Nucleotide identification

And I am afraid that the American counterpart journal, Science, has suffered a similar deterioration. It, too, has abandoned multidisciplinary interest, but in a different direction. They are now dedicated to chromosomes, and nucleotide identification, and are totally captivated by the attention paid to, and the apparent importance of, the human genome project. There is where you automatically go to publish, now, if you have unraveled some DNA sequence from the Latvian cockroach. 

Many databases use their own protein or nucleotide identification system. Therefore it is difficult to map the information obtained on the database-specific identifier from one database to another. Every Harvester page therefore contains database identifiers from various sources as shown in Table II. Among the most frequently used IDs are ... 

A potentially general method of identifying a probe is, first, to purify a protein of interest by chromatography (qv) or electrophoresis. Then a partial amino acid sequence of the protein is deterrnined chemically (see Amino acids). The amino acid sequence is used to predict likely short DNA sequences which direct the synthesis of the protein sequence. Because the genetic code uses redundant codons to direct the synthesis of some amino acids, the predicted probe is unlikely to be unique. The least redundant sequence of 25—30 nucleotides is synthesized chemically as a mixture. The mixed probe is used to screen the Hbrary and the identified clones further screened, either with another probe reverse-translated from the known amino acid sequence or by directly sequencing the clones. Whereas not all recombinant clones encode the protein of interest, reiterative screening allows identification of the correct DNA recombinant. 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Hijikata M, Ohta Y, Mishiro S. Identification of a single nucleotide polymorphism in the MxA gene promoter (G/T at nt -88] correlated with the response of hepatitis C patients to interferon. Intervirology 2000 43[2] 124—127. 

Verma R et al. Proteasomal proteomics identification of nucleotide-sensitive pro-teasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol Biol Cell 2000 11 3425-3439. 

Ohnishi Y, Tanaka T, Yamada R, Sue-matsu K, Minami M, Fujii K, Hoki N, Kodama K, Nagata S, Hayashi T, Ki-noshita N, Sato H, Sato H, Kuzuya T, Takeda H, Hori M, Nakamura Y. Identification of 187 single nucleotide polymorphisms (SNPs) among 41 candidate genes for ischemic heart disease in the Japanese population. Hum Genet 2000 106 288-292. 

Wang DG, Fan JB, Siao CJ et al. Large-scale identification, mapping, and geno-typing of single-nucleotide polymorphisms in the human genome. Science 1998 280 1077-1082. 

Anthony, T. G., Fabian, J. R., Kimball, S. R., and Jefferson, L. S. (2000). Identification of domains within the epsilon-subunit of the translation initiation factor eIF2B that are necessary for guanine nucleotide exchange activity and eIF2B holoprotein formation. Biochim. Biophys. Acta 1492, 56—62. 

Gomez, E., and Pavitt, G. D. (2000). Identification of domains and residues within the epsilon subunit of eukaryotic translation initiation factor 2B (eIF2Bepsilon) required for guanine nucleotide exchange reveals a novel activation function promoted by eIF2B complex formation. Mol. Cell Biol. 20, 3965—3976. 

Yang, W., and i linnebuscli, A. G. (1996). Identification of a regulatory subcomplex in the guanine nucleotide exchange factor eIF2B that mediates inhibition by phosphorylated eIF2. Mol. Cell Biol. 16, 6603—6616. 

Wang, D.G., et al., "Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome," Science 280, 1077-1082 (1998). 

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