2023 - Issue 2

IS-MPMI > COMMUNITY > Interactions > Categories
Jun 29
2023​ - Issue 2
Issue 2 • 2023
All eligible voting members of IS-MPMI have been sent an electronic ballot to vote in this year's Board of Directors election. Three of six candidates will be elected to the Board of Directors to serve a 4-year term. Those elected will be installed during the Board meeting at the 2023 IS-MPMI Congress. Cast your vote by July 6, 2023 (midnight CDT).
SHARE Share Share with Facebook Share with Twitter Share with Linkedin Share with SMS
Also in this issue...
The 2023 IS-MPMI Congress is less than a month away, and we're excited to see everyone in Providence, Rhode Island. There is still time to register and join us in July for our first in-person meeting in four years!
Congratulations to Jonathan D. G. Jones, the 2023 Outstanding Achievement Award recipient, and to Cara Haney and Xiufang Xin, the 2023 Early Career Achievement Award recipients. The awardees will be recognized and celebrated at the 2023 IS-MPMI Congress.
ISMPMI is seeking a new Editor-in-Chief for IS-MPMI Interactions. Learn more about the responsibilities, resources, and opportunities associated with this position. The term for the position will officially begin after the 2023 IS-MPMI Congress.
"The Next Big Idea" Session at 2023 IS-MPMI Congress
The 2023 IS-MPMI Congress will include an innovative and interactive plenary pession focused on the "WHY" behind our research. During the "The Next Big Idea" session, five IS-MPMI community members from diverse backgrounds and career stages will convey why you should care about their research and answer audience questions.
Interact with MPMI at 2023 IS-MPMI Congress: Attend a Special Session, Visit the Editors of MPMI, and Potentially Win a Poster Award!
MPMI editors are providing several opportunities to engage with and learn more about the journal and publishing during the 2023 IS-MPMI Congress. MPMI editors will host "The Making of a Story—Building Narratives and Communicating Science Effectively" session; the MPMI booth, and the Student Poster Award competition.
InterView with Dr. Wenbo Ma
Tianrun Li, Ph.D. candidate in the Plant Pathology program at the University of California, Davis, interviewed Dr. Wenbo Ma, senior group leader at The Sainsbury Laboratory and honorary professor at the University of East Anglia. Li spoke with Dr. Ma about being named a 2022 AAAS Fellow, her career journey, and what the future may hold.
InterView with Dr. Maeli Melotto
Aline Sartor Chicowski recently interviewed Dr. Maeli Melotto, professor and scientist at the University of California, Davis. Chicowski spoke with Dr. Melotto about being named a 2022 AAAS Fellow, how she became interested in plant pathology, her research goals, and challenges in her career.
InterView with Munir Nur and Kelsey Wood
Munir Nur, software engineer, Big Data, and Kelsey Wood, postdoctoral scholar, Michelmore Lab, University of California, Davis, answered questions about their collaboration on the EffectorO project and publication of their paper, "EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage-Specificity," in MPMI.
InterView with Dr. Bing Yang
Ashley C. Nelson, Ph.D. student in the Plant Pathology Department at North Dakota State University, interviewed Dr. Bing Yang, principal investigator and member at the Donald Danforth Plant Science Center, professor of plant science and technology, University of Missouri–Columbia, and 2022 AAAS Fellow. Nelson spoke with Dr. Yang about his career, the importance of collaboration in science, and his advice for young scientists.
InterView with Dr. Cyril Zipfel
Dr. Amelia H. Lovelace, postdoctoral researcher at The Sainsbury Laboratory, interviewed Prof. Cyril Zipfel, chair of Molecular and Cellular Physiology at the University of Zurich, and senior group leader at The Sainsbury Laboratory. Dr. Lovelace spoke with Prof. Zipfel about the evolution of his research interests, his approach to mentorship, and his advice for early-career researchers.
InterConnections: Get to Know Munir Nur and Kelsey Wood
Learn about Munir Nur and Kelsey Wood and how their diverse backgrounds led to a fruitful collaboration on EffectorO and publication of their paper, "EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage-Specificity," in MPMI.
InterConnections: Get to Know Stefan Sanow
Learn about Stefan Sanow, coauthor of the review paper "Molecular Mechanisms of Pseudomonas Assisted Plant Nitrogen Uptake—Opportunities for Modern Agriculture" recently published in MPMI, and the unexpected bacterium that led to new insights into the complex genus Pseudomonas.
Review Highlight: Molecular Mechanisms of Pseudomonas Assisted Plant Nitrogen Uptake—Opportunities for Modern Agriculture
Dr. Borjana Arsova, Root Dynamics group in the Plant Sciences Institute in the Research Center in Jülich (IBG-2), discusses how receipt of an unexpected Pseudomonas strain led to experiments with plants grown under low-nitrogen conditions and compilation of evidence about known processes relevant to the Pseudomonadaceae. The resulting review paper published in MPMI offers a novel perspective on this complex genus.
MPMI Journal Publishes Special Focus Issue on a Critical, Emerging Area of Study
The recently published MPMI Focus Issue on “The Plant Endomembrane System in Molecular Plant–Microbe Interactions” explores how microbes affect the plant endomembrane system and its role in plant disease, defense, and beneficial interactions.
Opportunity for Scientists in Under-Resourced Countries to Publish in MPMI
Microbes Biosciences is generously sponsoring MPMI to cover the publication fees for a limited number of authors from countries with low-income or lower-middle income economies who elect to publish in MPMI.
Catch Up on MPMI Editor's Picks and Virtual Seminars
Discover the Editor's picks from the March, April, and May issues of MPMI and listen to the What's New in MPMI Virtual Seminar presented by Janak Joshi, Amy Charkowski, and Adam Heuberger on their MPMI Editor's Pick.
We are always looking for content for Interactions. Please contact Interactions Editor-in-Chief Dennis Halterman with questions or article ideas.

Jun 28
2023 IS-MPMI Board of Directors Election

All eligible voting members of IS-MPMI have been sent an electronic ballot to vote in this year's Board of Directors election. Three of the six candidates (Yang Bai, Patricia Baldrich, Xin Li, Wenbo Ma, Ryohei Terauchi, and Xiufang Xin) will be elected to the Board of Directors to serve a 4-year term. Those elected will be installed during the Board meeting at the 2023 IS-MPMI Congress. Meet your candidates and cast your vote by July 6, 2023 (midnight CDT).​​

Jun 28
It's Almost Time for the IS-MPMI Congress

The 2023 IS-MPMI Congress is less than a month away, and we're excited to see everyone in Providence, Rhode Island! There is still time to register and plan to join us in July for groundbreaking special sessions, a dive​rse plenary program, and all-new engaging concurrent sessions.

Register Today

Jun 28
Congratulations to our 2023 IS-MPMI Awardees

Congratulations to Jonathan D. G. Jones, the 2023 Outstanding Achievement Award recipient and to Cara Haney and Xiufang Xin, the 2023 Early Career Achievement Award recipients.​ The awardees will be recognized and celebrated at the 2023 IS-MPMI Congress.

Learn more about the awardees.​

Outstanding Achievement Award

This award recognizes an investigator who has a high international reputation as a research leader for groundbreaking and original research in the area of molecular plant–microbe interactions. The award also recognizes their strong commitment to one or more activities that advance the IS-MPMI field, including teaching, mentoring, educational outreach, international collaborations, service to the community, and/or advancing diversity, equity, inclusion and belonging.

Early Career Achievement Award

This award recognizes outstanding investigators who are known internationally as emerging research leaders in the area of molecular plant–microbe interactions.

​Jonathan D. G. Jones

Cara Haney

Xiufang Xin​​
Jun 28
IS-MPMI Is Looking for a New Interactions EIC

Dennis Halterman, Editor-in-Chief Interactions

It is hard to believe that it has been almost seven years since I started as Editor-in-Chief of IS-MPMI Interactions. I entered the position with the idea of giving back to the society that has meant so much to me during my career. I have enjoyed seeing the society change and grow during this period, and I am constantly in awe of everyone's accomplishments and sense of community. But, the time has come for me to step aside and allow someone else to incorporate fresh ideas and express their own personality in this society publication. If you would like to learn more about the responsibilities, resources, and opportunities associated with this position, please contact me or current President Roger Innes. The term for the position will officially begin after this year's IS-MPMI Congress, but I will be available to provide guidance, consultations, and reviews to ensure a smooth transition period.

Jun 28
"The Next Big Idea" Session at 2023 IS-MPMI Congress

Ryan and Pat, Organizers of "The Next Big Idea" Session

​Dear IS-MPMI community,

As you might know, the 2023 IS-MPMI Congress is coming up in July, and it will include an innovative and interactive plenary session focused on the "WHY" behind our research. We have selected five IS-MPMI community members from diverse backgrounds and career stages who will try to convey why you should care about their research.

Participants will have five minutes to present the rationale and justification behind their research. Following each pitch, there will be three minutes for questions from the audience. The winner of the challenge, based on audience votes, your vote, will receive a monetary prize and eternal community recognition!

Join us on Thursday, July 20, for this unique session and be part of "The Next Big Idea" Session at IS-MPMI 2023!​

Jun 28
Interact with MPMI at 2023 IS-MPMI Congress: Attend a Special Session, Visit the Editors of MPMI, and Potentially Win a Poster Award!

​At the 2023 IS-MPMI Congress, the five assistant feature editors for MPMI will host a standalone session, "The Making of a Story—Building Narratives and Communicating Science Effectively," on Sunday, July 16, from 10:00 a.m. to 12:00 p.m. Learn how to utilize different media to effectively communicate science to diverse audiences in engaging, creative ways. This session will also include a live recording of the MPMI podcast Microgreens.​

In addition to attending this session, visit the editors of MPMI at the MPMI booth over the course of the meeting to learn more about publishing in the journal, signing up to be a reviewer, and engaging with the journal in other ways. Grab a few free "show your science" stickers while you are there!

MPMI is also host a Student Poster Award competition at the meeting, judged by the editors of the journal. The first-place winner will receive $300, the second-place winner will receive $200, and the third-place winner will receive $100. Any poster by a student is eligible for the award; winners will be announced at the meeting.​

Jun 28
InterView with Dr. Wenbo Ma

Tianrun "Jerry" Li​

Tianrun Li

Tianrun Li is a fourth-year Ph.D. candidate in the Plant Pathology program at the University of California, Davis, working under the guidance of Dr. Gitta Coaker. He completed his bachelor's degree from Northwest A&F University, China, in 2019. His current research focuses on exploring the utility of pattern recognition receptor (PRR) triggered immunity to control vector-borne disease. He is also investigating novel plant flagellin receptors with expanded ligand recognition specificity and their potential for receptor engineering.

Dr. Wenbo Ma

Dr. Wenbo Ma is a senior group leader at The Sainsbury Laboratory (TSL) and an honorary professor at the University of East Anglia, UK. Her group's long-term research interest has been to understand the plant–pathogen coevolutionary arms race, with a focus on microbial pathogenesis and effector biology. She is also one of the pioneers in determining the role of small RNAs in plant immunity against nonviral pathogens.

Conversation with Dr. Ma

Not only is Wenbo a recipient of the 2021 Ruth Allen Award from The American Phytopathological Society (APS), she was recently elected as a 2022 Fellow of the American Association for the Advancement of Science (AAAS). To mark the occasion, I had the privilege of speaking with Wenbo about her scientific journey, accomplishments, and forward-thinking perspectives.

Wenbo initiated her research journey in China, where she obtained her M.S. degree at the Chinese Academy of Sciences. Subsequently, in 2003, she attained her Ph.D. degree from the University of Waterloo in Canada, after which she pursued a postdoctoral position at the University of Toronto.

In 2006, Wenbo started as an assistant professor at the University of California, Riverside (UCR) and was later promoted to associate professor with tenure, eventually attaining the rank of full professor. Several years ago, she joined TSL, where she established new research programs centered around major host–pathogen systems.

When asked how she feels about being honored as an AAAS Fellow, Wenbo states that she's extremely fortunate and grateful for the recognition she has received as a reflection of her scientific journey. She adds that the honor is shared with her team.

I had the privilege of working with many amazing students and postdocs. Without their support and effort, my research would not be possible.

Throughout her career, Wenbo has devoted substantial time to conducting research on diverse continents, including Asia, America, and Europe. These experiences have provided her a comprehensive understanding of the unique challenges, cultural dynamics, and opportunities that each research environment offers. This journey has helped her cultivate a deep appreciation for the value of collaboration and diversity in her scientific pursuits.

She highlights two key elements of interdisciplinary collaborations: concepts and methodologies. Because scientists can sometimes become deeply immersed in their own field, limiting their perspectives, Wenbo encourages them to deliberately venture outside their comfort zone and broaden their scope by learning from other fields. This approach, she believes, helps researchers enhance their understanding of diverse concepts.

Simultaneously, Wenbo points out the role of technological advancements in fostering scientific breakthroughs. Invaluable knowledge can be obtained from structural biologists, and their insights have now become an indispensable part of her research program. As the popularity of AI-based analysis tools grows, there is great potential for them to become an integral part of the toolkit of every early-career researcher in biology-related fields.

This spirit of cooperation is crucial, especially in a field as intricate as MPMI, where bringing ideas from different perspectives and utilizing interdisciplinary methodologies often pave the way to the most exciting and fundamental discoveries in plant immunity and pathogen effector biology.​

The potential for translating discoveries from our basic biological research into practical applications, particularly in the area of disease resistance in crops, is what drives our work…. For me, effectors are one of the most intriguing components of these systems, providing critical insights into plant pathogenesis.

By understanding plant immunity, scientists learn how plants become resistant. However, without an understanding of pathogens we wouldn't know how plants become susceptible. Wenbo envisions a future where the knowledge gathered from studying virulence mechanisms utilized by pathogens will pave a new passage to generate resistant crops.

However, challenge is everywhere. A key hurdle in crop improvement is the perpetual coevolutionary battle between pathogens and plants.​

Pathogens are always evolving, which is why our goal is to enhance the durability of resistance in plants.

She adds that "there is no silver bullet solution" and underlines the importance of a comprehensive understanding of plant–pathogen coevolution to develop integrated resistance strategies.

The effects of climate change add layers of complexity to plant pathology research. Recent studies have found plant stress and immune signaling are dampened in a warming climate. Global warming and ecological shift are altering the delicate balance between plants and their microbial "partners."

"Environmental factors are integral to plant–pathogen interactions. With climate change, both the plant's immune system and pathogen's virulence mechanisms can be affected, altering disease patterns. Our research needs to incorporate more of these environmental aspects," explains Wenbo, emphasizing the importance of actively integrating environmental factors into MPMI research programs.

Looking toward the future, Wenbo is excited about the role of small molecules in immune signaling as a promising research frontier. She shares that her research group's goal is to use effector proteins as molecular probes to dissect the complex immune signaling process and adds that "It also provides an opportunity to incorporate metabolome analysis and structural biology, which is truly exciting for us."

"This field is witnessing a wave of really cool technologies," says Wenbo, specifically calling out the impact of structure prediction. "Now with structural models, we can gather a wealth of information that can help us generate testable hypotheses." It's a game-changer that has opened up previously unexplored avenues to investigate protein functions.

Wenbo's contributions to the scientific community extend far beyond her exceptional research. Over the span of 17 years as a professor and mentor, her laboratory has nurtured numerous postdoctoral fellows, graduate students, and undergraduate students. Many of them have gone on to flourish in their scientific pursuits.

Wenbo feels strongly about mentoring early-career professionals and wants to help them make their mark in the field of MPMI. She emphasizes the importance of motivation, open-mindedness, and persistence.

She believes that we are at a fascinating juncture where we have already accumulated a lot of important knowledge and are poised to make the next jump. "Seeing the opportunities of making potential breakthroughs should fuel your motivation," she urges early-career researchers. "We are in an exciting time for MPMI research. There are many exciting projects aiming to answer some of the most pressing questions."

Being open-minded is key to advancing in this field, and researchers should embrace new technologies and explore novel approaches.

You need to be very adaptable to new technologies, willing to try new things. Try it, try different things.

When AlphaFold was first announced, Wenbo was enthused by how many in the scientific community "immediately tried to model their favorite proteins." This eagerness to embrace and experiment with new technologies is something she views as vital.

With all these exciting prospects in mind, Wenbo is also fully aware that any scientific pursuit can be riddled with challenges and potential frustrations. Experiments may not always align with initial hypotheses and require series of adjustments and readjustments. This is where the importance of resilience and persistence comes into play—maintaining a positive attitude, viewing these roadblocks not as failures but as opportunities to refine hypotheses and seek alternative methods, is crucial.

Wenbo concluded our enlightening conversation with a final piece of wisdom, encouraging early-career researchers to "keep a positive energy and challenge yourself by stepping out of your comfort zone; be persistent but flexible; the sky is unlimited."​

Jun 28
InterView with Dr. Maeli Melotto
Aline Sartor Chicowski

Maeli Melotto

Aline Sartor Chicowski

Dr. Maeli Melotto is a professor and scientist at the University of California, Davis, where she has worked for the past nine years. Ever since she was an undergraduate in biology at São Paulo State University (UNESP), Brazil, Maeli knew she wanted to be a plant scientist. For her B.S. thesis, she surveyed biological nitrogen fixation efficiency in trees using a collection of native rhizobium isolates from local forests. From that moment on, she has studied plant–microbe interactions. First, she worked on cowpea and soybean associations with rhizobia for her M.S. degree at the University of São Paulo (USP), Brazil. For her Ph.D. thesis at Michigan State University (MSU), she worked on bean–Colletotrichum lindemuthianum interactions. Finally, during her postdoctoral training at the MSU-DOE Plant Research Laboratory, she worked on tomato and Arabidopsis interactions with the bacterium Pseudomonas syringae.

When she started her lab, first at the University of Texas in Arlington in 2008 and then at UC Davis in 2014, she expanded her research interests to study plant colonization by human bacterial pathogens. She chose to work with Escherichia coli O157:H7 and Salmonella enterica because they are the top microbial contaminants of freshly consumed foods in the United States and the world. Besides, "UC Davis is a perfect location to carry out projects focused on solving this problem that affects the national and international fresh produce market. Leafy greens production in California accounts for 70–80% of the national market, and multiple foodborne disease outbreaks have originated in the field," she explained.

Her main research goal is to uncover the mechanisms that allow these bacteria to survive and multiply in healthy leaves using lettuce and Arabidopsis as models. Even though these bacteria are not pathogenic on plants, lettuce and Arabidopsis serve as hosts for them and react to their presence. "At the molecular level, there are many similarities between Arabidopsis and lettuce responses to phytobacteria such as Pseudomonas syringae and these human pathogens," she explained. Her group discovered that some lettuce cultivars mount a strong immune response (pattern-triggered immunity, or PTI) against O157:H7 and S. enterica, but other cultivars allow for bacterial growth, posing a greater risk for the occurrence of foodborne illnesses.

For Dr. Melotto, one of the most important discoveries in plant immunity during the past few years was the work by Matsumura et al. (2022): "Mechanosensory Trichome Cells Evoke a Mechanical Stimulus-Induced Immune Response in Arabidopsis thaliana." This study explains the mechanosensory role of trichomes in Arabidopsis. Disease is the exception of all possible plant–microbe interactions, and many things happen on the leaf surface before a pathogen can internalize the leaf and damage internal tissues. "The leaf surface is an exposed, complex environment that plays a crucial role in protecting the plant from invaders. This work presented a fascinating story on how mechanical stimuli at the trichome triggers a wave of calcium signaling that triggers plant immunity systemically. It sounds like a danger-detecting antenna," she said.

Dr. Melotto's favorite paper is her first: "Development of a SCAR Marker Linked to the I Gene in Common Bean." This article was a product of her overcoming scientific barriers and a turning point in her career. "It marked a point in time when molecular marker-assisted selection to improve disease resistance was the state-of-the-art for crop breeding," she mentioned. The marker she developed is still useful to breeding programs focused on virus diseases. Her paper has been cited 239 times, including 2023 citations. "To me, that paper represents a molecular technology that made it to real applications towards developing genetically resistant, commercial cultivars of beans in many countries."

Her favorite part of her job as a professor and scientist is to study the literature to fully interpret data from her research. She loves to write discussions and review articles to create a big picture and think about the next steps in science. "The desire to be a scientist came naturally, and, to this day, I can't think of being anything else but a scientist," she said. Maeli points out that the hardest part of her work is that it lies in the intersection of three major disciplines: molecular plant–microbe interactions, food science, and agronomy, "which do not have a history of working together," she noted. "Our audience is highly diverse, and we must navigate through 'discipline-specific vocabularies' when communicating our science."

When talking about challenges in her career, Dr. Melotto mentioned that her first biggest obstacle was overcoming the English language barrier, as her native language is Portuguese. She mentioned that it took her a while to start thinking in English and stop translating everything in her mind before speaking, "a tiresome task that any non-native English speaker will understand." She also pointed out that the second biggest obstacle she had to overcome, and according to her "once in a while still is," is to cope with "impostor syndrome." Dr. Melotto advises someone starting their career to seek opportunities to ask questions of those they consider successful individuals and learn from their experiences. Maeli said she had excellent mentors who answered all the questions she had as they became relevant to each stage of her career. "I am very grateful to Dr. James D. Kelly, my Ph.D. advisor, and Dr. Sheng ​Yang He, my postdoctoral mentor, who guided me to be the best scientist I could be and helped me reach my potential," she proudly said.

Ten years from now, Dr. Melotto hopes to have trained great scientists and advanced the knowledge of how hormonal signaling drives plant immune responses at the cell and tissue levels. "I would like to uncover new regulatory nodes that connect plant growth and defense, which could be used for metabolic engineering toward crop resilience under biotic stresses," she explained.

When asked what being recognized as a Fellow of the American Association for the Advancement of Science (AAAS) means to her, she said, "I have never dreamt about receiving this honor. I am so very grateful to the anonymous person who nominated me. It still doesn't feel like I deserve it, but I am happy to share this recognition with my advisees who contributed to the discoveries and publications from our lab."​

Jun 28
InterView with Munir Nur and Kelsey Wood

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

Munir Nur

Kelsey Wood

Question: What was the inspiration for EffectorO?

Kelsey: When I started my Ph.D. program on oomycete effector genomics in 2013, it seemed like everyone was really only using the same motifs (RXLR or LFLAK) to predict effectors. But as I dove deeper into the genome of the lettuce downy mildew pathogen, I found that there were some real effectors that did not have these motifs and published a paper on my findings (Wood et al., 2020). That got me thinking of alternative ways to predict effectors.

The first way to predict effectors that I thought of was to leverage lineage specificity, which is a characteristic of many effectors from species with narrow host ranges, to find effectors. I realized this would be pretty simple in principle using BLAST. However, the downside would be that there are other lineage-specific genes besides effectors and a lot of misannotated junk from genomes would probably be picked up. It also would depend a lot on what other organisms are sequenced for comparison.

In my search for a more accurate way to predict effectors, I found a paper on EffectorP 2.0 (Sperschneider et al., 2018) that used machine learning to predict effectors from fungi. I tried to use it on my oomycete genome, but it didn't work and I was sad.

That is, until I met Munir.

Question: How did you two find each other?

Munir: During my undergraduate studies, I was eager to apply what I've learned in computer science and bioinformatics classes to help solve research problems. I saw an ad for a bioinformatics intern in the Michelmore lab and applied by email.

Kelsey: Funny story, I posted a few job ads for undergraduate interns for summer 2017 on the Michelmore lab website, and we didn't take them down even after the job openings had expired. Munir saw the (old) ad for the bioinformatics intern and emailed me right around the time I was wanting to develop a machine-learning pipeline for oomycete effectors, and I interviewed and hired him on the spot. Moral of the story: never update your lab website. And, if you are an undergrad, don't wait for an official job ad to reach out to labs for internships!

Question: What did you think bioinformatics research would be like versus what it was actually like?

Munir: Bioinformatics research is much more data wrangling than I thought! I think this is also true for the entire field of data science—it typically takes a lot more work to get the data ready than it does to build models and perform analyses!

Kelsey: What Munir said. And, I'm always surprised at how much you have to reperform the same or similar analysis until it's "done." Using R for most of the graphics was a life saver because if something ended up changing we could easily rerun the scripts with the new data.

Question: What lessons did you learn during the preparation of this manuscript?

Munir: Write clean code in a reusable manner the first time around. And if you don't, definitely get to it the second time you use the same code! Research analyses typically get rerun multiple times, as you're constantly pulling the latest datasets that get released in the research world or tweaking some parameters to compare different models/hypotheses.

Constantly write lab notes and code documentation, since you will often be looking back at analyses you performed and code you wrote several weeks, months, or years ago.

Kelsey: I learned how valuable reviewer feedback could be, even (or especially?) criticism. One reviewer in particular had a lot of excellent critiques that forced me to rewrite several sections, which resulted in a much clearer argument for the manuscript.

Question: How did reviewers help to improve the manuscript?

Kelsey: One very useful suggestion was to perform domain prediction on our effector candidates using Pfam, which I didn't think would be a good idea because most effector domains are not well studied. This is what the results ended up showing, but the domains that were found were mostly known effector domains, which helped support the conclusions of the paper. Also, there were many reverse-transcription–related domains that I think also support the conclusions, as it is known that effectors live in transposon-rich regions of the genome. The ones with RT-related domains are probably pseudogenes though, so it is another criteria that one could use to refine the list of candidates.

One reviewer also asked if BLE01, which was the Bremia lactucae effector that we predicted with EffectorO and that we found to be an Avr candidate, was also predicted by EffectorP 3.0 (Sperschneider and Dodds, 2021). We found that it was not predicted by their pipeline. This was important because EffectorP 3.0 came out while our paper was under review. However, this showed that the two machine-learning algorithms predict distinct (but overlapping) sets of proteins and, thus, can be used together for prediction of oomycete effectors. Thank you so much Reviewer #2!

Question: Why was the collaboration between you two especially fruitful?

Kelsey: I brought the biology knowledge, and Munir brought the coding skills. I learned Unix, Perl, and R scripting during grad school, but Munir knew how to code really well in Python, which was essential for this project. He was able to write code very quickly and elegantly and came up with the various evaluation metrics used for the machine-learning models. He also spent a long time working on a convolutional neural network model that was more computationally complex, in the end giving us similar results to the simpler Random Forest classifier we ended up using.

Munir: One of the first things I learned while collaborating with Kelsey was how to effectively digest research papers. My first exercise at the lab was summarizing a collection of research articles relevant to our projects, which was immensely invaluable in teaching me how to look in the right places for information. Kelsey's research background also played a significant role in coming up with fresh hypotheses and methods to test them, and her plant genetics background allowed us to make better sense of the large amount of data we had.

Also, at the end of the EffectorO project, I got the opportunity to do my first PCR! This was really fun for me to do, as computer scientists and bioinformaticians don't always have much exposure to the wet lab.

Question: What are you excited to see in future MPMI research?

Kelsey: I'm excited to see how advances in protein structure prediction will expand our knowledge of effectors with uncharacterized protein domains. I'm also excited about high-throughput assays for testing predicted effectors.

Munir: Making machine learning more accessible! I think it would be great to standardize self-service model-building interfaces, since training sets are ever expanding. This would be a way to further improve classifiers like EffectorO whenever new effectors are discovered.

Learn more about Munir and Kelsey in their InterConnections article.


Sperschneider, J., and Dodds, P. N. 2022. EffectorP 3.0: Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. Mol. Plant-Microbe Interact. 35:146-156.

Sperschneider, J., Dodds, P. N., Gardiner, D. M., Singh, K. B., and Taylor, J. M. 2018. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol. Plant Pathol. 19:2094-2110.

Wood, K., Nur, M., Gil, J., Fletcher, K., Lakeman, K., et al. 2020. Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif. PLOS Pathog. 10:e1009012.

1 - 10Next

 ‭(Hidden)‬ Blog Tools