Young PIs in action: Interview with Iro Tsipa

In our next post of our young PI series, I had the pleasure to interview Iro Tsipa, who will shortly start in her new role as as a Lecturer in Environmental Biotechnology at the University of Cyprus.

Kostas Vavitsas: You recently moved to Cyprus from the UK and you are going to start your own lab very soon. What are the most striking differences between the two research environments?

Iro Tsipa: In the UK, I was working in a world-leading institution, Imperial College London, and in a cutting-edge research centre, SynbiCITE. So, the research could run smoothly in terms of support in equipment and consumables, communicating ideas, being able to attend and participate in conferences.  In Cyprus, these are not for granted, I had to prioritize the tasks in the projects I participate in, as the budgets are much lower. I feel more responsible for the choices I make. This was quite challenging in the beginning but now I understand better the priorities of a lab and a project and it helped a lot to be prepared for my next job.


Kostas: Do you feel prepared to start your new role?

Iro: I’m very excited to start working as a PI, have my lab and contribute to realistic solutions for environmental bioremediation and bioprocessing. I feel prepared about that. It seems like a natural next step to my academic career. The main challenges are: (i) get funded to be able to have the necessary equipment and working environment, (ii) find young people who share the same passion for environmental biotechnology to make a strong team and (iii) make a multi-disciplinary network of partners and collaborators who appreciate science to share ideas and try to answer key scientific questions.


Kostas: What is the true potential of environmental biotechnology and synthetic biology? Any interesting application that came up recently or will be out soon?

Iro: Environmental sustainability is at the core of the challenges of synthetic biology community. Engineered microbes and synthetic microbial consortia can substantially assist in limiting CO2 levels, recovering phosphorus, bioremediating and biodegrading resistant and toxic compounds that natural strains cannot process (yet)… Plastics and micropollutants biodegradation assisted by engineered microbes is an interesting field of emerging concern, which has attracted attention in recent years. Further, bioprocessing is a bottleneck in synthetic biology. We recently submitted a paper with my academic mentor, Sakis Mantalaris, and close collaborator, Gizem Buldum, of a kinetic model of synthetic genetic circuits predicting product formation towards microbial cell factories bioprocessing. I hope that this project will provide a different point of view of mathematical modelling and process intensification in synthetic biology.

Kostas: What is the single most important piece of advice you would give to an early career researcher in synthetic biology?

Iro: I would say ‘follow your own path’, find what fascinates you the most based on your background and knowledge, do your own research in the literature and start building on. Also, perform a thorough research of which groups work on similar projects and try to be inspired. Research and science are based on team efforts which can result in a great individual result.


In August 2019, Argyro (Iro) Tsipa will start working as a Lecturer in Environmental Biotechnology in the Department of Civil and Environmental Engineering and Nireas International Research Centre, at University of Cyprus.Currently, she has been a Senior Researcherin the Department of Environmental Science and Technologyat Cyprus University of Technology. She obtained a Diploma in Chemical Engineering from the National Technical University of Athens, an MSc in Chemical Engineering with Biotechnology from Imperial College London where she also got her PhD in Bioprocess Systems Engineering. Before her current appointment, she worked as a Research Associate at the UK’s National Innovation and Knowledge Centre for Synthetic Biology (SynbiCITE) and the London DNA Foundry. Iro is considered as an expert in transcriptomics and proteomics. She has been instrumental in developing an integrated experimental-modelling framework to design optimal bioprocesses with applications in Industrial and Environmental Biotechnology, and Synthetic Biology. She developed and is responsible for the molecular biology facility of her current lab and the OzoneBioPro project developing a hybrid ozonation-bioremediation treatment of drill cuttings of the drilling operations in Cyprus.


Young PIs in action: Interview with Kaspar Valgepea

Our next blog in our Young PI series features Kaspar Valgepea (lab website), a group leader from Tartu University (and old lab mate of mine at the University of Queensland).

Kostas Vavitsas: You have worked both in academia and in the industry. What do you miss and what you don't miss from working in a company such as Genomatica?

Kaspar Valgepea: My work experience in Genomatica was a bit special, as I was there as a Visiting Scholar and I ran an independent project. Thus I did not exactly have “corporate” deadlines, which maybe let me work under less stress. Nevertheless, the momentum of work and research in such a fast-growing biotech company was impressive and addictive in a good way. I greatly enjoyed working together with highly ambitious and professional people who had the highest goal: to make biology work for mankind. My co-workers, but most importantly the work atmosphere at Genomatica, truly inspired me to dream big and set the highest goals.

One thing that I do not find in academia is this special teamwork atmosphere where a significant number of people are all working towards one single goal. There is nothing I can think of that Ireally don’t like in the industry, but I would say that one benefit of academia is the freedom to be curious and investigate things that might not necessarily lead to near-term financial gains.

Kostas: Biotechnology and synthetic biology have set high expectations on potential applications and societal impact. Where do you see the field in the next 5-10 years?

Kaspar: Indeed, biotech and synbio have set the bar high but I am optimistic that they will deliver! I think we need a few more breakthroughs that are obvious for both investors, science funders, and people in general to kick-start the snowballing effect. The revolution has clearly started, just last week I felt great when I found out that there is a company in Estonia that is making biodegradable plastic bags from the 1,4-butanediol produced by the Genomatica process! And there will be an increasing push towards sustainable solutions, in terms of biotech, for chemicals and fuels due to climate change. Europe has set several ambitious goals recently, e.g. the new Renewable Energy Directive, single-use plastic ban, waste recycling etc. These actions are essential to fast-track innovation both in academia and industry.

One focus of Kaspar’s research is systems biology of gas fermentation, recently exemplified in a Cell Systems paper (DOI:  10.1016/j.cels.2017.04.008 )

One focus of Kaspar’s research is systems biology of gas fermentation, recently exemplified in a Cell Systems paper (DOI: 10.1016/j.cels.2017.04.008)

I am personally most excited about the idea of seeing waste as a resource for its conversion into sustainable fuels and chemicals through bioprocesses. I am obviously biased, but I see that gas fermentation technologies for capturing waste and renewable carbon have a huge potential. LanzaTech is proving this by currently operating one and building four industrial scale plants world-wide. There are many other examples and exciting fields, I highly recommend the recent Economist story on synbio for a good overview.

Kostas: What was the biggest challenge you had to face in your professional life so far?

I think things have worked out quite smoothly for me so far. I was lucky to be invited to join the unique lab of Professor Raivo Vilu during my Bachelors in Estonia, and enjoyed working there a lot until my PhD with a few stints abroad in between to the US and Japan. For a postdoc, I searched around quite intensively and it paid off. My postdoctoral experience at Esteban Marcellin’s lab at The University of Queensland was probably as good as it gets, for me at least. I think these steps paved a good way to the startup of my own lab back home in Estonia with help from Professor Mart Loog. And this startup I have been doing since March is surely the biggest challenge I have faced. I have to set up an experimental lab basically from scratch, hire people, start innovative projects, collaborate with industry... a lot on the plate. We will see in about four years how did I do. I am super excited to have this privileged and great opportunity. Fingers crossed that I can transform this excitement into creating a lab where people want to work and can do cutting-edge science!

Kostas: How easy was it to transition from postdoc to PI? Was as you had imagined it?

Kaspar: As I said above, the transition went quite smoothly. I thought it would be harder but it might have turned out smoother due to a few things. First, I started thinking and planning about post-postdoc during the first half of my postdoc. This might help you to have a clearer vision about potential trajectories early on, so you could react faster once options pop up. Second, I was networking and keeping old contacts active in light of potential future research options or collaborations. These two things likely had an important effect on me being awarded two personal research grants and on being selected as the group leader of the ERA Chair in Gas Fermentation Technologies.

Kostas: If you could change one thing in your career trajectory, what would it be? What is the single most important piece of advice you would give to an Early Career Researcher in synthetic biology?

Kaspar: I was happy to conclude that I would actually not change anything! If research at the first lab I worked in in Estonia had not been that exciting, I would have potentially went to do MSc or PhD abroad. I did not do that as I believed that exciting research will lead into results and these are more important later than “just” having more locations on your CV.

My advice for an ECR would be to dream big and then work towards that dream as hard as possible while maintaining work-life balance. If you are passionate about it and enjoy it all along, I think you are all good.


Kaspar Valgepea is leading the ERA Chair in Gas Fermentation Technologies at the University of Tartu that employs gas fermentation technologies together with systems and synthetic biology methods to address global challenges of biosustainability

Young PIs in action: Interview with Amanda Jarvis

In the next post of our young PI series, Jo interviews Amanda Jarvis from the University of Edinburgh.


Jo Sadler: You are working at the interface of biology and chemistry. Do these two disciplines talk well to each other?  

Amanda Jarvis: I think that depends on which area of the interface you focus. There has been a long tradition of medicinal chemists collaborating with biologists, and I think that works well from what I see on the outside. In catalysis there is less history of talking across this interface, and there are language barriers – words such as ligand have different meanings and chemists talk in TON/TOF whereas enzymologists talk about kcat and Km. When you have scientists who are really interested in bridging the divide, the disciplines can talk well with each other, but mutual respect, interest and vision helps a lot.


Jo: How can we better integrate practices in interdisciplinary research?

 Amanda: I think, for each discipline,having an awareness of what knowledge they assume is important, and making sure that acronyms, specialist techniques etc are explained when talking to an interdisciplinary audience would help a lot.  This is also great for including younger members of the audience, or those from different subdisciplines, who may not have come across those techniques and terms. I think encouraging openness, curiosity, and creativity in teaching at all levels is vital for interdisciplinary research. As is creating an environment that brings people together (joint meetings, networks, places for informal meetings on campuses etc).


Jo: What can artificial enzymes do better than the ones found in nature?

Amanda: It is not so much they will be better, but that artificial metalloenzymes can do reactions that nature has never evolved to do. Introducing unnatural metal sites will, I believe, open up numerous possibilities for catalysis, biomaterials and novel healthcare approaches, that go beyond what just chemistry or biology can do alone.


Jo: How did you find your transition to PI?

 Amanda: In some ways the transition to PI was very similar to what I had been doing as a senior postdoc, except with more grant writing. I had been coordinating a subgroup within my previous group, which involved group management, recruitment and finance decisions. For the last few months all this this was taking place after my supervisor moved to Germany.

However, this doesn't mean there haven’t been challenges. A big one has been how to divide my time between lab work and applying for funding, as well as teaching, and admin, and making sure I keep up with the literature! Another challenge has been recruitment – how to find PhD students and postdocs who are interested in interdisciplinary projects and have the skills and background needed. As a small group working at the interface of chemistry and biology there are a lot of skills I am looking for but it is hard to find that in just 1 or 2 people, so working out what is the most important skill needed now and trusting I will be able to hire more people later has been important.


 Jo: What is the one most important piece of advice you would give to an early career researcher who aspires to become a group leader?

Amanda: If you have an idea, go for it, don’t feel you have to wait until you have 3 years’ experience or 10 papers. The process of writing a proposal really helps you focus on your ideas and what more experience\training you will need to get where you want to be. Conversely if you worry that you don’t have any ideas, start small and see where your reading takes you.

I would also say enjoy it and be curious, if there is a scientist who you admire and would like to go and work for, contact them. The time between PhD and PI is where you have the opportunity to explore and there are lots of fellowships that will allow you to work with the groups you want, regardless of what you might do in the future.

Amanda Jarvis.jpg

Dr Jarvis started her independent career at the University of Edinburgh as a Christina Miller Research Fellow in 2017, and has recently been awarded a UKRI Future Leaders FellowshipPrior to this she studied and worked in the UK, France and Canada. She graduated in 2007 from the University of St. Andrews with a Masters in Chemistry and then went on to receive a PhD from the University of York under the supervision of Professor Ian Fairlamb.  Amanda then joined the group of Dr Philippe Dauban (ICSN, Gif-sur-Yvette) as a postdoctoral research fellow and worked on the development of Rh(II)-catalysed nitrene reactions.  In 2013, she moved to Professor Paul Kamer’s group to work on sustainable catalysis, and subsequently received a Marie Curie Individual Fellowship to continue working in Professor Paul Kamer’s group on Artificial Metalloenzymes for the Oxidation of Alkanes (ArtOxiZymes).

Young PIs in action: Interview with Arren Bar-Even

For the next instalment of our young PI series, we interview Arren Bar-Even from the Max Planck Institute (Potsdam-Golm)

Kostas Vavitsas: You are working on redesigning carbon fixation and photosynthetic reactions. Do you think that we can we really improve photosynthesis?

Arren Bar-Even: That is a good question, and the answer is not very clear. There are indications that modifications in both the light and dark reactions can increase certain aspects of photosynthetic efficiency. For example, if we tamper with photorespiration, productivity can increase in crop plants, as reported recently by South et al.

The real problem is that generally we can not transfer observations and insights from one organism to the other, or even from one condition to the other. The main issue is that we don’t really know the precise metabolic and physiological mechanisms. Again in the example by South et al, they claim that the increase in crop productivity is due to the local increase in carbon dioxide. But every model we have run disagrees with this as the full oxidation of glycolate is highly counterproductive, so the reasoning for the observed increase in productivity upon expression of the pathway might be different than the one suggested.

Generally speaking, the high complexity of plants - as compared for example to bacteria - make them behave in an almost chaotic manner upon modification, that is, small modifications can have a substantial impact that is very difficult to predict. This makes many of the observed results difficult to interpret or repeat.

KV: Modern research is interdisciplinary. Do you think the way Universities and research institutes are structured facilitates this kind of research?

ABE: My first answer would be no. My research approach is dependent on close inteartion between biotic and an abiotic systems. Hence, I’m involved in multiple collaborations with chemists. I established this on my own without institutional support.

I think collaborative research is not built into the system. That is especially true within the Max Planck Society, where every Institute focuses on a very narrow research field. Universities might be a bit different, as they harbour multiple departments. However, people tend to stay in their field and within their comfort zone.

I must admit that I don’t know how this can be improved in a systematic manner. But I encourage researchers to seek interdisciplinary collaborations and not focus only on their day-to-day research and short-term outcomes. The benefits might be long-term, but keep in mind that such collaborations can substantially contribute to your research.

KV: How was the transition from a PhD student to a PI? Was it as you had imagined it?

ABE: The transitions was actually as I had imagined it. There was a lot of work and the amount of stress definitely increased. But in a way it is “my” fault, as I decided to run a big lab and multiple ambitious research goals. I could have stayed small, but I chose otherwise. What I maybe didn’t expect is the extent by which such continuous work erodes you over time.  

KV: What was your biggest professional challenge?

BE: I would say the biggest challenges come from the research itself. I set ambitious goals and they are not easy to accomplish. Besides research, I would say the workload. There is always a huge amount of stuff to do and issues to deal with.

KV: What is the one most important piece of advice you would give to an Early Career Researcher in synthetic biology?

ABE: Generally speaking, you need to find the right balance between identifying and focusing on one or few research fields in which you can become the expert and spreading out to avoid being dependent on the success of a single project. Finding this balance is tricky...


Arren Bar-Even completed his Bachelor studies at the Technion, Israeli institute of technology, as part of the excellence program. He completed his Masters studies in the Weizmann Institute of Science (Israel) in Bioinformatics. At 2012 received his PhD from the Weizmann Institute of Science in Biochemistry. In 2015, he established the “Systems and Synthetic Metabolism” lab at the Max Planck Institute of Molecular Plant Physiology as an Independent Research Group Leader.

The answers were edited for length and clarity

Young PIs in action: Interview with Pierre Crozet

For the next blog in our Young PI series, we interview Pierre Crozet from Sorbonne Université in Paris, Frence.

Kostas Vavitsas: What is the biotechnological and synthetic biology potential of microalgae, and why did you choose to work in this area?

Pierre Crozet: As you work in the field, you have a few answers of your own, but I will try to answer with a twist. I want to work on photosynthetic organisms, for all the advantages you can imagine. There is a strong focus on the community on plants for agriculture, but in photosynthetic algae you can do more. Chlamydomonas has a bigger potential to answer biological questions and do synthetic biology. So plants can provide food, and algae could do anything else.

And here is the twist. I come from an Arabidopsis research background; Arabidopsis is easy to work with but slow to grow. Transitioning to algae was great! The algae synbio community is still small and the European GMO legislation is not very helpful, but we’re getting there. See for example the strong algae research by ExxonMobil; I think that practical applications are coming soon!

KV: How was the transition from postdoc to Associate Professor? Was it as you had imagined it?

PC: No, it was totally different. I have to note that technically I am not a PI, in the French system an Associate Professor is normally not a group leader. However, I have a significantly higher level of independence as I am the leader of my projects and already co-supervising a PhD student.

Well, for the first year in my new position I didn’t even touch a pipette. I had to do admin, write grants, teaching, teaching, and teaching. There is a lot of hidden administration work that PhD students and postdocs never see. So the nature of my job has changed.

But not all changes are bad. The interaction with the society is different, you are no longer a postdoc and people start contacting you – like you guys did – to draw on your expertise. For example, I am at the scientific advisory board of a startup biotech company named Neoplants, a position I think I wouldn’t have without being an Associate Professor.

KV:You emphatically mentioned teaching as a major part of your work routine. Do you find it a hindrance to your research role?

PC: Look, I love teaching. I never pictured myself in any other role other than professor. I wouldn’t exchange this position with anything else – maybe a full Professor position!

I really value the time I spend with the students. But teaching has more to it: administration work, marking essays and exams, preparing lecturing content… I could do with less of that.

Teaching has some benefits to the teacher. It forces you to see outside the box, and gives an incentive to improve your knowledge, especially when you are teaching something you feel unqualified for. For example, I had to train engineers in food and feed industry. As the subject was not within my immediate field of expertise, I had to become competent.

Last but not least, teaching makes you feel that you are making a difference to your students’ lives. You interact with them, you help them make a career, and some of them might choose to join in your lab for projects or research positions.

KV: And speaking of mentorship, what is the one most important piece of advice you would give to an Early Career Researcher in synthetic biology?

PC: Do what you like! This is the only important thing, do it for real and never give up!

Pierre Crozet.jpg

Pierre is interested in the molecular mechanisms allowing Plants to adapt to stresses. One of the major integrators of these environmental cues is the SnRK1 complex that allows maintenance of energy homeostasis. He studied its complex post-translational regulations that allow specific signal transduction during both his PhD at Université Paris-Sud, France, with Martine Thomas and Jean Vidal, and his postdoc at Instituto Gulbenkian de Ciência, Portugal, with Elena Baena-Gonzalez.

Since 2016, he shifted towards Synthetic Biology of carbon fixation in Chlamydomonas aiming at making this alga a better chassis to study the Calvin-Benson Cycle regulation through synthesis. He joined the team of Stéphane Lemaire and was appointed Assistant Professor in 2017 at Sorbonne Université to continue his work on developing Synthetic Biology in microalgae.

The answers were edited for length and clarity.