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| 4. | Ärkin, A P; Youvan, D C " Optimizing nucleotide mixtures to encode specific subsets of amino acids for semi-random mutagenesis (Journal Article) Biotechnology (N.Y.), 10 (3), pp. 297–300, 1992. @article{pmid1368102, title = {Optimizing nucleotide mixtures to encode specific subsets of amino acids for semi-random mutagenesis}, author = {A P Ärkin and D C " Youvan}, year = {1992}, date = {1992-03-01}, journal = {Biotechnology (N.Y.)}, volume = {10}, number = {3}, pages = {297--300}, abstract = {In random mutagenesis, synthesis of an NNN triplet (i.e. equiprobable A, C, G, and T at each of the three positions in the codon) could be considered an optimal nucleotide mixture because all 20 amino acids are encoded. NN(G,C) might be considered a slightly more intelligent "dope" because the entire set of amino acids is still encoded using only half as many codons. Using a general algorithm described herein, it is possible to formulate more complex doping schemes which encode specific subsets of the twenty amino acids, excluding others from the mix. Maximizing the equiprobability of amino acid residues contributing to such a subset is suggested as an optimal basis for performing semi-random mutagenesis. This is important for reducing the nucleotide complexity of combinatorial cassettes so that "sequence space" can be searched more efficiently. Computer programs have been developed to provide tables of optimized dopes compatible with automated DNA synthesizers.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In random mutagenesis, synthesis of an NNN triplet (i.e. equiprobable A, C, G, and T at each of the three positions in the codon) could be considered an optimal nucleotide mixture because all 20 amino acids are encoded. NN(G,C) might be considered a slightly more intelligent "dope" because the entire set of amino acids is still encoded using only half as many codons. Using a general algorithm described herein, it is possible to formulate more complex doping schemes which encode specific subsets of the twenty amino acids, excluding others from the mix. Maximizing the equiprobability of amino acid residues contributing to such a subset is suggested as an optimal basis for performing semi-random mutagenesis. This is important for reducing the nucleotide complexity of combinatorial cassettes so that "sequence space" can be searched more efficiently. Computer programs have been developed to provide tables of optimized dopes compatible with automated DNA synthesizers. |
| 3. | An algorithm for protein engineering: simulations of recursive ensemble mutagenesis (Journal Article) Proc. Natl. Acad. Sci. U.S.A., 89 (16), pp. 7811–7815, 1992. @article{pmid1502200, title = {An algorithm for protein engineering: simulations of recursive ensemble mutagenesis}, year = {1992}, date = {1992-00-01}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, volume = {89}, number = {16}, pages = {7811--7815}, abstract = {An algorithm for protein engineering, termed recursive ensemble mutagenesis, has been developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Starting from partially randomized "wild-type" DNA sequences, a highly parallel search of sequence space for peptides fitting an experimenter's criteria is performed. Each iteration uses information gained from the previous rounds to search the space more efficiently. Simulations of the technique indicate that, under a variety of conditions, the algorithm can rapidly produce a diverse population of proteins fitting specific criteria. In the experimental analog, genetic selection or screening applied during recursive ensemble mutagenesis should force the evolution of an ensemble of mutants to a targeted cluster of related phenotypes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An algorithm for protein engineering, termed recursive ensemble mutagenesis, has been developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Starting from partially randomized "wild-type" DNA sequences, a highly parallel search of sequence space for peptides fitting an experimenter's criteria is performed. Each iteration uses information gained from the previous rounds to search the space more efficiently. Simulations of the technique indicate that, under a variety of conditions, the algorithm can rapidly produce a diverse population of proteins fitting specific criteria. In the experimental analog, genetic selection or screening applied during recursive ensemble mutagenesis should force the evolution of an ensemble of mutants to a targeted cluster of related phenotypes. |
| 2. | Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra (Journal Article) Biotechnology (N.Y.), 8 (8), pp. 746–749, 1990. @article{pmid1366901, title = {Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra}, year = {1990}, date = {1990-00-01}, journal = {Biotechnology (N.Y.)}, volume = {8}, number = {8}, pages = {746--749}, abstract = {Digital imaging spectroscopy has been used to obtain the grayscale spectrum of colored bacterial colonies directly from petri dishes. Up to 500 individual colony spectra can be simultaneously recorded and processed from a single plate. Spectra can be obtained in the visible to near infrared region (400nm-900nm) with 10nm resolution. Instrument response is normalized through run-time radiometric calibration such that each grayscale spectrum can be converted to the ground-state absorption spectrum of the colony. In this study, mutants of the photosynthetic bacterium Rhodobacter capsulatus have been differentiated by the absorption spectra of their pigment-protein complexes. This imaging technique is applicable to chromogenic systems in which colony and/or media color (e.g. indicator plates) provides a quantitative indicator of gene expression.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Digital imaging spectroscopy has been used to obtain the grayscale spectrum of colored bacterial colonies directly from petri dishes. Up to 500 individual colony spectra can be simultaneously recorded and processed from a single plate. Spectra can be obtained in the visible to near infrared region (400nm-900nm) with 10nm resolution. Instrument response is normalized through run-time radiometric calibration such that each grayscale spectrum can be converted to the ground-state absorption spectrum of the colony. In this study, mutants of the photosynthetic bacterium Rhodobacter capsulatus have been differentiated by the absorption spectra of their pigment-protein complexes. This imaging technique is applicable to chromogenic systems in which colony and/or media color (e.g. indicator plates) provides a quantitative indicator of gene expression. |
| 1. | Daliang Ning Mengting Yuan, Linwei Wu Ya Zhang Xue Guo Xishu Zhou Yunfeng Yang Adam Arkin Mary Firestone P K; Zhou, Jizhong A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming (Journal Article) 0000. @article{ning2020quantitative, title = {A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming}, author = {Daliang Ning , Mengting Yuan , Linwei Wu , Ya Zhang , Xue Guo, , Xishu Zhou , Yunfeng Yang , Adam P. Arkin , Mary K. Firestone , and Jizhong Zhou}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } |
