InterConnections

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Mar 17

KEK on 3/17/2025 4:27 PM

Damaris Barminga is a passionate molecular biology and biotechnology researcher currently serving as a research assistant and graduate fellow at Kenyatta University, Nairobi, Kenya. She is pursuing her M.S. degree in biotechnology, focusing on plant-pathogen interactions, with a particular emphasis on the parasitic plant Striga. In her recent paper published in MPMI, "Cell Wall Dynamics in the Parasitic Plant (Striga) and Rice Pathosystem," she delves into the intricate offensive and defensive mechanisms involved in the interaction between Striga and its host plant. Her work provides groundbreaking insights into the complex molecular strategies deployed by Striga to invade its host, as well as the corresponding defensive responses of rice, paving the way for innovative approaches to combat this devastating agricultural weed.

1. What do you think is the most important or exciting finding from your paper?

In our paper, we utilized simultaneous RNA sequencing to unravel the cell wall dynamics in rice and the parasitic plant Striga. On rice, we did a comparison on the cell wall modification processes in a susceptible and resistant interaction. Similarly, a comparison of Striga infecting the two. Interestingly, the study revealed the flip side of the interaction—Striga infecting a resistant versus a susceptible rice genotype, highlighting its dual role as both a plant and a pathogen. This duality showcases an intriguing dynamic between offense and defense. A highlight of strategies such as cell wall degradation is observed as the offense plays through the induction of endo-1,3-β-glucosidase, resonating with other pathosystems during triggered immune responses.

Another exciting finding from the paper is the phenotype from the resistance assay on the rice genotype Nipponbare showed Striga wasn't able to breach the endodermis and took a detour at the Casparian strip and exited the host root.

2. Was there a piece of data that was particularly challenging to obtain, or a part of the project that was particularly difficult?

Obtaining high-quality RNA from Striga-infected root tissues, particularly from the resistant rice genotype Nipponbare, was challenging. However, through optimization of the RNA extraction process and repeated sampling, we successfully got high-quality RNA.

3. What research project are you most excited about right now?

I'm particularly excited about leveraging the synergistic potential of epigenomics, spatial transcriptomics, and single-cell transcriptomics to deepen our understanding of plant-pathogen interactions and uncover distinct cellular immune states.

4. What drew you to your current lab?

Steven's lab is at the forefront of host-pathogen interactions and plant transformation research, perfectly aligning with my interests. Its cutting-edge work in these fields provides a dynamic environment for scientific research. Additionally, having a PI who fosters professional growth was a significant factor in my decision.

5. How did you choose to join your current graduate program?

During my undergraduate studies, I had the opportunity to intern at the National Plant Health Laboratory, which sparked my fascination with plant-pathogen interactions and their critical role in agriculture and food security. This experience also ignited my interest in applying molecular techniques to better understand these interactions, ultimately shaping my choice of graduate program. I'm pleased to say that this field continues to captivate me to this day.

6. What advice would you give to starting graduate students?

Simply put, challenges are an inevitable part of research, from failed experiments to unexpected obstacles. The key is not to shy away from adjusting your strategy. Resilience and adaptability are invaluable traits in overcoming these hurdles. Embrace these challenges as learning opportunities and don't hesitate to seek support when needed. Beyond data generation, graduate school is a transformative journey that sharpens problem-solving skills. Most importantly, stay curious!

7. Who has inspired you scientifically? Why?

In my field of research, Gebisa Ejeta stands out as an inspiring figure. His groundbreaking work on Striga has significantly improved the livelihoods of millions of farmers in Sub-Saharan Africa (SSA). His career exemplifies how a scientist can create meaningful impact, particularly through a steadfast commitment to advancing SSA agriculture—a path I aspire to follow.

8. Are/were you involved in other scientific/
professional development activities? How do/did these contribute to your training?

I've actively participated in science communication training and workshops to enhance my ability to share my research, along with other related studies, with both technical and nontechnical audiences, particularly my fellow youth. My goal has always been to highlight how my work can contribute to solving the societal challenges we face today. Additionally, I've been involved in a mentorship program offered by AuthorAid, which helped me cultivate my skills in scientific research writing and presentation. These experiences have been instrumental in shaping my ability to contribute to research with tangible societal impact, particularly in the area of food security.

9. What is the greatest challenge you have encountered in your career? What did you do to overcome this challenge?

Early in my career, my goal was perfection in all aspects of science. However, this pursuit often led to disappointment and made me question my abilities. Over time, I've realized that this focus on perfection was a significant setback. Now, I value progress in place of perfection. Consistent growth and learning have become essential tools for advancing in my field and continually improving.

10. How can people find you on social media?

You can find me on the following platforms:

X: @DBarrminga
LinkedIn: www.linkedin.com/in/damaris-barminga-634422159
Research Gate: Damaris Barminga

11. Is there anything else you would like to share in your Spotlight? If so, what is it?

I appreciate the opportunity offered by IS-MPMI to be able to share my experience.

12. Bonus question: What's your favorite pathogen or disease?

Although Striga is at the heart of my current research, I find maize lethal necrosis disease particularly intriguing. This interest most likely stems from it being the first disease I worked on when I began my research career during my internship.

13. Bonus question: What's your favorite molecular plant pathology-related article?

That would be the review article on "The Plant Immune System" (Jones and Dangl, 2006). This article really laid a foundation for my comprehension of immune responses in plants.

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Mar 17

Bridging Academia and Industry

KEK on 3/17/2025 4:23 PM

Sandra Gomez is a Ph.D. candidate at Purdue University working on effector proteins in Zymoseptoria tritici. Her research integrates computational biology with molecular plant pathology techniques. In addition to her primary work, she has collaborated on projects involving comparative genomics of extremophilic fungi within Dothideomycetes, isothermal amplification methods for pathogen detection, and transcriptomics analysis of Phyllachora maydis. Alongside her Ph.D. degree, Sandra is earning a concentration in computational life sciences. Her passion for bioinformatics led her to a co-op internship in computational biology at Corteva Agriscience^TM, where she worked for six months under the supervision of Dr. Achal Rastogi on the Biologicals and Natural Product Discovery team. This experience played a key role in shaping her career path. She interviewed Dr. Rastogi to gain insights into his perspective on the career transition from academia to industry and the advice he has to offer to the new generation of scientists.

Dr. Achal Rastogi is a senior data scientist at Corteva Agriscience^TM. He holds a Ph.D. degree in bioinformatics from Ecole Normale Supérieure, France, and an M.S. degree in bioinformatics from Jamia Millia Islamia, India. His professional journey includes significant roles at Corteva, ENS, Genoscope (CEA), Personal Genomics Institute, ICGEB, and NIPGR. He has authored numerous high-impact publications in the field of microbial ecology and bioinformatics and has received several prestigious awards, including the Early Career Achievement Award from Corteva Agriscience^TM. Dr. Rastogi is dedicated to advancing microbial genomics and bioinformatics for crop health and is currently focusing on biologicals and natural product discovery.

1. Can you describe your path to becoming a senior data scientist at Corteva Agriscience^TM?

I have been fortunate to be able to work with some of the best people and research groups, and I owe my progress to their support. I began with an M.S. degree in bioinformatics from Jamia Millia Islamia in India, followed by a Ph.D. degree in bioinformatics from Ecole Normale Supérieure in France. My professional career started with research roles at the National Institute of Plant Genome and Research (NIPGR) and the International Center for Genetic Engineering and Biotechnology (ICGEB) in India, where I developed my skills in genomics data analytics and machine learning while working with plant and viral genomes. I then worked as a researcher at the Personal Genomics Institute in South Korea, focusing on human genomics. My Ph.D. and postdoctoral research at ENS and Genoscope (CEA) in France introduced me to microbial ecology and diatom biology and allowed me to delve into big data analytics. In 2018, I transitioned from academia to industry and joined Corteva as a bioinformatics scientist, where I advanced my learning toward sustainability and applied genomics and got the opportunity to explore insect biology. Currently, my research focuses on microbial genomics for biological and natural product discovery.

2. Can you tell us about your past and present research?

During my Ph.D. research with Prof. Leila Tirichine in Chris Bowler's lab at Ecole Normale Supérieure, Paris, I studied the interplay between genomics and epigenomics to understand how microbial populations adapt to changing environment. By analyzing the genetic diversity and population structure of Phaeodactylum tricornutum, a marine model diatom species, we demonstrated how genetic variations support adaptability. Concurrently, my work on histone modifications, specifically H3K27me3, supported the idea that epigenetic regulation enables rapid responses to environmental changes in this species. This integrative approach established a crucial crosstalk between stable genetic variations and flexible epigenetic changes, which together enhance the resilience and ecological success of diatoms. During my postdoctoral studies with Prof. Olivier Jaillon at Genoscope, I extended my research to study these complex interactions, leading to insights into the molecular functional preferences of microbial communities in the open ocean. After transitioning to industry, I have leveraged my bioinformatics and data science expertise in leading complex research projects aligned with sustainable crop protection and active discovery and product development.

3. What skills are most important in your role as senior data scientist?

In my role as a senior data scientist, several skills are crucial for success. First, a strong foundation in data science and computational biology is essential—this is what I bring to the table. Proficiency in programming languages like Python, R, and Bash, as well as experience with high-performance computing and cloud platforms is vital for handling large-scale genomics data. Leading projects requires effective management and leadership abilities for guiding teams and ensuring timely delivery of high-quality results. I work with large, dynamic, and interdisciplinary teams, so communication skills are necessary to collaborate and bring a clear understanding of complex scientific problems. Continuous learning and adaptability are also critical given the fast-paced nature of the field.

4. How do you define success in your role?

Success in my role at Corteva is defined by the expertise and impact that I bring to projects and the organization. This includes delivering high-quality, reproducible data and analysis workflows, advancing our understanding of microbial genomics, and accelerating the discovery of new biologicals and natural products. Success also means fostering collaboration across diverse teams, mentoring colleagues, and continuously improving our data science capabilities. Ultimately, it's about driving innovation, achieving our research goals, and contributing to the broader scientific community while ensuring that our work translates into tangible benefits for our stakeholders and customers.

5. How do you stay current with developments in your field?

Big thanks to social media platforms and active academic social networks! It is easier than ever to follow what's new—I read, attend seminars, and talk to people around me to stay current. I prioritize continuous education to update my skills time-to-time through formal and, many times, through self-guided training. Also, I mentor students and interns, which allows me to stay connected with fresh perspectives and emerging technologies in the field. Most importantly, active contributions and collaborations on scientific projects keep me curious, which I believe is the key driver that pushes me to learn more.

6. What are some common misconceptions about your field of expertise?

There are several common misconceptions about the field of bioinformatics. One major misconception is that it's solely about coding and data analysis. While these are important aspects, bioinformatics requires a deep understanding of biological concepts and the ability to interpret complex biological data. Another misconception is that bioinformatics is only relevant to academic research. In reality, it has significant applications in various industries, including agriculture, healthcare, and pharmaceuticals, where it drives innovation and is key to product development. Also, some people think that bioinformatics is a solitary field, but collaboration is a key component, involving teamwork with scientists, researchers, and engineers. Bioinformatics is constantly evolving with new technologies and methodologies, requiring continuous learning and adaptation.

7. What advice would you give to people starting in the job market or looking for a career like yours?

The current job market is very dynamic, but the foundation of it hasn't changed and will never change. Organizations need to attract talent to grow and stay competitive. Based on your career aspirations and training, seek out suitable open positions and apply with dedication. Pay close attention to job descriptions for the roles you aspire to, identify any skill gaps, and work on advancing your expertise. While focusing on your technical skills, invest time in improving your communication and soft skills. Last, be patient and persistent; the job search can be challenging, but staying focused and positive will help you find the right opportunity.

8. Can you share a memorable experience or achievement in your career?

I have had many! One that is close to my heart is the day I defended my Ph.D.—becoming a scientist had always been my dream. There was not a single crazy moment on that day, everything was blissful. I still clearly recall each moment of the day, from picking the right outfit to setting up the defense room to welcoming my thesis advisor and committee members. The presentation went smoothly, the audience was engaged, and I had a wonderful, thought-provoking discussion with the committee members—it all felt so right. Then, the president of the committee congratulated me on successfully obtaining a Ph.D. degree—that was the moment! We celebrated with a fantastic after-party, and I ended the day with a pleasant walk along the Seine with my wife.

9. Oh, by the way. How could people find you on social media?

I am active on LinkedIn and am always happy to connect.

10. Is there anything else you would like to share in your Spotlight? If so, what is it?

Drive yourself with a purpose for an enriching career journey. When deciding between career options weigh three things and maneuver accordingly. Do you love what you do? Does the world need what you do? Are you good at what you do?

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Dec 20

InterConnections: Plant-Microbe Interaction Careers in Government

KEK on 12/20/2024 3:00 PM

Careers in plant-microbe interactions span more than research. Suma Chakravarthy is a senior science advisor at the USDA-APHIS-Biotechnology Regulatory Service. She earned her Ph.D. degree in genetics at Delhi University, working in plant biology, and was a postdoctoral researcher in Dr. Greg Martin's lab at the Boyce Thompson Institute. Read how she made her way to her current position and her role at APHIS.

1. What drew you to your current job?

The availability of new techniques for genome engineering allows developers to introduce desirable traits into plants and other organisms, with the promise of enhancing sustainability and food security. This is an exciting period for countries trying to enable innovation and revise or adapt their regulatory processes for the oversight of products of agricultural biotechnology. In my current job, I work with federal partners and coordinate international communication to support science- and risk-based regulatory decision-making, while also providing support for APHIS BRS regulatory processes.

The chance to learn constantly, provide technical advice and influence policy, and work on international cooperation with many countries and organizations is exciting and motivating for me and drew me to my current job.

2. How did you choose molecular plant-microbe interactions as your focus of research?

My Ph.D. degree was in the field of plant biotechnology and focused on modification of the CaMV 35S promoter for transgene expression. The "clever" 35S promoter is a perfect example of plant-pathogen coevolution, as this viral promoter has cis-elements found in plant promoters and is responsive to the defense hormone salicylic acid, among other stimuli. My interest in plant transcription serendipitously led me to the lab of Prof. Greg Martin, where I started my postdoc studying the role of transcription factors in plant defense responses. During my years in academia, I was fortunate to be able to study plant defense responses, as well as bacterial virulence strategies.

3. What advice would you give to starting graduate students?

Remember that graduate school is only the start of your career, which could take different turns in your life. During grad school, it is important to focus on your project, work hard, and not get disappointed by failures. Have a backup project (or two) in case your main project is not successful. This is a good time to develop writing skills. Most important, do not box yourself in a niche field: read broadly, network, be interested in what other graduate students do, and enjoy the journey. A side hobby is a great way to decompress and take a mental break.

4. What advice would you give to people starting out in the job market?

Take time to prepare a good resume tailored to the advertised job and seek feedback from someone senior in your organization to polish the resume. It may take a few iterations till the application looks sharp. Prepare a list of potential interview questions and practice your answers, preferably with a colleague or senior, paying attention to content and timing. Be focused on the requirements of the job during your preparation phase.

Do not be afraid to contact potential employers and express your interest to learn about their work. Networking is critical because it will improve your understanding of opportunities and the scope of jobs in your field. Although it is important to find the right job for your background, sometimes the dream job will not come your way and it may be more realistic to accept the next-best position and do your best in it. Over time, other opportunities for growth will present themselves. A very important piece of advice, in my opinion, for young professionals is not to switch jobs too quickly—take time to learn the subject area and contribute to the mission of your employer. Important skills that will make you successful in the job market are good teamwork, collaboration, clear communication, and integrity.

5. Who has inspired you scientifically? Why?

Gregor Johann Mendel, who laid the foundation of the science of genetics, has inspired me scientifically. Despite facing tremendous personal struggles, he had many aspirational qualities that contributed to his success in laying down the foundational rules of inheritance. He had astute powers of observation and was rigorous, methodical, analytical, and persistent. He displayed courage to stand up for what he believed was right.

6. How did you make the transition from science to policy?

The Science and Technology Policy Fellowship (STPF) program of the American Association for the Advancement of Science (AAAS) helped me segue from science to policy. I listened to some lectures by invited scientists at Cornell University and became aware of the prospects the AAAS STPF gives to scientists to contribute their knowledge in the policy realm. The stories of former fellows were inspiring and offered a glimpse into an exciting and relevant career path. As a STPF Fellow in USDA APHIS BRS, the transition process was difficult, and I missed being on the bench and doing active research. I had to learn about biotechnology regulations, how they are implemented, how to apply science to perform risk assessments, and decision-making in the face of uncertainty. Every bit of my education, research experience, and soft skills were utilized during this transition. In my current position I am a regulatory scientist doing science and policy work, applying scientific skills to support complex evaluation of products to make regulatory determinations, and keeping up with advancements that will inform future policy.

7. What is the greatest challenge you have encountered in your career? What did you do to overcome this challenge?

I worked as regulatory manager at CropLife International (CLI), an international trade association that promotes agricultural technologies. The job at CLI pushed me out of my comfort zone because it was a new work environment and I had to interact with industry colleagues and a dynamic team of legal, trade policy, and communication professionals whose purpose was to promote trade and globally harmonized regulatory policies. This meant I had to zoom out and look at the big picture instead of focusing on details. I used the lessons from my academia workbook to overcome the challenge. I observed the workstyle of different member companies; learned about business pipelines and the importance of deadlines; was goal oriented; collected and organized information; used data for problem solving and presenting solutions; and was open to critical suggestions. My experience working in different sectors now helps me in my current job.

8. How can people find you on social media?

I have a LinkedIn profile, which is the easiest way to find me on social media.

9. What's your favorite story from an IS-MPMI Society meeting?

The first IS-MPMI meeting I attended was in Madison, WI, in 2001, when I was a postdoc in Greg Martin's lab working on the ethylene response factor Pti4. During the meeting, our lab met Charles Després who is now professor, biological sciences, at Brock University in Canada. Charles had an interest in studying plant signaling pathways, and after the meeting, we went on to become collaborators and coauthors on a 2003 paper on Pti4-mediated gene expression and its role in plant defense. This is a favorite story because it showcases the power of networking prior to the explosion of social media!

10. Have you ever conducted research in a country other than the United States? What were the challenges and good parts?

I completed my Ph.D. degree in India under the guidance of Dr. P.K. Burma and Dr. D. Pental. I was part of the first cohort of Ph.D. students from the lab and worked with researchers who focused on transformation and improvement of Brassica, cotton and pigeon pea using Agrobacterium and biolistic based methods. It was a stimulating environment, and I learned a lot though the discoveries and experiences of fellow scientists. At that time, it was challenging to access scientific literature, and I had to commute to a different institution to prepare photocopies of articles to read. Visits to the library often turned into a full-day event, which allowed me to detach from the bench and spend time browsing journals and books.

11. Is there anything else you would like to share? If so, what is it?

In my opinion, it is important to find ways to pay forward the support we obtain during our career to other colleagues and younger professionals. This could be by mentoring, offering career advice, or volunteering in schools and the local community.

12. Bonus question: What's your favorite molecular plant pathology-related article?

This paper I am a co-author on is by far my favorite—it was published when I was a research associate in Dr. Alan Collmer's lab: “Genetic Disassembly and Combinatorial Reassembly Identify a Minimal Functional Repertoire of Type III Effectors in Pseudomonas syringae. (Cunnac, S., Chakravarthy, S., Kvitko, B. H., Russell, A. B., Martin, G. B., and Collmer, A. 2011. Proc. Natl. Acad. Sci. 108:2975-2980).

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Dec 20

Spotlight on Early Career Researchers

KEK on 12/20/2024 2:58 PM

Meet recently graduated student Dr. Alexandra Margets, aka "Allie," from Prof. Roger Innes' lab at Indiana University Bloomington. Her research focuses on Identifying and understanding the intricate components of the plant-pathogen interface, which motivates her research questions. Allie was awarded the prestigious Agriculture and Food Research Initiative Predoctoral Fellowship by the USDA National Institute of Food and Agriculture to investigate the molecular mechanisms of soybean cyst nematode effector proteins. Her research work led to the identification of a key protease effector of soybean cyst nematode (SCN), and this work translated into her first-author paper recently published in the November issue of MPMI, which was selected as an Editor's Pick. With her current and future research, she hopes to gain information that expands our knowledge of plant immunity and use that information to address problems that impact agriculture. We congratulate Allie on her recent achievements and wish her a stroke of good luck in her future endeavors.

1.What do you think is the most important or exciting finding from your paper?

The most exciting finding from my paper was identifying a soybean target of the SCN effector protease, CPR1. It was an important finding to not only to provide a snapshot as to where/how CPR1 functions in plant cells, but now we can use this target to identify CPR1's preferred cleavage sequence to generate PBS1 decoys that elicit immune responses upon cleavage.

2.Was there a piece of data that was particularly challenging to obtain or a part of the project that was particularly difficult?

Identifying the soybean target of CPR1 was the most challenging piece of data to obtain. Before pursuing biotin-based proximity labeling (miniTurbo) in composite soybean roots, I tried several different approaches to identify soybean targets of CPR1 and other SCN proteases. I tried to optimize several different approaches to perform these experiments in soybean. The techniques I pursued before using the composite plant system included soybean protoplasts, transient expression in soybean, and hairy root cultures. At first, I was using GFP fluorescence to identify transgenic roots, which was challenging, but incorporating the screenable marker, RUBY, into these experiments was a game changer that saved me a lot of time! However, miniTurbo yielded a list of interesting targets to test, which meant there was a lot of cloning and negative results along the way. Once I confirmed GmBCAT1 as a target of CPR1, the challenge made the result that much more exciting.

3. What research project are you most excited about right now?

I have now defended my thesis work but am happy to see that my projects are continuing in the lab. I am most excited to see the Innes-Baum labs work together to generate and test PBS1 decoys for SCN resistance. Stay tuned, as we hope to publish our findings on this system in roots in the near future. I also left the lab with an idea for using the composite plant system to identify the R gene in soybean that recognizes PBS1 cleavage.

4. What drew you to your current lab?

Despite rotating through two other great labs where I learned a lot, I was fascinated by the complexity between plant-pathogen interactions. I had very little exposure to this field at the time but loved molecular plant biology and the idea of learning about not only plants, but the pathogens that infect them in agriculture. I also was drawn to the idea of doing research, with the goal of developing resistance strategies as I was interested in a future career in industry/biotechnology. During my rotation in the Innes lab, I had a great mentor who routinely took the time to discuss his projects and the field of molecular plant-pathogen interactions, while challenging me to think about potential future directions of the lab's research. I felt like there was a great support system among the Innes lab members and thoroughly enjoyed showing up each day. Dr. Innes and I established good communication early on, and I felt that it was a place where I would be able to grow into an independent scientist.

5. How did you choose to join your current graduate program?

I was looking for a broad graduate program that would allow me to explore different areas of biology research before choosing a thesis lab. The Genome, Cell, Developmental Biology Ph.D. program at IU was exactly that. This program also allowed me to explore labs under microbiology, biochemistry, and evolution/ecology through rotations. Since I was coming from undergraduate studies, I didn't want to "think" I knew what I wanted/needed but rather wanted to explore different labs and mentors through hands-on experiences. Before joining, there were several labs I was interested in, so I knew that I would be able to make an educated decision on where I would thrive. Upon visiting IU, I immediately got a sense of diversity at the university and within the community that reminded me of where I grew up in New York. The graduate students during my visit were extremely friendly and honest, which allowed me to truly envision what it would be like to be a student there. Additionally, Bloomington, IN, is a beautiful small town that had everything I needed to focus on my thesis work but enjoy where I was living.

6. What advice would you give to starting graduate students?

Find a thesis lab that is going to give you the support that you need to reach your scientific goals and communicate those goals with your PI as early as possible. If you are doing rotations, have this conversation during the rotation and before joining. It is reasonable for graduate students to have high expectations for their research mentor. However, it is easy to forget we are just one of their responsibilities among many others. Establishing healthy, clear, and direct communication early on will help you both get what you need out of the professional relationship.
Build your scientific community early on in your career. It is always intimidating to put yourself out there in those early years, as many of us of get self-conscious about the amount of data we have in year one or two (especially if we are working on a newer project)—but do it! Whether that is attending a meeting with a "future directions" poster or attending a mixer where you may not know anyone. Once you make connections, remember to maintain them. The relationships in your network should be a give and take. Don't only reach out when you need something.
Try and leave the "self-doubt" at the door. Grad school is a marathon, not a race. There are going to be rough times and that's okay. Find constructive ways to handle the lows and don't resort to thinking you aren't good enough. It's normal to feel these things from time to time, but don't let them consume you. Having a healthy perspective and trying to find the positive in these instances will keep you motivated and happier in the long run.

7. Who has inspired you scientifically? Why?

I have always been inspired by my undergraduate PI, Dr. Michelle Barthet, at Coastal Carolina University. She was the first to show me the great world of research during my first year as an undergrad. Being at a primarily undergraduate institution, there were the obvious restraints when it came to funding, resources, and time in the lab. However, this never stopped Dr. Barthet. She was so passionate about her research and the productivity of her lab, she always came up with a way to accomplish her research questions while mentoring several undergrads. Not only was she creative, but the passion she had for her students in her lab and in her classrooms was unmatched. She genuinely cared about our long-term goals and tailored our experiences around them. I am truly inspired by the scientist she is and the dedication she has to her role in academia. My time working with Dr. Barthet shaped how I approach my science today and interact with mentees and colleagues.

8. Are you or have you been involved in other scientific/professional development activities? And how have they contributed to your training?

At IU, I served as the vice president of my graduate student organization that we started during COVID. It allowed me to build upon my leadership skills and adapt to new ways to communicate with our graduate student community during a challenging time. The organization is thriving today, and I love seeing how the new leaders have used the organization to promote a supportive community. I also worked closely with Dr. Innes on outreach initiatives in the Bloomington community. Each fall, we would visit third-grade classrooms and teach students what plants needed to grow through a hands-on experiment. This experience helped me immensely with my communication skills, and it was rewarding to watch the students get excited about plant science. Since I loved outreach, I wanted to branch out beyond IU, which led me to getting involved in The American Phytopathological Society Office of Public Relations and Outreach (APS OPRO). For two years, I served as the graduate student representative, where I had the pleasure of communicating plant science with different target audiences. Since my program at IU was not plant-specific, APS gave me a great community that I had the pleasure of meeting with regularly.

9. What is the greatest challenge you have encountered in your career? What did you do to overcome this challenge?

My greatest challenge during my academic career occurred during my undergrad studies. To pay for college, I was working full-time as a waitress at the Hard Rock Café. Luckily, I had a great support system there, and my managers fully supported my education. However, balancing work, school, and research was a real challenge both physically and mentally. Registering for the upcoming semesters was always a stressful time as I was working hard to pay off the current semester on time to be sure I could register for the classes I needed. To overcome this challenge, I had to become really (really) good with time management and sticking to a routine. Sometimes that meant having flash cards for an upcoming test in my apron at work or waking up before an 8 a.m. class to go to the library. I used my future goals as my source of motivation. At Coastal Carolina University, I got my first taste of research and really fell in love with it. Luckily, I was able to stay work in the same lab for the three years I was at Coastal, which helped me develop a routine. While I wouldn't necessarily want go through this period again, it really shaped how I approached grad school, and I had such appreciation for being able to immerse 100% of myself in my research and education during my Ph.D. studies.

10. How can people find you on social media?

X: @_acmargets

LinkedIn: https://www.linkedin.com/in/alexandra-margets

11. Is there anything else you would like to share? If so, what is it?

To students interested in pursuing a Ph.D. degree or those navigating grad school, always feel free to reach out to me if you need someone to talk to or have questions. I was lucky enough to have several more senior scientists to go to with my questions and concerns throughout my graduate experience, and I genuinely love helping others.

12. What's your favorite pathogen or disease?

Soybean cyst nematode (but any sedentary plant parasitic nematode sparks my interest).

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Sep 18

InterConnections: Letter from IS-MPMI President Adam Bogdanove

KEK on 9/18/2024 5:58 PM

Here in Ithaca, NY, the days are getting shorter and cooler as summer comes to a close, but with the start of our new academic year, it is a time of excitement and promise. For our Society too there is a lot to look forward to in the coming year.

Not least, the 20th IS-MPMI Congress next July, in the beautiful city of Cologne, Germany, a science hub rich in history and culture. The program will feature a variety of speakers from around the world to showcase the most exciting findings in plant-microbe interactions, with ample time for human interactions. Plan now on "Making Global Connections in Plant-Microbe Interactions" in Cologne 2025!

I also am happy to report that the IS-MPMI Board of Directors, beyond its historical role of selecting a locale and assisting the organizers for the biannual congress, has been building on transformative initiatives developed during the pandemic—in professional development for our early-career members and in community building that promotes geographic and social diversity. We have been working on new initiatives too, in open science and public outreach, that we hope will help members better share their research and its importance.

You can look forward to several things already in the works, including more frequent episodes of the Microgreens podcast, a new slate of What's New in MPMI Virtual Seminars, a reprisal of the 2022 Online Early Career Showcase, first author interviews and other engaging new content in the Interactions newsletter, and, as offered for the 19th IS-MPMI Congress, a permanent switch to open access to all congress posters and talks by authors and speakers who sign on.

More is being planned, and the board will need your help. Keep an eye out for calls to get involved, and send me or any other board member your thoughts and ideas on how together we can best advance the IS-MPMI mission of supporting member achievement, as well as realize our vision to "embody a diverse, engaged, international community of scientists, educators, and other stakeholders to create and share foundational knowledge in plant-microbe interactions toward greater understanding, appreciation, and sustainable use of plants and the environments in which they grow."

Whether the days are getting shorter or longer where you are, and wherever you may be in your calendar, my sincere best wishes for the year ahead. On behalf of all the board members, we look forward to your successes and to working together to strengthen our community and the positive impact of our discipline.

With best regards,

Adam Bogdanove
IS-MPMI President

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Jun 19

InterFaces: Spotlight on Early-Career Researchers: Danielle Stevens and Alba Moreno Perez

KEK on 6/19/2024 12:32 PM

Alba Moreno Perez (left) and Danielle Stevens (right)

This is the first spotlight in our series highlighting early-career scientists and their recent discoveries. Meet graduate student Danielle Stevens and postdoctoral scientist Dr. Alba Moreno Pérez from the Coaker lab at UC Davis. Their work on the natural variation of immune epitopes was recently published in PNAS. Learn about their advice for choosing and navigating graduate school, their scientific inspirations, and their new paper.

Q&A with Dani Stevens

Q What research project are you most excited about right now?

A As I am wrapping up my Ph.D., the discoveries I made have only led to more questions and more future project ideas. During the heart of the pandemic, I noticed most of the MAMP research was focused on characterizing the biochemical and immune outcomes of a handful of MAMPs. With so many bacterial genomes already in NCBI, I quickly realized there is an opportunity to understand the impact of epitope evolution on immune outcomes. For example, I found that multicopy csp22 epitopes can have differential immune outcomes in tomato, impacting pathogen colonization. This was one of our findings in our recent PNAS paper.

Now, I have many follow-up questions on these interactions. For example, how do different immune outcomes impact bacterial protein function? Does an intermediary PTI response provide any resistance locally or induce SAR distally? How do perception and immune outcomes change in other relative plants?

In particular, the csp22 receptor CORE is restricted to the Solanaceous family, which contains hundreds of species, and other plant species are found to respond to csp22 epitopes, though they do not encode a CORE homolog. Currently, we do not have a great understanding of the evolution of CORE, other convergently evolved csp22-receptors, and their receptor perception capabilities. With tens to thousands of receptors encoded within land plants, how do we better understand ligand-receptor interactions at scale and potentially engineer de novo receptors. These are questions I am hoping to answer during my postdoc research in Dr. Ksenia Krasileva's lab at UC Berkeley.

But, if you ever meet me in person, I have (maybe too) many questions around PTI and microbial evolution. J

Q What drew you to the Coaker lab?

A I leaned about the Coaker lab after reading a paper published in MPMI for a class I was taking during my senior year of as an undergraduate student. I had spent several years working on an actinobacterial pathogen and wanted to keep working on these understudied organisms. Additionally, Gitta Coaker was highly recommend for her mentorship abilities, and I could quickly tell it was a great fit. I feel thankful for my colleagues who helped point me in her direction and for having the opportunity to be part of her lab.

Q How did you choose to join the graduate program at UC Davis?

A I have worked in host-pathogen interactions since my first research project, yet I don't see myself as a plant pathologist, at least not in the traditional sense. My undergraduate degree is in biochemistry and biophysics, and I spent a summer at the Max Planck Institute for Evolutionary Biology. I always have valued diverse training and, thus, sought graduate programs with this in mind, particularly focusing on those that emphasize bioinformatics, computational biology, or genomics and that allow me to conduct research in plant-microbe interactions. I landed at UC Davis as it has numerous well-regarded plant-focused departments and a well-established genetics and genomics graduate program.

Q What advice would you give to graduate students who are just starting out?

A Be curious and flexible, read broadly and often, yet keep focused on the major questions, areas, and systems that most interest you. Sometimes the most interesting and worthwhile projects are ones you may have not planned for. Alternatively, there are far more opportunities and ideas than any one person has the time for, so it also is important to be selective. Trying to maintain this balance with funding in mind is not easy, but it is incredibly rewarding.

Q Who has inspired you scientifically? Why?

A As any young scientist, I use to look up the "greats" in our field. As I have gotten older, however, I have come to realize I am much more inspired by the handful of incredible scientists who have mentored me professionally and personally. These individuals have taught me so much, treated me with kindness and respect, and provided me opportunities and independence, all while maintaining a positive life outside of their academic careers.

Q Are you involved in other scientific/professional development activities? How do these contribute to your training?

A As I approach graduation, I am gradually winding down some activities to refresh before starting my next position. I want to highlight two key scientific activities that shaped my training. First, I served on my graduate group's admissions committee for three years. This role was incredibly rewarding, as I could provide a diverse perspective and impact our incoming class. Second, I organized and ran a student-focused seminar series for genetics students. Unlike some graduate programs, genetics (also known as IGG) spans many departments and buildings, making it difficult for our community to come together. The seminar provided an opportunity for students to gather, share their science, and support each other's progress. Both experiences were rewarding and contributed significantly to my training.

Q What is the greatest challenge you have encountered in your career? What did you do to overcome this challenge?

A I think the most rewarding and challenging aspects of my career all revolve around people. I found it is important to stick to and stand up for one's values. However, also having grace and patience can do wonders in conflict.

Q How can people find you on social media?

A X: @Dani_M_Stevens

Q What's your favorite story from an IS-MPMI society meeting?

A I don't have a particular story to share, but I have enjoyed my last two IS-MPMI meetings and look forward to the next.

Q Is there anything else you would like to share in your spotlight?

A While I am thankful for the chance to highlight myself, Alba, and our recent publication, I am also excited to wrap up some other work to share with the MPMI community in the coming month or so. Be on the lookout if you are interested!

Q Bonus question: What's your favorite pathogen or disease?

A Any actinobacterial pathogen of course. J

Q&A with Alba Moreno Pérez

Q What research project are you most excited about right now?

A During my collaboration with Dani on this project, we made an exciting discovery: some elf18 variants can induce early, but not late, plant immune responses. These MAMPs, known as deviants, have opened up intriguing questions. I am particularly fascinated by how these natural deviants manage to reduce the PTI responses. Recently, I've started a new project with the goal of uncovering how these deviant peptides activate the receptor and why they fail to trigger later plant immune responses. I'm really thrilled about this opportunity to identify the mechanisms by which deviants evade plant immunity and to explore their potential role in avoiding pathogen recognition.

Q What drew you to the Coaker lab?

A In 2018, during my Ph.D. research, I did a four-month short stay in Dr. Gitta Coaker's laboratory in order to learn the GFP strand system. In my thesis, I investigated how pathogens inhibit plant defense systems and promote disease. My time in the Coaker lab sparked a deep curiosity about understanding the defense mechanisms plants use to prevent pathogen infections. Given the Coaker lab's extensive experience in biochemical, posttranslational, and genetic investigations of immunological signaling, I chose to pursue a postdoctoral position there. I believe this will allow me to learn new methodologies that complement my training, providing a comprehensive understanding of both sides of plant-pathogen interactions. Additionally, during my four-month stay, I observed Dr. Coaker's dedication as a mentor who fosters intellectual growth, critical thinking, and creativity. This positive experience motivated me to work with her on applications for various postdoctoral fellowships, ultimately securing two opportunities that enabled me to join the Coaker lab.

Q How did you choose to join the graduate program at the University of Malaga?

A During the third year of my bachelor's degree studies in biology, I began working on a project as an undergraduate student in the lab of Dr. Cayo Ramos at the Department of Cellular Biology, Genetics, and Physiology at the University of Malaga, Spain. This project awakened my curiosity for studying plant-pathogen interactions. After completing my master's degree, I joined the doctoral program in advanced biotechnology to pursue my Ph.D. degree under the supervision of Dr. Ramos. His research focuses on studying the role of virulence factors in the host range of Pseudomonas savastanoi, a bacterium that causes knots in woody hosts. I was particularly interested in investigating the mechanisms that bacteria use to overcome plant immunity and cause disease.

Q What advice would you give to graduate students who are just starting out?

A My advice is, if you decide to pursue a Ph.D. degree, choose a project that you are truly passionate about. Science can be challenging, and your passion and curiosity will help make the journey easier. When you find a paper or project that excites you, don't hesitate to contact the principal investigator. Send your CV and express your interest in the project. Don't be afraid of rejection; if you don't try, the answer is always no.

Q Who has inspired you scientifically? Why?

A At the beginning of my career, I was inspired by Rosalind Franklin and Marie Curie, women who broke barriers and fought hard for their scientific careers in times when women were not often allowed to do so. Throughout my career, I have met many remarkable and strong women who serve as excellent examples of how it is possible to have a successful career in science without sacrificing family life. Everything is possible if you have passion and dedication.

Q Are you involved in other scientific/professional development activities? How do these contribute to your training?

A I am involved in mentoring undergraduate students in the lab. Mentoring is a crucial part of our development, especially if you aspire to be an academic professor. Every student is different, so learning how to help them and bring out their best is very important. I also participate in the review of articles and serve on evaluation committees for the Postdoctoral Scholar Association. These experiences have contributed to my scientific career by enhancing my critical thinking skills, broadening my understanding of current research trends, and providing valuable insights into the peer-review process. Additionally, during my Ph.D. program, I participated in outreach activities with the goal of bringing the real image of scientists closer to the public and showing that they are people just like them. I believe outreach is very important because it provides the opportunity to connect current science with future generations.

Q What is the greatest challenge you have encountered in your career? What did you do to overcome this challenge?

A One of my biggest challenges has been overcoming the language barrier. I am from Spain, and English has been particularly challenging for me, but I have worked hard to improve my speaking and oral presentation skills. One piece of advice: don't hesitate to speak if your English is not perfect. It's more important to express yourself and seize the opportunity to interact and connect with people.

Q How can people find you on social media?

A You can find me on X: @Alba_MorenoP.

Q What's your favorite story from an IS-MPMI society meeting?

A The IS-MPMI meetings are among my favorite conferences. They provide the perfect opportunity to reconnect with former colleagues, meet new people, and stay up-to-date with the latest discoveries in plant-pathogen interactions. A very fun moment from the IS-MPMI meeting held in Glasgow, Scotland, in 2019 was during the diversity party when everyone ended up dancing to the Spanish song "La Macarena."

Q Is there anything else you would like to share in your spotlight?

A I would like to thank Dani and Gitta for giving me the opportunity to be part of this amazing project and MPMI for highlighting our work.

Q Bonus question: What's your favorite pathogen or disease?

A Pseudomonas syringae has always been my favorite pathogen due to its diverse virulence factors and its value in studying plant-pathogen interactions. However, since working with Ralstonia, the causative agent of bacterial wilt disease, I've come to appreciate it equally. Ralstonia's sophisticated strategies for invading and colonizing plant tissues make it an excellent model for studying plant-pathogen interactions at both single-cell and spatial resolution levels.

Q Bonus question: What's your favorite molecular plant pathology-related article?

A One of my favorite plant pathology-related articles associated with MAMP perception is the article titled "Co-incidence of Damage and Microbial Patterns Controls Localized Immune Responses in Roots," published in the journal Cell by the group of Niko Geldner. In this study, they analyzed MAMP receptor expression and responses at cellular resolution in Arabidopsis roots. They demonstrated that only a restricted subset of Arabidopsis root zones directly responds to the flagellin MAMP in the absence of damage.

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Mar 19

InterConnections: Get to Know Kamesh Regmi

KEK on 3/19/2024 3:41 PM

Three-Dimensional Ultrastructure of Arabidopsis Cotyledons Infected with Colletotrichum higginsianum

Name: Kamesh Regmi

Current Position: Assistant Professor, Kenyon College (Gambier, Ohio)

Education: B.A. degree, Reed College; Ph.D. degree, Arizona State University

Non-scientific interests: Visual media

Brief Bio: I grew up in Nepal and arrived at Reed College to pursue my college education, graduating with a degree in biology. Then I met Dr. Roberto Gaxiola on a visit to Arizona State University (ASU) and was immediately fascinated by the mechanisms of photosynthate transport in phylogenetically diverse lineages of plants. During my pursuit of a Ph.D. degree at Dr. Gaxiola's lab, I studied sugar transport and partitioning in a vascular monocot rice and a nonvascular moss, Physcomitrium, and showed that the molecular toolkit required for sugar transport evolved before phloem itself. Overall, trying to understand how structure recapitulates function in the biological universe has been the primary driving force of my research. I ultimately landed as a postdoctoral researcher in Dr. Roger Innes' lab at Indiana University, where I optimized and utilized state-of-the-art imaging methods like serial block-face and focused ion beam scanning electron microscopy to elucidate and reconstruct the three-dimensional ultrastructure of various Colletotrichum fungi in the process of infecting host plants like Arabidopsis, sorghum, and Medicago. Last summer, I moved to Kenyon College, a small, primarily undergraduate, liberal arts institution, to establish my own plant biology lab. At Kenyon, I have really enjoyed teaching a wide array of classes—ranging from introductory labs and lectures to upper-division courses in plant physiology and pathology. Specifically, integrating hypothesis-driven, research-oriented, publication-quality science in the classes that I teach to highly motivated undergraduate students has been a rewarding experience.

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Mar 19

InterConnections: Get to Know Tom Waksman

KEK on 3/19/2024 3:38 PM

Computational Prediction of Structure, Function, and Interaction of Myzus persicae (Green Peach Aphid) Salivary Effector Proteins

Name: Thomas Waksman

Current Position: Postdoctoral Research Assistant, Bos Group, Department of Plant Sciences, University of Dundee, UK

Education: Master's degree in biochemistry, University of Oxford; Ph.D. in plant science, University of Glasgow

Non-scientific Interests: Nature, hiking, music

Brief Bio: My passion for nature, science, and the environment came from my parents, education, and hiking activities. From an early age, I thought I would like to be a biologist, and I enjoyed math and chemistry, so I studied for a biochemistry degree. My research activities have focused on protein structure and interactions, plant-microbe interactions and environmental signaling.

During my master's research project, I was involved in determining the structure of the UDP-glucose:glycoprotein glucosyltransferase (UGGT). UGGT is the glycoprotein folding quality-control checkpoint in eukaryotes—it transfers glucose to short glycans in misfolded glycoproteins, causing retention and refolding of these incorrect proteins in the endoplasmic reticulum. UGGT must be able to interact with misfolds and glucosylate glycans in any misfolded glycoprotein, covering a very wide range of protein structures—this interactive adaptability is intriguing from a protein structure perspective. Multiple crystal structures of UGGT suggested how interdomain conformational flexibility allows the enzyme to cover a great range of misfold-to-glycan distances.

Initially, I wanted to pursue a Ph.D. degree in protein structure and molecular machines. However, an inspiring summer project about nitrogen-fixing symbiosis in the group of Prof. Sharon Long at Stanford University, as well as a growing desire to work in a nature and environment context, led me to plant molecular biology research. During my Ph.D. program, I investigated blue-light signaling in Arabidopsis in Prof. John Christie's group at the University of Glasgow. I developed a novel in vitro phosphorylation assay method for phototropin (phot) blue-light receptor kinases, based on "gatekeeper" technology in which a kinase is engineered to use an enlarged ATP analogue. Gatekeeper-engineered Arabidopsis phot was expressed in a cell-free system and used to identify thiophosphorylate substrate candidates, which is detected by immunoblotting. I discovered that NPH3/RPT2-like proteins, known to be key signaling components since phot was discovered in the 1990s, are in fact phot substrates. Phosphorylation of a conserved phosphorylation site at the protein C-terminus contributes to blue-light response in plants.

I am now finally combining my main research interests as part of the APHIDTRAP project in the group of Jorunn Bos at the University of Dundee. My aim is to determine the structure of protein complexes comprised of aphid effectors and plant-host target proteins. For my article published in the MPMI Focus Issue on effectors, properties (including structure) of effector candidate proteins found in green peach aphid saliva were computationally predicted. We realized that many of these proteins are relatively unknown to science, unpredictable, and probably contain intrinsic disorder in their structure. Some of these unusual proteins have effector activity, so I intend to study those. I would like to use mass spectrometry methods to determine the structure of the effector-target complexes at medium to high resolution, followed by computational modeling to achieve accurate structures. X-ray crystallography or electron microscopy can be used to determine high-resolution structure if necessary, after removal of disordered regions.

As part of University of Dundee Plant Sciences, I am affiliated with the James Hutton Institute, which exposes me to diverse biological science approaches applied to agriculture and the environment. In addition, volunteering in the United Kingdom's invasive tree disease observation program (Observatree) has reinforced my regard for environmental monitoring and nature restoration. In the future, I hope to do research in the MPMI area, linking the evolution of interspecies protein complexes to ecosystems and engineering plant resistance to insect effectors for agricultural application.

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Dec 18

InterConnections: Get to Know Mohamed Hafez

KEK on 12/18/2023 12:37 PM

Evolution of the ToxB Gene in Pyrenophora tritici-repentis and Related Species

Name: Mohamed Hafez

Current Position: Research Biologist, Agriculture and Agri-Food Canada

Education: B.S. and M.S. degrees in microbiology, Suez Canal University, Egypt; Ph.D. degree in microbiology, University of Manitoba, Canada

Nonscientific Interests: Photography and chess

Brief Bio: Earlier my career, I conducted research in the field of molecular biology and fungal genetics as a Ph.D. student in Dr. Georg Hausner's lab (Department of Microbiology, University of Manitoba, Canada), then as a postdoctoral fellow in Dr. Franz Lang's group (Department of Biochemistry and Molecular Medicine, University of Montreal, Canada). In Dr. Hausner's lab, my work aimed to understand the evolutionary dynamics of mobile introns and their encoded open reading frames (such as DNA-cutting meganucleases). An important finding from my Ph.D. project was the characterization of two novel DNA-cutting enzymes (i.e., I-OmiI and I-OmiII) with applications in genome editing. In Dr. Lang's lab, my research was part of a large-scale project titled “GenoRem," the goal of which was to improve bioremediation of polluted soils through environmental genomics. My research in GenoRem led to one of the biggest achievements in my career, which was the discovery and characterization of a novel RNA family called mitochondrial transfer-messenger RNA (mt-tmRNA) encoded within the mitochondrial genomes of many Oomycetes. My second postdoctoral position in Dr. Fouad Daayf's lab (Plant Science Department, University of Manitoba, Canada) introduced me to the basics of plant pathology by being involved in a project to investigate the cross-pathogenicity of some Fusarium spp. between cereal and pulse crops in Manitoba (a prairie region of Canada producing mainly cereals and pulses). During this project, we developed the first specific molecular marker for the important Fusarium head blight pathogen F. graminearum sensu stricto and reported an emerging disease, soybean root rot caused by F. cerealis. Currently, I am working as a research biologist in Dr. Reem Aboukhaddour's lab (Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre). In Dr. Aboukhaddour's lab (Cereal Pathology), my research is centered on investigating plant pathogens associated with cereal crops in western Canada (and worldwide through international collaboration), as well as studying plant–microbe interactions and how disease-causing microorganisms (mainly fungi) sustain themselves within their hosts. Moreover, we investigate virulence gene diversity and its impact on pathogenicity, as well as the discovery and biochemical characterization of novel effectors encoded by necrotrophic fungal plant pathogens. In addition to research experience, I have built substantial teaching and supervision experience. I have taught a variety of biology, microbiology, and molecular biology courses during my work as a lecturer at Suez University (Egypt) and as a session instructor with the Department of Microbiology, University of Manitoba (Canada). I also have supervised many masters and Ph.D. students in Egyptian and Canadian universities.

In Dr. Aboukhaddour's lab, I combine my long experience in microbiology, molecular biology, plant pathology, and bioinformatics to answer many important research questions regarding the diversity and evolution of effector-encoding genes. We have designed molecular tools to detect and characterize the neglected ToxB gene (encoding chlorosis-inducing effector), and its homolog (toxb) in the tan spot pathogen Pyrenophora tritici-repentis and related species. We have explored ToxB/toxb in a large number of P. tritici-repentis isolates that represent all known pathotypes from different geographic regions and have identified the presence of toxb homologs in P. teres (the barley pathogen) and many other plant fungal pathogens for the first time. This work has provided novel insights into ToxB, its homologs, and its evolution via duplication or loss of function and the variation in its upstream regulatory sequences in various isolates or species, which add significant value to the effector research community.

I hope to continue my research on understanding the molecular basis underlying the interactions between necrotrophic fungal pathogens and their host crops. This can help us to develop long-term effective management options for necrotrophs infecting economically important cereal crops.

Learn more about the research project in "Research Highlight: Evolution of the ToxB Gene in Pyrenophora tritici-repentis and Related Species" by Reem Aboukhaddour.

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Jun 28

InterConnections: Get to Know Munir Nur and Kelsey Wood

KEK on 6/28/2023 3:38 PM

EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage-Specificity

Name: Munir Nur

Current Position: Software engineer, Big Data

Education: B.S. degree in computer science, concentration in computational biology, University of California, Davis

Nonscientific Interests: Cooking, hiking, reading, animals, plants, music

Brief Bio: I grew up developing a keen interest in how we can build technology to better understand the world around us. Applications in ecology and agriculture specifically intrigue me, and as I learned more about computer science in my university studies, I became increasingly eager to apply it to the natural sciences. I soon dove into computational biology and bioinformatics courses, and I was fortunate to start working with Kelsey Wood in Dr. Richard Michelmore's lab at UC Davis, assisting with plant–microbe interaction research. I learned how to parse research papers, relevant background information about oomycetes, and how to apply academic knowledge to approach research problems. This opportunity allowed me to perform analyses and build tools for published research papers, and I'm grateful for the experience. I'm continuing a career in the data science field as an engineer and also helping to maintain the published tools we've built.

LinkedIn: www.linkedin.com/in/munir-nur

Name: Kelsey Wood

Current Position: Postdoctoral scholar, Michelmore Lab, University of California, Davis

Education: B.A. degree in biology, Reed College; Ph.D. degree in integrative genetics and genomics, University of California, Davis

Nonscientific Interests: Music, poetry, art, fashion, travel, food, cats

Brief Bio: I grew up in Boise, ID, where I became fascinated with plants, animals, and mushrooms from a young age during camping trips and in the ecological habitat of my own backyard. I attended Reed College in Portland, OR, where I had my first taste of genomics research during my senior thesis on the behavioral genomics of cichlid fish with Dr. Suzy Renn. After graduation, I returned to Boise, where I began working with potatoes at a biotechnology company called Simplot Plant Sciences. This was my first introduction to the microscopic battle between plants and pathogens, which I found irresistibly exciting and led me to pursue a Ph.D. degree at UC Davis with Dr. Richard Michelmore, studying the interaction between lettuce and the lettuce downy mildew pathogen. I am continuing these studies as a postdoctoral scholar and look forward to a career in plant–microbe interaction research.

Twitter: https://twitter.com/klsywd

LinkedIn: www.linkedin.com/in/dr-kelsey-wood

Learn more about Munir and Kelsey's fruitful collaboration in their InterView.

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12. Bonus question: What's your favorite pathogen or disease?

13. Bonus question: What's your favorite molecular plant pathology-related article?

1. Can you describe your path to becoming a senior data scientist at Corteva AgriscienceTM?

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1. What drew you to your current job?

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4. What advice would you give to people starting out in the job market?

5. Who has inspired you scientifically? Why?

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11. Is there anything else you would like to share? If so, what is it?

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1.What do you think is the most important or exciting finding from your paper?

2.Was there a piece of data that was particularly challenging to obtain or a part of the project that was particularly difficult?

3. What research project are you most excited about right now?

4. What drew you to your current lab?

5. How did you choose to join your current graduate program?

6. What advice would you give to starting graduate students?

7. Who has inspired you scientifically? Why?

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Q&A with Dani Stevens

Q&A with Alba Moreno Pérez

Evolution of the ToxB Gene in Pyrenophora tritici-repentis and Related Species​

EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage-Specificity​

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Evolution of the ToxB Gene in Pyrenophora tritici-repentis and Related Species

EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage-Specificity