MERG - Universitetet i Oslo

More documents

Recommendations

Info

Microlab MERG has established a new infrastructure for microbiology research at the University of Oslo, Department of Biology. Access will be granted to staff, guests and students at UiO working with microorganism cultures and/or eukaryotic cells, as well as ”field” material. For access and questions contact Cecilie Mathiesen and Kathrine Schou. More about the Microlab, see: http://www.mn.uio.no/bio/english/research/groups/merg/ Major achievements in 2011 Publications In 2011 MERG published 4 more articles than in 2010, and is the most productive year since the group was established. Altogether 31 articles were published. Inter-disciplinary publications Several of our papers have a clear cross-disciplinary profile where different types of expertise have been combined to achieve common goals. Two of these are presented here. The article by Kumar et al. presents a new bioinformatics pipeline named CLOTU dedicated to processing of DNA sequences generated by the 454 technology. In this work expertise in microbiology, informatics and statistics worked together. The other paper by Krabberød et al. investigates the phylogeny of a group of unculturable group of eukaryotes by applying fieldwork, whole genome amplification MERG’s main goal is to achieve a status as an excellent research environment within 2012. We reached this goal in 2011 by participating on a proposal for a Centre for Integrative Microbiology, which received the score Excellent by an international review panel. The finalists will be announces in May. and phylogenetic analyses. To accomplish the work, experts in biochemistry, micropaleontology, bioinformatics and evolutionary biology where brought together. • Krabberød, Anders Kristian; Bråte, Jon; Dolven, Jane Karine Lønne; Ose, Randi Frida; Klaveness, Dag; Kristensen, Tom; Bjørklund, Kjell Rasmus et al. (2011). Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny . PLoS ONE. doi: 10.1371 • Kumar, Surendra; Carlsen, Tor; Mevik, Bjørn-Helge; Enger, Pål; Blaalid, Rakel; Shalchian-Tabrizi, Kamran & Kauserud, Håvard (2011). CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation . BMC Bioinformatics. doi: 10.1186/1471-2105- 12-182
Impact factor The two papers published in 2011 with highest impact factor (IF) were: • Buntgen U, Kauserud H, Egli S. 2011. Linking climate variability to mushroom productivity and phenology. Frontiers in Ecology and the Environment, in press (IF: 8.8) • Eastwood et al. 2011. The Plant Cell Wall‚ Decomposing Machinery Underlies the Functional Diversity of Forest Fungi. Science 333, 762 (IF: 31) All 2011 publications see the appendix 2. Highly cited papers In 2011 two articles were on the top cited articles in two international peer reviewed journals. Burki et al. 2008 and 2009 are currently at top cited list in Biology Letters Genome Biology and Evolution. • Burki, F; Shalchian-Tabrizi, Kamran & Pawlowski, J (2008). Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes. Biology Letters. ISSN 1744-9561. 4, s 366- 369 . doi: 10.1098/rsbl.2008.0224 • Burki, Fabien; Inagaki, Yuji; Bråte, Jon; Archibald, John M; Keeling, Patrick J; Cavalier-Smith, Thomas; Sakaguchi, Miako et al. (2009). Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates. Genome Biology and Evolution. ISSN 1759-6653. 1(1), s 231-238 . doi: 10.1093/gbe/evp022 research and serVice aPPlications In 2011 MERG staff took part in 11 larger grant applications to national and international grant offices. These are the following highlight: Centre of Excellence (CoE) MERG applied for a Centre of Excellence named Centre for Integrative Microbiology (CIM) together with three other microbial biology research groups at the University of Oslo (Glyconor, LaMDa, MERG and Tone Tønjumgroup) and external collaborators to maximize the potential synergies. The assessment gave an overall score excellent. The outcome of the prequalification round will be announced in May 2012. ERC starting grant application In November 2011 Håvard Kauserud submitted an ERC starting grant application to the European Research Council entitled “Linking microbial communities in boreal forest soils to plant diversity and productivity – a metagenomics approach”. The goal of this project is to make fundamental progress in the understanding of the community ecology of microorganisms in boreal forest soils and how they are organized spatiotemporally. The diversity, composition and activity of microbial communities will be related to the diversity and productivity of co-occurring plants. Grants from Research Council of Norway and UiO Project leader Dag Klaveness, got funded the project: “X-cell parasites: an emerging threat to marine fish”. This project is a collaboration with Kamran Shalchian-Tabrizi, Mark Freeman, University of Malaya, David Bass, Natural History Museum, London and Håkon Hansen, Norwegian Veterinary Institute, Norway. The project ”Regulatory RNA and the origin of animal multicellularity” got funded by an UiO PhD position (Ralf Neumann) and a, postdoc position to Jon Bråte. The projects aims to investigate whether the RNAi machinery was lost from the genomes of single-celled ancestors of animals multiple times and if the miRNA pathway evolved independently in animals with respect to other eukaryotic supergroups. All scientific project see the appendix 1 high PerforMance coMPuting The capabilities of the Bioportal will be expanded to meet the Life Science users’ computational needs. The major objective with the requested project from NOTUR is to implement the Galaxy infrastructure at the computational resources at UiO and develop this system to handle jobs from the Bioportal. Porting jobs from the Bioportal to the Galaxy system will have several advantages. This project is a collaboration between BIO, USIT and CLSi. eValuation In the BIO-fag evaluation from 2010 the research program MERG got a good – very good score. The BIO-fag evaluation is based on achievement from 2000-2009. infrastructure The Microlab facility at Department of Biology was opened in December 2011. The facility is designed and managed by MERG. The Microlab is established for storage and growth of microbial cells of prokaryotes and eukaryotes species a well as virus, and other kinds of cell tissues from multicellular organisms such as animals and plant. The Microlab will be used for research on algea, fungi, protozoa, several bacteria strains and salmon cells. More about this infrastructure see MERG web-pages. new web-Pages New MERG web pages have been made - see http://www.merg.uio.no new coMMunication Profile for Merg New profile including power-points, posters, newsletters, colour pallet and elements was ready September 2011. This is intended for MERG internal and external use. all achieVeMent 2011 in the JiPPi rePort Activities in MERG has been reported in the JIPPI, more information about JIPPI and the activities in MERG 2011, see appendix 2.
Page 1 and 2: merg info NEW KNOWLEDGE by CrOssiNG
Page 3 and 4: Goals and Visions for MERG Visions
Page 5: VisualiZation of Merg Administrativ
Page 9 and 10: adVanced equiPMent aPPlication The
Page 11 and 12: MERG Annual report 2011 APPENDIX 1:
Page 13 and 14: MERG A molecular phylogeny of the b
Page 15 and 16: MERG Alkaloid profiles in Claviceps
Page 17 and 18: MERG Bioinformatics applications fo
Page 19 and 20: MERG Ectomycorrhiza on Salix repens
Page 21 and 22: MERG Evolutionary diversification a
Page 23 and 24: MERG Fungi and climate change Objec
Page 25 and 26: MERG High throughput sequencing of
Page 27 and 28: MERG Microbial ecology of mycorrhiz
Page 29 and 30: MERG Phylogenomic and single cell w
Page 31 and 32: MERG Population genetics and phylog
Page 33 and 34: MERG Regulatory RNA and the origin
Page 35 and 36: MERG Annual report 2011 Appendix 2:
Page 37 and 38: MERG JIPPI numbers 2011 Based on JI
Page 39 and 40: MERG Entered activities 1.1. PUBLIC
Page 41 and 42: MERG 1.5 PUBLICATION: Posters 1 Evo
Page 43 and 44: MERG 13 High throughput cell sorter
Page 45 and 46: MERG 4.5 COURSES/WORKSHOP: Further
Page 47 and 48: MERG Annual report 2011 APPENDIX 3:
Page 49: MERG Jon Bråte K. Shalchian-Tabriz

MERG - Universitetet i Oslo

Create successful ePaper yourself

Delete template?

Save as template?