Alicia Camuel is a Ph.D. student at the Plant Health Institute of Montpellier working with Eric Giraud on the Symbiotic Mechanisms in Tropical Legumes team. Her current research is focused on identifying an alternative symbiotic pathway independent of Nod factors by studying the symbiosis between Aeschynomene spp. and Bradyrhizobium spp. Alicia was the recipient of a Ko Shimamoto Travel Award to attend the 2023 IS-MPMI Congress.
Simona Radutoiu is currently a professor and group leader at the University of Aarhus in Denmark, and her main research area is the identification of the genes involved in nitrogen-fixing symbiosis, with the aim of designing biotechnological tools that will enable us to transfer this ability to nonlegumes.
Conversation with Dr. Radutoiu
Between two sessions at the 2023 IS-MPMI Congress in Providence, RI, and over a lunch break, I had the chance to chat with Simona Radutoiu. Of course, we talked about science—it could not be any other way in such a context. But, we also talked about many other aspects of the life of a woman scientist, career choices, and building a personal life in line with her plans and wishes. In the following article, I recount this informal interview with Simona, which I will remember for a long time. Our conversation began with scientific topics. As I am also working on nitrogen-fixing symbiosis, I wanted Simona's opinion on questions that were more or less open and that I thought would be useful to discuss later on in my thesis. However, unlike most legumes capable of associating with rhizobia, I am studying an alternative symbiotic model that does not depend on Nod factors but on the bacteria's type 3 secretion system (T3SS). In a recent paper, Simona and colleagues described the importance of LysM domain receptors that have adapted for nodule organogenesis. I, therefore, asked her about the fact that in my subject of study, the bacteria bypass this signaling mediated by LysM receptors and whether, in her opinion, other key symbiotic players could also be avoided. Our opinion on this question was similar, since it could very well be that other players in the symbiotic pathway are not required. However, it should be noted that "infection by infection threads remains the most efficient…and that CCaMK and CYCLOPS are central players for nodulation."
Furthermore, the symbiotic model that I use to observe this T3SS-dependent process (Aeschynomene spp./Bradyrhizobium spp.) can only be observed under in vitro conditions. Often genetically associated with the Nod genes, T3SS in nature does not play a role in nodule organogenesis on its own. Nevertheless, a large majority of Bradyrhizobium spp. able to nodulate soybean possess both nod and T3SS genes (1), suggesting that T3SS could play a decisive role in symbiotic efficiency. Indeed, during my Ph.D. study I was able to show that effectors could directly trigger nodulation (2). I asked Simona if there is any real interest in studying this alternative process. According to her, there is: "These two processes [Nod-dependent and T3SS-dependent] should work together" in order to optimize symbiotic efficiency. Indeed, bacteria are known to use T3SS to modulate host specificity, as observed for several legumes (3,4). In this symbiotic model, however, T3SS is not just a host specificity factor, and thus, its role would be broader and complementary with Nod factors in nature. A response like this reinforced my choice of subject for my thesis, which is very fundamental but could ultimately have a broader scope.
I immediately wanted to know what Simona thought about the "dream" of one day transferring the symbiotic capacity of legumes to cereals, which are plants of major agronomic interest. Indeed, as a member of the ENSA (Engineering Nitrogen Symbiosis for Africa) scientific consortium, she is at the heart of this question, which many scientists have been asking themselves for several years. For sure, it represents "a real challenge…coordination between organogenesis and infection is essential but difficult to achieve…and many players have yet to be discovered." Despite more than 20 years of research, this transfer to cereals remains a real challenge, requiring a great deal of resources and rigor.
Our conversation then moved on to subjects that some might consider 'lighter,' but which taught me so much in such a short space of time and which are just as important in a woman's scientific career. Having completed her doctorate in Romania, Simona found her calling, so to speak, after her Ph.D. stage at the University of Tennessee in the United States. On her return, she became a mother, but this in no way hindered her career. On the contrary, she says she is "passionate about science," but still attaches great importance to her family: "I talk a lot with my daughter." I could see in her eyes how obvious and authentic this was for her, although "managing these two sides of life is a constant learning process." Being a woman in science has not always been easy, and it still is not, depending on the laboratories and countries in which we work. In France, for example, only around 30% of scientists are women. So, I told Simona about my doubts and misgivings about this aspect, as well as about becoming a mother one day. Although she was happy and fulfilled to be a mother, she advised me "not to let motherhood get in the way, to continue your career and always believe in yourself so that you can keep moving forward." In a laboratory or elsewhere, it is important to "share your doubts and experiences with other women, with people you trust." I felt at that moment that this is also what gives us the strength that we do not think we have, but which is always deep within us. Her words touched me deeply, and I invite everyone else to follow her precious advice.
I then asked her about choosing a postdoc position; what would be her career advice in light of her own experience? Should I change my research subject or move to another country? For Simona, it is essential to change subjects and above all to learn new techniques. She invited me to leave my comfort zone and start researching at least one year in advance. Even if changing subjects and leaving your country may seem like a challenge that is not so easy to overcome, you have to "believe in yourself and have confidence in yourself."
Finally, now living in Denmark, Simona is far from her family and her country of origin. So, I wanted to find out if it had been difficult and how she managed this aspect of her life. For her, it was important for her career to leave Romania, and she was able to find a place where she and her family could blossom and make new friends with the people living there. In the end, she told me that although part of her family is still far away, "having moments to share with them becomes even more precious given the distance."
Our whole exchange was a real pleasure, both on the scientific side and on the personal side. I hope that my feedback on the time I spent with Simona will also be of interest to young women like me, who are starting out on their scientific careers while trying to make the most of their life choices.
1. Teulet, A., Gully, D., Rouy, Z., et al. 2020. Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium. Microb. Genom. 6(9):mgen000407. DOI: 10.1099/mgen.0.000407
2. Camuel, A., Teulet, A., Carcagno, M., et al. 2023. Widespread Bradyrhizobium distribution of diverse type III effectors that trigger legume nodulation in the absence of Nod factor. ISME J. DOI: 10.1038/s41396-023-01458-1
3. Yang, S., Tang, F., Gao, M., Krishnan, H. B., and Zhu, H. 2010. R gene-controlled host specificity in the legume-rhizobia symbiosis. Proc. Natl. Acad. Sci. U.S.A. 107:18735-18740. DOI: 10.1073/pnas.1011957107
4. Miwa, H., and Okazaki, S. 2017. How effectors promote beneficial interactions. Curr. Opin. Plant Biol. 38:148-154. DOI: 10.1016/j.pbi.2017.05.011
Tianrun "Jerry" Li
Tianrun Li is a fourth-year Ph.D. candidate in the Plant Pathology program at the University of California, Davis, working under the guidance of
Dr. Gitta Coaker. He completed his bachelor's degree from Northwest A&F University, China, in 2019. His current research focuses on exploring the utility of pattern recognition receptor (PRR) triggered immunity to control vector-borne disease. He is also investigating novel plant flagellin receptors with expanded ligand recognition specificity and their potential for receptor engineering.
Dr. Wenbo Ma
Dr. Wenbo Ma is a senior group leader at The Sainsbury Laboratory (TSL) and an honorary professor at the University of East Anglia, UK. Her group's long-term research interest has been to understand the plant–pathogen coevolutionary arms race, with a focus on microbial pathogenesis and effector biology. She is also one of the pioneers in determining the role of small RNAs in plant immunity against nonviral pathogens.
Conversation with Dr. Ma
Not only is Wenbo a recipient of the 2021 Ruth Allen Award from The American Phytopathological Society (APS), she was recently elected as a 2022 Fellow of the American Association for the Advancement of Science (AAAS). To mark the occasion, I had the privilege of speaking with Wenbo about her scientific journey, accomplishments, and forward-thinking perspectives.
Wenbo initiated her research journey in China, where she obtained her M.S. degree at the Chinese Academy of Sciences. Subsequently, in 2003, she attained her Ph.D. degree from the University of Waterloo in Canada, after which she pursued a postdoctoral position at the University of Toronto.
In 2006, Wenbo started as an assistant professor at the University of California, Riverside (UCR) and was later promoted to associate professor with tenure, eventually attaining the rank of full professor. Several years ago, she joined TSL, where she established new research programs centered around major host–pathogen systems.
When asked how she feels about being honored as an AAAS Fellow, Wenbo states that she's extremely fortunate and grateful for the recognition she has received as a reflection of her scientific journey. She adds that the honor is shared with her team.
I had the privilege of working with many amazing students and postdocs. Without their support and effort, my research would not be possible.
Throughout her career, Wenbo has devoted substantial time to conducting research on diverse continents, including Asia, America, and Europe. These experiences have provided her a comprehensive understanding of the unique challenges, cultural dynamics, and opportunities that each research environment offers. This journey has helped her cultivate a deep appreciation for the value of collaboration and diversity in her scientific pursuits.
She highlights two key elements of interdisciplinary collaborations: concepts and methodologies. Because scientists can sometimes become deeply immersed in their own field, limiting their perspectives, Wenbo encourages them to deliberately venture outside their comfort zone and broaden their scope by learning from other fields. This approach, she believes, helps researchers enhance their understanding of diverse concepts.
Simultaneously, Wenbo points out the role of technological advancements in fostering scientific breakthroughs. Invaluable knowledge can be obtained from structural biologists, and their insights have now become an indispensable part of her research program. As the popularity of AI-based analysis tools grows, there is great potential for them to become an integral part of the toolkit of every early-career researcher in biology-related fields.
This spirit of cooperation is crucial, especially in a field as intricate as MPMI, where bringing ideas from different perspectives and utilizing interdisciplinary methodologies often pave the way to the most exciting and fundamental discoveries in plant immunity and pathogen effector biology.
The potential for translating discoveries from our basic biological research into practical applications, particularly in the area of disease resistance in crops, is what drives our work…. For me, effectors are one of the most intriguing components of these systems, providing critical insights into plant pathogenesis.
By understanding plant immunity, scientists learn how plants become resistant. However, without an understanding of pathogens we wouldn't know how plants become susceptible. Wenbo envisions a future where the knowledge gathered from studying virulence mechanisms utilized by pathogens will pave a new passage to generate resistant crops.
However, challenge is everywhere. A key hurdle in crop improvement is the perpetual coevolutionary battle between pathogens and plants.
Pathogens are always evolving, which is why our goal is to enhance the durability of resistance in plants.
She adds that "there is no silver bullet solution" and underlines the importance of a comprehensive understanding of plant–pathogen coevolution to develop integrated resistance strategies.
The effects of climate change add layers of complexity to plant pathology research. Recent studies have found plant stress and immune signaling are dampened in a warming climate. Global warming and ecological shift are altering the delicate balance between plants and their microbial "partners."
"Environmental factors are integral to plant–pathogen interactions. With climate change, both the plant's immune system and pathogen's virulence mechanisms can be affected, altering disease patterns. Our research needs to incorporate more of these environmental aspects," explains Wenbo, emphasizing the importance of actively integrating environmental factors into MPMI research programs.
Looking toward the future, Wenbo is excited about the role of small molecules in immune signaling as a promising research frontier. She shares that her research group's goal is to use effector proteins as molecular probes to dissect the complex immune signaling process and adds that "It also provides an opportunity to incorporate metabolome analysis and structural biology, which is truly exciting for us."
"This field is witnessing a wave of really cool technologies," says Wenbo, specifically calling out the impact of structure prediction. "Now with structural models, we can gather a wealth of information that can help us generate testable hypotheses." It's a game-changer that has opened up previously unexplored avenues to investigate protein functions.
Wenbo's contributions to the scientific community extend far beyond her exceptional research. Over the span of 17 years as a professor and mentor, her laboratory has nurtured numerous postdoctoral fellows, graduate students, and undergraduate students. Many of them have gone on to flourish in their scientific pursuits.
Wenbo feels strongly about mentoring early-career professionals and wants to help them make their mark in the field of MPMI. She emphasizes the importance of motivation, open-mindedness, and persistence.
She believes that we are at a fascinating juncture where we have already accumulated a lot of important knowledge and are poised to make the next jump. "Seeing the opportunities of making potential breakthroughs should fuel your motivation," she urges early-career researchers. "We are in an exciting time for MPMI research. There are many exciting projects aiming to answer some of the most pressing questions."
Being open-minded is key to advancing in this field, and researchers should embrace new technologies and explore novel approaches.
You need to be very adaptable to new technologies, willing to try new things. Try it, try different things.
When AlphaFold was first announced, Wenbo was enthused by how many in the scientific community "immediately tried to model their favorite proteins." This eagerness to embrace and experiment with new technologies is something she views as vital.
With all these exciting prospects in mind, Wenbo is also fully aware that any scientific pursuit can be riddled with challenges and potential frustrations. Experiments may not always align with initial hypotheses and require series of adjustments and readjustments. This is where the importance of resilience and persistence comes into play—maintaining a positive attitude, viewing these roadblocks not as failures but as opportunities to refine hypotheses and seek alternative methods, is crucial.
Wenbo concluded our enlightening conversation with a final piece of wisdom, encouraging early-career researchers to "keep a positive energy and challenge yourself by stepping out of your comfort zone; be persistent but flexible; the sky is unlimited."
Aline Sartor Chicowski
Aline Sartor Chicowski
Dr. Maeli Melotto is a professor and scientist at the University of California, Davis, where she has worked for the past nine years. Ever since she was an undergraduate in biology at
São Paulo State University (UNESP), Brazil, Maeli knew she wanted to be a plant scientist. For her B.S. thesis, she surveyed biological nitrogen fixation efficiency in trees using a collection of native rhizobium isolates from local forests. From that moment on, she has studied plant–microbe interactions. First, she worked on cowpea and soybean associations with rhizobia for her M.S. degree at the
University of São Paulo (USP), Brazil. For her Ph.D. thesis at Michigan State University (MSU), she worked on bean–Colletotrichum lindemuthianum interactions. Finally, during her postdoctoral training at the
MSU-DOE Plant Research Laboratory, she worked on tomato and Arabidopsis interactions with the bacterium
When she started
her lab, first at the University of Texas in Arlington in 2008 and then at UC Davis in 2014, she expanded her research interests to study plant colonization by human bacterial pathogens. She chose to work with
Escherichia coli O157:H7 and
Salmonella enterica because they are the top microbial contaminants of freshly consumed foods in the United States and the world. Besides, "UC Davis is a perfect location to carry out projects focused on solving this problem that affects the national and international fresh produce market. Leafy greens production in California accounts for 70–80% of the national market, and multiple foodborne disease outbreaks have originated in the field," she explained.
Her main research goal is to uncover the mechanisms that allow these bacteria to survive and multiply in healthy leaves using lettuce and Arabidopsis as models. Even though these bacteria are not pathogenic on plants, lettuce and Arabidopsis serve as hosts for them and react to their presence. "At the molecular level, there are many similarities between Arabidopsis and lettuce responses to phytobacteria such as
Pseudomonas syringae and these human pathogens," she explained. Her group discovered that some lettuce cultivars mount a strong immune response (pattern-triggered immunity, or PTI) against O157:H7 and
S. enterica, but other cultivars allow for bacterial growth, posing a greater risk for the occurrence of foodborne illnesses.
For Dr. Melotto, one of the most important discoveries in plant immunity during the past few years was the work by Matsumura et al. (2022): "Mechanosensory Trichome Cells Evoke a Mechanical Stimulus-Induced Immune Response in
Arabidopsis thaliana." This study explains the mechanosensory role of trichomes in
Arabidopsis. Disease is the exception of all possible plant–microbe interactions, and many things happen on the leaf surface before a pathogen can internalize the leaf and damage internal tissues. "The leaf surface is an exposed, complex environment that plays a crucial role in protecting the plant from invaders. This work presented a fascinating story on how mechanical stimuli at the trichome triggers a wave of calcium signaling that triggers plant immunity systemically. It sounds like a danger-detecting antenna," she said.
Dr. Melotto's favorite paper is her first: "Development of a SCAR Marker Linked to the
I Gene in Common Bean." This article was a product of her overcoming scientific barriers and a turning point in her career. "It marked a point in time when molecular marker-assisted selection to improve disease resistance was the state-of-the-art for crop breeding," she mentioned. The marker she developed is still useful to breeding programs focused on virus diseases. Her paper has been cited 239 times, including 2023 citations. "To me, that paper represents a molecular technology that made it to real applications towards developing genetically resistant, commercial cultivars of beans in many countries."
Her favorite part of her job as a professor and scientist is to study the literature to fully interpret data from her research. She loves to write discussions and review articles to create a big picture and think about the next steps in science. "The desire to be a scientist came naturally, and, to this day, I can't think of being anything else but a scientist," she said. Maeli points out that the hardest part of her work is that it lies in the intersection of three major disciplines: molecular plant–microbe interactions, food science, and agronomy, "which do not have a history of working together," she noted. "Our audience is highly diverse, and we must navigate through 'discipline-specific vocabularies' when communicating our science."
When talking about challenges in her career, Dr. Melotto mentioned that her first biggest obstacle was overcoming the English language barrier, as her native language is Portuguese. She mentioned that it took her a while to start thinking in English and stop translating everything in her mind before speaking, "a tiresome task that any non-native English speaker will understand." She also pointed out that the second biggest obstacle she had to overcome, and according to her "once in a while still is," is to cope with "impostor syndrome." Dr. Melotto advises someone starting their career to seek opportunities to ask questions of those they consider successful individuals and learn from their experiences. Maeli said she had excellent mentors who answered all the questions she had as they became relevant to each stage of her career. "I am very grateful to
Dr. James D. Kelly, my Ph.D. advisor, and
Dr. Sheng Yang He, my postdoctoral mentor, who guided me to be the best scientist I could be and helped me reach my potential," she proudly said.
Ten years from now, Dr. Melotto hopes to have trained great scientists and advanced the knowledge of how hormonal signaling drives plant immune responses at the cell and tissue levels. "I would like to uncover new regulatory nodes that connect plant growth and defense, which could be used for metabolic engineering toward crop resilience under biotic stresses," she explained.
When asked what being recognized as a Fellow of the American Association for the Advancement of Science (AAAS) means to her, she said, "I have never dreamt about receiving this honor. I am so very grateful to the anonymous person who nominated me. It still doesn't feel like I deserve it, but I am happy to share this recognition with my advisees who contributed to the discoveries and publications from our lab."
A Fruitful Symbiosis Between an Undergrad in Computer Science and a Graduate Student in Genetics and Genomics
Question: What was the inspiration for EffectorO?
Kelsey: When I started my Ph.D. program on oomycete effector genomics in 2013, it seemed like everyone was really only using the same motifs (RXLR or LFLAK) to predict effectors. But as I dove deeper into the genome of the lettuce downy mildew pathogen, I found that there were some real effectors that did not have these motifs and published a paper on my findings (Wood et al., 2020). That got me thinking of alternative ways to predict effectors.
The first way to predict effectors that I thought of was to leverage lineage specificity, which is a characteristic of many effectors from species with narrow host ranges, to find effectors. I realized this would be pretty simple in principle using BLAST. However, the downside would be that there are other lineage-specific genes besides effectors and a lot of misannotated junk from genomes would probably be picked up. It also would depend a lot on what other organisms are sequenced for comparison.
In my search for a more accurate way to predict effectors, I found a paper on EffectorP 2.0 (Sperschneider et al., 2018) that used machine learning to predict effectors from fungi. I tried to use it on my oomycete genome, but it didn't work and I was sad.
That is, until I met Munir.
Question: How did you two find each other?
Munir: During my undergraduate studies, I was eager to apply what I've learned in computer science and bioinformatics classes to help solve research problems. I saw an ad for a bioinformatics intern in the Michelmore lab and applied by email.
Kelsey: Funny story, I posted a few job ads for undergraduate interns for summer 2017 on the Michelmore lab website, and we didn't take them down even after the job openings had expired. Munir saw the (old) ad for the bioinformatics intern and emailed me right around the time I was wanting to develop a machine-learning pipeline for oomycete effectors, and I interviewed and hired him on the spot. Moral of the story: never update your lab website. And, if you are an undergrad, don't wait for an official job ad to reach out to labs for internships!
Question: What did you think bioinformatics research would be like versus what it was actually like?
Munir: Bioinformatics research is much more data wrangling than I thought! I think this is also true for the entire field of data science—it typically takes a lot more work to get the data ready than it does to build models and perform analyses!
Kelsey: What Munir said. And, I'm always surprised at how much you have to reperform the same or similar analysis until it's "done." Using R for most of the graphics was a life saver because if something ended up changing we could easily rerun the scripts with the new data.
Question: What lessons did you learn during the preparation of this manuscript?
Munir: Write clean code in a reusable manner the first time around. And if you don't, definitely get to it the second time you use the same code! Research analyses typically get rerun multiple times, as you're constantly pulling the latest datasets that get released in the research world or tweaking some parameters to compare different models/hypotheses.
Constantly write lab notes and code documentation, since you will often be looking back at analyses you performed and code you wrote several weeks, months, or years ago.
Kelsey: I learned how valuable reviewer feedback could be, even (or especially?) criticism. One reviewer in particular had a lot of excellent critiques that forced me to rewrite several sections, which resulted in a much clearer argument for the manuscript.
Question: How did reviewers help to improve the manuscript?
Kelsey: One very useful suggestion was to perform domain prediction on our effector candidates using Pfam, which I didn't think would be a good idea because most effector domains are not well studied. This is what the results ended up showing, but the domains that were found were mostly known effector domains, which helped support the conclusions of the paper. Also, there were many reverse-transcription–related domains that I think also support the conclusions, as it is known that effectors live in transposon-rich regions of the genome. The ones with RT-related domains are probably pseudogenes though, so it is another criteria that one could use to refine the list of candidates.
One reviewer also asked if BLE01, which was the
Bremia lactucae effector that we predicted with EffectorO and that we found to be an Avr candidate, was also predicted by EffectorP 3.0 (Sperschneider and Dodds, 2021). We found that it was not predicted by their pipeline. This was important because EffectorP 3.0 came out while our paper was under review. However, this showed that the two machine-learning algorithms predict distinct (but overlapping) sets of proteins and, thus, can be used together for prediction of oomycete effectors. Thank you so much Reviewer #2!
Question: Why was the collaboration between you two especially fruitful?
Kelsey: I brought the biology knowledge, and Munir brought the coding skills. I learned Unix, Perl, and R scripting during grad school, but Munir knew how to code really well in Python, which was essential for this project. He was able to write code very quickly and elegantly and came up with the various evaluation metrics used for the machine-learning models. He also spent a long time working on a convolutional neural network model that was more computationally complex, in the end giving us similar results to the simpler Random Forest classifier we ended up using.
Munir: One of the first things I learned while collaborating with Kelsey was how to effectively digest research papers. My first exercise at the lab was summarizing a collection of research articles relevant to our projects, which was immensely invaluable in teaching me how to look in the right places for information. Kelsey's research background also played a significant role in coming up with fresh hypotheses and methods to test them, and her plant genetics background allowed us to make better sense of the large amount of data we had.
Also, at the end of the EffectorO project, I got the opportunity to do my first PCR! This was really fun for me to do, as computer scientists and bioinformaticians don't always have much exposure to the wet lab.
Question: What are you excited to see in future MPMI research?
Kelsey: I'm excited to see how advances in protein structure prediction will expand our knowledge of effectors with uncharacterized protein domains. I'm also excited about high-throughput assays for testing predicted effectors.
Munir: Making machine learning more accessible! I think it would be great to standardize self-service model-building interfaces, since training sets are ever expanding. This would be a way to further improve classifiers like EffectorO whenever new effectors are discovered.
Learn more about Munir and Kelsey in their
Sperschneider, J., and Dodds, P. N. 2022. EffectorP 3.0: Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. Mol. Plant-Microbe Interact. 35:146-156.
Sperschneider, J., Dodds, P. N., Gardiner, D. M., Singh, K. B., and Taylor, J. M. 2018. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol. Plant Pathol. 19:2094-2110.
Wood, K., Nur, M., Gil, J., Fletcher, K., Lakeman, K., et al. 2020. Effector prediction and characterization in the oomycete pathogen
Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif. PLOS Pathog. 10:e1009012.
Ashley C. Nelson
Ashley C. Nelson is a second year Ph.D. student in the Plant Pathology Department at North Dakota State University. She is working in
Tim Friesen's lab, focusing on functional characterization of necrotrophic effectors in the
Parastagonospora nodorum–wheat interaction.
Dr. Bing Yang currently holds a joint position as a principal investigator and member at the Donald Danforth Plant Science Center, as well as being a professor of plant science and technology at the University of Missouri–Columbia. His current research uses bacterial blight of rice as a model to understand the resistant and susceptible interactions between the host and pathogen. Dr. Yang's group has used the bacterial blight–rice system to master genome-editing technologies for improvement in rice, as well as other crops, including wheat, sorghum, and soybean. Dr. Yang's work led to the development of the Healthy Crops Project, which creates an opportunity to collaborate with labs worldwide to develop crop resistance in multiple host–pathogen combinations. Dr. Yang's career work and dedication to science has been rewarded, as he was recently elected as a Fellow of the American Association for the Advancement of Science (AAAS).
Originally from China, Dr. Yang obtained his bachelor's and master's degrees from the Southwest Forestry University, where much of his effort was spent on trees. In 1995, he made his way to the United States as a Ph.D. student in the Department of Plant Pathology at Kansas State University, working with
Dr. Frank White. In Dr. White's lab, his project focused on bacterial blight of rice, and this interest in rice health continued even after obtaining his Ph.D. degree as Dr. Yang remained as a postdoc in the White lab for five more years. Working on rice hit home for Dr. Yang, since rice was a staple food source that is nutritious and essential for the daily diet for not only him and his family, but for much of China. This familiarity and passion continued when Dr. Yang took his first job as an assistant professor at Iowa State University. Wanting to ensure the health and productivity of rice, Dr. Yang continued his work on bacterial blight of rice and subsequently expanded into plant biology using genome editing, first with TALEN and then CRISPR. In 2018, he took a joint position with the Donald Danforth Plant Science Center and University of Missouri–Columbia, where his bacterial blight and genome-editing work continues.
Bacterial blight remains an important disease that is well studied and serves as a model for characterizing interactions to gain fundamental understanding of plant diseases. This understanding aids in the strategy of resistance engineering to make it applicable to other crops by presenting targets to engineer resistance and connect advanced biological techniques to solve real-world problems. Dr. Yang has observed these innovations unfold over his career and has had a direct impact through his Healthy Plants Project, which promotes international collaborations with groups focusing on various host–pathogen systems. Dr. Yang finds motivation in answering scientific questions that lead to new discoveries and technologies resulting in worldwide solutions. He believes that scientific discoveries are not due to individuals, but to collaborative efforts.
Dr. Yang is as excited as he was in the beginning by how science seemingly has no end and has some advice for young scientists navigating their early career. Dr. Yang outlines that identifying the root problem and formulating a scientific question is challenging, but just the beginning of a project. He stresses that answering the scientific question correctly, in a timely manner, and with integrity, while garnering public support are just as important as the question itself. Dr. Yang recommends working toward your passion and finding a way to collaboratively reach goals and find answers to the difficult questions. Dr. Yang also believes finding a mentor is critical, as the support and advocacy will be helpful throughout your career. Last, he encourages preparation, active participation, and networking at conferences to ensure a beneficial experience.
Amelia H. Lovelace
Dr. Amelia H. Lovelace (she/her) is a postdoctoral researcher in Dr. Wenbo Ma's group at The Sainsbury Laboratory (TSL). Her current research focuses on characterizing effector proteins from the citrus greening pathogen 'Candidatus Liberibacter asiaticus'. In general, she is interested in pathogenic bacterial interactions with plants. Amelia is an assistant feature editor for MPMI and enjoys sharing her passion for science communication with others.
Prof. Cyril Zipfel (he/him) is chair of Molecular and Cellular Physiology at the University of Zurich, Switzerland, and is a senior group leader at The Sainsbury Laboratory (TSL) in Norwich, UK. In general, his group studies immunity and signaling mediated by plant receptor kinases. He has been widely recognized for his contributions to the field of MPMI, including being elected to the European Molecular Biology Organization (EMBO) and being awarded the Charles Albert Shull Award from the American Society of Plant Biologists (ASPB) and the Tsuneko & Reiji Okazaki Award from Nagoya University, Japan.
I had the pleasure of interviewing Cyril. We discussed the evolution of his research interests throughout his career, as well as his approach to mentorship and his personal life. Cyril is a keynote speaker for the IS-MPMI Congress Meeting in Rhode Island, USA. The title of his talk is "Connecting the Dots of Surface Immune Signaling."Background
Prof. Zipfel's path to studying plant immune signaling was a bit unorthodox. He started by studying biology at Strasbourg University in France and quickly switched to studying environmental science in Nancy in France, with the ultimate aim to study forestry, because his uncle and grandfather were both forest engineers. He was first introduced to plant signaling through a summer internship where he investigated the molecular biology of auxin signaling during mycorrhizal fungal interaction with trees. This experience inspired him to study molecular biology. He continued to work on auxin signaling during his M.S. degree studies at the University of Paris–Orsay. He was originally going to continue studying auxin signaling there for his Ph.D. program until he heard about an exciting international Ph.D. program at the Friedrich-Miescher Institute for Biomedical Research in Basel, Switzerland.
Prof. Zipfel received his Ph.D. degree in botany at The University of Basel working under Prof. Thomas Boller. In 2004, Cyril and colleagues discovered that the pattern recognition receptor (PRR) FLAGELLIN-SENSING 2 (FLS2)—the receptor for flg22, the highly conserved 22 amino acid epitope of bacterial flagellin—limits bacterial growth (Zipfel et al., 2004, Nature). This landmark discovery opened the flood gates to study additional pathogen-associated molecular patterns (PAMPs) and corresponding PRRs besides flagellin, such as EFR and its ligand elf18, the highly conserved 18 amino acid epitope of bacterial EF-Tu (Zipfel et al., 2006, Cell). During his Ph.D. studies, he collaborated with a student of Prof. Jonathon Jones, a senior group leader at TSL. At the time, he was excited by recent findings in animal innate immunity, such as Toll receptors, but after meeting Prof. Jones at a conference, he joined his group in 2005 for a postdoc, where he was funded by a long-term EMBO postdoctoral fellowship. In just two years, Cyril joined the ranks of his mentors and became a group leader at TSL and eventually a senior group leader (2011) and then head of TSL (2014). Prof. Zipfel expressed his gratitude for the respect and support of his mentors and colleagues during his transition from postdoc to group leader at TSL. In 2010, Prof. Zipfel's group demonstrated just how powerful PRRs can be for breeding sustainable broad-spectrum disease resistance. More specifically, by transferring the Arabidopsis EFR into tomato, they were more resistant to a range of phytopathogenic bacteria (Lacombe et al., 2010, Nature Biotechnology).
In 2018, he moved his group to the University of Zurich, Switzerland, where he is now professor of Molecular and Cellular Plant Physiology. His lab currently supports two-dozen members across two institutes and countries (TSL and UZH). He describes his lab as more of a signaling lab than an MPMI lab, as this move has allowed him to participate in more interdisciplinary research. He currently collaborates with many colleagues, ranging from structural biologists to chemists to systems biologists, who have given him a more holistic approach to studying plant signaling.Interview Summary
Prof. Zipfel's success has been due, in part, to the tremendous support from his mentors. When asked how they have influenced his own mentorship style, Cyril stated that he takes aspects that work for him and his group. In academia, there, unfortunately, is generally little management training, and of the courses he has taken, he has learned to pick what fits best for him and his group based on an individual's personality and project. Everyone has different needs, thus it is important to tailor your mentorship to each person. Now that his lab has expanded to around 25 members, he breaks down his group into 5 subgroups based on research topic. Within each group there is no team leader, but he always pairs a Ph.D. student with a postdoc to ensure that the students have someone on which they can rely. Given that his team is split between two different locations, he has subgroup meetings every other week and a long weekly lab meeting with his entire group.
It's hard to believe that it has been almost 20 years since publishing his FLS2 Nature paper. What's even more surprising is how much we still don't know about plant innate immunity!
When asked to comment on this and identify research directions that he finds most exciting, Cyril stated that his lab is more interested in receptor kinases in general, which, yes, are involved in plant immunity, but are also involved in regulating other stress responses. There are still many mechanisms yet to be explored. This includes investigating the biochemical and structural biology of these receptor kinases, signaling and regulation of plant immunity cross-talk, execution function of immunity, stress-regulating signaling peptides, translational application of these receptors, and synthetic biology or bioengineering of these signaling pathways. His lab members are kept busy exploring all these diverse avenues. Cyril is impressed by the undergraduate students whom he could mentor in recent years as part of the UZH International Genetically Engineered Machine (iGEM) team. As many of these students are traditionally more attracted to biomedicine, Cyril gets joy out of showing them the power that plants can provide to the field of synthetic biology. As for what the future holds for plant signaling, he remarked that previous findings have used crude methods to answer general questions. He hopes to answer these same questions but in a more precise way. For instance, on a single-cell level how does one cell activate a stress response and signal to a neighboring cell? Developing technologies to achieve this precision will be key to advancing the field of plant immunity.
When asked if he has any advice for early-career researchers, he stated that there were three aspects in one's work life that are important for success: 1) Having a project or research topic that excites you; 2) working with a mentor or group that you respect and that respects you; and 3) having a safe environment outside of work that can fulfill your other needs in life. Ideally, you want to have all three, but he cautions that if you have to compromise to only compromise on one. Which one you choose to compromise on depends on your own personality and needs. Prof. Zipfel is not immune to imposter syndrome either. He reflects on his feelings of early success in his career and remembers worrying whether he was just lucky. These thoughts fueled him to push further, and his work has provided a landscape for further discovery of plant immunity and plant signaling. Cyril strives for balance in his personal life. He enjoys cooking every day to decompress after work. He tries to not work on weekends (except when there is a tight deadline) and uses this time to listen to live music and explore cities around the world.
Dr. Ajayi Olaoluwa Oluwafunto
Dr. Ajayi Olaoluwa Oluwafunto
Dr. Ajayi Olaoluwa Oluwafunto recently completed her Ph.D. degree from the University of Ibadan, Nigeria, and works in the Soil Microbiology unit of the International Institute of Tropical Agriculture, Ibadan, Nigeria. Her major research interest is in plant–microbe interactions, particularly in promoting the yield and health of legumes using plant growth-promoting bacteria, nitrogen-fixing bacteria, and molecular approaches.
Dr. Blake Meyers is a senior member of IS-MPMI who holds joint appointments at the Donald Danforth Plant Science Center and the University of Missouri-Columbia. Dr. Meyers' current research emphasizes bioinformatics and plant functional genomics to understand the types of RNA they produce, particularly pollen and plant reproduction, gene regulation and small RNA, and secondary siRNAs in anther development, working in collaboration with scientists in other labs. He has been widely recognized for his major research contributions in the field of disease resistance, small RNAs, and evolutionary biology. He is an elected Fellow of the American Association for the Advancement of Science (AAAS) and the American Society of Plant Biology (ASPB). He became a reviewing editor at The Plant Cell in 2008 and then a senior editor in 2017. He was also recently elected to the National Academy of Sciences as a member of the 2022 class of inductees.
Dr. Meyers grew up in the college town of Williamsburg, where his father worked as a professor of English. His numerous adventures with nature in fields and outdoors helped him develop an early interest in plants and food production. He completed his undergraduate studies at the University of Chicago, and afterward, he had the opportunity to work on a team that had access to the most advanced DNA sequencing equipment in the field. He formed a second interest in genomic research during his M.S. and Ph.D. degree studies with Dr. Richard Michelmore at UC Davis, where he was funded by an NSF predoctoral fellowship focused on characterizing the diversity of nucleotide-binding, leucine-rich repeat (NB-LRR or NLR) disease-resistance genes in lettuce.
His first postdoctoral assignment was at Dupont-Pioneer (where he met his wife), and his second assignment was at the Michelmore lab, where his work focused on disease resistance genes. At the Michelmore lab, he manually re-annotated NLR-encoding genes for the then just released Arabidopsis thaliana Col-0 genome, the results of which were published in The Plant Cell (Meyers et al., 2003). His findings showed that the 150 Arabidopsis NLR genes often formed in segmentally duplicated clusters, similar to those in lettuce, and that the automated gene prediction tools misannotated nearly one-third of the NLR genes and still required human inputs.
Dr. Meyers began working as a faculty member at the University of Delaware in 2002, where his lab used multiple sequencing approaches to analyze mRNA and small RNAs. In 2005, with collaborator Pam Green, his lab was the first to perform large-scale, genome-wide analysis of small RNAs, and in 2008, the Green and Meyers labs codeveloped a new and widely adopted method for the genome-wide analysis of cleaved mRNAs. Dr. Meyers' career progressed rapidly at the University of Delaware, and he became the Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences in 2010. In 2012, he was named a Fellow of AAAS.
Dr. Meyers started his laboratory at the Donald Danforth Plant Science Center in 2016. Research at the Donald Danforth Center is focused on developing tools and resources to help breeders and farmers make agriculture more sustainable, reduce our dependence on water, protect the soil, and provide nutritious crops for communities around the world. The Meyers lab has developed and used a wide variety of bioinformatics tools and pipelines, provided a customized genome browser, and developed apps for analysis of small RNA targets, cleavage, etc., which are available to the public using their tools.
Dr. Meyers' lab group was the first to demonstrate the targeting of transcripts from NLR genes directly by microRNAs and indirectly through the production of “phased," short, interfering RNAs (phasiRNAs) (Zhai et al., 2011). Their work on phasiRNAs has identified roles in posttranscriptional control of numerous pathways, with much of their current work focused on understanding the functions and evolutionary history of two genetically separable pathways that are highly active in premeiotic and meiotic maize anthers (Zhai et al., 2015). Dr. Meyers copublished a seminal 2005 manuscript in Science, “Elucidation of the Small RNA Component of the Transcriptome," that has generated more than 2 million reads, providing the most expansive and detailed data set view of small RNAs in any plant, animal, or fungal species at the time.
I interviewed Dr. Meyers and asked several questions related to his research, lab, and thoughts on various topics important to junior scientists. I have summarized his responses in my own words, but you can read the direct responses from Dr. Meyers here.
Looking back over the years, when he was a younger scientist, like most graduate students, postdocs, and early-career scientists, Dr. Meyers felt the pressure to make progress on his projects, publish, and make a name for himself while balancing his personal life with work and a myriad of other things. During the early stages of his career, he felt that success was an uncertain thing, with moments of success that he was worried would be short-lived. He warns young scientists that there are a lot of decisions to be made along the way—which way to go, which goal to pursue, etc.—stating that success is a product of how you set and measure up to your own goals, plus some hard work to meet those goals and a measure of serendipity. He also tries to spend time doing things outside of work that he enjoys, although at certain times he has put more effort into work than he should have. Putting it in one piece of advice, he says that we should appreciate both failures and successes along the way for the learning moments that they represent. And, appreciate the great people we meet, the moments when good fortune occurs, and the remarkable career that we as scientists can have relative to many other professions.
When setting up his lab, about 10 or 20 years ago, he had to spend a lot of time finding and training people, working directly with them to build up systems for data management. He also had to juggle the many responsibilities of early-career faculty, including teaching and generating data for grant proposals, having to make tough decisions about where to focus his limited time, and building stories that would result in papers and good talks. These experiences have helped, and he can now do most tasks, such as writing and evaluation, much quicker than when he first started out. However, while there are aspects of the work that, over time, get quicker or easier, other tasks, such as mentoring, designing experiments, and thinking creatively, still take the same amount of time. He has found that selective investment of time early in your career can yield time savings later through greater efficiency and experience.
In recent years, Meyers says that he has also been fortunate to be able to attract and retain talented staff, postdocs, and research scientists with whom he can share the work of managing the group. This has allowed continuity and retained institutional memory of how things work, why things might fail, and who to go to when assistance is needed. This is all important to managing one's time, leaving him free to work on other things, as he can depend more on many people, from administrative assistants to academic staff. Meyers says that it is not him per se, but “all of us working as a team, and when it is a well-oiled operation, we are that much better," which is why they are a high-achieving and successful group. He also says they are a cohesive, collaborative group that works well together, which is important to success. He notes that a good personality is a winning trait, arguably even more so than technical skills among group members, and that when conflicts and complications occur within a group, or communication is poor, it slows things down.
Since he has a dependable team, Meyers' personal work revolves around his email inbox, as this is where he diligently manages his time. The emails in his inbox represent his “to do" list—as soon as he finishes a task, he files or deletes the email. Over the last couple of years, he has tried to keep his inbox to around 20 emails, at least as a regular weekly low point. He even hit the legendary “inbox zero" over the last winter holiday, which was the first time in over a decade. Jokingly, he commented that he would file the email for this interview, removing it from his to-do list as taken care of after the interview.
As an accomplished writer, he points out that experience is important for efficiently writing good publications and successful grant proposals. He provides a few tips that he also reminds his lab members about:
- Write for a reader who does not know your work at all but has the ability to learn it quickly.
- Pay close attention to the clarity of your text, avoiding hasty writing that comes off as sloppy.
- Use good transitions, continuity, and logical flow by ensuring one sentence follows from the former and into the next.
- Pay attention to the conclusions of paragraphs and sections to end on your strongest point made in that block of text; don't simply let the text fizzle out with a minor or tangential point.
- Work with a mentor or instructor to critique your writing, or even read a few books on the topic, as there are many.
Meyers advises that when preparing a good paper there is a lot to think about at the submission/evaluation stage of publishing and that the inputs by reviewers should be greatly appreciated, as they help to improve your work. He also points out that there is a need to develop a thick skin, as you occasionally get reviewers who are mean, nitpicky, or just do not share your enthusiasm for the topic, and at such times, even if you are feeling irritated by a reviewer or editor, you should make sure you take an extra day or so to get over the emotions and purge your responses of adjectives or opinions—focusing on the science and keeping a neutral tone. It is also important to do as much extra work to address the comments as possible, as reviewers and editors appreciate it when you fix a concern and do not argue everything.
He points out that writing grant proposals is different in many ways from writing papers and requires good ideas along with preliminary data, which can sometimes take months (or years) to generate. In other words, you need to play the long game, building a story over time with the anticipation that you will be able to work it in as preliminary data for a proposal. That is what start-up funds are for, and even when you have a grant, you need to be thinking about the dual needs of addressing the objectives of the current funding while planning for the next round. All this has to be done while ensuring that your team has interesting projects that are going to yield publications. When asked this question, he said, “Now that you are asking me to think about it, it is kind of stressing me out, but in real life, it seems to work out but can take a lot of planning."
There are so many interesting areas within plant biology in which breakthroughs are needed and are likely to come. On the biological side, his interests continue to focus on small RNAs—how are they made, how they function, where they go, how different organisms exploit them for signaling, etc. For the last decade, his lab group has been working with collaborators, mainly the lab of
Virginia Walbot at Stanford University, to determine why many flowering plants accumulate extraordinarily high levels of several classes of small RNAs in their anthers during pollen development. Understanding why this occurs and what those small RNAs are doing would be a major breakthrough. Being able to answer those questions is likely to require technical breakthroughs, including single-cell analysis of small RNAs and spatial transcriptomics of small RNAs, so these are also major (technical) breakthroughs to look forward to, whether from his lab or someone else's.
In the context of IS-MPMI, Meyers would also say that another major breakthrough would be to fully understand the small RNAs that mediate communication between plant hosts and their pathogens and symbiotic microbes. He states that only in recent years have we begun to characterize these RNAs, and there are many things yet to learn about the mechanism of movement, perception, and response, which will require several major breakthroughs, by many people in the field, perhaps with contributions by his group—although not his primary area of work, it is an exciting field in which he will be pleased to be involved.
Dr. Mariana Schuster
Jones (Photo courtesy JIC Photography)
Dr. Mariana Schuster
Dr. Mariana Schuster is a post-doctoral researcher in the Plant Chemetics laboratory at the University of Oxford. Her research currently focuses in unravelling the role of immune cysteine proteases of tomato against the devastating pathogen Phytophthora infestans.
Dr. Jonathan Jones is a professor of biology at the University of East
Anglia, Norwich, UK, and a group leader at The Sainsbury Laboratory (TSL) in Norwich. His
group studies the defense mechanisms that plants use to resist pathogen attack
and the strategies that pathogens deploy to overcome the plant immune system.
Jonathan has made landmark contributions to the field of plant immunity, and
his work has been recognized with honors, including an EMBO
membership, a Fellowship of
the Royal Society, and an International
Membership in the U.S. National Academy of Sciences. Jonathan was recently awarded an Honorary
Membership in the British Society of Plant Pathology. On occasion of the award, I had the pleasure of
interviewing him and discussing his exceptional academic career, the challenges
of living as an academic and bringing one's science to public use, and getting
a glimpse of the man behind the scientist.
Jonathan recognized that he wanted to be a scientist
from early on. However, he says he is an "accidental plant pathologist."
Initially interested in physics and chemistry, but always motivated by research
on the mechanisms that govern life, Jonathan started his Ph.D. program in the
early years of molecular genetics and working with plant DNA. He and his team
then needed to acquire protein biochemistry skills to understand the mechanisms
by which the genes revealed in their cloning contributed to a phenotype (1). Looking back, he highlights the benefits of the
lifestyle of a scientist: "typically, in life, the more you think about
yourself, the unhappier you are. When you are doing science, you become very
preoccupied with thinking about your research problem, which is much more fun
than thinking about yourself."
It is no secret that
the career path to become an academic has changed since Jonathan started out.
He acknowledges that "now it is much tougher than back then." But, as
in the past, the key go/no-go moment to secure an academic post is when people
are applying for a faculty position. Looking back, he admits that after his Ph.D.
degree he "caught the wave of plant molecular genetics, where I was one of
a leading group of scientists who had the skills to chase down interesting
genes to begin to figure out their function" and that it was the "skill
he brought to bear on the problem." The skill was important back then and
is still relevant, but now most labs have these skills: "To get a job you
have to present yourself as someone who is particularly good at something, who
can bring those skills to tackle a problem—and it has to be an important and
interesting problem—where no one has applied those skills and methods before."
In addition, what Jonathan now looks for in applicants for group leader
positions is a unique, original, and independent-minded engagement with the
biological problem; a mature knowledge of the field that allows the applicant
to recognize a relevant research question; and a size and outlook of the
project that lies within "that sweet spot of what is ambitious yet
feasible" and is also "a project that has legs."
In his case, Jonathan
became a group leader and entered the field of plant pathology by applying his
skills in plant molecular genetics to the identification of the then-enigmatic Resistance (R) genes. R genes were
known to confer disease resistance against pathogens. Using transposon tagging,
his group was able to identify Cf-9, a gene that confers tomato resistance against the
fungal pathogen Cladosporium
fulvum (2). "It was very satisfying to develop a lethal
selection that enabled almost effortless recovery of dozens of mutants in Cf-9," Jonathan
Cf-9 encodes a cell-surface immune receptor containing
leucine-rich repeats—the first such receptor to be discovered. Immune receptors
are key proteins that detect molecules from invading pathogens and then
initiate the signaling that ultimately leads to defense responses. Jonathan's
group identified many such receptors and soon started researching their
I have listed only a
couple examples of the fundamental discoveries that Jonathan's group has made
in our understanding of the proteins that confer resistance to pathogen attack.
In fact, when asked which contribution to plant
pathology he is proudest of, he answers: "I could mention a few." Hunting for the
mechanism of action of receptor-like proteins (RLPs), he devised a theoretical framework for how
receptors could be activated, now known as the guard hypothesis (3). "This
was my first theoretical contribution to be
later validated experimentally in a nice collaboration with the group of Pierre de Wit,"
he said. He referred to work on Cf-2, another immune receptor from tomato that monitors
(guards) the activity status of tomato cysteine protease Rcr3, an important
component of the plant's defense repertoire. Rcr3 is targeted by the pathogen
effector Avr2, a cysteine protease inhibitor. Once the pathogen tries to disarm
the plant by inactivating Rcr3, it falls into the trap of the guard mechanism that
ends in a strong Cf-2-dependent
defense response (4). He's also proud to have contributed to the success of
TSL, alongside his superb set of colleagues who continue to do pioneering
science at TSL, and of the success of the alumni who are former students or
postdocs from his lab, such as Tina Romeis, Martin Parniske, Brande Wulff, and
Cyril Zipfel. He's also hugely grateful to all the students and
postdocs who've contributed to the success of his lab over the last 32 years,
and to David Sainsbury's Gatsby
Foundation for their sustained
and generous funding of TSL.
Inspired by the work
of the Brian Staskawicz lab that showed that a pepper immune receptor can confer
disease resistance in tomato (5), Jonathan decided to open an applied research
stream in his group that aims to tackle crop losses due to diseases. The idea
is elegant and powerful: generate pathogen-resistant crop varieties by
introducing immune receptors into plants that lack them. When asked about how
that experience compares to life as an academic, he starts by stressing that
fundamental discoveries in science are the major source of solutions for "real
life problems," and that although he is satisfied with the balance between
applied and basic research in his group, he is conscious that "you cannot
do everything, so any time I spend in applied research, is time I do not spend
making fundamental discoveries, although work with an applied intent can reveal
new and interesting scientific problems."
Some examples of
resistant plant varieties developed with contributions from Jonathan's group
can be found in the June 2016 edition of Nature Biotechnology: soybean resistant to
Asian soybean rust (6), potato resistant to late blight (7), and wheat
resistant to stem rust (8). Two of these three papers were dependent on RenSeq
(8), the sequence capture method for R gene cloning developed in his lab.
Jonathan is happy to have contributed to applied plant science but acknowledges
that he did not predict, and thus underestimated, the fact that people would
find problems in the solutions he provided. He finds the need to work around
these problems frustrating, but acknowledges that even scientists must have
faith and hopes that his solutions will be implemented eventually.
Jonathan is a happy
husband, father, and proud grandfather of four: "two 2‑year olds, one 5‑year
old, and one 8‑year old. Seeing them develop and grow is a great source of
happiness!" On work–life balance and family, he points out that "it's
hard enough to get your own life right, let alone anybody else's." He
highlights his appreciation for his illustrious partner Professor
Dame Caroline Dean. Their family features in the book Mothers in
When asked about his
passion aside from science and family, Jonathan told me that he likes to sail
on the weekends and that he owns a sailing boat called "zigzagzig," which is both the
name of what one must do to take a sailboat upwind and of the model describing
the immune system for which he is famous (8). "The Zig-zag-zig model was proposed to bring together two schools of
thought: the geneticists investigating gene-for-gene interactions, and the
biochemists who added elicitors to cell cultures and defined what happens."
According to this model, plants use cell-surface receptors to recognize the
presence of a pathogen and mount an immune response termed
pattern-triggered-immunity (PTI). Adapted pathogens use effectors to inactivate
PTI and cause disease (effector-triggered-susceptibility [ETS]). In turn,
resistant plants deploy specialized receptors, generally intracellular, to
detect these effectors and mount a stronger defense response termed
As to what is Jonathan up to today, on April 1 (not a
joke) of this year, his group published a new paper in
which they further explain the relation between PTI and ETI (10). This was independently
verified by another lab's report published in the same issue of Nature. Beforehand,
the nature of ETI was rarely studied in the absence of PTI. "These papers show that ETI replenishes and
restores PTI, not only helping us better understand the dynamics of the plant
immune system but also why R gene stacking
for disease resistance works so well. It's been very satisfying to see how the
basic and applied science in my lab has (dare I say?) mutually potentiated."
and chemistry to plant biology. Plant Physiology (nih.gov)
of the tomato Cf-9
gene for resistance to Cladosporium
fulvum by transposon tagging. Science (sciencemag.org)
pathogens and integrated defence responses to infection. Nature
Avr2 inhibits tomato Rcr3 protease required for Cf-2-dependent disease resistance. Science
Expression of the Bs2 pepper gene
confers resistance to bacterial spot disease in tomato. PNAS (pnas.org)
gene confers resistance to Asian soybean rust in soybean. Nature Biotechnology
cloning of a potato late blight-resistance gene using RenSeq and SMRT
sequencing. Nature Biotechnology (nature.com)
of disease-resistance genes in plants using mutagenesis and sequence capture.
Nature Biotechnology (nature.com)
immune system. Nature (nature.com)
Mutual potentiation of plant immunity
by cell-surface and intracellular receptors. Nature (nature.com)
and Jennifer D. Lewis
(left to right): Ilea Chau, Jamie Calma, Yuritzy Rodriguez, Yuan Chen, Karl
Schreiber. Back row (left to right): Jana Hassan, Hunter Thornton, Jennifer
Lewis, Maël Baudin, Jacob Carroll-Johnson, Jack Kim.
Yeram Hong is an undergraduate at the University of California, Berkeley, in her
third year. She is double majoring in forestry and in genetics and plant
biology. From a young age, Yeram has been interested in the natural
environment, with a particular interest in plant biology. Her current research
interests include protein function in plant nuclear membranes and bacterial
plant pathology. Outside of academia, Yeram enjoys drawing, caring for her many
houseplants, and reading literary fiction.
Jennifer Lewis is a principal investigator at the U.S. Department of
Agriculture and an adjunct associate professor at UC Berkeley. Her lab studies
the plant immune system and its response to the bacterial pathogen Pseudomonas syringae.
The Lewis lab is committed to diversifying plant sciences. To encourage this,
we are carrying out interviews with prominent scientists in the field to
discuss their research and their perspectives on diversifying science.
Dr. Wenbo Ma
Dr. Wenbo Ma has been selected to receive the 2021 Ruth Allen Award from The American Phytopathological Society. This
award honors individuals who have made an outstanding, innovative research
contribution that has changed, or has the potential to change, the direction of
research in any field of plant pathology.
Dr. Ma currently holds a position as the senior group
leader at the Sainsbury Laboratory in Norwich, UK, where she is a leading
expert in the field of plant-microbe interactions. Her specialty is effector
proteins: these are proteins produced and delivered by microbial pathogens into
plant hosts, where they can directly manipulate host physiology and immunity.
After introduction into a host, effectors can overwhelm the immune system and
promote vulnerability to infection.
Effector genes are the fastest evolving feature of
pathogens, and Dr. Ma finds the evolutionary race between effectors and hosts
fascinating. She states, "One of [my personal interests] is coevolution. I
feel that effectors and pathogens always surprise us. They always come up with
amazing things, strategies, mechanisms, to fight back against the host."
Dr. Ma believes that effectors hold a key to unlocking more knowledge about
plant pathology: "If we know how effectors function in the host cell, then
we understand how pathogens become a pathogen, how they cause disease."
She also believes that once researchers can identify what pathogens attack in
their hosts, a more selective and strategic defense plan can be created to make
plants more resistant to the disease. Her eventual goal is to "use [the]
fundamental knowledge [she gains] to identify these fundamental principles in
disease and use this knowledge to develop strategies that enhance disease
resistance in crops."
Dr. Ma's current research focuses on effectors
produced by Phytophthora species, an oomycete pathogen
that is linked to a large variety of devastating diseases and that targets a
broad range of hosts. One such disease with a global impact is the late potato
blight, which can cause total crop failure if not properly dealt with in
fields. Dr. Ma was able to identify novel functions of Phytophthora
effectors. She found that many of these effectors perform suppressor activities
that can inhibit the activity of small interfering RNAs (siRNA) in plant
defense pathways. In normal situations, a plant infection can prompt siRNAs to
selectively target and deactivate alien nucleic acids introduced by pathogens.
However, in a plant infected by pathogens carrying these suppressor effectors,
this defense system is shut down. Although small RNAs are usually associated
with viral infections, the presence of Phytophthora
effectors that silence siRNA suggested that siRNAs are actually contributing to
plant defense against nonviral pathogens. From this discovery, Dr. Ma was able
to identify a specific class of plant siRNAs that are important for a nonviral
pathogen defense process called host-induced gene silencing. She is now
continuing this line of research to better understand "how this specific
class of siRNA is regulated during plant response to pathogens, and how we can
use this knowledge to implement this defense mechanism, which is quite
different from [other mechanisms]."
Dr. Ma is also pursuing another significant line of
research into the devastating citrus huanglongbing disease (HLB) caused by the
bacterium Candidatus Liberibacter asiaticus. Citrus HLB is different from
well-studied apoplastic pathogen systems because the bacteria colonize phloem
tissue. Therefore, much of the knowledge gained by studying apoplastic-type
pathogens may not apply. Interested in this new challenge, Dr. Ma proceeded to
conduct research on how to deal with this pathogen, which colonizes a unique
cellular environment. Through her work, Dr. Ma was able to identify a class of
proteases that most likely contributes directly to plant immunity within the
phloem. Currently, she is working on systematically characterizing effectors
from Ca. L. asiaticus and finding their targets in
the phloem or neighboring tissues. Her focus is on phloem colonization by the
bacteria, and she plans to use the knowledge of induced molecular events to
provide more sustainable solutions against citrus HLB.
While Dr. Ma has been a leader in her field of plant
pathology for many years, she did not originally intend to study the subject.
She received her bachelor's degree in general biology while attending college
in Beijing at the Chinese Academy of Science: Institute of Microbiology. During
her undergraduate studies, Dr. Ma participated in research and discovered her
passion for microbiology while studying under Dr. Huarong Tan, who worked on Streptomyces genetics. She then continued to pursue her master's
degree in microbial genetics under his mentorship. While studying in China, Dr.
Ma had the support of her parents in her career path, which she feels was very
quite fortunate or lucky [because] my parents were university professors. I grew
up in an environment where my parents were very supportive of me becoming a
very fortunate to have the support from my family and also my husband.
This level of support was not always the case in her
community, and Dr. Ma said, "I feel there was a lot of bias in the culture
of Chinese communities, especially at that time. Women were usually the
supportive role in the family or in society." Outside the circle of her
close family, Dr. Ma still experienced the criticism of people who questioned
her ability to balance her professional work and her expected familial duties
of raising children. But to this, she exclaimed:
these other opinions or comments from these people become a motivation rather
than discouragement. I began to think that this is nothing I should be stopped
by. I feel now, I almost have a responsibility [to be] that person that can
tell other people, other young female scientists, that this is quite normal. We
can all do it!
She believes that the presence of role models is very
valuable and strives to inspire others to seek their dreams. She commented:
very important to have role models, to have those examples there so that the
younger generations of young kids can see this is nothing impossible. This is
very very possible. There are opportunities, and there are ways, and you can
get here also.
After finishing her master's degree in microbial
genetics, Dr. Ma pursued her Ph.D. degree in Canada at the University of
Waterloo, working with Prof.
Bernard Glick. He is a major pioneer in biotechnology, and his
expertise was the use of bacteria to remediate plants under stress conditions.
Under Prof. Glick, Dr. Ma worked on her Ph.D. thesis, for which she isolated
beneficial rhizosphere bacteria that may help with plant growth from plants
growing in contaminated soil. After receiving her Ph.D. degree, Dr. Ma's
attention was captured by the groundbreaking research of Prof. David Guttman
at the University of Toronto, who, along with his colleagues, had published a
milestone paper on the identification of type 3 secreted effectors from the
bacterial pathogen Pseudomonas syringae.
This paper provided her with a much better understanding of the effector
repertoire produced by bacteria pathogens, and Dr. Ma was hooked. She worked
with Guttman as his first postdoc in Toronto and began her research on
After the University of Toronto, Dr. Ma then pursued
an academic path in the United States, where she worked for 14 years as a
professor of plant pathology in the Department of Microbiology and Plant
Pathology at the University of California, Riverside. Of these 14 years as a
primary investigator, she stated that, "I'm very proud of not only our
solid science and the novel insights that it can provide, but how, through this
research, we were able to train some young scientists. And now, several of them
have their own independent research programs." During her stay at UC Riverside,
Dr. Ma trained more than 50 undergraduate students in her lab. She believes a
large part of the value of her research at UC Riverside came from her ability
to use it as a training program to encourage students, who she sees as the next
generation of scientists and researchers.
Dr. Ma believes that a large part of the beauty of
science is the collaboration that occurs behind the scenes, as doing research
gives her many opportunities to work with collaborators, colleagues, students,
postdocs, and staff scientists. She stated, "I really like working
together with people of different expertise and strengths, and I think it is
more important than ever to work together." She enjoys the diversity of
different perspectives and people within science working together, commenting, "I
think that's my favorite part of research."
Along with her love of collaboration, she is also
passionate about providing resources and opportunities for anyone of any
background to pursue science. She emphasized the need for this, stating, "We
need to provide opportunities. We need to really reach out to people, and I
want to emphasize the importance of providing research opportunities…as early as possible
when they are in high school, middle school, or even earlier." She
believes there are good programs available to specifically support
underrepresented minority groups and women that encourage them to pursue
science and provide resources for them to perform research, such as summer
internship programs. Dr. Ma believes that "we will see fruit from all
these programs in some years. Nothing can happen overnight, but this requires
continuous proactive effort."
For Dr. Ma, research is an ongoing job that does not
end after working hours. She states, "[Research] is not a 9 to 5 job. I
spend time during the weekends, in the evenings; I still spend the time I have
[doing] something research-related." However, in the free time she gives
herself, Dr. Ma spends much of it with her husband and two children. She enjoys
seeing different landscapes and likes to hike with her family on the weekends.
Dr. Ma is also an avid sports fan and is currently keen on the soccer scene of
the United Kingdom where she is now living.
Ani Chouldjian and Jennifer D. Lewis
Front row (left to
right): Ilea Chau, Jamie Calma, Yuritzy Rodriguez, Yuan Chen, Karl Schreiber.
Back row (left to right): Jana Hassan, Hunter Thornton, Jennifer Lewis, Maël
Baudin, Jacob Carroll-Johnson, Jack Kim.
Dr. Kimberly Webb
Ani Chouldjian is currently a senior at the University of
California, Berkeley, majoring in microbial biology. She is interested in
plant-microbe interactions, infectious diseases, and genetics. After graduation,
she wishes to take a year or two off from school to pursue research
opportunities and later enter a microbiology and immunology Ph.D. program.
Jennifer Lewis is a principal investigator at the U.S. Department of
Agriculture and an adjunct associate professor at UC Berkeley. Her lab studies
the plant immune system and its response to the bacterial pathogen Pseudomonas syringae.
The Lewis lab is committed to diversifying plant sciences. To encourage this,
we are carrying out interviews with prominent scientists in the field to
discuss their research and their perspectives on diversifying science.
Dr. Kimberly Webb
Webb is a plant pathologist with the U.S. Department of Agriculture
Agricultural Research Service (USDA ARS) in Fort Collins, CO. Her research
primarily focuses on diseases in Beta vulgaris (sugar beets) caused by Fusarium species, Beet necrotic
yellow vein virus (BNYVV), and Rhizoctonia species. It is
important to study these diseases because sugar beet is an important commercial
crop that accounts for 50–60% of
sucrose production within the United States. Fusarium species, BNYVV, and Rhizoctonia species cause foliar symptoms in B. vulgaris. Fusarium invades the
vascular system of the plant and produces toxins, causing yellowing of the
leaves and necrosis. BNYVV causes rhizomania, whose symptoms include taproot
constriction and proliferation of small feeder roots with reduced sugar content.
BNYVV also causes wilting and yellowing of leaves. Rhizoctonia causes stunted leaf growth
and wilting of foliage. By preventing these plant diseases, growers can
decrease crop losses and increase sugar beet yields.
Dr. Webb studies many isolates within many species of Fusarium and tries to
identify isolates that cause disease in the field. A major tool she uses to do
this is phylogenetics. In one of her studies, Dr. Webb and her team identified
multiple species of Fusarium
that are able to cause disease in sugar beets; they found a greater number
of virulent strains than people previously thought existed. Dr. Webb says, "Phylogenetics
is a really good tool to see if there are genetic mechanisms that are
associated with these pathogen phenotypes." She also studies the effects
of temperature and soil moisture on Fusarium virulence. She has found that
temperatures of 24°C
or higher lead to more Fusarium yellows; however, symptoms do not worsen as
temperatures increase past 24°C.
Higher soil moisture also correlates with an increase in Fusarium yellows.
However when looking at the effect of temperature and soil moisture on Fusarium virulence,
the results ultimately depend on the Fusarium strain under study.
Dr. Webb also studies sugar beet resistance and
susceptibility to BNYVV and Rhizoctonia species. In both cases, she uses proteomics and metabolomics
to look at the proteins and metabolites present in healthy and infected B. vulgaris. She also
looks at the difference in protein and metabolite content in infected
susceptible or resistant strains of sugar beets. Looking at these differences
allows her to identify certain pathways that are related to BNYVV and Rhizoctonia infection
and resistance within sugar beets. These studies help identify specific genes
in B. vulgaris that
confer resistance to these pathogens.
Dr. Webb is proud of the fact that through her
research she is able to help farmers solve problems they are experiencing in the
field. She says, "Within my research, being able to help people solve
problems has been the most exciting part of it, even in my private industry
days I really enjoyed being able to solve a problem for my customers and
farmers at the time." Dr. Webb believes that her research is important for
the future because she is "building little pieces of knowledge that other
researchers can use to not only help sugar beet growers but also agricultural
Although she really enjoys solving problems in her
field of research, Dr. Webb never planned on becoming a plant pathologist. When
she first started her undergraduate degree at Colorado State University, her
intended major was business. However, during her senior year she decided to
change her major to agronomy after taking a plant biology course in which her
professor really challenged her. She said,
When I was an undergraduate I actually started as a business major, science was not even in my mindset. I was in business courses, and I needed to have three more credits to fill out my year. The only class I could get into was a plant biology class, so I ended up taking it. I think that just having really good professors really got me interested in plant biology, and so I switched my undergraduate major when I was a senior and ended up completing a whole agronomy degree within a year and a half in addition to an agricultural business minor.
After finishing her undergraduate degree, Dr. Webb
took a job as a crop consultant in western Kansas, where she was responsible
for advising dry bean growers on general agronomic practices. She was
responsible for looking at pinto bean fields and helping farmers decide how to
better manage their irrigation, soils, and plant diseases. It was this job that
led her to the decision to attend graduate school and learn more about plant
pathogens. She said,
plants had a ton of diseases. Every week I seemed to tell them to spray more
chemicals, and it didn't seem to do any good. They asked me why I was telling
them to spray chemicals when it wasn't doing anything, and I said 'I don't
really know.' That made me decide that I wanted to go to graduate school to
learn more about plant pathology, and I'm glad I did.
Dr. Webb believes that her greatest accomplishment so
far is the fact that she is the first person in her family to go to college and
be able to work her way through college on her own. She says, "I was the
first person in my family to go to college and to go all the way and get a Ph.D.,
when we really had no knowledge of what a college education was; this is the
thing I am most proud of in my career." She participated in a Ph.D.
program at Kansas State University and conducted her studies under the
supervision of Dr. Jan
Leach. Dr. Webb studied Xanthomonas oryzae pv. oryzae, which is a bacterium that causes rice blight.
Because rice is not grown in Kansas, Dr. Webb spent most of her time in the
Philippines at her rice plots and "looked at different combinations of how
to use rice resistance genes and collect bacteria that was in the field."
She would then bring the bacteria she collected back to the United States and
study them. She said, "[We would] characterize the bacterial population using
phylogenetics to see if we were maintaining resistance or if we were
encouraging the bacterial population to mutate to be more virulent."
the very day she received her Ph.D. degree in plant pathology in 2005, Dr. Webb
had her son. She then decided to work in industry. She said, "It's been a
unique path for me; most people take a traditional postdoc path after a Ph.D.
[program] and then move into research or academia. I actually went into
industry instead of a traditional postdoc." While working in industry, Dr.
Webb had the title of seed health manager at STA Laboratories and managed seed
health testing at two facilities—one in Colorado and one in California. She
made sure that testing followed industry standards for quality. She said, "What
our company did was, test all commercial agricultural seed for the presence of
seedborne pathogens. It was basically a diagnostic laboratory. I worked with
over 40 different crops and disease interactions to identify and determine if
they were actually colonizing the seed prior to being sold to the market."
After three years of working in industry, Dr. Webb joined the USDA ARS and
continues to conduct research there today.
When asked if anyone ever discouraged her from
pursuing a career in science because she is a woman, Dr. Webb said, "I
wouldn't necessarily say because I'm a woman"; however, she believes that
biases toward women definitely exist within academia and the workplace. Dr.
Webb was strongly discouraged from having kids, and she believes that women
having to choose between having a career or a family is a big issue in today's
society. She said,
I had an
amazing female mentor; however, she was probably the biggest one who
discouraged me from having kids. I was actually discouraged against either
starting a family or staying in science. There is still this perception that
the most successful female scientists tend to not have kids. I think that is
one of the hardest things for women in science to deal with, because women also
tend to be the primary child carer and to take care of the home. I don't need
to be the most prestigious scientist. I want to do my job to the best of my
abilities, but I may not ever win a Nobel Prize. I really wanted to put my
family as a priority. I think that there is still this stigma that if you don't
want to be the best, then you're somehow not successful, and I think it's a
particular issue in academia. Or, you have to delay everything until after you
get tenure; you have to do "x," "y," and "z"
first, then you can have kids. It's almost a competition type mentality.
Dr. Webb also believes that biases against women exist
within the workplace. She said, "There's this stereotype that women tend
to be more empathetic, gentle, or more understanding, and if you're not falling
into that group then you're being judged on how you communicate with your
coworkers. I have been criticized for not being emotional enough; I don't think
that would ever be told to a man." She believes that a solution to this
problem can be to incorporate training or classes on leadership into graduate programs,
where students learn how to deal with certain communication problems or
personality differences. She said, "I think this is where business does a
much better job than science, because they teach students how to interact with
different people and different personalities. When I was in private industry, I
had to take a couple supervisor and manager training courses. They were week
long sessions, and they were great. I think we should provide more
opportunities like that to our undergraduate and graduate students in science
and plant pathology." Dr. Webb also said that in her 16 years of working
in plant pathology she hasn't seen a decrease in these biases toward women,
which is why these training courses and classes would be important to not only
decrease biases toward women but also toward minorities.
When asked if she thinks the inclusion of women in
plant pathology will increase in the future, Dr. Webb stated that she believes
it will; however, women should also be educated so that they know that careers
in plant pathology exist. She stated that, "It's still a primarily male-dominated
field. Within the USDA, at my location up until two years ago we only had two
female scientists. I think we are doing a better job at the high school and
undergraduate levels of bringing females into the sciences. It would be nice,
especially in rural and agricultural communities, to let women know that there
is more to agricultural careers than just traditional farming. Most women go
into the family farm and business but don't know that there is more technical
science and research that they could do in agriculture outside of just farming."
Aside from educating students on how to deal with
certain biases and women about their career options, Dr. Webb also believes
that the public should be educated on how food is grown. She says, "I wish
that we would teach people more about agriculture than just trying to pick
sides over which agricultural system is better than the other." Dr. Webb
believes that many people fear new scientific technologies, like those used in
agriculture, and, therefore, believes that the public should be educated about
topics like genetically modified crops.
In her free time, Dr. Webb loves to spend time with
her son, who sometimes accompanies her to the lab. She also loves being
outdoors and hiking. One piece of advice that Dr. Webb has for the younger
generation is to "make sure you have a life outside of work. For your
mental health, you have to have activities and other things that you like to