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Annual report 2012

Production SciLifeLab uppsala AdministrationGrAPhic deSiGn Matador kommunikationPhotoS 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

3scilifelab uppsala annual report 2012

SciLifeLab Uppsala

ManagementKerstin Lindblad-tohDirector, Chair, Program Board

Johan elfVice Director

Karin Forsberg nilssonVice Director

ulf LandegrenVice Chair, Program Board

Maria SörbySite Director

Program BoardKerstin 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 CouncilStellan 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 CoordinatorsAgneta Siegbahn, MedicineLars rönnblom, MedicineSiv Andersson, Biology

Contact information: Administrative staff at SciLifeLab UppsalaSite DirectorMaria Sö[email protected] Project Coordinator, education and outreachelina hjertströ[email protected] Communications OfficerSara engströ[email protected]

EconomistAnna [email protected]

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 Scientificcommunitybreedsinterdisciplinaryexploration

14 Education that enables the science of the future

16 Interaction increases collaboration

20 ScientificHighlights

42 ScientificResources

p.8

p.29

p.25

p.16


Rising to the challenges: SciLifeLab Uppsala 2012SciLifeLab 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 interdiscipli-

nary 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 showsthatourplatformsalreadydeliveronanationallevel.Weaimtofurtherincreasetheproportionofexternalprojects.

Furthermore,ourassociatedscientistspublishedalargenumberofpeer-reviewedscientificarticles,37ofwhichappearedinhigh-profilejournals.Youcanreadaboutsomeofthesediscoveriesinthisreport.Everyoneofthesearticlesdeservesmentioning;highlights include the use of genomic signatures to investigate human migration and new mechanisms for killing cancer cells.

Severalnewpilottechnicalplatformswereestablishedin2012;abiomaterialsplatform,aclinicalproteomicsplatform,andaplatformforhigh-throughput,single-cellanalysis.Asourrangeoffacilitiesisexpanding,bothestablishedandnovelplatforms often initiate joint technology development projects.

WeestablishnewconnectionsandcollaborationsasourscientificcommunityatSciLifeLabUppsalaisgrowing,andhavenowexceeded800researchers,includingassociatedmembersandtheirlabs.Lastyear,werecruitedoutstandingscientistsin several key areas, including disease genetics, host-parasite relations for microorganisms, single-cell genomics, bioinfor-matics, and RNA biology to further strengthen the research environment within SciLifeLab Uppsala.

Sharing our knowledge – for the benefit of many

Community-andcollaboration-buildingwashighonouragendafor2012,andwehaveundertakenanextensiverangeofactivities. 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 betweencommercialenterprisesandthescientificcommunity,whichhascontributedtothegrowingnumbersofcollabora-tions 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

6 scilifelab uppsala annual report 2012

System biologyBiological processes

Medical biologyTranslational medicine

Evolutionary biologyEnvironment

Energy

SciLifeLab combines advanced methods development and instrumentation with a broad knowledge base in technolo-gy-driven molecular bioscience and translational medicine. We enhance this competence by providing a computa-tionalinfrastructureforhypothesis-basedandexplorativeresearch in biology and medicine. We aim to be an interna-tionally leading research center, providing both bioscience technologyandexpertise.

The SciLifeLab Uppsala community brings together academic and professional staff scientists united in a com-mitment to developing new and transformative approaches to biomedical research. Our goal is to understand the fundamental basis of genome and cell biology within the broaderfieldoflifesciences,andtoadvancediagnosticsandtreatment of diseases with unmet needs.

SciLifeLab Uppsala

Organization of SciLifeLab Uppsala

SciLifeLab uppsala’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.

Genomics

Proteomics

Bioimaging

Data storage and bio

informatic support

Comparative genetics

Emerging platforms

Management and boards SciLife Innovation

Research programs Associated membersTechnology platforms


3%

34%

63%

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%

Research programs 34%the strategic recruitments during 2011 and 2012 of carefully selected junior research group leaders will contribute to high-profile interdisci-plinary research; they will be important drivers of the SciLifeLab community. With the imple-mentation 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.

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

Enabler for Life Sciences

evolutionary biology, environment, energy Medical biology, translational medicine System biology, Biological processes

evoLutionAry BioLoG

y – env

iron

Men

t – enerG

y

SySt

eM B

ioLo

Gy

– Bi

oLo

GicAL P

roceSSeS

MedicAL BioLoGy – trAnSLAtionAL Medicine


In its 2012 Research and Innovation Bill, the Swedish Gov-

ernment 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 ongoingefforts.Forinstance,althoughourscientificresources are available nationally, we needed to further developthemtomeettheextendedresponsibilityofbeingpartofanationwideinfrastructure.Oneexampleoftheextensiveeffortstosimplifyroutinesforaccessingourresources, especially in genomics, bioinformatics and data storage, is the new web portal shared by all genom-ics 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• Earlyandbroadexploitationofuniquetechnologies,

reagents and sample resources• Undertaking large-scale projects and generation of mo-

lecular 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 Sci LifeLab efforthaveintensifiedstrategicplanningtomeetthechallengeof creating a national infrastructure. One important actor playing a major part in these discussions is the National Ref-erence Committee of SciLifeLab, established in 2010. This committee includes representatives from the major universi-ties in Sweden, thus serving as a vital link to SciLifeLab for researchers from all over Sweden.

The pilot project with the working title SciLife Inno-vation, was initiated together with Uppsala University Innovation and aims to facilitate innovation partner-ships. Through this, we are building momentum towards enhanced industrial liaisons.

Building the SciLifeLab national infrastructure


The year 2012 was a particularly productive year for Sci-LifeLab Uppsala. Many important achievements, both for infrastructure and research, have been accomplished. The broadrangeofscientificresourcesavailable,allbasedonstate-of-the-art technologies, has proven attractive both on national and international levels. Moreover, the research performedatSciLifeLabreceivedexcellentratingsintheuniversities’externalresearchevaluations.Inaddition,arecord 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.Asaverificationofitshigh-leveltechnology,UppsalaGenome Center was also chosen as one of only two Euro-pean centers to gain early access to IonProton, a novel tech-nology allowing human genome sequencing for less than a thousand US dollars.

High-impact research

Research projects performed at SciLifeLab Uppsala resultedin126publicationsspecificallyaffiliatedwiththeSciLifeLabUppsalacommunity.However,theactualuseofourscientificresourceswasevengreater,resultingin 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 inhigh-profilejournalssuchasNature,ScienceandNatureGenetics.Wesummarizeaselectionofthesescientific

highlights starting on page 20. Furthermore, within the community,85PhDstudentswereawardedtheirDoctor’sdegree 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 sci-entificresourceswereledbyprincipalinvestigatorsfromuniversitiesotherthanUppsalaUniversity.Byextendingthe knowledge and competence of these resources and tech-nologies further, we aim to further increase the proportion ofexternalusers.

Wealsoaddedtoouralreadysizablescientificplatformsduring 2012. New pilot facilities include single-cell anal-ysis, biomaterial characterization and the introduction of PLA-technologyforproteinanalysesinaclinicalcontext.In 2012, SciLifeLab Uppsala also initiated an effort within drug discovery and development by supporting the previ-ously established Uppsala University Drug Optimization andPharmaceuticalProfilingPlatform.Wealsocontinuedtechnologydevelopmentcentraltoourexistingresources.During2012,theseeffortsresultedin26scientificpublica-tions describing new and improved methodologies.

Ourscientificresourcesaredescribedindetailbeginningon page 42.

Cutting-edge platforms deliver outstanding science

Selection of novel methods developed in 2012

• Methods for sample preparation from difficult sources

• unique methods for using biomaterials for gene therapy

• A canine exome capture array

• novel protocols for epigenetic genotyping

• 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

• e-infrastructure for life science

• new bioinformatics methods

Universities using our resources

uppsala university, royal institute of technology, Stockholm univer-

sity, Karolinska institutet, Swedish university of Agricultural Science,

umeå university, university of Gothenburg, Linköping university,

Örebro university, Lund university, Ludwig institute for cancer research

Hospitals/government agencies using our resources

Sahlgrenska Academy at the university of Gothenburg & the Queen Silvia

children’s hospital Gothenburg, Falu hospital, uppsala university hospital,

the Swedish national veterinary institute, Örebro county council, Foi

0

30

60

90

120

150

120

150

International media National media

62

143

0

30

60

90

120

150

120

150

8

2010 2011 2012

80

126

37high-profile

publicationas

26high-profile

publicationas

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

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.

Publications in general media referring to SciLifeLab uppsala.

294

529

242

699Emerging platforms: 48 projects

Bioimaging: 60 projects

Comparative genetics: 59 projects

Proteomics: 205 projects

Genomics: 327 projects

0

100

200

300

400

500

600

700

2010 2011 2012

Scientific publications

Projects performed at the technology platforms

General media 2012

UPPNEX projects 2012

242


The scientific community of SciLifeLab Uppsala continued

to grow during 2012, partly due to active recruiting, partly

also because of our growing reputation as an attractive

research environment. At the end of the year, we had more

than 160 research groups with more than 800 research-

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 inter-disciplinaryscientificcollaboration,activebothatnationaland international levels. Community activities are all designed to bring members together, strengthen interactions, andtolearnfromeachother’sexperiencehowtouseourscientificresourcesinnewandchallengingways.In2012,our activities focused on reaching new life science research groups within academia, industry, health and governmental agencies.OurSciLifeLabdaysandseminarseriesreflected

thisinitiative,targeting,forinstance,thefieldsofdrugdis-covery, biomaterials and technology development.

Recruiting gifted group leaders

SciLifeLab Uppsala has concluded the 2012 strategic recruitmentofthreecarefullyselectedresearchgroups;ErikIngelsson’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 andwillcontributetotheinterdisciplinaryprofileoftheSciLifeLab 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,wehaveemployedeightnewbioin-formaticians/computational biologists to meet current and future needs. These recruitments complement our specially designed courses to increase the bioinformatics competence of our users.

Scientific community empowers interdisciplinary exploration

A selection of our invited speakers on seminars and SciLifeLab days

Tarjei Mikkelsen, Broad Institute of MIT and HarvardFunctional genomics enabled by integrated DNA synthesis and sequencing

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

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

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

Xiao Yonghong, Zhejiang UniversityChanging policies to meet the challenge of antibiotic resist-ance in China

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


Per Ahlberg, Göran Akusjärvi, Marie

Allen, Kjell Alving, Göran Andersson, Jan

Andersson, Leif Andersson, Siv Andersson,

Per Andrén, Göran Annerén, Gunnar Antoni,

Per Artursson, Anders Backlund, Sandra

Baldauf, Lars Baltzer, Jonas Bergquist, Peter

Bergsten, rolf Bernander, Stefan Bertilsson,

Bryndis Birnir, Pernilla Bjerling, Marie-Louise

Bondeson, Mikael Brandström durling,

Jyoti chattopadhyaya, Lena claesson-

Welsh, erica comasco, niklas dahl, helena

danielson, Anna dimberg, christina dixelius,

Jan dumanski, Måns ehrenberg, Johan

elf, hans ellegren, Maija-Leena eloranta,

ulf emanuelson, håkan engqvist, Magnus

essand, henrik von euler, claes Fellström,

Lars Feuk, Karin Forsberg nilsson, Anthony

Forster, urban Friberg, Pär Gerwins,

valeria Giandomenico, Manfred Grabherr,

Mats Gustafsson, ulf Gyllensten, Anders

Götherström, håkan hall, Finn hallböök,

Margareta hammarlund-udenäs, Peter

hansell, My hedhammar, Åke hedhammar,

carl-henrik heldin, Paraskevi heldin, eva

hellmen, Mats hellström, Per hellström, Lars

hennig, Jöns hilborn, Andrea hinas, Patrice

humblot, Jens häggström, torleif härd, Jacob

höglund, Simone immler, Anders isaksson,

Mattias Jakobsson, christer Jansson, elena

Jazin, Per Jemth, Patric Jern, helena Jernberg

Wiklund, Staffan Johansson, Alwyn Jones,

Masood Kamali-Moghaddam, chandrasekhar

Kanduri, Anders Karlén, Manfred Kiliman,

Andreas Kindmark, Leif Kirsebom, Lena

Kjellén, Stefan Knight, Jan Komorowski, dirk-

Jan de Koning, Johan Kreuger, Klas Kullander,

olle Kämpe, ulf Landegren, Marene

Landström, Lars Lannfelt, dan Larhammar,

Mats Larhed, Lars Larsson, Martin Lascoux,

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

Lindblad-toh, Anna Lobell, Angelica Loskog,

Magnus Lundgren, Bengt Långström,

Aleksei Maklakov, cecile Martijn, Johan

Meijer, håkan Melhus, Karl Michaëlsson,

Aristidis Moustakas, Sherry Mowbray, Marika

nestor, Antti niemi, Fredrik nikolajeff, Mats

nilsson, Peter nygren, Luke odell, ernst

oliw, Anna-Karin olsson, ingela Parmryd,

ulf Pettersson, Fredrik Pontén, richard

rosenquist Brandell, Kristofer rubin, Lars

rönnblom, hans rönne, Anja Sandström,

Jens Schuster, Bo Segerman, Maria Selmer,

Agneta Siegbahn, tobias Sjöblom, tanja

Slotte, david van der Spoel, Maria Strömme,

inger Sundström Poromaa, richard Svanbäck,

catharina Svensson, Staffan Svärd, Ann-

christine Syvänen, ola Söderberg, Fredrik

Söderbom, Kenneth Söderhäll, Mattias

thelander, Birgitta tomkinson, hans törmä,

Lene uhrbom, Anders virtanen, claes

Wadelius, Mia Wadelius, Gerhart Wagner,

Lars Wallentin, Matthew Webster, nils Welsh,

Bengt Westermark, Gunnar Westin, Jochen

Wolf, carolina Wählby, Anki Wästljung,

helena Åkerud, Johan Åqvist, Fredrik Öberg,

Kjell Öberg

Associated members of SciLifeLab Uppsala at the end of 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.

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

Attendees at the bioinformatics course Computational Methods for Massively Parallel Sequencing

“excellent lectures describing current problems within bioinformatics”

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

“very good balance of lectures and practical examples”

“Advice on study design was invaluable”

“this was really what i needed to kick start”


SciLifeLab Uppsala conducted education at both undergrad-

uate and graduate levels during 2012. Researchers from the

SciLifeLab community together with scientific resource per-

sonnel 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.

Theeducationaleffortsalsorepresentsomethingnew;our courses now target researchers who have not previously been aware of or had access to the technologies we provide. Theycannowbenefitfromlearningwhatourscientificresources 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 bioin-formatics to meet the increasing demand for user sup-port. 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 occa-sions during 2012. These courses were very popular, and attractedatotalof80participantsfromalloverSweden.Upon request from Umeå University, we gave one of these courses in Umeå.

Other educational efforts during 2012 include:• Thethreeproteomicsplatforms(ProximityLigationAssays,TissueProfilingandMassSpectrometry)in SciLifeLab Uppsala together organized the PhD-level course Advanced Molecular Technology and Instrumentation for Proteome Analyses. The course was attended by participants from Uppsala University, the Swedish University of Agri-cultural Sciences and The Royal Institute of Technology.

• The Comparative Genetics platform organized the two-week 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.

Education that enables the science of the future

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.

Collaboration partners and groups taking advantage of

SciLifeLab services are found in many national and interna-

tional organizations within academia, research, industry

and society – including healthcare providers, schools

and policymakers.

During2012,anextensiverangeofactivitieshasbeen 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 rightpeoplemeettheycanreinforceexistingnetworksand 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 pro-viders and undertaking joint research projects, to repre-senting the life science region of Uppsala together rather than as separate organizations. An important initiative that shouldbementionedinthiscontext,isthecommitmentfrom Astra-Zeneca to support projects related to SciLifeLab, starting 2013.

Common entry to innovation partnerships

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.

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 Med-ical Products Agency and the municipal agency Världsklass Uppsala to promote the region.

Engaging schools

2012 also witnessed an increase in our efforts to engage schoolchildreninthemarvelsoflifescience.Forexample,we arranged research projects for high school students and organized open lectures and supplementary training of school teachers.

Interactions with industry and society add value


COMMERCIAL ENTERPRISESACADEMIA

HEALTH PROvIDERS

GOvERNMENT AND MUNICIPAL AGENCIES

SOCIETY AND SCHOOLS


Navet

during 2012, we started to build navet (the hub) – a specially-designed meet-ing 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.


Entering healthcare

UCR-PEA/PLA,ournovelscientificresource,isintegratedwith Uppsala Clinical Research Center at Uppsala Univer-sityHospital.Thisplatformoffershigh-throughputanalysisofproteinbiomarkercandidatesinbodyfluidsbasedonaunique, 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 importancetothem,andresearchersfromdifferentfieldsparticipateinworkshopstosharetheirexpertiseinthesequestions.Theseeventshaveprovenanexcellentmeansof bringing industry and academia together to formulate

andaddressproblemsidentifiedbyindustryandsoci-ety. 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 Econ-omist conference ‘Bridging the gap between science and healthcare’ with several SciLifeLab researchers partici-pating. 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.

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.

Scoring fluorescence distribution patterns with the Wormtoolbox. Fluorescence microscopy images show clec-60øGFP expression (green) in wild-type 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.

pmk-1

wt


scientific highlights

When biological pathways and diseases

cannot be reduced to purely biochem-

ical or cell-based assays, the free-liv-

ing nematode worm Caenorhabditis

elegans has proven an excellent model

organism for studying relevant bio-

logical processes. Despite its small size

and short generation time it has organ

systems similar to those of more com-

plex animals and shares many molecu-

lar and physiological homologies with

humans. A new image analysis toolbox

now improves the way we capture

quantitative information from individ-

ual 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 mostassays,forexample,thedensityof worms causes them to touch or cluster, which has prohibited accurate measurements of individuals thus limiting automated analyses to popu-lation averages.

In collaboration with researchers in Massachusetts, USA, we have devel-opedWormToolbox,atoolboxforauto-

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-through-put image-based assays of C. elegans, WormToolboxwillunderpinthestudyof biological pathways relevant to human disease. Initial testing and com-parisonsarepromising.Forexample,compared with visual viability scoring of random samples and hits from a high-throughput viability assay, 97% accuracy was achieved in a few min-utes, compared with 20 hours for visual scoring.Thetoolboxwasalsoevalu-atedforitsabilitytoscorefluorescencedistribution patterns within worms. Variations in signaling pattern could not be scored using simple approaches suchastotalsignalperworm.How-ever, digital worm straightening and atlasmappingfromtheWormToolboxquantitatively detected elevated signal in the anterior intestine.

WormToolboxisbelievedtobethefirstsystemtoautomatically,quanti-tatively and objectively score a variety

of phenotypes in individual C. elegans in static, high-throughput images. Furthermore,thetoolboxhasbeenimplemented as modules in the free andopen-sourceCellProfilersoftware.CellProfileremphasizesease-of-use,itis compatible with cluster computing, andisflexibleenoughtoaccommo-date new assays being developed by thescientificcommunity.

FutureworkislikelytoextendWormToolboxbyaddingmoreworm-specificmeasurementsbasedontheir unique anatomy, and incorpo-ratingbettermethodsformixeswithworms in various stages of development. TheWormToolboxisamethodthatfur-ther 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. ele-gans assays. Nature Methods, Vol. 9 No. 7, 714-716.

Quantitative information captured from individual C. elegans worms in high-throughput assays

Contact

Carolina Wählby [email protected]



Genetic mutations that increase the

availability to the brain of two essen-

tial long-chain polyunsaturated fatty

acids were likely to be favored when

dietary access to the required pre-

cursors was limited. However, in the

modern Western world, this phenom-

enon 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 doco-sahexaenoicacid(DHA)andomega-6arachidonic acid (AA). As neither can be synthesized de novo, both need to be supplied via dietary intake. Two key enzymes involved in the conversion of18-carbonprecursorstoDHAandAA 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 remedythisdeficiency.

Genome-wide genotyping of theFADSregioninfiveEuropean

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 posi-tive selection.

The age of the diversity seen in hap-lotype D and its present geographic distribution indicate that both haplo-type A and D appeared after the split from Neanderthals (around 500,000 years ago) but prior to the time of the exodusofmodernhumansfromAfrica50,000 –100,000 years ago.

Both haplotypes are thus present in European, Asian and Oceanian popu-lations. In Africa, haplotype D appears to have continued to increase in fre-quencyaftertheexodusuntilitreachedits 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 witharelaxationoftheselectivepressure due to a diet with higher levelsofessentialLC-PUFAs.How-ever, a low frequency of haplotype D may augment the synthesis of arachi-donic-acid-derivedproinflammatoryeicosanoids, which are associated with increased risk of atherosclerotic vascular damage.

It thus seems that while FAD haplo-typeDhasbeenbeneficialwhenfoodsources rich in essential LC-PUFAs were limited, it now represents a risk factor for Western lifestyle-related dis-eases, such as coronary artery disease.

Reference

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

FAD-diets – how evolution may be turning the tables on us

Contact

Ulf Gyllensten [email protected]



The 2011 European outbreak of

bloody diarrhea with high rates of

severe complications caused much

public concern and attracted the inter-

est of researchers keen to investigate

a rare and poorly-understood tox-

in-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 causedbyShigatoxin-producingE. coli O104:H4duringthesummerof2011highlighted the potential of this rare E. 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 withspecialfocusontheShigatoxin.

Prior to the outbreak, which was largely concentrated to Germany (3,816cases),littlewasknownofthis

rarely-reporteddisease;itsdiversityandevolutionwerepoorlyexplored.Muchattention was thus given to analyzing the genomic diversity of E. coliO104:H4and one group of scientists soon pre-sentedfindingssuggestingthatinde-pendent isolates from later outbreaks, e.g. in France, were not derived from theGermanoutbreakstrain;thediver-sity in the small French outbreak was much larger than in the German out-break. Together with colleagues from other parts of Sweden, we have argued thatthisconclusionisnotjustified.

Ourre-identificationofsinglenucleotide 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 substitu-tions accounted for 31.2% of SNPs in coding regions and another 11.1% at intergenic sites in the German outbreakstrains,figuresthatareverysimilar to 36% and 14.3%, respec-tively, for the French strains.

Ourfindingsthattheaveragenumber 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 pop-ulation 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 escheri-chia coli o104:h4. Letter. PNAS Vol. 109, No. 52.

New insights into outbreak of illness caused by Shiga toxin-producing E. coli strains

Contact

Siv Andersson [email protected]



Studies that genotype millions of SNPs

are now providing remarkable data that

improve our understanding of human

evolutionary history and the emer-

gence of modern-day civilizations. Two

recent investigations provide fascinat-

ing insights into the complex history of

adaptation in Africa and the arrival of

the farming culture in northern Europe.

Genetic, anthropological and archae-ological 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 extanthumanpopulations.Thestudygenotypedapproximately2.3millionsingle-nucleotide polymorphisms (SNPs) in 220 individuals representing eleven key populations from southern Africa (1). Analyses included reconstructing the demographic history of sub-Sa-haran populations using a powerful genealogical concordance approach.

It was found that the Khoe-San diverged from other populations ≥100,000yearsago,andthatthepopulation structure within the Khoe-San dated back to about 35,000 years. Genetic variation in the vari-ous sub-Saharan populations did not

localize the origin of modern humans to a single geographic region within Africa, but instead indicated a history ofadmixtureandstratification.Strongevidence of recent and ancient adapta-tion targeting muscle and skeletal (i.e. bone and cartilage) development was noted.Thisfinding,combinedwiththefact that no currently studied popula-tion diverged from the ancestral human population before the ancestors of the Khoe-San, suggests that anatomical modernityappearedpriortothefirstmodernhumandiversificationevent.

The origins and genetic legacy of human populations has also been investigated in a study of the transition from the hunter-gath-erer 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 directgenomicevidenceofstratifica-tion between the two Neolithic cultural groups. The farmer is genetically most similartoextantsouthernEuropeans,while the hunter-gatherers had a distinct genetic signature that is most similar tothatofextantnorthernEuropeans.

These results suggest that migration from southern Europe catalyzed the

spread of agriculture, and that barriers togeneflowbetweenresidenthunt-er-gatherers and colonizing farming groups persisted during the initial stages ofexpansionandsettlement.Thiscon-trasts strongly with earlier models that proposedanexpansionoffarmingwith-out substantial replacement of resident hunter-gatherer populations.

The observation that most Euro-pean populations appear genetically intermediate to the two Neolithic groups also suggests that the barriers perhaps became more permeable overtimeandthatgeneflowbetweenfarmer and hunter-gatherer popu-lations, possibly over a long period, eventually gave rise to the present pattern of genetic variation in Europe.

References

1. Schlebusch et al (2012) genomic varia-tion 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.

Pivotal studies of genomic diversity chart human evolution and development

Contact

Mattias Jakobsson [email protected]

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.



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 mito-

genic signaling.

The four members of the epidermal growth factor receptor family of type-1 tyrosine kinases (EGFR and ErbB2toErbB4)arewidelyexpressedin normal skin epithelial cells. Sign-aling 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,forexam-ple, disrupts normal tissue homeosta-sis and contributes to the formation of many epithelial cancers.

Mig6, a negative feedback regu-lator 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 sup-pressor since knockout mice are highly susceptible to cancer formation, while Mig6expressionisfrequentlylostinvarious human cancers. Interfering withitsfunction,forexample,leadstodisrupted mammary morphogenesis characterizedbyductalluminalfillingdue 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(encodingMig6)andinhibit-ing RNAi silencing of c-Abl causes impairedapoptosisandluminalfillingof 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 phosphorylationonc-Abl-Tyr488.Theseresultsrevealareceptor-proxi-mal switch mechanism by which Mig6 actively senses EGF deprivation and directly activates proapoptotic c-Abl.

This double-edged tumor suppres-sor role of Mig6 challenges today’s ideas about how growth factor dep-rivation might induce apoptosis via passivemechanisms.Thefindingisof particular interest considering that acquisition of growth factor-independ-ent 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.

The double-edged tumor suppressor Mig6 links ErbB receptor inactivation to apoptosis

Contact

Ingvar Ferby [email protected]



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 illus-

trates 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 onacomplexcoordinationofmusclecontractions 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/gallop-ing. Some horses, e.g. Icelandic breeds, can use alternate gaits, typically at intermediate speed. In an attempt to explainwhysomeIcelandichorsescanpace but others cannot, a genome-wide association analysis using 30 Icelandic horses was performed. This revealed that a single gene, DMRT3, largely explainsthegeneticdifferencebetweenpacers and non-pacers.

Independently, other SciLifeLab researchers discovered that the same geneisexpressedinapreviouslyunknown 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 biologicalfindingwasimminent.Notonlydidthediscoveryextendour understanding of spinal neu-ronal 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 pro-tein, and that this mutation shows a strong positive association with perfor-mance 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 dis-qualificationinraces.Themutationthus 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 connec-tion with motor neurons that control flexorandextensormuscles.Inter-estingly, 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 cen-tral 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.

Breakthrough study shows single gene has a major impact on gait in horses and mice

Contact

Leif Andersson [email protected]

Klas Kullander [email protected]



Although we know that the hippocam-

pus region of the brain is involved in

spatial navigation and memory, the

mechanisms underlying these functions

are not well understood. A newly-

discovered 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.

Humansthink,learnandmemorizewith 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.

Butexactlyhowtheseprocessesfunction is poorly understood and the lackofcell-specifictoolshasham-pered detailed investigation. Never-theless, recent evidence has suggested that receptors containing the nicotinic acetylcholine receptor α2 subunit (Chrna2)arespecificallyexpressedinoriens lacunosum-moleculare (OLM) cells and that direct cholinergic excitationofOLMcellsmightbeinvolvedinswitchinginformationflow

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, SciLife-Lab researchers at Uppsala Univer-sity, together with Brazilian collabo-rators, were able to discover that light activation of the OLM-α2 gatekeeper cellsalterstheflowofinformationinthe hippocampus in the same way as nicotine does.

Via research on a transgenic mouselineexpressingCrerecombi-nase under the control of the Chrna2 promoter (Chrna2isthemostspecificmarker of a morphologically well-de-finedhippocampalinterneuronpopulation 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 tar-gets. Nicotine activates the gatekeeper cell, thereby prioritizing the formation of memories via local inputs.

Althoughthebeneficialeffectsofnicotine on cognitive processes such

as learning and memory are recog-nized,thiswasthefirsttimethatanidentifiednervecellpopulationcould be linked to the phenomenon. The new study literally ‘sheds light’ onthisintriguingmechanism;thenewly discovered gatekeeper nerve cellsofferanexplanationtohowtheflowofinformationiscontrolledinthe hippocampus. Thanks to this new knowledge, it may be possible to stimulatethesenervecellsbyartificialmeans,forexamplebyselectivenic-otine-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.

Study ‘sheds new light’ on the brain’s learning and memory mechanisms

Contact

Klas Kullander [email protected]

Richardson Leão [email protected] [email protected]



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 genome-

wide study, it is now also a model

organism for population genetic stud-

ies of adaptation and natural selection.

The Atlantic herring (Clupea haren-gus) 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 regionhasbeenclassifiedasasub-species, Clupea harengus membras, of the herring found in North Atlantic waters. Previous studies based on few genetic markers have revealed a con-spicuous lack of genetic differentiation between these two geographic regions, a result that is considered to be con-sistent with huge population sizes and minute genetic drift.

In collaboration with other Swed-ish researchers we have employed a cost-effective, genome-wide sequenc-ing strategy that overcomes the otherwise challenging requirement for a high-quality draft genome. By com-bining a transcriptome assembly with whole-genome shotgun sequencing, weconstructedan‘exomeassembly’that permitted genome-wide screening for genetic polymorphisms.

Thisapproachidentified440,817SNPs, the great majority of which showed no appreciable differences in allele frequency among the pop-ulations.However,3,847SNPsdiddisplay striking differences, some even approachingfixationfordifferentalleles.AsimulationstudyconfirmedthatthedistributionofthefixationindexFSTdeviatedsignificantlyfromexpectationforselectivelyneutralloci.

Thesefindingsprovidecompellingevidencefortheexistenceofanumberof genetically differentiated popula-tions of Atlantic herring and support theclassificationoftheBalticherring

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 geneflowbetweensub-populationscontributes to the lack of genetic dif-ferentiation at selectively neutral loci, while natural selection is the dominat-ing force that determines the frequency of non-neutral alleles. The results also establish the herring as a model organ-ism for evolutionary genetics.

Reference

Lamichhaney (2012) population-scale sequencing reveals genetic differ-entiation due to local adaptation in atlantic herring. PNAS Vol. 109 No. 47 19345–19350.

Distinguishing genetic drift from selection: the Atlantic herring enters the debate

Contact

Leif Andersson [email protected]

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.

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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 recep-

tor that can specifically kill appropri-

ate prostate and breast cancer cells

suggest that there are good grounds

for optimism regarding future thera-

peutic developments.

Recent clinical trials for cancer have demonstrated that immunotherapy can lead to improvements in overall survival. Genetically-engineered T-cellshave,forexample,inducedcomplete remission in patients with otherwise treatment refractory B-cell leukemia.However,thepromiseofT-cell-based immunotherapy has beenlimitedbydifficultiesinisolatingandexpandingT-cellsspecificfortumor-associated antigens.

To produce genetically engineered T-cells directed against prostate and breast cancer cells, a T-cell receptor (TCR)withspecificityforaprostatedifferentiation antigen was cloned.

The targeted antigen, TCRγ chain alternate reading-frame protein (TARP),isexclusivelyexpressedinnormal prostate epithelium, as well as in prostate and breast cancer cells. TARP may be a particularly relevant immunological target for T-cell ther-apy 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 circulat-ing T-cells against both TARP4–13 and TARP27–35 epitopes.

TCR-engineered T-cells, which recognizetheHLA-A2–restrictedTARP4–13 epitope (FPPSPLFFFL), proliferatedwellwhenexposedtopeptidespecificstimuli,andexertedpeptide-specificIFN-©productionandcytotoxicactivity.Significantly,theywerebothspecificandefficientinkillingTARP-expressingHLA-A2+ 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 aphysiologicallyrelevantHLA-A2epitopeofahighlyandspecificallyexpressedantigencaneffectivelykillprostate and breast cancer cells. This report, which to the best of our knowl-edge is unique, suggests that T-cell-based immunotherapy may have an important future role in combating both cancer forms.

Reference

Hillerdal et al., (2012) t cells engi-neered 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.

Unique report: T cells with cloned T-cell receptor specifically kill prostate and breast cancer cells

Contact

Magnus Essand [email protected]



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 combina-

tion 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 theexpressionofgenesbybindingtosequence-specificsitesonthechromo-some. This process, which is both fast andaccurate,hasbeenexplainedbyafacilitated diffusion mechanism com-bining 3D cytoplasmic diffusion and 1D sliding along the DNA. This sliding wouldeffectivelyextendthetargetregion to the sliding distance and facili-tate the search for the binding site.

Facilitated diffusion has been demonstrated in vitro, but the physi-ological 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 investi-gate the sliding process in living bacte-ria, and that should also show just how far a transcription factor slides on chromosomal DNA.

Usingayellowfluorescentprotein- labeled lac repressor (LacI) in E. coli cells, we developed an assay for measur-ing search time based on the distinction betweenlocalizedanddiffusefluores-cence signals. We determined that the time required for a single repressor molecule to bind a single chromosomal operator (lacOsym)areinexcellentagreement with recent theoretical bind-ing-time predictions (3.5 min) based on facilitated diffusion by sliding.

To directly evaluate whether the lac repressorslidesonnon-specificDNAsequences in vivo – and if so, how far – bacterial strains with two identi-cal 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

astwoindependenttargets.Howfastthe lacrepressorfindsanyoneofthesesites 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 theoret-ical 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-specificsequencesandfastbind-ingatthespecificsite.

Reference

Hammar et al (2013) the lac repressor displays facilitated diffusion in living cells. Science Vol. 336 1595-1598.

Sliding rules: 45 base pairs on chromosomal DNA for the lac repressor

Contact

Johan Elf [email protected]



Opinion is divided regarding the

genetic and molecular basis of adap-

tive evolution. Do regulatory changes

or protein-coding changes predomi-

nate? A detailed investigation using a

high-quality reference genome assem-

bly for three-spine sticklebacks now

helps resolve this dilemma.

Accumulatingsufficientexamplesin any particular study group has remained a barrier to gaining an overall picture of the molecular mechanisms underlying evolutionary change, particularly for clearly adap-tive phenotypes in wild organisms.

Three-spine sticklebacks, however, provide a powerful system for studying the molecular basis of adaptive evolu-tion in vertebrates. After the retreat of Pleistocene glaciers, marine stickle-backs colonized and adapted to many newly-formed freshwater habitats, evolving repeated changes in body shape, skeletal armour, trophic special-izations, pigmentation, salt handling, life history and mating preferences, all traits that are likely to evolve by natural selection. In addition, distinc-tive 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 marine–fresh-water adaptation.

Forexample,thesignalresolu-tion of repeatedly used adaptive loci approaches 5 kb, which will often identify single genes or intergenic regions.Thisoffersasignificantadvantage over the several hundred kilobase candidate intervals typically identifiedingeneticmappingcrosses,or the megabase or larger regions identifiedinearlierselectionscansofthe 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.Analyzingthepatternsofgenetic variation indicates that parallel evolution of marine and freshwater sticklebacks occurs by dynamic reas-sembly of many ‘islands’ of divergence distributed across many chromosomes.

Reassembly by linkage is probably strengthened by inversions that distin-guish marine and freshwater ecotypes

Comparative data suggest that both regulatory and protein-coding differences contribute to parallel sticklebackevolution.However,regu-latory 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-fresh-water divergent loci, the substantial fraction of loci mapping entirely to non-coding regions, as well as thesignificantenrichmentofgeneswithexpressiondifferencesnearkeyregions used for parallel evolution.

Reference

Jones et al (2012) the genomic basis of adaptive evolution in threespine stickle-backs Nature Vol. 484 55-61.

Regulatory changes or protein-coding changes: which dominate adaptive evolution?

Contact

Kerstin Lindblad-Toh [email protected]



The absence of non-invasive biomark-

ers for this debilitating infant disor-

der 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, cerebel-lum and retina in infancy is part of the clinical spectrum of lysosomal storage disorders, mitochondrial respiratory chain defects, carbohydrate glycosyla-tiondefects,andinfantileneuroaxonaldystrophy. The typical disease course is characterized by failure to acquire developmental milestones and culmi-nates in profound psychomotor retar-dation 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.

Extensivelaboratoryinvestigations,including complete blood count, routine serum chemistry, glucose, lactate, ammonia, thyroid functions, and cre-atine kinase were all normal, as was the urinaryorganicacidprofile.Cerebro-spinalfluidanalysesforcells,glucose,protein, lactate, amino acids, and neurotransmitters also revealed normal

findings.Musclebiopsiesofthreeindi-viduals disclosed normal histology.

Eventheactivitiesofthefiveenzy-maticcomplexesofthemitochondrialrespiratory chain and the pyruvate dehydrogenasecomplexwerenormalin mitochondria isolated from muscle. However,theoxidationofglutamatewas slightly reduced (to 62.7%) of the controlmean,whiletheoxidationsofrelated mitochondrial substrates were 88.3%,86.7%and90.3%.

To localize the mutated gene, we searched for homozygous regions com-mon 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, exomesequencingwasalsoemployed.

Weidentified112homozygoussingle-nucleotide variants in the region, and 42 variants were located in coding exonsandflankingintronicsequencing(512nt).Variantswerefiltereduntilonlya 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 ‘proba-bly 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.Noneofthe128anony-mous individuals of the same ethnic origincarriedit.Specificaconitaseactivitywasshowntobesignificantlyreducedinpatients’fibroblasts.Wealsoshowed that the human mutated ACO2 failed to rescue a yeast ACO1 deletion mutant, providing further functional supportforthegeneticfinding.

ACO2consistsof18exonsthatencode mitochondrial aconitate hydratase,an805-aminoacidTCA-cycle protein. We recom-mend 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 cerebel-lar-retinal degeneration associated with a mutation in mitochondrial aco-nitase, aco2. American Journal of Human Genetics 90, 518–523.

Pathogenic mutation identified in Infantile Cerebellar-Retinal Degeneration

Contact

Lars Feuk [email protected]


Technology PlaTforms

Mission

To offer SNP genotyping and sec-ond-generation sequencing as a service to researchers in Sweden and abroad. The unit’s genotyping and sequencing procedures are accredited by SWE-DAC,andthefacilityisCsPro-certifiedas a service provider using Illumina genotyping and sequencing technology.

Management

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

Services

SNP genotyping:• SNP genotyping for projects ranging

in size from 1- >5,000,000 SNPs per sample in hundreds or thousands of samples

• SNPidentificationfromdatabasesand bioinformatics-assisted primer and assay design

• Analyzing genotype, copy number and methylation data using the analy-sis software of each genotyping system

• Delivering quality-assessed geno-typingresultsintextfileformat

• 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 sequenc-ing 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 includ-ingdatafiltering,sequencealignments, coverage statistics, SNV-calling,andexpression levels/RNA counts

• Compiling materials and methods for publications

Equipment includes

• iScan system (Illumina)• BeadExpress(Illumina)• GenomeLab SNPstream

(Beckman Coulter)• GeniosPro (Tecan)• HiSeq2000sequencers(Illumina)• MiSeq sequencer (Illumina)

(available Q2 2012)• Genome Sequencer FLX+

(Roche/454

SNP&SEQ technologies

Contact

TomasAxelsson +46-18-6112644,070-1679458 [email protected]

www.genotyping.se

Ulrika Liljedahl +46-18-6114934,070-1679459 [email protected]

www.sequencing.se

GENOMICS

scilifelab uppsala annual report 2012


Mission

ToprovideNextGenerationSequenc-ingserviceswithSOLiD5500xl/SOLiD5500xl-W,IonTorrentinstru-ments, including Ion Proton, as well as Sanger sequencing and genotyping. Tailor-made,cost-effectiveandexpe-dient solutions for all types of genetic/genomic projects are also key parts of the offering.

Management

Ulf Gyllensten (platform director)Inger Jonasson (manager)

Services

• Capillary electrophoresis on frag-ment analysis or Sanger sequencing samples

• Sanger sequencing service• Next-generationsequencingon

SOLiD5500 and Ion Torrent systems

Equipment includes

• SOLiD5500XL instruments• Ion Torrent PGM instruments• ABI3730XL DNA Analyzers• ABI7900HT

Application examples

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

sequencing

Uppsala Genome Center

Contact

Inger Jonasson +46-70-1679082 [email protected] [email protected]

GENOMICS

TECHNOLOGY PLATFORMS

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 analyz-ing clinical samples in conjunction with the rest of the clinical ’omics plat-form. Our bioinformatics competence will continue to support the develop-ment and introduction of both array-based and sequencing-based clinical analyses throughout Sweden.

Management

Anders Isaksson (platform director and manager)

Services

Wet lab service:• mRNAquantification• SNP genotyping• Copy number analysis of genomic

DNA

• Loss-of-heterozygosity• Alternative splicing• miRNAquantification• Mapping protein-genomic DNA

interactions

Bioinformatics service:

• Experimentaldesign• 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 identi-fying/annotating non-coding RNAs, etc. Practical courses on data analysis, demonstrations and other types of support are also available.

Equipment includes

• AffymetrixGeneChipSystem30007G

• Fluidic stations FS 450• Hybridizationovens640/645• Agilent 2100 Bioanalyzer• ABI 9700 Thermocycler


• Genomic analysis of 400 samples from patients with chronic lympho-cytic leukemia

• Developing bioinformatic tools for allele-specificcopynumberanalysisin tumor samples

• Identifying non-coding RNA bind-ing to chromatin

Array and Bioinformatics

Contact

Anders Isaksson +46-18-6119782 [email protected] [email protected]

GENOMICS




Mission

Toutilizethefacility’sexpertiseinsam-pling, sample preparation (e.g. selective extraction,affinitypurification,deple-tion of abundant proteins), separation (e.g. 1-D and 2-D gel analysis, capillary electrophoresis, gas and liquid chro-matography), mass spectrometry and general protein and peptide chemistry. The unit’s instruments provide high res-olution and accurate mass determina-tionsforconfidentstructuralelucidationand quantitative analysis.

Management

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

Services

• Analyzing and comparing pro-teomes using selected sample prepa-ration technologies

• Quantitative proteome analysis using label-free as well as stable isotope label technologies

• Identifying proteins in protein spots/bands by mass spectrometry

• Analyzingexpressedproteinsforquality control

• Analyzing proteins for post-transla-tionalmodification

• 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 (UltraflexIIBruker)

• ESI-TOF (Agilent)

• Q-STAR XL and Q-TRAP 3200 (Sciex)


• Distinctcerebrospinalfluidpro-teomes that differentiate post-treat-ment Lyme disease from Chronic Fatigue Syndrome

• Fish peptidome patterns that can distinguishfromexposuretoantro-pogenic pollution

• Analyzing membrane and hy-drophilic proteins simultaneously derived from the mouse brain using cloud-pointextraction

• Moving toward a comprehensive characterization of the phosphoty-rosine proteome

• Exploringliquidchromatogra-phy-massspectrometryfingerprintsof urine samples from patients with prostate or urinary bladder cancer

MS Proteomic Resource Center

Contact

Jonas Bergquist +46-18-4713675

[email protected]

Margareta Ramström +46-18-4713678

[email protected]

Åke Engström +46-18-4714206

[email protected] e-mail: [email protected]

PROTEOMICS



Mission

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

Management

Fredrik Pontén (platform director)Caroline Kampf (manager)

Services

• ProducingTMAs(paraffinblockscontaining cores of selected tissue or cell preparations assembled together toallowmultiplexhistologicalanal-ysis in a high-throughput setting)

• OfferingIHCtovisualizeantigensusingantibodiesorotheraffinityreagents

• 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

• Tissuemicroarrayers;oneautomat-ed system (Beecher ATA-27), one manual system (Beecher MTA-1) and one semi-automated system (Pathology Devices)

• Waterfall microtomes (MicromHM355S)

• Automated image scanners (Aperio Scanscope XT)

• Automated liquid handler (Gilson Quad-Z 215)

• Automated slide-staining system for deparafinizationanddehydration(Leica Autostainer XL)

• Automated glass coverslipper system (Leica CV 5030)

• Automated slide-staining systems forIHCstaining (LabVisionAutostainer480)

• Brightfieldmicroscopes


• Construction of 1200 TMAs con-tainingover86,400tissuecores,180CMAscontainingover23,800cell cores, staining over 190,000 slidesforIHCandscanningover70,000 slides

• Diagnostic pathology to determine the origin of poorly differentiated tumors and to stratify tumors for optimized treatment regimes

• IHCwidelyusedtostudycellularprocesses or localization

• 500 to 600 new antibodies tested everymonthaspartoftheHumanProtein Atlas project

Tissue-profiling Center

Contact

Caroline Kampf +46-18-4714879

[email protected]

PROTEOMICS


Mission

TousetheinsituProximityLigationAssay (in situ PLA) to visualize and quantify proteins, post-translational modificationsandproteininteractionswithgreatsensitivityandspecificityincellsandtissues.Specificitycanbe increased compared to standard immunoassays(e.g.IHC)sincetwo,three or more antibodies are required for recognition. The facility combines insituPLAwithDNAamplificationto generate the detection signal, which ensures highly sensitive detection.

Management

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

Services

• in situ PLA for detecting proteins and their interactions using either client-selected antibodies or previ-ously validated antibodies from a constantly updated list

• Validation, optimization and assay development for client-selected antibodies

Equipment includes

• Epi-fluorescencemicroscopes• Confocal microscope • Fluorescence scanner


• Visualizationandquantificationof proteins, their interactions and

post-translationalmodificationsincells and tissues

• Analyses of biological pathways and cell signaling

• Quantitative analyses of the effect of drugcandidatesonproteinexpres-sion,interactionsandmodifications

in situ PLA Facility

Contact

Masood Kamali-Moghaddam +46-18-4714454

[email protected]

PROTEOMICS


Mission

To provide an infrastructure and indi-vidually-tailored support for projects utilizing this popular model system for vertebrate development and disease. Zebrafishembryosaretransparentand 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 zebrafishmodelsystem,andprovidesinitialadviceonfeasibilityandexper-imental design as well as running support over the course of the project.

Management

Per Ahlberg (platform director)Johan Ledin (manager)

Services

• Facility services• Consultancy• Access to the facility• Techniques for reverse and for-wardgeneticexperiments,aswellas methods to visualize biological processesforextendedperiodsinintact embryos

Equipment includes

• Fish facility, including tank systems, fishlines,workstations,incubatorsand injectors

• Light microscopy, including confo-cal microscopy

• Electron microscopy


• Gain-andlossoffunctionexperi-ments

• Expressionanalysis• Generation- and analysis of trans-

genic lines

Zebrafish Facility

Contact

Johan Ledin [email protected]

+46-70-447 39 94

KatarinaHolmborn-Garpenstrand katarina.garpenstrand@

scilifelab.uu.se +46-18-4712684

COMPARATIVE GENETICS




Mission

To offer a unique possibility to utilize the disease mechanisms of domestic animals to identify genetic risk factors, exploregenotype-phenotyperelation-ships, and identify candidate genes that can be of relevance for human diseases. The domestic animal facility offersalreadydefineddiseasemodelsfor a large number of diseases as well asexpertiseforevaluatingnewmodelsfor the disease of interest.

Management

Leif Andersson (platform director)Cecilia Johansson (manager)

Services

• Assistance with evaluating the availability and validity of domestic animalmodelsforspecificdiseases

• Assistance with planning, organiz-ing and interpreting whole genome wide association analysis to identify disease loci in the animal model

• DNA preparation and storage of sam-ples in the SLU SciLifeLab Biobank

Equipment includes

• QIAsymphony instrument for DNA and RNA preparation

• LIMS system for registering bio-bank samples (at the SLU SciLife-Lab Biobank)


• Identifying genetic risk factors in domestic animals

• Comparative studies in human counterparts (can be applied to ho-mologous diseases between domesti-cated animals and humans)

• Mapped traits in the dogs:• HAS2forperiodicfeverinthe

Sharpei breed• Genes involved in T-cell activation

in an SLE-like disease in Nova Sco-tia Duck Tolling Retriever.

• SOD 1 for ALS in Pembroke Welsh Corgi

• CDH2forOCDinDobermanPinscher

Domestic Animals

Contact

Cecilia M Johansson [email protected]

+46-18-4714525

COMPARATIVE GENETICS



Mission

Toprovidetechnologyandexpertisefor high-resolution biological imaging and visualization at tissue, cell and sub-cellular levels, including sup-porting 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 includefluorescence,confocalandmultiphoton microscopy plus elec-tronmicroscopyandflowcytometry

• Flow sorting and microdissection microscopy for upstream sample purification

• Ultrastructural studies

Equipment includes

• Zeiss 710 multiphoton and Confocal microscope

• Zeiss 510 confocal microscope• ZeissAxioObservermicroscope

with ApoTome• Arcturus microdissection micro-

scope• BDLSRIISORPanalyticalflow

cytometer• BDFACSAriaflowsorter• FEI Tecnai BioTwin transmission

electron microscope• Workstations for analysis of imagingandflowdata,includ-ing Imaris 3D image analysis software.


• Co-localization studies on both cell- and tissue levels with several simultaneous markers

• Ultrastructural morphology and IHCstudies

• Analysis of the 3D-distribution of markers of interest in the cell or cell environs

• Quantitative analysis of cell popula-tionsandmarkerexpression

• Preparativeexperimentstoisolatecells or tissue sections of interest for downstream processing

BioVis Facility

Contact

[email protected]

BIOLOGICAL VISUALISATION


Mission

To provide high-performance comput-ing 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.

Management

Ola Spjuth (manager)

Services

• High-performancecomputingandlarge-scale storage for bioinformatics

• Computing and storage resources, primarilyfortheNextGenerationSequencing (NGS) community in Sweden, and SciLifeLab in particular

• Expertmanagementofcomputa-tional hardware and system admin-istration

• 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 edu-cation at SciLifeLab and Uppsala University

• Participates in the national bio-informatics support forum www.biosupport.se

Hardware includes

• Computer cluster with 1 M comput-ing 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 Univer-

sity Network (SUNET) backbone

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:

• Primaryfocusonnext-generationsequencing

• Large-scale storage and archiving of image data.

UPPNEX – UPPmax NExt generation sequencing Cluster & Storage

Contact

Ola Spjuth, Coordinator UPPNEX [email protected]

+46-18-4714281www.uppmax.uu.se/uppnex

BIOINFORMATICS




Mission

Toexploittheimmensepotentialofsingle-cell genomics, which allows explorationofthegenomecontentof individual cells without the need for laboratory cultivation, by becom-ing a leading single-cell genomics center in Europe. The center will offer single-cell sorting, whole-genome amplificationandsingle-cellscreen-ing and sequencing services to the scientificcommunityinSwedenand beyond.

Management

Stefan Bertilsson (platform director)Thijs Ettema (manager)

Services

• Single-cell sorting in microwell plates using FACS-based approaches

• Streamlined lysis and whole-ge-nomeamplification(WGA)ofindividual cells

• QPCRscreeningofamplifiedsinglecell 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

• BDInFluxFACS• Apricot TPS-24 12-channel pipet-

ting robot• Clean-room, PCR hoods and UV-basedreagentpurificationequipment

• Sealer, incubator and centrifuge for microwell plates

• LeicaDM-IRBinvertedfluores-cence microscope

• BeckmanBiomekNxP robotic handler (available soon)


• Assessing the genomic content of a given environmental or medical sample at the individual cell level

• Studying the phylogenetic distribu-tion of target genes in a microbial population, such as antibiotic resist-ance genes

• Denovoidentificationofmetabolicnetworks in microbial communities (‘Who is doing what?’)

• Studying genomic variability within microbial populations

SiCell single-cell genomics

Contact

Stefan Bertilsson [email protected]

+46184712712

Thijs Ettema [email protected]

+46184716129

EMERGING TECHNOLOGY PLATFORMS


Mission

To offer services for high-throughput, high-specificityanalysesofproteinbiomarkercandidatesinbodyfluidsand other biological samples by integrating molecular tools such as proximityextensionandproximityligation technologies (PEA and PLA) with the internationally recognized and accredited laboratory plat-form at Uppsala Clinical Research Center (UCR).

Management

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

Services

• Multiplexandsingle-plexanalysesof proteins using just 1-µl samples

• Chips that include a panel of 92 proteins relevant to cancer, or 92 proteins/biomarkers in cardiovas-cular diseases

• Detectingsingleproteinswithex-tremely high sensitivity

• Analyzingalltypesofbodyfluids,e.g. serum, plasma, cerebrospi-nalfluidsandotherbiologicalmaterials such as cells and tissue lysates

• Consultation in study design and statistical data analyses

Equipment includes

• Real-time PCR instruments, auto-matic liquid dispenser, etc.


• Detecting and quantifying single proteins and panels of proteins

• Quantitative analyses of the effect of drugcandidatesforproteinexpression

UCR-PEA/PLA Facility

Contact

Agneta Siegbahn [email protected]

+46186114251.

Masood Kamali-Moghaddam [email protected]

+46-18-4714454



Mission

To provide access to analytical techniquesandscientificsupporttodecode protein, cell and tissue response in relation to biomaterial properties. Biomaterials have wide-ranging appli-cations 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 scien-tificcommunity.

Management

JönsHilborn(platformdirector)Marjam Ott (manager)

Services

• Fee-based access to state-of-the-art instrumentsandscientificsupportfor 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 Ther-mogravimetric Analyzer (TGA)

• TA Instruments DSC Q1000 Differential Scanning Calorimetry (DSC)

• TA Instruments AR 2000 Rheom-eter

• JeolEclipse+400MHzNuclearmagnetic resonance (NMR)

• Micromeretics, AccyPyc 1340 labo-ratorydensitymeter(Hepycnometry)

• Malvern, Zetasizer Nano ZS parti-cle 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 Spec-trometer (FTIR)

• Nano Indenter CSM Instruments UNHT

• High-performanceliquidchroma-tography(HPLC)AllianceHPLC2695

Applications examples

Researchfieldsthatcanbenefitfromthe BioMat facility include:• Stem cell research in relation to the influenceofthematrix

• Disease-related research, e.g. in-flammation,cancer,diabetes

• Orthopedics and dentistry• Drug delivery and development of

drug devices• Minimal invasive therapies• Cardiovascular research• Skinrepairdevices(artificialtissue)• Extracorporalbloodtreatment

research

Biomaterial Characterization – BioMat Facility

Contact

Marjam Ott [email protected]

+46-18-4717243



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