bluuebunny/crossref_metadata_2025_split huggingface dataset:
Das Geheimnis der Austrocknungstoleranz: Wiederauferstehungspflanzen
Authors: Hilbricht Tobias , Bartels Dorothea 
Published: February 2003

AbstractWiederauferstehungspflanzen wie Craterostigma plantagineum besitzen im vollentwickelten Zustand eine Eigenschaft, die man bei den meisten Embryonen der Samenpflanzen antrifft: sie sind austrocknungstolerant und überdauern einen beinahe vollständigen Entzug des Zellwassers ohne Vitalitätsverlust. Vermutlich sind die Biosynthese von LEA‐Proteinen und die Bildung von Saccharose aus 2‐Octulose an der Ausprägung der Trockentoleranz in C. plantagineum maßgeblich beteiligt. Das Phytohormon ABA als wichtiges Signalmolekül im Zusammenhang mit Trockenstress reguliert unter anderem die Aktivitäten von Transkriptionsfaktoren, die an der Expression von lea‐Genen beteiligt sind. Die Ausprägung der Trockentoleranz bei C. plantagineum wird allerdings durch viele Faktoren und Prozesse bestimmt, die sich in gleicher oder ähnlicher Form auch im Embryo der Samenpflanzen stattfinden.
Auf den Duft kommt es an
Authors: Wendler Silke 
Published: February 2003

AbstractPflanzen können auf die Anwesenheit von pflanzenfressenden Insekten mit der Erzeugung von Duftstoffen reagieren, um beispielsweise natürliche Feinde des Insektes anzulocken oder eine Eiablage zu verhindern. Bisher unbekannt war, dass Insekten die Zusammensetzung von pflanzlichen Duftcocktails für eigene Zwecke nutzen können, wie die Gallwespe Antistrophus rufus zeigt.
The HUPO Proteomics Standards Initiative meeting: towards common standards for exchanging proteomics data
Authors: Orchard Sandra , Kersey Paul , Hermjakob Henning , Apweiler Rolf 
Published: February 2003

AbstractThe Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields of protein–protein interactions (PPI) and mass spectroscopy have been targeted and the inaugural meeting of the PSI addressed the questions of data storage and exchange in both of these areas. The PPI group rapidly reached consensus as to the minimum requirements for a data exchange model; an XML draft is now being produced. The mass spectroscopy group have achieved major advances in the definition of a required data model and working groups are currently taking these discussions further. A further meeting is planned in January 2003 to advance both these projects. Copyright © 2003 John Wiley & Sons, Ltd.
Building ontologies in DAML + OIL
Authors: Stevens Robert , Wroe Chris , Bechhofer Sean , Lord Phillip , Rector Alan , Goble Carole 
Published: February 2003

AbstractIn this article we describe an approach to representing and building ontologies advocated by the Bioinformatics and Medical Informatics groups at the University of Manchester. The hand‐crafting of ontologies offers an easy and rapid avenue to delivering ontologies. Experience has shown that such approaches are unsustainable. Description logic approaches have been shown to offer computational support for building sound, complete and logically consistent ontologies. A new knowledge representation language, DAML + OIL, offers a new standard that is able to support many styles of ontology, from hand‐crafted to full logic‐based descriptions with reasoning support. We describe this language, the OilEd editing tool, reasoning support and a strategy for the language's use. We finish with a current example, in the Gene Ontology Next Generation (GONG) project, that uses DAML + OIL as the basis for moving the Gene Ontology from its current hand‐crafted, form to one that uses logical descriptions of a concept's properties to deliver a more complete version of the ontology. Copyright © 2003 John Wiley & Sons, Ltd.
The MGED ontology: a framework for describing functional genomics experiments
Authors: Stoeckert Christian J. , Parkinson Helen 
Published: February 2003

AbstractThe Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts used and a common need to capture experimental information in a standardized manner. In building the MGED ontology, it was recognized that it would be impractical to cover all the different types of experiments on all the different types of organisms by listing and defining all the types of organisms and their properties. Our solution was to create a framework for describing microarray experiments with an initial focus on the biological sample and its manipulation. For concepts that are common for many species, we could provide a manageable listing of controlled terms. For concepts that are species‐specific or whose values cannot be readily listed, we created an ‘OntologyEntry’ concept that referenced an external resource. The MGED ontology is a work in progress that needs additional instances and particularly needs constraints to be added. The ontology currently covers the experimental sample and design, and we have begun capturing aspects of the microarrays themselves as well. The primary application of the ontology will be to develop forms for entering information into databases, and consequently allowing queries, taking advantage of the structure provided by the ontology. The application of an ontology of experimental conditions extends beyond microarray experiments and, as the scope of MGED includes other aspects of functional genomics, so too will the MGED ontology. Copyright © 2003 John Wiley & Sons, Ltd.
A relational database for the discovery of genes encoding amino acid biosynthetic enzymes in pathogenic fungi
Authors: Giles Peter F. , Soanes Darren M. , Talbot Nicholas J. 
Published: February 2003

AbstractFungal phytopathogens continue to cause major economic impact, either directly, through crop losses, or due to the costs of fungicide application. Attempts to understand these organisms are hampered by a lack of fungal genome sequence data. A need exists, however, to develop specific bioinformatics tools to collate and analyse the sequence data that currently is available. A web‐accessible gene discovery database (http://cogeme.ex.ac.uk/biosynthesis.html) was developed as a demonstration tool for the analysis of metabolic and signal transduction pathways in pathogenic fungi using incomplete gene inventories. Using Bayesian probability to analyse the currently available gene information from pathogenic fungi, we provide evidence that the obligate pathogen Blumeria graminis possesses all amino acid biosynthetic pathways found in free‐living fungi, such as Saccharomyces cerevisiae. Phylogenetic analysis was also used to deduce a gene history of succinate‐semialdehyde dehydrogenase, an enzyme in the glutamate and lysine biosynthesis pathways. The database provides a tool and methodology to researchers to direct experimentation towards predicting pathway conservation in pathogenic microorganisms. Copyright © 2003 John Wiley & Sons, Ltd.
An approach to inferring transcriptional regulation among genes from large‐scale expression data
Authors: Herrero Javier , Díaz‐Uriarte Ramón , Dopazo Joaquín 
Published: February 2003

AbstractThe use of DNA microarrays opens up the possibility of measuring the expression levels of thousands of genes simultaneously under different conditions. Time‐course experiments allow researchers to study the dynamics of gene interactions. The inference of genetic networks from such measures can give important insights for the understanding of a variety of biological problems. Most of the existing methods for genetic network reconstruction require many experimental data points, or can only be applied to the reconstruction of small subnetworks. Here we present a method that reduces the dimensionality of the dataset and then extracts the significant dynamic correlations among genes. The method requires a number of points achievable in common time‐course experiments. Copyright © 2003 John Wiley & Sons, Ltd.
Early gene expression in wounded human keratinocytes revealed by DNA microarray analysis
Authors: Dayem Manal A. , Moreilhon Chimène , Turchi Laurent , Magnone Virginie , Christen Richard , Ponzio Gilles , Barbry Pascal 
Published: February 2003

AbstractWound healing involves several steps: spreading of the cells, migration and proliferation. We have profiled gene expression during the early events of wound healing in normal human keratinocytes with a home‐made DNA microarray containing about 1000 relevant human probes. An original wounding machine was used, that allows the wounding of up to 40% of the surface of a confluent monolayer of cultured cells grown on a Petri dish (compared with 5% with a classical ‘scratch’ method). The two aims of the present study were: (a) to validate a limited number of genes by comparing the expression levels obtained with this technique with those found in the literature; (b) to combine the use of the wounding machine with DNA microarray analysis for large‐scale detection of the molecular events triggered during the early stages of the wound‐healing process. The time‐courses of RNA expression observed at 0.5, 1.5, 3, 6 and 15 h after wounding for genes such as c‐Fos, c‐Jun, Egr1, the plasminogen activator PLAU (uPA) and the signal transducer and transcription activator STAT3, were consistent with previously published data. This suggests that our methodologies are able to perform quantitative measurement of gene expression. Transcripts encoding two zinc finger proteins, ZFP36 and ZNF161, and the tumour necrosis factor α‐induced protein TNFAIP3, were also overexpressed after wounding. The role of the p38 mitogen‐activated protein kinase (p38MAPK) in wound healing was shown after the inhibition of p38 by SB203580, but our results also suggest the existence of surrogate activating pathways. Copyright © 2003 John Wiley & Sons, Ltd.
Genomics and ethics: the case of cloned and/or transgenic animals
Authors: de Montera Béatrice 
Published: February 2003

AbstractThe point of the present study is to illustrate and, if possible, promote the existing link between genomics and ethics, taking the example of cloned and transgenic animals. These ‘new animals’ raise theoretical and practical problems that concern applied ethics. We will explore more particularly an original strategy showing that it is possible, starting from philosophical questioning about the nature of identity, to use a genomic approach, based on amplification fragment length polymorphism (AFLP) and methylation‐sensitive amplification polymorphism (MSAP) detection, to provide useful tools to define more rigorously what cloned animals are, by testing their genetic and epigenetic identity. We expect from the future results of this combined approach to stimulate the creativity of the philosophical and ethical reflection about the impact of biotechnology on animals, and to increase scientific involvement in such issues. Copyright © 2003 John Wiley & Sons, Ltd.
Why chloroplasts and mitochondria contain genomes
Authors: Allen John F. 
Published: February 2003

AbstractChloroplasts and mitochondria originated as bacterial symbionts. The larger, host cells acquired genetic information from their prokaryotic guests by lateral gene transfer. The prokaryotically‐derived genes of the eukaryotic cell nucleus now function to encode the great majority of chloroplast and mitochondrial proteins, as well as many proteins of the nucleus and cytosol. Genes are copied and moved between cellular compartments with relative ease, and there is no established obstacle to successful import of any protein precursor from the cytosol. Yet chloroplasts and mitochondria have not abdicated all genes and gene expression to the nucleus and to cytosolic translation. What, then, do chloroplast‐ and mitochondrially‐encoded proteins have in common that confers a selective advantage on the cytoplasmic location of their genes? The proposal advanced here is that co‐location of chloroplast and mitochondrial genes with their gene products is required for rapid and direct regulatory coupling. Redox control of gene expression is suggested as the common feature of those chloroplast and mitochondrial proteins that are encoded in situ. Recent evidence is consistent with this hypothesis, and its underlying assumptions and predictions are described. Copyright © 2003 John Wiley & Sons, Ltd.
Pressures in archaeal protein coding genes: a comparative study
Authors: Chattopadhyay Sujay , Sahoo Satyabrata , Kanner William A. , Chakrabarti Jayprokas 
Published: February 2003

AbstractOur studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC‐rich to AT‐rich protein‐coding gene‐containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons. These findings suggest that the deviations from the second parity rule (through the increasing differences between complementary base contents) and the increasing purine load hinder the chance of formation of the intra‐strand Watson–Crick base‐paired secondary structures in mRNAs (synonymous with the protein‐coding genes we dealt with), thereby increasing the translational efficiency. We hypothesize that the AT‐rich protein‐coding gene‐containing archaeal species might have better translational efficiency than their GC‐rich counterparts. Copyright © 2003 John Wiley & Sons, Ltd.
Turning informal thesauri into formal ontologies: a feasibility study on biomedical knowledge re‐use
Authors: Hahn Udo 
Published: February 2003

AbstractThis paper reports a large‐scale knowledge conversion and curation experiment. Biomedical domain knowledge from a semantically weak and shallow terminological resource, the UMLS, is transformed into a rigorous description logics format. This way, the broad coverage of the UMLS is combined with inference mechanisms for consistency and cycle checking. They are the key to proper cleansing of the knowledge directly imported from the UMLS, as well as subsequent updating, maintenance and refinement of large knowledge repositories. The emerging biomedical knowledge base currently comprises more than 240 000 conceptual entities and hence constitutes one of the largest formal knowledge repositories ever built. Copyright © 2003 John Wiley & Sons, Ltd.
Building a cell and anatomy ontology of Caenorhabditis elegans
Authors: Lee Raymond Y. N. , Sternberg Paul W. 
Published: February 2003

AbstractWe are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell‐based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress. Copyright © 2003 John Wiley & Sons, Ltd.
Bringing ontology to the Gene Ontology
Authors: Williams Jennifer , Andersen William 
Published: February 2003

AbstractWe present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine‐processible ontology, reflecting principles of formal ontology. GO is a controlled vocabulary that is intended to facilitate communication between biologists by standardizing usage of terms in database annotations. Making such controlled vocabularies maximally useful in support of bioinformatics applications requires explicating in machine‐processible form the implicit background information that enables human users to interpret the meaning of the vocabulary terms. In the case of GO, this process would involve rendering the meanings of GO into a formal (logical) language with the help of domain experts, and adding additional information required to support the chosen formalization. A controlled vocabulary augmented in these ways is commonly called an ontology. In this paper, we make a modest exploration to determine the ontological requirements for this extended version of GO. Using the terms within the three GO hierarchies (molecular function, biological process and cellular component), we investigate the facility with which GO concepts can be ontologized, using available tools from the philosophical and ontological engineering literature. Copyright © 2003 John Wiley & Sons, Ltd.
The S. cerevisiae HAP complex, a key regulator of mitochondrial function, coordinates nuclear and mitochondrial gene expression
Authors: Buschlen S. , Amillet J‐M , Guiard B. , Fournier A. , Marcireau C. , Bolotin‐Fukuhara M. 
Published: February 2003

AbstractWe have compared Saccharomyces cerevisiae global gene expression in wild‐type and mutants (Δhap2 and Δhap4) of the HAP transcriptional complex, which has been shown to be necessary for growth on respiratory substrates. Several hundred ORFs are under positive or negative control of this complex and we analyse here in detail the effect of HAP on mitochondria. We found that most of the genes upregulated in the wild‐type strain were involved in organelle functions, but practically none of the downregulated ones. Nuclear genes encoding the different subunits of the respiratory chain complexes figure in the genes more expressed in the wild‐type than in the mutants, as expected, but in this group we also found key components of the mitochondrial translation apparatus. This control of mitochondrial translation may be one of the means of coordinating mitochondrial and nuclear gene expression in elaborating the respiratory chain. In addition, HAP controls the nuclear genes involved in several other mitochondrial processes (import, mitochondrial division) that define the metabolic state of the cell, but not mitochondrial DNA replication and transcription. In most cases, a putative CCAAT‐binding site is present upstream of the ORF, while in others no such sites are present, suggesting the control to be indirect. The large number of genes regulated by the HAP complex, as well as the fact that HAP also regulates some putative transcriptional activators of unknown function, place this complex at a hierarchically high position in the global transcriptional regulation of the cell. Copyright © 2003 John Wiley & Sons, Ltd.
An upper‐level ontology for the biomedical domain
Authors: McCray Alexa T. 
Published: February 2003

AbstractAt the US National Library of Medicine we have developed the Unified Medical Language System (UMLS), whose goal it is to provide integrated access to a large number of biomedical resources by unifying the vocabularies that are used to access those resources. The UMLS currently interrelates some 60 controlled vocabularies in the biomedical domain. The UMLS coverage is quite extensive, including not only many concepts in clinical medicine, but also a large number of concepts applicable to the broad domain of the life sciences. In order to provide an overarching conceptual framework for all UMLS concepts, we developed an upper‐level ontology, called the UMLS semantic network. The semantic network, through its 134 semantic types, provides a consistent categorization of all concepts represented in the UMLS. The 54 links between the semantic types provide the structure for the network and represent important relationships in the biomedical domain. Because of the growing number of information resources that contain genetic information, the UMLS coverage in this area is being expanded. We recently integrated the taxonomy of organisms developed by the NLM's National Center for Biotechnology Information, and we are currently working together with the developers of the Gene Ontology to integrate this resource, as well. As additional, standard, ontologies become publicly available, we expect to integrate these into the UMLS construct. Published in 2003 by John Wiley & Sons, Ltd.
What is the Nature of the First‐Formed Intermediates in the Electrophilic Halogenation of Alkenes, Alkynes, and Allenes?
Authors: Lenoir Dieter , Chiappe Cinzia 
Published: February 2003

AbstractThe π complexes first formed as essential intermediates from alkenes, alkynes, and allenes with bromine have been investigated in different solvents by UV‐spectroscopy in combination with stopped‐flow techniques allowing the determination of the equilibrium constants, Kf. Using alkenes with sterically protected double bonds, such as di‐tert‐butylstilbene and tetraneopentylethylene, the reaction stops at the stage of the 1:1 and 1:2 π complex of the alkene with bromine as persistent species in 1,2‐dichlorethane as solvent. Calculations by state‐of‐art ab initio and DFT methods reproduces the experimentally determined thermodynamic values quite well, and reveal the preferred structures and nature of both complexes for ethene, ethyne, and allene. Consideration of the entropy term reveals that complexes are stabilized in solution owing to reduction of the entropy loss by restricted translations and rotation. According to calculations these species are Mulliken‐outer‐type complexes with no or little charge transfer from bromine to the double or triple bond, respectively. The 1:2 complex has a close structural relationship to the bromonium‐ or bromirenium ion, which is the subsequent intermediate on the reaction coordinate. Steric influences show a strong effect on the Kf value, which can be explained by the polarizibility of the parent system. Addition–elimination often occurs. In bromination of adamantylidenadamantane and its derivatives the reaction stops at the stage of the bromonium ion. The effect of various polar groups situated in equatorial homoallyl positions on the stability of corresponding π complex and bromonium ion has been studied in this series.
Catalytic Hydrogenation by Triruthenium Clusters: A Mechanistic Study with Parahydrogen‐Induced Polarization
Authors: Blazina Damir , Duckett Simon B. , Dyson Paul J. , Lohman Joost A. B. 
Published: February 2003

AbstractThe reactivity of the cluster family [Ru3(CO)12−x(L)x] (in which L=PMe3, PMe2Ph, PPh3 and PCy3, x=1–3) towards hydrogen is described. When x=2, three isomers of [Ru3(H)(μ‐H)(CO)9(L)2] are formed, which differ in the arrangement of their equatorial phosphines. Kinetic studies reveal the presence of intra‐ and inter‐isomer exchange processes with activation parameters and solvent effects indicating the involvement of ruthenium‐ruthenium bond heterolysis and CO loss, respectively. When x=3, reaction with H2 proceeds to form identical products to those found with x=2, while when x=1 a single isomer of [Ru3(H)(μ‐H)(CO)10(L)] is formed. Species [Ru3(H)(μ‐H)(CO)9(L)2] have been shown to play a kinetically significant role in the hydrogenation of an alkyne substrate through initial CO loss, with rates of H2 transfer being explicitly determined for each isomer. A less significant secondary reaction involving loss of L yields a detectable product that contains both a pendant vinyl unit and a bridging hydride ligand. Competing pathways that involve fragmentation to form [Ru(H)2(CO)2(L)(alkyne)] are also observed and shown to be favoured by nonpolar solvents. Kinetic data reveal that catalysis based on [Ru3(CO)10(PPh3)2] is the most efficient although [Ru3(H)(μ‐H)(CO)9(PMe3)2] corresponds to the most active of the detected intermediates.