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Undergraduate Research in Biology

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.


The Study of Protein and Basic Molecular Structures via Computational Chemistry

Ian Poveda ’21; Advisor: Roberto Garza-Lopez

Square lattices model diffusion-controlled reactions on Euclidean surfaces, such as catalytic surfaces. A first-order reaction like Aà products shows “A” as a diffusing atom. Once it achieves the “reaction center” or 100% absorbing trap, the process terminates. A single deep trap under periodic and confining boundary conditions determines the mean walk length for a random walker transiting on a family of d=2 square lattices. We establish as a function of the size N for the case of a deep trap (100% absorbing) as a centrosymmetric reaction center under periodic boundary conditions. Later such trap is moved to active sites of each square lattice nxn where n= 5, 7, 9, 11, 13 and 15. Our research is still in progress, but can be expanded in two directions. We would consider stacked square lattices to model smectite clays and would investigate the case where active sites have shallow traps instead of 100% active traps. Two-layer systems mimic the behavior of stacked clays and measure the efficiency of diffusion in such systems. Therefore we would like to study the efficiency of the reactant, walker or diffusing particle “A” and its movement on the space to achieve the trap to mimic the reaction A à products. We have obtained preliminary results on one-layer systems that demonstrate as N increases the average walk length increases. The results show that when the surrounding sites to the reaction center are shallow traps, the diffusing particle could be absorbed too.

Leveraging Liquid Biopsy to Predict Metastatic Risk in Uveal Melanoma Patients

Mirenna Scott ’20; Advisor: Karl Johnson

Uveal melanoma (UM), a cancer of the eye, currently requires an invasive biopsy to determine metastatic risk. Understanding risk is crucial as once this cancer has spread, it is universally fatal. However, the procedure carries risk of vision loss and provoking metastasis. Therefore, there is a critical need for a non-invasive analyte of UM to detect metastatic risk early on, enabling tailored therapeutic intervention. Recently, a novel cell population was discovered and named circulating hybrid cells (CHCs). CHCs are found in peripheral blood of patients with cancer and are formed by the fusion of a cancer cell and macrophage. CHCs are an overlooked population that could be leveraged as a liquid biopsy for disease monitoring in UM patients. Peripheral blood mononuclear cells were isolated from whole blood. CHCs were then separated using FACS and sent to Castle Biosciences for qtPCR to determine metastatic risk.

Results: CHC genetic profile based classification accurately detects a Class 1 tumor (low metastatic risk), however additional data is needed to understand how macrophage fusion may impact gene expression. Further successful completion of this study has the potential to demonstrate CHCs as a robust circulating analyte of disease status in UM. This may contribute to a burgeoning potential for metastasis prognosis via liquid biopsy, requiring nothing more than a blood draw and circumventing the need for tumor biopsy entirely.

Landscaping Matters: Suburbanization Enhances Decomposition and Soil Respiration

Emma van der Veen ’21; Advisor: Wallace M. Meyer III

Large swaths of natural habitat in southern California are being converted to suburban landscapes. These conversions affect decomposition and soil respiration, two key ecosystem functions that release CO2 to the atmosphere. Decomposition rates depend on plant and microbial assemblages and abiotic conditions associated with management. We examined if decomposition and soil respiration rates differed among five common habitats (lawn, shrub, water wise with and without mulch, natural) at seven institutions across the region. Live oak and sycamore leaves were used to assess the importance of different litter types. We found lower decomposition rates in the natural habitat relative to the suburban habitats suggesting that suburbanization facilitates decomposition. We also found that the lower quality (high C:N ratio) sycamore leaves decomposed 22% more slowly than oak litter indicating that plant palate can influence C cycling. Soil respiration rates increased according to our assumptions with regard to soil humidity and water subsidies across habitats: low respiration in natural and water wise habitats, and high in water wise with mulch, shrub, and lawn habitats. Results demonstrate that decisions regarding how we landscape southern California are critical for combating climate change. Sustainable landscaping should limit water subsidies and other modifications that enhance soil moisture (mulch) and use plants that have recalcitrant litter to curb carbon emissions.

Potential Role of Sonic Hedgehog in Tissue Fibrosis during Chronic Graft vs Host Disease

Ash Maria ’22; Advisor: Elizabeth Glater

Sonic hedgehog (SHH) is a protein involved in cell growth, tissue specialization, and body patterning pathways. Chronic graft vs. host disease (cGvHD) is an immune condition which can occur after allogeneic hematologic stem cell transplants (HCT). In cGvHD the donor graft sees the recipient as foreign, causing malignant immune response in recipient. SHH may promote unregulated fibrosis in many recipient organs. Preliminary evidence suggests that SHH is overexpressed early after HCT in vivo. Given this, we hypothesized that SHH is critical in unregulated fibrosis of various organs during cGvHD. To determine patient SHH levels, we examined plasma samples from HCT patients with or without cGVHD, and healthy donors, for abundance of SHH through an ELISA assay. An ELISA is where a plate is pre-coated with the capture antibody, then the following are added in order: plasma samples/standard, biotinylated secondary antibody, Streptavidin-HRP, and finally TMB colorimetric substrate. We found a leaning-towards significant positive trend between SHH abundance and active plasma samples. Further supporting our hypothesis, in a recent Phase 1 clinical trial, SHH pathway inhibitor sonidegib was effective in fighting some cGvHD symptoms, but patients found worse quality of life from harmful side effects, leading to early trial termination. Thus, our goal of this project was to get a better understanding of the SHH pathway to aid in development of safe and effective inhibitors to treat cGvHD.

Glypican-1 and Novel Biomarkers Show Differential Expression in Dielectrophoretic isolated Exosomes from Healthy versus PDAC Plasma Samples

Katherine Pelz ’20; Advisor: Sharon Stranford

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease that is extremely difficult to diagnose in its early stages, due to late onset of symptoms which are often misdiagnosed. Developing a method for early detection that is cost-effective and non-invasive is crucial. Exosomes are nano-sized vesicles that can affect the tumor microenvironment and facilitate cell-to-cell communication and are, therefore, of great interest in cancer research. Cancer derived exosomes are abundant in PDAC patient plasma and carry unique proteins that have the potential to be biomarkers for the early detection of PDAC and other cancers. However, current technologies to isolate exosomes from undiluted plasma are time intensive (typically overnight centrifugation) and require several milliliters of diluted plasma. Dielectrophoretic isolation (DEP) using a microelectrode array chip allows for exosome isolation in 15 minutes and requires small amounts of plasma (30 μL). On-chip immunofluorescence using this DEP technology shows differential expression of glypican-1 and other novel proteins in healthy patient plasma versus PDAC patient plasma. Although these data are preliminary, further research aims to develop a panel of biomarkers for clinical early detection of PDAC and other cancers.

Nitrogen Excretion during Embryonic Development in the Terrestrial Isopod Genera Ligidium and Ligia

Stephanie Yu ’22; Advisor: Jonathan Wright

This study aimed to isolate the modes of nitrogen excretion in terrestrial and marine-littoral isopod crustaceans of the family Ligiidae, Ligidium and Ligia, and determine whether the form of waste nitrogen changes during embryonic development. Previous studies performed on embryos of the fully terrestrial Armadillidium vulgare, found increasing ammonia excretion until the manca stage, in which ammonotelism was supplanted by uric acid storage. In this study, ammonia and uric acid assays were conducted across all stages of development. Embryos of Ligia occidentalis were found to excrete increasing levels of ammonia with each transition to a later embryonic stage, suggesting ammonotelism in all stages. Levels of uric acid production did not change significantly during embryonic development and remained low, demonstrating that Ligia embryos do not store uric acid as a primary mode of nitrogen excretion in any stage. This contrasts with the findings of research on A. vulgare. Specifically, in A. vulgare , marsupial fluid in the closed marsupium is provisioned from the maternal blood, with limited capacity for replenishment; therefore, the shift to uric acid storage could protect the mancae from ammonia toxicity. In Ligia, the marsupial fluid in the open marsupium is provisioned from external seawater and can be replenished regularly, preventing long-term accumulation of ammonia and rendering uric acid storage unnecessary.

The Metabolic Cost and Energy Budget of Ultra-Fast Mites

Shan Ming Gao ’21; Advisor: Jonathan Wright

The fastest land animal relative to body size is the terrestrial mite Paratarsotomus macropalpis (Rubin et al., 2016), yet little is known about how its metabolism and ecology are able to support such tremendous speeds. In this project, we used stop-flow respirometry and field observations, including the use of high frame-rate filming, to study the mite’s metabolism at temperatures from 20.5 - 56.4°C, calculate Q10, observe and capture footage of feeding behavior, identify prey species, and calculate the mite’s water balance demands. We found 10 arthropods that are potential prey and observed mites feeding on dead specimens of 4 of these species. Due to its high operative temperatures, P. macropalpis probably specializes on dead or heat-succumbed prey. Calculations showed that preformed water from prey is more important than metabolic water to offset evaporative water loss. Animals had lower metabolic rates (measured as VCO2) than predicted by body mass and cost of transport allometric scaling. P. macropalpis’s Q10 value of 1.86 was lower than the reported Q10 values for temperate and cold-adapted mites (Block, 1977). These may be adaptations for the high operative temperatures.

The Effect of the Rab Cycle and Phagocytosis on Drosophila Hemocyte Proliferation

Claire Goldman ’21; Advisor: Cris Cheney

Previous studies have found that knocking down rab5 in Drosophila melanogaster causes an overabundance of hemocytes. Rab5 is a G-protein that acts as a molecular switch, existing in one of two states: active or inactive. Rabex-5 and rabaptin-5 are involved in activating rab5. Rab5 is known for its role in vesicle transport, including initiation of the phagocytosis pathway. It was therefore of interest whether other proteins involved in this pathway, such as rab7 and rab9, would have the same effect. Rab5 works along the cellular membrane, forming vesicles, while rab7 directs vesicles to the lysosome for degradation, and rab9 mediates migration to the trans Golgi network. The hypothesis was that knockdowns of rabex-5, rabaptin-5, rab7, and rab9 would increase the abundance of hemocytes. The GAL4-UAS system was employed to express these gene knockdowns in Drosophila. Larval hemocytes of stocks with genetic knockdowns were then counted and compared to control stocks. No statistically significant increase was observed, suggesting that another pathway may be responsible. Rab5 also directs vesicles to the early endosome for recycling. Clathrin is involved in coating vesicles during this process. Next steps may include investigating the effect of a clathrin knockdown on hemocyte proliferation. Continuing this research is important because overproliferation of hemocytes essentially constitutes leukemia, so understanding the associated mechanisms may be of medical significance.

The reversal in orientation of a C. elegans migratory cell does not require the presence of nicotinic receptors

Amy Kaneshiro ’22; Advisor: Mihoko Kato

We are studying cell migration using Caenorhabditis elegans, a small, transparent nematode. In the male, an epithelial cell, the linker cell (LC), leads the gonad migration from the mid body region to the posterior. This migration uses acetylcholine signaling which can occur through two plasma membrane localized receptor types: muscarinic and nicotinic. The LC expresses one muscarinic receptor and multiple nicotinic receptors. The drug aldicarb increases the amount of extracellular acetylcholine and causes the LC to reverse its orientation. GAR-3, a muscarinic receptor, was previously found to be important for LC reversals to occur, but the role of nicotinic receptors is unknown. We tested whether LC reversals depend on two of the LC nicotinic receptors by creating null mutants of acr-15 and acr-16 using CRISPR/Cas9 genome editing. We found that this double mutant resulted in 12.19% reversal and 53.66% no reversal which is not statistically different from the number of reversals in the control that expresses both receptors. We conclude that acr-15 and acr-16 are not required for LC reversal to occur since there was a normal number of reversals without these receptors. For future studies, we developed a marker that expresses red fluorescent protein (RFP) in the LC nucleus and green fluorescent protein (GFP) in the mitochondria. Since the mitochondria is normally in front of the nucleus during LC migration, this marker will be used to more accurately determine LC orientation.

Knockout of Gene DIT1 in Yeast for the Production of Chitosan

Alex Kleinman ’20; Advisor: Sara Olson

Chitosan (CS) is a promising candidate for drug delivery, yet the current process of harvesting CS from crustaceans contains impurities that render it unsafe. Yeast spores naturally synthesize CS as part of their ascospore wall. Our ultimate goal is to produce pure spore-derived CS as an alternative. CS extracted from wild-type Saccharomyces cerevisiae ascospores is contaminated with other polysaccharides and dityrosine. Dityrosine is the outermost layer of the ascospore wall. Previous work sought to eliminate the dityrosine layer by using a disruption cassette to silence DIT1, the gene that controls the assembly of the dityrosine layer. We verified the existence of a DIT1 disruption via polymerase chain reaction (PCR) and then converted the DIT1 disruption to a deletion. The absence of dityrosine was confirmed by microscopic analysis with a CS specific fluorescent dye, Calcofluor White (CFW). The CFW does not stain wild-type spores but can penetrate and stain the CS layer in DIT1 mutants. Our work served as an important step toward creating yeast strains that are amenable to producing pure chitosan.

Investigating the movement of the dancing plant Codariocalyx motorius

Jason Lu ’22; Advisor: Fabien Jammes

Codariocalyx motorius, the dancing plant also known as the telegraph plant is a species that is native to India and China. The telegraph plant possesses terminal and lateral leaflets. Remarkably, its lateral leaflets move in an elliptical shape at a speed visible to the naked eye. While light and sound have been reported to affect the movement of the dancing plant, no one knows how plants could benefit from it. Our goals this summer were to (i) optimize the germination and growth of this tropical plant (ii) observe and quantify its movement in response to environmental cues and (iii) develop a protocol for the transformation, tissue culture and regeneration of the dancing plant. We show that the poor germination rate of Codariocalyx motorius seeds can be improved by scarification of the seed coats. By testing different types of soil, we optimized the growing conditions that allowed us to grow 3-4-week old healthy plants showing moving lateral leaflets. By analyzing video recordings, we then tried to characterize, in a quantitative manner, the elliptical movement of the leaflets in order to further understand how environmental stimuli can affect it. Finally, we optimized a protocol of dancing plant transformation, tissue culture and regeneration. This tool will allow us to generate transgenic plants in which particular cellular compartments or signaling pathways contributing to the movement could be tracked by fluorescence microscopy.

Cyclic Voltammetric Determination of Sulfide Reduction

Edwin Lopez Gonzalez ’21; Advisor: Edward Crane

Sulfur plays a key role in all life on earth, especially in the biological systems of extremophiles. These are organisms capable of living under extreme conditions such as really high temperatures and anaerobic environments. However, sulfur is a highly reactive element making it a very difficult substance to study with traditional analytical tools. In this study, we employed cyclic voltammetry to determine the sulfur species present in numerous solutions. We used mercury-plated gold working electrodes, created by the Crane Lab, to measure the reduction potentials of sulfur compounds, particularly sulfide, HS-. The reduction potential of sulfide was measured under various conditions including different concentrations of sulfide and in the presence of various pH levels. We found the reduction potential of sulfide with our electrodes to be between -0.60V and -0.75V. The reduction potential remained fairly consistent between conditions.

New Hominin Fossil Identified

Caleb Caton ’20; Advisor: Bob Gaines

This project identified a fossil mandible discovered in Ethiopia as belonging to a specific hominin species of either Australopithecus afarensis, early Homo (habilis sensu lato or rudolfensis), or Paranthropus boisei. Which species it is cannot be revealed until the team of international scientists publishes the paper, but this significant discovery extends the hitherto known range of one of these species. In order to quantitatively identify the species, we micro-CT scanned the fossil to create a 3D model than can be cross-sectioned in Avizo software. This allows non-invasive measuring of unexposed surfaces within the fossil. We collected tooth-root dimensions of the fossil and also created a new database of tooth-root dimensions of 30+ Ethiopian fossils belonging to the three genera listed above. The measurements were buccal-lingual distance, which is the width of the root from cheek side to tongue side, measured at the point of greatest width. We measured both premolars (P3 and P4) and the first two molars (M1 and M2). The three genera neatly grouped by buccal-lingual distance, with Homo as the smallest and Paranthropus the widest. Our new fossil clearly belongs to one of these three groups, and the presence of this species in a site where it has never been found will prove interesting to paleoanthropology scholars when published. Knowing the species’ range is important for theorizing about its preferred habitat and which other hominins it coexisted with.


How do MIXTA-like transcription factors regulate cell shape in flower petals?

Tessa Finley ’18; Advisor: Fabien Jammes

In plants, the epidermis serves numerous important functions that mediate the plant’s interactions with its environment: it is the plant’s first line of defense against infection, helps facilitate pollinator attraction, and controls transpiration. In the majority of angiosperms, conical epidermal cells in petals represent an ongoing problem with multiple competing hypotheses: they may be involved in petal hydrophobicity, pollinator attraction, and/or light scatter. We approach this problem from two main perspectives: a) an evolutionary phylogenetic analysis, which involves quantifying cell shape in various Mimulus species and comparing genes identified in silico and via qPCR as candidates for influencing petal cell shape; b) a protein functional analysis, which involves generating transgenic mutants for our candidate genes to isolate the phenotypic effects of each gene, which will help us understand what regulatory pathways they’re involved in. Preliminary confocal imaging studies suggest that cutin deposition plays a significant role in conical cell formation, so we plan to use transcriptomics to explore the up/down-regulation of hormones involved in cutin formation in our mutant lines.
Funding Provided By: The Professors Corwin Hansch and Bruce Telzer Undergraduate Research Fund

Using SCA to Predict Functionally Related Residues in eRF1

Anran Tang ’18; Advisor: André Cavalcanti

Statistical Coupling Analysis (SCA) is a method originally developed by Ranganathan (2009) based on the idea that amino acid residues within a protein function cooperatively and that its amino acid sequence should be reflective of this interaction. Through the calculation of covariance between positions weighted by measures of positional conservation in a multiple sequence alignment, SCA identifies groups of correlated residues, termed “sectors”. Owen and I have performed substantial modifications to the published versions of SCA, aiming for precise and automated analysis that incorporates high-quality and intuitive result visualizations. A Python implementation of the method was developed this summer and applied to the identification of functionally related residues in the eukaryotic releasing factor 1 family (eRF1). SCA was able to identify three sectors of residues spatially grouped in the crystal structure of eRF1. Several residues cluster around previously identified essential motifs, indicating their biochemical significance. Inter-covariance between sectors was also observed, suggesting cooperation between sectors. Following the Python implementation of SCA, I plan to apply the method to other well-studied protein families and incorporate contact mapping and in silico simulation of correlated motions within and between sectors, serving as measures of sector validity.
Funding Provided By: The Professors Corwin Hansch and Bruce Telzer Undergraduate Research Fund

Excretion of nitrogenous waste throughout embryotic development of Armadillidium vulgare

Alfredo Reyes-Guzman ’20; Advisor: Jonathan Wright; Collaborators: Kenna Schammel ’19

Throughout the different stages of their development, embryos of Armadillidium vulgare were tested for their nitrogenous waste products, including urea, uric acid, and ammonia, the three common nitrogenous waste products of animals. Marsupial fluid was also tested for ammonia and volume per embryo. Glutamine concentrations of embryos as well as juveniles were determined. During the final manca stage of embryonic development, uric acid storage excretion increased significantly while ammonia excretion declined. Marsupial fluid volume was consistent throughout development until the manca stage where it dramatically reduced. By switching to uric acid storage excretion during this period, mancas avoid exposure to potentially harmful ammonia concentrations.
Funding Provided By: Paul K. Richter and Evalyn E. Cook Richter Memorial Fund AND Rose Hills Foundation SURP Grant

Aerial and Aquatic Respiration of Littoral Isopods

Zechariah Harris ’18; Advisor: Jonathan Wright

The terrestrial isopods (suborder Oniscidea) include several basal families that inhabit the marine littoral zone. Many of these littoral species are regularly submerged in water by wave splash or high spring tides for extended periods of time. However, the respiratory structures differ between species and some are better adapted for aquatic gas exchange than others. This research focused on the respiratory capacity of six different littoral isopod species in air and seawater. Generally, it was found that most species had a decrease in VCO2 and VO2 when submerged in water with the exception of Ligia occidentalis and Ligidium lapetum, both of which possess unmodified pleopodal gills for gas exchange. Despite the possession of elaborate internal lungs, Tylos punctatus also is capable of efficient gas exchange when immersed, likely due to an ability to trap an air bubble over the pleopodal surface. Metabolic rates in air scaled allometrically with animal mass as predicted by Kleiber's Law, though the submerged rates scale with a significantly steeper exponent. All species tested survived in water for at least seven hours.
Funding Provided By: The Professors Corwin Hansch and Bruce Telzer Undergraduate Research Fund

Using CRISPR-Cas9 to identify genes involved in plant immunity

Adam Haochun Yang ’20, Advisor: Michael Brown

Understanding the genetics of plant immune system is vital, as it will help us determine how plants operate and combat pathogens. More importantly, with more insight into plant immunity, we can not only develop more nutritious crops that will grow in less-than-ideal soils, but also reduce our reliance on pesticides and fertilizers. Therefore, it is crucial to identify genes involved in immunity. In this project, from our RNAseq dataset which indicates genes that are upregulated as a response to pathogens, we were able to select the LIN6 gene, whose upregulation was then confirmed via qPCR. In order to demonstrate LIN6’s importance in plant immunity, we would also like to show increased resistance from plants when LIN6 is overexpressed, and decreased resistance when it is silenced. However, targeted gene knockout is difficult, so we have planned to use CRISPR, which involves using a Cas9-gRNA complex to remove existing genes. To accomplish this in plants, we have to clone Cas9 and the gRNA into agrobacterium to then express them in plants. Currently, Cas9 has been cloned into agrobacterium, while gRNA is still in the Ti plasmid. In the future, we would like to conduct the proof of concept experiment where we silence GFP, then knockouts of genes we’re interested in, like LIN6. Finally, we are also interested in using a dead Cas9, which will reduce expression without altering the plant DNA.
Funding Provided By: Paul K. Richter and Evalyn E. Cook Richter Memorial Fund

The Plight of the Younger Siblings in Common Terns

Clare Flynn ’19; Advisor: Nina Karnovsky

The purpose of this study was to track the productivity and growth of many species of Seabirds in the National Audubon Society’s Seabird Restoration Program (NASSRP) in the Gulf of Maine, including the Common Tern, Sterna hirundo. In the NASSRP’s islands, the inshore islands have higher S. hirundo productivity than the outer islands. I hypothesized that the difference in productivity affects the growth of the second and third chicks hatched per nest more than the first hatched. To test this hypothesis, I worked on Seal Island National Wildlife Refuge for the 2017 breeding season, where I monitored the S. hirundo nests every other day for 12 weeks. I recorded the number of nests and clutch sizes, the number of eggs per nest, and chick mass and wing chord every other day until they fledged. Using these data, along with those from the other islands and those collected in past years, I will compare the mean linear growth rates of chicks between the inshore and offshore islands. I expect that the mean growth rates of younger chicks will be significantly higher on the inshore islands than the offshore islands, but that the mean growth rate of first hatched chicks will not differ amongst colonies. I will also analyze the difference in growth rates over time to assess interannual differences in S. hirundo chick growth. This study could indicate that islands with lower availability of food have less successful younger chicks because parents focus more on the first hatched chicks.
Funding Provided By: Faucett Catalyst Fund SURP Grant

Are the maxillary glands of isopods hyper-regulatory organs?

Clayton Ziemke ’18, Advisor: Jonathan Wright

In terrestrial isopods (suborder Oniscidea), the maxillary glands are excretory organs that produce urine. In some species, the maxillary glands are capable of producing dilute urine and may be involved in hyper-regulation for other species that are regularly subject to hypo-osmotic conditions. This study examines the ability of two sand-burrowing isopod species (Alloniscus perconvexus and Tylos punctatus) to hyper-regulate their blood osmolality during immersion in hypo-osmotic solution by producing dilute urine. The study found that both species had low osmotic permeabilities and are capable of hyper-regulation, but did not find evidence for dilute urine production.
Funding Provided By: Fletcher Jones Foundation

A better vALUe: redesign of the final BIOL40 lab

Ana Stevens ’20, Advisor: Andre Cavalcanti

The PCR Lab is the final lab of the semester for Pomona College’s Introductory Genetics course (BIOL40).  Students test their own DNA for the Alu gene insert and compare the class’ data to data from ethnic populations from all over the world.  The lab is meant to leave students with a positive association with the program and with biology in general, regardless of their intended career path.  However, the web application that has been used to analyze the PCR results from the lab is outdated and inconvenient. It often crashes, especially when used by multiple groups of students at once. This wastes time and can be a source of frustration among students and instructors. Our project was to modernize the lab by completely rewriting the application used to analyze the data. We used Python and JavaScript to create a responsive interface for the data analysis of the project. Additionally, the new application is hosted at Pomona College’s domain rather than that of a third party. The redesigned lab is more efficient and user-friendly than the old version and we plan to integrate it into the BIOL40 course for the Fall 2017 semester.
Funding Provided By: Department Funding

The Degradation of Crude Oil by the Salton Sea Mud Volcano Microbes

Cleo Forman ’20; Advisor: Andre Cavalcanti; Collaborators: Micayla George ’20, Erin Su ’19

The microbes that live in the Salton Sea mud volcanoes undergo anaerobic respiration, using sulfur instead of oxygen as their final electron acceptor. This lab examines two different mud volcanoes at the Salton Sea, one at 65C, the other at 100C. The lab's previous research and outside sources, through GCMS analysis, have shown strong evidence that certain sulfate-reducing bacteria and archaea in the Salton Sea mud, do anaerobically degrade many of the BTEX compounds. However, without the presence of sulfur as the electron acceptor, no such degradation is done (Lee, 2016; Rueter et al., 1994). Therefore, there is reason to believe that the sulfur cycle, which this lab specializes in, and hydrocarbon degradation in crude oil, are linked. Analysis this summer focused on previous mud samples’ metagenomics data and we found there were significant differences in the microbial communities between 65C and 100C and that many BTEX compound degradation pathways were shown to be completed by the 65C and 100C microbe sets, to different degrees.
Funding Provided By: Rose Hills Foundation SURP Grant and The Professors Corwin Hansch and Bruce Telzer Undergraduate Research Fund

Mutating Naa20 in Drosophila using CRISPRCas9

Ellen Wang ’20; Advisor: Clarissa Cheney

N-terminal acetyltransferase B (NatB) co-translationally modifies GDP Dissociation Inhibitor (GDI), which plays a key role in the Rab-GTPase Pathway. NatB is comprised of the catalytic subunit, known as Naa20, and the non-catalytic subunit, Psidin. We will mutate the CG14222 gene in Drosophila using the CRISPR/Cas9 system, as there are currently no effective fly mutations for that gene. Previous research indicates that knockdown of the CG14222 gene using RNA interference (RNAi) yields only a few female survivors with male pigmentation on the abdomen. Knockout of the CG14222 gene can give us a deeper understanding of how Naa20 functions, in comparison to Psidin.
Funding Provided By: The Elgin Fund for Summer Student Research

Isolation and Amplification of Mitogen-Activated Protein Kinase 9 in Arabidopsis Thaliana

Michaela Ince ’18; Advisor: Fabien Jammes

Abscisic acid (ABA) is a plant hormone responsible for the regulation of stomatal aperture. Stomata are the main source of water loss in plants, and their closure is an example of an adaptive response to drought conditions. The biochemical pathway that triggers stomatal closure via ABA signaling includes two MAPK genes, MPK9 and MPK12, which are both preferentially expressed in guard cells. Previous research has shown that MPK9 and MPK12 function downstream of reactive oxygen species in the ABA-mediated pathway, and upstream of anion channel activation. Several questions involving the protein localization and the presence of protein partners of MPK9 are still unanswered. However, before beginning to study MPK9, it was necessary to isolate this gene of interest from wild type Arabidopsis thaliana. The MPK9 gene was then amplified, and cloned into an expression vector for further use on this project.
Funding Provided By: Dean’s Diversity Fund

Sphagnum Moss: Nature’s Air Gun

Michelle Lee ’20; Advisor: Dwight Whitaker; Collaborator: Pulkit Bansal ’19

Sphagnum moss uses vortex rings to disperse its spores. These vortices carry the spores up to a height of 15 cm., where they can be easily carried by the wind. In this experiment, we aim to analyze these vortex rings using computational fluid dynamics. We hypothesize that unlike the vortex rings created by animals, these rings are suboptimal. We use ANSYS Fluent to model the flow fields from Sphagnum capsules. This summer, we are simulating a simpler vortex ring system, “slug flow,” to test the validity of our models and eventually test our hypothesis.
Funding Provided By: Schulz Fund for Environmental Studies and Department Funding

Plant-Pathogen Interactions: Beans and Peas as Alternative Model Organisms for Heterologous Gene Expression

Paula Reyes Daza ’19; Advisor: Michael Brown

Understanding the genetics of the plant immune system is essential for optimizing agricultural production, since successful crops are those which effectively combat pathogens. Once a gene is proposed to be involved in defense, its role can be confirmed by gene overexpression, since an abundance of a beneficial protein should confer greater resistance. Nicotiana benthamiana is a popular model organism for this kind of research because it is susceptible to transient overexpression via agrobacterium. The goal of this project was to evaluate beans/peas as alternative organisms in which to overexpress genes. We engineered a Ti plasmid coding for green fluorescent protein (GFP) and then transformed it into agrobacterium, which we used to infect the plants and deliver the GFP gene. Our preliminary data suggests that this method for heterologous expression is successful for some beans/peas. While fava showed GFP expression only when infiltrated at two and three weeks old, peas were best infiltrated about two weeks later. The optimal age at which to infiltrate garbanzos remains unclear. Altogether the potential for peas, fava, and garbanzo beans to be alternative model organisms for immunological studies shows promise. In the future, since our preliminary transcriptional analysis suggested that expansin-like protein 1 is upregulated in tomatoes in response to multiple pathogens, this cell wall modification protein may be the first immunological-relevant gene we test in these organisms.
Funding Provided By: Biology Department Funding


Bacterial and fungal nest pathogens of Caretta caretta

Jessica Hernandez ’15; Mentor: Nina Karnovsky

Sea turtles have inhabited this planet for more than 210 million years. Even today, they are among the largest reptiles in the world, but unfortunately they are one of the most endangered animals. All sea turtles are considered endangered or vulnerable to extinction, with population declines of 30-80% in most of the seven sea turtle species. While bycatch, coastal development, predators, and pollution detrimentally impact sea turtles, another prominent threat includes opportunistic bacterial and fungal pathogens. The potential pathogens of interest in this project were Serratia marcescens and Fusarium solani, both of which have been previously found in or on sea turtle eggs and are associated with mortalities of the species Caretta caretta. To test for the presence of S. marcescens, I collected samples of cloacal mucous from the nesting mother, sand from inside the nest, and sand from 1 meter away from the nest. To test for the presence of F. solani, I collected fungal infected eggs from the nest (post-hatching). I then inoculated nutrient agar-filled petri dishes with each sample and stored them at room temperature to incubate for three days. While I have thus far observed growth of mixed colonies on all inoculated plates, all samples have been negative for S. marcescens and F. solani.
Funding Provided By: Rose Hills

Bioreactivity and Cytotoxicity of Community-Associated Methicillin-Resistant Staphylococcus Aureus (MRSA) Metabolites

Maria Vides ’18; Mentors: Julieta Aguilar (UC San Diego), Michael Dores (UC San Diego)

In recent years, methicillin-resistant Staphylococcus aureus (MRSA) has become a major challenge to public health, affecting 80,000 individuals each year and causing 11,000 deaths in the United States alone. Two main strains of MRSA have been identified, hospital-associated methicillin resistant S. aureus (HA-MRSA) and community-associated MRSA (CA-MRSA). Currently, the virulence of CA-MRSA is poorly understood. Using a peptidomics approach, six bioactive peptides were identified in CA-MRSA, which are absent in HA-MRSA. These peptides robustly stimulate primary immune cells and cause lysis of blood cells. Since CA-MRSA typically cause skin and soft tissue infection, this study will test the effects of the 6 peptides on immune cells and skin cells. Preliminary studies show that these peptides cause cell death. Further studies will identify the process of cell death by mass spectrometry and microscopy. This project will provide a new understanding of how CA-MRSA peptides damage mammalian tissues, and will lead to the development of new pharmacological avenues of intervention for the treatment of MRSA infections.
Funding Provided By: Pomona College Research Fund

Common Murres in Uncommon Numbers: The Effects of Common Murre Resurgence on Brandt’s Cormorants Nesting Behavior

Leo Estrada ’16; Mentor: Nina Karnovsky; Collaborators: Ramoncito Caleon ’15, Nicole McDuffie ‘15

The purpose of this project was to better understand the breeding habits of different species on Gualala Point Island (GPI), an important breeding site for marine seabirds in Sea Ranch, Sonoma County, California. The California Coastal National Monument Stewardship Taskforce has been using citizen science to collect data on this island from two land-based vantage points and aerial photography taken approximately every two to three weeks during the summer breeding season for the last eight years, monitoring each seasons’ individual nests, chicks, and species counts of Western gulls, pelagic cormorants, Brandt’s cormorants, pigeon guillemots, and black oystercatchers. Within this last decade, a resurgence in the presence of common murres - once native to the area but diminished by anthropogenic disturbances such as oil spills in earlier years- poses a new challenge to the ecosystem of nesting seabirds which has formed in their absence. We hypothesized that the abundance of common murres on GPI was related to the abundance of Brandt’s cormorants and predicted that the increasing number of common murres would result in a decrease of nesting Brandt’s cormorants due to competition for space in prime nesting niches. We then tested our hypothesis by comparing the nest abundance and nest density of Brandt’s cormorants before and after the arrival of the common murres - utilizing the aerial photography of GPI over the course of several years to discern the count and location of nests.
Funding Provided By: Rose Hills (Caleon), Howard Hughes Medical Institute (McDuffie, Estrada)

Computational investigation of Queuosine nucleoside tRNA modification in Eukaryotes, Bacteria and Archaea

Sathya Citturi ’18; Mentor: Andre Cavalcanti; Collaborator: Zachary Wilson ‘17

Codon usage bias refers to the observation that synonymous codons are not used with the same frequency. One major hypothesis to explain this phenomenon posits that codon usage will be optimized for translational efficiency and hence tRNA abundance should be a predictor of codon usage bias. Studies have generally found that correlation of tRNA abundance and codon usage is approximately 0.6. Further, the incorporation of domain-specific tRNA modifications into these models leads to higher correlations (Novoa et al., 2012). We studied the Q-tRNA modification present in the three domains of life with the hope of constructing a linear model to better predict codon usage. The Q-modification applies to the amino acids Aspartic Acid, Asparagine, Histidine and Tyrosine. It involves the modification of a Guanine to Queuosine in the third tRNA anticodon position. Queuosine has greater affinity for Uracil than it does for Cytosine – thus deviating from the normal Watson-Crick base-pairing. We created Python scripts to study codon usage and genomic GC content and used an open source program, tRNAScan, to determine the number of tRNA coding genes in each of the genomes. / Our preliminary study suggests that the amino acids cognate to the tRNAs containing the Q-modification have higher frequencies of U codon usage relative to amino acids that do not have the modification. This is consistent with our predictions. Further analyses must be performed for verification purposes.
Funding Provided By: Howard Hughes Medical Institute (Chitturi), Beckman (Wilson)

Dirty Water: What's in it for honey bees?

Salvatore Daddario ’18; Mentor: Philip Starks (Tufts University); Collaborator: Rachel Bonoan (Tufts University)

The agricultural crisis of disappearing honey bee colonies is alarming – the number of managed honey bee colonies has halved in the past sixty years. Although honey bees are important pollinators, there is very little known about their mineral requirements. Honey bees are often observed to forage in dirty water sources, even with clean water sources present. What is the nutritional benefit of this dirty water foraging? We conducted preference assays in the field in order to determine the water-soluble minerals that bees prefer. We also sought to explore how these mineral preferences might change across the seasons. We found that honey bees preferred sodium in both summer and fall, and showed preference to calcium, potassium, and magnesium in the fall, but not the summer. As pollen contains these three micronutrients in the highest amount (1), we believe that this variation is due to the available floral resources. In the summer, more flowers are available; therefore, the bees do not show a preference for these three nutrients. From these findings, we learned that honey bees selectively forage for minerals, suggesting that they have an optimal diet. With this new knowledge, beekeepers can develop more precise, less expensive diet supplements that will improve hive health – specifically, for monoculture-subjected hives. (1) Herbert, E.W., Miller-Ihli, N.J. 1986. Seasonal Variation of Seven Minerals in Honey Bee Collected Pollen. Am. Bee J. 127: 367-369
Funding Provided By: National Science Foundation (Tufts University)

Factors Driving Early Decomposition Processes in Low Elevation Habitat Types of Southern California

Madison Dipman; Mentor: Wallace Meyer

Type conversion of California sage scrub (CSS) to non-native grasslands is dramatically changing the landscapes in low elevation areas of Southern California. Because type conversion alters many functional attributes, it is necessary to assess how these ecosystems function following landscape transformations. Litter decomposition is a key ecosystem process that releases carbon to the atmosphere and provides nutrients in forms that can be used for respiration. Broadly, litter decomposition is influenced by factors related to litter quality, climate, and site quality. In this experiment, we manipulated litter quality (C:N), UV radiation, and macroinvertebrate access in CSS and non-native grassland habitats to provide a framework for understanding the factors driving early decomposition processes in the LA Basin. Litter type, UV, and habitat all significantly affected the rate of decomposition; however, UV played the largest role, and its relative contribution was dependent on habitat type. The primary driver of decomposition varied seasonally, suggesting simple models of decay lacking a temporal component fail to account for additional effects of landscape changes on decomposition processes. Overall, decomposition was significantly accelerated in the non-native grassland, which supports previous research that type-converted grasslands store less C in stable pools than native CSS and contradicts work from studies limited to grass-invaded CSS systems.
Funding Provided By: Howard Hughes Medical Institute

Knocking Down GDI in Drosophila Melanogaster

Taurean Brown ’18; Mentor: Clarissa Cheney

GDP Dissociation Inhibitor (GDI) is a protein found in Drosophila melanogaster, as well as other organisms, which has been found to be an integral part of vesicle transport in cells due to its control over the G-protein family of Rabs (Figure1). In order to test this mechanism for vesicle transport we attempted to knock down GDI in the pigment granules in the eye of Drosophila melanogaster, which are essentially modified vesicles (Figure 2). By eliminating GDI in the eye there should be a visible loss in pigmentation. / We were able to knock down GDI by manipulating Gal4/UAS system and a GDI/RNAi transgene. Three eye drivers 9146, 8605, and 1104 were crossed with the RNAi 57502 and subsequently the progeny of these crosses was scored. The results of the crosses yielded no observable pigmentation changes in the eye. As a result of this we attempted to test the effectiveness of the eye drivers and the RNAi we were using by crossing them with the 36328- tomatoRFP and 4414 Actin Gal 4 driver respectively. The results of these crosses revealed that all of the drivers as well as the RNAi were functional, however the RNAi may not be that strong. On a western blot probing with an anti-GDI antibody the amount of GDI present in the 4414 Actin Gal 4 ;RNAi showed a equal or negligible decrease in the amount of GDI present indicating also that this particular RNAi is weak.
Funding Provided By: Pomona Unrestricted

Measurement of Endogenous Phenolic Content of Intact Chloroplasts

Irene Hsiung ’16; Mentor: David Becker

Phenolics, a class of organic compounds that consist of one or more hydroxyl groups bonded directly to an aromatic hydrocarbon, are the most abundant secondary plant metabolites. Such compounds include cannabinoids, capsaicin, and salicylic acid. We are interested in the ability of phenolic compounds to act as alternate electron donors to photosystem I (PSI), when photosystem II (PSII), the normal source of electrons, is inhibited due to heat stress, a process that we have shown to occur in vitro. Because the photosynthetic electron transport chain is localized to the chloroplasts, we used a recent, rapid method to isolate intact chloroplasts from spinach leaves, which we measured for endogenous phenolic content by two independent spectrophotometric assays. Both the Folin-Ciocalteu (FC) and Prussian Blue (PB) assays are based on the transfer of electrons from phenolics to a colorimetric reagent and are susceptible to interference from other oxidation substrates especially ascorbate, which is abundant in chloroplasts. Using the method of standard additions, we were able to correct for ascorbate and other interferents. We determined a net phenolic content of 2.85±0.17 •moles/•mole chlorophyll in spinach chloroplasts via both assays. Next, we will make these measurements in isolated Larrea chloroplasts to assess whether they contain sufficient endogenous phenolics to support significant amounts of electron donation to PSI, as we hypothesize.
Funding Provided By: Steller

Microbial Community Analysis of the Mud Volcanoes at the Salton Sea (CA)

Marlie Shelton ’16; Mentors: EJ Crane, Andre Cavalcanti;

Located in the San Andreas Rift Valley of California is the Salton Sea, an environment which experiences a high degree of both geologic and thermodynamic activity. An interesting phenomenon within this environment are the mud volcanoes, which are anoxic and extremely hot gurgling vents that lend themselves to extremophilic microbial activity. An understanding of the microbes present in these mud volcanoes is the first step in determining their mechanisms of sulfur reduction and their greater role in biogeochemical cycles. The highly conserved gene in the 16s rRNA region is targeted in this study, through both clone library production and next-generation sequencing, in order to provide a catalog of the microbial species present.
Funding Provided By: Fletcher Jones

Nest location as a predictor of success in two species of nesting seabirds

Jeffrey Allen ’17; Mentor: Nina Karnovsky

Gualala Point Island (GPI) is a small offshore island off the coast of The Sea Ranch, in Sonoma County, California where seabirds have been studied since 2007. In 2014 and 2015 students from Pomona College studied the nesting success of Brandt’s cormorants (Phalacrocorax penicillatus) and Western gulls (Larus occidentalis) nesting on the island. . The purpose of my study was to better understand the factors that influence nest success and failure for these seabirds. In particular I am interested in how nest location influences reproductive success, particularly whether past success at a nest site predicts future success. I predicted that prior success would predict future success, and that areas that supported successful nests in 2014 would support successful nests in the 2015. To test this hypothesis I made almost daily observations of Brandt’s cormorants and Western gulls breeding on GPI through a spotting scope. I recorded nest location and the number of eggs laid, and hatched and the number of chicks fledged. I used high quality photos to compare these data to those collected in 2014. This season there were nine new Brandt’s cormorant nest locations with eight of those locations failing before their chicks had hatched. / While nest site is not the only factor influencing reproductive outcomes, it appears to be an important predictor of success.
Funding Provided By: Faucett

Pollinator foraging at resources with variable rewards

Tessa Finley ’18; Mentor: Matina Donaldson-Matasci (HMC); Collaborator: Clayton Ziemke ‘18

Pollinator habitats are undergoing major shifts as a result of rapid environmental change. Pollinators with different traits – life histories, foraging strategies – are differently equipped to be part of communities in flux. How do organisms with a certain set of evolved behaviors respond to a variable environment? In Southern California, most native pollinators’ foraging seasons are synchronized with the blooming periods of host plants, but honeybees forage all summer, which seems to confer a disadvantage. However, their foraging strategy, which is based on the waggle dance colony communication system, is versatile in the sense that it enables them to quickly locate and mobilize to good resources. To compare the foraging strategies of honeybees and native pollinators at resources with different rewards, we observed pollinator visitation per flower at selected ‘large’ and ‘small’ resource patches as blooms senesced over time. Previous research suggests that, compared to native pollinators, 1) honeybees are more able to take advantage of rewarding resources due to efficient colony communication, and 2) honeybees can afford ‘exploratory’ foraging at less rewarding resources by risk-sharing within the colony, whereas native pollinators (mostly solitary, or living in smaller groups) must concentrate on foraging at certainly rewarding resources. Based on these hypotheses, we predicted that 1) more honeybees would visit flowers in ‘large’ than ‘small’ patches while native pollinators would visit each equally, and 2) honeybees would forage more persistently at senescing resources, unless their versatile foraging strategy allows them to respond to the regional costliness of ‘exploratory’ foraging by concentrating on the most rewarding resources. Initial data suggest that honeybees do forage more frequently at large patches, while native pollinators show no preference; and honeybees continue to visit senescing resources while native pollinators quit those resources, suggesting that ‘exploratory foraging’ is regionally maladaptive.
Funding Provided By: Howard Hughes Medical Institute

Telomerase Activity of Aging Hydra and Telomere Length Across Species

Ian Thomas ’17; Mentor Daniel Martinez

Asexually reproducing Hydra vulgaris can be maintained in a laboratory setting for many years without showing any signs of senescence (Martinez 1998). When cultured at 10°C, however, Hydra oligactis become sexual and exhibit physiological deterioration and eventual death (Yoshida et al., 2006). Telomeres have long been held to play a role in aging and the maintenance of stem cells. Hydra telomeres possess the same repeating sequence found in vertebrates (TTAGGG), capping the ends of chromosomes, as well as telomerase, the enzyme responsible for elongating telomeres. Understanding the telomere biology of hydra may help us understand aging and stem cell maintenance. Tan et al. (2012) revealed that in planarian flatworms, the type of reproduction (sexual or asexual) mediated the expression of telomerase. Further, Bertozzi (2015) characterized the telomerase activities of sexually induced female H. oligactis. This project aims to provide a similar profile for male H. oligactis, thus creating a more comprehensive view of telomerase activity throughout the process of sexual induction in Hydra. Further we hoped to uncover whether telomere length varies across the species of hydra. It was hypothesized that males exhibit an increase in telomerase activity during the first 11 days of induction, as had been shown in female hydra. It was also hypothesized that telomere length would not vary significantly between species of hydra.
Funding Provided By: Howard Hughes Medical Institute

The Effect of Fire on Vertebrate Species Composition at the Bernard Field Station

Elika Nassirinia ’17; Mentors: Nina Karnovsky, Wallace Meyer

The purpose of this study was to examine differences in vertebrate species composition between burned and unburned areas in the BFS. In 2013 a fire burned approximately 20 percent of the Bernard Field Station, providing an opportunity to study the effects of fire on vertebrate species. I hypothesized that species composition differs between burned and unburned areas. I predicted that species that prefer open areas would be more common in burned areas, and those that prefer more densely vegetated areas would be more common in unburned areas. I tested this hypothesis by setting up 11 motion sensing cameras, with 6 in burned areas and 5 in unburned areas. I studied pictures from each camera from the months of February until June, and noted the type and number of species “trapped.” I ran an ANOSIM test using the Bray Curtis similarity coefficient to examine if species composition differed between burned and unburned sites, and carried out SIMPER analysis to determine which species contributed to differences in composition. I found that species composition differed significantly in burned and unburned areas. While the woodrat, Neotoma sp., Western scrub jay, Aphelocoma californica, and California thrasher, Toxosoma redivivum, were only found in unburned sites, the Northern flicker, Colaptes auratus, and the majority of kangaroo rats, Dipodomys agilis, were found in burned sites. Results may be explained by species preference for either densely vegetated or open areas.
Funding Provided By: Thoreau Foundation and Rose Hills Foundation

The Effects of the 2015 El Niño on the Nesting and Breeding of Western Gulls and Pelagic Cormorants

Kyle Jensen ’17; Mentor: Nina Karnovsky; Collaborator: Ramoncito Caleon ‘15

The purpose of this project was to compare the breeding habits and success of two seabird species breeding in the area of Sea Ranch, Sonoma County, CA during two years, one of which (2015) had anomalous oceanographic conditions (El Niño). Seabirds get all their food from the ocean and are therefore sensitive to changes in the ocean that impact availability of their prey. We hypothesized that El Niño has a negative impact on breeding seabirds. We predicted that the timing of nesting would be later and that the success of raising chicks until they are flight capable would be lower in the El Niño year. We tested this hypothesis by collecting data for ten weeks on nest conditions, the number of eggs and chicks visible, and the developmental stage of chicks by observing mapped nests through spotting scopes in both years. A group of pelagic cormorants (Phalacrocorax pelagicus) at Breakers Reach and a group of Western gulls (Larus occidentalis) at Gualala Point Island were the focus of our study. Western gull chicks were first observed to take short flights around 7/25 in both 2014 and 2015. Pelagic cormorant chicks were observed at Breakers Reach as early as 6/2 in 2014, but were not observed in 2015 until 7/7. It seems likely then that pelagic cormorants may be more affected by the anomalous oceanographic conditions of 2015 than Western gulls, though further analysis will need to be conducted to fully assess the nesting success and timing of these birds between the two years.
Funding Provided By: Schulz (Jensen), Rose Hills (Caleon)

The Effects of Type Conversion and Suburban Development on Southern California Arthropod Communities

Savanah Bird ’18; Mentor: Wallace Meyer; Collaborator: Savannah Meadors ‘18

California Sage Scrub (CSS) is an endangered ecosystem type threatened by type-conversion to non-native grasslands (NNG), and encroaching urban/suburban development. Estimates suggest that less than 10% remains from its prehistoric range. To examine how landscape modifications influence ground dwelling arthropod (GDA) communities, we surveyed GDA communities using 120 pitfall traps (passive collection for ground-dwelling arthropods) at 40 sites (3 pitfall traps per site) in CSS (16 sites), NNG (8) and suburban habitats (16) at and near the Bernard Field Station for 5 seasons (Spring 2013 to Spring 2014). In total, 17,902 individuals and 279 species from at least 11 arthropod orders were inventoried. CSS, NNG, and suburban habitats significantly differed from one another in arthropod composition. Many species were only collected in one habitat type: suburban (87; 31%), CSS (51; 20%) and NNG (17; 6%) further supporting that each habitat supports a unique fauna. While species richness was highest in the suburban habitat, 50% of the 10 most abundant species are known non-natives. The NNG habitat had the lowest species richness and few species unique to that habitat (17) indicating an overall loss of GDA diversity following type conversion. As such, our results highlight that preventing type-conversion and preserving CSS is essential for supporting native arthropod species, and that conditions in non-suburban sites may limit establishment of many non-natives.
Funding Provided By: Pomona Unrestricted (Bird), Thoreau Foundation and Pomona College Research Fund (Meadors)

The Role of Anrkd2 in insulin Sensitivity

Nhu Y Doan ’18; Mentor: Angelina Hernandez-Carretero (UC San Diego); Collaborator: Natalie Weber (UC San Diego)

Obesity is a disease that is correlated with a decrease in the body’s ability to respond to insulin, also known as insulin resistance. Patients with diabetes are either insulin deficient or insulin resistant, causing them to have impaired functional processes such as insulin-stimulated glucose uptake of the muscle. In order to further study insulin sensitivity of the muscle, we have used RNA-seq to discover novel genes that change in conditions of lean (LF), obese (HF), or previously obese mice that have restored insulin sensitivity (SW). We found that expression of ankyrin repeat domain protein 2 (Ankrd2) was reduced in muscle tissue of HF group and reversed in SW group. It is hypothesized that Ankrd2 contributes to insulin sensitivity in the muscle and that reduction of Ankrd2 results in impaired insulin-stimulated glucose uptake. To this end, siRNA-mediated knockdown of Ankrd2 was utilized in a dose dependent manner on rat L6 myotube cells. In addition, radiolabeled glucose uptake assays were performed to measure insulin sensitivity of L6 cells under these conditions. Preliminary results show that about 75% knockdown of Ankrd2 expression impairs insulin-stimulated glucose uptake by 1.5-fold. These data suggest that methods to increase Ankrd2 will improve insulin sensitivity in the muscle. Overall, this study will determine whether Ankrd2 is a useful therapeutic target to enhance insulin sensitivity of obese and diabetic individuals.
Funding Provided By: UC San Diego Institutional Research and Academic Career Development Award Summer Undergraduate Research Fellowship

The Role of PLK-1 Phosphorylation on SPD-5 PCM Assembly in C. elegans

Delfina Gonzalez ’17; Mentors: Sara Olson, Karen Oegema (UC San Diego), and Stacy D. Ochoa (UC San Diego)

Animal cells require centrosomes to nucleate and anchor microtubules (MT) during mitosis. Centrosomes consist of a centriole pair enveloped in a network of pericentriolar material (PCM). Once PCM maturation has occurred, microtubules anchor to the γ–TuRC complex for proper spindle assembly. Several proteins are required for PCM assembly and maturation, including SPD-5, a scaffolding protein, and polo-like kinase (PLK-1), a phosphorylating protein. Previous research has shown that PLK-1 aids in the recruitment and assembly rate of SPD-5 complexes in the PCM both in vitro and in vivo. This mechanism however, remains poorly understood. We have thus identified potential PLK-1 phosphorylation sites on SPD-5 to mutate in order to understand how Plk1 contributes to PCM assembly. We are analyzing the consequences of making transgenic worms with these mutations. After knocking down the endogenous SPD-5 gene using RNAi, we conducted embryonic lethality and single-cell embryo fluorescence imaging studies. Preliminary results show increased embryonic lethality, decreased SPD-5 fluorescence, and decreased γ-tubulin fluorescence in both a single-point mutant and a four-point mutant. These results indicate that phosphorylation at these sites have an effect on PCM assembly and maturation. This in turn affects cell cycle dynamics and overall embryonic survivability.
Funding Provided By: UC San Diego Institutional Research and Academic Career Development Award Summer Undergraduate Research Fellowship


Studies on the eye color mutation in Drosophila

Bianca Rodriguez ’17; Mentor: Clarissa Cheney;

Funding Provided By: Howard Hughes Medical Institute

What's the scoop on skua poop? Ages and sizes of Electrona antarctica and Pleurogramma antarcticum consumed by South Polar skuas on King George Island

Miranda Starr ’15; Mentor: Nina Karnovsky; Collaborator: Joel Llopiz (Woods Hole Oceanographic Institution)

The purpose of this study was to determine the ages and sizes of fish consumed by South Polar skuas (Catharacta maccormicki) breeding on King George Island on the Antarctic Peninsula. By analysing guano samples collected over 7 breeding seasons, I was able to determine that two fish species dominated their diets (>95% of all fish consumed): Electrona antarctica and Pleurogramma antarcticum. I hypothesized that there is a positive relationship between the size of the otolith and the size and age of the fish. To test this hypothesis, I measured and aged otoliths from high-resolution photographs taken after several weeks in immersion oil. Preliminary results indicate that otolith size is predictive of both size and age of fish. Furthermore, our findings suggest that specific cohorts of fish can be detected in skua diets. These data will be used to identify and track cohorts in seabird diets to link ice conditions and cohort success, and ultimately to present a mechanism through which the reproductive success of these birds is impacted by climate change.
Funding Provided By: Schulz

The Effects of Fire and Type Conversion on Southern California Vertebrate Composition

Savannah Meadors ’18; Mentor: Wallace Meyer; Collaborator: Savanah Bird ‘18

California Sage Scrub (CSS) is an endangered ecosystem type, threatened by type-conversion of CSS to non-native grasslands (NNG), which is facilitated by increasing fire frequency. Once non-native grasses are established, they promote more frequent fires perpetuating a cycle of grass dominance. To understand how vertebrate community composition is affected by these disturbances at the Bernard Field Station, motion-activated cameras were used to track vertebrate activity in CSS, NNG and burned habitats. We used a total of 15 downward facing cameras set up on t-posts, with 5 cameras in each habitat type. Photos were collected for one week each month. Over five months (Feb-June), 21 vertebrate taxa, 5 mammal, 5 reptile and 11 bird, were inventoried. Through ANOSIM analysis, we also found that CSS, NNG, and burned habitats significantly differed in vertebrate composition. While 29% of species were unique to CSS, NNG and the burned habitat supported species like the side-blotched lizard, kangaroo rat, and whiptail lizard in greater abundance than CSS. From this, we determine that CSS is vital for native species survival, but that NNG and burned habitats may also support some native species as supplements to CSS. Combined, our results underscore that fire is a natural component of the ecosystem and critical to maintaining a diversity of species. However, if fire becomes too frequent, facilitating type-conversion of CSS to NNG, loss of local diversity should be expected.
Funding Provided By: Pomona Unrestricted (Bird), Thoreau Foundation and Pomona College Research Fund (Meadors)

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 sulfur, 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 Fairchild 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 altricial 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 Institute)

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 analyzed 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