ABSTRACT
Chlamydomonas reinhardtii cells have been in the focus of research for more than a decade, in particular due to its use as alternative source for energy production. However, the molecular processes in these cells are still not completely known, and 3D visualisations may help to understand these complex interactions and processes. In previous work, we presented the stereoscopic 3D (S3D) visualisation of a complete Chlamydomonas reinhardtii cell created with the 3D modelling framework Blender. This animation contained already a scene showing an illustrative membrane model of the thylakoid membrane. During discussion with domain experts, shortcomings of the visualisation for several detailed analysis questions have been identified and it was decided to redefine it.
A new modelling and visualisation pipeline based on a Membrane Packing Algorithm was developed, which can be configured via a user interface, enabling the composition of membranes employing published material. An expert user study was conducted to evaluate this new approach, with half the participants having a biology and the other half having an informatics background. The new and old Chlamydomonas thylakoid membrane models were presented on a S3D back projection system. The evaluation results reveal that the majority of participants preferred the new, more realistic membrane visualisation. However, the opinion varied with the expertise, leading to valuable conclusions for future visualisations. Interestingly, the S3D presentation of molecular structures lead to a positive change in opinion regarding S3D technology.
- 2001. 1jb0 - Photosystem I of cyanobacteria - Orientations of Proteins in Membranes (OPM) database. http://opm.phar.umich.edu/protein.php?search=1jb0Google Scholar
- 2004. 1rwt- Light-Harvesting Complex II- Orientations of Proteins in Membranes (OPM) database. http://opm.phar.umich.edu/protein.php?search=1rwtGoogle Scholar
- 2014. 2014-09-21 | 4th Int. CeBiTec Research Conference Bielefeld. http://www.webcitation.org/6xjDvOwr2Google Scholar
- 2017. AlgaeTEM - 6/17: Chlamydomonas#80501. http://remf.dartmouth.edu/images/algaeTEM/source/6.htmlGoogle Scholar
- 2017. Avanti Polar Lipids, Inc. https://avantilipids.comGoogle Scholar
- 2017. Jmol: an open-source browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D. http://jmol.sourceforge.net/Google Scholar
- 2017. MCell Home. http://www.mcell.org/Google Scholar
- 2017. Stereoscopic Displays and Applications conference - 3D Theatre Session. http://stereoscopic.org/3dcinema/index.htmlGoogle Scholar
- 2018. CELLmicrocosmos.org - project. http://cellmicrocosmos.orgGoogle Scholar
- N. Biere, M. Ghaffar, A. Doebbe, D. Jäger, N. Rothe, R. Klein K, Hofestädt, F. Schreiber, O. Kruse, and B. Sommer. 2018 in print. Heuristic modeling and 3D stereoscopic visualization of a Chlamydomonas reinhardtii cell. Journal of Integrative Bioinformatics 2, 15 (2018 in print), e53293.Google Scholar
- Christian Bogen, Viktor Klassen, Julian Wichmann, Marco La Russa, Anja Doebbe, Michael Grundmann, Pauliina Uronen, Olaf Kruse, and Jan H. Mussgnug. 2013. Identification of Monoraphidium contortum as a promising species for liquid biofuel production. Biores. Techn. 133 (2013), 622--626.Google ScholarCross Ref
- Yusuf Chisti. 2007. Biodiesel from microalgae. Biotechnology advances 25, 3 (2007), 294--306.Google Scholar
- Sébastien Doutreligne, Tristan Cragnolini, Samuela Pasquali, Philippe Derreumaux, and Marc Baaden. 2014. UnityMol: interactive scientific visualization for integrative biology. In Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium on. IEEE, 109--110.Google ScholarCross Ref
- Blender Foundation. 2017. blender.org - Home of the Blender project - Free and Open 3D Creation Software. blender.org (2017). https://www.blender.org/Google Scholar
- Paul Green-Armytage. 2010. A colour alphabet and the limits of colour coding. JAIC - Journal of the International Colour Association 5 (2010), 1--12.Google Scholar
- Sebastian Grottel, Michael Krone, Christoph Müller, Guido Reina, and Thomas Ertl. 2015. MegaMol - a prototyping framework for particle-based visualization. IEEE Trans. Visualization and Computer Graphics 21, 2 (2015), 201--214.Google ScholarCross Ref
- B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. 2008. Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput 4, 3 (2008), 435--447.Google ScholarCross Ref
- E. Hummel, P. Guttmann, S. Werner, B. Tarek, G. Schneider, M. Kunz, A. S. Frangakis, and B. Westermann. 2012. 3D ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography. PloS One 7, 12 (2012), e53293.Google ScholarCross Ref
- S. Jo, J. Lim, J. Klauda, and W. Im. 2009. CHARMM-GUI Membrane Builder for Mixed Bilayers and its Application to Yeast Membranes. Biophysical Journal 97, 1 (2009), 50--58.Google ScholarCross Ref
- G. Johnson, D. Goodsell, L. Autin, S. Forli, M. Sanner, and A. Olson. 2014. 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discussions 169 (2014), 1--21.Google ScholarCross Ref
- G. T. Johnson, L. Autin, D. S. Goodsell, M. F. Sanner, and A. J. Olson. 2011. ePMV Embeds Molecular Modeling into Professional Animation Software Environments. Structure 19, 3 (2011), 293--303.Google ScholarCross Ref
- Rex A. Kerr, Thomas M. Bartol, Boris Kaminsky, Markus Dittrich, Jen-Chien Jack Chang, Scott B. Baden, Terrence J. Sejnowski, and Joel R. Stiles. 2008. Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces. SIAM journal on scientific computing 30, 6 (2008), 3126--3149. Google ScholarDigital Library
- T. Klein, L. Autin, B. Kozliková, D. S. Goodsell, A. Olson, M. E. Gröller, and I. Viola. 2017. Instant construction and visualization of crowded biological environments. IEEE Trans. Visualization and Computer Graphics (2017).Google Scholar
- M. A. Lomize, I. D. Pogozheva, H. Joo, H. I. Mosberg, and A. L. Lomize. 2012. OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Research 40, D1 (2012), D370--D376.Google ScholarCross Ref
- L. Martínez, R. Andrade, E. G. Birgin, and J. M. Martínez. 2009. Packmol: a package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry 30, 13 (2009), 2157--2164.Google ScholarCross Ref
- Teresa M. Mata, Antonio A. Martins, and Nidia S. Caetano. 2010. Microalgae for biodiesel production and other applications: a review. Renewable and sustainable energy reviews 14, 1 (2010), 217--232.Google Scholar
- L. Mendiola-Morgenthaler, W. Eichenberger, and A. Boschetti. 1985. Isolation of chloroplast envelopes from Chlamydomonas. Lipid and polypeptide composition. Plant Science 41, 2 (Oct. 1985), 97--104.Google ScholarCross Ref
- The Presidents and Fellows of Harvard College. 2007. BioVisions: the Inner Life of the Cell. http://web.archive.org/web/20081215222914/http://multimedia.mcb.harvard.edu/Google Scholar
- Nivedita Rajendiran and Jacob D. Durrant. 2017. Pyrite: a blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques. Journal of Computational Chemistry (2017).Google Scholar
- Mark A. Scaife, Alexandra Merkx-Jacques, David L. Woodhall, and Roberto E. Armenta. 2015. Algal biofuels in Canada: Status and potential. Renewable and Sustainable Energy Reviews 44 (2015), 620--642.Google ScholarCross Ref
- John Sheehan, Terri Dunahay, John Benemann, and Paul Roessler. 1998. Look back at the US department of energy's aquatic species program: biodiesel from algae; close-out report. Technical Report. National Renewable Energy Lab., Golden, CO.(US).Google Scholar
- S. J. Singer and G. L. Nicolson. 1972. The fluid mosaic model of the structure of cell membranes. Science 175, 23 (1972), 720--731.Google ScholarCross Ref
- Björn Sommer. 2013. Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. Computational and Structural Biotechnology Journal 5, 6 (2013), e201302014.Google ScholarCross Ref
- B. Sommer, C. Bender, T. Hoppe, C. Gamroth, and L. Jelonek. 2014. Stereoscopic cell visualization: from mesoscopic to molecular scale. Electronic Imaging, Proceedings of Stereoscopic Displays and Applications XXVIII 23, 1 (2014), 011007.1--10.Google Scholar
- B. Sommer, T. Dingersen, C. Gamroth, S. E. Schneider, S. Rubert, J. Krüger, and K. J. Dietz. 2011. CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous Membrane Packing Problems. Journal of Chemical Information and Modeling 5, 51 (2011), 1165--1182.Google ScholarCross Ref
- B. Sommer, B. Kormeier, P. S. Demenkov, P. Arrigo, K. Hippe, Ö. Ates, A. V. Kochetov, V. A. Ivanisenko, N. A. Kolchanov, and R. Hofestädt. 2013. Subcellular Localization Charts: A new visual methodology for the semi-automatic localization of protein-related data sets. Journal of Bioinformatics and Computational Biology 11, 1 (2013), 1340005.Google ScholarCross Ref
- M. F. Zini, Y. Porozov, R. M. Andrei, T. Loni, C. Caudai, and M. ZoppÃĺ. 2010. BioBlender: fast and efficient all atom morphing of proteins using Blender game engine. Arxiv preprint arXiv:1009.4801 (2010).Google Scholar
Index Terms
- 3D Modelling and Visualisation of Heterogeneous Cell Membranes in Blender
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