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Research Presentation Video

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

Alternate Phenolic Electron Donors to Photosystem I

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

Abstract removed upon request.

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

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

Abstract removed upon request.

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

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

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

Climate Linked Range Shift in Southern California Endemic Conifer

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

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

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

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

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

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

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

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

Natural Revertants in Hydra oligactis

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

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

Evolution of Adaptive Immunity

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

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

Evolutionary Origins of Adaptive Immunity

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

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

The role of SGEF in glioblastoma multiforme invasion

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

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

Biomimcry in Architecture and Engineering: Innovation from Nature

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

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

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

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

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

Color Morph Specific Predation on Clay Models of Uta stansburiana

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

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

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

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

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