Laura is our Meet the Fellow this week! She works with robotized SELEX.
I am collaborating with the Life & Medical Sciences (LIMES) Institute for my PhD. This Institute is part of Bonn University, in Germany. The LIMES Institute is an internationally oriented center for biomedical research. The main scientific focus of the institute is to explore the regulation of lipid metabolism and the immune system in health and disease, and decipher the signaling processes that take place both within and on biomembranes. I am working in Günter Mayer’s lab, focused on aptamer selection by Systematic Evolution of Ligands by Exponential Enrichment (SELEX link to post). We are many international scientists with different backgrounds in our working group. Our work is connected, helping each other as a team so we can reach our particular goals leading to the final selection of great aptamers.
Aptamers are short and stable nucleotide molecules that bind with high specificity and affinity to a certain target. They have plenty useful applications like diagnosis, drug delivery, therapeutic and bio-imaging. The SELEX procedure is very time consuming as each selection cycle consists of multiple steps and to select a good aptamer, 5 to 15 selection cycles are necessary.
So, to solve this issue, we now have a wonderful SELEX robot that will do the hard work for us. This robot will work day and night without any distractions, so it will be able to do one whole SELEX in 3 days. It can also run different SELEX in parallel, multiplying by 20 the speed of selection. I am in charge of this robot: I have to set everything and make sure that everything works; I have to program the different SELEX protocols and check that they are correct.
With this delightful SELEX robot we will be able to select many aptamers. This aptamers carry a lot of information that will be stored in a SELEX database I am building. All this information will be accessible for the members of the lab so they can compare results and improve SELEX protocols.
With the introduction of new generation sequencing (NGS) technologies it is possible to massively parallelize the sequencing process. That makes it easy to gather large amounts of sequence data in relatively short periods of time. All these huge amount of data can be analyzed with bioinformatic tools in regard to the enrichment fold of the sequences and motifs to identify patterns and identify the best aptamers.
So, as you can see, I have three pretty projects that will make aptamer selection much easier: the SELEX robot, the SELEX database and the NGS analysis.
My motivations to work on this PhD? Well, who could say no to such an opportunity! I am in a new nice place, with great colleagues as people and scientist and working in a really interesting and promising European project. We also keep on learning new matters and visiting new places all over Europe! Lovely… For my own projects I also have to go to other labs and enterprises related to bioinformatics, so I will also have the chance to travel to new places like Switzerland, Munich and Phoenix.
I have always liked genetics since I was at school and I wanted to work with something related to it. Then, I realized that bioinformatics are really promising for the analysis of all these huge amount of data we have gathered, giving us new and great results to understand better this world to discover. So I tried this field of knowledge and it looks like I’m good at it and I do like it so I decided to focus in this new field.
As I have told you before, my lab is located at Bonn (Germany). This means I am hearing a new strange language all day long. I already learned a little bit of German two years ago, so this has helped me a lot to be able to understand the basic and important things. My colleagues at the lab have also helped me a lot with every problem I have encountered. I am pretty happy here at Bonn and I do like my PhD, so for now everything looks good ☺. I am also improving my German little by little although I think it is a really hard language to learn. Maybe next year I can start having some easy conversations… We’ll see!
I always liked travelling and knowing new places and people, so to come to a different country for my PhD was not that traumatic, otherwise, I quite like it. Now I live in a pretty little apartment on the top of a mountain surrounded of green places and nice quiet neighborhood.
After my PhD, I will have improved my biotechnological and bioinformatics backgrounds; I will have learned a new language; I will have visited many different places and I will have improved my presentation skills to show my work and knowledge to the public. I hope this helps to take me where I will like to go for my post-doc: California!
To end up this short blog about me, I would like to add that apart from science, what I really like is to go out and meet new people and places. I like stories from all over the world and learn about different cultures and behaviors. I like nature and animals also. I have two nice cats living with me; they are part of the family! I also like to relax watching some film and drinking some sangria. And I really like eating tasty food like paella ^^.