Research Projects by Subject

Note: Each research project will involve background reading for the interns provided by their mentors. Each research project will involve a final presentation by the interns.

Interns are expected to work collaboratively on the same project and/or data set. This may preclude rising seniors from submitting papers based on such projects to the Intel Science Talent Search competition.

Ecology & Evolutionary Biology

Code Research Project Descriptions
EEB-01 Title: Parasite Contamination of Soil from Community Gardens and Playgrounds Associated to Free-roaming Cats
Primary mentor: Luz De Wit
Faculty advisor: Prof. Donald Croll
Location: Other
Number of interns: 3

Project description: Throughout the Central coast of California native populatoins of small mammals, migratory birds and birds of prey are threatened by either predation or competition from free-roaming cats. Management of free-roaming cats is a contentious topic due to opposing social, ethical, and environmental views posed by animal rights activists and conservationists. Understanding the public health impacts of free-roaming cats can open a new channel of communication between these stakeholders that can potentially lead to more effective management programs. Cats are the only known definitive hosts of the parasite Toxoplasma gondii. Following acute infection, cats can shed hundreds of millions robust T. gondii oocysts in their feces, leading to subsequent contamination of soil and water. High densities of free-roaming cats can result in high T. gondii loads in the environment, potentially increasing risk of exposure for people. This project aims to evaluate the public health threat of 30 free-roaming cat colonies located in the greater San Francisco Bay area. SIP interns that participate in this project will aid in measuring abundance of free-roaming cats near playgrounds and community gardens located in the greater San Francisco Bay area, and will use lab techniques to analyze samples from these locations in order to assess whether the soil is contaminated with T. gondii.  

Tasks: SIP interns will be assigned three main tasks: (1) to become acquainted with literature that is relevant to this project. Topics include the impact of free-roaming cats in native wildlife, the life cycle of Toxoplasma gondii, and the different diagnostic techniques that are currently used to detect T. gondii in soil; (2) to aid in measuring the abundance of cats in 30 free-roaming cat colonies located in the greater San Francisco Bay area. This includes visiting different sites that have been identified as holding a free-roaming cat colony, and count cats to estimate relative abundance; and (3) to aid in laboratory analysis of soil that was previously sampled from community gardens and playgrounds located within movement range of free- roaming cats. This includes soil processing, DNA extraction, PCR amplification, and DNA sequencing of positive samples. 

Required skills for interns prior to acceptance: Lab work
Skills intern(s) will acquire/hone: Lab work; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON REM REM ON ON

Special age requirement: The applicant must be 16 years old by June 12, 2017.

Code Research Project Descriptions
EEB-02 Title: Environmental Effects on Rockfish (Sebastes spp) Reproduction in California
Primary mentor: Sabrina Beyer
Faculty advisor: Prof. Suzanne Alonzo
Other mentors: Susan Sogard
Location: Other
Number of interns: 2

Project description: Rockfishes in the genus Sebastes are live-bearers that release pelagic offspring every year off the coast of California. The SIP interns will participate in an on-going study to examine the effects of maternal size, body condition and oceanographic conditions on larval quality and quantity released by the females. Data for this study come from both collections of wild fish sampled in California coastal waters since 2005 and a laboratory study on Rosy Rockfish, which is a dwarf species commonly found in California. In the laboratory study, the mentor's research group is directly testing the effects of water temperature and food availability on reproductive output with a working hypothesis that eggs and larvae will develop more quickly at warmer water temperatures (up to a physiological constraint) and that females on high ration diets (greater food availability) will produce greater numbers of larvae a year and of higher quality, in terms of size and energy reserves. Results from this study will inform our understanding of how variability in oceanographic conditions and potential future effects of climate change will affect female health and reproductive output with implications for sustainable management of these economically valuable species.

Tasks: The internship is located at the NOAA National Marine Fisheries Service on the UCSC Marine Science Campus. The SIP interns will assist with basic animal husbandry duties and larval collection in support of the Rosy Rockfish laboratory study. Additionally, the interns will process samples of preserved eggs and larvae from previous field collections and work on image analysis of archived photographs of larvae released in the aquarium during year 1 of the study. Other activities may include data entry, data quality control and summary data analysis to compare quality and quantity of larvae to maternal condition and experimental treatment. The SIP interns will be required to complete a safety training in order to work with live fish. The training will be completed the first week of the internship with the NOAA aquarium manager. Required skills: (1) enthusiasm to work alongside fishery biologists, (2) interest in learning about the reproductive ecology of rockfishes, and (3) demonstrated attention to detail. Desired skills (but not required): (1) previous husbandry experience working with live animals, and (2) laboratory skills gained through course work or other professional experience.

Required skills for interns prior to acceptance: Attention to detail, ability to follow protocol, enthusiasm to work with a fisheries biologist
Skills intern(s) will acquire/hone: Lab work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON

Special age requirement: The applicant must be 16 years old by June 12, 2017.

Code Research Project Descriptions
EEB-03 Title: Impacts of Pesticides on Intrinsic Plant Defenses
Primary mentor: Julie Herman
Faculty advisor: Prof. Kathleen Kay
Location: UCSC Main Campus
Number of interns: 3

Project description: Application of pesticides is a key measure used in agriculture to protect plants from insect herbivores and pathogens. However, it is not well known how these extrinsic applications of chemicals impact plants’ intrinsic defensive traits or how application of pesticides may alter growth rates. The SIP interns will investigate these questions using a species that is closely related to many agricultural varieties but has a shortened generation time.

Tasks: The SIP interns will design standardized environments in which they will grow Wisconsin FastPlants (Brassica rapa). The interns will execute treatments to examine the effects of herbivore damage and pesticide application. They will analyze these plants for growth-related markers such as leaf expansion rate, height, reproductive output, total above and below-ground biomass, chemical/physical defense production, and leaf nutrient content. The SIP interns will also analyze the soil before and after plants are grown in it to determine how nutrient compositions have changed.

Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-04 Title: Selective Patterns on Pierid Detoxification Enzymes
Primary mentor: Hanna Dort
Faculty advisor: Prof. Kathleen Kay
Other mentors: Julie Herman
Location: UCSC Main Campus
Number of interns: 2

Project description: Insect herbivores have developed a variety of strategies for exploiting food resources. In cases where plants have developed toxic chemicals as defensive strategies, insects have several options to respond. One method, used by Pierid butterflies to detoxify glucosinolate compounds found in mustard species, involved shunting chemical intermediates into non-toxic end products. However, plants often escalate their defense traits when herbivores are successful at overcoming them, meaning insects are likely under selective pressure to improve their detoxification mechanisms. In this project, interns will explore selective patterns in detoxification enzymes across the Pierid butterfly family.

Tasks: The SIP interns will obtain samples of Pierid butterflies from public and private collections. The interns will extract DNA from organisms and and use PCR to amplify the nitrile specifier proteins (NSP) responsible for detoxification, as well as the barcoding gene COII. The interns will then obtain DNA sequences for these genes and construct phylogenetic trees to determine relationships. The interns will analyze the NSPs for patterns of natural selection and examine these patterns in light of speciation rates.

Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-05 Title: Evolutionary Scaling Patterns of Musteloid Bite Forces
Primary mentor: Chris Law
Faculty advisor: Prof. Rita Mehta
Location: Long Marine Lab
Number of interns: 2

Project description: Bite force is a widely used measure of feeding performance. Although many scientists have used bite forces to examine relationships between skull morphology and dietary ecology, few have examined the scaling patterns of bite forces across evolutionary time. As animals increase in body size across evolutionary history, it is expected that their bite forces also increases (e.g. a lion's bite force is much larger than that of a cat's). However, whether these bite forces increase proportionally or disproportionally is not known. In this summer project, the SIP interns and mentor will examine the scaling patterns of estimated bite forces in musteloids. Musteloids (otters, weasels, minks, and ferrets) are a diverse group of carnivores that exhibit great dietary variation from rodents to hard-shelled invertebrates. The group will test the hypothesis that the scaling patterns of bite forces will differ between the different feeding ecologies.

Tasks: The SIP interns will learn the basic concepts of evolutionary scaling (isometry and allometry) and its importance in the evolution of different animal body forms and functions. Next, the interns will learn to estimate bite forces from musteloid skull photos using the program ImageJ. With these data, the interns will be able to use phylogenetic comparative methods to infer the evolutionary history of biting ability across different musteloid lineages, examine the variation in craniodental traits related to biting, and examine the scaling relationships of bite force through evolutionary time. All data analyses will be conducted using the statistical program R.

URL: http://research.pbsci.ucsc.edu/eeb/cjlaw/
Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Computer programming; lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON REM REM ON ON ON ON


Code Research Project Descriptions
EEB-06 Title: Aquatic Community Ecology of Bar Built Estuaries
Primary mentor: Ben Wasserman
Faculty advisor: Prof. Eric Palkovacs
Other mentors: Travis Apgar
Location: Long Marine Lab
Number of interns: 2

Project description: Due to California's mediterranean climate, coastal streams in the Santa Cruz Mountains are closed off from the ocean by a sandbar during the dry summer months. Water from the stream builds up in a coastal lagoon or bar-built estuary during this time. Over the winter, the rain breaches the sandbar. The mass of water drains into the ocean and a free-flowing stream is restored. This natural process repeats annually, but differently depending on the watershed area, rain conditions, etc. We are interested in how the biological community responds to this large disturbance. The aim of this study is to understand how the abundance and diversity of aquatic organisms including fish, invertebrates, plankton, and plants respond to differences in hydrological regime.

Tasks: The SIP interns will be involved in field surveys of aquatic organisms at six field sites, all located within an hour's drive of the UCSC Long Marine Lab. Most of the work will be completed in the wet lab. SIP interns will identify, count, and measure samples of fish, aquatic invertebrates, and zooplankton that they helped collect in the field.

URL: https://wasserman.sites.ucsc.edu/
Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work; statistical data analysis; field work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON REM ON


Code Research Project Descriptions
EEB-07 Title: The Effects of Incline on Terrestrial Locomotion in Fish
Primary mentor: Christiane Jacquemetton
Faculty advisor: Prof. Rita Mehta
Location: Long Marine Lab
Number of interns: 2

Project description: The transition from a fully aquatic to a semi-terrestrial lifestyle about 470 million years ago was a pivotal time in vertebrate evolution as it led to the diversity of all terrestrial vertebrates. Much research has focused on the fossil record (e.g., Tiktaalik), which has shown the importance of limbs in terrestrial locomotion. More recently, researchers have looked at extant aquatic species that are known to make forays on land such as the mudskipper. These studies of mudskipper movements up an incline demonstrate the importance of an elongate tail for propulsion. This project will examine the ability of eels and eel-like fishes to move across the water-land interface and quantify movement patterns of eels up an incline.

Tasks: In this project, SIP interns will help conduct trials where they simulate the incline fish encounter when moving across the water-land interface. This will involve conducting trials at 5, 10, and 15 degree elevations across a pebble substrate. Trials will involve handling and filming our various fish species including the snowflake moray eel (Echidna nebulosa) and the ropefish (Erpetoichthys calabaricus). The SIP interns will learn how to analyze high-speed video, organize data, create graphs using both Excel and R, interpret results, and present their results in the larger context of vertebrate evolution.

URL: http://mehta.eeb.ucsc.edu/
Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
EEB-08 Title: Understanding How and Why New Species Evolve: A Case Study in California Wildflowers
Primary mentor: Shelley Sianta
Faculty advisor: Prof. Kathleen Kay
Location: UCSC Main Campus
Number of interns: 2

Project description: One of the most fascinating aspects of biology is the vast diversity of species on this planet. The field known as "speciation" is concerned with how populations of a species split to become new species. The mentor's research interests are specifically in how adaptation to a new type of environment affects the process of speciation. The SIP interns will work with California native wildflowers that grow on a naturally-toxic soil type – serpentine soil. Speciation on serpentine soils is thought to happen when serpentine-adapted populations of a species split from non-serpentine-adapted populations of the same species, resulting in a new species that only occurs on serpentine (a.k.a., a serpentine endemic). However, there are many species with populations both on- and off-serpentine (a.k.a., serpentine tolerators), suggesting that speciation hasn't happened in serpentine tolerators. The mentor's goal is to understand why speciation hasn't happened in serpentine tolerators. One hypothesis is that serpentine-adapted populations haven't had enough time to speciate from non-serpentine-adapted populations, whereas serpentine endemics have had more time to successfully speciate from their non-serpentine relatives. SIP interns will use genetic tools to estimate the ages of multiple serpentine endemic species and populations within multiple serpentine tolerator species in order to test this hypothesis.

Tasks: The SIP interns will learn how to use genetic techniques to build phylogenetic trees and determine the age of speciation events. Specifically, SIP interns will learn how to: make laboratory solutions, use micropipettes, perform DNA extractions, use PCR (polymerase chain reaction) to amplify a certain gene, get genes sequenced, build phylogenetic trees, and estimate divergence times of species. In addition, there will also be opportunities for side-research projects in the UCSC greenhouse. Greenhouse projects will involve learning how to rear caterpillars to use in plant-herbivore interaction tests, and growing plants species in different soil types to assess their tolerance for serpentine soils.

Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON OFF ON ON ON REM ON ON OFF