Foundational Knowledge

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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 Field Concentrations.

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
       
  • 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

Here in SIPS we are making breakthroughs in understanding the important and fundamental processes at work in plants and their environments from which solutions to global challenges will emerge. Essentially, we are figuring out how plant do what they do and how we can use that knowledge to help them do it better.

Greater understanding of plant processes and development reveals 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
  • 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.
  • June Nasrallah's research group focuses on the genetic basis of self-incompatibility in Arabidopsis, understanding of which will allow for more effective use of germplasm when breeding crop plants tailored to particular environments
  • Susheng Gan's research group is focused on regulation of senescence as a strategy for increasing crop yield and minimizing post-harvest loss

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.
  • David Stern’s research group investigates assembly of RuBisCO, the enzyme that catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere

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

New technologies for biomolecular characterization  and computational analysis are transforming our understanding of genome variation, evolution, and regulatory networks

  • 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.  
  • 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

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 - David Stern - Robert Turgeon - Klaas van Wijk - Olena Vatamaniuk - Randy Wayne


Soil Properties and Impact

In the School of Integrative Plant Science (SIPS) we are making breakthroughs in understanding properties of soils and the basis for soil impact on plant productivity and microbial communities. Essentially, we are unraveling the complex network of interactions occurring within the soil so they can be optimized optimizing for the long term health and benefit of plants.

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

  • Jenny Kao-Kniffin's group 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
  • Dan Buckley's research group characterizes the soil microbial processes involved in decomposition, in order to better understand soil geochemical cycles and identify novel microbes with useful digestive capabilities
  • Anthony Hay's group is focuses on identification and genetic analysis of soil microbes capable of degrading toxic compounds with potential applications for environmental restoration

Water quality, availability, and its influence on other soil factors

  • Tammo Steenhuis's research group investigates the fate of agricultural nutrients and sediment transport in local and African watersheds to improve and protect water resources
  • Susan Riha's group investigates the the impact of shale gas drilling and climate change on water resources, providing predictive models to inform public policy

Understanding and manipulating nutrient cycling in the soil to optimize plant nutrition

  • Johannes Lehmann's group investigates how biochar can be used as a soil amendment to enhances soil and sequester carbon
  • Janice Thies's research group looks at the fate of insecticidal Bt-toxin in the soil, its impact on plant physiology, and how different agricultural practices alter soil properties.
  • Carmen Enid Martinez's research group focuses on the movement of major, trace, and toxic elements through plants and soil
  • Christine Goodale's research group investigates how nitrogen is cycled through a forest environment and how its presence impacts soil decomposition and the fitness of different tree species
  • Tim Fahey's group investigates how acid rain changes the chemistry of elements in the soil and how this influences growth of different plant species.

Faculty and senior researchers working in this area:
Daniel Buckley - Timothy Fahey - Christine Goodale - Anthony Hay - Jenny Kao-Kniffin - Johannes Lehmann - Carmen Enid Martinez - Susan Riha - Dawit Solomon - Tammo Steenhuis - Janice Thies - David Wolfe


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. 

Mathematical models of pathogen populations and host-pathogen interaction provide valuable information for growers and policy makers

  • Bill Fry's research group focuses on changes in Phytophthera infestans populations that influence virulence and strategies for disease control. Development and refinement of the BlightPro decision support system (DSS) helps users improve their crop protection strategy.
  • Michael Milgroom's group is is using molecular markers to characterize population structure of powdery mildew fungus on grape. This work is providing insights into patterns of disease spread worldwide.

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