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Complete profiles of the multiple research interests of many faculty and senior academics can be found in the Faculty and Senior Academics Directory. To search for faculty in specific disciplinary areas, see lists in the various Graduate Fields.

Foundational Knowledge

  • Plants as model systems

    • Uncovering new targets for enhancing agronomic qualities
    • Manipulation of chloroplasts and photosynthesis for increased plant productivity
    • Imaging technologies provide novel insights into plant development
    • Biomolecular characterization and computational analysis tools
       
  • Systematics and biodiversity
         

  • Soil properties and impact on plant productivity

    • Understanding and manipulating soil microbes for improved soil and plant health
    • Water quality, availability, and its influence on other soil factors
    • Understanding and manipulating nutrient cycling in the soil
       
  • Plant-associated microbes

    • Promote plant health through exploration of beneficial interactions with other organisms
    • Identify virulence factors and their targets to uncover sources of resistance
    • Predictive modeling of pathogen populations and interactions

Plants as Model Organisms

SIPS researchers are making breakthroughs in understanding the important and fundamental processes at work in plants and their environments, as well as understanding the principles underlying plant evolution and diversification.

Molecular mechanisms of plant development

  • Margaret Frank uses grafting as a tool to look at the coordination of growth and development between root and shoot systems, and the molecular mechanisms underlying grafting-induced traits.
  • Jian Hua’s research explores the molecular mechanisms underlying how plants respond to temperature variation and associated regulation of development and immunity.
  • Robert Turgeon investigates the physiology of phloem transport and its relation to leaf development and the structure and function of plasmodesmata.
  • Kenong Xu is focused on characterization of regulatory networks in apple with an emphasis on those involved in stress resistance and fruit quality and longevity.

Identification of new targets for enhancing agronomic qualities

  • Lailiang Cheng's research group is finding new ways to manipulate the sugar and acid content in apples in ways that enhance fruit quality.
  • Olena Vatamaniuk's research group is identifying proteins involved in metal transport and signaling with potential use in creation of iron fortified foods
  • Susheng Gan's research group is focused on regulation of senescence as a strategy for increasing crop yield and minimizing post-harvest loss
  • Li Li's research group is investigating plant genes involved in biosynthesis of pigments like carotenoids, as a means of enhancing nutritional value in crop plants
  • Jim Giovannoni, Carmen Catala and their research groups are characterizing developmental changes associated with ripening, revealing new genetic targets for improving flavor in tomatoes.

Increased plant productivity through manipulation of chloroplasts and photosynthesis

  • Klaus van Wijk’s research group investigates the development and repair of photosynthetic apparatuses in plants using different photosynthetic pathways
  • Maureen Hanson’s research group has successfully re-engineeered chloroplasts of higher plants with high efficiency Rubisco from an alga and is working on transferring additional algal components to allow high efficiency function under normal atmospheric conditions
  • Mike Scanlon's research group investigates the developmental biology of leaves, revealing new strategies for optimizing leaf angles so light is more efficiently captured by the whole plant.

Read more about improving photosynthetic efficiency as an important strategy for increasing agricultural productivity in the perspective piece, “Redesigning photosynthesis to sustainably meet global food and bioenergy demand” (PNAS 2015,112:8529).

Advanced imaging technologies provide novel insights into plant development

  • Adrienne Roeder analyzes plant developmental patterning over time by generating computational models from confocal microscope images (news)
  • Wojtek Pawlowski studies meiotic recombination using genetics, biochemistry and several advanced microscopy methods, such as restorative deconvolution, multiphoton excitation, and structured illumination microscopy.
  • Taryn Bauerle images very fine-scale spatial relationships between competing tree roots in a 3D space using X-ray computed tomography.

New technologies for biomolecular characterization  and computational analysis

  • Gaurav Moghe’s research involves in silico process modeling and creation of predictive computational models to reveal enzyme function, pathway organization, and secondary metabolite pools (news
  • Joss Rose's research group is developing new protocols and computational tools to characterize cell wall proteins with particular emphasis on cell wall changes during fruit development and molecular interactions with pathogens
  • Zhangjun 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
  • Lukas Mueller's group coordinates the SOL Genomics Network which provides resources for genome analysis and genomic selection of solanaceous crop plants including tomato, potato, pepper, and eggplant.

Faculty and senior researchers working in this area:
Taryn Bauerle - Carmen Catala - Lailiang Cheng - Yong Gu Cho - William Crepet - Jerrold Davis - Zhangjun Fei - Giulia Friso - Susheng Gan - James Giovannoni - Maureen Hanson - Jian Hua- Dan F. Klessig - Joanne Labate - Li Li - Lukas Mueller - June Nasrallah - Karl Niklas - Kevin Nixon - Maria Gandolfo Nixon - Thomas Owens - Wojciech Pawlowski - Robert A. Raguso - Adrienne Roeder - Jocelyn Rose - Michael Scanlon - Chelsea Specht - Robert Turgeon - Klaas van Wijk - Olena Vatamaniuk - Randy Wayne


Systematics and biodiversity

Biodiversity resources such as the L.H. Bailey Hortorium and Cornell Plant Pathology Herbarium are becoming ever more important for genomic study of biodiversity and evolution. The Hortorium's mission includes systematic studies of wild and cultivated plants, ethnobotany, molecular systematics, paleobotany, phylogenetic theory, biodiversity studies, and pharmaceutical studies of tropical plants.

  • Chelsea Specht investigates the processes and patterns involved in the evolution and diversification of monocots, with a focus on the Zingiberales.
  • M. Alejandra Gandolfo’s research centers on paleobotany, answering questions about the origin of angiosperms, the evolution of seed plant characters, and evolution of floras in the Southern Hemisphere.
  • Kevin Nixon focuses on evolution and systematics of angiosperms with emphasis on the Fagaceae. He has also written software packages used for phylogenetic analysis.
  • Jeff Doyle’s research concerns the origin and evolution of polyploidy in plants, also focusing on legume systematics and the evolution of nodulation
  • Kathie Hodge works on the biodiversity and ecology of fungi with a focus on insect-associated and food-spoilage fungi and is a national expert on fungal identification and poisoning

Faculty and senior researchers with involvement in Systematics and Biodiversity:
Bill Crepet - M. Alejandra Gandolfo - Jerrold Davis - Kevin Nixon - Jeff Doyle - Chelsea Specht - Kathie Hodge - Gaurav Moghe

Soil Properties and Impact

Understanding the properties of soils, soil impact on plant productivity, and the soil microbial communities is foundational to both environmental conservation and food security.

Characterization and manipulation of soil microbes for enhanced soil and plant health

  • Dan Buckley investigates the soil microbiome and its impacts on ecosystem health, the plants we grow, the water we drink, and the air we breathe.
  • Jenny Kao-Kniffin investigates how soil microbes can be used to confer selective growth benefits to plants, providing a potential strategy for promoting growth of desirable plants and suppressing weeds without the use of chemicals
  • Janice Thies looks at the fate of insecticidal Bt-toxin in the soil, the role of the rhizosphere microbial community, and how different agricultural practices alter soil properties.

Understanding and manipulating nutrient cycling in the soil

  • Johannes Lehmann’s research is focused on understanding of biogeochemical cycles of carbon and nutrient elements in soil, developing methods for soil carbon sequestration with biochar, resource recycling from waste to fertilizers, and providing important insight into regional and global element cycles. (news)
  • Harold Van Es’s program concerns precision soil management, with emphases on a holistic soil health management framework, and a computational tool for precision nitrogen management (Adapt-N) that was recently commercialized (news)
  • Enid Martínez focuses on molecular scale investigations of the interaction of organic carbon and nitrogen at mineral surfaces and the movement of major, trace, and toxic elements through plants and soil.

Faculty and senior researchers working in this area:
Dan Buckley - Jenny Kao-Kniffin - Johannes Lehmann - Enid Martínez - Janice Thies - David Wolfe -  Dawit Solomon - Jeffrey Melkonian


Plant-Associated Microbes

In the School of Integrative Plant Science (SIPS) we are making breakthroughs in understanding how microbes and other organisms interact with plants leading either to beneficial interactions or disease.

Exploring beneficial interactions with other organisms to more effectively promote plant health

  • Maria Harrison 's group studies arbuscular mycorrizhal fungi which form associations with the roots of flowering plants and provide plants with phosphate in exchange for other nutrients. Understanding the molecular interactions that underlie phosphate transfer and development of symbiotic interactions may reveal new strategies for optimizing nutrient transfer to the host plant
  • Teresa Pawlowska's group studies also studies arbuscular mycorrizhal fungi and how bacterial endosymbionts of the fungi contribute to the symbiotic relationship.
  • Robert Raguso's research group studies how volatile plant chemicals influence behavior of insect pollinators and pests. By understanding the biosynthetic pathways responsible for production of these chemicals as well as the receptors and biochemical response pathways in insects, these interactions can be manipulated to promote plant growth and health.

Identification of virulence factors and their targets to uncover sources of susceptibility and resistance

  • Adam Bogdanove's research group works on TAL effector proteins that are injected into host plant by pathogenic bacteria and activate expression of genes that determine susceptibility and resistance. By identifying new effectors and their target sequences in host plants, the targets can be genetically altered to promote disease resistance. TAL effectors are additionally being used as biotechnological tools for DNA modification.
  • Michele Heck's  group uses affinity purification and mass spectroscopy to identify factors in host plants and insect vectors that interact with viruses and bacterial pathogens during different stages of transmission and disease development.  Factors important for virus transmission can be targeted by genetic modification of RNA silencing
  • Alan Collmer's group works on Pseudomonas syringaes that produce a vast array of virulence factors. By selectively recombining these factors in a strain from which they have all been deleted, Collmer's group is understanding how these toxins and type III effectors work together to interfere with plant defense pathways.
  • Greg Martin's group collaborates closely with the Collmer group, identifying defense pathways and proteins in tomato that trigger resistance in response to pathogen cultivars.  By screening for variation in responses among different tomatoes, Martin's group is identifying novel sources of host resistance.
  • Xiaohong Wang's research group is identifying nematode virulence factors that promote parasitism in potato.  RNA-silencing of nematode parasitism genes may prove an effective strategy for generating resistant cultivars. 

Faculty and senior researchers working in this area:
Adam Bogdanove - Michelle Heck - Alan Collmer - Melanie J. Filiatrault - Stewart Gray - Maria Harrison - Kathie Hodge - Georg Jander - Andre Kessler - Gregory Martin - Teresa Pawlowska - Bryan Swingle - B. Gillian Turgeon - Xiaohong Wang