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

Aquatic snails have been used to study the neural processes that govern behaviors such as memory, feeding and reproduction.  The freshwater snail, Lymnaea stagnalis, has been used in neurophysiological studies and is known to respond to carbohydrates such as sucrose and maltose, but little is known of their response to amino acids. The purpose of this study was to determine the effects of amino acids on the feeding response of snails. The feeding response of snails was tested using shallow, water-filled glass bowls containing four sets of four agar pellets. Each set consisted of one control agar pellet, one pellet containing 20 mM maltose, one pellet containing 100 mM of an amino acid, and one pellet with a combination the amino acid and maltose. Snails were placed in a holding tank without food for at least 18 hours prior to testing. Duplicate groups of 8 snails were placed in bowls with the pellets and the number snails feeding on a pellet was recorded every 15 minutes for one hour.  All twenty standard L-amino acids were tested in addition to some D-amino acids. I also tested organic compounds that are similar to amino acids, e.g., taurine, citrulline, and sarcosine. Lymnaea stagnalis were attracted to the combination pellets of taurine + maltose, L-isoleucine + maltose and D-proline + maltose.  L-glycine and L-threonine without maltose were also strongly attractive.   I plan to extend this research by testing responses to selected amino acids using intracellular and extracellular preparations, and I will test whether electrophysiological responses correlate with feeding behavior. 

Program: Culver Behavioral Science Research Fellowship
Faculty: Professor David Grannis, Communication
Student:

The drought in California has significantly impacted the state as a whole. Farmers have had to fallow their fields, water bills have risen, and more people will be talking about conserving water. Park managers and residents have pulled out their grass to put in turf and drought tolerant plants. In this research, we hope to raise awareness about the drought as well as the efforts being made to improve community living conditions that work to combat the drought. Making a documentary about this issue allows us to visually show how bad the drought is. We traveled to various locations including, Fresno State, Santa Barbra, and here in Thousand Oaks to interview various experts about the water crisis and to hear their views and opinions on the subject. We didn’t realize the severity of this drought until we started researching. Visiting places that have been affected by the drought has also been eye opening. Stratford was one of those places. The ground water had completely dried up and the town was almost completely vacant. At that point, we were able to see what a drought can do to a community. This was one of many cities that have been affected by the drought. A challenge that we faced during this research was having different companies agree to interview with us. The issue of “where the water should go” is a big controversy between northern and southern California. We didn’t realize this until we interviewed both sides of the issue. We have finished filming but we still need to finish editing it all together and do the marketing for it as well as send it to various film festivals. Hopefully this documentary will help inform and educate others about the drought. We also hope that we will get people thinking about ways that they can save and conserve water in their own homes and communities. If we don't work together to fix this issue, it’ll only get worse. Our ground water could possibly dry up and water could become very expensive. We don't want to wake up one day with no water in our homes and communities.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Robert Richards, Biology
Student:

Infectious bovine Keratoconjunctivitis (IBK), commonly referred to as “pinkeye” in cattle, is an ocular disease that is endemic in cattle herds worldwide. Moraxella bovis is a gram-negative, rod shaped bacteria that has been identified as the main organism responsible for this disease, although other contributing pathogenic organisms have also been identified. In this study, Illumina’s New Generation Sequencing (NGS) technology was utilized to launch a shotgun metagenomic analysis of the microbial community in the eyes of both healthy cattle and cattle displaying objective symptoms of Keratoconjunctivitis. A total of 15,762,090 sequences were identified and were analyzed by using two different software algorithms, Genius Metagenomics: Know Now, and Kraken Metagenomics. In order to strengthen the efficacy of bacteria identification, these two software programs were used in tandem. Each program identified the same bacteria in the samples approximately 67% of the time. M. bovis was not found in significant quantities in any of the infected samples. However, six of the seven infected samples contained bacteria known to cause conjunctival infection in mammals. Software analysis also revealed a large number of bacterial biofilms in both healthy and infected subjects. Multiple biofilm inhabitants within the genus Ralstonia were found in all but two samples. This genus has been recognized in several studies as the most common type of bacteria in the healthy human eye. These results suggest that the presence of biofilms could give the pathogenic bacteria protection from the immune system and as well as protection from being washed away by lacrimal secretions. The existence of a biofilm and the diversity of pathogenic bacteria other than M. bovis could help explain the failure of vaccines against M. bovis observed in larger studies. 

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Dennis Revie, Biology Department
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: Swenson Science Summer Research Fellowships
Faculty: Dr. Michele LeBlanc, Exercise Science
Student:

Stair descent has been rated as one of the most challenging tasks of daily living for the elderly (Williamson and Fried, 1996). Being able to safely maneuver stairs greatly affects an individual’s ability to live independently. It is estimated that 10% of all fall-related deaths occur on stairs (Starzell et al., 2000). Falls have been reported to be more prevalent for females than males (Svanstrom, 1974). Previous research found kinetic and kinematic gender differences in a younger population during stair-to-ground descent transition in the sagittal plane (Hong and Shin, 2015). They found that females exhibited body positions that would make them more at risk for falls.  The purpose of this study was to determine gender differences in stair-to-ground descent kinematics and kinetics in an elderly population in both the sagittal and frontal plane. Males (n=15) and females (n=17), aged 65-91 years, participated in this study.  There was no significant difference in their ages. All subjects signed university IRB-approved consent forms and filled out a brief health history to ensure eligibility. Eighteen reflective markers were placed on various body landmarks to determine lower body kinematics. Subjects descended a set of three stairs (each step 92 cm wide, 26 cm deep and 20cm high) without the use of the handrails.  Two force plates were imbedded in the floor immediately in front of the stairs, capturing the first and second step onto the floor. Subjects descended the set of stairs multiple times with lead leg order randomized. Six Vicon Vantage V5 cameras (120 Hz) captured their movement along with two Kistler force plates (1200 Hz). Leg strength was measured using the Biodex System 3 isokinetic dynamometer. Data was analyzed for both the continuous phase (stair to stair) and the transition phase (stair to floor) of stair descent. Independent t-tests were used to compare joint angles, joint torques and ground reaction forces between females and males (p < 0.05).  Knee joint torque values were normalized for strength using the peak torque values from the dynamometer.

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

Aziridines are highly reactive, 3-membered nitrogen containing rings that undergo a variety of ring opening reactions in high yield and with defined regio-and stereoselectivities. I am interested in harnessing the ring strain in vinyl aziridines in unexplored ways. Many studies have shown how phenyl substituted vinyl aziridine can undergo various ring-opening reaction to yield a variety of stereochemically rich heterobicycles. However, only few examples are known involving vinyl aziridine reorganization by [3,3] aza Claisen rearrangements. A significant end goal for vinyl aziridine ring opening reactions is in the formation of phenyl substituted 7-membered nitrogen ring. In the substrate route that I proposed, esterification was performed on cinnamic acid, a commercially available starting material, followed by aziridination to afford tert-butyl aziridine ester. The ester was later reduced and Wittig reaction was finally performed to give 2-phenyl-3-vinyl aziridine. Using NMR spectroscopy, I was able to confirm that the ester aziridine was successfully synthesized in high purity and moderate yield (64%). However, when the ester was reduced, a new amino aldehyde functional group was created. The amino aldehyde functional group is highly reactive and it differed the reaction from its original path. Fortunately, through various experiments, a new method was found that allows the ester to be reduced without activating the amino aldehyde functional group. This method will allow for continuation to the vinyl aziridine. Therefore, once the vinyl aziridine is synthesized in large quantities, we would have ample quantities to begin testing a novel methodology for transformation to 7-member azacycles. If successful, our efforts could revolutionize and expand the opportunities for everyday manufacture of pharmaceuticals and other biological probes.

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

Siderophores are small molecules that are secreted from bacteria to retrieve iron to help the bacteria thrive. The siderophore product of the protein Francisella tularensis (FslA) is a virulence factor in the veterinary infection tularensemia, one of the most pathogenic bacterial infections. It is, moreover, one carboxylate group away from the multidrug-resistant MRSA siderophore, a virulence factor that helps MRSA infects up to 75,000 people per year in the United States. With increasing drug resistance in pathogenic bacteria, new antibiotic drug classes are required, and the synthesis pathways of siderophores are a possible drug target. Studying how different chemicals bind in the protein pocket of FslA will help us decide the structure that binds the tightest within the pocket and creates the siderophore. We will utilize the MicroCal Peaq Isothermal Titration Calorimetry (ITC) to determine how tightly different chemicals bind in the pocket, and the structures that fit the best. Our long term plan is then to design an inhibitor that binds tighter than the naturally binding chemicals, in turn becoming a new class of antibiotics. In order to experiment with the ITC, an abundance of protein is needed to run all of the experiments. Overexpression and purification of the protein have been optimized with E. Coli cultures and purified in a Fast Protein Liquid Chromatography (FPLC) machine. Using the purified protein and the ITC, we were able to determine that AMP, ADP, and a non-hydrolysable form of ATP did not bind in the protein pocket. We still have further experiments with different substrates and chemicals to determine the best fitting structure. 

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

Due to their characteristic ring-opening properties, aziridines have been proven useful as building blocks in the production of molecules with possible pharmaceutical applications. This study aimed to better understand the reactions in the proposed path of synthesis for these molecules and determine the requirements necessary for their ring-opening rearrangement.  This research aimed to bypass the challenge of making enantiomerically pure starting material by using a commercially available starting material called Phenylglycinol. Schlenk line technique was used to flame-dry reaction vessels under vacuum and backfill with nitrogen to ensure the absence of moisture and oxygen in our reactions. Products were isolated and purified using thin layer and column chromatography. Identity of products was determined using H NMR and Mass spectroscopy. The first reaction attempted was the Mitsunobu reaction, which aimed to convert our free amine into an aziridine. This reaction was first attempted in THF using DEAD and Ph3P. These conditions resulted in a number of different products that were not the aziridine. In response to this, the Mitsunobu reaction was attempted again in Toluene using ADDP and Bu3P, which are commonly accepted as more powerful reagents. Although the product of this reaction was isolated in reasonably pure form, it did not match the data for our aziridine that had been reported in scientific literature. Since we were unable to determine the exact structure of this unknown product, we worked around this issue by performing a formylation first. Phenylglycinol was formylated using ammonium formate in acetonitrile. After developing a method to cleanly formylate our starting material, we once again attempted the Mitsunobu reaction using ADDP and Bu3P. While we were unable to make the formylated aziridine, we synthesized a unique Mitsunobu product not previously reported in literature and developed a method to cleanly formylate our amine.

Program: Culver Behavioral Science Research Fellowship
Faculty: Professor David Grannis, Communication
Student:

The California drought is a serious problem that has caused significant detrimental effects on
several communities throughout the state. From the state government implementing water cuts, a cost increase on water bills, sod farms losing business, and farmers in the Central Valley having to pump groundwater to meet demands, everyone has been affected negatively in one way or another. There are varying opinions on why the drought has impacted the state so gravely, and on who should be responsible for saving water and how they should do it, but there hasn’t been much research that has taken information and opinions from various sources and compiled it all to show a larger picture. My research partner Kristiann, my mentor Professor David Grannis, and I worked tirelessly this summer to open up the conversation between different experts and organizations involved in the issues surrounding water conservation and water rights in order to create a documentary. We traveled many places to film, from the thirsty farms in the San Joaquin Valley to the offices of local government officials, to gain a greater understanding about how the issue is being addressed both locally as well as up north. With this research, we hope to provide a more in depth look on the efforts being made in the small community of Thousand Oaks, CA and how they have made a difference to improve living conditions to combat the drought as well as to inform the masses on just how awful the serious conditions that have resulted from the drought truly are. The aim behind this research is to tell a visual story that will educate others on what we have come to learn throughout the time we spent on this project: The drought is about more than just a lack of water, it is about a huge controversy between northern and southern California, and it is about people having to transform their lives, from how they live to how they make their livelihood. We are currently in the post-production phase of this film and we hope to submit the final production to various Eco-film festivals throughout the country.

Program: Swenson Science Summer Research Fellowships
Faculty: Professor Candace Kelman, Bioengineering
Student:

According to a 32 years Nurses’ health study (1976-2008) on a total of 118,177 women aged 30-55, type II diabetes was found to be highly associated with an increased risk of renal cancer.
In the current study, the relationship between renal cancer and type II diabetes was studied at the cellular level. Human proximal tubule epithelial renal cells donated from diabetic patients were compared with the same type of cells donated from healthy individuals. Their growth and survival rates were observed, where the diseased cells were hypothesized to perform poorly as compared to healthy ones. A basic cell culture research was done on the growth rates of the two categories of cells. Two sets of experiments were conducted:
1.         Both diabetic and healthy proximal tubule epithelial cells were grown separately in 75 cm² flasks for a time period of 12 days and a cell count was done on day 12 in quest for cell growth rates of both categories.
2.         Both diabetic and healthy proximal tubule epithelial cells were grown in 25 cm² flasks and growth rate was observed based on confluence. Pictures of the flasks were taken daily at three designated areas and the progress in cell confluence was observed.
Based on the cell count done during the first part of the research, diabetic cells were observed to have higher growth (replication) rate than healthy cells, which was unexpected and opposes the hypothesis. However, results from the second part of the research, where cell % confluence was recorded daily, and the healthy cells resulted in higher growth rates as compared to the diseased cells. These two contradictory results are to be analyzed as, for future work; the experiment is to be repeated by considering other factors such as the hormones, growth factors and other nutrients that are added in the media in addition to maintaining favorable environment such as temperature. This will be a continuing project for the 2016-2017 academic year.

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

With the recent detection of gravitational waves by the Laser Interferometer Gravitational Wave Observatory (LIGO) a new era of gravitational wave astronomy is beginning to open. Finding an approximation for the background noise experienced by a gravitational wave detector would lead to more accurate readings and provide more information for the design of such instruments. This project aims to produce an estimate of the background noise in gravitational wave signals for that purpose. Gravitational radiation background noise is emitted by massive compact objects (such as black holes, white dwarfs and neutron stars) in orbit around supermassive black holes (SMBH) at the centers of galaxies. To calculate the background noise we take approximations for the energy released per compact object-SMBH interaction, an approximation for the rate at which these interactions occur, an approximation for the number of events per supermassive black hole, an estimated number density of galaxies per volume of space, and lastly the cosmological evolution of these parameters. The resulting signal is redshifted due to the expansion of the universe. The goal of this project was to create a code to calculate the necessary values listed above. To date, a calculation incorporating only the black hole-SMBH interactions has been made. The background noise emitted by other compact objects will be included in the future work. Fortunately, the black hole-SMBH interactions emit most of the gravitational radiation experienced. Once these are incorporated, we will continue to improve the approximations used. Specifically, we will look to improve the approximations for the energy per event, redshift value and number of events per supermassive black hole. The final resultant from this project will be useful in the design of future gravitational wave detectors such as the Laser Interferometer Space Antenna (LISA) set to start soon.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Katherine Hoffman, Chemistry Department
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 Department
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: Swenson Science Summer Research Fellowships
Faculty: Dr. Grady Hanrahan, Chemistry and Physics
Student:

Semiconductor photocatalysis has been applied to a variety of problems of environmental interest, such as towards the remediation of a wide variety of contaminants and microorganisms in aqueous systems. In this regard, archetypal semiconductors (e.g., TiO₂, ZnO, Fe₂O₃, and CdS) can act as sensitizers for light-reduced redox processes. Using the Cr(VI) ion as a model contaminant, the purpose of this study will focus on using aqueous solutions of ZnO under UV/vis radiation as a method of photocatalytically reducing Cr(VI) to the less harmful Cr(III). In order to optimize experimental reactor conditions we will utilize the exploratory power of Factorial Designs to examine the continuous factors (e.g. solution pH, concentrations of Cr(VI), reaction time, etc.). In regards to methodology, all photocatalytic degradation of Cr(VI) will be performed in a slurry batch reactor with a .250-L volume, a stirring mechanism and radiation from a mercury lamp (UV/visible). By applying JMP software-based Full Factorial Designs we will be able to find the most important experimental factors (and at what levels) are needed for both efficient co-precipitation and determination of reaction kinetics of the conversion of Cr(VI) to Cr(III). The simplest version of Full Factorial Designs is referred to as a two-level design, 2k. This means that there will be two factors and each factor will have two factor levels: low and high. Optimized conditions will help us study reaction kinetics associated with the conversion of Cr(VI) to Cr(III). We will consider various kinetic models such as pseudo zero, first, and second order models. The integral treatment of differential rate equations will yield integrated rate laws which will profile the decay models that will be observed when Cr(VI) undergoes photocatalytic degradation. This study will provide insight into the catalytic reduction of toxic environmental species and allow us to determine reaction kinetics under optimal experimental conditions determined by dedicated mathematical modeling techniques.

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

Infectious bovine keratoconjunctivitis (IBK), also known as pinkeye, is a disease commonly endemic in cattle herds found in the United States.  The manifestations are mild conjunctivitis, ulceration, and blindness which can result in significant financial loss to the rancher.  The most common pathogen that is associated with IBK is Moraxella bovis, a gram negative non-motile coccobacillus bacterium that exists in both a hemolytic and non-hemolytic growth.  The hemolytic type has been shown to be virulent whereas the non-hemolytic version does not cause the disease.  Current dogma suggests that the pathogen is transmitted by animal handlers, head flies and animal-to-animal contact.  It has been shown that outbreaks of IBK usually occur in warmer months and it has been suggested that M. bovis might reside in the nasal passages of the cattle during winter time lying dormant until the warmer months of the year.  The purpose of this study was to investigate the possibility that M. bovis could be isolated from a typical water trough located in a cattle pasture and moreover, function as another method of transmitting the disease.  Water samples were collected on a monthly basis from a water trough located in a cattle pasture in Moorpark, California from February to July 2016.  Total colony forming units (CFUs) were counted and the bacterial growth increased in a manner consistent with the ambient temperature.  Samples were transmitted to blood bovine agar plates using cloxacillin as a semi-isolation method.  M. bovis was isolated and identified by 16s sequencing from the initial samples, however, in April three other bacteria were cultured on the agar plates along with M. bovis with resistance to cloxacillin.  One of those bacteria was isolated and identified via 16s sequence as Aeromonas voronii. M. bovis exists in both a hemolytic (infectious) and non-hemolytic (non-infectious) form.  Investigation of the intergenic spacer region (ISR) of both forms suggests significant genome variability between the hemolytic and non-hemolytic varieties.

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

Collagen is a structural protein found throughout the connective tissues of the animal body.  It plays a large role in determining the tensile strength of tissue.  Collagen is a major component of the extracellular matrix and is responsible for many of its functionalities including tissue structure, growth, repair, and renewal. The purpose of this study was to investigate how collagen affects the growth and survival of D17 canine cancer cells.  We hypothesized that the D17 cells would survive longer in a collagen-coated plate compared to a standard plastic culture plate. The cells were grown under standard cell culture methods; incubated at 37 C in 5% CO2 and fed with Eagle’s MEM.  A clonogenic assay performed resulted in a higher yield of D17 colonies in collagen compared to plastic (Avg. # of colonies per 10⁴ cells; 17 in plastic, 79 in collagen).  Flow cytometry was used to determine whether the difference in the number of colonies was due to cell survival.  Samples were stained with 7AAD to discriminate dead or dying cells from living cells; results revealed no difference in the number of 7AAD positive cells in collagen versus plastic, indicating a separate explanation for the increased number of colonies in the collagen assay, possibly increased proliferation.  Further experimentation is required to determine if the rate of proliferation in collagen will account for the disparity in the clonogenic assay colony count.  Studying the effects of collagen on canine cancer cells can help us determine the conditions by which cancer cells proliferate most efficiently.  Consequently, we can better understand how to limit their proliferation in canines and eventually humans in vivo.

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

Navigating stairs is considered a difficult and dangerous task for elderly adults (Cohen et al., 1985; Alcock et al., 2015). Past research has found that falls on stairs account for 10% of fatal fall accidents, and this difficulty with stairs for older adults could be due to visual impairments, musculoskeletal strength or joint disease (Startzell et al., 2000). It has been reported that when elderly ascend stairs, most prefer to use their stronger limb during the transition cycle from the floor surface to the stairs (Alcock et al., 2013). The purpose of this study was to determine if there is a link between knee joint muscle strength and transition step preference in stair descent in elderly subjects. Additionally, kinematic and kinetic values were compared between preferred and non-preferred lead legs. Individuals 65 years and older were recruited for the study (17 females, 15 males). All subjects were free of physical impairments, neurological disease and vision challenges not correctable with lenses. Subjects also had to be comfortable going down a short set of stairs without using a handrail. After completing a university IRB-approved consent form, subjects filled out a health questionnaire to ensure eligibility. Stair descent was done on a set of three standard sized stairs, leading with their right foot or leading with their left foot, in random order. Motion capture data was recorded using 6 Vantage V5 cameras collecting at 120 Hz and two Kistler Force Plates collecting at 1200 Hz. Data was analyzed using Vicon Nexus 2.0. Knee extensor and knee flexor strength was determined by a Biodex System 3 isokinetic dynamometer at 180º/s and at 60º/s. After data collection, subjects were asked to identify which was their preferred lead leg for the stair descent. 28 subjects had a definite preferred lead leg. The lead leg matched the stronger knee extensor leg for 16 of the subjects who had a preference. A dependent t-test was used to determine differences in joint angles, joint torques and ground reaction forces between the preferred and non-preferred legs (p < 0.05).

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

Hepatitis C (HCV) is able to avoid the immune system and apoptosis because the core protein inhibits the kinase activity of the cyclin E protein. The cyclin E protein helps control the G1/s checkpoint and thus helps the cells to evade apoptosis. In addition to preventing infected cells from moving beyond the G0/1 checkpoints, the core protein seems to stop NFKB activation, which can change the immune response. Cells that have successfully evaded apoptosis remain in the G0 and G1 checkpoints of their cell growth cycle and overexpress interleukin 10 (IL-10). This causes a shift from Th1 to Th2 immune response. Real Time Polymerase Chain Reaction will measure the levels of cytokine mRNA, which will tell us about the changes in infected cell gene expression. Performing Western Blots will detect the presence of proteins and Flow Cytometry will measure the cell-viability by the cell count. My hypothesis is that when interleukin 10 is blocked, the immune system will be directed at fighting the virus instead of the protein decoy. The Escherichia Coli cells were incubated and grown in RPMI-1640 and Fetal Calf Serum media. Once the cells reached maturation, they were treated in order to knockout the IL-10 gene. The plates turned up dry and the experiment needs to be repeated. From this assay, cytokine expressions of IL-2, IL-4, IL-6, IL-10 and IL-12 will be compared, as well as INF gamma and HCV concentrations. The data will thus help us see the effect of the knocked out gene on other cytokines and HCV concentrations. With more than 350,000 annual, HCV-related casualties and almost 3-4 million new victims each year, the search for an HCV vaccine is an ongoing priority. Because of its asymptomatic characteristic, HCV has been inferred to avoid the human body’s immunological response to infections by lymphocytes (B and T cells) and monocytes. Out of the many cytokines expressed during typical immunological responses, the interleukin 10 (IL-10) cytokine has demonstrated a particular overexpression in HCV infected cells (2,3).

Program: Darling Summer Research Fellowships for Applied Scientific Computing
Faculty: Dr. Craig Reinhart, Computer Science Department
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: Darling Summer Research Fellowships for Applied Scientific Computing
Faculty: Dr. John Deisz, Physics Department
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: John Stauffer Research Fellowships in the Chemical Sciences
Faculty: Dr. Jason Kingsbury, Chemistry
Student:

Homochiral aziridines are useful precursors for ring-opening chemistry that generates novel pharmaceutical compounds. Specifically, functionalized and stereodefined vinylaziridines represent a class of compounds previously unexplored for producing complexity in novel drug compounds. Previous research has shown successful preparation of homochiral aziridines by various methods. Unfortunately, these methods are limited to a small range of aziridines, all with specific functional groups that are not conductive to further transformations. The objective of my research was to efficiently synthesize functionally-versatile and stereochemically-defined vinylaziridines in a cost-effective manner. A double-protected, serine-derived amino alcohol was subjected to reduction by lithium aluminum hydride and a Swern oxidation, producing an L-serine aldehyde. Significant product loss was evident by 1H NMR when product isolation was attempted, likely due to the unstable nature of the L-serine aldehyde. However, when the resulting crude product was immediately employed in a Wittig reaction, useful quantities of olefinated L-serine aldehyde were produced and confirmed by GC/MS and 1H NMR analysis. The olefinated L-serine aldehyde is now being employed in a double-deprotection reaction with Pd/C in the presence of hydrogen gas. This is expected to afford the amino alcohol vinylaziridine, which will immediately be employed in a pseudo-Claisen rearrangement to afford a functionalized azacycle. Mitsunobu reactions will also be attempted on a deprotected variant of the serine-derived amino alcohol as well as a variant that was deprotected and underwent a formylation reaction. If successful, these reactions will constitute a remarkably direct and scalable entry to this valuable synthon, with points of diversification easily anticipated. This will usher in a new method for functionalizing azacycle cores that can be tuned for pharmaceutical intention.

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

Integrins are transmembrane proteins present of the surface of cells Integrins aid the cell in many tasks, such as adhesion, proliferation, migration, growth, cell-to-cell contact, and connecting the cell to the extracellular matrix. The purpose of this study is to determine which integrins are present on the surface of a line of canine cancer cells, named D17. Cells were handled in a biohazard, sterile hood and fed with Eagle MEM media. Several assays were conducted to test for presence or function of integrins on D17s, including an integrin inhibition assay, scratch wound assay, and the cells were run through the flow cytometer to determine the presence of integrins on the surface of the cells. The integrin inhibition assay tests the adhesion and attachment of the cells via integrins. The scratch wound assay is a test of migration potential and data from flow cytometry is an indicator of which integrins are present on the surface of the cells and which are not. So far we know that 6 and 1 integrins are present on the surface of D17 cells. We are beginning to understand the relationship between integrins and adhesion, migration or attachment of the cells. By learning more about D17 cells, they can be used as a model to better understand other cancer cell lines. 

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

As global ocean temperatures rise, fish populations migrate north in search of colder waters.  In effect, California sea lions, Zalophus californianus, inhabiting the Channel Islands must travel farther north to forage, leaving their pups for longer periods of time between feedings. The extended separation between mother and pup results in malnourishment and leads to disease. Unable to care for themselves, these pups are often found stranded on the shores of the California coast. The Channel Islands Marine and Wildlife Institute (CIMWI) is a local rescue organization committed to rescuing, providing medical attention, and rehabilitating marine mammals in need. Once healthy and rehabilitated, these animals are released back into the wild. With the assistance of CIMWI staff and chief veterinarian, Dr. Sam Dover, we are studying the gut microbial population of California sea lion pups in hopes of finding new ways to improve treatment during rehabilitation.

The purpose of this research is to compare the gut microbial population of sea lion pups before, during, and after CIMWI care, which includes the administration of antibiotics, probiotics, and a controlled diet within a regulated environment. CIMWI staff collected fecal samples from sea lion pups upon entering rehabilitation, twenty days after antibiotic administration, and before release. We extracted metagenomic DNA from 55 samples and performed PCR to amplify Bacterial and Archaeal DNA sequences of the small subunit ribosomal RNA (ssu rRNA). Each sample was tagged with a unique barcode. Samples were pooled, diluted, and sequenced using the Illumina^Ⓡ MiSeq Next-Generation Sequencer. To analyze the ssu rRNA sequence data, we are using QIIME software to evaluate sequence quality and determine phylogenetic identity. Using the HHMI Cluster, we are comparing microbial communities between sea lions and along the time course of their rehabilitation. We expect that the gut microbial populations will differ between sea lions upon admission to CIMWI, become similar during treatment, and healthy prior to release.

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

Much research has been performed to understand how superconducting materials could be changed in order for them work at room temperature; which would make them commercially affordable. Such materials offer two unique properties: quantum levitation and zero electrical resistance. One method for altering the material is to apply different levels of strain. After various decades of research, our current understanding of how strain affects materials is not as accurate as we may think. The purpose of this study was to determine how the electronic and superconducting properties of Strontium Ruthenate were affected by applying different levels of strain. By using a computer program, known as Cygwin, I wrote a total of around 600 lines of the computer code. This task was performed to be able to model this material’s composition, and consequently be able to model different strain levels to it. As we applied different levels of strain we obtained contradictory results with respect to the electronic properties of the material. First, when we looked at how the energy of one single electron was affected by strain, the results showed a significant change to the material’s electronic properties. Second, we now looked at how the energy of all electrons changed with strain, yet this time the results showed no significant change. We then looked at how superconductivity/magnetism was impacted by strain. Our expectations were that as we increased the strain, the temperature at which the material became magnetic would also increase. However, our results showed that this temperature decreased as we increased strain. In order to successfully analyze this material we must implement a 3D model. My code, being only a 2D model, accounts for the movement of electrons between the atoms that are within the same plane. The 3D model would not only account for the horizontal movement between planes, but also analyze the vertical movement of electrons from plane to plane. We believe that this might resolve the discrepancies that we have observed thus far.

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Andrea Huvard, Environmental Science
Student:

Fouling communities are groups of marine organisms that can be found on artificial surfaces. On the California coastline, increasingly common invasive species such as Bugula neritina pose a threat to marine ecosystems including the keystone species Mytilus californianus.  This study investigates how succession in fouling communities located in Channel Islands Harbor can be affected by abiotic factors (temperature, salinity, etc.) as well as biotic factors (species composition, abundance, etc.).  This was studied at two research sites in the harbor 576 miles apart with each location being either 0.396 or 0.697 miles away from the mouth of the harbor. Research samples included PVC plates and ceramic pots that were placed at both study sites. On a monthly basis, environmental parameter data was collected in the form of temperature, conductivity, salinity, and oxygen measurements. Plankton and nutrient samples involving chemical compounds such as ammonium, nitrate, nitrite, and phosphate were also taken. Data was analyzed using graphs, tables, visual identification, and the open source image processing program known as Image J to calculate species abundance and % coverage. The results indicated there is a greater amount of biodiversity of fouling species at the first study site located 0.697 miles away from the mouth of the harbor. While it is clear succession occurs at both locations, the first study site has a larger presence of Mytilus californianus on the outside and the inside of ceramic pots in both length and number along with higher average % species coverage of 33.6%. The results are not statistically significant according to the student’s T-Test that was used to determine significance. This hypothesis was formulated under the assumption that the closest study site to the mouth of the harbor would have a greater biodiversity due to more nutrients and water flow, however, it can be inferred that factors such as increased eutrophication from runoff fertilizer could explain our current results. 

Program: Swenson Science Summer Research Fellowships
Faculty: Dr. Joel Berrier, Physics
Student:

The universe is constantly evolving and growing, as time goes on more structure is seen forming. The largest objects in our universe are galaxy clusters which can house anywhere from 10s to thousands of galaxies. Each cluster is surrounded by a halo of dark matter. Within clusters galaxies show major differences from non-cluster galaxies, in star formation, color and internal structure, one question we wish to answer is whether this change has happened at an earlier time in the formation of the universe when the galaxies were still not members of a cluster or if the interior environment of the cluster is the driving force for these differences.  We look at when galaxies fall into the cluster and how clusters gain their mass. We use the Multidark Plank Simulation which is accessible for querying on the Comso-sim website and look at around 10 clusters (Masses > 10¹⁵ Solar Masses).  We then obtain data on the history of each of the clusters and the objects that contribute to their growth. All the data is collected we looked at each time step of the simulation and determined the total number of in falls at each time step for the 10 clusters. The results show that most galaxies currently in the cluster fell into the cluster more recently in cosmic history. The time spent in the clusters suggests that fast acting processes are required to change a galaxy’s properties in the clusters.

Program: Culver Behavioral Science Research Fellowship
Faculty: Dr. Jean Kelso Sandlin and Dr. Monica Gracyalny, Communication
Student:

Much of the past research on public apology has conceptualized the behavior as mass communication, using a media framework to analyze effective rhetorical strategies and opinion polls outcomes. With the rise of new communication technologies, however, public figures are now using social media to communicate their apologies through new “mass-interpersonal” channels. Despite the popularity of social media apologies, few studies have examined public perceptions of this new form of communication. Specifically, it is important to understand whether audiences perceive social media apologies as sincere, and how these perceptions relate to audiences’ willingness to forgive. As the first in a program of research on social media apologies, the current study examined verbal and nonverbal behaviors used by public figures to apologize on social media. Thirty-six video apologies recorded between 2009-2014 were analyzed. Apologies were included if mentioned in at least one of the top two television news networks and posted to YouTube. Using content analysis, videos were coded for verbal and nonverbal behaviors. Nonverbal emotion expression was coded using a modified version of Ekman & Friesen’s FACS. Verbal apologies were coded using Darby & Schlenker’s interpersonal apology framework and Benoit’s media image repair strategies. Results of the nonverbal analysis showed the following emotion: 33.4% sadness, 12.5% anger, 11.5% contempt, and 29.3% no negative emotion. Regarding verbal behaviors, Darby & Schlenker’s interpersonal analysis found: 37.1% admitted fault, 14.5% admitted damage, 23.4% expressed remorse, and 22.3% offered compensation. According to Benoit’s media image repair analysis, the apologies included 8.9% evasion, 9.5% reduced offensiveness of event, 15.4% corrective action, and 61.2% mortification. Finally, none of the apologies included nonverbal expressions of fear, surprise, or denial, and no public figure specifically asked for forgiveness. Phase two (public sentiment analysis) and three (public forgiveness study) will be conducted this fall and spring.