FY2014 Annual Report

Structural Cellular Biology Unit

Professor Ulf Skoglund

Abstract

The Title of this section, the "Abstract" above, should be Header 3 or H3. All the section headers here should be H3. The abstract is a concise overview of the work of that fiscal year for the unit.

1. Staff

  • Dr. Ulf Skoglund, Professor
  • Dr. Lars-Göran Öfverstedt, Staff Scientist
  • Dr. Gunnar Wilken, Staff Scientist
  • Dr. Setsuko Nakanishi, Staff Scientist
  • Dr. Bill Söderström, Postdoctoral Scholar
  • Mr. Qingyuan Tian, Technician
  • Mr. Faisal Mahmood, Graduate Student
  • Mr. Märt Toots, Graduate Student
  • Ms. Jiafu Zeng, Research Intern
  • Ms. Shizuka Kuda, Research Administrator

Departed Memgers:

  • Dr. Yumiko Mishima, Researcher (departed 4/30/15)
  • Dr. Pan Soonsawad, Researcher (departed 4/30/15)
  • Dr. Cayho Budiman, Researcher (shred with IPB Unit, departed 5/30/14)
  • Mr. Jakub Kolodziejczyk, Technician (departed 7/31/14)
  • Ms. Ruby May Andales, Technician (departed 7/31/14)
  • Ms. Olivia Leavitt, Research Intern (departed end of Term 2, 2015)

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: CEMOVISel
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Lars Norlën
      • Dr. Ichiro Iwai
  • Theme: Structure and function of Glucocorticoid receptor protein
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Masataka Kinjo, Hokkaido University
  • Theme: Structure and function of proteins involved in Malaria infection
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Mats Walgren, Karolinska Institutet
  • Theme: Characterization of synaptic vesicles in brain tissue
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Shigetoshi Oiki, University of Fukui

3. Activities and Findings

Our Unit has continued to develop our 3D tomographic software. The latest version, 6.2.2, is now a stable and robust software and a version has been installed at Professor Shigetoshi Oikis lab at University of Fukuji., at the Mats Wahlgren lab at Karolinska Institutet, Sweden and Dr. Lars Norléns lab at Karolinska Institutet, Sweden. The Krios cryo-TEM has now been actively used to collect new and very high quality datasets of molecules within our collaborations. 

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 have filed a first patent in the area of calculation of Fast Fourier Transforms without the degrading series termination errors from non-periodic functions. We also filed a patent for removal of noise in 3D reconstruction that emanates from the detector, EFIRT (Extended Field Iterative Reconstruction Tomography).

The second PhD project concerns cryo-electron tomography of protein nano-crystals. So far we have shown that nano-crystals can be harvested and visualized. Subsequently lattice parameters can be refined after 3D reconstruction of these crystals. This project contains a significant amount of software development.

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 are at the publication stage of of our first article in this area.  In this project we show, through 3D tomographic analysis, how the human primary immune defense, via IgM, is being used by the invading Malaria parasite to form giant complexes, the rosetting phenomenon, in thin blood-capillaries, and they are probable candidates for causing fever.

We have started a project to characterize synaptic vesicles in brain tissue. Another started projected concerns the membrane-bound proteins in the bacterial-wall membranes.

4. Publications

4.1 Journals

  1. Efghijk, S., Uxyaabc, E., Defgh, K., Cdefg, HI. Article Title Here as It Appears in the Publication. Publication Title in Italics, doi:doi: 10.1177/1059712310397633 (2011).
  2. Efghijk, S., Uxyaabc, E., Defgh, K., Cdefg, HI. Article Title Here as It Appears in the Publication. Publication Title in Italics, doi:doi: 10.1177/1059712310397633 (2011).

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

1. Skoglund, U., (2014) Molecular characterization in three dimensions using cryo_electron microscopy, OIST-Members.of .the.CAO.Panels.for.Future.Issues, OIST Campus

2. Skoglund, U., (2014) Progress in developing the technology to see individual proteins in three dimensions, OIST-Members of the Budget Bureau-Ministry of Finance Visit, OIST Campus

3. Skoglund, U., (2014)  OIST has a functioning technology to study individual proteins in three dimensions using cryo electron microscopy, Members of the Austrian IST Visit, OIST Campus

4. Skoglund, U., (2015) Analysis of individual protein molecules in 3D with Molecular Electron Tomography, SCB Unit Review Seminar, OIST Campus

5. Skoglund, U., (2015) Analysis of individual protein molecules in three dimensions with cryo electron electron tomography, SCB Student Seminar, OIST Campus

6. Skoglund, U., (2014). 3D visualization of individual protein molecules using Molecular Electron Tomography. Single Protein Dynamics in Cellulo SPDC 2014 , OIST Seaside House, Okinawa, Japan

7. Kumar, P., F. Mahmood, J. Dauwels and e. al (2014). A Study on the Effect of Subliminal Priming on Subjective Perception of Images: A Machine Learning Approach. 36th IEEE Engineering in Medical & Biological Conference (EMBC), Chicago, IL.

8. Wilken, G. (2014). Extending Goodstein Principles. Logic Seminar, Yonsei University, Seoul, South Korea.

9. Wilken, G. (2014). Goodstein sequences for prominent ordinals up to the ordinal of Pi(1.1)-CAo. Colloquim Logicum 2014, Universitatet der Bundeswehr Muenchen.

10. Mahmood, F., L. Ofverstedt and U. Skogldund (2014). Extended Field Iterative Reconstruction Technique (EFIRT) for Correlated Noise Removal from 3D Tomographic Reconstructions. 36th IEEE Engineering in Medical & Biology Conference (EMBC). Chicago, IL.

11. Skoglund, U., (2014). Visualizing Individual protein molecules in 3D with Molecular Electron Tomography. OIST Campus

12. Soderstrom, B., A. Hjelm, J. W. de Gier and U. Skoglund (2015). Bacterial ghosts: One platform, multiple possibilities. Focus on Microscopy. Gottingen, Germany.

13. Soderstrom, B. (2015). Bacteria, not all are bad…?Using Bacteria in Vaccine research. OIST Campus.

5. Intellectual Property Rights and Other Specific Achievements

5.1 Patent

1. Mahmood, F., L. Ofverstedt and U. Skogldund (2014). Extended field iterative reconstruction technique (efirt) for correlated noise removal

6. Meetings and Events

6.1 Seminar

  • Date:           April 14, 2014
  • Venue:        OIST Campus, Lab 1
  • Speaker:     Dr. Suchi Goel (Karolinska Institutet)

6.2 Seminar

  • Date:           April 17, 2014
  • Venue:        OIST Campus, Lab 1
  • Speaker:     Professor Vladana Vukojevic (Karolinska Institutet)

6.3 Seminar

  • Date:           August 18, 2014
  • Venue:        OIST Campus, Lab 1
  • Speaker:     Dr. Bill Söderström (Stockholm University)

6.4 Seminar

  • Date:           January 15, 2015
  • Venue:        OIST Campus, Lab 1
  • Speaker:     Professor Takashi Yonetani (University of Pennsylvania)

6.2 Conference/Workshop

  • Title: Single Protein Dynamics in Cellulo - 2014
  • Date: April 21 - 25, 2014
  • Venue: OIST Seaside House
  • Organizer: Ichi Maruyama, Ulf Skoglund
  • Co-organizers: Masataka Kinjo, Thorsten Wohland
  • Speakers:
    • Dr. Shigetoshi Okiki (Unversity of Fukui)
    • Dr. Paul Wiseman (McGill University)
    • Dr. Tomoko Masaike (Tokyo University of Science)
    • Dr. Akihiro Kusumi (Kyoto University)
    • Dr. Thorsten Wohland (National University of Singapore)
    • Dr. Hiroko Bannai (Nagoya University)
    • Dr. Duccio Fanelli (University of Florence)
    • Dr. Masataka Kinjo (Hokkaido University)
    • Dr. Vladana Vukojevi'c (Karolinska Institutet)
    • Dr. Charlotte Fourrnier (OIST)
    • Dr. Takayuki Uchihashi (Kanazawa University)
    • Dr. Jun Liu (University of Texas)
    • Dr. Mike Heilemann (Goethe-University)
    • Dr. Yasushi Sako (Riken)
    • Dr. Andrew Clayton (Swinburne University of Technology)
    • Dr. Ichi Maruyama (OIST)
    • Dr. Ulf Skoglund (OIST)

7. Other

Nothing to report.