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Undergraduate Research in Biology

Student Research in Biology

Click to watch Peter Pellitier '14 discuss his research project.


Student-faculty research is an essential part of Pomona’s educational mission. In biology, the research process teaches students how to think like a scientist. Students engaged in research work closely with faculty to develop the skills needed to form a biological question and answer it in a rigorous way.

All biology majors either carry out an original experimental or field research project or develop an original research proposal for their senior capstone experience, but students are encouraged to engage in research before their senior year. Some students first become engaged with a research lab as an assistant — helping the faculty member and advanced students with their projects and carrying out lab support tasks. The department also encourages students to spend a summer or a semester involved in biological research, either working with a faculty member on campus or through one of many available research internship programs or biological field station programs.

Students interested in research or laboratory assistant positions in the biology department should contact the potential faculty mentor.

Recent Student Research in Biology


Computer Simulation of Phenotypic Assortment in Ciliates

John Bryan (2016); Mentor(s): Andre Cavalcanti

Abstract: Ciliates are unicellular eukaryotes characterized by the presence of cilia and nuclear dimorphism. During vegetative growth, the somatic macronucleus (MAC) divides amitotically. This process distributes the DNA to the two daughter cells at random, creating the potential for either daughter cell to not receive the correct number of chromosomes or even the necessary genes to survive. Phenotypic assortment can occur through this process when alleles are silenced as they are eliminated from the MACs of a ciliate population through successive generations of asexual division. Using python computer simulations, we are examining the time that it takes for phenotypic assortment to occur. We are exploring the effects of different population sizes, gene copy numbers, and fitness costs on this process. As anticipated, higher fitness costs result in a shorter time to assortment. The same is true for higher copy numbers. Additionally, we have compared the differences in assortment times when total gene copy number is kept constant or allowed to fluctuate. Such comparisons have demonstrated that the two cases behave nearly identically in terms of assortment times and the way they are influenced by the parameter changes that we have examined. We are now exploring phenotypic assortment when multiple chromosomes are present. We expect that as more chromosomes are present in the genome, the power of selection will be diminished. We are currently working to implement a Moran process into the simulation, which will hopefully resolve past issues that were apparent with high chromosome numbers. 
Funding Provided by: Howard Hughes Medical Institute

Automating the analysis of Cassin’s auklets diving patterns using time-depth recorders (TDRs) and python programming

Nicole McDuffie (2015); Mentor(s): Andre Cavalcanti; Nina Karnovsky

Abstract: The purpose of this study is to investigate the diving behavior of Cassin’s auklets (Ptychoramphus aleuticus) using TDRs and python programming. These seabirds feed on zooplankton by diving near their nest sites on the Farallon Islands, just west of San Francisco and are highly sensitive to environmental changes impacting the ocean. Raising one chick at a time, the auklets create self-dug burrows but will also use man-made nests, allowing easy access for studying. TDRs or Time-Depth Recorders were glued to the body feathers of adults raising chicks in nest boxes for multiple days at a time. The TDRs recorded time, depth, temperature, and pressure every 5 seconds when attached to a bird as well as additional measurements every .5 seconds when a bird was under water. Using Python coding language I organized both the 5 second and .5 second data into Dive and DiveBout objects, both with calculated multiple attributes allowing further analysis of the dives. One such calculation is the percentage U-shaped a dive is, which indicates the purpose of the dive. Auklets make more V-shaped dives for finding underwater pockets of zooplankton while more U-shaped dives are for actual sustained feeding. To calculate dive shape, the number of data points in the lowest 25% of the dive depth was divided by the total number of data points in the dive. These data will allow me test further hypotheses about the responses of these birds to oceanographic variability for me senior thesis. 
Funding Provided by: Howard Hughes Medical Institute

Temperature sensitivity of the RW allele of quartet in Drosophila melanogaster

Samuel Chen (2016); Mentor(s): Clarissa Cheney

Funding Provided by: Rose Hills Foundation

Uncovering red in Drosophila menalogaster

Bianca Rodriguez (2017); Mentor(s): Clarissa Cheney

Abstract: Red malpighian tubules (red) is a gene in Drosophila melanogaster that is commonly used as a phenotypic marker, as it is one of the few phenotypes visible in the larvae. Its phenotypes include red malpighian tubules in larvae and red- brown eyes in adult flies. red is found in over four hundred publicly available fly stocks, even though its function and genomic location are unknown. Various eye color changes in flies have been attributed to mutations in genes involved in vesicle transport. It is possible that red could also be involved in vesicle transport. The location of red was narrowed down through deletion mapping, and three potential corresponding genes were identified: Aftiphilin (Afti), involved in AP-1 adaptor complex binding and protein transporter activity; CG12207, whose function is unknown; and CG3259, which is involved in microtubule binding. We sequenced these genes in both wild type and red1 backgrounds to look at any point mutations that result in translational changes and potential protein alterations. Two missense mutations were observed in the red1 Afti gene, however these point mutations are located in poorly conserved areas of the gene and could simply be polymorphisms. In the mutant CG12207 gene, a non-conservative missense mutation was found within a highly conserved region. No sequencing results have been obtained for CG3259. While the current sequencing results point to CG12207 as the red gene, the search will continue by sequencing these genes in red2 mutants, as well as conducting a series of crosses with RNAi deletions of each gene.
Funding Provided by: Howard Hughes Medical Institute

Effects of GDI mutations on hemocytes in Drosophila melanogaster

Vian Zada (2016); Mentor(s): Clarissa Cheney

Funding Provided by: Rose Hills Foundation

The characterization and localization of telomerase reverse transcriptase (TERT) in Hydra oligactis

Tessa Bertozzi (2015); Mentor(s): Daniel Martinez

Funding Provided by: Elgin Fund

Macerate Immunofluorescence to Locate Gamma- H2AX in Hydra Nuclei

Madeline Cowen (2016); Additional Collaborator(s): Anthony Bellantuono; Mentor(s): Daniel Martinez

Funding Provided by: Fletcher Jones Foundation

Phylogenetic affinities of Hydra: a molecular analysis

Alonso Iñiguez (2015); Additional Collaborator(s): Richard Campbell (University of California Irvine); Mentor(s): Daniel Martinez

Funding Provided by: Kenneth T. and Eileen L. Norris Foundation

Stopped-flow kinetic study of the reductive half reaction of the NADH-dependent polysulfide reductase (Npsr) from Archaeoglobus fulgidus

Wuyi Li (2017); Mentor(s): EJ Crane

Abstract: Archaeglobus fulgidus is an anaerobic archaeon which metabolizes sulfate and thiosulfate in hyperthermal environments.The NADH- dependent polysulfide reductase from Archaeoglobus fulgidus belongs to a group of enzymes which catalyze NAD(P)H-dependent reduction of sulfer, poly- and disulfide, oxygen, and peroxide. Previous steady-state kinetic study from this laboratory have revealed insignificant per and polysulfide reduction activity with this enzyme. Thus the actual physiological role of Npsr in Archaeoglobus fulgidus remains unknown. We have characterized the reductive half reaction of the enzyme with NADH/ NADD using stopped flow spectroscopy. In a one-second reaction between NADH/ NADD and enzyme, we observed at least three steps with rate constants of about 300, 100, and 10 per second, respectively. These constants don’t show consistent trends of change when the concentration of substrate increases. Previous studies on other Npsr homologues suggest the first two steps to be the binding and internalization of nucleotide substrate to the active site of the enzyme, while the last step to be the transfer of hydride from substrate to the mixed-disulfide between the active site cysteine residue and a tightly bound Coenzyme A. An obvious isotope effect (kH/ kD around 3) is observed in the third step, which indicates it is the hydride-transfer step. However more data is needed to draw a conclusion for the first two steps. Besides, we found another slow step occurring at the end of 1-second interval, whose rate constant is close to the third step that it is masked in some runs. 
Funding Provided by: Pomona College SURP

Phylogeny of Purple Sulfur Bacteria in Lakes of the American Midwest

Marlie Shelton (2016); Mentor(s): EJ Crane

Abstract: Photosynthetic bacteria are crucial members of ecosystems. They, like plants, can produce a primary carbon source that an entire microclimate is dependent upon. A particularly interesting type of photosynthetic microbes are known as purple sulfur bacteria (PSB). As well as providing a carbon source to a microclimate, they also play an important role in sulfur cycling. It is thusly important to know which species of PSBs are present and how they are related to each other. Using a highly conserved gene, 16s ribosomal RNA, the phylogeny of these crucial bacteria can be deduced. 
Funding Provided by: Fletcher Jones Foundation

Spatial and Temporal Variation in the Pollinator Assemblage of Eriastrum sapphirinum

Maria Pettis (2017); Student Collaborator(s): Aidan Orly (2016); Mentor(s): Frances Hanzawa

Abstract: In order to understand plant-pollinator interactions, it is important to determine the composition of pollinators that visit the plant at a site, or the pollinator assemblage. The pollinator assemblage can reveal crucial information especially in areas where specialized pollinators play key roles in pollination. These pollinators are often more affected by habitat degradation that may eliminate pollinator populations even when viable plants still remain in the habitat. In this study, we examined the pollinator assemblage of the wildflower Eriastrum sapphirinum at various sites at the Bernard Field Station (BFS) across space and time. We found that sites displayed differences in pollinator assemblage at different sites and between hours and weeks, and the distance between sites was not a predictor of similarity in their pollinator assemblages. Our results indicate that degradation of patches at the BFS may eliminate specialist pollinator populations even if the BFS E. sapphirinum population is not eliminated. 
Funding Provided by: Sherman Fairchild Foundation (MP); Schulz Fund for Environmental Studies (AO)

Morphological Variation in Sceloporus occidentalis: a Comparison Along an Urbanization Spectrum.

Maria Caruso (2017); Student Collaborator(s): Jonathan Feingold (2015), Brenna Gormally (2015); Additional Collaborator(s): Lauren Chan (W.M. Keck Science Department); Mentor(s): Kristine Kaiser

Abstract: Morphological variation is a central focus of evolutionary biology. Many studies have looked at how microhabitat and the environment affect morphological evolution, but the impact of urbanization on lizards remains understudied. We aimed to evaluate the effects of habitat change due to urbanization on lizard morphology. Western Fence Lizard (Sceloporus occidentalis) specimens were obtained from the Natural History Museum of, Los Angeles County representing six different regions across the LA Basin. These specimens were collected in the 1950’s and 1960’s from regions with varying levels of urbanization. We used principle component analysis (PCA) to compare head, body, limb, and toe measurements between the six populations. We found that there are significant differences in morphology between sexes, among sites, and among years. We found a general trend for lizards collected in protected areas to be larger than those in urban areas. Comparison between the years revealed that the 1950’s lizards were larger than those from the 1960’s. No significant interactions were found between the sex, site, and year, which could possibly be explained by small sample sizes. We plan to investigate how urbanization over the years has affected these populations by taking present day measures in the same regions. 
Funding Provided by: Schulz Fund for Environmental Studies (MC); Howard Hughes Medical Institute (JF); Sherman Faircild Foundation (BG)

Does the predator paradox affect urban lizards?

Jonathan Feingold (2015); Mentor(s): Kristine Kaiser

Abstract: Urbanization is occurring worldwide at an increasing rate, altering the wildlife communities that live in and around human development. Predator-prey interactions are altered in urban environments, as previous research has shown that predator populations tend to be larger in cities while prey generally experience lower predation rates. This predator paradox has been well studied for songbirds and some mammalian species, but has not been explored for urban lizards. In this study we aim to measure relative predator pressure experienced by lizards living in an urban gradient in the Los Angeles Basin. We use clay lizard models monitored with camera traps in order to measure predator presence and attacks in undeveloped habitat, habitat fragments, and urban matrix. No attacks have been recorded thus far. This study will provide a better picture of selective pressures experienced by lizard populations faced by different degrees of human development. 
Funding Provided by: Howard Hughes Medical Institute

Validation of corticosterone enzyme immunoassay for Sceloporus occidentalis

Brenna Gormally (2015); Student Collaborator(s): Maria Caruso (2017), Jonathan (2015); Additional Collaborator(s): Lauren Chan (Keck Science Department); Mentor(s): Kristine Kaiser

Abstract: The steroid hormone corticosterone (CORT) is released from the adrenal cortex in response to a stressor as a result of a cascade of signals secreted through the hypothalamic- pituitary-adrenal (HPA) axis. It is the primary glucocorticoid in reptiles, birds, amphibians, and rodents, whereas cortisol is the primary glucocorticoid in humans. One way of quantifying CORT concentrations is through the use of an enzyme immunoassay (EIA) kit. Most kits are initially validated for use in rodents and humans, and therefore must first be demonstrated to be accurate for other species before further use. In this study, the Cayman Chemical (Ann Arbor, MI) CORT EIA was validated for the Western fence lizard (Sceloporus occidentalis). Plasma samples were taken from both males and female lizards at the Bernard Field Station (Claremont, CA) and two validation assays were completed. The parallelism assay determined that dilutions of the plasma pools fall on trendlines parallel to the standard curve (F3,10=0.57, p=0.65). The accuracy assay determined that a known concentration of CORT added to the samples could be successfully recovered from the assay. Since both the parallelism and accuracy assays were effective, the Cayman Chemical CORT EIA is now validated for future studies involving S. occidentalis. 
Funding Provided by: Sherman Fairchild Foundation (BG); Howard Hughes Medical Institute (JF); Schulz Fund for Environmental Studies (MC)

Effects of Long-Term Aspirin Exposure on Protease Activity and Pro-Metastatic Behaviors in Breast Cancer Cells

Taylor Fortson (2016); Mentor(s): Melissa Petreaca

Abstract: Doctors often recommend that high-risk patients take daily doses of Aspirin, an anti- inflammatory drug, to prevent heart attacks, arthritis, and other health complications. However, in recent years, this large population of aspirin users has helped researchers to identify a relationship between regular aspirin use and decreased risk of colon, prostate, and breast cancer metastasis [1]. Our preliminary study (2013) showed that in vitro, aspirin treatment significantly inhibited the migration of a highly metastatic breast cancer cell line, MDA-MB-231. This breast cancer cell line relies on matrix metalloproteinase activity, and particularly that of gelatinase “MMP-9”, in order to degrade the extracellular matrix and invade into surrounding tissues [2]. This study investigates potential mechanisms for the effects of aspirin treatment observed in our preliminary study, by examining the breast cancer cells’ MMP-9 activity and ability to adhere in the presence of aspirin. Under our conditions, aspirin treatment did not significantly inhibit MMP-9 activity or adhesion, and may have instead increased cell death in vitro. 
Funding Provided by: Rose Hills Foundation

TNSF14 (LIGHT) alters rate of Apoptosis in Neutrophils

Vince Morgan (2015); Mentor(s): Melissa Petreaca

Abstract: Neutrophils are leukocytes, or white blood cells, that are responsible for the in vivo killing of bacteria and removal of cell debris in an inflamed area. Soon after arriving in the inflamed area, neutrophils undergo apoptosis, a type of programmed cell death that is considered anti- inflammatory, as it removes the inflammatory neutrophils while preventing release of cell contents into the surrounding area. In this study, we investigated the role of LIGHT (TNSF14), a protein known to induce apoptosis in some cancer cells and macrophages, on neutrophil apoptosis. We examined the effect of LIGHT on cell survival and apoptosis in neutrophils isolated from C57BL/6 wild type and LIGHT-/- mice, as well as human HL-60 cells differentiated to act as neutrophils. Initial trends in the data suggest that LIGHT can lead to both increases and decreases in cell survival, depending upon total LIGHT concentrations. 
Funding Provided by: Elgin Fund

LIGHT alters NET formation and MPO release in neutrophils

Philip Woods (2015); Mentor(s): Melissa Petreaca

Abstract: Neutrophils are a type of inflammatory cell specializing in the removal of potentially harmful bacteria from tissues. Stimulation by certain cytokines and small molecules can activate neutrophils, which can result in release of antimicrobial molecules from granules and the formation of neutrophil extracellular traps (NETs). These NETs, which consist of extruded chromatin, can trap bacteria in an environment with locally high concentrations of the neutrophil-derived antimicrobial compounds. LIGHT (TNFSF14) is a protein which may be important in neutrophil- mediated bacterial clearing, as suggested by the increased severity of wound infection found in some LIGHT-/- mice when compared with wild type mice. To examine the role of LIGHT in neutrophil function, we evaluated neutrophil release of a granule component, myeloperoxidase (MPO), and NET formation in human neutrophil-like HL-60 cells, and also compared these processes in neutrophils derived from C57BL/6 wild type and LIGHT-/- mice. Preliminary results indicate that LIGHT may facilitate NET formation and MPO release in neutrophils, suggesting a possible role for LIGHT in neutrophil-mediated bacterial killing. 
Funding Provided by: Howard Hughes Medical Institute

The More You Breed, The More You Feed: Clutch Size and Offspring Provisioning Among Pelagic Cormorants

Ramoncito Caleon (2015); Student Collaborator(s): Sophie Wang (2014), Jamie Canepa (2014); Mentor(s): Nina Karnovsky

Abstract: The purpose of this study was to investigate the factors that influence the foraging behavior and offspring provisioning among pelagic cormorants (Phalacrocorax pelagicus) that nest along shoreline cliffs of Sonoma County. As indicator species, seabirds reflect the changes that occur within the marine ecosystem and although pelagic cormorants are widely spread in the North Pacific, there is little information about their foraging and reproductive behavior. We tested the hypothesis that foraging trip duration decreases and feeding rates increase with chick size and clutch size as opposed to tide height. We observed nesting cormorants with binoculars and recorded adult departure and arrival times, as well as feeding rates and tide height. We found that adults with more chicks fed their young at a higher rate, and hence, parents maintain a per capita feeding effort as clutch sizes increase. Additionally, foraging trip duration decreased with chick size and there was no relationship with tide height. These results extend upon Lack’s hypothesis that parents of alticial birds adjust their clutch size based on the number of young that they can successfully feed. The study is ongoing; we hope to repeat the study in future years to determine how provisioning behavior relates to reproductive success and oceanographic conditions. 
Funding Provided by: Howard Hughes Medical Institute (SW); Rose Hills Foundation (RC)

Interactions between common murre population shifts and Brandt's cormorant breeding behavior

Sophie Wang (2014); Mentor(s): Nina Karnovsky

Abstract: Gualala Point Island (GPI) has historically been host to several species of breeding seabirds during the summer, including western gulls (Larus occidentalis), Brandt’s cormorants (Phalacrocorax penicillatus), pigeon guillemots (Cepphus columba), black oystercatchers (Haematopus bachmani), and pelagic cormorants (Phalacrocorax pelagicus). However, over the past several years, a new population of common murres (Uria aalge) has begun breeding atop GPI, within and around the Brandt’s cormorant nesting areas. By using aerial imagery and weekly population records, we are able to determine if there are correlations between the arrival of the breeding murres and changes in the Brandt’s cormorant population size, density, and nest distribution. This, coupled with data on common murre population size changes at breeding grounds to the north and to the south, may allow us to see how patterns of murre movement and migration interact with cormorant breeding behavior and success. 
Funding Provided by: Howard Hughes Medical Institute

Investigating the roles of PERM-2 and PERM-4 in C. elegans eggshell assembly

Helen Lamb (2015); Mentor(s): Sara Olson

Funding Provided by: Pomona College SURP

Y. Pseudotuberculosis Ascarylose Biosynthetic Protein Expression

Estela Sanchez (2017); Student Collaborator(s): Liliana Mora (2017); Mentor(s): Sara Olson

Funding Provided by: Sherman Fairchild Foundation (ES)

Examining the Factors that Influence Rates of Litter Decomposition in Native and Non-Native Habitat Types in Southern California

Madison Dipman (2015); Mentor(s): Wallace Meyer

Abstract: Litter decomposition is a critical process by which carbon is released to the atmosphere and other nutrients are released in forms that allow for plant and microbial production. To better understand the factors (biotic and abiotic) that drive decomposition of leaf litter in semi-arid, low elevation habitats types of Southern California, I designed a 2 x 2 x 2 factorial experiment with: (1) two litter types, high or low quality, represented by golden currant leaves and non-native grasses, respectively; (2) two invertebrate treatments, including or excluding macro-invertebrates from the boxes; and (3) two UV treatments, allowing or blocking the majority of UV radiation. This summer I set up my year-long experiment by constructing and installing 768 litter boxes in grassland and Coastal Sage Scrub sites at the Bernard Field Station that will be collected in different seasons during the year. Ultimately, the goal of the experiment is to provide an organized framework for understanding decomposition processes in Southern California, which is critical in determining how ecosystems respond to climate change and landscape transformations. 
Funding Provided by: Sherman Fairchild Foundation

Comparison of ant communities in coastal sage scrub, non-native grassland and suburban habitats in Los Angeles County: Conservation implications

Weston Staubus (2014); Mentor(s): Wallace Meyer

Abstract: Coastal sage scrub (CSS) has been eliminated from over 85% of its historic range and replaced by non-native grasslands and suburban habitats. CSS fragments have also been invaded by Argentine ants (Linepithema humile), which competitively exclude native ants where they become established. In this study, I investigated the ant communities in and around a CSS fragment at the Robert J Bernard Biological Field Station (BFS) in Claremont, California. In addition to CSS, the BFS contains a distinct non-native grassland habitat. The close proximity of these habitats to each other and the surrounding suburban matrix presents a rare opportunity to examine differences among ant communities in each habitat, while limiting confounding variables such as dispersal or climate variation. I used pitfall traps to survey ants and compared the richness and composition of ant communities in each habitat type. I also compared the ant community at the BFS to CSS fragments previously surveyed in San Diego. I found that ant richness and composition vary significantly among all three habitat types, and that the BFS supports a unique and unusually diverse ant community compared to fragments in San Diego. The BFS seems less susceptible to invasion by Argentine ants than coastal fragments. This demonstrates that both CSS and grassland habitats are required to preserve native ant diversity and that inland CSS fragments are of higher conservation value since they harbor more native ant species per area. 
Funding Provided by: Howard Hughes Medical Institute

Taxonomic Classification of Octocoral Species Using mutS and COI Barcode Marker Genes

Ah Yeon (Alice) Chung (2017); Student Collaborator(s): Nimrah Imam (2017 SC); Mentor(s): Catherine McFadden (HMC)

Abstract: Currently, there is still a void in our knowledge of the biodiversity present in coral reefs. The diversity of the octocorals, also known as soft corals, has yet to be fully understood because of the difficulties that arise in attempting to distinguish species. Genetic “barcode markers” are genes universal to all organisms that can serve as a more reliable method of identifying and differentiating species through DNA sequencing. In this project, we sequenced the genes mutS and COI in octocorals from Madagascar and Dongsha Atoll, Taiwan. DNA was extracted from these coral samples, then the mutS and COI genes were amplified using polymerase chain reactions and sequenced. Sequences were compared to reference databases of known species to identify the specimens from Madagascar and Dongsha. 
Funding Provided by: Howard Hughes Medical Institute (AC)

Dispersal and homing behavior of Gyrinophilus porphyriticus across two freshwater predation regimes in the White Mountains of New Hampshire

Jessica Hernandez (2015); Additional Collaborator(s): Brett Addis (University of Montana); Mentor(s): Jon Davenport (Southeast Missouri State University)

Abstract: The goal of this project was to better understand the influence of behavioral traits on the dispersal and homing behavior of the northern spring salamander, Gyrinophilus porphyriticus. More specifically, we sought to determine if 1) G. porphyriticus exhibited homing behavior after displacement episodes of 10-m, 2) ascertain if the behavioral syndrome of G. porphyriticus influenced homing behavior, and 3) deduce if the aquatic habitat affected the behavioral syndrome and/or the ability of G. porphyriticus to home. As an REU student, I had the incredible opportunity to research salamanders at the Hubbard Brook Long Term Ecological Research (LTER) site in the White Mountains of New Hampshire. My mentors included Professor Jon Davenport, Professor Winsor Lowe, and PhD student Brett Addis. This REU position was made possible thanks to Plymouth State University, the Hubbard Brook Research Foundation (HBRF), the U.S. Forest Service, and the amazing community of scientists of the Hubbard Brook Ecosystem Study. 
Funding Provided by: National Science Foundation (University of Montana)

Lizard Functional Biology: Vertical Running and Egg Water Uptake

Andrea Omonte (2015); Student Collaborator(s): Margaux Hujoel (2016 HMC), Ryan Jones (2016 HMC); Mentor(s): Stephen Adolph (HMC)

Abstract: Our lab group conducted research on a species of lizard native to Claremont, CA: the Western Fence Lizard (Sceloporus occidentalis). We ran two simultaneous projects, the first of which dealt with Sceloporus occidentalis eggs and the significant water uptake that is exhibited when they are laid in the soil. In order to obtain fence lizard eggs, we made two trips into the field; on both trips, we went up to Mount Baldy where we hiked on the Bear Canyon trail in search of gravid females. Gravid females were caught and taken to the lab where we placed them in sand-filled tanks until they were ready to lay their eggs. The sand was kept moist in order to provide a suitable environment for the eggs and the lizards were fed crickets regularly. Once we observed eggs present in the sand, we collected them and carried out the process of incubation. The eggs were placed in vermiculite with water added (80 ml for 100g of vermiculite), covered with aluminum foil and placed in an environmental chamber. We then took weekly measurements of their mass, length, and diameter. Our results showed that water uptake did in fact take place as the eggs doubled in mass while length and diameter increased slightly. Meanwhile, in our other project, we caught mainly male fence lizards as well as a couple non-gravid female lizards from areas around Harvey Mudd College. These lizards were collected in order to study the vertical running behavior of fence lizards. We constructed a vertical track in the lab that consisted of a tree truck obtained from a lumberyard, which was then mounted on a wooden 
Funding Provided by: Howard Hughes Medical Institute (AO)

A Method to Identify Biomarkers in Children with Type I Diabetes

Hannah Robertson (2015); Additional Collaborator(s): Jim Koziol (The Scripps Research Institute); Mentor(s): Joanna Davies (San Diego Diabetes Research Insititute)

Abstract: Type I Diabetes (TID) is an autoimmune disease characterized by the destruction of insulin producing β-cells in the pancreas. Patients with less severe disease respond better to immunotherapy. This blinded pilot study tested the ability of multi parameter flow cytometry to identify novel cellular biomarkers to predict disease severity. To test this hypothesis, blood samples from 20 children newly diagnosed with TID were compared to blood samples from healthy subjects. The cellular biomarkers are immune T cell subsets selected based on previous data showing their role in protecting against TID. Subsets of interest were distinguished using eight-color flow cytometry. The relative frequency of each cell subset was calculated using FloJo, a data analysis software. After locking the cellular biomarker data, the study was unblinded and the clinical history of each patient was revealed. The clinical history included gold standard measurements of disease severity. The association between the relative frequency of T cell subsets and measures of disease severity were analyzed using regression and correlational methods. The results show that usable data can be obtained from over 90% of samples using multi parameter flow cytometry. Linear regression analysis was used to test reproducibility of T cell subset relative frequency over time within the same patient. The conclusion of the study is that flow cytometry can be used to identify cellular biomarkers for disease progression in TID. 
Funding Provided by: San Diego Diabetes Research Institute

Role of STING in the Innate Immune Response Against Babesia microti

Alexandra Sanchez (2017); Additional Collaborator(s): Henry Wortis (Tufts University), Olivia Umaña (UMass Medical School); Mentor(s): Henry Wortis (Tufts University), Roberto Garza Lopez

Abstract: Babesia microti is a haemoprotozoan parasite which causes Babesiosis across United States. All age groups can be infected by the parasite, but young individuals remain asymptomatic while those over fifty years old can develop severe symptoms. To understand this difference, it is necessary to establish a mechanism for resistance. The importance of T-cells-dependent adaptive immunity for resistance has been established; however, the role of innate immunity remains unknown. Recently, STING (stimulator of interferon genes) was identified as a DNA sensor essential for resistance against Plasmodium falciparum. P. falciparum and B. microti share similar life cycles, host cells, and zoonosis – making STING a strong candidate as B. microti’s DNA sensor. We hypothesized that STING and Type I interferons are required for the early clearance of B. microti through the activation of phagocytes as part of the innate response. To test our hypothesis, STING-knockout and wild-type mice were infected with B. microti. Using flow cytometry, the percentages of parasitized red blood cells (pRBCs) were quantified over 32 days. Both groups reached high levels of pRBCs on the ninth day post-infection with the KO mice’s average of 5.1% and WT’s average of 4.9%. Both groups cleared the infection by the thirty-second day. Using a t-test on the average Area under the Curve of each population, we calculated the WT and KO parasitemia values to be statistically insignificant (p=0.43). Thus, STING was determined to be nonessential for resistance. The role of Type I interferons is unknown. 
Funding Provided by: National Institute of Health (Tufts University)

An Investigation of the Relationship between Sunscreen and Nevus Development

Catherine Song (2017); Additional Collaborator(s): Alexander Tran (University of Colorado, Denver); Mentor(s): Lori Crane (University of Colorado, Denver)

Abstract: Sunscreen is promoted as a means of prevention against melanoma, but little research has been done on it. The existing research shows controversial results, some showing that sunscreen decreases melanoma risk whilst others show that it is associated with a greater risk. Also, nevi are the strongest predictor of melanoma and some studies have found that sunscreen use is associated with a higher nevus count. Longitudinal data collected through the Colorado Kids Sun Care Program was analyzed to determine the relationship between sunscreen use and nevus counts at age 15 in 505 white Hispanic and non-Hispanic participants in this cohort. Sunscreen use was analyzed in the form of a sunscreen scale, which was created using the answers to sunscreen usage questions from parent interviews. Total body nevus counts were determined through skin exams, and natural log transformed for analysis to correct for positive skew. Chronic sun exposure, sunburns, waterside vacations, skin color, phenotype, and use of other sun protection were controlled for and different stratifications of the sample were analysed using multivariable regression procedures in SPSS. We found that for the most part, sunscreen use was not associated with number of nevi. The only exception was in lighter skinned kids with more than 3 sunburns from 2010-2012. This finding is consistent with previous research showing that there is a threshold of sunburns after which risk for skin cancer increases. Also, phenotype and sun exposure variables were found to be significantly associated with nevus counts, as with past studies. 
Funding Provided by: University of Colorado Cancer Center; Cancer League of Colorado


Studies on Vesicle Transport in Drosophila

Alan Chen (2014); Student Collaborator(s): Karen Leung (2014 CMC); Michelle Ozaki (2016 SCR); Additional Collaborator(s): Zhaohua Irene Tang (W.M. Keck Science Center of the Claremont Colleges); Ruye Wang (HMC); Mentor(s): Clarissa Cheney

Abstract withheld upon request.
Funding Provided by: Howard Hughes Medical Institute

Studies on Vesicle Transport in Drosophila

Evenson William (2014); Mentor(s): Clarissa Cheney

Abstract withheld upon request. 
Funding Provided by: Howard Hughes Medical Institute

Mechanisms of FAD and NAD(P)H-dependent persulfide and polysulfide reducing enzymes of Pyrococcus and Archaeoglobus

Brian Zhu (2014); Mentor(s): EJ Crane

Abstract: FAD and NAD(P)H-dependent coenzyme A disulfide/polysulfide reductases (CoADR/Psr) have been proposed to be important in the sulfur metabolism of the SO-reducing anaerobic hyperthermophiles Pyrococcus and Thermococcus. In these studies, we determined the structure for the FAD and coenzyme-A containing holoenzyme from P. horikoshii and characterized its substrate specificity. The enzyme is capable of reducing a variety of persulfide, disulfide, and polysulfide compounds. The results suggest that likely in vivo substrates are NAD(P)H and per and polysulfide derivatives of coenzyme-A, although the aerobic rapid recycling of persulfide substrate observed may explain findings that CoADR is non-essential for SO respiration in Pyrococcus or Thermococcus and instead participates in oxidative defense in the presence of SO. One homologue of CoADR, Npsr, is usually found only in mesophilic bacteria. We are currently characterizing the Npsr of the sulfate (but not sulfur) reducing Archaeoglobus fulgidus, the only Npsr found in archaea or hyperthermophiles to date.
Funding Provided by: Class of 1971 SURP Fund

Analysis of Reproduction and Regeneration in an Endemic California Conifer

Scott Lindburg (2014); Mentor(s): Frances Hanzawa

Abstract: As the climate warms, some plant populations can respond by shifting their geographic or elevation range, and some individuals can acclimate physiologically. Pseudotsuga macrocarpa, a Southern California native tree, exists across a wide elevation gradient, but previous research showed that the low elevation populations are not regenerating since no young trees are found. We examined one cause of this likely range contraction by analyzing P. macrocarpa reproduction across a 1366-meter elevation gradient. We also measured two variables related to water use efficiency, stomatal density and δ13C, to assess how the trees are responding to environmental conditions across elevations. We found that the number of developing cones, stomatal density, and δ13C all display a quadratic relationship with elevation. In addition, we found that the number of initiated cones has a linear relationship with elevation. This is most likely due to adverse climate conditions or low pollination rates at the higher sites, which caused a larger proportion of the cones to abort at those elevations. The results suggest that low reproduction, as well as low survival rates of seedlings, contributes to lack of replacement of the populations at the low elevations. Existing trees, however, adjust to warmer, drier conditions by increasing their water-use efficiency. It is likely that the low elevation populations of this tree will eventually go locally extinct due to the unfavorable conditions caused by rising temperatures and reduced precipitation at the lower sites.
Funding Provided by: Sherman Fairchild Foundation

Effects of TiO2 and C60 nanoparticles on development and survivorship in Pieris rapae larvae

Helen Lamb (2015); Mentor(s): Frances Hanzawa

Abstract: The long-term effects of increasing environmental nanoparticle (NP) deposition on natural populations are poorly understood; NP concentration and effects could amplify as NPs move through the food web. In this experiment, we fed Pieris rapae (cabbage white butterfly) larvae with an artificial food containing NP TiO2 or C60 to determine whether NP consumption affects the development or survivorship of P. rapae. We tested two concentrations of each NP. We recorded each larva’s instar and survival daily, and measured body weight on days 9, 14, 21, and 28 (day 0 = day eggs were laid). We found that nano-TiO2 decreases survivorship and growth of larvae while C60 does not affect either. Nano-TiO2 and C60 both reduce the developmental rate of larvae, but the effect of nano¬TiO2 is stronger. These results call for further study of C60 in the environment and increased regulation of nano-TiO2 manufacture and disposal.
Funding Provided by: Schulz Fund for Environmental Studies

Significance of Snow Leopard Hemoglobin B Gene in High Altitude Adaptivity in the face of Climate Change

Mitsuko Yabe (2014); Additional Collaborator(s): Peggy Barr (Western University of Health Sciences College of Veterinary Medicine); Andrea Wournell (Western University of Health Sciences College of Veterinary Medicine); Mentor(s): Richard Hazlett

Abstract: Snow leopards (Uncia uncia) are endangered species threatened by habitat loss caused by climate change effects such as desertification and anthropogenic threats such as hunting. In order to combat high altitude, hypoxic environments, they may have adaptive modifications that are genetically based in single nucleotide polymorphisms (SNPs). In natural populations of deer mice, four amino acid substitutions in the hemoglobin B (HBB) protein have been attributable to allelic differences that are responsible for better fitness in high altitude environments. The purpose is to examine if there are parallel mutations in snow leopard HBB genes. Without these mutations, snow leopards may experience higher susceptibility to global warming conditions where CO2 concentrations are richer and oxygen is low in these environments. Genotyping-by-sequencing (GBS) technology, an approach for mapping traits in high diversity organisms, was chosen to identify SNPs across the entire snow leopard genome, including HBB. We extracted DNA from blood from 75 captive and 11 wild snow leopards and sent it to Cornell University for GBS; however, data has not been returned. As an alternative method, we amplified the HBB gene from snow leopard genomic DNA using primers based on a comparative analysis of the HBB gene of other species, including dog, pig, mouse and human. The optimization PCR resulted in multiple faint bands, and a single stronger 0.7 kb band (vs. expected 1.2 kb size), suggesting primer binding with non-HBB regions of the snow leopard genome. New primers will be designed and tested.
Funding Provided by: Koe Family Fund

Localization of two arginine vasotocin receptor types in Litoria caerulea

Jonathan Feingold (2015); Mentor(s): Kristine Kaiser

Abstract withheld upon request.
Funding Provided by: Schulz Fund for Environmental Studies; National Science Foundation (UCR)

The effect of anthropogenic noise on luteinzing hormone receptor and testosterone levels in White's treefrog testes

Neha Savant (2014); Mentor(s): Kristine Kaiser

Abstract withheld upon request.
Funding Provided by: Rose Hills Foundation

Effect of corticosterone levels on the rate of wound healing

Maria Arciniega (2016); Additional Collaborator(s): Sarah DuRant (Tufts University); Carolyn Bauer (Tufts University); Mentor(s): Jane Liu

Abstract: The stress response is characterized by increased secretion of glucocorticoids (CORT) into the bloodstream. While the stress response is adaptive in the short-term, prolonged stressors can result in chronic stress. Chronic stress, typified by increased exposure to CORT, can cause several pathological effects including decreased growth, inhibition of reproduction, and immunosuppression. We hypothesized that increased exposure to CORT prior to wounding would slow the rate of healing. We chronically stressed house sparrows (Passer domesticus) and manipulated their CORT levels to analyze the effect of prior CORT exposure on wound healing. One treatment group received injections of mitotane, which decreases CORT levels. Another treatment group received exogenous CORT. All birds were chronically stressed for 10 days, after which mitotane and CORT treatment was discontinued. All birds were wounded on Day 11 and wound healing rate was recorded until all birds were completely healed. Blood samples were taken periodically to confirm the manipulation of CORT levels. While we successfully decreased CORT levels in mitotane birds and increased CORT levels in exogenous CORT birds compared to control birds, we still found no significant difference in healing rates between treatments. Contrary to our predictions, increased CORT exposure prior to wounding did not slow the rate of healing. In conclusion, these findings indicate that the relationship between stress and wound healing is complex.
Funding Provided by: National Science Foundation # CBET-1258307

The Role of the Retinoblastoma Protein in Calcific Aortic Valve Disease

Maxine Garcia (2016); Student Collaborator(s): Marina Freytsis (Sackler Graduate School of Biomedical Sciences); Additional Collaborator(s): Gordon Huggins (Tufts Molecular Cardiology Research Institute); Philip Hinds (Sackler Graduate School of Biomedical Sciences); Mentor(s): Jane Liu

Abstract: Calcific aortic valve disease is a progressive disease that involves calcification of aortic valve leaflets. A better understanding of the biological mechanisms responsible for calcification of the aortic valve is required to develop better therapies. The retinoblastoma protein (pRb), expressed by the RB1 gene, has been identified as a key protein in osteogenesis. pRb forms a complex with RunX2, a transcription factor that enhances expression of bone-specific promoters. The role of pRb in osteogenesis led us to question the role this protein plays in aortic valve calcification. We hypothesize that pRb is directly involved in the biological mechanisms that cause aortic valve calcification. We hypothesized that we can knockdown pRb using a lentivirus containing shRNA. We also hypothesized pAVICs would calcify in response to osteogenic signals and that the intensity of response would differ between lots of fetal bovine serum. Through puromycin selection and western blot analysis, we found that though there was successful transduction of the lentivirus, knockdown of pRb did not ensue. Additionally, all serum lots exhibited calcific nodules when stained with alizarin red S. In two lots, osteogenic markers were highly expressed in serums treated with osteogenic signals. We will further study the role of pRb using the serums tested with osteogenic signals; we also hope to optimize parameters of the lentivirus infection to develop mutant pAVICs with pRb knockdown.
Funding Provided by: Molecular Cardiology Research Institute

Hydra viridissima and its Chlorella endosymbiont

Alonso Iñiguez (2015); Mentor(s): Daniel Martínez

Abstract: The origin and evolution of the endosymbiosis between the green hydra and its algal endosymbionts remains to be explored. Physiological studies performed to characterize the relationship between the endosymbiotic algae and hydra hosts suggest a mutualistic relationship due to the bi¬directional flow of nutrients. In order to better understand this relationship and the taxonomy of green hydra, we have undertaken a molecular phylogenetic study including green hydra collected from all over the world. Using nuclear and mitochondrial nucleotide sequences, we have reconstructed the phylogenetic relationship of the hydra hosts and algal endosymbionts. The endosymbiotic algae cluster in five distinct clades within a deeper Chlorella clade. Interestingly, the hydra hosts also group in five clades each with its unique alga. We found no evidence of co¬evolution, that is, of phylogenetic congruence, between the phylogenies of the hydra and the algae. The different algae that have established stable endosymbioses with hydra are not closely related to one another. Instead, they are related to different kinds of free-living algae. Our current working hypothesis is that after the initial establishment of the endosymbiosis between green hydra and algae, different algal replacement events have occurred.
Funding Provided by: Elgin Fund; National Institute of Health #1R01AG037965

The effects of stress and epigenetics on senescence in Hydra oligactis

Lauren Penfield (2014); Additional Collaborator(s): Emma Burdekin (2016); Mentor(s): Daniel Martínez

Abstract: The lack of senescence in hydra has raised many questions about the causes of aging. One hydra species, Hydra oligactis, can live indefinitely with constant budding rates at 18 °C. At a colder temperature of 10 °C, the majority of H. oligactis begin to reproduce sexually and show signs of aging. However, in a recent study in our laboratory, only 60% of hydra died from physiological decay. The remaining 40% of hydra reverted back to asexual or were never induced (~1%). These natural revertant hydra have been maintained at 10 °C for over one year. It is thought that testes formation is related to revertance because the natural revertants developed significantly more testes at a later time compared to the aging hydra. However, the exact mechanism behind revertance is unknown. To test for an epigenetic component of revertance, buds of the natural revertant hydra were collected and maintained at 18 °C for one month. These hydra then were induced at 10 °C. The natural revertant buds had significantly fewer testes compared to the aging hydra and had similar testes rate and formation compared to the original revertants. Additionally, to determine if stress is a factor in revertance, a cohort of H. oligactis were stressed by a long term heat shock prior to induction at 10 °C. Compared to the controls, the hydra stressed before induction had significantly fewer testes and fewer buds at early stages. These data suggest both health and genetics could play an important role sexual induction.
Funding Provided by: Sherman Fairchild Foundation

Alcyoniid Biodiversity of Dongsha Atoll

Samuel Du (2016); Student Collaborator(s): Sara Shi (2016); Prudence Hong (2016 HMC); Mentor(s): Catherine McFadden (HMC)

Abstract: The tropics of Cancer and Capricorn delineate the tropical zone, where conditions are ideal for coral reef formation. Dongsha Atoll, located south of Taiwan in warm water, sits squarely within this area and has substantial coral development of the family Alcyoniidae. Penghu Archipelago, west of Taiwan in cold water, is located on the very edge of the tropical zone, which is considered too north to have true coral reef development. However, despite its location, many species that inhabit usually reefs can be found there. A research interest of this lab is to compare the two reefs and see how much overlap there is between the two locations. Because it is difficult to identify species by physical characteristics, our understanding of the biodiversity of these different reefs is limited. To enhance our ability to identify species quickly and accurately, previous work has found a genetic “barcode” of three genes unique to each species: cytochrome oxidase I, mitochondrial mutS and 28S rDNA. We received samples from Dongsha Atoll, extracted DNA, and then amplified and sequenced the three genes. The samples were then proofread and aligned to a tree with representative species from previous surveys of Taiwan and elsewhere. We have found representatives from eleven genera at Dongsha, compared to only six from Penghu. At this time, we have not been able to identify all the samples at a species level, though the number varies by genera.
Funding Provided by: Howard Hughes Medical Institute

Xeniid Biodiversity of Green Island

Sara Shi (2016); Student Collaborator(s): Samuel Du (2016); Prudence Hong (2016 HMC); Mentor(s): Catherine McFadden (HMC)

Abstract: Green Island lies east of Taiwan at the limits of the tropical zone at about 22.6°N, supporting the family of soft corals, Xeniidae. There has been growing interest in Xeniidae because of their rapid colonization after reef disturbances. Identifying species of this family by sight, however, has proven difficult for field researchers as physical characteristics that differentiate species are not well defined. From Indonesian xeniids, it has been determined that there are several genes that can be used as “barcodes” to better identify xeniid species. Using these molecular “barcodes” from the cytochrome oxidase I (COI) gene, the mitochondrial mutS gene, and the 28S rDNA gene, we have been able to more accurately identify species of xeniids. We extracted DNA from samples we received from Green Island, amplified, purified, and sequenced each barcode gene, and analyzed the sequences. We have been able to compile phylogenetic trees for our samples, and using the three different genes, we have been able to identify some species and determine the closest relatives of others. Future work will involve analyzing and comparing barcodes of previously studied Indonesian xeniids against Green Island xeniids to compare species diversity among locations.
Funding Provided by: Howard Hughes Medical Institute

What a Tangled Web We Weave: Preserving Spider Biodiversity in Suburban Southern California

Dakota Spear (2015); Student Collaborator(s): Weston Staubus (2014); Mentor(s): Wallace Meyer; Jonathan Wright

Abstract: Spiders (order Araneae), as the largest and most diverse taxon of terrestrial predators, fulfill a vital ecological function, yet are poorly studied, with species of many regions still unknown. The coastal sage scrub (CSS) ecosystem is currently listed as endangered by the USGS, and has declined by 85 to 98% of its original distribution. Further study of spider communities in this endangered habitat type is required in order to make informed decisions regarding the management and preservation of the CSS ecosystem and the spider species that depend on it for their survival. In this study we use pitfall trap sampling to examine differences in the spider communities between the Bernard Field Station (BFS) in Claremont, CA, an 86 acre protected region consisting of CSS, grassland and recovering CSS habitats, and the surrounding suburban area. Significant differences in the spider community exist between the BFS and suburban Claremont, and species richness is significantly greater within the BFS. Spider communities also significantly differ among the three habitat types within the BFS. The BFS is a habitat island that provides refuge for a spider community unique from that of the surrounding suburban area; therefore, protected areas like the BFS are critical to the preservation of spider diversity.
Funding Provided by: Howard Hughes Medical Institute

Comparing ant communities among habitat types in a Southern California suburban matrix: conservation implications

Weston Staubus (2014); Student Collaborator(s): Dakota Spear (2015); Mentor(s): Wallace Meyer; Jonathan Wright

Abstract: Coastal sage scrub (CSS) once flourished in Southern California’s Mediterranean climate, extending from Baja California to the Central Coast. However, human incursion has eliminated CSS from over 85% of its historic range. Much of the remaining CSS exists as habitat islands surrounded by an urban/suburban matrix. The effects of such dramatic habitat loss on native ant communities are unknown. As such, managers are ill-equipped to make informed conservation decisions. In this study, we investigated the ant communities in and around a single CSS fragment located within the Robert J Bernard Biological Field Station (BFS), an ~ 90 acre research station belonging to the Claremont colleges. In addition to CSS, the BFS also contains a non-native grassland habitat and a transitional habitat where the grassland is being recolonized by CSS shrubs. The close proximity of these habitats presents a rare opportunity to examine differences among ant communities in each habitat type, without confounding variables such as climate variation or dispersal. Ants were collected from 48 sites (3 pitfall traps per site) in CSS, grassland, transitional, and suburban habitats. We found that the ant community within the BFS significantly differed from the community outside, but that the communities did not differ among CSS, grassland, and transitional sites. Our results indicate that preservation of undeveloped lands in Southern California is essential for conservation of ant diversity.
Funding Provided by: Howard Hughes Medical Institute

Variable Lymphocyte Receptor Gene Regulation in Lamprey Provides Insight into the Evolutionary Origins of Adaptive Immunity

Wanyi (Jennifer) Jia (2016); Mentor(s): Jonathan Moore

Abstract: In jawless vertebrates, leucine rich repeats encoded by DNA cassettes flanking the variable lymphocyte receptor (VLR) genes generate equal diversity present jawed vertebrates’ B cell immunoglobulins and T cell receptors. One of the two remaining jawless vertebrates, the lamprey, has three types of VLRs: A, B, and C. Although VLRA and VLRB are analogous to T cell and B cell receptors, it is still unknown whether jawless and jawed adaptive immunities are convergent or divergent evolutionarily. In the VLRB gene, an 862 base pair region was discovered to have regulatory properties of the variable lymphocyte receptor B. Specifically, the first 150 base pair segment contains transcription factor binding sites. Located upstream of the VLRB gene is a putative regulatory element of 494 base pairs called B.2. From previous research results, B.2 exhibited inhibitory effects on the expression of luciferase when transfected into catfish B and T cells. To determine the function of B.2, we engineered a B.2 tetramer and introduced it into a vector with an EGFP reporter gene for lamprey embryo injections. Furthermore, B.2 was broken into three segments of similar lengths to test which part is sufficient in carrying out VLRB transcription inhibition in catfish.
Funding Provided by: Howard Hughes Medical Institute

Novel Minor Histocompatability Antigen Discovery

Tyler Hill (2014); Additional Collaborator(s): Tanya Cunningham (Fred Hutchinson Cancer Research Center); Mentor(s): Marie Bleakley (Fred Hutchinson Cancer Research Center)

Abstract: Minor histocompatibility (H) antigens play an essential role in mediating graft vs. host disease and graft vs. tumor response in allogeneic bone marrow transplants. Few minor H antigens have been molecularly characterized, hindering clinical assessment of their importance in transplant medicine. Genome Wide Association Studies (GWAS) incorporates phenotype data obtained from functional assays, in conjunction with well-studied and SNP mapped collections of lymphoblastic cell lines (LCL) from the Centre d’Etude du Polymorphism (CEPH), to allow for relatively efficient identification of minor H antigen loci. Minor H antigen specific T cell clones were generated by primary in vitro stimulation of naïve T cells. The restricting HLA alleles for each T cell clone were determined through lysis assays of LCL expressing only one of the potential HLA-restricting alleles. CTL clone 1 is restricted by HLA-B7 and CTL clone 3 is restricted by HLA-A2. The frequency of minor H antigen recognized by CTL 1 is 84% (n=19) and 3 is 23% (n=13). HLA expression of cell lines transfected by vaccinia with restricting HLAs were confirmed by flow cytometry. Successful transfection of many target LCL was not achieved. The variation in rate of transfection was due in part due to innate differences between LCL. In the future, stable transfected LCL will be created by lentiviral transfection followed by fluorescence aided cell sorting. The identity of the two minor H antigens will be determined after further phenotyping of CEPH LCL and GWAS.
Funding Provided by: Cancer Center Support Grant (CCSG) CURE Supplement: NCI 5 P30 CA015704-39; K23CA154532-01 from the National Cancer Institute

Investigating lymphangiogenesis in the adult mammary gland during normal and tumor development

Sarah Black (2014); Additional Collaborator(s): Pepper Schedin (University of Colorado Cancer Center); Mentor(s): Traci Lyons (University of Colorado Cancer Center)

Abstract: Breast cancer diagnosed in the postpartum period often has a poor prognosis, in part because of the increased metastatic potential of this type of cancer. In the postpartum period, after the cessation of milk production, or after birth in the absence of lactation, postpartum mammary gland involution occurs. During postpartum involution, the microenvironment within a mammary gland changes dramatically to exhibit multiple pro-tumorigenic and pro-metastatic characteristics normally associated with wound healing and inflammation. The Schedin lab has observed increased lymphangiogenesis, a hallmark of wound healing and inflammation, during postpartum involution in rodent and human mammary tissues. Furthermore, in xenograft and isograft models of postpartum breast cancer increased tumor associated lymphatic vessel density was observed. Here, we evaluated postpartum lymphangiogenesis in an additional immune competent model of postpartum breast cancer. Further, the lab’s previous results indicated that pro-lymphangiogenic molecule Semaphorin 7a (Sem7a) is upregulated in postpartum tumors. Thus, we evaluated the expression and function of Sem7a to determine if Sem7a contributes to lymphangiogenesis associated with postpartum tumors.
Funding Provided by: University of Colorado Cancer Center: Cancer Research Summer Fellowship

A Protein Complex Directs Assembly of the Vitelline Layer of the C. elegans Eggshell

Diana Partida (2014); Mentor(s): Sara Olson

Abstract withheld upon request
Funding Provided by: Sherman Fairchild Foundation; Pomona College Department of Biology

The Role of Lipid Droplets in Early Embryonic Development in C. elegans

Brian Wysolmerski (2014); Mentor(s): Sara Olson

Abstract withheld upon request
Funding Provided by: Sherman Fairchild Foundation

Activation of Neutrophil-like Cells by Zymosan

Alyssa Cook (2016); Student Collaborator(s): Lorraine Beck (2014); Mentor(s): Melissa Petreaca

Abstract: Neutrophils are critical for the innate immune response, and play a central role in inflammatory disorders. This study investigates the ability of a fungal cell wall component, zymosan A, to activate neutrophil-like HL-60 cells. These cells were treated with zymosan A or with a positive control, phorbol myristic acid (PMA). Cell death and cell release of myeloperoxidase (MPO), a component of neutrophil primary granules, were used as indicators of activation. Cell death was determined using trypan blue exclusion, and release of MPO was determined via enzyme assays of cell extracts and supernatants. MPO assay results were normalized to total and living cell numbers. Both PMA and zymosan increased cell death and MPO release from cells, suggesting that zymosan A, like PMA, can activate neutrophil-like HL-60 cells.
Funding Provided by: Pomona College SURP (AC); Fletcher Jones Foundation (LB)

Effect of Aspirin Exposure on Migration and Survival of Breast Cancer Cells

Katherine Taylor Fortson (2016); Mentor(s): Melissa Petreaca

Abstract: Chronic inflammation is commonly treated with aspirin and other NSAID pain relievers, which target the cyclooxygenase (COX) enzymes. Due in part to the vast population of aspirin users, several studies have identified a relationship between regular aspirin use and a decreased risk of invasive and metastatic cancers. We investigated the effect of aspirin treatment on the survival and migration of a metastatic breast cancer cell line, M DA-MB-231. Under our conditions (0, 5, and 10 mM aspirin active ingredient, acetylsalicylic acid), aspirin had little effect on cell survival, but significantly inhibited cell migration. Our results suggest that aspirin use may also decrease cancer cell migration in vivo, providing one possible mechanism for its inhibitory effect on cancer invasion and metastasis.
Funding Provided by: Pomona College SURP

Evaluating a new method of modeling plant populations using data for a rare California plant

Eric Pasewark (2015); Mentor(s): Diane Thomson

Abstract: Matrix models have long been the standard for modeling plant populations. In the past decade a new method, called the Integral Projection Model, has emerged that promises to give a more accurate model based on the same data that the standard matrix models use. Both of these models assume that individual plant survival and their offspring are related to some continuous parameter such as size. Matrix models split the plant data into a few size classes, and calculate survival and fertility rates for these classes while the Integral Projection Model represents survival and fertility rates as continuous functions of size, which should represent the data more accurately. Few studies have analyzed the differences of these models on real data. I have been building the Integral Projection Model for population data on the Oenothera deltiodes, which is an endangered California plant whose population has been in decline for the past few decades. A previous paper supplies a matrix model for the data, which I will compare to the Integral Projection Model.
Funding Provided by: Howard Hughes Medical Institute

The Distribution of Tardigrade and Rotifer Species on Mt. Baldy and their Rates of Accumulation of Molecular Desiccation Protectants

Parth Patel (2015); Mentor(s): Jonathan Wright; Charles Taylor

Abstract: Tardigrades and rotifers both have the ability to enter cryptobiosis—a reversible state of suspended animation in which an organism is able to survive with minimal metabolic activity. In this state, cryptobiotic organisms can withstand various extreme climate conditions and survive for extended periods of time without any outside food or water. Initially, I collected local tardigrade and rotifers species and investigated the distribution patterns of tardigrades along a vertical transect of Mount Baldy. Particular importance was placed on species characterization and variance among different, indigenous lichen and moss communities. Tardigrades from four different genera were found in the study—Hypsibius, Milnesium, Macrobiotus, and Echiniscus. There did not appear to be any correlation between elevation and tardigrade species. Currently, I am using LC-MS to detect the presence and rate of accumulation of any molecular desiccation protectants in the collected tardigrade and rotifer samples. In order to run the animal samples through the LC-MS, I am first desiccating the animals in controlled humdities using saturated potassium nitrate solutions. Next, I pestle and sonicate the animals and use a centrifuge to concentrate the sugars and lighter molecules in the sample’s supernatant. Ultimately, I will compare the accumulation of these molecular protectants in the rotifers and tardigrade species against the elevation and microenvironment in which the species were found.
Funding Provided by: Paul K. Richter and Evelyn E. Cook Richter Memorial Fund; Pomona College Department of Biology

Exceptional Locomotory Performance in Paratarsotomus macropalpis Mites

Maria Young (2016); Student Collaborator(s): Yoni Rubin (2015 PIT); Mentor(s): Jonathan Wright; Anna Ahn; Dwight Whitaker

Abstract: Arachnids can achieve remarkably high velocities and extreme maneuverability, making them beneficial to biomechanical analysis of muscle utility and kinematic modeling. The local endemic mite species, Paratarsotomus macropalpis, was filmed using a Red Lake high frame-rate video camera in both the field and lab to analyze speed, stride frequency and gait changes during acceleration, deceleration and turning. Mites running in the field on concrete substrates at high temperatures (40°C to 60°C) were shown to travel at mean relative speed of 192.4 bl s−1 (body lengths per second), exceeding highest currently documented value for land animals (171 bl s−1) achieved by an Australian tiger beetle (Cicindella eburneola). Despite this exceptional value, it is consistent with interspecific scaling of relative speed as a function of body mass. The mites maintained exceptionally high stride frequencies (as fast as 135 Hz), which increased significantly with substrate temperature. Calculations showed that air resistance was not sufficient to explain measured deceleration. Although mites accelerate and decelerate extremely rapidly (on average 7.2 ms−2 and −10.1 ms−2, respectively), the forces involved are comparable to those found in other running animals. We recorded higher resolution lab footage of mites starting, stopping and turning to analyze gait and kinematic mechanisms. During normal running, adjacent and opposite tarsi are 180 degrees out of phase. This gait cycle is preserved during turning, although the two front pairs of tarsi initiate acceleration cycles and duty factors increase for inner tarsi during turns.
Funding Provided by: Howard Hughes Medical Institute


Alternate Phenolic Electron Donors to Photosystem I

Caroline Davis (2013); Student Collaborator(s): Connie Clarke (2012); Mentor(s): David Becker

Abstract removed upon request.

Photosynthetic Activity of Nicotiana tabacum Grown in Low-Light and Full Sun

Elan Small (2013); Additional Collaborator(s): Robert Grebenok*; Mentor(s): David Becker
*Canisius College

Abstract removed upon request.

Effects of Soil Temperature and Moisture on Stomatal Density and Water Use Efficiency in Pseudotsuga macrocarpa

Daniel Mendes (2014); Student Collaborator(s): Peter Pellitier (2014); Mentor(s): Frances Hanzawa

Abstract: Pseudotsuga macrocarpa is a conifer endemic to mountain ranges in southern California. Our goal was to determine abiotic stresses such as hotter temperatures and decreased soil moisture being placed on P. macrocarpa trees at various elevations along Mount Baldy Road, near Claremont, California. Additionally, we wished to measure stomatal density and Delta C 13 of year old needles, and compare them with the abiotic factors. As a montane-tree, P. macrocarpa is more sensitive to climate changes, and more susceptible to range shifts across elevation. We found that Delta C 13 increased across elevation, indicating that trees at lower elevations have a higher water use efficiency, which suggests that they are faced with a more intense water deficit at the lower elevations. We also found that stomatal density decreased as soil temperature increased, suggesting that the trees at hotter sites have been selected for higher resource use efficiencies. 
Funding Provided by: Schulz Fund for Environmental Studies (DM); Sherman Fairchild Foundation (PP); Pomona College Biology Department

Climate Linked Range Shift in Southern California Endemic Conifer

Peter Pellitier (2014); Student Collaborator(s): Danniel Mendes (2014); Mentor(s): Frances Hanzawa

Abstract: In response to continuing climatic warming, plant species worldwide have shifted in geographic 6 distribution to be in suitable growing conditions. Detailed measurement of population age structure and environmental conditions can reveal past events and disturbances affecting the population. We determined current numbers of Pseudotsuga macrocarpa seedlings, saplings, and adults in stands on Mt Baldy, with the long term goal of predicting the likelihood of a range shift or contraction as climate continues to change. This study examined the seedling, sapling, and adult distribution of P. macrocarpa, a large, long-lived conifer, endemic to the Southern California mountains. Diameter at breast height (DBH) and fire marks were recorded for each individual tree in 11 stands. Soil moisture, soil temperature, and ambient temperature were measured throughout the study at each stand. Hottest and driest soils were found at lowest elevations 595m-965m, producing low levels of seedling survival, 13.6% juveniles. At mid elevations 1190m-1760m, where soil and air temperatures were among the coolest, recruitment was highest, 28% juvenile. At the highest elevations >1950m, recruitment is occurring to maintain the current population, yet data remains inconclusive. These findings suggest that P. macrocarpa is experiencing an upwards range shift on Mt Baldy, with low elevation populations going locally extinct. 
Funding Provided by: Sherman Fairchild Foundation (PP); Schulz Fund for Environmental Studies (DM)

Genomic engineering of light-harvesting and gene expression analysis for increased isoprene production in the cyanobacterium Synechococcus sp. PCC 7002

Sarah Black (2014); Student Collaborator(s): Justin Zangl*; Devin Hundt* (2015); Meghan Giese* (2015); Additional Collaborator(s): Matthew Nelson*; Mentor(s): Toivo Kallas*; *University of Wisconsin - Oshkosh

Abstract: Through photosynthesis, cyanobacteria such as Synechococcus capture energy from sunlight and use this energy, along with CO2 and water to produce carbohydrates and evolve oxygen. The light absorbing pigments used by Synechococcus include chlorophyll as well as the phycobiliproteins, which form antennae-like structures on PSI and PSII, allowing the bacteria to absorb a broad spectrum of light. Our work with Synechococcus has focused on genetic engineering of the photosynthesis pathway to obtain isoprene, an environmentally and economically valuable high-density liquid biofuel, as an end product rather than glucose. The bacteria contain a methyl-erythritol-4-phosphate (MEP) pathway which can be used in conjunction with an inserted, codon-optimized IspS gene to produce isoprene. Previously, research has shown that minimizing the chlorophyll antennae in cyanobacteria could maximize cell density and product yields within a culture (Melis et al., 2009). A megaprimer method was used to insert a chloramphenicol resistance cassette into the native apcF (allophycocyanin β-subunit) gene of a wild type and an isoprene producing strain of Synechococcus PCC 7002. ΔApcF transformants exhibited altered phycobilisome complexes, resulting in different light-harvesting properties. Preliminary data suggest that these mutants can grow to high densities, and can grow faster at high light intensities than the wild-type.
Funding Provided by: National Science Foundation (Research Experience for Undergraduates); Proteomics and Functional Genomics Facility, University of Wisconsin - Oshkosh

Seasonal changes in the diet of the large mouth bass (Micropterus salmiodes)

Garret Bell (2014); Mentor(s): Nina Karnovsky

Abstract: When introduced into a new ecosystem, an invasive species can wreak havoc on the already existing food chain. The purpose of this experiment was to investigate the diet of non-native large-mouth bass (Micropterus salmoides), found in the Bernard Field station, and to determine if their diet fluctuated with season. I hypothesized that seasonal differences in diet would arise due to changes in prey availability. I captured 103 bass using lures such as plastic worms. I collected and cataloged their stomach contents and compared these data to those from collections made in fall, 2011. I found that in the Spring/Summer of 2012 the majority of the bass’ diet was made up of amphipods, while in fall, 2011 the majority of their diet was made up of damsel fly larvae. I did not find any evidence that the bass fed upon the native Western pond turtle but further investigation is necessary.
Funding Provided by: Pomona College Biology Department

Natural Revertants in Hydra oligactis

Lauren Penfield (2014); Student Collaborator(s): Anne-Claire Saint Georges Chaumet (2013); Additional Collaborator(s): Ashley Brutto; Diane Bridge*; Mentor(s): Daniel Martínez; Glenn Freund; Gang Chen
*Elizabethtown College

Abstract: Multiple studies report that Hydra oligactis, a fresh-water cnidarian, live indefinitely when reproducing asexually. However, upon sexual induction, through keeping the polyps at colder temperatures (10oC), these H. oligactis appear to age through a decline in physiological functions ultimately leading to death. While most studies found that all individuals die following sexual induction, one study observed a revertance of some sexual polyps to asexual reproduction, while maintained at 10oC. Our study was designed to reproduce these results and quantify the number of revertants. We collected budding and testes rates over 10 weeks. We have yet to see any revertants, but the study is still in progress. At 10oC, hydras’ stenoteles, prey-stinging nematocysts found in hydra tentacles, diminished in number over time. These are made from interstitial cells, which also differentiate into gametes. The observed decrease suggests that interstitial cells are depleted to make gametes, causing fewer to differentiate into stenoteles.
Funding Provided by: Kenneth T. and Eileen L. Norris Foundation (LP); Sherman Fairchild Foundation (AS); National Institute of Health - 1R01AG037965-01

Evolution of Adaptive Immunity

Alex Bell (2014); Student Collaborator(s): Sophie Wang (2014); Mentor(s): Jonathan Moore

Abstract: Jawed vertebrates have an adaptive immune system containing B cells, T cells, and antibodies. Jawless vertebrates, such as lamprey and hagfish, have a different adaptive immune system involving variable lymphocyte receptor (VLR) genes, with VLRA cells and VLRB cells analogous to T cells and B cells, respectively. This summer, we studied the regulation of VLRB cells in lamprey by transcription factors from the Ets family in an attempt to discern whether the evolution of these adaptive immune systems was convergent or divergent. The two Ets factor binding sites we were interested in are located in a 150 base pair area studied last summer. In lamprey they have been shown to regulate VLRB expression. Starting with lamprey cDNA previously constructed, we designed primers for lamprey Ets binding domains based on similarity to transcription factors in jawed vertebrates. If the primers designed from jawed vertebrate transcription factors related to immunity led to Ets factor domain binding in the gel shift of an EMSA, it would suggest divergent evolution. After amplifying the lamprey DNA by PCR, we used an in vitro transcription translation (IVTT) system to make the peptides of the Ets binding domains, which we then ran through a gel and Western blot. We could not tell if the DNA had actually been transcribed and translated because the proteins involved in the IVTT system were fluorescing at the same protein size as the binding domains should have been. 
Funding Provided by: Vaille Biology Fund (AB); Pomona College Biology Department (SW)

Evolutionary Origins of Adaptive Immunity

Sophie Wang (2014); Mentor(s): Jonathan Moore

Abstract: The jawless vertebrates, lamprey and hagfish, have adaptive immunities that function without the familiar components of jawed vertebrate immune systems, such as T and B cells, immunoglobulins, a spleen, or a thymus. Instead, in lamprey, variable lymphocyte receptors (VLRs) VLRA and VLRB function as the primary antigen recognition proteins. These are thought to be respectively analogous to the Tcell receptors and immunoglobulins found in jawed vertebrates. However, the evolutionary relationship between the two adaptive immune systems is of yet unknown. To determine whether the parallels between the two systems are the result of convergent or divergent evolution, we studied the regulation of the VLRB gene by Ets family transcription factors that influence jawed vertebrate immune function. Results from previous research indicate that a 150 base-pair region containing two Ets factor binding sites are necessary for the transcription of an mCherry reporter gene, suggesting that the Ets family transcription factors drive VLR production. However, this only illustrates that the reporter is being expressed in some class of circulating cells. In order to determine whether the observed fluorescing cells produce VLR proteins, we employed immunohistochemistry to determine if mCherry, VLRA, and VLRB proteins co-localize. We found significant levels of staining for VLRA and lower levels for VLRB, but no staining patterns were localized, suggesting the need for further research.
Funding Provided by: Pomona College Biology Department

The role of SGEF in glioblastoma multiforme invasion

Molly Kupfer (2014); Mentor(s): Nhan Tran*; Shannon Fortin*; Frances Hanzawa
*Translational Genomics Research Institute

Abstract: Glioblastoma multiforme (GBM) is the most malignant form of brain tumor. The current treatments of surgical resection, chemotherapy with temozolomide (TMZ) and radiation specifically target proliferative cells. However, due to the highly invasive capacity of glioblastoma cells, tumors frequently recur after treatment and patient survival is poor. There are currently no treatments that target invading glioma cells, and thus understanding the genes responsible for invasion may help identify new therapeutic targets to treat GBM. A genome wide analysis of genes controlled by the pro-invasive, pro-survival transcription factor NF-κB in TMZ resistant xenografts revealed an increased occupancy of NF-κB on the promoter region of one potential target, the src-homology 3 domaincontaining guanine nucleotide exchange factor (SGEF). SGEF belongs to the GEF family of proteins known to play a role in cell motility, and our lab has found that SGEF is overexpressed in glioblastoma cells and is correlated with poor patient survival. SGEF expression is induced under signaling through the pro-invasive receptor fibroblast-growth factor inducible 14 (Fn14) and its ligand the tumor necrosis factor-like weak inducer of apoptosis (TWEAK). We hypothesize that SGEF promotes TWEAK/Fn14-increased migration and invasion of glioblastoma cells. Here we show increased SGEF expression when compared to normal brain tissue in patient tumor samples. Depletion of SGEF via shRNA decreased the rate of radial migration and ex vivo invasion of GB cells into murine brain slices. In addition, the ectopic expression of SGEF in human embryonic kidney cells resulted in an increase in cell ruffling as well as the co-localization of SGEF with actin at the cell edge. Further investigation into the role of SGEF in glioma migration and invasion will show whether SGEF is a reliable therapeutic target for GBM.
Funding Provided by: Helios Education Foundation; National Institute of Health via Translational Genomics Research Institute

Biomimcry in Architecture and Engineering: Innovation from Nature

Ann Dennis (2013); Mentor(s): Jonathan Wright

Abstract: Biomimcry is the modeling of biophysical innovation such as heterogeneous, anisotropic, hierarchical, and multi-functional materials and the modeling of biological production methods such as creation by growth, low-temperature processes, few materials and self-repair. In addition to exploring nature’s design principles further, this research presents three case studies. The first is a façade shading system inspired by torsional buckling of a material when a mechanical force is applied, found in the Bird of Paradise flower. The second is a water gathering material inspired by the hierarchical structure of a desert beetle whose exoskeleton is a patchwork of hydrophilic and hydrophobic surfaces that nucleates condensation. The third designs a building along the principles of a termite colony including thick walls, a thermal mass, narrow chambers connected to a chimney that ventilates air passively cooling the structure. At a time of rising energy cots and shrinking resources, a new era of materials called biomimcry is needed. 
Funding Provided by: Schulz Fund for Environmental Studies; Oldenborg Travel Grant

Right off the Road: An Investigation of the Impact of Road Construction on Plant Community Structure in a Chaparral Ecosystem

Molly Shallman (2013); Mentor(s): Jonathan Wright

Abstract: The negative impacts of roads stem from both their physical presence and the presence of the motor vehicles that use them. These harmful effects include changes in soil density, temperature, dust, soil water content, light, surface-water flow, run-off patterns, sedimentation and pollutant prevalence, all of which can have visible effects on the structure of roadside plant communities. This research project was aimed at investigating whether there is any difference in impact on chaparral plant communities depending on whether the community is next to a stretch of paved road or a gravel turnout area. Our methods included taking plant surveys along Mt. Baldy Road near the Pomona College campus; sampling both paved and unpaved roadside communities. We hypothesized that plant communities beside the unpaved areas are more negatively impacted and therefore display lower species diversity, plant abundance and percent ground coverage as well as a higher proportion of nonnative plant species, as they are exposed to more idling vehicles, dust clouds, trash and foot traffic. Our results support this hypothesis as paved road communities display a higher average value for species diversity (1.183 vs. .993), plant abundance (46.2 vs. 16.1), and percent ground coverage (53.4 vs. 16.6) as well as a lower average proportion of nonnative species (.56 vs. .65). Future study will be focused on determining the causative basis for these differences in impacts on plant community structure. 
Funding Provided by: Schulz Fund for Environmental Studies

Color Morph Specific Predation on Clay Models of Uta stansburiana

Nikki Becich (2013); Mentor(s): Pete Zani

Abstract: Well-documented populations of Uta stansburiana on Wright’s Point near Burns-Hines, OR, are subjected to mammalian, avian and reptilian predation pressures. Clay models were used to measure attack interval and attack rate for blue, yellow, and orange color morphs. Each clay model morph was exposed for approximately 3500 model hours during biologically relevant activity times for U.stansburiana. It was found that blue models were nearly three times as likely to be attacked as both orange and yellow models. A difference in predation across color morphs of U.stansburiana may indicate selection pressures for certain morphs and suggest possible explanations for population color morph differences.
Funding Provided by: Sherman Fairchild Foundation

Insect subsidies providing for differences in density distribution of northern side-blotched lizard (Uta stansburiana)

Cassandra Owen (2014); Mentor(s): Pete Zani

Abstract: We tested whether the Malheur wetlands surrounding a dry, high desert site in eastern Oregon provide subsidies in terms of food for higher trophic levels, specifically insect prey for the side-blotched lizard, Uta stansburiana. Higher density or diversity of insects closer to the cliff edge and/or where the long, narrow lava outcrop projects into wetter habitat could justify the distribution patterns of Uta observed at the study site. We quantified insect density and diversity using pitfall traps along the length of the site and at varying distances from the cliff edge, and also quantified plant density at those points. We found no significant correlation between insect/plant density/diversity and distance from tip, nor distance from cliff edge, suggesting either that the Malheur wetlands do not provide insect subsidies, or that subsidies are uniform along the site. However, in analyzing flightless and flying insects separately, we did find a positive correlation between flightless insect density and distance from cliff edge, contrary to the distribution pattern of Uta, which prefer to occupy cliff edge microhabitats. The implications of these results provide a direction for future experiments relating to the causal determinants of lizard population density.
Funding Provided by: Pomona College Biology Department