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 Štourač 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.
Jan: In my case, it’s more IT than biology or work in laboratories… I started programming in elementary school, my first programming “language” was Baltík and his simple programming of the wizard by graphical chaining of actions. At the gym I was a classic webmaker, so HTML, cascading styles, JavaScript, then PHP, SQL and in high school in the Pascal seminar. Currently, it’s mainly Java for more complex applications and Python as a fast prototyping language.
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.
Experts from Kardiovize will offer preventive check-ups
The Kardiovize team from the International Clinical Research Centre of St. Anne’s University Hospital in Brno has prepared preventive examinations for the public, aimed at the possible detection of cardiometabolic diseases. Interested people will undergo a medical examination by a doctor, a sonograph or a nutritional counsellor.
Preventive check-ups – especially for cardiometabolic diseases – are very important. “According to the results of our Kardiovize study, approximately 60% of the adult population in Brno meets the criteria for starting lifestyle intervention programmes at an early stage of the disease. Our centre can contribute to the detection and stratification of at-risk subjects and provide effective interventions. Currently, the Kardiovize Lifestyle Centre offers screening and lifestyle interventions as part of primary prevention (i.e. before the onset of any complication). Effective interventions in the early stages of the disease prevent the development of complications and are especially designed for people who are overweight – obesity, prediabetes, hypertension, dyslipidemia, type 2 diabetes – but without the presence of complications (stroke, heart attack, etc.),” said Juan Pablo Gonzalez Rivas, head of the Kardiovize research team, adding: “Unhealthy lifestyles are the cause of most common diseases worldwide. Unhealthy diet, lack of physical activity, tobacco use and excessive alcohol consumption are the main drivers of non-communicable diseases. Lifestyle medicine offers an opportunity to prevent these diseases and complications in their early stages.”
Kardiovize is offering three packages to interested parties based on the number of tests and collections. This is a paid service. For more information, interested parties can visit the website at www.fnusa-icrc.org or contact Kardiovize experts directly at 549 185 592, 603 299 683 or email infokardiovize@fnusa.cz.
Martin Toul won an award for the best poster at the FEBS Congress
Mgr. Martin Toul, a member of the Protein Engineering team at International Clinical Research Center of St. Anne’s University Hospital Brno (FNUSA-ICRC), won the poster of the day award at the 45th Congress of the Federation of European Biochemical Societies (FEBS). In addition, he also won the Outstanding poster of FEBS Open Bio Editor prize, which was given to only 4 out of a total of 1285 participants. The poster was titled “Engineering protein dynamics for the understanding of the divergent evolution of the Renilla luciferase” and described research on the role of protein dynamics and their high efficiency to understand the evolution of luciferase in Sea pansy (Renilla reniformis) on a molecular level.
Luciferase is the name of enzymes that allow animals to produce light (bioluminescence). The best-known example of an animal using bioluminescence is a firefly. The light is produced as a result of an oxidation reaction of a luciferin molecule in the presence of the enzyme luciferase. The range of bioluminescence colors is relatively extensive, ranging from blue-violet, found mainly in marine organisms including the sea pansy Renilla, to red, which can be seen on the beaches of California during so-called “red tides.”
Luciferase is beneficial not only for organisms in nature but also for laboratory use. It serves as an imaging technique for processes in living organisms, such as insulin secretion imaging. It can also monitor genes, their expression, or their interaction with other biomolecules. Luciferase is also used to monitor the spreading of labeled viruses or cancer cells. Using dynamics engineering of luciferase, Toul, in collaboration with other colleagues from the research team, constructed a new type of luciferase with a 100 times prolonged bioluminescence compared to the original short flash.
“The result is of great importance wherever the enzyme luciferase is used as a diagnostic system for monitoring gene expression or as an imaging technique. The prolongation of bioluminescence can extend the practical application of luciferase even more and make it more efficient, as the original short flash luminescence was not suitable for long-term monitoring of a stable bioluminescence signal. The newly modified protein makes this possible, “concluded Toul.
Comparison of the accuracy of different measuring methods for myocardial deformation
When it comes to evaluating myocardial deformations (strains), cardiovascular magnetic resonance (CMR) imaging is a widely used tool and offers a number of techniques for this purpose. The method of tagging is considered to be the gold standard for the evaluation of myocardial strain using CMR. But due to its specific requirements (need to scan additional sequences), this technique is used relatively little. On the other hand, CMR feature tracking (FT), a new imaging technique, is more practical and beneficial in clinical settings, but the verification of measurement accuracy is limited. The comparison of different methods of measuring myocardial deformation and comparison of used software is what the research in collaboration with doc. MUDr. Roman Panovský, Ph.D., the head of the Cardiovascular Magnetic Resonance Research Team at International Clinical Research Center of St. Anne’s University Hospital Brno (FNUSA-ICRC), focused on.
The research involved 61 participants, of which 18 were healthy, and 43 had heart conditions such as chronic heart attack, dilated cardiomyopathy, or left ventricular hypertrophy. For all participants, different dimensions of myocardial strains were measured. The measurements included global and regional longitudinal strain (LS), circumferential strain (CS), and radial strain (RS). All measurements were performed using 3 different post-processing software, and the measured values were compared within individual techniques and against tagging.
While the global LS and global CS data among software and tagging were similarly accurate, significant differences were seen for global RS and all strain dimensions on a regional level. “The reliability of global strain measurement for longitudinal and circumferential strains is important information for the introduction of the FT method into routine clinical practice. On the contrary, due to the significant variability of regional strains, it is not possible to recommend this evaluation for the purpose of drawing clinical conclusions,” stated associate professor Panovský.
The full research can be found here.
Supported by the European Regional Development Fund – Project ENOCH (No. CZ.02.1.01/0.0/0.0/16_019/0000868).
The hospital launched a cannabis cultivation facility
The St. Anne’s University Hospital Brno has launched a trial run of its own experimental cannabis cultivation facility. It has become the first medical facility in the Czech Republic to grow medicinal cannabis. For the time being for research purposes.
St. Anne’s University Hospital Brno (FNUSA) is the leading Czech institution in the development and use of medical cannabis treatment. “We use it at our department for pain treatment. It also has indications for the treatment of many problems in other medical fields. In general, cannabis treatment raises a number of unanswered questions, yet it meets the requirements for high safety breadth. For further development of treatment and understanding of the effects, we want to follow up the clinical practice with research,” said Radovan Hřib, MD, Head of the Pain Management Centre of the Anaesthesiology and Resuscitation Clinic of FNUSA and the Faculty of Medicine MU, and added: “The cultivation facility will allow us to have our own, precisely defined material for pharmacological, preclinical or other clinical research without additional huge costs. This includes, for example, new therapeutic forms such as extraction tailored to the patient, the development of other medical varieties of medicinal cannabis, modern forms of drugs with, for example, nanoparticles, etc.”
“Our hospital was the first state medical facility in the Czech Republic to start using medical cannabis. For the first time ever, we also introduced its use in capsules, which are produced by our pharmacy. The cultivation and research is therefore the logical next step,” said the director of St. Anne’s University Hospital Brno Ing. Vlastimil Vajdák. “We hope that in the foreseeable future, with the change of legislation in the Czech Republic, we will be able to use the grown products not only for science and research, but also as medicines. The effort to link the scientific, medical and business strategies of FNUSA and FNUSA-ICRC is one of our strategic goals and the way we want to go,” added Pavel Iványi MBA, LLM, Executive Director of the International Clinical Research Centre of St. Anne’s University Hospital Brno (FNUSA-ICRC).
The combination of clinical and research at FNUSA is ideal thanks to its International Clinical Research Centre. “Connecting our own research cultivation facility to the teams at our research centre brings countless research opportunities literally under one roof. This connection and the guarantee of standardised material for our own research, in addition to the possibility of applying the results in practice, i.e. with patients, is even unique in the world,” emphasised MVDr. Václav Trojan, Ph.D., Head of the Clinical Pharmacology Unit of the International Clinical Research Centre of FNUSA.
The hospital already has a special permit to handle plants with high THC content. The cultivation plant is now in trial operation. “The cannabis grown must be of pharmaceutical quality. For example, there must be no introduction of infection from outside. Workers must observe strict hygiene measures, the possibility of pathogens being transferred from clothing or hands is a major risk. This is one of the reasons why only a very limited number of people have access to the growing areas,” explained Václav Trojan, adding that it goes without saying that no pesticides or other substances are used to promote plant growth or yield. “We have chosen a basalt wool growing system with drip irrigation control. There is also precise monitoring and control of all external factors – light, heat or humidity. We will be able to fully control and monitor the growing equipment online and remotely.”
The actual operation of the grow room is one part of the cannabis research. Scientists will investigate the effects of external conditions on the growth of the plants or the actual production of content in the inflorescence. “The extract obtained is actually a mixture of active substances from the cannabis plant. Some of them like THC have detailed effects. But what about the others? Scientists are working hard to isolate the substances and study them separately. For example, CBD cannabidiol is of great interest for its regenerative properties after exertion. Research into the preclinical part, i.e. the possibility of processing the flower for other forms of application, will also be carried out in the pharmacy areas of our clinical pharmacology unit. There are a number of methods of extracting the contents – mechanical, by organic solvents or through carbon dioxide. The extract obtained is the basis for the preparation of creams or suppositories, for example. There are many possibilities, and our research will be able to map everything thoroughly thanks to the cultivation facility,” summarises scientist Václav Trojan.
The substances extracted from cannabis, or mixtures thereof, will be tested first on cell cultures by scientists from the International Clinical Research Centre at St. Anne’s University Hospital. “The road to a clinical trial is very long for substances that are expected to become medicines. For dietary supplements, which include CBD cannabidiol, for example, it is easier. That’s why a clinical trial with CBD substances and CBD nano-forms will take place this autumn. It involves monitoring one parameter in 30 volunteers. The whole process from the preparation for the study to its completion takes a year,” added Václav Trojan. “The main goal of the whole research is the development of cannabis treatment. It has many unexplored areas and so far also many poorly scientifically based promising results. The most elaborated is the treatment of pain, but the use in neurology or dermatology also seems very promising. The question of research is definitely not a question for one “summer season” but a comprehensive development of the whole scientific discipline on the cannabis plant,” added Radovan Hřib.
Day in the life of Research Scientist – Sofia Morazzo
A typical day starts with going over the experimental planning of the day, and then starting the experiments or data analysis, studying, or writing scientific papers. There is some flexibility and some level of control over your day. However, all experiments are very time-consuming and require a constant level of attention to detail, keeping track of your timings, and great planning. Almost every task is time-consuming, from planning the experiments, to doing them, redoing them, analyzing the data, and so on. It is common to be doing more than one experiment at a time and so sometimes the juggling can go wrong.
My research is focused on studying the molecular mechanisms in the invasion process of breast and lung cancer. In research, we each focus on a very narrow subject, on a specific group or even just a single protein, and try to determine the impact it has on different cellular processes. This helps us find new diagnostic tools, new treatments and potentially even cures.
I, personally, work with different techniques, so there is no specific routine, which is something I enjoy. But for instances, a day could be, starting in the morning with taking care of orders necessary for my research and replying to emails. Then I would go to a laminar flow hood to work with my cell cultures, either to maintain them or to perform experiments on them. After the experiment is done, I could extract protein from my cells, then do protein quantification and prepare the samples to run on what we call gel electrophoresis or Western Blot.
After this experiment is done, I would block and incubate the resulting membranes to evaluate the next day. Other times the experiment could be to fixate my cells and incubate with specific antibodies to visualize using a confocal microscope. Or I could be cloning my cells with specific genes and then tracking their effect using live imaging or some biochemical assay. Other times I will be receiving training in either some specific equipment or technique or in overall topics specific to my fields through webinars and conferences.
Working overtime is also very common and when working with living disease models (cell cultures, mouse models) working the weekends is also normal.
It’s also busy, hard work, and a lot of stress due to the constant stream of deadlines but also rewarding and exciting when you finally get some nice results and definitely always a nice challenge. The great part of doing research is to satisfy curiosity and the challenge of figuring out how to get the answers you seek.
Sofia Morazzo (in the middle) and Molecular Control of Cell Signaling Research Team.
Research on the use of senolytic drugs to treat liver disease has shown an unexpected increase in disease severity.
Manlio Vinciguerra, Ph.D., MSc, the head of the Epigenetics, Metabolism and Aging research team at International Clinical Research Center of St. Anne’s University Hospital Brno (FNUSA-ICRC), collaborated with colleagues from other institutions to publish a study on the use of senolytic drugs dasatinib and quercetin (D+Q) in targeting obesity and age-dependent nonalcoholic fatty liver disease (NAFLD) in mice xenografted with human hepatocellular carcinoma (HCC) cells.
NAFLD affects more than 25% of the population and is the most common chronic liver disease. It poses a challenge in both prevention and treatment and can lead to the development of fibrosis, cirrhosis, and even HCC, which is the main cause of cancer-related deaths.
The study used senolytic drugs, which target and eliminate senescent cells. Senescent cells are those that have permanently stopped dividing but did not die. While senescence is essential for many functions such as homeostasis or limiting tumor growth, many studies have already shown that when senescent cells accumulate, they can become harmful to other healthy tissues. “In the context of liver disease progression, the concept of selective elimination of senescent cells using senolytics holds a great therapeutic potential,” states Vinciguerra, as the use of senolytics presents a promising way to treat not only NAFLD but also many other age-related diseases.
The results have shown that the specific combination of (D+Q) used to treat NAFLD in mice has unexpectedly led to a mild increase in the severity of the disease, and the study thus concluded that the combination of senolytics used was ineffective in the treatment of NAFLD-caused HCC. “While elimination of some senescent cells is beneficial for healthy aging and overall lifespan, it is very important to identify which senescent cells are targeted by specific senolytics and their overall effects on health span,” explained Vinciguerra.
You can find the study here:
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Significant award for Giancarlo Forte
On Friday, June 25, Giancarlo Forte was bestowed upon the title of Cavaliere dell’Ordine della Stella d’Italia (Knight of the Order of the Star of Italy) from the Ambassador of Italy, H.E. Mr. Francesco Saverio Nisio. This award – the second highest civilian commendation in Italy – is given as a special recognition of merit in promoting friendly relations, promoting Italian prestige abroad and cooperating with other countries.
Giancarlo Forte works at the International Clinical Research Center of St. Anne’s University Hospital Brno (FNUSA-ICRC) for the eighth year. He came to the Czech Republic from Japan, where he worked in one of the largest research centers, the National Institute for Materials Science. In FNUSA-ICRC, he built the Center for Translational Medicine, which operates in the premises of Biology Park Brno.
He is the principal investigator of the research team Mechanobiology of Disease. In his work he deals with the properties of stem cells, which have the potential to replace and regenerate damaged tissues, and can be used in the treatment of serious cardiovascular, metabolic, neurological and oncological diseases.
During the coronavirus pandemic, he and his team actively participated in research related to COVID-19. Part of his team helped set up and participated in the testing activities of the covid lab. Moreover, thanks to contacts in his native Italy, Brno scientists helped test nanotray filters and determined their permeability for certification purposes, as Italian laboratories were overwhelmed by testing and evaluating samples.
During the ceremony, held at the Institute of Italian Culture in Prague, Dr. Forte and his group gave as special present to the Ambassador: they printed a high quality microscopy picture of human stem cells, which rwe elaborated as to recall the colors of the Italian flag. The gift was highly appreciated by the Ambassador.
Congratulations to Giancarlo Forte and we wish many more successes!
The Saste Roma project will teach not only Roma how to take care of their health
How to improve health not only in excluded localities is solved by the project Saste Roma (Healthy Roma), which started in the International Clinical Research Center of St. Anne’s University Hospital Brno. The three-year project aims to increase health literacy about the most serious diseases and a number of experts across the Czech Republic are involved in its solution.
The average life expectancy for Romani men is 57 and for Romani women 65 years. This is approximately 18 years less compared to the majority population. Compared to the majority of the population, Roma also suffer twice as often from multiple diagnoses (more than one serious disease). It is often due to ignorance of how to take care of their health, lack of information and support for lifestyle changes or shyness from visiting a doctor. This should be changed by the Saste Roma project aimed at the prevention of serious diseases in excluded localities, the most frequent inhabitants of which are the Roma.
The result of the almost three-year project will be a number of educational tools, from information brochures, through cultural events, educational e-learning, to a mobile application. “The project will focus on the development, implementation and evaluation of a multi-year health campaign in excluded localities. We will cover the most serious diseases, whether cerebrovascular, cardiovascular, oncological or mental illnesses, “explained Hana Maršálková, head of the Saste Roma project and head of the Public Health group within the Cerebrovascular research program that implements the project. “Online tools, applications and awareness-raising events will also be available and usable for the general public, and we also dedicate a special part to schoolchildren,” added Maršálková.
An expert team is working on the outputs, which now includes about 40 experts from the ranks of doctors, sociologists, educators, health marketing specialists and experts on excluded localities. A number of institutions also took part in the project – several clinics of the St. Anne’s University Hospital Brno, the University Hospital Brno or the Masaryk Memorial Cancer Institute. An important factor of success will also be the involvement of field workers from the State Health Institute, the Regional Hygiene Station or organizations supporting Roma communities.
“Every project focused on the health of the population in socially excluded localities is very much needed and the positive effects on the health of the population are also reflected in the overall improvement of the social situation,” confirms the importance of the project MUDr. Marie Nejedlá, Head of the Public Health Support Center of the State Institute of Public Health. Dr. Nejedlá and her team of field workers will ensure the dissemination of the project’s educational tools directly in the target communities.
“The project will be complemented by a questionnaire survey in the target areas, which map the knowledge and attitudes of the population and also verify how effective the health intervention was. Thanks to the scientific approach, we want to ensure that the project and its follow-up activities will be as effective as possible, “concludes Professor Robert Mikulík, expert guarantor of the project from the St. Anne’s University Hospital Brno and guarantor of the cerebrovascular diseases section.
The Saste Roma project – Developing health in excluded localities is financed from the EEA Funds 2014-2021, project no. ZD-ZDOVA2-002.
The involvement of the SZÚ takes place within the project Effective support of the health of persons at risk of poverty and social exclusion OPZ ESF, reg. No. CZ.03.2.63 / 0.0 / 0.0 / 15_039 / 0009439.
Programming for research – Ondřej Vávra and Jan Štourač
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 Štourač 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.
Jan: In my case, it’s more IT than biology or work in laboratories… I started programming in elementary school, my first programming “language” was Baltík and his simple programming of the wizard by graphical chaining of actions. At the gym I was a classic webmaker, so HTML, cascading styles, JavaScript, then PHP, SQL and in high school in the Pascal seminar. Currently, it’s mainly Java for more complex applications and Python as a fast prototyping language.
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.