FY2013 Annual Report

Structural Cellular Biology Unit

Professor Ulf Skoglund


Our unit runs research projects that concern method developments, applications, and rewarding and exciting collaborations with other groups in order to understand more of the function of proteins in cells and tissues.
In addition we are also developing basic mathematics to establish a more generalized information theory enabling a more quantitative use of the information in measured data.

We mainly use the techniques of electron microscopy, including molecular electron tomography, as the main tools in our unit, though we will draw upon well-established complementary techniques when called for.

This 4th year we have been very busy developing further our experimental protocols for our high-end electron microscopes and continuing developing our software, hiring more coworkers and starting data acquisition in our ongoing structural projects.  We are now in the middle of data acquisition for several of the projects mentioned.

Our method is well suited for use in pharmaceutical drug research in industrial collaborations, so a big leap forward was that we managed to get a MEXT grant that funds a spin-off formation. Currently this spin-off is being created. Towards the end of the FY 2013 it was clear that the company would be created in the early FY 2014.

1. Staff

  • Dr. Ulf Skoglund, Professor
  • Dr. Lars-Göran Öfverstedt, Researcher
  • Dr. Gunnar Wilken, Researcher
  • Dr. Yumiko Mishima, Researcher
  • Dr. Pan Soonsawad, Researcher
  • Dr. Cahyo Budiman, Researcher (shared with IPB Unit) departed May 2014
  • Mr. Hirotoshi Furusho, Technician
  • Mr. Jakub Kolodziejczyk, Technician (departed July 2014)
  • Ms. Ruby May Andales, Technician (departed July 2014)
  • Mr. Faisal Mahmood, Graduate Student
  • Mr. Märt Toots, Graduate Student
  • Ms. Olivia Leavitt, Intern
  • Ms. Shizuka Kuda, Research Administrator

2. Collaborations

  • Theme: Lipid Membrane Ion Channel KcsA, a Potassium ion-channel
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Shigetoshi Oiki, University of Fukui
  • Theme: Human Skin Structure
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Lars Norlën, Stockholm University
  • Theme: CEMOVIS
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Lars Norlën, Stockholm University
      • Dr. Ichiro Iwai, Shiseido
  • Theme: Structure and function of Glucocorticoid recepotr protein
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Örjan Wrange, Karolinska Institutet (Collaboration ends in FY2014 due to Retirement of Prof Wrange)
  • Theme: Structure and function of proteins involoved in Malaria infection
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Mats Wahlgren, Karolinska Institutet
  • Theme: Structure and function of the Ryanodine receptor and its complexes
    • Type of collaboration: Research Collaboration
    • Researchers:
      • ProfessorIchiro Maruyama, OIST

3. Activities and Findings

3.1 Title of Activity or Finding.

Our Unit has continued to develop our 3D tomographic software. The latest version, 6.0, is now a stable representation and a version has been also installed at Professor Shigetoshi Oikis lab at University of Fukuji. The Krios cryo-TEM has now been actively used to collect new and very high quality datasets of molecules within our collaborations. 

We managed to show MEXT that we could use our software to successfully finalize a proof-of-concept structural determination-project on a smaller sized protein (about 32 kD) in collaboration with a well-known Japanese pharmaceutical company. The result was that MEXT prolonged our grant until the company has been formed, which is now scheduled to happen in July, 2014.

Our regularization software COMET has also been updated to include local geometry refinement. This is the first time this has been achieved, and we are in the process of writing an article on this. This new feature helped in a test case for another OIST Unit (Sowwan’s) where they wanted to see if our methods could be used in their quest for understanding the atomic structure layout in the synthesized nanoparticles. Our 3D regularized nanoparticle structure shows the lattice in large regions of the small nanoparticle. As a feasibility study we regard this as successfully concluded.

We have started two PhD-student projects. One is related to hardware implementation of our technology to greatly increase speed and thus be an enabling technology for many more diverse applications. We are in the build-up stage. The second concerns cryo-electron tomography of protein nano-crystals. This project is also at the build-up stage, but we have shown that nano-crystals can be harvested and visualized.

The CEMOVIS project is now starting up. CEMOVIS is cryo electron microscopy of vitrified sections. We now have all the equipment. Dr. Ichiro Iwai is at the Shiseido facility in Yokohama and a CEMOVIS expert on the ultra-microtome cutting of high-pressure frozen tissue. We are now planning for him to pay us a visit so he can transfer his expertice on CEMOVIS experimental procedures to us.

Our Malaria-related project is closing in on it’s first phase so we can start writing an article.

4. Publications

4.1 Journals

  1. Weiermann, A. and G. Wilken (2013). "Goodstein sequences for prominent ordinals up to the ordinal of Pi(1)(1)-CA(0)." Annals of Pure and Applied Logic 164(12): 1493-1506.

4.2 Books and Other One-Time Publications

Nothing to report

4.3 Oral and Poster Presentations

  1. Wilken, G. (2013). Elementary Patterns of Resemblance. Seoul, Korea.
  2. Wilken, G. (2013). A short introduction to Patterns of Resemblance. Vienna, Austria.

5. Intellectual Property Rights and Other Specific Achievements

5.1 Patent

Title Extended field iterative reconstruction technique (EFIRT) for correlated noise removal
Filing date 2014-03-05 (PCT); OIST/ID/0040-PCT; Application No.: PCT/JP2014/001214
Inventors Faisal Mahmood, Lars-Göran Öfverstedt and Ulf Skoglund
Content: A method to remove noise from an image that comes from uncorrelated noise in the image-source, e.x. the detector

5.2 Grant

MEXT Grant-Project for Creating New Industries from University (Nov 2012 – July 2014)

6. Meetings and Events

6.1 Seminar

  • Date:    December 6, 2103
  • Venue:  OIST Campus, Lab 1
  • Speaker: Professor Mats Wahlgren (Karolinska Institutet)

6.2 Seminar

  • Date:    February 4, 2014
  • Venue:  OIST Campus, Lab 1
  • Speaker: Professor Gyesik Lee (Hankyong Nationa University)

6.3 Seminar

  • Date:    February 13, 2014
  • Venue:  OIST Campus, Center Bldg
  • Speaker: Professor Kuniaki Nagayama (NIPS)

6.4 Seminar

  • Date:    February 13, 2014
  • Venue:  OIST Campus, Center Bldg
  • Speaker: Dr. Nagatani (NIPS)