In the past decade, researchers have witnessed an explosive growth in the amount of information available to them at internet-based sites. In this day and age, researchers requiring supplementary information to a particular aspect of a research technique can do so by using a search engine or browsing through the internet, but this is more often than not a timeconsuming and frustrating endeavour where one ends up having to deal with thousands of hits that are not relevant to the initial query.
This section lists outstanding resources for cell and molecular biology research that complement and extend the usefulness of the research protocols described in the previous sections. We have found the sites listed here to be comprehensible, useful, and generally well run and consequently we recommend them as good starting points for any researcher rummaging around for information. Nonetheless, this compilation is intended solely as a valuable aid to the research techniques described throughout this book rather than a stand-alone guide of laboratory procedures or an exhaustive listing of Web resources.
II. INTERNET RESOURCES FOR CELL BIOLOGISTS
A. Cells and Tissue Culture
1. The World Federation for Culture Collections (wFcc)
The WFCC is a federation concerned with the collection, authentication, maintenance, and distribution of cultures of microorganisms and cultured cells. The WFCC, through the World Data Center for Microorganisms (WDCM), developed an international database on culture resources worldwide. This data resource is now maintained at the National Institute of Genetics (NIG, Japan) and has records of nearly 469 culture collections from 62 countries (http:// wdcm.nig.ac.jp/hpcc.html). The records contain data on the organisation, management, services, and scientific interests of the collections. Each of these records is linked to a second record containing the list of species held.
2. European Collection of Cell Cultures (ECACC)
In addition to being a bank of cell lines and hybridomas, ECACC also provides an EBV immortalisation service to establish lymphoblastoid cell lines from patients and their families with genetic and chromosomal abnormalities. This site boasts a full 25,000 cell lines and approximately 420 hybridomas.
3. RIKEN Cell Bank
The RIKEN cell bank has been organized as a unique, nonprofit public collection for deposit, isolation, preservation, and distribution of cultured animal cell lines produced by the life science research community. It houses a large number of cell lines as well as hybridomas established by its staff.
4. American Type Culture Collection (ATCC)
The ATCC Cell Biology Collection (http://www. atcc.org/SearchCatalogs/CellBiology.cfm) includes a very comprehensive and diverse cell bank, consisting of 4000 cell lines from more than 150 different species. It holds 950 cancer cell lines (including 700 human cancer cell lines) and over 1200 hybridomas for the production of monoclonal antibodies, as well as a variety of special collections.
5. The Mammalian Genetics Unit at Harwell (MGU)
Home page of an integrated campus for mouse genetics research with facilities for molecular genetics, genomics, mutagenesis, transgenesis, and bioinformatics. The MGU has a large collection of mouse stocks containing over 200 mutant, chromosome abnormality, and inbred lines. The stocks are maintained for experimental and breeding purposes and are available to investigators on request.
6. Stem Cell Information at NIH
A Web site provided by the National Institutes of Health (NIH) hosting information and links on stem cells.
7. The Stem Cell Database (SCD)
A joint project of the laboratories of Ihor R. Lemischka (Princeton University) and G. Christian Overton (University of Pennsylvania), the SCD contains data on the molecular phenotype of hematopoietic stem cells.
1. All the Virology on the WWW
A site that collects many virology-related Web sites of interest for virologists and others interested in learning more about viruses.
2. The Universal Virus Database (ICTVdB)
The directory of ICTVdB is an index of viruses, a list of approved virus names linked to virus descriptions coded from information in "Virus Taxonomy: The Seventh Report of the International Committee on Taxonomy of Viruses" by van Regenmortel et al. (eds.), Academic Press (2000), and includes updates subsequently approved by ICTV. It also incorporates the plant virus database VIDEdB and is illustrated with EM pictures, diagrams, and images of symptoms contributed by virologists around the world.
1. The Antibody Resource Page
A site that provides a broad collection of links to companies that sell antibodies or antibody-related products on the internet. Furthermore, it also presents sections containing links to online educational resources about antibodies and databases and software with immunological relevance.
AbCam features an extensive compilation of antibody information and advice for locating specific antibodies with a large selection of antibodies available online and a search engine to other antibody companies. In addition, AbCam provides a conference calendar, a database of conferences that have been submitted by research scientists.
A site that provides information on antibody structure and sequence as well as other useful links.
4. Information Resources for Adjuvants and Antibody Production
A very useful Web page for any researcher interested in antibody production. A rather comprehensive set of references is an added value.
5. Developmental Studies Hybridoma Bank (DSHB), at the University of Iowa
The DSHB supplies investigators with low-cost monoclonal antibodies useful for studies in developmental and cell biology. They may be ordered as tissue culture supernatants, ascites, or partially purified immunoglobulins. Certain selected hybridomas are also available as frozen or growing cells.
6. IMGT, the International ImMunoGeneTics Information System
An integrated information system specializing in immunoglobulins, T-cell receptors, major histocompatibility complex, and related proteins of the immune system of human and other vertebrate species. This site contains standardized and annotated data on proteins of the immune system, which include databases of nucleotide and protein sequences, gene maps, genetic polymorphisms, specificities, 2D and 3D structures, and a collection of interactive tools.
D. Flow Cytometry
1. Flow Cytometry Core Laboratory at the University of Florida
One of the core laboratories that compose the Interdisciplinary Center for Biotechnology Research at the University of Florida in Gainesville, Florida. This Web page provides a wealth of information and links related to flow cytometry. Included is the database for antibody cross-reactivity (htt-p://www.keithbahjat .com/abcxr/), a repository for flow cytometry software, and protocols for FACS-based analysis.
2. Flow Cytometry on the Web
A collection of links for those interested in flow cytometry. A good starting point if one is looking for software, protocols, instrumentation, protocols, or any flow cytometry-related subject.
An immunohistochemistry database query system to help determine the best panel of immune stains that will aid in the differential diagnosis of tumors. It lists antibodies that can differentiate between tumors entered by the user (e.g., lung adenocarcinoma vs breast carcinoma), ranks the antibodies in terms of their ability to differentiate between tumors, and provides instant references to journal articles describing the reactivity of these antibodies.
2. IHC World
A Web site dedicated to everything related to immunohistochemistry. Provides comprehensive and updated information regarding tissue processing, antigen retrieval, antibody selections, antibody protocol database, image analysis, protocol links, books, and journals.
3. DAKOCytomation's Immunochemical Staining Methods Online Handbook (3rd Ed.)
This site features a pdf-based online version of DAKO's IHC handbook. A very useful book, with detailed information on basic immunohistochemistry techniques including protocols and reviews of alternative methods.
4. PathBase: The European Mutant Mouse Pathology Database
Pathbase is a database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. This site containes a searchable database of histopathological images mainly from transgenic and knockout mice with effects on cell proliferation and cancer, and the response of adult and fetal animals to environmental insults such as radiation at high and low doses relevant to accidental, environmental, and medical irradiation of humans.
A site comprising a histology search engine for searches over 20,000 Web pages from histology-related sites on the internet, hyperlinks to other histology sites, and to relevant newsgroups and archives.
F. Transgenes and Gene Knockout and -down Technology
1. C. elegans Gene Knockout Consortium
This consortium aims at facilitating genetic research of this important model system through the production of deletion alleles at specified gene targets. Targets are chosen based on investigator requests. Strains produced by the consortium are freely available with no restrictions to any investigator.
2. BioMedNet's Mouse Knockout and Mutation Database
A comprehensive database of phenotypic and genotypic information on mouse knockouts and classical mutations with more than 8000 database entries covering over 3000 unique genes.
3. The Nagy Laboratory Cre Transgenic Database
This Web site contains a database of published as well as unpublished and in the making Cre transgenic lines. Also some mouse genetics protocols and links. All in all, a good site for those researchers with an interest in ES cell-mediated rodent genome alterations.
4. Database of Gene Knockout
A mouse gene knockout database with strains classified alphabetically or according to the viability of the knockout: viable mice, or resulting in prenatal, postnatal, or perinatal mortality.
5. Gene Targeting Protocols
A set of 23 gene targeting protocols from Practical Approach Online (in pdf format).
6. Antisense Gene Targeting
GeneTools produces antisense morpholino oligosnucleotides to shut down selected RNA sequences. Provides a very good alternative to phosphorothioates. Microinjection or electroporation of Morpholino oligosnucleotides into the embryos of frogs, zebrafish, chicks, and sea urchins has been shown to successfully and specifically shuts down the expression of desired mRNAs. Another alternative is locked nucleic acid oligosnucleotides that can be obtained through http://www.exiqon.com.
7. RNA Interference Resources
A resource containing a wealth of information on siRNA-mediated gene silencing, with many useful reviews, rererences, and link to other sites of interest. An additional site of interest is McManus home page (http://web.mit.edu/mmcmanus/www/RNAi. html), a very good Web site for researchers interested in the process of RNA interference.
G. Organelle Systems
1. Cell Biology Topics: Organelles
A collection of links to Web pages providing basic information on organelle systems. Most of the topics focus on structure/function correlations.
2. The Virtual Cell Web Page
A nice presentation on cell organization and function/ structure relations. A similar resource can be found at http://www.life.uiuc.edu/plantbio/cell.
1. DNA Microarray Web Site
A Web page boasting a collection of links to academic and industrial sites of interest for researchers with an interest in microarrays (DNA as well as protein chips).
2. Grid It
A useful resource for researchers interested in microarray technology. Includes an introduction to microarray technology and links to sources of equipment, analysis software, and other microarray sites.
3. LGM Microarray Links
A collection of links to microarray resources.
4. Genomics: A Global Resource
A gateway to a plethora of genomic resources.
1. Meta-Database Catalog of Two-Dimensional Gel Images Found in Web Databases (2DWG)
A catalog of some of the 2D gel images that can be found in 2D gel databases on the Web.
2. Two-Dimensional Gel Electrophoresis Tutorial
http://www.aber.ac.uk/parasito logy/Proteome/ Tut_2D.html
A tutorial written by Dr James R. Jefferies. Sections covering this topic include 2D gel electrophoresis, immobilized pH gradients, 2D procedure, sample preparation, sample solubilisation, chaotrophe, reductants, detergents-surfactants, ampholytes, interfering substances, protein estimation, gel electrophoresis, IEF run, strip equilibration, SDS-PAGE run, staining, general considerations, and references.
3. The Danish Centre for Human Genome Research's 2D PAGE Databases
A site containing proteomic databases developed for the study of global cell regulation in health and disease, focusing on skin biology and bladder cancer. Procedures are illustrated with still images and videos. The site also features a gallery of 2D gels of cells, tissues, and fluids, as well as 2D gel immunoblots.
4. EXPASy World 2DPAGE Index
A site containing references to known 2D PAGE database servers, as well as to 2D PAGE-related servers and services.
1. Spectroscopy Now
A gateway to various spectroscopy resources, including mass spectrometry, RAMAN, and NMR.
2. Protein Prospector
A collection of proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments.
K. Cell Signaling
1. The Alliance for Cell Signaling
The AfCS-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in cell signaling. The AfCS is an initiative with the aim of performing comprehensive experimental analyses of selected signaling systems, providing these data freely to the research community. Several tools of interest to investigators within the signalling community are also available here.
A database of phosphorylation sites, including two implementations of algorithms for prediction of potential phosphorylation sites.
3. List of Apoptosis Regulators
A Web site providing general and specific information of apoptosis regulators and signalling pathways, as well as quick access to relevant papers and sequences.
4. Science's Signal Transduction Knowledge Environment
A global resource useful to scientists who specialize in signal transduction, as well as the many scientists who need to follow and apply the current findings of this field even though their primary interest may not be in signal transduction mechanisms themselves.
A Web-based resource for inositols, phosphoinositides, phosphatidylinositols, and other essential cellsignaling molecules.
6. BioCarta's Pathways
A Web site containing interactive graphic models of molecular and cellular pathways.
L. Databases of Molecular Interactions and Pathways
1. Biomolecular Interaction Network Database (BIND)
This site consists of a search engine, PreBIND, that allows the user to mine the biomedical literature for protein-protein interactions and a database, BIND, that stores descriptions of interactions, molecular complexes, and pathway records.
2. General Repository of Interaction Databases (GRID)
A database of genetic and physical interactions containing interaction data from many different sources. This site is also home to the Osprey Network Visualization System (http://biodata.mshri.on.ca/osprey/ servlet/Index), a powerful application for graphically representing physical and genetic biological interactions that is coupled to the GRID database.
3. Database of Interacting Proteins (DIP)
A database of experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
4. Molecular Interactions Database (MINT)
A database of functional interactions between biological molecules (proteins, RNA, DNA). Beyond cataloguing the formation of binary complexes, MINT also stores other type of functional interactions, namely enzymatic modifications of one of the partners.
5. Curagen's PathCalling Yeast Interaction Database
PathCalling is a proteomic technology designed to identify protein-protein interactions on a genomewide scale.
6. Biomolecular Relations in Information Transmission and Expression (BRITE)
BRITE is a database of binary relations for computation and comparison of graphs involving genes and proteins. It contains diverse sets of binary relations, including the generalized protein interactions that underlie the KEGG pathway diagrams, systematic experimental data on protein-protein interactions by yeast two-hybrid systems, sequence similarity relations by SSEARCH, expression similarity relations by microarray gene expression profiles, and crossreference links between database entries.
7. KEGG Pathway Database
A part of the Kyoto Encyclopedia of Genes and Genomes, this graphical interface for pathway diagrams is very user friendly and a boon of information for any researcher looking for relational information for a given protein. Two diagrammatical databases are available, a metabolic pathway database (http:// www.genome.ad.jp/kegg/metabolism.html) and a regulatory pathway database (http://www.genome. ad.jp/kegg/regulation.html); each one of these divided in subsections. In addition to the possibility to perform searches on particular objects or sequences in the various pathways, one can also generate possible reaction pathways.
8. Yeast Interacting Proteins Database
A companion site to a publication reporting on the comprehensive two-hybrid analysis of the budding yeast proteome. One can download the complete datasets or analyse them as well as previously reported protein-protein interactions using a graphical system for viewing gene regulatory networks.
M. Gateways to Scientific Resources
1. The DEAMBULUM-BIONETosphere Thematic Exploration
A gateway to useful online resources for molecular biology, biocomputing, medicine, and biology. It includes hyperlinks to databases (sequence, bibliographic, organisms, etc.), sequence analysis tools, software, and many others.
2. The WI4rW Virtual Library of Cell Biology
A very large repository of cell biology information. It includes numerous sections with hyperlinks to various cell biology laboratories, databases, journals, methods, organizations, and meetings, among others.
3. Pedro's Biomolecular Research Tools
An extensive and quite comprehensive collection of links to resources useful to molecular and cell biologists.
4. The Canadian Bioinformatics Resource
A Web site providing convenient, effective access to widely used bioinformatic tools and databases.
5. Atelier BioInformatique, aBi Online Analysis Tools
An extensive collection of hyperlinks to various bioinformatics tools available online. A similar but complementary Web site is the home page of Dr. Andrew Kropinski (http://molbiol-tools.ca/).
6. bioWl4rW a Resource for Life Science Researchers
A forum for life science researchers containing information and links to protocols, news groups, and many other resources.
7. Molecular Biology Gateway
A gateway to Web resources for molecular biology, genetics, microbiology, and biochemistry.
N. Sequence Databases and Analysis Tools
This is arguably the largest single group of scientific Web sites in existence. The number of sites featuring sequence analysis tools (of proteins as well as nucleic acids), database queries, and prediction algorithms, among others, is overwhelming and many times the hardest task is to choose which one to use. Listing of even just the most interesting and relevant sites would exceed by far the scope of this resource section. We have chosen instead to provide a few select Web pages of major biology servers containing a large and well-curated collection of databases and tools that allow them be used as entry points for broader searches.
1. The European Bioinformatics Institute (EBI)
The European Bioinformatics Institute is a nonprofit academic organisation that forms part of the European Molecular Biology Laboratory (EMBL). The EBI manages databases of biological data and provides a comprehensive range of very useful bioinformatics tools.
2. The Catalog of Databases (DBCAT)
A near-exhaustive list of existent databases for various application fields, such as DNA, RNA, and proteins.
3. The National Center for Biotechnology Information (NCBI)
One of the major bioinformatics servers, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information. It provides an extensive collection of tools and resources, including, but not limited to, molecular databases such as GenBank, Entrez, and dbEST; literature databases such as PubMed and OMIM; and tools such as BLAST, Cn3D, and LinkOut.
4. Genome Net
A Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology. A gateway providing entry points to resources, including, but not limited to, DBGET (Integrated Database Retrieval System), KEGG (Kyoto Encyclopedia of Genes and Genomes), and SSDB (Sequence Similarity Database) (http://www.genome.ad.jp / dbget / dbget.links.html).
5. The Protein DataBank at Brookhaven (PDB)
PDB is the repository for the processing and distribution of 3D biological macromolecular structure data. In addition to containing structural data deposited by crystallographers and spectroscopists (NMR), worldwide PDB also presents a large collection of software for structural work and educational resources.
6. Center for Biological Sequence Analysis Server (CBS)
The server at CBS provides a set of very useful tools for sequence analysis, such as TMHMM for the identification of transmembrane helices in proteins; TargetP for the determination of subcellular location of proteins; and NetNGlyc for the identification of N-linked glycosylation sites in human proteins, as well as a very nice collection of links to other sites of interest.
7. The Expert Protein Analysis System (ExPASy) Molecular Biology Server
The ExPASy proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to protein analysis and contains a large number of tools as well as links to biology servers. The Amos Bairoch's WWW links page within the ExPASy server (http://www.expasy. org/alinks.html) contains pointers to information sources for life scientists with an interest in biological macromolecules. Additionally, this site is also home to Biohunt (http://www.expasy.org/BioHunt), a molecular biology search engine.
8. The Institute for Genomic Research (TIGR)
A not-for-profit research institute whose primary research interests are in structural, functional, and comparative analysis of genomes and gene products from a wide variety of organisms. This site contains a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants, and humans. Particularly interesting is the TIGR microarray resources page, where one can find many software tools available for free download.
A database of human genes, their products, and their involvement in diseases. A search engine useful for people who wish to find information about genes of interest.
O. Educational and General Information Resources
1. Cell and Molecular Biology Online
A site containing general information and links for cell and molecular biologists. It features several hyperlinks to many resources such as online journals, methods, protocols, and laboratories.
2. The Glossarist
A searchable glossary directory. Looking for the definition of a term in a particular subject can be difficult and time-consuming. That is where the Glossarist can help you look. This Web page contains links to several online dictionaries and glossaries, including, but not limited to, the online version of the book published by Lackie and Dow (1999) (http://on.to/ dictionary) and BioABACUS (http://www.nmsu. edu/-molbio/bioABACUShome.htm), a searchable database of abbreviations and acronyms in biotechnology.
3. Kimball's Biology Pages
A Web site containing an online biology textbook. Even though some of the information in this Web site has been taken from the sixth edition of the author's general biology text "Biology" published in 1994 by Wm. C. Brown, frequent updates make this site well worth a visit.
4. Online Biology Book
A college-level introduction biology text with an interesting set of lectures with many illustrations.
5. The Biology Project
An online interactive resource for biology. This site consists of student-oriented, highly interactive learning materials that can be used to support lectures for laboratory meetings, and discussion sessions of general education courses.
6. Biotech's Scientific Dictionary
A dictionary on general terminology of biochemistry, biotechnology, botany, cell biology, and genetics, as well as more specific brief definitions of the cell constituents.
7. Biology Online
A source of basic biological information, with tutorials and a dictionary of biology, as well as links to hundreds of related biology sites.
8. The Visible Mouse
A Web site providing a very nice introduction to the anatomy, physiology, histology, and pathology of the laboratory mouse with emphasis on genetically engineered mice.
9. Lee M. Silver's Mouse Genetics
The electronic version of Silver's book.
10. The Zebrafish Book
A guide for the laboratory use of zebrafish (Danio rerio).
11. Mark Blaxter's Home Page
http://nema.cap.ed.ac.uk/Caenorhabditis/C_e legans_ genome/Celegansgenome.html
It contains "The Genetics of Caenorhabditis elegans, an Introduction," a very well-written introduction to the biology of C. elegans.
A gateway to evaluated internet resources in the basic biological and biomedical sciences, aimed at students, researchers, academics, and practitioners in biological or biomedical science.
P. Safety, Ethical Issues, Legislation, and Patents
1. International Centre for Genetic Engineering and B io techno lo gy-B io safety
The ICGEB Biosafety Web pages, containing information on biosafety, international biosafety regulations (USA, Europe and others), handling of GMOs, and links to other related sites.
2. European Agency for Safety and Health at Work (OSHA)
This is the corporate Web site of the OSHA. It provides useful information and access to full-text versions of all OSHA's publications.
3. European Chemical Bureau (ECB)
The ECB is the focal point in Europe for data and the assessment procedure on dangerous chemicals. This site provides information on the classification and labelling of substances, import/export of dangerous chemicals, legislation, and a collection of links to other related sites.
4. Material Safety Data Sheet (MSDS) Databases Search
A search engine for MSDS libraries. MSDSSEARCH is a reliable starting point for obtaining the most updated MSDS documents from the manufacturer and provides a single, international, database with all MSDSs available in text format at no cost to users.
5. EUROPA Steering Committee on Bioethics
http://www.coe.int/T/E/Legal_Aff airs/Legal_ co-operation/Bioethics/CDBI
This Web site contains information concerning meetings and documentation produced by the CDBI as well as links to other relevant sites.
6. The International Bioethics Committee (IBC)
The Bioethics Programme is part of UNESCO's Division of the Ethics of Science and Technology in the Social and Human Sciences Sector and, through its committees, produces advice, recommendations, and proposals to submit to the Director-General for consideration by UNESCO's governing bodies. In addition to providing access to IBC's documents, this Web site has various links to legislative institutions, databases of bioethics institutions, and other related websites.
7. Institutional Animal Care and Use Committee at University of Iowa
This Web site has a very descriptive collection of basic biomethodology for mouse, rat, rabbit, and guinea pig animal husbandry, as well as a large number of established guidelines/regimens for various animal uses (e.g., recommendations for the production of ascitic fluid; regimens for anesthesia and analgesia of laboratory animals).
8. Animal Care at Johns Hopkins
A lot of useful information on regulations and polices on animal care and use.
9. UCAR Manual on the Responsible Care and Use of Laboratory Animals
A resource from the University of Rochester Medical Center. It includes a manual on care and use of laboratory animals and links to other resources, such as the dosage calculator (http://www.fda.gov/cder/cancer/ animalframe.htm).
10. OECD Principles of Good Laboratory Practices
A Web site containing information on OECD guidelines for GLP, and principles of GLP, as well as links to national GLP sites.
11. U.S. Environmental Protection Agency (EPA)
EPA's home page to the Good Laboratory Practice Standards (GLPs) compliance monitoring program.
Europe's network of patent databases. Search published worldwide patent applications with an English abstract and title as well as published patent applications in their original language from various European countries. A real trove of information, reagents, and sequences is sometimes buried in patent applications.
5. The Wellcome Library
One of the world's greatest collections of books, manuscripts, pictures, and films around the meaning and history of medicine.
A catalog of books, journals, and audiovisuals in the National Library of Medicine collections.
Q. Literature Datasets
1. BioMed Central
An open access, independent publishing house committed to providing immediate free access to peerreviewed biomedical research.
PubMed is a service of the National Library of Medicine providing access to over 12 million MEDLINE citations back to the mid-1960s and additional life science journals. PubMed also includes links to many sites providing full text articles and other related resources. A similar service is provided by High Wire (http://highwire.stanford.edu).
3. Online Mendalian Inheritance in Man (OMIM)
A resource provided by NCBI containing curated reviews on human genes of interest with many references and embedded hyperlinks to other resources.
4. The Cochrane Library
This site consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews, which provide high-quality information to people providing and receiving care and those responsible for research, teaching, funding, and administration at all levels. The Cochrane Library is available on a subscription basis, but there are several countries that have arranged national provisions and thus allow all residents to access The Cochrane Library for free (e.g., Australia, England, Norway, Finland).
A large medical reference site including an exhaustive list of medical journals and medical associations and similar resources in the biological sciences. Other research tools include medical glossaries, disease databases, clinical trials and guidelines, and medical journals offering full-text article.
8. BioMail Service
Biomail is an automatic service that regularly (weekly by default) searches for articles, that have recently appeared in the PubMed Medline database using customized search terms. Then it emails lists of the found articles to the user.
R. General Protocols
This Web site features a collection of protocols contributed by scientists from over 125 academic laboratories covering a variety of life science disciplines. A large site with a plethora of links and many useful protocols.
An initiative by a team of MIT-affiliated researchers and local software engineers to develop a free Web site containing research protocols used in biological sciences.
A specialized Web site containing a collection of links to more than 2000 online protocols. You can discuss these protocols with researchers that share a similar interest. The protocols are indexed into eight categories: anatomy and histology, biochemistry and molecular biology, biotechnology, cell biology, developmental biology, genetics, immunology, and neuroscience.
4. Protocol Online
A database of research protocols in a variety of life science fields. It features user-submitted protocols as well as links to other Web sites.
S. General Reagents and Techniques
1. The Biocurrents Research CentermDatabase of Pharmocological Compounds
A NIH-funded database providing its user with a useful forum on the use of pharmacological compounds in cellular research. It lists over 500 compounds with details on their mode of action and employ, including references.
A buying guide for life sciences. Even though this site is commercially oriented it allows one to search a wide range of product-related technical information for the life science researcher in a rather comprehensive manner. If you need something and do not know where to buy it and whom to buy it from, this site may be just what you need. Included is Biocompare's Antibody Search, which allows you to search over 60,000 antibodies from various antibody suppliers. A similar service provider is BioSupplyNet (http://www.biosupplynet. com/) where you can browse and search for suppliers in a variety of areas of life science research.
3. Bioresearch Online
A sourcing site for bioresearch. In addition to it belong a buyer's guide and a free newsletter, it contains a search engine for product information.
4. LabVelocity's Biowire
A Web site containing user-written laboratory product reviews pertaining to the life sciences community. It holds a very large number (ca. 25,000) of product reviews, which are a good aid not only when deciding on purchasing a particular item, but also if you are searching for a specific product. A complementary site is SciQuest (http://www.sciquest.com/ commerce/CommerceRouter/Index), a site providing search possibilities for scientific products.
A search engine for finding health sciences information.
T. Model Organisms
1. The Mouse Genome Resources
A gateway to mouse resources. This site is an entry point to access information pertaining to the NCBI mouse genome sequence as well as other extramural mouse resources.
2. Whole Mouse Catalog
A collection of links to internet resources of particular interest to scientific researchers using mice or rats in their work.
3. The Jackson Laboratory Home Page
JAX online consists of a series of resources of interest for mouse researchers, including databases (http" / / www.jax.org / resources / search_databases.ht ml) and a mouse strain repository (http://jaxmice.jax. org/index.html) for the collection and distribution of genetically engineered mice, as well as a Mouse Genome Informatics (MGI) site that provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
4. The Mouse Phenome Database
A collection of comprehensive phenotypic and genotypic data on inbred laboratory mouse strains.
5. The Edinburgh Mouse Atlas Project (EMAP)
This Web site is the home page of a collaborative project within the University of Edinburgh aiming at the creation of a digital atlas of mouse embryonic development. It consists of a series of interactive threedimensional computer models of mouse embryos at successive stages of development with defined anatomical domains linked to a stage-by-stage ontology of anatomical names. Additionally, the EMAP atlas underlies an image-mapped gene-expression database (EMAGE; http://genex.hgu.mrc.ac.uk/ Emage/database/intro.html). These two databases are interoperable.
This database system provides access to comprehensive public repositories for genome mapping data from farmed and other animal species (e.g., cat, chicken, cow, deer, horse, pig, salmon, sheep, tilapia, turkey). Data stored include details of loci and markers, references/papers, authors, genetic linkage map assignments, cytogenetic map assignments, experimental techniques, PCR primers and conditions, and any other data pertaining to genome mapping.
7. Rat Genome Database (RGD)
A Web site providing a large amount of rat genetic and genomic resources. It includes curated data on rat genes, quantitative trait loci (QTL), microsatellite markers, and rat strains used in genetic and genomic research. In addition, RGD provides a large number of tools for gene prediction, radiation hybrid mapping, polymorphic marker selection, and more.
A database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae, but the primary species represented is Drosophila melanogaster. This site also contains several links to resources of interest for Drosophila researchers.
9. The Zebrafish Information Network (ZFIN)
ZFIN is a database resource for the laboratory use of zebrafish. It provides integrated zebrafish genetic, genomic, and developmental information, together with links to corresponding data in other model organism and human databases.
10. The HGMP-RC Fugu Genome Project
In addition to containing the publicly available draft sequence of the Fugu genome, this site also provides a collection of protocols, publications, and much data for the scientific community with an interest in Fugu rubripes (the Japanese puffer fish).
11. Caenorhabditis elegans WWW Server
A Web site aimed at the community of C. elegans researchers. This site boasts a large number of resources, including literature search, methods, a list of meetings, labs, and researchers, links to Bionet. celegans, etc. A companion site is WormBase (http://www.wormbase.org/). A Web site displaying a large amount of relevant information and hyperlinks for the C. elegans scientific community.
12. WWW Virtual Library for Xenopus
A site dedicated to Xenopus laevis, a commonly used model system for studying vertebrate early development. One of the main uses of this site is as a reference for researchers looking for molecular probes. It also contains a collection of whole mount staining patterns using both antibody and nucleic acid probes, a methods book, supplier listing, Xenopus scientific community white pages, and more.
An informatics resource for Dictyostelium discoideum, it consists of a comprehensive genomic Dictyostelium database, lab protocols and strain availability, and a list of researchers, among many other links.
14. The Arabidopsis Information Resource (TAIR)
A comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. TAIR consists of a searchable relational database, which includes many different data types. In addition, pages on news, information on the Arabidopsis Genome Initiative (AGI), Arabidopsis lab protocols, and useful links are provided. Additional sites and nonlisted model organisms can be found at the following sites:
The WWW Virtual Library: Model Organisms (http://ceolas.org/VL/mo/)
The Sanger Institute's Model Organisms Resources Links (http://www.sanger.ac.uk/Info/Links / modelorgs.shtml)
Infobiogen's list of genomes and organisms (http://www.infobiogen,fr/services/deambulum/english/genomesl.html)
NIH's Model Organisms for Biomedical Research website (http://www.nih.gov/science/models/).
III. IMAGING TECHNIQUES IN CELL BIOLOGY
One of the paramount interests of cell biologists is to observe cellular themes, temporally as well as spatially resolved. No longer just structures, but also proteins and their cellular localisation, dynamics, and interaction(s). The field of cellular imaging is currently one of the cornerstones of cell biology and microscopy constitutes arguably its single most important technique. For this reason, we have chosen to list and highlight Web sites dealing with the subject of microscopy in a more comprehensive manner then hitherto. This part of the resources section is thus devoted to microscopy techniques and covers the subject in a broad manner with sites that should be of great use to the novice and experienced user alike.
A. Light Microscopy
1. A Brief History of Optics
A part of the laser-optics UK Web site giving a historical summary of the important discoveries in the field of optics.
2. Properties of Light and Introductory Optics
The Molecular Expressions Microscopy Primer is an excellent microscopy Web site from Florida State University (principal authors: Michael W. Davidson, FSU and Mortimer Abramowitz-http://micro.magnet. fsu.edu/). An extensive series of tutorials on light and colours can be found on this Web site: nature of light (electromagnetic radiation, duality of light, definition of colours), physical properties (reflection, refraction, diffraction, polarisation, interference), and fundamental tools to generate and direct light (lenses, filters, sources of light, laser). A good introduction about light microscopy written by these authors can be downloaded at: http: //screensavers.magnet.fsu.edu/pdfs/ microscopy.pdf.
3. Anatomy of a Light Microscope and Basic Concepts in Optical Microscopy
The complete description of the different parts of a microscope can be found within this link: microscope components configuration, optical train components, perfect lens characteristics, objectives, and other important parts of the microscope.
4. Concepts and Formulas in Microscopy
A part of the Nikon's MicroscopyU Web site (http://www.microscopyu.com/). This Web site was originally designed to provide an educational forum for all aspects of optical microscopy, digital imaging, and photomicrography and complements the Molecular Expressions Microscopy Primer microscopy Web site (http://micro.magnet.fsu.edu/). This Web site part covers concepts and formulas in microscopy and includes definitions on some very important and often not well-understood parameters (numerical aperture, depth of field, resolution, and many others).
5. Sources of Visible Light
Description of various sources of light used for fluorescence microscopy.
6. Köhler Illumination
Köhler illumination is a basic requirement of all modern light microscopy. The purpose is to obtain an evenly lit field of view and as wide a cone of radiation as possible in order to achieve maximum resolution. This Web page explains clearly what the Köhler illumination is and how to set it up.
7. Specialised Microscopy Techniques
Microscopic techniques can be separated into two categories: microscopy using polychromatic light (basic light microscopy) and microscopy using specific wavelength (fluorescence microscopy) that need specific filters. Here you will find a description of different nonfluorescent microscopy techniques: bright-field and dark-field microscopy, Nomarski (or DIC), phase contrast, and so on.
B. Fluorescence Microscopy
1. What Is Fluorescence? The Stokes Law
Cell biologists want to observe the localisation, dynamics, and relocalisation of proteins. Unfortunately, proteins are not directly visible; in order to monitor their localisation they need to be tagged with fluorescent probes. This site gives the necessary background about how fluorescence is generated.
A link about George Gabriel Stokes.
2. Fluorescence Microscopy Tutorials
Fluorescence microscopy is the most common technique today in medical and biological sciences. This link focuses on excitation and emission fundamentals, light sources, lasers, and filter cubes. The section interactive Java tutorials give very useful information about fluorochrome data tables, excitation/emission wavelengths, and filter cube suggestions listed by applications.
3. Laser and Fluorescence Microscopy
Section about laser fundamentals from the Olympus Web site. Lasers can be found in CD players and various other commonly used objects. In the field of microscopy, lasers are used for their monochromatic properties, light coherence, and power. This link gives useful and accessible information about laser physics. Many Java tutorials are also available.
C. Image Acquisition
1. Cameras and CCD Detectors
Originally, mechanisms of image capture were restricted to photomicrography on film. Currently, the development of sensitive and low noise cameras gives the possibility to acquire digitally images from the microscope. These cameras with high sensitivity are at the core of the development of video microscopy. Digitalized images, as an ordered matrix of integers rather than a series of analog variations in colour and intensity, give the interesting possibility to post process images in order to enhance features and extract information. This section addresses a variety of current topics in image acquisition and processing. http://www.roperscientific.com/ library_encyclopedia.shtml A part of the Roper scientific Web site (http://www.roperscientific.com) called encyclopedia and describing many camera concepts, such as binning, gain, and dynamic range, among others. A very useful reference to understand basic principles of cameras and CCD detectors.
Comparison of technical characteristics of several cameras.
D. Filter Sets and Fluorescence Filter Cubes
Filter sets are designed to select a specific wavelength for specimen illumination with polychromatic light sources and are essential for selectively collecting fluorescent light coming from the sample. Proper selection of filters is the key to successful fluorescence microscopy. This section describes characteristics of excitation and emission filters used in combination with dichroic mirrors to design filter cubes.
The Curvomatic application from the Omega Web site (http://www.omegafilters.com) is a tool helping microscopists to choose their filters set according to fluorophores used. A very useful application.
E. Fluorescence Tables
This link provides a table that summarizes several peak excitation and emission wavelengths of commonly used fluorochromes. These different fluorescence tags can be coupled with proteins or drugs (e.g., phalloidin or taxol) to monitor localisation of proteins in cells.
The Bio-Rad fluorescence database has been designed to allow the user to superimpose graphical fluorochrome data from various fluorochromes onto a normalised axis. Both emission and excitation spectra can be plotted from any fluorochrome in the database. These can subsequently be overlaid with filter data curves and laser lines, which aids the microscopist in selection of the correct fluorochrome for use with their samples and microscope.
The fluorescence spectrum viewer from bdbiosciences. This can be used as an alternative to Bio-Rad fluorescent database and the curvomatic application from Omega.
F. Fluorescent Probes for Light Microscopy
1. Fluorophores and Fluorescents Reagents
An electronic version of the Molecular Probes Handbook. Molecular Probes is one of the most interesting providers of fluorescent probes for cell biology. This Web edition of the handbook is an updated version of the 9th edition and is presented in two formats. Very useful information can be found in this Web handbook, such as cross-linking techniques, photoreactives reagents, probes for cytoskeletal proteins, membranes, organelles, and endocytosis, as well as pH indicators, and ions indicators.
This link points to the complete list of fluorescent Probes available from Molecular Probes. For each probe a sheet summarizes some characteristic of the probe (emission and excitation spectra, physical properties, etc...). Spectra are also available for download.
A base/dye ratio calculator from molecular probes. This applet allows the possibility to calculate fluorescence characteristics (maximum wavelength, extinction coefficient) of a nucleotide coupled to a fluorescent dye.
2. Secondary Antibodies for Immunohistochemistry
A part of the analytical imaging facility Web site from Albert Einstein college of medicine (New York, http://www.aecom.yu.edu/aif/). This link points to a troubleshooting guide on immunofluorescence nonspecific labelling; very useful for understanding staining problems in immunofluorescence experiments.
Jackon immunoresearch and Zymed are providers (although not unique) of secondary antibodies used in fluorescence microscopy. Secondary antibodies are classical tools used in cell biology to reveal localisation of proteins by fluorescence microscopy. Molecular Probes also provides some secondary antibodies.
3. GFP. Background and Properties of GFP and Related Tags
These Web pages about green fluorescent protein (GFP) have been developed as a dissertation project for the principles of protein structure using the internet course (http://www.cryst.bbk.ac.uk/PPS2/top.html). You will find the in vivo role of the GFP and some basic properties. Biosynthesis, chemical structure of the fluorophore, and spectrum characteristics of this protein are also available.
4. Commercial Web site of Fluorescent Proteins
This link points to the Clontech Web site, with emphasis on GFP vectors. Clontech is historically the first provider of GFP-expressing vectors.
G. Immunohistochemistry and Immunofluorescence Protocols
1. Protocols Database
Protocol Links Web page of IHC world Web site (http://www.ihcworld.com/; online information center for immunohistochemistry). An extensive list of Web sites, pdf files, and protocols covering fields of general histology, immunohistochemistry, immunofluorescence, in situ hybridisation, and electron microscopy protocols.
Link to the protocols database of the IHC Web site. You can query the protocol database for a specific antibody-staining protocol.
2. Immunohistochemistry and in situ Hybridization
Link to a Web site explaining theory and techniques of immunolabelling. Some protocols are available and many Powerpoint presentations are downloadable. Useful teaching resource.
3. Other Immunofluorescence Protocols
Web site of the imaging technology group from the Beckman Institute for Advanced Science and Technology (http://www.itg.uiuc.edu/). Link includes technical bulletin providing an introduction to fluorescent microscopy and a collection of various protocols for specific applications of fluorescence.
H. Other Microscopy Techniques
1. Three-Dimensional Laser Confocal Microscopy
Web site from Lance Ladic, Department of Physiology, University British Columbia, giving a basic introduction to 3D laser-scanning microscopy.
Link to the course "Looking inside cells and tissues by optical sectioning with a confocal laser scanning microscope" prepared by M. Diirrenberger and R. SiRterlin. Also some basics about confocal microscopy.
Home page of the scanning laser microscopy lab (also known as the confocal microscopy group) of the physics department at the University of Waterloo. This site is designed for researchers who use (or might like to use) confocal microscopes. This Web site describes optical design, problems of lateral and axial resolution, and problems of confocal slicing in confocal microscopy. Some formulae can also be found.
A complete section about confocal microscopy from the Molecular Expressions Microscopy Primer Web site. Basic concepts, imaging modes, specimen preparation and imaging, laser systems for confocal microscopy, etc... A very nice interactive java tutorial showing how a confocal microscope is working. This tutorial also shows effects of pinhole aperture on the quality of the confocal image.
2. Spinning Disk Confocal Microscopy
A short Web page that describes differences between confocal scanning microscopy and the new technique of spinning disk confocal microscopy.
3. Multiphoton Fluorescence Microscopy and Two Photon Theory
Multiphoton fluorescence microscopy is a powerful research tool that combines the advanced optical techniques of laser-scanning microscopy with long wavelength multiphoton fluorescence excitation. Multiphoton microscopy is generally used to specifically excitate fluorophores in a specific Z location. This link gives much information about this technique complementary to confocal microscopy.
4. Fluorescence Resonance Energy Transfer (FRET) Microscopy
FRET microscopy uses the same physical principle as FRET spectroscopy. FRET is a technique used to determine the interaction (or proximity) of two fluorescent labelled molecules. This site gives the mathematical background necessary to explain FRET spectroscopy. Observations and equations described here are applicable to FRET microscopy.
Molecular Probes Web page about fluorescence resonance energy transfer microscopy. Information about primary conditions of FRET, F6rster radius, and fluorophore pairs used for FRET can be found.
5. Fluorescent Lifetime Imaging Microscopy (FLIM)
Time-resolved fluorescence emission spectroscopy of a photoexcited sample is a powerful tool for the study of living cells in both space and time of their internal biochemistry. The Web page of the W.M. Reck Center for Cellular Imaging (University of Virginia) provides theory, images, and references about FLIM.
6. An Archive of Electron Micrographs
A collection of electron micrography images from the Institute for Molecular Virology, University of Wisconsin-Madison.
7. Atlas of Microscopy Anatomy
MicroscopicAnatomy/MicroscopicAnatomy.html Electronic version of the Atlas of Microscopic Anatomy: A Functional Approach: Companion to Histology and Neuroanatomy, second edition.
8. A Video Tour of Cell Motility
Contribution to the EAMNET network (http:// www.embl.de/eamnet) from the John Victor Small laboratory. An original gallery of video microscopies describing the phenomenon of cell motility.
9. Free Software for Microscopy
A part from Lance Ladic Web site (Department of Physiology, University British Columbia) giving many links for microscopy and image processing softwares.
10. ImageJ-Freeware Java Image Processing Software
ImageJ is a very good image processing software, written in Java and available for all types of platforms (Linux/UNIX, Windows and Mac-based computer).
11. Power Point Presentations on Microscopy
General teaching resource about light microscopy available as powerpoint presentations.
12. The European Advanced Light Microscopy Network (EAMNET) Network
EAMNET is a EU-funded network of eight European laboratories and two industrial partners working in the field of light microscopy. The aim of EAMNET is to assist scientists in exploiting the power of imaging by organizing practical teaching courses, creating online teaching modules, and offering software packages for microscopy.
13. Cell Migration Consortium
Movies and photo from the cell migration consortium (http://www.cellmigration.org/).
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569-4574.
Lachie, J. M., and Dow, J. A. T. (1999). "The Dictionary of Cell and Molecular Biology," 3rd Ed. Academic Press, London.
© 2018 Biocyclopedia | All rights reserved.