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Bioinformatic methods for metagenomics and comparative genetics in veterinary medicine

Norling, Martin (2014). Bioinformatic methods for metagenomics and comparative genetics in veterinary medicine. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2014:73
ISBN 978-91-576-8094-5
eISBN 978-91-576-8095-2
[Doctoral thesis]

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Abstract

Good science includes innovation, investigation, and rigor. This thesis’ first study is related to rigor. This study was performed at the International Livestock Research Institute (ILRI) in Nairobi, as part of the Arbovirus Incidence and Diversity (AVID) project. A field sample recording system was developed, which saves time and location metadata from the global positioning system (GPS), as well as a connected system monitoring the biobank, freezer, incubators and servers. This monitoring system more than once prevented loss of resources due to freezer failure by alerting responsible personnel, and was later published in 'Biopreservation and Biobanking'.

The sampling system was re-used in the second study, a Ugandan project aimed to identify African swine fever (ASF) in pigs. In this study Ndumu virus, a relatively unstudied virus previously only found in culicine mosquitoes, was discovered in domestic pigs.

For the third study, collaboration with ILRI continued with a study analyzing the 'Muguga Cocktail', the live vaccine currently used to control Theileria parva, a protozoan parasite causing East Coast Fever (ECF) in cattle. Live vaccines have many problems, such as high costs, difficult manufacturing, and the risk that misused vaccine will spread the disease. An in-depth study of the three parasite stocks included in the vaccine was performed, where genomic differences were identified with the goal of explaining the success of the vaccine, as well as identify a potential set of antigens which may in the future replace the live vaccine with a subunit vaccine.

Finally, for the fourth study, the metagenomic theme continued with the development of the MetLab, a tool for experimental design and analysis for viral metagenomics projects. The tool consists of three parts: (i) tools to estimate the sequencing needs of a metagenomic project, (ii) simulation tools, allowing users to simulate metagenomics sequencing data, and (iii) the system runs metagenomic analysis pipelines.

Authors/Creators:Norling, Martin
Title:Bioinformatic methods for metagenomics and comparative genetics in veterinary medicine
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :19 September 2014
Volume:2014:73
Number of Pages:62
Papers/manuscripts:
NumberReferences
I.Charles Masembe, George Michuki, Maria Onyango, Cecilia Rumberia, Martin Norling, Richard P Bishop, Appolinaire Djikeng, Stephen J Kemp, Alan Orth, Robert A Skilton, Karl Ståhl, and Anne Fischer (2012). Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus. Virology Journal vol 9(11).
II.Martin Norling, Absolomon Kihara, and Steve Kemp (2013). Web-Based Biobank System Infrastructure Monitoring Using Python, Perl, and PHP. Biopreservation and Biobanking vol 11(6), 355-358.
III.Martin Norling, Richard P. Bishop, Roger Pelle, Weihong Qi, Sonal Henson, Kyle Tretina, David Odongo, Stephen Mwaura, Thomas Njoroge, Erik Bongcam-Rudloff Claudia A. Daubenberger, Joana C. Silva. Whole Genome Comparisons of the Three Major Stocks Comprising the Live Sporozoite Theileria parva Vaccine. (Manuscript)
IV.Martin Norling, Oskar Karlsson, Erik Bongcam-Rudloff, Juliette Hayer. MetLab: An In Silico Experimental Design, Simulation and Validation Tool for Viral Metagenomics studies. (Manuscript)
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8094-5
ISBN for electronic version:978-91-576-8095-2
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:L Animal production > L70 Veterinary science and hygiene - General aspects
L Animal production > L73 Animal diseases
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
Agrovoc terms:bioinformatics, swine, cattle, african swine fever, african swine fever virus, east coast fever, theileria parva, genomes, genomics, vaccines, vaccination, east africa
Keywords:bioinformatics, metagenomics, virology, infection biology, next generation sequencing
URN:NBN:urn:nbn:se:slu:epsilon-e-2140
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2140
ID Code:11537
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
External funders:FORMAS and Swedish International Development Cooperation Agency
Deposited By: Martin Norling
Deposited On:26 Sep 2014 13:05
Metadata Last Modified:14 Dec 2014 00:40

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