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. Scientists work in different lab environments at BTI. Some labs are involved primarily in bioinformatics, while other labs operate in a wet lab or conduct field work. Read below for descriptions of bioinformatics and wet lab and field work. In general, most of our research projects are grouped into ones that involve a strong understanding and willingness to work with computers, and projects that involve laboratory or field work.
Bioinformatics involves work related to creating programming and software to understand and manage the large data sets that result from the research. This could involve creating programming, coding, and creating software that scientists will use. These are important and valuable skills to scientists since research often results in a lot of data—and a need to understand it! While a foundation of computer science skills (i.e. programming or coding) is important to bioinformatics projects, you can learn skills during your research project! A willingness to learn is key. Previous high school bioinformatics projects have involved using and helping create software to analyze data sets containing traits of wild watermelons to understand genes that might be important to plant breeders.
Wet Lab and field work involves working within a lab and/or in a field or greenhouse to conduct experiments and collect data. This could involve using techniques like DNA isolation and extraction and gel electrophoresis. Field work could involve planting and caring for the plants, as well as accurately collecting data for analysis. This work involves learning important skills to conduct experiments across many disciplines. Previous high school wet lab projects have involved looking at the impacts of salt stress on plants and finding genes within plants that can better handle salt stress in the environment. Previous high school field work projects have involved accurately documenting the number of bees visiting certain flowers in a greenhouse environment to understand if there are certain plant traits they like more.
Note: Some research could be mostly in a wet lab, and some mostly in a field, or a mix of both. Often times a project won’t involve field work. Below you will see labs labeled as ‘Wet lab and field work’, but not all will involve field work.
The following list reflects typical research programs and projects where students may be placed. Read through this list to help you better understand the types of lab placements and determine which type of lab experience you are interested in. We ask all high school students who are applying through our application form to select the type of lab experience they are interested in, not which lab they want to be placed in. However, if one of these projects seems very interesting to you, you may indicate that within your essay.
To learn more about potential projects and their faculty sponsors, click on the topics below.
Bioinformatics and genomics to understand important traits of agricultural crops - Fei Lab, BTI
Bioinformatics Lab
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
Developing computerd vision approaches to visualize long-distance transport - Frank Lab, Cornell
Bioinformatics lab
Project description:
Xylem-mobile dye moving through a pepper leaf (image credit: Hannah Thomas)
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
Molecular and genetic analysis of fruit ripening and related nutrient pathways, using tomato as the model system - Giovannoni Lab, BTI
Wet lab and field work
Project description:
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
Genetic and biochemical mechanisms of plant defense against insects - Jander Lab, BTI
Wet lab and field work
Project description:
Plants 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
Understanding stress-induced changes in plant architecture for improved resilience - Julkowska Lab, BTI
Wet lab and field work
Project description:
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
Seed-free plant genomics and symbioses– Li Lab, BTI
Bioinformatics lab
Project description:
The 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
Pollinator health - pesticide, pathogen, and nutritional stress on bees - McArt Lab, Cornell
Wet lab and field work
Project 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
Bioinformatics lab
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
The role of small-molecules in plant adaptation to stress - Skirycz Lab, BTI
Wet lab and field work
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
Bioinformatics lab
Project Description:
Project1 : A genomic framework for informing conservation of the Threatened plant species Aconitum noveboracense
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.
Project3 : Creating a Raspberry Pi device capable of quantitating disease progression of black speck and environmental conditions affecting progression
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.
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.
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