Team:UNAM-CU/Collaborations

Collaborations

We make a collaboration with the UNAH iGEM team from Honduras, they are working on a project to fight Dengue, so we decided to help them with their project in the modeling and wetlab parts; for this purpose we designed a working plan to help a part of their team to get started. We also gave them the opportunity to present their project to researchers of the UNAM from physiology, biotechnology, genomic sciences and medicine areas. They came to Mexico and worked 4 weeks in June in the institutes of chemistry, physiology and in the faculties of science and medicine.

Modeling area.

The section of our team who was more devoted to board mathematical modeling decided to give a course to our guests on the general ideas for developing a mathematical model, in order to do this, a 5-days system was implemented.

The first day was devoted to general problem solving, presenting some problems of mathematical logic, while trying to maintain a biological related subject in the problems, some of the listeners seemed enthusiastic with this idea and even used some extra time to discuss more problems. The computing part focused on principles of programing and getting to know the commands.
The second day was used to present a general idea on how functions work, in order to avoid confusions while working on derivatives and forming a solid basis for next few days.The computing part focused on first problems and starting to make their own programs.
We began the third day with a demonstration on derivatives and how they express change, which is a powerful weapon on biological systems modeling.The computing part focused on how to program the derivatives and some basic biological problems.
Once the listeners were comfortable with this kind of equations, some general models of this kind were discussed, for this purpose, we asked for systems that they thought that could be analyzed under this perspective.The computing part focused on how to program models using our own as an example, after that we started programing the first drafts of their model.
On the last day, it was decided to present some other branches of mathematics that are also useful in actual biology, like game theory or graph theory, with useful examples on how they work in different biological systems. We continued programing their model draft and trying different simulations to get the best results.

Wetlab work

They were taught on the basics of molecular biology, techniques like competent cells, growing mediums, pcr, transformations and bioinformatics on how to design their biobrick. The focus here was on the direct wet lab work and biobrick design, we used space provided in the Chemistry Institute and the Cellular Physiology Institute for giving them these classes.

Some members of the team, especially Lizbeth Bolaños, Alejandro Rodríguez and Xrysw Hernández, were closely involved in teaching our guests from the UNAH the following things during the second half of our guests stay in Mexico:

In our first session, we pointed out the requirements of the iGEM competition regarding the bioparts design, synthesis and testing.

In the second session, we checked with them some Molecular Biology principles, such as replication and transcription mechanisms as well as translation ones. We also covered some differences between eukaryotic and prokaryotic ways of protein expression.

Then, in another session, we began checking basic proteins’ structures principles, the main challenges in Molecular Dynamics that research groups involved have, as well as the ones they could affront during their project, and the different ways to study and purify proteins.

We also had a special session in which we taught them how to use: - Specialized softwares like PyMOL and Serial Cloner - Databases like the Biobrick Seeker and the Protein Data Bank - Servers online to run Molecular Dynamics programs

Finally, after these theoretical sessions, we began some practices at the lab in which we discussed with them the proceedings, what we expected and the possible results. The experiments done include competent cells and bacterial transformation. We also discussed some other techniques that would be useful for their project.

The feedback was good and they felt confident with being able to continue their work back on their home country.

Project presentation

The team got the chance to present their project on the IBT ( Institute of Biothecnology), CCG ( Center of Genomic Science), IQ ( Chemistry Institute), IFC (Institue of Celullar Physiology. They presented it in group seminars or in special appointments with the researchers, they got feedback and learned ways to improve their project and biobricks. The researchers were:

• Dr. Rafael Peña

• Dra. Laura Palomares

• Dr. Julio Freyre

• Dr. Gerardo Corzo.

• Dr. Ayari Fuentes

• Dr. Maximino Aldana

• M in B. Jose Alonso.

• Dr. Enrique Amador Guzmán

• Dra. Gloria Gutiérrez Venegas.

• Dr. David Romero.

https://2015.igem.org/File:Colaboration_letter_Pi_UNAH.pdf