2014 SURF Research Projects - Descriptions

Lihini Aluwihare – Associate Professor, Geoscience Research Division

Research in the Aluwihare Lab aims to understand the biogeochemistry of carbon and nitrogen partitioning in aquatic environments. The lab combines organic and analytical chemistry with molecular biology and isotope geochemistry to better understand the processes by which the lowest trophic levels in the ocean transform carbon and nitrogen. Potential projects include (1) examination of nitrogen cycling in lakes and the ocean by focusing on the types of nitrogen containing organic compounds (amino acids, nucleic acids, pigments) that accumulate in the water column and (2) examination of the suite of natural halogen containing molecules that closely resemble anthropogenic contaminants, such as PCBs and DDT, which accumulate in fish and squid, to understand the pathways by which natural organic compounds are biomagnified in marine food webs. Previous SURF mentoring: Khanh Dam (2011), “What can we learn from marine mammals lipids?” and Keifer Forsch (2011) “Investigation on lipid composition and abundance across metabolically diverse environments; GC-MS Analysis of particulate samples of the Santa Barbara Basin water-column”.

Katherine Barbeau –  Professor, Geoscience Research Division

Research in the Barbeau lab seeks to understand the chemical and biological cycling of trace metals in marine systems. This work focuses on iron, important as a limiting micronutrient for oceanic phytoplankton, and also copper, a toxic element in impacted coastal environments. Potential projects focus on chemical analyses of trace element species in natural waters, as well as projects related to the ecological effects of trace elements in marine systems. Previous SURF mentoring: Teresa Fukuda (2012).  Fukuda accompanied our group on a month-long oceanographic research cruise in the Southern California Current, sampling for trace metals and conducting incubation experiments.

Douglas H. Bartlett – Professor, Marine Biology Research Division 

The Bartlett laboratory studies the characteristics of microbial communities present in some of the most remote areas on the planet, deep-ocean trenches and deep subsurface environments. Potential projects include the opportunity to explore the phylogenetic breadth of deep microbes, their genomic characteristics, their “extremophilic” growth properties, physiological characteristics and genetic adaptations.   Previous SURF mentoring: Laura Filliger (2012) “Culturing piezophilic marine actinomycetes from the Deep Sea” and Alexandra Wheatley (2013) “Pressure adaptation of deep subsurface sulfate-reducing bacteria.”

Ron Burton - Professor, Marine Biology Research Division

Burton’s research focuses on evolutionary genetics and molecular ecology of marine organisms. A potential project explores the molecular basis of thermal tolerances in different populations of marine copepods collected along a latitudinal gradient. Another potential project employs DNA “barcoding” of plankton samples to identify species of fish spawning in La Jolla Marine Protected Areas.  Previous SURF mentoring:  Sonya Vargas Lima (2012) “Intraspecific variation across populations of the marine snail Chlorostoma funebralis:  Phenotypic Evidence for local adaptation?” and Reggie Blackwell (2013), “Osmotic stressed Serpin gene expression in a euryhaline copepod:  Tigriupus Califonicus.”

Paterno Castillo - Professor, Geoscience Research Division

Castillo’s research focuses on the composition and origin of magmas produced within and along divergent and convergent margins of tectonic plates as well as on mantle convection and evolution. A potential project is to investigate the origin of intrusive and extrusive igneous rocks of mostly middle Miocene age that crop out in widely separated areas near the coast in central and southern California and the offshore islands. These generally consist of bimodal basalt and rhyolite suites of mostly calc-alkalic compositions, similar to those erupted along active convergent margins, but also include some alkalic basalts, similar to those erupted in ocean islands in the middle of oceanic plates. Previous SURF mentoring: Ashley Davies (2013) “Relationship between magmatism and basin architecture in Guaymas and Cabo-Puerto Vallarta Basins, Gulf of California.”

Dimitri Deheyn – Associate Research Scientist and Lecturer, Marine Biology Research Division

The Deheyn laboratory is interested in 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) research on light production in organisms to identify and characterize the processes, actors and co-factors of new biochemical reactions that involve bioluminescence, and (2) research to identify new biomarkers for assessing sub-lethal toxicity, and factors affecting the bioavailability of contaminants to organisms. 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:  Navanx 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 aspects of nudibranchs” and Ahiram Rodriguez (2012) “The effects of multiple chemical reagents on the light production of Bioluminescent Chaetepterus Mucus.”  Mosley presented her results at the 2012 Ocean Sciences meeting.  Ewell and Schultz presented their results at the 2013 Aquatic Sciences meeting. 

William Gerwick – Distinguished Professor, Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy, UCSD

The Gerwick laboratory investigates diverse marine algae, cyanobacteria and other classes of microbial species for their unique secondary metabolites.  The major theme in this work is discovery of natural products with potential as anticancer, anti-inflammatory, anti-parasitic and neuromodulatory activity.   A potential project is to produce organic extracts of collected samples (in our freezers from previous expeditions), evaluate these in a few biological assays available in our laboratory, and then use these to direct the isolation of active compounds in a bioassay-guided chromatographic process.   Previous SURF mentoring: Alexis Brown (2012)Effect of modified pH environments on Moorea producens growth and production of adaptive secondary metabolites” and Ariana Remmel (2013) “Isolation and characterization of known and novel nucleocides from Tectitethya crypta.”

Sarah Gille – Professor, Center for Atmospheric Science and Physical Oceanography

Gille’s interests involve satellite oceanography, Southern Ocean dynamics, eddy mixing, air-sea interaction and the ocean’s response to bathymetry. There are opportunities for students to analyze upper ocean processes in the Drake Passage (between South American and Antarctica) using both observations and numerical model results. The goal is to determine physical mechanisms governing biological productivity and atmosphere--ocean exchanges.  Previous SURF mentoring: Angelica Gilroy (2011), “Oceanic heat sources near Pine Island Glacier.”  Gilroy presented this work at the 2012 Ocean Sciences meeting.  This work will lead to a first-authored student publication (Gilroy et al., in prep). 

Paul Jensen - Researcher, Center for Marine Biotechnology & Biomedicine 

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.

Carolyn Kurle, Assistant Professor, Section of Ecology, Behavior and Evolution

Research in the Kurle lab focuses on foraging ecology, food webs, and reconstructing vertebrate trophic ecology and movement patterns primarily in marine systems. A potential  project is to employ compound specific stable isotope analysis of archived marine zooplankton to determine a) patterns of environmental variability in the Pacific and Atlantic oceans over decadal time scales and b) the impacts of that potential environmental variability on the food web structures in the two ocean basins. This research will provide insight on marine vertebrate ecology and life history parameters.Previous SURF mentoring: Tricia Mae Zapanta Caraig (2012) "Determining Coastal California's anthropogenic, eutrophying pollution sources using stable isotope analyses" and Michelle McCartha (2013) " Developing techniques fo isotoping collagen in sea turtle bones for carbon stable isotope analyses."

Tony Koslow Researcher, Integrative Oceanography Division and previous Director of CalCOFI

Koslow’s research interests include the influence of climate change on marine ecosystems and the design of global ocean observing systems in the 21st century to assess climate impacts. At present, ocean observation systems to monitor the changing ecology of the oceans are embarrassingly inadequate, but there is considerable uncertainty about the cost and feasibility of improving this situation. A potential project will use the CalCOFI data set to examine how ecological observations may be optimized to characterize changes to fish and zooplankton communities.  Previous SURF mentoring: Xochitl Rojas-Rocha (2013) “Exploring new waters:  Biogeography and oceanographic controls of the southern California Current midwater fish community.”  Rojas-Rocha’s work is accepted as an oral presentation at the 2013 SACNAS conference and will be presented as a poster at the 2013 annual CalCOFI conference. A manuscript is in preparation for publication in the peer-reviewed journal, Marine Ecology Progress Series.

Lisa A. Levin, Professor of Biological Oceanography, Integrative Oceanography Division

Levin is interested in ecology of wetland, coastal and deep- sea benthic ecosystems. Two potential projects are (1) response of echinoderm, squid and fish populations to low oxygen (hypoxia) and pH on the California slope, and (2) animal roles in wetland and biofilter ecosystem services.  Previous SURF mentoring: Anai Novoa (2011) “Effects of ocean acidification on the growth and survival of sea urchin Strongylocentrotus Purpuratus larvae”,  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”; and Travonya Kenly (2013) “Size at Settlement of Mytilis californianus and Mytilis galloprovincialis.  Novoa presented her work at the 2012 Ocean Sciences meeting, Andrews and Lederer also participated in a 10-day student led research cruise off the coast of Southern California during their 2012 SURF experience.   

Joel Norris – Professor, Atmospheric and Climate Science

Norris does research on the role of clouds in climate.  If cloud cover increases with global warming, more solar radiation will be reflected back to space, thus mitigating the warming, but if cloud cover decreases with global warming, less solar radiation will be reflected back to space, thus exacerbating the warming.  The proposed project will examine cloudiness and atmospheric circulation simulated by global climate models to understand how and why clouds have been changing in the models over recent decades.  Previous experience with analyzing and plotting data using a software package is required.

Richard Norris - Professor of Paleobiology, Geoscience Research Division

Norris’ research focuses on the evolution of life in the oceans, with particular emphasis on the mechanisms of extinction and speciation of plankton and the processes of assembly of marine ecosystems during past periods of climate change. Norris also works on the recent fossil record of reefs and coastal environments to evaluate the impact of human activities on marine and terrestrial ecosystems.  Two proposed projects are (1) a study of the record of fossil brittlestars, urchins, molluscs, fish and sediment geochemistry in sediment cores collected through modern reefs in Panama to document the timing and sequence of ecosystem 'Phase shifts" associated with transformation of the coral community, and (2) examination of  the record of fish teeth preserved in deep sea sediment cores through the "Paleocene-Eocene Thermal Maximum"- an interval of intense global change 56 million years ago- as an ancient analog to potential future global change impacts on pelagic fish communities.  Previous SURF mentoring: Christian Brown (2013), “Geochemical and ecological observations on coral reefs in the Caribbean Panama.”

Brian Palenik – Professor of Marine Biology, Marine Biology Research Division

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. A potential project would involve characterizing cyanobacterial diversity using molecular biology techniques.  Previous SURF mentoring: Amanda Hodo (2012) “Characterization of Tetraselmis isolates and their use for algal biofuels.”

Greg Rouse – Professor, Marine Biology Research Division

 The Rouse lab studies the evolutionary relationships of marine animals, including many invertebrates and the fabulous seadragons. The research on seadragons focuses on the biology and population genetics of both seadragon species in Australia. Potential student projects include 1) Development of a non-invasive DNA sampling technique of seadragons at Birch Aquarium and assessment of relatedness among individuals. 2) Identification and tracking of individual seadragons from photographs taken in the field. 3) Investigation of potential sound production in seadragons.

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.  Proposed projects involve the analysis of the results collected from a major funded atmospheric field campaign, entitled, “Organic functional groups in atmospheric aerosol particles”. 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.”

Stuart Sandin  – Assistant Professor, Marine Biology Research Division

Research in the Sandin lab addresses questions of community ecology, with a specific focus on natural and anthropogenic factors that influence the composition and the functioning of coral reef ecosystems. The group uses a variety of approaches, including field work, laboratory analyses and experiments, and mathematical modeling, to answer questions prominent to the field of coral reef ecology and conservation. A potential project is the study of how predation influences the growth and diet patterns of fishes from coral reefs. The student would learn techniques of dissection, histology, taxonomic analysis of stomach contents, and advanced approaches in the preparation of otoliths (ear stones) for age analysis. Previous SURF mentoring: Atalani Jackson (2012) “The effects of variations in algal biomass on the selectivity of Acanthurus nicricans in the Northern Line Islands.”

Brice Semmens  – Assistant Professor, Marine Biology Research Division

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).

Lisa Tauxe – Distinguished Professor of Geophysics, Geosciences Research Division, PI-current proposal

Tauxe’s research focuses on the behavior of the ancient geomagnetic field and applications of magnetic measurements to help solve geological and archaeological problems.  Tauxe collaborates with archaeologists to obtain artifacts for analyzing their magnetic properties, including records of the ancient magnetic field.  A potential project is to choose a selection of these artifacts for analysis in the Scripps Paleomagnetic Laboratory, and possibly also participate in an excavation.  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” and James Holmes (2011; co-advisor)A new visualization of the motion of the Indian Plate in the Cenozoic.” 

Jennifer Taylor – Assistant Professor,  Marine Biology Research Division, SURF Program co-Director

The Taylor lab studies the biomechanics of marine invertebrates and its influence on animal behavior, ecology, and evolution. A potential project would be to study the structure and material properties of the exoskeleton of crustacean species from different habitats.  Previous SURF mentoring: Jasmine Gilleard (2013), “Effects of ocean acidification on the structure and function of Red Rock Shrimp’s, Lysmata Californica, exoskeleton”.  Gilleard will submit an abstract to the 2014 Ocean Sciences meeting.