Krishna Niyogi, Professor

Closed (1) Efficient photosynthesis is essential for productive food crops.

Applications for fall 2021 are now closed for this project.

Natural light is highly dynamic and often in excess, resulting in damage to pigments, proteins, and lipids within the chloroplast. To cope with saturating light, plants dissipate excess energy through a process called non-photochemical quenching (NPQ). Our lab and collaborators have shown that if we modulate the kinetics of NPQ we can increase growth in the field-grown model crop Nicotiana tabacum by 15%. Given this success, the Niyogi lab is interested in improving the recovery of slowly-relaxing photoinhibitory quenching – caused by high light damage to core photosynthetic machinery and subsequent reduction in CO2 assimilation. However, the mechanisms underlying photoinhibition are poorly understood. First-time undergraduate researchers will work alongside a graduate student to identify and characterize genes involved in NPQ and photoinhibition.

In saturating light, photosynthetic light harvesting is regulated by nonphotochemical quenching (NPQ) processes that dissipate excess absorbed light energy as heat. Our goal is to elucidate the molecular mechanism(s) and physiological importance of NPQ in different organisms. We are currently investigating NPQ in various microalgae using a combination of genetics, CRISPR/Cas9-mediated genome editing, biochemistry, and spectroscopy.



Motivated undergraduates will be involved in screening transgenic Nicotiana tabacum and Nicotiana benthamiana lines for differences in photosynthetic capacity and high-light tolerance. Mentees will learn and apply 1) PCR for cloning and genotyping, 2) Analysis of photosynthetic efficiency by chlorophyll fluorescence and gas exchange, 3) protein analysis techniques such as SDS-PAGE and western blotting, and 4) biochemical assays for in vitro investigation of photosynthetic complex structure and function. Additional biochemical techniques, as well as opportunities for independent research projects, may also be incorporated based on mentee interest and as the project develops.


Qualifications: Minimum qualifications: Biology 1A or 1B (may be taken concurrently), 3.0 GPA, and interest in genetics. Hours are negotiable, but a commitment of at least 12 hours per week is expected.

Weekly Hours: 12 or more hours

Related website: https://plantandmicrobiology.berkeley.edu/profile/niyogi#profile-main

Closed (2) Expanding the Molecular Toolbox for a Biomineralizing Microalgal Model System

Applications for fall 2021 are now closed for this project.

Hierarchically organized biominerals are characteristic of many aquatic microeukaryotes. Marine diatoms are single-celled microalgae responsible for ~20% of planetary primary production. A hallmark feature of diatom biology is their exquisitely shaped biosilica cell wall. Despite much progress in deciphering the molecular and cellular mechanisms of this vesicle-based, sunlight-driven biomineralization pathway, knowledge gaps remain. Studying biosilica morphogenesis in these environmentally ubiquitous organisms is advancing our understanding of global nutrient cycles and inspiring nanotechnology and biomaterials science research. Undergraduate researchers will work alongside a postdoctoral scientist with diatom biology expertise to design, build, and test novel protein expression vectors for genetic engineering of Thalassiosira pseudonana, a model marine diatom. This work will expand the potential of this relatively nascent microalgal model system for basic biology discoveries and biotechnology advances.

The primary project will involve characterizing a set of constitutive and inducible promoters in Thalassiosira pseudonana. Fluorescent proteins alone and as translational fusions with known and predicted biosilica-localized proteins will be delivered to Thalassiosira pseudonana using bacterial conjugation. The resulting diatom strains will be screened for fluorescence. Mentees will have the opportunity to learn about all aspects of diatom biology, biomineralization, and synthetic biology research. They will apply (1) polymerase chain reaction (PCR) for molecular cloning and genotyping, (2) Escherichia coli engineering to prepare conjugation donors, (3) bacterial conjugation to transform Thalassiosira pseudonana, and (4) fluorescence microscopy to characterize engineered diatom strains. Students will be encouraged to think beyond their immediate work and come up with ideas for future (independent) projects. Thus, the outlined aims may evolve depending on students’ interests and project progress.

Qualifications: Interest in at least one, ideally more, of the following: (marine) microbiology, unconventional (microbial) model systems, natural materials, molecular, cell, and synthetic biology. Hours are negotiable, but a commitment of at least 12 hours per week is expected. Minimum qualifications: Biology 1A or 1B (may be taken concurrently), 3.0 GPA, and interest in genetics. Hours are negotiable, but a commitment of at least 12 hours per week is expected.

Weekly Hours: 12 or more hours

Related website: https://plantandmicrobiology.berkeley.edu/profile/niyogi#profile-main

Closed (3) Photosynthesis is a fundamental process to the productive growth of plants and algae.

Applications for fall 2021 are now closed for this project.

Light in natural environments is often fluctuating and photosynthesis is optimized to be maximally productive in shade. In saturating light, green organisms must dissipate excess energy by a process called non-photochemical quenching (NPQ) to prevent damage to delicate photosynthetic tissues. However, the transition between photosynthesis and NPQ is not optimized in crops and the strategies to deploy NPQ differ between species. Undergraduate researchers will work alongside a graduate student to create genetic constructs from diverse organisms to express NPQ-related genes from algae and moss into model flowering plants.


This project will involve molecular cloning to generate constructs for expression of NPQ genes from algae and moss into Nicotiana benthamiana plants and measuring the transiently expressed genes’ effect on N. benthamiana NPQ. Mentees will learn and apply: 1) Golden Gate cloning and E. coli transformations, 2) PCR and Sanger sequencing, including primer design and sequence analysis, 3) agrobacterium-based transient expression assays in N. benthamiana, and 4) analysis of non-photochemical quenching efficiency by chlorophyll fluorescence. Additional biochemical techniques, as well as opportunities for independent research projects, may also be incorporated based on mentee interest.

Qualifications: Minimum qualifications: Biology 1A or 1B (may be taken concurrently), 3.0 GPA, and interest in genetics. Hours are negotiable, but a commitment of at least 12 hours per week is expected.

Weekly Hours: 12 or more hours

Related website: https://plantandmicrobiology.berkeley.edu/profile/niyogi#profile-main

Closed (4) Photosynthetic organisms as a promising sources for sustainable solutions to meet the growing global needs for energy and products.

Applications for fall 2021 are now closed for this project.

Microalgae utilize solar energy, consume CO2,can be cultivated on non-arable land and grow quickly. Algae can reveal new biological insights for more cost-effective biofuel andbioproduct opportunities, particularly when combined with bioengineering to reroute metabolism towardbioproducts for energy, food or pharmaceuticals. The unicellular green algae Chromochloris zofingiensis and Auxenochlorella protothecoides have strong economic potential because they are amongstthe highest producers of triacylglycerols (TAG), the preferred precursor for biofuels. Moreover, in
C.zofingiensis high accumulation of TAG can be paired with amassing large amounts of the commerciallyvaluable antioxidant astaxanthin and increasing biomass. In this project, we will identify and distinguish keymolecular pathways, metabolites, and regulatory factors involved in carbon utilization and thereby,redirecting the carbon flux towards AG/astaxanthin production. First-time undergraduate researchers will workalongside a postdoctoral student to identify and characterize various signaling pathways regulating TAG production.


The primary project will involve a understanding signaling pathways using biochemical and physiological assays.Mentees will learn to do techniques such as 1) Protein analysis techniques such as SDS-PAGE and western blotting, 2)various assays to monitor TAG and astaxanthin accumulation such as TLC, HPLC etc, and 3) Analysis ofphotosynthetic efficiency by chlorophyll fluorescence. Additional biochemical techniques, as well as opportunities forindependent research projects, may also be incorporated based on mentee interest and as the project develops.

Qualifications: Minimum qualifications: Biology 1A or 1B (may be taken concurrently), 3.0 GPA, and interest in genetics. Hours are negotiable, but a commitment of at least 12 hours per week is expected.

Weekly Hours: 12 or more hours

Related website: https://plantandmicrobiology.berkeley.edu/profile/niyogi#profile-main