Simone Baumann-Pickering - Assistant Researcher, Marine Physical Laboratory
The Scripps Acoustic Ecology Lab, under the lead of Simone Baumann-Pickering, investigates phenological patterns and spatial ecology of pelagic nekton, interactions of predators and prey, and adaptations of animals to natural and anthropogenic changes in the environment. We are mostly using acoustical and sometimes environmental sampling technologies for our research. Specific summer research topics range from 1) Soundscape analysis in the Southern California Bight; 2) Towed array analysis: cetaceans encountered during CalCOFI; 3) Cetaceans on long-term acoustic data in the central Pacific.
Jeff Bowman - Assistant Professor, Integrative Oceanography Division
The Bowman Lab explores many aspects of marine microbial ecology. We use sequence data (RNA and DNA) to assess the structure and function of marine microbial communities, flow cytometry and other approaches to describe microbial physiology, and models to tie it all together. Much of our work is focused on understanding the flow of carbon and energy through marine ecosystems in the Arctic and Antarctic. The dynamic microbial communities that occupy these ecosystems are particularly vulnerable to climate change, and poorly studied due to logistical challenges. Available projects include (1) isolating, culturing, and characterizing marine phytoplankton to develop appropriate model systems needed to expand our culture collection of ecologically significant phytoplankton. (2) a bioinformatics project to validate a new approach to 16S rRNA gene phylotyping to describe bacterial and archaeal communities and (3) predicting harmful algal bloom (HAB) species using a long-term time series of HAB forming phytoplankton and environmental parameters is available from the Scripps Pier sampling program and the application of machine-learning algorithms. This project will provide an opportunity to learn or improve skills in linear modeling and give an introduction to emergent self-organizing maps (a class of machine learning algorithms). No prior experience with programming language R is necessary, however, some familiarity with statistics will be helpful. Previous SURF mentoring: Tia Rabsatt (2017) “The effects of eelgrass on the abundance of marine microorganisms in San Diego Bay, CA.”
The Deheyn laboratory develops research in the field of biomimicry that spans topics such as biochemical characterization and identification of light producing compounds (occurring through bioluminescence and fluorescence), environmental health assessment (ecotoxicology), and the biology and ecology of light production in invertebrates. Two potential projects are (1) investigating light production in organisms to identify and characterize the processes, actors and co-factors of new biochemical reactions and (2) assessing bioavailability and sub-lethal toxicity of certain contaminants, especially under varying conditions from global climate change and (3) characterize biomaterials for engineering mimics. Previous SURF mentoring: Carolyn Mosley (2011) “Effects of copper on the correlation between Acropora yongei coral fluorescence and health”, Coleman Ewell (2012) “Coloration in nudibranchs: Navanax inermis”, Darrin Schultz (2012) “Ferrous iron's role in the bioluminescence of Chartopterus variopedatus”, Torrin McDonald (2013) “Evidence of reflective proteins associated with iridescence in various species of nudibranchs”, Ahiram Rodriguez (2013) “The effects of multiple chemical reagents on the light production of the bioluminescent Chaetopterus mucus”, Isabel Herrera (2014) "Reflectin proteins in nudibranch species", Franco Migliolo (2014) "Relationship between redox potential and light production in the mucus of the marine tubeworm Chaetopterus sp.” Noah Hamlish (2015) "Functional characterization of a new ferritin from the polychaete Chaetopterus sp.", Xochitl Clare (2016) “Effect of ocean acidification on the capacity of light production from the brittlestar Amphipholis squamata” and Isaiah Klimek (2017) “Characterizing the biochemistry of bioluminescence in the deep sea octocoral Umbellula magniflora.”
Jeff Gee – Professor, Geoscience Research Division
Gee’s research focuses on the use of magnetic data, both remotely sensed magnetic anomaly data and the magnetization of rock samples, to understand a variety of geological problems. He uses the magnetic record in geological samples to study topics ranging from the formation of new crust at oceanic spreading centers to the processes of melt redistribution and cooling in large magma chambers. One possible project for 2017 would involve samples and magnetic anomaly data from a tectonic exposure of the lower oceanic collected during a cruise to Pito Deep in early 2017 (https://www.pitodeep.org/). The exposures span two reversals of the earth’s magnetic field and the goal is to use the magnetic signature of these reversals to understanding cooling of the lower oceanic crust. A second potential project would use samples from a 1.43 billion-year-old intrusion to construct a time series of geomagnetic field variations in the Precambrian. Previous SURF mentoring: Zoe Burns (2017) “Toward constructing a time series of geomagnetic field variations from thermal remanence in slowly cooled igneous rocks” and Michelle Gess (2017) “Magnetic constraints on the formation of fast-spread lower oceanic crust at Pito Deep.”
Gille's research interests focus on the Southern Ocean and global satellite oceanography. The student project could be related to the Southern Ocean Carbon and Climate Observations and Modeling project (http://soccom.princeton.edu/), which is a major multi-institutional effort deploying biogeochemical sensors on profiling floats throughout the Southern Ocean. The student project will focus on analyzing physical and biogeochemical processes in the Southern Ocean using profiling float data and output from the Southern Ocean State Estimate. Key science questions relate to upper-ocean processes and exchanges of heat, momentum, and CO2 across the air-sea interface. The student will have the opportunity to work as part of the SOCCOM team at Scripps, with guidance from several members of the team. Other potential student projects could include research in preparation for the Surface Water and Ocean Topography (SWOT) satellite mission due to launch in 2021. Previous SURF mentoring: Angelica Gilroy (2011) “Oceanic heat sources near Pine Island Glacier”, Matthew Hurley (2014) "Spatial and Temporal Variability of the Upper Ocean in the Drake Passage", Anna Simpson (2015) "Remineralization ratios in the Antarctic Circumpolar Current using profiling float data", Phoebe Thompson (2016; co-mentored) “The seasonal cycle of macronutrients and net community production in the Southern Ocean”, Francisco Spaulding-Astudillo (2016, co-mentored) “The role of polynyas in ice export of Ross Sea”, Casey Brayton (2017, co-mentored) “Understanding preconditioning of the Maud Rise Polynya” and Maya Chung (2017, co-mentored) “Variability of ice production in the Ross Sea in 2006-2010 and its relationship to the Amundsen Sea Low.”
Research in the Grassian Lab aims to understand the atmospheric chemistry and global impacts of atmospheric aerosols. For example, it has become increasingly clear that all kinds of particles - including ice, sea spray and mineral dust - are present in the Earth's atmosphere and that the surfaces of these particles play a role in the chemistry of the atmosphere. The ozone hole is one example of how heterogeneous chemistry involving chlorine-reservoir species on ice particles can decrease ozone levels in the stratosphere. In the troposphere, the region closest to the Earth's surface, there are many more particles and the heterogeneous chemistry of these particles with trace gases such as nitrogen oxides, ozone and volatile organics is not well understood. In the Grassian research group, we are using a combination of spectroscopy, microscopy and particle analysis to gain a detailed molecular level understanding of these reactions. Reaction rate data measured in our laboratory are currently being incorporated into global chemistry models. We are also trying to understand how the particles can impact other global processes besides the chemical balance of the atmosphere. These processes include climate, biogeochemical cycles, ocean-atmosphere exchange and human health. Previous SURF mentoring: Meagan Marciano (2016) “Phase transitions of biologically-derived components in sea spray aerosols” and Jimmy Ge (2017) “Analysis of atmospherically relevant glyoxal reactions using Raman spectroscopy techniques.”
Jade d'Alpoim Guedes – Assistant Professor, Geoscience Research Division
Research in the Guedes lab aims to understand how humans adapted their agricultural regimes during episodes of climatic change. Her research group uses modeling to translate paleoclimate records into spatialized models of crop performance and uses archaeobotanical data derived from archaeological sites to examine how humans responded to these strategies. Possible projects for summer research include using wood charcoal data to understand changing forest composition around sites in Israel, China and Pakistan and using weed seed data to reconstruct ecology and steppe composition surrounding these sites.
Haase's research focuses on remote sensing of the atmosphere to improve forecasting of storms and advance understanding of the role moisture plays in the weather and climate system. She develops new methods of remote sensing using GPS signals recorded from airborne platforms. Current projects Haase's group is working on include studies of atmosphere-ocean-sea ice coupling in the Antarctic and Arctic regions, improving hurricane forecasting using airborne GPS radio occultation observations, and studying transport of moisture in atmospheric rivers bringing precipitation to California and the north American monsoon bringing precipitation to the southwestern US. She also collaborates with other researchers on the use of high rate precise GPS positioning for measuring earthquake ground motions. Possible undergraduate research projects are 1) intercomparisons of atmospheric measurements made by different Earth observation satellites or 2) visualization of weather model output in the regions of interest to the group. A new collaborative project with Universities in Mexico means Spanish-speaking students are being actively recruited. Previous SURF mentoring: Kelsey Malloy (2015), "February 6th, 2015, Case Study of Atmospheric River Event" and Samuel Kekuewa (2016), “GPS observations of the North American Monsoon.”
Ryan Hechinger - Associate Professor, Marine Biology Research Division
The research in the Hechinger lab seeks to better understand parasites and how they fit into ecological, evolutionary, and behavioral science. For Summer 2018, we can involve a SURF student or two on a project involving soldier worms. That's right: soldier worms. Trematode parasitic worms form colonies that live in snail bodies, and several marine trematode species have a specialized caste of worms that attack invaders and defend the parasite colony. We are studying how trematode colonies and caste structure develop and respond to enemies.
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" and Magdalena Lara (2017) “Co-culture of marine bacteria induces increase metabolite production in Salinispora tropica.”
Levin and her students are interested in ecology of wetland, coastal and deep- sea benthic ecosystems. Current research focuses on the ecology of animals in chemosynthetic ecosystems (methane seeps) off Costa Rica, and their interaction with the surrounding deep sea. Unusual invertebrates, strange bacteria and basic principles of biodiversity and ecosystem function combine to reveal how methane seepage controls life at the sea floor. Additional research explores the effects of low oxygen on vision in marine animals, and the use of natural treatment systems to clean stormwater. Previous SURF mentoring: Anai Novoa (2011) “Effects of ocean acidification on the growth and survival of sea urchin Strongylocentrotus Purpuratuslarvae”, Milinda Thompson (2011), “A buyer's guide to deep-sea homes: analysis of community composition on substrates at hydrothermal vents”, Jesse Andrews (2012) “Dissolved oxygen, temperature, and pH effects on benthic mobile organisms along the continental shelf in the Southern California Bight”, Blanka Lederer (2012) “Macrofaunal colonization of wood substrates at hydrate ridge methane seeps”; Travonya Kenly (2013) “Size at Settlement of Mytilis californianus and Mytilis galloprovincialis"; Kieu Tran (2014)“Biogeographic shifts and species density of echinoid (sea urchin) species along the Southern California Bight assessed using GIS”; Aissa Yazzie (2014), "Using stable isotope analysis to access cross-slope trophic patterns in benthic and demersal fish communities in an upwelling region”; Jackson Powell (2015) "Testing the feasibility of S. fragilis as a potential, climate change tolerant fishery through measurement of gonad color and texture characteristics”, Onyeweenu Ogene (2016) “Changes in deep-sea community composition with environmental conditions" and Zandria Acosta (2016) “Biological communities associated with biofilters in Los Angeles" and Jaxine Wolfe (2017) “Temporal dynamics of a demersal fish community residing within an oxygen limiting zone of the Southern California Bight.”
The Lubin research group studies fundamental physics processes that govern terrestrial climate change, with emphasis on observations and particular emphasis on the Earth's polar regions. The student project this summer will focus on data analyses related to US Department of Energy Atmospheric Radiation Measurement Program (ARM) West Antarctic Radiation Experiment (AWARE; https://scripps.ucsd.edu/expeditions/aware). This project will analyze atmospheric and remote sensing data collected in Antarctica using US Department of ARM instruments deployed on Ross Island and in West Antarctica. The student will work with data from instruments such as Micropulse Lidar, scanning and Doppler cloud radars, spectroradiometers, pyranometers, pyrgeometers, and rawinsondes to investigate the surface energy balance at the Antarctic ice sheet surface as it relates to climate warming. Special emphasis is placed on the properties and role of clouds in the lower atmosphere. Prior experience with Matlab, IDL, or other programming is desirable. Previous SURF mentoring: Alexis Wilson (2016) “West Antarctica as a Natural Laboratory for Single- and Mixed-Phase Cloud Microphysics” and Caitlin Glennon (2017) “Influence of meteorological regimes on cloud microphysics over Ross Island, Antarctica.”
Dierdre Lyons – Assistant Professor, Marine Biology Research Division
The Lyons lab is interested in understanding how changes in cellular processes, and their underlying gene regulatory networks, have led to diverse animal morphologies. 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 snails and echinoderms (sea urchins, sand dollars) 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. Some possible student projects include: 1) Live-imaging of shell gland formation in snails, and gene expression analysis of biomineralization genes and 2) Studying the role of matrix-metalloproteinases and their inhibitors in neural development of sea urchin larvae. Previous SURF mentoring: Bryant Jew (2017) “Mouth formation in Crepidula fornicate.”
Palenik studies the ecology, physiology and genomics of marine microalgae. His laboratory participated in the first whole genome sequencing projects for several isolated microalgae and currently employs environmental metagenomics techniques to understand strain diversity in situ. His lab is currently using microarray and proteomic analyses to characterize the effects of environmental stressors on growth rates and gene expression in marine microorganisms. This has led to recent work on microalgae with biofuel production potential. Diverse projects involving marine cyanobacteria or eukaryotic phytoplankton are possible. Previous SURF mentoring: Amanda Hodo (2012) “Characterization of Tetraselmis isolates and their use for algal biofuels”, Natalia Gutierrez (2014) "Investigating the presence of polyhydroxybutyrate, in cyanobacteria, using fluorescent microscopy and bioinformatics for its potential use in constructing biodegradable plastics", Courtney Swink (2015) "Raffinate waste as a nitrogen replacement to increase the self-sustainability of using marine microalgae for biofuel production", Morrie Lam (co-advised; 2015) "Identification and Characterization of a Novel Algal Pathogen" and Ivan Moreno (2017) “Characterizing the thermophilic microbial community of hot springs in the Black Canyon of the Colorado.”
Sarah Purkey- Assistant Professor, Center for Atmospheric Science and Physical Oceanography
Purkey’s research focuses on the use of in-situ ocean observations to assess variability in the large-scale global ocean circulation to further our understanding of the feedbacks between the strength of the circulation and climate. Her primary interest is on the formation and circulation of the cold, dense waters formed in polar regions and found throughout the deep ocean basins around the world. Student projects could focus on a large array of topics around observational physical oceanography ranging from the deep ocean to the surface. A student project could be built around looking at the recent data collected using the new Deep Argo floats, capable of profiling the full water column (up to 6000 m!). These floats have been deployed in both the North Atlantic and Southern Ocean and offer an exciting new platform for deep ocean observations. Purkey also works closely with the Southern Ocean Carbon and Climate Observations and Modeling Project (http://soccom.princeton.edu/) group at Scripps Institution of Oceanography and welcomes students with general interest in Southern Ocean circulation and could suggest a student project focusing on anything from small scale Antarctic coastal processes to large-scale features of the Antarctic Circumpolar Current.
Lynn Russell – Professor, Center for Atmospheric Science and Physical Oceanography
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) Analyzing the role of ocean surface mixing in contributing to sea spray aerosol particles (co-mentored with Janet Sprintall. 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” and Jeramy Dedrick (2017) “Analyzing hydroscopic particle growth of West Antarctic Boundary Layer aerosols.”
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" and Kayla Martinez-Soto (2017) “Egg morphometrics and fertilization rates from recovering and unexploited populations: Nassau Grouper and Tiger Grouper in the Cayman Islands.”
Dave Stegman – Associate Professor, Institute for Geophysics and Planetary Physics
Professor Stegman uses high-performance computing and advanced four-dimensional visualization systems to explore the intricate details of how planets evolve and why plate tectonics are unique to Earth. Current research projects in his lab investigate global scale dynamics by reconstructing the history of where tectonic plates have been recycled into the earth’s mantle over the past 300 million years. Previous SURF mentoring: Molly James (2016) “The role of viscous coupling in determining subduction style within numerical models of mantle convection" and Amrit Bal (2017) “Using geodynamic models to investigate how sediments influence subduction.”
Talley's research interests include general ocean circulation, climate change in the ocean, and hydrology and water masses. The student project will be related to the Southern Ocean Carbon and Climate Observations and Modeling project (http://soccom.princeton.edu/), which is a multi-institutional effort deploying biogeochemical sensors on profiling floats throughout the Southern Ocean. The student project will focus on analyzing physical and biogeochemical processes in the Southern Ocean using profiling float data and output from the Southern Ocean State Estimate. Key science questions relate to upper-ocean processes and exchanges of heat, momentum, and CO2 across the air-sea interface. The student will have the opportunity to work as part of the SOCCOM team at Scripps, with guidance from several members of the team. Previous SURF mentoring: Derek Grimes (2012), “The character of stratification in the Arabian Sea” and Phoebe Thompson (2016; co-mentored) The seasonal cycle of macronutrients and net community production in the Southern Ocean, Francisco Spaulding-Astudillo (2016, co-mentored) “The role of polynyas in ice export of Ross Sea”, Casey Brayton (2017, co-mentored) “Understanding preconditioning of the Maud Rise Polynya” and Maya Chung (2017, co-mentored) “Variability of ice production in the Ross Sea in 2006-2010 and its relationship to the Amundsen Sea Low.”
Tauxe’s research focuses on the behavior of the ancient geomagnetic field and applications of magnetic measurements to help solve geological and archaeological problems. One current area of interest in the lab is the behavior of the Earth’s magnetic field over the last 5 million years, in particular the strength of the magnetic field. One of the problems with the current data base is that, unlike the directional data which clearly point to a dominance of a “bar magnet” at the center of the earth, the data regarding strength do not show such a signal. We have new samples from Hawaii which we hope will shed light on the source of the discrepancy which would be an exciting summer project. Previous SURF mentoring: Miranda Mikesh (2011) “Applications of magnetic measurements on local igneous rocks to examine the record of the magnetic field during the Cretaceous”, James Holmes (2011; co-advisor) “A new visualization of the motion of the Indian Plate in the Cenozoic”, Hannah Asefaw (2014) "Paleointensity Estimates of Neoprotorezoic North Shore Volcanic Samples", Nicolas Santiago (2016) “Exploring the geomagnetic field anomaly during the first millennium CE: Evidence from new archaeointensity data from China”, Carlos Anguiano (2016) “First archaeomagnetic results from Armenia: toward a regional curve” and Justin Higa (2017) “Preliminary archaeointensity results from the historical period of Cambodia, Southeast Asia.”
Research in the Taylor lab focuses on the biomechanics of marine invertebrates. We combine biology with engineering and physics to explore the form and function of animals and their adaptations to various environments. Some of the research questions pursued in the lab include: how is the structure of the crustacean exoskeleton adapted for functions such as locomotion, defense, and acoustic communication? How are invertebrate skeletons built and adapted for different physical and chemical environments? We use a range of microscopy, materials testing, and experimental physiological, biomechanical, and behavioral approaches to answer these questions. Some possible focal projects include tree climbing mechanics of crabs and mechanical properties of skeletal materials. Previous SURF mentoring: Jasmine Gilleard (2013) “Effects of ocean acidification on the structure and function of Red Rock Shrimp’s, Lysmata Californica, exoskeleton” and Amanuel Weldemariam (2014) "Physiological Effects of Ocean Acidification on the Striped Shore Crab,Pachygrapsus crassipes", Jorge Rivera (2015) "Biomechanics of climbing in the striped shore crab Pachygrapsus crassipes” and Anya Byrd (2016) “Locomotion biomechanics of the tree-climbing mangrove crab, Aratus pisonii, and the intertidal shore crab, Pachygrapsus crassipes.”
Jane Willenbring, Associate Professor, Geoscience Research Division
Research in the Willenbring lab aims to understand the evolution of the Earth’s surface – especially how landscapes and soils are affected by tectonics, climate change, and life. She and her research group use geochemical techniques, high-resolution topographic data, field observations, and, when possible, couple these data to landscape evolution numerical models. The geochemical tools she uses and develops often include cosmogenic nuclide systems, which provide powerful, novel methods to constrain rates of erosion and mineral weathering. The lab has also started to organize citizen science campaigns and apply basic science principles to problems of human health with an ultimate broader impact goal of cleaning up urban areas and environments impacted by agriculture. Projects for summer research include (1) understanding the hillslope erosional response to differing fire regimes comparing Tijuana and San Diego, (2) studying the impact of bedrock weathering and vegetation on waterfall retreat rates in the El Yunque National Forest, Puerto Rico, (3) linking nutrients in soils to local vegetation patterns, and (4) measuring contaminant input and cycling in urban soils and coastal systems. Previous SURF mentoring: Omar Roseles-Cortez (2017) “Measuring tropical gnamma pool erosion rates on bedrock surfaces using cosmogenic nuclide beryllium-10.”