Summer 2012 Research Project: Peter Pellitier '14

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.

2014 Summer 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