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  • Genetics  (8)
  • SWISS-2DPAGE  (4)
  • Wiley-Blackwell  (12)
  • American Institute of Physics (AIP)
  • 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
    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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  • 4
    Electronic Resource
    Electronic Resource
    Disruption of six Saccharomyces cerevisiae genes from chromosome IV and basic phenotypic analysis of deletion mutants (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 14 (1998), S. 1199-1208 
    Details
    ISSN: 0749-503X
    Keywords: LFH deletion cassette ; functional analysis ; chromosome IV ; Saccharomyces cerevisiae ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We report here the construction of six deletion mutants and the analysis of their basic phenotype. Deletion cassettes containing the KanMX4 marker module and long flanking regions homologous to the target locus were constructed for each of the six open reading-frames (ORFs YDL088c, YDL087c, YDL086w, YDL085w, YDL084w and YDL082w) located on chromosome IV. Sporulation and tetrad analysis of heterozygous deletant strains revealed that, in the FY1679 genetic background, ORFs YDL088c, YDL087c and YDL084w are essential genes for vegetative growth whereas YDL086w, YDL085w and YDL082w are non-essential. ydl088cΔ and ydl084wΔ haploid strains are viable in the CEN. PK2 genetic background although ydl084wΔ grows at a slower rate than the wild type. Complementation tests by corresponding cognate genes confirmed that gene inactivation was responsible for these growth defects. © 1998 John Wiley & Sons, Ltd.
    Additional Material: 1 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    Understanding Candida albicans at the Molecular Level (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 12 (1996), S. 1677-1702 
    Details
    ISSN: 0749-503X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: No Abstract
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    DNA Sequence Analysis of a 23 002 bp DNA Fragment of the Right Arm of Saccharomyces cerevisiae Chromosome VII (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 13 (1997), S. 357-363 
    Details
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; yeast genome ; genome sequencing ; chromosome VII ; QCR9 ; UBR1 ; TYS1 ; TFG1 ; HGH1 ; BUB1 ; tRNALeu3 ; tRNATrp ; tRNALys1 ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We report the sequence of a 23 002 bp fragment located on the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of this region revealed 14 complete open reading frames (ORFs) with more than 300 base pairs. Six of them correspond to previously known genes. G7164 is the QCR9 gene coding for subunit 9 of the cytochrome c reductase; G7168 is UBR1, encoding an ubiquitin protein ligase; G7522 is the TYS1 gene, which encodes for the tyrosyl tRNA synthetase; G7526 is TFG1, the gene coding for the RNA polymerase transcription initiation factor TFIIF (factor G); G7538 is the gene HGH1 which encodes a protein related to the mammalian HMG1 and HMG2 proteins. G7542 is the BUB1 gene which encodes a ser/thr protein kinase involved in spindle assembly during the cell cycle. One of the ORFs, G7553, shares significant homologies with the gene UTR2 from S. cerevisiae. None of the seven remaining ORFs shows similarity to any of the sequences within the public databases. Three ORFs are internal ORFs of the above-described known genes, and two small ORFs are completely contained in larger ORFs on the complementary strand, and therefore probably do not correspond to real genes. This region also contains three genes specifying tRNAs for Leu, Lys and Trp, and several LTR elements. The sequence described in this paper has been deposited in the EMBL data library under the Accession Number X99074. © 1997 John Wiley & Sons, Ltd.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    The deletion of six ORFs of unknown function from Saccharomyces cerevisiae chromosome VII reveals two essential genes: YGR195w and YGR198w (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 14 (1998), S. 853-860 
    Details
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; chromosome VII ; ribonuclease PH ; HGH1 ; YGR187c ; YGR189c ; YGR194c ; YGR195w ; YGR196c ; YGR198w ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have deleted six different ORFs of unknown function located on the right arm of Saccharomyces cerevisiae chromosome VII; namely, YGR187c/HGH1, YGR189c, YGR194c, YGR195w, YGR196c and YGR198w. No basic phenotypes could be attributed to the strains deleted in any of genes YGR187c/HGH1, YGR189c, YGR194c and YGR196c. These deletants did not show mating, sporulation or growth defects under any of the conditions tested. However, spores bearing deletions in either the YGR195w or YGR198w genes were unable to develop into macroscopical colonies. The YGR195w gene product shows significant homology with bacterial ribonuclease PH, an enzyme hitherto undescribed in yeasts, and its deletion causes a loss of viability after one to three rounds of cell division. Overexpression of this gene, using a tetracycline-regulatable promoter system, did not cause any effect on the cells. Contrary to what has been reported for prokaryotic homologs, this enzyme could play an essential role in yeast cell biology. The product encoded by the other essential ORF, YGR198w, shows no significant homology with any protein of known function in the databases. Spores bearing the deletion usually germinate and give rise to microcolonies of 50-100 non-viable cells. © 1998 John Wiley & Sons, Ltd.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Cloning and sequencing of the URA5 gene from the yeast Yarrowia lipolytica (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 11 (1995), S. 425-433 
    Details
    ISSN: 0749-503X
    Keywords: Yarrowia lipolytica ; orotate phosphoribosyl transferase ; nucleotide sequence ; transcription ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The URA5 gene of Yarrowia lipolytica encoding the orotate phosphoribosyl transferase (OPRTase, EC2.4.2.10) was isolated by target integration in a mutant strain originally named ura2.21. The nucleotide sequence of the gene predicts a protein with high similarities with the OPRTases from Saccharomyces cerevisiae, Podospora anserina and Escherichia coli and to a lesser extent with that of Dictyostelium discoideum. The transcription start point has been mapped by primer extension analysis and indicates the existence of a long leader sequence in the corresponding mRNA. Northern-blot hybridization revealed the URA5 transcript to be approximately 0·94 kb. Deletion of the URA5 gene in Y. lipolytica produced a leaky phenotype similar to the one described for the ura5 mutation in S. cerevisiae. The URA5 gene of Y. lipolytica was able to complement functionally the ura5 mutation of S. cerevisiae. The sequence presented here has been submitted to the EMBL data library under Accession Number Z22571.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/yea.320110505
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  • 9
    Electronic Resource
    Electronic Resource
    Yeast exo-β-glucanases can be used as efficient and readily detectable reporter genes in Saccharomyces cerevisiae (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 10 (1994), S. 747-756 
    Details
    ISSN: 0749-503X
    Keywords: β-glucanases ; Saccharomyces cerevisiae ; flow cytometry ; reporter genes ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Yeast exo-1,3-β-glucanases are secretable proteins whose function is basically trophic and may also be involved in cell wall glucan hydrolytic processes. Since fluorescein di(β-D-glucopyranoside) is a fluorogenic substrate detectable and quantifiable by flow cytometry, it was used for testing the ability of the EXG1 gene product of Saccharomyces cerevisiae and its homologous gene in Candida albicans to function as reporter genes. These open reading frames were coupled to different promoters in multicopy plasmids, and exoglucanase activity quantified at flow cytometry. Exoglucanases were found to be useful tools for the study of promoter regions in S. cerevisiae. This technique has the advantage over other reporter gene systems - such as β-galactosidase fusions - that it does not require permeabilization of yeast cells and therefore it allows the recovery of viable cells - by sorting - after flow cytometry analysis.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/yea.320100606
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  • 10
    Electronic Resource
    Electronic Resource
    Flow cytometric analysis of Saccharomyces cerevisiae autolytic mutants and protoplasts (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 8 (1992), S. 39-45 
    Details
    ISSN: 0749-503X
    Keywords: Flow cytometry ; autolytic mutants ; protoplasts ; yeast ; viability assay ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Simple methods, based on the technique of flow cytometry, have been developed for the phenotypic characterization of yeast autolytic mutants and for the analysis of the formation and regeneration of the yeast protoplasts. The expression of lytic mutations determined uptake of the fluorescent dye propidium iodide, which could be carefully monitored by flow cytometry. Mixed populations of lysed and viable cells were precisely quantified and sorted, and the technique was also applied to demonstrate protection from lysis of mutant cells with cell wall defects, in the presence of osmotic stabilizers. Protoplast formation and regeneration was monitored by analysing relative cell size; this was facilitated by the preparation of homogeneous protoplast preparations. The technique of flow cytometry proved superior to other conventional methods for these types of study.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/yea.320080104
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