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An interview with Kildare Miranda

Posted by , on 10 May 2022

MiniBio: Kildare Miranda is the director of the Advanced Microscopy Unit and vice-director of the National Centre for Structural Biology and Bioimaging (CENABIO), Professor of Biophysics and Cell Biology and Head of the Cell Biology and Parasitology Department of the Biophysics Institute at the Federal University of Rio de Janeiro, and holds several CNPq fellowships. He did his PhD at the Federal University of Rio de Janeiro, and postdoc at the University of Konstanz, Germany and Georgia, USA. His research work focuses on structural biology and physiology of organelles found in protozoan parasites. He divides his time between scientific research, network development for Latin American Bioimaging community, and creating teaching programs for the next generation of microscopists. He also presides the Interamerican Committee of the Societies for Microscopy (CIASEM), which is bundle Microscopy Societies from North, Central and South Americas.

Brazil has a long-standing history of contributions to science both, in Latin America and world-wide. It is the land of scientists as renowned as Carlos Chagas and Oswaldo Cruz. It is also a country of fascinating biodiversity, attractive the whole world around. Before becoming a scientist, were you aware of this heritage? Was this something that inspired you to become a scientist?

For me this really happened in two phases. Firstly, I have an uncle who was a professor at USP (University of São Paulo). He is very famous here in Brazil – perhaps you remember a book on histology called ‘Junqueira and Carneiro’? Carneiro is a cousin of my father’s. So in my family there was already great awareness regarding science. Perhaps at the time I didn’t know what scientific research and publications meant, but I knew about the book! This book was translated to various languages, and used worldwide. When I chose my bachelors, I wasn’t sure if I wanted to be a physician or a scientist. My uncle was a physician. Around that time, he became aware of the creation of a new University which was really focused on scientific research. So he told me about this, and I decided to go to this University. The second phase started when I got there: I became very interested in cell biology. The leading group of cell biology was actually a group working on infectious diseases. All the part about ultrastructure and cell biology was applied to investigate T. cruzi, Toxoplasma gondii, and other pathogens. So my entry into the microscopy world was already directed towards infection biology. In the end I didn’t study medicine! I thought I’d give scientific research a try. During this time my family was hoping I would switch my interests to medicine, but this didn’t happen. I never looked back or wondered whether I had made the right choice. I received a fantastic education as a scientist.

You have a career-long involvement in microscopy and infectious diseases. What inspired you to choose this career path? 

About a direct interest in infectious diseases, this was more of an accident. Of course I was familiar with Carlos Chagas and Oswaldo Cruz, but what interested me first was the structural organization of the cell. I was a young man and the philosophy of the lab I joined was that people were responsible for their own projects, independently of their position in the lab – so since I did ‘Iniciação científica’ I had several responsibilities in the lab: do cell culture, do several experiments, use the microscopes. As a young student I was already using very sophisticated electron microscopes- perhaps the most sophisticated biological electron microscope in the country at the time was in this lab. The main research line in the lab was ultrastructure and cell biology applied to parasitology, and host-pathogen interactions. We also focused on anti-parasitic chemotherapy. So, I ended up entering the parasitology area as an accident really.

Brazil has renowned and historical institutions dedicated to research (and microscopy). Can you tell us a bit about what you have found uniquely positive about becoming a researcher in Brazil, from your education years?

I think the education in Brazil has a very strong experimental component, especially during the ‘Iniciação científica’. The novel things I learned as a graduate student or as a postdoc or PI, are relatively few compared to the immense knowledge I acquired during my ‘Iniciação científica’. During this period of my career, I had access to everything available at the time: immunogold labelling, analytical microscopy, cryo-methods, etc. By the time I started my masters degree, I was independently doing experiments. For me this early stage of my career was pivotal. I was also lucky to have been in such a strong lab. I had a supervisor, Prof. Marlene Benchimol, who was as concerned about her students having a solid education as about advancing their research project per se. I believe this always depends on the supervisor. Some supervisors get students to do the ‘dirty work’ – some trivial or boring task that no one else wants to do. This was not my case. Even if my project advanced more slowly, the main focus was on me learning and having a solid basis. This was very important for me. Now as PI I try to replicate this: everyone in my group is responsible for their own projects and I give them space to learn a lot.  

Throughout your career you have belonged to various world-renowned centres of microscopy? Can you tell us a bit about how did this shape you as a microscopist both at home and abroad?

In Brazil there is a very heterogeneous distribution of resources, and this is reflected in the microscopy infrastructure. A while ago we published a study where we mapped the microscopy infrastructure and expertise in Brazil. We have over 700 electron microscopes around the country, but there is a huge concentration in the region South and Southeast. So, during my education I was lucky I was in one of these big centres in this region, where I had access to many different techniques, some of which were very sophisticated. Another thing is that in biology, there is a tendency for scientists to show some ‘tropism’ or attraction towards understanding biological phenomena, rather than instrumentation. In this context, I was actually equally attracted to understanding and developing instrumentation. I used to fix microscopes, develop and adapt small tools, etc. This helped a lot in my education as a microscopist. Unfortunately, in many areas of the country we are more ‘consumers’ of technology, rather than creators.

Now as a leader, I noticed that many places have some sort of ‘jealousy’ over the equipment and its users: they don’t allow all users to learn and use the equipment. I think this is a very shorth sighted vision. As a scientist, I think it is important to facilitate this access. The net outcome is always positive. In places where access exists, this is fantastic.

You now lead a world-renowned centre of microscopy (at CENABIO). Can you tell us what your day to day job is, and the role that microscopy plays?

            Currently, we are working towards establishing a fair integration of technicians in microscopy. We are discussing the career opportunities for imaging scientists (what the career and portfolio means), and putting a lot of effort towards training technicians and platform members of staff, both at national and Latin American level. We recently approved at UFRJ a graduate program called Technologies for Bioimaging and Biostructure. The idea is that a professional graduate (masters and doctoral) program will allow students to learn about the technical parts of an imaging career, as well as interacting with industries and other sectors related to microscopy. This is an area that is gaining momentum in the world. Recently we won a grant from the CZI which is mainly focused on strengthening the Latin American Bioimaging community. One of the main challenges is to convince people (early career microscopists or imaging scientists) that this investment (training, specialization) is worthy of funding and worth embarking on. A good microscopist will never be out of a job. The idea is to strengthen this career within institutes. Currently the only open option is to become a PI for someone who is interested in instrumentation and research. In Brazil, some institutes have solved this: the career of a technician is the same as that of a regular researcher, with different responsibilities. It’s the same salary range, but different positions. In some Universities this is still not the case: a microscopy technician will earn half of what a PI does. This has to change urgently and we hope that, if we are successful, this may bring recognition to the career of microscopist, and stimulate this career. For instance, there is a member of staff here who is exceptional. He went to a course in Campinas to learn about non-linear optics, super-resolution microscopy, CARS, etc. Then he came back here and added his certificate to his portfolio on career progression, and it wasn’t accepted because his career is technical/administrative. If he had instead attended a course on dactylography, it would have been accepted. This has to change. We are trying to generate mechanisms that value this career in terms of salary, career opportunities, etc.  

            Regarding the CENABIO, the idea arose of unifying the major equipment in big platforms. In the past, equipment belonged to one specific group rather than being centralized. The design was not made for the usage to be multi-user based. At some point, colleagues including Wanderley de Souza,  Jerson Lima, Antonio Carlos Campos de Carvalho, decided to bring together all this equipment in a single centre. When I arrived here to the place where the Advanced Microscopy Unit now stands, it was a football field. We already had the centre for macro-molecular characterization by NMR, there was a site assigned for animal imaging, and microscopy was the last building to be built. At this point I joined this loop. The idea was to remove the big infrastructure from within individual labs, and make it available to all researchers, especially but not exclusively those that need biological microscopy. Another aspect is that we have a responsibility to make progress: to detect what are new and upcoming technologies. My main job is to look for funding, opportunities, organize training for professionals and scientists: to create this bridge that allows the growth of microscopy within CENABIO. Nowadays, CENABIO has 3 units: macromolecules, animal imaging, and microscopy. Our responsibility is to make progress within each area individually, but also to create bridges between these 3 major areas. The great aim is to be able to analyse a biological phenomenon all the way from atomic level to the whole animal. For instance a pipeline like the following is what we envisage for say, T. cruzi: identify a molecule that could be used as a drug -> collaborate with groups in Chemistry for drug synthesis -> perform experimental chemotherapy -> infect an animal and accompany by bioluminescence -> treat the animal and accompany cardiac lesions or other pathology by nuclear magnetic resonance -> then treat the animal and see regression of infection -> then inject stem cell and see if this regenerates the cardiac fibers. This is a phenomenon across all scales. Our wish is then to do translational research based on these findings.

            While we believe this setting will facilitate research, there is some resistance. There are people who believe multi-user platforms are not so efficient. But this is also being identified. My impression was that some people took longer to realize that multi-user platforms are good business in various aspects: funding is good and projects proposed in this context have good probabilities of being funded. While still asymmetric, there is an effort for improvement in various areas: building centres, improving education, improving funding, etc.

Do you have many opportunities to interact with other Latin American groups, outside of Brazil?

            I have had a chance to work with various scientists from Latin America. The lack of funding doesn’t facilitate these interactions. We had a program from the federal government called ProSul, which aimed to promote interactions between groups of MercoSur. This allowed scientists from everywhere in MercoSur countries to come to the CENABIO. More recently I have had a chance to interact with scientists from Institut Pasteur Montevideo, and the University of Buenos Aires, and discuss the consolidation of the Latin America Bioimaging Network (LABI). This is a movement that has brought about results. The hope is that we (Latin America) become an area of expertise worldwide. We have great people doing great things in our region despite the financial hardship. There’s room for improving interactions still and we look forward to this.  

Having worked abroad, what were some of the things you found to be very different between doing research in Brazil, and abroad?

            I worked in several places abroad. I worked at Konstanz University in Germany. I did a postdoc at the University of Georgia, in a centre dedicated to Global and Emerging diseases. I also visited the University of Duke several times to do analytical microscopy and I also did a short internship at the University of Illinois. In terms of challenges, things seem to be easier abroad. For instance, I recently bought an air conditioning system from my own grant. There is no institutional support for this. I never saw any of my foreign bosses worried about this. This is both resource- and time-consuming here. However, these difficulties teach us a lot. It helps us to have a deeper understanding of the overall effort to keep the structure running, from equipment to protocols. For instance, here we cannot call a technician to fix a microscope and expect they will be in the lab the next day. It takes a very long time. With knowledge and understanding of the equipment, this gives us a lot of flexibility and the opportunity to fix it ourselves.

            At an institutional and governmental level, cyclical funding is lethal: it is very unstable. At various points, however, I lived good financing cycles. The COVID19 pandemic was important to create awareness. CENABIO never closed in this time, because the institute continued to address the needs of various groups as well as from the population. But we do have this worry of keeping the centres up and running, and moving forward, with uncertain funding. During the pandemic, we implemented remote access: people were able to interact with each other and perform research from sites other than ‘on site’. I think this came to stay, and we have to improve this to link the country better. So someone from the Amazonia or further away, with difficulties to re-locate, can have access to this instrumentation. Regarding cyclical funding: last year the federal government did huge financing cuts. We were dealing with funding that was 10% of what we had 10 years ago, so this was a violent cut. This was a plan for scientific destruction. Despite presidential vetoes, the scientific community was able to pass a law that secure science resources. The hope is that in coming years we will have continuous funding rather than cyclical. This would be wonderful.

Who are your scientific role models (both Brazilian and foreign)?

            It’s difficult for me to choose one or two people. During my career I tried to find my bearings relative to positive and negative examples. These days I feel I have responsibilities (as leader) that go beyond research. I dedicate a relative large amount of my time to what I’d call ‘collective work’ or service to the scientific community. For example my first mentor, prof. Marlene Benchimol, dedicated a lot of time to communicate science and train children and young people from school level (primary or slightly older). This is not part of the general research duties, but it’s essential. Prof. Wanderley (de Souza) and I have also done a lot of things together in this aspect: we established the centre in Manaus, in INMETRO, etc. When I was vice-director of a new UFRJ campus next to INMETRO, there was a school (one of the worse in the state of Rio de Janeiro) and we worked on a project lead by Wanderley de Souza that ended up creating a building next to the school, with labs on biology, chemistry, physics and IT for the students at this school. A few years later, a number of students of this school gained entry to the public (State and Federal) Universities. We wanted to make a change. I feel that everyone who dedicates their time for something that transcends beyond their own benefit, is a great role model to me. 

From my personal experience, I have only worked in 2 countries world-wide, where the gender gap in science is not so pronounced: Brazil and Portugal. Was this something that influenced you? How?

            I grew up as a scientist in an environment quantitatively dominated by women. But women were rarely at the top of the leadership chain. I think this is not good. Currently I am also the head of the program of Cell Biology and Parasitology at the Institute of Biophysics. Within our program, until recently, we were 2 men and 9 women (PIs). But the main leader was a man. I think there’s a historical component too. Among the technical staff at CENABIO, 77% are woman. But I have this concern often. In my department, the calls for positions are public, so there’s no way of knowing if the candidates are men or women, but we can see that we were nonetheless able to give equal training. In other areas I also try to keep this balance: every time I organize a symposium, I invite equal numbers of women and men to be speakers. I see also that our community is much more aware of gender inequalities. But I think moving forward, we also have to think of women in positions of leadership, reaching the highest possible ranks. But in terms of opportunities to do research, I think we are doing our best to reach gender equality. [Joking] I personally believe women are better multi-taskers! I think in research, beyond microscopy, this is a differential. Anyway, we are doing baby steps: the next leader of the Brazilian Academy of Sciences is a woman – she is already chosen!

What is your favourite type of microscopy and why?

I love all types of microscopy, but I have dedicated myself various years to multidimensional analytical microscopy. We get samples processed with cryo-methods and localize ion nano-domains within organelles.

What is the most extraordinary thing you have seen by microscopy? An eureka moment for you?

There’s two things for me. During my postdoc, we described a new organelle in Toxoplasma, which forms when the parasite is extracellular (in-between cellular infections). Another eureka moment: within Trypanosomes, we identified ion nanodomains – so instead of having a soup of ions, we see that they organize in clusters: anions and cations form within nanodomains. I was very excited and am very proud of these findings. While this had been hypothesized, we managed to visualize this.

What is an important piece of advice you would give to future Brazilian scientists? and especially those specializing as microscopists?

            We live an environment with metrics (sometimes meaningless): impact factors, etc. I think you should focus on doing a good research job. Don’t let vanity and ego take the lead of what you do. What is it to do a good job? To do it with enthusiasm, with interest, with dedication and rigor. A good job addresses good questions in a systematic way and gets great answers. Forget about having to work with an organism that is of medical relevance because this will increase the impact of your work -this is irrelevant in the big picture– you should do what you love. I’ll give you an example: Linus Pauling published his work on vitamin C in a low impact factor journal. The impact comes from the relevance of the work, not the journal. Worldwide there are already mechanisms in place to address this bias towards journal impact factors- which does not really reflect anything in my opinion. About being a good scientist, I received a good advice from a colleague: if you want to know how good a scientist someone is, ask around.   

Where do you see the future of microscopy heading over the next decade in Brazil, and how do you hope to be part of this future?

            Brazil is a bit behind in the areas of image analysis, and in creating custom-made equipment. CENABIO for instance, does not have a specialist on IT, machine learning, big data management, etc. The current members of staff are experts in one or several microscopy techniques, but perhaps not specialists in ML, AI, and its uses for BioImaging questions. But I do see this is the future. I think these tools will be essential to move forward – it is being slowly organized in Brazil and I think it will result in scientific growth. Currently I am looking for personnel with this expertise and for ways to support this area, which I think is vital. All major centres worldwide are investing a lot in image analysis. Currently we are still very shy in this area.

Finally, Brazil is the largest Latin American country, and one of the largest in the world. Beyond the science, what do you think makes Brazil a special place to visit and go to as a scientist?

I think there are great things about Brazil! Brazilians are very warm-hearted! I remember we were giving a course on cryo-microscopy here at CENABIO and I invited a colleague of mine from abroad. In the last day of the course we were doing a barbecue (churrasco) outside, and he and I were at the microscope. And then one of our colleagues brought in a plate with “linguiça” (sausage) and a beer for him. He almost cried because he said that in his institute he can’t even handle an osmium ampoule because his ID card is administrative – so he doesn’t have access to the labs. We have this aim of being welcoming. Another thing is that we have a rich biodiversity, which gives us incredible models (tropical infectious diseases, for example). To paraphrase a friend of mine, ‘it’s important we know better the bugs before they get to know us’. We have model organisms that are not found elsewhere. The Brazilian biodiversity is a huge attraction for anyone wanting to do science – and this is at various levels. An example I can think of, there is a population in Manaus where a river divides two regions –with tribes living at opposite ends of the river. In one of the ends, no one has oral cavities, and nobody knows why. I think this is extraordinary, because the genetic background is the same. Anyway, I think working here is great!

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