2023 SURF Research Projects - Descriptions

this list will be updated occasionally. check back for new projects.


Sarah Aarons - Assistant Professor, Geoscience Research Division Research Areas: Geochemistry, Polar Science

The Earth’s surface is diverse, with different chemical compositions, mechanisms of formation, and weathering histories. Isotopes in natural substances vary as a result of physical, chemical, and biologic processes, and they can be used as a tool for understanding and interpreting Earth’s history throughout time. The Aarons lab uses isotope compositions of natural materials such as mineral dust, weathering profiles, river sediment and rocks to reconstruct paleo-environmental conditions and more broadly to understand the geochemical evolution of Earth’s surface. Potential SURF student projects for summer of 2021 include laboratory chemistry to understand the role of mineral dust on soil nutrient content and vegetation fertilization, and determining primary mineral phases in dust transported to mountain ecosystems. Previous SURF mentoring: Rain Blankenship (2020) “Preliminary Characterizations of Aeolian Dust Transport to the San Jacinto Mountains.”

Simone Baumann-Pickering - Associate Professor, Marine Physical Laboratory Research Areas: Marine Ecology, Acoustics

The Scripps Acoustic Ecology Lab investigates biological and ecological questions that range from a basic understanding of short and long-term behavioral patterns and geographic distribution of animals, to questions like habitat preference and quality, predator-prey interactions, or adaptations to anthropogenic impacts and a changing environment. A broad range of invertebrates and vertebrates use sound for communication and sensing of their environment. Each ecosystem contains a unique symphony of sounds, a soundscape, that informs us about its species composition, possibly abundance, and together with information about the physical environment leads to the characterization of the ecology and behavior of the species producing and interpreting sound. The group is using active and passive acoustic methods, optics and auxiliary environmental measurements to monitor and understand ecosystem adaptations. Previous SURF mentoring: Alexis Cugini (2018) “Passive acoustic monitoring of odontocetes at the California Current Ecosystem (CCE-1) site,” Chelsea Field (2020) “Evaluation of a Neural Network for Automated Classification of Beaked Whale Echolocation Clicks,” and Kelly Bishop (2020) “Diel Patterns of Bocaccio Rockfish Communication.”

Cathy Constable – Professor, Institute of Geophysics and Planetary Physics. Matti Morzfeld - Associate Professor, Institute of Geophysics and Planetary Physics Research Area: Geophysics, Geomagnetism

The geomagnetic field is generated by movement of liquid iron in Earth’s core 3000 km below our feet and is a fundamental property of our planet. The field shields the surface environment and low-orbiting satellites from solar radiation and also provides a means to probe the structure, dynamics and evolution of otherwise inaccessible regions of the Earth. Constable and Morzfeld are interested in exploring how Earth’s magnetic field has changed in the past, using a combination of paleomagnetic data with statistical and numerical modeling. Current research projects focus on decadal to million-year variations in the geomagnetic field, how quickly the magnetic field can change in time, and how the changing structure of the magnetic field and events like geomagnetic reversals can inform scientists about processes in Earth’s deep interior. Establishing the fastest variations of the field is important for understanding its past evolution and predicting future behavior and has gained much recent interest with new paleomagnetic research suggesting that field variations around 1000 BC and during the last polarity reversal 780,000 years ago were over 100 times faster than changes seen at the present day. However, these observational results have been controversial, in part because it has not been clear what physical process could have caused them. Recent work comparing results from computer simulations with global reconstruction of the geomagnetic field for the past 100 ky reveal rapid changes in both direction and intensity have occurred, but in different locations and at different times. This SURF project will be focused on identifying and understanding geographic variability in these rapid changes and their relation to geomagnetic spikes in intensity and geomagnetic excursions.

Julia Diaz – Assistant Professor, Geoscience Research Division Research Area: Biogeochemistry

The Diaz lab explores how microbes, the ocean’s smallest living inhabitants, interact with their chemical environment to shape the natural world in big ways, including impacts on ecosystem health, natural resources and global climate. We conduct this work using a combination of lab-based experiments with model organisms and field work in diverse ocean settings, from coastal to open ocean environments. Among other projects, the Diaz lab studies how marine microbes obtain the chemical nutrients they need from seawater, such as phosphorus.  One strategy that marine microbes use to deal with low availability of phosphorus is to employ the enzyme alkaline phosphatase, which releases phosphate from dissolved organic matter. This summer, we invite a SURF student to contribute to our research on alkaline phosphatase enzyme activity off the Scripps pier. The project will involve two sampling trips per week to the Scripps pier, followed by immediate analysis of samples using a standard fluorescent enzyme activity assay on a multimode plate reader.  The student will also filter and preserve water samples, analyze data, and present their results at weekly group meetings.

Wenyuan Fan - Assistant Professor, Institute of Geophysics and Planetary Physics Research Area: Seismology

Wenyuan Fan is an observational seismologist. His research program focuses on seismic sources and uses onshore and offshore, dense array seismic observations to investigate earthquakes, slow earthquakes, subduction zone processes, environmental processes, and their interaction and triggering.

Jack Gilbert - Professor, Center for Marine Biotechnology & Biomedicine. Sarah Allard - Assistant Project Scientist. Research Area: Microbial Oceanography.

The Gilbert lab studies the role of microorganisms and environmental and human health. Research in our lab spans 3 major areas: the human microbiome in nutrition, disease, and mental health; microbial ecology of the built environment; and marine microbial ecology in human and environmental health. Our lab is particularly interested in understanding how host-associated microbiomes influence disease ecology and how microbial interactions present opportunities to ameliorate anthropogenic impacts in marine environments. Research work in the Gilbert lab includes hands-on microbiology lab work and computer-based data analysis work, and some occasional field work. The SURF student will work with a graduate student to conduct inoculation experiments evaluating the role of the microbiome in viral infection of oysters exposed to different temperatures.

Sarah Gille – Professor, Physical Oceanography.  Matthew Mazloff - Associate Researcher, Physical Oceanography.  Lynne Talley - Professor, Physical Oceanography. Research Areas: Physical Oceanography, Polar Science.

Multiple Projects:

  • Southern Ocean Eddies:  Lydi Keppler - Postdoctoral Scholar.  The Southern Ocean (around Antarctica) is a key region of carbon dioxide uptake from the atmosphere. In this region, there are also a lot of eddies (swirling currents) that are known to influence the carbon uptake. Thus, a deeper understanding of Southern Ocean eddies will be useful to better understand the effect of eddies on the exchange of carbon between the ocean and the atmosphere and would contribute greatly to our knowledge of the global carbon cycle. The project:  A dataset has been prepared containing eddies in the Southern Ocean, based on data from satellites. Eddies can be cyclonic (clockwise) or anticyclonic (anti-clockwise) and they are labeled as such in the dataset. This rotation direction impacts the eddy influence on the carbon cycle. The student will determine which type of eddy is more prevalent in different regions. If time allows, this analysis can be deepened by doing a similar analysis during different seasons.
  • Estimating ocean mixed layer depth parameters in the California Current System:  Manuel Gutierrez, PhD Student. The ocean mixed layer is the upper part of the ocean where properties such as temperature, salinity and density are uniform. Estimating the depth of this layer is useful for oceanographers because of its importance for understanding ocean circulation, and how ocean temperature and salinity change in time and location. Nonetheless, the mixed layer depth varies depending on the criteria and properties used to define it. In this project, we will estimate the mixed layer depth in the California Current System using various criteria and parameters, such as temperature, salinity and density, and examine seasonal changes using the Massachusetts Institute of Technology global climate model (MITgcm) data. This hands-on project will help the student learn to analyze oceanographic data, and understand fundamental oceanographic principles.
  • DDT distribution in the Santa Monica Basin: DDT+ has been detected in high concentrations in the sediment in most places of the Southern California Bight. One of the biggest challenges in assessing DDT+ exposure in ecosystems comes in understanding how readily contaminants within the sediment can be disturbed and thus how exposure risks can vary over time. The Southern California Bight is characterized by highly intermittent flow patterns, with stable, nearly stationary bottom water undergoing infrequent flushing events that replace bottom water. We have developed a numerical model of the region, and now want to use the model to assess the frequency of "flushing" and the implications for contaminant exposure throughout the region. The project will take advantage of model simulations to examine properties of bottom water and its variability. Time permitting, the project will examine the residence time of bottom water within the basin and pathways by which water is carried out of the basin.
  • Carbon uptake in the Southern Ocean: Ben Taylor, PhD Student. Most of the carbon on earth is stored in the deep ocean; this dissolved carbon escapes to the atmosphere in only a few regions, such as near Antarctica in the Southern Ocean. Meanwhile, these oceans are absorbing some of the atmospheric carbon dioxide emitted by humans, which increases the amount of carbon - and decreases the pH - of the Southern Ocean. To better understand these processes, scientists at SIO have created B-SOSE, an ocean climate model that includes the latest observations of Southern Ocean chemistry. The intern will run existing Matlab scripts to analyze the model's output and help discover what this model is telling us about how currents, rain, snow, sea ice, and phytoplankton growth affect ocean carbon dioxide exchange with the atmosphere.

Paul Jensen - Professor, Center for Marine Biotechnology & Biomedicine Research Area: Marine Natural Products

Research in the Jensen lab addresses fundamental questions about the diversity and distributions of bacteria in the marine environment. These studies frequently target bacteria such as the actinomycetes, which are capable of producing biologically active secondary metabolites. The compounds produced by these bacteria represent an important resource for drug discovery and provide opportunities to explore the functional roles of secondary metabolites in marine systems. Potential projects include 1) culturing marine bacteria and testing to see if they produce new antibiotics or other potential medicines, 2) testing the effects of bacterial natural products on other bacteria to determine if they play a role in chemical defense, and 3) developing new methods for natural product discovery using genome sequence data. Previous SURF mentoring: Allan Somers (2014) "Isolation and Identification of Halogenated organic compounds," Joe Rodriguez (2015) "Examining Secondary Metabolite Expression in the Marine Actinomycete Genus Salinispora," Neha Prasad (2016) "Modulation of secondary metabolite production in Salinispora via co-culturing," Magdalena Lara (2017) “Co-culture of marine bacteria induces increase metabolite production in Salinispora tropica,” Monica Cisneros (2018), and Itzel Lizama Chamu (2019) "The search fo specialized metabolite production by S. pacifica," and Ivan Chavez (2020) “Characterizing new Pseudoalteromonas genomes and their natural product potential.

Deirdre Lyons – Assistant Professor, Marine Biology Research Division Research Area: Developmental Marine Biology

Why are animals shaped the way they are? How can humans, starfish, and squids look and behave so differently, when they all begin as single-celled, fertilized eggs? The Lyons lab is interested in understanding how changes in cellular processes, and their underlying gene regulatory networks, have led to the evolution of diverse animal shapes. Cells are the fundamental units of all biological structures and phenomena—the evolution of novel phenotypes and physiologies is ultimately the result of changes in cellular characteristics, including fate specification. The lab uses marine molluscs (snails, nudibranchs) and echinoderms (sea urchins, sea stars) as model systems, because they have unique, and complementary, advantages for studying the evolution of cell fate and behaviors in a phylogenetic context. A range of techniques are available in these animals such as in vivo-imaging, cell-lineage analysis, gene perturbation, and construction of gene regulatory networks. This summer, some possible student projects include, but are not limited to: 1) Comparison of cell shape, size, and asymmetry between early embryos of sea stars and sea urchins to understand how endoderm and mesoderm cell fates are segregated, and 2) using molecular biology to build fluorescent reported tags to study cell dynamics in vivo. Previous SURF mentoring: Bryant Jew (2017) “Mouth formation in Crepidula fornicate,” Milagros Esmerode (2018) “Shell formation in the marine gastropod, Crepidula fornicate,” and Abegail Bigasin (2020) “Transcriptomic analysis to determine genes involved in the sequestration of nematocysts from Exaiptasia pallida by Berghia stephanieae.”

Center for Western Weather and Water Extremes - CW3 Research Area: Meteorology

The Center for Western Weather and Water Extremes (CW3E, cw3e.ucsd.edu) aims to revolutionize the physical understanding, observations, weather predictions and climate projections of extreme events in Western North America, including atmospheric rivers and the North American summer monsoon as well as their impacts on floods, droughts, hydropower, ecosystems and the economy. The research interests of the group span multiple disciplines, including meteorology from micro- to synoptic scale, hydrology, air-sea interactions, drought, aerosols, machine learning, numerical weather prediction, and data assimilation. This summer, possible student projects include, but are not limited to: 1) evaluating the hydrological, ecological, and/or economic impacts of extreme precipitation on California watersheds, 2) investigating how any number of physical processes (e.g. mesoscale frontal waves, teleconnections) and/or climate change modulate atmospheric river intensity and duration, and 3) statistical and/or case study based analyses using observational datasets collected by CW3E and CA DWR to support research goals. Students working in the CW3E will be paired with an additional senior and junior researcher from the center for enhanced mentoring and project guidance.

Lynn RussellProfessor of Climate and Atmospheric Sciences Research Area: Atmospheric Chemistry

Russell is interested in aerosol chemistry and physics, aerosol-cloud interactions, air-sea exchange, organic aerosols, and atmospheric nanoparticles. Her work focuses on the role of atmospheric aerosols in climate. Two proposed summer projects are 1) Organic functional groups in atmospheric aerosol particles and 2) Atmospheric aerosol composition at Pismo Beach. Students will be trained in sample preparation, analysis, and collection of atmospheric aerosols and will have the opportunity to study the chemical composition of atmospheric aerosols, learn about the impacts of aerosol particles on climate and air quality. Previous SURF mentoring: Grace Wiessner (2012) “Organic composition of atomized seawater from the eastern Pacific during EPEACE 2011,” Emily Kraemer (2014) “Comparison of aerosol composition relative to clouds events on Mt. Soledad determined by HR-ToF-AMS,” Jeramy Dedrick (2017) “Analyzing hydroscopic particle growth of West Antarctic Boundary Layer aerosols,” Joanne Chung (2018) “Particle budget and chemical comparison of seabird guano aerosol during different campaigns,” and Nicole Posadas (2019) "Quantifying organic functional group composition of aerosol particles from Pismo Beach, CA."

Brice Semmens – Associate Professor, Marine Biology Research Division Research Area: Marine Ecology

The Semmens Lab focuses on applied questions in marine ecology, conservation biology, and fisheries management. Our approaches to these questions are varied and typically involve fieldwork, labwork, and modeling. The lab has particular strength in quantitative theory and tools, including mark-recapture analysis, stable isotope mixing models, stock assessment, and time series analysis. Possible projects include (1) Advancing Bayesian stable isotope mixing models used in trophic ecology (2) Using genetics and stable isotopes to investigate the recovery of a Nassau grouper spawning aggregation and (3) Estimating movement patterns, population abundance, and mortality of coastal marine fishes (acoustic telemetry, mark/recapture models). Previous SURF mentoring: Bethany Fowler (2015) "Passive Acoustic Monitoring of Grouper in the Cayman Islands," Jarvon Stout (2015) "Fingerprinting Fish: Computer- aided pattern matching of the Nassau grouper Epinephelus striatus," Lauren Arnold (2016) "Identification of Nassau grouper eggs in the plankton: is size a valid metric?" Brian Cohn (2016) "Using in-situ length data to test a data-poor stock assessment model and asses stock status of protected aggregating fish species Epinephelus striatus," Kayla Martinez-Soto (2017) “Egg morphometrics and fertilization rates from recovering and unexploited populations: Nassau Grouper and Tiger Grouper in the Cayman Islands,” Mary Cozy (2018) “Assessing the effectiveness of the facial recognition software, i3s, on the Nassau Grouper (Epinephelus striatus),” Joe Molina (2018) “Estimating the effort required for generating a photographic database on Nassau grouper (Epinephelus striatus): recommendations for potential mark and recapture studies,” and Youssef Dous (2019) "A small foray into the realm of giants: Investigating the movement ecology of Giant Sea Bass (Stereolepis gigas)," and Charles Hendrickson (2020) “Using Diver Operated Stereo-Video to Assess Nassau Grouper (Epinephelus striatus) Spawning Aggregation Demographics.

Maria Vernet – Researcher, Integrative Oceanography Division Research Areas: Marine Ecology, Polar Science. Tammy Russell - PhD Candidate, Oceanography. 

The Vernet Lab studies polar phytoplankton ecology and long-term changes in marine ecosystems (see https://polar.center/vernet-lab/). This summer there is an opportunity for a student to learn exciting lab techniques while contributing to our research on microplastics in the Antarctic food web and locally here in San Diego. Project tasks would include working closely with graduate student Tammy Russell, to process our collected Antarctic penguin-derived samples, and/or samples collected from local seabirds, for microplastic abundance. Potential projects include investigating trends in plastic type, by species of bird, or comparing results to previous research. There is no previous lab experience necessary. The participant will be trained in current microplastic extraction methods and coding in R programming. Previous SURF mentoring: Karina Halliman (2020) "Using Ecosystem Modelling to Explore Microplastic Pathways Through the Antarctic Peninsula Food Web."