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Common standards for genomics and proteomics
442
News & Comment
Never mind the quality…
Plants to make silk
Comparative genomics intended to reveal important primary conserved sequences in the Xist gene showed instead that it could be the structure of the message and not its content that is important in spreading this X-silencing signal. Xist produces an untranslated transcript in female mammalian cells that is responsible for silencing the X chromosome, thus equalizing gene expression to male cells. Nesterova et al. compared genomic sequences for Xist from four species of vole against those from mouse and human. They found that, although the overall genomic structure is conserved, the primary exonic sequence has been mutated to the same extent as the intron sequences, indicating little selective pressure to retain the coding sequence of the transcript. Regions flanking Xist were found to be ‘saturated’ with repeats, lending further support to the hypothesis that tandemly repeated sequences might act cooperatively to amplify the silencing function of the Xist transcript. [Nesterova, T.B. et al. (2001) Genome Res. 11, 833–849] CH
Common standards for genomics and proteomics A prototype of a common data platform for genomics and proteomics data was recently launched by the Biotechnology Industry Organization, USA. This platform, with Java programming language and extensible markup language (XML) standards, can be used by biotechnology, pharmaceutical or information technology sectors for exchanging genomic and proteomic data. Unlike the Internet, which is guided by standards set by the World-Wide Web consortium, biology-related databases have yet to be standardized. Lack of such standards requires various groups to develop their own tools to analyze and handle data. Depending on the source of datasets, different tools are often necessary. However, if the data exchange is standardized, the information management and analysis will be made simple. This standardization will not only help laboratories, but also smaller companies engaged in life science research and product development. The groundwork for this was laid by bringing several life science and information technology experts under one umbrella, designated the Informatics Interoperable Infrastructure Consortium (I3C), which has over 30 members including Sun Microsystems, IBM and the National Cancer Institute, USA among others. AP http://tig.trends.com
TRENDS in Genetics Vol.17 No.8 August 2001
A group of scientists at the Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany, have succeeded in engineering tobacco and potato plants to produce silk from spiders (Nephilia clavipes). Dragline silk is one of seven kinds of silk made by spiders. It has high tensile strength and elasticity, making it ideal for many industrial and medical purposes. Using microorganisms to produce these silk proteins from synthetic genes is difficult because of constant genetic instability and inefficient translation owing to repetitive sequences in the cDNAs for these genes. Conrad and colleagues designed synthetic cDNAs up to 3600 bp long and were able to express them efficiently in the leaves and tubers of the plants. The recombinant protein is exceptionally heat stable, so the purification is simple and gives good yields. The group is now collaborating with Nexia Biotechnologies Inc. to produce other silk genes, as well as to evaluate the use of fibers for spinning purposes. [Scheller, J. et al. (2001) Nat. Biotechnol. 19, 573–577] AP
Copper transport meets development Knockout of the gene encoding the copper transport protein Ctr1 in mice shows that copper is essential for embryonic development. Embryos lacking ctr1 die 10–12 days after fertilization. These embryos are smaller than normal and have major abnormalities in organ development. Although researchers knew that ctr1 was involved in copper transport in yeast, no one knew how this gene worked in mammals, until now. ‘Since the genetic structure and function of ctr1 is nearly identical in mice and humans, it is very likely that ctr1 is essential for human embryonic development as well’ says Dennie J. Thiele, professor of biological chemistry at the University of Michigan, who directed the study. [Lee, J. et al. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 6842–6847] PL
Immunophenotyping leukemia by microarray Australian scientists have developed a new technique that increases the efficiency and accuracy of immunophenotyping leukemias. The technique relies on the fact different leukemias present different cluster-of-differentiation (CD) antigens on their surface. Previously, only a small number of these antigens could be used for the identification of leukemia types, because the standard technique, flow cytometry, usually only identifies three CDs per assay. To get around this limitation, Christopherson and colleagues developed a microarray incorporating 60 different CD antibodies, and used it to distinguish between normal leukocytes and various leukemias, including chronic lymphocytic leukemia (CLL). Potentially this new development could be used to diagnose leukemia, and it paves the way for the identification of new prognostic markers and antigens to measure minimal residual disease following treatment. [Belov, L. (2001) Cancer Res. 61, 4483–4489] SG
Genetic diversity and conservation efforts Measurements of genetic diversity influence decisions on how to protect endangered or threatened species – because the most genetically diverse populations are assumed to be ‘fitter’, that is where resources are concentrated. However, a recent study questions this argument. Biologists at the University of California, San Diego, and the Louisiana State University measured the genetic diversity of populations of Acanthinucella spirata, a common marine gastropod, on the coast of California. The snail’s genetic diversity was highest in Los Angeles and lowest in the northern part of its range. However, the greatest variation in morphology was in northern populations because of the presence of a shell form not found elsewhere. ‘The difference is apparent to anyone collecting in the field’, says Kaustuv Roy at UCSD, ‘because the new form has shells that are clearly shorter, thicker and broader than the shells found to the south or in fossil deposits. If Acanthinucella spirata was a threatened species, efforts to protect only populations that are genetically diverse would risk eliminating this distinct shell form’. [Hellberg, M.E. et al. (2001) Science 292, 1707–1710] PL
0168–9525/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved.
News & Comment
Never mind the quality…
Plants to make silk
Comparative genomics intended to reveal important primary conserved sequences in the Xist gene showed instead that it could be the structure of the message and not its content that is important in spreading this X-silencing signal. Xist produces an untranslated transcript in female mammalian cells that is responsible for silencing the X chromosome, thus equalizing gene expression to male cells. Nesterova et al. compared genomic sequences for Xist from four species of vole against those from mouse and human. They found that, although the overall genomic structure is conserved, the primary exonic sequence has been mutated to the same extent as the intron sequences, indicating little selective pressure to retain the coding sequence of the transcript. Regions flanking Xist were found to be ‘saturated’ with repeats, lending further support to the hypothesis that tandemly repeated sequences might act cooperatively to amplify the silencing function of the Xist transcript. [Nesterova, T.B. et al. (2001) Genome Res. 11, 833–849] CH
Common standards for genomics and proteomics A prototype of a common data platform for genomics and proteomics data was recently launched by the Biotechnology Industry Organization, USA. This platform, with Java programming language and extensible markup language (XML) standards, can be used by biotechnology, pharmaceutical or information technology sectors for exchanging genomic and proteomic data. Unlike the Internet, which is guided by standards set by the World-Wide Web consortium, biology-related databases have yet to be standardized. Lack of such standards requires various groups to develop their own tools to analyze and handle data. Depending on the source of datasets, different tools are often necessary. However, if the data exchange is standardized, the information management and analysis will be made simple. This standardization will not only help laboratories, but also smaller companies engaged in life science research and product development. The groundwork for this was laid by bringing several life science and information technology experts under one umbrella, designated the Informatics Interoperable Infrastructure Consortium (I3C), which has over 30 members including Sun Microsystems, IBM and the National Cancer Institute, USA among others. AP http://tig.trends.com
TRENDS in Genetics Vol.17 No.8 August 2001
A group of scientists at the Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany, have succeeded in engineering tobacco and potato plants to produce silk from spiders (Nephilia clavipes). Dragline silk is one of seven kinds of silk made by spiders. It has high tensile strength and elasticity, making it ideal for many industrial and medical purposes. Using microorganisms to produce these silk proteins from synthetic genes is difficult because of constant genetic instability and inefficient translation owing to repetitive sequences in the cDNAs for these genes. Conrad and colleagues designed synthetic cDNAs up to 3600 bp long and were able to express them efficiently in the leaves and tubers of the plants. The recombinant protein is exceptionally heat stable, so the purification is simple and gives good yields. The group is now collaborating with Nexia Biotechnologies Inc. to produce other silk genes, as well as to evaluate the use of fibers for spinning purposes. [Scheller, J. et al. (2001) Nat. Biotechnol. 19, 573–577] AP
Copper transport meets development Knockout of the gene encoding the copper transport protein Ctr1 in mice shows that copper is essential for embryonic development. Embryos lacking ctr1 die 10–12 days after fertilization. These embryos are smaller than normal and have major abnormalities in organ development. Although researchers knew that ctr1 was involved in copper transport in yeast, no one knew how this gene worked in mammals, until now. ‘Since the genetic structure and function of ctr1 is nearly identical in mice and humans, it is very likely that ctr1 is essential for human embryonic development as well’ says Dennie J. Thiele, professor of biological chemistry at the University of Michigan, who directed the study. [Lee, J. et al. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 6842–6847] PL
Immunophenotyping leukemia by microarray Australian scientists have developed a new technique that increases the efficiency and accuracy of immunophenotyping leukemias. The technique relies on the fact different leukemias present different cluster-of-differentiation (CD) antigens on their surface. Previously, only a small number of these antigens could be used for the identification of leukemia types, because the standard technique, flow cytometry, usually only identifies three CDs per assay. To get around this limitation, Christopherson and colleagues developed a microarray incorporating 60 different CD antibodies, and used it to distinguish between normal leukocytes and various leukemias, including chronic lymphocytic leukemia (CLL). Potentially this new development could be used to diagnose leukemia, and it paves the way for the identification of new prognostic markers and antigens to measure minimal residual disease following treatment. [Belov, L. (2001) Cancer Res. 61, 4483–4489] SG
Genetic diversity and conservation efforts Measurements of genetic diversity influence decisions on how to protect endangered or threatened species – because the most genetically diverse populations are assumed to be ‘fitter’, that is where resources are concentrated. However, a recent study questions this argument. Biologists at the University of California, San Diego, and the Louisiana State University measured the genetic diversity of populations of Acanthinucella spirata, a common marine gastropod, on the coast of California. The snail’s genetic diversity was highest in Los Angeles and lowest in the northern part of its range. However, the greatest variation in morphology was in northern populations because of the presence of a shell form not found elsewhere. ‘The difference is apparent to anyone collecting in the field’, says Kaustuv Roy at UCSD, ‘because the new form has shells that are clearly shorter, thicker and broader than the shells found to the south or in fossil deposits. If Acanthinucella spirata was a threatened species, efforts to protect only populations that are genetically diverse would risk eliminating this distinct shell form’. [Hellberg, M.E. et al. (2001) Science 292, 1707–1710] PL
0168–9525/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved.