bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractMotivation: 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.chSupplementary 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

AbstractMotivation: 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.govSupplementary 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

AbstractMotivation: 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.deSupplementary 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

AbstractMotivation: 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.htmlContact: 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

AbstractA 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.
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

Abstract
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

AbstractDEFECTIVE 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

Abstract
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 &gt;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

AbstractTwo 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

AbstractBioactive 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

PurposeThe 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/approachPrime source of data is interviews with 60 pig farmers. Supplementary sources are research reports and statistics, specifications of the quality schemes.FindingsOn 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/valueThe 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

PurposeThe 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/approachThe 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.FindingsThe 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/implicationsThe 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 implicationsThe 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/valueThis 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

PurposeThe 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/approachIn 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.FindingsFarmers' 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/valueThis 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.