Programming for research - Ondřej Vávra and Jan Šťourač
17. 6. 2021 |
The prize of the Dean of the Faculty of Science of Masaryk University was awarded to two researchers from the Protein Engineering team of the International Clinical Research Center of St. Anne's University Hospital Brno. In the category of the Best Student of the Doctoral Study Program, Ondřej Vávra and Jan Šťourač received it, as an evaluation and thanks for their work so far in the Loschmidt Laboratories of the Faculty of Science, Masaryk University and FNUSA-ICRC. On this occasion, we asked both colleagues who specializes in bioinformatics for a short interview.
I imagine bioinformatics as such IT guys in the laboratory. Is it true? And what have you already programmed in?
Ondřej: I probably wouldn't describe it that way, it's about a combination of IT and biology, but we are not programmers in laboratories například For example, I consider myself a self taught IT guy. I started at the high school, with Pascal. Then I worked in Bash, but in Loschmidt's labs I needed more complex scripts to process the data, so now I'm working in Python, where I'm still a slightly advanced user and I'm happy to be sitting in the office with Jan, who can help me.
So how did you get into Loschmidt's labs?
Ondřej: My journey was quite steep, I come from Hradec Králové and I had no idea about any Loschmidt laboratories. I chose to study at university mainly because of biology, which always attracted me the most. I got to Masaryk University, majoring in molecular biology. In the first semester, we had a seminar with the heads of all laboratories, where they presented their research activities. There I learned about Loschmidt's labs for the first time and I was very interested in the combination of IT and biology. And when I met structural biology in my sophomore year, it was decided. I have already done my bachelor's thesis here and I am satisfied here.
Jan: It was easier for me and a little earlier. Im from Brno and we had to take part in Secondary School professional activities at our gym. And in the search for a suitable topic, I was fascinated by bioinformatics as a fascinating connection between computer science and biology, and that was only a step to Masaryk University and Loschmidt's laboratories. I then continued working on the projects even after the completion of it and I have already stayed here.
What are your results during your time here and what are your next goals?
Ondřej: My probably biggest result is that I participated in the development of a method for rapid analysis of the passage of molecules through protein tunnels. We successfully performed several other analyzes with this method, thanks to an internship abroad, we established further cooperation, so we managed to evaluate it well. Three years ago, I also received the Brno Ph.D. The talent of the South Moravian Center for International Mobility (JCMM), however, I am now in the fourth year of doctoral studies, so it is most important for me to combine work here with writing a doctoral thesis. So the closest goal is to complete my project and finish it successfully.
Jan: I primarily deal with the design and development of bioinformatics tools and databases. And it can be said that in some way I have been involved in almost everyone who has come out of our lab in the last ten years, which is twelve or thirteen programs. What makes me most happy is that they are popular in the scientific community and are really used by thousands of scientists around the world. As for studying, I'm in my second year, so in a while I will have a state exam and then I'll see. And if the pandemic situation allows, I would like to go on an internship at the European Bioinformatics Institute in Great Britain this year. But now it's hard to plan anything, so it's hard to say how it will all turn out in the end.
The most difficult you have encountered in your work so far, and what obstacle do you face now?
Ondřej: It was a purely professional problem, within the project in foreign cooperation I needed to integrate a special kind of simulations, which we have not done here yet. Long story short - it took about a year before I managed to find and put into operation a usable method and everything finally worked out. Now I face another obstacle. So far, there is no reliable automated method that can decide whether a protein has a ligand binding site on the surface or inside. If this problem could be solved and we could use software tools to determine the nature of these places, it would be a huge step forward. Using machine learning, we could apply this knowledge to the entire protein database and then better design changes to proteins or ligands, which would have an impact not only on applications in medicine, but also in industry.
Jan: I deal with one very difficult matter somehow continuously. It is about the robustness of our programs. Our calculations are quite demanding and run simultaneously on many computers. And as we all know, from time to time one stops randomly working or responding, and this then leads to a false calculation failure, which is a problem. So we're working to keep the running task running as well as possible, and for example to restart automatically, without the user noticing anything and we have to apologize for the technical inconvenience. But this is more of a technical matter, from a scientific point of view, the biggest challenge for me at the moment is the development of the PredicSNP Onco tool. It is a software aimed at the personalized treatment of children's cancer, which aims to analyze the effect of mutations found in the cancer tissue of a particular patient on the functioning of key proteins and their interaction with known drugs. The results obtained by us will then be used by physicians in deciding and preparing a suitable therapeutic plan.
What do bioinformatics say about the threats posed to us by filmmakers like Matrix or Terminator?
Ondřej: Probably nothing, we have fun like other viewers :) I have no specific fear of any IT thing. I don't have an Internet of Things facility at home, but it's more of a question that I don't care so much. And if I want to adjust the household to some automatic mode, then in the first place I will deal with security, which is something that a lot of people forget. As far as machine learning is concerned, it's more of a question for Elon Musk or Bill Gates, where they are going to go, I've never thought about it. It will definitely affect our lives, for example, let's take semi-autonomous cars, so we will see what it will look like in ten years.
Jan: Rather than the plots of the mentioned films, I am frightened by the "big brother" and the associated loss of privacy. Today, we almost always communicate to third parties, whether search engines, visited sites or social network operators, an awful lot of information that can be used to extract incredible details about our lives, habits and so on. And they can be easily abused, as in China in their social credit system, which seems very scary to me. And unfortunately it's not sci-fi, but it's here and now, and using it anywhere in the world is "just" a matter of justification. This is associated with the risk of theft of private data or identity by a completely stranger. Although I am glad that the state is gradually digitizing, I have no major illusions about information security. Globally, IT security is often perceived as an unnecessary and expensive luxury, and is basically not addressed until a problem arises. Unfortunately.
Let's leave the IT topic - what about free time?
Ondřej: I recently found a new hobby - I make mechanical keyboards. Otherwise, music or reading to take a break from that computer.
Jan: For me, it's definitely nature and trips. I like to walk in the mountains, in the woods and try to spend as much free time as possible outside the computer and the Internet. On weekends, I prefer to volunteer with the Brontosaurus to take care of valuable natural sites or monuments.
Obesity as a trigger of neurodegenerative diseases?
15. 6. 2021 |
RNDr. Jan Fröhlich, Ph.D. and Dr. Manlio Vinciguerra of the Epigenetics, Metabolism and Aging FNUSA-ICRC Research team, in collaboration with a research institute at the Medical University in Varna, published a successful review summarizing current knowledge on the effect of adipomyokines / metabotrophic factors on the development and progression of cardiometabolic (CMD) and neurodegenerative diseases. The work was published in the International Journal of Molecular Sciences.
"Over the last 30 years, there has been a significant change in the view of adipose tissue, which is now understood as an important regulator of metabolism and one of the main endocrine organs of the human body," says Dr. Jan Fröhlich with the fact that adiopobiology has thus become an important scientific field, dealing, among other things, with the study of the origin and consequences of obesity. It plays an important role in the pathophysiology of cardiometabolic and neurometabolic diseases, including Alzheimer's disease (AD).
"According to the latest findings, one of the main risk factors for the onset and progression of Alzheimer's disease is obesity and the associated hypertension, high LDL cholesterol and diabetes. On the contrary, numerous studies in mouse models and volunteers have shown that starvation-induced diets or short-term exercise have a beneficial effect and slow the development and progression of neurodegenerative diseases, including AD, ”explains Dr. Jan Fröhlich.
It has been shown that mediators of positive effects are factors / hormones secreted from skeletal muscle and adipose tissue, so-called adipomyokines. Adipomyokines are a heterogeneous group of metabolites and proteins that have a direct effect on metabolism and are therefore also nicknamed metabotrophic factors. "In our work, we point out that therapies based on the modulation of metabolism through the administration of metabotrophic factors could in the future help patients suffering from serious cardiometabolic and neurodegenerative diseases," points out Dr. Jan Fröhlich.
The full article is available HERE.
CZECRIN Annual Scientific Conference
4. 6. 2021 |
The CZECRIN research infrastructure invites all interested parties to its annual scientific conference 2021. The conference program is already out there and you can view it on the CZECRIN website. If you are interested in a topic, but you have already blocked the date, you can still register for the conference and get a record of the entire conference.
If you are already looking forward to the conference and would like to shorten the wait, CZECRIN has prepared a small competition quiz for you, in which you can test your knowledge of CZECRIN and clinical research and you can also participate in the prize draw by participating. Attention, if you want to participate in the draw, you must be registered for the conference. The evaluation of the quiz will take place at the end of the CZECRIN Conference.
The CZECRIN research infrastructure, which is part of the pan-European ECRIN-ERIC network, offers its support, services and expertise to all research-oriented physicians in order to join forces in a rapid approach to the initiation of national and especially transnational clinical trials.
St. Anne's University Hospital Brno and International Clinical Research Center, together with Masaryk University, is a founding member and main coordinator of this Czech national infrastructure.
2nd Hands-on Computational Enzyme Design Course
15. 5. 2021 |
The Hands-on Computational Enzyme Design Course is a highly practical and interactive course meant primarily for protein and metabolic engineers with no prior experience in computer modelling and bioinformatics. Other experts willing to broaden their current computational protein design toolbox can also benefit from this course. A team of experts and software developers provide training on how to operate several software tools devoted to different aspect of enzyme engineering, and how to properly interpret the results. Four main topics covered are: (i) Mining and analysis of novel enzymes, (ii) Engineering protein stability, (iii) Engineering enzyme activity and specificity, and (iv) Engineering protein solubility. The theoretical background and practical exercises are provided in a dynamic discussion environment.
The first edition of this course was carried out in the classical on-site format for 3.5 days, in Brno, Czech Republic, in February 2020. The course was organized by the Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University and International Clinical Research Center, St. Anne’s University Hospital Brno. Due to the COVID-19 pandemic, the second edition of the course was performed on-line in May 2021. Both editions were fully booked and the feedback from the participants was very positive. The great majority of the participants was highly satisfied and would recommend the course to a colleague. The 2nd edition was fully booked after only 2 weeks, with participants from 16 countries and 4 continents, 12% of them coming from industry. Our experience shows that: (i) by running an on-line edition we shortened distances, allowing participants from farther regions of the globe to join, (ii) the demand for training on computational enzyme design tools is high, and (iii) the reputation of the Loschmidt Laboratories as providers of valuable tools and training is growing.
We plan to run in the future both on-site and on-line versions of the course. If you are interested in participating in the next edition, you can access the course website and sign up to our newsletters to stay tuned!
The European Commission has awarded the prestigious HR Excellence in Research Award (HR Award) to our center
14. 5. 2021 |
Improving the quality of care for human resources, transparent recruitment and selection of employees, support for the development of professional growth, equal working and salary conditions for women and men and many other benefits. All this means the HR AWARD, which confirms that the International Clinical Research Center of St. Anne's University Hospital Brno (FNUSA-ICRC) guarantees excellence in caring for the working conditions of her researchers.
The award given by the European Commission is one of the most prestigious in the field of HR and is widely recognized in the international scientific community. "In the case of a foreign job applicant at our center, inquiries about the HR AWARD are very common," confirmed Silvia Vašulková, HR Award Officer of FNUSA-ICRC. The share of foreign workers in our center is very high, out of the total number of 425 employees it is almost twenty-five percent.
However, the work on improving processes in the field of HR does not end there, on the contrary. "Now we have and want to fulfill all the projects and tasks contained in our action plan, in two years we will have an internal evaluation and its eventual revision," added Silvia Vašulková. After its implementation, our center awaits evaluation directly by the European Commission.
All information about HR AWARD can be found here:
Kardiovize is Co-leading a Consortium of Cardiometabolic Risk Factors METRICS
13. 5. 2021 |
An important research team within the International Clinical Research Center of St. Anne's University Hospital Brno (FNUSA-ICRC) is Kardiovize. It is a cardiovascular prevention program in Central and Eastern Europe based on population analysis. One percent of the population of the city of Brno participates in it and the data from the research have a large international overlap. Its importance is also confirmed by the head of the research team, Dr. Juan Pablo Gonzalez Rivas: "Cardiometabolic risk factors, including obesity, diabetes, hypertension and dyslipidemia, are the leading cause of death and disability worldwide."
However, this burden affects populations disproportionally, „It is very important to understand how to stop the consequences of cardiometabolic risk factors globally, and the heterogeneity of the drivers that creates the disease varies considerably across regions, cultures, and ethnic groups, for this reason, it is mandatory to approach the understanding of this problem using a multicultural perspective“, says Dr. Gonzalez Rivas.
This fact was also the reason for the creation of the international consortium METRICS, which was established last year. Kardiovize is a founding member of the consortium and Dr. Gonzalez Rivas is its secretary. METRICS is the result of a long-term collaboration with a group of scientists from Venezuela, led by Ramfis Nieto-Martinez and Dr. Jeffrey I. Mechanick of Mount Sinai, NY, USA. "We have published sixteen articles with this group in the last seven years," said Dr. Gonzalez Rivas. "We meet regularly every month and continue to actively cooperate on our projects."
Currently, the consortium has 29 members from four continents, such as Masaryk University in Brno, Universidade Federal Fluminese in Rio de Janeiro, Charles University in Prague, Harvard School of Public Health in Boston and the Mayo Clinic. These are not only medical and PhD students, but also top scientists. "We are very proud of our diversity and I would like to emphasize that this is not a closed society, anyone can join us and will be welcome," added Dr. Gonzalez Rivas. Five members of Kardiovize itself are involved, each of whom presented at least one project related to public health issues last year, and another five projects are currently being prepared.
We asked Dr. Gonzalez Rivas - can a medical student from Masaryk University in Brno, for example, get involved in the activities of the consortium?
Of course, one of the core values we have in our research team is to support junior researchers and interns. For example, Anna Zimovjanová, one of our interns, approached us with the idea of a project aimed at evaluating the impact of social determinants on the mental health of medical students. Both mental health and the social situation are among the risk factors associated with cardiovascular disease. So we in Kardiovize helped her with the preparation of the project and she also introduced it to the members of METRICS. They provided it with feedback and in June she will present a supplemented proposal for the implementation of this project and its implementation in seven countries, which we consider a huge success. This is exactly the goal of the cooperation between the Kardiovize team and the METRICS consortium, ie to offer a platform for the development of our own projects. I would just like to add that Anna Zimovjanová is also a recent research assistant in our team while studying at Masaryk University.