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Jun 14
InterView with Dr. Jonathan Jones
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Dr. Mariana Schuster
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Dr. ​Jonathan Jones (Photo courtesy JIC Photography)

Dr. Mari​ana 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. 

D​r. Jon​athan Jones

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 commented.

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 function.

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 Science.

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 effector-triggered-immunity (ETI).

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."

References

  1. ​From physics and chemistry to plant biology. Plant Physiology (nih.gov)

  2. Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science (sciencemag.org)

  3. Plant pathogens and integrated defence responses to infection. Nature (nature.com)

  4. Cladosporium Avr2 inhibits tomato Rcr3 protease required for Cf-2-dependent disease resistance. Science (sciencemag.org)

  5. Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. PNAS (pnas.org)

  6. A pigeonpea gene confers resistance to Asian soybean rust in soybean. Nature Biotechnology (nature.com)

  7. Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing. Nature Biotechnology (nature.com)

  8. Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nature Biotechnology (nature.com)

  9. The plant immune system. Nature (nature.com)

  10. Mutual potentiation of plant immunity by cell-surface and intracellular receptors. Nature (nature.com)

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Jun 14
InterView with Dr. Wenbo Ma
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 Yeram Hong
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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.

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Dr. Wenbo Ma
Yeram Hong and Jennifer D. Lewis

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 fortunate:

I'm 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 professional. I'm 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:

Eventually, 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:

It's 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 pathogenic bacteria.

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 opportunitiesas 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.

Jun 14
InterView with Dr. Kimberly Webb
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Ani Chouldjian
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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.
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Dr. Kimberly W​​ebb
Ani Chouldjian and Jennifer D. Lewis

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

Dr. Kimberly 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 5060% 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 producers everywhere."

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,

My farmers' 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."

On 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 do."

Mar 19
InterView with Professor Emeritus Dr. Valerie Williamson

Ani Chouldjian and Jennifer D. Lewis

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Ani Chouldjian

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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.

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Dr. Valerie M. Williamson

 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, they are performing interviews with prominent scientists in the field to discuss their research and their perspectives on diversifying science.

Dr. Valerie M. Williamson

Dr. Valerie M. Williamson is a professor emeritus at UC Davis in the Department of Plant Pathology. Throughout her career at UC Davis, she has studied the Mi gene, a gene found in tomato, which confers resistance to root-knot nematodes, such as Meloidogyne incognita. M. incognita infects thousands of crops and forms biotrophic interactions with host roots. These nematodes establish feeding sites on tomato plant roots and release chemicals that induce nuclear division of root cells without cytokinesis, leading to the formation of enlarged cells called galls. The Mi gene, like other resistance genes, has conserved leucine-rich repeat (LRR), leucine zipper (LZ), and nucleotide binding-site (NBS) domains, which allow for pathogen recognition and signal transduction; therefore, tomato plants that have this gene are resistant to root-knot nematodes.

Dr. Williamson’s greatest scientific achievement was cloning the Mi gene, which allowed for its insertion into plants that are susceptible to root-knot nematode infection. This gene was discovered in a wild tomato plant and had other “bad” genes associated with it. Cloning the gene allowed Dr. Williamson’s lab to insert the Mi gene, alone, into other plant genomes to see it could confer resistance to nematodes. When asked why she thinks her research is important for the future, Dr. Williamson said,

This root knot nematode is all over the world, every continent has it, except Antarctica; it’s a huge problem in agriculture everywhere, and the way it’s controlled is with pesticides. And, they’re nasty pesticides, and there is a need to come up with new control measures. So, modifying [plants] with the Mi gene would be another control. Another project that I’ve been working on for the past 10 years is trying to figure out what attracts nematodes to roots. If you could understand what attracted them to roots and repel them, or trap them so that they are not attracted to roots anymore, that would be another way of controlling them.

Dr. Williamson’s discovery and cloning of the Mi gene was monumental; however it took some time for her to find what she is truly passionate about. Dr. Williamson grew up in a town in New Hampshire and had never planned to become a plant pathologist. Instead, her plan had been to become a medical technician. She said, “I was assuming that I would probably do some kind of medical technician type of work, because that’s the only thing I knew about that would be a good career. I loved biology, and I had always loved biology.”

As a first-generation college student, she attended Northeastern University for her undergraduate education, where she participated in a cooperative education program. The program encompassed six months of schooling and six months of clinical experience that focused on blood research. However, this type of research did not interest her. She said, “I did some karyotyping of human chromosomes, drawing blood, and analyzing blood—but I didn’t really like that.”

While looking for other research opportunities during her undergraduate education, Dr. Williamson was discouraged at times from pursuing a career in science and faced gender-based discrimination. She said, “Yes, there have been discouraging things. When I was an undergraduate and was doing these research stints in different places, there was one place I went to. They said that they had never had a woman before, and if they hired me, they would have to put in a new restroom.”

Although she was discouraged at times, Dr. Williamson did not give up. After graduation, she married a man in the army and moved to Alaska with him, where she obtained a job at the University of Alaska’s Institute of Marine Science. There she did research on trace metal contaminants of sea water; however, she was more interested in the biological samples that her colleagues were collecting. She said, “The people around me were collecting biological samples, and I thought that was much more interesting. I was frustrated because I was really interested in science, but I couldn’t do what I wanted to do. When you’re a technician, you can’t do what you want to do. You have to do what you’re assigned.”

Wanting to learn more about research, Dr. Williamson applied and was accepted into a biochemistry graduate program at UC Davis. Her thesis work was on RNA polymerase in Bacillus subtilis, and she received her Ph.D. degree in biochemistry in 1978. After obtaining her Ph.D. degree, Dr. Williamson became a postdoctoral fellow at the University of Washington in Seattle, where she worked on alcohol dehydrogenase in yeast. She said, “I got excited about alcohol dehydrogenase, so I cloned the gene that encodes it, which turned out to be very useful.” Alcohol dehydrogenase is an enzyme that converts acetaldehyde into ethanol during glucose fermentation in yeast. It is used in industry to reduce ketones into chiral alcohols.

After completing her postdoc, Dr. Williamson accepted a job in Dublin, CA, at a company called Arco Plant Cell Research Institute. During this time, oil was scarce due to the Cold War, and a lot of effort was being put into biofuel production. While there, she continued studying yeast and alcohol dehydrogenase, because the company was interested in fermentation. While working at Arco Plant Cell Research Institute, Dr. Williamson noticed that her colleagues were working on plants, and so she decided to start a project on plants as well. She said, “The other people hired there were doing research on plants, so I decided to start a project on plants. I started looking into what I would like to do. I knew that I liked nematodes, because I had met some C. elegans researchers in Seattle, and I looked into plant pathogens and thought I want to do something on plant–pathogen interactions.” However, when oil prices lowered, the company decided not to pursue agricultural research anymore. The company was sold, and at the same time, a position opened up in the Department of Nematology at UC Davis.

At the time, Dr. Williamson was not confident in her abilities to become a faculty member. She said, “I did not plan on being a faculty member. I thought that was something that I could not handle. There weren’t many role models of women being successful in it. They were mostly men then.” However, when Dr. Williamson applied for the UC Davis faculty position, she got the job.

When she started working at UC Davis, Dr. Williamson did feel the pressure of being one of the only women in a faculty position. She said, “When I first started at UC Davis, a lot of the committees I would get put on I would be the only woman there. I would be stuck onto all these committees because they wanted to have a woman there. That’s kind of hard on the woman or minority to be the only one, and you also get stuck with a lot of stuff.” Times did improve, however; Dr. Williamson persevered and found what she was most passionate about. She has been doing research as a UC Davis faculty member on the Mi gene and root-knot nematodes ever since.

When asked if she sees growth in the inclusion of women and minorities in STEM, she said,

It’s improved enormously since I started, and I think the women are holding their own really well. It’s not like we had to put them there so that we could have more women. We have a better proportion [of women]. They are really making major contributions and that helps too, because then you get more [women] in. They see that women can do this, and they can do a really good job in this.

There are a lot of young people who don’t realize that [research] is a career option, and for them to see it, they need to be given chances in high school or early undergrad [courses] to just see what science is.

Minorities have been harder to get in science. Maybe they are still at the stage where they need to be exposed more. Interacting with high-school teachers is a good way [and] having summer programs where they come in and look at labs and hang around the labs. It’s really good to have undergraduates in the lab, especially [students] who have not been exposed to science and have these programs where they come in and make friends with people who have been more exposed to science.

Although Dr. Williamson is now retired, she continues to perform research. Mi gene-resistant nematodes have been found throughout California; therefore, Dr. Williamson is initiating efforts to find differences between resistant and nonresistant nematodes through comparison of their genomes.

In her free time, Dr. Williamson likes to travel, be outside, and hike along the coast at Point Reyes and Bodega Bay. She also likes to garden because she can “look at [her] plants and think about their diseases.”

Mar 19
InterStellar: Interview with Newly Elected AAAS Fellow Dr. Barbara Kunkel
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Yeram Hong 

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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.

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Dr. Barbara Kunkel

Yeram Hong and Jennifer D. Lewis

Yeram Hong is an undergraduate student at UC Berkeley in her third year. She is double majoring in forestry and genetics and plant biology. From a young age, Yeram was 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, they are performing interviews with prominent scientists in the field to discuss their research and their perspectives on diversifying science.

Dr. Barbara Kunkel

Dr. Barbara Kunkel is a professor at Washington University in the Department of Biology, where she leads a research group and teaches courses in general and plant biology. Her lab is interested in the complex biological communication between bacterial plant pathogens and their hosts, as well as the bacteria’s virulence mechanisms. Her research group takes a genetic and molecular approach in looking at both bacteria and their plant hosts to develop a more clear and integrative view of disease. Currently, Dr. Kunkel is interested in investigating the molecular mechanisms of disease caused by Pseudomonas syringae in Arabidopsis thaliana. More specifically, she works to understand how auxin, a plant growth hormone, may play a role in these plant–bacteria interactions. She is particularly interested in understanding how bacteria sense auxin and respond to it and the significance of this interaction. Prof. Kunkel’s research is important in obtaining a fundamental understanding of the virulence strategies pathogens use. This knowledge can be used in the future to develop breeding, cultivation, and control strategies to address the global issues of crop failure and agricultural pathogen outbreaks. By providing fundamental knowledge about the interactions between bacterial pathogens and plants, she believes that her discoveries may be crucial to developing novel biological technologies to address crop losses from disease.

One of her major discoveries was the identification of the coronatine virulence factor as a jasmonic acid mimic in the Arabidopsis–Pseudomonas pathogenic interaction. Her lab stumbled upon CORONATINE INSENSITIVE 1 (COI1), a gene that encodes the coronatine receptor, while examining plant mutants that were particularly resistant to bacterial infection. At the same time, another researcher in her lab, who was focused on the bacterial side, isolated several mutants in a biosynthetic gene cluster in P. syringae that coded for coronatine. Connecting these observations, her lab realized coronatine was particularly significant. Although coronatine had been previously identified, her lab was able to find their “first indication that manipulation of plant hormone biology [aside from purely defense hormones] was important in these pathogen interactions.” They had discovered a virulence factor that the pathogen used as a hormone mimic to modulate the biology of its host!

To recognize her considerable and valuable contributions to the scientific community as an educator, mentor, and researcher, Dr. Kunkel was awarded the AAAS Fellowship as one of the elected Fellows of 2020. In response, Dr. Kunkel commented: “I was surprised to tell you the truth…but I was also very thrilled [as] it gives me some exposure that I would not have had otherwise.” This opportunity allows people to learn about her research and become more interested in the topics that she is researching. Through her achievement, she is paving the way in science as a role model for future women scientists to look up to and have the conviction that success is possible.

Despite her research successes, she had not originally planned on entering this career path. From a young age, Dr. Kunkel had a love for horses and other large animals and dreamed of becoming a veterinarian. Following her dreams, she attended the University of California, Davis. There, she became drawn to the pastoral life of working in the agricultural sector and began studying agricultural sciences. However, this was not meant to be, as she stated, “it was unrealistic because I’m not a farm kid, I’m a city kid.” In her second year of college, Dr. Kunkel found her true passion in a genetics course taught by Dr. Francisco Ayala. She became a genetics major, specializing in plant biology and bacteriology.

After graduating from UC Davis, Dr. Kunkel was unsure about her next steps. However, she loved to learn and was just being introduced to the world of scientific experimentation; graduate school seemed like the next step. Interested in symbiotic relationships, she looked for a graduate school where she could study plant–microbe interactions. Although she was not able to find the right opportunity in this line of interest, she obtained her Ph.D. degree at Harvard studying gene expression in Bacillus subtilis in Dr. Richard Losick’s Lab. For her postdoc, Dr. Kunkel decided to pursue research in the area of plant–pathogen interactions because she wanted to work with plants again and she “wanted to study a system where you could do the bacterial part and the plant host was genetically tractable.” She completed her postdoc at the University of California, Berkeley, with Dr. Brian Staskawicz, studying disease resistance in plants using a genetics approach to investigate which genes control the ability of a plant to detect the pathogen and activate defense responses.

Although Dr. Kunkel had never planned on becoming a university professor, she realized while obtaining her Ph.D. degree and completing her postdoc that she loved the scientific process. During her postdoc, Dr. Kunkel decided she wanted to run her own lab. While she was working in the Staskawicz lab researching disease resistance, she continued to wonder, “What’s the pathogen’s part in this?” She began planning to start a lab that would also study the pathogen as well as the plant host. At this time, researchers had discovered the type III secretion system (T3SS) in bacteria. Using this system, bacteria can inject into their plant hosts proteins that directly affect plant physiology and make the plant more susceptible to infection. Fascinated by the recent discovery of the T3SS, Dr. Kunkel decided that one of her first projects would be to study virulence mechanisms in P. syringae and find out more about the proteins being injected.

02Kunkel_Image2.jpgAs a woman in science, Dr. Kunkel wondered if she could manage a full-time, professional career as a professor. Her mother expressed concerns about her career path as a researcher, intimately aware of the time and dedication required for the job as Dr. Kunkel’s father was a professor of physics at the University of California, Berkeley. Although her parents did encourage her curiosity and to pursue the opportunity, her mother did not believe that Dr. Kunkel, who was in a serious relationship at the time, would be able to “be a mom with kids and a homelife and be a professor.” Along with these concerns, Dr. Kunkel found there was a lack of role models who could show her that this was in fact possible. She stated, “I wanted to look around and try to find role models or examples of what I wanted to do…[but] there weren’t a lot of role models for me at the time.” From her perspective as a professor, Dr. Kunkel emphasized the importance of role models. She said,

There has to be that first role model…. I think if you’re going to be the only woman, and if everybody is white, the only woman of color, that’s two barriers. You have to be the first one, and you have to be the role model? That’s a lot to do…. I teach a freshman biology class in which we have a lot of attrition in that first semester because it’s a challenging class. A lot of people go, ‘Oh my gosh, I can’t handle this.’ And, what we think would be helpful would be…that all the students could see themselves as scientists regardless of their background, [whether they’ve] taken AP Biology [or are] the first generation to go to college [or if] they’re black. How can we help them see themselves as succeeding there?

Another difficulty with being a woman in science was that she found it hard to be recognized for her accomplishments. When she was receiving more opportunities than some of her male colleagues, she said, “Some of them [said], ‘You’re getting all of these interviews because you’re a woman.’ Like ouch, I’m a good scientist and I’m a woman.” She also recalled a story from her years as a postdoc:

I think I did experience some of that when I was a postdoc, and I remember at some point [my co-postdoc] was trying to tell the boss about my results. And finally I just said, ‘Let me tell him. I did this.’ I don’t know if he was consciously trying to grab the credit for it, if he was thinking I couldn’t speak for myself, or what was he doing. The funny thing is this guy is a very very good friend of mine to this day. We had a few rough times in there where I had to just say, ‘Back off guy!’

Despite these past experiences, Dr. Kunkel believes that things are changing for the better. She believes that while the situation is still not perfect, there has been an increase in the number of role models that women can look to to know that they can actively pursue science. With additional focus on the effect of implicit bias and more strategic dispersal of funding for small labs and minorities to pursue research, Dr. Kunkel believes that we can continue to work toward a more diverse and inclusive scientific community.

When she is not busy in her lab, Dr. Kunkel loves to be outdoors. She enjoys hiking and gardening, which she says could be why she likes plants so much. She is also an avid reader and is currently part of a book club where she is exposed to many different genres and authors. When asked about her favorite types of books she exclaimed, “I like books with strong women!”

Mar 19
InterStellar: Interview with APS Award of Distinction Honoree Dr. Jan Leach

Kamal Kumar Malukani

Dr. Jan Leach (Colorado State University) was the recipient of the 2020 Award of Distinction from The American Phytopathological Society. This award, the highest honor APS can bestow, is presented on rare occasions to persons who have made truly exceptional contributions to plant pathology. Dr. Kamal Kumar Malukani, a postdoc in the lab of Dr. Ramesh V. Sonti at the CSIR-Centre for Cellular and Molecular Biology in Hyderabad, India, recently interviewed Dr. Leach to learn more about the qualities that one needs to become a leader in the field of plant pathology.

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​Dr. Kamal Kumar Malukani

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Dr. Jan Leach


1. Many scientists, especially those early in their careers, find it difficult to manage a balance between their professional and personal life. How do you manage it?

I don’t know that I did manage it particularly well! My husband, also a plant pathologist, and I started our faculty positions at the same time, so we were both going through the tenure and promotion process together. We shared an understanding of the pressures and demands of our positions. We respected and, very importantly, supported each other’s choices and challenges, which really helped as we worked through the ranks. We joked that we often passed each other in the door, one coming and one going, much of the early parts of our careers. So, I would say understanding and respecting each other’s situation played a big role.

2. Thinking back to the beginning of your career, can you provide one or two things you wished you had known that might have made starting your career easier?

As passionate scientists, we focus our early training on getting deeper into the science. We are frequently very focused on learning what is needed to support our research. But, unfortunately, we are often not well-trained in how to manage people, which is a critical part of running a successful lab. For me, it was “on-the-job” learning, and as a young faculty member trying to build my program, it was a hard go. Fortunately, I found good mentors to reach out to for sound advice. I still do that; more than 30 years of experience, and I still reach out to mentors, some decades younger than me, for guidance on how to handle tough people problems.

3. What do you believe is the biggest question in the field of MPMI today, and why?

One of our biggest questions is how we will identify and stabilize plant disease resistance in the face of a changing climate. Adapting crops to withstand disease in the face of changing temperatures and unpredictable weather patterns is not trivial. We have observed that some disease-resistance genes lose efficacy with a few degrees of increase in temperatures. Other resistance genes are more effective at high temperatures but may fail under drought conditions. Successful crop production in the future will likely depend on more complex solutions, discovered by studying the plant, pathogen, and environment as an interacting system (phytobiome) and integrating more diverse options into our tool kits. Successful translation of those solutions will likely require those of us in MPMI to work even more closely with those nearer to the field and the growers, including breeders, agronomists, and extension specialists.

4. You have been involved in a lot of science, as well as the administrative side of work. How do you manage this transformation?

The secret is working with talented, independent, and smart people who are patient with my split position. I have kept my research program running because it is the candy in my job, i.e., the part of the job where I am most comfortable and find the most joy. It also helps keep me grounded in the issues and challenges faced by the faculty I serve as associate dean for research. Balancing the two parts of the job is difficult, and I battle the constant feeling that I am not doing either job very well. But, we all have a limited time, and I try to give the best output in both parts with the help of people around me.

5. What advice would you like to give to emerging scientist that will help them in the long run?

Probably the best advice I received as an assistant professor was “Choose your battles wisely!” In other words, consider carefully if this is a cause or battle that is really important and worth investing your time and energy. You only have so much energy and time…conserve them for the important causes and issues.​

Mar 19
InterStellar: Interview with World Agriculture Prize Recipient Dr. Pamela Ronald
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Nick Colaian​ni​


Nick Colaian​ni

I had ​the pleasure of interviewing Dr. Pamela Ronald who was recently awarded the 2020 World Agriculture Prize for her ach​ievements in agricultural research and science education. Dr. Ronald is a leader in the research field of plant responses to environmental and pathogen stresses. Additionally, she is an advocate and educator for sustainable food practices and modern crop breeding strategies. She has a fabulous TED talk and has written a book with her husband on modern crop science and organic farming practices titled Tomorrow’s Table: Organic Farming, Genetics and the Future of Food. This Q&A session was designed to learn more about her accomplishments, understand the challenges humanity faces in fo​od production, and the ways science has and continues to address these issues.

1. In your own words, can you provide a brief introduction of your research and interests?

“I have been working on the interaction between plants and microbes for many years. My interest in this research started when I was an undergraduate. My plant physiology professor at Reed College taught me about plant–microbe interactions, and it sparked my interest. Then, while doing my masters at Stanford, Dr. Brian Staskawicz came and gave a talk on his lab’s work, and it left an impression on me. After my Ph.D. work, I decided to work in Dr. Staskawicz’s lab. There I focused on plant–microbe interactions, where I have now spent a bulk of my career.”

At the helm of her own lab, Dr. Ronald and her team identified Xa21, a receptor in rice, using positional cloning. This receptor confers resistance to the devastating Xanthomonas oryzae pv. oryzae pathogen. Almost immediately after publication, “a colleague of mine that I had known for several years, Dr. Dave Mackill, came by my office and asked if I would help him isolate another gene in rice that plays a role in stress tolerance. I was immediately interested.” This gene, Sub1A, turned out to be instrumental for conferring tolerance to submergence. Its discovery led to an, “exciting international project to create flood-tolerant rice varieties for farmers in India and Bangladesh.”

2. Can you go a bit more in-depth about the creation and distribution of Sub1A rice varieties?

“Well this whole process was started by the International Rice Research Institute (IRRI). The mission of IRRI is to help abolish poverty and hunger in regions that depend on rice for most of their calories.

Rice fields in India and Bangladesh were constantly being flooded, resulting in devastating yield losses, so farmers looked to the scientists at IRRI to help. At the time, IRRI had built up a large and diverse rice seed collection, which they used to screen rice varieties for submergence tolerance.

Dave Mackill had worked in South Asia before working at UC Davis and knew how important this work was. Researchers at IRRI had identified a rice variety with tolerance to submergence. Dave then mapped the submergence tolerance (Sub1) trait as a quantitative trait locus (QTL). This was when Dave came to me and asked if we could collaborate on isolation of Sub1 using positional cloning. We were successful and named the key gene Sub1A.

Dave used marker-assisted breeding to introgress Sub1A into commonly used rice varieties. This breeding practice is not considered a genetically modified organism (GMO) and is not regulated. IRRI researchers collaborated with breeders at breeding stations in India and Bangladesh to test the performance of the Sub1 varieties.” Last year, 6 million farmers in India and Bangladesh grew Sub1 rice with an average yield advantage of 60% after flooding.” See this perspective for more information.

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Dr. Pamela Ronald

​​3. If you were to make the argument for GMO products to someone against it, what would you tell them?

“Well, I would first try to understand what they were afraid of. The term GMO means something different to everyone. Interestingly, GMO isn’t even used by the FDA because genetically modified organism doesn’t accurately describe any breeding process really. Often, a person who identifies as ‘anti-GMO’ is afraid of large corporations like Monsanto, or they heard that ‘GMOs’ require more chemicals, and they don’t like that. This is why it’s really important to understand the root of each person’s fears of GMOs, so you can narrow the discussion to address individual questions.

When trying to explain to a group of people why modern genetics is useful in agriculture, I think it’s important to give specific examples. That’s the one thing that just changes people’s mind. Two examples I usually give are genetically engineered papaya that are resistant to the deadly Papaya ringspot virus and Bt eggplant in Bangladesh that reduces the need to spray chemical insecticides. Both genetically engineered crop varieties have improved plant yields and the lives farmers.

Now in the world of COVID-19, more people are familiar with viruses and their infective nature. This is a good example, because some people may be interested to know that viruses also infect plants. This allows you to then engage people by using their knowledge about the vaccine for COVID-19 to explain the techniques used by plant scientists to ward off pathogens. Also, something I realized while writing my book was, why would the average American know a lot about farming? And, how much would they actually know about it? This is also a really important thing to keep in mind when talking about GMOs with people. Many people may not understand or know the farming practices used today and what challenges farmers face.”

4. In your point of view, what are some of the toughest challenges facing agriculture right now? And, how might agriculture look in 2040 to address these problems?

“I think problems associated with climate change, like increased flooding, which I’m now more aware of, droughts, and unpredictable insect infestations, like the fall armyworm sweeping through Africa, are going to be tough. There are scientists and modelers trying to predict new infestation events, but it is proving very difficult. The work we do now is similar to what breeders have been doing for 100 years or so, but we now have to work smarter and faster to keep up with all of the changes occurring around the world.

Additionally, we will have to start growing more food, while reducing emissions. This is something that wasn’t really being talked about when I first entered the field. It was more about reducing chemical inputs. So, now we have to also think about enhancing soil fertility, reducing greenhouse gas emissions, and using water more efficiently.

This is seemingly a daunting task; however, Dr. Ronald is optimistic that scientists can work toward solutions. “The field is rapidly advancing, and new technologies are now starting to be developed and tested to address these problems.”

5. In your mind, what are some of the most intriguing questions concerning pattern recognition receptors and their role in plant immunity?

“Well, I think an emerging topic that is still sort of a black box is the relationship between development and immunity. There is great work from Dr. Joanne Chory and others on the SERK receptors that are involved in both immunity and development. When this relationship was discovered years ago it was pretty surprising, and now there are many great examples of the relationship between development and immunity.

I think the other complicated aspect of this area is that immunity has been traditionally thought of as a linear concept—immunogen interacts with receptor, and this induces a linear pathway that results in a response. However, we now know that the responses to immunogens are much more complex than this. For instance, there are receptor complexes and receptors that can double dip into immunity and development. I think trying to sort out the balance and inner workings of this is really fascinating and will be studied for a long time.”

6. For pattern recognition receptors (PRRs) and resistance (R) genes, what needs to be done to increase their use and efficacy against pathogens?

“There are examples where different resistance genes have been stacked [placing multiple R genes into a plant], and this provided additive and, hopefully, more durable resistance. I think some steps to improve the process will be trying to predict how resistant and durable these added genes will be in a crop plant. This involves doing epidemiological studies where you think about the population diversity of the pathogen in the field. This allows you to predict the types of mechanisms the pathogen has to overcome and the methods being placed into plants to confer durable resistance. You really need to know the effector repertoire of a pathogen population and the interactions they have with the receptors of interest. This allows you to answer the question, ‘Are there pathogen strains in the field that can already overcome the R gene(s) or PRR(s) being added?’ There really is no shortcut to the process of engineering durable resistance.

We are still learning a lot about utilizing plant immune components to increase pathogen resistance. For example, being able to introduce many R genes at a single time in a cassette of genes would be a great step forward. Currently, it takes a long time to breed many R genes into a population. If people become more accepting of genetic engineering, this could decrease the time needed to introduce resistance genes into plants, which is exciting.

For a long time, there has been the hypothesis that PRRs that recognize conserved virulence factors or immunogens would be more durable in the field than R genes. However, I don’t think this has been very well validated or tested in the field. One reason may be because much of the research on PRRs, like FLS2, is carried out on non-crops. So there are very few studies that examine if these theories hold up in the field. Even for Xa21, where plants carrying this gene have been grown in the field for years now, there really hasn’t been any thorough epidemiological studies to determine if this resistance is indeed more durable than the resistance provided by other types of resistance genes such as NBS-LRR genes. Researchers have discovered bacterial strains that evade Xa21 in the field; however, to my knowledge it is not known if they become problematic to farmers. So, what does that mean? Does the evolution of the ability to evade Xa21-mediated immunity result in strains that are compromised in virulence somehow? You really can’t determine this unless you do large-scale field trials that look at the pathogen population over time.”

Sep 16
​An Interview with Dr. Hailing Jin

This InterView with Hailing Jin, Professor of Genetics at the University of California-Riverside, was conducted by Sowmya Ramachandran, a PhD candidate in the Department of Plant Pathology at Washington State University. If you are interested in completing your own InterView, please contact​ Interactions Editor-in-Chief Dennis Halterman.

Hailing_Jin_photoR.pngDr. Hailing Jin is the Cy Mouradick Endowed Chair and Professor of Genetics at The Institute of Integrative and Genome Biology, University of California (UC), Riverside. Her group works on plant–pathogen interactions with emphasis on cross-kingdom RNA interference and small RNA trafficking between plants and fungi.

Sowmya Ramachandran (SR): Thank you for giving me the opportunity to speak with you today. I would like to know what motivated you to enter plant science and eventually establish a program on host–pathogen interactions?

Hailing Jin (HJ): When I was young, my grandpa used to grow flowering plants at home. The beautiful and vivid flowers of jasmine and chrysanthemum attracted me toward plants from a very young age. More specifically, my interest in small RNAs started to develop when I was a post-doc at John Innes Center while studying transcription factors and gene regulation. Around this time, Andrew Fire and Craig Mello discovered RNA interference (RNAi) in Caenorhabditis elegans. A year later, David Balcombe, then a scientist at Sainsbury Laboratory, published a seminal study on posttranslational gene silencing, and together with Craig and Mello’s work, this opened up a new area of research. So, when I joined Barbara Baker’s lab at UC Berkeley Plant Gene Expression Center (PGEC), I utilized the RNA interference-based approach—specifically, virus-induced gene silencing to dissect the signaling transduction pathway of the N gene-mediated resistance to Tobacco mosaic virus in Nicotiana tabacum and N. benthamiana, which piqued my interest for small RNA-mediated gene regulation. By 2004, when I started my own lab at UC Riverside, studies had established the role of small RNAs in development, but very few had looked at their involvement in other processes, especially biotic stress responses. Combining my expertise in gene silencing and gene regulation in plants, I wanted to explore the role of small RNAs in plant–microbial interaction. I was particularly interested to understand plant endogenous small RNA silencing during bacterial and fungal infections. At the time, this was a unique niche and not many scientists were working in this area.

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SR: Do you see small RNAs as effective management tools for plant diseases?

HJ: Yes, this is something our group is excited about. Now we can generate double-stranded RNAs or small RNAs that target fungal virulence genes in the plant. These small RNAs can be delivered into the plant and then enter the fungus to silence specific target genes. This strategy also allows us to custom design constructs for controlling diseases in different regions and against different pathogens at the same time. For example, if Botrytis and Sclerotinia are major pathogens in California, we can design constructs to target essential fungal genes, like Dicers, and control both diseases at the same time. The study was published in Nature Plants in 2016. Basically, now we can generate transgenic plants that can target multiple pathogens based on our needs in different regions and different seasons. But at the same time, transgenic plants and GMOs are still a technical challenge for many crops, such as tree crops, vegetables, and flowers, and some require a long time. It is also a concern for consumers in many regions of the world. So in this case, it would be ideal to develop an ecofriendly, easy-to-use, and non-GMO way to combat plant diseases. This led us to discover RNA uptake by fungal pathogens. 

Over the years, people have observed that Caenorhabditis elegans and other nematodes can take up RNAs from the environment. Since nobody had shown this for fungal cells, our group decided to give it a try. We put Botrytis spores on plates containing fluorescence-labeled RNA and saw RNA being efficiently taken up into fungal cells. This allowed us to use synthetic double-stranded RNAs or small RNA duplexes in the form of sprays on the plants or postharvest products, including vegetables, flowers, and fruits. This strategy offers an ecofriendly and natural alternative to fungicides. These small RNA fungicides will eventually degrade in the soil and leave no toxic residues, unlike chemical fungicides. They can also be designed in a way that they hardly have any off-target effect and at the same time be more durable. As most fungi have already developed complete or partial resistance to fungicides, there is an urgent need to develop a new generation of fungicides. So I think this discovery of RNA uptake will lead to development of a new class of RNA-based, ecofriendly fungicides.

SR: Through your research on Botrytis and cross-kingdom RNA, you show small RNAs can act as effectors that interfere with host processes, similar to protein effectors. Is it possible to develop resistance to small RNAs in the pathogen?

HJ: There are several ways for pathogens to develop resistance to RNAi. One is to change the sequence of the RNA to escape RNAi. But we now know that small RNAs can tolerate many mismatches in their target region. We can also overcome this by targeting essential genes, which cannot mutate rapidly owing to the importance of protein functions. Another strategy that may be employed by the pathogens is to kick out their RNAi machinery. However, this will depend on the genome complexity of the pathogen, like the presence of transposons, and the importance of the RNAi machinery in the pathogen’s growth and defense. A third way of developing resistance is through eliminating the RNA uptake pathway. However, since RNA uptake is an important nutrient acquisition strategy, removing this pathway may not be feasible for the pathogen. Based on this, it seems it will be harder for pathogens to develop resistance to small RNA fungicides. These are some possibilities I can think of currently, based on which it will be harder for pathogens to develop resistance to small RNA fungicides. Even otherwise, we routinely use more than 100 bps dsRNA fragment for one gene, so even if there are a few mutations in this region, there is still enough homology to silence that gene. We also use a mix of small RNAs targeting multiple genes, which should make it harder for the fungus to develop resistance to the small RNAs.

Hailing_Jin_lab-2.jpegSR: Since RNA is unstable in nature, how do you suppose small RNAs will remain stable when delivered in the field?

HJ: Our group recently published a paper in Science in which we reported that fungi can take up small RNA-containing extracellular vesicles from the plant hosts. This process is very efficient, as within 2 hours of delivery, all the vesicles are taken up by the fungus. Based on this finding, we are developing a way to package small RNAs into artificial vesicles to prolong its life in the environment and also increase the fungal uptake. Also, Neena Mitter’s lab at the University of Queensland, Australia, has developed nanoparticles that can increase the stability of these small RNAs and protect them. We are now collaborating with Neena’s lab to come up with formulations that will best protect these small RNA fungicides in the fields.

SR: RNAi machinery is under sophisticated regulation to ensure precise functions in growth and defense. Your lab recently found that Arabidopsis Argonaute 2 (AGO2) is regulated through arginine methylation upon bacterial infection. How does arginine methylation-mediated dual regulation modulate plant defense? 

HJ: This is an interesting question. In a recent paper published in Nature Communications, we show that the RNAi machinery is under a very sophisticated regulatory control. We have shown that Arabidopsis AGO2 protein is regulated by posttranslational modification. Quite a few years ago, our lab discovered that AGO2 protein is the only AGO in Arabidopsis that is highly induced by bacterial infection. In case of miR393, we know that it targets auxin receptors as well as functions in plant defense. We found that miR393 is loaded into AGO1, while the other strand of miR393 duplex, miR393*, is loaded into AGO2. This miR393* version can target a SNARE protein to promote secretion of pathogenesis-related protein PR1. Although we know AGO2 play an essential role in plant defense against bacterial pathogens, their regulation is poorly understood. To this end, our group recently found that the N-terminal of AGO2 has arginine-glycine (GR/RG) repeats. The arginine residues of these repeats are methylated by protein arginine methyltransferase 5 (PRMT5). This modification can lead to a dual regulation of AGO2: one leading to AGO2 degradation and another to recruit Tudor-domain proteins (TSNs), which degrade AGO2 bound to small RNAs. 

Under normal conditions, when plants don’t need immune responses to be activated, this mechanism can dampen AGO2-mediated plant immunity. However, upon bacterial infection, PRMT5 is down-regulated and the arginine methylation is reduced so AGO2 proteins can be accumulated to a high level, along with AGO2-associated small RNAs. Together, this dual regulation of AGO2 can precisely modulate RNAi and immune responses during infection. 

SR: Based on your experience as a professor and a biologist, can you identify some qualities that are needed to be successful in this field?

HJ: To be successful in science, one needs to have passion and dedication for their work. If you love what you are doing, you will invariably do a good job! Personally, I feel motivated when my work can benefit the environment and the society in some way. If I can help the world through my work and through my teaching, then my time is well spent and my life is meaningful! My work with plant protection and disease resistance, such as developing environmental-friendly fungicides, seems fulfilling, as it can directly help the planet. 

Sowmya_MPMI.jpgSR: Thank you very much for your time. It was fascinating to know more about your research. I am sure your inspiring words will be valuable to young scientists aspiring to careers in plant biology.


Mar 15
Interview with Jeanne Harris, Editor-in-Chief of MPMI

Harris.jpgJeanne Harris, new editor-in-chief (EIC) of Molecular Plant-Microbe Interactions (MPMI), looks forward to building on MPMI’s reputation as a leading journal by continuing to focus on key research questions while attracting new readership by expanding the scope to include more population genomics/comparative genomics. She envisions a series of review articles that examine the effects of climate change on plant-microbe interactions and wants MPMI to engage more with junior scientists, who can raise awareness of the journal and increase its position within the community. In addition to her duties as EIC, Harris serves as an associate professor in the Department of Plant Biology at the University of Vermont, where her research interests include plant-microbe interactions, signaling networks, and developmental genetics. She holds a PhD in cell biology from the University of California, San Francisco.

What is your vision for the journal and your board over the next 3 years?

Jeanne Harris: I’d like to build on MPMI’s reputation as the leading journal for high-quality research in the MPMI field, helping us to identify and focus on the major research questions, expanding our scope to include more population/comparative genomics, and continuing the very successful Distinguished Review article series that John McDowell started. 

The new MPMI board brings a geographic breadth and depth of expertise that will help us to attract, evaluate, and publish foundational research from colleagues around the world on key questions regarding the molecular interactions of plants and the many microbes, insects, and parasitic plants in their environment. Over the next 3 years, I’d like to have MPMI engage more with junior scientists, helping to increase awareness of the journal to maintain and strengthen its position in the research community, and to be a leader in the discussion of the big questions in our field.

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What is the “Top 10 Questions in MPMI” campaign?

JH: The MPMI Editorial Board has planned a new interactive campaign to work with the scientific community on the “Top 10 Questions in MPMI.” The idea is to engage the community in a process of identifying the top 10 unanswered questions in MPMI. The result will be an editorial by the board reporting the results of this community discussion, followed by a series of Perspectives or Reviews on the questions over the course of a year. My goals are to engage the community in more of a dialogue with the journal and to draw the focus of the journal to the big research goals in the field. I also have plans to create a series of podcasts accompanying these perspectives to help showcase these unanswered questions: What is the background or context? Why are the questions so compelling? What do we know so far?


Why focus on these questions? 

JH: As scientists, we focus on trying to answer the big unanswered questions in our field. Journals naturally publish what has been figured out. As we chip away at these big questions, we publish pieces of it. How do we make people aware of the big unanswered questions that motivate this work? The goal is to make the journal MPMI a central place for the community to discuss and focus our attention on the big unanswered questions that motivate us and drive our research.

I think a focus on the unanswered questions is especially important for students and younger scientists, who may find it hard to identify the big questions amid a proliferation of journal articles. The editorial, Perspectives, and Reviews that will result from this community discussion should provide an important resource for students, post-docs, and junior faculty while helping to strengthen their familiarity with the journal MPMI and increase their connection to it.


What about John’s stewardship has made your transition to EIC more approachable?

JH: John’s leadership at MPMI has put the journal in an excellent position, attracting attention with a series of timely and fascinating focus issues while fostering a culture of research excellence and high ethical standards, as well as improving the experience for our submitting authors.  The Distinguished Review Article Series that John initiated, focusing on “Conceptual and Methodological Breakthroughs in Molecular Plant-Microbe Interactions,” started with a bang with an outstanding review by Dan Klessig and is a series I’m excited to continue. On a personal level, John’s mentorship has been hugely helpful as I take on the EIC role at MPMI, and I know I will continue to draw on his expertise and intuition.


Dec 17
​InterView: Detlef Weigel

Detlef Weigel is a Director at the Max Planck Institute for Developmental Biology. Interactions recently spoke with Weigel about his membership with IS-MPMI, his research, and more.

Interactions: What guided your decision to dedicate the next stage of your research career to MPMI?

Detlef Weigel: My path to MPMI was rather circuitous. Genetics is my first love, and genetic phenomena of any kind appeal to me. Almost 15 years ago, Janne Lempe and Kirsten Bomblies in my lab discovered a syndrome of Arabidopsis hybrid weakness that we at first interpreted as a developmental abnormality. We quickly learned that this syndrome was not specific to Arabidopsis spp. and that it was already well known from many wild and cultivated plants, for which it is called “hybrid necrosis.” Anybody in the MPMI field knows that necrosis is often a hallmark of pathogen infection. Nevertheless, we were apparently the first ones to recognize that inappropriate immune reactions in the absence of pathogens were most likely the defining characteristics of this phenomenon, rather than developmental defects.

For us, one of the attractions of studying hybrid necrosis was that we thought it would teach us about speciation, but after many thousands of crosses and having cloned quite a few of the causal genes, we realized that hybrid necrosis has much more to do with how the plant balances the demands on its immune system. With too little immunity, the plant will succumb too quickly to infection, but with too much immunity, the plant will damage itself. Hybrid necrosis occurs when components of the immune system are mismatched, and these components begin to signal even if there is no pathogen trigger. Satisfyingly, the molecular observations in Arabidopsis spp. seemed to match similar observations in several other species. As a matter of fact, with hindsight we realized that the first case of hybrid necrosis that was molecularly understood predated our own work in Arabidopsis—namely, the study of the tomato Cf-2/Rcr3 system by Jonathan Jones.

In parallel with our efforts to clone the causal genes for hybrid necrosis in Arabidopsis spp., we could confirm through our whole-genome resequencing and sequencing studies that immune genes—particularly those of the NLR class but also of other smaller families—are the most diverse genes in the Arabidopsis genome. This, in turn, made us wonder what drives this diversity—hence, our current obsession with trying to understand the relationship between Arabidopsis and its natural pathogens in the real world.

I: What do you see as the next big challenge in this field of research?

DW: The MPMI field has already revealed in exquisite detail many of the molecular mechanisms that allow pathogenic and symbiotic microbes to infect plants, as well as a plethora of mechanisms that plants use to either accommodate or ward off microbes. It is also clear that many of these molecular interactions are evolutionarily very fluid—perhaps the best example being the ease with which pathogens often jettison effectors. However, what this means in an ecological context is much less obvious. I therefore see as a big challenge how we can integrate the advanced molecular knowledge with an understanding of the interaction between wild plants and their microbes in the real world and how this changes over ecological and evolutionary time scales. To begin to dissect these, we need to know much more not only about the spatial and temporal distribution of hosts and microbes but also about their fine-scale genetic variation in effectors, resistance genes, and so on. My dream is to learn how genetic diversity in wild plant species maps onto the diversity of their microbiota (and vice versa) and what genetic, molecular, and ecological mechanisms relate the two. To this end, we recently started an ambitious effort, which we call “Patho(gens in Arabi)dopsis,” or “Pathodopsis” for short, to generate such foundational data. It would be fantastic to initiate such efforts in many other species. So far, the focus has mostly been on local populations, such as the impressive long-term studies by Anna-Liisa Laine in Finland and Jeremy Burdon and colleagues in Australia. I would love to see the sorts of insights they have gathered across the entire geographic ranges of many different plant species.

I: Symbiotic relationships between plants and microbes have been occurring for hundreds of millions of years, and we are only studying a tiny “snapshot” in the history of these interactions. How can we extrapolate our observations to better understand MPMI and improve the resistance capacity of agricultural crops?

DW: I agree that we need to have a better understanding of how wild plant pathosystems are different from agricultural systems. Whether the information from the wild systems is directly useful for agricultural systems is difficult to know beforehand, although it is probably safe to assume that increased immune system diversity in individual agricultural fields would most likely be helpful—an idea that has been advocated, for example, by Bruce McDonald. I like to think that with agriculture, we have often “broken” long-term stable interactions, and we need to learn what confers long-term stability before we can fix the broken state. I realize that to this end, I need to learn a lot more ecology, and I am benefitting in this area greatly from my collaboration with Joy Bergelson.

I: Your recent paper in PLoS Genetics highlights how interactions between NLRs from different species might affect the fitness of progeny. Do you feel that NLR interactions are a driving force in speciation?

DW: It is an attractive hypothesis, and I would not be surprised if there are cases of speciation or population divergence caused by inappropriate NLR interactions, but they are unlikely to be major drivers, because NLR variants typically do not become fixed in species. Having said this, there is a minority of NLR genes that seem to have very little, if any, variability, and these highly conserved NLR genes probably deserve more attention.

I: Do you plan to continue your research on plant development and adaptation? What do you hope to gain from your IS-MPMI membership?

DW: There is very little developmental work going on in my lab these days, as we have pivoted almost completely to genomic variation and plant immunity. As plant biologists, we are sometimes annoyed when animal biologists lump us all together simply because we all study plants, but I actually see this as a great advantage of our field. Beginning with the very first Arabidopsis conference that I attended in 1990, a large fraction of the plant meetings I have gone to have included at least a bit of plant immunity. Moreover, at the Salk Institute, I worked next to the late Chris Lamb, who was an important early figure in MPMI, and I have been lucky enough to have had Jeff Dangl as a friend for many years—a friendship that eventually turned into a very productive and enjoyable long-term collaboration. In addition, I have had the good fortune of having served on the board of The Sainsbury Laboratory (TSL) for several years, where I have received a tremendous education in MPMI from colleagues such as Cyril Zipfel, Sophien Kamoun, Silke Robatzek, David Baulcombe, and John Rathjen.

Even though I’m still somewhat of an amateur when it comes to MPMI, it is what I think about most these days, so it seemed only natural to join IS-MPMI. Not a small contributor to this step was that I have come to know the work of the three most recent IS-MPMI presidents very well: Sophien Kamoun’s work because of my association with the TSL and also through several collaborative projects, Sheng Yang He’s work because of my recently emerged interest in Pseudomonas biology, and Regine Kahmann’s work because she is a Max Planck colleague with whom I meet very regularly.

I: Much of your research engages interdisciplinary and international interactions. What methods/tools do you use to initiate and foster these interactions?

DW: Tool number 1: an open mind. I strongly believe that almost everybody we meet can teach us something—both inside and outside science. In other words, if one respects others and their research, even if it’s not automatically one’s own “cup of tea,” then productive interactions with a wide range of colleagues, both in different disciplines and in a wide range of institutions, are essentially preprogrammed.

I: Many students and some early post-docs are undecided on their ultimate career paths academia/industry/government/other). What advice do you give students and early post-docs in your research group who might need help making this decision?

DW: Many colleagues, both old and young, equate science only with academia, which is very shortsighted. Science has many different incarnations, from blue-sky discovery to translational and applied research, but also when we use the tools of scientific thinking and reasoning to make the world around us a better place. In the end, it is about personal proclivities and what career paths best fit one’s own personality along with the demands of family and friends. Somebody who is geographically more constrained because of a partner or parents must, of course, be more open minded about different careers—which is perfectly OK!

 

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