20001
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Jia HP, Schutte BC, Schudy A, Linzmeier R, Guthmiller JM, Johnson GK, Tack BF, Mitros JP, Rosenthal A, Ganz T, McCray PB. Discovery of new human beta-defensins using a genomics-based approach. Gene 2001; 263:211-8. [PMID: 11223260 DOI: 10.1016/s0378-1119(00)00569-2] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Epithelial beta-defensins are broad-spectrum cationic antimicrobial peptides that also act as chemokines for adaptive immune cells. In the human genome, all known defensin genes cluster to a <1 Mb region of chromosome 8p22-p23. To identify new defensin genes, the DNA sequence from a contig of large-insert genomic clones from the region containing human beta-defensin-2 (HBD-2) was analyzed for the presence of defensin genes. This sequence survey identified a novel beta-defensin, termed HBD-3. The HBD-3 gene contains two exons, is located 13 kb upstream from the HBD-2 gene, and it is transcribed in the same direction. A partial HBD-3 cDNA clone was amplified from cDNA derived from IL-1beta induced fetal lung tissue. The cDNA sequence encodes for a 67 amino acid peptide that is approximately 43% identical to HBD-2 and shares the beta-defensin six cysteine motif. By PCR analysis of two commercial cDNA panels, HBD-3 expression was detected in adult heart, skeletal muscle, placenta and in fetal thymus. From RT-PCR experiments, HBD-3 expression was observed in skin, esophagus, gingival keratinocytes, placenta and trachea. Furthermore, in fetal lung explants and gingival keratinocytes, HBD-3 mRNA expression was induced by IL-1beta. Additional sequence analysis identified the HE2 (human epididymis secretory protein) gene 17 kb upstream from the HBD-3 gene. One splice variant of this gene (HE2beta1) encodes a beta-defensin consensus cysteine motif, suggesting it represents a defensin gene product. HE2beta1 mRNA expression was detected in gingival keratinocytes and bronchial epithelia using RT-PCR analysis. The discovery of these novel beta-defensin genes may allow further understanding of the role of defensins in host immunity at mucosal surfaces.
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Affiliation(s)
- H P Jia
- Department of Pediatrics, University of Iowa College of Medicine, Iowa City, IA 52242, USA
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20002
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20003
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Morel CM. Present and future control of malaria. Science 2001; 291:435-6. [PMID: 11228137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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20004
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Breithaupt H. Reaching out. Scientists met in Heidelberg and discussed methods of restoring public trust in science. EMBO Rep 2001; 2:12-3. [PMID: 11252715 PMCID: PMC1083812 DOI: 10.1093/embo-reports/kve016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20005
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Abstract
A response to Whither genomics by Andrew W Murray, Genome Biology 2000, 1 :comment003.1-003.6
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20006
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Affiliation(s)
- S B Hedges
- Department of Biology, Institute of Molecular Evolutionary Genetics, and Astrobiology Research Center, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA.
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20007
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Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim SK. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2001; 98:218-23. [PMID: 11134517 PMCID: PMC14571 DOI: 10.1073/pnas.98.1.218] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have constructed DNA microarrays containing 17,871 genes, representing about 94% of the 18,967 genes currently annotated in the Caenorhabditis elegans genome. These DNA microarrays can be used as a tool to define a nearly complete molecular profile of gene expression levels associated with different developmental stages, growth conditions, or worm strains. Here, we used these full-genome DNA microarrays to show the relative levels of gene expression for nearly every gene during development, from eggs through adulthood. These expression data can help reveal when a gene may act during development. We also compared gene expression in males to that of hermaphrodites and found a total of 2,171 sex-regulated genes (P < 0.05). The sex-regulated genes provide a global view of the differences between the sexes at a molecular level and identify many genes likely to be involved in sex-specific differentiation and behavior.
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Affiliation(s)
- M Jiang
- Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA
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20008
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Plume SK. A healthcare systems leadership perspective on organizational challenges posed by genomics. Front Health Serv Manage 2001; 17:29-33; discussion 39-44. [PMID: 11299703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Affiliation(s)
- S K Plume
- Dartmouth Medical School, Hanover, New Hampshire, USA
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20009
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Affiliation(s)
- T K Sawyer
- ARIAD Pharmaceuticals, Cambridge, MA, USA.
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20010
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Abstract
A report on the thirteenth international Caenorhabditis elegans meeting, University of California, Los Angeles, USA, 22-26 June 2001.
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Affiliation(s)
- A G Fraser
- Wellcome/CRC Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
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20011
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Abstract
The blood-brain barrier (BBB) is formed by the brain microvascular endothelium, and the unique transport properties of the BBB are derived from tissue-specific gene expression within this cell. The current studies developed a gene microarray approach specific for the BBB by purifying the initial mRNA from isolated rat brain capillaries to generate tester cDNA. A polymerase chain reaction-based subtraction cloning method, suppression subtractive hybridization (SSH), was used, and the BBB cDNA was subtracted with driver cDNA produced from mRNA isolated from rat liver and kidney. Screening 5% of the subtracted tester cDNA resulted in identification of 50 gene products and more than 80% of those were selectively expressed at the BBB; these included novel gene sequences not found in existing databases, ESTs, and known genes that were not known to be selectively expressed at the BBB. Genes in the latter category include tissue plasminogen activator, insulin-like growth factor-2, PC-3 gene product, myelin basic protein, regulator of G protein signaling 5, utrophin, IkappaB, connexin-45, the class I major histocompatibility complex, the rat homologue of the transcription factors hbrm or EZH1, and organic anion transporting polypeptide type 2. Knowledge of tissue-specific gene expression at the BBB could lead to new targets for brain drug delivery and could elucidate mechanisms of brain pathology at the microvascular level.
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Affiliation(s)
- J Y Li
- Department of Medicine, UCLA School of Medicine, Los Angeles, California 90095-1682, USA
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20012
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Rai AK. The information revolution reaches pharmaceuticals: balancing innovation incentives, cost, and access in the post- genomics era. Univ Ill Law Rev 2001; 2001:173-210. [PMID: 16493845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Recent developments in genomics--the science that lies at the intersection of information technology and biotechnology--have ushered in a new era of pharmaceutical innovation. Professor Rai advances a theory of pharmaceutical development and allocation that takes account of these recent developments from the perspective of both patent law and health law--that is, from both the production side and the consumption side. She argues that genomics has the potential to make reforms that increase access to prescription drugs not only more necessary as a matter of equity but also more feasible as a matter of innovation policy. On the production end, so long as patent rights in upstream genomics research do not create transaction cost bottlenecks, genomics should, in the not-too-distant future, yield some reduction in drug research and development costs. If these costs reductions are realized, it may be possible to scale back certain features of the pharmaceutical patent regime that cause patent protection for pharmaceuticals to be significantly stronger than patent protection for other innovation. On the consumption side, genomics should make drug therapy even more important in treating illness. This reality, coupled with empirical data revealing that cost and access problems are particularly severe for those individuals who are not able to secure favorable price discrimination through insurance, militates in favor of government subsidies for such insurance. As contrasted with patent buyouts, the approach favored by many patent scholars, subsidies would take account of, and indeed capitalize on, the institutional realities of health care consumption. These subsidies should, however, be linked to insurance regulation that works to channel innovation in a cost-effective direction by requiring coverage of drugs that provide significant benefit relative to their cost.
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Affiliation(s)
- A K Rai
- University of San Diego Law School, USA
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20013
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Abstract
The power of genomics in transforming the biotechnology industry will be evident in all areas of drug discovery and development. This will be particularly true in safety evaluation, where the field will be forced to adapt to new schemes of e-R&D and e-business in general. Toxicologists will be required to create information-rich, real-time systems that can be used for decisions in the earliest phases of discovery and throughout development. The largest growth area in specific product types will be those that can move genomics information from the laboratory to the clinic the fastest.
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Affiliation(s)
- D E Johnson
- ddplatform LLC, Emeryville, California, USA.
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20014
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20015
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Affiliation(s)
- B Graham
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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20016
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Forman DS, Diner BC. Emerging new biotechnologies and the patent attorneys' struggle to best protect them. Trends Biotechnol 2001; 19:4-5. [PMID: 11193732 DOI: 10.1016/s0167-7799(00)01525-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- D S Forman
- Finnegan, Henderson, Farabow, Garrett & Dunner, L.L.P., Washington, DC 20005-3315, USA.
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20017
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Mizuno M, Yoshida J. [Perspectives on postgenome medicine: Gene therapy for brain tumors]. Nihon Rinsho 2001; 59:76-80. [PMID: 11197866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Recent development of therapeutic modalities in neurosurgery has brought about dramatic improvement for prognosis of brain tumors. Nevertheless, malignant glioma is one of the most formidable neoplasms in humans. According to a report by the Committee of Brain Tumor Registry of Japan, five-year relative survival rate of malignant gliomas is less than 10%. Malignant gliomas grow aggressively infiltrating into the surrounding normal brain tissue. So that total surgical resection is impossible. The tumors respond to radiation and chemotherapy, however, the efficiency has sustained transiently. The advert of new strategies for the treatment of malignant gliomas has long been awaited. We have developed a cytokine gene therapy for malignant glioma since about 10 years ago. Here, we introduce both suicide gene therapies and immune gene therapies including our case(IFN-beta gene therapy).
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Affiliation(s)
- M Mizuno
- Department of Molecular Neurosurgery, Nagoya University, Graduate School of Medicine
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20018
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Abstract
OBJECTIVE To review the advances in clinically useful molecular biological techniques and their applications in clinical practice as presented at the Ninth Annual William Beaumont Hospital DNA Symposium. DATA SOURCES The 10 manuscripts submitted were reviewed and their major findings were compared with literature on the same topic. STUDY SELECTION One manuscript reviewed the development of pharmacogenetics, 3 described analytic approaches to detect aneuploidy or cancer, 1 described transcription factor E2F-1 increase during apoptosis, 2 reported on genetic and pharmacologic factors that influence platelet aggregation, 2 described molecular methods for detecting long QT syndrome or mycobacteria, and 1 reported a modification in collection of buccal DNA. DATA SYNTHESIS Genomic and proteomic approaches to develop clinically useful assays have been successful. Aneuploidy can be easily detected by comparative genomic hybridization, which does not require cell culture like cytogenetics. Mutations have been characterized for a variety of hereditary cancer syndromes, 2 inherited long QT syndromes, and thromboembolism. PlA1 and PlA2 polymorphisms in platelets are associated with a difference in aggregation inhibition by estrogen, another example of genotypic pharmacogenetics. Protein expression differences may define colorectal cancer stage and explain apoptotic signal transduction. Mycobacterial detection by nucleic acid amplification and simplified buccal DNA collection demonstrate cost-effective strategies. CONCLUSION The working draft of the Human Genome Project is completed and the number of clinically useful molecular pathologic techniques and assays will expand as additional disease-associated mutations are defined. Expanded use of database software for genomic and proteomic screening should increase the efficiency of clinical useful assay development.
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Affiliation(s)
- F L Kiechle
- Department of Clinical Pathology, William Beaumont Hospital, Royal Oak, Mich 48073-6769, USA.
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20019
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Affiliation(s)
- S R McCouch
- Plant Breeding Department, 418 Bradfield Hall, Cornell University, Ithaca, New York 14853-1901, USA.
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20020
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Kakizoe T. [Ethical issues in relation to genetic analysis research]. Nihon Rinsho 2001; 59:185-7. [PMID: 11197853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
On April 2000, the so-called Millennium project which was launched by Japanese Government has started. Genetic research is one of the important subject in this project. Since there has been no official guideline for ethical issues in relation to genetic analysis research, Ministry of Health and Welfare arranged a special committee to prepare such a guideline. The process and key points of this guideline which has been published on April 2000 by Ministry of Health and Welfare was described.
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20021
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Hagiwara K, Saijo Y. [Perspectives on postgenome medicine: Gene therapy for lung cancer]. Nihon Rinsho 2001; 59:81-4. [PMID: 11197867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The gene therapy or the immunotherapy targeting specific molecule(s) have just introduced into the clinical field in Japan. The first gene therapy for the human lung cancer is underway; an adenoviral vector harboring wild type p53 gene is intratumorally injected. A cancer immunotherapy using the Cyclophilin B derived peptide is in the phase I clinical trial. As the next generation cancer therapies, a variety of strategies are planned and investigated at the laboratory level. They range from the usage of a new viral vector to the introduction of genes with specific biological functions into the cells. In this article, by reviewing the possible approach, an ideal combination of the future remedies is discussed.
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Affiliation(s)
- K Hagiwara
- Respiratory Medicine and Translational Research Clinic, Tohoku University Hospital
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20022
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Affiliation(s)
- G A Petsko
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA.
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20023
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Titus K. Reclassifying cancer, guided by genomics. CAP Today 2001; 15:1, 14-6, 18 passim. [PMID: 11317550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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20024
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Boenning DA, Kalfoglou AL. The future of clinical research: the role of genomics, informatics, and evidence-based medicine. J Investig Med 2001; 49:10-1. [PMID: 11217137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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20025
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Abstract
A report from HGM2001, the sixth annual International Human Genome Meeting organized by The Human Genome Organisation (HUGO), Edinburgh, UK, 19-22 April 2001.
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Affiliation(s)
- C A Semple
- Department of Medical Sciences, Molecular Medicine Centre, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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20026
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Abstract
Nuclear pore complexes, the conduits for information exchange between the nucleus and cytoplasm, appear broadly similar in eukaryotes from yeast to human. Precisely how nuclear pore complexes regulate macromolecular and ionic traffic remains unknown, but recent advances in the identification and characterization of components of the complex by proteomics and genomics have provided new insights.
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Affiliation(s)
- S A Adam
- Department of Cell and Molecular Biology, Northwestern University Medical School, Chicago, IL 60611, USA.
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20027
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20028
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Abstract
MOTIVATION Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for high-throughput analysis of large biological sequence sets and the genome analysis server associated with it. RESULTS The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual assignment of gene products to a number of functional and structural categories, (iv) extensive hyperlinked protein reports, and (v) advanced DNA and protein viewers. The system is easily extensible and allows to include custom methods, databases, and categories with minimal or no programming effort. PEDANT is actively used as a collaborative environment to support several on-going genome sequencing projects. The main purpose of the PEDANT genome database is to quickly disseminate well-organized information on completely sequenced and unfinished genomes. It currently includes 80 genomic sequences and in many cases serves as the only source of exhaustive information on a given genome. The database also acts as a vehicle for a number of research projects in bioinformatics. Using SQL queries, it is possible to correlate a large variety of pre-computed properties of gene products encoded in complete genomes with each other and compare them with data sets of special scientific interest. In particular, the availability of structural predictions for over 300 000 genomic proteins makes PEDANT the most extensive structural genomics resource available on the web.
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Affiliation(s)
- D Frishman
- GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany.
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20029
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Abstract
Those studying the genus Brassica will be among the early beneficiaries of the now-completed Arabidopsis sequence. The remarkable morphological diversity of Brassica species and their relatives offers valuable opportunities to advance our knowledge of plant growth and development, and our understanding of rapid phenotypic evolution.
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Affiliation(s)
- A H Paterson
- Center for Applied Genetic Technologies, Riverbend Research Lab, University of Georgia, Athens, GA 30602, USA.
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20030
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Abstract
Chemical genomics requires continued advances in combinatorial chemistry, protein biochemistry, miniaturization, automation, and global profiling technology. Although innovation in each of these areas can come from individual academic labs, it will require large, well-funded centers to integrate these components and freely distribute both data and reagents.
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Affiliation(s)
- G MacBeath
- Center for Genomics Research, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
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20031
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Abstract
Rapid accumulation of biological data from novel high throughput technologies characteristic of genomic and proteomic research as well as advances in more traditional biological disciplines are leading to wider use of detailed and complex computational models of cell behavior. These models address a variety of dynamic intracellular processes ranging from interactions within a gene regulation network to intracellular and intercellular signal transduction. This review focuses on the current trends in computation cell biology, particularly emphasizing the role of experimental validation. The recent successes and future challenges facing computational cell biology are also discussed.
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Affiliation(s)
- A Levchenko
- The Whitaker Institute for Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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20032
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Peerenboom E. German genomics effort. Nat Biotechnol 2001; 19:6. [PMID: 11135521 DOI: 10.1038/83554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20033
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Affiliation(s)
- Michael G. Kahn
- Affiliations of the author: Fellow, merican College of Medical Informatics; Vice President, Fast Track Systems, San Mateo, California
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20034
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Dosne Pasqualini C. [The human genome]. Medicina (B Aires) 2001; 61:243-6. [PMID: 11374152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
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20035
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Brenna JT. Natural intramolecular isotope measurements in physiology: elements of the case for an effort toward high-precision position-specific isotope analysis. Rapid Commun Mass Spectrom 2001; 15:1252-1262. [PMID: 11466780 DOI: 10.1002/rcm.325] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Chemical information available in organisms can be categorized into three major domains, macromolecular, small molecules, and isotope ratios. Information about physiological state is commonly obtained by qualitative and quantitative analysis in the macromolecular and small molecule domains. Genomics and proteomics are emerging approaches to analysis of macromolecules, and both areas yield definitive information on present physiological state. There is relatively little record of past physiological states of the individual available in these domains. Natural isotopic variability, particularly on an intramolecular level, is likely to retain more physiological history. Because of ubiquitous isotopic fractionation, every stereochemically unique position in every molecule has an isotope ratio that reflects the processes of synthesis and degradation. This fact highlights a vast amount of organismal chemical information that is essentially unstudied. Isotope measurements can be classified according to the chemical complexity of the analyte into bulk, compound-specific, and position-specific or intramolecular levels. Recent advances in analysis of isotope ratios are transforming natural science, and particularly answering questions about ecosystems using bulk methods; however, they have had relatively little impact on physiology. This may be because the vast complexities of physiological questions demand very selective information available in position-specific isotope analysis (PSIA). The relatively few high-precision PSIA studies, based on isotope ratio mass spectrometry (IRMS), have revealed intramolecular isotope ratio differences in pivotal physiological compounds including amino acids, glucose, glycerol, acetate, fatty acids, and purines. The majority of these analyses have been accomplished by laborious offline methods; however, recent advances in instrumentation presage rapid PSIA that will be necessary to attack real physiological problems. Gas-phase pyrolysis has been shown to be an effective method to determine (13)C/(12)C at high precision for molecular fragments, and technologies to extend C-based PSIA to N and other organic elements are emerging. Two related efforts are warranted, (a) development of rapid, convenient, and sensitive methods for high-precision PSIA, a necessary precursor to (b) a concerted investigation into the relationship of metabolic state to intramolecular isotope ratio. Inherent in this latter goal is the need to identify long-lived molecules in long-lived cells that retain a record of early isotopic conditions, as has been shown for post-mortem human neuronal DNA. Using known metabolic precursor-product relationships between intramolecular positions, future studies of physiological isotope fractionation should reveal the relationship of diet and environment to observed isotope ratio. This science of isotope physiology, or simply isotopics, should add an important tool for elucidation of early factors that effect later health, probably the most difficult class of biomedical issues.
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Affiliation(s)
- J T Brenna
- Division of Nutritional Sciences, Savage Hall, Cornell University, Ithaca, New York 14853, USA.
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20036
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Pearl FM, Martin N, Bray JE, Buchan DW, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA. A rapid classification protocol for the CATH Domain Database to support structural genomics. Nucleic Acids Res 2001; 29:223-7. [PMID: 11125098 PMCID: PMC29791 DOI: 10.1093/nar/29.1.223] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In order to support the structural genomic initiatives, both by rapidly classifying newly determined structures and by suggesting suitable targets for structure determination, we have recently developed several new protocols for classifying structures in the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath). These aim to increase the speed of classification of new structures using fast algorithms for structure comparison (GRATH) and to improve the sensitivity in recognising distant structural relatives by incorporating sequence information from relatives in the genomes (DomainFinder). In order to ensure the integrity of the database given the expected increase in data, the CATH Protein Family Database (CATH-PFDB), which currently includes 25,320 structural domains and a further 160,000 sequence relatives has now been installed in a relational ORACLE database. This was essential for developing more rigorous validation procedures and for allowing efficient querying of the database, particularly for genome analysis. The associated Dictionary of Homologous Superfamilies [Bray,J.E., Todd,A.E., Pearl,F.M.G., Thornton,J.M. and Orengo,C.A. (2000) Protein Eng., 13, 153-165], which provides multiple structural alignments and functional information to assist in assigning new relatives, has also been expanded recently and now includes information for 903 homologous superfamilies. In order to improve coverage of known structures, preliminary classification levels are now provided for new structures at interim stages in the classification protocol. Since a large proportion of new structures can be rapidly classified using profile-based sequence analysis [e.g. PSI-BLAST: Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402], this provides preliminary classification for easily recognisable homologues, which in the latest release of CATH (version 1.7) represented nearly three-quarters of the non-identical structures.
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Affiliation(s)
- F M Pearl
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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20037
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Abstract
A report on the talks presented at the Cold Spring Harbor 2000 Meeting on Arabidopsis Genomics, New York, 7-10 December, 2000.
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Affiliation(s)
- Pablo D Rabinowicz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. E-mail:
| | - Mary E Byrne
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. E-mail:
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20038
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Takei Y, Sawada T, Sameshima S, Nagasako K. [Post-genome challenges against inflammatory bowel diseases]. Nihon Rinsho 2001; 59:180-4. [PMID: 11197852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Advancement of genome analysis might give great impact to the treatment of inflammatory bowel diseases(IBD). IBD patients are treated by sulfadrugs, steroids and anti-immune drugs. For difficult cases, leukocytapheresis, beclomethasone dipropionate, anti-TNF therapy, anti-LTB4 therapy and other new methods are applied. Developing epoch-making drugs will be achieved by finding new molecular targets. Histologic identification of dysplasia is important in the surveillance of long-standing ulcerative colitis. The molecular diagnosis is required for the distinction of dysplasia from the regenerative inflammatory changes. P53 immunostaining have been proved useful. Various molecular targets will be taken into discussion as additional procedures. Recent genome analysis have revealed some genetic factors contribute to pathogenesis of IBD, which are HLA, IL4, MUC3, IBD1 locus, IBD2 locus and so on. More information about genes concerning IBD will be provided by analyzing dense SNP map using DNA tip. They will open the way to the tailored therapy.
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20039
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Imai E, Takenaka M, Ito T, Isaka Y, Moriyama T, Hori M. [Gene therapy and tissue engineering in nephrology and renal transplantation]. Nihon Rinsho 2001; 59:65-71. [PMID: 11197863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Human genome project will be completed in 2003 and we will soon obtain the information of the whole DNA sequence of the human genome. This should affect the therapy of progressive renal diseases since we have no effective remedy to cure the renal diseases. Gene therapy, renal engineering and generation of new drug can be achieved by using the information of human genome. In this context, we described our recent endeavors concerning the gene therapy of transplant kidney, seeking the renal stem cells and reprogramming factors, and exploring genes related to renal fibrosis. Completion of bioinformatics, can facilitate the above post-genome project.
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Affiliation(s)
- E Imai
- Department of Internal Medicine and Therapeutics, Osaka University Graduate School of Medicine
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20040
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Abstract
The fungi are the most economically important plant pathogens and continue to be the focus of extensive research with a wide variety of methodologies. Enhancements in microscopy techniques have increased our ability to visualize the intimate interaction of fungi and their host plants. Improving methods allow pharmacological inhibition and genetic dissection of the determinants of fungal pathogenicity in a gene-by-gene approach. Identification and analysis of genes differentially transcribed in ways pertinent to pathogenicity continues to be a frequent research approach. Genome-wide analysis is gaining favor in biological research and fungal plant pathogens are no exception. Several industrial research groups are exploring fungal plant pathogenesis based on genomic sequence data and genome-wide mutagenesis. In March 2001 the first publicly available complete genome of a filamentous fungus (Neurospora crassa) was released. N. crassa is of course a saprophyte and there is no complete sequence available for a plant pathogenic fungus in public databases. However, freely accessible entire genome sequences for both plant pathogenic fungi and their hosts are on the horizon. Sequence availability promises to revolutionize the rate at which data relevant to disease processes will be accrued. In this review we describe approaches currently applied to the study of plant pathogenic fungi and explore developments of potential future benefit with existing technologies not yet applied to this group of important organisms.
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Affiliation(s)
- S E Gold
- Department of Plant Pathology, University of Georgia, Athens, Georgia 30602-7274, USA.
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20041
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Dierssen M, Martí E, Pucharcós C, Fotaki V, Altafaj X, Casas K, Solans A, Arbonés ML, Fillat C, Estivill X. Functional genomics of Down syndrome: a multidisciplinary approach. J Neural Transm Suppl 2001:131-48. [PMID: 11771739 DOI: 10.1007/978-3-7091-6262-0_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The availability of the DNA sequence of human chromosome 21 (HSA21) is a landmark contribution that will have an immediate impact on the study of the role of specific genes to Down syndrome (DS). Trisomy 21, full or partial, is a major cause of mental retardation and other phenotypic abnormalities, collectively known as Down syndrome (DS), a disorder affecting 1 in 700 births. The identification of genes on HSA21 and the elucidation of the function of the proteins encoded by these genes have been a major challenge for the human genome project and for research in DS. Over 100 of the estimated 300-500 genes of HSA21 have been identified, but the function of most remains largely unknown. It is believed that the overexpression of an unknown number of HSA21 genes is directly or indirectly responsible for the mental retardation and the other clinical features of DS. For this reason, HSA21 genes that are expressed in tissues affected in DS patients are of special interest.
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Affiliation(s)
- M Dierssen
- Down Syndrome Research Group, Medical and Molecular Genetics Center-IRO, Hospital Duran i Reynals, L'Hospitalet de Llobregat, Barcelona, Spain
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20042
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Shiojima S, Tsujimoto G. [A model for clinical study based on genome science--trials in disorders of the immune system and allergies]. Nihon Rinsho 2001; 59:53-8. [PMID: 11197861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Disorders of the immune system, such as allergies, have multi-factorial etiologies that include both genetic and environmental components. The recent advances in genome science have facilitated two strategies for studying the genetic basis of disease: (1) systematic analysis of gene expression profiles and (2) comprehensive analysis of gene variations, such as polymorphisms. Here, we describe a unique research institute, Genox Research Inc., that can relate the clinical profile of a patient to genotyping and molecular profiling. Systematic gene expression analyses using differential display have been performed to explore genes related to allergy, and revealed 93 differentially expressed candidate genes in T-cells. Also, a single nucleotide polymorphism(SNP) analysis project has been designed to mine disease-related and/or drug-response-related genes involved in allergic disorders using biochip technologies. As exemplified above, clinical studies based on these applications of genome science would be of considerable value in clarifying our understanding of multi-gene disorders.
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Affiliation(s)
- S Shiojima
- Department of Molecular Cell Pharmacology, National Children's Medical Research Center
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20043
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Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P, Lengieza C, Lew-Smith JE, Tillberg M, Garrels JI. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res 2001; 29:75-9. [PMID: 11125054 PMCID: PMC29810 DOI: 10.1093/nar/29.1.75] [Citation(s) in RCA: 245] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The BioKnowledge Library is a relational database and web site (http://www.proteome.com) composed of protein-specific information collected from the scientific literature. Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins and other relevant data. This report describes four species-specific volumes of the BioKnowledge Library, concerned with the model organisms Saccharomyces cerevisiae (YPD), Schizosaccharomyces pombe (PombePD) and Caenorhabditis elegans (WormPD), and with the fungal pathogen Candida albicans (CalPD). Protein Reports of each species are unified in format, easily searchable and extensively cross-referenced between species. The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins involved in disease.
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Affiliation(s)
- M C Costanzo
- Proteome, Inc., 100 Cummings Center, Suite 435M, Beverly, MA 01915, USA.
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20044
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Posey KL, Jones LB, Cerda R, Bajaj M, Huynh T, Hardin PE, Hardin SH. Survey of transcripts in the adult Drosophila brain. Genome Biol 2001; 2:RESEARCH0008. [PMID: 11276425 PMCID: PMC30707 DOI: 10.1186/gb-2001-2-3-research0008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2000] [Revised: 01/22/2001] [Accepted: 01/24/2001] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Classic methods of identifying genes involved in neural function include the laborious process of behavioral screening of mutagenized flies and then rescreening candidate lines for pleiotropic effects due to developmental defects. To accelerate the molecular analysis of brain function in Drosophila we constructed a cDNA library exclusively from adult brains. Our goal was to begin to develop a catalog of transcripts expressed in the brain. These transcripts are expected to contain a higher proportion of clones that are involved in neuronal function. RESULTS The library contains approximately 6.75 million independent clones. From our initial characterization of 271 randomly chosen clones, we expect that approximately 11% of the clones in this library will identify transcribed sequences not found in expressed sequence tag databases. Furthermore, 15% of these 271 clones are not among the 13,601 predicted Drosophila genes. CONCLUSIONS Our analysis of this unique Drosophila brain library suggests that the number of genes may be underestimated in this organism. This work complements the Drosophila genome project by providing information that facilitates more complete annotation of the genomic sequence. This library should be a useful resource that will help in determining how basic brain functions operate at the molecular level.
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Affiliation(s)
- Karen L Posey
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
| | - Leslie B Jones
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
| | - Rosalinda Cerda
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
| | - Monica Bajaj
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
| | - Thao Huynh
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
| | - Paul E Hardin
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
| | - Susan H Hardin
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
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20045
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Yasuda K. [Perspectives on postgenome medicine: Gene therapy for diabetes mellitus]. Nihon Rinsho 2001; 59:157-61. [PMID: 11197848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Several topics in diabetes research and practice in the coming 'post-genomic era' are described. 1) Insulin-producing pancreatic beta cells are a plausible target of gene therapy for type 1 diabetes mellitus. Functional genomics will reveal the mechanism of beta cell growth and regeneration. Attempts are being made to differentiate non-beta cells(including ES cells) into insulin-producing cells in vitro or in vivo. 2) Very recently, an intron variation in calpain 10 gene was found to be associated with type 2 diabetes, which confirmed the importance of SNPs in common diseases. More and more SNPs related to type 2 diabetes will be discovered and, in combination with pharmacogenomics, 'personalized medicine' based on SNP information of the individuals will hopefully be achieved.
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Affiliation(s)
- K Yasuda
- Department of Metabolic Disorder, Research Institute, International Medical Center of Japan
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20046
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Banerjee-Basu S, Sink DW, Baxevanis AD. The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information. Nucleic Acids Res 2001; 29:291-3. [PMID: 11125116 PMCID: PMC29851 DOI: 10.1093/nar/29.1.291] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2000] [Accepted: 10/25/2000] [Indexed: 11/15/2022] Open
Abstract
The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 3.0 contains 795 full-length homeodomain-containing sequences, 32 experimentally-derived structures and 143 homeo-box loci implicated in human genetic disorders. Entries are fully hyperlinked to facilitate easy retrieval of the original records from source databases. A simple search engine with a graphical user interface is provided to query the component databases and assemble customized data sets. A new feature for this release is the addition of DNA recognition sites for all human homeodomain proteins described in the literature. The Homeodomain Resource is freely available through the World Wide Web at http://genome.nhgri.nih.gov/homeodomain.
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Affiliation(s)
- S Banerjee-Basu
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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20047
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Abstract
In the post-genomics era, molecular evolutionary geneticists have come to possess the molecular, statistical, and computational tools for estimating the relative importance of selection and random genetic drift in virtually any gene in almost any organism. We have examined single-nucleotide polymorphisms (SNPs) and nucleotide divergence across a region of approximately 1 kb in the promoter of the human tumor necrosis factor alpha (TNF-alpha) gene. TNF-alpha, which plays an important role in lymphocyte biology and in the pathogenesis of infectious and autoimmune diseases, is tightly regulated at the level of transcription through sequence-specific binding of transcription factors to cognate binding sites in a relatively small region of the 5' non-coding region of the gene. Analysis of the promoter region in 207 human chromosomes revealed nine SNPs, none of which were located in regions known to be important in transcriptional activation. Comparison with one promoter sequence in each of seven species of primates revealed 162 nucleotide sites occupied by a monomorphic nucleotide in the human sample but occupied by a different nucleotide in at least one of the primate sequences (a 'fixed human difference'). The fixed human differences were found outside the regions known to be important in transcriptional activation, and their large number suggests that they might be effectively neutral (Ns<<1). With regard to the human SNPs, although the hypothesis Ns approximately 0 cannot be rejected, the sample configurations suggest that the substitutions might be mildly deleterious. We emphasize the analytical insight to be gained from interspecific comparisons: through the interspecific comparisons, 3.1% of the total sequence information yielded 94.7% of the variable nucleotides. This combined approach, using interspecific comparisons and human polymorphism together with data from functional analyses, provides valuable insights into the evolutionary history and regulation of a key gene in the human immune response.
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Affiliation(s)
- A E Goldfeld
- The Center for Blood Research and Department of Medicine, Harvard Medical School, 800 Huntington Avenue, Boston, MA 02115, USA
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20048
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DNA alley. A map of Montgomery County, Md. Time 2000; 156:114-5. [PMID: 11187842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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20049
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Abstract
2000 was a banner year for scientists deciphering the "book of life"; this year saw the completion of the genome sequences of complex organisms ranging from the fruit fly to the human. Science marks the production of this torrent of genome data as the Breakthrough of 2000; it might well be the breakthrough of the decade, perhaps even the century, for all its potential to alter our view of the world we live in.
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20050
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