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Glycomics is the comprehensive study of glycomes, including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology. The term glycomics is derived from the chemical prefix for sweetness or a sugar, "glyco-", and was formed to follow the omics naming convention established by genomics and proteomics.
The glycome is the entire complement of sugars, whether free or present in more complex molecules, of an organism. An alternative definition is the entirety of carbohydrates in a cell. The glycome may in fact be one of the most complex entities in nature. "Glycomics, analogous to genomics and proteomics, is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology.
The Consortium for Functional Glycomics (CFG) is a large research initiative funded in 2001 by a glue grant from the National Institute of General Medical Sciences (NIGMS) to “define paradigms by which protein-carbohydrate interactions mediate cell communication”. To achieve this goal, the CFG studies the functions of:
Defined in the narrowest sense, glycobiology is the study of the structure, biosynthesis, and biology of saccharides that are widely distributed in nature. Sugars or saccharides are essential components of all living things and aspects of the various roles they play in biology are researched in various medical, biochemical and biotechnological fields.
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
The terms glycans and polysaccharides are defined by IUPAC as synonyms meaning "compounds consisting of a large number of monosaccharides linked glycosidically". However, in practice the term glycan may also be used to refer to the carbohydrate portion of a glycoconjugate, such as a glycoprotein, glycolipid, or a proteoglycan, even if the carbohydrate is only an oligosaccharide. Glycans usually consist solely of O-glycosidic linkages of monosaccharides. For example, cellulose is a glycan composed of β-1,4-linked D-glucose, and chitin is a glycan composed of β-1,4-linked N-acetyl-D-glucosamine. Glycans can be homo- or heteropolymers of monosaccharide residues, and can be linear or branched.
Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.
Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry. The individual resources are hosted in a decentralized way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions.
Chi-Huey Wong is a Taiwanese-American biochemist. He is currently the Scripps Family Chair Professor at the Scripps Research Institute, California in the department of chemistry. He is a member of the United States National Academy of Sciences, as awarded the 2014 Wolf Prize in Chemistry and 2015 RSC Robert Robinson Award. Wong is also the holder of more than 100 patents and publisher of more 700 scholarly academic research papers under his name.
Glycoinformatics is a field of bioinformatics that pertains to the study of carbohydrates involved in protein post-translational modification. It broadly includes database, software, and algorithm development for the study of carbohydrate structures, glycoconjugates, enzymatic carbohydrate synthesis and degradation, as well as carbohydrate interactions. Conventional usage of the term does not currently include the treatment of carbohydrates from the better-known nutritive aspect.
Anne Dell is an Australian biochemist specialising in the study of glycomics and the carbohydrate structures that modify proteins. Anne's work could be used to figure out how pathogens such as HIV are able to evade termination by the immune system which could be applied toward understanding how this occurs in fetuses. Her research has also led to the development of higher sensitivity mass spectroscopy techniques which have allowed for the better studying of the structure of carbohydrates. Anne also established GlycoTRIC at Imperial College London, a research center that allows for glycobiology to be better understood in biomedical applications. She is currently Professor of Carbohydrate Biochemistry and Head of the Department of Life Sciences at Imperial College London. Dell's other contributions to the study of Glycobiology are the additions she has made to the textbook "Essentials of Glycobiology" Dell was appointed Commander of the Order of the British Empire (CBE) in the 2009 Birthday Honours.
EuroCarbDB was an EU-funded initiative for the creation of software and standards for the systematic collection of carbohydrate structures and their experimental data, which was discontinued in 2010 due to lack of funding. The project included a database of known carbohydrate structures and experimental data, specifically mass spectrometry, HPLC and NMR data, accessed via a web interface that provides for browsing, searching and contribution of structures and data to the database. The project also produces a number of associated bioinformatics tools for carbohydrate researchers:
Carbohydrate Structure Database (CSDB) is a free curated database and service platform in glycoinformatics, launched in 2005 by a group of Russian scientists from N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences. CSDB stores published structural, taxonomical, bibliographic and NMR-spectroscopic data on natural carbohydrates and carbohydrate-related molecules.
In biochemistry, paucimannosylation is an enzymatic post-translational modification involving the attachment of relatively simple mannose (Man) and N-Acetylglucosamine (GlcNAc) containing carbohydrates (glycans) to proteins. The paucimannosidic glycans may also be modified with other types of monosaccharides including fucose (Fuc) and xylose (Xyl) depending on the species, tissue and cell origin.
The Minimum Information Required About a Glycomics Experiment (MIRAGE) initiative is part of the Minimum Information Standards and specifically applies to guidelines for reporting on a glycomics experiment. The initiative is supported by the Beilstein Institute for the Advancement of Chemical Sciences. The MIRAGE project focuses on the development of publication guidelines for interaction and structural glycomics data as well as the development of data exchange formats. The project was launched in 2011 in Seattle and set off with the description of the aims of the MIRAGE project.
The Symbol Nomenclature For Glycans (SNFG) is a community-curated standard for the depiction of simple monosaccharides and complex carbohydrates (glycans) using various colored-coded, geometric shapes, along with defined text additions. It is hosted by the National Center for Biotechnology Information at the NCBI-Glycans Page. It is curated by an international groups of researchers in the field that are collectively called the SNFG Discussion Group. The overall goal of the SNFG is to:
- Facilitate communications and presentations of monosaccharides and glycans for researchers in the Glycosciences, and for scientists and students less familiar with the field.
- Ensure uniform usage of the nomenclature in the literature, thus helping to ensure scientific accuracy in journal and online publications.
- Continue to develop the SNFG and its applications to aid wider use by the scientific community.
Charles E. Warren was an assistant professor of biochemistry and molecular biology at the University of New Hampshire.
Glycan nomenclature is the systematic naming of glycans, which are carbohydrate-based polymers made by all living organisms. In general glycans can be represented in: (i) text formats: These includes commonly used CarbBank, IUPAC name, and several other types and (ii) symbol formats: These are consisting of Symbol Nomenclature For Glycans and Oxford Notations.
Nicki Packer FRSC is a distinguished professor of glycoproteomics in the School of Natural Sciences at Macquarie University and principal research leader at Griffith University's Institute for Glycomics. Packer is a Fellow of the Royal Society of Chemistry and in 2021 received the Distinguished Achievement in Proteomic Sciences Award from the Human Proteome Organization. Her research focuses on biological functional of glycoconjugates by linking glycomics with proteomics and bioinformatics.
References
- ↑ "UniCarb-DB". unicarb-db.expasy.org. Retrieved 2016-11-14.
- ↑ Lisacek, Frederique; Mariethoz, Julien; Alocci, Davide; Rudd, PaulineM.; Abrahams, JodieL.; Campbell, MatthewP.; Packer, NicolleH.; Ståhle, Jonas; Widmalm, Göran (2017-01-01). "Databases and Associated Tools for Glycomics and Glycoproteomics". In Lauc, Gordan; Wuhrer, Manfred (eds.). High-Throughput Glycomics and Glycoproteomics. Methods in Molecular Biology. Vol. 1503. Springer New York. pp. 235–264. doi:10.1007/978-1-4939-6493-2_18. ISBN 9781493964918. PMID 27743371.
- ↑ Campbell, Matthew P.; Nguyen-Khuong, Terry; Hayes, Catherine A.; Flowers, Sarah A.; Alagesan, Kathirvel; Kolarich, Daniel; Packer, Nicolle H.; Karlsson, Niclas G. (2014-01-01). "Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1844 (1 Pt A): 108–116. doi:10.1016/j.bbapap.2013.04.018. ISSN 0006-3002. PMID 23624262.
- ↑ Hayes, Catherine A.; Karlsson, Niclas G.; Struwe, Weston B.; Lisacek, Frederique; Rudd, Pauline M.; Packer, Nicolle H.; Campbell, Matthew P. (2011-05-01). "UniCarb-DB: a database resource for glycomic discovery". Bioinformatics. 27 (9): 1343–1344. doi: 10.1093/bioinformatics/btr137 . ISSN 1367-4811. PMID 21398669.
- ↑ Rojas-Macias, Miguel A.; Mariethoz, Julien; Andersson, Peter; Jin, Chunsheng; Venkatakrishnan, Vignesh; Aoki, Nobuyuki P.; Shinmachi, Daisuke; Ashwood, Christopher; Madunic, Katarina (2018-08-27). "e-workflow for recording of glycomic mass spectrometric data in compliance with reporting guidelines". bioRxiv. doi: 10.1101/401141 .