Technology Transfer

Ensuring That Society Benefits from BTI Research

The Boyce Thompson Institute (BTI) makes fundamental discoveries in plant biology with support from federal and private grants. An important part of our mission is to identify basic research results that can be applied to commercial or humanitarian goals: to improve agriculture, enhance human health, or protect the environment. Discoveries with commercial potential are submitted for patent protection. By reaching out to scientists in industry, we identify opportunities for licensing, collaborative research, or consulting.

Featured Technology

BTI’s Research Advances Cancer Prevention

An insect cell line BTI-TN5B1 (The High-Five™), developed at Boyce Thompson Institute by Dr. Robert Granados while doing basic research on insects viruses, is now being used to produce Cervarix™ made by GlaxoSmithKline. This is one of two currently available vaccines that target the HPV virus, a major cause of cervical cancer. The vaccine is currently being used in more than one hundred countries around the world.

Paul Debbie, BTI Director of Technology Transfer and Licensing, talks to Bob Granados, BTI Emeritus.

Discoveries Making an Impact

Seminal BTI discoveries include:

  • Vaccine and other protein production in insect cell lines
  • Natural small molecules in plant and human health
  • Plant disease resistance
  • Plant and bacterial proteins in innate and effector-triggered immunity
  • Salicylic acid pathway for systemic acquired resistance
  • Plant insect resistance—plant genes and small signaling molecules
  • Plant-based vaccines

Collaborations and Consulting

The expertise of BTI scientists includes such diverse areas as plant disease and insect resistance; fundamentals of photosynthesis and abiotic stress tolerance; and genome-scale capabilities, including DNA and RNA sequencing, bioinformatics, small molecule chemistry, and functional proteomics. In addition, we have expertise in plant transformation and insect cell culture.

For Inventors

Inventors may download this fillable word document.

Invention Disclosure Form

Patents

For a full list of BTI’s patents click here.

Contact

For further inquiries, please contact:

Paul Debbie
Director of Technology Transfer and Licensing
Office/Lab: 200A
Email: ppd2@cornell.edu
Phone: (office) 607-254-8729

Research Utilization

BTI research often has practical applications. The research application statements highlight the utility of our professors’ research.

Gary Blissard

Research in the Blissard lab addresses fundamental and applied topics related to baculovirus infection and gene expression in insect cells. Baculoviruses are virulent pathogens of a number of insects, including many pests of agricultural importance. The baculovirus AcMNPV has been developed as a widely used expression system for secreted or membrane-bound proteins, or those requiring eukaryotic post-translational processing. Baculoviruses have been used for the development of vaccines and therapeutic proteins. They are also used to efficiently introduce DNA into mammalian cells and are being explored as potential vectors for human gene therapy. The laboratory focuses on several aspects of the baculovirus infection cycle, as well as on insect cell lines used in protein expression.

A major objective of our studies is to understand the complex nature of baculovirus entry into, and exit from insect cells. The major viral envelope protein, GP64, is critical for both attachment to host cells and fusion of viral and cellular membranes. Studies in the lab delve into the structure and function of this critical envelope protein, as well as the cellular pathways that deliver the virus to the nucleus, where viral replication occurs. The budding of baculovirus particles from infected cells is also under study. Understanding the mechanisms involved in baculovirus budding will be critically important for developing high quality virus-like particle (VLP) vaccines, which reduce or eliminate baculovirus particles from VLP preparations.

Another major objective is to understand viral gene expression, which is divided conceptually into early and late phases, mediated by host and viral RNA polymerases, respectively. The viral late RNA polymerase is critically important for biotechnological applications, as this polymerase mediates the exceptionally high levels of protein production from the baculovirus expression system, which is among the highest protein expression known in all eukaryotes. Using high throughput sequencing, we recently characterized the complete transcriptome of the baculovirus AcMNPV through the viral infection cycle in a High Five-derived cell line. In addition, we are analyzing the specific transcriptional changes and responses of the cell line to AcMNPV infection. This information will permit precise engineering of the virus and cell lines for optimized utilization in many biotechnological applications.

The laboratory also studies insect cells, focusing on the development of cell lines and most recently, on the model insect Manduca sexta. In collaboration with scientists from Kansas State University and the Baylor College of Medicine, the Manduca sexta genome was recently sequenced. Our transcriptome studies have examined gene expression in a variety of tissues over a range of developmental stages of the animal.

Recent studies are also focused on understanding how certain viruses are transmitted by insects. We are using several approaches to examine how viruses interact with and traffic through the midgut cells of vector and host insects. These studies will be important understanding how plant and animal viruses effectively utilize insects as vectors for the transmission of plant and animal diseases.

Joyce Van Eck
  • Transformation Technology and Plant Nutrition

    The focus of research in the Van Eck laboratory is biotechnological approaches for the study of gene function and crop improvement. The lab focuses on developing genetic transformation technology. This makes it possible to design and introduce gene constructs into plant cells, which subsequently regenerate into plants with altered phenotypes.

    The Van Eck group is experienced in the design of tissue culture and Agrobacterium tumefaciens-mediated transformation methods, which can be used to 1) study gene function, 2) unravel the intricacies of metabolic networks, and 3) further the development of novel model systems to discover genes that can be used to improve crop species. Most recently, the Van Eck group has developed transformation systems for the rapid cycling C4 grass, Setaria viridis, which is expected to become a valuable model system for corn, and forTaxus, in order to make it possible to metabolically engineer this species to produce higher quantities of taxol; Taxol is used as a chemotherapy treatment. Currently, they are developing methods for Asclepias(milkweed) and Solidago (goldenrod) because both have the potential to be used as model systems for the study of plant/insect interactions.

    In addition to developing transformation technology, the Van Eck group also performs transformations on a fee for service basis. The plant species they transform routinely include tomato, potato, Brachypodium distachyon, Setaria viridis, Medicago truncatula, Nicotiana benthamiana, N. tabacum, and NT1 suspension cultures.

    The Van Eck laboratory has collaborated with Dr. Li Li’s lab, at the USDA Federal Nutrition Lab on the Cornell campus, to study the Or gene, which was discovered as a dominant mutation in cauliflower that promotes chromoplast development, resulting in orange florets and substantially increased carotenoid accumulation. When transferred to potato, the mutant cauliflower Or gene enhances carotenoid accumulation in tubers, which increases further during cold storage. This gene has substantial promise to alleviate vitamin A deficiency, a cause of childhood blindness and death. A second approach takes a different metabolic strategy in the same pathway that has been modified in Golden Rice. The Crtb gene product transforms beta-carotene, a Vitamin A precursor, into zeaxanthin. Silencing this gene in potato results in beta-carotene levels about 30 times higher than in wild-type plants. These two approaches have great promise to increase beta-carotene and thus enhance the vitamin A content of vegetables and grains.

    Collaboration and Consulting Opportunities

    • Service: Creating transgenics to demonstrate gene efficacy
    • Collaboration: Plant transformation system development and improvement
    • Consulting: Transferring technology to enable transformation in C3 or C4 models
    • Collaboration or Licensing: Manipulation of plastid maturation and carotenoid biosynthesis to increase beta-carotene accumulation
David Stern

Chloroplasts are the organelles in which photosynthesis occurs, incorporating atmospheric carbon dioxide into sugars and carbohydrates. Thus, chloroplast function plays a key role in determining crop yield. Chloroplasts also carry out other metabolic functions and mediate responses to environmental stress. It is now possible to alter the chloroplast genome, raising the possibility of modifying stress responses or introducing new metabolic pathways into plants and algae.

The Stern laboratory investigates and manipulates gene expression and protein assembly in the chloroplast. Plant systems in use include green algae, which offer promise for bioenergy production; maize and the related “monocot model organism Setaria viridis; and the widely adopted dicot model Arabidopsis, Over the years, the laboratory has defined many aspects of chloroplast gene regulation, leading to two current projects that may have practical applications.

1)    Biofuel production: In the context of a multidisciplinary consortium, genes from Botryococcus braunii, a slow-growing microalga that produces high levels of triterpene oils, have been re-coded to facilitate efficient gene expression and inserted into the chloroplast of Chlamydomonas reinhardtii, which is much more tractable than Botryococcus, but does not harbor this pathway. The objective is to use a high-throughput genetic screen to obtain a rapidly-growing, high production Chlamydomonas strain that has gained the capacity to produce these oils. An additional goal is to engineer the green alga Chlorella, which is better adapted to scaled-up production,in a similar manner.

2)    Engineering photosynthesis: The laboratory has discovered two previously unknown proteins that are required in maize for the assembly of Rubisco, the enzyme complex that is responsible for fixing carbon during photosynthesis. Rubisco is a key target for improvement via biotechnology, partly because a competing reaction uses oxygen instead of carbon dioxide, and limits the efficiency of carbon fixation. Biotechnology approaches to engineer improved Rubisco have been limited in part by the challenge of assembling altered protein into functional complexes. The newly-discovered proteins may underpin the ability to assemble Rubisco in bacterial or cell-free systems. Furthermore, the assembly proteins themselves offer targets for improvement of plant yield through manipulation of Rubisco abundance in plants.

Collaboration and Consulting Opportunities

  • Chloroplast engineering for biofuel production
  • Assembly of Rubisco to enable enzyme engineering, manipulation of Rubisco abundance in plants

Public NSF

The multi-disciplinary research team will develop microfluidic lab-on-chip devices with capabilities to precisely assay and manipulate parallel samples at single-cell resolution. The devices will enable the integration of multiple experimental parameters on a single user-friendly platform. These devices will then be used to analyze and optimize the growth and hydrocarbon production potential of an engineered recombinant photosynthetic microalgae. The specific test case will be a recombinant, fast growing Chlamydomonas reinhardtii algal strain that will be engineered to express a high-yielding hydrocarbon biosynthetic gene system derived from the slow-growing microalaga, Botryococcus braunii. These specific hydrocarbons produced by these organisms are of particular interest because they can be readily converted into petroleum-equivalent fuels.

w.nsf.gov/awardsearch/showAward?AWD_ID=1240478&HistoricalAwards=false

Frank Schroeder

Nematode Metabolomics

The past few years have seen a surge of interest in using NMR-spectroscopic techniques for characterizing complex metabolite mixtures. The Schroeder lab has developed new computational and statistical methods to identify individual components in complex metabolite samples and determine their biological function(s). This approach accelerates the pace of natural products research because it reduces the need for chromatographic fractionation and enables the identification of previously inaccessible small molecules, for example compounds that are prone to chemical decomposition and thus cannot be isolated. In particular, comparative metabolomics, based on statistical analyses of NMR spectra and HPLC-MS data has proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype.

The nematode Caenorhabditis elegans is one of the most important model organisms for biomedical research, because of its experimental tractability and because many of its physiological pathways show strong analogies to corresponding pathways in humans. In addition, discoveries in C. elegans are relevant for human health, given that more than 2 billion people are currently infected with parasitic nematodes, which cause devastating disease and disability. Understanding chemical signaling in C. elegans will aid in developing new approaches toward control and eradication of nematode-derived disease. Lastly, C. elegans research is highly relevant to the agricultural industry since nematode pests are a significant source of crop loss.

The Schroeder lab aims to complement the highly developed genomics and proteomics resources for C. elegans with a comprehensive structural and functional characterization of its metabolome. This effort has revealed that small molecules play important roles in C. elegans endocrine and exocrine signaling, specifically in key pathways regulating lifespan, development, and metabolism. Two-dimensional NMR spectroscopy permits the comparison of complex metabolite samples derived from different C. elegans mutant strains to identify and characterize compounds whose biosynthesis is strongly up- or down-regulated as a result of a specific mutation. The Schroeder lab has selected a number of C. elegans mutant strains whose phenotypes suggest a defect in small-molecule signaling that affect conserved pathways regulating lifespan, development, and fat metabolism. These studies have identified several series of novel small molecules that delay ageing, control sexual attraction, or play important roles in C. elegans development. To validate the biological function of these novel small molecules, samples of the identified compounds are synthesized and used for chemical genetic screens to determine effects on lifespan, development, and fat metabolism. Compounds that show activity in wild-type C. elegans are subjected to additional assays with mutant or RNAi strains representative of key genetic pathways related to ageing and development.

Of particular interest is a class of molecules called ascarosides, which are synthesized by C. elegansand many other nematodes, but have not yet been detected outside of nematodes. Ascarosides are often active at exceedingly low concentrations, and affect a number of behavioral and developmental processes in nematodes. They have the potential to be useful for controlling pathogenic nematodes, including nematodes that cause human and animal disease, as well as pathogens of economically important crop plants. They may also be useful for attracting beneficial nematodes, for example entomopathogenic nematodes that kill insect pests. Nematodes have co-evolved with their hosts for millions years and appear to evade immune surveillance, suggesting that these parasites actively modulate their host’s immune system. Experiments to characterize effects of ascarosides on animal and plant immune responses are currently under way.

Collaboration and Consulting Opportunities

  • Identification of molecules that control parasitic nematodes in humans, livestock and plants
  • Identification and validation of signaling molecules and other bioactive small molecules in complex metabolite mixtures
  • 2D NMR-based comparative metabolomics for connecting genetic changes with changes in small molecule production
  • Synthesis of small molecules for validation of biological activity
Eric Richards

Plant Epigenetics

Epigenetics encompasses regulatory mechanisms (e.g., cytosine methylation, chromatin protein modification, changes in chromatin packaging, and RNA interference) that alter the information content of the genome without changing nucleotide sequences. Differential epigenetic states associated with gene expression changes can be propagated at high fidelity through cell division, and in some cases, from parents to offspring. Consequently, epigenetics represents an independent form of inheritance, one that allows a single genotype to specify different phenotypes.

Epigenetic phenomena are widespread and have enormous impacts in agriculture. For example, transgene instability due to epigenetic silencing is a major concern in agricultural biotechnology, and epigenetic research is being applied to avoid silencing through better transgene design, identification of favorable insertion sites, and modification of host epigenetic systems. Research in the Richards lab has highlighted the importance of inherited “epimutations,” which can mimic stable Mendelian traits but are caused by differential DNA methylation and associated epigenetic marks. The generation, selection and manipulation of stable epigenetic alleles in agricultural breeding programs remain an underexplored frontier.

Plants serve as powerful experimental platforms for dissecting and elucidating epigenetic pathways and the ways that aberrations in these pathways can lead to epimutations. They are remarkably tolerant of epigenetic perturbation, providing the opportunity to identify and manipulate epigenetic modifiers while maintaining viability. Two of the epigenetic modifier proteins studied in the Richards lab, the nucleosome remodeler DDM1 and the VIM family of methylcytosine-binding proteins, are required for epigenomic stability in plants. Further, DDM1 and VIM1 have human orthologs that have been implicated in cell cycle control and tumorigenesis. Our work in plants to elucidate the mechanisms through which these proteins operate is being applied to understand the role that these proteins play in epigenetic phenomena, including transgene silencing and control of higher order chromatin organization.

Collaboration and Consulting Opportunities

  • The role of epigenetics in position effect and transgene expression stability
  • Inherited epigenetic variation in breeding programs
Lukas Mueller

Plant Bioinformatics

Bioinformatics tools and databases are a cornerstone of modern plant research. The Mueller lab is developing resources such as the SOL Genomics Network (SGN, http://solgenomics.net) and Cassavabase (http://cassavabase.org/), which help researchers navigate and exploit vast amounts of information. These websites contain genomic, genetic, and phenotypic data and provide easy-to-use tools for researchers to query, analyze and visualize the data.

SGN is database for the Solanaceae family, which includes such agronomically important crops as tomato, potato and peppers. The database is centered around the tomato reference sequence generated by the International Tomato Genome Sequencing Project released in 2012. SGN stores genomic and breeding data, including genetic and physical maps with markers, QTLs, gene sequences, functional genomics data, including expression and pathway data, and phenotypic data. The database also supports community curation, which enables users to contribute annotation and other data, such as images, to locus and stock pages.

Cassavabase is the database for the Nextgen Cassava project (http://nexgencassava.org/), which has the goal of improving Cassava breeding by applying high throughput genotyping technologies, and using genomic selection to accelerate the breeding cycle. The database contains genotypic data for lines in the breeding program, as well as extensive phenotypic data for training populations, the tools to correlate genotypes with phenotypes and to predict breeding values from genotypic information.

All code developed in the Mueller lab is open-source and freely available.

The website code created for SGN and Cassavabase represents a generic, reusable, modular and flexible platform, suitable for use by other organism databases. The long-term goal is to provide opportunities for academic and private organizations to cooperate more closely on software development, reducing the re-implementation of the same site features by different databases. Not only would adoption of a common platform reduce the syndrome of re-inventing the wheel, but it would also benefit users, and would greatly facilitate the integration of public data into proprietary databases. The Mueller lab also welcomes collaborations involving the assembly, annotation, and analysis of next generation genome and transcriptome data for a wide variety of plants.

Collaboration and Consulting Opportunities

Custom bioinformatics tools and databases

Greg Martin

Bacterial Pathogenesis and the Plant Immune Response

Infectious diseases caused by pathogenic bacteria, fungi, oomycetes, viruses, and nematodes pose major economic and environmental challenges to agriculture throughout the world. It is estimated that 15% of food, fiber, and fuel crops is lost annually to diseases worldwide. One way to address this problem is to develop plant varieties that are inherently more resistant to diseases as a result of classical plant breeding or genetic engineering.

Research in the Martin lab is focused on understanding the molecular details of the infection process as well as the host immune response, from the perspective of both the pathogen and the plant. On the pathogen side, the lab studies the causative agent of speck disease in tomato, Pseudomonas syringae pv. tomato. As part of its infection process, this bacterial pathogen delivers a large number of virulence proteins directly into the plant cell where they interfere with the host immune system. The lab is determining which features of these virulence proteins are responsible for undermining host immunity and investigating the mechanisms they use to compromise specific host proteins. This research lays the foundation for developing genetic resistance in plants that avoids or counteracts the activities of virulence proteins. Discoveries from this work could have implications in both agriculture and medicine as it has recently become apparent that many disease-causing organisms of plants and humans use fundamentally similar virulence mechanisms to infect their hosts.

On the plant side, the lab uses tomato because it is the natural host for Pseudomonas syringae and it is an economically important and experimentally tractable plant species. A major goal has been to determine the structural basis of the interactions between pathogen and host proteins. This knowledge is expected to enable the design of host proteins that evade interference by pathogen virulence strategies, resulting in plants with more durable, broad-spectrum disease resistance.

In the near term, the research will add to the understanding of pathogenesis and plant immunity not only in the tomato – Pseudomonas syringae system but also in other important vegetable crops. Moreover, because it is now apparent that all plants (both monocots and dicots) appear to use fundamentally similar resistance mechanisms, the research is relevant to many economically important plant species and to the control of diseases caused by diverse pathogens.

Three projects with potential application in the Ag and Pharma industry are described below.

1)    Plant Disease Resistance: Engineering the plant BAK1 gene to enhance PAMP-triggered immunity. (Include link to slide deck).

To infect plants, Pseudomonas syringae pv. tomato delivers ∼30 type III effector proteins into host cells, many of which interfere with PAMP-triggered immunity (PTI). One effector, AvrPtoB, suppresses PTI using a central domain to bind to the host BAK1 protein, a kinase that functions with several pattern recognition receptors to activate defense signaling. The structure of the AvrPtoB-BAK1 interaction surface has been solved, and AvrPtoB mutations at the interface have been shown to disrupt bacterial virulence. These results suggest approaches for altering the plant BAK1 protein to increase plant resistance to this bacterial pathogen. Though this work is most immediately applicable to tomato, analogous approaches to disrupt host:pathogen protein interactions can be envisioned for other host:pathogen interactions.

2)    Therapeutic Proteins: Effector proteins that can modulate programmed cell death (PCD) and immune responses in diverse eukaryotes.

Programmed cell death is an important physiological process and is in fact required for maintenance of a healthy organism. PCD is well-conserved across evolution, from bacteria and plants to humans. A number of neurological diseases, including Parkinson’s and Huntington’s disease, are linked to an abnormal increase in PCD in neurological tissues. PCD is also a major component of the plant immune response to bacterial infection. Pathogenic bacteria have developed mechanisms to counteract this plant immune response. The Martin lab has discovered a number of bacterial effectors involved in PCD. One such effector is AvrPtoB (US patent number 7,888,467), which has been shown to prevent PCD in plants and other eukaryotic organisms.   Given the conservation of these types of proteins, this or related effector proteins could prove to be useful in the treatment and prevention of diseases related to an abnormally high rate of PCD or other diseases related to disorders of the immune system.

3)    Vaccine and Protein Production: Enhancing accumulation of proteins in diverse eukaryotic expression systems.

The ability to express recombinant proteins in eukaryotic cells is the basis for the

production of many vaccines and industrial enzymes It is also an essential step in fundamental studies of protein structures important in medicine and agriculture. However, expressing large amounts of protein is often challenging. The effector protein AvrPtoB is a potent suppressor of programmed cell death (PCD) induced during the plant immune response. It also suppresses PCD induced by expression of foreign proteins in plants. Furthermore, AvrPtoB suppresses PCD in yeast induced by hydrogen peroxide or menadione (vitamin K), suggesting that targets of effector proteins may be highly conserved across evolutionary space. The Martin lab has shown that AvrPtoB suppresses PCD that is induced by the expression of certain vaccine proteins in N. benthamiana, resulting in enhanced accumulation of the vaccine protein in this transient plant expression system. Thus, AvrPtoB, and presumably many other effector proteins, have the potential to enhance the synthesis of “hard-to-express” proteins in diverse eukaryotic expression systems.

Collaboration and Consulting Opportunities

  • Engineering plant disease resistance: effector-triggered immunity and basal immunity
Dan Klessig

Plant Disease Resistance

The central objective of research in the Klessig lab is to understand plant defense responses to pathogens. To this end the lab has identified a number of critical defense components, several of which are related to the central role that salicylic acid (SA, the active ingredient of aspirin) plays in activating plant immune responses. Three are SA-binding proteins (SABPs): catalase and ascorbate peroxidase, the two major enzymes for detoxifying hydrogen peroxide, and SABP2, a methyl esterase that converts biologically inactive methyl salicylate (MeSA) into active SA. SABP2 plays a key role in systemic acquired resistance in tissue distal to the sites of infection, where it converts the long-distance mobile signal MeSA to SA. This conversion results in the induction and/or priming of plant defense responses, resulting in a heightened defense response.

There are striking similarities between plant and animal defense mechanisms. The Klessig lab has developed novel, effective and sensitive approaches to identify SABPs, revealing many more targets of SA, with potential applications in both plant and animal disease management. Human SABPs have recently been identified that play key roles in important diseases, including heart disease, arthritis, certain cancers, and neurodegenerative diseases such as Alzheimer’s or Parkinson’s. The identification of these SABPs provides insight into how aspirin, one of the oldest drugs known to humanity, may carry out its remarkable and myriad therapeutic effects and provides an avenue to identify novel natural or synthetic derivatives of SA/aspirin with improved therapeutic properties.

In a separate project, the lab has identified a novel ATPase named CRT1 (Compromised for Recognition of Turnip Crinkle Virus), that plays important roles in regulating disease resistance. It is closely related to the mammalian MORC1 gene (Microchidia), which appears to play a role in epigenetic modification of DNA. Silencing or inactivating CRT1 in plants affects four distinct levels of immunity: resistance (R) gene-mediated resistance, basal resistance, non-host resistance, and systemic acquired resistance in Arabidopsis, tobacco, tomato, potato, soybean, and barley. Moreover, CRT1 is involved in immunity against a broad spectrum of pathogens including virus, bacteria, fungi, and oomycetes. Overexpression or suppression of these defense components has a significant impact on disease susceptibility, suggesting biotech approaches to modulating plant disease susceptibility.

In a collaboration with Frank Schroeder’s lab at BTI, the Klessig lab has been studying the effects of ascarosides, small molecules synthesized by nematodes, on plant responses to disease and pathogenic nematodes. Plant pathogenic nematodes are important agricultural pests, and the possibility of enhancing nematode and disease resistance via treatment with small molecules has significant practical potential. Preliminary results in Arabidopsis, tobacco, tomato, potato, and barley are very encouraging.

Collaboration and Consulting Opportunities

  • Engineering plant disease resistance: effector-triggered immunity and basal immunity
  • Plant immunity
    • Role(s) of salicylic acid, signaling in systemic acquired resistance
    • Engineering broad spectrum disease resistance with CRT1- a player in 4 levels of immunity
  • Role of salicylic acid binding proteins in human disease
Maria Harrison

The Arbuscular Mycorrhizal Symbiosis

Except for members of the Brassica family, all crop species of agronomic significance have the capacity to form symbioses with arbuscular mycorrhizal (AM) fungi. These beneficial associations have a profound effect on plant phosphorus nutrition and consequently impact plant growth and health. Phosphorous (P) is one of the mineral nutrients essential for plant growth but is relatively difficult for plants to obtain. Although the total P content of soils may be high, P exists in inorganic and organic complexes that are unavailable to plants. Consequently, after nitrogen, P is the mineral nutrient that is most frequently limiting for plant growth.

In many agricultural soils, P availability limits plant growth, a problem which is addressed by the input of phosphate (Pi) fertilizers. This has both economic and environmental costs as the immediate recovery of Pi by plants is low, and excess fertilizer run-off contributes to the pollution of aquatic ecosystems. Furthermore, rock Pi, the raw material for superphosphate fertilizers, is a non-renewable resource and reserves are being depleted. Beyond food crops, the future use of marginally fertile lands for the production of biofuel crops will further increase the need for sustainable fertilization strategies. Consequently, it is essential that we understand and deploy partnerships such as the AM symbiosis to maximize agricultural productivity in an economically and environmentally sustainable manner.

To ensure that crop plants contain the optimal set of alleles for a maximally functioning AM symbiosis, it is necessary first to understand which genes control the AM symbiosis and the molecular basis of their function. The long-term goals of Dr. Harrison’s research program are to understand the molecular mechanisms underlying development and regulation of the AM symbiosis, and symbiotic phosphate (Pi) transport. Medicago truncatula and Brachypodium distachyon are used as model plant hosts, along with 3 AM fungi, Glomus versiforme, G. intraradices and Gigaspora gigantea. Using these systems, the lab has taken an integrated approach to analyzing the AM symbiosis, and several genes that that are essential for regulation of the symbiosis and symbiotic Pi transport have been identified.

Collaboration and Consulting Opportunities

  • Improving nutrient acquisition by modulating the Arbuscular Mycorrhizal symbiosis
Jim Giovannoni

The Giovannoni lab deploys genetic, genomic, and molecular approaches to study the biology of fruit development and ripening, primarily in tomato with some activities in melon, apple and banana. Tomato is an economically important crop, as well as an experimentally tractable model system for fleshy fruit development. As such, genes identified and characterized in the course of our research are likely to find application across the Solanaceae (e.g. tomato, pepper eggplant) and in additional fruit crops.

The lab currently has two major focus areas: transcriptome/epigenome dynamics during fruit development and ripening, and functional characterization of genes involved in ripening and nutrient quality. The lab works with numerous international collaborators to address these questions and to translate research findings from tomato to other fruit crops.

The Giovannoni lab has been a major contributor to the international tomato sequencing project and together with collaborators at BTI and around the world has generated a high quality whole-genome sequence. The lab will continue to lead efforts to close remaining gaps so that the Solanum lycopersicum genome can serve as a robust reference genome for comparison with wild relatives and breeding varieties. The lab is currently embarking on research projects that utilize the genome sequence for genome scale analyses focused on fruit biology.

In recent years the lab has discovered a number of genes that are important in overall ripening control, including several that underlie important fruit quality and shelf-life traits of interest to plant breeders. Current efforts focus on identifying genes controlling overall ripening processes in addition to specific pathways affecting fruit nutrient quality. We are currently testing several candidate genes in transgenic plants. Many genes identified in the lab have potential application toward crop improvement through traditional breeding, molecular breeding or transgenic approaches.

Collaboration and Consulting Opportunities

  • Genetic control of fruit quality and ripening
  • Fruit biology and physiology (pre and post-harvest)
  • Genome and epigenome sequencing and analysis
  • Transcriptome profiling
Zhangjun Fei

Computational Bioinformatics and Databases

The development of high throughput technologies has given rise to a wealth of genome-wide data, including DNA sequence, transcriptome, proteome, and metabolome data from samples representing environmental, genetic, and evolutionary diversity. It remains a major challenge to digest the massive amounts of data and use them to make hypotheses and predict phenotypes. To address this challenge, 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.

Using next-generation sequencing for crop improvement. The Fei group is using next-generation sequencing (NGS) technologies to investigate genomes, epigenomes and transcriptomes of several economically important crops including tomato, cucurbits, apple, sweetpotato and kiwifruit, and to perform global virus survey of crops such as tomato and sweetpotato. They are developing new computational tools to process and analyze the ultra-large scale data generated by NGS platforms.

Computational tools for omics data analysis. Several computational tools/pipelines have been developed to mine and analyze large scale genomics datasets. Here is a list of tools developed so far:

  • Plant MetGenMAP – a web-based tool for comprehensive mining and integration of gene expression and metabolite changes in the context of biochemical pathways.
  • iAssembler – A de novo assembly package for transcriptome sequences generated using 454 or Sanger platforms
  • iTAK – A package to identify and classify plant transcription factors and protein kinases.

Inferring gene regulatory networks. Plant phenotypes are the product of gene expression programs involving the regulated transcription of thousands of genes. A gene regulatory network describes the interaction of transcription factors with their target genes in response to development or environmental perturbations. New algorithms are being developed to infer gene regulatory networks by integrating datasets from different sources, including gene expression data, metabolomics data, promoter sequences, and microRNA information.

Databases. Making genome-scale data available to users is critical for capturing value from large and diverse datasets.

    • Tomato Functional Genomics Database archives publicly available gene expression, metabolite profile and small RNA information. The database also includes a set of query interfaces and computational tools that allow users to mine, analyze, and integrate tomato expression, metabolite and small RNA datasets.
    • Tomato Epigenome Database presents single-base resolution methylomes of tomato.
    • Cucurbit Genomics Database is a web-accessible data resource for genomics and functional genomics analysis of cucurbit species, including cucumber, melon, watermelon, and pumpkin. Currently the database contains the genome and EST sequences, small RNAs, and genetic maps for all cucurbit species.
    • RadishBase is a genomics and genetics database of radish. Currently the database contains radish mitochondrial genome sequences, EST sequences and annotations, biochemical pathways, EST-derived single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, and genetic maps

Collaboration and Consulting Opportunities

Carmen Catala

The successful initiation and development of fruit is a critical component of plant fitness and a strong determinant of crop yield. Fruit formation follows successful pollination and fertilization, which activates the rapid enlargement of the ovary, first by cell division and later via cell enlargement and culminates in ripening to facilitate seed dispersal. The process of fruit initiation is under the control of environmental factors and endogenous signals such as phytohormones. The plant hormone auxin controls many aspects of fruit development, including fruit set and growth, ripening, and abscission. For example the dependence of fruit set on pollination and fertilization can be bypassed by exogenous auxin application or by expression in the ovary of bacterial auxin biosynthetic genes. This leads to the formation of fertilization-independent or parthenocarpic (seedless) fruit. However, the molecular mechanisms by which auxin regulates fruit development remain mostly unknown.

Research in the Catalá lab addresses the molecular and genetic mechanisms of fruit formation using tomato, an economically important crop, and a model system for studies of fleshy fruits. The knowledge generated through our research will help develop strategies to enhance plant productivity and crop yield through improved fruit set that can have wide application in other crop species.

There are two main focus areas in the lab:

Developing a comprehensive understanding of auxin homeostasis during fruit development. The precise spatial and temporal synthesis and action of auxin are required for proper fruit development. However, the dynamics of auxin biosynthesis and the mechanisms for its distribution to fruit tissues remain mostly unknown. We monitor the levels and distribution of auxin and related metabolites and the temporal and cell-specific expression of auxin transporters and auxin biosynthetic genes, and test their function by manipulating their expression in transgenic plants. Many of these genes have the potential to control the formation of fruit without seeds as well as to influence other fruit quality traits such as size, weight and ripening characteristics.

Tissue-specific transcript profiling using laser capture microdissection (LCM) coupled to next generation mRNA sequencing to uncover genes and transcriptional networks regulating fruit set and development. LCM is a powerful tool to isolate specific tissues or cell types which can be combined with RNA-seq to generate high-resolution expression maps of a plant organ through its development. This approach dramatically increases the discovery of rare and cell-type specific transcripts and can lead to the discovery of novel regulators of fruit set and development.

Collaboration and Consulting Opportunities

  • Improving fruit set under unfavorable climatic conditions by regulating auxin homeostasis and signaling.
  • Discovery of genes and transcriptional networks regulating fruit set and development.