FY2020

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 over five years as independent company.

Part of our image processing software, i.e. for 2D-processing are being ported and implemented on reconfigurable FPGA hardware. This was initially supported with an OIST Proof-of-concept (POC) grant.

1. Staff

  • Dr. Ulf Skoglund, Professor
  • Dr. Lars-Göran Öfverstedt, Staff Scientist (Retired Oct.31, 2020)
  • Dr. Gunnar Wilken, Staff Scientist
  • Dr. Reetesh Akhouri, Staff Scientist
  • Dr. Endang Rinawati Purba, Technician
  • Mr. Seigen Nakasone, Technician
  • Dr. Hong Huat Hoh, Junior Research Fellow (departed Mar 31, 2021)
  • Ms. Shizuka Kuda, Research Unit Administrator

Departed members:

  • Dr. Helena Chan, Postdoctoral Scholar (departed Dec 2019)
  • Bill Söderström, Staff Scientist (departed Dec 2019)
  • Dr. Cassie-Marie Peigne, Postdoctoral Scholar (departed Aug 2018)
  • Dr. Faisal Mahmood, Student (graduated 3/30/2017)
  • Dr. Märt Toots, Student, (graduated 3/30/2017)
  • Dr. Setsuko Nakanishi, Staff Scientist (departed 12/31/2016)
  • Ms. Jiafu Zeng, Research Intern (departed March 2016)
  • Ms. Olivia Leavitt, Research Intern (departed end of Term 2, 2015)
  • Dr. Yumiko Mishima, Researcher (departed 4/30/15)
  • Dr. Pan Soonsawad, Researcher (departed 4/30/15)
  • Mr. Hirotoshi Furusho, Technician (departed 4/30/15)
  • Dr. Cayho Budiman, Researcher (shared with IPB Unit, departed 5/30/14)
  • Mr. Jakub Kolodziejczyk, Technician (departed 7/31/14)
  • Ms. Ruby May Andales, Technician (departed 7/31/14)

2. Collaborations

2.1 Combining Molecular Dynamics and Molecular Electron Tomography to create a procedure to reach a reliable atomic resolution structure of a protein.

  • Type of collaboration: Research Collaboration
  • Researchers:
    • Professor Maria Bykhovskaia, Wayne State University

2.2 A New Molecular Machine required for Bacterial Development into Spores.

  • Description: 3-year grant from Australian Research Council
  • Type of collaboration: Research Collaboration
  • Researchers:
    • Professor Christopher Rodriguez, University of Technology Sydney, Australia

We are also on project-basis collaborating with faculty at OIST. Mostly with Professor Amy Shen and Professor Ichi Maruyama.

3. Activities and Findings

This 11th year we have continued to be very busy with further developments of our experimental protocols for our high-end light and electron microscopes and continued to intensively develop our software and also acquiring data in our ongoing structural projects. 

In our first project, we aim at getting a significant speed increase for noise removal and focus deconvolution for acquired images. To date, we have been able to generate high speed Fast Fourier Transforms via programmed FPGA (field-programmable-gated-arrays) chips. We have now managed to implement a floating-point FFT at high speed. Further, we have just managed to implement our full 2D image processing software for very fast noise-removal via our COMET technology. We were initially rewarded a Proof-of-Concept grant to achieve this. Currently we are busy improving our COMET technology in 2D to the FPGA chips, using the latest hardware version of the FPGA. We are also extending this to include 2D images from SEM microscopes in a collaboration with Hitachi. Very high-speed computations are 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.

Our second project is aimed to understand how malaria parasite uses our serum proteins to cause severe malaria in pregnant women and cause deaths and morbidity to fetus in the womb as well as women who are pregnant. In order to understand that we have resolved large complex of Var2CSA and IgM. We are now in the end-phase of data acquisition also preparing for a manuscript. In this project we show, through 3D tomographic analysis and biochemical experiments, how the human IgM, our primary immune defense, forms well defined giant complexes and stabilizes host parasite interaction. We have mapped domains that play important role in this interaction.

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

In this project we have been using super-resolution fluorescence microscopy and correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) in order to correlate protein localization with membrane ultra-structure during division. We have identified that the core proteins involved in this process forms multiple concentric rings, and specific well-defined supramolecular complexes and that the process of disassembly is a multistep process. In a related project we are also looking at spores, and their membrane channels. This project will proceed at slower speed, because both main researchers have got a postdoc position and an assistant professorship, respectively, in Australia. However, we continue to collaborate. At the moment Prof. Bill Söderström has not been able to visit OIST to complete some measurements. We are eagerly waiting for covid-19 restriction to allow for this.

The fourth project concerns the co-interpretation of 15Å->12Å->?Å .

Tomograms of synaptotagmin in different states are being analyzed. But as Proof-of-concept we are first analyzing data from Catalase and Albumin.  Our initial results are indeed very exciting.

In particular we now have a very competent and experienced technician working on the biochemistry of synaptotagmin, so that we for the first time can image the full length and membrane spanning protein. Currently we seem to have a reproducible way of reaching about 10Å, or better, resolution in 3D. We do seem to get better than 10Å resolution in 3D also for both of the Proof-of-concept proteins analyzed. It’s the first time for biological imaging that sub nanometer resolution is reached for 3D reconstructions without any averaging at all and seem to allow for secondary structure identification for a first type of tracing when comparing with published work. We are currently intensively investigating data acquisition parameters for optimal 3D resolution.

 

4. Publications

4.1 Journals

  1. Chan H., Söderström B., Skoglund U.  Spo0J and SMC are required for normal chromosome segregation in Staphylococcus aureus. MicrobiologyOpen 2020. DOI: 10.1002/mbo3.999
  1. Joshua W. McCausland, Xinxing Yang, Zhixin Lyu, Bill Söderström, Jie Xiao, and Jian Liu Treadmilling FtsZ polymers drive the directional movement of sPG-1 synthesis enzymes via a Brownian ratchet mechanism. BioRxiv https://doi.org/10.1101/857813
  1. Bill Söderström, Alessandro Ruda. Göran Widmalm and Daniel Daley. An OregonGreen488-labelled D-amino acid for visualizing peptidoglycan by super-resolution     STED nanoscopy. Microbiology 2020, 1-7, DOI 10.1099/mic.0.000996 
  1. Katsuya Fuchino, Helena Chan, Ling Chin Hwang and Per Bruheim Ethanologenic bacterium Zymomonas mobilis divides asymmetrically and exhibits heterogeneity in DNA content.  AEM, DOI: 10.1128/AEM.02441-20

4.2 Books and other one-time publications

  1. Gunnar Wilken: A glimpse of Sigma_3-Elementarity. R. Kahle and M. Rathjen (eds.): The Legacy of Kurt Schuette. 415-441 (Chapter 21), Springer September 2020

4.3 Oral and Poster Presentations

Nothing to report

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Nothing to report

7. Other

Nothing to report.