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  • 1
    Electronic Resource
    Electronic Resource
    Inside SWISS-2DPAGE database (1995)
    Weinheim : Wiley-Blackwell
    Electrophoresis 16 (1995), S. 1131-1151 
    Details
    ISSN: 0173-0835
    Keywords: SWISS-2DPAGE ; Two-dimensional gel electrophoresis ; Protein database ; Protein mapping ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Several two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) databases have been established and updated for more than 15 years. Only recently have developments of computer networks and high-speed transfer protocols provided the required tools for sharing comprehensive and hypermedia 2-D PAGE databases. This publication describes the SWISS-2DPAGE database structure. Proteins present in samples of human tissue, cells, cell lines and body fluids are assembled and described in an accessible uniform format. SWISS-2DPAGE can be freely accessed through the World-Wide Web (WWW) network on the ExPASy molecular biology server.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.11501601190
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  • 2
    Electronic Resource
    Electronic Resource
    The yeast SWISS-2DPAGE database (1996)
    Weinheim : Wiley-Blackwell
    Electrophoresis 17 (1996), S. 556-565 
    Details
    ISSN: 0173-0835
    Keywords: Yeast ; SWISS-2DPAGE ; Two-dimensional polyacrylamide gel electrophoresis ; Protein database ; Protein mapping ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The systematic sequencing of the yeast genome will soon be completed. A new challenge has been launched by the EUROFAN (European Functional Analysis) project whose goal is to elucidate the physiological and biochemical function of newly discovered open reading frames (ORF) from yeast. One of the approaches is to use protein-based technologies such as two-dimensional gel eletrophoresis and protein identification in order to establish a yeast reference map. Modified protein patterns can be compared to the reference map which hopefully will help identify changes related, for example, to growth processes or developmental events. This paper describes the yeast SWISS-2DPAGE database in which charge separation was obtained using immobilized pH gradient (IPG). Proteins identified by gel comparison, amino acid composition analysis and/or microsequencing are recorded and described in an accessible uniform format. We have identified more than one hundred polypeptides, several of which were newly mapped. In addition, the yeast SWISS-2DPAGE database can be freely accessed through the World Wide Web (WWW) network on the ExPASy molecular biology server.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150170326
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  • 3
    Electronic Resource
    Electronic Resource
    Make2ddb: A simple package to set up a two-dimensional electrophoresis database for the World Wide Web (1997)
    Weinheim : Wiley-Blackwell
    Electrophoresis 18 (1997), S. 2755-2758 
    Details
    ISSN: 0173-0835
    Keywords: SWISS-2DPAGE ; Two-dimensional polyacrylamide gel electrophoresis ; Protein database ; Federated database ; World Wide Web ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Two-dimensional electrophoresis (2-DE) has become a highly reproducible protein separation technique that currently serves as the main basis for proteome research and in particular for protein identification. Also, the Internet provides large utilities for exchanging data, and we can observe increased interest among scientists to build remote 2-DE databases, since many members of the concerned community are now able to access the data. By preparing the data and programs that are required to create a federated 2-DE database, the Make2ddb package, described here, helps to build such a database on the user own World Wide Web site.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150181509
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  • 4
    Electronic Resource
    Electronic Resource
    Federated two-dimensional electrophoresis database: A simple means of publishing two-dimensional electrophoresis data (1996)
    Weinheim : Wiley-Blackwell
    Electrophoresis 17 (1996), S. 540-546 
    Details
    ISSN: 0173-0835
    Keywords: SWISS-2DPAGE ; Two-dimensional polyacryamide gel electrophoresis ; Protein database ; World Wide Web ; Federated data-base ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150170324
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  • 5
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    Control of the DNA damage checkpoint by chk1 and rad53 protein kinases through distinct mechanisms (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-05
    Description: In response to DNA damage, cells activate checkpoint pathways that prevent cell cycle progression. In fission yeast and mammals, mitotic arrest in response to DNA damage requires inhibitory Cdk phosphorylation regulated by Chk1. This study indicates that Chk1 is required for function of the DNA damage checkpoint in Saccharomyces cerevisiae but acts through a distinct mechanism maintaining the abundance of Pds1, an anaphase inhibitor. Unlike other checkpoint mutants, chk1 mutants were only mildly sensitive to DNA damage, indicating that checkpoint functions besides cell cycle arrest influence damage sensitivity. Another kinase, Rad53, was required to both maintain active cyclin-dependent kinase 1, Cdk1(Cdc28), and prevent anaphase entry after checkpoint activation. Evidence suggests that Rad53 exerts its role in checkpoint control through regulation of the Polo kinase Cdc5. These results support a model in which Chk1 and Rad53 function in parallel through Pds1 and Cdc5, respectively, to prevent anaphase entry and mitotic exit after DNA damage. This model provides a possible explanation for the role of Cdc5 in DNA damage checkpoint adaptation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, Y -- Bachant, J -- Wang, H -- Hu, F -- Liu, D -- Tetzlaff, M -- Elledge, S J -- GM44664/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Nov 5;286(5442):1166-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10550056" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase ; Anaphase-Promoting Complex-Cyclosome ; CDC2 Protein Kinase/metabolism ; Cell Cycle Proteins/genetics/metabolism ; Checkpoint Kinase 2 ; Cyclin B/genetics/metabolism ; *DNA Damage ; DNA, Fungal/metabolism ; Fungal Proteins/genetics/metabolism ; Intracellular Signaling Peptides and Proteins ; Ligases/metabolism ; *Mitosis ; Mutation ; Nuclear Proteins/metabolism ; Phosphorylation ; Protein Kinases/genetics/*metabolism ; *Protein-Serine-Threonine Kinases ; RNA-Binding Proteins ; Recombinant Fusion Proteins/metabolism ; S Phase ; Saccharomyces cerevisiae/*cytology/*enzymology/genetics ; *Saccharomyces cerevisiae Proteins ; Securin ; *Ubiquitin-Protein Ligase Complexes ; Ubiquitin-Protein Ligases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Regulation of RAD53 by the ATM-like kinases MEC1 and TEL1 in yeast cell cycle checkpoint pathways (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-01-19
    Description: Mutants of the Saccharomyces cerevisiae ataxia telangiectasia mutated (ATM) homolog MEC1/SAD3/ESR1 were identified that could live only if the RAD53/SAD1 checkpoint kinase was overproduced. MEC1 and a structurally related gene, TEL1, have overlapping functions in response to DNA damage and replication blocks that in mutants can be provided by overproduction of RAD53. Both MEC1 and TEL1 were found to control phosphorylation of Rad53p in response to DNA damage. These results indicate that RAD53 is a signal transducer in the DNA damage and replication checkpoint pathways and functions downstream of two members of the ATM lipid kinase family. Because several members of this pathway are conserved among eukaryotes, it is likely that a RAD53-related kinase will function downstream of the human ATM gene product and play an important role in the mammalian response to DNA damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, Y -- Desany, B A -- Jones, W J -- Liu, Q -- Wang, B -- Elledge, S J -- DK07696/DK/NIDDK NIH HHS/ -- GM44664/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jan 19;271(5247):357-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Mars McLean Department of Biochemistry, Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8553072" target="_blank"〉PubMed〈/a〉
    Keywords: Ataxia Telangiectasia Mutated Proteins ; Base Sequence ; *Cell Cycle ; *Cell Cycle Proteins ; Checkpoint Kinase 2 ; *DNA Damage ; DNA Replication ; DNA-Binding Proteins ; Fungal Proteins/*genetics/metabolism ; Gene Expression Regulation, Fungal ; *Genes, Fungal ; Intracellular Signaling Peptides and Proteins ; Molecular Sequence Data ; Mutation ; Phosphorylation ; Protein Kinases/*genetics/metabolism ; *Protein-Serine-Threonine Kinases ; Proteins/genetics/metabolism ; Saccharomyces cerevisiae/cytology/*genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Signal Transduction ; Tumor Suppressor Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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