Summer Experiences - Scripps Institution of Oceanography
TIER 2 SUMMER RESEARCH PROGRAM
Aynchronous, 6/22-6/26; In Person, 7/6-7/24
Have you ever imagined designing your own research project, exploring new scientific questions, and presenting your findings? Our Tier 2 summer residential course offers select students the opportunity to engage in hands-on, cutting-edge research at the Scripps Institution of Oceanography. Students will be matched with research themes that align with their interests. Each research theme will be guided by experts in the field, providing students with mentorship and insight from professionals who specialize in their chosen area of study. For students interested in pursuing marine science as a career, this course offers a valuable head start, giving them practical experience and a deeper understanding of what it means to be a researcher in the field of marine science.
2026 Research Themes
Sonya Timko
Christian Johnson
Nicole Yen
Dr. Ariel Rabines
📷🦀Monitoring Coastal Ecosystems: Using Thermal Imaging to Assess Climate Change Impacts
Coastal ecosystems such as wetlands are highly accessible and ecologically rich environments, offering significant commercial, recreational, and educational value. However, they are increasingly vulnerable to climate-driven threats such as rising temperatures, sea-level rise, invasive species, and pollution. As global climate change intensifies, effective monitoring of these ecosystems becomes essential for understanding and mitigating its impacts.
Thermal imaging cameras, which detect infrared radiation emitted by warm objects, are now widely used in ecology to study temperature variability and identify heat stress in marine organisms. In addition to imaging, students can also assess heat stress by measuring changes in metabolic rate (e.g., oxygen consumption), respiration, behavior, and fluorescence —such as altered movement, feeding patterns, or habitat use. Together, these indicators help reveal how organisms respond to thermal extremes. Students will be working within our UC Reserves System and present their final posters at an informal poster session with our partners, at Birch Aquarium.
🐟🧬Field Genomics for Ocean Health: Exploring Marine Biodiversity with eDNA
Students in our Field Genomics for Ocean Health Research Pathway will play a pioneering role in biomonitoring efforts across San Diego by utilizing environmental DNA (eDNA), a non-invasive method that detects genetic material shed by marine organisms into the water, to better understand both ecosystem and human health. By collecting and comparing samples from three distinct coastal environments 1) La Jolla Cove, a high marine mammal–use site with resident sea lions and seals; 2) Dike Rock Tide Pools, a dynamic rocky intertidal ecosystem; and 3) Scripps Pier, representing a more open coastal and ocean-influenced site—students will investigate how biological communities shift across habitats and how varying levels of wildlife presence and human activity shape microbial and eukaryotic biodiversity.
Students will assess ecosystem health at the community level using both conventional field techniques, such as water quality testing and quadrat sampling, and cutting-edge molecular biomonitoring tools, including metabarcoding and shotgun sequencing, leveraging portable nanopore technology for real-time genomic analysis. Working within the UC Natural Reserve System and alongside leading researchers, students will develop their own research questions and explore how eDNA can be applied to pressing issues such as pollution, climate change, biodiversity loss, and public health challenges. Through this hands-on experience, they will generate and interpret real-world genomic data and present their findings in an informal poster session with program partners at Birch Aquarium, positioning themselves not only as learners of ocean science but as active contributors to understanding and protecting coastal ecosystems.
PAST SUMMER RESEARCH PROJECTS
Global biodiversity is declining faster than ever from direct consequences of climate change. The rocky intertidal is one of the most accessible marine coastal environments teeming with an incredibly diverse living community. Because of this unique quality it has immense commercial, recreational, and educational value to communities worldwide. However, this quality also makes these habitats highly susceptible to changing ocean conditions such as sea-level rise, invasive species, and pollution. Monitoring intertidal ecosystems becomes increasingly important as we continue to see global climate changes.
Thermal imaging cameras record infrared radiation (IR) and convert it to a visible image. The primary source of IR is heat or thermal radiation – the warmer something is, the more infrared radiation it emits. Infrared thermography (IRT) is being increasingly utilized by ecologists and physiologists to observe and investigate small-scale thermal variability and thermal stress on the distribution and abundance of marine species.
Students explore how heat transfers between organisms and their environment using a FLIR thermal camera at various marine ecosystems in San Diego (rocky intertidal, sandy seashore, salt marsh). We will relate our data to organismal anatomy, physiology, thermoregulation, species adaptability, ecology, and/or climate change.
Project Lead: Sonya Timko (MS, PhD Student)
Publications: Bravo, M., C.B. Cracamontes, S. Foss, N. Gottlieb, L. Kelly, E. Li, M. Liskov, L. Maschler, P. Randolf, A. Ringler, S. Timko., and N.K. Yen. 2023. Climate Change and its Implications on the Heat Flux of Rocky Intertidal Organisms. Research Scholars Marine Science Journal, 1(1).
Overfishing has become one of the most significant drivers in the decline of wild fish populations – this compounded with climate-related threats will have potentially detrimental effects on marine ecosystems worldwide. Global fisheries provide a vital economy for many communities, especially in developing nations. The goal of fisheries management is to provide sustainable resources with social, economic, and biological benefits. However, even with well managed fisheries many unreported, illegal, and mislabeled catches threaten the effectiveness of conservation practices.
Seafood is an important protein source worldwide and thus susceptible to a variety of fraudulent practices. Seafood mislabeling is surprisingly common in both domestic and international markets and has long been a known problem worldwide; however difficult to regulate. Past studies using DNA barcoding have reported alarmingly high rates of mislabeling. We are part of a long-term monitoring project of seafood fraud in San Diego Region.
Project Lead: Nicole Yen (MS, MAT); Advisors: Sarah Mesnick (PhD), Mar Mancha-Cisneros (PhD)
Project 1: As climate change and pollution drive changes to the chemical properties of the ocean, the activity of enzymes responsible for the functioning of countless cellular processes are being affected. In the research experience, students will generate their own research question to investigate the impact of environmental changes on bioluminescence. To accomplish this we will focus specifically on the chemical and molecular mechanisms that govern bioluminescence. We will be isolating the genes associated with bioluminescence from Aliivibrio fischeri and transforming them into a model organism, Escherichia coli, to specifically study the enzyme luciferase and the supporting genes needed to express a functional enzyme. Students will then generate their own hypothesis on how changes to the environments where host organisms of A. fischeri live, such as the Hawaiian bobtail squid, could change the catalytic ability of luciferin.
Project 2: As climate change and pollution alter ocean chemistry, they impact enzymes crucial for cellular processes. In this research experience, students will explore how environmental changes affect fluorescence, focusing on the GFP (Green Fluorescent Protein) from the bioluminescent jellyfish Aequorea victoria. Using the pGLO plasmid, students will transform bacteria to express GFP, causing them to glow green under UV light. Students will investigate the process of DNA > RNA > Protein > Trait and examine how internal and external factors influence gene regulation. They will also hypothesize how environmental changes could affect the expression and activity of fluorescence in marine organisms with GFP-like proteins.
Project Lead: Marc Piercy (PhD)
STUDENT RESEARCH ARTICLES
Xu, C, M. Piercy, S. Timko and N.K. Yen. 2026. Aluminum and its Impacts on the Bioluminescence of Aliivibrio fischeri. Research Scholars Marine Science Journal 1(3): 1-5.
Chiu, O., M. Cho, Z. Lai, T. Schiff, A. Suh, E. Tomala, M. Piercy, and N.K. Yen. 2025. Changing Ocean Conditions and it’s Impacts on Bioluminescent Bacteria, A. fischeri. Research Scholars Marine Science Journal 1(2): 1-12.
Bravo, M., C.B. Cracamontes, S. Foss, N. Gottlieb, L. Kelly, E. Li, M. Liskov, L. Maschler, P. Randolf, A. Ringler, S. Timko., and N.K. Yen. 2023. Climate Change and its Implications on the Heat Flux of Rocky Intertidal Organisms. Research Scholars Marine Science Journal, 1(1): 1-11.
STUDENT RESEARCH POSTERS
Summer 2025
Biomonitoring using eDNA
Summer 2025
Fluorescence and the Environment
Summer 2025
Life on the Edge
Summer 2024
Basis of Bioluminescence and the Environment
Summer 2024
Life on the Edge
Summer 2023
Life on the Edge
Spring 2023
Seafood Fraud Detectives
Summer 2022
Life on the Edge
MEDIA
