Three decades of the Human Genome Organization.

The Human Genome Organization (HUGO) was initially established in 1988 to help integrate international scientific genomic activity and to accelerate the diffusion of knowledge from the efforts of the human genome project. Its founding President was Victor McKusick. During the late 1980s and 1990s, HUGO organized lively gene mapping meetings to accurately place genes on the genome as chromosomes were being sequenced. With the completion of the Human Genome Project, HUGO went through some transitions and self-reflection. In 2020, HUGO (which hosts a large annual scientific meeting and comprises the renowned HUGO Gene Nomenclature Committee [HGNC], responsible for naming genes, and an outstanding Ethics Committee) was merged with the Human Genome Variation Society (HGVS; which defines the correct nomenclature for variation description) and the Human Variome Project (HVP; championed by the late Richard Cotton) into a single organization that is committed to assembling human genomic variation from all over the world. This consolidated effort, under a new Executive Board and seven focused committees, will facilitate efficient and effective communication and action to bring the benefits of increasing knowledge of genome diversity and biology to people all over the world

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

Online Mendelian Inheritance in Man (OMIM™) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (http://www.ncbi.nlm.nih.gov/omim/) is now distributed electronically by the National Center for Biotechnology Information, where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, HUGO nomenclature, MapViewer, GeneTests, patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics

The Light Microscopy of Triglyceride Digestion

During fat digestion (lipolysis) a number of physiochemical events can be seen directly by light microscopy. Hydrolysis of emulsified fat droplets bylipases at pHs above about 6.5 proceeds with the formation of visible product phases that may include both crystalline as well as liquid crystalline phases. The crystalline phase is primarily calcium-fatty acid soap and its formation is favored by high calcium concentrations, alkaline pHs, and inhibited by low pH and monoglycerides. The formation of liquid crystalline product phases are favored by low calcium-concentrations. monoglycerides and lipid saturated bile salt solutions. Both phases are solubilized by bile salts but the crystalline phase to a much lesser degree. Colored and fluorescent hydrophobic solutes that a re dissolved in long cha in triglyceride appear to flow directly into the liquid crystalline product phases where they can be codispersed with the digested lipid by bile salts. Measurements of the shrinking diameters of digesting fat droplets show that enzyme activity on individual droplet~ falls rapidly during lipolysis. This suggests that lipase molecules a re physically displaced from the substrate interface during lipolysis and dispersed in the product phases

Les réseaux sociaux numériques de chercheurs en SHS

Que ce soit Research gate, academia.edu ou des sites avec une fonction sociale  (Mendeley, Zotero), les outils se diversifient. Sont-ils nécessaires ? Utiles ? Qui est vraiment demandeur ? Prennent-ils en compte les besoins des chercheurs en SHS ? Quelles fonctions seraient les plus indispensables à la communauté des SHS

SNP and Mutation Data on the Web – Hidden Treasures for Uncovering

SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many years, is still stored in disparate sources, although moves are afoot to move to a similar central database. These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease. The impending availability of a complete human genome presents us with an ideal framework to integrate both these forms of data, as our understanding of the mechanisms of disease increase, the full genomic context of variation may become increasingly significant

Systematic review of fatty acid composition of human milk from mothers of preterm compared to full-term infants

Background: Fatty acid composition of human milk serves as guidance for the composition of infant formulae. The aim of the study was to systematically review data on the fatty acid composition of human milk of mothers of preterm compared to full-term infants. Methods: An electronic literature search was performed in English (Medline and Medscape) and German (SpringerLink) databases and via the Google utility. Fatty acid compositional data for preterm and fullterm human milk were converted to differences between means and 95% confidence intervals. Results: We identified five relevant studies publishing direct comparison of fatty acid composition of preterm versus full-term human milk. There were no significant differences between the values of the principal saturated and monounsaturated fatty acids. In three independent studies covering three different time points of lactation, however, docosahexaenoic acid (DHA) values were significantly higher in milk of mothers of preterm as compared to those of full-term infants, with an extent of difference considered nutritionally relevant. Conclusion: Higher DHA values in preterm than in full-term human milk underlines the importance of using own mother's milk for feeding preterm babies and raises the question whether DHA contents in preterm formulae should be higher than in formulae for full-term infants. Copyright (c) 2008 S. Karger AG, Basel

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

A particular challenge in biomedical text mining is to find ways of handling ‘comprehensive’ or ‘associative’ queries such as ‘Find all genes associated with breast cancer’. Given that many queries in genomics, proteomics or metabolomics involve these kind of comprehensive searches we believe that a web-based tool that could support these searches would be quite useful. In response to this need, we have developed the PolySearch web server. PolySearch supports >50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is ‘Given X, find all Y's’ where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences. PolySearch's performance has been assessed in tasks such as gene synonym identification, protein–protein interaction identification and disease gene identification using a variety of manually assembled ‘gold standard’ text corpuses. Its f-measure on these tasks is 88, 81 and 79%, respectively. These values are between 5 and 50% better than other published tools. The server is freely available at http://wishart.biology.ualberta.ca/polysearc

SNPedia: a wiki supporting personal genome annotation, interpretation and analysis

SNPedia (http://www.SNPedia.com) is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Online since 2006 and freely available for personal use, SNPedia has focused on the medical, phenotypic and genealogical associations of single nucleotide polymorphisms. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). In this article, we discuss the growth of this resource and its use by affiliated software to create personal genome reports