Author: "Viktor Stolc" / Topic: biology - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Viktor Stolc"' showing total 38 results

Start Over Author "Viktor Stolc" Topic biology

38 results on '"Viktor Stolc"'

1. Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program

Author: Tomoyoshi Soga, Cornelia Amariei, Viktor Stolc, Masaru Tomita, Douglas B. Murray, and Rainer Machné
Subjects: Applied Microbiology, Biochemistry, Genetics and Molecular Biology (miscellaneous), Microbiology, Applied Microbiology and Biotechnology, Transcriptome, chemistry.chemical_compound, Virology, Genetics, Oscillation (cell signaling), Transcriptional regulation, Nucleosome, histone modification, lcsh:QH301-705.5, Molecular Biology, Gene, energetics, respiratory oscillation, biology, anabolism, catabolism, Cell Biology, Chromatin, Cell biology, Histone, lcsh:Biology (General), chemistry, biology.protein, chromatin dynamics, Parasitology, transcription regulation, DNA
Abstract: The structural dynamics of chromatin have been implicated in the regulation of fundamental eukaryotic processes, such as DNA transcription, replication and repair. Although previous studies have revealed that the chromatin landscape, nucleosome remodeling and histone modification events are intimately tied into cellular energetics and redox state, few studies undertake defined time-resolved measurements of these state variables. Here, we use metabolically synchronous, continuously-grown yeast cultures to measure DNA occupancy and track global patterns with respect to the metabolic state of the culture. Combined with transcriptome analyses and ChIP-qPCR experiments, these paint an intriguing picture where genome-wide nucleosome focusing occurs during the recovery of energy charge, followed by clearance of the promoter regions and global transcriptional slow-down, thus indicating a nucleosome-mediated “reset point” for the cycle. The reset begins at the end of the catabolic and stress-response transcriptional programs and ends prior to the start of the anabolic and cell-growth transcriptional program, and the histones on genes from both the catabolic and anabolic superclusters are deacetylated.
Published: 2014
Full Text: View/download PDF

2. ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases

Author: Kamrun Zargar, Alison Conrad, Chad W. Saltikov, David L. Bernick, Viktor Stolc, Ronald S. Oremland, Todd M. Lowe, John F. Stolz, and Shelley E. Hoeft
Subjects: DMSO reductase, Oxidase test, Operon, Aroa, Arsenate, Biology, Reductase, biology.organism_classification, Microbiology, chemistry.chemical_compound, Biochemistry, chemistry, Ecology, Evolution, Behavior and Systematics, Bacteria, Arsenite
Abstract: Summary Arsenotrophy, growth coupled to autotrophic arsenite oxidation or arsenate respiratory reduction, occurs only in the prokaryotic domain of life. The enzymes responsible for arsenotrophy belong to distinct clades within the DMSO reductase family of molybdenum-containing oxidoreductases: specifi- cally arsenate respiratory reductase, ArrA, and arsen- ite oxidase, AioA (formerly referred to as AroA and AoxB). A new arsenite oxidase clade, ArxA, repre- sented by the haloalkaliphilic bacterium Alkalilimni- cola ehrlichii strain MLHE-1 was also identified in the photosynthetic purple sulfur bacterium Ectothiorho- dospira sp. strain PHS-1. A draft genome sequence of PHS-1 was completed and an arx operon similar to MLHE-1 was identified. Gene expression studies showed that arxA was strongly induced with arsenite. Microbial ecology investigation led to the identifica- tion of additional arxA-like sequences in Mono Lake and Hot Creek sediments, both arsenic-rich environ- ments in California. Phylogenetic analyses placed these sequences as distinct members of the ArxA clade of arsenite oxidases. ArxA-like sequences were also identified in metagenome sequences of several alkaline microbial mat environments of Yellowstone National Park hot springs. These results suggest that ArxA-type arsenite oxidases appear to be widely dis- tributed in the environment presenting an opportunity for further investigations of the contribution of Arx- dependent arsenotrophy to the arsenic biogeochemi- cal cycle.
Published: 2012
Full Text: View/download PDF

3. High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

Author: Jiming Jiang, Kun He, Songgang Li, Hang He, Xing Wang Deng, Xiangfeng Wang, Weiwei Jin, Xueyong Li, Waraporn Tongprasit, Viktor Stolc, William Terzaghi, Ning Su, and Yeqin Ma
Subjects: Chromatin Immunoprecipitation, Transcription, Genetic, Plant Science, Biology, Methylation, Polymerase Chain Reaction, Epigenesis, Genetic, Euchromatin, Histones, Epigenetics of physical exercise, Gene Expression Regulation, Plant, Histone methylation, Epigenetics, Methylated DNA immunoprecipitation, RNA-Directed DNA Methylation, Research Articles, Epigenomics, Reverse Transcriptase Polymerase Chain Reaction, food and beverages, Oryza, Cell Biology, DNA Methylation, Molecular biology, Differentially methylated regions, DNA methylation, Genome, Plant
Abstract: We present high-resolution maps of DNA methylation and H3K4 di- and trimethylation of two entire chromosomes and two fully sequenced centromeres in rice (Oryza sativa) shoots and cultured cells. This analysis reveals combinatorial interactions between these epigenetic modifications and chromatin structure and gene expression. Cytologically densely stained heterochromatin had less H3K4me2 and H3K4me3 and more methylated DNA than the less densely stained euchromatin, whereas centromeres had a unique epigenetic composition. Most transposable elements had highly methylated DNA but no H3K4 methylation, whereas more than half of protein-coding genes had both methylated DNA and di- and/or trimethylated H3K4. Methylation of DNA but not H3K4 was correlated with suppressed transcription. By contrast, when both DNA and H3K4 were methylated, transcription was only slightly reduced. Transcriptional activity was positively correlated with the ratio of H3K4me3/H3K4me2: genes with predominantly H3K4me3 were actively transcribed, whereas genes with predominantly H3K4me2 were transcribed at moderate levels. More protein-coding genes contained all three modifications, and more transposons contained DNA methylation in shoots than cultured cells. Differential epigenetic modifications correlated to tissue-specific expression between shoots and cultured cells. Collectively, this study provides insights into the rice epigenomes and their effect on gene expression and plant development.
Published: 2008
Full Text: View/download PDF

4. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

Author: Mark Gerstein, Ugrappa Nagalakshmi, Jiang Du, Joel Rozowsky, Deyou Zheng, Sherman M. Weissman, Alexander E. Urban, Olof Emanuelsson, Viktor Stolc, Michael Snyder, and Zheng Lian
Subjects: Genetics, Transcription, Genetic, Genome, Human, Chromosomes, Human, Pair 22, Gene Expression Profiling, Quantitative Trait Loci, Chromosome Mapping, Locus (genetics), Replicate, Computational biology, Gene Annotation, Biology, ENCODE, Genome, Cell Line, Gene expression profiling, Methods, Humans, Human genome, DNA microarray, Genetics (clinical), Oligonucleotide Array Sequence Analysis
Abstract: Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated with each tiling experiment (e.g., experimental protocols and genomic tiling density). Here, we assess the role of these parameters as they are manifest in different tiling-array platforms used for transcription mapping. First, we analyze how a number of published tiling-array experiments agree with established gene annotation on human chromosome 22. We observe that the transcription detected from high-density arrays correlates substantially better with annotation than that from other array types. Next, we analyze the transcription-mapping performance of the two main high-density oligonucleotide array platforms in the ENCODE regions of the human genome. We hybridize identical biological samples and develop several ways of scoring the arrays and segmenting the genome into transcribed and nontranscribed regions, with the aim of making the platforms most comparable to each other. Finally, we develop a platform comparison approach based on agreement with known annotation. Overall, we find that the performance improves with more data points per locus, coupled with statistical scoring approaches that properly take advantage of this, where this larger number of data points arises from higher genomic tiling density and the use of replicate arrays and mismatches. While we do find significant differences in the performance of the two high-density platforms, we also find that they complement each other to some extent. Finally, our experiments reveal a significant amount of novel transcription outside of known genes, and an appreciable sample of this was validated by independent experiments.
Published: 2006
Full Text: View/download PDF

5. Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway

Author: Manoj P. Samanta, Waraporn Tongprasit, Viktor Stolc, Chen-Shan Chin, and Himanshu Sethi
Subjects: Genetics, RNA, Untranslated, Saccharomyces cerevisiae Proteins, Multidisciplinary, Tiling array, Base Sequence, RNase P, Genes, Fungal, Molecular Sequence Data, Saccharomyces cerevisiae, Gene Expression, RNA, Fungal, Biological Sciences, Biology, biology.organism_classification, Genome, Intergenic region, Endoribonucleases, Coding region, RNA, Antisense, RNA Processing, Post-Transcriptional, DNA, Fungal, Gene, Ribonucleoprotein
Abstract: Noncoding RNAs (ncRNAs) perform essential cellular tasks and play key regulatory roles in all organisms. Although several new ncRNAs in yeast were recently discovered by individual studies, to our knowledge no comprehensive empirical search has been conducted. We demonstrate a powerful and versatile method for global identification of previously undescribed ncRNAs by modulating an essential RNA processing pathway through the depletion of a key ribonucleoprotein enzyme component, and monitoring differential transcriptional activities with genome tiling arrays during the time course of the ribonucleoprotein depletion. The entire Saccharomyces cerevisiae genome was scanned during cell growth decay regulated by promoter-mediated depletion of Rpp1 , an essential and functionally conserved protein component of the RNase P enzyme. In addition to most verified genes and ncRNAs, expression was detected in 98 antisense and intergenic regions, 74 that were further confirmed to contain previously undescribed RNAs. A class of ncRNAs, located antisense to coding regions of verified protein-coding genes, is discussed in this article. One member, HRA1 , is likely involved in 18S rRNA maturation.
Published: 2006
Full Text: View/download PDF

6. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

Author: Clark J. Nelson, John L. Markley, Sebastian Y. Bednarek, David M. Rancour, Himanshu Sethi, Michael R. Sussman, George N. Phillips, Adrian D. Hegeman, Manoj P. Samanta, Craig S. Newman, Waraporn Tongprasit, David C. Nelson, Viktor Stolc, Russell L. Wrobel, Brian G. Fox, Eldon L. Ulrich, Qin Zhao, and Shoudan Liang
Subjects: Proteomics, Optics and Photonics, Spectrometry, Mass, Electrospray Ionization, DNA, Complementary, DNA, Plant, Transcription, Genetic, Arabidopsis, Computational biology, Biology, Photography, RNA, Antisense, RNA, Messenger, Small nucleolar RNA, Gene, Chromatography, High Pressure Liquid, Oligonucleotide Array Sequence Analysis, Genetics, Multidisciplinary, Tiling array, Base Sequence, Arabidopsis Proteins, Reverse Transcriptase Polymerase Chain Reaction, Oligonucleotide, Gene Expression Profiling, Intron, RNA, Exons, Biological Sciences, Introns, RNA, Plant, Transfer RNA, Genome, Plant, Small nuclear RNA
Abstract: Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of the plant Arabidopsis thaliana . RNA expression was determined for the complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated Arabidopsis cell culture line. Transcripts were detected from at least 60% of the nearly 26,330 annotated genes, which included 151 predicted genes that were not identified previously by a similar genome-wide hybridization study on four different cell lines. In comparison with previously published results with 25-mer tiling arrays produced by chromium masking-based photolithography technique, 36-mer oligonucleotide probes were found to be more useful in identifying intron–exon boundaries. Using two-dimensional HPLC tandem mass spectrometry, a small-scale proteomic analysis was performed with the same cells. A large amount of strongly hybridizing RNA was found in regions “antisense” to known genes. Similarity of antisense activities between the 25-mer and 36-mer data sets suggests that it is a reproducible and inherent property of the experiments. Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage.
Published: 2005
Full Text: View/download PDF

7. The ENCODE (ENCyclopedia Of DNA Elements) Project

Author: Jonathan H. Dennis, Michael Brudno, Anindya Dutta, Richard M. Myers, Ian Dunham, Eduardo Eyras, S. S. Marticke, Alexandre Reymond, Anason S. Halees, Greg Schuler, M. G. Rosenfeld, Mikhail Nefedov, Robert E. Kingston, Elizabeth Anton, Tyra G. Wolfsberg, Alice C. Young, Kris A. Wetterstrand, C. K. Glass, Nancy F. Hansen, Gayle K. Clelland, Diane I. Schroeder, Jean L. Chang, H. Shin, Zhou Zhu, Nigel P. Carter, William Stafford Noble, Jenny McDowell, Ugrappa Nagalakshmi, Heike Fiegler, Philipp Kapranov, Peggy J. Farnham, Joanna C. Fowler, S. C. Harvey, Michael O. Dorschner, D. R. Inman, George V. Popescu, Jan-Jaap Wesselink, P. Groth, Baoli Zhu, H. Hirsch, James C. Wallace, Elise A. Feingold, S. Jin, Gabriel Robins, Thomas R. Gingeras, F. Denoeud, W. Tongprasit, Robert Castelo, Ross C. Hardison, John A. Stamatoyannopoulos, Joel Rozowsky, Eric A. Stone, Zheng Lian, J. E. Norton, Y. S. Kwon, Viktor Stolc, Michael C. Pirrung, Min-Feng Yu, A. Yang, W. J. Kent, Peter J. Sabo, Stephen Hartman, Stylianos E. Antonarakis, Tae Hoon Kim, H. Kim, Baishali Maskeri, Thomas Royce, R. Luna, Sherman M. Weissman, Tim Hubbard, Oliver M. Dovey, Ewan Birney, Kate R. Rosenbloom, Robert M. Andrews, Damian Keefe, Arend Sidow, D. Zhou, Jane Grimwood, Ulas Karaoz, Zhiping Weng, H. Burden, Michael C. Zody, Hiram Clawson, Gerry Bouffard, S. van Calcar, Mark Dickson, Kevin Struhl, Ingeborg Holt, Emmanouil T. Dermitzakis, T. J. Vasicek, Peter J. Good, Charles R. Cantor, Hari Tammana, Josée Dostie, Prachi Shah, Elliott H. Margulies, Peter D. Ellis, Mark S. Guyer, Christopher M. Taylor, Patrick A. Navas, Dione Kampa, Colin N. Dewey, Lior Pachter, Christof Koch, George Asimenos, James R R Whittle, Gregory E. Crawford, Jane B. Lian, Pamela J. Thomas, Kazutoyo Osoegawa, Webb Miller, Chunxu Qu, Nele Gheldof, Keith D. James, Sandeep Patel, Todd Richmond, Jacquelyn R. Idol, Michael A. Singer, Tomoko M. Tabuchi, Adam Siepel, Yutao Fu, David Vetrie, Long H. Nguyen, Michael Snyder, William H. Majoros, Michael R. Brent, Nathan D. Trinklein, Leah O. Barrera, Mark Gerstein, Srinka Ghosh, Sara J. Hartman, Jade P. Vinson, C. L. Middle, Sambath Chung, George Stamatoyannopoulos, Y. Nakayama, George M. Church, Job Dekker, Olof Emanuelsson, Julien Lagarde, Roderic Guigó, Marco A. Marra, Jeremy Schmutz, Daryl J. Thomas, Yong Yu, M. R. McCormick, Xiang-Dong Fu, Richard Humbert, Jennifer L. Ashurst, Alexander E. Urban, Sarah Wilcox, Ghia Euskirchen, Michael Kamal, Cordelia Langford, Jacquie Schein, Gregory M. Cooper, Paul Bertone, Eric S. Lander, C. Ding, Antonio Piccolboni, Steven L. Salzberg, Rhonda Harrison, Matthew J. Oberley, E. A. Sekinger, Mihaela Pertea, Bing Ren, H. K. Kim, Roland Green, Shelley Force Aldred, Laura Elnitski, Michael Hawrylycz, Andrew J. Mungall, Kerstin Lindblad-Toh, David B. Jaffe, Andreas D. Baxevanis, L. Liefer, Michele Clamp, David Haussler, Jill Cheng, John L. Rinn, S. Kamholz, Vicki L. Wraight, H. Sethi, Francis S. Collins, Steven J.M. Jones, Serafim Batzoglou, P. J. De Jong, Matthew E. Portnoy, Stefan Bekiranov, M. McArthur, Shu-Jin Luo, Eric D. Green, Robert W. Blakesley, Tarjei S. Mikkelsen, Z. Ye, Pawandeep Dhami, and Neerja Karnani
Subjects: Pilot phase, Pilot Projects, Computational biology, Regulatory Sequences, Nucleic Acid, Biology, ENCODE, Access to Information, Evolution, Molecular, Annotation, chemistry.chemical_compound, Animals, Humans, International HapMap Project, Conserved Sequence, Publishing, Genetics, Internet, Multidisciplinary, Genome, Human, Information Dissemination, GENCODE, Computational Biology, Proteins, Genomics, Sequence Analysis, DNA, United States, National Institutes of Health (U.S.), chemistry, Encyclopedia, Human genome, Databases, Nucleic Acid, DNA
Abstract: The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (∼1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.
Published: 2004
Full Text: View/download PDF

8. Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains

Author: Olufisayo Jejelowo, Robert G. Eason, Zelek S. Herman, Ronald W. Davis, Nader Pourmand, Waraporn Tongprasit, Kevin Anthony, and Viktor Stolc
Subjects: Genetics, Mutation, Multidisciplinary, biology, Oligonucleotide, Genes, Fungal, Saccharomyces cerevisiae, Nucleic Acid Hybridization, Biological Sciences, biology.organism_classification, medicine.disease_cause, Polymerase Chain Reaction, Yeast, law.invention, Nucleic acid thermodynamics, law, medicine, Pyrosequencing, DNA, Fungal, Gene, Gene Deletion, Polymerase chain reaction, DNA Primers
Abstract: Incorporation of strain-specific synthetic DNA tags into yeast Saccharomyces cerevisiae gene-deletion strains has enabled identification of gene functions by massively parallel growth rate analysis. However, it is important to confirm the sequences of these tags, because mutations introduced during construction could lead to significant errors in hybridization performance. To validate this experimental system, we sequenced 11,812 synthetic 20-mer molecular bar codes and adjacent sequences (>1.8 megabases synthetic DNA) by pyrosequencing and Sanger methods. At least 31% of the genome-integrated 20-mer tags contain differences from those originally synthesized. However, these mutations result in anomalous hybridization in only a small subset of strains, and the sequence information enables redesign of hybridization probes for arrays. The robust performance of the yeast gene-deletion dual oligonucleotide bar-code design in array hybridization validates the use of molecular bar codes in living cells for tracking their growth phenotype.
Published: 2004
Full Text: View/download PDF

9. Rpp2, an essential protein subunit of nuclear RNase P, is required for processing of precursor tRNAs and 35S precursor rRNA in Saccharomyces cerevisiae

Author: Sidney Altman, Viktor Stolc, and Alexander Katz
Subjects: Mitochondrial RNA processing, Multidisciplinary, Nuclear RNase P, RNase P, Protein subunit, Genes, Fungal, Molecular Sequence Data, RNA, Fungal, Saccharomyces cerevisiae, Biological Sciences, Biology, Ribosomal RNA, Molecular biology, RNase PH, Ribonuclease P, RNase MRP, RNA, Transfer, Biochemistry, Endoribonucleases, Transfer RNA, RNA Precursors, Humans, RNA, Catalytic, Sequence Deletion
Abstract: RPP2 , an essential gene that encodes a 15.8-kDa protein subunit of nuclear RNase P, has been identified in the genome of Saccharomyces cerevisiae . Rpp2 was detected by sequence similarity with a human protein, Rpp20, which copurifies with human RNase P. Epitope-tagged Rpp2 can be found in association with both RNase P and RNase mitochondrial RNA processing in immunoprecipitates from crude extracts of cells. Depletion of Rpp2 protein in vivo causes accumulation of precursor tRNAs with unprocessed introns and 5′ and 3′ termini, and leads to defects in the processing of the 35S precursor rRNA. Rpp2-depleted cells are defective in processing of the 5.8S rRNA. Rpp2 immunoprecipitates cleave both yeast precursor tRNAs and precursor rRNAs accurately at the expected sites and contain the Rpp1 protein orthologue of the human scleroderma autoimmune antigen, Rpp30. These results demonstrate that Rpp2 is a protein subunit of nuclear RNase P that is functionally conserved in eukaryotes from yeast to humans.
Published: 1998
Full Text: View/download PDF

10. Rpp1, an essential protein subunit of nuclear RNase P required for processing of precursor tRNA and 35S precursor rRNA inSaccharomyces cerevisiae

Author: Viktor Stolc and Sidney Altman
Subjects: Saccharomyces cerevisiae Proteins, Macromolecular Substances, RNase P, Genes, Fungal, Molecular Sequence Data, Endoribonuclease, Saccharomyces cerevisiae, Biology, Autoantigens, RNase PH, Ribonuclease P, RNA, Transfer, Endoribonucleases, RNA Precursors, Genetics, Humans, RNA, Catalytic, Amino Acid Sequence, Cloning, Molecular, RRNA processing, Base Sequence, Sequence Homology, Amino Acid, Nuclear RNase P, RNA, RNA, Fungal, Molecular biology, RNase MRP, RNA, Ribosomal, Transfer RNA, Sequence Alignment, Research Paper, Developmental Biology
Abstract: The gene for an essential protein subunit of nuclear RNase P fromSaccharomyces cerevisiae has been cloned. The gene for this protein, RPP1, was identified by virtue of its homology with a human scleroderma autoimmune antigen, Rpp30, which copurifies with human RNase P. Epitope-tagged Rpp1 can be found in association with both RNase P RNA and a related endoribonuclease, RNase MRP RNA, in immunoprecipitates from crude extracts of cells. Depletion of Rpp1 in vivo leads to the accumulation of precursor tRNAs with unprocessed 5′ and 3′ termini and reveals rRNA processing defects that have not been described previously for proteins associated with RNase P or RNase MRP. Immunoprecipitated complexes cleave both yeast precursor tRNAs and precursor rRNAs.
Published: 1997
Full Text: View/download PDF

11. Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis

Author: Viktor Stolc, Xing Wang Deng, Mikiko Kojima, Mikhail Kovtun, Hitoshi Sakakibara, Hongchang Cui, and Yueling Hao
Subjects: Chromatin Immunoprecipitation, Cytokinins, Physiology, Green Fluorescent Proteins, Arabidopsis, Plant Science, Phloem, chemistry.chemical_compound, Gene Expression Regulation, Plant, Genetics, Cluster Analysis, Homeostasis, cardiovascular diseases, Lateral root formation, Transcription factor, Body Patterning, Oligonucleotide Array Sequence Analysis, Regulation of gene expression, Microscopy, Confocal, biology, Arabidopsis Proteins, fungi, Development and Hormone Action, food and beverages, Meristem, biology.organism_classification, Molecular biology, Cell biology, Pericycle, Phenotype, chemistry, Stele, Cytokinin, Mutation, cardiovascular system, Plant Vascular Bundle, Genome, Plant, circulatory and respiratory physiology, Transcription Factors
Abstract: SHORT-ROOT (SHR) is a key regulator of root growth and development in Arabidopsis (Arabidopsis thaliana). Made in the stele, the SHR protein moves into an adjacent cell layer, where it specifies endodermal cell fate; it is also essential for apical meristem maintenance, ground tissue patterning, vascular differentiation, and lateral root formation. Much has been learned about the mechanism by which SHR controls radial patterning, but how it regulates other aspects of root morphogenesis is still unclear. To dissect the SHR developmental pathway, we have determined the genome-wide locations of SHR direct targets using a chromatin immunoprecipitation followed by microarray analysis method. K-means clustering analysis not only identified additional quiescent center-specific SHR targets but also revealed a direct role for SHR in gene regulation in the pericycle and xylem. Using cell type-specific markers, we showed that in shr, the phloem and the phloem-associated pericycle expanded, whereas the xylem and xylem-associated pericycle diminished. Interestingly, we found that cytokinin level was elevated in shr and that exogenous cytokinin conferred a shr-like vascular patterning phenotype in wild-type root. By chromatin immunoprecipitation-polymerase chain reaction and reverse transcription-polymerase chain reaction assays, we showed that SHR regulates cytokinin homeostasis by directly controlling the transcription of cytokinin oxidase 3, a cytokinin catabolism enzyme preferentially expressed in the stele. Finally, overexpression of a cytokinin oxidase in shr alleviated its vascular patterning defect. On the basis of these results, we suggest that one mechanism by which SHR controls vascular patterning is the regulation of cytokinin homeostasis.
Published: 2011

12. Polymorphism of Cyclic 3´,5´-Adenosine Monophosphate Stimulation in Rat Erythrocytes

Author: Viktor Stolc
Subjects: Male, Adenosine monophosphate, medicine.medical_specialty, Erythrocytes, Stimulation, Biology, chemistry.chemical_compound, Species Specificity, 1-Methyl-3-isobutylxanthine, Rats, Inbred BN, Internal medicine, Cyclic AMP, medicine, Animals, Polymorphism, Genetic, Isoproterenol, Rats, Inbred Strains, Hematology, General Medicine, Propranolol, Rats, Rats, Inbred ACI, Red blood cell, medicine.anatomical_structure, Endocrinology, chemistry, Rats, Inbred Lew, Female, Adenylyl Cyclases
Abstract: Significant differences were found in the cyclic 3',5'-adenosine monophosphate (cAMP) levels in (-)-isoproterenol-stimulated rat erythrocytes. The BN strain had the highest level (13.1 +/- 1.29 pmol cAMP/10 mg Hb) and the LEW strain had the lowest cAMP level (3.29 +/- 1.76 pmol cAMP/10 mg Hb) in the erythrocytes. The high levels were inherited in three intercrosses in a dominant fashion. The results of the backcross breeding suggested diallelic inheritance. However, the polygenic effect was not ruled out.
Published: 1991
Full Text: View/download PDF

13. LINKAGE OF NEUTROPHIL RESPONSE TO A MUTAGEN GENE (Nrm-1) TO THE AGOUTI LOCUS IN THE RAT

Author: Viktor Stolc
Subjects: Male, Genetic Linkage, Neutrophils, Offspring, Neutrophile, Immunology, Locus (genetics), Immunogenetics, Biology, Leukocyte Count, Species Specificity, Gene mapping, hemic and lymphatic diseases, Genetics, Animals, Allele, Gene, Alleles, Crosses, Genetic, Methylnitrosourea, Phenotype, Molecular biology, Rats, Genes, Female, Mutagens
Abstract: SUMMARY The ACI or BDIV rats responded with decreased or increased neutrophil levels in blood after the N-methyl-N-nitrosourea (MNU) administration. The F1 hybrids had decreased neutrophil counts, and the BDIV × (BDIV × AC1)Fl backcross offspring showed two phenotypes. The sex of the rats and the neutrophil response to MNU assorted independently. The results indicated that the neutrophil response to MNU was regulated by autosomal gene Nrm-1 with two alleles. The Nrm-Id regulates the decrease and the Nrm-1i regulates the increase of neutrophils in blood after the MNU administration. The results were confirmed by the SKUMIX computer program. We found that the Nrm-1 gene was linked to the agouti locus (chi-square = 10–3, P < 0.001). The map distance between two genes was 33 ± 5 cM. The Nrm-1 gene thus resides on the linkage group IV of the rat.
Published: 1990
Full Text: View/download PDF

14. Analysis of oligo hybridization properties by high-resolution tiling microarrays in rice

Author: Xiangfeng Wang, Jun Wang, Waraporn Tongprasit, Viktor Stolc, Lei Li, Xing Wang Deng, Chen Chen, and Songgang Li
Subjects: In situ, Genetics, Oligonucleotide, Microarray analysis techniques, Complementary DNA, Computational biology, DNA microarray, Oligonucleotide synthesis, Biology, DNA sequencing, GC-content
Abstract: Rice genome sequencing and computational annotation provide a static map for understanding this model of Gramineae species. With the development of in situ oligonucleotide synthesis technology, tiling-path microarrays have become a dynamic and efficient way for monitoring large-scale transcriptional activities and detecting novel transcribed elements missed by software. Unlike conventional cDNA or oligonucleotide arrays, tiling-path platforms employ the full extent of oligos covering given genomic regions, and thus offer excellent experimental conditions in which to assay the properties of oligos in terms of their specificity and efficiency of hybridization to their corresponding targets. Here, we report a tiling-path microarray analysis of a 1-Mb region (10 to 11 Mb) in japonica rice chromosome 10, which was tiled by a 36-mer oligo set at a resolution of 5 bp. Our analysis focused on three major factors of oligo hybridization properties, including GC content, melting temperature (Tm), and the repetitiveness of oligo sequences.
Published: 2007
Full Text: View/download PDF

15. Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

Author: Zhengdong D. Zhang, Michael Snyder, Wah Heng Lee, Sherman M. Weissman, Chia-Lin Wei, Olof Emanuelsson, Joel Rozowsky, Ghia Euskirchen, Stephen Hartman, Yijun Ruan, Viktor Stolc, and Mark Gerstein
Subjects: Chromatin Immunoprecipitation, Computational biology, Biology, ENCODE, DNA sequencing, chemistry.chemical_compound, DNA Microarray Analysis, Genetics, Hardware_INTEGRATEDCIRCUITS, Methods, Animals, Humans, Genetics (clinical), Oligonucleotide Array Sequence Analysis, Tiling array, Hardware_MEMORYSTRUCTURES, Binding Sites, Oligonucleotide, Genome, Human, Sequence Analysis, DNA, Microfluidic Analytical Techniques, STAT1 Transcription Factor, chemistry, Human genome, Chromatin immunoprecipitation, DNA, HeLa Cells
Abstract: Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%–86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies.
Published: 2007

16. Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development

Author: Xing Wang Deng, Jungeun Lee, Pablo Figueroa, Hongyu Zhao, Kun He, Waraporn Tongprasit, Ilha Lee, Viktor Stolc, Horim Lee, and Ying Gao
Subjects: Chromatin Immunoprecipitation, Light, Arabidopsis, Plant Science, Biology, Genes, Plant, Epitopes, Gene Expression Regulation, Plant, Binding site, Photosynthesis, Promoter Regions, Genetic, Gene, Transcription factor, Research Articles, Genetics, Binding Sites, Arabidopsis Proteins, Gene Expression Profiling, Nuclear Proteins, Promoter, Cell Biology, Plants, Genetically Modified, Circadian Rhythm, DNA binding site, Gene expression profiling, Basic-Leucine Zipper Transcription Factors, Organ Specificity, Transcription Factor Gene, Chromatin immunoprecipitation, Acyltransferases, Genome, Plant, Protein Binding
Abstract: The transcription factor LONG HYPOCOTYL5 (HY5) acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here, we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using a high-density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis thaliana genome, we mapped genome-wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed >3000 chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light-responsive genes and transcription factor genes. Our data thus support a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis.
Published: 2007

17. Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays

Author: David C. Nelson, Michael R. Sussman, Matthew J. Rodesch, Manoj P. Samanta, Viktor Stolc, and Dana J. Wohlbach
Subjects: Transcription, Genetic, Microarrays, Biophysics, Expression, Biology, Biochemistry, Genome, Chips, chemistry.chemical_compound, Structural Biology, Genetics, Molecular Biology, Gene, Oligonucleotide Array Sequence Analysis, Artifact (error), Tiling array, Base Sequence, Nucleotides, DNA, Cell Biology, Genes, chemistry, RNA, DNA microarray, Primer (molecular biology), Sequence motif, Artifacts
Abstract: This study identified the widely used T7 in vitro transcription system as a major source of artifact in the tiling array data from nine eukaryotic genomes. The most affected probes contained a sequence motif complementary to the +1 to +9 initial transcribed sequence (ITS) of the T7-(dT)24 primer. The abundance of 5′ ITS cRNA fragments produced during target preparation was sufficient to drive undesirable hybridization. A new T7-(dT)24 primer with a modified ITS was designed that shifts the artifactual motifs as predicted and reduces the effect of the artifact. A computational algorithm was generated to filter out the likely artifactual probes from existing whole-genome tiling array data and improve probe selection. Further studies of Arabidopsis thaliana were conducted using both T7-(dT)24 primers. While the artifact affected transcript discovery with tiling arrays, it showed only a minor impact on measurements of gene expression using commercially available ‘gene-only’ expression arrays.
Published: 2007

18. A core transcriptional network for early mesoderm development in Drosophila melanogaster

Author: Waraporn Tongprasit, Marc Brehme, Viktor Stolc, Charles Girardot, Thomas Sandmann, and Eileen E. M. Furlong
Subjects: Mef2, Mesoderm, Chromatin Immunoprecipitation, animal structures, Embryonic Development, Genetics, medicine, Animals, Drosophila Proteins, Gene Regulatory Networks, Gene, Transcription factor, biology, Microarray analysis techniques, Twist-Related Protein 1, Gene Expression Regulation, Developmental, ChIP-on-chip, biology.organism_classification, Cell biology, medicine.anatomical_structure, Drosophila melanogaster, Enhancer Elements, Genetic, embryonic structures, Chromatin immunoprecipitation, Developmental Biology, Research Paper
Abstract: Embryogenesis is controlled by large gene-regulatory networks, which generate spatially and temporally refined patterns of gene expression. Here, we report the characteristics of the regulatory network orchestrating early mesodermal development in the fruitfly Drosophila, where the transcription factor Twist is both necessary and sufficient to drive development. Through the integration of chromatin immunoprecipitation followed by microarray analysis (ChIP-on-chip) experiments during discrete time periods with computational approaches, we identified >2000 Twist-bound cis-regulatory modules (CRMs) and almost 500 direct target genes. Unexpectedly, Twist regulates an almost complete cassette of genes required for cell proliferation in addition to genes essential for morophogenesis and cell migration. Twist targets almost 25% of all annotated Drosophila transcription factors, which may represent the entire set of regulators necessary for the early development of this system. By combining in vivo binding data from Twist, Mef2, Tinman, and Dorsal we have constructed an initial transcriptional network of early mesoderm development. The network topology reveals extensive combinatorial binding, feed-forward regulation, and complex logical outputs as prevalent features. In addition to binary activation and repression, we suggest that Twist binds to almost all mesodermal CRMs to provide the competence to integrate inputs from more specialized transcription factors.
Published: 2007

19. Global identification and characterization of transcriptionally active regions in the rice genome

Author: Runsheng Chen, Lei Li, Wei Deng, Jan O. Korbel, Xuewei Chen, Xiangfeng Wang, Hang He, Rajkumar Sasidharan, Mark Gerstein, Waraporn Tongprasit, Viktor Stolc, Pamela C. Ronald, and Xing Wang Deng
Subjects: Transcriptional Activation, 0106 biological sciences, DNA, Complementary, DNA, Plant, Transcription, Genetic, lcsh:Medicine, Biology, Genes, Plant, 01 natural sciences, Genome, Genetics and Genomics/Plant Genetics and Gene Expression, DNA, Antisense, Conserved sequence, Transcriptome, 03 medical and health sciences, Genetics and Genomics/Genomics, lcsh:Science, Gene, Conserved Sequence, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Tiling array, Oryza sativa, Genetics and Genomics/Functional Genomics, Gene Expression Profiling, lcsh:R, Life Sciences, food and beverages, Genetics and Genomics, Genetics and Genomics/Gene Expression, Oryza, Exons, Genome project, Genetics and Genomics/Bioinformatics, Gene expression profiling, RNA, Plant, Nucleic Acid Conformation, Genetics and Genomics/Gene Discovery, lcsh:Q, Genome, Plant, Research Article, 010606 plant biology & botany
Abstract: Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.
Published: 2007

20. The Transcriptome of the Sea Urchin Embryo

Author: R. Andrew Cameron, Eric H. Davidson, Manoj P. Samanta, Waraporn Tongprasit, Viktor Stolc, Sorin Istrail, and Qiang Tu
Subjects: Embryo, Nonmammalian, RNA, Untranslated, Transcription, Genetic, ved/biology.organism_classification_rank.species, Embryonic Development, Molecular Probe Techniques, Biology, Genome, Transcriptome, Intergenic region, Animals, RNA, Messenger, Model organism, Strongylocentrotus purpuratus, Gene, Oligonucleotide Array Sequence Analysis, Genetics, Multidisciplinary, Tiling array, ved/biology, Gene Expression Profiling, Intracellular Signaling Peptides and Proteins, Computational Biology, Gene Expression Regulation, Developmental, Nucleic Acid Hybridization, Gastrula, Genome project, Blastula, biology.organism_classification, embryonic structures, Signal Transduction, Transcription Factors
Abstract: The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.
Published: 2006

21. The Genome of the Sea Urchin Strongylocentrotus purpuratus

Author: Amro Hamdoun, Virginia Brockton, Huyen Dinh, Qiang Tu, Richard O. Hynes, Maria Ina Arnone, Wratko Hlavina, L. Courtney Smith, Mariano A. Loza, David R. Burgess, Matthew P. Hoffman, Florian Raible, Qiu Autumn Yuan, Geoffrey Okwuonu, Mark Y. Tong, Jennifer Hume, Donna Maglott, Manisha Goel, Olivier Fedrigo, Manuel L. Gonzalez-Garay, Celina E. Juliano, Judith Hernandez, Gary M. Wessel, William F. Marzluff, Audrey J. Majeske, Christian Gache, Louise Duloquin, Xingzhi Song, François Lapraz, Fowler J, Alexandre Souvorov, Jared V. Goldstone, Georgia Panopoulou, Sandra Hines, Kyle M. Judkins, Clay Davis, Christine G. Elsik, Paul Kitts, Mariano Loza-Coll, Greg Wray, Taku Hibino, Eric Röttinger, Allison M. Churcher, Annamaria Locascio, Arcady Mushegian, Masashi Kinukawa, Anna Reade, Katherine M. Buckley, I. R. Gibbons, Bert Gold, Aleksandar Milosavljevic, David Epel, Victor D. Vacquier, Ling Ling Pu, Vincenzo Cavalieri, Erin L. Allgood, Lan Zhang, Lynne V. Nazareth, Constantin N. Flytzanis, Ian Bosdet, Yi-Hsien Su, Zeev Pancer, Matthew L. Rowe, Robert C. Angerer, David R. McClay, William H. Klein, Rachel F. Gray, Julian L. Wong, Shunsuke Yaguchi, Robert Bellé, Aaron J. Mackey, Herath Jayantha Gunaratne, Karl Frederik Bergeron, Bruce P. Brandhorst, Greg Murray, Avis H. Cohen, Stephanie Bell, Kristin Tessmar-Raible, Ian K. Townley, Bertrand Cosson, Thomas D. Glenn, Jongmin Nam, Cynthia A. Bradham, Michael Dean, Joseph Chacko, Anthony J. Robertson, Margherita Branno, Valeria Matranga, K. James Durbin, Esther Miranda, Lili Chen, Eran Elhaik, Robert D. Burke, Rita A. Wright, Paola Oliveri, Sandra L. Lee, Gary W. Moy, Alexander E Primus, Shawn S. McCafferty, Cristina Calestani, David A. Garfield, Erica Sodergren, Karen Wilson, Joel Smith, Marco A. Marra, Cynthia Messier, Julia Morales, Kim D. Pruitt, Rachel Thorn, Rachel Gill, John S. Taylor, Mark E. Hahn, Victor Sapojnikov, Meredith Howard-Ashby, Lynne M. Angerer, Maurice R. Elphick, Kathy R. Foltz, Anne Marie Genevière, Justin T. Reese, Blanca E. Galindo, Kim C. Worley, Andrew Leone, Glen Humphrey, Kevin Berney, Olga Ermolaeva, George Miner, David P. Terwilliger, Elly Suk Hen Chow, Lora Lewis, Dan Graur, C. Titus Brown, Gerard Manning, Kevin J. Peterson, Angela Jolivet, Michele K. Anderson, Francesca Rizzo, Ekaterina Voronina, Thierry Lepage, Giorgio Matassi, Antonio Fernandez-Guerra, Mamoru Nomura, Charles A. Whittaker, James R.R. Whittle, James A. Coffman, George M. Weinstock, Mohammed M. Idris, Ashlan M. Musante, Sebastian D. Fugmann, Katherine D. Walton, Sorin Istrail, Shu-Yu Wu, Cerrissa Hamilton, Jonah Cool, Jacqueline E. Schein, Stacey M. Curry, Athula Wikramanayke, Seth Carbonneau, Blair J. Rossetti, Christopher E. Killian, Melissa J. Landrum, Amanda P. Rawson, Jenifer C. Croce, Ryan C. Range, Rahul Satija, John J. Stegeman, Yufeng Shen, Cavit Agca, Terry Gaasterland, Rocky Cheung, Takae Kiyama, Nikki Adams, Jonathan P. Rast, Robert Piotr Olinski, Andrew Cree, Mark Scally, Shuguang Liang, David A. Parker, Rebecca Thomason, Gretchen E. Hofmann, Michelle M. Roux, Ronghui Xu, Robert A. Obar, Enrique Arboleda, Odile Mulner-Lorillon, Shannon Dugan-Rocha, David J. Bottjer, Gabriele Amore, Manoj P. Samanta, Waraporn Tongprasit, Véronique Duboc, La Ronda Jackson, Fred H. Wilt, Viktor Stolc, Anna T. Neill, Michael Raisch, Pei Yun Lee, Jia L. Song, Margaret Morgan, Brian T. Livingston, Sofia Hussain, Zheng Wei, Bryan J. Cole, Tonya F. Severson, Victor V. Solovyev, Finn Hallböök, Donna M. Muzny, Christine A. Byrum, Albert J. Poustka, Xiuqian Mu, Andrew R. Jackson, Shin Heesun, Euan R. Brown, Nansheng Chen, Patrick Cormier, Ralph Haygood, Pedro Martinez, R. Andrew Cameron, D. Wang, Wendy S. Beane, Eric H. Davidson, Christie Kovar, Hemant Kelkar, Charles A. Ettensohn, Sham V. Nair, Robert L. Morris, Stefan C. Materna, Michael C. Thorndyke, Richard A. Gibbs, Dan O Mellott, Department of Physiology and Biophysics, Stony Brook University [The State University of New York] ( SBU ), Astronomy Unit ( AU ), Queen Mary University of London ( QMUL ), Urban and Industrial Air Quality Group, CSIRO Energy Technology, Commonwealth Scientific and Industrial Research Organisation Energy Technology ( CSIRO Energy Technology ), Commonwealth Scientific and Industrial Research Organisation, Center for Polymer Studies ( CPS ), Boston University [Boston] ( BU ), Physics Department [Boston] ( BU-Physics ), Max Planck Institute for Psycholinguistics, Max-Planck-Institut, Department of Biology [Norton], Wheaton College [Norton], Mathematical Institute [Oxford] ( MI ), University of Oxford [Oxford], Centre for the Analysis of Time Series ( CATS ), London School of Economics and Political Science ( LSE ), Thomas Jefferson National Accelerator Facility ( Jefferson Lab ), Thomas Jefferson National Accelerator Facility, Laboratoire d'Energétique et de Mécanique Théorique Appliquée ( LEMTA ), Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Evolution, Génomes et Spéciation ( LEGS ), Centre National de la Recherche Scientifique ( CNRS ), Department of Geology, University of Illinois at Urbana-Champaign [Urbana], Department of Electrical and Computer Engineering [Portland] ( ECE ), Portland State University [Portland] ( PSU ), Saint-Gobain Crystals [USA], SAINT-GOBAIN, Institute for Animal Health ( IAH ), Biotechnology and Biological Sciences Research Council, Center for Agricultural Resources Research, Chinese Academy of Sciences [Changchun Branch] ( CAS ), Ipsen Inc. [Milford] ( Ipsen ), IPSEN, Department of Physics [Berkeley], University of California [Berkeley], Institute for Climate and Atmospheric Science [Leeds] ( ICAS ), University of Leeds, Chung-Ang University ( CAU ), Chung-Ang University [Seoul], Antarctic Climate and Ecosystems Cooperative Research Center ( ACE-CRC ), Institute of Aerodynamics and Fluid Mechanics ( AER ), Technische Universität München [München] ( TUM ), Mer et santé ( MS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Imperial College London, Radio and Atmospheric Sciences Division, National Physical Laboratory [Teddington] ( NPL ), International Research Institute for Climate and Society ( IRI ), Earth Institute at Columbia University, Columbia University [New York]-Columbia University [New York], Soils Group, The Macaulay Institute, Department of Haematology, University of Cambridge [UK] ( CAM ), School of Biology and Biochemistry, Queen's University, Leslie Hill Institute for Plant Conservation ( PCU ), University of Cape Town, Institute for Microelectronics and Microsystems/ Istituto per la Microelettronica e Microsistemi ( IMM ), Consiglio Nazionale delle Ricerche ( CNR ), Laboratoire d'acoustique de l'université du Mans ( LAUM ), Le Mans Université ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Interactive Systems Labs ( ISL ), Carnegie Mellon University [Pittsburgh] ( CMU ), Dalian Institute of Chemical Physics ( DICP ), Architectures, Languages and Compilers to Harness the End of Moore Years ( ALCHEMY ), Laboratoire de Recherche en Informatique ( LRI ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique ( Inria ), Clean Air Task Force ( CATF ), Clean Air Task Force, Space Physics Laboratory, Indian Space Research Organisation ( ISRO ), Centre d'études et de recherches appliquées à la gestion ( CERAG ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Microbiology and Immunology, College of Medicine and Health Sciences-Sultan Qaboos University, European Molecular Biology Laboratory [Heidelberg] ( EMBL ), Department of Biostatistics, University of Michigan [Ann Arbor], Department of Radiation Oncology [Michigan] ( Radonc ), Department of Physics and Astronomy [Leicester], University of Leicester, Informatique, Biologie Intégrative et Systèmes Complexes ( IBISC ), Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut für Meteorologie und Klimaforschung ( IMK ), Karlsruher Institut für Technologie ( KIT ), Physics Department [UNB], University of New Brunswick ( UNB ), Laboratoire Parole et Langage ( LPL ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ), Institut des Sciences Chimiques de Rennes ( ISCR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Ecole Nationale Supérieure de Chimie de Rennes-Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Bioprojet, Laboratoire de Matériaux à Porosité Contrôlée ( LMPC ), Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique ( CNRS ), School of Information Engineering [USTB] ( SIE ), University of Science and Technology Beijing [Beijing] ( USTB ), Laboratory for Atmospheric and Space Physics [Boulder] ( LASP ), University of Colorado Boulder [Boulder], Department of Applied Mathematics [Sheffield], University of Sheffield [Sheffield], School of Mathematics and Statistics [Sheffield] ( SoMaS ), Laboratoire de Mécanique de Lille - FRE 3723 ( LML ), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Centre National de la Recherche Scientifique ( CNRS ), Computer Science Department [UCLA] ( CSD ), University of California at Los Angeles [Los Angeles] ( UCLA ), Développement et évolution ( DE ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie du Développement de Villefranche sur mer ( LBDV ), Laboratoire Pierre Aigrain ( LPA ), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris ( FRDPENS ), Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Mathematics and Statistics [Mac Gill], McGill University, Departamento de Botánica [Comahue], Universidad nacional del Comahue, Bioénergétique Cellulaire et Pathologique ( BECP ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Environnements et Paléoenvironnements OCéaniques ( EPOC ), Observatoire aquitain des sciences de l'univers ( OASU ), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Jacques Monod ( IJM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratori Nazionali del Sud ( LNS ), National Institute for Nuclear Physics ( INFN ), Departament de Matemàtiques [Barcelona], Universitat Autònoma de Barcelona [Barcelona] ( UAB ), Max-Planck-Institut für Kohlenforschung (coal research), Institute of Oceanology [CAS] ( IOCAS ), National Chiao Tung University ( NCTU ), Department of Hydrology and Water Resources ( HWR ), University of Arizona, Centre for Educational Technology, Environment Department [York], University of York [York, UK], State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Peking University [Beijing], Department of Physics and Astronomy [Iowa City], University of Iowa [Iowa], NASA Ames Research Center ( ARC ), Department of Materials, Digital Language & Knowledge Contents Research Association ( DICORA ), Hankuk University of Foreign Studies, Department of Physics [Coventry], University of Warwick [Coventry], Space Science and Technology Department [Didcot] ( RAL Space ), STFC Rutherford Appleton Laboratory ( RAL ), Science and Technology Facilities Council ( STFC ) -Science and Technology Facilities Council ( STFC ), Institut de biologie et chimie des protéines [Lyon] ( IBCP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), H M Nautical Almanac Office [RAL] ( HMNAO ), Rutherford Appleton Laboratory, United Kingdom Met Office [Exeter], University College of London [London] ( UCL ), Department of Pathology and Laboratory Medicine [UCLA], University of California at Los Angeles [Los Angeles] ( UCLA ) -School of Medicine, School of Earth and Environmental Sciences [Seoul] ( SEES ), Seoul National University [Seoul], Department of Chemistry, Seoul Women's University, MicroMachines Centre ( MMC ), Nanyang Technological University [Singapour], Regroupement Québécois sur les Matériaux de Pointe ( RQMP ), École Polytechnique de Montréal ( EPM ) -Université de Sherbrooke [Sherbrooke]-McGill University-Université de Montréal-Fonds Québécois de Recherche sur la Nature et les Technologies ( FQRNT ), Département de Physique [Montréal], Université de Montréal, School of Earth and Environment [Leeds] ( SEE ), Centre for Ecology and Hydrology ( CEH ), Natural Environment Research Council ( NERC ), Norwegian Institute for Water Research ( NIVA ), Norwegian Institute for Water Research, Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Astronomy Unit [London] (AU), Queen Mary University of London (QMUL), Commonwealth Scientific and Industrial Research Organisation Energy Technology (CSIRO Energy Technology), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Department of Biochemistry and Molecular Biology [Houston], The University of Texas Medical School at Houston, Mathematical Institute [Oxford] (MI), University of Oxford, Centre for the Analysis of Time Series (CATS), London School of Economics and Political Science (LSE), Thomas Jefferson National Accelerator Facility (Jefferson Lab), Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA ), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), University of Illinois System-University of Illinois System, Department of Electrical and Computer Engineering [Portland] (ECE), Portland State University [Portland] (PSU), Saint-Gobain, Institute for Animal Health (IAH), Biotechnology and Biological Sciences Research Council (BBSRC), Chinese Academy of Sciences [Changchun Branch] (CAS), Ipsen Inc. [Milford] (Ipsen), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, Chung-Ang University (CAU), Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Institute of Aerodynamics and Fluid Mechanics (AER), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Mer et santé (MS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), National Physical Laboratory [Teddington] (NPL), International Research Institute for Climate and Society (IRI), Macaulay Institute, University of Cambridge [UK] (CAM), Queen's University [Kingston, Canada], Leslie Hill Institute for Plant Conservation (PCU), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Interactive Systems Labs (ISL), Carnegie Mellon University [Pittsburgh] (CMU), Dalian Institute of Chemical Physics (DICP), Architectures, Languages and Compilers to Harness the End of Moore Years (ALCHEMY), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Clean Air Task Force (CATF), Indian Space Research Organisation (ISRO), Centre d'études et de recherches appliquées à la gestion (CERAG), Université Pierre Mendès France - Grenoble 2 (UPMF)-Centre National de la Recherche Scientifique (CNRS), Sultan Qaboos University (SQU)-College of Medicine and Health Sciences [Baylor], Baylor University-Baylor University, European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Michigan System-University of Michigan System, Department of Radiation Oncology [Michigan] (Radonc), Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute for Meteorology and Climate Research (IMK), Karlsruhe Institute of Technology (KIT), University of New Brunswick (UNB), Laboratoire Parole et Langage (LPL), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Matériaux à Porosité Contrôlée (LMPC), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), School of Information Engineering [USTB] (SIE), University of Science and Technology Beijing [Beijing] (USTB), Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], School of Mathematics and Statistics [Sheffield] (SoMaS), Laboratoire de Mécanique de Lille - FRE 3723 (LML), Université de Lille, Sciences et Technologies-Centrale Lille-Centre National de la Recherche Scientifique (CNRS), Computer Science Department [UCLA] (CSD), University of California [Los Angeles] (UCLA), Développement et évolution (DE), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Pierre Aigrain (LPA), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics and Statistics [Montréal], McGill University = Université McGill [Montréal, Canada], Departamento de Botánica [Bariloche], Centro Regional Universitario Bariloche [Bariloche] (CRUB), Universidad Nacional del Comahue [Neuquén] (UNCOMA)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), Bioénergétique Cellulaire et Pathologique (BECP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratori Nazionali del Sud (LNS), Istituto Nazionale di Fisica Nucleare (INFN), Departament de Matemàtiques [Barcelona] (UAB), Universitat Autònoma de Barcelona (UAB), Max-Planck-Institut für Kohlenforschung (Coal Research), Max-Planck-Gesellschaft, CAS Institute of Oceanology (IOCAS), Chinese Academy of Sciences [Beijing] (CAS), National Chiao Tung University (NCTU), Department of Hydrology and Water Resources (HWR), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), University of Iowa [Iowa City], NASA Ames Research Center (ARC), Digital Language & Knowledge Contents Research Association (DICORA), Space Science and Technology Department [Didcot] (RAL Space), STFC Rutherford Appleton Laboratory (RAL), Science and Technology Facilities Council (STFC)-Science and Technology Facilities Council (STFC), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), H M Nautical Almanac Office [RAL] (HMNAO), University College of London [London] (UCL), University of California (UC)-University of California (UC)-School of Medicine, School of Earth and Environmental Sciences [Seoul] (SEES), Seoul National University [Seoul] (SNU), MicroMachines Centre (MMC), Regroupement Québécois sur les Matériaux de Pointe (RQMP), École Polytechnique de Montréal (EPM)-Université de Sherbrooke (UdeS)-McGill University = Université McGill [Montréal, Canada]-Université de Montréal (UdeM)-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal (UdeM), Centre for Ecology and Hydrology (CEH), Natural Environment Research Council (NERC), Norwegian Institute for Water Research (NIVA), SEA URCHIN GENOME SEQUENCING CONSORTIUM, SODERGREN E, WEINSTOCK GM, DAVIDSON EH, CAMERON RA, GIBBS RA, ANGERER RC, ANGERER LM, ARNONE MI, BURGESS DR, BURKE RD, COFFMAN JA, DEAN M, ELPHICK MR, ETTENSOHN CA, FOLTZ KR, HAMDOUN A, HYNES RO, KLEIN WH, MARZLUFF W, MCCLAY DR, MORRIS RL, MUSHEGIAN A, RAST JP, SMITH LC, THORNDYKE MC, VACQUIER VD, WESSEL GM, WRAY G, ZHANG L, ELSIK CG, ERMOLAEVA O, HLAVINA W, HOFMANN G, KITTS P, LANDRUM MJ, MACKEY AJ, MAGLOTT D, PANOPOULOU G, POUSTKA AJ, PRUITT K, SAPOJNIKOV V, SONG X, SOUVOROV A, SOLOVYEV V, WEI Z, WHITTAKER CA, WORLEY K, DURBIN KJ, SHEN Y, FEDRIGO O, GARFIELD D, HAYGOOD R, PRIMUS A, SATIJA R, SEVERSON T, GONZALEZ-GARAY ML, JACKSON AR, MILOSAVLJEVIC A, TONG M, KILLIAN CE, LIVINGSTON BT, WILT FH, ADAMS N, BELLE R, CARBONNEAU S, CHEUNG R, CORMIER P, COSSON B, CROCE J, FERNANDEZ-GUERRA A, GENEVIERE AM, GOEL M, KELKAR H, MORALES J, MULNER-LORILLON O, ROBERTSON AJ, GOLDSTONE JV, COLE B, EPEL D, GOLD B, HAHN ME, HOWARD-ASHBY M, SCALLY M, STEGEMAN JJ, ALLGOOD EL, COOL J, JUDKINS KM, MCCAFFERTY SS, MUSANTE AM, OBAR RA, RAWSON AP, ROSSETTI BJ, GIBBONS IR, HOFFMAN MP, LEONE A, ISTRAIL S, MATERNA SC, SAMANTA MP, STOLC V, TONGPRASIT W, TU Q, BERGERON KF, BRANDHORST BP, WHITTLE J, BERNEY K, BOTTJER DJ, CALESTANI C, PETERSON K, CHOW E, YUAN QA, ELHAIK E, GRAUR D, REESE JT, BOSDET I, HEESUN S, MARRA MA, SCHEIN J, ANDERSON MK, BROCKTON V, BUCKLEY KM, COHEN AH, FUGMANN SD, HIBINO T, LOZA-COLL M, MAJESKE AJ, MESSIER C, NAIR SV, PANCER Z, TERWILLIGER DP, AGCA C, ARBOLEDA E, CHEN N, CHURCHER AM, HALLBOOK F, HUMPHREY GW, IDRIS MM, KIYAMA T, LIANG S, MELLOTT D, MU X, MURRAY G, OLINSKI RP, RAIBLE F, ROWE M, TAYLOR JS, TESSMAR-RAIBLE K, WANG D, WILSON KH, YAGUCHI S, GAASTERLAND T, GALINDO BE, GUNARATNE HJ, JULIANO C, KINUKAWA M, MOY GW, NEILL AT, NOMURA M, RAISCH M, READE A, ROUX MM, SONG JL, SU YH, TOWNLEY IK, VORONINA E, WONG JL, AMORE G, BRANNO M, BROWN ER, CAVALIERI, V, DUBOC V, DULOQUIN L, FLYTZANIS C, GACHE C, LAPRAZ F, LEPAGE T, LOCASCIO A, MART, University of California-University of California, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), University of California-University of California-School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), University of Manchester Institute of Science and Technology (UMIST), Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Brookhaven National Laboratory [Upton, NY] (BNL), UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE), Baylor College of Medicine (BCM), Baylor University, Laboratoire de Traitement de l'Information Medicale (LaTIM), Université européenne de Bretagne - European University of Brittany (UEB)-Université de Brest (UBO)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire de Modélisation et Simulation Multi Echelle (MSME), Université Paris-Est Marne-la-Vallée (UPEM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Duke University [Durham], Instituto Andaluz de Geofísica y Prevención de Desastres Sísmicos [Granada] (IAGPDS), Universidad de Granada (UGR), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), University of New South Wales [Sydney] (UNSW), Celera Genomics (CRA), Celera Genomics, Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma Tor Vergata [Roma], Unité de recherches forestières (BORDX PIERR UR ), Institut National de la Recherche Agronomique (INRA), Deptartment of Neuroscience, Uppsala University, State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology (NIGPAS-CAS), Chinese Academy of Sciences [Nanjing Branch]-Chinese Academy of Sciences [Nanjing Branch], Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China, Université Paris Diderot - Paris 7 (UPD7), Department of Physical and Environmental Sciences [Toronto], University of Toronto at Scarborough, inconnu temporaire UPEMLV, Inconnu, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Atmospheric Sciences [Seattle], University of Washington [Seattle], National Institute of Advanced Industrial Science and Technology (AIST), Department of Pharmacy, Università degli studi di Genova = University of Genoa (UniGe), Interdisciplinary Arts and Sciences Department, St. Vincent's Hospital, Sydney, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Electrical Engineering (DEE-POSTECH), Pohang University of Science and Technology (POSTECH), Centre Suisse d'Electronique et de Microtechnique SA [Neuchatel] (CSEM), Centre Suisse d'Electronique et Microtechnique SA (CSEM), Human Genome Sequencing Center [Houston] (HGSC), Brookhaven National Laboratory, Meteorological Service of Canada, 4905 Dufferin Street, Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Mines-Télécom [Paris] (IMT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Paris-Est Marne-la-Vallée (UPEM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Forestières, Department of Physical and Environmental Sciences, University of Toronto [Scarborough, Canada], National Institute for Nuclear Physics (INFN), University of Genoa (UNIGE), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Universidad de Granada = University of Granada (UGR), Laboratoire d'Energétique et de Mécanique Théorique Appliquée (LEMTA ), Technische Universität München [München] (TUM), Queen's University [Kingston], Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Grenoble Alpes (UGA), Institut für Meteorologie und Klimaforschung (IMK), Karlsruher Institut für Technologie (KIT), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille, Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Universitat Autònoma de Barcelona [Barcelona] (UAB), École Polytechnique de Montréal (EPM)-Université de Sherbrooke [Sherbrooke]-Université de Montréal [Montréal]-McGill University-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal [Montréal], U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, MESH: Signal Transduction, MESH: Sequence Analysis, DNA, MESH : Transcription Factors, MESH : Calcification, Physiologic, Genome, MESH : Proteins, 0302 clinical medicine, MESH : Embryonic Development, MESH: Gene Expression Regulation, Developmental, Innate, MESH: Embryonic Development, Developmental, Nervous System Physiological Phenomena, MESH: Animals, MESH: Proteins, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Complement Activation, ComputingMilieux_MISCELLANEOUS, MESH: Evolution, Molecular, MESH : Strongylocentrotus purpuratus, Genetics, 0303 health sciences, MESH: Nervous System Physiological Phenomena, Multidisciplinary, biology, Medicine (all), MESH: Immunologic Factors, Gene Expression Regulation, Developmental, Genome project, MESH: Transcription Factors, MESH : Immunity, Innate, MESH : Complement Activation, MESH: Genes, Bacterial artificial chromosome (BAC)DeuterostomesStrongylocentrotus purpuratusVertebrate innovations, Echinoderm, MESH : Nervous System Physiological Phenomena, embryonic structures, MESH: Cell Adhesion Molecules, MESH : Genes, MESH: Immunity, Innate, Sequence Analysis, Signal Transduction, MESH: Computational Biology, Genome evolution, MESH: Complement Activation, Sequence analysis, Evolution, MESH: Strongylocentrotus purpuratus, MESH : Male, Embryonic Development, MESH : Immunologic Factors, Article, MESH: Calcification, Physiologic, Calcification, MESH : Cell Adhesion Molecules, Evolution, Molecular, 03 medical and health sciences, Calcification, Physiologic, Animals, Immunologic Factors, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Physiologic, Gene, Strongylocentrotus purpuratus, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH : Signal Transduction, Bacterial artificial chromosome, Immunity, Molecular, Computational Biology, Proteins, Cell Adhesion Molecules, Genes, Immunity, Innate, Transcription Factors, Sequence Analysis, DNA, DNA, biology.organism_classification, MESH: Male, Gene Expression Regulation, MESH : Animals, MESH : Gene Expression Regulation, Developmental, MESH : Genome, 030217 neurology & neurosurgery, MESH : Computational Biology, MESH : Sequence Analysis, DNA
Abstract: We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus , a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
Published: 2006
Full Text: View/download PDF

22. Insights into social insects from the genome of the honeybee Apis mellifera

Author: George M. Weinstock, Andrew K. Jones, Katherine A Aronstein, Irene Gattermeier, Kiyoshi Kimura, Susan E. Fahrbach, Laura I. Decanini, Christina M. Grozinger, Evgeny M. Zdobnov, Susan J. Brown, Jonathan V. Sweedler, Kazutoyo Osoegawa, Christian A. Ross, Joseph J. Gillespie, Ngoc Nguyen, Geert Baggerman, Frank Hauser, Dan Graur, Michelle M. Elekonich, Alison R. Mercer, Amanda F. Svatek, Jean Marie Cornuet, Cornelis J. P. Grimmelikhuijzen, Aleksandar Milosavljevic, Anand Venkatraman, Andrew J. Schroeder, Huaiyang Jiang, Michael R. Kanost, Justin T. Reese, Margaret Morgan, Tomoko Fujiyuki, Kim C. Worley, Susanta K. Behura, Jun Kawai, Robert Kucharski, Gildardo Aquino-Perez, Miguel Corona, Diana E. Wheeler, Kathryn S. Campbell, William M. Gelbart, Amy L. Toth, Yanping Chen, Mira Cohen, Noam Kaplan, Michihira Tagami, Miguel A. Peinado, Peter K. Dearden, Glenford Savery, Liliane Schoofs, Takeo Kubo, Giuseppe Cazzamali, Sylvain Forêt, Thomas C. Newman, Ross Overbeek, Piero Carninci, Ryszard Maleszka, Barbara J. Ruef, Michal Linial, Alexandre S. Cristino, Mary A. Schuler, Huyen Dinh, J. Troy Littleton, Manoj P. Samanta, Waraporn Tongprasit, L. Sian Grametes, Eran Elhaik, Jean-Luc Imler, Zhen Zou, Rodrigo A. Velarde, Tanja Gempe, Dorothea Eisenhardt, Juan Manuel Anzola, Graham J. Thompson, Aaron J. Mackey, René Feyereisen, Mrcia M.G. Bitondi, Lora Lewis, Guy Bloch, Richard A. Gibbs, Jane Peterson, Jay D. Evans, Robert E. Page, Amanda B. Hummon, Viktor Stolc, Donna M. Muzny, Yair Shemesh, Francis M. F. Nunes, Dawn Lopez, Judith H. Willis, Martin Hasselmann, Mark S. Guyer, John G. Oakeshott, Pinglei Zhou, Eriko Kage, Dominique Vautrin, Kevin J. Hackett, Sandra L. Lee, Clay Davis, Christine Emore, Gene E. Robinson, Alexandre Souvorov, T.A. Richmond, Rachel Thorn, Jurgen Huybrechts, Elad B. Rubin, Craig Mizzen, Deborah R. Smith, Walter S. Sheppard, Takekazu Kunieda, Adam Felsenfeld, Bingshan Li, Jeffrey G. Reid, La Ronda Jackson, Jamie J. Cannone, Robin R. Gutell, Jireh Santibanez, Megan J. Wilson, David B. Sattelle, Azusa Kamikouchi, George Miner, Hideaki Takeuchi, Geoffrey Okwuonu, Jennifer Hume, Jonathan Miller, Kazuaki Ohashi, Angela Jovilet, Yoshihide Hayashizaki, Joseph Chacko, Paul Kitts, Erica Sodergren, Charles Hetru, Andrew V. Suarez, Brian P. Lazzaro, Susan E. St. Pierre, Evy Vierstraete, Haobo Jiang, Sandra Hines, Teresa D. Shippy, Greg J. Hunt, Peter Kosarev, Dan Hultmark, Stefan Albert, Susan M. Russo, Chung Li Shu, Michel Solignac, H. Michael G. Lattorff, Xu Ling, Grard Leboulle, Miklós Csürös, Neil D. Tsutsui, Lynne V. Nazareth, Ying Wang, Florence Mougel, Beverly B. Matthews, Kevin L. Childs, Rita A. Wright, Hugh M. Robertson, Lan Zhang, Peter Verleyen, Daniel B. Weaver, Christie Kovar, Chikatoshi Kai, Charles W. Whitfield, Madeline A. Crosby, Natalia V. Milshina, Reed M. Johnson, Michael A. Ewing, Peter L. Jones, Sandra L. Rodriguez-Zas, Michael B. Eisen, Klaus Hartfelder, Karl H.J. Gordon, W. Augustine Dunn, Ling Ling Pu, M. Monnerot, Stephen Richards, Richa Agarwala, Judith Hernandez, Pieter J. de Jong, Michael Williamson, Marcé D. Lorenzen, Zilá Luz Paulino Simões, Mark D. Drapeau, Donna Villasana, Katarína Bíliková, J. Spencer Johnston, David I. Schlipalius, Xuehong Wei, Laurent Duret, Venky N. Iyer, Andrew G. Clark, Christine G. Elsik, Hilary Ranson, Kyle T. Beggs, Mireia Jordà, Shiro Fukuda, Seth A. Ament, Vivek Iyer, Jozef Šimúth, Stewart H. Berlocher, May R. Berenbaum, Robin F. A. Moritz, Tatsuhiko Kadowaki, Charles Claudianos, Gro V. Amdam, Yue Liu, Naoko Sakazume, Morten Schioett, Paul Havlak, Anita M. Collins, Dirk C. de Graaf, Derek Collinge, Ivica Letunic, Carlos H. Lobo, Mizue Morioka, Martin Beye, Rachel Gill, C. Michael Dickens, Daisuke Sasaki, Victor V. Solovyev, Peer Bork, Sunita Biswas, David A. Wheeler, Heidi Paul, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), and Physical and genetic mapping
Subjects: Male, 0106 biological sciences, Transposable element, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Proteome, Genome, Insect, Molecular Sequence Data, Genes, Insect, Genomics, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Article, Evolution, Molecular, 03 medical and health sciences, Molecular evolution, Phylogenetics, Animals, Gene, Phylogeny, abeille domestique, 030304 developmental biology, Whole genome sequencing, Genetics, Base Composition, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Behavior, Animal, Reproduction, SOCIAL BEHAVIOR, [SDV.BA]Life Sciences [q-bio]/Animal biology, Immunity, APIS MELLIFERA, food and beverages, Bees, Telomere, Physical Chromosome Mapping, INSECTE, Gene Expression Regulation, DNA methylation, DNA Transposable Elements, Female, GENETIQUE DES POPULATIONS, Signal Transduction
Abstract: Ce travail résulte de la collaboration de très nombreux chercheurs. Seuls les auteurs de la rubrique Physical and Genetic Mapping sont cités explicitement.; Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes, the A. mellifera genome has high A1T and CpG contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, RNA interference and DNA methylation genes, among others. Furthermore, A.mellifera has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen utilization, consistent with its ecology and social organization. Compared to Drosophila, genes in early developmental pathways differ in Apis, whereas similarities exist for functions that differ markedly, such as sex determination, brain function and behaviour. Population genetics suggests a novel African origin for the species A.mellifera and insights into whether Africanized bees spread throughout the New World via hybridization or displacement
Published: 2006
Full Text: View/download PDF

23. Genome-wide transcription analyses in rice using tiling microarrays

Author: Lei Li, Xing Wang Deng, Waraporn Tongprasit, Xiangfeng Wang, Xueyong Li, Viktor Stolc, Songgang Li, Dongfen Zhang, Zhukuan Cheng, Jun Wang, and Ning Su
Subjects: Genetics, Expressed Sequence Tags, Expressed sequence tag, Oryza sativa, Models, Genetic, Transcription, Genetic, food and beverages, Chromosome, Oryza, Biology, Genome, Homology (biology), Chromosomes, Intergenic region, Gene Expression Regulation, Plant, Tandem Repeat Sequences, DNA, Intergenic, DNA microarray, Gene, Genome, Plant, Oligonucleotide Array Sequence Analysis
Abstract: Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species. We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome. Udgivelsesdato: 2006-Jan
Published: 2005
Full Text: View/download PDF

24. Global identification of human transcribed sequences with genome tiling arrays

Author: Alexander E. Urban, Paul Bertone, Michael Snyder, Xiaowei Zhu, Sherman M. Weissman, Mark Gerstein, Joel Rozowsky, John L. Rinn, Thomas Royce, Manoj P. Samanta, Waraporn Tongprasit, and Viktor Stolc
Subjects: DNA, Complementary, Transcription, Genetic, Computational biology, Biology, Genome, Conserved sequence, Mice, Intergenic region, Sequence Homology, Nucleic Acid, Databases, Genetic, Animals, Humans, RNA, Messenger, Gene, Conserved Sequence, Oligonucleotide Array Sequence Analysis, Genetics, Multidisciplinary, Tiling array, Base Sequence, Genome, Human, Reverse Transcriptase Polymerase Chain Reaction, Computational Biology, Nucleic Acid Hybridization, Proteins, Reproducibility of Results, Genome project, Exons, Introns, Human genome, CpG Islands, DNA, Intergenic, DNA microarray, Oligonucleotide Probes
Abstract: Elucidating the transcribed regions of the genome constitutes a fundamental aspect of human biology, yet this remains an outstanding problem. To comprehensively identify coding sequences, we constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome. Transcribed sequences were located across the genome via hybridization to complementary DNA samples, reverse-transcribed from polyadenylated RNA obtained from human liver tissue. In addition to identifying many known and predicted genes, we found 10,595 transcribed sequences not detected by other methods. A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins.
Published: 2004

25. Functional profiling of a human cytomegalovirus genome

Author: Walter Dunn, David A. Patterson, Viktor Stolc, Rong Hai, Hong Li, Hua Zhu, Cassie Chou, and Fenyong Liu
Subjects: Human cytomegalovirus, Chromosomes, Artificial, Bacterial, viruses, Population, Molecular Sequence Data, Clone (cell biology), Cytomegalovirus, Genome, Viral, Biology, Virus Replication, Open Reading Frames, medicine, Humans, ORFS, education, Gene, Tropism, Genetics, education.field_of_study, Multidisciplinary, Gene Expression Profiling, Biological Sciences, medicine.disease, Virology, Gene expression profiling, Viral replication, Mutagenesis, DNA, Viral, Gene Deletion
Abstract: Human cytomegalovirus (HCMV), a ubiquitous herpesvirus, causes a lifelong subclinical infection in healthy adults but leads to significant morbidity and mortality in neonates and immunocompromised individuals. Its ability to grow in different cell types is responsible for HCMV-associated diseases, including mental retardation and retinitis, and vascular disorders. To globally assess viral gene function for replication in cells, we determined the genomic sequence of a bacterial artificial chromosome (BAC)-based clone of HCMV Towne strain and used this information to delete each of its 162 unique ORFs and generate a collection of viral mutants. The growth of these mutants in different cultured cells was examined to systematically investigate the necessity of each ORF for replication. Our results showed that 45 ORFs are essential for viral replication in fibroblasts and 117 are nonessential. Some genes were found to be required for viral replication in retinal pigment epithelial cells and microvascular endothelial cells, but not in fibroblasts, indicating their role as tropism factors. Interestingly, several viral mutants grew 10- to 500-fold better than the parental strain in different cell types, suggesting that the deleted ORFs encode replication temperance or repressing functions. Thus, HCMV encodes supportive and suppressive growth regulators for optimizing its replication in human fibroblasts, epithelial, and endothelial cells. Suppression of viral replication by virus-encoded temperance factors represents a novel mechanism for regulating the growth of an animal virus, and may contribute to HCMV's optimal infection of different tissues and successful proliferation among the human population.
Published: 2003

26. Pyrosequencing

Author: Mostafa Ronaghi, Viktor Stolc, and Nader Pourmand
Subjects: Massive parallel sequencing, Pyrosequencing, Computational biology, Biology, DNA sequencing
Published: 2001
Full Text: View/download PDF

27. Characterization of two scleroderma autoimmune antigens that copurify with human ribonuclease P

Author: Viktor Stolc, Ramesh Kekuda, Sidney Altman, and Paul S. Eder
Subjects: RNase P, Protein subunit, Immunoblotting, Molecular Sequence Data, Biology, Molecular cloning, Cross Reactions, Autoantigens, Ribonuclease P, Antigen, Complementary DNA, Endoribonucleases, medicine, Humans, RNA, Catalytic, Amino Acid Sequence, Cloning, Molecular, Autoimmune disease, Multidisciplinary, Scleroderma, Systemic, Base Sequence, Nuclear RNase P, RNA, Sequence Analysis, DNA, Biological Sciences, medicine.disease, Molecular biology, Precipitin Tests, HeLa Cells
Abstract: Human RNase P has been purified more than 2000-fold from HeLa cells. In addition to the RNA component, H1 RNA, polypeptides of molecular masses 14, 20, 25, 30, 38, and 40 kDa copurify with the enzyme activity. Sera from two different patients with the autoimmune disease scleroderma were used to immunodeplete human RNase P activity. These same sera cross-reacted on immunoblots with two of the copurifying polypeptides, p30 and p38, whereas an autoimmune serum that does not immunodeplete RNase P activity did not react with these proteins. Peptide fragments derived from purified p30 and p38 facilitated the molecular cloning and sequencing of cDNAs coding for these two polypeptides, which are now designated as Rpp30 and Rpp38, respectively. RPP38 cDNA encodes a polypeptide that may be identical to a previously identified antigen of ≈40 kDa, which is immunoprecipitated by Th and To autoimmune antisera, and that has been implicated as a protein subunit of human RNase P by virtue of its ability to bind to H1 RNA in vitro . The second autoimmune antigen, Rpp30, as such, has not been described previously.
Published: 1997

28. [Untitled]

Author: Lei Li, Songgang Li, Xiping Wang, Jun-Jun Wang, Viktor Stolc, Mian Xia, Ning Su, Xiangfeng Wang, Zhiyu Peng, and Xing Wang Deng
Subjects: 2. Zero hunger, 0106 biological sciences, Genetics, 0303 health sciences, Euchromatin, Microarray analysis techniques, Heterochromatin, food and beverages, Genome project, Biology, 01 natural sciences, Genome, Gene expression profiling, 03 medical and health sciences, DNA microarray, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: Background: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. Results: We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18% increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. Conclusion: These results demonstrated the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray analysis further revealed a chromosomewide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice.
Published: 2005
Full Text: View/download PDF

29. GENETIC CONTROL OF BLOOD NEUTROPHIL CONCENTRATION IN THE RAT

Author: Viktor Stolc
Subjects: Genetics, Neutrophils, Offspring, Neutrophile, Immunology, Rats, Inbred Strains, Immunogenetics, Quantitative trait locus, Biology, Phenotype, Rats, Andrology, Leukocyte Count, Backcrossing, Animals, Lymphocytes, Allele, Alleles, Crosses, Genetic, Hybrid
Abstract: SUMMARY Two phenotypes that characterize low and high neutrophil concentrations in blood were found in the rat. It is possible that either two regulating alleles control the high (Nr-1a) and the low (Nr-1b) neutrophil concentration or that a polygenic system affects the neutrophil concentration in blood. The F1 hybrids of four intercrosses had low neutrophil levels in blood that suggested a dominant effect of the Nr-1b allele. The backcross progeny showed abnormal segregation of the neutrophil phenotypes. The high phenotype was expressed in only 5% of the offspring. The presence of the two phenotypes and their distribution in the backcross progeny was confirmed by the computer program SKUMIX that resolved the quantitative traits into two discrete distributions with 95% and 5% representation. Because the logistic of SKUMIX can not rule out the polygenic effect, only further breeding studies using linked markers can resolve the mechanism of the genetic control of neutrophil concentration in the rat.
Published: 1988
Full Text: View/download PDF

30. Genetics of meprin in the rat

Author: Viktor Stolc
Subjects: Genetics, chemistry.chemical_classification, Kidney, Locus (genetics), Biology, Molecular biology, Centimorgan, Enzyme, medicine.anatomical_structure, chemistry, Backcrossing, medicine, High activity, Allele, Gene
Abstract: The locus encoding for meprin activity in kidney was found polymorphic in the rat. The BDIV and COP strains that carried theMep-1a allele had high meprin concentration in the kidney, while the ACI, BN, LE and LEW strains that carried theMep-1b allele had low meprin levels. TheMep-1a allele that controlled the high activity enzyme was expressed in a dominant fashion in the (BN × COP) F1 progeny. The backcross studies showed that the segregation of alleles at theMep-1 and theGlo-1 loci was normal and that the genes were linked (x2 = 4.06,P < 0.05). The map distance between theMep-1 andGlo-1 genes was 41 ± 4 centimorgans.
Published: 1986
Full Text: View/download PDF

31. Linkage ofaconitase-1 andmajor urinary protein-1 loci in male rats

Author: Viktor Stolc
Subjects: Genetics, Urinary protein, Backcrossing, Male rats, Group ii, Locus (genetics), Allele, Biology, Gene, Molecular biology, Synteny
Abstract: A new major urinary protein alleleMup-lc with “null” activity was detected in males of the COP strain. The (BN X COP)F1 X COP backcross had significant segregation distortion of theMup-lc andAco-1 alleles that indicated a linkage between the genes, at a map distance of 13 ± 4 cM. The loci reside on the linkage group II of the rat with theb locus. According to our data and the results published previously, the map distance and the orientation of genes isb - 8 ± 4 -Mup-1 - 13 ±4-Aco-1. These genes form a syntenic group in both the mouse and the rat.
Published: 1986
Full Text: View/download PDF

32. Inhibitory EflEect of Pituitary Factor on Phagocytosis and Iodine Metabolism in Human Leukocytes

Author: Viktor Stolc
Subjects: Monoiodotyrosine, medicine.medical_specialty, Pituitary gland, Latex, Chromatography, Paper, Phagocytosis, medicine.medical_treatment, Serum albumin, Thyrotropin, chemistry.chemical_element, In Vitro Techniques, Iodine, chemistry.chemical_compound, Endocrinology, Anterior pituitary, Pituitary Hormones, Anterior, Iodine Isotopes, Internal medicine, Leukocytes, medicine, Humans, biology, Insulin, Blood Proteins, Iodides, Luteinizing Hormone, Microspheres, Thyroxine, medicine.anatomical_structure, Myoglobin, chemistry, Depression, Chemical, Growth Hormone, biology.protein, Follicle Stimulating Hormone, Ceruloplasmin, Diiodotyrosine, Protein Binding
Abstract: A pituitary factor decreasing iodine uptake and protein-bound iodine formation in human leukocytes was found in semi-purified preparations of TSH, LH, FSH, GH and in crude anterior pituitary extract. ACTH, insulin, serum gamma globulin, myoglobin and ceruloplasmin were ineffective in comparison to control samples incubated with serum albumin. TSH, in relation to dose (0.01–0.5 U/ml), significantly decreased the total uptake, formation, and release of iodocompounds from phagocytic leukocytes. The amount of iodocompounds released from resting or phagocytic leukocytes into the media was twice as high as the amount of organically bound iodine that remained in the cells. These data suggest that iodine-containing compounds are actively formed, metabolized, and released from human leukocytes. Because TSH also decreases engulfment of latex microparticles, the observed changes in iodine metabolism are probably secondary, due to the reduced phagocytosis. The presence of an unknown factor in the semipurified prepara...
Published: 1972
Full Text: View/download PDF

33. TSH and Dibutyryl-Cyclic-AMP Stimulation of Hormone Release from Rat Thyroid Glandsin Vitro

Author: Teiichiro Tonoue, Winton Tong, and Viktor Stolc
Subjects: Male, Thyroid Hormones, endocrine system, medicine.medical_specialty, Epinephrine, endocrine system diseases, Chromatography, Paper, Vasopressins, medicine.medical_treatment, Thyroid Gland, Thyrotropin, Stimulation, In Vitro Techniques, Endocrinology, Antithyroid Agents, Thyroid peroxidase, Iodine Isotopes, Internal medicine, Cyclic AMP, Animals, Medicine, Incubation, biology, Adenine Nucleotides, business.industry, Thyroid, Dibutyryl Cyclic AMP, Stimulation, Chemical, In vitro, Rats, Thyroxine, medicine.anatomical_structure, biology.protein, Autoradiography, Triiodothyronine, Thyroglobulin, business, Adenylyl Cyclases, Hormone
Abstract: The release of hormones from thyroid glands in vitro was observed by incubating the whole thyroid lobes taken from rats which had been injected 3 hr previously with 131I. The release of free 131I-T3 and T4 from 131I-thyroglobulin that occurred in the tissues during 2 hr incubations was measured by paper chromatographic analysis of the tissues and media. TSH (50–500 mU/ml) increased the free T3, T4 content of the incubated specimens by 2- to 4-fold. Cyclic-AMP, ATP and AMP were without effect, but dibutyryl-cyclic-AMP (3 mm) stimulated T3, T4 release in a TSH-like manner. Furthermore, incubation with TSH led to prompt increases in the cyclic-AMP content of the thyroid lobes. These findings provide another example of a TSH action which may be mediated by the adenyl cyclase-cyclic AMP system. (Endocrinology 86: 271, 1970)
Published: 1970
Full Text: View/download PDF

34. Orientation of loci in the major histocompatibility complex of the rat and its comparison to man and the mouse

Author: D. J. Schaid, J. L. VandeBerg, Viktor Stolc, Heinz W. Kunz, and Thomas J. Gill
Subjects: Male, Pan troglodytes, Swine, Immunology, Genes, MHC Class II, Guinea Pigs, Neuraminidase, Major histocompatibility complex, law.invention, Major Histocompatibility Complex, Mice, Dogs, law, Genetics, Animals, Humans, Gene, Crosses, Genetic, Muridae, Recombination, Genetic, MHC class II, biology, Lactoylglutathione Lyase, Chromosome Mapping, Rats, Inbred Strains, biology.organism_classification, Macaca mulatta, Histocompatibility, Rats, Backcrossing, Recombinant DNA, biology.protein, Female, Recombination
Abstract: Among 290 F2 progeny of an r10 X ACP cross were two recombinants which allowed the loci for glyoxalase-1 and neuraminidase-1 to be mapped relative to the RT1.A and dw-3 loci in the major histocompatibility complex (MHC) of the rat. In 673 progeny of the same cross there was a recombinant between ft and dw-3, and in 403 progeny of the backcross BY1 X (BY1 X BDIX)F1 there was another recombinant between ft and dw-3. These data, combined with those from previous studies, provide the information for constructing a detailed map of the rat major histocompatibility complex: the gene order and size in the rat are very similar to those in the mouse and different from those in man and in the other species that have been studied. Comparison of the structures of the MHC in the various species leads to a hypothesis about the evolution of the MHC which involves sequential duplications of the genes coding for class I and class II loci and an inversion in the prototypic muridae which placed the class II loci between the class I loci.
Published: 1982

35. Linkage and polymorphism of a gene controlling lactate dehydrogenase in the rat

Author: Thomas J. Gill and Viktor Stolc
Subjects: Male, Genotype, Genetic Linkage, Macromolecular Substances, Protein subunit, Biology, Biochemistry, chemistry.chemical_compound, Sex Factors, Species Specificity, Polymorphism (computer science), Lactate dehydrogenase, Genetics, Animals, Allele, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Alleles, Crosses, Genetic, Regulator gene, chemistry.chemical_classification, Polymorphism, Genetic, L-Lactate Dehydrogenase, Rats, Inbred Strains, General Medicine, Molecular biology, Rats, Isoenzymes, Enzyme, Phenotype, chemistry, Genes, Female, Hemoglobin
Abstract: The amount of lactate dehydrogenase subunit A in rat serum is under the control of the lactate dehydrogenase regulatory gene Ldr-1, and it is determined by two alleles, Ldr-1 a (high) and Ldr-1 b (low). Sex and LDH-A level segregate independently, so the Ldr-1 gene is autosomal. The genes for albino, red eye, hemoglobin, and Ldr-1 are linked (linkage group I), and their order is Ldr-1-Hbb-r-c. Our data put Ldr-1 45 cM from Hbb, and Hbb is 7 cM from c. Data in the literature separate r and c by 0.3 cM.
Published: 1983

36. Stimulation of adenosine 3',5'-monophosphate formation in mononuclear leukocytes by toad venoms

Author: Viktor Stolc
Subjects: medicine.medical_specialty, Neutrophils, Stimulation, Toad, Species Specificity, biology.animal, Internal medicine, 1-Methyl-3-isobutylxanthine, medicine, Cyclic AMP, Animals, Humans, Alprostadil, Bufo, Molecular Biology, Incubation, biology, urogenital system, Prostaglandins E, Cell Biology, American toad, biology.organism_classification, Adenosine, Bufonidae, Enzyme Activation, Kinetics, Endocrinology, Colorado river toad, Bufo arenarum, Amphibian Venoms, Bufo marinus, sense organs, hormones, hormone substitutes, and hormone antagonists, medicine.drug
Abstract: The content of adenosine 3',5'-monophosphate in human mononuclear leukocytes was enhanced 3-5-times by venoms obtained from African toad (Bufo africanus), American toad (Bufo americanus), Colorado river toad (Bufo arenarum) and Marine toad (Bufo marinus) at 25 micrograms/ml for 5 min of incubation at 37 degrees C. The maximum stimulation was observed after 1-5 min of incubation. The half-maximal stimulation was observed at 0.1 micrograms/ml venom obtained from Colorado river toad (Bufo arenarum). The increased content of adenosine 3',5'-monophosphate in the mononuclear leukocytes persisted without significant change for at least 30 min of incubation at 37 degrees C.
Published: 1982

37. Hemoglobin polymorphism in inbred strains of rats (Rattus norvegicus)

Author: Thomas J. Gill, Viktor Stolc, and Heinz W. Kunz
Subjects: Male, Genetic Linkage, Major histocompatibility complex, medicine.disease_cause, Biochemistry, symbols.namesake, Hemoglobins, Inbred strain, Polymorphism (computer science), Genetics, medicine, Animals, Molecular Biology, Polyacrylamide gel electrophoresis, Ecology, Evolution, Behavior and Systematics, Crosses, Genetic, Mutation, Sex Characteristics, Polymorphism, Genetic, biology, Rats, Inbred Strains, General Medicine, Phenotype, Molecular biology, Rats, biology.protein, Mendelian inheritance, symbols, Electrophoresis, Polyacrylamide Gel, Female, Hemoglobin
Abstract: Hemoglobin phenotypes A and B were determined by polyacrylamide gel electrophoresis of erythrocyte lysates from 29 inbred strains of rats. Fourteen strains have phenotype A and fifteen have phenotype B, which are characterized by five and six hemoglobin bands, respectively. Breeding studies showed that the phenotypes are codominant and that they segregate in a simple Mendelian fashion in the (A x B) F1 x A backcross. Sex and hemoglobin phenotype assort independently, and the hemoglobin phenotype is not linked to the major histocompatibility complex (RT1) and to two erythrocyte alloantigenic systems (RT2 and RT3).
Published: 1982

38. Microgranular promyelocytic leukemia: a multiparameter examination

Author: Lila Penchansky, Sandra S. Kaplan, Viktor Stolc, and John R. Krause
Subjects: Acute promyelocytic leukemia, Adult, Antigens, Differentiation, T-Lymphocyte, medicine.medical_specialty, Pathology, Myeloid, Biology, Flow cytometry, Antigen, Leukemia, Promyelocytic, Acute, medicine, Humans, Aged, Aged, 80 and over, Blood Cells, medicine.diagnostic_test, Histocytochemistry, Cytogenetics, Antibodies, Monoclonal, Hematology, Gene rearrangement, medicine.disease, Flow Cytometry, Leukemia, medicine.anatomical_structure, Cytochemistry
Abstract: Six cases of microgranular variant acute promyelocytic leukemia (M3v) were studied by use of a multiparameter approach including morphology, cytochemistry, flow cytochemistry, flow cytometry, cytogenetics, and gene rearrangement. Three of six cases demonstrated both myeloid and monocytoid associated surface markers by flow cytometry. One of six cases had strong alpha-naphthyl-butyrate esterase (alpha-NBE) activity in addition to myeloperoxidase activity. There was no correlation between percentage of positive monocytoid surface markers and intensity of cytoplasmic alpha-NBE activity. Four of six cases also had a T-cell-associated surface antigen. Further studies indicated that the T-cell markers appeared to be on the promyelocytes and that the T-B receptor gene was not rearranged. Similarly, cytogenetics studies indicated only one clonal abnormality t(15q+; 17q-). Whether these cases represent true "lineage infidelity" remains to be answered. Future important studies are needed on normal hematopoietic progenitor cells at early stages of development and childhood to study lineage-specific characteristics and to determine whether co-expression normally exists during early development.
Published: 1989

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Journal

Database

Publisher

38 results on '"Viktor Stolc"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources