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Imbim Annual Report 2016 Department of Medical Biochemistry and Microbiology IMBIM ANNUAL REPORT 2016 DEPARTMENT OF MEDICAL BIOCHEMISTRY AND MICROBIOLOGY ANNUAL REPORT 2016 Pictures taken by Eva Garmendia IMBIM Day, February and September, 2016 Edited by Veronica Hammar ISBN no 978-91-983979-0-1 PREFACE I would like to take the opportunity to welcome two new research groups to IMBIM, Both Örjan Carlborg and Mikael Sellin, with their coworkers joined our Department during 2016. Örjans group joined us during summer whereas Mikaels group will move physically to their new laboratory, hopefully before summer 2017. During 2016 a position as a University Lecturer in Computational Genomics was filled. Örjan, who comes from SLU, was ranked as number one by the expert reviewers and was offered the position. With all the positive comments from the expert reviewers we took the opportunity to also offer Matthew Webster, who came in at second place, a position as a University Lecturer in Computational Genomics. Thus, in one stroke the number of permanent staff at the Genomic section at IMBIM doubled. Mikael Sellin was recruited as an Associate Senior Lecturer “biträdande universitetslektor (BUL)” in Medical Infection Biology sponsored by the SciLifeLab Uppsala. Mikael was ranked as number one among fifteen national and international applicants. We were pleased that Mikael decided to place his laboratory at IMBIM. BUL positions are a new type of career development positions. In fact, Mikael is the first BUL appointed at the Medical Faculty. Mikael started to work with us in December 2016 but his group will physically move to the B9:3 corridor during spring 2017. During the year IMBIM also announced a position as Senior Lecturer in “Experimental Immunology”. Among the twelve applicants Jenny Hallgren Martinsson was placed first and offered this new position. IMBIM congratulates Örjan, Matthew, Mikael and Jenny for their well-deserved new positions and expects them to do wonders as scientists and teachers at IMBIM during many years to come. An exciting development that was cooking during 2016 was the planning for the merger between IMBIM and the Ludwig Institute for Cancer Research. Thus, after more than 30 years as an independent research organization the Ludwig Institute will from August 2017 become part of Uppsala University via a merger with IMBIM. This change is most welcomed since the research theme at the Ludwig Institute fits like a glove (better than for OJ) with the research interest at IMBIM. The merger will also overnight add some 30 new persons to the list of IMBIM workers. Currently, the Department has a stable staff consisting of some 150 people. Including project workers, post doc etc. we are around 240 persons that spend our daily work hours at the Department. To this we now add some 30 people. During the year the Uppsala Antibiotic Center (UAC) was established with plentiful of support from the University under much media attention. Dan Andersson and Linus Sandegren are top figures in the steering committee of this new initiative. Hopefully this strategic investment will result in the development of the much-needed new antibiotics. The cover to this annual report consists of pictures taken during the two IMBIM days that were arranged in 2016. Both were hugh successes. The topic for the meeting in Sigtuna (February) was equality “All animals are equal, but some animals are more equal than others”. The second IMBIM day was held at Skarholmen (September) and dealt with scientific misconduct “Shortcut to success”. Kudos to the people who organized these two meeting and to Eva Garmendia who took these beautiful pictures. Prizes and Awards: Two scientists at IMBIM have received prestigious prices and awards during 2016. Lena Kjellén received the Rudbeck medal for “extraordinarily prominent achievements in science, 3 to be conferred primarily for such accomplishments or findings attained at Uppsala University”. She has done exceptional contributions to the understanding of the molecular biology of carbohydrates and proteoglycans in health and disease. Sangeet Lamichhaney received the “Hwasser price” from Uppsala Läkareförening for the best PhD thesis from the Medical Faculty “Genetic basis for adaptation”. Normally the “Hwasser price” is divided between two newly graduates. However, this year no one could compete and Sangeet got the prize alone. Scientific Highlights: Ongoing research projects at IMBIM are summarized later in this annual report. Below I have picked out a few examples of studies that illustrate the high quality and wide range of research carried out at our Department. The genomic groups, with Leif Andersson, Kerstin Lindblad-Toh, Matthew Webster and Carl-Johan Rubin as the central PIs, had a very productive year with multiple high quality papers published in high impact journals. These include studies of the genetics of ruff sex (Lamichhaney et al., Nature Genetics 48, 84-88), the ecological adaptation in the Atlantic herring (Martinez Barrio et al., eLife 5, e12081), new insights into the evolution of beak morphology among Darwin finches (Science 352, 470-474), and the function of the TBX3 transcription factor in hair pigmentation (Imsland et al., Nature Genetics 48, 152-158). Diarmaid Hughes group has worked on the selective power of codon usage in highly expressed bacterial genes. They have shown that discrimination between alternative codons for the same amino acid in a gene can have profound effects on the evolutionary selection (Brandis and Highes. PLoS Genetics 12, e1005926. A team of researchers led by Cecilia Annerén has identified an enhanced method for generating human pluripotent stem cell cultures. This discovery could lead to the more economical and rapid large-scale industrial production of these cells. This technology holds great promise in disease modeling, drug screening and cell-based therapeutics (Pijuan-Galitó et al. Nature Communications 13, 12170). Lena Kjelléns group published the “Paper of the week” in Journal of Biological Chemistry where they showed that the enzyme that transfers sulfate groups to heparan sulfate also regulates the length of the heparan sulfate polysaccharide chains (Deligny et al. J. Biol. Chem. 291, 18600-18607). During 2016 Aris Moustakas group reached a long-term milestone by identifying, via a chemical screen, novel compounds that block epithelial to mesenchymal transition. Further, they could demonstrate that these compounds work via inhibition of TGFß signaling (Carthy et al., Science Report 6, 29868). Teaching: Teaching of undergraduate and graduate students is a primary undertaking for IMBIM. During 2016 a total of ten students received their doctoral degree. The teachers at IMBIM does an excellent job something that is illustrated by the fact that Linus Sandegren received yet another pedagogic prize. This time the “pedagogic rose” from the Medical students at the 4 Faculty for his exceptional contributions to the education in Bacteriology. Also, Birgitta Tomkinson was bestowed the title “Excellent teacher”. Birgitta is the first, and only, teacher at IMBIM that carries this fine title. The course "Homeostasis and endocrine regulation", given at the second semester of the Medical program was awarded the Optimus prize for the spring semester 2016. The prize is given to the course at the Medical program that receives the best course evaluations. Lena Kjellén is course leader and Eva Engström is course administrator. I would also like to thank all of those who left IMBIM during the past year for your participation in building up this fantastic scientific environment. I wish you all the best for the future and hope that you have mostly fun memories from your time at IMBIM. At the same time I welcome all new students/scientists etc. to this exciting environment and hope that you will actively take part in the future development of this Department. In closing: I will end my term as the Head of the Department this summer and will try to return to science full-time for the last 3-4 years of active service. I have served as the chairman for almost five years. These years have been stimulating with many fun moments but also with some more difficult times to survive. Thanks to the superb help from the administrative and technical staff at IMBIM my life as the Head of the Department has been bearable. I would like to thank them all; Veronica, Malin R, Malin S, Susanne L, Rehné, Eva, Susanne T, Alexis, Lasse and Mervi. However, now is the time to handover the torch to someone else. Thus, “It´s time to say goodbye, but goodbyes are so sad that I´d much rather say hello. Hello to a new adventure”1. Uppsala March 2017 Göran Akusjärvi Not for long Head of the Department 1 Ernie Harwell, famous sports commentator 5 LIST OF CONTENTS ADDRESS LIST 8 ORGANIZATION 12 SCIENTIFIC REPORTS OF RESEARCH GROUPS 15 Comparative Genetics and Genomics 16 Andersson Leif: Functional genomics in domestic animals and natural populations 18 Axelsson Erik: Genetic and functional characterisation of dog domestication 27 Bjerling Pernilla: Epigenetics and new antifungal drugs 28 Carlborg Örjan: Computational genomics 30 Grabherr Manfred: Evolutionary bioinformatics and computational biology 34 Jern Patric: Retrovirus-host evolution 37 Lindblad-Toh Kerstin: Comparative genomics and genetics 39 Meadows Jennifer: Genetic dissection of autoinflammatory disease 50 Rosengren Pielberg Gerli: Comparative genetics of immunological diseases towards functional genomics 54 Rubin Carl-Johan: Identification and characterization of genes
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