An Interview with Gözde S. Demirer: Plant Genetic Engineering Tools for the 21st Century and Beyond
Dr. Gözde S. Demirer (X: @Demirer_GozdeS) obtained her Bachelor’s degree in Chemical and Biological Engineering from Koç University in Turkey, before moving to the University of California Berkeley for her PhD. There, she worked on the development of carbon nanotubes as tools for the genetic engineering of plants, under the supervision of Prof. Markita Landry. She then moved to the University of California Davis, in the team of Prof. Siobhan Brady, to investigate the response of tomato plants to nitrate and phosphate deficiencies with the aim of engineering better nutrient use efficient crops. In 2022, Gözde started her own lab at the California Institute of Technology in Pasadena as an Assistant Professor of Chemical Engineering.
The diverse research themes of her group all share an engineering-oriented approach aimed at solving the most pressing challenges in plant science and society. One of the primary lines of research is concerned with the development of new nanoparticle-based tools for genetic engineering of plants without relying on Agrobacterium-mediated transformation and regeneration in tissue culture. Another interest of her team is the engineering of plant-microbe interactions in the rhizosphere, through the genetic manipulation of root exudates, to increase the nutrient use efficiency of plants in nutrient-depleted soils. Although much of her research is foundational, Gözde and her team do not lose sight of their overarching aim: contributing to a more sustainable and climate-resilient agriculture.
Carlo Pasini: What fascinates you most about your research? Why did you choose to work at the interface of chemical engineering and biology?
Gözde S. Demirer: Since my undergraduate studies, I’ve always been interested in the biological applications of chemical engineering. I started by working on topics related to drug delivery and ended up working on nanoparticle-mediated delivery for mammalian cells. At that point, I realized that this kind of technologies, which were already quite developed and researched in the biomedical field, were still severely lacking in plants and for agriculture. That’s when I started my PhD studies with Prof. Landry focusing on the cargo delivery and genetic engineering of plants using carbon nanomaterials.
Carlo: Many readers might not be familiar with the use of nanomaterials for genetic engineering. What are the potential benefits compared to the classic Agrobacterium-mediated transformation?
Gözde: There are several aspects where Agrobacterium-mediated transformation falls short: first, not all plants can be transformed with it. Second, Agrobacterium cannot target all plant tissues, such as roots, germ cells, or stem cells. In addition, it cannot deliver any other cargo than DNA, where there is a lot of recent interest in protein delivery. Lastly, Agrobacterium causes random transgene insertion into the plant genome that requires further time and effort for removal. Nanomaterials have the advantage of not being dependent on the biology of the host to deliver their cargo and their effectiveness depends on physiochemical parameters, such as their size compared to that of plant cell walls (they need to be small enough to pass that barrier). Therefore, they have the potential for more universal delivery. They can technically deliver all cargo types to all plant tissues, and they typically do not cause gene insertion when used to deliver DNA cargoes, all of which offers interesting new opportunities. For example, using nanoparticles, we could potentially target CRISPR-Cas DNA vectors or proteins specifically to the shoot apical meristem (i.e. plant stem cells), and then obtain homozygous mutants directly from the seeds of the transformed plants, without the tedious regeneration process in tissue culture and screening multiple generations to remove transgenes.
Carlo: Working in your lab, which techniques would one expect to use?
Gözde: Different topics employ very different techniques in our lab. The projects relating to the engineering of nanomaterials usually start from the synthesis of the nanoparticles (NPs) or their purification from plants, in the case of protein-based NPs that we express in the model plant Nicotiana benthamiana. This is followed by the characterization of these NPs in terms of size, morphology, and surface charge using techniques such as transmission electron microscopy, atomic force microscopy, and dynamic light scattering. Then we load the desired cargoes on these NPs and infiltrate them into the plants, and we validate their efficacy in-vivo using confocal microscopy imaging, qPCR, sequencing, or other relevant techniques.
We also have more biology-oriented projects that employ the usual molecular techniques such as cloning, gene expression analysis, … etc. Recently, we started working on engineering the rhizosphere microbiome and to do that we are using new approaches that we were previously not familiar with, like metagenomics and metabolomics of soil samples and organisms.
Carlo: Have you ever come across any plant-related fact that you found especially intriguing and that has influenced your research interests?
Gözde: Well, when we first started investigating microbiome engineering for better nutrient use efficiency, we found out that plants can release up to 40% of their fixed carbon to the rhizosphere, depending on the circumstances. This to me is a mind-boggling number! And it also hints at the importance of plant-microbe interactions for plant fitness.
Carlo: Where do you see your research going in the future?
Gözde: Concerning genetic engineering tools, I think the challenge is now to develop nanomaterial platforms that are suitable for the stable transformation of plants. Right now, the techniques work well only for transient expression. We are also seeing advancements in the type of nanomaterials we use: when I started as a PhD student, we were using single-walled carbon nanotubes, which cannot be applied at an agricultural scale in field conditions. So, we are now optimizing protein-based biocompatible NPs, which can be produced and purified from plants, and carbon nanodots with easy and scalable synthesis that have a very small diameter (< 2 nm) and can thus easily penetrate the cell wall. Both are easier, more sustainable, and more scalable to synthesize, and less cytotoxic.
In the field of plant-microbe interactions, we are focusing on engineering the plant host to favour the growth of specific microbe species, which can help in nutrient acquisition. Nowadays, there are commercially available inoculants that contain this type of “healthy” microbes; however, they often don’t work as advertised because soil types and microbial communities vary a lot between different places. Our aim is to find ways to keep the good microbes alive and enriched in the plant microbiome. We are aiming to engineer plants that can release specific carbon substrates used preferentially by desired microbes to promote the growth of these beneficial microbes over others.
Carlo: Any other scientific topic you would like to investigate in the future?
Gözde: The applicability of my research to real-world problems is of vital importance to me. While our research is currently focused on model organisms like Arabidopsis and Nicotiana, we aim to translate our findings to different plant species. I am especially interested in crops that are important in developing or underdeveloped countries and that have received less attention in terms of biotechnology and breeding, but can be crucial for our future food security, crop diversification, and climate-resiliency efforts, such as millets, nuts, yams, amongst others.
Carlo: What are your favourite and least favourite parts of the job?
Gözde: My favourite part is definitely the mentoring of my lab members, which is also why I decided to become a professor. I love our one-on-one meetings and the brainstorming sessions to come up with solutions to problems or new ideas, relating to our research. On the other hand, just like everyone else, I really dislike grant rejections. But unfortunately, they are part of this job, and I am learning to not take them as a negative evaluation of our research and capabilities.
Carlo: You have a very interdisciplinary background, from chemical engineering to molecular biology. Is there any advice based on your experience that you would like to share?
Gözde: Don’t be afraid to enter a new field! When I first considered working on plants, I initially felt intimidated by all the things I would have to learn, and I thought that staying in a familiar field would be easier. But after having switched fields, I saw how easy it was to learn new areas and I first-hand experienced the added value of interdisciplinary approaches. I think that when you put together the contributions of people with different backgrounds and views, you end up finding new, innovative solutions that would have been otherwise difficult to conceive. That’s what I’m seeing also in my own lab, where we have team members from chemistry, chemical engineering, biology, bioengineering, and environmental science backgrounds.
Carlo: What kind of obstacles did you encounter in your career so far, and what advice do you have for people that want to follow your path?
Gözde: During the first two years of my PhD, my research progress was slower than desired. This was discouraging and I started doubting my skills as a researcher. I was also an international student in the US with a visa and had to pass the qualifying exam to keep my status, which put even more pressure on me. I am not sure I would have made it if it wasn’t for the positive, optimistic, and supportive attitude of my supervisor, who kept being very encouraging throughout the whole process. A few months before the exam, things did start to work out and I collected a lot of data in a very short time span, probably the most data dense portion of my whole PhD.
So, try to keep an optimistic outlook when things are not working. Keep asking good scientific questions, troubleshooting, and understanding what may be happening in one small experiment and step at a time. It is also important to make sure to have supportive people around, like mentors, friends, and colleagues, that can support you and motivate you under these circumstances.
Carlo: Is there anything (or anyone) that helps you cope with difficult times?
Gözde: When I first got my current position, it was very busy to start the lab, research, and teaching at the same time, and the first thing I did was cutting physical exercise, thinking that working longer hours would solve the issue. Looking back, that was a mistake and I have changed my habits since then. I now have a routine in place, where no matter what happens at work, I still find some time for myself. Physical exercise helps a lot with finding my mental focus and releasing negative emotions. My two cats have also been helping me a lot in coping with daily work stress.
Carlo: If you could change one thing about academia, what would that be?
Gözde: I would focus on inclusivity. Not just having a diverse population in STEM but also creating the resources needed to support those people, such as in terms of policies like parental leave and the way we assess academic performance for the academic job market and promotion. Often people with families, women, and people from historically excluded backgrounds have a disadvantage because of the way these performance metrics are designed. Although things are already improving in this area, I think progress should and could be faster.
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About the Author
Carlo Pasini is a PhD student at ETH Zurich, and a 2024 Plantae Fellow. He studies the links between carbon metabolism and abiotic stresses, primarily focusing on guard cells. In his free time, Carlo enjoys reading, playing ice hockey and any kind of snow-related activity. You can find him on X: @Crl_Psn.
