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Monday, May 23, 2011
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A transcriptome is a blueprint, a snapshot of all the transcripts a cell produces. My work revolves around analyzing different transcriptomes and comparing them to derive what makes a cell's blueprint and phenotype. I am also interested in the transcriptional regulation specifically how transcription factor perturbations influence the transcriptome.
Going up the scale... looking at the shape of cells. In suspension, a cell is round - just like a droplet of water or a soap bubble - because this shape minimizes its surface tension as Laplace tells us. A cell, however, likes to adhere and bind to the surface. Its shape can still be explained by the minimizing of its energy if you take into account the adhesive energy, using a thermodynamical model (Cellular Potts Model)
I am working on how cells reorganize their cytoskeleton, and how they distribute the adhesions spots when you constrain their shapes and spreading possibilities. Looking at one side of the "ECM topology -> cell shape -> cell internal organization -> function" loop.
One other very interesting thing is the dynamics of change in cell shape and organization and the plasticity of most biological systems.
Striped or not?
The nanoparticle size, shape, surface charge and chemical composition are some of the factors that play a crucial role on its cellular uptake. Sometimes a striped surface pattern may be enough to avoid cytotoxicity or cell death. In my studies, I perform Molecular Dynamics simulations to investigate into the effect of specific patterns on the nanoparticle's surface and its effect on the nanoparticle-membrane interactions. Stripes, helical shapes or a random distribution of hydrophilic groups on the nanoparticles surface?
shape of a single protein is its folding; having good shape means fold properly, and we always need forces to be well shaped ;). using single molecule force spectroscopy we learn more about shapes of life in single molecule manner, and using Atomic Force Microscopy based single molecule force spectroscopy we can see the process of getting shaped of a single protein from fully unstructured to properly folded one.
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