Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Project Description I want to develop a synthetic assymetrical-cell-division system to enable synthetic cell differentiation; as a toolkit for engineer multicellular organization, development, pattern formation and others. To futher detail, see the page of the final project The project have two major subprojects: A mitotic counter: a circuit capable of counting as states how many cell division the linage have sense since the system has been activated (firts division, second, third, and so on). The system uses the natural fluctuations of the cell’s cycle regulators to induce or activate distinct proteins. When the system is activated, a TF would be activated by an cell-cycle-dependent kinase (at the G1 phase), that would induce the expression of a recombinase, that would inverse the sequence of its own promoter, inducing the expression of an inactivated, second, TF. This TF2 would be activated via a second cell-cycle-dependent kinase, one that would be activated in the final of the cell cycle and not be expressed at the same time with the firts kinase. The phosphorylation upon TF2 would, for example, link two homodymers together, in an activated form (an option, but not necessarily how it would work). When the kinase 2 activates TF2, gene expression would not be available because of chromatin condesation upon mitosis. After the cell divides, at G1, TF2 could induce the activation of other genes, that, in consenquence and, using the architecture, enables the activation of other genes at the second cell division, and so on, making possible to count cell division in the cell lineage. The system also needs other things such as a degradation system, repression for past states, etc. Assymetrical component: ¿How can we engineer an assymetrical distribution of molecules to induce the assymetrical cell division? It should be transferable to other organisms. The proposed one is to used an synthetic phased segregated condensate that is capable of create one individual and stable condensate upon the cell. It should carry an mRNA that would express a TF. It should be formated upon the activation of the scaffolds and dissegregated upon the cell division, enabling the translation of the mRNA selected. The mRNA should be sequestred in the condensate, where its translation-initiation site would be blocked, and it would be protected of degradations by directed nucleases over that mRNA. All of this via linking the sites of union of the scaffolds with this important sites of the mRNA (nuclease recognition site, translation initiation site, rybozome binding site, etc). The scaffolds should be inactivated upon cell division via phosphorylation at the binding sites, liberating the mRNA. But how we can make a single condensate exist? The idea is to use the pyrenoid (a rubisco aggregate condensate that makes CO2 fixation more efficient) as an example for this, where, in a dynamics between phosphatases and kinases, the algae maintains the pyrenoid as a single condensate or multiple when needed. ¿So how all of this is going to work in order to make the assymetrical cell division system function?
Week 2 HW: DNA read, write and edit
Homework