Chapter 6: Molecular and Cellular Biology
Chapter 6: 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 (Chapter 5) and genetics (Chapter 7). Given this very substantial overlap, it is essential to review the sources annotated in these chapters for a more complete understanding of the literature of molecular biology.
- American Society for Cell Biology (ASCB). 8120 Woodmont Ave., Ste. 750, Bethesda, MD 20814-2762. E-Mail: firstname.lastname@example.org. URL: http://www.ascb.org.
Founded in 1960. 9,000 members. Includes scientists with educational or research experience in cell biology or an allied field. Placement service is offered. Publications: ASCB Newsletter, Molecular Biology of the Cell, and CBE—Life Sciences Education. Web site provides membership information and access to the Society’s products and services, meetings, news, publications, public policy, and careers.
- European Molecular Biology Laboratory (EMBL). Meyerhofstrasse 1, D-69117 Heidelberg, Germany. E-Mail: email@example.com. URL: http://www.embl.de.
Founded 1975. 16 member countries. Conducts molecular biological research in a wide array of areas. Their Website lists their outstation locations and provides access to information about each site. Formerly European Laboratory for Molecular Biology.
- International Federation of Cell Biology (IFCB). c/o Dr. W. Elaine Hardman, Treas., Marshall University School of Medicine, 1542 Spring Valley Dr., Huntington, WV 25704-9388. URL: http://www.ifcbiol.org.
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 and Cell Biology International Reports. Formerly: International Society for Cell Biology and International Society for Experimental Cytology.
- RNA Society (RNA). 9650 Rockville Pike, Bethesda, MD 20814-3998. E-Mail: firstname.lastname@example.org. URL: http://www.rnasociety.org.
Founded 1993. 1000 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.
- Society for in Vitro Biology (SIVB). 514 Daniels St., Ste. 411, Raleigh, NC 27605-1317. E-Mail: email@example.com. URL: http://www.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, In Vitro-Plant, and In-Vitro Report. Their Web site provides access to society information and links to educational material.
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Molecular biology information is available extensively on the 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 (currently volume 42, issue D1 or at http://nar.oxfordjournals.org/content/42/D1.toc). The associated 2013 Molecular Biology Database (http://www.oxfordjournals.org/nar/database/a/) lists 1,512 databases, and there are many others as well.
- DDBJ (DNA Data Bank of Japan). Mishima, Japan: National Institute of Genetics, 1986- . http://www.ddbj.nig.ac.jp/.
Collaborates with GenBank and EMBL (both below) to collect nucleotide sequences, which are compiled to form the INSD: International Nucleotide Sequence Database.
- Entrez. Bethesda, MD: National Center for Biotechnology Information, 1990s- . http://www.ncbi.nlm.nih.gov/sites/gquery.
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.”
- European Nucleotide Archive. Heidelberg, Germany: EMBL Data Library, 1980- . http://www.ebi.ac.uk/ena/.
A nucleotide sequence database, created by EMBL in collaboration with GenBank and DDBJ.
- Genbank. Bethesda, MD: National Center for Biotechnology Information, 1982- . http://www.ncbi.nlm.nih.gov/genbank/.
NIH's “annotated collection of all publicly available DNA sequences”. Contained over 165 million sequence records from 260,000 species in July 2013. Accessible via ENTREZ, above.
- Protein Data Bank (PDB). Research Collaboratory for Structural Bioinformatics (RCSB), 1993- . http://www.rcsb.org/pdb/home/home.do.
“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 and by December 2013, there were 96,250 structures. The PDB Web site provides links to many molecular biology databases and other resources. There are three other mirror sites in Europe, Japan, and the US.
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Guides to the Literature
- National Center for Biotechnology Information (NCBI). Bethesda, MD: National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/.
The NCBI is one of the primary resources for molecular biology worldwide. Its Web site provides access to dozens of databases, software products, projects, tutorials and training opportunities, and literature.
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Methods and Techniques
- Guidelines for Human Embryonic Stem Cell Research. Washington, DC: National Academies Press, 2005. 166 p. $34.95 (pa). ISBN 0309096537 (pa); 9780309096539 (pa).
Provides recommendations for safe and ethical research on human stem cells. Also available as a free PDF download at the NAP web site (http://www.nap.edu/catalog.php?record_id=11278).
- OpenHelix. http://www.openhelix.com/. Bellevue, WA: OpenHelix, 2010. Price varies.
"The OpenHelix Search Portal provides a mechanism to search for, and evaluate, online bioinformatics and genomics resources by providing contextual displays of search results." Individual and institutional subscriptions are available, although some tutorials are free.
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Textbooks and Treatises
- DNA Learning Center. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, Dolan DNA Learning Center, 1993- . http://www.dnalc.org/.
"The DNA Learning Center (DNALC) is the world's first science center devoted entirely to genetics education and is an operating unit of Cold Spring Harbor Laboratory, an important center for molecular genetics research." The learning center offers on-site courses but also provides numerous Web sites and tools for educators and students.
- Mount, David W. Bioinformatics: Sequence and Genome Analysis. 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2004. 692 p. $95.00 (pa). ISBN 0879696877; 9780879696870; 0879697121 (pa); 9780879697129 (pa).
This guide is a comprehensive introduction to bioinformatics at both the undergraduate and graduate level. Unlike most bioinformatics texts, it includes information on collecting and storing sequences, not just analyzing them. It also discusses programming using Perl and analysis of genomes and microarrays. The text is augmented by a Web site, http://www.bioinformaticsonline.org/.
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- Bioscience Reports. v. 1- , 1981- . London: Portland Press. Bimonthly. Open Access. ISSN 0144-8463.
"Bioscience Reports publishes articles in the cellular and molecular life sciences." Starting in mid-2012 the journal became fully Open Access; articles are available at http://www.bioscirep.org/bsr/toc.htm.
- BMC Genomics. v. 1- , 2000- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2164.
Publishes "articles on all aspects of genome-scale analysis, functional genomics, and proteomics." Articles available at http://www.biomedcentral.com/bmcgenomics.
- BMC Molecular Biology. v. 1- , 2000- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2199.
Publishes "articles on all aspects of DNA and RNA in a cellular context, encompassing investigations of chromatin, replication, recombination, mutation, repair, transcription, translation and RNA processing and function." Articles available at http://www.biomedcentral.com/bmcmolbiol.