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Dec 18
MPMI InterView with Prof. Adam Bogdanove

Pritha Kundu​

Pritha Kundu is currently a postdoctoral fellow at the University of Nebraska-Lincoln (UNL), USA, with Prof. Joe Louis, investigating the molecular intricacies mediating crop defense physiology against a wide range of pests, with particular interest in the monolignol biosynthetic pathway. She pursued her Ph.D. degree from the Indian Institute for Science, Education and Research (IISER-Kolkata) in wheat fungal pathogenesis, deciphering the phytohormonal crosstalk and the regulatory transcription factors providing resistance. Later, she moved on to study insect calcium signaling and the role of different calcium nucleotide gated channels (CNGCs) and their interaction with the eATP receptor molecule, DORN1 in Arabidopsis–Spodoptera litura herbivory with Dr. Jyothilakshmi Vadassery at the National Institute of Plant Genome Research (NIPGR), New Delhi, India. Her major interest lies in deciphering the key components of the plant defense system that modulates its growth-defense trade off against pests and pathogens.

Adam Bogdanove is presently a professor in the Department of Plant Pathology and Plant-Microbe Biology at Cornell University, with a major research focus on understanding the TAL effectors and their targets in diseases of rice and other crop plants caused by Xanthomonas spp. TAL effectors are those transcription factors that are injected by the bacterium into the host cell, which in resistant host varieties target genes that block disease progression. Bogdanove was one of the discoverers of the modular mechanism by which the TAL effectors recognize specific DNA sequences (the others being co-author Matthew Moscou and, in a simultaneous publication, a group led by Jens Boch and Sebastien Schornack in Ulla Bonas’ lab at the time). Bogdanove’s lab also established computational models to identify key TAL effector binding sites in complex plant genomes. With more than 62 publications and 21,000 citations, Bogdanove also helped pioneer the use of TAL effectors as customizable DNA-targeting tools for applications like targeted gene regulation and genome editing.

It was my pleasure to host an interview with Prof. Bogdanove, which is detailed below, and I want to thank MPMI for this exclusive opportunity.

My interest in Prof. Bogdanove's long journey from Yale to Japan—he was an English instructor there—to Purdue, Iowa, and now Cornell prompted me to ask him whether it was a strategic move or happened one move after another. Bogdanove remembered his years in Japan as very formative, and he decided then to start his work on a long-standing interest in environmental protection and a newfound interest in agriculture and biotechnology and sort of merge the two in the late 1980s. At this inflection point in a field like plant pathology, plant breeding was interested in generating innovations that would ultimately reduce our dependence on agrochemicals. The intensive, but limited, agricultural facilities (limited land), triggered in him the interest to apply for graduate school at Cornell University. When questioned about the struggles of life as a Ph.D. student, he mentioned that his rotation across three amazing labs at Cornell helped him immensely in choosing his Ph.D. lab, which had successfully purified the first microbial elicitor for hypersensitive reaction. He also mentioned that it was quite challenging to raise his three kids during graduate school but that the process was made smooth by his wife. ​He was particularly driven by some exciting ideas for research that kept him moving forward.

When asked about his entry into the field of TAL effectors and being one of the pioneers, he remembered the tremendous influence rice pathologist and friend Jan Leach had, the then recently published fully sequenced rice genome, and his strong interest in studying tissue specificity in plant–pathogen interactions. He decided to study the interactions of rice with the two pathovars (vascular and nonvascular)​ of X. oryzae—pv. oryzae and pv. oryzicola—infecting different plant tissues. His scientific interest revolved around two questions:

  • What determines tissue trophism for bacterial pathogens and plants?
  • Does the plant respond differently to these two pathovars?

He further developed an inoculation method for both pathovars and examined the differences that these pathovars had on reprogramming the plant transcriptome. The challenge was to connect the bacterial effectors to their targets, which led him to study the comparative genomics on the pathogen side and specifically to the detailed study of the largest effector family found in Xanthomonas spp., the AvrBs3/PthA or TAL (transcription activator-like) family. He then moved on to study individual TAL effectors targeting individual host genes, which ultimately led to the mechanism for TAL effector binding specificity. At a later stage, Bogdanove collaborated with Dan Voytas and others to develop TAL effector-based targeted nucleases for genome editing.

Bogdanove also suggested that being mindful and intentional helps in developing a research group with a strong foundation of research interests that keeps you moving. "Science is a social enterprise"; thus, building a strong network to gain information and facilitate collaborations is definitely helpful in the long run. When questioned about the struggles he faced while running his lab, he emphasized the importance of giving the freedom to young enthusiasts to be intellectual drivers who share the same interests and getting the lab funded. "Research can be stressful at times"; thus, he mentioned the acute importance of providing a healthy lab environment. Drive, curiosity, and intellectual leadership are essential components in each member that determine the success of an enterprise. An important challenge he faced was retraction of an article from his group, and he stressed the imperative to correct the literature openly and the importance of eliminating any stigma related to it.

When questioned about the critical factors in running a lab successfully, he emphasized the importance of creating a space in which people feel free to be critical of one another. Valuing one another's views is another important component that determines team success—the idea that everyone must critically look through the data and then give critical feedback. "There is an increased tendency to get medals for everyone," which he suggests is a generational issue and that we should be critical of our data and maintain a balance. He also stressed that celebrating lab successes and milestones together help you develop as a group.

When asked about work–life balance, he mentioned that's been very easy for him. He mentioned his family to be his most important hobby, besides gardening and hiking. He loves to spend quality time with his family. Presently, he is basking in the happiness of having his first 6-week-old grandchild.

When asked about the key advice he has for the scientific community, he suggested that we follow our dreams. To do something that wakes you up in the morning and does not let you sleep at night ("sometimes"). Something that interests you. Science is not a profession to pursue if you have no passion for it. Try to engage with the community and seek out help and be open with the science that you perform. Scientists all over the world are advocating for open science, which is essential for the development of the global scientific community. We are working together in this world to pull each other up, as he mentioned that our mentors and mentees should be our examples. He suggested all early-career researchers be an example for their mentees.

Altogether, it was a wonderful experience to interview Dr. Bogdanove, the new IS-MPMI president and be enlightened by his ideas for working together in a collaborative environment and being open with our science and scientific community as a whole.

Dec 18
InterView with Cara Haney

Siva Sankari

Siva Sankari is a new assistant investigator at the Stowers Institute for Medical Research. Her research focuses on understanding the mechanism of action of plant peptides on symbiotic bacteria. She is an assistant feature editor for the MPMI journal.

Cara Haney is a recipient of the 2023 IS-MPMI Early Career Achievement Award. Haney is an associate professor at the University of Pittsburgh, PA. After a very successful journey with her lab at the University of British Columbia, she recently moved her lab to Pitt, which is in her hometown. Her lab works on understanding the genetic factors that regulate the functional outcome of plant–microbe interactions.

I was very excited to interview Cara, mainly because I love her research questions. These were questions that I wondered about when I started working with symbiosis. What determines whether a symbiotic microbe will become a pathogen, mutualist, or commensal? How does a host plant distinguish between beneficial and pathogenic bacteria? Being a new PI myself, I was also interested in knowing more about the nitty gritty things one should know as an early-career scientist. Our Zoom call was more like a fireside chat rather than a formal interview. Following are some important excerpts from our chat.

I was very curious about why she was interested in her research questions and what led her to start asking these questions in her lab. Cara said,

I first developed an interest in plant–microbe interactions as an undergraduate. I was a plant science major, and my academic advisor suggested I take Plant Pathology, which included a lab component. Isolating microbes from plant tissues opened up an entire world for me. After working in a plant pathology research lab, I then did my Ph.D. on rhizobia–legume symbiosis. Over time, I became more and more fascinated with the microbes that just were there—not the devastating pathogens and not the closely co-evolved mutualists. I was fixated on the idea that these microbiota might hold some clues to why pathogens are pathogens and how mutualists first evolved. During my postdoc, I wanted to develop a system that would let me start to ask questions about the origins of symbiosis. As a postdoc in Fred Ausubel's lab, I started working on Arabidopsis–Pseudomonas as a model microbiome system, which became the model system in my own lab. This system has let us answer questions about bacterial lifestyle transitions and how plants distinguish closely related pathogens and mutualists.

I asked her what an early-career scientist should focus on to be successful in their field. She replied,

I don't think there is just one way to be successful in science, and I think a lot of what academia needs is to rethink and broaden our ideas around metrics of success. I would advise early-career scientists to first and foremost define their own metrics of success, as there are a lot of ways to make meaningful and impactful contributions to science. For me, success is mentoring students and postdocs to reach their self-defined career goals and generating data for field-specific publications that advance scientific knowledge.

When asked what would be her advice for postdocs in particular, Cara replied,

It's essential to find a supervisor who is supportive of your personal career goals and who will be a champion for you. I also think postdoctoral positions should be targeted training for a specific end goal; many jobs don't require a postdoc, or just require a short postdoc, and so I always ask trainees what they want out of their training. Finally, I also think many postdocs with goals of securing a faculty position spend too much time in pursuit of a single high-impact paper and forego developing the depth of an independent research program. I think the latter is much more important for long-term success in academia.

There are numerous commitments that come with being a faculty member, especially in the first few years of starting a lab. I asked how she does it all! She said,

An amazing thing about running a research lab is that you're now not alone in answering questions that are of interest to you. But at the same time, it means a lot of people are depending on you to advance their career and research goals. l try and prioritize the things that are rate limiting for people in my lab—whether it is discussing an experiment, sending an email to connect them to a key resource, or editing a manuscript draft. I'm also not someone who is willing to work around the clock, so I allot specific amounts of time for tasks and do what I can in the time I have to give. Sometimes the result is not to the standard I wish it was, but I have learned to accept 'good enough' in many areas of my job. Finally, I've learned to say no. I recently got advice that for everything I say yes to, I need to drop something else. That has been helpful in making sure I can reserve time for the parts of my job I really enjoy, like the science itself and mentorship.

When asked if she faces any additional challenges being a woman in science, Cara replied very calmly,

I have certainly experienced challenges ranging from tokenism to overt sexism. This sometimes results in the rather contradictory internal narrative where I simultaneously feel like I need to be better than my male counterparts to be taken seriously, and at the same time like I've only gotten to where I am because of my gender. Now ,I prioritize academic spaces, interactions, and collaborations where I feel valued for what I bring. And times where I feel I'm being included just because I'm a woman, I remind myself that it doesn't mean I don't belong.

I thoroughly enjoyed this interview. I have followed Cara's scientific work, yet it was a delight to know her as a person. This interview also led to me borrowing some bacterial strains from Cara, which she happily shared. I hope early-career readers take home a few key points from this interview.​

Dec 18
MPMI InterView with Xiufang Xin

Eilyn Mena

Eilyn Mena is a scientist at the Clemente Estable Biological Research Institute of Montevideo, Uruguay, where she has worked for the past seven years. Her main research is focused on Diaporthe–soybean interactions and the identification of genes involved in fungal pathogenicity and plant defense. Eilyn was the recipient of a Ko Shimamoto Travel Award to attend the 2023 IS-MPMI Congress.

Xiufang Xin received the 2023 IS-MPMI Early Career Achievement Award at the IS-MPMI Congress in Providence, RI. She leads a research group in the Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology and Ecology.

It's a pleasure to me to have been selected for the interview with her. I listened to her talks at the 2023 IS-MPMI Congress: "Environmental Impacts on Plant–Microbe Interactions" and "Understanding Plant–Pathogen Environment Interactions." I really liked her talks even though I don't work with environmental factors in the Diaporthe–soybean pathosystem. Regarding her scientific work and experience in the plant–pathogen interactions field, I asked her some questions.

For Xiufang it's definitely a great honor to have received the IS-MPMI Early Career Achievement Award in recognition of her academic career. About the award, she said, "There are many great and young scientists in the field, and I feel lucky to receive the award."

Question: Can you provide an overview of your research and your specific focus within the field of plant–pathogen interactions?

Xiufang Xin: We try to understand the mechanisms underlying the interplay between plant, pathogen, and environmental factors. More specifically, we study the plant immune system, particularly the interplay between PTI and ETI, and how high air humidity affects plant immunity and pathogen virulence to promote plant disease. We also have projects investigating the regulation of plant leaf microbiota.

Question: How do you approach disease resistance in plants, and what strategies do you use to develop resistant crop varieties?

Xiufang Xin: By studying PTI-ETI interplay, we hope to offer new ways of strengthening disease resistance in plants. In addition, our study shows that high air humidity suppresses plant immune pathways. By understanding the specific plant elements/modules and humidity affects, we hope to develop plants that are resistant to the influence of high humidity and, therefore, retain immunity vigor under high humidity.

Question: What challenges do you encounter in your research, and how do you work to overcome them?

Xiufang Xin: I think for areas that many people are working on, like plant immunity, there is potential competition. Collaborating with people is always better, and finding unique angles/directions of research is also important. For air humidity-related projects, one challenge is that there is little information, since not much work has been done previously. It's good that people are becoming more interested and more labs are starting to work on related topics. I think the progress in this field will be faster.

Question: I work in plant–pathogen interactions with Diaporthe species in soybean. I want to understand both the pathogen virulence and plant immunity. For these, I sequenced the genome of the fungus, and I analyzed the transcriptome of the fungus and plant at 8- and 48-h postinoculation with respect to control. Now, I believe that other work is necessary to determine the function of the genes and to be able to have an approach to the molecular mechanisms. What do you recommend to me?

Xiufang Xin: I do not have much background information on your project. From your description, I think you need to obtain a list of fungal and plant genes, based on transcriptome analysis, that you want to work on further. One approach is to generate the fungal/soybean mutants and determine which mutants have infection- or disease-related phenotypes. Then, you may narrow the list down to one or several genes and determine how they function, e.g., by investigating their regulatory mechanisms on transcription, protein stability, protein modification, or others.

Question: What do you think about the future of immunity in plants induced by effectors?

Xiufang Xin: I'm guessing that you are talking about ETI. There have been many breakthroughs on ETI and NLR activity in recent years. It's one of the fastest evolving fields in MPMI. I feel it's an exciting time and anticipate there will be many advances in the future.

Throughout her career, Xiufang received her bachelor's degree in biology at China Agricultural University, after which she has developed studies in the United States and China. She is an example for me because I'm from Cuba, where I received my bachelor's and master's degrees. I have been living in Uruguay since 2016, and I finished my Ph.D. study at Clemente Estable Biological Research Institute. Now, I'm looking for a postdoc position, and I talked about these challenges with Xiufang and asked her for career advice based on her experience. I want to share with you two of the answers to questions that may be useful for other young researchers like me.

Question: Should I change my research subject or move to another country?

Xiufang Xin: The most important thing is probably finding a research project/direction in which you are interested. If you want to pursue an academic career afterward, finding a supportive mentor is also important. There are always many other factors to consider: for example, location, living expenses, and family. It's up to you which factors are most important to consider. I would encourage contacting PIs as early as possible, and after going through the process (emails, interviews, negotiations, etc.), you will know where you want to go.

Question: Do you have any advice for early-career researchers?

Xiufang Xin: Try to identify important, and ideally new, scientific questions. If possible, do something different (this is the advice my previous mentor Dr. Sheng Yang gave to me, which I think is quite important, especially for early-career researchers).​

Sep 18
InterView with Dr. Simona Radutoiu

​​​Alicia Camuel ​

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 

03InterView_Radutoiu.jpgBetween 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 scienceit 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 efficientand 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 challengecoordination between organogenesis and infection is essential but difficult to achieveand 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. ​

03InterView_Camuel2.jpgOur 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

Jun 28
InterView with Dr. Wenbo Ma

Tianrun "Jerry" Li​

Tianrun 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."​

Jun 28
InterView with Dr. Maeli Melotto
Aline Sartor Chicowski

Maeli Melotto

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 Pseudomonas syringae.

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."​

Jun 28
InterView with Munir Nur and Kelsey Wood

​A Fruitful Symbiosis Between an Undergrad in Computer Science and a Graduate Student in Genetics and Genomics

Munir Nur

Kelsey Wood

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 InterConnections article.


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.

Jun 28
InterView with Dr. Bing Yang

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.

Jun 28
InterView with Dr. Cyril Zipfel

​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."

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.

Jun 22
InterView with Dr. Blake Meyers, Newly Elected Member of the National Academy of Sciences
Dr. Aj​ayi Olaoluwa Oluwafunto​

Dr. Blake Myers

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​.

Interview Summary

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.

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