TED Fellow Christina Warinner is an expert on ancient diets. So how much of the diet fad the "Paleo Diet" is based on an actual Paleolithic diet? The answer is not really any of it.
Dr. Christina Warinner has excavated around the world, from the Maya jungles of Belize to the Himalayan mountains of Nepal, and she is pioneering the biomolecular investigation of archaeological dental calculus (tartar) to study long-term trends in human health and diet. She is a 2012 TED Fellow, and her work has been featured in Wired UK, the Observer, CNN.com, Der Freitag, and Sveriges TV. She obtained her Ph.D. from Harvard University in 2010, specializing in ancient DNA analysis and paleodietary reconstruction.
UniProt:
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
ExPASy
ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu). On this portal you find resources from many different SIB groups as well as external institutions.
Unimod
http://www.unimod.org/login.php?message=expired (Login as guest)
Unimod is a public domain database, distributed under a copyleft licence: "a copyright notice that permits unrestricted redistribution and modification, provided that all copies and derivatives retain the same permissions."
The aim is to create a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).
Prosite
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them [More details / References / Commercial users].
PROSITE is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids [More details].
PROSITE is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids [More details].
Virtual Proteomics Laboratory
The Proteomics Virtual Laboratory provides in-depth information about modern, high-throughput proteomic techniques available and their application to various proteomic studies. The field of proteomics has gained popularity following the successful completion of several genome sequencing projects and large amounts of gene data being made available to researchers. The genome, however, represents only the first step towards understanding complex biological processes. Significant amount of information regarding molecular and cellular processes can be obtained from the products of gene expression – the proteins. “Proteomics” is the study of the entire protein complement of a cell, organ or organism at a given time including the set of protein isoforms and all its complements. The high-throughput analysis of several proteins simultaneously requires robust platforms that can detect extremely small quantities of proteins with high sensitivity and specificity. The Proteomics Virtual Laboratory aims to provide students a first-hand experience of commonly used proteomic techniques with the help of animations and video footage of actual lab experiments. In addition to this, users will be provided reading material to enhance their theoretical knowledge about these techniques, which find wide applications such as discovery of biomarkers, immunological studies, protein-protein interaction studies etc. There has been a surge in the number of proteomics techniques developed over the last decade which have increasingly facilitated proteomics studies. The data generated through these experiments will also be made available, which will enable researchers and students to carry out data analysis and interpretation with the help of suitable software
Human Proteome Map
Kim et al. A draft map of the human proteome. 2014. Nature. 509, 575-581. [PubMed]
The Human Proteome Map (HPM) portal is an interactive resource to the scientific community by integrating the massive peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. All mass spectrometry data including precursors and HCD-derived fragments were acquired on the Orbitrap mass analyzers in the high-high mode. Currently, the HPM contains direct evidence of translation of a number of protein products derived from over 17,000 human genes covering >84% of the annotated protein-coding genes in humans based on >290,000 non-redundant peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. This includes 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues. The HPM portal provides an interactive web resource by reorganizing the label-free quantitative proteomic data set in a simple graphical view. In addition, the portal provides selected reaction monitoring (SRM) information for all peptides identified.
Proteomics
Proteomics clinical applications
Special Issue: Reviews 2014
February 20l4
Volume 8, Issue 1-2 Pages 1-126
Issue edited by Michael J. Dunn
Journal of Proteomics
http://www.journals.elsevier.com/journal-of-proteomics/Journal of Proteomics is the official journal of the European Proteomics Association (EuPA) and is aimed at both European and international protein scientists and analytical chemists in the field of proteomics, biomarker discovery, protein analytics, plant proteomics, microbial and animal proteomics, human studies and protein bioinformatics. The journal welcomes papers in new and upcoming areas such as metabolomics, genomics, systems biology, toxicogenomics and pharmacoproteomics. Journal of Proteomics unifies both fundamental scientists and clinicians, and includes translational research.Suggestions for reviews, webinars and thematic issues are welcome. All manuscripts are strictly peer reviewed and conform the highest ethical standards. Journal of Proteomics also publishes official EuPA reports and participates in the International Proteomics Tutorial Programme with HUPO and other partners.
Proteome Science considers manuscripts based on all aspects of functional and structural proteomics. Proteome Science is an open access, peer-reviewed, online journal considering research in proteomics. The journal is specifically interested in manuscripts that integrate functional or structural proteomic analysis with cell or developmental biology. Proteome Science will consider studies in the area of structural biology, mass spectrometry, protein arrays, bioinformatics, HTS assays, protein chemistry, cell biology, signal transduction and physiology - as long as a component of the study relates to proteomics.
Molecular & Cellular Proteomics
http://www.mcponline.org/In summary, Molecular & Cellular Proteomics will publish three types of original articles: research papers, database articles, and technology development articles. Mini-reviews and articles discussing important unresolved issues (perspective articles), as invited contributions, will also be published. Suggestions for appropriate topics will be welcome. Letters to the editor dealing with material published in MCP will be published at the discretion of the Editors.
Translational Proteomics
http://www.journals.elsevier.com/translational-proteomicsTranslational Proteomics covers all areas of human proteomics using multi-disciplinary approaches to untangle complex disease processes. Emphasis is placed on linking basic sciences to clinical research (from patient to bench to bedside). It focuses on the rapid dissemination of novel discoveries. Topics included but not limited to are:
Translational Systems Biology and Integrative Bioinformatics
Clinical Proteomics and Personalized medicine
Comparative proteomics and drug development
Medical bioinformatics and biostatistics
Food and Health
Clinical Proteomics and Personalized medicine
Comparative proteomics and drug development
Medical bioinformatics and biostatistics
Food and Health
Translational Proteomics is intended to academic, industrial and clinical researchers, physicians, pharmaceutical scientists, biochemists, clinical chemists, disease molecular biologists in the fields of applied human proteomics. Examples of diseases include oncology, neurology, immunity, cardiovascular disease, infectious diseases and any internal medicine disorder.
International Proteomics Tutorial Programme – supported by HUPO and EuPA
The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts have launched the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org
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