FY2016 Annual Report

Structural Cellular Biology Unit
Professor Ulf Skoglund

Abstract

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

Our methods are 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. The created spin-off has now been successfully running for three years as independent company.

1. Staff

  • Dr. Ulf Skoglund, Professor
  • Dr. Lars-Göran Öfverstedt, Staff Scientist
  • Dr. Gunnar Wilken, Staff Scientist
  • Dr. Setsuko Nakanishi, Staff Scientist
  • Dr. Reetesh Akhouri, Staff Scientist
  • Dr. Bill Söderström, Postdoctoral Scholar
  • Dr. Cassie-Marie Peigne, Postdoctoral Scholar
  • Dr. Helena Chan, Postdoctoral Scholar
  • Mr. Qingyuan Tian, Technician
  • Mr. Faisal Mahmood, Student
  • Mr. Märt Toots, Student
  • Ms. Shizuka Kuda, Research Administrator

Departed members:

  • 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. Hirotoshi Furusho, Technician (departed 4/30/15)
  • 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)
  • Ms. Jiafu Zeng, Research Intern (departed March 2016)

2. Collaborations

2.1 Cell division in E.coli

  • Description: Cell division in E.coli
  • Type of collaboration: Joint research
  • Researchers:
    • Professor Daniel Daley, Stockholm University

2.2 Structure and fucntion of proteins involved in Malaria infection

  • Description: Structure and function of proteins involved in Malaria infection
  • Type of collaboration: Joint research
  • Researchers:
    • Professor Mats Wahlgren, Karolinska Institutet

3. Activities and Findings

3.1 Activities and Findings

This 7th year we have been very busy with further development of our experimental protocols for our high-end light and electron microscopes and continued to develop our software, hiring more coworkers and starting data acquisition in our ongoing structural projects. 

To get a significant speed increase we have been able to generate high speed Fast Fourier Transforms via programmed FPGA (field-programmable-gated-arrays) chips. It’s clear that these chips can be augmented with full image processing software for very fast noise-removal via our COMET technology. We are now applying for a Proof-of-Concept grant to achieve this. Very high-speed computations are very enabling in structural biology because it allows for more thorough mappings of experimental parameters as well as allowing for more experiments to be processed and using more accurate mathematical models with less truncating approximations.

We are now in the middle of data acquisition for a Malaria related project, with the first major publication reported below.

The second concerns the mysteries of bacterial division, which surprisingly is not very well understood at the molecular level. This project is rapidly evolving with nice publications.

The third project concerns the co-interpretation of 15Å-12Å resolution tomograms of synaptotagmin and the molecular dynamics result after extensive simulations. This is in collaboration with an expert neuroscience group in the US.

Marrying the methods of tomography and molecular dynamics is totally new and potentially very powerful. We are exploiting this.

4. Publications

4.1 Journals

This 7th year we have been very busy with further development of our experimental protocols for our high-end light and electron microscopes and continued to develop our software, hiring more coworkers and starting data acquisition in our ongoing structural projects. 

To get a significant speed increase we have been able to generate high speed Fast Fourier Transforms via programmed FPGA (field-programmable-gated-arrays) chips. It’s clear that these chips can be augmented with full image processing software for very fast noise-removal via our COMET technology. We are now applying for a Proof-of-Concept grant to achieve this. Very high-speed computations are very enabling in structural biology because it allows for more thorough mappings of experimental parameters as well as allowing for more experiments to be processed and using more accurate mathematical models with less truncating approximations.

We are now in the middle of data acquisition for a Malaria related project, with the first major publication reported below.

The second concerns the mysteries of bacterial division, which surprisingly is not very well understood at the molecular level. This project is rapidly evolving with nice publications.

The third project concerns the co-interpretation of 15Å-12Å resolution tomograms of synaptotagmin and the molecular dynamics result after extensive simulations. This is in collaboration with an expert neuroscience group in the US.

Marrying the methods of tomography and molecular dynamics is totally new and potentially very powerful. We are exploiting this.

4. Publications

4.2 Journals

  1. Wahlgren, M., S. Goel and R. R. Akhouri (2017). "Variant surface antigens of Plasmodium falciparum and their roles in severe malaria." Nat Rev Microbiol.
  2. Peigne, C.-M., A. Leger, M.-C. Gesnel, F. Konczak, D. Olive, M. Bonneville, R. Breathnach and E. Scotet (2017). "The Juxtamembrane Domain of Butyrophilin BTN3A1 Controls Phosphoantigen-Mediated Activation of Human Vgamma9Vdelta2 T Cells." J Immunol 198(11): 4228-4234.
  3. Söderström, B., K. Mirzadeh, S. Toddo, G. von Heijine, U. Skoglund and D. O. Daley (2016). "Coordinated disassembly of the divisome complex in Escherichia coli." Molecular Microbiology.
  4. Daley, D. O., U. Skoglund and B. Soderstrom (2016). "FtsZ does not initiate membrane constriction at the onset of division." Sci Rep 6: 33138.

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. Sy-David Friedman (Universität Wien, A., S. Dilip Raghavan (NUS, S. Yue Yang (NUS and G. Tracking Chains Revisited (Wilken, Eds. (2017). Lecture Notes Series, Institute for Mathematical Sciences, National University of Singapore. Singapore.
  2. Soderstrom, B. (2017). Using advanced imaging to understand bacterial cell division. Germany, New Approaches and Concepts in Microbiology, EMBO/EMBL Symposia,.
  3. Soderstrom, B. (2017). Cell division through a different perspective; super-resolution fluorescence microscopy on standing cells, Madrid, Spain, Spanish National Center for Biotechnology, Madrid.
  4. Bailey, D. G., F. Mahmood and U. Skoglund (2017). Reducing the cost of removing border artefacts in Fourier Transforms., Bochum, De, Interna'onal Symposium on Highly-efficient accelerators and reconfigurable technologies, HEART2017,.
  5. Tian, Q., L.-G. ø. W. Öfverstedt and U. Skoglund (2016). Xpix2: Software to Pick the Fiducial Markers Semi-Automatically in Electron Tomography Tilt Images. The 4th International Conference on Intelligent Systems and Image Processing 2016, Kyoto, Japan.
  6. Söderström, B., D. O. Daley and U. Skoglund (2016). Correlating protein localization with membrane geometry at a nanometer scale. Single-Molecule Microscopy: Life at a Higher Resolution. Single Molecule Approaches to Biology.
  7. Söderström, B., D. O. Daley and U. Skoglund (2016). Correlating protein localization with membrane geometry at a nanometer scale. Single-Molecule Microscopy: Life at a Higher Resolution. Single Molecule Approaches to Biology.
  8. Soderstrom, B. and D. O. Daley (2016). "The bacterial divisome: more than a ring?" Curr Genet.
  9. Söderström, B. (2016). Correlating protein localization with envelope constriction during cell division in Escherichia coli. EMBO workshop. Bacterial cell division: Orchestrating the ring cycle., Czech Republic.
  10. Soderstrom, B. (2016). The bacterial cell division machinery is built in modules. Tampa, Florida, Protein secretion in bacteria.
  11.  Skoglund, U. (2016). Individual protein molecules in 3D seen with Molecular Electron Tomography. JEOL, Tokyo.
  12. Skoglund, U. (2016). Analysis of individual protein molecules in 3D with Molecular Electron Tomography. OIST.
  13. Nakanishi, S. (2016). "A spider toxin, ω-agatoxin IVA, binds to fixed as well as living tissues: cytochemical visualization of P/Q-type calcium channels." Microscopy.

​5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 Seminar: Signal Processing on Graphs: From Principle Component Analysis to Biomedical Applications

  • Date: March 8, 2017
  • Venue: OIST Campus Lab3
  • Speaker: Mr. Nauman Shahid (Ecole Polytechnique Federale De Lausanne (EPFL)

7. Other

Nothing to report.