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Program: Jung Summer Research Fellowship for Biological Science
Faculty: Dr. Chad Barber, Biology
Student: Tristen Burt

With over 7.6 million people losing their life to various cancers every year, a demand exists for answers to how cancer metastasizes, regulates, and proliferates. As of 2007, promising advancements were suggested in the area of altered cancer metabolism as a potential therapeutic target. Characterized by Otto Warburg in the 1920’s, the glycolytic phenotype describes an up-regulation of glycolysis in transformed cells. Little is understood of this aberrancy observed in cancer cells, however it is thought to aide as a key promoter of cancer metastasis. An investigation was conducted into identifying and characterizing the glycolytic phenotype in Canine in situ carcinomas across different tumor lines, in order to confirm the presence of the glycolytic phenotype. Several tumor lines (mast cell tumors from multiple specimens across varied anatomical locations) MCT1, MCT2, MCT3, MCT4, and (sebaceous adenomas) SA3 and SA4 were harvested from Arroyo Vista Veterinary Hospital and grown in vitro. Concurrently, mRNA was purified from the samples via RT-qPCR. 3T3 Mouse Fibroblast cDNA was used as a control. Key genes contributing to the glycolytic phenotype were found to be upregulated in canine tumor cells when compared to control cells. Further optimization of real-time conditions, using the organism’s blood as a control, will yield more certainty.  The cell lines observed in this study are candidates for further study of the Warburg Effect in canine cancers. 

Program: Darling Summer Research Fellowships for Applied Scientific Computing
Faculty: Dr. John Deisz, Physics
Student: Dominic Lunde

Several experimental studies have revealed that atomic-scale striped structures appear in several superconducting compounds. These stripes are believed to represent regions of enhanced magnetism and/or electron density. Despite extensive work by many researchers, there is still no accepted explanation for why stripes appear and whether these stripes are accidental or central to superconductivity. The aim of my work is to address this issue via computer simulations.

Procedure: Using C++ I created a model of a superconductor. I made simplifying assumptions in order to make the calculation time reasonable and therefore the code is less accurate but quicker than other models. I created the ability to nudge the model in different striping patterns and used that to test which type of striping patterns that the model reacted to most strongly. This hopefully tells us what type of striping patterns that the physical superconductors might actually be experiencing. I compared my code with a similar lower level code created by my adviser, Dr. Deisz, to confirm that they match. I am currently testing whether 2 different striping patterns are affected by different temperatures near the super-critical temperature, using a more accurate code developed by Dr. Deisz.

Results: I tested my code to confirm that it compared to physical experiments and all tests were positive. Secondly, I found that striping the magnetization in oscillating directions had the most potential to be part of the striping pattern in physical superconductors. However, in my preliminary results from the more accurate code I have found that there does not seem to be a correlation between striping strength and temperature, as is observed in real superconductors. 

Conclusions and further directions: I am performing my simulations for larger systems of atoms with the hope that this will produce more conclusive results that are in alignment with experimentation. However, these calculations will take weeks or months using a powerful scientific workstation to find conclusive results. We will also explore other potential striping patterns that might explain the striping observed in superconductors.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Katherine Hoffmann, Chemistry
Student:

A lack of iron inside bacteria leads to the secretion of siderophores (small molecule metal chelators) to acquire iron from the external environment. Siderophores have high affinity for ferric iron (Fe³⁺) outcompeting host chelators, and making them virulence factors in infection. Some siderophores are assembled via a nonribosomal peptide synthetase (NRPS)-dependent pathway, a well-studied and understood pathway utilizing large complexes and poly-ketide reactions. A second pathway for siderophore biosynthesis is the NRPS-independent siderophore (NIS) pathway. In this different pathway, enzymes are small and independent, and create siderophores with hydroxamate and carboxylate functional groups, using ATP as the energy source to drive the reaction. NIS synthesized siderophores are increasingly associated with virulence in pathogenic bacteria, and evade the human immune response during infection. Understanding the structure of NIS siderophore biosynthesis enzymes may lead to the design of specific inhibitors, or antibiotics, to fight pathogenic bacteria.

The Hoffmann lab uses x-ray crystallography to determine the protein structure of NIS synthetase DesD, from Streptomyces coelicolor. DesD makes the siderophore desferrioxamine, requiring three iterative bonds and a macrocyclization event. DesD is one of the best biochemically characterized NIS synthetases so far, and this structure is solved as a model for the rest. DesD has an active site for substrate binding, which enables it to function; if mutated carefully, the active site is functionally changed and cannot do the chemistry on the substrates, thus inactivating the enzyme. The goal of this project was to crystalize DesD bound to various substrates, as well as apo (empty of substrates), in order to characterize the conformational changes that may occur with binding. Mutant DesD both apo and bound to ATP and desferrioxamines were found in a crystal solution of 0.16 M magnesium chloride hexahydrate, 0.08 M TRIS hydrochloride pH 8.5, 24% PEG 4,000, and 20% glycerol. X-ray diffraction data will be collected and used to solve and refine the structures of DesD. This structural information may allow for the design of an inhibitor that will prevent the binding of substrate in future work.

Program: Jung Summer Research Fellowship for Biological Science
Faculty: Dr. Theresa Rogers, Biology
Student:

Cancer is one of the leading causes of death in the world, killing over 8 million people a year (World Health Organization, 2015). Many successful anticancer compounds are produced by terrestrial plants, marine plants, slime molds, and microorganisms isolated from soils (Cragg & Pezzuto, 2015; Kahn, et al., 2011). Soil is abundant with microorganisms that produce chemical weapons, such as antibiotics, in order to compete for resources by killing or inhibiting the growth of other microorganisms (Hibbing, et al., 2010). In the search for novel anticancer compounds, I isolated microorganisms from soil associated with the roots of a pomegranate tree in California Lutheran University’s very own SEEd Garden and then screened for the inhibition of cancer cell growth and induced cancer cell death. First, the soil sample was serially diluted, plated on glycerol yeast extract media, and incubated at 25°C for 3-5 days. Two hundred isolates were organized and grown on master plates. Each colony and the immediate surrounding media was cut out of the plate, placed in a microfuge tube, and frozen at -20°C. To extract potential antibiotics, the agar plugs were incubated at 4°C in 1.5 ml of RPMI media for 24 hours. Each extract was filtered twice through a 0.22 µm filter and then added to U937 cancer cells (male histiocytic lymphoma cells) (Chanput et al., 2015). To screen the extracts for anticancer effects, U937 cells were counted using hemocytometry to determine cell concentration. Most colony extracts had no noticeable effect on U937 cell growth or death.  One of the screened colonies, #62, reduced U937 cell concentration relative to negative controls. In future work, extract toxicity to non-cancer cells will be tested against 3T3 mouse fibroblast cells (American Type Culture Collection, 2016). If non-toxic to non-cancer cells, the anticancer compound can be further isolated from cell extracts and identified. 

Program: Steven Dorfman Research Fellows Program in the Environmental Sciences
Faculty: Richard W. Hurst, Geology
Student: William P. Zimmerle

The Desert Pupfish is an endangered species that inhabits small ponds and springs in the Amargosa River Basin (ARB) and other areas proximal to Death Valley.  The sources of water for the pupfish habitats are derived from groundwater aquifers.  One aquifer is a deeper, regional carbonate aquifer.  The second groundwater source is comprised of numerous shallow, silica-rich alluvial aquifers.  Little is known about the relative contributions of the deeper versus shallower aquifers to the ponds and springs that the desert pupfish inhabit.  A conflict arose when a solar facility was proposed in the area by a German company, Solar Millennium.  The operation of the solar facility would require extraction of groundwater not only to produce electricity, but also for use by the personnel working at the facility.  However, given the uncertainty in the source or sources of water feeding the pupfish habitats, extraction of groundwater could seriously impact this endangered species of fish as well as local ecosystems and people living/working in the region.  The objective of the present study was to integrate isotopic and major element geochemical analyses of pond and spring waters in order to further:

• Assess the relative contributions of the deeper carbonate versus shallower silica-rich alluvial aquifers to the pupfish habitats; and
• Evaluate the amount of mixing among groundwater in the Amargosa River Basin.

Geochemical data from 22 separate wells were statistically analyzed via multivariate plots of the isotopic and major element data.  The data define linear arrays indicating ARB groundwater feeding the desert pupfish habitats is commingling.  Results show minimal hydraulic connections between the shallow alluvial and deep carbonate aquifer.  However, there is hydraulic connectivity among shallow groundwater aquifers feeding the pupfish habitats. The latter conclusion indicates that extraction of groundwater from any shallow groundwater aquifers in the ARB would likely have detrimental effects on the desert pupfish habitats.

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Michael McCambridge, Education
Student:

Many teachers overlook the importance of knowing their students and choose to focus solely on the basic knowledge that students need to learn in order to get to the next level of their education. It is the teacher’s duty to not only teach but to also assist in the journey of development and growth students go through, as this is the basis for positive working relationships with our students in and out of the classroom The purpose of our research was to explain how adolescents develop physically, cognitively, socially and personally to deepen understanding, and then use this information to develop teaching practices to give students the best chance at success.  In the beginning stages of our research, we looked at adolescent development from two different standpoints, books and articles found in the Cal Lutheran database and CDC surveys which focused on different aspects of adolescent development. We took these findings from each and compared the themes found in both. Then, researched how teachers can use this information to appropriately and efficiently teach their students.  We found that risk-taking behavior; leadership and peer relationships were the three factors that strongly affected student learning. Teaching performance expectations are important in the classroom and go hand in hand with the prevalent factors found in adolescent development. For example, TPE #8: Learning about students, is one of the most important because in order to successfully teach your students, you must know them, which could be something as simple as greeting them at the door. TPE #13: Professional growth, is important as well and through various programs, teachers can help students achieve higher education and beyond.  These findings provided the foundation for Phase 2 of our research, which will include interviews with adolescents. 

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Theresa Rogers, Biology
Student:

Antibiotic resistance is a growing issue, as the introduction of new antibiotics cannot compete with the increase of resistance in pathogens. One opportunistic pathogen that has acquired resistance to multiple antibiotics is methicillin-resistant Staphylococcus aureus (MRSA). S. aureus is a common bacterium found on the skin and in the noses of individuals where it is generally harmless. This bacterium can cause an infection when introduced into an open wound and may even lead to death if it enters the blood stream. With the increasing incidence of MRSA infections and acquisition of resistance to the so-called “last resort” antibiotics, such as vancomycin and daptomycin, treatment of multi-drug resistant S. aureus has become a major obstacle in medicine.

The majority of antibiotics used in clinical settings, such as penicillin, streptomycin, and tetracycline, were originally derived from soil microbes that produce antibiotics in order to compete with other microbes for resources. The plethora of microbial diversity in soil has yet to be fully investigated; therefore soil remains a potential reservoir for the discovery of novel antibiotics. In this study, we joined a collaborative research effort, The Small World Initiative (Hernandez, Tsang, & Handelsman, 2015), in the search for novel antibiotics produced by soil microbes that will inhibit the growth of multi-drug resistant pathogens such as MRSA.  We collected soil surrounding the roots of Heavenly Bamboo, Nandina domestica, and cultured soil microorganisms by plating dilutions of the soil onto a variety of microbiological media. Over 200 colonies were isolated and screened for production of antibiotics that inhibit the growth of Staphylococcus cohnii, a safe relative of S. aureus. Some notable isolates that inhibit S. cohnii growth are KB20, KB36, KB103, KB151, KB152, and KB159. The antibiotic produced by isolate KB20 has been successfully extracted from KB20 culture media. We are currently purifying the antibiotic in order to perform structural analysis to determine if we have in fact isolated a novel antibiotic.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Craig Reinhart, Computer Science
Student: George Nasr

This research focuses on a design for a live simulation of the physics of a droplet of fluid hitting the ground, bouncing and sloshing around, as if it was a droplet of water interacting with a large flat surface of water in slow motion, or gelatin hitting the ground.         

The model was assumed to be in two-dimensions, to be later expanded to m dimensions. A particle system was used to design the physical interactions that dictate the motion of the droplet. The particles were represented as corners on an n-sided regular polygon (n-gon). In order to simulate interactions between particles, forces were defined. Specifically, there were three forces utilized: the force of gravity (pulling all particles in a particular direction), the force of particles pushing on one-another (with the magnitude dependent on the distance between particles), and the force of neighbors (keeping the distance between all particles that share an edge on the n-gon the same as the desired length of sides of the n-gon). Newtonian physics was used to determine the acceleration from the sum of forces acting on each particle (by simply dividing by the mass of the particle). Then, the Runge-Kutta fourth order numerical integration technique was used to approximate the position of each particle at every time step for the duration of a given simulation. The simulation was created in Java, including a graphical user interface, which allows for live visibility of the droplet, interactions between user and the droplet (external forces), and the manipulation of system parameters (such as the number of particles, the magnitude of gravity, and more).      

The simulation environment included all the above described features in both two and three dimensions, with the exception of user interactions (allowed only in two dimensions). For systems consisting of up to 200 particles, the simulation ran in near real time on a standard off-the-shelf laptop computer. For larger numbers of particles, the system did not meet desired performance goals. Future research will consider optimizing algorithmic implementations.

Program: Darling Summer Research Fellowships for Applied Scientific Computing
Faculty: Dr. John Deisz, Physics
Student:

Superconductors are materials that have one-hundred percent electrical efficiency at very low temperatures. Superconductors have different properties based on how the electrons are paired in the material. We can use computer modeling to find the type of electron pairing in these superconductors. The purpose of this research was to determine if purple bronze, Li_0.9Mo₆O₁₇, is a spin triplet superconductor. In spin triplet pairs, the magnetic north poles of the paired electrons are aligned in the same direction. We used numerical models to determine this. In order to make these numerical models, we used the C++ programming language, the GNU Scientific Library, and the emacs text editor. First, we constructed basic tight binding models for electrons in metals. These models describe the movement of electrons between atoms in the material. We then can find the eigenpairs of a specially constructed matrix called the Hamiltonian and place them into the Green’s function, a function that tells us the energy of the system and whether the system is magnetic. This is important because spin triplet superconductors originate in materials that become magnetic at low temperatures. Since purple bronze is believed to be a spin triplet superconductor, we want to see these special magnetic properties in the results of our model. We found that our results show that purple bronze is a good candidate to be a spin triplet superconductor. We showed that the critical temperature at which the material becomes magnetic increases as the interaction strength increases. This research could show us why purple bronze is a superconductor and why it has certain properties. Once we can find what makes a material act like a superconductor, we can increase these factors in materials. This would allow us to form superconductors that could work at higher temperatures. This could make superconductors more accessible which could make the use of electrical energy more efficient.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Dennis Revie, Biology
Student:

Previous studies have shown that Hepatitis C Virus (HCV) not only infects hepatocytes, but also leukocytes. Receptors known to be used for viral entry of HCV are: CD81, SRB1, CLDN1, OCLN, and NPC1L1. Expression of LDLR, ANKRD1, CD5, TFRC and PIM1 have also been shown to be involved in HCV entry. To determine if the known genes responsible for viral entry were differentially expressed in monocytes before and after infection with HCV, RNA from U937 cells was sequenced. To prepare samples for sequencing, the Illumina TruSeq Stranded mRNA Library Prep Kit was used to convert RNA into DNA. The Illumina MiSeq was used for sequencing the samples. BaseSpace Sequence Hub was used to analyze the data generated by the MiSeq system. First, RNA-Seq Alignment was performed using the STAR Aligner to map the reads, estimate FPKM of reference genes, and assemble novel transcripts.  Second, Cufflinks Assembly and DE was used to perform differential expression of novel and reference transcripts with Cuffdiff 2 using the reference Homo sapiens genome. After sequencing, 7.9 million high quality reads for the sample from uninfected cells were obtained. For the sample from the infected cells, 11.6 million reads were obtained.  Two genes that code for proteins involved in cell entry were upregulated in infected cells: SCARB1 (2.07-fold), which encodes the SRB1 receptor protein, and LDLR (1.90-fold). Two genes for proteins involved in cell entry were downregulated: PIM1 (2.19-fold) and TFRC (3.2-fold).

Genes that had the largest fold-changes were also determined.  Of these, 13 of 21 are involved in preventing viral entry. These results suggest that SRB1, LDLR, PM1 and TFRC may be involved in HCV entry in these cells. CD5, ANKRD1, CLDN1, NPC1L1, and CD81 were not significantly expressed according to these results. The proteins that had the largest fold-changes included ones that decreased the innate host immune response, reduced response to DNA damage, reduced degradation of viral RNA, and decreased inflammatory response. Genes that increased in expression included ones involved in viral export. 

Program: Steven Dorfman Research Fellows Program in the Environmental Sciences
Faculty: Dr. Andrea Huvard, Biology
Student:

Previous studies have determined that the succession of invertebrates in fouling communities is influenced by environmental factors. The purpose of my study was to determine how man-made coastal structures like bays change the water flow, oxygen levels and other abiotic and biotic conditions influencing the succession of fouling communities. From these changes we see different communities that we normally do not see in the area form.  The materials needed to complete this study are four different types of settling plates. The four different types of settling plates were flowerpot (porous), wooden box, rock and plexiglass (plastic). Once getting those materials, I had to decide what knot was the best route to take to tie them all together. The next step was choosing a location at Ventura Harbor. I chose one location at the mouth of the harbor (Whales Tale), and the other location towards the back of the harbor (Oxnard Marine Lab). Once I chose the location, I tied the settling plates to two public docks that had fences facing the open water of the harbor. For the first two months, I was checking the settling plates daily because I had to photograph the change of the settling plates. While waiting for organisms to settle and grow, I took samples of water and recorded the pH with a refractometer, and I also took the temperature at each location. Each factor was logged, dated and timed because these two abiotic factors could contribute to the succession of the settling of the organisms in each location. Since my study is an ongoing process, earlier this summer I took two mature fouling communities from the same two locations. At the mouth of the harbor the mature fouling communities showed a more abundance in diversity, and the back of the harbor mature fouling communities had multiple species of tunicate. But between the two locations there is an organism that ties in both communities, the mussels (Mytilus californianus). Besides the mussels each location has a different diversity. So in conclusion, I can say the location of the settling plates plays a big role in the succession of invertebrates as well as the abiotic and biotic conditions. 

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Graham Matthews, Computer Science
Student:

As more work becomes dependent on interpretation of data, flexible ways to visualize large and varied data sets have become desirable in both academic and industry settings. Common graphics-generating software tends to be rigid in their approach, limiting the number of different graphics that may be displayed in one window or restricting the type of graphics to a set of specified options. Therefore, a flexible and expandable system is desired. By building on Hadley Wickham's existing work in R called ggplot2, this work aims to develop a system of composable graphics. By using different combinations of independent components, new or specialized graphics can be created. These individual parts of graphics are divided into different categories, the key ones being geoms, stats, and scales. Geoms are the geometric objects, the actual shapes that are plotted for each observation in the data. Stats are the statistical transformations made on the data—an example of this would be generating a line of best fit from a group of x and y values. Scales are transformations to the data that occur to fit the visual representations of the data to the viewing window. Components of a category are independent from those of other categories, and so there exists little restriction on which can be used with which. A bar graph and a histogram may both use a rectangle geom, but utilize different stats to display the same data in different ways. For this implementation of the system, JavaFX is used due to its support for hardware acceleration (which allows faster render times) and ability to be ported to web or mobile platforms. The various categories of components are written as interfaces, so that any user-created component that fits the rules of the category can be added to the system and used successfully. Thus, the system is a fast, flexible, and expandable way to generate visualizations of data.

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Jason Kingsbury, Chemistry
Student:

Previous research on the cytotoxicity and mutagenicity of a new organic non-linear optical (NLO) dye hinted at a rough and unorganized trend of harmful effects in yeast cells.  Nonetheless, a more extensive investigation was needed, especially with more appropriate control dyes.

Purpose: The purpose of this project was to analyze the cytotoxicity of the dye in two eukaryotic mammalian cell lines.

Methods: Utilizing cell growth assays where the addition of the DNA dye was varied in concentration and run in triplicate to form a control, I was able to look at how the DNA dye affected growth rates in two cell lines – 3T3s and U937s – over the course of three days.  When the cells were plated, I would need to continuously return to analyze if they had become contaminated with bacteria or fungi and at what stage of growth they were at.  After determining that the cells were in an appropriate growth phase, I would proceed by placing the cells in an incubator to promote cell division.  At the start of the assay, after 24 hours, and after 72 hours I was able to take small samples from the plated cell colonies and perform hemocytometry.  The hemocytometry was run in order to get cell counts and determine whether the cells were dying, growing in number, or stagnating.  After the three-day trials, the data was collected, cells were disposed of, and a duplicate assay was initiated to test for reproducibility in the assay.

Results: Thus far, my findings show that the dye is cytotoxic overall, but there may be applicability for its use in DNA visualization at low concentrations.  The fact that the pyridinium-based dye is highly fluorescent and tunable is most advantageous in this context 

Conclusion: My future work seeks to provide a better understanding of the dye’s potential hazards, and has pointed me in a direction to further understand its overall intracellular behavior and possible mechanism of DNA association.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Chad L. Barber, Biology
Student:

Tumors are the result of a rapid proliferation that can be triggered by various cellular factors, primarily genetic mutations. Alternative methods to treat cancer are progressively being developed through current research. This study targets extracellular adhesion proteins known as integrins localized on canine tumor cells. It is expected that various types and expression levels of integrins will be displayed in an assortment of canine tumors. It is also expected that canine tumors with a greater amount of integrins will exhibit increased growth kinetics compared to other tumors. In order to successfully grow cancerous cells in vitro for experimentation, a protocol was developed with the usage of a collagen cleaving protein, collagenase. This protocol was tested on mouse (Mus musculus) organs before application to tumor samples. It was found that optimal conditions to retrieve living cells from mice organs was a 2.5 hour exposure to 125U/mg collagenase. Utilizing similar methods for the tumor samples, cells were acquired and maintained at 37ºC and 5% CO2. The protocol was then applied to retrieve tumor cells from four different canine samples. Cells were then cultured and observed for growth kinetics and morphology. Cells from an epithelial mass (English bulldog) increased in confluency by 1.6 fold in four days. Cells from a thigh epithelial and mammary mass (Yorkshire terrier) increased in confluency by  3.3 fold and 1.6 fold respectively in four days. Cells from a lipoma (Labrador) increased in confluency by 10 fold in four days. After sufficient growth, these cells were tagged with fluorescent integrin antibodies and analyzed for specific integrin expression utilizing flow cytometry. Results of flow cytometry are pending. The tumor cells with the highest growth rate may be attributed to many factors including a greater concentration of a specific integrin subtype. We plan to use integrin antagonists on cells in vitro to measure apoptosis (cell death). We hope to demonstrate the importance of integrins in cell growth and the possibility of using anti-integrin strategies to inhibit proliferation of canine tumor cells.   

Program: Steven Dorfman Research Fellows Program in the Environmental Sciences
Faculty: Dr. Theresa Rogers, Biology
Student: Christina Geldert

The vitality of honey bees is essential for crop pollination and production of honey. Prior to the recent, rapid decline of the global honey bee population, a healthy population has been taken for granted. This devastating population decline, named “Colony Collapse Disorder”, has been explored from a multitude of standpoints, but no singular cause has been determined. One factor that may contribute to Colony Collapse Disorder is the confinement of honey bees to monoculture crops, as is common in today’s agricultural practices, rather than allowing bees to forage on a diverse diet. This change in diet is expected to change the microbial community of the honey bee gut. Given that honey bees express one third of the innate immunity genes of most insects, antimicrobial producing microbes that reside in honey bee guts are predicted to contribute to a bee’s ability to ward off invading pathogens and ultimately affect the health of the entire hive (Vásquez et al., 2012).

The aim of the present study is to compare the antimicrobial production by bacteria cultured from the honey stomach of honey bees that forage on a diverse or monoculture diet. Honey bees were collected from hives exposed to one of the two diet types (n = 13 diverse diet, n = 15 monoculture citrus diet). Diverse and monoculture diets were confirmed by morphological characterization of pollen collected from hind legs of sampled bees. Honey stomachs were aseptically excised, homogenized, and plated for bacterial isolation on MRS agar at 35°C for 48 hours. To determine antimicrobial production, bacterial isolates were screened for inhibition of Bacillus subtilis. Bacteria isolated from honey bees with a diverse diet exhibited more diverse colony morphologies and antimicrobial production against B. subtilis than the bacteria isolated from honey bees with a monoculture citrus diet. These results support the hypothesis that more antimicrobial-producing bacteria reside in the honey stomachs of bees that forage on a diverse diet than a monoculture diet. We plan to expand our study to screen for inhibition of various types of bacteria that are differentially inhibited by different antibiotics and to repeat the study with a different monoculture crop at a different time of year.

Program: Steven Dorfman Research Fellows Program in the Environmental Sciences
Faculty: Dr. Grady Hanrahan and Dr. Haco Hoang, Environmental Science, Chemistry, and Political Science
Student:

In 2013, the California Department of Food and Agriculture reported that California produces approximately half of all nuts, fruits and vegetables grown in the U.S. Additionally, the state produced 14.7% of all U.S. exports in 2013. The success of California's agricultural industry is in part due to the widespread use of pesticides, herbicides and fungicides. According to the California Department of Pesticide Regulation, 194 million pounds of pesticides were reportedly used in 2013. While the use of pesticides has grown, regulations that monitor this usage have not been rigorous enough to effectively protect communities.  The focus of this research is to develop an environmental monitoring approach for assessing pesticide exposure in these environments and provide recommendations for improving relevant public policy. In this research a chemical analysis was done of urine samples using a gas chromatograph mass spectrometer that identified pesticides, pesticide residues and metabolites. Additionally, the mass spectrum for each urine sample was found. This allowed for a focus on the number of pesticides identified throughout the data, the average amount of pesticides found in each sample, the specific hit rates of particular pesticides and the sample percentage for each pesticide. This data was then statistically analyzed looking at factors such as occupation, site location, age and gender. A review of legislation, statistical analysis and chemical identification inform the following public policy recommendations.

1. Increased education for the communities exposed to pesticides is necessary to create an informed dialogue about pesticide use.
2. Improvements for regulations that mitigate the dangerous exposure constituents are faced with.
3. Organize appropriate oversight measures to ensure that farms are compliant with the improved regulations.

Additional research examining legislation would allow for a more specific approach to policy recommendations, focusing on specific improvements that can be made to current legislation as well as future laws and regulations. Furthermore, access to a platform where these recommendations can be shared with policy makers and constituents would create the opportunity for significant progress in legislation.

Program: Darling Summer Research Fellowships for Applied Scientific Computing
Faculty: Dr. Chang-Shyh Peng, Computer Science
Student:

Drones are used widely around the world.  Predator drones in use by the United States military are the most familiar drones, but there are also companies who use drones to complete tasks such as Amazon for delivering packages and Parrot for consumer entertainment. Although drones are frequently used by individuals or larger organizations, college and university campuses can also utilize drones. Parking stickers are sometimes used in order to allow security to quickly identify if cars are parked in their designated areas. This project aims to simulate a artificial intelligence with target recognition so autonomous drones can patrol an area on campus. While security still requires patrols around campus, drones can allow security to focus on other tasks or reduce the frequency of patrols. The program that controls the drone in this project will be able to move around campus in a pre-programmed route, hover, scan cars, and take a picture of the parking sticker. The drone will then identify the sticker, flag any incorrect sticker, and continue along its pre-programmed path until it detects another car. Currently, the simulation correctly performs the tasks specified. While the drone can perform the tasks, there are case errors where the drone will incorrectly move or not perform a command, disrupting the simulation. More work is needed on this program to ensure the reliability and efficiency of the drone. Further improvements to the simulation should allow it to perform without any disruptions, assist us to more accurately evaluate the viability of deploying drones on campuses. With commercial-grade hardware and software, we believe this simulation already demonstrates the ability for a drone to perform these tasks in a real world environment. Autonomous drones can be a great complement to existing systems and further progress might open doors for security on university campuses.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Steven Hawkins, Exercise Science
Student:

Recent research has shown that an increase in muscle mass is linked to an increase in bone mineral density.  However, it remains unclear if muscle fiber type is a determinant of bone density.

Purpose: The purpose of this study was to determine if bone density is fiber type dependent both cross sectionally and longitudinally.

Methods: Twenty male master runners, aged 40-77 years, were recruited. Muscle biopsy samples were obtained by needle biopsy from the vastus lateralis and analyzed using standard histochemistry. Bone mineral density (BMD) of the lumbar spine, proximal femur, and total body were measured by dual energy x-ray absorptiometry. Subjects were divided by fiber type, and comparisons between groups and across time made using independent samples t – test.  Relationships between muscle and bone variables were examined using partial order correlation.

Results: There were no significant differences between groups 1 and 2 (48.0±6.5% vs. 38±5.6% type II fiber respectively) for Spine or Hip BMD.  These findings were likely influenced by the small sample size.  Lean body mass and aerobic fitness were also similar between groups.  Across time, there was no significant difference in change in spine (-.0149 ± .0321 vs. .0160 ± .0301, p = 0.07) or hip BMD (-.0015 ± .0360 vs. .0228 ± .0474, p = .250) between the two groups. However, significant positive relationships were found between type II fiber percentage and hip (r = .60, p = .019) and spine (r = .46, p = .043) BMD when controlling for lean body mass, age, weight, and VO₂ max.

Conclusion: Our findings show an association between fiber type and bone density that could suggest a greater influence of type II fibers on bone strength.

Program: Darling Summer Research Fellowships for Applied Scientific Computing
Faculty: Dr. Chang-Shyh Peng, Computer Science
Student:

Countless man-hours are spent by forensic photographers taking pictures of the ground and creating establishing shots of a crime scene. This work could be done more quickly and reliably by an autonomous drone. The use of an autonomous drone provides many advantages, it ensures that all ground in a specified area is recorded and avoids any disruption to the crime scene.
An android application was written for the DJI Phantom 3 Standard with Android Studio incorporating DJI’s software developers kit (SDK) and Google Map’s application programming interface (API). Two SDK tutorials put out by DJI, “GSDemo” and “FPVDemo”, were instrumental in understanding their SDK as well as Google’s API. Furthermore a desktop application was written using Eclipse and Java Swing. Lastly, DJI’s drone flight simulator was helpful in testing flight commands. An android app was written to issue commands to the drone to systematically take photos of a crime scene. Once complete the user takes the drone’s SD card and uses the desktop application to stitch the photos together into one large aerial view. To initiate the android app at the ‘crime scene’ the user inputs 4 outside boundaries and specifies an altitude safe for the drone to fly at. The app takes those two inputs and breaks the crime scene down into a grid and then instructs the drone to fly over each cell, using waypoints, and photograph the ground directly below it. During this time the user has the ability to look through the drone's camera or stop it in case of unforeseen circumstances. Upon photographing every cell in the grid the drone will fly higher and take establishing shots of the crime scene from the four corners, this option can be disabled if problematic. Finally the user can take the SD card and run it through the desktop application, this will organize the photographs into one large composite view. This project attempts to eliminate the ‘grunt work’ of forensic photography allowing human photographers to focus on the important shots in a crime scene.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. John Villalpando, Mathematics
Student:

Schedules play a critical role in how sports leagues are run. For many people, sports league schedules are created through the brute force method, a time consuming trial-and-error process. The mathematical world has become very interested in the creation of sports league schedules.  Different articles have approached the problem through various topics, such as time tabling, constraint logic programming, and graph theory. This project relates sports league schedules to graph theory. A graph is a set of points, called vertices, connected by a set of lines, called edges.  Hence, the vertices act as the teams and the edges represent a game occurring between the connecting teams. The project investigates the Edge Coloring Algorithm, an algorithm that produces a single round robin tournament, making sure that all the teams play against each other.  However, it only works for an even number of teams. The research expanded on the algorithm, applying it to an odd number of teams as well. Then, by adding directions to the edges the algorithm is able to assign home and away games. A break is two consecutive home or away games for a team, and a bye is when a team does not play a game in a certain round or play date.  A goal is to have the least amount of breaks and byes because they are seen as undesirable. A schedule might be considered optimal if it meets all the required criteria and is considered fair between the teams; for instance, all the teams playing each other team twice where each team has the same number of breaks and byes. The research resulted in a proof that for any round robin tournament with n teams, at least n-2 teams have breaks. The expanded algorithm creates a round robin tournament for n teams such that each team as no more than one breaks. The algorithm was tested on some CLU sports team schedules. The 2016 seasons for men’s football and men’s water polo are single round robin tournaments but most teams have 2 breaks (CLU football has 3 breaks). However, the expanded algorithm created more optimal schedules because each team had only one break.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. John Diesz, Physics
Student:

A superconductor is a material that exhibits a few exciting properties when cooled to below a certain critical temperature (about -200° F). One of these properties is the expulsion of magnetic flux during the transition of the material into its superconducting state. If the magnetic field is applied after the material has become superconducting, the flux cannot penetrate it and the magnetic field will not be present inside the material. This is even true if the superconductor is in the form of a ring. The field cannot even penetrate the center of the ring, where atoms are not physically present. However, if the ring is sufficiently thin, then magnetic flux values will be able to penetrate the ring. By passing a range of flux values through the center of this ring, we are able to calculate the superfluid density, which is a measurement of how good our superconductor is.  

Using the C++ language to model how atoms and electrons behave in a superconductor, I first started with developing a simple code that represented where the atoms and electrons physically existed in the system. I did this by implementing a range of different mathematical and physical parameters, to demonstrate real properties of superconductors.  I assured the accuracy of my code with the output of a few physical quantities, such as the energy per atom, the chemical potential, and the observance of zero magnetic flux inside the superconductor. By utilizing the power of scientific computing, we are able to quickly and efficiently model a superconductor on the atomic scale. We hope that by investigating superconductors at an atomic level we will be able to better understand the underlying principles of superconductivity, and contribute to the possibility of one day using superconductors at ambient temperatures. 

I contributed to the development of a new method of measuring the flux quanta in the modeling of a superconductor. My data supported the fact that these flux values are quantized, and that the energy per atom in my system charted a periodic function with a period of one. With the implementation of my more efficient and effective method, researchers will ultimately be able to incorporate that piece of code into a larger body of work allowing for quicker, and more calculations.

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Andrea Sell, Psychology
Student:

In this study we explored the use of intentional forgetting in the forgiveness process.

Purpose: Two experiments were conducted to assess individuals with differing levels of  inhibition resources (adults age 65+, and younger adults who have performed a self-control depleting task) in order to explore the role of inhibition in the forgiveness process. It was hypothesized that individuals with limited inhibition are less likely to use directed forgetting in the service of forgiveness.

Methods: In Experiment 1, fifty adults age 65+ were presented a 12 sentence story written in second person. Following each sentence was a forget, remember, or control (an asterisk) cue indicating whether they should, respectively: forget, remember, or read normally the previous sentence. The seventh sentence served as the target conflict sentence where antagonist of the story damages the protagonist’s car. Participants were randomly assigned to one of three groups which differed based on the cue presented for the target sentence. After the story, participants were asked to recall the story. They were then given a 7-point Likert Scale to indicate how likely they would be to forgive the antagonist (1=very unlikely to forgive, 7=very likely).

Experiment 2 followed similar methods, however participants included younger adults (18-65) sampled through an online data collection website (Mturk). These participants were presented with the same story as the older adults, with the same cue conditions. However, in order to limit inhibition levels in the younger adults, a self-control task was performed before reading the story. Participants in the self-control condition retyped a presented paragraph using all capital letters and omitting all vowels.

Results:  In Experiment 1, among the young-old (ages 65-78), there was a marginally significant effect for cue, F(2,11)=3.19, p=.09, =.415. For this group of participants, the forget and remember cues led to higher forgiveness scores (M_F=5.11, SD_F=.57, M_R=4.80, SD_R=..69) compared to forgiveness scores following the control cue (M_C=2.97, SD_C=.69). There was also a significant effect for recall such that among the young-old, those who recalled the target sentence (M=5.32, SD=.46) had higher forgiveness scores compared to those who did not recall the target sentence (M=3.27, SD=.56), F(1,11)=7.74, p=.02, =.462. Experiment 2 data is currently being analyzed.

Conclusion: Experiment 1 results are consistent with the hypothesis that older adults are less likely to use directed forgetting to forgive compared to younger adults. Rather than following the remember and forget cues to assist in the forgiveness process, older adults are likely using other cognitive tools.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Dennis Revie, Biology
Student:

Hepatitis C, caused by the Hepatitis C Virus (HCV), affects approximately 150 million people worldwide. HCV infects hepatocytes, liver cells, and causes liver cirrhosis and may even lead to liver cancer. Currently, there is no vaccine available for HCV and minimal information is known about the virus. The purpose of this project is to gain a greater understanding of the replication process of HCV, particularly to determine important sites of viral production. HCV viral proteins core and nonstructural protein 5A (NS5A) have been shown to associate with specific host cell organelles, namely the nuclei and lipid droplets. HCV core manipulates host cell functions including gene transcription and signaling pathways by interacting with host proteins, which can induce viral replication around and in the nucleus. NS5A plays important roles in viral replication, regulation of cellular pathways, and transcriptional activation functions, which are important for viral RNA replication. Like HCV core, NS5A interacts with host cell proteins to induce HCV RNA replication. Because HCV is also known to evade and manipulate immune system response, it is possible for HCV to infect macrophages, which are a precursor to monocytes (white blood cells). U-937 monocytes, which are cultured and infected by Dr. Revie, are used for this project. The monocytes are stained with various fluorescent dyes that attach to the nuclei, lipid droplets, and HCV proteins, if present in the samples. The stained samples are then analyzed with a fluorescence microscope that excites the dyes to fluoresce in their respective wavelengths, or colors. This allows for visualization of colocalization, spatial overlap between the organelles and viral proteins. Colocalization indicates the presence of HCV proteins on or in the host cell organelles and is represented as a different wavelength. Further analysis will be conducted on HCV core and NS5A and their associations with host cell organelles and other viral proteins by comparing uninfected and infected samples. If sites of HCV replication are established in monocytes, the information gathered from this research can potentially contribute to advancing antiviral treatments and developing a vaccine for HCV.

Program: Darling Summer Research Fellowships for Applied Scientific Computing
Faculty: Dr. Craig Reinhart, Computer Science
Student:

Over the years, many well-known companies have invested time and money into the idea of creating a self-driving car. One example of this is Google and their autonomous car project. An autonomous vehicle is one that is capable of sensing its environment and navigating without human input. The benefits of an autonomous car will include decreased accidents as well as increases in fuel economy. Autonomous cars use sensors and software to sense objects like pedestrians, cyclists, other vehicles and more, and are designed to safely drive around them. In this project, I studied sensors and devices required to achieve mobile vehicle autonomy. I began this process by understanding and learning the Arduino Programming language and IDE. To fully understand the different concepts and syntax of this language, I read the arduino documentation, programmers guide, and wrote many different pieces of code. In this project I used two different types of robots, a Boe-Bot to Shield-Bot Retrofit Kit with Arduino Uno, and a Vex Tank with the Arduino Uno mounted on the bot itself. This summer I tested three sensors, the Adafruit GPS Shield for location and navigation, the Pololu IR Beacon for robot detection, and the Hall-Effect Sensor for speed detection. With each sensor, I went through process of reading the documentation provided along with other information found on the web to fully understand the sensor, wrote code in respect to each sensor, then tested the sensor on each of the robots to compare the results. In the future, I plan to continue testing other devices and sensors, and hope to be able to combine the sensors onto a couple of robots to get them interacting. After I complete the autonomous vehicle I hope to take on the challenge of connecting the Arduino Uno with a Drone to create an autonomous drone.

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Jason Kingsbury, Chemistry
Student:

Aziridines are three-membered, nitrogen-containing cycles.  The chemistry of these molecules is dominated by ring-opening reactions, making them practical precursors for the synthesis of valuable azacyclic pharmaceutical building blocks.  Despite much research, a straightforward method of creating stereochemically-defined aziridines for use in azacycle synthesis continues to remain elusive, highlighting the need for an improved method for catalytic enantioselective aziridination.  Prior work by Cui and He (2003) revealed a practical disilver(I)-catalyzed aziridination reaction, effective only in the presence of a tridentate, 2,2',2''-linked terpyridine ligand.  Few chiral terpyridine ligands are known, and as such, our recent work has focused on synthesizing several novel terpryridine ligands for use in generating optically pure chiral aziridines that can then be used to produce medium-ring azacycles.

Previous work in the Kingsbury lab has produced large quantities of both saturated 2-bromopyrindane and unsaturated pyrindane as starting materials to stage chiral terpyridine ligand syntheses.  Attempts to N-oxidize the unsaturated pyrindane, so as to enable bromination at the 2 position, proved quite difficult.  Initial reactions with hydrogen peroxide in water and acetic acid were unsuccessful, and N-oxidation was only effected upon use of dimethyldioxirane (DMDO) as a mild oxidant.  Subsequent bromination using Baran et al.’s (2013) procedure with tetrabutylammonium bromide, tosic anhydride, and DMF also proved challenging.  However, Kugelrohr distillation of the unsaturated pyrindane starting material, followed by quick isolation and subjection to bromination conditions under argon gave promising NMR results. 

Ongoing experiments will be focused on dehydrogenation of the saturated 2-bromopyrindane, as well as bromination of the unsaturated pyrindane N-oxide using alternative conditions based on neat phosphorus oxybromide.  Upon successful generation of unsaturated 2-bromopyrindane, application of a Stille cross-coupling method, followed by ferrocene group addition, is expected to generate the desired novel terpyridine ligands needed for downstream aziridination reactions.

Program: Steven Dorfman Research Fellows Program in the Environmental Sciences
Faculty: Dr. Bryan Swig, Biology
Student:

Global climate change has begun to increase the temperature of the oceans. As the water temperatures increase, sharks have begun to modify their behaviors in an effort to locate resources. Additionally, the fishing industry has drastically reduced the global fish population and destabilized this fragile ecosystem. Together the reduction of prey and the increase in temperatures have changed shark-human dynamic, by increasing the likelihood of a shark swimming into waters that humans utilize, and making interaction more likely. White sharks (Carcharodon carcharias) are considered a valuable market fish and have been targeted by black market smugglers. While there has been an international effort to cut back on the illegal harvesting of these sharks, it is not only difficult to track and identify the smugglers but also the sharks after processing. Therefore a systems approach is needed to understand the modification of shark behavior. Carcharodon carcharias have mitochondrial microsatellites that are unique based on region. These sequences can be used to track the origin and movement of sharks, and will provide insight into behavioral modification, as well as the impact the illegal fishing industry is having on specific shark populations. DNA was extracted from 20.0 mg samples using the Qiagen dneasy Blood and Tissue kit. PCR was then performed with elasmocr15642f and Ccar 3.1R primers in 50 ul volumes through an initial denaturation of 5 minutes at 94 °C, 35 cycles of 15 seconds at 94 °C, 120 seconds at 63 °C, and 45 seconds at 72 °C with a final extension of 5 minutes at 72 °C. Varying concentrations of the contents were investigated, by altering the water, master mix, guanine enhancer and DNA sample ratios. PCR products were then purified with the Clontech nucleotrap kit. It was found that extraction of the DNA was viable, and that PCR was working, but not optimally. Future work will investigate the ideal annealing temperatures.

Program: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Jason Kingsbury, Chemistry
Student:

Previous research has identified successful conditions for cross-coupling hindered secondary organoborons, and tertiary boronic esters can be prepared from geminal diborons via deboronation and alkylation steps.  The purpose of my research is to explore reaction conditions that may allow for the transformation of a tertiary organoboron to an all-carbon-substituted, quaternary chiral center.  Achieving this goal would offer new reaction methodology relevant in carbon-carbon coupling, which can streamline the synthesis of new compounds in spite of extreme steric hindrance.  This investigation required multi-step synthesis to get from commercially available starting materials to the tertiary organoboron starting materials for these reactions.  Some of the precursor reactions necessary to pursue my research goal were quite sensitive, including reagents that had to be added under nitrogen in a glove box and products that had to be immediately stored in a –40 °C freezer.  Thin layer chromatography (TLC) of the reaction mixture after extraction gave a sense of purity by showing how many products existed and their relative proportions.  The use of NMR spectroscopy was essential to confirm which spot on a TLC plate was the desired product and its final purity.  Any impurities were removed by subjecting the mixture to a silica column that separated the components based on polarity.  Conditions for the sterically hindered coupling reaction remain an active area of interest, and several ways of improving the reaction methodologies for access to the precursors were developed and fully optimized.  Some reactions yielded diazo compounds that are novel, first time syntheses, and a number of secondary organoborons have been purified for use as “control” substrates for quaternary cross-coupling in future studies.

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Andrea Sell, Psychology
Student:

Past research has shown that information can be interpreted through spatial cognition, which involves imagining various visual domains in order to create a representation of our stimuli. Spatial representation has already been shown to be a key factor in interpreting language, as people implicitly assign visual image schemas to particular words. In this study, we explored the possibility that music employs a spatial representation as a form of organization. Specifically, it was hypothesized that melodies would elicit a horizontal spatial representation and chords would elicit a vertical spatial representation, due to the way they are printed in sheet music. Forty-nine people participated through the online data collection website, Mechanical Turk. The study employed a within-subjects design. Each participant was presented with two melodies and two chords. After each sound, participants saw two images. These images reflected either vertical or horizontal representations. One image was of a circle with an arrow pointed directly upwards to a square. The other image was of a circle with an arrow pointing to the right towards a square. Participants were asked to determine which direction they felt best corresponded to the sound. Each choice was coded as a 1 for the vertical image and a 2 for horizontal image. We calculated an average choice for the melodies and an average choice for the chords for each participant. A paired samples t-test was run in order to compare these averages. On average, participants more often chose the horizontal image for the chord (M=1.69, SD=0.37) and chose the vertical image for the melody (M=1.43, SD=0.43); t(48)=2.47, p = .017. This experiment tested the hypothesis that melodies would elicit a horizontal spatial representation while chords would elicit a vertical spatial representation. However, results show that people view chords as having a horizontal spatial representation while melodies have a vertical spatial representation.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. John Diesz, Physics
Student:

Experiments and research on strontium ruthenate have puzzled scientists since its superconducting state for temperatures below 1.5K was discovered in 1994. Results from previous studies suggest that strontium ruthenate has properties that are atypical of superconductors although some of the evidence appears to be contradictory. For example, there has been some, but not always consistent evidence of a change in phase of reflected polarized light within the superconducting state, magnetic flux quantization at atypical values, and the breaking of time reversal symmetry.  The inconsistent behavior of this material is what I intend to understand via computer simulations.

I performed this research computationally through a quantum simulation, using techniques from linear algebra and a momentum space model, which greatly contributes to the accuracy of the results, and the speed at which I obtain them. Through simulations we can make it easier to understand, define, and visualize what is happening physically while using different methods, models, and techniques. Our initial work has focused on determining the origin of flux quantization that appears to be occurring at unconventional values. We show that while our model reproduces the conventional flux quantization values expected for a superconductor and other aspects of the calculations are in agreement with the first principles study by Mazin and Pavarini, we have not yet been able to reproduce the flux quantization at the unconventional values through two different mechanisms, which might plausibly be present in strontium ruthenate.

We will describe the results that we have obtained so far as well as discuss the next steps that will be made as we continue to develop our simulation such that eventually it is able to reproduce all of the unusual behaviors observed in strontium ruthenate.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Michele LeBlanc, Exercise Science
Student:

Previous studies have used ultrasound to assess mechanical properties of tendon during ramped isometric contractions. Contraction duration has been reported to affect patellar tendon strain; however, the extremely slow contractions (10 seconds) studied by Person et al. (2007) are not particularly relevant to sporting activities or even everyday life.  Additionally, the previous studies have determined tendon strain using Tendon Elongation methods (Joseph et al., 2012).  The purpose of this study is to determine if the rate of torque development reflected by more realistic contraction times affects the strain and stiffness of the patellar tendon using acoustoelasticity. Nine recreationally active males between the ages of 18-25, with no previous knee injuries, volunteered to participate in the study. Each subject signed an IRB-approved consent form and filled out a fitness and knee health questionnaire.   After a warm up on a cycle ergometer, subjects were strapped in a Biodex System 3 isokinetic dynamometer to isolate preferred leg knee extension.  They performed a conditioning set of eight ramped knee extension isometric contractions.  Afterwards, they performed another set at regular (2-3 seconds), at fast (1-2 seconds), and at slow (at least four seconds) ramp up speeds. The order of the slow and fast ramp up conditions were randomized.  A Terason 3200 ultrasound collected images of the tendon during the isometric contractions at 25 Hz.  DICOM files were downloaded and opened with Echosoft software (Echometrix, Madison, WI).  A region of interest was chosen distal to the patellar apex for analysis.  Strain values over time were determined and paired with torque data which was collected at 100 Hz and resampled at 25 Hz.  Approximate patellar tendon moment arm values (Lu and O’Connor, 1996) were used to determine force and stress values which enabled the computation of tendon stiffness.  One-way ANOVA was used to determine the effect of contraction speed on strain and stiffness values.  Post hoc tests were performed using Bonferoni. Significance was determined with p < 0.05.   

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Dennis Revie, Biology
Student:

Humans infected with Hepatitis C virus may experience long term damage to liver cells, which can lead to symptoms such as liver disease, liver cancer and cirrhosis. There are approximately 130-170 million people living with Hepatitis C in the world.  Due to the large amount of people infected by the disease, most notably in poorer countries, it is vital to have treatment that is less expensive and more readily accessible. In this study, the main goals were to determine the effects of these two medications on monocytes alone, and in combination.  The medications used in this experiment were interferon alpha and ribavirin, which are broad-spectrum medications that aid the body in combatting the illness.   In addition to analyzing interferon alpha and ribavirin’s effects on monocytes, this experiment was also performed to determine the ideal amounts of each medication required in producing the highest yield of inhibition.  It was expected that both inhibitors in combination would yield greater successful rates of inhibition and that the cell cultures with the treatment of ribavirin alone will have no significant lowering of the cDNA in the culture supernatants. 

U-937 monocytic cells were infected via serums from patient’s infected blood.  After allotting time for viral transmission into the cells, the viral RNA was purified. The viral RNA was converted to cDNA using the enzyme reverse transcriptase then amplified using Polymerase Chain Reaction (PCR).  Once the cells were adequately infected and the virus was replicating within the cells, they were given interferon alpha and ribavirin individually, and then treated with a combination of the two medications. Real-time PCR was used to quantify the amount of virus within the cells and served as a proxy to measure viral activity inhibition.  Due to the inability of the monocytes to maintain the infection by HCV, there was no significant data collected at this time. This study will continue throughout the academic year. 

Program: Summer Undergraduate Research Fellowships (SURFS)
Faculty: Dr. Akiko Yasuike, Sociology and Global Studies
Student:

In today’s atmosphere of rapid globalization, there is a growing demand for avenues of prosperity that will allow actors to maintain or obtain positions of power, or secure their place as strong competitors in the global economic order. This drive, along with other motivations such as political stability, conflict resolution, and societal growth, is the main impetus for the emergence of regional integration. While the potential rewards of this type of integration include opportunities for economic growth, the negative societal implications for less developed nations and their citizens merits serious discussion, which can only begin once reliable and accurate measurements of progress and development are accepted and utilized on a broad scale. The aim of this study is to observe potential disparities in rates and outcomes of development for countries entering into regional integration agreements (RIAs). This research compares existing indices that seek to measure progress and development, to the Nighttime Light Development Index (NLDI), derived from the use of satellite images of the Earth’s anthropogenic lights at night, provided by the Defense Meteorological Satellite Program’s Operational Linescan System (DMSP-OLS), along with the Oak Ridge National Laboratory’s LandScan population grid (Elvidge et al. 2012). While economic studies of RIAs have often presumed positive growth outcomes for member countries, it is my proposition that by examining the broader effects on human and societal development we will be able to construct a deeper understanding of our future as an increasingly interdependent and integrated global society and of the sustainability of such changes. It is imperative to consider what these potential inconsistencies may mean for developing nations looking to RIAs as a path for economic growth, while simultaneously and unwittingly overlooking adverse effects on overall societal development and well-being. This approach is applied to an analysis of the holistic development outcomes of one particular regional integration agreement: the Association of South East Asian Nations (ASEAN), resulting in inconsistencies between the NLDI values and other indicators in the cases of the Philippines and Thailand. The possible reasons for these discrepancies are examined further within the context of regional integration.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Kristopher B. Karsten, Biology
Student:

Sceloporus occidentalis, the western fence lizard, is considered a territorial lizard because it has the following traits or behaviors: it has site fidelity, it defends that site, and it holds a near exclusive use of that site. However, physical combat, which may be used to defend their site, carries significant risks like potential injury or even death. As a result, this species has evolved displays to establish social dominance without physical confrontation, which take the form of a push-up like behavior that displays blue patches on their belly, or ventral side. I proposed that male S. occidentalis lizards with larger ventral blue patches would display territorial dominance (both size of home range and number of females present in that territory) over males with smaller blue patches. I tested this by surveying a site on the CLU campus and determining territories of males within that site. I identified the lizards by marking them, both semi-permanently with paint and permanently by toe-clipping. The paint markings were four markings of varying colors placed on the back of the legs of the lizards in order to identify them from afar. The paint markings corresponded to the toe clippings, which were three toes, specific to one lizard. When I surveyed the site, I would find the lizard, mark its location with a GPS, and continue searching. On the first sighting of the lizard, I would capture the lizard and bring it to the lab to measure sprint speed, morphology, bite force, and photograph the ventral patches. I also recorded spectral properties of each ventral patch with a spectrometer so that I can quantify the color of the patch into hue, saturation, and brightness. With that, I can compare the spectrometer data and the patch sizes to the size of the home ranges found using the GPS surveys in order to determine whether the patches are significant in determining competitive success. 

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Kristopher B. Karsten, Biology
Student:

As with many lizards, male Western Fence Lizards (Sceloporus occidentalis) are territorial. The more dominant males keep larger territories with better basking spots, hiding places, and food resources. A better territory means that the male will likely have more females nearby and therefore more mating opportunities. Also like other lizards, S. occidentalis can voluntarily lose their tails to avoid predation. However, because they store fat in their tails, losing them may lower the lizards’ chance of survival and their social status. We conducted this study to determine if tail loss in males affects ability to maintain territory or access to females.

We collected data from males and females in 2014 from May to August and in 2015 from March to August. Each time we spotted a lizard, we marked it for identification and collected a GPS point at the exact location where it was found. We mapped individual territories using these points through GIS software. In total, we found points for 29 males and 22 females. In June of 2015, we brought seven males into the lab. First, we measured their bite force, sprint speed, and morphology, and took high speed videos of each lizard sprinting at 1000 fps. We then removed tails from three of the males and measured and video recorded their sprint speed again. After a month of tail regrowth, we recorded the lizards again to assess if tail loss affected sprinting biomechanics. After recording video, we returned all lizards back to their original locations.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Jason Kingsbury, Chemistry
Student: Hasmik Jasmine Adetyan

Dimethylaminonaphthylpyridinum iodide is an ionic compound that can be used as a fluorescent dye molecule for routine biological staining.  Similar to the known intercalator ethidium bromide (EB), the dye shows high affinity for DNA.  If it were to prove less toxic then EB, it could be of promise for nucleic acid visualization in vivo.  Currently, the salt can be prepared in three steps on a multigram scale, but the commercial starting material 6-bromo-2-naphthalenamine is quite expensive (15 dollars/gram).  My aim was to test a “greener” method for access to 6-bromo-N,N-dimethyl-2-naphthalenamine.  In the original synthesis, the product is prepared by double SN2 methylation of the free amine.  The reaction gives a high yield, but it requires high temperature and affords a monomethylated byproduct. The mixture of the desired dimethylaniline and monomethylated byproduct must then be separated and purified by flash column chromatography.  The unwanted byproduct is then resubjected to the same reaction conditions in order to push it to the desired dimethylated product.  The entire process is tedious, time-consuming, and generates significant amounts of solvent waste, which is an added cost on larger scales.

To achieve a “cleaner and greener” synthesis with a one-step amination, a new starting material was chosen, and reaction conditions were tested using Pd-catalyzed amination methodology.  The substrate used was 2,6-dibromonaphthalene, which was coupled with dimethylamine.  The reaction conditions included using Pd(dba as the precatalyst, (tBu)XPhos as the ligand, toluene as the solvent, and KOtBu as the base.  The mixture was placed in a hot oil bath at 95 °C and left to stir for 11-27 hours.  One issue that required optimization was the stoichiometry of the dimethylamine, since it is a volatile secondary amine that tended to evaporate from the reaction mixture.  Nonetheless, success was achieved, and a hallmark of my findings is that no over-amination was observed.

Program: Overton Summer Research Program in Economics
Faculty: Dr. Kirk Lesh, Economics
Student:

In the last few years, the media has been flooded with violent interactions between police and the citizens they are sworn to protect. While the police have the legal power to use force, citizens are starting to question the legitimacy of that force. Though the media focuses on the violence that police commit, this issue is not properly described without talking about both sides of the issue: violence by and against police. Police use excess force because there is violence used against them. The literature regarding violence by and against police generally focuses on one direction of violence. Most of the research focuses on violence by police because of the significance of the officer’s position in society. When it came to trying to model this violence, studies looked into predictors of violence by police or violence against police but there was no literature that used violence against police as a predictor of violence by police, or vice versa. We believe that these two variables are codependent, as one moves so will the other. We also believe that they are significant predictors and the exclusion of either one will bias the regression results. Using a nationally collected representative data sample from various sources collected by the Bureau of Justice Statistics and the FBI, we are proposing a different way to model the violent interactions between the public and the police. Violence by and against police create a simultaneous system of equations. To solve this, we represent violence by police with unique identifiers in the violence against police regression. This eliminates the bias and allows us to look at both dependent variables simultaneously to see if there is any causal effect between the two. This econometric model has not been used to describe this issue before. We hope that this model will give policy makers a more holistic view of the problem and give them the tools to solve it.