bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cell cycle and seed germination
Authors: Vázquez-Ramos Jorge M. , de la Paz Sánchez María 
Published: May 2003

AbstractThe cell cycle is the series of molecular events that allows cells to duplicate and segregate their chromosomes to form new cells. The finding that a protein kinase, the product of the yeastcdc2gene, was fundamental in the regulation of the G2/M and G1/S transitions, associated with unstable proteins named cyclins, opened a very exciting and dynamic research area. The number of gene products that participate in the development and regulation of the cell cycle may be in the hundreds, and there is a high degree of conservation in protein sequences and regulatory pathways among eukaryotes. Although there are clear differences between plants and animals in cell structure, organization, growth, development and differentiation, the same types of proteins and very similar regulatory pathways seem to exist. Seed germination appears to be an excellent model system for studying the cell cycle in plants. Imbibition will reactivate meristematic cells – most initially with a G1DNA content – into the cell cycle in preparation for seedling establishment. Early events include a thorough survey of DNA status, since the drying process and seed storage conditions reduce chromosomal integrity. The initiation of cell cycle events leading to G1and S phases, and of the germination process itself, may depend on a G1checkpoint control. Most, if not all, cell cycle proteins appear to be already present in unimbibed embryos, although there is evidence of protein turnover in the early hours, suggesting the need forde novoprotein synthesis. Regulation also may occur at the level of protein modification, because existing G1, S and G2cell cycle proteins appear to be activated at precise times during germination. Thus, cell cycle control during seed germination may be exerted at multiple levels; however, knowledge of cell cycle events and their importance for germination is still scarce and fragmentary, and different species may have developed unique control mechanisms, more suited to specific germination characteristics and habitat.
Cell cycle and germination of fresh, dried and deteriorated sugarbeet seeds as indicators of optimal harvest time
Authors: Śliwińska Elwira 
Published: May 2003

AbstractSeeds of sugar beet (Beta vulgarisL.) were collected at weekly intervals from 3 weeks before to 1 week after commercial harvest time, dried and stored at room temperature (18–22°C). Laboratory germination tests and flow cytometric analyses were performed immediately after harvest (fresh seeds) and five times at weekly intervals during storage (dry seeds). After 6 months of storage, seeds were exposed to a controlled deterioration treatment (CD). The proportion of G2nuclei in the embryo was constant in the fresh seeds, regardless of their maturity. It decreased, however, after drying and CD, especially in those seeds harvested before maturation drying had commenced. The proportion of endosperm cells in the seed decreased with maturation, and a further decrease was observed after drying and CD. These observations suggest that nuclei with a higher nuclear DNA content were more sensitive to water stress caused by premature desiccation and to deterioration than nuclei with a lower DNA content. Fresh seeds exhibited some germination, but this increased after drying, suggesting that desiccation induced a switch from the developmental to the germination mode. Germination percentages were the highest in dry seeds collected at the commercial harvest time and a week after. This high germinability coincided with the highest proportion of G2cells in the embryo. It is concluded that flow cytometry provides information about the status of sugarbeet seed maturation, seed quality and storage potential, and can be used for estimation of optimal harvest time.
Distinct expression patterns of β-1,3-glucanases and chitinases during the germination of Solanaceous seeds
Authors: Petruzzelli Luciana , Müller Kerstin , Hermann Katrin , Leubner-Metzger Gerhard 
Published: May 2003

AbstractThe expression patterns of β-1,3-glucanases (βGlu) and chitinases (Chn) were investigated during the seed germination of members of theCestroideae(threeNicotianaspecies,Petunia hybrida) and theSolanoideae(Capsicum annuum,Physalis peruviana) subgroups of Solanaceous species. Rupture of the micropylar testa (seed coat) and rupture of the micropylar endosperm, i.e. radicle emergence, were distinct and temporally separate events during the germination ofCestroideae-type seeds. βGlu accumulation in imbibedCestroideae-type seeds, occurring after testa rupture but prior to endosperm rupture, was inhibited by abscisic acid (ABA) and promoted by gibberellins (GA) and light, in strict association with germination, and appeared to be caused by transcriptional regulation of the class I βGlu genes. The micropylar cap ofSolanoideae-type seeds does not allow a distinction between testa and endosperm rupture, but βGlu accumulation occurred prior to radicle emergence of pepper andP. peruvianaseeds. ABA inhibited endosperm rupture and βGlu accumulation in the micropylar cap of pepper seeds. In contrast to tomato, βGlu accumulation in pepper seeds was not only confined to the micropylar cap, was due to distinct, tissue-specific βGlu isoforms, and was not accompanied by Chn accumulation. In conclusion, ABA inhibition of germination and βGlu accumulation in the micropylar endosperm appears to be a widespread event during the seed germination of Solanaceous species. In contrast, accumulation of Chn and distinct βGlu isoforms in the embryo, prior to germination, appears to be a species-specific phenomenon within theSolanaceae. In addition, a post-germination co-induction of βGlu and Chn in the root of the emerged seedling was found in endospermic and non-endospermic species and could represent an evolutionarily conserved event during dicot seedling development.
Acquisition of desiccation tolerance in developing oil palm (Elaeis guineensis Jacq.) embryos in planta and in vitro in relation to sugar content
Authors: Aberlenc-Bertossi Frédérique , Chabrillange Nathalie , Corbineau Françoise , Duval Yves 
Published: May 2003

AbstractRelationships between desiccation tolerance and dry matter, water and sugar contents were studied throughout the development of oil palm (Elaeis guineensis Jacq.) zygotic embryos and in immature embryos cultured on a sucrose-enriched medium. Embryo dry weight during in planta development increased between 80 and 140 d after pollination (DAP) and was then stable until maturity. Embryos underwent dehydration until 120 DAP, but their moisture content remained high at maturity (c. 2 g H2O g-1 DW). Desiccation tolerance was acquired between 83 and 104 DAP, and was positively correlated with embryo age and dry weight, and negatively correlated with initial water content during this period. Sucrose, the main soluble sugar present throughout embryo development, accounted for an average of 24% of the dry weight. Glucose and fructose contents decreased to less than 1 mg g-1 DW in embryos at maturity. At 117 DAP, as embryos became tolerant to desiccation, the monosaccharides/sucrose ratio fell to 0.015 and raffinose was detected. Stachyose appeared later in 147-day-old embryos and accumulated until shedding. In vitro culture of immature embryos in the presence of high sucrose concentrations (350 and 700 mM) resulted in an increase in their dry weight and a decrease in their water content, and induced the acquisition of desiccation tolerance. Under these conditions, sucrose accumulated in embryos to 30–40% on a dry weight basis, but neither raffinose nor stachyose was detected. Acquisition of desiccation tolerance by oil palm immature embryos was associated both in planta and in vitro with an accumulation of dry matter, a reduction of moisture content, and a fall in the monosaccharides/sucrose ratio. In planta, survival to dehydration was also related with the deposition of oligosaccharides whereas in vitro, it was related with high sucrose accumulation. The role of sugars in the acquisition of desiccation tolerance in oil palm embryos is discussed.
Codon pairs in the genome of Escherichia coli
Authors: Boycheva Svetlana , Chkodrov Georgi , Ivanov Ivan 
Published: May 2003

Abstract
Motivation: The effect of two neighboring codons (codon pairs) on gene expression is mediated via the interaction of their cognate tRNAs occupying the two functional ribosomal sites during the translation elongation step. For steric reasons it is reasonable to assume that not all combinations of codons and therefore of tRNAs are equally favorable when situated on the ribosome surface. Aiming of identifying preferential and rare codon pairs, we have determined the frequency of occurrence of all possible combinations of codon pairs in the entire genome of Escherichia coli (E.coli).
Results: The frequency of occurrence of the 3904 codon pairs comprising both sense:sense and sense:stop codon pairs in the full set of E.coli 4289 ORFs was found to vary from zero to 4913 times. For most of the pairs we have observed a significant difference between the real and statistically predicted frequency of occurrence. The analysis of 334 highly expressed and 303 poorly expressed E.coli genes showed that codon pair usage is different for the two gene categories. Using an especially defined criterion (Δreg), the codon pairs are classified as ‘hypothetically attenuating’ (HAP) and ‘hypothetically non-attenuating’ (HNAP) and their possible effect on translation is discussed.
Availability: The program used in this study is available at http://www.bio21.bas.bg/codonpairs/
Contact: iviv@obzor.bio21.bas.bg; svetlana@obzor.bio21.bas.bg
* To whom correspondence should be addressed.
FPV: fast protein visualization using Java 3DTM
Authors: Can Tolga , Wang Yujun , Wang Yuan-Fang , Su Jianwen 
Published: May 2003

Abstract
Motivation: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D™ are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison.
Results: In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could.
Availability: FPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/
Contact: tcan@cs.ucsb.edu
* To whom correspondence should be addressed.
Terminology-driven mining of biomedical literature
Authors: Nenadic Goran , Spasic Irena , Ananiadou Sophia 
Published: May 2003

Abstract
Motivation: With an overwhelming amount of textual information in molecular biology and biomedicine, there is a need for effective literature mining techniques that can help biologists to gather and make use of the knowledge encoded in text documents. Although the knowledge is organized around sets of domain-specific terms, few literature mining systems incorporate deep and dynamic terminology processing.
Results: In this paper, we present an overview of an integrated framework for terminology-driven mining from biomedical literature. The framework integrates the following components: automatic term recognition, term variation handling, acronym acquisition, automatic discovery of term similarities and term clustering. The term variant recognition is incorporated into terminology recognition process by taking into account orthographical, morphological, syntactic, lexico-semantic and pragmatic term variations. In particular, we address acronyms as a common way of introducing term variants in biomedical papers. Term clustering is based on the automatic discovery of term similarities. We use a hybrid similarity measure, where terms are compared by using both internal and external evidence. The measure combines lexical, syntactical and contextual similarity. Experiments on terminology recognition and clustering performed on a corpus of Medline abstracts recorded the precision of 98 and 71% respectively.
Availability: Software for the terminology management is available upon request.
Contact: g.nenadic@umist.ac.uk
* To whom correspondence should be addressed at: Department of Computation/Department of BioMolecular Sciences, UMIST, Manchester, UK.
Inference of transcriptional regulation relationships
from gene expression data
Authors: Kwon Andrew T. , Hoos Holger H. , Ng Raymond 
Published: May 2003

Abstract
Motivation: In order to find gene regulatory networks from microarray data, it is important to first find direct regulatory relationships between pairs of genes.
Results: We propose a new method for finding potential regulatory relationships between pairs of genes from microarray time series data and apply it to expression data for cell-cycle related genes in yeast. We compare our algorithm, dubbed the event method, with the earlier correlation method and the edge detection method by Filkov et al. When tested on known transcriptional regulation genes, all three methods are able to find similar numbers of true positives. The results indicate that our algorithm is able to identify true positive pairs that are different from those found by the two other methods. We also compare the correlation and the event methods using synthetic data and find that typically, the event method obtains better results.
Availability: Software is available upon request.
Contact: hoos@cs.ubc.ca
* To whom correspondence should be addressed.
Approximate variance-stabilizing
transformations for gene-expression microarray data
Authors: Rocke David M. , Durbin Blythe 
Published: May 2003

Abstract
Motivation: A variance stabilizing transformation for microarray data was recently introduced independently by several research groups. This transformation has sometimes been called the generalized logarithm or glog transformation. In this paper, we derive several alternative approximate variance stabilizing transformations that may be easier to use in some applications.
Results: We demonstrate that the started-log and the log-linear-hybrid transformation families can produce approximate variance stabilizing transformations for microarray data that are nearly as good as the generalized logarithm (glog) transformation. These transformations may be more convenient in some applications.
Contact: dmrocke@ucdavis.edu
* To whom correspondence should be addressed.
ProPred1: prediction of promiscuous MHC Class-I binding
sites
Authors: Singh Harpreet , Raghava G.P.S. 
Published: May 2003

Abstract
Summary: ProPred1 is an on-line web tool for the prediction of peptide binding to MHC class-I alleles. This is a matrix-based method that allows the prediction of MHC binding sites in an antigenic sequence for 47 MHC class-I alleles. The server represents MHC binding regions within an antigenic sequence in user-friendly formats. These formats assist user in the identification of promiscuous MHC binders in an antigen sequence that can bind to large number of alleles. ProPred1 also allows the prediction of the standard proteasome and immunoproteasome cleavage sites in an antigenic sequence. This server allows identification of MHC binders, who have the cleavage site at the C terminus. The simultaneous prediction of MHC binders and proteasome cleavage sites in an antigenic sequence leads to the identification of potential T-cell epitopes.
Availability: Server is available at http://www.imtech.res.in/raghava/propred1/. Mirror site of this server is available at http://bioinformatics.uams.edu/mirror/propred1/
Supplementary information: Matrices and document on server are available at http://www.imtech.res.in/raghava/propred1/page2.html
Contact: raghava@imtech.res.in
* To whom correspondence should be addressed at Bioinformatics Centre, Institute of Microbial Technology, Sector 39A, Chandigarh, India.
Generating consensus sequences from partial
order multiple sequence alignment graphs
Authors: Lee Christopher 
Published: May 2003

Abstract
Motivation: Consensus sequence generation is important in many kinds of sequence analysis ranging from sequence assembly to profile-based iterative search methods. However, how can a consensus be constructed when its inherent assumption—that the aligned sequences form a single linear consensus—is not true?
Results: Partial Order Alignment (POA) enables construction and analysis of multiple sequence alignments as directed acyclic graphs containing complex branching structure. Here we present a dynamic programming algorithm (heaviest_bundle) for generating multiple consensus sequences from such complex alignments. The number and relationships of these consensus sequences reveals the degree of structural complexity of the source alignment. This is a powerful and general approach for analyzing and visualizing complex alignment structures, and can be applied to any alignment. We illustrate its value for analyzing expressed sequence alignments to detect alternative splicing, reconstruct full length mRNA isoform sequences from EST fragments, and separate paralog mixtures that can cause incorrect SNP predictions.
Availability: The heaviest_bundle source code is available at http://www.bioinformatics.ucla.edu/poa
Contact: leec@mbi.ucla.edu
* To whom correspondence should be addressed.
Pathways database system: an integrated system for biological pathways
Authors: Krishnamurthy L. , Nadeau J. , Ozsoyoglu G. , Ozsoyoglu M. , Schaeffer G. , Tasan M. , Xu W. 
Published: May 2003

Abstract
Motivation: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers.
Results: In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; (b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and (d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e. pathways data) to researchers in the community, giving them control on the use of pathways data.
Availability: Available on request from the authors.
Contact: mxo2@po.cwru.edu
Supplementary information: http://nashua.cwru.edu/pathways
* To whom correspondence should be addressed.
Hierarchical analysis of dependency in metabolic networks
Authors: Gagneur Julien , Jackson David B. , Casari Georg 
Published: May 2003

Abstract
Motivation: Elucidation of metabolic networks for an increasing number of organisms reveals that even small networks can contain thousands of reactions and chemical species. The intimate connectivity between components complicates their decomposition into biologically meaningful sub-networks. Moreover, traditional higher-order representations of metabolic networks as metabolic pathways, suffers from the lack of rigorous definition, yielding pathways of disparate content and size.
Results: We introduce a hierarchical representation that emphasizes the gross organization of metabolic networks in largely independent pathways and sub-systems at several levels of independence. The approach highlights the coupling of different pathways and the shared compounds responsible for those couplings. By assessing our results on Escherichia coli (E.coli metabolic reactions, Genetic Circuits Research Group, University of California, San Diego, http://gcrg.ucsd.edu/organisms/ecoli.html,‘ model v 1.01. reactions’) against accepted biochemical annotations, we provide the first systematic synopsis of an organism’s metabolism. Comparison with operons of E.coli shows that low-level clusters are reflected in genome organization and gene regulation.
Availability: Source code, data sets and supplementary information are available at http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html
Contact: julien.gagneur@cellzome.com
* To whom correspondence should be addressed.
† Present address: Cellzome AG, Meyerhofstr. 1, 69117 Heidelberg, Germany..
Visual representation of database search results: the RHIMS Plot
Authors: Martin David M.A. , Hill Pamela , Barton Geoffrey J. , Flavell Andrew J. 
Published: May 2003

Abstract
Summary: An algorithm and software are described that provide a fast method to produce a novel, function-oriented visualization of the results of a sequence database search. Text mining of sequence annotations allows position specific plots of potential functional similarity to be compared in a simple compact representation.
Availability: The application can be accessed via a web server at http://www.compbio.dundee.ac.uk. The RHIMS software may be obtained by request to the authors.
Contact: d.m.a.martin@dundee.ac.uk
* To whom correspondence should be addressed.
Ligand-Info, searching for similar small compounds using
index profiles
Authors: von Grotthuss Marcin , Pas Jakub , Rychlewski Leszek 
Published: May 2003

Abstract
Motivation: The Ligand-Info system is based on the assumption that small molecules with similar structure have similar functional (binding) properties. The developed system enables a fast and sensitive index based search for similar compounds in large databases. Index profiles, constructed by averaging indexes of related molecules are used to increase the specificity of the search. The utilization of index profiles helps to focus on frequent, common features of a family of compounds.
Results: A Java-based tool for clustering and scanning of small molecules has been created. The tool can interactively cluster sets of molecules and create index profiles on the user side and automatically download similar molecules from a databases of 250 000 compounds. The results of the application of index profiles demonstrate that the profile based search strategy can increase the quality of the selection process.
Availability: The system is available at http://Ligand.Info. The application requires the Java Runtime Environment 1.4, which can be automatically installed during the first use on desktop systems, which support it. A standalone version of the program is available from the authors upon request.
Contact: leszek@bioinfo.pl
* To whom correspondence should be addressed.