been documented in a small number of cases except for the imprinted regions and X chromosomes in females. We carried out a chromosome-wide survey of ASM across 16 human pluripotent and adult cell lines using Illumina bisulfite sequencing. We applied the principle of linkage disequilibrium (LD) analysis to characterize the correlation of methylation between adjacent CpG sites on single DNA molecules, and also investigated the correlation between CpG methylation and single nucleotide polymorphisms (SNPs). We observed ASM on 23%∼37% heterozygous SNPs in any given cell line. ASM is often cell-type-specific. Furthermore, we found that a significant fraction (38%∼88%) of ASM regions is dependent on the presence of heterozygous SNPs in CpG dinucleotides that disrupt their methylation potential. This study identified distinct types of ASM across many cell types and suggests a potential role for CpG-SNP in connecting genetic variation with the epigenome.
Short-term memories in Drosophila are governed by general and specific genetic systems
Authors: Zars Troy
Published: April 2010

In a dynamic environment, there is an adaptive value in the ability of animals to acquire and express memories. That both simple and complex animals can learn is therefore not surprising. How animals have solved this problem genetically and anatomically probably lies somewhere in a range between a single molecular/anatomical mechanism that applies to all situations and a specialized mechanism for each learning situation. With an intermediate level of nervous system complexity, the fruit fly Drosophila has both general and specific resources to support different short-term memories. Some biochemical/cellular mechanisms are common between learning situations, indicating that flies do not have a dedicated system for each learning context. The opposite possible extreme does not apply to Drosophila either. Specialization in some biochemical and anatomical terms suggests that there is not a single learning mechanism that applies to all conditions. The distributed basis of learning in Drosophila implies that these systems were independently selected.
The Arabidopsis Chaperone J3 Regulates the Plasma Membrane H+-ATPase through Interaction with the PKS5 Kinase
Authors: Yang Yongqing , Qin Yunxia , Xie Changgen , Zhao Feiyi , Zhao Jinfeng , Liu Dafa , Chen Shouyi , Fuglsang Anja T. , Palmgren Michael G. , Schumaker Karen S. , Deng Xing Wang , Guo Yan
Published: April 2010

The plasma membrane H+-ATPase (PM H+-ATPase) plays an important role in the regulation of ion and metabolite transport and is involved in physiological processes that include cell growth, intracellular pH, and stomatal regulation. PM H+-ATPase activity is controlled by many factors, including hormones, calcium, light, and environmental stresses like increased soil salinity. We have previously shown that the Arabidopsis thaliana Salt Overly Sensitive2-Like Protein Kinase5 (PKS5) negatively regulates the PM H+-ATPase. Here, we report that a chaperone, J3 (DnaJ homolog 3; heat shock protein 40-like), activates PM H+-ATPase activity by physically interacting with and repressing PKS5 kinase activity. Plants lacking J3 are hypersensitive to salt at high external pH and exhibit decreased PM H+-ATPase activity. J3 functions upstream of PKS5 as double mutants generated using j3-1 and several pks5 mutant alleles with altered kinase activity have levels of PM H+-ATPase activity and responses to salt at alkaline pH similar to their corresponding pks5 mutant. Taken together, our results demonstrate that regulation of PM H+-ATPase activity by J3 takes place via inactivation of the PKS5 kinase.
The effect of dyslexia on information retrieval
Authors: MacFarlane A. , Al‐Wabil A. , Marshall C.R. , Albrair A. , Jones S.A. , Zaphiris P.
Published: April 2010

Purpose

The purpose of this paper is to resolve a gap in the knowledge of how people with dyslexia interact with information retrieval (IR) systems, specifically an understanding of their information‐searching behaviour.

Design/methodology/approach

The dyslexia cognitive profile is used to design a logging system, recording the difference between two sets of participants: dyslexic and control users. A standard Okapi interface is used – together with two standard TREC topics – in order to record the information searching behaviour of these users.

Findings

Using the log data, the differences in information‐searching behaviour of control and dyslexic users, i.e. in the way the two groups interact with Okapi, are established and it also established that qualitative information collected (such as experience etc.) may not be able to account for these differences. Evidence from query variables was unable to distinguish between groups, but differences on topic for the same variables were recorded. Users who view more documents tended to judge more documents as being relevant, in terms of either the user group or topic. Session data indicated that there may be an important difference between the number of iterations used in a search between the user groups, as there may be little effect from the topic on this variable.

Originality/value

This is the first study of the effect of dyslexia on information search behaviour, and it provides some evidence to take the field forward.
Creativity and craft: the information‐seeking behavior of theatre artists
Authors: Medaille Ann
Published: April 2010

Purpose

The aim of this study is to explore the information needs and behaviors of practicing theatre artists. Psychological research into creativity provides a framework for understanding both theatre artists' information‐seeking behavior and the role of information seeking and gathering in the creative process.

Design/methodology/approach

The exploratory study presents findings from an online questionnaire of 73 practicing theatre artists and qualitative data gathered from eight interviews with theatre professionals.

Findings

The study reveals that theatre artists seek information for six primary purposes: understanding a work's historical, cultural, and critical background; finding sources of inspiration; learning about contemporary or historical theatre productions, artists, and events; learning technical or process information; finding performance materials; and furthering career goals. Theatre artists view the information search process as being essential to their creative activities, and their first‐hand accounts of their artistic experiences illuminate the critical role that information seeking and gathering play in the creative process.

Research limitations/implications

Some theatre professions, such as lighting or sound design, were represented in the questionnaire but were not represented in the interviews.

Practical implications

The study has practical implications for the delivery of library and internet theatre art collections and information services.

Originality/value

Few studies have examined the information‐seeking behavior of practicing theatre artists. The paper demonstrates that studies of artists can be used to understand the role of information seeking and gathering in the creative processes of people working in various subject domains.
Information about the synthesis of life forms: a document‐oriented approach
Authors: Kouper Inna
Published: April 2010

Purpose

This study aims to examine the forms of information about the synthesis of life forms in the public sphere.

Design/methodology/approach

A document‐oriented approach was used and a wide range of documents that discuss a particular technoscientific issue was sampled. The analysis of documents involved a combination of discourse and content analysis.

Findings

The study demonstrates that there is a significant growth of the diversity of document types over time. Overall, 24 document types and 21 publication formats were identified. Web‐based formats, such as blogs and news and information web sites, play a prominent role in the dissemination of information about the synthesis of life forms.

Research limitations/implications

The variety of document types identified here expands current understanding of the public documentary landscape and shows that the analysis of technoscientific debates and controversies can no longer be limited to traditional mass media documents such as news, feature articles, and editorials. However, a larger sample that includes more documents as well as non‐textual objects, such as images or even lab specimens, would expand the scope of this taxonomy and make conclusions more definitive. Further research into the specific digital types of documents identified in the study and their impact on the communication of scientific information to the public is needed.

Practical implications

Surveying and understanding the kinds of documents that circulate information about emerging technoscientific issues can help to provide better services for a variety of information users and develop better tools for access and dissemination of such information.

Originality/value

The study demonstrates that a document‐oriented approach can provide valuable insight into the circulation of information about science in the public sphere. It also offers an elaborate taxonomy of documents that can be used in further research as well as in information and science literacy instruction.
Scholarly output: print and digital – in teaching and research
Authors: Maynard Sally , O'Brien Ann
Published: April 2010

Purpose

The purpose of this paper is to report the outcomes of a Joint Information Systems Committee (JISC)‐sponsored study to determine the current state and trends in different forms of scholarly output used in teaching and research; and the nature and extent of problems associated with their use.

Design/methodology/approach

A total of 60 UK HE institutions were chosen at random and a selection of departments within these was contacted. An online questionnaire was distributed to the selected departments; resulting in responses from 304 academics across a broad range of subjects and institution types.

Findings

The study showed that printed output was still the preferred option in both teaching and research, although electronic journals now have a well‐established presence. Web‐based material is increasingly provided in teaching and used in research but this includes primarily traditional tools such as reading lists and links to scholarly resources. Some content creation was evident. Use of web 2.0 was not extensive, although respondents were making use of Institutional Learning Environments. Academics were aware of Intellectual Property Rights (IPR) issues but not always clear about their responsibilities in this area.

Research limitations/implications

The study revealed an essentially conservative approach to the developments in digital information. This may have been due to the sample size which was relatively small, and the age profile which clustered around the 45‐65 years range. In the case of research the influence of the Research Assessment Exercise (RAE) was clear.

Originality/value

No equivalent study has been reported on the transition between traditional and new forms of scholarly output used in teaching and research. In this fast developing area this research provides a benchmark for future studies.
Diversity in the e‐journal use and information‐seeking behaviour of UK researchers
Authors: Nicholas David , Rowlands Ian , Huntington Paul , Jamali Hamid R. , Hernández Salazar Patricia
Published: April 2010

Purpose

The purpose of this paper is to present some of the results of the project “Evaluating the usage and impact of e‐journals in the UK”. The particular research reported here evaluated the use of the ScienceDirect journals database with regard to Life Sciences, Economics, Chemistry, Earth & Environmental Sciences and Physics by ten major UK research institutions. The aim of the study is to investigate researchers' digital behaviour, and to ascertain whether their use and behaviours varied by subjects and disciplines, or in relation to the institutions in which they worked.

Design/methodology/approach

Raw logs for ScienceDirect were obtained for the period January to April 2007, were subject to deep log techniques and analysed using the Software Package for Social Sciences (SPSS).

Findings

Typically, 5 per cent of the ScienceDirect journals viewed accounted for a third to half of all use. A high proportion of researchers entered the ScienceDirect site via a third‐party site, and this was especially so in the case of the Life Sciences and in the highest‐ranked research institutions. There were significant institutional and subject differences in information‐seeking behaviour. In the most research‐intensive institutions, per capita journal use was highest and their users spent much less time on each visit. There were significant differences of the order of 100‐300 per cent in the age of material viewed between subjects and institutions. Just four months after ScienceDirect content was opened to Google indexing, a third of traffic to the site's Physics journals came via that route.

Originality/value

The research is one of the very few studies to investigate subject and institutional differences with regard to the information seeking and use of UK researchers, something UK academic librarians should particularly welcome.
The one‐stop shop search engine: a transformational library technology?
Authors: Joint Nicholas
Published: April 2010

Purpose

The purpose of this paper is to form one of a series which will give an overview of so‐called “transformational” areas of digital library technology. The aim will be to assess how much real transformation these applications are bringing about, in terms of creating genuine user benefit and also changing everyday library practice.

Design/methodology/approach

An overview of the present state of development of the one‐stop shop library search engine, with particular reference to its relationship with the underlying bibliographic databases to which it provides a simplified single interface.

Findings

The paper finds that the success of federated searching has proved valuable but limited to date in creating a one‐stop shop search engine to rival Google Scholar; but the persistent value of the bibliographic databases sitting underneath a federated search system means that a harvesting search engine could well answer the need for a true one‐stop search engine for academic and scholarly information.

Research limitations/implications

This paper is based on the hypothesis that Google's success in providing such an apparently high degree of access to electronic journal services is not what it seems, and that it does not render library discovery tools obsolete. It argues that Google has not diminished the pre‐eminent role of library bibliographic databases in mediating access to e‐journal text, although this hypothesis needs further research to validate or disprove it.

Practical implications

The paper affirms the value of bibliographic databases to practitioner librarians and the potential of single interface discovery tools in library practice.

Originality/value

The paper uses statistics from US LIS sources to shed light on UK discovery tool issues.