Student Research Symposium

Saturday, October 29th, 2016, 9am-12pm

Abstracts

Darling Summer Research Fellowships for Applied Scientific Computing

Interaction of Two Artificial Intelligences Using Seek and Destroy Algorithm

Nickel Revie, Dr. Craig Reinhart
Department of Computer Science

Description

Artificial Intelligences (AI) are very prevalent in many industries for their ability to autonomously accomplish tasks. As an example, a metro system in Hong Kong is managed by an artificial intelligence program and has seen significant improvement across the board which includes having a 99.9% on time record and saving two days of repair time a week. By relegating tedious tasks to AI controlled devices, it allows people to do other tasks that cannot be conducted by AIs. For example, a robot controlled by an AI can spend several hours a week cleaning a house autonomously instead of an individual (or several) doing the same job. Furthermore, a dependable and autonomous intelligence combined with reliable hardware will save costs and free up individuals for other jobs that require more technical skills or remove individuals out of hazardous occupations. In particular, sending teams on search and rescue operations has become a dangerous task. These teams are sent into the same environments that injure the traveler or travelers, making injured rescue personnel a real possibility. Having an AI control several drones may help ground teams locate the lost person or persons and will save money, lives and time during a search and rescue operation. This can cause a reduction of team sizes and injuries among rescuers in dangerous terrain. Using this as an inspiration, this study is aimed towards experimenting with the search and rescue algorithms and modifying them in order to investigate how two autonomous non-human intelligences interact. This will be implemented by using two different AI controlled robots; a “search and rescue” drone that will search, locate, and attempt to track a “fugitive” robot to evade the tracking AI. By doing so, we can see how the tracking AI will behave based upon the movements of the “fugitive” robot trying to evade the “search and rescue” drone.

Measuring the Efficiency of Rapid Application Development Languages (LiveCode) in Creating Cross-Platform Software

Carla De Lira, Dr. Craig Reinhart
Department of Computer Science

Description

Software development has become more complex with the need to provide applications on platforms (e.g. desktop, laptop, tablet, smart phone) and operating systems (e.g. MacOS, Windows, Linux). The time to develop cross platform application has also increased dramatically. Furthermore, cross platform development may require different programming languages (e.g. Objective C for iOS and Java for Android), further stressing resources. Much significance is made in cross-platform development's importance as key to an application's success, especially mobile applications. Recently, developers have turned to web-based applications that depend on internet connections for its accessibility. Although this solves the cross platform issue, it is not practical in its overall usability and imposes limitations in completing specifications with HTML 5 and JavaScript. The purpose of this study is to develop an application using LiveCode (livecode.com) to see how efficient it is in creating a usable, binary compatible, cross-platform application. Parameters to be studied include the consistency of the user interface, speed, disk space, and memory usage across each operating system and device. The application is S.E.A Navigation, a cross platform mapping application. S.E.A Navigation will be tested on different platforms on several devices with a specific test plan which focuses on specification fulfillment, resource usage, and speed. Each conducted test will be completely neutral to the operating system and device. By doing this, it will reveal insights for future development of other IDEs and programming languages that have a similar cross-platform centered design.

Foster Family Foundation Undergraduate Research Fellowship in Religion

Sex and the City: A Study of Sexual Theologies across Christian Denominations

Malina Keaton, Dr. Peter Carlson
Department of Religion

Description

Christian theologies on topics of gendered sexuality have been informed by many different sources throughout history. Theologians such as Augustine and Jerome are famous for their “sex negative” ideologies, views still manifested in many denominations today. Feminist, Lesbian/Gay, and Queer theologies have also opened the door for marginalized Christians to look at their bodies in different ways than before. Voices within this movement have shaped a new sex ethic, one that emphasizes the important potential of the church within sex education. Whether “conservative” or “progressive”, denominations are becoming part of the ever-increasing discussion about sexuality within the context of religious conviction, discourse that can sometimes empower or shame its laity. As more and more people—and, in particular, more and more college-age people—seek to find ways of integrating their sexuality and their spirituality, there is a need within the current scope of religious influence to connect the physical bodies we are now much more open about in the “secular” world with a theology that is created to deal with temporal issues. The world has shifted since the days of Augustine; sexuality has become more of a question rather than a statement. It is because of this that research of sexual theology is of vital importance individually, academically, and ecclesiastically. With the generosity of the Foster Family Foundation and Office for Undergraduate Research and Creative Scholarship, I conducted an ethnographic study involving eighteen semi-structured interviews with clergy in the Ventura and LA counties, and additionally collected the official denominational positions and legislation of thirteen Christian denominations pertaining to issues of gender, marriage, and sexuality. Research conducted this previous summer often showed disparity between denominational doctrine and congregational experience regarding issues of sexuality, placing clergy in a position of mediation between an official voice and lived reality. Due to the divisive nature of discussion that centers around these topics, my research additionally documents the forms of marginalization that occur within a congregation—a marginalization which repeatedly places clergy in situations of tension.

John Stauffer Research Fellowships in the Chemical Sciences

New Synthetic Applications of the Diazoalkane-Carbonyl Homologation Reaction

Jacob S. Burman, Dr. Jason Scott Kingsbury
Department of Chemistry

Description

In the laboratory, we often rely on heteroatoms (oxygen- and nitrogen-based functional groups) to create C–C bonds, which are the foundation upon which structure and function are realized in biological systems.  Contemporary research has shown that laboratory methods for functionalizing unactivated C–H bonds represent an impressive feat for chemical synthesis.  Today, a number of techniques exist for installing oxygen- or nitrogen-based groups in a selective fashion, and the resulting functionality imparts useful reactivity to the target molecules.  However, in spite of great achievements, we are still far from Nature’s perfection in building diverse and biologically active molecules from inert carbon frameworks.  Thus, identifying strategies for C–C or C–H insertion events will greatly advance the field. One reaction type that formally allows for carbon insertion is Diazoalkane-Carbonyl Homologation. This C-C bond forming system is a powerful catalytic transformation involving net insertion of carbon atoms from diazoalkane reagents into the C–C or C–H bond adjacent to C=O double bonds.  In addition to permitting formation of two new C–C bonds in one step, this method imparts a synthetically useful ring expansion or chain elongation.  Another advantage is that molecular nitrogen, a harmless gas comprising 60% of earth’s atmosphere, is the only stoichiometric byproduct of the process. Optimizing this reaction and rendering it scalable for the community/field will not only change the way we build up molecular complexity, but represent a victory in our quest to expand on the number of environmentally-friendly chemical practices.

Presently there are two related projects under investigation in the Kingsbury group that focus on the strategically powerful Diazoalkane-Carbonyl Homologation reaction. In the first, application of a 5-carbon diazo compound to the total synthesis of artemone, a natural product from the Indian sage Artemesia pallens is being pursued. In the second area of study, a 15-carbon diazoalkyl insertion is being applied to the synthesis of a mitochondrial marker for MPTP (Mitochondrial Permeability Transition Pore).

Toward Studying the Cytotoxicity of Common DNA Markers

Trevor Hougen, Dr. Jason Scott Kingsbury
Department of Chemistry

Description

Prior investigation into the field of fluorescent DNA markers has presented the need for a marker that could operate within a live cell, and whose binding mechanism to DNA did not cause mutations within the genome or other forms of cytotoxicity.

Purpose:  Our goal was to examine the synthetic route taken to prepare a recently discovered novel fluorescent DNA marker, and to determine the efficiency of each step in order to increase overall yield.  Methods:  The synthetic route for the target molecule had a crucial convergent step that needed optimization.  This step involved the joining of two molecules – one incorporating a boronic acid side chain and the other containing a halogen group in order to undergo a common synthetic process known as the Suzuki coupling.  We then altered the conditions with which we ran the Suzuki coupling, for instance we tested whether the more stable MIDA-boronate would create a higher yield than using the less stable, unprotected boronic acid.  Furthermore, we adjusted the concentration of the reactants in our reaction from 0.05 M – 0.1 M, the temperature from 75 oC – 95 oC, and the equivalents of the reactants to further increase the overall yield.  Lastly, we sought to ensure that the work up for the reaction was easy and efficient, so we compared the use of chromatography to properly separate our product to the use of hot filtrations and recrystallizations.  Results:  In the end, the highest yield we managed to achieve for the crucial intermediate synthetic step was ~85% from chromatography and ~40% from hot filtration and recrystallization.  We further optimized the final step and found roughly 80% conversion to the target DNA marker.  In addition, the purity of our final compound was high, so the overall performance of the synthetic route was very good.  Conclusion:  Studies are now underway to compare the mechanism of DNA visualization to that of other well-known DNA markers such as ethidium bromide and Disperse Red 1.

Direct Arylation Methodology for the Synthesis of Flexible Electronic Materials

Mickey Da Silva, Joseph Enders, Hillis Johnson,*Timothy Schwochert, Matthew Slaught, Dr. John Tannaci
Department of Chemistry

Description

Direct arylation is an effective way of synthesizing new molecules by forming carbon-carbon bonds. It offers a “greener” and more cost-effective method for generating many known compounds, as well as new ones. Applying direct arylation to the synthesis of conjugated materials and polymers greatly increases the viability of flexible electronics. This is because the direct arylation reaction tolerates a greater range of functionalities than previous methods of carbon-carbon bond formation, thus providing a more versatile tool for engineering devices at the molecular level.  However, there are still issues with controlling the unselective C-H activation observed during direct arylation reactions and polymerizations. The unselective activation leads to the formation of bonds in undesired locations on the molecules. In order to approach this problem, we used small molecule systems to optimize the reaction and minimize unselective activations. These optimizations included catalyst loadings, temperature, and time. Gas chromatography-mass spectrometry was used to analyze the experiments. Additionally, calibration curves for each model system were created in order to quantify the results. Despite extensive optimizations, unselective C-H activations were still observed. In addition to the optimizations, we studied the initiation of conjugated polymers using direct arylation. Careful initiation of a polymerization reaction can lead to increased control with minimal side reactions. The goal was to combine the findings of the optimizations with that of the initiators to produce a controlled reaction. Controlling the unselective coupling through experimentation will make direct arylation more competitive with current synthetic methods.

Pearson Scholars Summer Program for Leadership and Engagement in a Global Society

Latinas in the Los Angeles Street Art Culture

Marina Marisela Alverez, Dr. Rafaela Fiore Urízar
Department of Languages and Cultures

Description

In the urban setting that composes Los Angeles, graffiti, street art, and murals are visible in nearly every part of the city. They have been crucial to the formation of its identity, as well as the identities of the artists that produce the public art. Though few question the identity of these artists were due to the nature of this art, it has traditionally been a space dominated by men. It is important to acknowledge the female Latina artists who are leaving their mark in the history of this art form. Although many people would like to attribute its origins to New York’s Hip-hop scene of the 1970’s, its beginnings can be traced much further to 1930’s Los Angeles when Latino shoeshine boys would write their names on the walls of the neighborhoods they claimed. It was an act that proclaimed territorial spaces, but it was also an expression of identity and the attempt to survive a series of unfortunate circumstances. Latino gang members later used this concept to assert their dominance in neighborhoods as they struggled to find, and create, their spaces within American society and culture. When the writing developed into what is now known as Cholo writing, it had already become a pivotal aspect of Latino identity and culture in Los Angeles. Many of the Latina graffiti writers found themselves influenced by this epoch, along with Hip-hop music and New York-based ‘Wildstyle’ type graffiti in their artwork. The intimate world of street art is one that is not easy to get into. It takes practice, dedication, and hard work to be accepted and finally recognized. Not only have these Latina street artists and graffiti writers had to endure this code of the street world, but they have also had to maneuver through their culture’s stereotypes, one that promotes a patriarchal gender relation. It would be an understatement to say that they have proven every person wrong. Among them, they are world-renowned artists that have sold pieces in famous galleries, as well as continuing to be well-received artists in the communities they used to serve or still serve today. It is clear many of their experiences have shaped who they are, but they are the ones who ultimately claim the power when it comes to defining themselves, with a spray can or paintbrush in hand. Now is the time they are being credited with the recognition they deserve.

Summer Undergraduate Research Fellowships (SURFS)

Perceptions Regarding College from Adolescents with High Functioning Autism Spectrum Disorder

Chelsea M. Feller, Dr. Jodie Kocur
Department of Psychology

Description

Given recent research which indicates that a growing number of students with Autism Spectrum Disorder (ASD) are moving on to higher levels of education, it is important for colleges to discover how to best support students with ASD and for students with ASD to properly prepare for college. The present study aimed to better understand the feelings that individuals with High Functioning ASD have about attending college. Gaining insight into how these individuals feel about college and a better understanding of the challenges that a student with High Functioning ASD might face in the college setting will give valuable information to all those working to help these students transition successfully into post-secondary education. Seven male students with High Functioning ASD (ages 17-25) who were planning to attend college completed a fifteen minute interview regarding their perceptions of college. Students discussed when they started considering college, colleges they were considering and why, excitement and concerns about college, and their goals for college. A majority of participants started thinking about college in middle school and hoped to attend a 4-year university with a strong disability support services office.  Prominent concerns regarding college were socializing and managing their time to handle the work load. A majority of participants reported being excited about the opportunity to learn more about their particular field of interest. Other prominent college goals included making friends and getting a degree. Recommendations for future research as well as implications for how professionals and college personnel can best support students with ASD as they prepare for this transition are discussed.

Critical Thinking and Its Implications for the Acceptance of New Scientific Information

Lauren Neiger, Dr. Andrea J. Sell
Department of Psychology

Description

The scientific community currently faces a challenge in helping the general public understand and act on the current scientific conclusions published and supported by data.  For reasons unknown, the general public is critical of these new research findings and often chooses not to accept them. The present study aims to explore the connection between this criticism of new scientific findings and elements focused on in traditional critical thinking instruction. In this experiment, it was hypothesized that people who understand an article will be less likely to criticize it. Twelve undergraduate students from California Lutheran University who were enrolled in summer courses participated for extra credit. Participants read an article from a leading peer-reviewed psychology journal, and then wrote an open-ended response in paragraph form. Participants then answered questions for reading comprehension. Lastly, participants rated their perception of the article in terms of interest, believability, understandability and readability, using Likert scales. Two research assistants who were blind to the hypothesis read responses and coded each sentence as either criticizing or not criticizing, with fair agreement (K=0.368, p<.01).  Correlational analyses were run to test for relationships between perceptions of believability, readability, understandability and the critical sentence ratio and the ratio of critical sentences to total number of sentences for each response. Results show that participants who correctly answered all of the comprehension questions showed the hypothesized relationship between critical sentences and understandability r(12)=-.670, p=.048.  As perceived understandability increased, the number of critical sentences relative to total sentences decreased. This study is a good first step in exploring factors involved in critical thinking and criticism of new scientific findings. Future studies will further investigate how manipulating the difficulty of the article changes the ratio of critical sentences to total number of sentences in a response.

Forgetting as a Cognitive Mechanism of Forgiveness: Studying Intentional Forgetting in Older Adults

Alicia Vanessa Nuñez, Dr. Andrea J. Sell
Department of Psychology

Description

Intentional forgetting is forgetting information on purpose (MacLeod, 1998). Often, it involves inhibiting or limiting details of a memory from coming into awareness (Levy & Anderson, 2002). Previous research suggests that intentional forgetting is useful in the forgiveness process (Sell, under review; Noreen, Bierman, & MacLeod, 2014). However, previous research has only examined this process in younger adults. Older adults, on the other hand, are known to have trouble with tasks that rely on inhibition, including intentional forgetting (Hasher, Zacks, & Radvansky, 1996). The current study explores the ability of older adults to use intentional forgetting in the forgiveness process. Thirty adults over the age of 65 from the community readtwo short stories, one sentence at a time. Each sentence was followed by a forget (F) or remember (R) cue. Midway through each story, an antagonist character perpetrated a conflict. This target sentence was either followed by a (F) or a (R) cue. After the story, participants were asked how likely they would be to forgive the antagonist. In a second manipulation, participants read two more stories; in these stories, the antagonist was either closely related (brother) or not related (stranger). This manipulation was used to examine how these relationships predicted forgiveness scores. Findings from the first manipulation revealed that the forget and remember cues did not produce increased forgiveness [b=-0.11, SE=0.32, t(18)=-0.36, p=0.72].  However, forgiveness scores predicted whether or not participants subsequently remembered the conflict sentence [b=-0.89, SE=0.33, t(18)=-2.69, p=0.02]. Perhaps, for older adults, intentional forgetting does not produce increased forgiveness, but forgiveness on the other hand, can influence the availability of an offending memory trace. Findings for the second manipulation found that, closeness in relation to the antagonist affected forgiveness scores [b=1.09, SE=0.37, t(14)=2.91, p=0.01].  While low power is a limitation in this study, overall these findings support the hypothesis that older adults are less able to use intentional forgetting in the service of forgiveness. Likewise, participants are much more likely to forgive a family member than a stranger.

Swenson Science Summer Research Fellowships

Effects of Landing Direction and Gender on Lower Extremity Kinematics in Drop Landings

Tyler Berg, Dr. Michele LeBlanc
Biomechanics Laboratory, Department of Exercise Science

Description

Previous research has identified several factors that may contribute to ACL injury, including gender, improper landing mechanics, and landing direction. Purpose: The purpose of this study was to compare the effect of landing directions and gender on lower body landing kinematics.Methods: Twenty-nine physically active subjects (15 M, 14 F) age 18-25 years with no previous jump or landing training participated in this study. Drop landings were performed from a 60 cm box with lower extremity kinematics captured with a Vicon 6-camera motion capture system collecting at 120 Hz. Trials were performed from six equal distance directions (Right, Diagonal Right, Forward with Left foot, Forward with Right foot, Diagonal Left, Left) with direction order randomized.  Sagittal and frontal plane angles at the hip, knee and ankle for the lead leg were computed at touchdown (TD), at maximum knee flexion (LP), and the corresponding ROM with five clean trials per direction averaged for analysis.  Analysis was performed with a two-factor ANOVA (p < 0.05) with post hoc tests using Bonferoni.  Results: There were no gender differences or interactions for the hip or ankle angles in either plane.  Ankle angles did not differ based on direction in either plane.  Gender differences existed for the knee in the frontal plane at TD (-3.7° ± 10.4° for F, 6.1° ± 8.8° for M; p < 0.001), at LP (-7.1° ± 19.0 for F, 15.0° ± 13.3° for M; p < 0.001), and the ROM (-3.4° ± 11.1° for F, 8.8° ± 6.3° for M; p < 0.001) with females generally exhibiting valgus angles. Landing direction affected hip adduction and knee flexion angles.  In general, subjects had smaller hip adduction and greater knee flexion angles when landing in directions that had their right foot as lead.  Conclusions: Various landing directions maintained the knee frontal plane angle differences associated with gender.  Subjects altered landing mechanics based on lead foot which may affect injury potential.

The Effects of SOCS36E on JAK/STAT Signalling and Extra Eye Penetrance in Drosophila melanogaster

Jared I. Berman, Dr. David M. Marcey
Department of Biology

Description

The Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) pathway governs many developmental and pathological processes in Drosophila melanogasterExtra eye (ee) is an incompletely penetrant, variably expressed mutation located on chromosome 2L. Prior studies of JAK/STAT signaling and ee indicate that the penetrance of ee phenotypes increase as JAK/STAT activity is upregulated.SOCS36E is a known feedback inhibitor of the JAK/STAT pathway. Thus, loss of function of SOCS36E may be used to analyze the penetrance of ee in a scenario of intensified JAK/STAT signaling. Purpose: This investigation was intended to assess the amplification of ee phenotype penetrance in Drosophila populations bearing the ee mutation as a result of JAK/STAT activation.  Methods: The experiment utilized fourDrosophila lineages: Wild type individuals (1), ee individuals (JG1), and two lines containing SOCS36E loss of function mutations (35896 and 33106). Virgin JG1 females were simultaneously crossed in three separate instances to males of wild type, and both SOCS36E mutant populations. F1 generations for each of the three crosses were collected and evaluated for ee penetrance. Scored flies included 660 individuals from the 35896xJG1 population, 649 from the 33106xJG1 cross, and 200 1xJG1 individuals. Flies with an ee phenotype were recorded and used to determine penetrance levels in each respective F1 generation. Results were compared with chi square analysis to elucidate significant increases in penetrance. Results: An evaluation of the three crosses indicated that there was a significant increase in ee penetrance in both of the SOCS36E crosses in relation to the control wild type cross. The 33106xJG1 cross yielded a penetrance of 1.08% and the 35896xJG1 cross demonstrated a value of 1.82%. The 1xJG1 cross presented moderately lower expression, with a penetrance of 0.500%. Conclusion: It appears that ee penetrance is heightened by JAK/STAT activation. Future investigation should be devoted to considering other potential effectors of JAK/STAT signaling and ee penetrance.

Manipulation of Cytokine Expression and Its Effect on Hepatitis C Virus Infected U937 Monocyte

Salvador I. Brito, Dr. Dennis Revie
Department of Biology

Description

According to the World Health Organization, there are approximately 150 million people infected with the human Hepatitis C Virus (HCV) worldwide. Out of the ones infected, about 500,000 people die per year from HCV-related diseases, like liver cirrhosis and hepatocellular carcinoma. However, due to the elusive process of infection by HCV, discovering a proper vaccine has been difficult. Thus, it is important to obtain as much knowledge as possible on how HCV is expressed in infected cells. Because of its asymptomatic characteristic, HCV has been inferred to avoid the human body’s immunological response to infections. This evasion by HCV has thus brought forth an interest in cytokines, which are intercellular proteins that act as signals between different cells, including monocytes. The first part of this ongoing study is to quantify the expression of cytokines in monocytes before and after HCV infection. After the quantification step, manipulation of cytokine expression will be done through a gene knockdown in order to understand the role specific, over-expressed cytokines play during HCV infection. In the study, two samples of U937 monocytes were cultured by Dr. Dennis Revie: uninfected (U) and HCV infected (I) cells. RNA purification was then done on both cultured cells, which was followed by Reverse Transcriptase (RT) to obtain cDNA strands. Upon reaching this step, Real Time Polymerase Chain Reaction (qPCR) was done on uninfected and infected samples in order to compare cytokine expression. A standard curve composed of different concentrations of HCV and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were used in order to quantify the analyzed cytokines. Over the course of this study, approximately 25 unique genes were analyzed. From these 25 genes, 6 genes (TAF1L, TNF, TNFAPI3, TAX1BP1, PAK2, and API5) showed a considerable amount of up-regulation after infection. Five of the formerly mentioned genes, not including TAF1L, have been showed to be anti-apoptotic genes. Because liver cells are known to avoid apoptosis after HCV infection, these genes are of particular interest. Further quantification studies and analysis will be conducted on these anti-apoptotic genes as well as a gene knockdown to further study their role in HCV infected cells.

The Correlation Between Ventral Patches and Dominance in Sceloporus occidentalis

Luis Patricio Burgos, Dr. Kristopher B. Karsten
Department of Biology

Description

In many lizard systems, males often engage in physical confrontations for access to resources such as food, territory, or access to females. However, physical combat carries significant risks. As a result, many species have evolved displays to establish social dominance without physical confrontation. In western fence lizards, Sceloporus occidentalis, males signal with large ventral blue patches that they display via ‘pushup’ behavior. I proposed that male S. occidentalis lizards with larger ventral blue patches would display territorial dominance (both size of territory and number of females present in that territory) over males with “lesser” blue patches. In my research, I studied these displays but I mostly focused on identifying the territories of males correlated to the size of their blue patch. I did this by going out with a small team of researchers who aided in capturing and marking the lizards, both semi-permanently with paint and permanently by clipping their toes. 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 (toes 14 and 19 were not clipped because of their effect on sprint speed and possible fitness). After marking the S. occidentalis lizards, we would go out and do ecological surveys where we would identify the lizard by its markings and mark its location with a GPS device that saved all the locations. Over the course of the summer, we conducted over 20 surveys. Anytime we came across a previously unmarked male during the surveys, we would capture him and take him back to the lab for the spectroscopy measurements that quantified the blue of the patches. The males were released soon after the tests were completed.

The Analysis of Gene Sequences in Canine Tumors

Tristen Burt, Dr. Chad L. Barber
Department of Biology

Description

With over 33 commonly mutated gene loci an ever-increasing demand exists for mammalian model systems between human and canine cancers. As such, the canine genome has become a popular model for mammalian comparative genomics within the past decade. An investigation was conducted into identifying different genomic mutations in canine in situ carcinomas and comparing those mutations with those found in human cancers. It was expected that the tumor cells harvested and cultured in vitro should prove to be useful models for comparative genomic study. Four canine tumor lines (a mammary gland carcinoma (MG1), a canine lipoma (CL1), a sebaceous adenoma (SA1), and an osteosarcoma (OC1)) were harvested from dogs at Arroyo Vista Veterinary Hospital and grown in vitro. Meanwhile, DNA was extracted, purified, and amplified with 30 oligonucleotide primer sets, corresponding to common proto-oncogenes shared between canines and humans, using polymerase chain reaction. Their respective presence on the genome was verified via agarose gel electrophoresis, optimized, and then sequenced via capillary electrophoresis. In vitro studies concluded that the neoplasms harvested were not truly immortalized cell growths, with MG1 cultures going into quiescence after passage 11.  Molecular studies concluded and verified the presence of a majority of common proto-oncogenes among all four canine carcinomas, including genes of interest—TP53, KRAS, EGFR, and HMGA2 (common in human lipomas), all of which are common mutations observed in human cancers. Due to quality of genomic DNA, oligonucleotide design, and further optimization needed, only short sequences obtained were viable candidates for alignment and comparative analysis. In conclusion, our in vitro system can sustain most cell lines for at least 5-10 passages in culture.  In addition, primer sets for gene sequencing have been validated and should yield sequences in the next phase of the project.

The Social Effects of Tail Loss on Sceloporus occidentalis

Katherine Dubsky, Dr. Kristopher B. Karsten
Department of Biology

Description

Introduction: As in many species of 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 bigger and better territory means that the male will likely have more females nearby and therefore more access to mating opportunities. Lizards can voluntarily lose their tails to avoid predation. However, because they store fat in their tails, losing them may lower lizards’ chance of survival as well as their social status. Purpose: The purpose of this study was to determine if tail loss in males affects ability to maintain territory and/or access to females. Methods: Data were collected from late May to early August in the Briar Bluff region on Mount Clef. Males and females were marked with toe clippings and paint dots on their hind limbs for identification. Each time a lizard was spotted, a GPS point was taken at the exact location where it was found. Individual territories were mapped out using these GPS points. The number of females accessible to a male was determined by the number of female home ranges his territory overlapped. Results: This year, 18 males and 17 females were recorded. The GPS points for every lizard were plotted on a map of the region. Ten or more GPS points are required in order to accurately determine territory size. However, due to time and weather constraints, most lizards did not have enough points by the end of the season. Future Work: Next season, tails from half of the males will be removed. In addition, bite force, sprint speed, and the size of the blue patch on the underside of the male lizards will also be measured to observe any relation to territory size or access to females after tail loss.

The Role of sRNAother in Antibiotic Resistance in Bacillus thuringiensis

Jordan Felipe, Dr. Theresa Rogers
Department of Biology

Description

An extraordinary number of lives have been saved each year by the clinical use of antibiotics, but as we continue to use these drugs, bacteria evolve to withstand them. Antibiotic resistance, especially multidrug resistance, is a major public health concern as it not only increases morbidity and mortality rates, it also costs more money as hospital stays for the infected tend to be longer that those infected with a nonresistant bacterial strain. Purpose: The purpose of this study is to gain a better understanding of different methods of antibiotic resistance by investigating the naturally occurring increased multidrug antibiotic resistance found in the bacterium Bacillus thuringiensis.Methods: This investigation was done by selectively removing a gene sequence in B. thuringiensis, pseudotRNATrp, thought to be responsible for conferring an increase in antibiotic resistance. This selective deletion was achieved by a multistep method, generally: (a) obtain genomic DNA from stock B. thuringiensis; (b) selectively remove pseudotRNATrp via the use of specific primers and polymerase chain reaction, PCR, to create a sequence, ΔpseudotRNATrp, without our gene of interest; (c) insert ΔpseudotRNATrp into plasmid DNA of E. coli; (d) obtain modified plasmid from E. coli; (e) recombine E. coli plasmid DNA and B. thuringiensis genomic DNA in living B. thuringiensis bacteria to create deletion strain.  Future Work: Once this deletion strain of B. thuringiensis is obtained, we will perform growth analyses of this mutant alongside its wild type counterpart in the presence of varying levels of different antibiotics. This will help us understand the phenotypic differences betweenB. thuringiensis strains with the pseudotRNATrp sequence and those without said sequence. Outcomes: If pseudotRNATrp does as we expect, this would provide us with a platform to further study an actual mechanism of antibiotic resistance, specifically the intriguing method possibly employed by this bacterium. B. thuringiensis would be an ideal candidate for study because, as an insect pathogen, it can safely be handled by humans without the need for elevated health protocol or special certification.

Longitudinal Associations Between Anthropometric and Functional Measures of Sarcopenia and Osteopenia

1Amanda Hamilton, 2Jessica Tran, 1Dr. Steven Hawkins
1Department of Exercise Science (California Lutheran University), 2Cell and Molecular Biology and Public Health (Tulane University)

Description

The purpose of this study was to determine the longitudinal associations between anthropometric and functional measures of sarcopenia and osteopenia.  Fifty-three subjects (19 males and 34 females) aged 68-91 yrs were recruited from the previous study done in 2011. Bone mineral density was measured by a dual energy x-ray absorptiometry. A leg strength test, performed on a leg press machine, and a pinch strength and handgrip strength tests, performed with a dynamometer, were used to measure muscle strength. A get up and go test was performed as a measure of functionality. Data were compared across time by paired samples t-tests (p < 0.05).  For males, there was a significant decline in leg press (471±158 vs. 379±125 lbs, p < 0.05) and grip (40±8 vs. 37±7 kg, p < 0.05) strength.  GUG time (6.8± 1.3 vs. 7.8±2.9 s) and hip BMD (0.930±0.14 vs. 0.902±0.15 g/cm2) approached significance. For females, GUG time (6.7±1.1 vs. 7.1±1.3 s, p < 0.05), grip strength (27±5 vs. 25±6 kg, p < 0.05), and hip BMD (0.761±0.10 vs. 0.741±0.11 g/cm2, p < 0.05) changed significantly.  For both males and females, change in GUG time and change in grip strength were the strongest predictors of change in hip and spine BMD.  It appears that strength and functional measures may be useful to predict osteoporosis in older men and women.

Applying Queuing Theory to a Queuing System

Su Ji Hong, Dr. John Villapando
Department of Mathematics

Description

I waited over an hour for a ride at Magic Mountain even though the sign at the entrance said that the wait time is 30 minutes. This begged the question how does one estimate the length of time people wait in line.  In math terms the study of systems with lines is called queuing theory. In queuing theory a state represents the number of customers present at the system. Queuing theory uses flow balance equations derived from steady states to determine the probability of each state.  Then the expected number of customers and the expected time spent in the system can be figured out using the definition. I modeled the queuing system at the Centrum. After studying queuing system, I collected the data at the Centrum and formed models of the queuing system. Assuming that the arrival and service rates follow exponential distribution, I modeled the waiting line at the register and the network of queue line between the register and the kitchen.  From my observation, the queue system at the register followed M/M/1/FCFS: the arrival and service times are independent, there is one server, it has a first come first serve queue discipline, infinitely many people can be in the queue, and there are infinite many people from which customers are drawn. I figured out the arrival rate, and service rate. I computed the waiting time and compared it to the data. For the queuing system at the kitchen, it had M/M/1/FCFS: the arrival and service times are independent, there are n servers depending on what people ordered, it has a first come first serve queue discipline, infinitely many people can be in the queue, and there are infinite many people from which customers are drawn. I simplified this model to M/M/1/FCFS. Then I connected them using the fact that it depends on the register. This gave flow balance equations similar to the one before but with more variables. After calculating the probability of each steady state, I calculated the queue time at the register and the kitchen.

Where’s My Car? An AI Assisted-Living Android App

Blin Kazazi, Dr. Chang-Shyh Peng
Department of Computer Science

Description

Driving and using our cell phones is illegal and very dangerous. However in the 21st century when driving is part of our daily lives, finding our way in the maze of streets, highways and freeways has become almost impossible. People can no longer pull over to the side of the road and read a map to see where they want to go. There have been multiple attempts that big companies have made to solve this problem. Google has done an excellent job with the Google Maps. However operating the app still requires a lot of attention, and it is difficult to set the app and drive at the same time. My goal is to design a simple interface that is safe to use while driving, so that people can operate their phones and also drive at the same time. The goal of this project is to find ways to help people better use today’s technology to improve their efficiency. Technology is always changing, and keeping up with it is a challenge. This is why in this research project I intend to make a Map application that will be really simple to use, and in addition it will boost the user experience by already knowing where the user intends to go.

One area that needs serious consideration is parking in parking structures. With multi-story parking buildings and large parking areas, remembering where one parked is becoming more of a challenge everyday. Technology can  make the process of finding your car much easier. This is a problem amongst all age groups, however elderly people are more prone to forgetting where they parked. This can happen for multiple reasons, however Alzheimer’s disease is one of the main causes. This investigation will be part of the research project. By creating a simple to use application that will help people affected by memory loss, we will also indirectly expand the smartphone market to older age groups.

Using the Java programming language, in combination with a MySQL database, PHP scripts, and Javascript I am working on a revolutionary app that will change the way we use maps on our phones.

Antibiotic Resistance in Local Waterways and the Hill Canyon Wastewater Treatment Plant

Danielle Renee Montoya, Dr. Theresa Rogers
Department of Chemistry

Description

Antibiotic resistance has recently become a global concern. Over the past three decades, the level of antibiotic resistance in bacterial pathogens has increased dramatically due to the misuse and overuse of antibiotics in medicine and agriculture.  Antibiotic resistant bacteria from hospital and municipal waste collect in wastewater treatment plants where they can transfer genes conferring antibiotic resistance to other bacteria. Large and comprehensive studies have shown tetracycline, erythromycin, and sulfonamide resistance have been found in bacteria isolated from wastewater treatment plants around the globe. Various studies have demonstrated that some of these antibiotic resistant bacteria can pass through wastewater treatment plants into local waterways.  These studies may be underestimating the amount of antibiotic resistance entering local waterways because they relied on isolating bacteria in order to test for antibiotic resistance, yet only about 1% of bacteria can be cultured.  In this study, bacteria were collected by filtration and their DNA extracts analyzed for the presence of genes conferring resistance to tetracycline, erythromycin, and sulfonamides.

Localization of the ABCA4 Phospholipid Flippase in Developing Photoreceptors

Sharena Rice, Dr. Kenneth O. Long
Department of Biology

Description

Introduction: Flippases are proteins that transport lipids across cell membranes and serve as key regulators of cell polarity.  There are a number of flippases in the retina. A defect in the photoreceptor-specific flippase ABCA4 is linked to Stargardt macular degeneration in humans. In the adult fish retina there are developing photoreceptor cells at the periphery of the eye (close to the iris) along with fully differentiated photoreceptors throughout the rest of the retina.  Using goldfish retinas allows the visualization of the developmental appearance of ABCA4 and related proteins in photoreceptors.Purpose: The purpose of this study was to determine the effectiveness of different commercial antibodies in labeling flippases (ABCA4 and ATP8a2) in the goldfish retina.  These antibodies were not known to work in fish retina before.  The ultimate goal is to analyze the developmental appearance of flippases in photoreceptors and whether they appear before or after opsin, the light-capturing protein of photoreceptors. Materials and methods: Commercial goldfish were used.  SDS-PAGE and Western blotting were used to determine the molecular weights of the proteins and to tell which antibodies bound proteins of the goldfish retina.  The antibodies tested included Abcam's monoclonal anti-ABCA4, GeneTex’s polyclonal anti-ABCA4, Santa Cruz Biotechnology's anti-ATP8a2 (a related flippase) and anti-opsin.  Light and dark-adapted retinas were also fixed processed for immunocytochemistry. Results:This study demonstrated that GeneTex’s polyclonal anti-ABCA4 is effective in labeling ABCA4 in goldfish retinas.  Santa Cruz Biotechnology’s monoclonal anti-ABCA4 does not work as well, as it requires a great concentration of these antibodies to work.  Further studies will analyze the localization of the ABCA4 in the developing retinas.  Preliminary immunocytochemical results demonstrated ATP8a2 labeling of developing photoreceptors.  The anti-opsin also worked well in labeling.Conclusion: Since the polyclonal anti-ABCA4 from GeneTex and the anti-ATP8a2 were working for the goldfish retina, they can be used in further studies to find more about these flippases and their developmental appearance in the retina.

Modeling Catalyst Transfer and Exploring Initiators for Direct Arylation Polymerization

Timothy Schwochert, Dr. John Tannaci
Department of Chemistry

Description

The synthesis of conjugated materials with an application to organic photovoltaic devices has been an increasingly growing field of study in recent years. Traditionally, these conjugated polymers (CPs) have been synthesized using transmetallated monomers via Stille, Suzuki, or Grignard metathesis (GRIM) preparations. Direct arylation, a type of Palladium catalyzed C—H activation, presents a different potential synthetic process for these CPs without unstable and/or toxic monomer functionalization. Additionally a controlled chain growth polymerization in coordination with an initiator is ideal when developing a synthesis for CPs. To better understand catalyst transfer properties of Direct Arylation, four small molecule systems were used to model the polymerization reaction of poly-3hexyl thiophene(P3HT), a common conjugated polymer. These novel model molecules were synthesized on a gram scale, purified, and were used to quantify the effect of reaction conditions on C—H selectivity and catalyst transfer efficiency. After extensive optimization, we observed that lower catalyst loadings (1%) and a moderate temperature (70°C) was ideal for conversion. However, even for these optimized conditions we found that as our model systems better represented P3HT, we observed less C—H activation control.  Regardless of the lack of specific C—H activation, these reactions yielded very interesting data as only completely substituted products were observed throughout all systems strongly favoring a catalyst transfer mechanism. Preliminary work has been conducted on an initiator for the polymerization. This extensive optimization of reaction conditions yielded promising results due to catalyst transfer being strongly observed, as well as the finding of a potential initiator for Direct Arylation polymerization, but we believe that a more refined understanding of the reaction mechanism is still necessary. Through the development of a ligand specifically tailored for Direct Arylation this synthetic technique could yield polymers analogous to controlled polymerizations such as GRIM.

Suzuki Cross-Coupling Synthesis of a Fluorescent Dye Molecule

Brittany Smolarski, Dr. Jason Scott Kingsbury
Department of Chemistry

Description

Intracellular fluorescence staining, a common microscopy technique used to enhance image contrast, utilizes dye molecules to target specific parts of a cell for visualization.  Currently, ethidium bromide is the most widely used biological stain for nucleic acids such as DNA.  Unfortunately, ethidium bromide is extremely toxic and requires involved procedures for its use and disposal, pressing the need for other nontoxic dyes that stain DNA as efficiently.  Scientists have utilized molecular modeling to identify small biarylated pyridinium constructs that demonstrate high affinity for DNA and optical nonlinearity in excess of that of Disperse Red 1.  Further experiments have targeted higher hyperpolarizability variants and optimization of conditions for the incorporation of the dye into thin films for materials applications.  Regrettably, a first generation synthesis of such dye molecules based on Pd-catalyzed cross coupling was inefficient, with only a 30% yield in the key step.  The aim of our investigation was to develop new methodology that would be broadly applicable to the synthesis of electron-rich, 4-substituted pyridines.

A GC assay utilizing unprotected 2-amino-6-bromonaphthalene and 4-pyridinylboronic acid or its MIDA ester was implemented with tetramethylbenzene as an internal standard.  This allowed for rapid screening of reaction conditions.  Exhaustive N-methylation of the pyridine was then performed, allowing transformation to the cationic form of the dye in good yield.  Ongoing experiments are focused on further diversification of the alkyl moiety on the cation, testing the role of the counterion, and possible application of our catalyst system to other challenging pyridinyl and pyrrolo cross-couplings.

Cell Adhesion, Proliferation, and Morphology of PEGDA Hydrogels

Anthony Sotelo, Dr. Chad Barber
Department of Biology

Description

Hydrogels are increasingly being used in the developing field of tissue engineering and for drug delivery systems. Different monomer substituents and cross linkers are being used in the development of these gels which include macromolecules such as polyethylene glycol (PEG), poly(acrylamide) (PAAm), N-isopropylacrylamide (NIPA), poly(acrylic acid) (PAA), as well as other various monomers. These synthetic hydrogels have an advantage over natural hydrogels such as collagen plugs or Matrigel® by being able to manipulate the mechanical properties of the gel and the polymerization used to create the gels. While natural gels have a fix concentration, synthetic hydrogels can be tuned to a specific concentration of monomers, ligands, and spacers.  PEG gels can be selectively modified at different functional groups, are biocompatible, and resistant to protein adsorption or degradation. PEG hydrogels are an attractive platform for cell culture because of the potential to introduce different spacers, linkers, or binding sites into the gel network. PEG monomers are not limited to a linear network; branched PEGs provide a higher degree of spacing and branching which leads to a higher specificity for the gel’s mechanical properties. The stability of the gel can be influenced by the functional groups used in its synthesis. PEGDA hydrogels with ranging weight percent were used to determine the morphologic effect on 3T3 fibroblast and SMC cell lines. PEGDA hydrogels were cross-linked using TEMED and APS in solution. It was found that pure PEGDA hydrogels yields no cell adhesion on the gel platforms resulting in a spherical morphology in contrast to the branched morphology that the 3T3 cell line typically maintain. The PEGDA hydrogels are resistive to protein absorption, which leads to the inability for the cell lines to adhere to the platforms. The inclusion of an adhesion promoting peptide will be included to enhance the binding of the cells to the gel platform in hopes to create a biomimetic platform for cell culture.

©