ALBERT

Description: Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756445/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756445/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berriman, Matthew -- Haas, Brian J -- LoVerde, Philip T -- Wilson, R Alan -- Dillon, Gary P -- Cerqueira, Gustavo C -- Mashiyama, Susan T -- Al-Lazikani, Bissan -- Andrade, Luiza F -- Ashton, Peter D -- Aslett, Martin A -- Bartholomeu, Daniella C -- Blandin, Gaelle -- Caffrey, Conor R -- Coghlan, Avril -- Coulson, Richard -- Day, Tim A -- Delcher, Art -- DeMarco, Ricardo -- Djikeng, Appolinaire -- Eyre, Tina -- Gamble, John A -- Ghedin, Elodie -- Gu, Yong -- Hertz-Fowler, Christiane -- Hirai, Hirohisha -- Hirai, Yuriko -- Houston, Robin -- Ivens, Alasdair -- Johnston, David A -- Lacerda, Daniela -- Macedo, Camila D -- McVeigh, Paul -- Ning, Zemin -- Oliveira, Guilherme -- Overington, John P -- Parkhill, Julian -- Pertea, Mihaela -- Pierce, Raymond J -- Protasio, Anna V -- Quail, Michael A -- Rajandream, Marie-Adele -- Rogers, Jane -- Sajid, Mohammed -- Salzberg, Steven L -- Stanke, Mario -- Tivey, Adrian R -- White, Owen -- Williams, David L -- Wortman, Jennifer -- Wu, Wenjie -- Zamanian, Mostafa -- Zerlotini, Adhemar -- Fraser-Liggett, Claire M -- Barrell, Barclay G -- El-Sayed, Najib M -- 086151/Wellcome Trust/United Kingdom -- 5D43TW006580/TW/FIC NIH HHS/ -- 5D43TW007012-03/TW/FIC NIH HHS/ -- AI054711-01A2/AI/NIAID NIH HHS/ -- AI48828/AI/NIAID NIH HHS/ -- R01 GM083873/GM/NIGMS NIH HHS/ -- R01 GM083873-07/GM/NIGMS NIH HHS/ -- R01 GM083873-08/GM/NIGMS NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- R01 LM006845-09/LM/NLM NIH HHS/ -- U01 AI048828/AI/NIAID NIH HHS/ -- U01 AI048828-01/AI/NIAID NIH HHS/ -- U01 AI048828-02/AI/NIAID NIH HHS/ -- WT085775/Z/08/Z/Wellcome Trust/United Kingdom -- England -- Nature. 2009 Jul 16;460(7253):352-8. doi: 10.1038/nature08160.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Cambridge CB10 1SD, UK. mb4@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19606141" target="_blank"〉PubMed〈/a〉

Description: No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen alpha1- and alpha2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Welker, Frido -- Collins, Matthew J -- Thomas, Jessica A -- Wadsley, Marc -- Brace, Selina -- Cappellini, Enrico -- Turvey, Samuel T -- Reguero, Marcelo -- Gelfo, Javier N -- Kramarz, Alejandro -- Burger, Joachim -- Thomas-Oates, Jane -- Ashford, David A -- Ashton, Peter D -- Rowsell, Keri -- Porter, Duncan M -- Kessler, Benedikt -- Fischer, Roman -- Baessmann, Carsten -- Kaspar, Stephanie -- Olsen, Jesper V -- Kiley, Patrick -- Elliott, James A -- Kelstrup, Christian D -- Mullin, Victoria -- Hofreiter, Michael -- Willerslev, Eske -- Hublin, Jean-Jacques -- Orlando, Ludovic -- Barnes, Ian -- MacPhee, Ross D E -- England -- Nature. 2015 Jun 4;522(7554):81-4. doi: 10.1038/nature14249. Epub 2015 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] BioArCh, University of York, York YO10 5DD, UK [2] Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. ; BioArCh, University of York, York YO10 5DD, UK. ; Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen K, Denmark. ; Institute of Zoology, Zoological Society of London, London NW1 4RY, UK. ; CONICET- Division Paleontologia de Vertebrados, Museo de La Plata. Facultad de Ciencias Naturales y Museo de La Plata, Universidad Nacional de La Plata. Paseo del Bosque s/n, B1900FWA, La Plata, Argentina. ; Seccion Paleontologia de Vertebrados. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", 470 Angel Gallardo Av., C1405DJR, Buenos Aires, Argentina. ; Institute of Anthropology, Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 7, D-55128 Mainz, Germany. ; Department of Chemistry, University of York, York YO10 5DD, UK. ; Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK. ; Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA. ; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK. ; Applications Development, Bruker Daltonik GmbH, 28359 Bremen, Germany. ; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark. ; Department of Materials Science and Metallurgy, University of Cambridge, Cambridge CB3 0FS, UK. ; Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. ; 1] BioArCh, University of York, York YO10 5DD, UK [2] Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam OT Golm, Germany. ; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. ; Department of Mammalogy, American Museum of Natural History, New York, New York 10024, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25799987" target="_blank"〉PubMed〈/a〉

Description: The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies.