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Fundamental Research Projects

Basic research into the biology of plants, cyanobacteria, and algae. Projects include:

  • Modeling photosynthesis in dynamic environments
  • Resistance against pathogens, herbivores and environmental stress
  • Cell organization and metabolism


Characterization and disruption of bacterial microcompartment shells from human pathogens – National Institutes of Health (Kerfeld lab)

Many pathogenic bacteria contain bacterial microcompartments that confer a metabolic advantage to the pathogen. This project investigates the permeability of BMC shells to metabolites; understanding these principles may lead to the development of therapeutic strategies that disrupt the BMC-based competitive advantage. Read more.


Discovery of the mechanisms enabling the dynamic architecture of the plant ER – National Science Foundation (Brandizzi lab)

The major goal of this project is to identify and characterize genes that control the morphological integrity of the plant endoplasmic reticulum, which exhibits unique features to suit the intracellular dynamics of plant cells. Read more.


Illuminating Emergent Microbial Interactions via Modular Synthetic Consortia (Ducat Lab)

Microbial communities contribute a broad range of important functions towards human health, ecology and biotechnology (e.g., gut or soil microbiomes). Natural microbial consortia contain hundreds to thousands of different species, many of which may have limited prior research. The large number of microbial partners and the complexity of signaling networks between them can make natural consortia difficult to study. This research proposes a “bottom-up” strategy to learn about more complicated consortia through the design and engineering of simple 2-species communities. Specifically the research uses a cyanobacterium that has been modified to use light and CO2 to produce simple sugars that are secreted. We have shown that these cyanobacterial sugars can support the metabolism and growth of a variety of different heterotrophic microbes in a modular or “plug-and-play” fashion. Cyanobacteria have evolved natural symbiotic relationships that are partially analogous to these artificial communities – most famously the plant chloroplast and in lichens. The research activities funded by this Award will increase knowledge of interaction dynamics in microbial communities, potentially improve the ability to engineer microbial consortia and provide insight into the evolution of natural microbial symbioses. Read more.


Molecular mechanisms governing the cytoskeleton-mediated motility and distribution of peroxisomes and mitochondria in plants – National Science Foundation (Hu lab)

Organelle proliferation and motility are critical for healthy plant growth. We often envision plant cells as the classic textbook cartoon: Static organelles, spaced indiscriminately in the cytoplasm within the confines of rigid cell walls. However, organelles are highly dynamic and mobile, subject not only to cytoplasmic streaming but also targeted motility along the cytoskeleton by molecular motors. Peroxisomes, mitochondria and chloroplasts work in concert to carry out metabolic processes like photorespiration and fatty acid metabolism, which may require relocation to facilitate the proximity required for inter-organelle communication. The mechanisms governing organelle recruitment of myosin motors and association with actin filaments, as well as the conditions that trigger intracellular transport, remain unclear. An NSF-funded project in the Hu Lab aims to uncover these elusive mechanisms, with an emphasis on peroxisomes and mitochondria. We are characterizing several candidate genes predicted to be involved in organelle dynamics, distribution and motility. We use fluorescent markers and confocal microscopy to track and quantify peroxisomal and mitochondrial movement in relevant genetic mutants and under various stress and developmental conditions. By uncovering the mechanisms of organelle dynamics in plants, we can better understand the impact on plant growth and resilience. Read more.


ProteoCell – National Science Foundation (Kerfeld lab)

This multidisciplinary project seeks to build functional, lipid-free, ‘living’ cells by using proteins to create multi-compartment ‘ProteoCells’ that can self-generate, house reactions to produce products, interact with other ProteoCells, and in total, define a new type of cell-like structure with fundamentally novel properties. It remains unclear why nature chose to use lipids as its hallmark compartment-formers, and how compartmentalization enables a complex ‘soup’ of biological molecules to function as an autonomous and self-sustainable unit. This project addresses these questions by using engineering principles to design new protein synthesis reactions, new compartment-forming proteins and new protein catalysts, and by studying how these ‘designer’ protein molecules interact with one another to create collective cell-like units. Read more.


Unfolded Protein Response in the Model Plant Species Arabidopsis thaliana – National Institutes of Health (Brandizzi lab)

This project focuses on largely unexplored mechanisms that multicellular eukaryotes have evolved to grow and protect themselves from death and diseases caused by insufficiency and defects in secretory protein synthesis in the model plant species Arabidopsis thaliana. Read more.