Blog of Andrés Aravena

Bioinformatics + Biotech in high impact strategic industries: My talk at Yeditepe University

26 February 2018

The students of Genetics and Bioengineering at Yeditepe University have a club, that they call “Biotechnology Society”. They organized the “International Yeditepe University Genetics and Bioengineering Student Congress” and they invited academics from different institutions to present their research. They were very kind to invite me also.

What did I said?

My talk was titled “Bioinformatics + Biotech in high impact strategic industries”. On it I aimed to show how recent advances in biotechnology have changed dramatically the way we do research in science and technology.

Biotechnology has changed a lot in the last 10 years, and it will probably keep changing. The same is true in general for all science and technology. Experiments that used to be expensive and slow, are today cheap and fast. Producing and analyzing huge volumes of data is easy and inexpensive today. Everybody can build new instruments, or cheaper versions of the standard instruments at home, and even do synthetic biology in any lab. How are you going to succeed in this brave new world?

In this talk I showed some of the challenges that you as a biotechnologist will face in the following years, and what we can learn (if we can learn) from previous experiences. I focused on my experience in Chile, where biotechnology is used for the rational exploitation of natural resources (mainly copper, but also wood, fishes, fruits and wine), which are the main source of national income. Biotechnology has been essential for the efficient use of resources, transforming the industries and have a huge positive effect on the whole economy.

A key part of this successful biotechnological experience is due to bioinformatics and computational biology. Using mathematical and informatics tools allows us to design the best experiments, simulate the possible outcomes and extract meaningful knowledge from the results.

Other talks that I liked

One of the reasons why I like attending to these conferences is to see what other people are doing and learn a little on every subject. You can see what people said in the abstracts page or in the abstracts book.

I enjoyed very much the talk “Plant Cell Wall Biotechnology: Perspectives and Future Directions” by Dr.​ Andrew Harvey from Yeditepe Univ. He wisely prepared the first part of his talk as “an infomercial”, that is, giving first an overview of the area to attract the interest of the students. He gave several arguments to convince us that “plants are great”. That was a nice introduction for the rest of us which do not have previous knowledge on the subject. And hopefully was good to convince some students to work with him. It was a good inspiration to my talk, so I also tried to do some “infomercial”.

I also liked the talk “The role and therapeutic potential of invariant Natural Killer T (iNKT) cells in health and disease” by Dr. Gerhard Wingender from Izmir International Biomedicine & Genome Institute. Gerhard introduced us to the subject of immunology with a very clever motivation. Later I learned that he has formation on Pedagogy, which reflects on his talk. I met him again this month at the “Winter School” organized by our students at Istanbul University.

Dr. Christopher Mayack from Sabaci University presented the thought-provoking talk “Ecology, evolution and animal behavior” based on his work on bees. I liked how he created his own tools to observe and measure the behavior of the bees. It is a nice example of “making your own instruments”. Christopher’s contribution is not limited to the experimental part. To understand behavior you need models, and he has a nice one, which is very similar to the models used by behavioral economists. It seems that bees and humans act very much in the same way: we avoid risk if possible, but desperate times require desperate measures and when resources are scarce, we (bees and humans) do take more risky decisions. This suggests (to me) that we do not need a big brain to make extreme decisions; a bee-size brain will suffice in many cases. But we need a big brain to tell a story later to justify why we did what we did.

I’m always attracted to these interdisciplinary subjects that combine new tools, basic research and complex models, and that can be extrapolated to other contexts. Another talk that showed the need for good models was “RNA-mediated epigenetic heredity: experimental mouse models of an acquired pathology” Dr. Minoo Rassoulzadegan, from University of Nice-Sophia Antipolis, France. She described several experiments that show non-Mendelian heredity, where the evidence suggests that sperm RNA plays an epigenetic role on these paramutations. She stressed that to understand the complete phenomena we need better models. Obviously, I agree with her on this.

There was another talk about RNA, which was much technical. Dr. Yongsoo Park from Koç University presented “MicroRNA exocytosis by vesicle fusion as a novel neuromodulator”. He is a neuroscientist interested on the role of miRNA as neuromodulator. In his research he combines techniques from biochemistry, biophysics and cell biology. I like these interdisciplinary studies. Nature is not separated into disciplines, they are something we created to fit our way of thinking, or sometimes just to get more funding. This separation was useful in the nineteenth century and we got all the easy results from that. Now we have only hard questions which need vision from several disciplines at the same time. The more independent areas you understand, the better chances of success.

The last talk was the most biotechnological. Dr. Allen Liu​ from University of Michigan-Ann Arbor presented “Microfluidics for single cell mechanobiology”. He develop tools to measure the stiffness of cells. TO do that, he and his team use micro-engineering tools to make nanoscale pipes in a microscope plate, where they can flow cell-by-cell into small chambers where they can see what happens when the cell is compressed. It reminds me of the garbage compactor in the first Star Wars movie, but with single cells instead of Leia, Luke and Han Solo. Dr. Liu also showed some photos of his campus, which some of my friends have visited and praised, and make me think about visiting there someday.

I was very curious about the talk by Dr. Pedro Morouco from Polytechnic Institute of Leiria. Portugal is a very beautiful county with some of the nicest people, and I want to know more about their research. Dr. Morouco’s research is based on the availability of 3D printers that can produce biological tissues, a subject that interact with several of my interests as engineer. Unfortunately Dr. Morouco could not attend this time. I look forward to see him on a future occasion.

There was another professor initially invited that could not attend. Dr. Sreeparna Banerjee from Middle East Technical University spoke at “IU Winter School” and told me that she was also invited to Yeditepe but couldn’t manage to be there. Luckily she did manage to be at Istanbul University. But that will be for another post.

About the Conference Organization

This was the 7th conference, and the first “International” one. They tell me that they “have been organizing student congresses since 2013. Until this year we have been organizing these congresses in national level and we have been reached a participation population up to 600 people from all over Turkey”. Since 2013 was six years ago I guess that in one they made two conferences.

Since this was an “International Conference”, the talks were all presented in English. Yeditepe students speak and understand good English, and they seem very well prepared on the scientific matters. Unfortunately there were not too many students from other universities. Maybe the language was a barrier, maybe the fact that other student conference was held the same weekend. I personally think that the promotion was not very good and the registration was opened too late. Other conferences distribute promotional posters to all related departments. At Istanbul University the student club hires a good translation service for the people who needs help with English. Maybe that could have helped. The 150 people who finally attended were able to understand, but this number is significantly lower than the 600 of previous years.

The “international” label is used in a wide sense. Most of the speakers were foreigners, including myself, but then most of the foreigners are already in Turkey. So is kind of “national conference with foreigner speakers”. The real “international speakers” were Dr. Minoo Rassoulzadegan (France) and Dr. Allen Liu (US).

Despite the low attendance I liked the organization very much. The speakers were interesting and the students asked good questions.

A cable protector that looks like a plastic model of a virus.

My only complain is “Why not real coffee?” We had cookies and tea for the coffee break, and some kind of powder that people call “coffee” but is more like acid dirt. Turkey is famous worldwide for its coffee, and europeans learned it from Turkey. Is like Turkey invented coffee. Why cannot we have real coffee on Turkish conferences? In any other country, including the remote Chile, conferences provide either filter coffee in a jar (American style) or Italian coffee in a big tank, the same we use here only for tea.

Repeat after me: “Nescafe no es cafe”, “Nescafe is not coffee”.

Finally, in the conference pack, inside the bag, between the papers and the “ecological” pen, there was a mysterious test tube with a kind of plastic model of a virus. I couldn’t figure out what was it for, until Dilara explained to me: it is a protector for the charging cable. It is great. My MacBook charger cable is broken and usually does not work. With the new protector it works perfectly. Thank you very much.