Bilaga 7 – kemins forksningsinfrastruktur
KBC technical platforms:
KBC hosts four technical platforms with state of the art equipment. They offer service in the
following technical areas:
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Electron Microscopy
Proteomics
Metabolomics
NMR
The platforms provide service and support not only for research groups within KBC but for all
scientists in Umeå, and in some cases nationwide. Service is offered at different levels according
to the need of the specific project and due to financial and personnel resources. Analysis of a
limited number of samples can be made according to set cost but also larger projects including and
collaborations technical development are possible. The details vary between platforms.
The technical platforms play a major role also for teaching in research schools at KBC and Umeå
Centre for Microbial Research (UCMR). The courses offered are on three different levels. Short
introductory courses will give a basic understanding of the technique with its advantages and
limitations; more advanced courses will give detailed knowledge, and advanced “hands-on”
courses are offered for those who will make the analysis themselves.
The total budget for the platforms in 2009 is just over 7 MSEK with 1.5-2.1 MSEK per platform.
The largest contributors to the budget with about 20% each are user fees; KBC and the graduate
schools for KBC and UCMR; larger research grants (Berzelius, MIMS/UCMR and Small
molecules) and faculties at UmU and SLU but also VLL and individual departments give
substantial support. In addition to the support to individual platforms we are during 2009
upgrading the system for transfer and storage of data. The total cost for this is about 900 kkr,
which is supported by a grant from Kempe (600 kkr) and the rest from KBC. The system will
initially be used by the platforms in proteomics and metabolomics but will be available to the
other platforms as well. It also includes a common booking system.
The financing model varies between the platforms, as does the duration of secured economy (see
respective platform description for details). The present level of funding is sufficient for graduate
teaching and a basic level of service at the present level. However, to allow further development
of service offered some additional funding will be necessary. The planning for the future should
also take into account that the UmU support to KBC runs out in 2011 and the VR support to
graduate schools in 2012.
In order to secure stable funding for the platforms active support is required from all researchers
who see a value in maintaining them. However, platforms should only be maintained as long as
they are needed. Therefore it is important that platforms are evaluated at regular intervals (e.g.
every 3 years) and the future directions decided.
The platforms are presented on www.kbc.umu.se and an online booking system is at the moment
established with login access.
Electron Microscopy (EM) Platform:
Scientific Manager: Markus Grebe, markus.grebe, markus.grebe@plantphys.umu.se
Contact: Roland Rosqvist, roland.rosqvist@molbiol.umu.se;
Per Hörstedt, per.horstedt@medbio.umu.se
The EM platform at Umeå University is a joint resource for research and higher education in
electron microscopy techniques. By integrating all available electron microscopy techniques to the
platform the personnel is able to supply the scientists with a broad technical competence and high
quality service in routine electron microscopy techniques. The platform maintains and increases
the competence in the fields of Scanning electron microscopy (SEM) and Transmission electron
microscopy (TEM) in Umeå. It provides also course for graduate students in research schools of
KBC and UCMR.
The main current available services are:
 Transmission electron microscopy (TEM)
 Morphological Scanning electron microscopy (SEM)
 Analytical Scanning electron microscopy (SEM-EDX)
 Technical support and introductory training
Technical equipment:
 Cambridge Stereoscan 360 iXP scanning electron microscope
 Jeol electron microscope 1230
 Edwards S150A Sputter Coater and Edwards E12 Metal/Carbon evaporator
 Sectioning: LKB 7800 glass knife maker, Reichert Ultracut microtome with FCS cryo
attachment, RMC Power Tome XL, RMC glass knife maker
Examples for applications
Routine processing of cells/tissues (fixation, embedding), ultra-cryo sectioning,
immunolabelling of ultra-thin sections followed by TEM, ultra-thin sections from resinembedded specimens, routine morphological SEM and characterization of materials, energy
dispersive X-ray microanalyses, back-scatter detections, luminescence-based analyses.
Experiments will be carried out by EM platform personnel or by the applicants themselves after
adequate introductory training of techniques. All data and results belong to the customer and can
only be accessed by the researcher and the personnel of the EM platform.
Teaching
At the moment the following courses are offered:
 Basic course in Transmission and Scanning Electron Microscopy
 Practical course in Transmission and Scanning Electron Microscopy
 Advanced course SEM, TEM and Ultracryomicrotomy
The services are based on a fee-for-service basis and subsidised by the KBC departments.
Future developments:
The Proteomic Platform:
Scientific coordinator: Gunnar Wingsle, Gunnar.Wingsle@genfys.slu.se
Contact: Thomas Kieselbach, thomas.kieselbach@chem.umu.se
The proteomic platform provides infrastructure, service and development for research and
education in protein science, proteomics and mass spectrometry. Its instrumental and
bioinformatics equipment and infrastructure was enabled through considerable investments from
Umeå University, SLU, and The Swedish Research Council. As a result a complete proteomics
workflow is now available for the analysis of post-translational modifications (electron
dissociation mass spectrometer), which will considerably improve the current opportunities for all
research in protein science in Umeå.
The main current available services are:
 2-D DIGE automated spot picking
 protein analysis using MALDI-TOF and ESI-Q-TOF mass spectrometry.
The bioinformatics infrastructure includes:
 on-line booking of instruments
 data transfer
 a local Mascot server providing access to many important sequence databases.
Technical equipment:
 MALDI-TOF mass spectrometry: Voyager DE-STR mass spectrometer from Applied
Biosystems is used for both research and development, and protein analysis services
 Electrospray mass spectrometry: Q-tof Ultima ESI mass spectrometer from Micromass that
can be combined with a nanoACQUITY UPLC from Waters for LC/MS/MS applications.
Services on this instrument include currently protein identification by LC/MS/MS analysis.
Teaching in proteomics methods:
The personnel of the proteomic platform is not only organizing own courses, but has also
contributed to other courses including:
 Applied Mass Spectrometry
 Functional Genomics Course.
The future teaching activities will continue this work and also contribute to the KBC Research
School for graduate students. For no experienced scientists, the platform offers training courses
two to three times a year. The personnel has more than five years experience in mass
spectrometry training. The training includes usually three parts: theoretical introduction to protein
science, individual laboratory training, and a practical task to practice the newly learned
knowledge. Researchers, who are properly trained, are welcomed to use the MALDI-TOF mass
spectrometer for own research.
At the moment users are charged a yearly user fee, fees for access to expensive instrumenta–tion,
and for services of the facility. These charges are only used to maintain the instruments and
scientific infrastructure. Users of the MALDI-TOF mass spectrometer at Thomas Kieselbach’s
workbench are welcomed to use it on a self-cost basis.
Future developments:
Metabolomics Platform:
Scientific director: Thomas Moritz, thomas.moritz@genfys.slu.se (responsible MS-analysis);
Co-directors: Johan Trygg, johan.trygg@chem.umu.se, and Henrik Antti,
henrik.antti@chem.umu.se (responsible chemometrics and data evaluation)
Contact: Krister Lundgren, krister.lundgren@genfys.slu.se (service).
In the era of post-genomics, elucidation of gene function is a main target. Techniques enabling
metabolites to be identified and metabolic fluxes to be quantified are essential to complement the
information provided by genetic experiments and the large-scale analysis of transcript and protein
profiles in living organisms.
The main current available services are:
 Advice regarding design of metabolomics experiment;
 Extraction of samples, including extraction protocols (depending on the type of samples),
examples are online available
 Mass spectrometry analysis; protocols for derivatization for GC/MS analysis are online
available
 Basic multivariate analysis on obtained results (PCA, PLS, PLS-DA, O-PLS, OPLS-DA)
 Simple presentation of obtained results; differences between samples will be presented;
extensive identification of unknown compounds or multivariate analysis on obtained results
cannot be provided at the moment.
 Help scientists to find collaboration partners at KBC or other departments at UmU.
Technical equipment:
Mass spectrometers dedicated to metabolomics:
 LECO Pegasus III, gas chromatography- time-of-flight mass spectrometer (GC/TOFMS)
 Waters Acquity UPLC-LCT premier time-of-flight mass spectrometer (UPLC/TOFMS)
 ThermoScientific liquid chromatography-LTQ orbitrap-XL mass spectrometer (LC/MSMS)
 Agilent 6460 triple quadrupole liquid chromatography – mass spectrometer (LC/MSMS)
By the close collaboration with the proteomics and other platforms also these instruments are
available:
 JEOL JMS-MStation GC/MS (magnetic-sector mass spectrometer)
 Bruker Esquire 3000 plus, liquid chromatography - mass spectrometer
 Micromass Quattro Ultima LC/MS (triple quadrupole mass spectrometer)
 Micromass Q-TOF Ultima LC/MS (quadrupole/time-of-flight mass spectrometer)
 Applied Biosystem Voyager-DE STR (Maldi-TOF)
The Metabolomics facility at Umeå Plant Science received initially substantial support from the
Wallenberg Consortium North (WCN; www.wcn.se), and the facility is also open for the
Universities associated to the WCN.
The facility has one full-time research engineer and one part-time technician. The director and the
co-directors have long experience in mass spectrometry based analysis of small molecules in
biology samples and chemometrics, respectively.
Future developments:
The platform is now focusing on three directions:
1. Increased identification rates of metabolites. By extend the GC/MS and LC/MSMS spectra
libraries with more standards compound analysis, together with in-depth LC/MSMS
analysis of unknown metabolites the platform believes that a larger identification success
of obtained. It will inevitable help the interpretation of metabolomics studies in the future.
2. Develop methods for target analysis of specific compound classes, such as hormones,
amino compounds and lipids. As there are many metabolites that can’t be detected with
general metabolite profiling methodology there is important to extend the platform to
target analysis of biological important compound classes.
3. Further integration of bioinformatics in the metabolomics analysis, i.e. metabolic pathway
analysis, network analysis and other visualization tools. The goal is to be able to have all
tools web-based.
In the near future graduate courses in metabolomics as a part of the KCB graduate school will be
offered.
NMR-Platform
Scientific directors: NTFak: Gerhard Gröbner, gerhard.grobner@chem.umu.se
MedFak: Juergen Schleucher, jurgen.schleucher@chem.umu.se
Contact (NMR Platforms): Tobias Sparrman, tobias.sparrman@chem.umu.se
Based on major funding by Wallenberg and Kempe, the NMR platform provides NMR
instrumentation, which allows that all the different NMR techniques (solution, solid, diffusion,
imaging) can be used simultaneously in a highly synergetic way. The platform provides service
and access to all KBC and Campus groups, as well as training in state-of-the-art NMR
methodology. In addition, it has an open-access policy for academic/industrial partners at a
national/international level. Examples for the NMR based research in Umeå are projects on
membrane lipids and their proteins, amyloidogenic and allergenic proteins, proteins suitable for
dynamics and folding studies, bioactive RNA/DNA complexes. Many of these studies are of major
medical and pharmaceutical interest.
The main current available services are:
Solution NMR:
600 MHz (with cryoprobes), 500 MHz, 400 MHz, 360 MHz
Solid state NMR:
500 MHz narrowbore HR-MAS, 400 MHz widebore, MAS, Diffusion, 100 MHz
widebore, MAS, Diffusion
Imaging and pfg-NMR:
400 MHz microimaging, 400 MHz diffusion
Teaching:
The platform offers the following courses:
 Basic courses in NMR for students in chemistry
 Courses in the PhD training within the KBC and UCMR research schools covering basics
of the application of NMR in molecular biology.
The main service at the moment is to connect NMR groups and integrate NMR for all KBC
groups interested in this methods. For routine analysis more financial and personnel support is
needed.
Future developments: To maintain this platform at a high international level in the future and
make it available for a wider range or interested groups (nationally and internationally), the
current platform development is targeted towards the removal of the current critical shortage of
NMR time at high-field, the missing of an in-house, permanently accessible high-field (800-900
MHz) machine.
Needed financial support:
Running costs now and predicted för 2010-2014 (material, localities): 1.000.000 SEK/a
Costs for personnel: 1 fulltime researcher (FoA) and 1 partime - 50 % - researcher; ca. 900.000