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 Special Topics | Microbiology |
Microbiology is the scientific study of microorganisms (e.g. bacteria, viruses, and fungi). Originally this was directed towards their effects (e.g. in causing disease and decay), but during the 20th century the emphasis shifted to their physiology, biochemistry, and genetics. Microbes are now recognized as important vehicles for the study of biochemical and genetic processes common to all living organisms, and their rapid growth enables their laboratory culture in large numbers for studies in genetics and for biotechnological applications.1
eBooks
Encyclopedia of Environmental Microbiology, 6 Volume Set by ISBN: 0471354503Publication Date: 2002-02-25
Handbook of Culture Media for Food and Water MicrobiologyISBN: 1847551459Publication Date: 2011-12-07
Oxford Dictionary of Biochemistry and Molecular Biology by ISBN: 0198529171Publication Date: 2006-08-24
Mims' Medical Microbiology and ImmunologyISBN: 9780702072024
Protocols and Methods
- JoVE Science Education: Basic BiologyVideo library that covers "General Laboratory Techniques" and "Basic Methods in Cellular and Molecular Biology"
Coverage:Varies - Springer Nature ExperimentsLife and biomedical sciences laboratory protocols.
Coverage: Current
Microbiology Databases and Tools
- Cancer Cell Line Encyclopedia (CCLE)This encyclopedia is online and provided by OpenScholar, and captures the large-scale genetic characterization of ~1000 cancer cell lines.
- CellosaurusProvided through Expasy at the Swiss Institute of Bioinformatics (SIB), this is a knowledge resource on cell lines.
- CLO: Cell Line OntologyThe Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. Provided by EMBL-EBI.
- IPD-IMGT/HLAThe IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System.
Registries
- hPSCregThe Human Pluripotent Stem Cell Registry (hPSCreg®) is a freely accessible global registry for human pluripotent stem cell lines (hPSC lines). The registry allows searching for cell lines and for information available about these cell lines.
- SKiP (Stem cell knowledge and information network)SKIP is operated by Center for iPS Cell Research and Application from Kyoto University as an embodiment of the section of the stem cell information database
The European Bioinformatics Institute (EMBL-EBI) is an International Governmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. The EMBL-EBI maintains the world’s most comprehensive range of freely available and up-to-date molecular data resources.
- ChEMBL [EMBL]ChEMBL is a curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.
- Clustal Omega [EMBL]
Multiple sequence alignment of DNA or protein sequences. Clustal Omega replaces the older ClustalW alignment tools - Ensembl [EMBL]Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.
- Expression Atlas [EMBL]An added-value database that shows which genes/proteins are expressed under which conditions, and how expression differs between conditions.
- InterProScanInterProScan searches sequences against InterPro's predictive protein signatures.
- PDBe [EMBL]The European resource for the collection, organisation and dissemination of 3D structural data (from PDB and EMDB) on biological macromolecules and their complexes.
The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information. The NCBI is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH).
- PubMedArticles in medicine, life sciences, animal sciences, plant sciences, biomedical research, medical devices, nursing, biotechnology, the healthcare system, and the preclinical sciences.
Coverage: 1950 - present
- BLAST [NCBI]Basic Local Alignment Search Tool: BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
- Gene [NCBI]Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
- Nucleotide [NCBI]The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
- Protein [NCBI]The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.
- Taxonomy [NCBI]The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.
The JGI is the global leader in generating genome sequences of plants, fungi, microbes, and metagenomes.
- Genome Portal [JGI]The JGI Genome Portal provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes.
- MycoCosm [JGI]Access to data, visualization, and analysis tools for comparative genomics of fungi.
- PhycoCosm [JGI]Access to publicly available sequenced algal genomes and genome annotations generated by the JGI and by others. The web portal allows users to navigate these genomes and conduct comparative and genome-centric analyses of algae.
- Phytozome [JGI]Phytozome is the Plant Comparative Genomics portal of the Department of Energy’s Joint Genome Institute.
1 (2019). microbiology. In Hine, R. (Ed.), A Dictionary of Biology. : Oxford University Press. Retrieved 10 Feb. 2021, from https://www-oxfordreference-com.proxy.lib.uwaterloo.ca/view/10.1093/acref/9780198821489.001.0001/acref-9780198821489-e-2746.