High School Research Projects & Faculty

High School Research Internship Projects

BTI’s High School Research Program provides students with 6-7 weeks of hands-on research training with existing research projects happening within plant science. The following list reflect typical research programs and projects where students may be placed. We ask all high school students who are applying through our application form to select up to 5 projects of interest. It is not guaranteed you will be placed with those labs, but it is helpful for applicants to understand the kinds of projects available each summer.

To learn more about available projects and their faculty sponsors, click on the topics below.

Bioinformatics and genomics to understand important traits of agricultural crops - Fei Lab, BTI

Using integrated bioinformatics and genomics approaches to understand important traits of agricultural crops.

Project description:

The development of high throughput technologies has given rise to a wealth of information at system level including genome, transcriptome, proteome and metabolome. However, it remains a major challenge to digest the massive amounts of information and use it in an intelligent and comprehensive manner. To address this question, Dr. Fei’s group has focused on developing computational tools and resources to analyze and integrate large scale “omics” datasets”, which help researchers to understand how genes work together to comprise functioning cells and organisms.

Faculty advisor: Zhangjun Fei

Headshot of Zhangjun Fei

 

 

 

 

 

 

More about the Fei Lab

Developing computerd vision approaches to visualize long-distance transport - Frank Lab, Cornell

Project description:

Xylem-mobile dye moving through a pepper leaf (image credit: Hannah Thomas)

Xylem-mobile dye moving through a pepper leaf (image credit: Hannah Thomas)

The Frank lab studies the biology of plant grafting. Although grafting has been used as a tool to improve plant performance for over 2,000 years, there are many open questions about what makes particular graft combinations successful, how graft junctions are formed, and what moves between grafted organ systems. We use genetics, genomics, and phenomics to explore these questions. Our longterm aim is to be able to identify successful graft combinations in a predictive manner, and to engineer graft donor genotypes that provide sustainable solutions for crop protection in the face of biotic and abiotic pressures. 

Long-distance signals are transported between grafted root and shoot systems through the plant vascular network. Summer students will combine genetic engineering, fluorescence imaging, and computer vision based approaches to automate the detection of vascular tissue and track long-distance transport of mobile dyes and proteins through the plant vascular system.  This work will require some computational background as well as interest in plant physiology and microscopy.

Faculty advisor: Margaret Frank 

Headshot of Margaret Frank

 

 

 

 

 

 

More about the Fei Lab

Molecular and genetic analysis of fruit ripening and related nutrient pathways, using tomato as the model system - Giovannoni Lab, BTI

Project description:

Tomatoes in various stages of ripeness

Ripening is a process by which the texture, color, flavor, and nutritional content of fruit is enhanced. These traits contribute to the healthfulness and desirability of the fruit as a food source. Clearly, understanding the processes behind fruit ripening are important in terms of nutrition, but also for commercial applications such as transportation and shelf-life. Thus, the focus of research in the Giovannoni lab is molecular and genetic analysis of fruit ripening, related signal transduction systems and pathways leading to accumulation of nutritional compounds, using tomato as a model system. Researchers in the lab have characterized numerous genes related to ripening control and manifestation. In addition to identifying important genomic and regulatory components of ripening, the lab also investigates regulation of lycopene synthesis and accumulation in fruit. Lycopene is the pigment that gives tomatoes their red coloring and which is also suggested to inhibit degenerative diseases such as cancer and heart disease. Using a genomics approach, the lab is investigating the regulatory mechanisms behind accumulation of this important compound.

For more information about the Giovannoni lab, please visit the Plant Biology website. Additionally, the Giovannoni lab, in conjunction with other labs on campus has developed a resource for tomato genomics, the Tomato EST Database. Additional resources and information resulting from tomato genomics activities on the Cornell campus can be found at the Solanaceae Genomics Network site.

Faculty advisor: Jim Giovannoni

Headshot of Jim Giovannoni

Understanding how insects transmit plant pathogens - Heck Lab, USDA

Project description:

The Heck lab deciphers molecular mechanisms regulating insect transmission of plant pathogens and uses this knowledge to create practical solutions that mitigate vector-borne diseases in agriculture. We use a combination of computational and wet-lab approaches to study vector-pathogen-plant interactions. Students will receive training at the intersections of computational biology, plant pathology, entomology, microbiology, genetic engineering and synthetic biology. Projects involve research on citrus greening disease or diseases caused by aphid-borne poleroviruses, such as the invasive cotton leafroll dwarf virus

Faculty advisor: Michelle Heck

Headshot of Michelle Heck

 

Molecular genetic studies of temperature responses and immune responses in plants - Hua Lab, Cornell

Project description:

Two plants grown under different temperatures and how they differ from each other

Proper responses to environmental signals are essential for plant growth, reproduction, and fitness. Understanding the molecular genetic basis of such responses is not only fundamental to the central biological question of signaling and adaptation, but also better prepares us for global climate changes.
Research programs in Hua lab include molecular genetic studies of 1) temperature regulation of plant growth, 2) regulation of plant immunity, and 3) interplay between temperature and immunity. Both induced mutations and natural variations of Arabidopsis and rice are used to dissect signaling pathways and reveal adaptive changes in signaling. These studies aim at a deeper understanding of how plants adapt and evolve in a changing environment.

Faculty advisor: Jian Hua

Headshot of Jian Hua

Genetic and biochemical mechanisms of plant defense against insects - Jander Lab, BTI

Project description:

Aphids on a plantPlants in nature are subject to attack by wide variety of caterpillars, beetles, aphids, and other insect herbivores. Although there are a million or more species of herbivorous insects, any individual plant species is resistant to the vast majority of these. Insect feeding is inhibited by an array of chemical defenses that exhibits great variability both within and among different plant species. However, although it is known that any plant leaf contains several thousand different metabolites, most of these remain unidentified. In the Jander lab we are investigating natural variation in the herbivore resistance of maize, tomato, and potato to elucidate the molecular basis of plant defense traits. Through a combination of genetic crosses, gene expression assays, metabolite profiling, and insect growth experiments, we are able to identify specific plant genes, biosynthetic pathways, and metabolites that are required to mount an effective anti-herbivore defense.

Faculty advisor: Georg Jander

Headshot of Georg Jander

Understanding stress-induced changes in plant architecture for improved resilience - Julkowska Lab, BTI

Project description:

the root system architecture types that Julkowska lab has identified in wild tomato relative, S. pimpinellifollium.

The root system architecture types that Julkowska lab has identified in wild tomato relative, S. pimpinellifollium.

Plants adjust their development to the environmental conditions. This incredible flexibility is exhibited in tropic responses, like phototropism, but also extends beyond the individual organ scale. In Jukowska lab we are interested in how environmental stress shapes plant architecture. Stress exposure often induces quiescence of growth through modification of cell cycle activity, cell expansion and cell wall extensibility. The period of initial growth arrest and the extent of recovered growth differs between individual organs leading to altered plant architecture.

Interns in Julkowska lab will explore changes to plant architecture using timeseries experiments, where the changes in plant growth are recorded using Raspberry Pi computers connected to the cameras. The images are subsequently analyzed using PlantCV software and the dynamics are examined using pipelines in R. The environmental changes are explored in domesticated plant species, such as tomato or common beans, but also across resilient species, such as Solanum pimpinellifolium, which is a close relative to cultivated tomato, but exhibits tremendous resilience to heat and drought stress, as well as cowpea, which is known for its resilience to heat and drought, and performs well in subsistence farming across the world. The data collected during the internship will form a fundaments for future genetic studies, including GWAS and RNAseq experiments, to identify the genetic components underlying changes in growth dynamics of individual organs, as well as changes in overall plant architecture. This will provide new insight into breeding targets and future strategies to ensure food security in changing climate.

Faculty advisor: Magdalena Julkowska

Magdalena Julkowska

Seed-free plant genomics and symbioses– Li Lab, BTI

Project description:

Sporophyte, Gametophyte, and Cyanobacteria colonyThe Li lab uses genomic tools to investigate the evolution and biology of seed-free plants: ferns, fern allies, and bryophytes (mosses, liverworts, and hornworts). We are particularly interested in their symbioses with N2-fixing cyanobacteria, which provide plants with their own source of nitrogen fertilizer. We aim to understand the evolution and mechanisms of plant-cyanobacteria symbioses, and the results of which will lay the foundation for future engineering of “self-fertilizing” crops with less reliance on synthetic nitrogen fertilizers. To this end, we are surveying the diversity of cyanobacterial symbionts in hornworts, and using RNA-sequencing to uncover putative symbiosis-related genes.

Faculty advisor: Fay-Wei Li

Headshot of Fay-Wei Li

 

 

 

 

 

 

More about the Li Lab

Pollinator health - pesticide, pathogen, and nutritional stress on bees - McArt Lab, Cornell

BeesProject description:

Why are pollinator populations declining and what can we do about it? These are core research motivations in the McArt lab. Some current projects include: 1) Understanding pathogen transmission in plant-pollinator networks. We’ve recently found that ~20% of individual flowers have bee pathogens on them (!) and are working to understand how disease spreads in bee communities via bee-flower visitation networks. 2) Investigating how fungicides impact bees during pollination of apple. We’re unraveling a complex system where interactions between fungicides, insecticides, bee microbiota, and pathogens are all at play. 3) Understanding how pollinator populations respond to mass flowering events in agricultural systems and habitat enhancements (e.g., large wildflower plantings underneath solar panels at new solar power facilities).

Approaches in our lab typically involve field and/or lab research with bees, chemical analyses (HPLC, etc.), and molecular techniques (PCR, etc.).

Bioinformatics and genomics - Mueller Lab, BTI

Project Description:

Interns in the Mueller lab work on a variety of bioinformatics and genomics projects and gain experience in the following areas: genome assembly, structural and functional annotation, biochemical pathways, comparative genomics, ontology development and data presentation and visualization.

Faculty Advisor: Lukas Mueller

Lukas Mueller

The role of small-molecules in plant adaptation to stress - Skirycz Lab, BTI

Project description:

How organisms respond to stress, from bacteria to humans, is a central question in biology. Because stress can cause permanent damage and threaten survival, stress resistance is a vital fitness trait directly related to productivity, health, and aging. Irrespective of the studied organism, stress is accompanied by a major rewiring of metabolism, largely driven by small-molecule regulation. We’ve recently discovered that proteogenic dipeptides, which accumulate as a consequence of stress-induced protein degradation, constitute a previously uncharacterized class of small-molecule regulators important for metabolic remodeling. For instance, binding of a dipeptide Tyr-Asp to a glycolytic enzyme GAPDH inhibits its activity and redirects glucose to the production of antioxidant compounds. Remarkably, Tyr-Asp’s exogenous application improves stress tolerance of plants and extends the lifespan of a model worm C.elegans. Because of their “health-promoting” effects and evolutionary conservation, dipeptides constitute promising leads for drugs and agrochemicals.
Interns in the Skirycz lab will further investigate stress-protective properties and underlying molecular mechanisms of the selected dipeptides using combination of metabolomics, enzymatic assays, and phenotypic screens. They will also be involved in mining available enzyme-dipeptide interactions networks to explore the breadth of dipeptide-enzyme interactions involved in plant metabolic adaptation to stress.

Faculty Advisor: Aleksandra Skirycz

 

BTI Computational Biology Center - Suzy Strickler, BTI

Project Description:

Project1 : A genomic framework for informing conservation of the Threatened plant species Aconitum noveboracense

Wolfsbane in the wild

The genus Aconitum (known colloquially as monkshood and wolfsbane) is important both for its use in Traditional Chinese Medicine and for the range of metabolites it can produce. Relatively little is known about the North American Aconitum, including the federally threatened Aconitum noveboracense. Because A. noveboracense is normally found in cool environments and prefers rare ecosystems such as talus slopes, we hypothesize that climate change may pose a threat to the species. In order to establish that conservation efforts are necessary, however, we must determine whether or not A. noveboracense is taxonomically distinct from species such as the closely related and less threatened A. columbianum. To build a phylogeny of the North American Aconitum, we performed a large-scale genomic analysis of 80 individuals using RAD-seq, calling SNPs using STACKS 2.4. Our results indicate that A. noveboracense is monophyletic, which, in combination with high pairwise FST and low admixture between A. noveboracense and A. columbianum, implies that A. noveboracense is a distinct species. Now that we have a better understanding of the evolutionary history and relationships between the North American Aconitum species, we can investigate possible forces that are threatening A. noveboracense. A future direction in ecological niche modeling in order to understand how Earth’s changing conditions affect the distribution of A. noveboracense may allow us to hone in on specific dangers to this threatened species.

 

Project2 : Progress towards mapping tomato loci involved in response to Bacterial Speck

 

The purpose of our research was to locate the genes responsible in the tomato’s response to speck, a bacterium known as Pseudomonas syringae that manifests itself in the form of black spots on the leaves of tomato plants and in drastic cases can cause the leaves to shrivel, wilt, and die. This bacterium is not only limited to tomatoes, and has been known to spread to other crops. Our goal for this project was to correctly identify the gene of the tomato that is involved in its response to the bacterial speck. Our hope is that by doing this it will become possible to produce a breed of tomatoes that contained a natural resistance to the bacterial speck, and aid agriculturalists whose economic stability depends on tomatoes. By producing a breed of tomato that can resist the effects of the tomato speck, we will be to preserve tomatoes grown in farms and other agricultural centers. It is important to note that this research can also be applied to other studies that involve similar circumstances and is not simply limited to tomatoes. Pseudomonas syringae possesses the ability to infect a large variety of plant and crop species aside from tomatoes, meaning the research we acquire in this study could potentially be used to help other crops create a breed of plants with a stronger resistance to the bacterium. We hypothesize that by using genetic markers based on primers and PCR we can identify the DNA sequence responsible in plants producing a novel (different) response and plants that maintained the wild type response to Pseudomonas. The response typically demonstrates signs of infection through black specks. Novel responses to speck include galls, a swelling of the tissues of the plants, or reduced response.

 

 
Tomato plant Tomato plant Tomato plant
 

 

Project3 : Creating a Raspberry Pi device capable of quantitating disease progression of black speck and environmental conditions affecting progression

Raspberrry Pi

Bacterial speck is a common disease caused by the bacterium Pseudomonas syringae pv. tomato, that occurs in tomatoes, which is an important agricultural crop. The disease significantly reduces the yield of the crop, therefore not only posing health risks (through the creation of fruit blemishes that allow for easier intake of harmful pathogens), but also destroying crops that possibly represent the livelihood of farmers across the world. The disease takes the form of black and brown dots on leaves that spread to the fruit, translating to large areas of tissue damage, as well as the wilting of leaves on the fruit. The bacteria easily spreads from plant to plant often through splashing water in the form of rain or watering by sprinkling, therefore making it an even bigger problem. All in all, it is clear that bacterial speck is a major threat to tomatoes in wetter climates, and understanding the growth and conditions that allow for the best growth of the bacteria may help in the fight against disease to improve the production of tomatoes worldwide. Additionally, a standardized and automated method of quantitating disease progression would be invaluable in plant phenotyping.In this project we used a micro-computer Raspberry Pi to control multiple interfaces through which we were able to create peripherals that combine to create a device that is able to monitor the growth of bacterial speck on plant leaves over time, as well as the conditions that the bacterial speck is growing in. Specifically, we used a camera module that takes pictures over certain intervals (similar to a time lapse) so we can observe speck growth over time. Also, we have many micro sensors that came in a Raspberry Pi SmartGardenSystem Kit that will allow for the measurement of environmental variables such as temperature, humidity, sunlight, and soil moisture. With this data we will make charts using the R language that will tell us relationships between growth in bacterial speck and its environment. Finally, with the pictures that we collect we will quantitate the disease progression over time using software called ImageJ. The way I will use this software is measuring the amount of total pixels that are seen in the image of the leaves and then I will see how many are a different color (dark green) and then subtracting that from the total. Then I will divide the new total by the reference to get a percentage representing disease progression. The reference image will be the most infected tomato leaves.

 

 

 

 

Plant-Insect Ecology - Thaler Lab, Cornell

Project Description:

Dr. Thaler’s lab goals are to develop a predictive framework for understanding the complex interactions that occur between plant and insect species.  Studies of fundamental ecological processes, in both agricultural and wild systems, can provide insight into controlling insect pests and understanding the natural world. Thaler’s research focuses on ecological interactions between plants, herbivores, and carnivores in agricultural and wild Solanaceous plants. Current research projects focus on understanding the non-consumptive effects of predators on prey; how plants balance interactions between mutualists and antagonists such as pollinators and herbivores, and understanding how plants integrate their defenses against multiple attackers.

Faculty Advisor: 
Jennifer Thaler

Headshot of Jennifer Thaler

NSF Logo
USDA Logo
Emerson Foundation
Ithaca Garden Club Logo
John Ben Snow logo
Legacy Foundation of Tompkins County Logo
Rheonix Logo
Triad-Foundation Logo
Yunis Realty Logo

Internships are funded by the National Science Foundation, Research Experiences for Undergraduates Award #1358843, individual faculty grants, and the generosity of donors including the Emerson Foundation , Ithaca Garden Club, John Ben Snow, the Legacy Foundation of Tompkins County, Rheonix, Triad Foundation Inc, Yunis Realty , and many individual donors.

 

Contact:

Boyce Thompson Institute
533 Tower Rd.
Ithaca, NY 14853
607.254.1234
contact@btiscience.org