| 1. |
- Niazi, Adnan, et al.
(författare)
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Genome Analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: A Rhizobacterium That Improves Plant Growth and Stress Management
- 2014
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plantbacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.
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| 2. |
- Karlsson Lindsjö, Oskar, et al.
(författare)
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MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies
- 2016
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens' theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab.
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| 3. |
- Manzoor, Shahid, et al.
(författare)
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Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036
- 2013
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Ingår i: Genome Announcements. - 2169-8287. ; 1, s. e00111-13
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Tidskriftsartikel (refereegranskat)abstract
- We announce here the genome sequence of Bacillus amyloliquefaciens strain UCMB5036, a plant growth-promoting bacterium isolated from a cotton plant. Its genome contains gene clusters involved in nonribosomal synthesis of secondary metabolites known for their antimicrobial activities. The availability of this genome will provide novel insights into plant-bacterium-associated activities.
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| 4. |
- Truvé, Katarina, et al.
(författare)
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Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
- 2016
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Ingår i: Plos Genetics. - : Public Library of Science (PLoS). - 1553-7404 .- 1553-7390. ; 12:5
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Tidskriftsartikel (refereegranskat)abstract
- Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10(-8)). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility.
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| 5. |
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| 6. |
- Bongcam Rudloff, Erik
(författare)
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2013 Annual General Meeting: Executive Board Report
- 2013
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Ingår i: EMBnet.journal. - 2226-6089. ; 19.1, s. 24-25
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- During the past year, the Executive Board (EB) met regularly and held frequent meetings with the Operational Board via Skype. These meetings allowed discussion of a range of issues relating to the Project Committees (PCs), to EMBnet.journal, to the website, the Stichting accounts, membership, etc. In alternate months, we also endeavoured to convene Skype meetings open to the full EMBnet constituency; however, for larger numbers of attendees, technical issues continued to cause problems. Attempting to address these issues, we took the first steps towards evaluating the various tools and technologies available for online meetings, by creating a list of existing tools, and a protocol on how to test them. The test will be realised in the same spirit as the ‘ping project1' of the ‘80s. The 2013 AGM allowed us to convene a working group to discuss the issues in more detail, and to initiate a common experiment with different software and different Nodes. The ultimate goal is to write a white paper and to publish the results in EMBnet.journal. The last year has been both busy and productive, building substantially on the programme of work we outlined in 2010. In particular, working closely with Itico2 to improve the EMBnet ‘brand', we finally launched the new website, which now includes a new online fee-payment module for individual members. We call on all members to help augment the content of the new site and to help keep it up-to-date. Since the 2012 AGM in Uppsala, EMBnet's training strategy has been dominated by our leadership of GOBLET3 (the Global Organisation for Bioinformatics Learning, Education and Training), which has been established as a Stichting, registered in the Netherlands, following the successful model of EMBnet. Working through GOBLET has significantly increased our level of interaction and cooperation with a range of major international societies and networks (including ISCB4, ASBCB5,ISB6, APBioNet7, SoIBio8, ABN9 and so on) - from the original 10 members who signed the Memorandum of Understanding to establish GOBLET, a further 16 organisations and several individuals have committed to join the Foundation. Another profound advance for EMBnet this year has been the final ratification of the new statutes, which were voted in during the Uppsala 2012 AGM - these statutes became legally binding in April 2013. The most significant result of the change is that we are now able formally to accept individual members (this allows, say, former Node managers to join, or any individual to participate in EMBnet's activities but whose organisation is not a member). Since ratification of the statutes, we have already had several membership applications, and welcomed one new organisation; new memberships will be processed without delay via the online payment system. The new statutes also ushered in changes to the internal structure of the organisation, obliging the PC Chairs and the EB to work together much more closely than they have done in the past; it has also allowed us to streamline the way in which EMBnet's activities
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| 7. |
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| 8. |
- Bongcam Rudloff, Erik
(författare)
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Capacity building and bioinformatics challenges
- 2014
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Ingår i: The SLU Global Food Security Research and Capacity Development Programme 2012-2014 – A Swedish Government Initiative. ; 2014:6, s. 68-71
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Moderna biotekniska framgångar bidrar till att skapa nya möjligheter inom den globala jordbrukssektorn och till att på lång sikt minska fattigdom och hunger. Nya växtgenotyper som till exempel är toleranta mot torka eller översvämning eller som klarar av insekt- eller svampangrepp är några exempel. Metodutveckling inom bioinformatik ligger till grund för många av dessa framgångar. Få afrikanska forskare har fått utbildning i hur man använder och drar nytta av dessa verktyg och det saknas en utvecklad infrastruktur inom området bioinformatik i det afrikanska vetenskapssamhället. Projektet syftar till att bygga upp bioinformatikkapacitet inom afrikanska jordbruksuniversitet och institutioner. Detta kommer att bidra till ett förbättrat bioteknikstöd i jordbrukets kamp mot hunger. Forskare från SLU tillsammans med afrikanska partners (från ILRI-BecA (International Livestock Research Institute - Biosciences of Eastern and Central Africa), ICPE (International Center for Insect Physiology and Ecology) and ICRISAT (International Crops Research Institute for the Semi-Arid Tropics)) arbetar för att öka samarbetet mellan svenska och afrikanska forskare inom bioinformatik och för att bygga upp en afrikansk bioinformatikinfrastruktur. Flera workshops och utbildningstillfällen har genomförts i Sverige och Afrika under 2013. I december hålls en bioinformatikkurs vid Mikocheni Agricultural Research Institute (MARI) i Dar es Salaam, Tanzania och vid PWANI University i Kilifi, Kenya. Där har projektet möjliggjort att servrar som är till endast för bioinformatikdata (eBioKit-servrar) installerats. Detta gör att forskare inom olika "Life Sciences"områden får tillgång till "open source" mjukvaror och att alla databaser som behövs finns tillgängliga så att forskare kan bygga sina egna databaser anpassade till egna forskningsområden.
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| 9. |
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| 10. |
- Bongcam Rudloff, Erik
(författare)
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Next NGS Challenge – Data Processing and Integration’ Conference – Conference report
- 2013
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Ingår i: EMBnet.journal. - 2226-6089. ; 19.1, s. 14-15
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Abstract. The ‘Next NGS Challenge - data processing and integration' Conference (held on 15-16 May 2013, in Valencia, Spain), a joint event of EU COST Action BM1006, SeqAhead, the Global Bioinformatics Network, EMBnet, the International Society for Computational Biology, ISCB, and the FP7 Project, STATegra was a true success in terms both of the high number of participants from a wide diversity of countries and backgrounds, and of the quality of the keynote and contributed talks.
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