Current Project(s) :
Throughout all different scales within organism, movement is a basic function of the organism. In multicellular tissue, cells migrate coordinately but flexibly to generate specific forms and to maintain homeostasis. Cell migration is driven by the robust mechanics between cytoskeleton and motor proteins. These proteins are not only involved in the movement of the whole cell, but also for the transport of cellular components to specific sites within the cell, for proper function of proteins at appropriate places. My general interest is to know how these movements are organized within organism.
Movements we observe at these levels are very different from that we know in our daily life. Unlike automobile or trains, movements within organism are associated with chaotic and random movements, which seemingly are very inefficient. The tendency of this randomness becomes evident as the scale becomes smaller. At single protein level, the energy required for a motor protein to make one step is comparable to the thermal energy passively given to the motor protein, which is the Brownian motion (Osawa, 1998). At organelle and cellular levels, polarized movement appears by spontaneous breaking of symmetric random movements (Verkovsky et al. 1999; Theriot, 2000). In microscopic scale between single proteins and unit of cells, there seems to be hidden answers for how this randomness-containing system is organized.
By approaching the biology from the point-of-view focused on “movement” vertically along from microscopic to macroscopic scale and by establishing analytical methods for studying biological movement in detail, I wish to contribute my limited potential towards the understanding of how biological system is operating.
1. Vesicle movement
Within cell protein cargos are packaged in membrane-bound vesicles and actively transported. At the micrometer scale, the cargo transport is elegantly organized from an organelle to the others as it has been shown by analyzing the ensemble movement of proteins e.g. using Fluorescence Recovery After Photobleaching (FRAP). On the other hand at the nanometer scale, cargo movement could be spontaneous and not fully deterministic, such as shown by Single Particle Tracking (SPT) techniques. To resolve this discrepancy, the project aims at the mezoscopic analyses of cargo proteins using optical flow estimation. Link: More details
2. Structured Cell Biology
Recent advances in surface chemistry techniques enabled fine modifications of the substrate we use for studying cell movements (Chen et al.). This advancement has permitted controlling cell shapes to study its functions. Many evidences indicate that the cell shape is an important cue for gene expressions and cellular metabolisms (e.g. Ingber). In turn, for studying the intracellular dynamics, cell shape must be under a stable experimental control to acquire precise data. In addition, recent cell biological studies involve computer simulations of the experimental results to evaluate the interpretation of results and for a deeper understanding of the biological system. Simulation requires defined boundary conditions, and one of which is the constant cell shape. For these reasons, we call cell biology with the cellular shape under experimental control “Structured Cell Biology”. Currently substrate structure that is linear, plane and three-dimensionally controlled is under development.
This project is in collaboration with Emmanuel Reynaud (Pepperkok lab), Julien Colombeli (Stelzer lab) and Francois Pouthas (Boulin Lab).
3. Multicellular movement
Maintenance of multicellular morphology is not static but dynamic. Cells constituting the multicellular structure are continuously changing their positions while the whole multicellular structure remains to have certain shape. How this is organized both during and after the development however is still uncertain ( Link on More details: Dictyostelium Phototaxis). One approach is to search for genes governing these processes, but how actually cell movement is organized must be studied in detail to know the actual mechanics. For this reason, cell movement tracking technique is indispensable.
Currently, three-dimensional tracking algorithms are under development using three-dimensional optical flow estimation and three-dimensional cross-correlation based tracking. The former tracking technique is in development in association with a devising of microscope to study three-dimensional multicellular movement using novel flat laser illumination technology called SPIM (Single Plane Illumination Microscopy, in collaboration with Jan Huisken and Klaus Greger in the Stelzer Lab). The latter technique is under collaboration with Wittbrodt Group to study single cell migration within Medaka fish embryo. In addition to the tracking technique, detailed analytical method using mean-squared-displacement plotting is under examination to separate random and non-random behaviour of cells.
4. Image Processing Algorithms
Image processing is becoming more and more important in cell biology. This is due to the digitalization of image data acquired through high-end microscopes and for extracting more information from image data at a higher precision. Projects I am involving are all related to movement of cellular components and thus require processing of image sequences. One way to analyze movement is by tracking the movement. There are many techniques rapidly appearing in everyday basis for analyzing movement in digital image sequences. Besides the algorithms mentioned in above sections, I am also examining other tracking algorithms (see (Miura, 2005)). Recently, a custom tracking program was written using two dimensional Gaussian fitting and further analytical approaches for SPT are under development.
In addition to the object tracking, protein mobility is studied also by other technology such as FRAP, which enables measurements of the averaged movement of proteins in vivo. The recovery curves must be studied by fitting model equations to measure the diffusion and interaction of the molecules under research interest. There are many equations and approaches proposed for this purpose, so I am now trying to make a computer program, which enable comparison of these different model equations for fitting experimental data.
Image data we acquire through studying biological system are astonishingly dynamic and beautiful. To share these scientific and artistic results and to increase the public knowledge on science, there is a new format of presentation using multimedia technology called “BioClip”. Scientific results are presented like a movie clip in association with background music. Two bioclip presentations have been created in 2002 and 2003, and I plan to put effort for further production. (Links: Bioclip web site; 2003 bioclip.)