bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating protein models from electron-density maps using particle-filtering methods
Authors: DiMaio Frank , Kondrashov Dmitry A. , Bitto Eduard , Soni Ameet , Bingman Craig A. , Phillips George N. , Shavlik Jude W.
Published: October 2007

Motivation: One bottleneck in high-throughput protein crystallography is interpreting an electron-density map, that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed Acmi (Automatic Crystallographic Map Interpreter), an algorithm that uses a probabilistic model to infer an accurate protein backbone layout. Here, we use a sampling method known as particle filtering to produce a set of all-atom protein models. We use the output of Acmi to guide the particle filter's sampling, producing an accurate, physically feasible set of structures.

Results: We test our algorithm on 10 poor-quality experimental density maps. We show that particle filtering produces accurate all-atom models, resulting in fewer chains, lower sidechain RMS error and reduced R factor, compared to simply placing the best-matching sidechains on Acmi's trace. We show that our approach produces a more accurate model than three leading methods—Textal, Resolve and ARP/WARP—in terms of main chain completeness, sidechain identification and crystallographic R factor.

Availability: Source code and experimental density maps available at http://ftp.cs.wisc.edu/machine-learning/shavlik-group/programs/acmi/

Contact:  dimaio@cs.wisc.edu
MDQC: a new quality assessment method for microarrays based on quality control reports
Authors: Cohen Freue Gabriela V. , Hollander Zsuzsanna , Shen Enqing , Zamar Ruben H. , Balshaw Robert , Scherer Andreas , McManus Bruce , Keown Paul , McMaster W. Robert , Ng Raymond T.
Published: October 2007

Motivation: The process of producing microarray data involves multiple steps, some of which may suffer from technical problems and seriously damage the quality of the data. Thus, it is essential to identify those arrays with low quality. This article addresses two questions: (1) how to assess the quality of a microarray dataset using the measures provided in quality control (QC) reports; (2) how to identify possible sources of the quality problems.

Results: We propose a novel multivariate approach to evaluate the quality of an array that examines the ‘Mahalanobis distance’ of its quality attributes from those of other arrays. Thus, we call it Mahalanobis Distance Quality Control (MDQC) and examine different approaches of this method. MDQC flags problematic arrays based on the idea of outlier detection, i.e. it flags those arrays whose quality attributes jointly depart from those of the bulk of the data. Using two case studies, we show that a multivariate analysis gives substantially richer information than analyzing each parameter of the QC report in isolation. Moreover, once the QC report is produced, our quality assessment method is computationally inexpensive and the results can be easily visualized and interpreted. Finally, we show that computing these distances on subsets of the quality measures in the report may increase the method's ability to detect unusual arrays and helps to identify possible reasons of the quality problems.

Availability: The library to implement MDQC will soon be available from Bioconductor

Contact:  gcohen@mrl.ubc.ca

Supplementary information: Supplementary data are available at Bioinformatics online.
Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data
Authors: Tai Feng , Pan Wei
Published: October 2007

Motivation: Discriminant analysis for high-dimensional and low-sample-sized data has become a hot research topic in bioinformatics, mainly motivated by its importance and challenge in applications to tumor classifications for high-dimensional microarray data. Two of the popular methods are the nearest shrunken centroids, also called predictive analysis of microarray (PAM), and shrunken centroids regularized discriminant analysis (SCRDA). Both methods are modifications to the classic linear discriminant analysis (LDA) in two aspects tailored to high-dimensional and low-sample-sized data: one is the regularization of the covariance matrix, and the other is variable selection through shrinkage. In spite of their usefulness, there are potential limitations with each method. The main concern is that both PAM and SCRDA are possibly too extreme: the covariance matrix in the former is restricted to be diagonal while in the latter there is barely any restriction. Based on the biology of gene functions and given the feature of the data, it may be beneficial to estimate the covariance matrix as an intermediate between the two; furthermore, more effective shrinkage schemes may be possible.

Results: We propose modified LDA methods to integrate biological knowledge of gene functions (or variable groups) into classification of microarray data. Instead of simply treating all the genes independently or imposing no restriction on the correlations among the genes, we group the genes according to their biological functions extracted from existing biological knowledge or data, and propose regularized covariance estimators that encourages between-group gene independence and within-group gene correlations while maintaining the flexibility of any general covariance structure. Furthermore, we propose a shrinkage scheme on groups of genes that tends to retain or remove a whole group of the genes altogether, in contrast to the standard shrinkage on individual genes. We show that one of the proposed methods performed better than PAM and SCRDA in a simulation study and several real data examples.

Contact:  weip@biostat.umn.edu
Steady-state expression of self-regulated genes
Authors: Fournier T. , Gabriel J.P. , Mazza C. , Pasquier J. , Galbete J.L. , Mermod N.
Published: October 2007

Motivation: Regulatory gene networks contain generic modules such as feedback loops that are essential for the regulation of many biological functions. The study of the stochastic mechanisms of gene regulation is instrumental for the understanding of how cells maintain their expression at levels commensurate with their biological role, as well as to engineer gene expression switches of appropriate behavior. The lack of precise knowledge on the steady-state distribution of gene expression requires the use of Gillespie algorithms and Monte-Carlo approximations.

Methodology: In this study, we provide new exact formulas and efficient numerical algorithms for computing/modeling the steady-state of a class of self-regulated genes, and we use it to model/compute the stochastic expression of a gene of interest in an engineered network introduced in mammalian cells. The behavior of the genetic network is then analyzed experimentally in living cells.

Results: Stochastic models often reveal counter-intuitive experimental behaviors, and we find that this genetic architecture displays a unimodal behavior in mammalian cells, which was unexpected given its known bimodal response in unicellular organisms. We provide a molecular rationale for this behavior, and we implement it in the mathematical picture to explain the experimental results obtained from this network.

Contact:  christian.mazza@unifr.ch, nicolas.mermod@unil.ch

Supplementary information: Supplementary data are available at Bioinformatics online.
Carbon-fate maps for metabolic reactions
Authors: Mu Fangping , Williams Robert F. , Unkefer Clifford J. , Unkefer Pat J. , Faeder James R. , Hlavacek William S.
Published: October 2007

Motivation: Stable isotope labeling of small-molecule metabolites (e.g. 13C-labeling of glucose) is a powerful tool for characterizing pathways and reaction fluxes in a metabolic network. Analysis of isotope labeling patterns requires knowledge of the fates of individual atoms and moieties in reactions, which can be difficult to collect in a useful form when considering a large number of enzymatic reactions.

Results: We report carbon-fate maps for 4605 enzyme-catalyzed reactions documented in the KEGG database. Every fate map has been manually checked for consistency with known reaction mechanisms. A map includes a standardized structure-based identifier for each reactant (namely, an InChI™ string); indices for carbon atoms that are uniquely derived from the metabolite identifiers; structural data, including an identification of homotopic and prochiral carbon atoms; and a bijective map relating the corresponding carbon atoms in substrates and products. Fate maps are defined using the BioNetGen™ language (BNGL), a formal model-specification language, which allows a set of maps to be automatically translated into isotopomer mass-balance equations.

Availability: The carbon-fate maps and software for visualizing the maps are freely available (http://cellsignaling.lanl.gov/FateMaps/).

Contact:  wish@lanl.gov

Supplementary information: Supplementary data are available at Bioinformatics online.
Conformational analysis of alternative protein structures
Authors: Domingues Francisco S. , Rahnenführer Jörg , Lengauer Thomas
Published: October 2007

Motivation: Alternative structural models determined experimentally are available for an increasing number of proteins. Structural and functional studies of these proteins need to take these models into consideration as they can present considerable structural differences. The characterization of the structural differences and similarities between these models is a fundamental task in structural biology requiring appropriate methods.

Results: We propose a method for characterizing sets of alternative structural models. Three types of analysis are performed: grouping according to structural similarity, visualization and detection of structural variation and comparison of subsets for identifying and locating distinct conformational states. The alpha carbon atoms are used in order to analyse the backbone conformations. Alternatively, side-chain atoms are used for detailed conformational analysis of specific sites. The method takes into account estimates of atom coordinate uncertainty. The invariant regions are used to generate optimal superpositions of these models. We present the results obtained for three proteins showing different degrees of conformational variability: relative motion of two structurally conserved subdomains, a disordered subdomain and flexibility in the functional site associated with ligand binding. The method has been applied in the analysis of the alternative models available in SCOP. Considerable structural variability can be observed for most proteins.

Availability: The results of the analysis of the SCOP alternative models, the estimates of coordinate uncertainty as well as the source code of the implementation are available in the STRuster web site: http://struster.bioinf.mpi-inf.mpg.de.

Contact:  doming@mpi-sb.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
A congruence index for testing topological similarity between trees
Authors: de Vienne Damien M. , Giraud Tatiana , Martin Olivier C.
Published: October 2007

Motivation: Phylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made.

Results: We propose an index, Icong, for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level.

Availability: A web site has been created that allows rapid and easy online computation of this index and of the associated P-value at http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html

Contact:  damien.de-vienne@u-psud.fr
Evolution of the Xenopus piggyBac Transposon Family TxpB: Domesticated and Untamed Strategies of Transposon Subfamilies
Authors: Hikosaka Akira , Kobayashi Toshihiro , Saito Yumiko , Kawahara Akira
Published: October 2007

A new family, termed TxpB, of DNA transposons belonging to the piggyBac superfamily was found in 3 Xenopus species (Xenopus tropicalis, Xenopus laevis, and Xenopus borealis). Two TxpB subfamilies of Kobuta and Uribo1 were found in all the 3 species, and another subfamily termed Uribo2 was found in X. tropicalis. Molecular phylogenetic analyses of their open reading frames (ORFs) revealed that TxpB transposons have been maintained for over 100 Myr. Both the Uribo1 and the Uribo2 ORFs were present as multiple copies in each genome, and some of them were framed by terminal inverted repeat sequences. In contrast, all the Kobuta ORFs were present as a single copy in each genome and exhibited high evolutionary conservation, suggesting domestication of Kobuta genes by the host. Genomic insertion polymorphisms of the Uribo1 and Uribo2 transposons (nonautonomous type) were observed in a single species of X. tropicalis, indicating recent transposition events. Transfection experiments in cell culture revealed that an expression vector construct for the intact Uribo2 ORF caused precise excision of a nonautonomous Uribo2 element from the target vector construct but that for the Kobuta ORF did not. The present results support our viewpoint that some Uribo2 members are naturally active autonomous transposons, whereas Kobuta members may be domesticated by hosts.
Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells
Authors: Loh Yuin-Han , Zhang Weiwei , Chen Xi , George Joshy , Ng Huck-Hui
Published: October 2007

Embryonic stem (ES) cells are pluripotent cells with the ability to self-renew indefinitely. These unique properties are controlled by genetic factors and chromatin structure. The exit from the self-renewing state is accompanied by changes in epigenetic chromatin modifications such as an induction in the silencing-associated histone H3 Lys 9 dimethylation and trimethylation (H3K9Me2/Me3) marks. Here, we show that the H3K9Me2 and H3K9Me3 demethylase genes, Jmjd1a and Jmjd2c, are positively regulated by the ES cell transcription factor Oct4. Interestingly, Jmjd1a or Jmjd2c depletion leads to ES cell differentiation, which is accompanied by a reduction in the expression of ES cell-specific genes and an induction of lineage marker genes. Jmjd1a demethylates H3K9Me2 at the promoter regions of Tcl1, Tcfcp2l1, and Zfp57 and positively regulates the expression of these pluripotency-associated genes. Jmjd2c acts as a positive regulator for Nanog, which encodes for a key transcription factor for self-renewal in ES cells. We further demonstrate that Jmjd2c is required to reverse the H3K9Me3 marks at the Nanog promoter region and consequently prevents transcriptional repressors HP1 and KAP1 from binding. Our results connect the ES cell transcription circuitry to chromatin modulation through H3K9 demethylation in pluripotent cells.
RINGO/cdk1 and CPEB mediate poly(A) tail stabilization and translational regulation by ePAB
Authors: Kim Jong Heon , Richter Joel D.
Published: October 2007

One activity that controls mRNA translation in vertebrate oocytes, embryos, and neurons is cytoplasmic polyadenylation. In Xenopus oocytes, where much of the biochemistry of this process has been elucidated, nuclear pre-mRNAs containing a cytoplasmic polyadenylation element (CPE) in their 3′ untranslated regions (UTRs) have long poly(A) tails; once the RNAs are spliced and transported to the cytoplasm, the tails are shortened. Following the resumption of meiosis, the poly(A) tails are lengthened and translation ensues. CPEB is a sequence-specific RNA-binding protein that coordinates these events and does so by binding to the CPE as well as several factors including Gld2, a poly(A) polymerase, and PARN [poly(A)-specific ribonuclease], a deadenylase. Here, we show that ePAB, embryonic poly(A)-binding protein, transiently associates with the polyadenylation complex; it initially interacts with CPEB, but after polyadenylation, it binds the poly(A) tail. ePAB dissociation from CPEB is regulated by RINGO (Rapid Inducer of G2/M progression in Oocytes), a cyclin B1-like cofactor that activates cdk1, a protein kinase that phosphorylates CPEB. Subsequent ePAB binding to the poly(A) tail is necessary to protect the homopolymer from degradation by deadenylating enzymes. Poly(A)-bound ePAB also interacts with eIF4G, which instigates translation initiation of CPEB-bound mRNAs.
Regulation of the σE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress
Authors: Hasselblatt Hanna , Kurzbauer Robert , Wilken Corinna , Krojer Tobias , Sawa Justyna , Kurt Juliane , Kirk Rebecca , Hasenbein Sonja , Ehrmann Michael , Clausen Tim
Published: October 2007

The unfolded protein response of Escherichia coli is triggered by the accumulation of unassembled outer membrane proteins (OMPs) in the cellular envelope. The PDZ-protease DegS recognizes these mislocalized OMPs and initiates a proteolytic cascade that ultimately leads to the σE-driven expression of a variety of factors dealing with folding stress in the periplasm and OMP assembly. The general features of how OMPs activate the protease function of DegS have not yet been systematically addressed. Furthermore, it is unknown how the PDZ domain keeps the protease inactive in the resting state, which is of crucial importance for the functioning of the entire σE stress response. Here we show in atomic detail how DegS is able to integrate the information of distinct stress signals that originate from different OMPs containing a ϕ-x-Phe C-terminal motif. A dedicated loop of the protease domain, loop L3, serves as a versatile sensor for allosteric ligands. L3 is capable of interacting differently with ligands but reorients in a conserved manner to activate DegS. Our data also indicate that the PDZ domain directly inhibits protease function in the absence of stress signals by wedging loop L3 in a conformation that ultimately disrupts the proteolytic site. Thus, the PDZ domain and loop L3 of DegS define a novel molecular switch allowing strict regulation of the σE stress response system.
Identification and Mutational Analysis of Arabidopsis FLS2 Leucine-Rich Repeat Domain Residues That Contribute to Flagellin Perception
Authors: Dunning F. Mark , Sun Wenxian , Jansen Kristin L. , Helft Laura , Bent Andrew F.
Published: October 2007

Mutational, phylogenetic, and structural modeling approaches were combined to develop a general method to study leucine-rich repeat (LRR) domains and were used to identify residues within the Arabidopsis thaliana FLAGELLIN-SENSING2 (FLS2) LRR that contribute to flagellin perception. FLS2 is a transmembrane receptor kinase that binds bacterial flagellin or a flagellin-based flg22 peptide through a presumed physical interaction within the FLS2 extracellular domain. Double-Ala scanning mutagenesis of solvent-exposed β-strand/β-turn residues across the FLS2 LRR domain identified LRRs 9 to 15 as contributors to flagellin responsiveness. FLS2 LRR-encoding domains from 15 Arabidopsis ecotypes and 20 diverse Brassicaceae accessions were isolated and sequenced. FLS2 is highly conserved across most Arabidopsis ecotypes, whereas more diversified functional FLS2 homologs were found in many but not all Brassicaceae accessions. flg22 responsiveness was correlated with conserved LRR regions using Conserved Functional Group software to analyze structural models of the LRR for diverse FLS2 proteins. This identified conserved spatial clusters of residues across the β-strand/β-turn residues of LRRs 12 to 14, the same area identified by the Ala scan, as well as other conserved sites. Site-directed randomizing mutagenesis of solvent-exposed β-strand/β-turn residues across LRRs 9 to 15 identified mutations that disrupt flg22 binding and showed that flagellin perception is dependent on a limited number of tightly constrained residues of LRRs 9 to 15 that make quantitative contributions to the overall phenotypic response.
Subcellular Localization and Functional Domain Studies of DEFECTIVE KERNEL1 in Maize andArabidopsisSuggest a Model for Aleurone Cell Fate Specification Involving CRINKLY4 and SUPERNUMERARY ALEURONE LAYER1
Authors: Tian Qing , Olsen Lene , Sun Beimeng , Lid Stein Erik , Brown Roy C. , Lemmon Betty E. , Fosnes Kjetil , Gruis Darren (Fred) , Opsahl-Sorteberg Hilde-Gunn , Otegui Marisa S. , Olsen Odd-Arne
Published: October 2007

DEFECTIVE KERNEL1 (DEK1), which consists of a membrane-spanning region (DEK1-MEM) and a calpain-like Cys proteinase region (DEK1-CALP), is essential for aleurone cell formation at the surface of maize (Zea mays) endosperm. Immunolocalization and FM4-64 dye incubation experiments showed that DEK1 and CRINKLY4 (CR4), a receptor kinase implicated in aleurone cell fate specification, colocalized to plasma membrane and endosomes. SUPERNUMERARY ALEURONE LAYER1 (SAL1), a negative regulator of aleurone cell fate encoding a class E vacuolar sorting protein, colocalized with DEK1 and CR4 in endosomes. Immunogold localization, dual-axis electron tomography, and diffusion of fluorescent dye tracers showed that young aleurone cells established symplastic subdomains through plasmodesmata of larger dimensions than those connecting starchy endosperm cells and that CR4 preferentially associated with plasmodesmata between aleurone cells. Genetic complementation experiments showed that DEK1-CALP failed to restore wild-type phenotypes in maize and Arabidopsis thaliana dek1 mutants, and DEK1-MEM also failed to restore wild-type phenotypes in Arabidopsis dek1-1 mutants. Instead, ectopic expression of DEK1-MEM under the control of the cauliflower mosaic virus 35S promoter gave a dominant negative phenotype. These data suggest a model for aleurone cell fate specification in which DEK1 perceives and/or transmits a positional signal, CR4 promotes the lateral movement of aleurone signaling molecules between aleurone cells, and SAL1 maintains the proper plasma membrane concentration of DEK1 and CR4 proteins via endosome-mediated recycling/degradation.
Manipulation of Phytoene Levels in Tomato Fruit: Effects on Isoprenoids, Plastids, and Intermediary Metabolism
Authors: Fraser Paul D. , Enfissi Eugenia M.A. , Halket John M. , Truesdale Mark R. , Yu Dongmei , Gerrish Christopher , Bramley Peter M.
Published: October 2007

In tomato (Solanum lycopersicum), phytoene synthase-1 (PSY-1) is the key biosynthetic enzyme responsible for the synthesis of fruit carotenoids. To further our understanding of carotenoid formation in tomato fruit, we characterized the effect of constitutive expression of an additional tomato Psy-1 gene product. A quantitative data set defining levels of carotenoid/isoprenoid gene expression, enzyme activities, and metabolites was generated from fruit that showed the greatest perturbation in carotenoid content. Transcriptional upregulation, resulting in increased enzyme activities and metabolites, occurred only in the case of Psy-1, Psy-2, and lycopene cyclase B. For reactions involving 1-deoxy-d-xylulose5-phosphate synthase, geranylgeranyl diphosphate synthase, phytoene desaturase, ζ-carotene desaturase, carotene isomerase, and lycopene β-cyclase, there were no correlations between gene expression, enzyme activities, and metabolites. Perturbations in carotenoid composition were associated with changes in plastid type and with chromoplast-like structures arising prematurely during fruit development. The levels of >120 known metabolites were determined. Comparison with the wild type illustrated that key metabolites (sucrose, glucose/fructose, and Glu) and sectors of intermediary metabolism (e.g., trichloroacetic acid cycle intermediates and fatty acids) in the Psy-1 transgenic mature green fruit resembled changes in metabolism associated with fruit ripening. General fruit developmental and ripening properties, such as ethylene production and fruit firmness, were unaffected. Therefore, it appears that the changes to pigmentation, plastid type, and metabolism associated with Psy-1 overexpression are not connected with the ripening process.
Class-Specific Interaction of Profilin and ADF Isovariants with Actin in the Regulation of Plant Development
Authors: Kandasamy Muthugapatti K. , Burgos-Rivera Brunilís , McKinney Elizabeth C. , Ruzicka Daniel R. , Meagher Richard B.
Published: October 2007

Two ancient and highly divergent actin-based cytoskeletal systems have evolved in angiosperms. Plant genomes encode complex actin and actin binding protein (ABP) gene families, most of which are phylogenetically grouped into gene classes with distinct vegetative or constitutive and reproductive expression patterns. In Arabidopsis thaliana, ectopic expression of high levels of a reproductive class actin, ACT1, in vegetative tissues causes severe dwarfing of plants with aberrant organization of most plant organs and cell types due to a severely altered actin cytoskeletal architecture. Overexpression of the vegetative class actin ACT2 to similar levels, however, produces insignificant phenotypic changes. We proposed that the misexpression of the pollen-specific ACT1 in vegetative cell types affects the dynamics of actin due to its inappropriate interaction with endogenous vegetative ABPs. To examine the functionally distinct interactions among the major classes of actins and ABPs, we ectopically coexpressed reproductive profilin (PRF4) or actin-depolymerizing factor (ADF) isovariants (e.g., ADF7) with ACT1. Our results demonstrated that the coexpression of these reproductive, but not vegetative, ABP isovariants suppressed the ectopic ACT1 expression phenotypes and restored wild-type stature and normal actin cytoskeletal architecture to the double transgenic plants. Thus, the actins and ABPs appear to have evolved class-specific, protein–protein interactions that are essential to the normal regulation of plant growth and development.
Global Analysis of DELLA Direct Targets in Early Gibberellin Signaling inArabidopsis
Authors: Zentella Rodolfo , Zhang Zhong-Lin , Park Mehea , Thomas Stephen G. , Endo Akira , Murase Kohji , Fleet Christine M. , Jikumaru Yusuke , Nambara Eiji , Kamiya Yuji , Sun Tai-ping
Published: October 2007

Bioactive gibberellins (GAs) are phytohormones that regulate growth and development throughout the life cycle of plants. DELLA proteins are conserved growth repressors that modulate all aspects of GA responses. These GA-signaling repressors are nuclear localized and likely function as transcriptional regulators. Recent studies demonstrated that GA, upon binding to its receptor, derepresses its signaling pathway by binding directly to DELLA proteins and targeting them for rapid degradation via the ubiquitin-proteasome pathway. Therefore, elucidating the signaling events immediately downstream of DELLA is key to our understanding of how GA controls plant development. Two sets of microarray studies followed by quantitative RT-PCR analysis allowed us to identify 14 early GA-responsive genes that are also early DELLA-responsive in Arabidopsis thaliana seedlings. Chromatin immunoprecipitation provided evidence for in vivo association of DELLA with promoters of eight of these putative DELLA target genes. Expression of all 14 genes was downregulated by GA and upregulated by DELLA. Our study reveals that DELLA proteins play two important roles in GA signaling: (1) they help establish GA homeostasis by direct feedback regulation on the expression of GA biosynthetic and GA receptor genes, and (2) they promote the expression of downstream negative components that are putative transcription factors/regulators or ubiquitin E2/E3 enzymes. In addition, one of the putative DELLA targets, XERICO, promotes accumulation of abscisic acid (ABA) that antagonizes GA effects. Therefore, DELLA may restrict GA-promoted processes by modulating both GA and ABA pathways.
Attitudes of French pig farmers towards animal welfare
Authors: Kling‐Eveillard Florence , Dockès Anne‐Charlotte , Souquet Catherine
Published: October 2007

Purpose

The purpose of this paper is to describe the main characteristics of the animal welfare specifications in different quality schemes of the French pig sector; to present the French pig farmers' attitudes towards animal welfare in general, and illustrate different quality schemes.

Design/methodology/approach

Prime source of data is interviews with 60 pig farmers. Supplementary sources are research reports and statistics, specifications of the quality schemes.

Findings

On many themes, the responses and attitudes of the farmers differ according to their participation or not in a quality assurance scheme, and according to the level of stringency of their scheme regarding animal welfare. For instance, farmers in the most stringent schemes define animal welfare as providing natural living conditions for the animals, whereas for farmers in no schemes, or in more intensive schemes, animal welfare is above all an animal in good health, for which one must provide correct housing and a balanced and sufficient diet. Animal welfare is almost always a part of more global quality schemes including environmental and high flavour quality aspects.

Originality/value

The paper provides insights into the different definitions of good animal welfare by French pig farmers, as well as their attitudes towards public regulations and different types of private schemes. This is interesting from a scientific point of view and to fuel the debate between a high level of regulation for all farmers, a market segmentation based on welfare specification, or a market segmentation in which animal welfare is one aspect of the specifications.
Italian pig producers' attitude toward animal welfare
Authors: Menghi Alberto
Published: October 2007

Purpose

The purpose of this paper is to explore the attitude of pig farmers toward animal welfare in light of the state‐of‐the‐art legislation on animal welfare and production schemes in Italy.

Design/methodology/approach

The general framework regarding pig production, legislation and production schemes will be described by a literature review and personal communications from experts in the field. The results of farmers' attitudes toward animal welfare are based on a survey carried out among pig producers.

Findings

The main findings of the research are related to the survey results among pig producers. The paper presents a short description of the Italian pig sector and the results of the animal welfare legislation and production schemes.

Research limitations/implications

The main limitation of the study is the relatively limited number of survey interviews. For this reason the sample cannot be considered statistically representative of the whole country.

Practical implications

The information collected in this article could represent a useful source for farmers, policy makers, and retailers, as well as consumers interested in animal welfare issues.

Originality/value

This is the first time that pig producers have been asked to express their opinion on animal welfare as defined by the legislation in force and the existing production schemes.
Attitudes of Dutch pig farmers towards animal welfare
Authors: van Huik M.M. , Bock B.B.
Published: October 2007

Purpose

The purpose of this paper is to provide insights into the rationale of Dutch pig farmers concerning animal welfare and animal‐friendly production. It aims to show the interrelations between farmers' production logic, their ideas about good farming and animal welfare and the characteristics of Dutch pig production.

Design/methodology/approach

In total, 62 Dutch pig farmers, participating in quality assurance schemes with different focuses on animal welfare, were interviewed about animal welfare, legislation, quality assurance schemes, and possibilities for animal‐friendly production.

Findings

Farmers' attitudes towards animal welfare and the implementation of animal welfare measures follow their understanding of good farming practices, which in turn are strongly influenced by the rationale of the market in which they operate. Two groups can be distinguished. Farmers operating in markets that focus on price and production‐efficiency tend to define animal welfare in terms of animal health and optimal zoo‐technical performance. Farmers operating in markets with a broader sense of quality, which incorporates values such as naturalness, animal welfare and care for the environment, define animal welfare in terms of the room the animals have to express natural behaviour.

Originality/value

This article provides insights into the perception of Dutch pig farmers about animal welfare and their readiness to change towards more animal‐friendly production methods. It points to the interrelations between animal welfare attitudes and behaviour, farmers' perception of good farming and the production logic of the farm. These interrelated influences should be borne in mind by policy makers and researchers seeking to raise welfare levels in pig production.
Swedish pig producers and their perspectives on animal welfare: a case study
Authors: Bruckmeier Karl , Prutzer Madeleine
Published: October 2007

Purpose

The purpose of this paper is to identify the views of Swedish pig producers concerning animal welfare, the schemes practised for animal welfare in Sweden, and the ramifications of animal welfare for Swedish retailers and consumers.

Design/methodology/approach

The Swedish study for animal welfare covers a pig‐production sector of 2,794 producers (2005). The pig production study was one of three such studies conducted as part of the EU's Welfare Quality project with semi‐structured interviews (the other two studies were on cattle and poultry production). The stratified sample included 60 pig producers, both conventional and organic, selected from all areas of Sweden.

Findings

The main results show a high level of animal care exercised in the Swedish pig production sector. Although there are no specific animal welfare schemes implemented, there is a high level of animal care provided by farmer participation in quality assurance schemes that include animal welfare stipulations, among other criteria.

Practical implications

The results from this pig production study will serve as input for a subsequent study of the on‐farm practice of animal welfare for the Welfare Quality project and as information material for policy to argue for more compatible criteria of welfare schemes at national level as well as for more homogeneous practice and standards of animal welfare within the EU.

Originality/value

This is the first in‐depth study on animal welfare in Swedish agriculture that takes into account a wide array of views and experiences of both conventional and organic producers. Prior to this animal welfare study only studies with a narrow focus on animal welfare, for example about organic production, and the State Audit Institution's report, which focuses on the effectiveness in animal welfare monitoring, have been produced.
Animal welfare: the attitudes and behaviour of European pig farmers
Authors: Bock B.B. , van Huik M.M.
Published: October 2007

Purpose

The purpose of this paper is to provide insights into the behaviour and attitudes of European pig producers towards animal welfare. It looks at the relationship of these factors with farmers' understanding of good farming and production logic, together with national characteristics of production, and market and policy arrangements.

Design/methodology/approach

This article synthesises the results of six national studies in which circa 360 pig farmers were interviewed. It compares the differences in attitudes and behaviour of farmers across different countries forming quality‐assurance schemes. This allows for an understanding of how participation in different types of schemes affects farmers' definitions and practice of animal welfare and how this is embedded in specific national contexts.

Findings

Farmers' readiness to implement stricter animal welfare regulations and their belief in animal‐friendly production differ according to their definition of animal welfare and the importance they attach to it, but are also linked to their participation in schemes. In general two groups of farmers can be distinguished. Farmers participating in basic or top quality‐assurance schemes define animal welfare in terms of animal health and production‐performance. By contrast, farmers who participate in organic or specific welfare schemes emphasise the animals' opportunity for expressing natural behaviour. These different attitudes towards the animal welfare issue are underpinned by differences in farming style, or production logic.

Originality/value

The article provides insights into how pig farmers across Europe perceive and construct animal welfare. By relating these factors with farmers' understanding of good farming and production logic and national characteristics of production, market and policy arrangements, it contributes to the scientific understanding of animal welfare attitudes and behaviour. It provides insights into the factors that influence farmers' readiness to engage in animal‐friendly production, which may be of use to policymakers.
Newly qualified librarians and their professional associations: UK and US comparisons
Authors: Joint Nicholas
Published: October 2007

Purpose

The purpose of this paper is to argue that, for historical reasons related to the manner in which career progression and professional accreditation has developed in the UK, newly qualified LIS professionals are uniquely positioned to reshape the role of their professional association in this country.

Design/methodology/approach

An opinion piece based on a brief and selective conference report from the 2007 American Library Association conference held in Washington DC.

Findings

Newly qualified professionals in the UK may well find good models for reshaping the UK profession by taking some of the best examples of professional association practice from the USA.

Research limitations/implications

The suggestions made in this paper are entirely value‐based, but their acceptability at the practitioner level is a potential avenue for further investigation.

Practical implications

This piece attempts to give newly qualified LIS practitioners some very clear ideas about how to develop their own professional practice by reference to broader principles of professional ethics, law and the role of the professional association.

Originality/value

This paper attempts to give an original synthesis of viewpoints from two different national perspectives.
The question of faculty status for academic librarians
Authors: Bryan Jacalyn E.
Published: October 2007

Purpose

Faculty status for academic librarians is an issue that has been the subject of much debate in recent decades. The purpose of this paper is to examine the key points raised during this debate, in the hope of achieving a suitable resolution.

Design/methodology/approach

This paper begins with an overview of the issue of faculty status for academic librarians from an historical perspective and then continues with a review of literature from the past three decades. The pros and cons of granting faculty status are examined, as well as alternate models, followed by a proposed recommendation.

Findings

While there are a number of concerns regarding the value of faculty status for academic librarians, such as disagreement with the basic tenet that librarians are primarily teachers, the weight of the evidence seems to support the granting of faculty status to academic librarians. This status provides academic freedom, recognition of librarians in their role as educators, and financial benefits and job security and is supported by the Association of College and Research Libraries, the Association of American Colleges, and the American Association of University Professors.

Research limitations/implications

While this paper is a review of selected relevant literature, only a small portion of the literature was of an empirical nature. There is a need for more studies which directly measure the impact of faculty status for academic librarians on the librarians themselves and the students, faculty, and institutions they serve.

Originality/value

The paper shows that with faculty status, academic librarians receive the same rights and privileges as other faculty and participate in college or university governance, thereby increasing the integration of the library with the institution.
The naked librarian: health librarians in the modern era
Authors: Steyn Christelle , de Wee Janice A.
Published: October 2007

Purpose

The purpose of this paper is to discuss the ever‐changing profession of the Health Information Specialists.

Design/methodology/approach

The paper is a literary essay.

Findings

Health Information Specialists/librarians need to adapt and change constantly, in order to keep up with all new developments.

Practical implications

This paper should be of interest to anyone involved in academic health libraries.

Originality/value

The paper offers a viewpoint on the current and possible future situation of Health Information Specialists, especially in South Africa.
The evolving landscape of the learning commons
Authors: Lee Roberts Regina
Published: October 2007

Purpose

Libraries are exploring the meaning of the “information commons” and have responded to the technological needs of the diversity of digital access trends. The purpose of this conceptual article is to explore the possibilities of the next step of developing dynamic “learning commons” using examples of projects and ideas presented by librarians in the field.

Design/methodology/approach

The “learning commons” model has the potential to be a laboratory for students, librarians and faculty. It is a collaboration space and requires partnerships and cooperation across disciplines. Ideas about user behavior and types of projects to be explored are included.

Findings

Funding for learning commons is linked to measured outcomes. The role of the librarian changes to include advocacy and project planning.

Practical implications

This paper demonstrates that the change in library service via the learning commons concept requires planning, interdisciplinary collaboration and a certain amount of risk taking.

Originality/value

This paper is useful for librarians who are designing and/or implementing “learning commons” spaces and concepts into their libraries and library services.
Interaction among diet, genes, and exercise affects athletic performance and risk for chronic disease
Authors: Demmig‐Adams Barbara , Carter Jared
Published: October 2007

Purpose

The purpose of this review is to provide a comprehensive summary, for both experts and non‐experts, of new findings on interactions among diet, genes, and exercise in determining the risk for chronic disease.

Design/methodology/approach

The present review focuses on the key role of exercise in modulating the ratio of muscle fiber types and the resulting effects on overall health.

Findings

Exercise and a diet rich in omega‐3 (n‐3) fatty acids modulate human gene expression and lower the risk for chronic disease. Emerging evidence, synthesized here, shows that a family of gene regulatory proteins, the PPAR (peroxisome proliferator‐activated receptor) transcription factor family, regulates the synthesis of human muscle fibers and thereby affects glucose metabolism and the risk for obesity, diabetes, and heart disease. Dietary fatty acids, in particular n‐3 polyunsaturated fatty acids, act on PPAR family members, and thereby enhance the synthesis of specific muscle fiber types. Human muscle fibers contain a heterogeneous mix of slow‐oxidative, fast‐oxidative, and fast‐glycolytic muscle fibers. At the extremes of the spectrum, low‐oxidative fibers, important for endurance activities, rely on a complete oxidation of sugars as well as fats for energy, and are associated with high insulin sensitivity. In contrast, fast‐glycolytic fibers, important for short, intense exercise, predominantly use a quick, but only partial breakdown of sugars (glycolysis) for energy. Not surprisingly, sprinters have more fast‐glycolytic fibers, while endurance athletes have more slow‐oxidative fibers. The relative ratio of these different fiber types, in part genetically fixed and in part respondent to diet and exercise, determines not only what type of activities an individual performs best, but also affects the risk for chronic disease. Recent research has identified correlations between muscle fiber type and PPAR type as well as between even modest levels of endurance training and a lowering of the risk for insulin resistance, obesity, diabetes, and heart disease.

Practical implications

This review synthesizes recently discovered mechanisms into a framework supporting the conclusion that even moderate levels of endurance exercise, combined with a sufficient intake of n‐3 fatty acids, lower the risk for chronic disease.

Originality/value

This article provides accessible and comprehensive information to researchers, nutritionists, and consumers who are interested in using lifestyle management (such as exercise and diet) to lower the risk for chronic disease.
Cancer: the role of exercise in prevention and progression
Authors: Thomas Robert , Davies Nicola J.
Published: October 2007

Purpose

The paper's purpose is to examine evidence for the benefits of exercise in relation to cancer development, progression and prevention.

Design/methodology/approach

The reviewed literature was divided into categories according to the role exercise plays in cancer prevention and progression, during treatment, and in relapse prevention.

Findings

There is now persuasive evidence that exercise improves the physical and psychological function of patients with cancer, reduces the risk of recurrence and possibly improves survival.

Originality/value

Previous research highlights the importance of exercise in cancer prevention and throughout the cancer experience. However, current knowledge of the mechanisms by which physical activity may positively influence the activity of cancers is poorly understood; these mechanisms are explored in this paper.
Assessing body types, diet, exercise, and sedentary behavior of American and Japanese college students
Authors: Kobayashi Futoshi
Published: October 2007

Purpose

The present study aims to investigate the prevalence of overweight and obesity in both American and Japanese college students and their diet, exercise, and sedentary behavior.

Design/methodology/approach

The total of 407 college students from the USA (162 students aged 17‐53 years) and from Japan (245 students aged 18‐32 years) answered the survey in order to assess their body types, diet, exercise, and sedentary behavior.

Findings

Although the author found a lower mean BMI (body mass index) in the Japanese sample than in their American counterparts, there were not many differences in their diet, exercise, and sedentary behavior between them. The Japanese sample consumed their breakfast more regularly, were more likely to live with their parents, went to fast food restaurants less often and spent less money there than their American counterparts.

Research limitations/implications

The present study used self‐report survey method and it can be considered as a pilot study. In the future study, the height and weight of participants may be actually measured for obtaining more reliable data. Breakfast skipping, single living, and frequent usage of fast food restaurant might be crucial factors for overweight and obesity problems in American college students.

Originality/value

The present study is the first cross‐cultural study regarding body types, diet, exercise, and sedentary behavior between American and Japanese college students.