FY2015 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. To get a significant speed increase we have lately started to generate high speed Fast Fourier Transforms via programmed FPGA (field-programmable-gated-arrays) chips. When finalized as useful we will try to incorporate these chips with our computer processing setup. Very high speed computations are very enabling in structural biology because it allows for more thorough mapping of experimental parameters as well as allowing for more experiments to be processed and using more accurate mathematical models with less truncating approximations.

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 6th 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 projects of biological nature. Basically we are engaged in 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.

The third project concerns the large-scale dynamics of proteins.

We are also developing the CEMOVIS technology to be a practical tool for our laboratory.

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. The created spin-off has now been successfully running for two 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. Bill Söderström, Postdoctoral Scholar
  • Mr. Qingyuan Tian, Technician
  • Mr. Faisal Mahmood, Graduate Student
  • Mr. Märt Toots, Graduate Student
  • Ms. Evropi Toulkeridou, Graduate Student
  • Ms. Shizuka Kuda, Research Unit 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 function 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

Our Unit has continued to develop our 3D tomographic software. The latest version, 6.2.4.8, is now a stable and robust software and a version has been installed at several international labs. The Krios cryo-TEM has now been actively used to collect new and very high quality datasets of molecules within our collaborations. 

We have two PhD-student projects that are now almost ready for thesis defense. 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 e.g. detector, EFIRT (Extended Field Iterative Reconstruction Tomography). The EFIRT full paper is now at an advanced state of reviewing. The FFT full paper is in the state of being written. A limited FFT paper is already published in an IEEE journal.

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. A full paper of this analysis on a sample protein which is well characterized already is now being written.

The CEMOVIS project is now getting functional. CEMOVIS is cryo electron microscopy of vitrified sections. We have all the equipment and we have been busy implementing experimental protocols. We are now beginning to acquire high quality images of thin sections of the high-pressure frozen tissue.

In our Malaria-related project we now have 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 engaged a new post-doctoral researcher to continue this collaborative project.

We have started a project to characterize synaptic vesicles in brain tissue.

In the project regarding the bacterial cell division we have been using super-resolution fluorescence microscopy and identified that the core proteins involved in this process forms multiple concentric rings, and that the process of disassembly is a multistep process. These findings are about to be written up and published. Furthermore have we started to use correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) in order to correlate protein localization with membrane ultra structure during division.

Finally, we have also initiated a project aiming to characterize membrane proteins in their native membrane environment using the bacterial ghost technology and cryo-ET.

The third image, Figure 3, is a single image with the caption below it.

 

4. Publications

4.1 Journals

  1. Akhouri, R., R, S. Goel, H. Furusho, U. Skoglund and M. Wahlgren (2016). "Architecture of Human IgM in Complex with P. falciparum Erythrocyte Membrane Protein 1." Cell Reports

    Bel, G., C. P. Connaughton, M. Toots and M. M. Bandi (2016). "Grid-scale fluctuations and forecast error in wind power." New Journal of Physics 18.

    Cardiel, J. J., H. Furusho, U. Skoglund and A. Q. Shen (2015). "Formation of crystal-like structures and branched networks from nonionic spherical micelles." Scientific Reports 5.

    Mahmood, F., N. Shahid, P. Vandergheynst and u. Skoglund (2016). "Graph Based Sinogram Denoising for Tomographic Reconstructions." Computer Vision and Pattern Recognition.

    Mohan, D. M., P. Kumar, F. Mahmood, K. F. Wong, A. Agrawal, M. Elgendi, R. Shukla, N. Ang, A. Ching, J. Dauwels and A. H. D. Chan (2016). "Effect of Subliminal Lexical Priming on the Subjective Perception of Images: A Machine Learning Approach." PLoS ONE.

    Mahmood, F., M. Toots, L.-G. W. Öfverstedt and U. Skoglund (2015). "2D Discrete Fourier Transform with Simultaneous Edge Artifact Removal for Real-Time Applications." IEEE.

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. B.Söderström, A. Hjelm, J-W. de Gier and U. Skoglund (2015). Bacterial ghosts: One platform, multiple possibilities. Focus on Microscopy Conference. Göttingen, Germany.

    B.Söderström, A. Hjelm, J-W. de Gier and U. Skoglund (2015). The bacterial cell envelope at single protein level. New Approaches and Concepts in Microbilogy, EMBO/EMBL Syposia, Germany

    B.Söderström, A. Hjelm, J-W. de Gier and U. Skoglund (2015) The bacterial cell envelope at single protein level. Seeing in Believing, EMBO/EMBL Symposia, Germany

    Mahmood, F., M. Toots, L.-G. W. Öfverstedt and U. Skoglund (2015). 2D Discrete Fourier Transform with Simultaneous Edge Artifact Removal for Real-Time Applications. IEEE Field Programmable Technology (FPT) 2015, Queenstown, NZ. Quessntown, NZ.

    Mohan, D. M., P. Kumar, F. Mahmood, K. F. Wong, A. Agrawal, M. Elgendi, R. Shukla, N. Ang, A. Ching, J. Dauwels and A. H. D. Chan (2016). "Effect of Subliminal Lexical Priming on the Subjective Perception of Images: A Machine Learning Approach." PLoS ONE.

    Nakanishi, S. (2015). High-resolution FIB-SEM reveals plasma membrane dynamics at the neuronal-glial synaptic interface. Glia Study Group. Nagoya University.

    Nakanishi, S. (2015). Endocytosis occurs spontaneously in the synaptic plasma membrane facing glial process-Analysis by focused ion beam scanning electron microscopy. OIST.

    Tian, Q., L.-G. W. Öfverstedt and U. Skoglund (2015). Automatically Pick Fiducial Markers in Electron Tomography Tilt Images. The International Conference on Intelligent Informatics and Biomedical Sciences, OIST.

    Wilken, G. (2015). Pure Patterns and Ordinal numbers. Program on Sets and Computations, National University of Singapore.

    Wilken, G. (2015). On the well-quasi-orderedness of pure patterns of resemblance of order two. Minisymposium-Well-quasi-orders: from theory to applications, Hamburg, Germany.

    Wilken, G. (2015). Pure Patterns of Resemblance.  Section Logic and Theoretical Computer Science, Annual meeting of the German Mathematical Society (DMV), Hamburg, Germany.

    Skoglund, U. (April. 2015) At OIST for Fraunhofer. “Analysis of individual protein molecules in 3D with Molecular Electron Tomography.”

    Skoglund, U. (May. 2015) At OIST for Hodgson & Hedman. “Analysis of individual protein molecules in 3D with Molecular Electron Tomography.”

    Skoglund, U. (Nov. 2015) At OIST for the Forein Press Center. “Individual protein molecules in 3D seen with Molecular Electron Tomography.”

    Skoglund, U. (Mar. 2016) At OIST for the Students at OIST. “Analysis of individual protein molecules in 3D with Molecular Electron Tomography.”

5. Intellectual Property Rights and Other Specific Achievements

On OIST file

6. Meetings and Events

6.1 Super-resolution imaging in neuroscience and nephrology

  • Date: June 24, 2015
  • Venue: Meeting Room C016, Lab 1
  • Speaker: Prof. Hans Blom, The Royal Institute of Technology, Sweden

6.2 Mathematical models for controlling seizures and neurosurgical planning

  • Date: June 29, 2015
  • Venue: Seminar Room C210, Center Bldg
  • Speakers: Prof. Justin Dauwels, Nanyang Technological University, Singapore

6.3 Ultrafast noise-resilient phase reconstruction from intensity images

  • Date: June 30, 2015
  • Venue: Seminar Room C700, Lab 3
  • Speakers: Prof. Justin Dauwels, Nanyang Technological University, Singapore

6.4 Salmonella in vivo habitats – surprises and implication

  • Date: Aug 4, 2015
  • Venue: Meeting Room B729, Lab 3
  • Speakers: Dr. Christopher Bleck, University of Basel

7. Other

Nothing to report.