Projects and Faculty

As world leaders in plant genome research, Cornell University, Boyce Thompson Institute (BTI), the USDA-ARS, and the U.S. Plant, Soil, and Nutrition Laboratory are host to many outstanding research labs. These research facilities have built on Cornell’s long tradition of research in plant genetics and breeding to develop novel technologies, the application of which has sought to improve the scientific understanding of many aspects of plant biology. The research interests of the labs are quite varied, ranging from identifying disease resistance in crop plants to understanding how plants sense and respond to light. Please click the following text to learn more about the faculty members associated with the research projects in the various summer internship opportunities at BTI.

Internship Projects

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

Chemical ecology and coevolution of monarchs and milkweeds - Agrawal Lab, Cornell

Project description:

Our lab studies the ecology and evolution of plant-insect interactions, including aspects of plant defense (the spines and toxins plants produce to reduce herbivory), induced defense (the immune-like system of plants in response to attack), chemical ecology (how interactions between species are mediated by chemistry), and coevolution (long-term reciprocal adaptation and “arms race” evolution when species battle). We work on local biodiversity and especially milkweed plants and monarch butterflies.

Approaches in our lab are diverse, and typically involve field research, chemical analyses, genetic techniques, and rearing lots of bugs. Our work has advanced both basic questions in ecology, evolution, and plant biology, as well as applications to insect pest management (especially in cucurbit crops) as well as conservation biology (of monarch butterflies).

For more information about Agrawal’s lab, publications, and his blog please click here

 

Faculty advisor:  Anurag Agrawal

 

TAL effector biology for durable plant disease prevention and DNA targeting applications - Bogdanove Lab, Cornell

Project description:

TAL effector illustration - Jon Bogdanove

TAL effector PthXo1 bound to its target. Illustration by Jon Bogdanove

Research in the Bogdanove laboratory is directed at understanding mechanisms of bacterial plant pathogenesis and plant defense to develop better means of disease control. We focus on the interactions of the globally important staple crop rice with Xanthomonas oryzae, in which transcription activator-like (TAL) effector proteins of the bacterium play an important role. TAL effectors are injected into plant cells by the bacterium, enter the nucleus, and activate specific plant “susceptibility” (S) genes that contribute to disease development. TAL effectors recognize their DNA targets in a modular way: tandem, variable structural repeats in these proteins independently specify single contiguous bases in the DNA. This correspondence makes it possible to rapidly identify TAL effector targets, to engineer novel TAL effectors with custom assortments of repeats to bind DNA sequences of choice, and even to customize genes for TAL effector activation (or prevent it!). Major areas of activity in our lab include 1) identification and characterization of Sgenes, 2) genomic analyses to identify the diversity of TAL effectors in pathogen populations and understand their evolution, and 3) structural and biochemical studies to better harness the unique properties of these proteins for applications such as targeted gene regulation and genome editing. REU opportunities in the lab are available in each of these areas.

Faculty advisor: Adam Bogdanove

 

 

 

 

 

 

More about the Bogdanove Lab

Investigating the molecular mechanisms underlying fruit set and development- Catala Lab, BTI

Project description:

Fruit development is a crucial process in the sexual reproduction of flowering plants and of critical importance for seed dispersal, plant fitness and agricultural yield. Fruit are complex organs that arise from the coordinated growth and development of floral tissues following pollination. Research in the Catala lab focuses on the molecular regulation of fruit formation and early development using tomato as a model system. We use molecular and genetic techniques to investigate the complex interplay of gene expression changes, signaling events, and hormonal activity, controlling fruit development. The lab also studies the effect of drought stress, an increasing problem in crop production, on tomato fruit set and growth. We are taking advantage of the genetic diversity of wild tomato species, to examine the molecular basis of adaptations to water stress as well as of other fruit quality traits.

Students participate in projects aimed to identify new genes, small molecules or chemical signals playing a key role during fruit initiation. One of these projects involves the functional characterization of an ovule specific small secreted protein (OSP), specifically expressed in the inner ovule integument of tomato ovaries. OSP belongs to the cysteine-rich peptide class of small, secreted peptides, which have been involved in short-term signaling. We hypothesize that OSP, produced in the tomato female gametophyte, may participate in signaling events regulating pollen tube guidance, sperm reception and gamete activation, or in embryo development after fertilization. To characterize the function of OSP, the students involved in this project will use a range of techniques such as gene expression analysis by quantitative PCR, CRISPR-mediated gene editing, and protein localization using confocal microscopy.

Faculty advisor:  Carmen Catalá

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

 

 

 

 

 

 

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)

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 

 

 

 

 

 

 

More about the Fei Lab

Molecular and genetic analysis of fruit ripening - Giovannoni Lab, BTI

Molecular and genetic analysis of fruit ripening and related signal transduction systems, using tomato as the model system

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 and related signal transduction systems, using tomato as the model system. Recently, researchers in the lab isolated two genes, RIN and NOR, that are part of the master switch to induce ripening in tomatoes. In addition to identifying important regulatory components of ripening, the lab also investigates lycopene production. 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 in different tomato varieties.

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

Genomic analysis of leaf cuticle development and functional diversity in maize - Gore Lab, Cornell

Project Description:

Protecting crop plants from diseases and adverse growing conditions is key to achieving sustainable food production. The cuticle is a waxy, water-proof layer on the outer surfaces of plant leaves and stems that plays a vital role in preventing water loss. It is also where plants first interact with most insects and diseases. Therefore, the cuticle is important to keep plants healthy while preventing them from drying out in the breeze. While many prior projects have contributed insights into cuticle composition, development and function, very few have focused on the adult leaves of cereal crops, whose cuticle has a significant impact on the agricultural performance of these key crops. This project will discover genes that control cuticle development and function in corn, evaluate the potential for improvement of the leaf cuticle to help produce crops with increased drought tolerance and resistance to diseases, and generate tools to guide these efforts.

Faculty Advisor: Michael Gore

 

 

 

 

 

 

More about the Gore Lab

Genetic engineering of photosynthesis - Hanson Lab, Cornell

Project description:

Life on earth is dependent on the process of photosynthesis, which captures light energy and carbon dioxide to create essential molecules. The efficiency of carbon fixation in land plants is limited by the properties of the enzyme Rubisco, which is relatively slow and also sometimes reacts with oxygen instead of carbon dioxide.  The properties of Rubisco may potentially be improved by observing natural variation in its amino acid sequence and biochemical properties, or by performing mutational analysis. We are using transgenic plants to probe ways to improve Rubisco.  Another way to enhance photosynthesis is to increase the concentration of carbon dioxide surrounding the enzyme. We are using a synthetic biology approach to incorporate microcompartments into chloroplasts that will increase carbon dioxide near Rubisco.

Faculty Advisor: Maureen Hanson

 

 

 

 

Molecular analyses of arbuscular mycorrhizal (AM) symbiosis - Harrison Lab, BTI

Project description:

Phosphorus is a critical macronutrient for proper plant growth. While phosphorus deficiencies can be improved by the application of phosphate fertilizers, it is costly, both to the farmer and to the environment. Furthermore, the crops only take up a small percentage of the applied fertilizer; the remainder is either immobilized in the soil, or carried into ground water and rivers, often resulting in pollution.

Interns in the  Harrison lab investigate two aspects of plant phosphorus nutrition. The first aspect seeks to understand the basis for the symbiotic relationships between vascular flowering plants and arbuscular mycorrhizal (AM) fungi. The fungi colonize root cells, gaining access to carbon supplied by the plant, while at the same time mobilizing mineral nutrients from the soil, including phosphorus, to be used by the plant. For this work, the lab uses the model legume, Medicago truncatula and the fungus Glomus versiforme. The Harrison lab also studies how plants find and take up phosphorus from the soil when they do not have these symbiotic relationships with fungi. This work toward understanding the mechanisms of perception and acquisition of phosphorus by plants may eventually lead to a more effective usage of fertilizers.

Faculty advisor: Maria Harrison

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

Project description:

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

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

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

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

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

 

 

 

 

 

 

More about the Li Lab

Molecular and genomic analysis of the plant immune system - Martin Lab, BTI

Project description:

Identifying natural variation in the plant immune system using cultivated and wild species of tomato and investigating the underlying mechanisms through gene mapping-by-sequencing and CRISPR/Cas9 genome editing methods.

Bacterial speck disease decreases yield and also creates unattractive black spots on tomato fruits, making them unmarketable. The disease is caused by the bacterium Pseudomonas syringae pv. tomato. (Photo by Gregory Martin)

Project description:

The Martin laboratory studies the molecular basis of plant immunity and bacterial pathogenesis. Our focus is on the infection of tomato by Pseudomonas syringae pv. tomato as this interaction results in bacterial speck, an economically important disease, and also serves as a powerful model system for understanding fundamental mechanisms involved in plant-pathogen biology. On the bacterial side, we study virulence proteins and associated mechanisms that the pathogen uses to interfere with the plant immune response. On the plant side, we identify and characterize genes, proteins and molecular mechanisms that play a role in host immunity and susceptibility. Our work relies on natural variation for these traits that is present in cultivated tomato and in the 12 wild relatives of tomato that originated in South America. For the characterization of both plant and bacterial genes and proteins, we use a variety of experimental approaches including biochemistry, bioinformatics, genetics, genomics, molecular biology, and structural biology.

Examples of research projects in my laboratory include: 1) Using tomato varieties that have natural variation in their immune system to clone and characterize the genes responsible; 2) Using CRISPR/Cas9 genome-editing methods to mutate immunity-associated genes and investigate alterations in the plant defense system; and 3) Investigating bacterial proteins that play a key role in promoting pathogenesis and virulence.

Representative publication: https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15788

Faculty advisor: Greg Martin

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

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.).

Understanding the evolution of plant metabolic pathways using comparative genomics - Moghe Lab, Cornell

Project Description:

Metabolic pathways in plants are quite dynamic, resulting in production of over a million metabolites across ~300,000 estimated plant species. These metabolic pathways are in a constant state of innovation due to gene duplication, transcriptional divergence, enzyme promiscuity etc. How have specific metabolic pathways originated and diversified? What is the role of positive selection and genetic drift in shaping metabolic diversity? How does enzyme promiscuity influence evolution of specialized metabolic pathways? We are investigating these and other allied questions using evolutionary genomic approaches, by performing comparative analyses of plant genomes, transcriptomes and proteomes. Research in the Moghe lab is highly integrative and comprised of both computational and wet-lab approaches.

Faculty Advisor: Gaurav Moghe

Gaurav Moghe

 

 

 

 

 

 

More about the Moghe Lab

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

Defense mechanisms in maize, with a focus on mycotoxigenic fungi - Nelson Lab, Cornell

Integrated field, greenhouse and lab studies to reduce the vulnerability of maize to fungi that cause disease

Project description:

Like other crops, maize is attacked by diverse microbes, including micro-fungi that produce toxic compounds. These toxins, including aflatoxin, fumonisin and deoxynivalenol, contaminate staple crops around the world and pose health threats to vulnerable human and animal populations. The Nelson lab is working to understand the genetic architecture of disease resistance in maize and sorghum as well as the mechanisms that enhance or reduce toxin accumulation in crops before and after harvest. We also contribute to plant disease management efforts in international contexts. We work at Cornell, with collaborating labs in North Carolina and Mississippi, and with collaborating teams in India, Tanzania and Kenya.

Faculty advisor: Rebecca Nelson

Rebecca Nelsom

Identifying factors that control distribution of recombination events along chromosomes - Pawlowski Lab, Cornell

Project description:

The goal of the research in the Pawlowski lab is to understand the basis of inheritance in plants by studying the mechanisms governing chromosome behavior and genetic recombination in meiosis.  Meiosis is a specialized type of cell division that leads to the production of gametes.  During meiosis, homologous chromosomes, one from the mother and the other one from the father, pair with each other and exchange parts (recombine).  These processes are essential for accurate transmission of genetic material from parents to progeny and for generating genetic variation.  Our research combines genetics, molecular biology, and cutting-edge microscopy to identify genes, and pathways that regulate meiosis.  These basic studies will provide means to investigating how meiotic processes can be modified to improve plant breeding methods.  We use two model plant systems, maize, one of the most important crop plants in the world, and a common weed, Arabidopsis thaliana.

Faculty advisor: Wojtek Pawlowski

Wojtek Pawlowski

 

 

 

 

 

 

More about the Pawlowski Lab

The role of membrane transport in root abiotic stress responses – Pineros Lab, USDA/Cornell

Project description:

Roots are the essential organ for plant nutrition, absorbing water and nutrients. Research in the Pineros lab focuses on the role of two distinct, but complementary aspects of root biology and plant adaptation to environmental stresses: root system architecture and membrane transport. Our goal is to understand the physiological and molecular processes underlying plant abiotic stress responses, as well as mineral nutrition-related processes. Current projects focus on A) structural and functional studies on membrane transporters that underlie Al resistance responses in crops by mediating Al exclusion or internal detoxification, and B) determining  the mechanisms underlying the expression and regulation of these membrane transporters. The outcome of this research will provide a new framework for identifying molecular determinants that confer high levels of Al resistance, with the ultimate goal of “engineering” their functional characteristics to enhance the plant’s adaptation responses.

Faculty advisor: Miguel Pineros

 

Chemical Ecology, Plant-Pollinator Interactions and Multi-Modal Behavior - Raguso Lab, Cornell

Project description:

My students and I study the full spectrum of chemically mediated interactions between flowering plants and their insect pollinators, including typical nectar- or pollen-based systems, obligate mutualism, mimicry and deception. These studies have compelled us to develop broader interests in the evolution of signals and communication, exploring the links between chemical signals and nutrition, physiology and foraging decisions. Our study of chemically-mediated interactions has expanded to include the impact of third parties (microbial symbionts, parasites and predators), and to apply what we have learned in pollination systems to those of host specificity and biological control, including recent work on yeasts, bacteria and the spotted wing drosophila fly.

Our laboratory environment provides students with opportunities to design and perform behavioral bioassays, to learn analytical chemistry, electrophysiology, dietary manipulation and performance assays with several species of insects, plants and microbes. Learn more about our projects, publications and lab history at:  http://pages.nbb.cornell.edu/neurobio/ragusolab/index.html

Faculty advisor: Robert Raguso

Cell size and sepal size in Arabidopsis - Roeder Lab, Cornell

Project Description:

Size is a critical property of plants, yet we know little about how it is controlled. In the Roeder laboratory, we ask how does a cell know how big to be and how does the whole organ (e.g. leaf, sepal or petal) made up of many cells know how big to be. To answer these questions we image living plants on a confocal microscope and measure the growth of cells, examine the cell division pattern, and quantify fluorescent proteins expressed.

Faculty Advisor: Adrienne Roeder

Adrienne Roeder

 

 

 

 

 

 

More about the Roeder Lab

Polymers and matrices of the cell wall and cuticle of tomato fruit - Rose Lab, Cornell

Characterization of key structural polymers and matrices of the cell wall and cuticle of tomato fruit, and mechanisms of their synthesis and modification.

Project Description:

Research in the Rose lab is focused on understanding the biological importance of the structural polymers that form plant cell walls, as well as the water resistant barrier, called the cuticle (the plant ‘skin’), which covers the above ground surfaces of land plants. We look at how those polymers are synthesized and assembled into complex polymer matrices, and how they contribute to factors such as plant architecture, resistance to pathogens and limiting drought stress. This involves a wide range of analytical approaches, including genomics, proteomics and imaging techniques. Much of the research uses tomato as a model system and the research aims to bridge basic science and practical applications geared towards enhancing fruit quality traits and food security.

Faculty Advisor: Jocelyn Rose

Jocelyn Rose

 

 

 

 

 

 

More about the Rose Lab

Evolution of floral traits in a California native plant lineage (Calochortus) - Specht Lab, Cornell

Project description:

Calochortus (Liliaceae) is a large genus (75 spp.) of bulbous herbs with flowers of kaleidoscopic vari­ety and exquisite complexity. It has a center of diversity in California and ranges north to British Colum­bia, west to the Dakotas, and south to Mexico and Guatemala. Calochortus has undergone strik­ing radiations in flower morphology, habitat, and substrate preference, and most taxa have narrow ranges. Floral syndromes include Mariposas with large, brightly colored, tulip-like blossoms with an erect perianth (tepals); Cat’s Ears with a smaller, spread­ing perianth densely covered with trichomes; Star Tulips with spreading, mostly glabrous tepals; and Fairy Lanterns with closed, globular nodding flowers. Calo­chortus petals are marked by unique, often brightly colored glands. Species inhabit deserts, grass­lands, chaparral, mead­ows, vernal pools, springs, montane woodlands, and forest under­stories. One quarter of all species occur on or are limited to serpentine; nearly as many are federally endang­ered or extinct. Several species are visited by a wide range of pollinators, while others attract a narrow range of visitors.

Given the diversity of habitats, geographic ranges, and floral forms seen in Calochortus, a well-resolved and densely sampled phylo­geny would provide the opportunity to address many questions at the interface of ecology, evolution, and biogeography: Are species with similar floral syndromes each other’s closest rela­tives, or have such syndromes arisen multiple times independently? What is the adaptive significance and developmental origin of each floral syndrome? Has the ability to tolerate serpentine evolved more than once within and among clades? What has been the historical pattern of geographic spread within the genus? Do closely related species occupy similar ecological distributions?

The selected student will work with graduate student Adriana Hernandez to develop a phylogeny for Calochortus and to investigate gene flow and diversification in floral form among various species native to California and Mexico.

Faculty Advisor: Chelsea Specht

Chelsea Specht

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

Biotechnological approaches to accelerate improvement of underutilized plant species - Van Eck Lab, BTI

Project Description:

Research in the Van Eck lab is focused on development of genetic engineering and gene editing approaches to support crop improvement efforts.  A current focus of her work is investigation of strategies to accelerate improvement of underutilized plant species and orphan crops to diversify our food supply.  By applying genetic engineering and gene editing of groundcherry and goldenberry as proof-of-concept, she has demonstrated the feasibility of targeting key genes for domestication traits to tame the wild nature of a plant species and increase its likelihood of adoption into large-scale agricultural production.

Faculty Advisor: Joyce Van Eck

 

 

 

 

 

 

Comparing leaf development and cellular differentiation - Van Wijk Lab, Cornell

Project Description:

Grasses such as rice, wheat, maize and sorghum are important cereal crops grown in different parts of the world. Plants are classified as C3 or C4 species based on the primary product of carbon fixation in photosynthesis. C4-type plants, such as maize, sorghum and sugarcane, have traits that greatly increase their efficiency of carbon-fixation especially when water or nitrogen are limiting and temperatures are higher; this makes C4 crop species particularly successful in warmer parts of the earth. The van Wijk lab is comparing leaf development and cellular differentiation in the C3 species rice to that in the C4 species maize mainly using large scale comparative protein (proteome) analysis. Since chloroplasts play such a key role in C3 and C4 photosynthesis and plant growth, we pay particular attention to chloroplasts. We focus on proteins, since most cellular functions are carried out by proteins. Proteome analysis relies on modern mass spectrometers, as well as the availability of sequenced genomes and bioinformatics tools. Therefore to facilitate our biological research, the van Wijk lab also tries to develop and implement proteomics tools. Together with our Cornell colleague Dr Qi Sun, we also developed the Plant Proteomics Database PPDB to provide an integrated resource for experimentally identified proteins in the plant species Arabidopsis, maize and rice.

Faculty Advisor: Klaas Van Wijk

Klaas van Wijk

 

 

 

 

 

 

More about the Van Wijk Lab

Molecular genetic and genomic analysis of mineral nutrients transport, regulation and signaling – Vatamaniuk Lab, Cornell.

Project Description:

The global demand for high-yield grain crops is increasing due to the current trend of population growth, global climate change, and environmental pollution. In this regard, micronutrients such as iron and copper are required for the growth and development of all organisms including plants and humans. These elements, however, are toxic when are accumulated in cells in access. Thus plants tightly regulate copper and iron uptake from the soil to avoid deficiency while precluding toxicity. This regulation involves the transcriptional control of genes mediating copper and iron uptake from the soil, root-to-shoot partitioning and shoot-to-root signaling of copper and iron status to accommodate the demands of the growing shoot. Many of the mechanisms involved in metal transport, its regulation and signaling as well as micronutrient utilization for ensuring successful developmental programs including fertility are not well understood.

Project 1: Copper transport, it’s regulation, and influence on pollen fertility.

Using RNA-seq analysis, we identified a novel transcription factor, CITF1 (Cu-deficiency Induced Transcription Factor1), that is strongly upregulated in Arabidopsis thaliana flowers subjected to copper deficiency. We demonstrated that CITF1 regulates copper uptake into roots and delivery to flowers and is required for normal plant growth under copper deficiency. We found that CITF1 acts together with a master regulator of copper homeostasis, SPL7, and the function of both is required for copper delivery to anthers and pollen fertility. We now aim to identify the sites of copper action in anthers and pollen, the role played by SPL7 and CITF1 in pollen development, SPL7, and CITF1 transcriptional regulatory networks and transport processes governing copper homeostasis in A. thaliana. We are also analyzing SPL7 and CITF1 pathways in a globally important crop, wheat, and its proxy, a model grass species, Brachypodium distachyon.

Project 2: Shoot-to-root signaling of iron deficiency

Despite significant progress in the understanding of how plants acquire iron from the soil and how iron is mobilized within the plant, not much is known about how shoots communicate their iron status to the root. We are using A. thaliana iron deficiency signaling mutants to address the question of the nature of systemic iron deficiency signal(s), its interactions with sensors in different tissues and cell types as well as the signal propagation to root epidermal cells to trigger transcriptional iron deficiency responses.

Faculty Advisor: Olena Vatamaniuk 

 

 

 

 

 

 

BTI Computational Biology Center - Suzy Strickler, BTI

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 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 North American Acontium, 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, imply that A. noveboracense is a distinct species. Now that we better understand the evolutionary history and relationships between NorthAmerican Aconitum species, we can investigate what possible forces are threatening A. noveboracense. A future direction in ecological niche modeling to understand how Earth’s changing conditions may affect the distribution of A. noveboracense and 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 tomatoes response to speck, a bacterium known as Pseudomonas syringae that manifests itself in the form of black spots on the leaves the tomato plants and in drastic cases can cause the leaves to shrivel, wilt, anddie. 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 possessesthe 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.
 

 

 
 

 

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 making it an even bigger problem. All in all, it’s 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 (like 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 local donors including the Ithaca Garden Club, the Legacy Foundation of Tompkins County, and the Tompkins Charitable Gift Fund.

 

Contact:

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