Microbiology and Immunology
Microbiology and Immunology
This chapter includes reference sources useful for microbiology and immunology. Microbiology is "the scientific study of microorganisms (e.g. bacteria, viruses and fungi)." For purposes of this discussion, however, fungi such as yeasts are included with plant biology in Plant Biology. Immunology is the study of immunity, "the state of relative insusceptibility of an animal to infection by disease-producing organisms". (Oxford Dictionary of Biology, 4th ed, 2000) Because microbial systems are convenient and effective for studying a whole range of life processes, there is a significant overlap between this section and the sections covering biochemistry and biophysics, molecular and cell biology, and genetics, respectively. Although medical microbiology and immunology are not comprehensively discussed in this chapter, some basic materials are included that pertain to the study of pathogenic microbiology and diagnostic immunology.
- American Academy of Microbiology (AAM).
Founded in 1955, 1,500 members. Honorific leadership component of American Society for Microbiology concerned with microscopic and submicro-scopic organisms. Encourages exchange of information among members. Publishes Academy News & Views. Web site primarily for membership information.
- American Association of Immunologists (AAI).
Founded 1913, 5,500 members. Scientists engaged in immunological research including aspects of virology, bacteriology, biochemis-try, genetics, and related disciplines. Goals are to advance knowledge of immunology and related disciplines and to facilitate the interchange of information among investigators in various fields. Promotes interaction between laboratory investigators and clinicians; conducts training courses, symposia, workshops, and lectures; bestows awards; compiles statistics. Publishes quarterly AAI Newsletter; periodic Directory; Journal of Immunology. Web site contains membership information, extensive educational material for K12 and the general public.
- American Society for Microbiology (ASM).
Founded in 1899, 42,000 members with 36 local groups. Scientific society of microbiologists promoting advancement of scientific knowledge in order to improve education in microbi-ology. Encou-rages the highest professional and ethical standards and the adoption of sound legislative and regulatory policies affecting the disci-pline of microbiology at all levels. Affiliated with the International Union of Microbiological Societies. Publishes over twenty scientific journals available in alternate formats; other professional pamphlets. Formerly: the Society of American Bacteriologists. Web site includes membership information, news, and educational materials for K12.
- American Type Culture Collection (ATCC).
Founded 1925. 225 staff. A private organization seeking to collect, propagate, preserve, and distribute authentic cultures of microorganisms and genetic materials for reference purposes for use in educational, research, and other scientific and industrial activities. Conducts research, maintains depository for cultures, aids in processing and packaging biohazardous materials, identifies cultures. Publishes ATCC Connections; ATCC Quality Control Methods for Cell Lines, brochures, catalogs (both in print and on the Web), manuals. Web site provides access to catalogs, news, information about the ATCC.
- Canadian Society for Immunology (CSI); Societe Canadienne d'Immunologie (SCI).
Immunologists and other health care professionals and scientists with an interest in immunology. Seeks to advance immunological study, research, and practice. Promotes ongoing professional development of members. Serves as a network linking members; sponsors research and educational programs. Web site contains membership information, links to other societies.
- Committee on the Status of Women in Microbiology (CSWM).
Founded in 1972. A committee of the American Society for Micro-biology who investigate the status of women in microbiology in relation to their male counterparts on the work place and within their professional society. Reports findings and conducts seminars at the annual meeting of ASM. Works toward full and equal opportunity for educational, career, and personal development for male and female microbiologists. Affiliated with the Federation of Organizations for Professional Women. Publishes The Communicator. Web site provides access to The Communicator.
- European Culture Collection Organization (ECCO).
Founded 1981. 61 members. Members of European organizations in 22 countries participating in the maintenance of biological material. Encourages communication and collaborative research among members. Informs members of current developments concerning taxonomy, culture identification, and patent information. Information services: Microbial Information Network Europe- MINE. Publishes European Culture Collections (in English). Web site has limited information
- European Federation of Immunological Societies.
Founded 1975, 16,000 members. Immunological societies from around the world focusing on Europe. Promotes the advancement of research and education in immunology. Web site includes links to databases, organizations of interest to immunologists.
- International Society for Microbial Ecology (ISME).
Founded 1998. 44 members. Multinational. Microbiology societies dealing with microbial ecology. Affiliated with the International Union of Biological Sciences and the International Union of Microbiological Societies. Publishes Microbial Ecology and annual Advances in Microbial Ecology and Symposium Proceedings. Web site includes extensive links to other sites of interest. Formerly: International Committee on Microbial Ecology.
- International Committee on Taxonomy of Viruses (ICTV).
Founded 1966. 120 members. Multinational. A committee of the Virology Division of the International Union of Microbiological Societies. Seeks to develop a standard, internationally accepted system of virus classification and nomenclature. Publishes triennial ICTV Reports. Web site provides extensive information on viral taxonomy.
- International Union of Immunological Societies (IUIS).
Founded 1969, 51 members. National professional societies of basic and applied immunologists. Encourages the orderly development and utilization of the science of immunology; promotes the applica-tion of new developments to clinical and veterinary problems and standardizes reagents and nomenclature; conducts educational symposia and scientific meetings. Publishes The Immunologist. Web site for membership information.
- International Union of Microbiological Societies (IUMS); Union Internationale des SociŽtŽs de Microbiologie.
Founded 1930. 106 members. Multinational. National microbiological societies in 62 countries representing 100,000 microbiologists. Publishes five scientific journals and IUMS Directory. Web site lists affiliated groups.
- Japan Collection of Microorganisms (JCM). RIKEN
A semi-governmental research institute supported by the Science and Technology Agency of Japan. It serves as a culture collection of microorganisms and contributes to domestic, regional, and global improvements of conservation of microbiological resources in cooperation with other culture collections and institutions. Web site provides access to culture catalogs, extensive links.
- Society for Applied Microbiology (SFAM).
Founded 1931, 1,800 members. Multinational. Individuals in-volved in the study of microbiology whose purpose is to promote and advance the study of microbiology, particularly bacteriology, in its application to agriculture, industry, and the environment. Publishes Journal of Applied Microbiology, Letters in Applied Microbiology, and Environmental Microbiology, annual symposium series, and a technical series. Holds three meetings each year. Formerly: Society for Applied Bacteriology. Web site has a particularly nice collection of other links.
- Society for General Microbiology (SGM).
Founded 1945, 5,500 members. Multinational. Works to advance the study of general microbiology. Bestows awards and grants. Affiliated with the International Union of Microbiological Societies, and the Federation of the European Microbiological Societies. Publishes International Journal of Systematic and Evolutionary Microbiology, Journal of General Virology, Micrbiology, and an annual symposium series. Web site contains membership information, news, and links.
- Society for Industrial Microbiology (SIM).
Founded 1948, 2,122 members and 2 local groups. Mycologists, bacteriologists, biologists, chemists, engineers, zoologists, and others interested in biological processes as applied to industrial materials and processes of microorganisms. Affiliated with the American Institute of Biological Sciences. Publishes Journal of Industrial Microbiology and Biotechnology, Membership Directory, and SIM News. Web site includes "KidsÕ Zone", Web picks from SIM News, and career information.
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Classification, Nomenclature, and Systematics
For more information concerning online nomenclature access sites, check the Databases section below. There is also overlap in the Methods section for techniques relevant to classification and systematics.
- American Type Culture Collection.
This non-profit repository collects, propagates, preserves, and distributes microorganisms, cell lines, and molecular biological materials all over the world. ATCC's catalogs of strains and materials are accessible online at the ATCC home page. The catalogs can serve as a convenient information resource on nomenclature and classification. See full annotation in the Associations section, above.
- BIOSIS Register of Bacterial Nomenclature (BRBN). Philadelphia: BIOSIS
The Register is a computerized database of more than 16,400 bacterial names containing information on nomenclature, synonyms, references, etc. It is no longer available as a standalone product. The data from BRBN has been added to the BIOSIS product Index to Organism Names. (Update: This resource is no longer available online.)
- European Culture Collection Organization (ECCO)
Members of European organizations in 22 countries participating in the maintenance of biological material. Encourages communication and collaborative research among members. Informs members of current developments concerning taxonomy, culture identification, and patent information. Information services: Microbial Information Network Europe- MINE. Publishes European Culture Collections (in English). Web site has limited information.
- Euzeby, J. P. List of Bacterial Names with Standing in Nomenclature. Toulouse, France: Centre universitaire de calcul de Toulouse, 1998- .
This site provides access to alphabetical files of nomenclature of bacteria cited in the Approved Lists of Bacterial Names.
- Index Virum: Catalogue of ICTV Approved Virus Names. Cornelia Buchen-Osmond, compiler. Canberra, Australia: Bioinformatics Group, Australian National University.
The gateway to the descriptions of viruses with links to electron micrographs and genomic sequences, on the Universal Virus Database at the Australian National University in Canberra. Information on more than 4,500 viruses, based on the 6th report of the ICTV (International Commission on Taxonomy of Viruses). For more details about the database itself, see "Databases" below.
- Japan Collection of Microorganisms. Saitama, Japan: Japan Collection of Microorganisms.
This culture collection of microorganisms was founded in 1980 at RIKEN (the Institute of Physical and Chemical Research), a semi-governmental research institute in Japan. JCM supplies authentic microorganisms to researchers in life sciences and biotechnology from over 3,700 strains of bacteria, over 2,300 strains of fungi, and over 130 strains of archaea. In the JCM On-line Catalogue Database, it is possible to search for microorganisms with key words; strain data is linked to other data, such as history, taxonomic information, references, and cultivation conditions with medium formulations. Also available in a printed catalog (7th ed. in 1999, ISSN 0913-0098, $42.00).
- National Center for Biotechnology Information
See main annotation in Genetics and Biotechnology chapter. In addition to its other resources, NCBI provides a Taxonomy Homepage with direct links to some of the organisms commonly used in molecular research projects, e.g. E. coli.
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Databases relevant to the Biochemistry and Biophysics, Molecular and Cellular Biology, and Genetics will likely be useful for microbiology and virology, also.
- CGSC: E. coli Genetic Stock Center. New Haven, CT: Yale University, 1998- .
The CGSC maintains a database of E. coli genetic information, including genotypes and reference information for the strains in the CGSC collections, gene names, properties, and linkage map, gene product information, and information on specific mutations. The public version of the database includes this information and is accessible in three forms: the CGSC DB_WebServer, the CGSC Gopher, and guest logins to CGSC Sybase database. The home page also provides links to other pertinent Web sites.
- EcoCyc: Encyclopedia of E. Coli Genes and Metabolism. Menlo Park, CA: Pangea Systems.
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli. The long term goal is to describe the molecular catalog of the E. coli cell as well as the functions of each of it molecular parts, and to facilitate a system-level understanding of E. coli. An account is required to access the database, but non-commercial use by individuals at academic and governmental institutions is free.
- Escherichia coli Database Collection (ECDC)
Provides the complete genome map for E.coli. (Release 28, March 1997 with complete sequence, 28 May, 1999).
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- Microbial Strain Data Network (MSDN). 63 Wostenholm Road, Sheffield, England, UK. Phone: +44 114 258 3397. Fax: +44 114 258 3402. E-mail: firstname.lastname@example.org.
This non-profit organization provides specialized information and communications services for life scientists worldwide. There is an international Committee of Management and a Secretariat based in Sheffield, UK. MSDN is sponsored by the United Nations Environment Programme (UNEP) and other organizations. MSDN provides a unique package of databases and bulletin boards covering microbiology, biotechnology, and biodiversity. There is information on microbial strains, culture collections from several nations (Russia, Slovenia, Czech Republic, India, Bulgaria, Argentina, UK), biotechnology publications and meetings, and environmental matters. The scope includes cell lines, hybridomas, molecular probes and recombinant materials as well as microorganisms. Access to MSDN is free through public data networks and the Web. The MSDN Directory of Information Resources is a database indexing microbial cultures of about 60 laboratories. (Update: This resource is no longer available online.)
- World Data Centre for Microorganisms (WDCM)
This site provides a comprehensive, worldwide directory of culture collections, databases on microbes and cell lines, and the gateway to biodiversity, molecular biology and genome projects.
Guides to Internet Resources
- All the Virology on the WWW. Society for Applied Microbiology, 1995- .
"All the Virology on the WWW seeks to be the best single site for Virology information on the Internet. We have collected all the virology related Web sites that might be of interest to our fellow virologists, and others interested in learning more about viruses." While no Web directory can be truly comprehensive, this one comes close. There are links to plant viruses, HIV and AIDS sites, biological warfare, and all the usual taxonomic information plus much more.
- Buchen-Osmond, Cornelia and M. J. Dallwitz. ICTVdB: Universal Virus Database. Canberra, Australia: Bioinformatics Group, Australian National University.
This database was developed under the auspices of the International Committee on Taxonomy of Viruses (ICTV) and is based on the 6th report of the ICTV. Index Virum, below, is one of its components, along with projects for Plant Viruses Online, a picture gallery, and a virus identification data exchange.
- Deutsche Sammlung von Mikroorganismenund Zellkulturen GmbH (DSMZ), German Collection of Microorganisms and Cell.
The DSMZ "is an independent, non-profit organization dedicated to the acquisition, characterization and identification, preservation and distribution of Bacteria, Archaea, fungi, plasmids, phages, human and animal cell lines, plant cell cultures and plant viruses."
- E. coli Index
"These pages contain a comprehensive guide to information relating to the model organism Escherichia coli." The site contains information on E. coli databases, researchers, societies, news, protocols, and much more. The site was created by Dr. Gavin H. Thomas at the Department of Molecular Biology and Biotechnology, University of Sheffield, UK. (Update: This resource is no longer available online.)
Billed as listing "the best sites that list the sites." This "Microbiology & Infectious Diseases" page lists primarily medical sites.
- MedWebplus. Decatur, GA: y-DNA, Inc., 1998- .
Provides links to focused information about E.coli: encyclopedias, genetics, microbiology and links to the Genetic Stock Center (CGSC) at Yale University, an organism index, an organism database collection (ECDC), EcoCyc, an Encyclopedia of E. coli Genes and Metabolism, and the E. coli Genome Center at the University of Wisconsin-Madison.
- Molecular Microbiology Jump Station. Highveld.com, 1996- .
A comprehensive collection of links for microbiologists, covering all areas of basic and applied microbiology. The site is sponsored by several corporations.
The global electronic reporting system for outbreaks of emerging infectious diseases and toxins, open to all sources; a program of the International Society for Infectious Diseases
- Stanford Genomic Resources
The genomic collections contains links to other Stanford databases, for example, the Saccharomyces Genome Database Project (SGC); genome centers, published datasets, software resources, research departments, and mirrored sites.
- WFCC-MIRCEN, World Data Centre for Microorganisms
"Provides a comprehensive directory of culture collections, databases on microbes and cell lines, and the gateway to biodiversity, molecular biology and genome projects."
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Two publishers that should be especially acknowledged are the American Society for Microbiology in Washington, DC and the Cold Spring Harbor Laboratory Press in Plainview, NY. Both of these publishers issue authoritative laboratory methods manuals and handbooks of importance to microbiologists, immunologists, and molecular biologists. Consult the biochemistry, genetics, and molecular biology chapters for other handbooks relevant to microbiology and immunology.
- IMI Descriptions of Fungi and Bacteria. 1964- . Kew, Surrey, England: CAB International Mycological Institute. 4 sets/yr. ISSN 0009-9716.
Title varies, Commonwealth Mycological Institute Descriptions of Fungi and Bacteria; continuation of CMI Descriptions of Pathogenic Fungi and Bacteria. Provides standardized, illustrated descriptions of organisms including disease caused, geographical distribution, physiological specialization, transmission, references to key literature. There is an electronic catalog of the Bacteria and Fungi published to date which is available by subscription only. It incorporates full text and high quality images. It is accompanied by a fully searchable word index with indices to organism name, host organism and geographical location.
Methods and Techniques
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 Chapters 5, "Biochemistry and Biophysics," and 7, "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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