User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/12/05

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To begin

These last days I have been not so organized and as a consequence I have not updated this notebook. The reasons are essentially the following ones:

  1. I took some holidays around thanksgiving day.
  2. I was involved with protein engineering stuff.
    • I worked with (Pablo Ceroni). The experience has been very good until now. In fact I am learning some standard techniques involved in the obtention of chimeric recombinant proteins. Last days I performed the purification of some of my samples, but it seems that this step is not working. I arrived to this conclusion because I can not see the presence of the protein when applying the SDS-PAGE protocol. It seems that the protein does not bound to the probond resin during the purification step. I think that the problem was caused by lack of care with the preparation of the native buffer. I will repeat the purification step working with a buffer made by Vera Mucaj of Faisal Fadaye. Or maybe it would be nice to make again my own buffer, taking into account all the small details involved in it (in particular I am having some difficulties when insuring the requested pH levels).
  3. I continued with the AKT-modified network modeling question. Now the problem is to create a model for the description of the nuclear FOXO dynamics. I suppose an enzymatic mechanism and the algebraic condition involved with the conservation of FOXO (i.e. the total quantity of FOXO is fixed and is the result of the addition of nuclear FOXO with cytoplasmatic FOXO). The model do what was expected, but David would like to see the saturation of FOXO (i.e. the transfer of all FOXO to the nucleus of the cell as a response to the presence of AKT) before the jump in the level of AKT due to the change in the stability region of the system. By the moment I am playing with the parameters of the system and the result looks nice, and maybe can be improved, but I am not so sure. I will continue with this model later, maybe next Monday.
  4. I am delayed with the study of the learning question concerning the paper that Eva Jablonka send to me. i will do this weekend and is the only thing that I will do. i need to guarantee it.
  5. I need to read the papers by Eduardo Sontag and the papers by Pilpel in order to clarify the discussion about robustness as a conserved quantity.
  6. I need to organize my mess. My bay is becoming increasingly out of order.
  7. I need also to think about the proposal to be given to Frenk concerning my interest in molecular medicine and synthetic biology.

The talk with Devin

Yesterday I had a very interesting talk with Devin Burill, who is working in the application of a memory device, based in a sustained loop, as a tracking system used to detect cells responding to a given stimulus. The idea is to link the tracking device to specific responses of the organism to specific stimulus. She is working with DNA damage problems. She explained that the memory device disappear affter some time. I will check this thing with her next week, and it would be good to read the involved papers.

The talk by Tzachi Pilpel

Today Tzachi gave a very interesting talk about the mechanism that some micro-organism display to predict changes in the environment. The idea is that an organism will preserve a mechanism allowing it to detect statistical patters associated to environmental changes ih what is gained is more valuable that the implied investment in energy. The Pilpel talk presented some very interesting experiments, which proposes techniques to measure affectation on fitness and ways to measure the predictive behavior (the most interesting thing concerned E. Coli behavior in different regios of the digestive tract, which has different food for the bacteria). I need to ask him for some more details. it seems that there exits a paper by Alon concernig this topic.