bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database
Authors: Yang Chia-Ying , Chang Chao-Hui , Yu Ya-Ling , Lin Tsu-Chun Emma , Lee Sheng-An , Yen Chueh-Chuan , Yang Jinn-Moon , Lai Jin-Mei , Hong Yi-Ren , Tseng Tzu-Ling , Chao Kun-Mao , Huang Chi-Ying F. 
Published: August 2008

Abstract
Motivation: To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s). However, of the 518 known human serine/threonine/tyrosine kinases, 35% of these have known substrates, while 14% of the kinases have identified substrate recognition motifs. In contrast, 85% of the kinases have protein–protein interaction (PPI) datasets, raising the possibility that we might reveal potential kinase–substrate pairs from these PPIs.
Results: PhosphoPOINT, a comprehensive human kinase interactome and phospho-protein database, is a collection of 4195 phospho-proteins with a total of 15 738 phosphorylation sites. PhosphoPOINT annotates the interactions among kinases, with their down-stream substrates and with interacting (phospho)-proteins to modulate the kinase–substrate pairs. PhosphoPOINT implements various gene expression profiles and Gene Ontology cellular component information to evaluate each kinase and their interacting (phospho)-proteins/substrates. Integration of cSNPs that cause amino acids change with the proteins with the phosphoprotein dataset reveals that 64 phosphorylation sites result in a disease phenotypes when changed; the linked phenotypes include schizophrenia and hypertension. PhosphoPOINT also provides a search function for all phospho-peptides using about 300 known kinase/phosphatase substrate/binding motifs. Altogether, PhosphoPOINT provides robust annotation for kinases, their downstream substrates and their interaction (phospho)-proteins and this should accelerate the functional characterization of kinomemediated signaling.
Availability: PhosphoPOINT can be freely accessed in http://kinase.bioinformatics.tw/
Contact: cyhuang5@ym.edu.tw; kmchao@csie.ntu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
Authors: Bansal Vikas , Bafna Vineet 
Published: August 2008

Abstract
Motivation: The goal of the haplotype assembly problem is to reconstruct the two haplotypes (chromosomes) for an individual using a mix of sequenced fragments from the two chromosomes. This problem has been shown to be computationally intractable for various optimization criteria. Polynomial time algorithms have been proposed for restricted versions of the problem. In this article, we consider the haplotype assembly problem in the most general setting, i.e. fragments of any length and with an arbitrary number of gaps.
Results: We describe a novel combinatorial approach for the haplotype assembly problem based on computing max-cuts in certain graphs derived from the sequenced fragments. Levy et al. have sequenced the complete genome of a human individual and used a greedy heuristic to assemble the haplotypes for this individual. We have applied our method HapCUTto infer haplotypes from this data and demonstrate that the haplotypes inferred using HapCUT are significantly more accurate (20–25% lower maximum error correction scores for all chromosomes) than the greedy heuristic and a previously published method, Fast Hare. We also describe a maximum likelihood based estimator of the absolute accuracy of the sequence-based haplotypes using population haplotypes from the International HapMap project.
Availability: A program implementing HapCUT is available on request.
Contact: vibansal@cs.ucsd.edu
Inter-species normalization of gene mentions with GNAT
Authors: Hakenberg Jörg , Plake Conrad , Leaman Robert , Schroeder Michael , Gonzalez Graciela 
Published: August 2008

Abstract
Motivation: Text mining in the biomedical domain aims at helping researchers to access information contained in scientific publications in a faster, easier and more complete way. One step towards this aim is the recognition of named entities and their subsequent normalization to database identifiers. Normalization helps to link objects of potential interest, such as genes, to detailed information not contained in a publication; it is also key for integrating different knowledge sources. From an information retrieval perspective, normalization facilitates indexing and querying. Gene mention normalization (GN) is particularly challenging given the high ambiguity of gene names: they refer to orthologous or entirely different genes, are named after phenotypes and other biomedical terms, or they resemble common English words.
Results: We present the first publicly available system, GNAT, reported to handle inter-species GN. Our method uses extensive background knowledge on genes to resolve ambiguous names to EntrezGene identifiers. It performs comparably to single-species approaches proposed by us and others. On a benchmark set derived from BioCreative 1 and 2 data that contains genes from 13 species, GNAT achieves an F-measure of 81.4% (90.8% precision at 73.8% recall). For the single-species task, we report an F-measure of 85.4% on human genes.
Availability: A web-frontend is available at http://cbioc.eas.asu.edu/gnat/. GNAT will also be available within the BioCreative MetaService project, see http://bcms.bioinfo.cnio.es.
Contact: joerg.hakenberg@asu.edu
Supplementary information: The test data set, lexica, and links to external data are available at http://cbioc.eas.asu.edu/gnat/
Optimal spliced alignments of short sequence reads
Authors: De Bona Fabio , Ossowski Stephan , Schneeberger Korbinian , Rätsch Gunnar 
Published: August 2008

Abstract
Motivation: Next generation sequencing technologies open exciting new possibilities for genome and transcriptome sequencing. While reads produced by these technologies are relatively short and error prone compared to the Sanger method their throughput is several magnitudes higher. To utilize such reads for transcriptome sequencing and gene structure identification, one needs to be able to accurately align the sequence reads over intron boundaries. This represents a significant challenge given their short length and inherent high error rate.
Results: We present a novel approach, called QPALMA, for computing accurate spliced alignments which takes advantage of the read's quality information as well as computational splice site predictions. Our method uses a training set of spliced reads with quality information and known alignments. It uses a large margin approach similar to support vector machines to estimate its parameters to maximize alignment accuracy. In computational experiments, we illustrate that the quality information as well as the splice site predictions help to improve the alignment quality. Finally, to facilitate mapping of massive amounts of sequencing data typically generated by the new technologies, we have combined our method with a fast mapping pipeline based on enhanced suffix arrays. Our algorithms were optimized and tested using reads produced with the Illumina Genome Analyzer for the model plant Arabidopsis thaliana.
Availability: Datasets for training and evaluation, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/qpalma.
Contact: Gunnar.Raetsch@tuebingen.mpg.de
An environmental perspective on large-scale genome clustering based on metabolic capabilities
Authors: Kastenmüller Gabi , Gasteiger Johann , Mewes Hans-Werner 
Published: August 2008

Abstract
Motivation: In principle, an organism's ability to survive in a specific environment, is an observable result of the organism's regulatory and metabolic capabilities. Nonetheless, current knowledge about the global relation of the metabolisms and the niches of organisms is still limited.
Results: In order to further investigate this relation, we grouped species showing similar metabolic capabilities and systematically mapped their habitats onto these groups. For this purpose, we predicted the metabolic capabilities for 214 sequenced genomes. Based on these predictions, we grouped the genomes by hierarchical clustering. Finally, we mapped different environmental conditions and diseases related to the genomes onto the resulting clusters. This mapping uncovered several conditions and diseases that were unexpectedly enriched in clusters of metabolically similar species. As an example, Encephalitozoon cuniculi—a microsporidian causing a multisystemic disease accompanied by CNS problems in rabbits— occurred in the same metabolism-based cluster as bacteria causing similar symptoms in humans.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: g.kastenmueller@helmholtz-muenchen.de
BioJava: an open-source framework for bioinformatics
Authors: Holland R. C. G. , Down T. A. , Pocock M. , Prlić A. , Huen D. , James K. , Foisy S. , Dräger A. , Yates A. , Heuer M. , Schreiber M. J. 
Published: August 2008

Abstract
Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.
Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher.
Contact: andreas.prlic@gmail.com. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.
Anglerfish discard estimates and patterns in Spanish Northeast Atlantic trawl fisheries
Authors: Díaz Paz , Santos Juan , Velasco Francisco , Serrano Alberto , Pérez Nélida 
Published: August 2008

Abstract
Díaz, P., Santos, J., Velasco, F., Serrano, A., and Pérez, N. 2008. Anglerfish discard estimates and patterns in Spanish Northeast Atlantic trawl fisheries. – ICES Journal of Marine Science, 65: 1350–1361. Estimates of Spanish bottom trawl discards of anglerfish Lophius budegassa and Lophiuspiscatorius in the Northeast Atlantic Ocean are presented. Both species are commercially valuable in ICES Subareas VI and VII, and Divisions VIIIc and IXa. Information was obtained from observers on board during discard-monitoring programmes. Raising by effort, rather than by landings and target species, was used to determine the total annual discards by weight and number, the discard percentage, and the discard length distribution by stock throughout the dataseries. By weight and number, discards varied interannually, ranging from 4 to 600 t (∼28 000–7 000 000 fish) in northern stocks of anglerfish, and from 1 to 100 t (∼20 000–400 000 fish) in southern stocks. The discard percentage for both species and northern and southern stocks therefore ranged between 2 and 76% by number. Length distributions of the discarded anglerfish show that most were juveniles, although the pattern differed in years with high or with low rates of discarding. The number of juveniles caught apparently increased in most areas after 2000. Correlations between the quantities discarded and recruitment indices from French and Irish trawl surveys were found for northern stocks and with Spanish trawl survey indices for southern stocks.
Spawning groups of European anchovy: population structure and management implications
Authors: Sanz Núria , García-Marín José-Luis , Viñas Jordi , Roldán Marina , Pla Carles 
Published: August 2008

AbstractSanz, N., García-Marín, J-L., Viñas, J., Roldán, M., and Pla, C. 2008. Spawning groups of European anchovy: population structure and management implications. – ICES Journal of Marine Science, 65: 1635–1644. Samples of Engraulis encrasicolus from the western Mediterranean and the eastern Atlantic spawning groups were examined by protein electrophoresis to investigate their relevance in the genetic structure of European anchovy, and how they fit with the current definition of anchovy fisheries. Samples from an earlier study were also included in the analyses to assess the temporal genetic stability of spawning groups. Gene diversity analysis indicated greater differentiation between spawning groups within seas (GRS = 0.046) than between seas (GSEA = 0.022), and lesser differentiation between locations within spawning groups (GLR = 0.003), as well as genetic stability of spawning groups (GCL = 0.002). The six spawning groups apparently involved three genetic units according to Structure results, and the results of other analyses also suggested genetic differences between the two Atlantic spawning groups. The genetic substructure detected within the Atlantic agrees with the spawning groups, but does not fit easily with ICES Subdivisions. Based on these results, a revision of the current anchovy management in both Alboran Sea and Bay of Biscay areas is suggested.
Stringent promoter recognition and autoregulation by the group 3 σ-factor SigF in the cyanobacterium Synechocystis sp. strain PCC 6803
Authors: Asayama Munehiko , Imamura Sousuke 
Published: August 2008

Abstract
The cyanobacteirum Synechocystis sp. strain PCC 6803 possesses nine species of the sigma (σ)-factor gene for RNA polymerase (RNAP). Here, we identify and characterize the novel-type promoter recognized by a group 3 σ-factor, SigF. SigF autoregulates its own transcription and recognizes the promoter of pilA1 that acts in pilus formation and motility in PCC 6803. The pilA1 promoter (PpilA1-54) was recognized only by SigF and not by other σ-factors in PCC 6803. No PpilA1-54 activity was observed in Escherichia coli cells that possess RpoF (σ28) for fragellin and motility. Studies of in vitro transcription for PpilA1-54 identified the region from −39 to −7 including an AG-rich stretch and a core promoter with TAGGC (-32 region) and GGTAA (-12 region) as important for transcription. We also confirmed the unique PpilA1-54 architecture and further identified two novel promoters, recognized by SigF, for genes encoding periplasmic and phytochrome-like phototaxis proteins. These results and a phylogenetic analysis suggest that the PCC 6803 SigF is distinct from the E. coli RpoF or RpoD (σ70) type and constitutes a novel eubacterial group 3 σ- factor. We discuss a model case of stringent promoter recognition by SigF. Promoter types of PCC 6803 genes are also summarized.
Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli
Authors: Perwez Tariq , Hami Danyal , Maples Valerie F. , Min Zhao , Wang Bi-Cheng , Kushner Sidney R. 
Published: August 2008

Abstract
RNase E of Escherichia coli is an essential endoribonuclease that is involved in many aspects of RNA metabolism. Point mutations in the S1 RNA-binding domain of RNase E (rne-1 and rne-3071) lead to temperature-sensitive growth along with defects in 5S rRNA processing, mRNA decay and tRNA maturation. However, it is not clear whether RNase E acts similarly on all kinds of RNA substrates. Here we report the isolation and characterization of three independent intragenic second-site suppressors of the rne-1 and rne-3071 alleles that demonstrate for the first time the dissociation of the in vivo activity of RNase E on mRNA versus tRNA and rRNA substrates. Specifically, tRNA maturation and 9S rRNA processing were restored to wild-type levels in each of the three suppressor mutants (rne-1/172, rne-1/186 and rne-1/187), while mRNA decay and autoregulation of RNase E protein levels remained as defective as in the rne-1 single mutant. Each single amino acid substitution (Gly→ Ala at amino acid 172; Phe → Cys at amino acid 186 and Arg → Leu at amino acid 187) mapped within the 5′ sensor region of the RNase E protein. Molecular models of RNase E suggest how suppression may occur.
Interactions between branched DNAs and peptide inhibitors of DNA repair
Authors: Kepple Kevin V. , Patel Namita , Salamon Peter , Segall Anca M. 
Published: August 2008

Abstract
The RecG helicase of Escherichia coli unwinds both Holliday junction (HJ) and replication fork DNA substrates. Our lab previously identified and characterized peptides (WRWYCR and KWWCRW) that block the activity of RecG on these substrates. We determined that the peptides bind HJ DNA and prevent the binding of RecG. Herein, we present further evidence that the peptides are competitive inhibitors of RecG binding to its substrates. We have generated structural models of interactions between WRWYCR and a junction substrate. Using the fluorescent probe 2-aminopurine, we show that inhibitors interact with highest affinity with HJs (Kd = 14 nM) and ~4- to 9-fold more weakly with replication fork substrates. The fluorescence assay results agree with the structural model, and predict the molecular basis for interactions between HJ-trapping peptides and branched DNA molecules. Specifically, aromatic amino acids in the peptides stack with bases at the center of the DNA substrates. These interactions are stabilized by hydrogen bonds to the DNA and by intrapeptide interactions. These peptides inhibit several proteins involved in DNA repair in addition to RecG, have been useful as tools to dissect recombination, and possess antibiotic activity. Greater understanding of the peptides’ mechanism of action will further increase their utility.
Innate Immunity Signaling: Cytosolic Ca2+ Elevation Is Linked to Downstream Nitric Oxide Generation through the Action of Calmodulin or a Calmodulin-Like Protein
Authors: Ma Wei , Smigel Andries , Tsai Yu-Chang , Braam Janet , Berkowitz Gerald A. 
Published: August 2008

Abstract
Ca2+ rise and nitric oxide (NO) generation are essential early steps in plant innate immunity and initiate the hypersensitive response (HR) to avirulent pathogens. Previous work from this laboratory has demonstrated that a loss-of-function mutation of an Arabidopsis (Arabidopsis thaliana) plasma membrane Ca2+-permeable inwardly conducting ion channel impairs HR and that this phenotype could be rescued by the application of a NO donor. At present, the mechanism linking cytosolic Ca2+ rise to NO generation during pathogen response signaling in plants is still unclear. Animal nitric oxide synthase (NOS) activation is Ca2+/calmodulin (CaM) dependent. Here, we present biochemical and genetic evidence consistent with a similar regulatory mechanism in plants: a pathogen-induced Ca2+ signal leads to CaM and/or a CaM-like protein (CML) activation of NOS. In wild-type Arabidopsis plants, the use of a CaM antagonist prevents NO generation and the HR. Application of a CaM antagonist does not prevent pathogen-induced cytosolic Ca2+ elevation, excluding the possibility of CaM acting upstream from Ca2+. The CaM antagonist and Ca2+ chelation abolish NO generation in wild-type Arabidopsis leaf protein extracts as well, suggesting that plant NOS activity is Ca2+/CaM dependent in vitro. The CaM-like protein CML24 has been previously associated with NO-related phenotypes in Arabidopsis. Here, we find that innate immune response phenotypes (HR and [avirulent] pathogen-induced NO elevation in leaves) are inhibited in loss-of-function cml24-4 mutant plants. Pathogen-associated molecular pattern-mediated NO generation in cells of cml24-4 mutants is impaired as well. Our work suggests that the initial pathogen recognition signal of Ca2+ influx into the cytosol activates CaM and/or a CML, which then acts to induce downstream NO synthesis as intermediary steps in a pathogen perception signaling cascade, leading to innate immune responses, including the HR.
LEAFY COTYLEDON1Is a Key Regulator of Fatty Acid Biosynthesis in Arabidopsis
Authors: Mu Jinye , Tan Helin , Zheng Qi , Fu Fuyou , Liang Yan , Zhang Jian , Yang Xiaohui , Wang Tai , Chong Kang , Wang Xiu-Jie , Zuo Jianru 
Published: August 2008

AbstractIn plants, fatty acids are de novo synthesized predominantly in plastids from acetyl-coenzyme A. Although fatty acid biosynthesis has been biochemically well studied, little is known about the regulatory mechanisms of the pathway. Here, we show that overexpression of the Arabidopsis (Arabidopsis thaliana) LEAFY COTYLEDON1 (LEC1) gene causes globally increased expression of fatty acid biosynthetic genes, which are involved in key reactions of condensation, chain elongation, and desaturation of fatty acid biosynthesis. In the plastidial fatty acid synthetic pathway, over 58% of known enzyme-coding genes are up-regulated in LEC1-overexpressing transgenic plants, including those encoding three subunits of acetyl-coenzyme A carboxylase, a key enzyme controlling the fatty acid biosynthesis flux. Moreover, genes involved in glycolysis and lipid accumulation are also up-regulated. Consistent with these results, levels of major fatty acid species and lipids were substantially increased in the transgenic plants. Genetic analysis indicates that the LEC1 function is partially dependent on ABSCISIC ACID INSENSITIVE3, FUSCA3, and WRINKLED1 in the regulation of fatty acid biosynthesis. Moreover, a similar phenotype was observed in transgenic Arabidopsis plants overexpressing two LEC1-like genes of Brassica napus. These results suggest that LEC1 and LEC1-like genes act as key regulators to coordinate the expression of fatty acid biosynthetic genes, thereby representing promising targets for genetic improvement of oil production plants.
Lipid Trafficking between the Endoplasmic Reticulum and the Plastid in Arabidopsis Requires the Extraplastidic TGD4 Protein
Authors: Xu Changcheng , Fan Jilian , Cornish Adam J. , Benning Christoph 
Published: August 2008

Abstract
The development of chloroplasts in Arabidopsis thaliana requires extensive lipid trafficking between the endoplasmic reticulum (ER) and the plastid. The biosynthetic enzymes for the final steps of chloroplast lipid assembly are associated with the plastid envelope membranes. For example, during biosynthesis of the galactoglycerolipids predominant in photosynthetic membranes, galactosyltransferases associated with these membranes transfer galactosyl residues from UDP-Gal to diacylglycerol. In Arabidopsis, diacylglycerol can be derived from the ER or the plastid. Here, we describe a mutant of Arabidopsis, trigalactosyldiacylglycerol4 (tgd4), in which ER-derived diacylglycerol is not available for galactoglycerolipid biosynthesis. This mutant accumulates diagnostic oligogalactoglycerolipids, hence its name, and triacylglycerol in its tissues. The TGD4 gene encodes a protein that appears to be associated with the ER membranes. Mutant ER microsomes show a decreased transfer of lipids to isolated plastids consistent with in vivo labeling data, indicating a disruption of ER-to-plastid lipid transfer. The complex lipid phenotype of the mutant is similar to that of the tgd1,2,3 mutants disrupted in components of a lipid transporter of the inner plastid envelope membrane. However, unlike the TGD1,2,3 complex, which is proposed to transfer phosphatidic acid through the inner envelope membrane, TGD4 appears to be part of the machinery mediating lipid transfer between the ER and the outer plastid envelope membrane. The extent of direct ER-to-plastid envelope contact sites is not altered in the tgd4 mutant. However, this does not preclude a possible function of TGD4 in those contact sites as a conduit for lipid transfer between the ER and the plastid.