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  • 1
    Electronic Resource
    Electronic Resource
    The rat liver epithelial (RLE) cell protein database (1991)
    Weinheim : Wiley-Blackwell
    Electrophoresis 12 (1991), S. 931-939 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Computer databases of rat liver epithelial (RLE) cellular polypeptides have been established using high resolution two-dimensional gel electrophoresis and computer-assisted analysis. Databases have been constructed utilizing both [35S]methionine- and [32P]orthophosphate-labeled as well as silver-stained polypeptides from normal RLE cells. The RLE database, which contains both qualitative and quantitative annotations, includes experiments with normal, chemically and oncogene transformed as well as spontaneously transformed cell lines. A total of 2537 [35S]methionine-labeled polypeptides from whole cell lysates (1920 acidic and 617 basic, separated in the first dimension using isoelectric focusing and nonequilibrium pH gradient electrophoresis, respectively) were analyzed and databases constructed using the Elsie 5 gel analysis system. To increase the “viewing window” and hence the usefulness of the RLE database, subcellular fractionation of whole cell preparations was performed and high resolution two-dimensional maps of the individual subcellular components were constructed. Databases representing 1229 cytosolic, 1539 acidic and 674 basic nuclear, 1746 membrane-associated, 415 mitochondrial, 773 in vitro translated and 350 phosphoproteins were established from these maps. The RLE databases contain the Elsie 5 identification number, protein name (if known), molecular weight and pI information, quantitative and spot shape data, and specific information regarding transformation-sensitive, growth-related (exponentially proliferating versus confluent) cell populations as well as those polypeptides modulated by specific growth factors. The RLE databases represent initial efforts toward the establishment of comprehensive databases of rat liver proteins and serve as a vital resource for on-going as well as future studies regarding the regulation of growth and differentiation as well as transformation of RLE cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150121112
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  • 2
    Electronic Resource
    Electronic Resource
    The rat liver epithelial (RLE) cell nuclear protein database (1993)
    Weinheim : Wiley-Blackwell
    Electrophoresis 14 (1993), S. 1199-1215 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The master two-dimensional computer database of rat liver epithelial (RLE) cellular proteins (Wirth et al., Electrophoresis 1991, 12, 931-954) has been expanded to include detailed information concerning 1100 nucleoplasmic (cytosolic) and 850 particulate associated [35S]methionine labeled as well as 215 nucleoplasmic and 269 particulate associated [32P]orthophosphate labeled RLE nuclear polypeptides, respectively. The RLE nuclear protein database developed using the Elsie 5 gel analysis system contains both qualitative and quantitative annotations including polypeptide identification number, protein name (if known), molecular weight and pI information, quantitation and polypeptide spot shape, subcellular location, as well as specific information regarding transformation (chemical and spontaneous) and growth-related characteristics. Microsequencing of polypeptides directly from two-dimensional (2-D) blotted membranes has recently been established in our laboratory and provides a highly efficient and rapid means of polypeptide identification in the absence of specific antibodies. At present the RLE protein database is still in the developmental stage and is continually being updated as additional information is obtained. Nonetheless, it is anticipated that knowledge obtained concerning the identification and characterization of specific transformation and/or growth regulatory proteins in the RLE in vitro cell system will not only have direct application to other rodent and human 2-D protein databases currently under development but will also complement them.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.11501401180
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  • 3
    Electronic Resource
    Electronic Resource
    Computer analysis of two-dimensional gels: Automatic matching (1984)
    Weinheim : Wiley-Blackwell
    Electrophoresis 5 (1984), S. 297-303 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: A program which automatically mathches the spot patterns resolved on two-dimensional gel electrophoretograms is described. The program does not require handmatched, landmark matches for initial alignment of the spot patterns. The matching algorithm is based on a hierarchical nearest neighbor analysis. Starting with the most intense spots in the two films, the program determines if spots are equivalent by attempting to match a list of all nearby spots (a “cluster”) from each film. “Clusters” are considered to be aligned if there is a low probability that the pairing of spots between them is due to a random process. The match is further tested by requiring that secondary clusters (i. e. those clusters that surround the spots matched between the central clusters) can also be aligned. Pairings found by cluster matching are checked for consistency and matches that are out of alignment with the majority of other mathces are eliminated. Finally, the program tries to match the remaining spots by mapping the coordinates of an unmatched spot in one gel into the coordinate system of the other using the matched spots in the cluster as landmarks. The formulas used for the transformation allow for localized rotation and stretching of the coordinate systems. The accuracy and robustness of the program are discussed. If high quality gels are used, the program will find, on average, 95% of the spots that are mathcable between the gels, and requires about 4.3 seconds per mathch. Most of the errors are found at the extreme edges of the gels.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150050510
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