Research Areas

Faculty mentors, research interests and proposed projects for SURF (REU), STARS, and other undergraduate research opportunities

 

Lihini Aluwihare

Associate Professor, Geoscience Research Division
Research interests

Research in the Aluwihare Lab aims to use individual molecules to inform our understanding of biogeochemical cycles in aquatic environments. In particular, they

  • Perform compound specific isotope measurements to asses stocks and dynamics of organic carbon and organic nitrogen
  • Develop and apply compound-specific (natural) radiocarbon analyses of dissolved organic molecules to understand the relationship between molecular structure and reactivity
  • Perform isotopic analyses (14C, 13C, 15N) of cellular components to study metabolisms and carbon-sources supporting microbial production
  • Develop chromatographic and analytical techniques to enable molecular level analyses of biomarkers in complex matrices
Potential project

One potential project is to generate a library of mass spectra for alicylic lipids isolated from laboratory cultures of phytoplankton and bacteria. The student would subsample cultures maintained by investigators at SIO and our other collaborators, perform a standard lipid extraction technique, and analyze samples by gas chromatography-mass spectrometry. One of lab’s current research goals is to use biomarkers to identify biological sources that contribute particulate and dissolved organic matter to the water column (surface, mesopelagic and bathypelagic ocean) and sediments of various aquatic environments. The ability to identify and quantify lipid biomarkers from known sources in complex organic samples enables a better understanding of the origin and transformations that affect these important reservoirs of reduced carbon.

Furthermore, mass spectral characteristics of known compounds enable the structures of unknown compounds to be determined and so, this has potential as a tool for describing new biomarkers.  Undergraduate students who would be best suited for this project would have one full year of college chemistry/biochemistry, including one semester/quarter of organic chemistry. Lab courses in chemistry/biochemistry and additional course work in biology or environmental science would be helpful.

 

 

Douglas H. Bartlett

Professor of Marine Microbial Genetics
Marine Biology Research Division and Center for Marine Biotechnology and Biomedicine
Research interests

The Bartlett laboratory studies the characteristics of microbial communities present in some of the most remote areas on the planet, deep-ocean trenches.  Students may have an opportunity to explore the phylogenetic breadth of trench microbes, their genomic characteristics and their “extremophilic” growth properties and physiological characteristics.  Most environmental microbes still cannot be cultured.  We are attempting to circumvent this problem by using single-cell imaging and isolation technologies in concert with multiple displacement amplification of DNA, genome sequencing and in silico analyses.  We are also attempting a variety of nontraditional culturing approaches. 

Major issues in this research relate to the adaptations of these microbes to darkness, low temperature, high pressure, and reduced and altered sources of nutrients. For example, deep-sea water, sediment and animal samples used for culturing must be kept at pressures as high as 15,000 pounds per square inch inside titanium or stainless steel pressure vessels.

Potential project

Students with interests in the diversity of microbial life, isolating new and unusual types of microbes, characterizing microbial ultrastructure, physiology and taxonomy, following microbial stress responses, or with interests in genetics, genomics, bioinformatics or biotechnology are all encouraged to consider a summer research experience “working in the trenches”.

 

 

Katherine Barbeau

Associate Professor, Geoscience Research Division
Research interests Research in the Barbeau lab is directed towards understanding the cycling of biologically active trace metals in marine systems. Much of our work has focused on iron, important as a limiting micronutrient in large areas of the ocean. My group has developed a highly interdisciplinary approach to the study of marine trace metal biogeochemistry. We employ techniques from bioinorganic and analytical chemistry as well as microbial and molecular biology, in both field and laboratory settings. Undergraduates regularly make contributions to our research program, and projects are possible in a range of subject areas.
Potential project

One area of active research in the lab concerns the biological availability of different chemical forms of iron. Heme complexes are a form of iron which occurs intracellularly and which we hypothesize may be an important source of iron to marine bacteria colonizing dead algal cells, such as during the aftermath of an algal bloom. Incubation experiments to study these phenomena can readily be set up with natural communities in water from the Scripps pier, or using cultured phytoplankton and bacteria maintained in the Barbeau lab.

To study the removal of heme from algal detritus as a result of microbial uptake, physical separation techniques will be combined with high performance liquid chromatography (HPLC) and chemiluminescence-based assays.  This project will help elucidate a little-studied aspect of the marine iron cycle by studying at a molecular level how biologically assimilated iron is recycled in the upper ocean by marine microbes.

Prerequisites:  undergraduates with course experience in both chemistry and biology, especially if they have had some laboratory classes (eg. general, analytical or organic chemistry laboratory, microbiology laboratory, biochemistry laboratory). We are also interested in students who have experience with computational bioinformatics methods.

Examples of recent REU projects conducted in the Barbeau lab (and others at SIO) are available online. Also see attached Biographical Sketch.

 

 

Ron Burton

Professor of Marine Biology, Marine Biology Research Division
Research interests

Research focuses on evolutionary genetics and molecular ecology of marine organisms.  Our work focuses on three major themes:

  • The genetic mechanisms underlying the formation of new species
  • The molecular basis of adaptation to environmental change
  • The use of molecular tools in understanding dispersal of marine larvae

Undergraduates have played significant roles in all of our projects. Their contributions often span a range of activities including experimental matings of animals in the lab, exposures to thermal or salinity stresses and biochemical and molecular analyses of animals subjected to stress.

Potential project

One potential project would be to explore thermal preferences and tolerances of different populations of marine copepods collected along a latitudinal gradient.  We are interested in understanding the molecular basis of population differences and would use assays of gene regulation and enzyme activities.  A full year of college biology would be required; additional work in biochemistry, molecular biology or physiology would be helpful.

 

 

Dave Checkley

Professor/Researcher, Integrative Oceanography Division
Research interests

Long-term change in pelagic zooplankton and fish, including climate-biota interactions Role of zooplankton in the marine nitrogen cycle.  Effects of weather and air-sea interactions on plankton and fishes.  Ecology of marine zooplankton and fish.  The biological pump, including the role of particles and plankton.  Ocean acidification

Potential project

Zooplankton and other particles interact to prime the biological pump in the euphotic zone, resulting in a downward flux of organic matter. The REU student would conduct experiments in the laboratory or work at sea on a cruise to investigate the dynamics of selected zooplankton interacting with particles, particularly phytoplankton. Laboratory experiments would be with live zooplankton collected near SIO and for which the rates of grazing, excretion, and/or defecation would be measured. Work at sea would include similar experiments and also assistance with the deployment and recovery of autonomous, profiling floats used to sense zooplankton and other particles, as well as ship-based measurements of water properties using a CTD and nets.

 

 

James Day

Assistant Professor, Geoscience Research Division
Research interests

The petrology and geochemistry of igneous and metamorphic rocks to understand planetary accretion and differentiation.

Potential project

Understanding how planets grew, or “accreted,” and how they transformed, or “differentiated,” is central to seemingly disparate fields of study in the astronomical, earth, and life sciences. Undergraduates that are interested and enthusiastic about the natural world are sought to choose from original research projects involving training in quantitative petrology and/or trace-element geochemistry.  The project will involve review and synthesis of published literature, preparation of data from the literature for entry into a database, and analysis and modeling of the new results obtained with the published data compilations. Projects could result in original publications, including conference participation, with possibility for independent study or a senior thesis.

 

 

Dimitri Deheyn

Associate Project Scientist- Marine Biology Research Division
Research interests

The Deheyn laboratory in interested in biochemical characterization of light producing compounds, environmental health assessment, biology of light production in invertebrates (bioluminescence and fluorescence).

Potential project

One potential project for undergraduates involved research on light production that is native to organisms. The goal of this research is to isolate, identify and characterize new compounds and/or biochemical reactions that lead to light production, with the long-term application being to have new powerful bioreporters to be used in the areas of biomedicine and biotechnology. Another area of research involves identifying new biomarkers for assessing sub-lethal toxicity, and in addressing factors affecting the bioavailability of contaminants to organisms. This research topic would be appropriate for students with interests in environmental issues, coastal management and policy.  In both cases, the REU student can be involved in field studies as well as laboratory work, and thus gain extensive experience in sampling organisms and collecting physico-chemical data in the field, as well as learn a variety of laboratory techniques, from molecular biology to protein biochemistry, and epifluorescence and confocal microscopy.

 

 

Andrew G. Dickson

Professor of Marine Chemistry, Marine Physical Laboratory
Research interests

Andrew Dickson and his group at the MPL oceanic CO2 laboratory are involved in a variety of projects aimed at improving our understanding of the chemistry of carbon dioxide in seawater and at studying upper- ocean biogeochemistry. These projects include the development of strategies for the quality control of oceanic carbon dioxide measurements including the production and distribution of appropriate reference materials; the improvement of techniques for measuring carbon dioxide parameters in seawater; and a detailed study of the chemistry of acid-base processes in seawater including aspects related to the understanding of ocean acidification.

In particular, his group is currently collaborating in a project directed by Prof. Victoria Fabry (California State University, San Marcos) and funded by the California Ocean Protection Council to study ocean acidification exacerbated by coastal upwelling on the California shelf, as well as in a project directed by Dr. Richard Feely (NOAA/PMEL) to ascertain changes in ocean pH or aragonite saturation along the California coast can be accurately inferred from hydrographic measurements such as salinity, temperature, oxygen concentrations.

Potential project

There are opportunities for undergraduates to work alongside other laboratory personnel in a variety of tasks associated with these projects, and in particular with the study of ocean acidification. Interested undergraduates would be involved with setting up and monitoring aquaria containing organisms that are being subjected to high-CO2 conditions. There will also be opportunities for both chemical and biological studies associated with these experiments.

 

 

William Fenical

Distinguished Professor
Director, Center for Marine Biotechnology and Biomedicine
Research interests

The ocean is the last great frontier in the discovery of natural drugs for the treatment of human disease.  At the Center for Marine BIotechnology and Biomedicine, the Fenical research program explores the oceans for microorganisms that produce novel molecules under cultivation in laboratory conditions.  The focus of the program is the discovery of new anticancer drug leads and new antibacterials for the treatment of the most dangerous of drug resistant human pathogens. The focus on cancer is the discovery of new intracellular protein targets by the application of new natural products isolated from marine bacteria.  In the infectious disease area, the group focuses on MRSA, the highly dangerous Methicillin-Resistant Staphylococcus aureus.

Potential project

REU students could be involved in all aspects of the research programs.  Samples collected from the oceans are brought into the lab, microorganisms are isolated and they are cultured.  The culture extract is tested against cancer cells and against MRSA and those of sufficient potency are then chemically examined.

 

 

William H. Gerwick

Professor of Oceanography and Pharmaceutical Sciences
Marine Biology Research Division and Center for Marine Biotechnology and Biomedicine
Research interests

The Gerwick laboratory integrates the subjects of basic marine biology, organic chemistry, biochemistry, genetics and pharmacology in our search for new pharmaceuticals from marine algae and cyanobacteria. Our laboratory has made collections of algae and cyanobacteria from around the world, cultured, and used as source materials of unusual organic molecules and toxins. Extracts from these are screened for anticancer, antimicrobial, neurotoxic and anti-inflammatory activity, and active materials are then further studied to isolate and define the chemical structures of active compounds.

We make extensive use of nuclear magnetic resonance (NMR) and mass spectrometry (MS) to define these unusual organic molecules.Our laboratory also studies how these molecules are made at the biochemical and genetic level, and also uses molecular biology and genetics to classify the producing strains of cyanobacteria.

Ultimately, these studies are providing new leads to the pharmaceutical industry by which to more effectively treat human disease, and simultaneously helping to describe the intricate chemical interactions between competing marine life forms.

While all aspects of the work are open to student participation, a particularly good starting project would be to evaluate various of our algal and cyanobacterial extracts in a series of easily performed but insightful biological assays.

Other students may be interested to use molecular genetics to help classify one of our natural product rich cyanobacteria, or to help in the isolation and characterization of a new bioactive natural product using chemical and analytical methods.Learn more of the lab interests, and take the “Lab Tour” at http://gerwick.ucsd.edu/

 

 

Sarah Gille

Professor, Center for Atmospheric Science and Physical Oceanography
Research interests

Satellite oceanography, Southern Ocean dynamics, eddy mixing, air-sea interaction and ocean response to bathymetry.

Potential project

One important question for understanding long-term climate change in the ocean is to understand how much heat the ocean transports poleward to the Antarctic ice margins (and how much this heat might destabilize ice on the Antarctic continent.)  The first step in evaluating this is to locate historic data from the Antarctic marginal seas.  Although oceanographers often assume that the ocean does not change in time and therefore group all historic data together, climate-change analyses require us to segregate data by year and to look closely at seasonal biases that might distort our interpretation of long-term climate change.  While the scientific issues are broad and potentially daunting, we would scope the REU project to focus on a small subset of the data.

 

 

Lisa A. Levin

Professor of Biological Oceanography, Integrative Oceanography Division
Research interests

Ecology of coastal and deep sea benthic ecosystems.  Research themes include biodiversity of extreme environments, climate change impacts on benthos (ocean acidification and deoxygenation), wetland structure and function, species invasion, restoration, and population connectivity. Undergraduates routinely participate in the laboratory activities through volunteering, BISP and SIO 199 research for credit, oral presentations at lab meetings, and collaboration at sea. 

Undergraduate mentoring activities include weekly meetings, training on preparation of scientific papers and powerpoint presentations, and statistical /data presentation guidance.  They are fully integrated into laboratory activities (including safety training, lab meetings, clean up, field work etc.).  Lisa routinely take undergraduates to sea on deep-sea research cruises and occasionally can provide submersible experiences.  Two undergraduates are currently at sea with Lisa right now on the RV Atlantis.

Potential project

Undergraduate research opportunities are available in the following areas: ecology of deep-sea methane seeps and hydrothermal vents, ocean acidification effects on marine larvae, and trophic ecology of restored wetlands

 

 

Todd Martz

Assistant Professor, Marine Chemistry
Research interests

Researchers in the Martz lab develop chemical sensors for seawater and other natural water applications. We focus primary on autonomous instrumentation - devices that run on internal power and computer control for extended periods without a human operator.  Research interests are centered on the marine inorganic carbon cycle and the related biogeochemical processes controlling it.

Potential project

The student would be involved in chemical sensor development in my lab. The sensors we work with measure seawater chemical parameters such as carbon dioxide, pH, and oxygen.  Chemistry majors would best fit the required skill set. Projects would include helping out with construction of sensor packages, conducting an evaluation of sensor performance/response on the benchtop, and participating in local sensor deployments in our test tank, off the pier and possibly on a mooring in the ocean.

 

 

Richard Norris

Professor of Paleobiology, Geoscience Research Division
Research interests

Paleoceanography of Paleogene and Cretaceous warm climates, the role of plankton evolution in biogeochemical cycles, origins of deep-sea unconformitie, oceanographic control on plankton distributions, structure and dynamics of large-scale diversification in the history of life.

Potential project

Climatology of the last two centuries from off shore California.  This project uses the geochemical analysis of marine sediment cores representing the last 2000 years of history of the California coast. The cores, analyzed with non-destructive XRF technology, should provide an annual to decadal resolution study of the history of el Nino events in southern California. The objective is to select cores form our sediment core collection for analysis, prepare them for XRF analysis, and plot the results.  The resulting geochemcial records can then be interpreted in terms of climatologically significant variables, particularly periods of drought and heavy rainfall years, and oceanic biological productivity.

 

 

Brian Palenik

Professor of Marine Biology, Marine Biology Research Division
Research interests

We study the ecology, physiology, and genomics of marine microalgae, focusing on cyanobacteria.  small green algae such as Ostreococcus and the ecologically important prymensiophyte Emiliania huxleyi and we have brought novel species from these groups into laboratory culture. We are have been involved in the first whole genome sequencing projects for several of these isolated microalgae and are using environmental metagenomics techniques to understand strain diversity in situ. Environmental stress is a common trigger of changes is lipid composition and secondary metabolite production. We are currently using microarray and proteomic analyses to characterize the effects of common environmental parameters or stressors on growth rates and gene expression in these marine microorganisms. This has also led to our recent work on finding new microalgae with  biofuel production potential.

Undergraduates have been involved in the whole range of these projects through UCSD “199” course work, ESYS major projects, NSF REU programs, and as hired student research assistants.

Potential project

Biofuels from algae are a possible source of liquid fuels in the future. Undergraduate students have been and can be involved in characterizing the growth of potential algal biofuel strains and lipid production under different growth conditions. The student with basic lab skills can  apply them learning to culture microalgae, analyze them using flow cytometry and microscopy, and look at the presence or expression of specific genes using basic molecular biology techniques.

 

 

Lynn Russell

Professor of Atmospheric Chemistry
Research interests

Aerosol chemistry and physics

Potential project

Organic Functional Groups in Atmospheric Aerosol Particles.  The project will be carried out in coordination with a major atmospheric field campaign as part of a multi-institution and multi-national project. To identify organic functional groups in particles, analytical methods will primarily involve filtration and Fourier Transform Infrared Spectroscopy analysis but may include operation of other instruments for environmental monitoring. The student will be trained in sample preparation, analysis, and collection of atmospheric aerosols. Students also will have the opportunity to participate in the analysis of the results collected. For related group research activities, please see http://aerosols.ucsd.edu.

This REU project is designed for students interested in atmospheric chemistry, who are pursuing a B.S. in Chemistry or a related discipline such as Earth or Environmental Sciences. The student should have completed laboratory coursework and training in college-level general chemistry.  In this project, the student will study the chemical composition of atmospheric aerosols, learning about the impacts of aerosol particles on climate and air quality.

 

 

David Sandwell

Professor of Geophysics, Institute for Geophysics and Planetary Physics
Research interests

Geodynamics, Satellite Remote Sensing and Geodesy, Charting the Remote Ocean Basins

Potential project

Global Bathymetry. The student would participate in the development of a global bathymetry and gravity models.  The research would range from editing bathymetry sounding data to the tectonic analysis of these data.  The student would be exposed to computer languages such as UNIX, C, and GMT and would learn how to edit data and maintain a rather complex database.  The student would  work side-by-side with SIO graduate students and professors who would help supervise their research project and prepare their final report.

 

 

Jennifer Smith

Assistant Professor, Marine Biology Research Division
Research interests

Research in the Smith Lab focuses on understanding the factors (natural and anthropogenic; physical and biological) that influence community structure in benthic marine ecosystems.  Members of the lab work in both pristine and degraded coral reef ecosystems that face a variety of anthropogenic impacts that affect coral reef community structure.  When coral reefs undergo degradation, a “phase-shift” usually occurs where reef-building corals are replaced by fleshy algae. Phase-shifts are often considered to be irreversible and the end result is an algal-dominated community that lacks the diversity, complexity and structure necessary to support a typical reef assemblage.  Members of the Smith Lab work both in the field and in the lab to answer questions about coral reef ecology, physiology, and health.

Potential project

The student will be engaged in a project investigating phase-shifts on coral reefs in Maui.  The project includes field and lab experience, as well as education and outreach with the public.  The project will focus on the role of herbivores on coral reefs, asking, “What is the level of functional redundancy of herbivores on Maui coral reefs?”  That is, are fishes and urchins generally eating the same species and amounts of algae on the reef, thus having a high functional redundancy (aka: fulfilling the same role on the reef)?  Or are some fishes and urchins eating different species or amounts of algae, thus having a low functional redundancy (aka: each herbivore plays a different role)?  These ecological questions are also important management questions with implications for reef health and fisheries management.

This project is a component of a larger research project, funded by the Hawaii Coral Reef Initiative and in collaboration with the Hawaii Division of Aquatic Resources, the agency tasked with coral reef management in the state, to look at the role of herbivores and their potential for improving Maui coral reef health.  The project will include a field component in which the SURF student will travel to Maui to work with members of the Smith Lab, state agency officials, and local spearfishermen in collecting herbivore guts from the annual Maui Father’s Day Spearfishing Tournament.  The student will participate in outreach education at various reef events, species identification of coral reef fishes, urchins, and algae, and data collection during the spearfishing tournament. 

Back in the lab at Scripps, the student will learn laboratory techniques to analyze the algae contents of herbivore guts.  Gut content analysis will include creating permanent slides of algae, analyzing algae functional type and species composition, and preparing an algae species list with relative abundance for a variety of Maui herbivores.  This project will produce a description of herbivore algae preferences and will be the first of its kind to this level of detail for Maui’s herbivores

 

 

Lisa Tauxe

Distinguished Professor of Geophysics
Research interests

Dr. Tauxe is interested in the behavior of the ancient geomagnetic field and applications of magnetic measurements to help solve geological and archaeological problems.

Potential project

The study of the ancient geomagnetic field requires that the enormous body of published data be assembled. To this end, Dr. Tauxe has collaborated on designing and populating the Magnetics Information Consortium (MagIC) database. Undergraduates choose small research projects involving scouring the published literature, preparing the data for entry into the database and analyzing the resulting compilations. This project could result in original publications and may even spawn new field campaigns in which the undergraduates could participate.

 

 

Maria Vernet

Research Biologist, Integrative Oceanography Division
Research interests

Research in the Vernet lab focuses on Antarctic Phytoplankton as a model system to link taxonomy, in-water optics and remote sensing to assess climate change in high-latitude ecosystems

Potential project

Adaptation to climate change in high-latitudes has been linked to possible changes in species phytoplankton composition, in particular a replacement of large cells by smaller ones, creating a potential change in primary production, food chain and nutrient dynamics, organic matter sedimentation and CO2 uptake. Both Arctic and Antarctic studies identify this process as an adaptation of phytoplankton communities to lower sea ice concentrations, change in the timing of maximum biomass accumulation and increases in ocean stratification. To test such a hypothesis over seasonal to interannual time scales and regional space scales, we use ocean color remote sensing data to identify potential changes in phytoplankton communities along the western Antarctic Peninsula (wAP). The project uses Antarctic coastal phytoplankton as a model to further develop algorithms for determination of phytoplankton composition. This research serves as a foundation for understanding the role of phytoplankton in oceanic carbon cycling. Results from this study provides a key element in determining phytoplankton composition from space on a regional scale applicable to adaptations of Antarctic communities to climate change.

Some possible focus areas for the REU students within the scope of the overall project include the following: retrieval and initial processing of historical remote sensing data for model development; processing of water column optical data for development of relationship between optics and phytoplankton composition; exploration of ecological models to define the relationship between oceanographic parameters and phytoplankton composition; webpage development for management of data sharing, project status and outreach; database development for project specific data management.

 

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