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Department of Plant Pathology

Research & Extension Experiences for UndergraduatesResearch & Extension Experiences for UndergraduatesResearch & Extension Experiences for UndergraduatesResearch & Extension Experiences for UndergraduatesResearch & Extension Experiences for Undergraduates
Department of Plant Pathology
Kansas State University
1712 Claflin Road
4024 Throckmorton PSC
Manhattan, KS 66506

Ph: +1-785-532-6176
Fx: +1-785-532-5692

2021 Projects - **2022 Projects Coming Soon! (early/mid December)

(Projects may be subject to change slightly)

You will list three projects on your APPLICATION FORM. We cannot guarantee that you will be placed in one of your top three selections, but your selections will help us place students in projects that are a good match for their interests.

You do not need to already have the skills mentioned in the project descriptions, just an interest to learn. You will gain hands-on training during the program.

Gene editing to develop improved wheat varieties

CRISPR/CAS9 technology can be used to rapidly generate new variants of genes with improved function. We use CAS9 technology to edit wheat genes that can increase yield and disease resistance, and improve nutritional quality. Intern will be involved in selecting genes that affect positively these traits in wheat, designing CRISPR/CAS9 reagents for gene editing using bioinformatical tools, and testing these reagents using next-generation sequencing (NGS) technologies available at the KSU Integrated Genomics Facility. She/he will conduct these experiments as part of the gene editing projects aimed at improving wheat traits.

60% lab, 40% computer.

Mentor: Eduard Akhunov


Wheat extension, diagnostics, and pathogen surveillance

So you want to be a plant doctor? Plants get sick too! This REEU internship will be focused on plant disease diagnostics and extension, with many hands-on opportunities to be a plant disease detective. Come learn techniques for diagnosing sick plants, characterizing and managing pathogen isolates, and reporting findings back to growers. Additionally, students will have the opportunity to shadow extension agents and develop video and print extension materials to directly help growers manage disease problems on their farms. The isolate characterization component of this project will be focused on the yield-limiting pathogen that causes Fusarium head blight of wheat, Fusarium graminearum.

60% lab, 40% field

Mentors: Kelsey Andersen Onofre and Jessica Rupp


Genome Engineering in fungi using CRISPR-Casdavid-cook

Have you heard about Genome Engineering or CRISPR-Cas and want to learn more? Maybe you know the basics details and you want to get some hands-on experience creating targeted DNA alterations to a genome. Complete an internship in the Cook lab as part of the K-State REEU program and you'll have the opportunity to learn out this exciting new technology and a whole lot more. You will learn basic microbiology techniques, some mycology, molecular biology, and about genetically modified organisms. You will leave with proficiency and knowledge about DNA editing using CRISPR and be on your way to changing the future!

Areas: Genome engineering, mycology, molecular-biology, CRISPR-Cas, plant pathology

MentorDavid Cook


Synthetic Biology to Make Super Seeds

 Seeds function as powerful biosynthetic factories that convert photosynthetically derived sugars into storage lipids, proteins and carbohydrates. My research group uses synthetic biology approaches to genetically modify metabolism so that seeds can produce novel compounds with functionalities useful for different applications. One particular focus involves modifying the chemical structure of vegetable oil to make a better, low-viscosity biofuel. You will have the opportunity to learn a variety of synthetic biology methods, including rapid assembly of gene constructs, CRISPR/Cas9 genome editing and plant transformation, as well as different biochemical methods to quantify lipids and amino acids in the modified seeds.

 Lab 100%

Mentor:Tim Durrett


Let’s Make Better Wheat 

Let’s help wheat fight off pests! Come help screen wheat breeding populations for pathogen and disease resistance to find the genetic factors that help produce our favorite breads and cereals. The intern will select resistant wheat to certain wheat pathogens, and using high throughput sequencing and genotyping techniques identify genetic regions involved in plant resistance using current bioinformatics tools. These genetic factors will be transferred into our breeding programs for improved wheat for future deployment and development. 

Greenhouse 20%, Lab 30%, Computer 50% 

Mentor:Katherine Jordan


Microbial interactions affecting plant pathogens and plant growth-promoting bacteria

Microbial communities associated with plant tissues (plant microbiomes) have significant consequences for plant growth and health. These diverse communities are the site of a wide range of microbe-microbe interactions. These interactions shape the effect these communities have on plants, in part because they can influence the establishment and success of functionally important taxa such as pathogens and plant growth-promoting bacteria. We are manipulating the composition of plant rhizosphere microbiomes and evaluating impacts on functionally important focal bacterial taxa and plant performance. This research may identify strategies to protect plants from pathogens and promote the establishment of beneficial bacteria.

Lab 75%/Greenhouse 25%

Mentor: Tom Platt

tania kim

Crop diversity effects on pest and beneficial insects

Crop plants are vulnerable to pest infestation. As such, the US spends $12.5 billion/year for pesticides, however, more sustainable measures are needed to control pest outbreak.  For example, planting different crop types or varieties can reduce the likelihood of damage to target crop plants. For this project, we will examine how crop diversity (monocultures versus polycultures, annual versus perennial crop species) affects the likelihood of infestation and damage by pests such as aphids.  We will also examine how crop diversity affects the likelihood of colonization of important predatory insects (e.g. lady beetles) that naturally feed on aphids and pollinators.

Field 50%/Greenhouse 25%/Lab 25%.

Mentor: Tania Kim

dal hoe

Wild wheat!

Just like we all have some interesting relatives, wheat has some wild in-laws of its own! Bread wheat was domesticated in Central Asia around Iran and Iraq and the wild relatives can still be found there today. Though they don’t really even look like wheat and aren’t any good for making bread, the wild relatives have important genes for disease resistance. Using chromosome engineering and bioinformatics, we are transferring these useful genes into wheat to make stronger wheat plants that are resistant to disease and other stress.

Areas: genetics and genomics, plant breeding, plant pathology, cytogenetics.

MentorsDal-Hoe Koo and Jesse Poland


Weed Management

 Weeds are one of the greatest challenges farmers have. Weed scientists work to find effective and economical soluweedtions to farmers’ weed management challenges and share that information with farmers and agribusinesses. In this internship, students will have the opportunity to work in the field on projects related to herbicide evaluation as well as nonchemical weed management practices. In addition, students will have the opportunity to participate in Extension-related activities, including summarizing data. If you enjoy biology or chemistry, gathering information, working outdoors, and helping people, this internship might be for you!

80% Field, 20% Lab + Greenhouse


Mentor:Sarah Lancaster


Biology of sorghum and soybean diseases

Sorghum and soybean are major crops in Kansas. My lab studies fungal disease of both crops, including characterizing seedborne fungi, mechanisms of resistance to stalk rot in sorghum, and working with crop breeders to identify resistance to diseases. Students in my lab will learn how to isolate and culture diverse fungi, microscopic techniques, and greenhouse inoculation assays.

Lab 50%/Greenhouse 50%

Mentor:Chris Little

s liu

What makes plants resistant to diseases?

Plants do not have immune systems like ours, but they fight off pathogens. Some plants have a strong capability to fight against diseases but some do not. In this project you will inoculate plant pathogenic bacteria on plants (e.g. wheat and corn), observe symptom developing through time-lapse imaging, and quantify disease resistant levels among plant individuals.  You will also use DNA technologies to find genomic regions causing resistance.You will learn basic programming, cutting-edge computation techniques for data processing and visualization, and knowledge in plant diseases, genetics, and genomics.

Lab 60%/Greenhouse 30%/Field 10%.

Mentor: Sanzhen Liu

brian mccornack

Blending ecology with technology to manage crop pests

Kansas crop growers face a diverse array of insect pests and need to adapt novel solutions to manage arthropods. In this project, you will learn how to use cutting edge technology to help develop integrated pest management (IPM) solutions to pest problems and learn how to deliver information to growers using novel technologies. You will learn how to scout and sample insects, map prevalence across production fields, use sampling tools, and/or contribute to existing extension programs. In this program you will learn how social networks are digitally connecting farmers with researchers and Extension personnel to provide established user-networks for improved response to pest incursions.

Lab 25%/Field 50%/Computer 25%.

MentorBrian McCornack


New insect-associated viruses: Friends or Foes?

Many plant pathogens rely on insect vectors for their transmission. Insects are occupied by native resident microorganisms from diverse groups ranging from bacteria to fungi to viruses, together called microbiome. Many of these microbes are not pathogen but they might be beneficial. We recently discovered/identified new insect-specific viruses associated with important insect vectors of plant pathogens. We consider the new viruses as natural components of the insect host`s microbiome. Join host-virus-vector interactions research team to explore the molecular interaction between the insect and its new viruses.

Areas: Virology, molecular biology, vector biology, and bioinformatics.

MentorShahideh Nouri


Establishing a high-throughput transformation platform for crop genome-phenome cause-effect studies

Functional genome analysis through genetic transformation and plant regeneration processes must enter the high-throughput stage in order to determine how these genome sequences generate crop phenotypes. However, functional genomics researches in most crops are constrained by low transformation efficiency. Establishment of a robust, reliable crop transformation and regeneration system for the use of ectopic overexpression, RNAi, and CRISPR/Cas9 gene editing approaches is crucial for understanding of the relationship between genomes and phenomes in the crops. You will learn crop (e.g., rice, maize, sorghum, tomato, lettuce, etc.) tissue culture, gene transformation, and genome editing technology.

MentorSanghun Park

y park

Insect hormone disruptors

Park team focuses on the development of new tools to disrupt insect endocrine system based on the knowledge of hormone receptors revealed in comparative genomics. Current project includes high throughput screening of chemical compounds that act on insect specific ecdysis triggering hormone receptor and mite specific neuropeptide receptors. Students will be trained for molecular biology and data analyses of bioassay depending on the background and the interests of the students assigned. Most of all, the students will have opportunities to play with arthropods, learn the fun biology, and perform modern molecular techniques to solve the problems in pest control.

MentorYoonseong Park

jesse poland

An eye in the sky...

Unmanned aerial vehicles (UAVs), sometimes called ‘drones’, are more than just fun toys to make cool videos. They are also powerful research tools that can help us quickly measure field experiments and farmer’s fields to measure plant growth and plant diseases. Join our research team to use UAVs for rapid measurements of plant traits and explore how this high-resolution data can be used for different analysis to understand plants.

Areas: physiology, engineering, genetics and genomics, high-throughput phenotyping.

MentorJesse Poland

deann presley

Going undercover

Cover crops are used to prevent erosion and improve soil structure and have the added benefit of increasing the plant biodiversity of a cropping system. Does increasing biodiversity aboveground lead to increased biodiversity belowground, and if so, how does it affect the plant pathogenic organisms? In this project, you will collect measurements in the field and soil sample experiments with and without cover crops to determine if there are any effects of cover crops on soil health.

50%, Field, 50% Lab.

MentorDeAnn Presley


My feet hurt! Investigating root rots in diversified cropping systems of wheat

Once upon a time, farmers used to grow wheat, followed by a year of giving the field a rest, called a fallow period. Fallow was meant to recharge the soil with moisture and fertility that could be used in the following cropping cycle. However, with the population growing and farming becoming an economic challenge, wheat growers are looking for new rotations that can make a profit. Peas are now being grown in place of fallow in many regions, including northern KS. While they do use the moisture saved for the wheat crop, their Rhizobia fix nitrogen to improve fertility. But, it may come with a cost. During this project, you will investigate if root rot pathogens that affect both wheat and pea are building up in the soil due to these cropping systems. This will include trips to sample wheat and pea across northern KS and culturing these pathogens in the lab. The pathogen communities will then be compared to wheat-fallow systems. Could we be driving a system we can't control?

Field 50%, Lab 50%

MentorJessica Rupp


Extracellular vesicles as intercellular messengers

Extracellular vesicles are important intercellular messengers in many organisms, but very little is known about them in insects or how they might be used for insect control and plant protection. My lab is working to address these shortcomings by enhancing our understanding of the composition of these vesicles and the roles they play in intercellular communication in insects. Experiments will focus on identifying protein and RNA content of insect-derived extracellular vesicles and examining their uptake by cultured insect cells in an effort to devise ways that they may be used in pest control. Interns will learn multiple molecular techniques including gene expression analysis and double-stranded RNA design, synthesis, and delivery. In addition, interns will also have the opportunity to learn cell culture and fluorescent microscopy techniques.

100% Lab

MentorKristopher Silver


Pollinator ecology and machine learning

Pollinators are important components of our ecosystem that help provide us with much of the food we eat, maintain diverse natural plant communities, and make for enjoyable creatures to observe in our gardens. Our lab studies the ecology of pollinator communities in grassland habitats and surrounding landscapes. Machine learning and computer vision are emerging technologies in our field that will help remove the bottleneck associated with sampling, processing, and identifying pollinators in the field. Students will have the opportunity to participate in our experiments on these topics by gathering pollinator specimens and images in the field and processing them in the lab for ecological analysis and incorporation into our deep learning models for bee identification and detection. We will work with students to develop independent research projects based on their particular interests in pollinator ecology, which may or may not feed into our ongoing research.

50% lab, 50% field

Mentor:Brian Spiesman


Fungal genomics to understand Fusarium pathogen diversity

Fusarium is a genus of filamentous fungi that contains many plant pathogens that cause diseases on major crops. In this project, you will use DNA sequence from fungal samples to analyze genetic diversity, infer the evolutionary history of populations, and associate genetic markers with important pathogen traits. This project will expand your knowledge of: microbiological techniques such as culturing fungal isolates and measuring growth rates; molecular techniques such as nucleic acid extraction and amplification, and DNA sequencing; and bioinformatics techniques such as next-generation DNA sequence processing and analysis of genetic diversity.

Lab: 50% Computer: 50%

MentorChristopher Toomajian


Help Control a Cereal Killer

A fungus, called Magnaporthe oryzae, causes blast disease that destroys enough rice every year to feed 60 million people.  This fungus adapted to infect wheat in the 1980s, and now threatens global wheat production as well.  Have a blast understanding how the fungus kills cereal crops at the molecular and cellular level.  You will learn live cell imaging using confocal and fluorescence microscopy to observe the fungus invading rice cells.  Learn to document locations and dynamics of fluorescently labeled fungal effector proteins, critical tools the fungus uses to hijack host cells and cause disease.  You will also gain skills in molecular biology, construction of fluorescent fungal strains, and rice infection assays. 

Lab 100% 

MentorBarbara Valent


Mechanisms affecting RNAi efficiency in insects

RNA interference (RNAi) is a Nobel Prize-winning discovery of the post-transcriptional gene regulatory mechanism and has shown great potentials for developing novel strategies for managing insect pests. However, RNAi efficiency is considerably variable among different insect species, which have currently hindered possible applications of RNAi-based strategies for managing insect pests in different taxonomic groups. Our lab is studying molecular mechanisms affecting RNAi efficiency in different insect species. In this research, you will learn various molecular techniques, including identification and analysis of insect genes, design and synthesis of double-stranded RNA (dsRNA), dsRNA delivery, and gene expression analysis.

Lab 100%

MentorKun Yan Zhu