bluuebunny/crossref_metadata_2025 huggingface dataset:
GOSSIP: a method for fast and accurate global alignment of protein structures
Authors: Kifer I. , Nussinov R. , Wolfson H. J.
Published: February 2011

Motivation: The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time.

Results: Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities.

Availability: A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

Contact:  wolfson@tau.ac.il; ilonak@post.tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Model annotation for synthetic biology: automating model to nucleotide sequence conversion
Authors: Misirli Goksel , Hallinan Jennifer S. , Yu Tommy , Lawson James R. , Wimalaratne Sarala M. , Cooling Michael T. , Wipat Anil
Published: February 2011

Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models.

Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC.

Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html.

Contact:  anil.wipat@ncl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists
Authors: Voss Björn , Hanselmann Michael , Renard Bernhard Y. , Lindner Martin S. , Köthe Ullrich , Kirchner Marc , Hamprecht Fred A.
Published: February 2011

Motivation: Alignment of multiple liquid chromatography/mass spectrometry (LC/MS) experiments is a necessity today, which arises from the need for biological and technical repeats. Due to limits in sampling frequency and poor reproducibility of retention times, current LC systems suffer from missing observations and non-linear distortions of the retention times across runs. Existing approaches for peak correspondence estimation focus almost exclusively on solving the pairwise alignment problem, yielding straightforward but suboptimal results for multiple alignment problems.

Results: We propose SIMA, a novel automated procedure for alignment of peak lists from multiple LC/MS runs. SIMA combines hierarchical pairwise correspondence estimation with simultaneous alignment and global retention time correction. It employs a tailored multidimensional kernel function and a procedure based on maximum likelihood estimation to find the retention time distortion function that best fits the observed data. SIMA does not require a dedicated reference spectrum, is robust with regard to outliers, needs only two intuitive parameters and naturally incorporates incomplete correspondence information. In a comparison with seven alternative methods on four different datasets, we show that SIMA yields competitive and superior performance on real-world data.

Availability: A C++ implementation of the SIMA algorithm is available from http://hci.iwr.uni-heidelberg.de/MIP/Software.

Contact:  fred.hamprecht@iwr.uni-heidelberg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
DDN: a caBIG® analytical tool for differential network analysis
Authors: Zhang Bai , Tian Ye , Jin Lu , Li Huai , Shih Ie-Ming , Madhavan Subha , Clarke Robert , Hoffman Eric P. , Xuan Jianhua , Hilakivi-Clarke Leena , Wang Yue
Published: February 2011

Summary: Differential dependency network (DDN) is a caBIG® (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG® 's In Silico Research Centers of Excellence (ISRCE) Program, DDN enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. DDN also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, CytoDDN, to integrate network analysis and visualization seamlessly.

Availability: The Java and MATLAB source code can be downloaded at the authors' web site http://www.cbil.ece.vt.edu/software.htm

Contact:  yuewang@vt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Gobe: an interactive, web-based tool for comparative genomic visualization
Authors: Pedersen Brent S. , Tang Haibao , Freeling Michael
Published: February 2011

Summary: Gobe is a web-based tool for viewing comparative genomic data. It supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive, exploratory research tool. Gobe can be used without installation through our web service, or downloaded and customized with stylesheets and javascript callback functions.

Availability: Gobe is a flash application that runs in all modern web-browsers. The full source-code, including that for the online web application is available under the MIT license at: http://github.com/brentp/gobe. Sample applications are hosted at http://try-gobe.appspot.com/ and http://synteny.cnr.berkeley.edu/gobe-app/.

Contact:  bpederse@berkeley.edu
Projected expansion of the subtropical biome and contraction of the temperate and equatorial upwelling biomes in the North Pacific under global warming
Authors: Polovina Jeffrey J. , Dunne John P. , Woodworth Phoebe A. , Howell Evan A.
Published: February 2011

Polovina, J. J., Dunne, J. P., Woodworth, P. A., and Howell, E. A. 2011. Projected expansion of the subtropical biome and contraction of the temperate and equatorial upwelling biomes in the North Pacific under global warming. – ICES Journal of Marine Science, 68: 986–995. A climate model that includes a coupled ocean biogeochemistry model is used to define large oceanic biomes in the North Pacific Ocean and describe their changes over the 21st century in response to the IPCC Special Report on Emission Scenario A2 future atmospheric CO2 emissions scenario. Driven by enhanced stratification and a northward shift in the mid-latitude westerlies under climate change, model projections demonstrated that between 2000 and 2100, the area of the subtropical biome expands by ∼30% by 2100, whereas the area of temperate and equatorial upwelling (EU) biomes decreases by ∼34 and 28%, respectively, by 2100. Over the century, the total biome primary production and fish catch is projected to increase by 26% in the subtropical biome and decrease by 38 and 15% in the temperate and the equatorial biomes, respectively. Although the primary production per unit area declines slightly in the subtropical and the temperate biomes, it increases 17% in the EU biome. Two areas where the subtropical biome boundary exhibits the greatest movement is in the northeast Pacific, where it moves northwards by as much as 1000 km per 100 years and at the equator in the central Pacific, where it moves eastwards by 2000 km per 100 years. Lastly, by the end of the century, there are projected to be more than 25 million km2 of water with a mean sea surface temperature of 31°C in the subtropical and EU biomes, representing a new thermal habitat. The projected trends in biome carrying capacity and fish catch suggest resource managers might have to address long-term trends in fishing capacity and quota levels.
Soft Rot Disease Severity Is Affected by Potato Physiology and Pectobacterium taxa
Authors: Marquez-Villavicencio Maria del Pilar , Groves Russell L. , Charkowski Amy O.
Published: February 2011

Pectobacterium species cause disease worldwide in many crop and ornamental plants, including potato. A new Pectobacterium subspecies, P. carotovorum subsp. brasiliensis was recently described in Brazil and later found in the United States, Israel, and South Africa. Its virulence traits and host range remain unknown. A comparison of three taxa commonly found on potato showed that both P. carotovorum subsp. carotovorum and subsp. brasiliensis are more aggressive in causing tuber and stem soft rot than P. atrosepticum. Also, despite bacterial growth inhibition in vitro of P. carotovorum subsp. carotovorum and P. atrosepticum strains by P. carotovorum subsp. brasiliensis, this new subspecies and P. carotovorum subsp. carotovorum are able to co-colonize in the same infected tissue. Both subspecies were motile in lesions. Pathogenesis assays showed that host ranges of all three overlap, but are not identical. The host ranges of individual strains of P. carotovorum subsp. carotovorum and subsp. brasiliensis are limited, whereas P. atrosepticum can macerate many plant species in addition to potato. There was high variability in virulence assays with potato tuber; thus physiological factors were investigated. Tuber size, maturity, and field location had significant effects on susceptibility to soft rot, with larger, more mature tubers being more susceptible.
Concentrations and size distributions of airborne influenza A viruses measured indoors at a health centre, a day-care centre and on aeroplanes
Authors: Yang Wan , Elankumaran Subbiah , Marr Linsey C.
Published: February 2011

The relative importance of the aerosol transmission route for influenza remains contentious. To determine the potential for influenza to spread via the aerosol route, we measured the size distribution of airborne influenza A viruses. We collected size-segregated aerosol samples during the 2009–2010 flu season in a health centre, a day-care facility and onboard aeroplanes. Filter extracts were analysed using quantitative reverse transcriptase polymerase chain reaction. Half of the 16 samples were positive, and their total virus concentrations ranged from 5800 to 37 000 genome copies m
−3
. On average, 64 per cent of the viral genome copies were associated with fine particles smaller than 2.5 µm, which can remain suspended for hours. Modelling of virus concentrations indoors suggested a source strength of 1.6 ± 1.2 × 10
5
genome copies m
−3
air h
−1
and a deposition flux onto surfaces of 13 ± 7 genome copies m
−2
h
−1
by Brownian motion. Over 1 hour, the inhalation dose was estimated to be 30 ± 18 median tissue culture infectious dose (TCID
50
), adequate to induce infection. These results provide quantitative support for the idea that the aerosol route could be an important mode of influenza transmission.
Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field
Authors: Wang Liang , An Dong-Shan , Kim Song-Gun , Jin Feng-Xie , Lee Sung-Taik , Im Wan-Taek
Published: February 2011

A novel gammaproteobacterium, designated LnR5-47T, was isolated from soil of a ginseng field in Liaoning province, China. The isolate was a Gram-negative, aerobic, non-motile, non-spore-forming rod. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LnR5-47T belonged to the genus Rhodanobacter. The isolate was most closely related to Rhodanobacter ginsengisoli GR17-7T, Rhodanobacter terrae GP18-1T, Dyella ginsengisoli Gsoil 3046T, Rhodanobacter soli DCY45T, Dyella soli JS12-10T and Dyella japonica IAM 15069T (98.0, 97.9, 97.7, 97.3, 97.2 and 97.1 % 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C16 : 0, iso-C17 : 1ω9c and iso-C15 : 0 as the major fatty acids) also supported the affiliation of strain LnR5-47T with the genus Rhodanobacter. However, DNA–DNA relatedness between strain LnR5-47T and its closest phylogenetic neighbours was <25.8 %. Moreover, physiological and biochemical tests phenotypically differentiated the isolate from other members of the genus Rhodanobacter. Therefore, strain LnR5-47T represents a novel species, for which the name Rhodanobacter panaciterrae sp. nov. is proposed; the type strain is LnR5-47T ( = KACC 12826T = KCTC 22232T = LMG 24460T).
Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov., isolated from Palythoa caribaeorum
Authors: Chimetto Luciane A. , Cleenwerck Ilse , Moreira Ana Paula B. , Brocchi Marcelo , Willems Anne , De Vos Paul , Thompson Fabiano L.
Published: February 2011

Two novel vibrio isolates (R-40492T and R-40493T) originating from the zoanthid Palythoa caribaeorum in Brazil in 2005 were taxonomically characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA), DNA–DNA hybridization (DDH), ΔT
m analysis and phenotypic characterization. Phylogenetic analysis based on 16S rRNA gene sequences showed that R-40492T and R-40493T fell within the genus Vibrio and were most closely related to each other with 99 % similarity; similarities of these two novel isolates towards Vibrio neptunius LMG 20536T, Vibrio coralliilyticus LMG 20984T, Vibrio nigripulchritudo LMG 3896T, Vibrio sinaloensis LMG 25238T and Vibrio brasiliensis LMG 20546T varied between 97.1 and 98.5 %. DDH experiments showed that the two isolates had less than 15 % relatedness to the phylogenetically most closely related Vibrio species. R-40492T and R-40493T had 55–57 % relatedness to each other. The ΔTm
between R-40492T and R-40493T was 6.12 °C. In addition, MLSA of concatenated sequences (16S rRNA, ftsZ, gyrB, recA, rpoA, topA, pyrH and mreB; 6035 bp in length) showed that the two novel isolates formed a separate branch with less than 92 % concatenated gene sequence similarity towards known species of vibrios. Two novel species are proposed to accommodate these novel isolates, namely Vibrio variabilis sp. nov. (type strain, R-40492T = LMG 25438T = CAIM 1454T) and Vibrio maritimus sp. nov. (type strain, R-40493T = LMG 25439T = CAIM 1455T).
Reclassification of Paralactobacillus selangorensis Leisner et al. 2000 as Lactobacillus selangorensis comb. nov.
Authors: Haakensen Monique , Pittet Vanessa , Ziola Barry
Published: February 2011

The taxonomic status of Paralactobacillus selangorensis is described and, based on evidence presented, transfer of the species to the genus Lactobacillus with the name Lactobacillus selangorensis comb. nov. is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and portions of the cpn60, pheS and rpoA genes. Mode of cell division and existing phenotypic information also show that P. selangorensis cannot be differentiated from the genus Lactobacillus. The type strain of Lactobacillus selangorensis comb. nov. is ATCC BAA-66T ( = LMG 17710T  = CIP 106482T).
Alkalibacterium subtropicum sp. nov., a slightly halophilic and alkaliphilic marine lactic acid bacterium isolated from decaying marine algae
Authors: Ishikawa Morio , Nakajima Kazuyuki , Ishizaki Shihomi , Kodama Kayo , Okamoto-Kainuma Akiko , Koizumi Yukimichi , Yamamoto Yasushi , Yamasato Kazuhide
Published: February 2011

Two novel strains of marine lactic acid bacteria, isolated from decaying marine algae collected from a subtropical area of Japan, are described. The isolates, designated O24-2Tand O25-2, were Gram-positive, non-sporulating and non-motile. They lacked catalase and quinones. Under anaerobic cultivation conditions, lactate was produced from glucose with the production of formate, acetate and ethanol in a molar ratio of approximately 2 : 1 : 1. Under aerobic cultivation conditions, acetate and lactate were produced from carbohydrates and related compounds. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. They were able to grow in 0–17.0 % (w/v) NaCl, with optimum growth of strains O24-2Tand O25-2 at 1.0–3.0 and 1.0–2.0 % (w/v) NaCl, respectively. Growth of strain O24-2Twas observed at pH 7.5–9.5, with optimum growth at pH 8.0–8.5. Comparative 16S rRNA gene sequence analysis revealed that the isolates occupied a phylogenetic position within the genusAlkalibacterium, showing highest similarity (99.6 %) toAlkalibacterium putridalgicolaT129-2-1T. Although sequence similarity was high, the DNA–DNA relatedness value between strain O24-2TandA.putridalgicolaT129-2-1Twas 27 %, indicating that they are members of distinct species. The DNA G+C contents of O24-2Tand O25-2 were 43.7 and 44.4 mol%, respectively, and DNA–DNA relatedness between the isolates was 89 %. The cell-wall peptidoglycan was type A4β, Orn-d-Asp. The major cellular fatty acid components were C14 : 0, C16 : 0and C16 : 1ω9c. Based on phenotypic characteristics and genetic distinctiveness, the isolates were classified as representatives of a novel species within the genusAlkalibacterium, for which the nameAlkalibacterium subtropicumsp. nov. is proposed; the type strain is O24-2T( = DSM 23664T = NBRC 107172T).
Frondihabitans cladoniiphilus sp. nov., an actinobacterium of the family Microbacteriaceae isolated from lichen, and emended description of the genus Frondihabitans
Authors: Cardinale Massimiliano , Grube Martin , Berg Gabriele
Published: February 2011

A novel actinobacterium, designated strain CafT13T, was isolated from the thallus of the reindeer lichen Cladonia arbuscula sampled in the Austrian Alps (Koralpe). The organism was aerobic, with rod- to irregular-shaped cells (often forming dense clusters of cells when grown in liquid medium), Gram-stain-positive, oxidase-negative, catalase-positive and non-motile. It was able to grow at 1 °C and at low to neutral pH, but not above 30 °C or at high pH. The peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The menaquinones were MK-7 and MK-8. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, three unidentified glycolipids and one unidentified aminolipid. The predominant fatty acids were C18 : 1, C14 : 0 2-OH, C17 : 1ω9c, C16 : 0 and anteiso-C15 : 0. The mean DNA G+C content of strain CafT13T was 69.0±0.17 mol%. 16S rRNA gene sequence analysis showed that strain CafT13T belongs to the family Microbacteriaceae, within the genus Frondihabitans. The mean level of DNA–DNA relatedness between strain CafT13T and the type strain of Frondihabitans australicus was 35.2±5.23 %. The enzyme spectrum of strain CafT13T differentiated it from recognized species of the genus Frondihabitans. Based on molecular, chemotaxonomic and physiological data, strain CafT13T is considered to represent a novel species of the genus Frondihabitans, for which the name Frondihabitans cladoniiphilus sp. nov. is proposed; the type strain is CafT13T ( = DSM 23273T = LMG 25550T).
Marinobacter daqiaonensis sp. nov., a moderate halophile isolated from a Yellow Sea salt pond
Authors: Qu Lingyun , Zhu Fengling , Zhang Jinxing , Gao Chunlei , Sun Xiuqin
Published: February 2011

A Gram-negative, oxidase- and catalase-positive, moderately halophilic strain, designated YCSA40T, was isolated from sediment of Daqiao saltern in Qingdao, on the east coast of China. Growth occurred at 10–45 °C, at pH 5–9 and with 1–15 % NaCl. Strain YCSA40T showed the highest 16S rRNA gene sequence similarity to Marinobacter segnicrescens SS011B1-4T (97 %) and M. gudaonensis SL014B61AT (96.9 %) and 16S rRNA gene sequence phylogenetic analysis assigned the isolate to the genus Marinobacter. Strain YCSA40T contained C18 : 1ω9c (34.8 %), C16 : 0 (11.6 %), C19 : 0 cyclo ω10c/C19 : 1ω6c (10.5 %), C16 : 1ω9c (8.4 %), C17 : 0 (6.3 %) and C12 : 0 3-OH (5.8 %) as the predominant fatty acids. The DNA G+C content was 60.8 mol% and the major ubiquinone was Q-9. These chemotaxonomic characters were all consistent with membership of the genus Marinobacter. DNA–DNA relatedness between the isolate and M. segnicrescens CGMCC 1.6489T, M. gudaonensis CGMCC 1.6294T and other type strains of species of the genus Marinobacter was ≤30 %. On the basis of the aforementioned data, it was concluded that strain YCSA40T represents a novel species of the genus Marinobacter, for which the name Marinobacter daqiaonensis sp. nov. is proposed. The type strain is YCSA40T ( = CGMCC 1.9167T  = NCCB 100308T  = LMG 25365T).
A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales
Authors: Papke R. Thane , White Emma , Reddy Prajwal , Weigel Griffin , Kamekura Masahiro , Minegishi Hiroaki , Usami Ron , Ventosa Antonio
Published: February 2011

Members of the orderHalobacterialesare obligate extreme halophiles that belong to the domainArchaea. The classification of theHalobacterialescurrently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with theHalobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the most frequently recombined gene between closely related species. Moreover, theHalobacterialesis a rapidly expanding group due to recent successes at cultivating novel strains from a diverse set of hypersaline environments; a fast, reliable, inexpensive, portable molecular method for discriminating species is required for their investigation. Recently, multilocus sequence analysis (MLSA) has been shown to be an effective tool for strain identification and taxonomic designation, even for those taxa that experience frequent lateral gene transfer and homologous recombination. In this study, MLSA was utilized for evolutionary and taxonomic investigation of theHalobacteriales. Efficacy of the MLSA approach was tested across a hierarchical gradient using 52 halobacterial strains, representing 33 species (including names without standing in nomenclature) and 14 genera. A subset of 21 strains from the genusHaloarculawas analysed separately to test the sensitivity and relevance of the MLSA approach among closely related strains and species. The results demonstrated that MLSA differentiated individual strains, reliably grouped strains into species and species into genera and identified potential novel species and also family-like relationships. This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic level within theHalobacteriales.
The genus Listonella MacDonell and Colwell 1986 is a later heterotypic synonym of the genus Vibrio Pacini 1854 (Approved Lists 1980) – a taxonomic opinion
Authors: Thompson Fabiano L. , Thompson Cristiane C. , Dias Graciela M. , Naka Hiroaki , Dubay Christopher , Crosa Jorge H.
Published: February 2011

We analysed the taxonomic position of the genus Listonella based on phylogenetic, genomic and phenotypic data. The species of the genus Listonella were nested within the genus Vibrio according to the 16S rRNA gene sequence-based phylogenetic tree. The closest neighbour of Vibrio (Listonella) anguillarum strains LMG 4437T and ATCC 68554 ( = strain 775) was Vibrio ordalii LMG 13544T, with more than 99.5 % 16S rRNA gene sequence similarity. Furthermore, Vibrio (Listonella) pelagius is highly related to Vibrio splendidus. According to average amino acid identity (AAI), multilocus sequence analysis (MLSA) and Karlin genome signature, the closest neighbour of L. anguillarum ATCC 68554 is V. ordalii LMG 13544T, with 95 % AAI, 98 % MLSA and 5 in Karlin. V. anguillarum ATCC 68554 and Vibrio cholerae N16961 had 77 % similarity in AAI, 85 % in MLSA and 14 in the Karlin signature. Phenotypic analyses of previously published data for V. (L.) anguillarum and V. (L.) pelagius revealed that the genus Listonella is extremely similar to the genus Vibrio. V. ordalii and L. anguillarum strains yielded up to 67 % DNA–DNA hybridization. There are only a few phenotypic features that might be used to discriminate these two species: L. anguillarum is positive for the Voges–Proskauer reaction, citrate utilization, starch hydrolysis, lipase activity and acid production from glycerol, sorbitol and trehalose, whereas V. ordalii is negative for these traits. We suggest that the genus Listonella is a later heterotypic synonym of the genus Vibrio and propose to use the names Vibrio anguillarum and Vibrio pelagius in place of Listonella anguillarum and Listonella pelagia, respectively.
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
Authors: MacNeil Lesley T. , Walhout Albertha J.M.
Published: February 2011

In any given cell, thousands of genes are expressed and work in concert to ensure the cell's function, fitness, and survival. Each gene, in turn, must be expressed at the proper time and in the proper amounts to ensure the appropriate functional outcome. The regulation and expression of some genes are highly robust; their expression is controlled by invariable expression programs. For instance, developmental gene expression is extremely similar in a given cell type from one individual to another. The expression of other genes is more variable: Their levels are noisy and are different from cell to cell and from individual to individual. This can be highly beneficial in physiological responses to outside cues and stresses. Recent advances have enabled the analysis of differential gene expression at a systems level. Gene regulatory networks (GRNs) involving interactions between large numbers of genes and their regulators have been mapped onto graphic diagrams that are used to visualize the regulatory relationships. The further characterization of GRNs has already uncovered global principles of gene regulation. Together with synthetic network biology, such studies are starting to provide insights into the transcriptional mechanisms that cause robust versus stochastic gene expression and their relationships to phenotypic robustness and variability. Here, we discuss GRNs and their topological properties in relation to transcriptional and phenotypic outputs in development and organismal physiology.
Coordinated histone modifications are associated with gene expression variation within and between species
Authors: Ha Misook , Ng Danny W-K. , Li Wen-Hsiung , Chen Z. Jeffrey
Published: February 2011

Histone modifications regulate gene expression in eukaryotes, but their effects on transcriptomes of a multicellular organism and on transcriptomic divergence between species are poorly understood. Here we present the first nucleotide-resolution maps of histone acetylation, methylation, and core histone in Arabidopsis thaliana and a comprehensive analysis of these and all other available maps with gene expression data in A. thaliana, Arabidopsis arenosa, and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their distribution patterns are associated with Gene Ontology (GO) functional classifications. Highly dense and narrow distributions of these modifications near transcriptional start sites are associated with constitutive expression of genes involved in translation, whereas broad distributions toward coding regions correlate with expression variation of the genes involved in photosynthesis, carbohydrate metabolism, and defense responses. Compared to animal stem cells, dispersed distributions of H3K27me3 without bivalent H3K4me3 and H3K9ac marks correlate with developmentally repressed genes in Arabidopsis. Finally, genes affected by A. thaliana histone deacetylase 1 mutation tend to show high levels of expression variation within and between species. The data suggest that genome-wide coordinated modifications of histone acetylation and methylation provide a general mechanism for gene expression changes within and between species and in allopolyploids.
Rice MADS3 Regulates ROS Homeostasis during Late Anther Development
Authors: Hu Lifang , Liang Wanqi , Yin Changsong , Cui Xiao , Zong Jie , Wang Xing , Hu Jianping , Zhang Dabing
Published: February 2011

The rice (Oryza sativa) floral homeotic C-class gene, MADS3, was previously shown to be required for stamen identity determination during early flower development. Here, we describe a role for MADS3 in regulating late anther development and pollen formation. Consistent with this role, MADS3 is highly expressed in the tapetum and microspores during late anther development, and a newly identified MADS3 mutant allele, mads3-4, displays defective anther walls, aborted microspores, and complete male sterility. During late anther development, mads3-4 exhibits oxidative stress-related phenotypes. Microarray analysis revealed expression level changes in many genes in mads3-4 anthers. Some of these genes encode proteins involved in reactive oxygen species (ROS) homeostasis; among them is MT-1-4b, which encodes a type 1 small Cys-rich and metal binding protein. In vivo and in vitro assays showed that MADS3 is associated with the promoter of MT-1-4b, and recombinant MT-1-4b has superoxide anion and hydroxyl radical scavenging activity. Reducing the expression of MT-1-4b causes decreased pollen fertility and an increased level of superoxide anion in transgenic plants. Our findings suggest that MADS3 is a key transcriptional regulator that functions in rice male reproductive development, at least in part, by modulating ROS levels through MT-1-4b.
An Arabidopsis Dual-Localized Pentatricopeptide Repeat Protein Interacts with Nuclear Proteins Involved in Gene Expression Regulation
Authors: Hammani Kamel , Gobert Anthony , Hleibieh Kamal , Choulier Laurence , Small Ian , Giegé Philippe
Published: February 2011

Following the endosymbiotic acquisition of mitochondria by eukaryotic cells, most of the genes in this organelle were transferred to the nucleus. To maintain mitochondrial biogenesis and function, nuclear and mitochondrial genomes require regulated and coordinated expression. In plant organelles, nuclear-encoded proteins targeted to the organelles control posttranscriptional and posttranslational mechanisms. Pentatricopeptide repeat (PPR) proteins are good candidates to play such regulatory roles. Here, we identify PNM1 (for PPR protein localized to the nucleus and mitochondria 1), a novel PPR protein that is dual localized to mitochondria and nuclei in Arabidopsis thaliana, as observed by green fluorescent protein fusions and immunodetection on subcellular fractions and on histological sections. Genetic complementation showed that loss of PNM1 function in mitochondria, but not in nuclei, is lethal for the embryo. In mitochondria, it is associated with polysomes and may play a role in translation. A genetic screen in yeast identified protein partners of PNM1. These partners, the nucleosome assembly protein NAP1, and the transcription factor TCP8 interact with PNM1 in the nucleus in planta. Furthermore, TCP8 can bind the promoter of PNM1. This suggests that PNM1 might be involved in the regulation of its own gene expression in the nucleus and could thus play a role in gene expression adjustments between mitochondria and the nucleus.
Inter‐organizational knowledge transfer needs among small and medium enterprises
Authors: Wei Chong Chin , Choy Chong Siong , Chew Gan Geok
Published: February 2011

Purpose

The purpose of this paper is to build upon Chen et al.'s work by investigating inter‐organizational knowledge transfer needs and practices among small and medium enterprises (SMEs) which have received relatively little research attention to date.

Design/methodology/approach

A questionnaire survey was conducted on SMEs which have been accorded the Multimedia Super Corridor Malaysia status. Data were analyzed using Statistical Package for the Social Sciences.

Findings

In total, nine important areas have been the focus of this study, i.e. the importance of external knowledge; the extent to which external knowledge is more important than internal knowledge to organizational success; areas in which insufficient knowledge contributes to costly errors or mistakes in the SMEs; SMEs' involvement in knowledge transfer activities; number of social networks involved; SMEs' perceptions about networks; use of tools and technologies to transfer inter‐organizational knowledge; constraints of inter‐organizational knowledge transfer; and SMEs' effectiveness in leveraging knowledge. The data collected from 70 owners/managers of SMEs suggest that to some extent external knowledge is believed to be an important need by the enterprises.

Research limitations/implications

The small sample size raises the question of generalizability of the findings.

Practical implications

Overall, the empirical findings point to the need for the SMEs to pursue inter‐organizational knowledge transfer practices.

Originality/value

This paper is one of the first to address the inter‐organizational knowledge transfer needs in Malaysian SMEs.
Key determinants of knowledge sharing in an electronics manufacturing firm in Malaysia
Authors: Mohammed Fathi Nurliza , Cyril Eze Uchenna , Guan Gan Goh Gerald
Published: February 2011

Purpose

The purpose of this paper is to examine the factors that affect knowledge‐sharing attitudes in Malaysia, with emphasis on a manufacturing firm and how this attitude influences their intention to share knowledge.

Design/methodology/approach

This is a survey research conducted within a manufacturing firm. The questionnaire was developed by adapting items and concepts from prior works, and by developing a new variable, kiasuism. A census sampling method was used to select participants for this research. The data derive from a case analysis in a manufacturing company in Malaysia. The analysis was based on 141 valid responses.

Findings

The findings indicate that collectivism, social network, social trust, shared goal, incentive systems, kiasuism and self‐efficacy emerged significant except for individualism. A unique finding is that kiasuism emerged as proposed, which suggest that future works could focus more on this variable to highlight its impact in a firm's ability to share knowledge. Overall, the data support our framework and indicate that knowledge sharing among employees in Malaysia's private companies is gaining grounds.

Research limitations/implications

The limitations of this research include the case study approach adopted, which does not allow the generalization of the results beyond that of the firm being studied. The implications emanating from this research is that the ability of a firm, especially electronic manufacturing firms, to harness internal resources and capabilities to enhance knowledge sharing among employees, would be critical for the firm to maintain a competitive position in the marketplace.

Originality/value

This paper provides specific backgrounds of the key factors that could affect the effective implementation of knowledge‐sharing initiatives in a firm, particularly those in the manufacturing sector. The findings suggest key implications for practice and research involved in knowledge‐sharing activities in their firms and related initiatives.
Knowledge innovation hindering factors at Latvian enterprises
Authors: Lukjanska Renate
Published: February 2011

Purpose

Over the last decade, the competitiveness of enterprise has been dictated by the availability of knowledge and its application into successful innovations. Innovation capacity indicators in Latvia stay low and enterprises are considerably lagging in comparison with other European Union countries, data reflected at “European Innovation Scoreboard 2008”, where Latvia took 30th place among 32 countries. The purpose of this paper is the identification of knowledge innovation (KI) hindering factors at Latvian enterprises. The focus is to develop a KI management framework for Latvian enterprises.

Design/methodology/approach

The research objective is achieved by analysing available statistical data, national development documents, empirical research and two discussions with participants involved with innovation systems. The author's practical interpretation of specific KIs basic elements is provided. The design of the paper is the following: theoretical aspects of KI, practical description of the current innovation and knowledge management (KM) in Latvian enterprise, the role of education and science in KI field, identification of hindering aspects of KI development, and conclusions and suggestions.

Findings

The main findings show that only a few elements of innovation and KM are functioning at Latvian enterprises. The role of science and education play a key role. Main hindering factors affecting KI are identified. There is a contradiction between some of the knowledge and innovation management research data, which is a subject for more complicated research.

Research limitations/implications

The paper compares analysis and comparison for time period 2004‐2009.

Originality/value

Identified problems of KI lagging can be successfully used as a base for KI management framework development. This paper reflects an original viewpoint of identification of the main hindering factors of KI as well as contradictory results of knowledge and innovation management research.
Formative assessment: transforming information literacy instruction
Authors: Kathleen Dunaway Michelle , Teague Orblych Michael
Published: February 2011

Purpose

This paper aims to describe the use of a pre‐assessment exercise and in‐session assessment questions to determine graduate students' existing information literacy skills and to adjust the content of the instruction session accordingly. The paper seeks to propose that the use of assessments to inform instruction increases the practicality of research instruction. The use of formative assessment creates effective information literacy instruction by acknowledging variation in information literacy skills among students.

Design/methodology/approach

A librarian partnered with a faculty member to create instruction sessions for graduate level business courses. An open‐ended pre‐assessment exercise was administered prior to the session, and students' responses were used to determine the content of the instruction session. Assessment questions administered during the session provided the librarian with a measure of the effect of the pre‐assessment exercise on students' information literacy skills, and provided students with feedback regarding their individual information literacy and engaged students in the learning process.

Findings

The pre‐assessment exercise and the session assessment questions together created an instruction session that included content that was appropriate for the students in each session. Therefore, these information literacy instruction sessions were more practical and beneficial to the students than sessions based on pre‐determined content.

Research limitations/implications

The paper presents a conceptual approach to the design of research instruction sessions rather than extensive empirical analysis of data. Therefore, the essay addresses the need for quantitative measures of the impact of formative assessment on students' information literacy skills.

Originality/value

The process of formative assessment has not been applied to one‐shot information literacy instruction sessions.
When coming to campus is not an option: using web conferencing to deliver library instruction
Authors: Barnhart Anne C. , Stanfield Andrea G.
Published: February 2011

Purpose

Owing to the growing number of online and commuting students at the University of West Georgia, the Instructional Services department at Ingram Library experimented with offering online synchronous library instruction. This paper aims to describe how it approached this problem and the findings from the initial attempts.

Design/methodology/approach

The authors wanted to provide library instruction to online graduate students at the university. They worked with the staff development department to develop a pilot program for an online library instruction course using WIMBA web‐conferencing software.

Findings

It was found that due to the limitations of technology, the authors had to reduce the amount of information they deliver in the same amount of time. It was also discovered that it is easy to be distracted by the technology and forget that clear communication with the users (students and faculty) are the key to any successful instruction program regardless of the delivery method.

Originality/value

Most libraries offer face‐to‐face library instruction and rely on tutorials to reach their distance education and non‐traditional students. Few libraries are using distance education tools to teach information literacy skills. As librarians begin to explore this avenue, they need to re‐evaluate how and what they teach students to better leverage the technology while reaching the same information literacy objectives.
“I can't find anything”
Authors: Stowe Brook
Published: February 2011

Purpose

The purpose of this paper is to describe the efforts of library faculty at Long Island University's Brooklyn Campus Library to design and implement a continuum of curriculum‐integrated, outcomes‐assessed library instruction in undergraduate writing‐intensive courses.

Design/methodology/approach

The literature review investigates various course‐integrated curriculum designs, how contemporary students learn, the challenges they face in academic research, and the significance of collaboration between library and teaching faculty in facilitating curriculum‐integrated library instruction (LI). Various components of LI design are examined, along with LI development in collaboration with other academic departments. The integration of new LI into a lower‐level undergraduate composition course as well as a pre‐existing LI component to an upper‐level undergraduate writing‐intensive course is explored.

Findings

The initial curriculum‐spanning continuum approach envisioned by the library and English department was necessarily scaled back and down due to personnel and budgetary restrictions. Integrating two library instruction sessions into 47 undergraduate composition courses produced challenges of scheduling, communication and content. Designing LI components with outcomes assessment (OA) measurement built‐in proved superior to retrofitting OA to previously designed, and implemented LI.

Practical implications

The paper contributes to the discussion of library pedagogy, curriculum‐integrated library instruction design and collaboration between library and teaching faculty.

Originality/value

This paper provides a step‐by‐step recounting of a mid‐sized, urban academic library's efforts to implement the first steps towards designing a “continuum” of library instruction for an undergraduate core curriculum. It offers valuable insights and information in designing, implementing and sustaining multiple library instruction components to aid students in seeking and locating authoritative sources for their research projects.
The librarian's role in combating plagiarism
Authors: Snyder Gibson Nancy , Chester‐Fangman Christina
Published: February 2011

Purpose

The paper aims to discuss the ways in which librarians of different types are addressing the issue of plagiarism at the institutional and pedagogical levels.

Design/methodology/approach

A 25‐question non‐quantitative online survey was conducted regarding: the institutional role of librarians in plagiarism prevention; the collaborations among librarians and instructors in helping students understand what plagiarism is and how to avoid it; and the interactions among librarians and students involved in combating plagiarism.

Findings

More than 90 percent of the 610 respondents report that they have assisted students with citing sources. Over 70 percent have instructed students about plagiarism in class. Approximately a quarter have collaborated with other departments regarding plagiarism, conducted or attended workshops on plagiarism, worked with instructors to redesign assignments, or helped faculty with tracking possible instances of student plagiarism.

Research limitations/implications

This paper reports on a survey which is not statistically valid. The results of this survey, however, can shed light on the librarian's role to date in combating plagiarism and suggest future directions.

Practical implications

This survey reports what librarians are doing to address plagiarism at all levels, and it reflects what is being practiced in the field.

Originality/value

While many librarians have written about plagiarism strategies, this national survey focuses on the work of librarians at the institutional and pedagogical levels.
Successful negotiation is 80 percent preparation
Authors: Rich Clive
Published: February 2011

Purpose

The purpose of the paper is to present preparation as a key to successful negotiation.

Design/methodology/approach

The paper presents the key factors in preparing for a negotiation.

Findings

Fail to prepare as a negotiator and you prepare to fail.

Practical implications

Preparation is an investment of time.Originality/valuePlanning your deal‐making can add as big a return for your company as effective business planning or effective marketing plans. Most people do not prepare properly when they negotiate, so this is an unusual perspective
Successful leadership practices during turbulent times
Authors: Cangemi Joseph P. , Lazarus Harold , McQuade Ted , Fitzgerald Jaime , Conner James , Miller Richard , Murphree William
Published: February 2011

Purpose

During difficult economic times the media often highlight examples of failing or failed business organizations. In some cases the demise of corporations is examined in considerable detail often resulting in the following take‐home messages: these are the sins that have brought about your failure; and if things had been done differently you might still be a viable company. This paper aims to point out success stories from creative leaders who successfully navigated through challenging environments.

Design/methodology/approach

The paper draws on existing cases from the literature highlighting leaders who led their organizations to positive ends during turbulent times.

Findings

There are opportunities for company success despite difficult business environments.

Originality/value

It is rare to read about successful leadership practices during turbulent times. Yet, they do exist. The overwhelming number of examples and cases written about, however, are indeed in the negative direction, not the positive.