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Mar 19
InterConnections: Get to Know Kamesh Regmi

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.

Mar 19
InterConnections: Get to Know Tom Waksman

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.

Dec 18
InterConnections: Get to Know Mohamed Hafez

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. ​

Jun 28
InterConnections: Get to Know Munir Nur and Kelsey Wood

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.


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.



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

Jun 28
InterConnections: Get to Know Stefan Sanow

Molecular Mechanisms of Pseudomonas Assisted Plant Nitrogen Uptake—Opportunities for Modern Agriculture

Name: Stefan Sanow

Current Position: JUMPA Ph.D. student, Root Dynamics Group, IBG-2, Forschungszentrum Jülich, Germany (Jülich–University of Melbourne Postgraduate Academy)

Education: M.S. degree in biotechnology at the University of Applied Sciences–FH Aachen (Campus Jülich), Germany; B.S. degree in biology at Heinrich-Heine University Düsseldorf, Germany

Nonscientific Interests: Videogames, music, traveling, nature, penguins

Brief Bio: I started my scientific journey in the group of Prof. Andreas Weber at Heinrich-Heine University, Düsseldorf, where (at that time) Privatdozentin Dr. Nicole Linka (now Prof. Linka) and Ph.D. student Björn Hielscher (now Dr. Hielscher) introduced me to plant biochemistry. During my B.S. thesis, I studied the colocalization of putative peroxisomal transporters, which further increased my interest in biology, especially molecular biology and plant science. As a result, I pursued my M.S. degree in biotechnology at FH Aachen (Campus Jülich). For my M.S. thesis, I worked with Dr. Borjana Arsova and Prof. Michelle Watt in the Root Dynamics Group at IBG-2, Forschungszentrum Jülich, and Prof. Ingar Janzik (FH Aachen). This is when I delved into studying the molecular mechanisms of plant–microbe interactions. While exploring the potential benefits of such interactions on plant performance, we encountered an unexpected development. The bacterium stock, sent to us by a colleague, was identified as a different strain than expected. Nonetheless, since the experiments showed promising results, I continued studying the new bacterium, which turned out to be a Pseudomonas strain. Another positive development occurred when I was offered a Ph.D. student position in the Jülich-Melbourne Postgraduate Academy (JUMPA) in 2019. This opportunity also included a one-year stay at the partner institution, the University of Melbourne in Victoria, Australia. Awesome! Additionally, I got an interdisciplinary supervisor team consisting of Dr. Borjana Arsova (IBG-2, FZJ), Prof. Pitter Huesgen (ZEA-3, FZJ), Prof. Michelle Watt (University of Melbourne), Prof. Ute Roessner (Australian National University), and Prof. Gabriel Schaaf (University of Bonn).

I accepted the offer without much hesitation, as I was already determined to understand the underlying mechanisms of plant–microbe interactions and wanted to utilize this time to optimize my studies. However, like everyone else, the outbreak of the COVID-19 pandemic in early 2020 brought about significant changes. Dealing with numerous restrictions, we decided to utilize the lockdown period to prepare a review on Pseudomonas–plant interactions, with a focus on the molecular mechanisms that increase nitrogen content in plants and the influence of the abiotic environment on this interaction.

Almost three years later, I finally had the opportunity to spend two months at the University of Melbourne. During this stay, I had the opportunity to interact with several great people, to learn about the challenges of untargeted lipid analyses (lipidomics), and to experience working on another continent. At the same time, I had the privilege of observing penguins (Eudyptula minor) in their natural habitat for the first time on Phillip Island, Victoria, Australia. I did not expect one of my childhood dreams to come true so quickly; thus, I had to adapt my plans: I now want to observe all penguin species in their natural habitats during my lifetime. Science makes this possible, as we are able to work on various continents. From my personal point of view, I highly recommend exchange programs for Ph.D. students, as it expands your perspective on the world, which also changes your perspective on science. Keep in mind that adapting to a new environment will take some time, so do not pack your schedule too tight (or you might miss your "penguins")!

I have now reached a point where I can summarize the findings of the past few years and prepare to embark on my first postdoc position after completing my Ph.D. degree. Plant–microbe interactions offer interdisciplinary research opportunities that incorporate a variety of methods to unravel the molecular mechanisms involved. This makes the field particularly fascinating, as I can grow alongside the project and gain insights into various factors influencing this complex system.

Learn more about the research project in "Review Highlight: Molecular Mechanisms of Pseudomonas Assisted Plant Nitrogen Uptake—Opportunities for Modern Agriculture" by Borjana Arsova.

Sep 20
InterConnections: Get to Know Jacob Botkin

A Reference Genome Sequence Resource for the Sugar Beet Root Rot Pathogen Aphanomyces cochlioides

Annie Harvieux, UMN Plant Pathology Communications and Relations Coordinator

Jacob Botkin, graduate research assistant

From his undergraduate plant pathology internship to his work assembling and annotating the Aphanomyces cochlioides genome, Jacob Botkin's plant pathology career thus far has been a testament to versatility and embracing the unknown.

While interning in the University of Minnesota Plant Disease Clinic (PDC) during his bachelor's degree program, Botkin discovered a love for examining plant samples and studying plant–microbe interactions. This great fit led to a subsequent job at the Forest Service research lab in St. Paul, MN, that was doing similar diagnostic work.

Botkin points out that what surprised him most when transitioning from coursework to the PDC was how much is still left to discover about plant health and plant genetics in particular. This theme of discovery held true as he pursued his master's degree in plant pathology at the University of Minnesota under the guidance of Drs. Ashok Chanda and Cory Hirsch. During his master's program Botkin picked up more skills on genome assembly and annotation, optimizing soil DNA isolations and qPCR-based detection of soilborne pathogens.

Minnesota is number one in the nation for sugar beet production, and sugar beet production is consistently challenged by A. cochlioides, especially during wet years. To sequence and annotate the A. cochlioides genome, Botkin unlocked an entirely new skill set through on-the-go learning and collaboration: computation and coding. Despite his lack of experience in this side of the work, Botkin was encouraged not to worry about it and to take on the new challenge. Botkin credits Dr. Hirsch, assistant professor of plant pathology, with giving him regular, detailed, and ongoing lessons in coding skills, as well as Hirsch's plant genomics coursework. Spending summers at the Northwest Research and Outreach Center and pursuing opportunities to present this research to sugar beet stakeholders were also rewarding experiences for Botkin.

When the COVID-19 pandemic began and universities sent staff and students home, Botkin's work continued. With his DNA sequence data in hand, Botkin was able to work from home and do the computational portion of the project utilizing the Minnesota Supercomputing Institute's computing power. Botkin identifies this as the steepest part of the learning curve, particularly installing and configuring new software being used for plant pathogen genome assembly and annotation.

This growth has all paid off by adding versatility and adaptability to Botkin's skills and career options. Beyond going from being a mild technophobe to being his new lab's bioinformatic troubleshooter, Botkin now has a variety of skills that can take him from the computer desk to the lab to the greenhouse in a single project. This ability to work in a variety of environments and to pick up new skills and bring them into any subsequent environment has helped Botkin break the assumption that plant pathology is too niche of a career path and move into embracing the variety of skills, settings, and job options available for him.

Mar 21
InterConnections: Get to Know Gongjun Shi

​A Conserved Hypothetic​al Gene Is Required but Not Sufficient for Ptr ToxC Production in Pyrenophora tritici-repentis​

Gongjun Shi

Current Position: Research Specialist, Department of Plant Pathology, North Dakota State University, ND, USA

Education: Ph.D. degree in genomics and bioinformatics at North Dakota State University, USA; Ph.D. and M.S. degrees in olericulture at Nanjing Agricultural University, China; and B.S. degree, with honors, in olericulture at Shandong Agricultural University, China

Nonscientific Interests: Hiking, running, photography, cooking, and volunteering

Brief Bio: I was born in a small village in Shandong Province, China, and had a dream to be a medical doctor one day. However, I was not accepted into medical school, which led me to pursue degrees in olericulture and then genomics and bioinformatics. Now, I am proud to be a plant pathologist. During my years working with Brassica, I was fascinated with the sophisticated mechanisms by which plants fertilize at the molecular level. How plants recognize self and non-self pollen particularly drew my attention. Joining the Key Lab of Southern Vegetable Crop Genetic Improvement led by Dr. Xilin Hou allowed me to pursue this project. At the same time, how plants distinguish self and non-self molecules captured my eye for understanding how plants can effectively balance energy for both growth and defense processes.

After enrolling in the Department of Plant Pathology at North Dakota State University, I worked in Dr. Justin Faris' lab and focused on the cloning of wheat sensitivity genes interacting with necrotrophic effectors produced by Parastagnospora nodorum. Collaborating with Dr. Tim Friesen's group, we found that necrotrophic specialists could hijack both PAMP-triggered immunity and the effector-triggered immunity pathway to cause disease. As a postdoc, I entered Dr. Daniel Kliebenstein's lab at the University of California, Davis, to work on a necrotrophic generalist, Botrytis cinerea, to understand its virulence across the plant kingdom. Currently, I am working on wheat tan spot disease and bacteria leaf streak research led by Dr. Zhaohui Liu. I continue to leverage my plant breeding background, together with my expertise in plant pathology, to unveil many more exciting stories of phytopathogens and plant immunity.​

Dec 20
InterConnections: Get to Know Hari Karki

Natural Genetic Diversity in the Potato Resistance Gene RB Confers Suppression Avoidance from Phytophthora Effector IPI-O4

Name: Hari Karki

Current Position: Molecular breeder (tomato) at Lipman Family Farms, Florida, USA

Education: M.S. and Ph.D. degrees in plant health at Louisiana State University, Baton Rouge, LA, USA

Brief Bio: Over the years, I have conducted research in the field of plant pathology, genetics, genomics, and molecular biology at Louisiana State University (LSU), The Sainsbury Laboratory (TSL) and U.S. Department of Agriculture (USDA). I was always attracted to different aspects of agriculture, which eventually led to my enrollment at the agriculture institute of Nepal. After completion of my undergraduate degree, I joined the Department of Plant Pathology and Crop Physiology at LSU to pursue a master's degree, studying the bacterial pathogen Burkholderia glumae. After completion of a M.S. degree in plant health, I continued studying for a Ph.D. degree and worked on understanding the virulence mechanism and population diversities of B. glumae through targeted sequencing and mutagenesis of pathogenic and nonpathogenic isolates. At TSL, I worked on a capture-based next-generation sequencing method, resistant gene enrichment and sequencing (RenSeq), and gene enrichment and sequencing (GenSeq) to map and clone resistance genes against late blight of potato caused by Phytophthora infestans. At the USDA, I worked on the molecular dissection of RB (also known as Rpi-blb1) mediated late blight resistance in potato. RB is a broad-spectrum late blight resistance gene cloned from Solanum bulbocastanum, which recognizes P. infestans effector IPI-O (in planta–induced gene O), also known as Avrblb1.

IPI-O is a multigene effector family that has been divided into three major classes. IPI-O class I and class II variants detect RB and initiate resistance activation; however, with class III variants, IPI-O4 not only escapes recognition by RB but is also capable of inhibiting the hypersensitive response (HR) by directly binding the RB CC domain. To identify the RB CC domain that does not interact with IPI-O4, we explored natural variations in the RB CC domain from different Solanaceae species and identified the RB CC domain from S. pinnatisectum (pnt) that does not interact directly with IPI-O4. We identified crucial amino acids in the RB CC domain that play an important role in the avoidance of suppression activity of IPI-O4 and, thus, could enable resistance activation even in the presence of this suppressor. We further modified these amino acids in a wild-type RB gene and concluded that modification of single amino acids within the RB CC domain can either diminish or increase the resistance capability of the RB gene. Our study provides a clue about engineering new variants of known R genes that can further expand the resistance spectrum.

Dec 20
InterConnections: Get to Know Maria Malvino

Influence of Flagellin Polymorphisms, Gene Regulation, and Responsive Memory on the Motility of Xanthomonas Species That Cause Bacterial Spot Disease of Solanaceous Plants

Name: Maria Laura Malvino

Current Position: Ph.D. candidate, crop sciences, University of Illinois at Urbana-Champaign, IL, USA

Education: B.S. degree in food science and technology and M.S. degree in biotechnology at the Universidad de Buenos Aires, Argentina; M.S. and Ph.D. degrees in crop sciences at the University of Illinois at Urbana-Champaign, IL, USA

Non-scientific Interest: Ice hockey, running, roller blading

Brief Bio: While I was wrapping up my studies in the food science and technology program, I realized that what I really wanted to do was to improve our food through altering its genetics, as I thought that was the way to make a bigger impact and lead to real change. Therefore, shortly after I finished my bachelor's degree, I pursued an M.S. degree in biotechnology. I also was fortunate enough to work for some years at a seed company performing biotechnology-related research. After a while, out of curiosity, I applied for a Fulbright Scholarship, and I won! This opportunity allowed me to fulfill my dreams of coming to the United States and studying what I love the most—how to improve the genetics of our crop plants. In my recently published research, I navigated the fascinating world of Xanthomonas bacteria and how they have evolved to evade recognition by their host plants. When I first found polymorphisms in the flagellin proteins that form the bacterial flagellum, I thought there could be a correlation between the different variants and bacterial motility, but this was not the case. Interestingly, I found some Xanthomonas species demonstrated a responsive memory, which is a phenomenon that has been observed in other bacterial species in response to different stimuli. This evidence supports previous work showing that bacteria deploy different strategies to improve their long-term fitness under constantly fluctuating environmental conditions. In terms of agricultural production, it is important to have a clear understanding of plant pathogens in order to defeat them.​

Dec 20
InterConnections: Get to Know Danielle Stevens

​​A Genetic Toolkit for Investigating Clavibacter Species: Markerless Deletion, Permissive Site Identification, and an Integrative Plasmid

Name: Danielle Stevens

Current Position: Integrative genetics and genomics Ph.D. candidate and USDA NIFA predoctoral fellow, University of California Davis, California, USA

Education: B.S. degree in biochemistry and biophysics at Oregon State University, OR, USA

Non-scientific Interest: Traveling, tech, hiking

Brief Bio: Often we hear of scientists who were driven by their passions as children. Growing up, I enjoyed science but nothing in particular perked my interests. At Oregon State University, I worked toward a B.S. degree in biochemistry and biophysics thinking I would work in the medical field to make a difference in people's lives. However, an accidental introduction to gram-positive actinobacterial plant pathogens and molecular plant–microbe interactions thanks to Dr. Jeff Chang changed much of my perspective and goals.

As an undergraduate student in his lab, I investigated the contribution of bacterial virulence loci to disease in plant-associated Rhodococcus and worked collaboratively in a team that elucidated the misdiagnosis of beneficial Rhodococcus bacteria as a pathogen in pistachio. During those formative years, I learned and loved what it meant to do science. I also witnessed the economic implications of the misdiagnosis on both pistachio growers and in the loss of time for many research groups as we tried to repeat incorrect findings. Since then, I have been committed to making my research, both data and code, accessible to others.

Now, I am fortunate to continue studying actinobacterial pathogens, focusing on important crop pathogens of the Clavibacter genus under the mentorship of Dr. Gitta Coaker. Using large-scale genomics and functional biology, I am investigating effector-driven host range, which has been a question in Clavibacter biology for over a decade. Additionally, I am investigating how these bacteria interact with the plant immune system, an area which has been relatively unexplored in the context of pattern-triggered immunity.

Compared to their gram-negative peers, actinobacterial pathogens are greatly understudied, in part, due to the limited number of genetic and biochemical tools. Thus, I wanted to first generate a genetic toolkit for Clavibacter during my Ph.D. studies, which could expand the type of questions that could be investigated. The work I published in MPMI highlights new genetic tools we have adapted and developed for Clavibacter with potential application in orphan systems. We have a vector designed for markerless deletion and another that can be combined with an R package, permissR, which aids in targeted integrated expression. These vectors build on tools designed for other actinobacterial pathogens, while taking advantage of the growing genomics-focused era of plant–microbe research today.

In the long run, I hope to continue combining computational and functional approaches to unravel how actinobacterial pathogens evolve and adapt to their hosts. In turn, this can help us develop long-term, sustainable solutions to managing actinobacterial pathogens.

Twitter: @Dani_M_Stevens

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