Using
the Biological Literature
Web Resources
|
Using
the Biological Literature |
Molecular and Cellular Biology
Molecular biology is defined as "The study of the structure and function of large molecules associated with living organisms, in particular proteins and the nucleic acids DNA and RNA" (Oxford Dictionary of Biology, 4th ed., 2000), while cellular biology is the study of cells, "the structural and functional unit of most living organisms" (Oxford Dictionary of Biology, 4th ed., 2000). Molecular biology is among the most rapidly growing fields within biology with recent success stories such as the sequencing of the entire human genome (reported in Science and Nature). Molecular biology is unusual in that the major information source for molecular biologists is not journal articles, but public databases such as GenBank, PDB, and DDBJ (annotated below in the database section). This is one reason why there are relatively fewer handbooks and treatises for molecular biology than there are for other biological subjects. There is a natural affinity between this chapter and the ones discussing reference materials for Biochemistry and Genetics. Given this very substantial overlap, it is essential to review the sources annotated in these sections for a more complete understanding of the literature of molecular biology.
Abstracts and Indexes
PubMed is the most important index for molecular biology. See the entry in Indexes and Abstracts, for full annotation.
American Society for Biochemistry and Molecular Biology (ASBMB). 9650 Rockville Pike, Bethesda, MD 20814, USA. Phone: (301)530-7145, Fax: (301) 571-1824, E-mail: asbmb@asbmb.faseb.org.
Founded 1906, 9,300 members. Biochemists and molecular biologists who have conducted and published original investigations in biological chemistry and/or molecular biology. Publishes Journal of Biological Chemistry. Formerly American Society of Biological Chemists. Web site primarily for society information..
American Society for Cell Biology (ASCB). 8120 Woodmont Ave., Suite 750, Bethesda, MD 20814-2755. Phone: (301)347-9300; Fax: (301) 347-9310. E-mail: ascbinfo@ascb.org.
Founded in 1960. 9,000 members. Includes scientists with educational or re-search experience in cell biology or an allied field. Placement service is offered. Publications: ASCB Newsletter, Molecular Biology of the Cell. Web site provides membership information and access to the Society's products and services, meetings, news, publications, public policy, and careers.
European Laboratory for Molecular Biology (EMBL) . Meyerhofstr. 1, D-69117 Heidelberg, Germany. Phone: 49 6221 3870; Fax: 49 6221 387306
Founded 1975. 16 member countries. Conducts molecular biological research in the following areas: cellular biology, differentiation, biological structures, genetics, biochemical instrumentation, and biocomputing. Their Web site lists their outstation locations and provides access to information about each site.
European Molecular Biology Organization (EMBO). Postfach 10 22 40, 69012 Heidelberg, Germany. Phone: 49 6221 383031; Fax: 49 6221 384879. E-Mail: embo@embl-heidelberg.de
Promotes the advancement of molecular biology in Europe and neighboring countries, administers programs funded by the Europe-an Molecular Biology Conference consisting of fellowships and courses. The organization holds courses and workshops, and presents an annual award. Publications: EMBO Journal and EMBO Reports. They hold periodic general assemblies and an annual symposium. Their Web site provides links to other European organizations, members' home pages, international university addresses, etc.
International Cell Research Organization (ICRO); Organisation Internationale de Recherche sur la Cellule. c/o UNESCO-House, SC/LSC, 1 rue Miollis, F-75732 Paris, France. Phone: 33 45688378; Fax: 33 45685818; E-Mail: icro@unesco.org
Founded 1962. 400 members. Scientists, researchers, and laboratories in 75 countries encour-age and facilitate the exchange of information on basic cell biology research. The organization organizes international training courses in microbiology, biotechnology, and cell and molecular biology; they compile statistics. Web site provides information on training courses and has a limited number of other useful links.
International Federation of Cell Biology (IFCB). c/o Dept. Of Cellular & Structural Biology, University of Texas Health Science Center, 7703 Floyd Curl Dr., San Antonio, TX 78229-USA. Phone: (210) 567-3817; Fax: (210) 567-3803
Founded 1972. 21 member associations. National and regional associations of cell biologists promoting international cooperation among scientists working in cell biology and related fields, and contributing to the advancement of cell biology in all of its branches. Publishes Cell Biology International. Formerly International Society for Cell Biology and International Society for Experimental Cytology.
International Union of Biochemistry and Molecular Biology (IUBMB). 18 Leyden Crescent, Saskatoon, Canada S7J 2S4-. Phone: (306) 374-1304, Fax: (#06) 955-1314, E-mail: fvella@sk.sympatico.ca.
Founded 1955. 65 members. National academies, research councils, or biochemical societies; associated bodies represent national biochemical and molecular biology societies; special members are organizations representing industrial and other groups. Publishes Biochemical Education, Biochemical Nomenclature and Related Documents, BioFactors, Journal of Biotechnology and Applied Biochemistry, and Trends in Biochemical Sciences. Web site primarily for society information.
RNA Society (RNAS). 9650 Rockville Pike, Bethesda, MD 20814-3998. Phone: (301) 530-7120; Fax: (301) 530-7049. E-Mail: rna@faseb.org
Founded 1993. 800 members. Professionals working in molecular, evolutionary, and structural biology, biochemistry, biomedical sciences, chemistry, genetics, virology, and related disciplines with an interest in the structure and functions of ribonucleic acid (RNA). Publishes RNA. Web site provides membership and conference information, and a limited list of related links.
Society for In Vitro Biology (SIVB). 9315 Largo Dr., Ste. 255, Largo, MD 20774. Phone: (301)324-5054; Fax: (301)324-5057; E-Mail: sivb@sivb.org
Founded 1946. 2,500 members. Professional society of individuals using mammalian,
invertebrate, plant cell tissue, and organ cultures as research tools in chemistry,
physics, radiation, medicine, physiology, nutrition, and cytogenetics. Publications: In
Vitro-Animal and In Vitro-Plant. Their Web site provides access to Society
information and links to the full text of Society publications.
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Molecular biology information is available extensively on the World Wide Web. Many of the databases discussed here provide access to gene or protein sequences. Each time a researcher sequences a gene or protein, he or she is expected not only to publish the sequence in a research journal, but also to submit the sequence to a sequence database. Sometimes journals will not accept articles until the sequences have appeared in a database, which is one of the few cases in which journals will accept data previously published elsewhere. The annual Nucleic Acids Research Database Issue is the best source for information on the major databases. The 2001 Database issue (volume 29, issue 1) lists 95 databases, and there are many others as well.
DDBJ (DNA Data Bank of Japan). Mishima, Japan: National Institute of Genetics. 1986-
Collaborates with GenBank and EMBL to collect nucleotide sequences.
EMBL (European Molecular Biology Laboratory). 1980- . Heidelberg, Germany: EMBL Data Library.
A nucleotide sequence database, created in collaboration with GenBank and DDBJ.
Entrez "is a search and retrieval system that integrates information from databases at NCBI. These databases include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE, through PubMed."
GenBank. 1982- . Bethesda, MD: National Center for Biotechnology Information.
NIH's "annotated collection of all publicly available DNA sequences". Contained over 7 million sequence records from 47,000 species in June 2000.
Protein Data Bank (PDB). 1993- . Research Collaboratory for Structural Bioinformatics (RCSB).
"The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR." (from the Web page). It was established at Brookhaven National Laboratories in 1971 and contained just 7 structures; by June 2000, there were over 12,500 structures. The PDB Web site provides links to many molecular biology databases and other resources.
Gannon, Pamela M. Cell and Molecular Biology Online: An Informational Resource for Cell and Molecular Biologists.
There are links to sites for research, communication, perspectives on careers, educational resources, and various other items for information.
European Bioinformatics Institute (EBI)
This center for research and services in bioinformatics manages databases of biological data including nucleic acids, protein sequences and macromolecular structures, with access to databases such as SRS, EMBL, SWISS-PROT, InterPro, etc.
Presented by the Pharmaceutical Research and Manufacturers of America and co-sponsored by the American Institute of Biological Sciences (AIBS). This site offers access to links for genome news, legislation, regulation, issues, bioinformatics databases, and much more. There is also a Genomics Lexicon. While the site is sponsored by a manufacturer's association, there is no detectable "spin" on the information presented. The site would be most useful for researchers and students, but there are a number of resources that would be of interest to the general public.
Human Genome Project. The Department of Energy.
A great deal of information on the Human Genome Project, including educational materials, information on genetics and medicine, and a collection of ethical, legal, and social issues.
LiMB (Listing of Molecular Biology Databases)
LiMB contains information about the contents and details of maintenance of databases related to molecular biology. Link is not working at the present time.
Links to sites for bioinformatics resources, nucleic acid analysis, protein analysis, genomics, software, educational resources, laboratory resources, protocols and methods, reference tools, and supplies are listed.
Molecular Biology Info & Search Engines. CMS Molecular Biology Resource.
Index of resources include Molecular Biology-Biotechnology Specific Search Servers, Biotechnology Searching Users Guides, Other Molecular Biology Compiled Internet Resources such as the List of WWW Biological Servers and the Molecular Biology Databases on the Internet.
National Biotechnology Information Facility (NBIF)
This Web site is divided into three main sections: Educational Resources, Internet Resources, and Products and Services. The Internet Resources list a wide assortment of compendiums and resource links for grant information; biotechnology products, careers and training; biotechnology-related science and resources; gene browser, other biotech centers; a database for standards and recommendations for naming and measuring in chemistry; Molecular Biology Gateway and other molecular biology links; National Library of Medicine, to name a few.
The National Center for Biotechnology Information (NCBI)
THE place to go for information on molecular biology, genomics, and biotechnology. This Web site provides links to information for researchers, ranging from news briefs and online tutorials to information on the latest tools for data mining. The site also includes links to the numerous federally-funded genomics projects, GenBank and other molecular biology databases, and much more.
The National Human Genome Research Institute (NHGRI)
A division of the National Institute of Health that is charged with directing the Human Genome Project. Its Web site contains a wealth of information on genetics and genome projects, including links to other sites, the Glossary of Genetic Terms (see Chapter 7, "Genetics"), downloadable handouts dealing with genetics and techniques used in the Human Genome Project, and news about the project.
UK Human Genome Mapping Project Resource Centre (HGMP-RC)
This site provides access to all the latest databases and bioinformatics tools for genetic and genomic research. Registration for use of these tools is free for academics.
Research Collaboratory for Structural Bioinformatics (RCSB)
This is a non-profit consortium dedicated to improving our understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. This group from Rutgers, the San Diego Supercomputer Center, and the Biotechnology Division of the National Institutes of Standards and Technology provide databases, software and software standards, education, and community service.
There are links to several model organism Web sites, concentrating on genome and genetics databases for Dictyostelium, zebrafish, and livestock genomes. This guide is less comprehensive than the WWW Virtual Library Model Organisms guide.
Smith, Christopher M. CMS Molecular Biology Resource. San Diego, CA: Computational Biology Group, San Diego Supercomputer Center.
"A compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Molecular Modeling" (from the home page). It is organized by function.
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Attwood, Teresa K. and David J. Parry-Smith. Introduction to Bioinformatics. Essex, England: Longman, 1999. (Cell and Molecular Biology in Action Series). 218 p. ISBN 0582327881.
This text on bioinformatics discusses the application of computers in biological science and the analysis of biological sequence data--essential tools in molecular biology. It is linked to a Web site and introduces key databases, tools and resources, and outlines pitfalls of methods.
Ibelgaufts, Horst. COPE: Cytokines Online Pathfinder Encyclopaedia. Version 4.0 (August 1999).
This online handbook was composed by a researcher at the University of Munich in an effort to help people cope with the number and actions of various cytokines. Arranged alphabetically, each cytokine is defined by function; there are over 6,650 hyperlinked entries. This site appears to be more comprehensive than the Cytokine Handbook although it has not received editorial review.
There are innumerable excellent books, series, and Web sites containing information on protocols for molecular biology. This selected list contains a great deal of redundancy in order to provide access to various levels and currency of techniques. It may be necessary and most effective to peruse several examples, concluding with protocols that have been updated in an online database. Also, refer to the sections on Biochemistry and Biophysics and Genetics, and see the section "Methods, Protocols and Software" listed in the WWW Virtual Library of Cell Biology.
Biological Procedures Online. Faculty of Science, University of Waterloo, 1998- . ISSN 1480-9222.
Science Med Central publishes four, peer reviewed electronic technique journals at this site: medicine, biology, chemistry, and physics. Archival issues of BPO are available on CD-ROM.
Gannon, Pamela. Cell and Molecular Biology Online. Concord, MA: Cell Biology Online, 1996- .
The "Methods and Protocols" section of this directory lists various online resources, primarily from specific research laboratories, for cell and molecular biology research protocols. Some of topics addressed are antibody design, cell biology, DNA sequencing, microscopy, molecular biology, PCR Jump Station, and vector database.
DoubleTwist: Protocol Online--Your Lab's Reference Book. DoubleTwist, Inc., 1999- .
This keyword-searchable site provides protocols and discussion forums for molecular biology, cell biology, and immunology; a BioMail News Group and BioResearch Chat. The "Quick Access Table" organizes the protocols by discipline and topic, aiding retrieval.
Strom, Mark. Molecular Biology Protocols. US Dept. of Commerce (NOAA, NMFS, NWFSC).
This Web site provides access to molecular biology protocols such as DNA Purification Techniques, DNA Transformation/Library Preparation, Southern/Northern Blotting, DNA Sequencing, Oligonucleotides, PCR and Related Methods, RNA Methods, Protein Electrophoresis, Protein Purification, Autoradiography Tips, Safety, and other references.
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