On the origins of Mendelian disease genes in man: the impact of gene duplication

Over 3,000 human diseases are known to be linked to heritable genetic variation, mapping to over 1,700 unique genes. Dating of the evolutionary age of these disease-associated genes has suggested that they have a tendency to be ancient, specifically coming into existence with early metazoa. The approach taken by past studies, however, assumes that the age of a disease is the same as the age of its common ancestor, ignoring the fundamental contribution of duplication events in the evolution of new genes and function. Here, we date both the common ancestor and the duplication history of known human disease-associated genes. We find that the majority of disease genes (80%) are genes that have been duplicated in their evolutionary history. Periods for which there are more disease-associated genes, for example, at the origins of bony vertebrates, are explained by the emergence of more genes at that time, and the majority of these are duplicates inferred to have arisen by whole-genome duplication. These relationships are similar for different disease types and the disease-associated gene's cellular function. This indicates that the emergence of duplication-associated diseases has been ongoing and approximately constant (relative to the retention of duplicate genes) throughout the evolution of life. This continued until approximately 390 Ma from which time relatively fewer novel genes came into existence on the human lineage, let alone disease genes. For single-copy genes associated with disease, we find that the numbers of disease genes decreases with recency. For the majority of duplicates, the disease-associated mutation is associated with just one of the duplicate copies. A universal explanation for heritable disease is, thus, that it is merely a by-product of the evolutionary process; the evolution of new genes (de novo or by duplication) results in the potential for new diseases to emerge

Lista preliminar dos Nematoda, Annelida e Chordata terrestres dos Açores

Apresenta-se uma lista preliminar dos Filos Nematoda, Annelida e Chordata terrestres dos Açores. Com base na recente lista de espécies animais terrestres da Europa, projecto “Fauna Europaea” (http://www.faunaeur.org), listam-se 80 espécies de nemátodos e 21 espécies de anelídeos terrestres. As cerca de 49 espécies de vertebrados (Chordata) listados correspondem às espécies que se reproduzem nos Açores.ABSTRACT: A preliminary list of the Phyla Nematoda, Annelida and Chordata was compiled. Based on the recent list of European terrestrial species, project “Fauna Europaea” (http://www.faunaeur.org), 80 species of Nematoda and 21 species of Annelida are listed. The listed 49 species of vertebrates (Chordata) are the species known to breed in the Azores

Food habits and dietary variability of pelagic nekton off Oregon and Washington, 1979-1984

The food habits of 20 species of pelagic nekton were investigated from collections made with small-mesh purse seines from 1979-84 off Washington and Oregon. Four species (spiny dogfish, Squalus acanthias; soupfin shark, Galeorhinus zyopterus; blue shark, Prionace glauca; and cutthroat trout, Salmo clarki) were mainly piscivorous. Six species (coho salmon, Oncorhynchus kisutch; chinook salmon, O. tshawytscha; black rockfish, Sebastes melanops; yellowtail rockfish, S. f1avidus; sablefish, Anoplopoma fimbria; and jack mackerel, Trachurus symmetricus) consumed both nektonic and planktonic organisms. The remaining species (market squid, Loligo opalescens; American shad, Alosa sapidissima; Pacific herring, Clupea harengus pallasi; northern anchovy, Engraulis mordax; pink salmon, O. gorbuscha; surf smelt, Hypomesus pretiosus; Pacific hake, Merluccius productus; Pacific saury, Cololabis saira; Pacific mackerel, Scomber japonicus; and medusafish, Icichthys lockingtom) were primarily planktonic feeders. There were substantial interannual, seasonal, and geographic variations in the diets of several species due primarily to changes in prey availability. Juvenile salmonids were not commonly consumed by this assemblage of fishes (PDF file contains 36 pages.

NG peptides: A novel family of neurophysin-associated neuropeptides

NOTICE: this is the author’s version of a work that was accepted for publication in GENE. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in GENE, [VOL 458, ISSUE 1-2, (2010)] DOI: 10.1016/j.gene.2010.03.00

Ascidiacea (Chordata, Tunicata) de Uruguay (Atlántico SO): Checklist y consideraciones zoogeográficas

The diversity of ascidians from the Southwestern Atlantic between 30°S and 40°S (southern Brazil, Uruguay and northern Argentina) remains as one of the poorest known of the West Atlantic. The objective of this work is to compile, analyze and discuss all published records of ascidians from Uruguay. They show the historical relevance of the studies performed by Herdman, Monniot F. and Monniot C. on ascidians collected at deep-sea stations by the HMS Challenger and the RV Atlantis II in the Argentine Basin. Total literature records include 38 ascidian species which are enumerated here for the first time. On the basis of the current knowledge, the ascidian fauna of Uruguayan waters encompasses: a) shallow-water species with temperate distribution (3 spp.); b) shelf and deep-sea species with Antarctic and Sub-Antarctic distribution (13 spp.); c) deep-sea species until now only collected off Río de La Plata (11 spp.); d) deep-sea species displaying a wide distribution (11 spp.). Only nine species have been recorded for the continental shelf; the remaining species were collected either from the slope (21) or the abyssal plain (5) or both deep-sea zones (3). Future research should be directed to record coastline and shelf species, assess the presence of exotic elements, and re-describe enigmatic species first described by Herdman (1882, 1886).Fil: Fabrizio Scarabino. Centro Universitario Regional del Este - CURE, Universidad de la República y Museo Nacional de Historia Natural, Montevideo, ; UruguayFil: Maggioni, Tamara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; ArgentinaFil: Taverna, Anabela Jesús. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; ArgentinaFil: Lagger, Cristian Fabian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Schwindt, Evangelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Biología de Organismos Marinos; ArgentinaFil: Guzmán López. Dirección Nacional de Recursos Acuáticos, Montevideo; UruguayFil: Leonardo Ortega. Dirección Nacional de Recursos Acuáticos, Montevideo; UruguayFil: Felipe García-Rodríguez. Centro Universitario Regional del Este -CURE, Universidad de la República, Montevideo ; UruguayFil: Tatian, Marcos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentin

Recovery at Morvin: SERPENT final report

Recovery from disturbance is poorly understood in deep water, but the extent of anthropogenic impacts is becoming increasingly well documented. We used Remotely Operated Vehicles (ROV) to visually assess the change in benthic habitat after exploratory hydrocarbon drilling disturbance around the Morvin well located at 380m depth in the Norwegian Sea.An ROV, launched directly from the rig drilling the well in 2006 was used to carry out video transects around the well before drilling and immediately after. On a return to the site three years after disturbance a larger survey was conducted with a ship-launched ROV in 2009. Transects were repeated at the disturbed area and random background transects were taken. Visible drill cuttings were mapped for each survey, and positions and counts of epibenthic invertebrate megafauna were determined, revealing a fauna dominated by Cnidaria (45% of total observations) and Porifera (33%).Immediately after disturbance a visible cuttings pile extended to over 100m from the well and megafaunal density was significantly reduced (0.07 individuals m-2) in comparison to pre-drill data (0.23 ind. m-2). Three years later the visible extent of the cuttings pile had reduced in size, reaching 60m from the well and considerably less in some headings. In comparison to background transects (0.21 ind. m-2), megafaunal density was significantly reduced on the remaining cuttings (0.04m-2), but beyond the visible disturbance there was no significant difference (0.15m-2). The investigation at this site shows a return to background densities of megafaunal organisms over a large extent of the area previously disturbed. However a central area, where the initial cuttings pile was deepest, demonstrated reduced sessile megafaunal density which persisted three years after disturbance. Elevated Barium concentration and reduced sediment grain size suggests persistence of disturbance beyond the remaining visibly impacted area which may result in changes to the infaunal communities undetectable by ROV video survey

Eliciting the Functional Taxonomy from protein annotations and taxa

The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules