Biere, Niklas

Doebbe, Anja

Huser, Thomas

Kruse, Olaf

Rothe, Nils

Sommer, Björn

English

BieColl - Bielefeld Electronic Collections

  Proceedings of CELLmicrocosmos neXt 2014 (DOI: 10.2390/biecoll-next2014-2)  7Towards a 3D Cell Model of Chlamydomonas reinhardtiiNiklas Biere1, Anja Doebbe2, Nils Rothe1,Thomas Huser3, Olaf Kruse2, Björn Sommer1,*1Bio-/Medical Informatics Department, Bielefeld University/Center for Biotechnology2Algae Biotechnology & Bioenergy, Bielefeld University/Center for Biotechnology3Biomolecular Photonics Group, Bielefeld UniversityUniversitätsstr. 25, 33615 Bielefeld, Germany1 IntroductionChlamydomonas reinhardtii is a green alga which is often used in Biotechnology as a modelorganism. This  single-cell  organism has a size of approx. 10 µm, contains a very largechloroplast relevant for the energy production which is partly used to move by using twoflagella. An important biotechnological application is the production of biofuels.2 Cell ModelingA visualization approach of the interpretative abstraction level is used to create the C.reinhardtii model [1]. By combining the information of different publications, microscopicimages and videos at multiple scales, this project aims to present a more precise three-dimensional structure of this cell type. The cell model is generated by using Blender [2]. Inaddition, 3D microscopy data was used as  a base to model the  Endoplasmic reticulumwhich was previously segmented with FIJI [3].To  visualize  the  energy-relevant  pathways  of  C.  reinhardtii,  a  simplified  network  wasmodeled  and  localized  using  the  CELLmicrocosmos  4.2  PathwayIntegration  [4].  Thispathway was afterwards used in Blender to illustrate the intracellular processes.Figure 1: An anaglyph stereoscopic rendering (red/cyan) of Chlamydomonas reinhardtii*bjoern@CELLmicrocosmos.org  Proceedings of CELLmicrocosmos neXt 2014 (DOI: 10.2390/biecoll-next2014-2)  83 Animation and VisualizationThe colors of the different cell components are basically derived from the natural colorswhich are visible using a light microscope. For example, the color of the Chloroplast isgreen, caused by the Chlorophyl. There is also a number of publications and videos whichare presenting the movement of the flagella. These sources have been taken into accountduring the modeling process [5].4 OutlookA first version of this video was presented at the conference “Prospects and challenges forthe  development  of  algal  biotechnology”  and  the  CELLmicrocosmos  neXt  workshop  inSeptember 2014. Future approaches may be the integration of the molecular level, e.g.,by modeling the photo system complexes, by using the MembraneEditor [6].AcknowledgmentsThis project is sponsored in part by the program “Bioinformatics of Signaling Networks” atthe Center for Biotechnology of Bielefeld University, and by the Ministry of Innovation,Science,  Research  and  Technology  of  North  Rhine-Westphalia  (MIWFT)  as  part  of  theresearch cooperation “MoRitS - Model-based Realization of intelligent Systems in Nano- andBiotechnologies” (grant no. 321 - 8.03.04.03 2012/02).References[1] B. Sommer. CELLmicrocosmos –  Integrative cell modeling at the molecular, mesoscopicand functional level. Doctorate Thesis, Bielefeld University, Bielefeld, Germany, 2012.[2] blender.org -  Home of the Blender project  -  Free and Open 3D Creation Software.[Online]. Available: http://www.blender.org/. [Accessed: 22-Jul-2014].[3] J.  Schindelin,  I.  Arganda-Carreras,  E.  Frise,  V.  Kaynig,  M.  Longair,  T.  Pietzsch,  S.Preibisch, C. Rueden, S. Saalfeld, and B. Schmid. Fiji: an open-source platform forbiological-image analysis. Nature Methods, 9(7):676–682, 2012.[4] B.  Sommer,  J.  Künsemöller,  N.  Sand,  A.  Husemann, M.  Rumming,  and B.  Kormeier.CELLmicrocosmos  4.1:  an  interactive  approach  to  integrating  spatially  localizedmetabolic networks into a virtual 3D cell environment. in  BIOSTEC  BIOINFORMATICS2010, 2010:90–95.[5] V. F. Geyer, F. Jülicher, J. Howard, and B. M. Friedrich. Cell-body rocking is a dominantmechanism  for  flagellar  synchronization  in  a  swimming  alga.  Proceedings  of  theNational Academy of Sciences, 110(45):18058–18063, 2013.[6] B. Sommer, T. Dingersen, C. Gamroth, S. E. Schneider, S. Rubert, J. Krüger, and K. J.Dietz.  CELLmicrocosmos  2.2  MembraneEditor:  a  modular  interactive  shape-basedsoftware approach  to  solve heterogeneous  Membrane Packing  Problems.  Journal  ofChemical Information and Modeling, 5(51):1165–1182, 2011.

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Towards a 3D Cell Model of Chlamydomonas reinhardtii

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Towards a 3D Cell Model of Chlamydomonas reinhardtii

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