A Greedy Algorithm for Aligning DNA Sequences
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Cottus Poecilopus Heckel, 1836, in the River Javorin- Ka, the Tatra
Oecologia Montana 2018, Cottus poecilopus Heckel, 1836, in the river Javorin- 27, 21-26 ka, the Tatra mountains, Slovakia M. JANIGA, Jr. In Tatranská Javorina under Muráň mountain, a small fish nursery was built by Christian Kraft von Institute of High Mountain Biology University of Hohenlohe around 1930. The most comprehensive Žilina, Tatranská Javorina 7, SK-059 56, Slovakia; studies on fish from the Tatra mountains were writ- e-mail:: [email protected] ten by professor Václav Dyk (1957; 1961), Dyk and Dyková (1964a,b; 1965), who studied altitudinal distribution of fish, describing the highest points where fish were found. His studies on fish were likely the most complex studies of their kind during that period. Along with his wife Sylvia, who illus- Abstract. This study focuses on the Cottus poe- trated his studies, they published the first realistic cilopus from the river Javorinka in the north-east studies on fish from the Tatra mountains including High Tatra mountains, Slovakia. The movement the river Javorinka (Dyk and Dyková 1964a). Feri- and residence of 75 Alpine bullhead in the river anc (1948) published the first Slovakian nomenclature were monitored and carefully recorded using GPS of fish in 1948. Eugen K. Balon (1964; 1966) was the coordinates. A map representing their location in next famous ichthyologist who became a recognised the river was generated. This data was collected in expert in the fish fauna of the streams of the Tatra the spring and summer of 2016 and in the autumn mountains, the river Poprad, and various high moun- of 2017. Body length and body weight of 67 Alpine tain lakes. -
Trout Stocking in SAC Rivers. Phase 1: Review of Stocking Practice
Trout stocking in SAC rivers. Phase 1: Review of stocking practice Science Report: SC030211/SR1 SCHO0707BMZC-E-P The Environment Agency is the leading public body protecting and improving the environment in England and Wales. It’s our job to make sure that air, land and water are looked after by everyone in today’s society, so that tomorrow’s generations inherit a cleaner, healthier world. Our work includes tackling flooding and pollution incidents, reducing industry’s impacts on the environment, cleaning up rivers, coastal waters and contaminated land, and improving wildlife habitats. This report is the result of research commissioned and funded by the Environment Agency (Habitats Directive Programme), English Nature and the Countryside Council for Wales. Published by: Author: Environment Agency, Rio House, Waterside Drive, Aztec West, N. Giles Almondsbury, Bristol, BS32 4UD Tel: 01454 624400 Fax: 01454 624409 Dissemination Status: www.environment-agency.gov.uk Publicly available ISBN: 978-1-84432-796-6 Keywords: Trout, stocking, cSAC rivers, salmon, bullhead, crayfish © Environment Agency July 2007 Research Contractor: All rights reserved. This document may be reproduced with prior Dr Nick Giles & Associates, permission of the Environment Agency. 50 Lake Road, Verwood, Dorset, BH31 6BX. The views expressed in this document are not necessarily Tel: 01202 824245 those of the Environment Agency. Email: [email protected] This report is printed on Cyclus Print, a 100% recycled stock, Environment Agency’s Project Manager: which is 100% post consumer waste and is totally chlorine free. Miran Aprahamian, Richard Fairclough House, Warrington Water used is treated and in most cases returned to source in better condition than removed. -
Baylisascariasis
Baylisascariasis Importance Baylisascaris procyonis, an intestinal nematode of raccoons, can cause severe neurological and ocular signs when its larvae migrate in humans, other mammals and birds. Although clinical cases seem to be rare in people, most reported cases have been Last Updated: December 2013 serious and difficult to treat. Severe disease has also been reported in other mammals and birds. Other species of Baylisascaris, particularly B. melis of European badgers and B. columnaris of skunks, can also cause neural and ocular larva migrans in animals, and are potential human pathogens. Etiology Baylisascariasis is caused by intestinal nematodes (family Ascarididae) in the genus Baylisascaris. The three most pathogenic species are Baylisascaris procyonis, B. melis and B. columnaris. The larvae of these three species can cause extensive damage in intermediate/paratenic hosts: they migrate extensively, continue to grow considerably within these hosts, and sometimes invade the CNS or the eye. Their larvae are very similar in appearance, which can make it very difficult to identify the causative agent in some clinical cases. Other species of Baylisascaris including B. transfuga, B. devos, B. schroeder and B. tasmaniensis may also cause larva migrans. In general, the latter organisms are smaller and tend to invade the muscles, intestines and mesentery; however, B. transfuga has been shown to cause ocular and neural larva migrans in some animals. Species Affected Raccoons (Procyon lotor) are usually the definitive hosts for B. procyonis. Other species known to serve as definitive hosts include dogs (which can be both definitive and intermediate hosts) and kinkajous. Coatimundis and ringtails, which are closely related to kinkajous, might also be able to harbor B. -
Abstracts Genome 10K & Genome Science 29 Aug - 1 Sept 2017 Norwich Research Park, Norwich, Uk
Genome 10K c ABSTRACTS GENOME 10K & GENOME SCIENCE 29 AUG - 1 SEPT 2017 NORWICH RESEARCH PARK, NORWICH, UK Genome 10K c 48 KEYNOTE SPEAKERS ............................................................................................................................... 1 Dr Adam Phillippy: Towards the gapless assembly of complete vertebrate genomes .................... 1 Prof Kathy Belov: Saving the Tasmanian devil from extinction ......................................................... 1 Prof Peter Holland: Homeobox genes and animal evolution: from duplication to divergence ........ 2 Dr Hilary Burton: Genomics in healthcare: the challenges of complexity .......................................... 2 INVITED SPEAKERS ................................................................................................................................. 3 Vertebrate Genomics ........................................................................................................................... 3 Alex Cagan: Comparative genomics of animal domestication .......................................................... 3 Plant Genomics .................................................................................................................................... 4 Ksenia Krasileva: Evolution of plant Immune receptors ..................................................................... 4 Andrea Harper: Using Associative Transcriptomics to predict tolerance to ash dieback disease in European ash trees ............................................................................................................ -
120421-24Recombschedule FINAL.Xlsx
Friday 20 April 18:00 20:00 REGISTRATION OPENS in Fira Palace 20:00 21:30 WELCOME RECEPTION in CaixaForum (access map) Saturday 21 April 8:00 8:50 REGISTRATION 8:50 9:00 Opening Remarks (Roderic GUIGÓ and Benny CHOR) Session 1. Chair: Roderic GUIGÓ (CRG, Barcelona ES) 9:00 10:00 Richard DURBIN The Wellcome Trust Sanger Institute, Hinxton UK "Computational analysis of population genome sequencing data" 10:00 10:20 44 Yaw-Ling Lin, Charles Ward and Steven Skiena Synthetic Sequence Design for Signal Location Search 10:20 10:40 62 Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads 10:40 11:00 178 Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq 11:00 11:30 coffee break Session 2. Chair: Bonnie BERGER (MIT, Cambrige US) 11:30 11:50 139 Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly 11:50 12:10 171 Yan Huang, Yin Hu and Jinze Liu A Robust Method for Transcript Quantification with RNA-seq Data 12:10 12:30 120 Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping 12:30 12:50 205 Dmitri Pervouchine Evidence for widespread association of mammalian splicing and conserved long range RNA structures 12:50 13:10 169 Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes 13:10 13:30 217 Rory Stark Differential oestrogen receptor binding is associated with clinical outcome in breast cancer 13:30 15:00 lunch break Session 3. -
Methodology for Predicting Semantic Annotations of Protein Sequences by Feature Extraction Derived of Statistical Contact Potentials and Continuous Wavelet Transform
Universidad Nacional de Colombia Sede Manizales Master’s Thesis Methodology for predicting semantic annotations of protein sequences by feature extraction derived of statistical contact potentials and continuous wavelet transform Author: Supervisor: Gustavo Alonso Arango Dr. Cesar German Argoty Castellanos Dominguez A thesis submitted in fulfillment of the requirements for the degree of Master’s on Engineering - Industrial Automation in the Department of Electronic, Electric Engineering and Computation Signal Processing and Recognition Group June 2014 Universidad Nacional de Colombia Sede Manizales Tesis de Maestr´ıa Metodolog´ıapara predecir la anotaci´on sem´antica de prote´ınaspor medio de extracci´on de caracter´ısticas derivadas de potenciales de contacto y transformada wavelet continua Autor: Tutor: Gustavo Alonso Arango Dr. Cesar German Argoty Castellanos Dominguez Tesis presentada en cumplimiento a los requerimientos necesarios para obtener el grado de Maestr´ıaen Ingenier´ıaen Automatizaci´onIndustrial en el Departamento de Ingenier´ıaEl´ectrica,Electr´onicay Computaci´on Grupo de Procesamiento Digital de Senales Enero 2014 UNIVERSIDAD NACIONAL DE COLOMBIA Abstract Faculty of Engineering and Architecture Department of Electronic, Electric Engineering and Computation Master’s on Engineering - Industrial Automation Methodology for predicting semantic annotations of protein sequences by feature extraction derived of statistical contact potentials and continuous wavelet transform by Gustavo Alonso Arango Argoty In this thesis, a method to predict semantic annotations of the proteins from its primary structure is proposed. The main contribution of this thesis lies in the implementation of a novel protein feature representation, which makes use of the pairwise statistical contact potentials describing the protein interactions and geometry at the atomic level. -
Paleolithic Fish from Southern Poland: a Paleozoogeographical Approach
10. ARCH. VOL. 22 (2ª)_ARCHAEOFAUNA 04/09/13 18:05 Página 123 Archaeofauna 22 (2013): 123-131 Paleolithic Fish from Southern Poland: A Paleozoogeographical Approach LEMBI LÕUGAS1, PIOTR WOJTAL2, JAROSŁAW WILCZYń SKI2 & KRZYSZTOF STEFANIAK3 1Department of Archaeobiology and Ancient Technology, Institute of History, University of Tallinn, Rüütli 6, EE10130 Tallinn, Estonia [email protected] 2Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Slawkowska 17, 31-016 Cracow, Poland [email protected], [email protected] 3Institute of Zoology, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland [email protected] (Received 5 August 2012; Revised 31 October 2012; Accepted 17 July 2013) ABSTRACT: The area covered by glaciers during the Last Glacial Maximum (LGM) includes a large territory in northern Europe. In this region, Paleolithic finds are rare and fish bones fair- ly unique. Analysis of Paleolithic fish bones outside of the LGM range was carried out with the intention of reconstructing the paleozoogeographical distribution of this animal group before the retreat of the ice cap from the Baltic Basin. This research focuses on an archaeological fish bone assemblage from Obłazowa Cave, southern Poland. Other samples examined are from Krucza Skała Rock Shelter (Kroczyckie Rocks), Biśnik Cave (Wodąca Valley), Borsuka Cave (Szklarka Valley), and Nad Tunelem Cave (Prądnik Valley). The latter sites are considered natu- rally accumulated deposits, but, at Obłazowa and Krucza Skała, anthropogenic factors also played an important role. The fish bones from the Paleolithic cave deposits of Obłazowa inclu- ded at least six fish genera: Thymallus, Coregonus, Salmo, Salvelinus, Esox, and Cottus. -
Subclase Secernentea
Orden Ascaridida T. 21. ASCARIDIDOS. Generalidades y Clasificación. Incluye parásitos con tres labios de gran tamaño. En los machos, cuando existen alas caudales, éstas se localizan Ascaridioideos y Anisakoideos. lateralmente. 1. GENERALIDADES Y CLASIFICACIÓN Los ascarídidos son nematodos con fasmidios (quimiorreceptores posteriores); pertenecen por tanto a la Clase Secernentea. Los machos presentan generalmente alas caudales o bolsas copuladoras. Los ascarídidos de interés veterinario se clasifican en base al siguiente esquema taxonómico: Orden Ascaridida Superfamilia Ascaridoidea Familia Ascarididae Género Ascaris Género Parascaris Género Toxocara Género Toxascaris Fig. 1. Extremo caudal del macho en Ascarididae. Superfamilia Anisakoidea Familia Anisakidae Género Anisakis Superfamilia Ascaridoidea Género Contracaecum Género Phocanema Por lo general son nematodos de gran tamaño. No Género Pseudoterranova presentan cápsula bucal y el esófago carece de bulbo posterior Superfamilia Heterakoidea pronunciado. En algunas especies el esófago está seguido de un Familia Heterakidae: G. Heterakis ventrículo posterior corto que puede derivarse en un apéndice Familia Ascaridiidae: G. Ascaridia 1 ventricular, mientras que otras presentan una prolongación del 2.1. GÉNERO ASCARIS intestino en sentido craneal que se conoce como ciego intestinal (Fig. 12, Familia Anisakidae). Existen dos espículas en los machos Ascaris suum y el ciclo de vida puede ser directo o indirecto. Es un parásito del cerdo con distribución cosmopolita y de 2. FAMILIA ASCARIDIDAE considerable importancia económica. Sin embargo, su prevalencia está disminuyendo debido a los cada vez más frecuentes sistemas Los labios, que como característica del Orden están bien de producción intensiva y a la instauración de tratamientos desarrollados, presentan una serie de papilas labiales externas e antihelmínticos periódicos. Durante años se ha considerado internas, así como un borde denticular en su cara interna. -
Gastric Nematode Diversity Between Estuarine and Inland Freshwater
International Journal for Parasitology: Parasites and Wildlife 3 (2014) 227–235 Contents lists available at ScienceDirect International Journal for Parasitology: Parasites and Wildlife journal homepage: www.elsevier.com/locate/ijppaw Gastric nematode diversity between estuarine and inland freshwater populations of the American alligator (Alligator mississippiensis, daudin 1802), and the prediction of intermediate hosts Marisa Tellez a,*, James Nifong b a Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA b Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, USA ARTICLE INFO ABSTRACT Article history: We examined the variation of stomach nematode intensity and species richness of Alligator mississippiensis Received 11 June 2014 from coastal estuarine and inland freshwater habitats in Florida and Georgia, and integrated prey content Revised 23 July 2014 data to predict possible intermediate hosts. Nematode parasitism within inland freshwater inhabiting Accepted 24 July 2014 populations was found to have a higher intensity and species richness than those inhabiting coastal es- tuarine systems. This pattern potentially correlates with the difference and diversity of prey available Keywords: between inland freshwater and coastal estuarine habitats. Increased consumption of a diverse array of Alligator mississippiensis prey was also correlated with increased nematode intensity in larger alligators. Parasitic nematodes Ascarididae Georgia Dujardinascaris waltoni, Brevimulticaecum -
Exploiting High Throughput DNA Sequencing Data for Genomic Analysis
Exploiting high throughput DNA sequencing data for genomic analysis Markus Hsi-Yang Fritz Darwin College A dissertation submitted to the University of Cambridge for the degree of Doctor of Philosophy 14th October 2011 Markus Hsi-Yang Fritz EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD United Kingdom email: [email protected] This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. No part of this work has been submitted or is currently being submitted for any other qualification. This document does not exceed the word limit of 60,000 words1 as defined by the Biology Degree Committee. Markus Hsi-Yang Fritz 14th October 2011 1 excluding bibliography, figures, appendices etc. To an exceptional scientist — my Dad. Exploiting high throughput DNA sequencing data for genomic analysis Summary Markus Hsi-Yang Fritz Darwin College The last few years have witnessed a drastic increase in genomic data. This has been facilitated by the shift away from the Sanger sequencing tech- nique to an array of high-throughput methods — so-called next-generation sequencing technologies. This enormous growth of available DNA data has been a tremendous boon to large-scale genomics studies and has rapidly advanced fields such as environmental genomics, ancient DNA research, population genomics and disease association. On the other hand, however, researchers and sequence archives are now facing an enormous data deluge. Critically, the rate of sequencing data accumulation is now outstripping advances in hard drive capacity, network bandwidth and processing power. -
Strategic Plan 2011-2016
Strategic Plan 2011-2016 Wellcome Trust Sanger Institute Strategic Plan 2011-2016 Mission The Wellcome Trust Sanger Institute uses genome sequences to advance understanding of the biology of humans and pathogens in order to improve human health. -i- Wellcome Trust Sanger Institute Strategic Plan 2011-2016 - ii - Wellcome Trust Sanger Institute Strategic Plan 2011-2016 CONTENTS Foreword ....................................................................................................................................1 Overview .....................................................................................................................................2 1. History and philosophy ............................................................................................................ 5 2. Organisation of the science ..................................................................................................... 5 3. Developments in the scientific portfolio ................................................................................... 7 4. Summary of the Scientific Programmes 2011 – 2016 .............................................................. 8 4.1 Cancer Genetics and Genomics ................................................................................ 8 4.2 Human Genetics ...................................................................................................... 10 4.3 Pathogen Variation .................................................................................................. 13 4.4 Malaria -
Toxocara Cati (Schrank, 1788) (Nematoda, Ascarididae) in Different Wild Feline Species in Brazil: New Host Records
Biotemas, 26 (3): 117-125, setembro de 2013 http://dx.doi.org/10.5007/2175-7925.2013v26n3p117117 ISSNe 2175-7925 Toxocara cati (Schrank, 1788) (Nematoda, Ascarididae) in different wild feline species in Brazil: new host records Moisés Gallas * Eliane Fraga da Silveira Departamento de Biologia, Museu de Ciências Naturais Universidade Luterana do Brasil, CEP 92425-900, Canoas – RS, Brasil *Autor para correspondência [email protected] Submetido em 07/03/2013 Aceito para publicação em 14/05/2013 Resumo Toxocara cati (Schrank, 1788) (Nematoda, Ascarididae) em diferentes espécies de felinos silvestres no Brasil: novos registros de hospedeiros. Esta é a primeira descrição detalhada de Toxocara cati parasitando felinos na América do Sul. Dezessete felinos silvestres (Leopardus colocolo, Leopardus geoffroyi, Leopardus tigrinus e Puma yagouaroundi) atropelados foram coletados em diferentes municípios do Estado do Rio Grande do Sul, Brasil. A morfometria de machos e fêmeas permitiu a identificação de espécimes como T. cati. Os helmintos foram encontrados no estômago e intestino dos hospedeiros com prevalência de 66,6% em L. colocolo, L. geoffroyi e L. tigrinus; e 60% em P. yagouaroundi. Foram calculados os parâmetros ecológicos para cada hospedeiro e, L. colocolo teve a maior intensidade de infecção (22,5 helmintos/hospedeiro). Este é o primeiro registro de T. cati parasitando quatro espécies de felinos silvestres no Sul do Brasil e, dois novos registros de hospedeiros para esse parasito. Palavras-chave: Felinos; Leopardus; Puma; Sul do Brasil; Toxocara Abstract This is the first detailed description ofToxocara cati parasitizing felines in South America. Seventeen run over wild felines (Leopardus colocolo, Leopardus geoffroyi, Leopardus tigrinus, and Puma yagouaroundi) were collected from different towns in the State of Rio Grande do Sul, Brazil.