Annual Report 2012 – SciLifeLab Uppsala (English) by SciLifeLab

Annual report 2012

Production SciLifeLab Uppsala Administration Graphic Design Matador kommunikation Photos Max Brouwers (p. 5), Matador kommunikation (illustrations p. 6, 7, 11, 14), Elf/Tremani (p. 7, 39), Hans Karlsson (p. 8, 51), Shutterstock (p.11), iStockphoto (p. 17, 23, 24, 32), Werket (p. 18), Carolina Wählby (p. 20), Göran Burenhult (p. 27), Ingvar Ferby (p. 28), Freyja Imsland (p. 31), Matton (p. 35), Claudia Bergin (p. 52), Johan Forsgren (p. 54), Mikael Wallerstedt (all other photos) Printing Kph, Uppsala 2013

scilifelab uppsala annual report 2012

SciLifeLab Uppsala Management Kerstin Lindblad-Toh Director, Chair, Program Board Johan Elf Vice Director Karin Forsberg Nilsson Vice Director Ulf Landegren Vice Chair, Program Board Maria Sörby Site Director

Content 5 Rising to the challenges 6 SciLifeLab Uppsala 9 Building a national infrastructure in Uppsala and Stockholm 10 Quality resources deliver outstanding science 12 Scientific community breeds interdisciplinary exploration 14 Education that enables the science of the future 16 Interaction increases collaboration 20 Scientific Highlights 42 Scientific Resources

Program Board Kerstin Lindblad-Toh (Chair), Ulf Landegren (Vice Chair), Karin Forsberg Nilsson, Johan Elf, Per Ahlberg, Leif Andersson, Siv Andersson, Mattias Jakobsson, Ulf Gyllensten, Aristidis Moustakas, Agneta Siegbahn, Ann-Christine Syvänen, Per Artursson, Jöns Hilborn, Jens Häggström (SLU) Program Council Stellan Sandler (Chair), Helena Danielson, Gerhart Wagner, Carl-Henrik Heldin, Johan Schnürer (SLU), Maria Fällman (UmU), Jan Stenlid (SLU), Kerstin Lindblad-Toh, Karin Forsberg Nilsson, Johan Elf, Ulf Landegren Program Coordinators Agneta Siegbahn, Medicine Lars Rönnblom, Medicine Siv Andersson, Biology Contact information: Administrative staff at SciLifeLab Uppsala Site Director Maria Sörby Maria.Sorby@scilifelab.uu.se Project Coordinator, education and outreach Elina Hjertström elina.hjertstrom@scilifelab.uu.se Communications Officer Sara Engström sara.engstrom@scilifelab.uu.se Economist Anna Lidin anna.lidin@scilifelab.uu.se

scilifelab uppsala annual report 2012

Rising to the challenges: SciLifeLab Uppsala 2012 SciLifeLab Uppsala continues to expand in its role as a national infrastructure for Swedish life science research. During 2012, we attracted much attention and, together with other major infrastructure initiatives, came to symbolize novel interdisciplinary collaborations in Sweden. We are proud that our achievement is acknowledged by the Swedish Government’s decision to increase funding for SciLifeLab Sweden to develop the two current sites – Uppsala and Stockholm – to form one national center for life science research.

During 2012, the platforms at SciLifeLab Uppsala performed nearly 700 research projects – a substantial increase compared to 2011. It is especially gratifying to note that 30% of the projects were led by researchers outside Uppsala University. This shows that our platforms already deliver on a national level. We aim to further increase the proportion of external projects. Furthermore, our associated scientists published a large number of peer-reviewed scientific articles, 37 of which appeared in high-profile journals. You can read about some of these discoveries in this report. Every one of these articles deserves mentioning; highlights include the use of genomic signatures to investigate human migration and new mechanisms for killing cancer cells. Several new pilot technical platforms were established in 2012; a biomaterials platform, a clinical proteomics platform, and a platform for high-throughput, single-cell analysis. As our range of facilities is expanding, both established and novel platforms often initiate joint technology development projects. We establish new connections and collaborations as our scientific community at SciLifeLab Uppsala is growing, and have now exceeded 800 researchers, including associated members and their labs. Last year, we recruited outstanding scientists in several key areas, including disease genetics, host-parasite relations for microorganisms, single-cell genomics, bioinformatics, and RNA biology to further strengthen the research environment within SciLifeLab Uppsala. Sharing our knowledge – for the benefit of many

Community- and collaboration-building was high on our agenda for 2012, and we have undertaken an extensive range of activities. We participated in collaborations with other actors within the life sciences, including government agencies and life science companies. SciLifeLab Uppsala also organized or co-organized several conferences aimed at increasing interactions between commercial enterprises and the scientific community, which has contributed to the growing numbers of collaborations between companies and SciLifeLab Uppsala. We have an important mission to foster knowledge about how advanced technology can be utilized, both in academic research and for industrial applications. The importance of our training courses and workshops with participants from all over Sweden cannot be overstated. Through activities like these, knowledge of the techniques and methods developed and offered at SciLifeLab has made our partners increasingly aware of our potential to enable their research. We are proud of our achievements in the past year and look forward to an even better 2013. We warmly invite our colleagues throughout Sweden!

Kerstin Lindblad-Toh, director SciLifeLab Uppsala

scilifelab uppsala annual report 2012

Management and boards

Technology platforms

Research programs

System biology Biological processes

Medical biology Translational medicine

SciLife Innovation

Associated members

Evolutionary biology Environment Energy

Genomics

Proteomics

Bioimaging

Data storage and bioÂ informatic support

Comparative genetics

Emerging platforms

Organization of SciLifeLab Uppsala SciLifeLab Uppsalaâ&#x20AC;&#x2122;s scientific resources provide scientists with the means to achieve key goals within the vast field of life science. From 2012 and onwards, we provide state-of-the-art resources within genomics, proteomics, bioimaging, comparative genetics, and data storage & bioinformatics support. We have also established new technology platforms for emerging fields such as biomaterial characterization, single-cell analysis, high-throughput protein biomarker analysis, and drug optimization and pharmaceutical profiling. Within the research programs, scientists are brought together to further science, form collaborations and to learn how to optimally use our resources. During 2012, we intensified our efforts to integrate the SciLifeLab centers in Uppsala and Stockholm as one national infrastructure. The pilot project SciLife Innovation, which aims to create a one-stop shop for academic life science innovation, was initiated during 2012.

SciLifeLab Uppsala SciLifeLab combines advanced methods development and instrumentation with a broad knowledge base in technology-driven molecular bioscience and translational medicine. We enhance this competence by providing a computational infrastructure for hypothesis-based and explorative research in biology and medicine. We aim to be an internationally leading research center, providing both bioscience technology and expertise.

The SciLifeLab Uppsala community brings together academic and professional staff scientists united in a commitment to developing new and transformative approaches to biomedical research. Our goal is to understand the fundamental basis of genome and cell biology within the broader field of life sciences, and to advance diagnostics and treatment of diseases with unmet needs.

scilifelab uppsala annual report 2012

SciLifeLab Uppsala 2012 Budget The SciLifeLab budget for 2012, with funding from the Government’s strategic areas (SFO) and co-financing from the university, has been allocated to enable the best possible conditions for building a strong research environment.

Management and Administration 3%

34%

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S y s t em b

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iolo

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–B

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Technology Platforms 63% Financing skilled personnel, instruments and licenses and service costs has allowed our technology platforms to deliver service as well as education and technology development.

63%

Research programs 34% The strategic recruitments during 2011 and 2012 of carefully selected junior research group leaders will contribute to high-profile interdisciplinary research; they will be important drivers of the SciLifeLab community. With the implementation of a wide range of activities (seminar series, conferences, workshops, and more), important interdisciplinary networks have been created. In addition, a number of scientific projects have been supported.

Enabler for Life Sciences Me

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Evolutionary biology, Environment, Energy Medical biology, Translational medicine System biology, Biological processes

scilifelab uppsala annual report 2012

Building the SciLifeLab national infrastructure In its 2012 Research and Innovation Bill, the Swedish Government decided to bring together SciLifeLab in Uppsala and Stockholm into one national infrastructure from 2013 and onwards. Also during 2012, The Knut and Alice Wallenberg Foundation pledged to support the SciLifeLab effort by strengthening key elements of the infrastructure through major financial support. These initiatives, together with the original strategic research area funding, plus the great commitment by Uppsala University to support the initiative, have provided a foundation for a strong initiative in the life sciences.

As a consequence, SciLifeLab Uppsala during 2012 readily accepted the challenge to prepare for the new organization and larger responsibility starting in 2013. These preparations often meant intensifying already ongoing efforts. For instance, although our scientific resources are available nationally, we needed to further develop them to meet the extended responsibility of being part of a nationwide infrastructure. One example of the extensive efforts to simplify routines for accessing our resources, especially in genomics, bioinformatics and data storage, is the new web portal shared by all genomics resources within SciLifeLab (Uppsala and Stockholm together). WABI (Wallenberg Advanced Bioindomatics Infrastructure) also provides bioinformatics support to researchers using the resources. One mission for 2013 is to develop a national platform within drug discovery and development (DDD) together with SciLifeLab Stockholm. The Uppsala and Stockholm

sites are now planning which activities should be part of the national DDD platform. All of these efforts have been implemented, together with corresponding initiatives in Stockholm, to streamline the resources to better accommodate national needs. Central goals include the following: • Nationwide access to state-of-the-art molecular biological technologies • Early and broad exploitation of unique technologies, reagents and sample resources • Undertaking large-scale projects and generation of molecular resources • Enhanced knowledge transfer through courses, symposia and on-site accommodation of guest researchers • Supporting translation of results for societal and industrial utility During 2012, the four universities involved in the SciLifeLab effort have intensified strategic planning to meet the challenge of creating a national infrastructure. One important actor playing a major part in these discussions is the National Reference Committee of SciLifeLab, established in 2010. This committee includes representatives from the major universities in Sweden, thus serving as a vital link to SciLifeLab for researchers from all over Sweden. The pilot project with the working title SciLife Innovation, was initiated together with Uppsala University Innovation and aims to facilitate innovation partnerships. Through this, we are building momentum towards enhanced industrial liaisons.

scilifelab uppsala annual report 2012

Cutting-edge platforms deliver outstanding science The year 2012 was a particularly productive year for Sci LifeLab Uppsala. Many important achievements, both for infrastructure and research, have been accomplished. The broad range of scientific resources available, all based on state-of-the-art technologies, has proven attractive both on national and international levels. Moreover, the research performed at SciLifeLab received excellent ratings in the universities’ external research evaluations. In addition, a record number of Wallenberg Fellow & Scholar and ERC Investor Awards were granted to SciLifeLab scientists in Uppsala. In 2012, we received 6 awards, compared to 4 in 2011. As a verification of its high-level technology, Uppsala Genome Center was also chosen as one of only two European centers to gain early access to IonProton, a novel technology allowing human genome sequencing for less than a thousand US dollars. High-impact research

Research projects performed at SciLifeLab Uppsala resulted in 126 publications specifically affiliated with the SciLifeLab Uppsala community. However, the actual use of our scientific resources was even greater, resulting in 130 additional publications. This research covers wide areas of science, including molecular mechanisms of human diseases, e.g. leukemia and autism, as well as evolutionary biology and environmental research. Clearly indicating the high international quality of our community, 37 of the 126 research articles were published in high-profile journals such as Nature, Science and Nature Genetics. We summarize a selection of these scientific

highlights starting on page 20. Furthermore, within the community, 85 PhD students were awarded their Doctor’s degree in 2012. Enhancing scientific resources

The facilities at SciLifeLab Uppsala have been used in 699 research projects. This represents a substantial increase over the projects conducted in 2010 and 2011. During 2012, our facilities were staffed with 150 people. Of these, 100 spend more than 50% of their working time within the facility. More than 30% of the projects conducted at our scientific resources were led by principal investigators from universities other than Uppsala University. By extending the knowledge and competence of these resources and technologies further, we aim to further increase the proportion of external users. We also added to our already sizable scientific platforms during 2012. New pilot facilities include single-cell analysis, biomaterial characterization and the introduction of PLA-technology for protein analyses in a clinical context. In 2012, SciLifeLab Uppsala also initiated an effort within drug discovery and development by supporting the previously established Uppsala University Drug Optimization and Pharmaceutical Profiling Platform. We also continued technology development central to our existing resources. During 2012, these efforts resulted in 26 scientific publications describing new and improved methodologies. Our scientific resources are described in detail beginning on page 42.

Scientific publications

General media 2012

150

120

143

126 120

37 High-profile publicationas

26 High-profile publicationas

30 8

0 2010

2011

International media

2012

The increase in scientific publications with SciLifeLab-Uppsala affiliation. High-profile publications have an impact factor larger than 5.

National media

Publications in general media referring to SciLifeLab Uppsala.

Projects performed at the technology platforms 700

699

600

Comparative genetics: 59 projects

529

500

Emerging platforms: 48 projects Bioimaging: 60 projects

UPPNEX projects 2012

Proteomics: 205 projects

400

242

300

294

242

200

Genomics: 327 projects

100 0 2010

2011

2012

Number of projects at the SciLifeLab Uppsala Technology Platforms. In 2012, more than 30% were projects from users other than Uppsala University.

UPPNEX projects during 2012.

Selection of novel methods developed in 2012

Universities using our resources

• Methods for sample preparation from difficult sources

Uppsala University, Royal Institute of Technology, Stockholm Univer-

• Unique methods for using biomaterials for gene therapy

sity, Karolinska Institutet, Swedish University of Agricultural Science,

• A canine exome capture array

Umeå University, University of Gothenburg, Linköping University,

• Novel protocols for epigenetic genotyping

Örebro University, Lund University, Ludwig Institute for Cancer research

• New approaches for allele-specific expression analysis • New methods for ling link generation – necessary for genome assembly • New ranges for protein interaction analyses in single-cells

Hospitals/government agencies using our resources Sahlgrenska Academy at the University of Gothenburg & The Queen Silvia

• E-infrastructure for life science

Children’s Hospital Gothenburg, Falu Hospital, Uppsala University Hospital,

• New bioinformatics methods

The Swedish National Veterinary Institute, Örebro County Council, FOI

scilifelab uppsala annual report 2012

Scientific community empowers interdisciplinary exploration The scientific community of SciLifeLab Uppsala continued to grow during 2012, partly due to active recruiting, partly

this initiative, targeting, for instance, the fields of drug discovery, biomaterials and technology development.

also because of our growing reputation as an attractive research environment. At the end of the year, we had more

Recruiting gifted group leaders

than 160 research groups with more than 800 research-

SciLifeLab Uppsala has concluded the 2012 strategic recruitment of three carefully selected research groups; Erik Ingelsson’s in molecular epidemiology, Bengt Persson’s in bioinformatics, and Thijs Ettema’s in metagenomics. All three will be important drivers of the Uppsala community and will contribute to the interdisciplinary profile of the SciLifeLab infrastructure. Recruitment of talented bioinformaticians to the community has also been an important strategic decision. The enormous amount of data generated at our platforms represents a challenge in itself, placing high demands on both the numbers of bioinformaticians and on their expertise. Therefore, we have employed eight new bioinformaticians/computational biologists to meet current and future needs. These recruitments complement our specially designed courses to increase the bioinformatics competence of our users.

ers, including mathematicians, engineers, evolutionary biologists and clinicians. Most members are researchers at Uppsala University, while others come from the Swedish University of Agricultural Sciences (SLU) and the National Veterinary Institute (SVA). The community shows great regional strength from which to expand nationally.

Our community forms the foundation of SciLifeLab’s interdisciplinary scientific collaboration, active both at national and international levels. Community activities are all designed to bring members together, strengthen interactions, and to learn from each other’s experience how to use our scientific resources in new and challenging ways. In 2012, our activities focused on reaching new life science research groups within academia, industry, health and governmental agencies. Our SciLifeLab days and seminar series reflected

A selection of our invited speakers on seminars and SciLifeLab days Tarjei Mikkelsen, Broad Institute of MIT and Harvard Functional genomics enabled by integrated DNA synthesis and sequencing

Fernando Baquero, Ramon y Cajal University Hospital, Madrid Predicting mechanisms and evolution of antibiotic resistance at the local and global scale

Jakob Zinsstag, Swiss Tropical and Public Health Institute One health: The added value of closer cooperation between human and animal health for the control of infectious disease

Xiao Yonghong, Zhejiang University Changing policies to meet the challenge of antibiotic resistance in China

Balganesh Tanjore, Council of Scientific and Industrial Research (CSIR), New Delhi New antibiotics- the need and the challenge. TB as an illustrative example

Michael Zody, Broad Institute of MIT and Harvard Viral Genetics and Serotype-Specific Immunity Interact to Determine the Dynamics of Dengue Virus Disease Severity

scilifelab uppsala annual report 2012

Any research group within the Swedish universities is welcome to seek associate membership. The application form is available at www.scilifelab.uu.se. We invite every researcher of the SciLifeLab Uppsala community to participate in the many activities organized by SciLifeLab. You do not have to be an associated member to use our scientific resources. They are available on the same conditions and at the same price to all academic researchers in Sweden.

Associated members of SciLifeLab Uppsala at the end of 2012: Per Ahlberg, Göran Akusjärvi, Marie

Hansell, My Hedhammar, Åke Hedhammar,

Aristidis Moustakas, Sherry Mowbray, Marika

Allen, Kjell Alving, Göran Andersson, Jan

Carl-Henrik Heldin, Paraskevi Heldin, Eva

Nestor, Antti Niemi, Fredrik Nikolajeff, Mats

Andersson, Leif Andersson, Siv Andersson,

Hellmen, Mats Hellström, Per Hellström, Lars

Nilsson, Peter Nygren, Luke Odell, Ernst

Per Andrén, Göran Annerén, Gunnar Antoni,

Hennig, Jöns Hilborn, Andrea Hinas, Patrice

Oliw, Anna-Karin Olsson, Ingela Parmryd,

Per Artursson, Anders Backlund, Sandra

Humblot, Jens Häggström, Torleif Härd, Jacob

Ulf Pettersson, Fredrik Pontén, Richard

Baldauf, Lars Baltzer, Jonas Bergquist, Peter

Höglund, Simone Immler, Anders Isaksson,

Rosenquist Brandell, Kristofer Rubin, Lars

Bergsten, Rolf Bernander, Stefan Bertilsson,

Mattias Jakobsson, Christer Jansson, Elena

Rönnblom, Hans Rönne, Anja Sandström,

Bryndis Birnir, Pernilla Bjerling, Marie-Louise

Jazin, Per Jemth, Patric Jern, Helena Jernberg

Jens Schuster, Bo Segerman, Maria Selmer,

Bondeson, Mikael Brandström Durling,

Wiklund, Staffan Johansson, Alwyn Jones,

Agneta Siegbahn, Tobias Sjöblom, Tanja

Jyoti Chattopadhyaya, Lena Claesson-

Masood Kamali-Moghaddam, Chandrasekhar

Slotte, David Van der Spoel, Maria Strömme,

Welsh, Erica Comasco, Niklas Dahl, Helena

Kanduri, Anders Karlén, Manfred Kiliman,

Inger Sundström Poromaa, Richard Svanbäck,

Danielson, Anna Dimberg, Christina Dixelius,

Andreas Kindmark, Leif Kirsebom, Lena

Catharina Svensson, Staffan Svärd, Ann-

Jan Dumanski, Måns Ehrenberg, Johan

Kjellén, Stefan Knight, Jan Komorowski, Dirk-

Christine Syvänen, Ola Söderberg, Fredrik

Elf, Hans Ellegren, Maija-Leena Eloranta,

Jan de Koning, Johan Kreuger, Klas Kullander,

Söderbom, Kenneth Söderhäll, Mattias

Ulf Emanuelson, Håkan Engqvist, Magnus

Olle Kämpe, Ulf Landegren, Marene

Thelander, Birgitta Tomkinson, Hans Törmä,

Essand, Henrik von Euler, Claes Fellström,

Landström, Lars Lannfelt, Dan Larhammar,

Lene Uhrbom, Anders Virtanen, Claes

Lars Feuk, Karin Forsberg Nilsson, Anthony

Mats Larhed, Lars Larsson, Martin Lascoux,

Wadelius, Mia Wadelius, Gerhart Wagner,

Forster, Urban Friberg, Pär Gerwins,

Jin-Ping Li, Lars Lind, Peter Lindblad, Kerstin

Lars Wallentin, Matthew Webster, Nils Welsh,

Valeria Giandomenico, Manfred Grabherr,

Lindblad-Toh, Anna Lobell, Angelica Loskog,

Bengt Westermark, Gunnar Westin, Jochen

Mats Gustafsson, Ulf Gyllensten, Anders

Magnus Lundgren, Bengt Långström,

Wolf, Carolina Wählby, Anki Wästljung,

Götherström, Håkan Hall, Finn Hallböök,

Aleksei Maklakov, Cecile Martijn, Johan

Helena Åkerud, Johan Åqvist, Fredrik Öberg,

Margareta Hammarlund-Udenäs, Peter

Meijer, Håkan Melhus, Karl Michaëlsson,

Kjell Öberg

Attendees at the bioinformatics course Computational Methods for Massively Parallel Sequencing

“Excellent lectures describing current problems within bioinformatics”

“This was really what I needed to kick start”

“I learned more in this course that I have ever done in any previous course I have attended”

“Advice on study design was invaluable”

“Very good balance of lectures and practical examples”

6 Chalmers University of Technology 6 Karolinska Institutet 4 Royal Institute of Technology 2 Linköping University 8 Lund University 12 Swedish University of Agricultural Sciences 11 Umeå University 4 University of Gothenburg 27 Uppsala University

scilifelab uppsala annual report 2012

Education that enables the science of the future SciLifeLab Uppsala conducted education at both undergraduate and graduate levels during 2012. Researchers from the SciLifeLab community together with scientific resource personnel were involved in undergraduate courses spanning a wide range of subjects, including biomaterials and polymer chemistry, molecular medicine, genome bioinformatics, separation techniques and mass spectrometry, regenerative medicine and clinical tumor biology.

SciLifeLab Uppsala associated resources were involved in novel graduate-level courses aimed at training PhD students and postdocs in advanced techniques and data analysis methods. During 2010 and 2011, we evaluated the need for education within different areas. In 2012, we began meeting this need. The educational efforts also represent something new; our courses now target researchers who have not previously been aware of or had access to the technologies we provide. They can now benefit from learning what our scientific resources allow them to achieve, how to plan their projects, and how to analyze the data that result. The courses are in great demand, and the participants’ positive reviews verify their top quality. Joined forces for education

A major focus has been to educate researchers in bioinformatics to meet the increasing demand for user support. For instance, the three genomics platforms together with UPPNEX, a sequencing cluster in Uppsala, have all contributed to the doctoral-level course Computational Methods for Massively Parallel Sequencing given on four occasions during 2012. These courses were very popular, and attracted a total of 80 participants from all over Sweden. Upon request from Umeå University, we gave one of these courses in Umeå.

Other educational efforts during 2012 include: • The three proteomics platforms (Proximity Ligation Assays, Tissue Profiling and Mass Spectrometry) in SciLifeLab Uppsala together organized the PhD-level course Advanced Molecular Technolog y and Instrumentation for Proteome Analyses. The course was attended by participants from Uppsala University, the Swedish University of Agricultural Sciences and The Royal Institute of Technology. • The Comparative Genetics platform organized the twoweek PhD-level course Gene Mapping and Population Genetics in Humans and Domestic Animals, attended by participants from Uppsala University, the Swedish University of Agricultural Sciences, Stockholm University and Gothenburg University. • A PhD-level course in Advanced Cell Culture was arranged within the area drug development and discovery. The course welcomed researchers within both academia and the pharmaceutical industry. • The BioVis platform arranged the PhD-level imaging course Methods for Cell Analysis together with other SciLifeLab researchers.

Biosupport.se – new web site for bioinformatics support SciLifeLab, in collaboration with other organizers, launched the bioinformatics forum Biosupport.se to answer questions from Swedish researchers and coordinate support efforts. Our bioinformaticians take turns in responding to queries from researchers. They provide support both in experimental design and data analysis in research projects.

scilifelab uppsala annual report 2012

Interactions with industry and society add value Collaboration partners and groups taking advantage of

Common entry to innovation partnerships

SciLifeLab services are found in many national and interna-

The pilot project SciLife Innovation was initiated during 2012, as a structure for industrial liasons, and developed together with Uppsala University Innovation. We anticipate that it will become a natural one-stop shop for SciLifeLab associated partnerships with companies.

tional organizations within academia, research, industry and society – including healthcare providers, schools and policymakers.

During 2012, an extensive range of activities has been carried out to facilitate interaction and collaboration between SciLifeLab Uppsala researchers and other stakeholders. Key members of the SciLifeLab community have been participating in these activities: when the right people meet they can reinforce existing networks and establish new collaborations. In part due to these efforts, the reported number of companies interacting with the SciLifeLab environment increased to more than 45 in 2012. On these occasions, we invited people from different areas to form new collaborations and interactions. These ranged from working closer together with healthcare providers and undertaking joint research projects, to representing the life science region of Uppsala together rather than as separate organizations. An important initiative that should be mentioned in this context, is the commitment from Astra-Zeneca to support projects related to SciLifeLab, starting 2013.

Collaborative representation

SciLifeLab Uppsala has participated in joint presentations with other life science stakeholders on several occasions. During BioPartnering Europe 2012, we collaborated with Uppsala BIO and Uppsala University Innovation to present Uppsala life sciences. At the Economist conference ‘Bridging the gap between science and healthcare’ held in Uppsala, SciLifeLab Uppsala, Uppsala BIO and Uppsala University Innovation joined forces with the Swedish Medical Products Agency and the municipal agency Världsklass Uppsala to promote the region. Engaging schools

2012 also witnessed an increase in our efforts to engage school children in the marvels of life science. For example, we arranged research projects for high school students and organized open lectures and supplementary training of school teachers.

Academia

Commercial Enterprises

government and municipal agencies

society and schools

health providers

scilifelab uppsala annual report 2012

Navet During 2012, we started to build Navet (The Hub) â&#x20AC;&#x201C; a specially-designed meeting place for all associated researchers and collaborating partners. Thanks to its unique shape and state-of-the-art design, this new building stands out from the existing biomedical research environment at Uppsala University. From 2013, Navet will host flexible work-spaces, conference facilities and rooms for guest researchers; it will thus catalyze communication among different SciLifeLab activities spread over Uppsala, Stockholm and the rest of Sweden.

scilifelab uppsala annual report 2012

The number of AIMdays increased from 1 in 2011 to 3 in 2012. We also noted a corresponding rise of reported collaborations from 4 in 2011 to at least 10 in 2012.

Entering healthcare

UCR-PEA/PLA, our novel scientific resource, is integrated with Uppsala Clinical Research Center at Uppsala University Hospital. This platform offers high-throughput analysis of protein biomarker candidates in body fluids based on a unique, high-performance assay technique developed and commercialized in Uppsala. We continue discussions with the hospital about how we best can establish routines and a platform for clinical sequencing during 2013. Academia meets industry

During 2012, SciLifeLab Uppsala co-organized three AIMdays, events where companies send in questions of importance to them, and researchers from different fields participate in workshops to share their expertise in these questions. These events have proven an excellent means of bringing industry and academia together to formulate

and address problems identified by industry and society. As a result, we are pleased to note that several of the companies participating in AIMday ® Diabetes in January, AIMday ® Imaging in March, and AIMday ® Cancer in June have now formed collaborations with our associated research groups. Healthcare conference and symposium

In November, SciLifeLab Uppsala supported the Economist conference ‘Bridging the gap between science and healthcare’ with several SciLifeLab researchers participating. At the same time, we took the opportunity to host the satellite symposium ‘In Joint Battle against Infectious Disease and Antibiotic Resistance’ on the day following the Economist conference. This international symposium attracted nearly 200 delegates from healthcare, national and international authorities, and public agencies.

pmk-1

Scoring fluorescence distribution patterns with the WormToolbox. Fluorescence microscopy images show clec-60Ă¸GFP expression (green) in wildtype worms (WT, top left) and in pmk-1 (km25) mutants (pmk-1, bottom left). The pharynx is marked with myo-2::mCherry (red). All the worms are digitally straightened and resampled to a straight shape (right), which enables us to obtain a low-resolution worm atlas.

scilifelab uppsala annual report 2012

scientific highlights

Quantitative information captured from individual C. elegans worms in high-throughput assays When biological pathways and diseases cannot be reduced to purely biochemical or cell-based assays, the free-living nematode worm Caenorhabditis elegans has proven an excellent model organism for studying relevant biological processes. Despite its small size and short generation time it has organ systems similar to those of more complex animals and shares many molecular and physiological homologies with humans. A new image analysis toolbox now improves the way we capture quantitative information from individual worms.

Since C. elegans is visually transparent, deviations from wild type are often readily apparent using image-based techniques. Visual analysis, however, is tedious and automated analysis has been suffering several drawbacks. In most assays, for example, the density of worms causes them to touch or cluster, which has prohibited accurate measurements of individuals thus limiting automated analyses to population averages. In collaboration with researchers in Massachusetts, USA, we have developed WormToolbox, a toolbox for auto-

mated, high-throughput screening of image-based phenotypes that can detect individual worms in liquid culture, regardless of crossing or clustering. The image analysis algorithms therefore permit measurement of morphological phenotypes in individual worms. By enabling objective, high-throughput image-based assays of C. elegans, WormToolbox will underpin the study of biological pathways relevant to human disease. Initial testing and comparisons are promising. For example, compared with visual viability scoring of random samples and hits from a high-throughput viability assay, 97% accuracy was achieved in a few minutes, compared with 20 hours for visual scoring. The toolbox was also evaluated for its ability to score fluorescence distribution patterns within worms. Variations in signaling pattern could not be scored using simple approaches such as total signal per worm. However, digital worm straightening and atlas mapping from the WormToolbox quantitatively detected elevated signal in the anterior intestine. WormToolbox is believed to be the first system to automatically, quantitatively and objectively score a variety

of phenotypes in individual C. elegans in static, high-throughput images. Furthermore, the toolbox has been implemented as modules in the free and open-source CellProfiler software. CellProfiler emphasizes ease-of-use, it is compatible with cluster computing, and is flexible enough to accommodate new assays being developed by the scientific community. Future work is likely to extend WormToolbox by adding more worm-specific measurements based on their unique anatomy, and incorporating better methods for mixes with worms in various stages of development. The WormToolbox is a method that further strengthens the role of C. elegans as a powerful model organism for studying biological pathways and diseases. Reference

Wählby et al (2012) an image analysis toolbox for high-throughput c . elegans assays . Nature Methods, Vol. 9 No. 7, 714-716.

Contact

Carolina Wählby carolina@cb.uu.se

scilifelab uppsala annual report 2012

scientific highlights

FAD-diets – how evolution may be turning the tables on us Genetic mutations that increase the availability to the brain of two essential long-chain polyunsaturated fatty acids were likely to be favored when dietary access to the required precursors was limited. However, in the modern Western world, this phenomenon may now be exerting a negative effect on our health.

Maintaining the function of the human brain requires large amounts of the two long-chain polyunsaturated fatty acids (LC-PUFA) omega-3 docosahexaenoic acid (DHA) and omega-6 arachidonic acid (AA). As neither can be synthesized de novo, both need to be supplied via dietary intake. Two key enzymes involved in the conversion of 18-carbon precursors to DHA and AA are coded from the FADS region located on chromosome 11. Great interest has been devoted to FADS as a key locus for LC-PUFA biosynthesis, but the potential role of FADS mutations in human evolution has never been addressed. Together with co-workers from a broad array of international institutes, we now remedy this deficiency. Genome-wide genotyping of the FADS region in five European

population cohorts, combined with an analysis of available genomic data from human populations, archaic hominins and more distant primates, revealed that present-day humans have two common FADS haplotypes. The most common, haplotype D, was associated with high lipid levels, whereas the less frequent haplotype A was associated with low levels. Furthermore, haplotype D has a high frequency in Africa, indicating positive selection. The age of the diversity seen in haplotype D and its present geographic distribution indicate that both haplotype A and D appeared after the split from Neanderthals (around 500,000 years ago) but prior to the time of the exodus of modern humans from Africa 50,000 –100,000 years ago. Both haplotypes are thus present in European, Asian and Oceanian populations. In Africa, haplotype D appears to have continued to increase in frequency after the exodus until it reached its present dominating position. This suggests further positive selection. Interestingly, data also show a low frequency of haplotype D in Native American populations, suggesting that this haplotype might have been lost

during colonization of the American continent, possibly in combination with a relaxation of the selective pressure due to a diet with higher levels of essential LC-PUFAs. However, a low frequency of haplotype D may augment the synthesis of arachidonic-acid-derived proinflammatory eicosanoids, which are associated with increased risk of atherosclerotic vascular damage. It thus seems that while FAD haplotype D has been beneficial when food sources rich in essential LC-PUFAs were limited, it now represents a risk factor for Western lifestyle-related diseases, such as coronary artery disease. Reference

Ameur et al (2012) genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the bio synthesis of long - chain omega-3 and omega-6 fatty acids . American Journal of Human Genetics, 90, 809–820.

Contact

Ulf Gyllensten ulf.gyllensten@igp.uu.se

scilifelab uppsala annual report 2012

scientific highlights

scilifelab uppsala annual report 2012

scientific highlights

New insights into outbreak of illness caused by Shiga toxin-producing E. coli strains The 2011 European outbreak of bloody diarrhea with high rates of severe complications caused much public concern and attracted the interest of researchers keen to investigate a rare and poorly-understood toxin-producing strain of Escherichia coli. Recent work by SciLifeLab scientists now challenges some of the initial conclusions regarding the original source of several outbreaks.

The widespread outbreak of diarrhea and hemolytic uremic syndrome caused by Shiga toxin-producing E.Â coli O104:H4 during the summer of 2011 highlighted the potential of this rare E.Â coli serogroup to cause severe disease and raised considerable public concern. On June 11th, 2011, the European Centre for Disease Prevention and Control and the European Food Safety Authority issued public health advice on the prevention of diarrheal illness with special focus on the Shiga toxin. Prior to the outbreak, which was largely concentrated to Germany (3,816 cases), little was known of this

rarely-reported disease; its diversity and evolution were poorly explored. Much attention was thus given to analyzing the genomic diversity of E.Â coli O104:H4 and one group of scientists soon presented findings suggesting that independent isolates from later outbreaks, e.g. in France, were not derived from the German outbreak strain; the diversity in the small French outbreak was much larger than in the German outbreak. Together with colleagues from other parts of Sweden, we have argued that this conclusion is not justified. Our re-identification of single nucleotide polymorphisms (SNPs) in isolates originating from Germany and France, including new isolates from Swedish patients travelling in Germany, revealed that they do share a similar genomic diversity. Furthermore, synonymous substitutions accounted for 31.2% of SNPs in coding regions and another 11.1% at intergenic sites in the German outbreak strains, figures that are very similar to 36% and 14.3%, respectively, for the French strains.

Our findings that the average number of SNPs per genome and their substitution patterns are similar in the French and German outbreaks argues against the previously published hypothesis that mutation rates vary in the two bacterial populations. Even if biased sampling cannot be ruled out (29% of the patient population was sampled in the French outbreak, compared with only 0.3% in the German outbreak), our data strongly suggest that the French and German outbreaks originated from a common source that contained at least two different genotypes. Reference

Guy et al (2012) genomic diversity of the 2011 european outbreaks of escherichia coli o104:h4. Letter. PNAS Vol. 109, No. 52.

Contact

Siv Andersson siv.andersson@ebc.uu.se

scilifelab uppsala annual report 2012

scientific highlights

Pivotal studies of genomic diversity chart human evolution and development Studies that genotype millions of SNPs are now providing remarkable data that improve our understanding of human evolutionary history and the emergence of modern-day civilizations. Two recent investigations provide fascinating insights into the complex history of adaptation in Africa and the arrival of the farming culture in northern Europe.

Genetic, anthropological and archaeological studies support an African origin of modern humans. Within Africa, click-speaking southern African Khoe and San populations (Khoe-San) harbor the deepest mitochondrial DNA lineages, have great genomic diversity and probably represent the deepest historical population divergence among extant human populations. The study genotyped approximately 2.3 million single-nucleotide polymorphisms (SNPs) in 220 individuals representing eleven key populations from southern Africa (1). Analyses included reconstructing the demographic history of sub-Saharan populations using a powerful genealogical concordance approach. It was found that the Khoe-San diverged from other populations ≥100,000 years ago, and that the population structure within the Khoe-San dated back to about 35,000 years. Genetic variation in the various sub-Saharan populations did not

localize the origin of modern humans to a single geographic region within Africa, but instead indicated a history of admixture and stratification. Strong evidence of recent and ancient adaptation targeting muscle and skeletal (i.e. bone and cartilage) development was noted. This finding, combined with the fact that no currently studied population diverged from the ancestral human population before the ancestors of the Khoe-San, suggests that anatomical modernity appeared prior to the first modern human diversification event. The origins and genetic legacy of human populations has also been investigated in a study of the transition from the hunter-gatherer lifestyle to a sedentary farming economy in northern Europe about 4,000–6,000 years ago (2). Detailed investigation of 249 million base pairs of genomic DNA obtained from around 5000-year-old remains of three hunter-gatherers and one farmer, separated by less than 400 km, provided direct genomic evidence of stratification between the two Neolithic cultural groups. The farmer is genetically most similar to extant southern Europeans, while the hunter-gatherers had a distinct genetic signature that is most similar to that of extant northern Europeans. These results suggest that migration from southern Europe catalyzed the

spread of agriculture, and that barriers to gene flow between resident hunter-gatherers and colonizing farming groups persisted during the initial stages of expansion and settlement. This contrasts strongly with earlier models that proposed an expansion of farming without substantial replacement of resident hunter-gatherer populations. The observation that most European populations appear genetically intermediate to the two Neolithic groups also suggests that the barriers perhaps became more permeable over time and that gene flow between farmer and hunter-gatherer populations, possibly over a long period, eventually gave rise to the present pattern of genetic variation in Europe. References

1. Schlebusch et al (2012) genomic variation in seven khoe-san groups reveals adaptation and complex african his tory. Science Vol. 338 374-379. 2. Skoglund et al (2012) origins and genetic legacy of neolithic farmers and hunter- gatherers in europe .

Science Vol. 336 466-469.

Contact

Mattias Jakobsson mattias.jakobsson@ebc.uu.se

Cross sections of mammary ducts in mice showing the hollow lumen of normal tissue and abnormal luminal filling due to lack of cell death in the absence of Mig6.

scilifelab uppsala annual report 2012

scientific highlights

The double-edged tumor suppressor Mig6 links ErbB receptor inactivation to apoptosis Together with European colleagues, we have uncovered a multi-adaptor protein that acts as a double-edged tumor suppressor; Mig6 not only attenuates ErbB-signaling but also directly triggers cell death when ErbB receptors are inactive. These findings challenge the common belief that deprivation of growth factors induces apoptosis passively by lack of mitogenic signaling.

The four members of the epidermal growth factor receptor family of type-1 tyrosine kinases (EGFR and ErbB2 to ErbB4) are widely expressed in normal skin epithelial cells. Signaling by EGFR is a highly-regulated process and the liganded receptor is known to alter key cell properties including differentiation, survival and programmed death (apoptosis). EGFR also affects cancer development and progression. Deregulation, for example, disrupts normal tissue homeostasis and contributes to the formation of many epithelial cancers. Mig6, a negative feedback regulator of ErbB receptors, is known to

act by directly binding to the active receptor kinase domain, thereby interfering with the formation of the activating dimer interface. It is known that Mig6 is an important tumor suppressor since knockout mice are highly susceptible to cancer formation, while Mig6 expression is frequently lost in various human cancers. Interfering with its function, for example, leads to disrupted mammary morphogenesis characterized by ductal luminal filling due to impaired cell death. Our studies have uncovered an ‘inverse’ mode of receptor tyrosine kinase signaling that directly links ErbB receptor inactivation to the induction of apoptosis. On ligand deprivation, Mig6 dissociates from the ErbB receptor, binds to the tyrosine kinase c-Abl and activates it in order to trigger p73-dependent apoptosis in mammary epithelial cells. Deleting Errfi1 (encoding Mig6) and inhibiting RNAi silencing of c-Abl causes impaired apoptosis and luminal filling of mammary ducts. Mig6 activates c-Abl by binding to the kinase domain, which is prevented in the

presence of epidermal growth factor (EGF) by Src family kinase-mediated phosphorylation on c-Abl-Tyr488. These results reveal a receptor-proximal switch mechanism by which Mig6 actively senses EGF deprivation and directly activates proapoptotic c-Abl. This double-edged tumor suppressor role of Mig6 challenges today’s ideas about how growth factor deprivation might induce apoptosis via passive mechanisms. The finding is of particular interest considering that acquisition of growth factor-independent survival is likely to be an early step of cellular transformation. Reference

Hopkins et al (2012) mig6 is a sensor of egf receptor inactivation that directly activates c -abl to induce apoptosis during epithelial homeostasis .

Developmental Cell 23, 547–559.

Contact

Ingvar Ferby ingvar.ferby@licr.uu.se

scilifelab uppsala annual report 2012

scientific highlights

Breakthrough study shows single gene has a major impact on gait in horses and mice Our understanding of spinal cord neuronal circuitry and its control of locomotion in vertebrates has been boosted by genetic studies of gait in horses combined with new insights into the function of certain neurons in the spinal cord of mice. The work illustrates how genetic studies of domestic animal evolution can lead to exciting new knowledge about gene function and key biological mechanisms.

Our ability to walk and run depends on a complex coordination of muscle contractions carried out by neuronal circuits in our spinal cord. To see how this works at cell and molecular levels, researchers studied locomotion in horses. In order of increasing speed, the three naturally occurring gaits are walking, trotting and cantering/galloping. Some horses, e.g. Icelandic breeds, can use alternate gaits, typically at intermediate speed. In an attempt to explain why some Icelandic horses can pace but others cannot, a genome-wide association analysis using 30 Icelandic horses was performed. This revealed that a single gene, DMRT3, largely explains the genetic difference between pacers and non-pacers.

Independently, other SciLifeLab researchers discovered that the same gene is expressed in a previously unknown type of neuron in the spinal cord of mice. The characteristics of these neurons suggested that they could take part in neuronal circuits coordinating movements. The two research groups compared data and realized that an important biological finding was imminent. Not only did the discovery extend our understanding of spinal neuronal circuits in mice, it implicated a tangible population of nerve cells as being critical for the control of gaits in horses. As the new type of nerve cell was dependent on DMRT3, it was tentatively named after the gene. Moreover, it was also demonstrated that a single base change in DMRT3 results in a truncated form of the protein, and that this mutation shows a strong positive association with performance in harness racing, also known as trotting. As a horse increases speed, it will normally switch from trot to gallop, which is the natural gait at high speed, but which leads to disqualification in races. The mutation thus appears to inhibit the transition

from trot to gallop, thereby allowing the horse to trot at very high speed. Further work on DMRT3 function revealed that DMRT3-neurons cross the midline of the spinal cord and thus connect the left with the right side. They also have a direct connection with motor neurons that control flexor and extensor muscles. Interestingly, knockout mice, which lack a functional DMRT3 gene, display an altered pattern of locomotion. Since DMRT3 is present in all vertebrates for which data are available, it is likely that DMRT3 nerve cells play a central role in coordinating movements in humans as well. Reference

Andersson et al. (2012) mutations in dmrt3 affect locomotion in horses and spinal circuit function in mice . Nature Vol. 488 642-646.

Contact

Leif Andersson leif.andersson@imbim.uu.se Klas Kullander klas.kullander@neuro.uu.se

scilifelab uppsala annual report 2012

scientific highlights

Study ‘sheds new light’ on the brain’s learning and memory mechanisms Although we know that the hippocampus region of the brain is involved in spatial navigation and memory, the mechanisms underlying these functions are not well understood. A newlydiscovered group of OLM-α2 nerve cells that act as ‘gatekeepers’ and that carry a nicotine receptor can now help explain our ability to remember and sort information.

Humans think, learn and memorize with the help of nerve cells sending signals between each other. Some nerve cells send signals far away to other areas of the brain, while other neurons send signals within the same area. Local nerve circuits in the hippocampus process impressions and turn some of them into memories. But exactly how these processes function is poorly understood and the lack of cell-specific tools has hampered detailed investigation. Nevertheless, recent evidence has suggested that receptors containing the nicotinic acetylcholine receptor α2 subunit (Chrna2) are specifically expressed in oriens lacunosum-moleculare (OLM) cells and that direct cholinergic excitation of OLM cells might be involved in switching information flow

in the brain. In addition, it was known previously that nicotine improves cognitive processes including learning and memory. Through a new technology called optogenetics in which light is used to stimulate selected nerve cells, SciLifeLab researchers at Uppsala University, together with Brazilian collaborators, were able to discover that light activation of the OLM-α2 gatekeeper cells alters the flow of information in the hippocampus in the same way as nicotine does. Via research on a transgenic mouse line expressing Cre recombinase under the control of the Chrna2 promoter (Chrna2 is the most specific marker of a morphologically well-defined hippocampal interneuron population to date), it was then shown that the gatekeeper cells connect to the principal cell of the hippocampus. Active gatekeeper cells prioritize local circuit signals arriving to the principal cell, while inactive gatekeeper cells allow inputs from long-distance targets. Nicotine activates the gatekeeper cell, thereby prioritizing the formation of memories via local inputs. Although the beneficial effects of nicotine on cognitive processes such

as learning and memory are recognized, this was the first time that an identified nerve cell population could be linked to the phenomenon. The new study literally ‘sheds light’ on this intriguing mechanism; the newly discovered gatekeeper nerve cells offer an explanation to how the flow of information is controlled in the hippocampus. Thanks to this new knowledge, it may be possible to stimulate these nerve cells by artificial means, for example by selective nicotine-like drugs, to improve memory and learning in humans. Reference

Leão et al (2012) olm interneurons differentially modulate ca3 and entorhinal inputs to hippocampal ca1 neurons .

Nature Neuroscience Vol. 15 No. 11 1524-1530.

Contact

Klas Kullander klas.kullander@neuro.uu.se Richardson Leão richardson.leao@neuro.ufrn.br richardson.leao@neuro.uu.se

scilifelab uppsala annual report 2012

scientific highlights

Distinguishing genetic drift from selection: the Atlantic herring enters the debate With around 20 billion individuals in the Baltic Sea alone, the Atlantic herring is one of the most abundant marine fishes in the world, as well as a critical food source in Northern Europe. Thanks to a breakthrough genomewide study, it is now also a model organism for population genetic studies of adaptation and natural selection.

The Atlantic herring (Clupea harengus) is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Based on its distinct phenotype (including smaller size and lower fat content), the herring found in this region has been classified as a subspecies, Clupea harengus membras, of the herring found in North Atlantic waters. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between these two geographic regions, a result that is considered to be consistent with huge population sizes and minute genetic drift.

In collaboration with other Swedish researchers we have employed a cost-effective, genome-wide sequencing strategy that overcomes the otherwise challenging requirement for a high-quality draft genome. By combining a transcriptome assembly with whole-genome shotgun sequencing, we constructed an â&#x20AC;&#x2DC;exome assemblyâ&#x20AC;&#x2122; that permitted genome-wide screening for genetic polymorphisms. This approach identified 440,817 SNPs, the great majority of which showed no appreciable differences in allele frequency among the populations. However, 3,847 SNPs did display striking differences, some even approaching fixation for different alleles. A simulation study confirmed that the distribution of the fixation index FST deviated significantly from expectation for selectively neutral loci. These findings provide compelling evidence for the existence of a number of genetically differentiated populations of Atlantic herring and support the classification of the Baltic herring

as a sub-species. Genetic differences among three samples of the Baltic herring are generally small compared with the allele frequency differences between Baltic and Atlantic herring. The overall results imply that low gene flow between sub-populations contributes to the lack of genetic differentiation at selectively neutral loci, while natural selection is the dominating force that determines the frequency of non-neutral alleles. The results also establish the herring as a model organism for evolutionary genetics. Reference

Lamichhaney (2012) population-scale sequencing reveals genetic differentiation due to local adaptation in atlantic herring .

PNAS Vol. 109 No. 47

19345â&#x20AC;&#x201C;19350.

Contact

Leif Andersson leif.andersson@imbim.uu.se

Image from: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15840-2. Epub 2002 Dec 2. T cells take aim at cancer. Pardoll D. Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.

T-cells transduced with a cloned T-cell receptor that can specifically kill appropriate prostate and breast cancer cells suggest that there are good grounds for optimism regarding future therapeutic developments.

scilifelab uppsala annual report 2012

scientific highlights

Unique report: T cells with cloned T-cell receptor specifically kill prostate and breast cancer cells T-cell therapy using the patient’s own T-cells is considered to hold great promise as a cancer treatment. T-cells transduced with a cloned T-cell receptor that can specifically kill appropriate prostate and breast cancer cells suggest that there are good grounds for optimism regarding future therapeutic developments.

Recent clinical trials for cancer have demonstrated that immunotherapy can lead to improvements in overall survival. Genetically-engineered T-cells have, for example, induced complete remission in patients with otherwise treatment refractory B-cell leukemia. However, the promise of T-cell-based immunotherapy has been limited by difficulties in isolating and expanding T-cells specific for tumor-associated antigens. To produce genetically engineered T-cells directed against prostate and breast cancer cells, a T-cell receptor (TCR) with specificity for a prostate differentiation antigen was cloned.

The targeted antigen, TCRγ chain alternate reading-frame protein (TARP), is exclusively expressed in normal prostate epithelium, as well as in prostate and breast cancer cells. TARP may be a particularly relevant immunological target for T-cell therapy of prostate cancer since antibody responses against TARP have been detected in prostate cancer patients treated with GM-CSF-secreting cellular immunotherapy. Early-stage prostate cancer patients have circulating T-cells against both TARP4–13 and TARP27–35 epitopes. TCR-engineered T-cells, which recognize the HLA-A2–restricted TARP4–13 epitope (FPPSPLFFFL), proliferated well when exposed to peptide specific stimuli, and exerted peptide-specific IFN-© production and cytotoxic activity. Significantly, they were both specific and efficient in killing TARP-expressing HLAA2+ prostate and breast cancer cells, demonstrating that the TARP4–13 epitope is a physiologically relevant

target for T-cell therapy of prostate and breast cancer. These results thus provide evidence that a cloned TCR directed against a physiologically relevant HLA-A2 epitope of a highly and specifically expressed antigen can effectively kill prostate and breast cancer cells. This report, which to the best of our knowledge is unique, suggests that T-cellbased immunotherapy may have an important future role in combating both cancer forms. Reference

Hillerdal et al., (2012) t cells engineered with a t cell receptor against the prostate antigen tarp specifically kill hla-a2+ prostate and breast cancer cells .

PNAS Vol. 109 No. 39

15877–15881.

Contact

Magnus Essand magnus.essand@igp.uu.se

scilifelab uppsala annual report 2012

scientific highlights

Sliding rules: 45 base pairs on chromosomal DNA for the lac repressor That transcription factors find their sequence-specific operator sites on the chromosome faster than the rate limit for three-dimensional (3D) diffusion in the cytoplasm has been explained by proposing a combination of 3D diffusion plus 1D sliding along the DNA. Sliding on DNA has previously only been studied in vitro. Now it has been measured for the lac repressor in living bacteria.

Transcription factor proteins regulate the expression of genes by binding to sequence-specific sites on the chromosome. This process, which is both fast and accurate, has been explained by a facilitated diffusion mechanism combining 3D cytoplasmic diffusion and 1D sliding along the DNA. This sliding would effectively extend the target region to the sliding distance and facilitate the search for the binding site. Facilitated diffusion has been demonstrated in vitro, but the physiological relevance of the long sliding distances observed at low in vitro salt concentrations has been questioned. We have now developed a single-mol-

ecule imaging assay that provides the time resolution necessary to investigate the sliding process in living bacteria, and that should also show just how far a transcription factor slides on chromosomal DNA. Using a yellow fluorescent proteinlabeled lac repressor (LacI) in E. coli cells, we developed an assay for measuring search time based on the distinction between localized and diffuse fluorescence signals. We determined that the time required for a single repressor molecule to bind a single chromosomal operator (lacOsym) are in excellent agreement with recent theoretical binding-time predictions (3.5 min) based on facilitated diffusion by sliding. To directly evaluate whether the lac repressor slides on non-specific DNA sequences in vivo – and if so, how far – bacterial strains with two identical lac operator sequences separated by different distances were used. The rationale is that if the distance between two operator sites is smaller than the sliding distance, they will appear as one search target, whereas two distant operator sites will appear

as two independent targets. How fast the lac repressor finds any one of these sites was then measured. The average sliding distance was found to equal 45 ± 10 bp, which is again close to in vitro estimates for high salt concentrations. Speed-up was modest, i.e. in vivo binding is not much faster than the theoretical limit for 3D diffusion alone. Sliding can also be obstructed by other DNA-bound proteins near the operator. Interestingly, the repressor almost always slides over its natural lacO1 operator several times before eventually binding. This suggests a trade-off between rapid search on non-specific sequences and fast binding at the specific site. Reference

Hammar et al (2013) the lac repressor displays facilitated diffusion in living cells .

Science Vol. 336 1595-1598.

Contact

Johan Elf johan.elf@icm.uu.se

scilifelab uppsala annual report 2012

scientific highlights

Regulatory changes or protein-coding changes: which dominate adaptive evolution? Opinion is divided regarding the genetic and molecular basis of adaptive evolution. Do regulatory changes or protein-coding changes predominate? A detailed investigation using a high-quality reference genome assembly for three-spine sticklebacks now helps resolve this dilemma.

Accumulating sufficient examples in any particular study group has remained a barrier to gaining an overall picture of the molecular mechanisms underlying evolutionary change, particularly for clearly adaptive phenotypes in wild organisms. Three-spine sticklebacks, however, provide a powerful system for studying the molecular basis of adaptive evolution in vertebrates. After the retreat of Pleistocene glaciers, marine sticklebacks colonized and adapted to many newly-formed freshwater habitats, evolving repeated changes in body shape, skeletal armour, trophic specializations, pigmentation, salt handling, life history and mating preferences, all traits that are likely to evolve by natural selection. In addition, distinctive marine and freshwater forms can still hybridize, making it possible to

map the genetic basis of individual traits. Furthermore, the highly parallel nature of stickleback evolution in different parts of the world provides clear molecular signatures that can be used to recover many loci consistently associated with parallel marineâ&#x20AC;&#x201C;freshwater adaptation. For example, the signal resolution of repeatedly used adaptive loci approaches 5 kb, which will often identify single genes or intergenic regions. This offers a significant advantage over the several hundred kilobase candidate intervals typically identified in genetic mapping crosses, or the megabase or larger regions identified in earlier selection scans of the stickleback genome. By sequencing individual genomes from a global set of marine and freshwater three-spine stickleback populations, a genome-wide set of loci that are consistently associated with marine-freshwater divergence could be identified. Analyzing the patterns of genetic variation indicates that parallel evolution of marine and freshwater sticklebacks occurs by dynamic reassembly of many â&#x20AC;&#x2DC;islandsâ&#x20AC;&#x2122; of divergence distributed across many chromosomes.

Reassembly by linkage is probably strengthened by inversions that distinguish marine and freshwater ecotypes Comparative data suggest that both regulatory and protein-coding differences contribute to parallel stickleback evolution. However, regulatory changes seem to account for a much larger proportion of the overall set of loci repeatedly selected during marine-freshwater divergence. This is suggested by the increased density of conserved non-coding intergenic sequences found near marine-freshwater divergent loci, the substantial fraction of loci mapping entirely to non-coding regions, as well as the significant enrichment of genes with expression differences near key regions used for parallel evolution. Reference

Jones et al (2012) the genomic basis of adaptive evolution in threespine sticklebacks

Nature Vol. 484 55-61.

Contact

Kerstin Lindblad-Toh kersli@broadinstitute.org

scilifelab uppsala annual report 2012

scientific highlights

Pathogenic mutation identified in Infantile Cerebellar-Retinal Degeneration The absence of non-invasive biomarkers for this debilitating infant disorder has driven the search for genetic mutations. Advanced mapping and sequencing techniques have now identified a pathogenic mutation in the gene for mitochondrial aconitase in eight affected individuals.

Degeneration of the cerebrum, cerebellum and retina in infancy is part of the clinical spectrum of lysosomal storage disorders, mitochondrial respiratory chain defects, carbohydrate glycosylation defects, and infantile neuroaxonal dystrophy. The typical disease course is characterized by failure to acquire developmental milestones and culminates in profound psychomotor retardation and progressive visual loss. As part of an international research team, we have studied eight individuals from two unrelated families who presented symptoms at 2 to 6 months of age. Extensive laboratory investigations, including complete blood count, routine serum chemistry, glucose, lactate, ammonia, thyroid functions, and creatine kinase were all normal, as was the urinary organic acid profile. Cerebrospinal fluid analyses for cells, glucose, protein, lactate, amino acids, and neurotransmitters also revealed normal

findings. Muscle biopsies of three individuals disclosed normal histology. Even the activities of the five enzymatic complexes of the mitochondrial respiratory chain and the pyruvate dehydrogenase complex were normal in mitochondria isolated from muscle. However, the oxidation of glutamate was slightly reduced (to 62.7%) of the control mean, while the oxidations of related mitochondrial substrates were 88.3%, 86.7% and 90.3%. To localize the mutated gene, we searched for homozygous regions common to three of the individuals and used selected short tandem repeat (STR) markers for genotyping remaining family members. Because of the large number of genes within the region, exome sequencing was also employed. We identified 112 homozygous single-nucleotide variants in the region, and 42 variants were located in coding exons and flanking intronic sequencing (512 nt). Variants were filtered until only a single coding homozygous variant remained. This variant was c.336C>G in ACO2, which causes p.Ser112Arg. This position is highly conserved and the substitution was scored as ‘probably damaging’ with PolyPhen2 (score of 0.992). All eight individuals were homozygous for the mutation and

further investigation indicated that Ser112Arg is a founder mutation in this population. None of the 128 anonymous individuals of the same ethnic origin carried it. Specific aconitase activity was shown to be significantly reduced in patients’ fibroblasts. We also showed that the human mutated ACO2 failed to rescue a yeast ACO1 deletion mutant, providing further functional support for the genetic finding. ACO2 consists of 18 exons that encode mitochondrial aconitate hydratase, an 805-amino acid TCA-cycle protein. We recommend measuring aconitase activity in lymphoblasts or determining the sequence of ACO2 in similarly affected individuals, as there are no noninvasive biomarkers. Reference

Spiegel (2012) infantile cerebellar-retinal degeneration associated with a mutation in mitochondrial aco nitase , aco2.

American Journal of Human Genetics 90, 518–523.

Contact

Lars Feuk lars.feuk@igp.uu.se

scilifelab uppsala annual report 2012

Technology Platforms Genomics

SNP&SEQ technologies Management

Ann-Christine Syvänen (platform director) Tomas Axelsson (manager, SNP genotyping) Ulrika Liljedahl and Olof Karlberg (managers, Sequencing) Services

Mission

To offer SNP genotyping and second-generation sequencing as a service to researchers in Sweden and abroad. The unit’s genotyping and sequencing procedures are accredited by SWEDAC, and the facility is CsPro-certified as a service provider using Illumina genotyping and sequencing technology.

SNP genotyping: • SNP genotyping for projects ranging in size from 1- >5,000,000 SNPs per sample in hundreds or thousands of samples • SNP identification from databases and bioinformatics-assisted primer and assay design • Analyzing genotype, copy number and methylation data using the analysis software of each genotyping system • Delivering quality-assessed genotyping results in text file format • Compiling materials and methods for publications • Maintaining database containing information on samples, genotypes, SNPs and primer sequences Second-generation sequencing:

• Project planning • Optimized sequencing library preparation, including target region enrichment • Single-read or paired-end sequencing of genomes, targeted genomic

regions, transcriptomes and tag-sequencing • Delivering sequence reads with quality information via the UPP NEX project at SNIC-UPPMAX • Bioinformatics support including data filtering, sequence alignments, coverage statistics, SNV-calling, and expression levels/RNA counts • Compiling materials and methods for publications Equipment includes

• iScan system (Illumina) • BeadExpress (Illumina) • GenomeLab SNPstream (Beckman Coulter) • GeniosPro (Tecan) • HiSeq2000 sequencers (Illumina) • MiSeq sequencer (Illumina) (available Q2 2012) • Genome Sequencer FLX+ (Roche/454 Contact

Tomas Axelsson +46-18-611 26 44, 070-167 94 58 contact@genotyping.se www.genotyping.se Ulrika Liljedahl +46-18-611 49 34, 070-167 94 59 contact@sequencing.se www.sequencing.se

scilifelab uppsala annual report 2012

Technology Platforms Genomics

Uppsala Genome Center Mission

Services

Application examples

To provide Next Generation Sequencing services with SOLiD5500xl/ SOLiD5500xl-W, Ion Torrent instruments, including Ion Proton, as well as Sanger sequencing and genotyping. Tailor-made, cost-effective and expedient solutions for all types of genetic/ genomic projects are also key parts of the offering.

• Capillary electrophoresis on fragment analysis or Sanger sequencing samples • Sanger sequencing service • Next-generation sequencing on SOLiD5500 and Ion Torrent systems

• Whole genome resequencing • Targeted resequencing • Whole transcriptome sequencing • Small RNA sequencing • ChIP sequencing • Methylation analysis and de novo sequencing

Equipment includes

Contact

• SOLiD5500XL instruments • Ion Torrent PGM instruments • ABI3730XL DNA Analyzers • ABI7900 HT

Inger Jonasson +46-70-167 90 82 inger.jonasson@scilifelab.uu.se info@genomecenter.uu.se

Management

Ulf Gyllensten (platform director) Inger Jonasson (manager)

Technology Platforms Genomics

Array and Bioinformatics Mission

To provide access to microarray technology and bioinformatics support for applications in both research and healthcare in Sweden. Particular focus is put on national support for analyzing clinical samples in conjunction with the rest of the clinical ’omics platform. Our bioinformatics competence will continue to support the development and introduction of both arraybased and sequencing-based clinical analyses throughout Sweden. Management

Anders Isaksson (platform director and manager) Services

Wet lab service: • mRNA quantification • SNP genotyping • Copy number analysis of genomic DNA

• Loss-of-heterozygosity • Alternative splicing • miRNA quantification • Mapping protein-genomic DNA interactions Bioinformatics service:

• Experimental design • Quality control • Normalization • Visualization • Univariate statistics • Multivariate analyses • Evaluation using databases • Data integration • Algorithm development • Cancer bioinformatics In addition, we develop algorithms for analyzing tumor samples and identifying/annotating non-coding RNAs, etc. Practical courses on data analysis, demonstrations and other types of support are also available.

Equipment includes

• Affymetrix Gene Chip System 3000 7G • Fluidic stations FS 450 • Hybridization ovens 640/645 • Agilent 2100 Bioanalyzer • ABI 9700 Thermocycler Application examples

• Genomic analysis of 400 samples from patients with chronic lymphocytic leukemia • Developing bioinformatic tools for allele-specific copy number analysis in tumor samples • Identifying non-coding RNA binding to chromatin

Contact

Anders Isaksson +46-18-611 97 82 anders.isaksson@medsci.uu.se arrayplatform@medsci.uu.se

scilifelab uppsala annual report 2012

Technology Platforms

MS Proteomic Resource Center Mission

To utilize the facility’s expertise in sampling, sample preparation (e.g. selective extraction, affinity purification, depletion of abundant proteins), separation (e.g. 1-D and 2-D gel analysis, capillary electrophoresis, gas and liquid chromatography), mass spectrometry and general protein and peptide chemistry. The unit’s instruments provide high resolution and accurate mass determinations for confident structural elucidation and quantitative analysis. Management

Jonas Bergquist (platform director) Margareta Ramström Jonsson (manager, MS) Åke Engström (manager, 2D-gel) Services

• Analyzing and comparing proteomes using selected sample preparation technologies

• Quantitative proteome analysis using label-free as well as stable isotope label technologies • Identifying proteins in protein spots/bands by mass spectrometry • Analyzing expressed proteins for quality control • Analyzing proteins for post-translational modification • Complementary analysis of organic compounds, trace elements, DNA, carbohydrates and lipids • 1-D and 2-D gel facility • Imaging mass spectrometry on the MALDI TOF/TOF platform • General MS analysis Equipment includes

• 7T LTQ FTICR MS and LTQ Orbitrap Velos Pro ETD MS (Thermo) • MALDI TOF/TOF (Ultrafl ex II Bruker) • ESI-TOF (Agilent)

Proteomics

• Q-STAR XL and Q-TRAP 3200 (Sciex) Application examples

• Distinct cerebrospinal fluid proteomes that differentiate post-treatment Lyme disease from Chronic Fatigue Syndrome • Fish peptidome patterns that can distinguish from exposure to antropogenic pollution • Analyzing membrane and hydrophilic proteins simultaneously derived from the mouse brain using cloud-point extraction • Moving toward a comprehensive characterization of the phosphotyrosine proteome • Exploring liquid chromatography-mass spectrometry fingerprints of urine samples from patients with prostate or urinary bladder cancer

Contact

Jonas Bergquist +46-18-471 36 75 jonas.bergquist@kemi.uu.se Margareta Ramström +46-18-471 3678 margareta.ramstrom@kemi.uu.se Åke Engström +46-18-471 42 06 ake.engstrom@imbim.uu.se Platform e-mail: ms@scilifelab.uu.se

scilifelab uppsala annual report 2012

Technology Platforms Proteomics

Tissue-profiling Center Mission

To provide facilities for tissue-based proteomic analyses. The facility focuses on histopathology with special emphasis on tissue microarray (TMA) production, immunohistochemistry (IHC) and slide scanning. Management

Fredrik Pontén (platform director) Caroline Kampf (manager) Services

• Producing TMAs (paraffin blocks containing cores of selected tissue or cell preparations assembled together to allow multiplex histological analysis in a high-throughput setting) • Offering IHC to visualize antigens using antibodies or other affinity reagents • Visualization of antigen-antibody interactions by direct enzyme, fuorophore or biotin conjugation of the primary antibody, or by a polymer technique

• Slide scanning to transform stained glass slides to digital images that can be saved, shared, annotated and used for automated image analyses Equipment includes

• Tissue microarrayers; one automated system (Beecher ATA-27), one manual system (Beecher MTA-1) and one semi-automated system (Pathology Devices) • Waterfall microtomes (Microm HM 355S) • Automated image scanners (Aperio Scanscope XT) • Automated liquid handler (Gilson Quad-Z 215) • Automated slide-staining system for deparafinization and dehydration (Leica Autostainer XL) • Automated glass coverslipper system (Leica CV 5030) • Automated slide-staining systems for IHC staining (Lab Vision Autostainer 480) • Bright field microscopes

Application examples

• Construction of 1200 TMAs containing over 86,400 tissue cores, 180 CMAs containing over 23,800 cell cores, staining over 190,000 slides for IHC and scanning over 70,000 slides • Diagnostic pathology to determine the origin of poorly differentiated tumors and to stratify tumors for optimized treatment regimes • IHC widely used to study cellular processes or localization • 500 to 600 new antibodies tested every month as part of the Human Protein Atlas project

Contact

Caroline Kampf +46-18-471 48 79 caroline.kampf@igp.uu.se

Technology Platforms Proteomics

in situ PLA Facility Mission

Services

To use the in situ Proximity Ligation Assay (in situ PLA) to visualize and quantify proteins, post-translational modifications and protein interactions with great sensitivity and specificity in cells and tissues. Specificity can be increased compared to standard immunoassays (e.g. IHC) since two, three or more antibodies are required for recognition. The facility combines in situ PLA with DNA amplification to generate the detection signal, which ensures highly sensitive detection.

• in situ PLA for detecting proteins and their interactions using either client-selected antibodies or previously validated antibodies from a constantly updated list • Validation, optimization and assay development for client-selected antibodies

post-translational modifications in cells and tissues • Analyses of biological pathways and cell signaling • Quantitative analyses of the effect of drug candidates on protein expression, interactions and modifications

Equipment includes

• Epi-fluorescence microscopes • Confocal microscope • Fluorescence scanner Contact

Management

Application examples

Ulf Landegren (platform director) Masood Kamali-Moghaddam (manager)

• Visualization and quantification of proteins, their interactions and

Masood Kamali-Moghaddam +46-18-471 44 54 masood.kamali@igp.uu.se

Technology Platforms Comparative genetics

Zebrafish Facility Mission

Services

Application examples

To provide an infrastructure and individually-tailored support for projects utilizing this popular model system for vertebrate development and disease. Zebrafish embryos are transparent and develop outside the mother’s body, which greatly facilitates manipulation and imaging of biological processes. The facility allows researchers to take advantage of the unique features of the zebrafish model system, and provides initial advice on feasibility and experimental design as well as running support over the course of the project.

• Facility services • Consultancy • Access to the facility • Techniques for reverse and forward genetic experiments, as well as methods to visualize biological processes for extended periods in intact embryos

• Gain- and loss of function experiments • Expression analysis • Generation- and analysis of transgenic lines

Equipment includes

Contact

• Fish facility, including tank systems, fish lines, workstations, incubators and injectors • Light microscopy, including confocal microscopy • Electron microscopy

Johan Ledin johan.ledin@scilifelab.uu.se +46-70-447 39 94

Management

Per Ahlberg (platform director) Johan Ledin (manager)

Katarina Holmborn-Garpenstrand katarina.garpenstrand@ scilifelab.uu.se +46-18-471 26 84

scilifelab uppsala annual report 2012

Technology Platforms Comparative genetics

Domestic Animals Mission

To offer a unique possibility to utilize the disease mechanisms of domestic animals to identify genetic risk factors, explore genotype-phenotype relationships, and identify candidate genes that can be of relevance for human diseases. The domestic animal facility offers already defined disease models for a large number of diseases as well as expertise for evaluating new models for the disease of interest.

• Assistance with planning, organizing and interpreting whole genome wide association analysis to identify disease loci in the animal model • DNA preparation and storage of samples in the SLU SciLifeLab Biobank Equipment includes

• QIAsymphony instrument for DNA and RNA preparation • LIMS system for registering biobank samples (at the SLU SciLifeLab Biobank)

• Mapped traits in the dogs: • HAS2 for periodic fever in the Sharpei breed • Genes involved in T-cell activation in an SLE-like disease in Nova Scotia Duck Tolling Retriever. • SOD 1 for ALS in Pembroke Welsh Corgi • CDH2 for OCD in Doberman Pinscher

Management

Leif Andersson (platform director) Cecilia Johansson (manager) Services

• Assistance with evaluating the availability and validity of domestic animal models for specific diseases

Application examples

• Identifying genetic risk factors in domestic animals • Comparative studies in human counterparts (can be applied to homologous diseases between domesticated animals and humans)

Contact

Cecilia M Johansson cecilia.m.Johansson@scilifelab.uu.se +46-18-471 45 25

scilifelab uppsala annual report 2012

Technology Platforms Biological Visualisation

BioVis Facility Mission

To provide technology and expertise for high-resolution biological imaging and visualization at tissue, cell and sub-cellular levels, including supporting analytical and preparative technologies. Management

Lena Claesson-Welsh (platform director) Dirk Pacholsky (manager) Services

• Fee-based access to state-of-the-art instruments and advice regarding methods and visualization-related problems • Analytical techniques available include fluorescence, confocal and multiphoton microscopy plus electron microscopy and flow cytometry

• Flow sorting and microdissection microscopy for upstream sample purification • Ultrastructural studies Equipment includes

• Zeiss 710 multiphoton and Confocal microscope • Zeiss 510 confocal microscope • Zeiss AxioObserver microscope with ApoTome • Arcturus microdissection microscope • BD LSR II SORP analytical flow cytometer • BD FACSAria flow sorter • FEI Tecnai BioTwin transmission electron microscope • Workstations for analysis of imaging and flow data, including Imaris 3D image analysis software.

Application examples

• Co-localization studies on both cell- and tissue levels with several simultaneous markers • Ultrastructural morphology and IHC studies • Analysis of the 3D-distribution of markers of interest in the cell or cell environs • Quantitative analysis of cell populations and marker expression • Preparative experiments to isolate cells or tissue sections of interest for downstream processing

Contact

biovis@scilifelab.uu.se

Technology Platforms Bioinformatics

UPPNEX – UPPmax NExt generation sequencing Cluster & Storage To provide high-performance computing and storage resources, maintain relevant bioinformatics software and data (e.g. reference genomes), and offer associated user support. UPPNEX is hosted at Uppsala Multidisciplinary Center for Advanced Computational Science (SNIC-UPPMAX), which is Uppsala University’s resource for high-performance computing and related know-how. Its reference group makes strategic and policy decisions, while a coordinator is responsible for daily operations.

• Expert management of computational hardware and system administration • Assistance with technical questions • Assistance with NGS analyses on UPPNEX systems • Assistance with installation of new or updates to current software applications • Training in bioinformatics education at SciLifeLab and Uppsala University • Participates in the national bioinformatics support forum www. biosupport.se

Management

Hardware includes

Ola Spjuth (manager)

• Computer cluster with 1 M computing hours per month • Storage resources of 2 PB • Large memory SMP with 2 TB RAM • Tape backup • Access to SweStore National Storage • Fast connection to Swedish University Network (SUNET) backbone

Mission

Services

• High-performance computing and large-scale storage for bioinformatics • Computing and storage resources, primarily for the Next Generation Sequencing (NGS) community in Sweden, and SciLifeLab in particular

Software includes

• Alignment programs (e.g. BWA, Mosaik, Bowtie, Tophat, MAQ, Bioscope and Lifescope) • De novo assembly software (e.g. Abyss, Velvet and Mira) • Downstream analysis programs (e.g. Cufflinks, MrBayes, SAM-tools, and Annovar) • General tools (e.g. BioPerl, Picard and GATK) Application examples:

• Primary focus on next-generation sequencing • Large-scale storage and archiving of image data.

Contact

Ola Spjuth, Coordinator UPPNEX ola.spjuth@farmbio.uu.se +46-18-471 42 81 www.uppmax.uu.se/uppnex

scilifelab uppsala annual report 2012

Technology Platforms Emerging technology platforms

SiCell single-cell genomics Mission

To exploit the immense potential of single-cell genomics, which allows exploration of the genome content of individual cells without the need for laboratory cultivation, by becoming a leading single-cell genomics center in Europe. The center will offer single-cell sorting, whole-genome amplification and single-cell screening and sequencing services to the scientific community in Sweden and beyond. Management

Stefan Bertilsson (platform director) Thijs Ettema (manager) Services

• Single-cell sorting in microwell plates using FACS-based approaches • Streamlined lysis and whole-genome amplification (WGA) of individual cells

• QPCR screening of amplified single cell genomes for marker genes (e.g. bacterial 16S rRNA, metabolic genes) • Advising in the design of single-cell experiments, whole-genome sequencing and genome assembly Equipment includes

• BD InFlux FACS • Apricot TPS-24 12-channel pipetting robot • Clean-room, PCR hoods and UV-based reagent purification equipment • Sealer, incubator and centrifuge for microwell plates • Leica DM-IRB inverted fluorescence microscope • Beckman Biomek NxP robotic handler (available soon)

Application examples

• Assessing the genomic content of a given environmental or medical sample at the individual cell level • Studying the phylogenetic distribution of target genes in a microbial population, such as antibiotic resistance genes • De novo identification of metabolic networks in microbial communities (‘Who is doing what?’) • Studying genomic variability within microbial populations

Contact

Stefan Bertilsson stebe@ebc.uu.se +46 18 471 2712 Thijs Ettema thijs.ettema@icm.uu.se +46 18 471 6129

Technology Platforms Emerging technology platforms

UCR-PEA/PLA Facility Mission

Services

Equipment includes

To offer services for high-throughput, high-specificity analyses of protein biomarker candidates in body fluids and other biological samples by integrating molecular tools such as proximity extension and proximity ligation technologies (PEA and PLA) with the internationally recognized and accredited laboratory platform at Uppsala Clinical Research Center (UCR).

• Multiplex and single-plex analyses of proteins using just 1-µl samples • Chips that include a panel of 92 proteins relevant to cancer, or 92 proteins/biomarkers in cardiovascular diseases • Detecting single proteins with extremely high sensitivity • Analyzing all types of body fluids, e.g. serum, plasma, cerebrospinal fluids and other biological materials such as cells and tissue lysates • Consultation in study design and statistical data analyses

• Real-time PCR instruments, automatic liquid dispenser, etc.

Management

Agneta Siegbahn (platform director) Masood Kamali-Moghaddam (manager)

Application examples

• Detecting and quantifying single proteins and panels of proteins • Quantitative analyses of the effect of drug candidates for protein expression

Contact

Agneta Siegbahn agneta.siegbahn@medsci.uu.se +46 18 611 42 51. Masood Kamali-Moghaddam masood.kamali@igp.uu.se +46-18-471 44 54

Technology Platforms Emerging technology platforms

Biomaterial Characterization – BioMat Facility Mission

To provide access to analytical techniques and scientific support to decode protein, cell and tissue response in relation to biomaterial properties. Biomaterials have wide-ranging applications in modern healthcare including diagnostics, medical devices, tissue regeneration tools, and advanced drug delivery systems. The BioMat facility aims to foster their use across the scientific community. Management

Jöns Hilborn (platform director) Marjam Ott (manager) Services

• Fee-based access to state-of-the-art instruments and scientific support for proteomics, bioengineering, stem cell research, biomechanics, and drug delivery applications Equipment includes

• Standard cell lab equipment • SEM/EDS - LEO 440, SEM/ EDS - Zeiss 1550, SEM/EDS -

Zeiss DSM 960A Scanning electron microscopes (SEM) • ESEM/e-beam lith - FEI XL30 environmental scanning electron microscope (ESEM) • TA Instruments TGA Q500 Thermogravimetric Analyzer (TGA) • TA Instruments DSC Q1000 Differential Scanning Calorimetry (DSC) • TA Instruments AR 2000 Rheometer • Jeol Eclipse + 400MHz Nuclear magnetic resonance (NMR) • Micromeretics, AccyPyc 1340 laboratory density meter (He pycnometry) • Malvern, Zetasizer Nano ZS particle size/zeta potential-meter (DLS) • Shimadzu, UV-1800, Shimadzu, UV-1650pc UV-VIS Spectrometers (UVVis) • Perkin Elmer LS 45 Luminescence Spectrometer (LS) • Perkin Elmer Spectrum One FTIR Fourier Transform Infrared Spectrometer (FTIR) • Nano Indenter CSM Instruments UNHT

• High-performance liquid chromatography (HPLC) Alliance HPLC 2695 Applications examples

Research fields that can benefit from the BioMat facility include: • Stem cell research in relation to the influence of the matrix • Disease-related research, e.g. inflammation, cancer, diabetes • Orthopedics and dentistry • Drug delivery and development of drug devices • Minimal invasive therapies • Cardiovascular research • Skin repair devices (artificial tissue) • Extra corporal blood treatment research

Contact

Marjam Ott marjam.ott@angstrom.uu.se +46-18-471 72 43