Fortifying Saint Cloud: Searching for Fort Holes

This thesis is about my efforts to locate Fort Holes – a civilian fortification built in September of 1862 in response to the nearby threats of Native American violence. A decade after the western parts of Minnesota were opened to Euro-American settlement, the actions of government agents, traders, and a small group of Native American actors led to violence on the frontier. The citizens of Saint Cloud constructed Fort Holes in a week and it only stood for a couple of years before they removed the lumber for the growing city. Throughout Minnesota, citizens constructed over 50 of these expedient “settlers’ forts,” sometimes in as little as 24 hours. As of 2014, none of these forts from the U.S. – Dakota War of 1862 had been examined archaeologically. In the summer of 2015, I began work on studying Fort Holes. The project included archival research, a gradiometer survey, and a targeted shovel test survey based on the results of the gradiometer survey to identify archaeological features or artifacts associated with the fort. The artifacts of that excavation were then cleaned, analyzed, and inventoried. While no definitive features or artifacts were found, the archival resources, as well as the gradiometer results show that this is likely the location of the fort, and larger excavations may reveal features missed in this project

Maurice Merleau-Ponty And Aesthetics: On Perception, Art, And Embodied Existence

French philosopher Maurice Merleau-Ponty is one of the 20th century’s greatest phenomenological thinkers. Merleau-Ponty’s main philosophical concern is understanding how humans experience and perceive the world around them. He grounds his thought in phenomenological inquiry and existential ontology, providing a rich understanding of what it means to be a human living in the world. In his examination of human situation in the world, Merleau-Ponty draws from art, in particular the work of French painter, Paul Cézanne, in outlining a theory of aesthetics that brings to light our being in the world as an embodied individual who is immersed in it, not outside of it. In my paper, I explore the various implications of Merleau-Ponty’s philosophy, arguing that his aesthetic theory is not simply ancillary to his general perspective, but instead unveils a new way of understanding what it means to be human living and existing in the world

Reverse transcriptases can clamp together nucleic acids strands with two complementary bases at their 3′-termini for initiating DNA synthesis

We present evidence that the reverse transcriptase (RT) of human immunodeficiency virus type-1 stabilizes in vitro very short (2-nt) duplexes of 3′-overhangs of the primer strand that are annealed to complementary dinucleotides tails of DNA or RNA template strands, provided that these sequences contain at least one C or G. This RT-induced strand ‘clamping’ activity promotes RT-directed DNA synthesis. This function is achieved only when the functional template strand is adjacent to a second DNA or RNA segment, annealed upstream to most of the primer (without gaps). The combined clamp/polymerase activity is typical to RTs, as it was found in different RTs from diverse retroviral groups, whereas cellular DNA-polymerases (devoid of 3′→5′ exonucleolytic activity) showed no clamp activity. The clamp-associated DNA-binding activity is markedly stabilized by dGTP, even when dGTP is not incorporated into the nascent DNA strand. The hereby-described function can help RTs in bridging over nicks in the copied RNA or DNA templates, encountered during reverse transcription. Moreover, the template-independent blunt-end synthesis of RTs can allow strand transfers onto compatible acceptor strands while synthesizing DNA. These RT properties can shed light on potentially-new roles of RTs in the reverse-transcription process and define new targets for anti-retroviral drugs

Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids

The crystal structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) bound to an RNA/DNA hybrid reveals an extensive network of contacts with the phosphate backbone of the DNA strand ∼4–9 bp downstream from the ribonuclease H (RNase H) catalytic center. Collectively designated as ‘the RNase H primer grip’, this motif contains a phosphate binding pocket analogous to the human and Bacillus halodurans RNases H. The notion that the RNase H primer grip mediates the trajectory of RNA/DNA hybrids accessing the RNase H active site suggests that locally neutralizing the phosphate backbone may be exploited to manipulate nucleic acid flexibility. To examine this, we introduced single and tandem methylphosphonate substitutions through the region of the DNA primer contacted by the RNase H primer grip and into the RNase H catalytic center. The ability of mutant hybrids to support RNase H and DNA polymerase activity was thereafter examined. In addition, site-specific chemical footprinting was used to evaluate movement of the DNA polymerase and RNase H domains. We show here that minor alteration to the RNase H primer can have a dramatic effect on enzyme positioning, and discuss these findings in light of recent crystallography of human RNase H containing an RNA/DNA hybrid

Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein

Annealing of the TAR RNA hairpin to the cTAR DNA hairpin is required for the minus-strand transfer step of HIV-1 reverse transcription. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. To gain insight into the mechanism of NC-mediated TAR RNA–DNA annealing, we used structural probes (nucleases and potassium permanganate), gel retardation assays, fluorescence anisotropy and cTAR mutants under conditions allowing strand transfer. In the absence of NC, cTAR DNA-TAR RNA annealing depends on nucleation through the apical loops. We show that the annealing intermediate of the kissing pathway is a loop–loop kissing complex involving six base-pairs and that the apical stems are not destabilized by this loop–loop interaction. Our data support a dynamic structure of the cTAR hairpin in the absence of NC, involving equilibrium between both the closed conformation and the partially open ‘Y’ conformation. This study is the first to show that the apical and internal loops of cTAR are weak and strong binding sites for NC, respectively. NC slightly destabilizes the lower stem that is adjacent to the internal loop and shifts the equilibrium toward the ‘Y’ conformation exhibiting at least 12 unpaired nucleotides in its lower part

Terminal Deoxynucleotidyl Transferase: The Story of A Misguided DNA Polymerase

Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal deoxynucleotidyl transferase with other well-characterized DNA polymerases that perform template-dependent synthesis. This includes a quantitative inspection of how terminal deoxynucleotidyl transferase binds DNA and dNTP substrates, the possible involvement of a conformational change that precedes phosphoryl transfer, and kinetic steps that are associated with the release of products. These enzymatic steps are discussed within the context of the available structures of terminal deoxynucleotidyl transferase in the presence of DNA or nucleotide substrate. In addition, we discuss the ability of proteins involved in replication and recombination to regulate the activity of the terminal deoxynucleotidyl transferase. Finally, the biomedical role of this specialized DNA polymerase is discussed focusing on its involvement in cancer development and its use in biomedical applications such as labeling DNA for detecting apoptosis

Maurice Merleau-Ponty And Aesthetics: On Perception, Art, And Embodied Existence

French philosopher Maurice Merleau-Ponty is one of the 20th century’s greatest phenomenological thinkers. Merleau-Ponty’s main philosophical concern is understanding how humans experience and perceive the world around them. He grounds his thought in phenomenological inquiry and existential ontology, providing a rich understanding of what it means to be a human living in the world. In his examination of human situation in the world, Merleau-Ponty draws from art, in particular the work of French painter, Paul Cézanne, in outlining a theory of aesthetics that brings to light our being in the world as an embodied individual who is immersed in it, not outside of it. In my paper, I explore the various implications of Merleau-Ponty’s philosophy, arguing that his aesthetic theory is not simply ancillary to his general perspective, but instead unveils a new way of understanding what it means to be human living and existing in the world

Guitar Performances

Wesley Park, Guitar SoloistProfessor Christopher Parkening, Faculty Mentor Wesley Park is a Freshman at Pepperdine University in Malibu California, studying classical guitar under Maestro Christopher Parkening. He is originally from Culver City, CA. In addition to the guitar, Wesley also plays the piano. Wesley started playing the piano when he was 5, and he started the classical guitar when he was 15 years old.. He placed as a finalist in the 2014 Pacific Guitar Festival in Monrovia, CA in the chamber mixed division and in the junior solo division. He was the Second Place Winner in the 2013 ASTA/Aron Green Classical Guitar Competition junior division in Los Angeles, CA. In 2004, he was the winner of the Loyola Marymount University First Annual Elementary Artists Competition on the piano. His brother, Alex Park, is a senior studying classical guitar here at Pepperdine University. “Koyunbaba” – Carlo Domeniconi (b. 1947) Carlo Domeniconi is a guitarist and composer. Domeniconi was born in Italy, but raised in Istanbul which gives the piece “Koyunbaba (The Shepherd)”, a Middle Eastern flavor. The music for “Koyunbaba” started from an improvisation then eventually grew into a full piece. The piece is unique for the classical guitar because of the tuning that is required. The guitar needs to be tuned to a C# minor chord, and the only string that remains at normal pitch is the 1st string. “Koyunbaba” is performed frequently by many guitarists. It has been recorded by great guitarists such as Christopher Parkening, John Williams, William Kanengiser, David Russell, and others. Kenneth Bender, Guitar SoloistProfessor Christopher Parkening, Faculty Mentor Kenneth Bender is currently a Freshman at Pepperdine University where he studies under Maestro Christopher Parkening. Kenneth is originally from Encinitas, California, and began studying Classical Guitar at age eight. He developed his appreciation for the arts at a young age through collaborating with many local organizations and artists including the Encinitas Guitar Orchestra and the Mira Costa College Guitar Ensemble. In 2011 Kenneth participated in his first Guitar Foundation of America event where he won a performance opportunity during the Western Regional Youth Competition. In the Fall of 2014, Kenneth began his undergraduate studies at Pepperdine. He will be performing a selection from Celedonio Romero’s Suite Andaluz. Fantasia Celedonio Romero (1913-1996)Fantasia is the final movement of the Suite Andaluz written by the Spanish guitarist and composer Celedonio Romero to celebrate the birth of his son Pepe. Romero composed the Suite as he and his family rebuilt their lives in post-Civil War Spain. It serves as an homage to Spanish ideals and a commemoration to the beauty of Spanish culture. It captures the sounds and essence of traditional Spain by taking the listener on a journey through the vibrant streets of Málaga. Joseph Peliska & Sergio Gallardo, Guitar DuetProfessor Christopher Parkening, Faculty Mentor Joseph Peliska is currently a Sophomore at Pepperdine University studying Classical Guitar Performance under the instruction of Maestro Christopher Parkening. Joseph began the guitar at age 7, and continued his studies with Rafael Padron at the University of Miami while in high school. Prior to attending Pepperdine, Peliska was active in his local arts community of Naples, Florida, teaching, participating in competitions, performing extensively, and collaborating with various music organizations. Joseph enjoys writing new music for the classical guitar, drawing upon influences of the diverse musical styles that inspire him. Sergio Gallardo, age 20, was born in La Paz, Bolivia. He began studying guitar when he was 8 at the Montessori School. In 2006 he entered the Escuela Contemporánea de Músicas and studied with Roberto Borda. He began studying under Marcos Puña in 2008. Gallardo has won prizes at international competitions including first prize at the International Guitar Festival of La Paz in 2011 and second prize in 2010, first place in the XX International Festival Abril en Tarija in the 16 and under category in 2010, first prize at the V Competition and International Guitar Festival of Cochabamba in the youth category in 2010, and first prize in the Pacific Guitar Festival in California in 2014. He is currently a sophomore studying classical guitar performance at Pepperdine University under the instruction of Maestro Christopher Parkening. JONGOJongo is arguably the Brazilian composer Paulo Bellinati’s (b. São Paulo, 1950) most successful work. Written in Switzerland in 1988 for solo classical guitar, Jongo won the 1st Prize for Composition in the “Carrefour Mondial de la Guitare” in Martinique that same year. Bellinati proceeded to write a duet version in 1989 for the world renowned guitar duo The Assad Brothers, who concertized the piece extensively. Eventually Bellinati created versions of the piece for jazz ensemble (guitar, piano, sax, bass, and drums), jazz ensemble and orchestra, and guitar and orchestra. The Jongo is heavily influenced by rhythms from South East Brazil which has a heavy African population. Bellinati is known for taking raw folk music rhythms and musical ideas, refining them with modern compositional techniques. The piece is written in a loose ABA format, unified by the constant Jongo rhythm. Bellinati’s use of the guitar is masterful, encompassing virtually every technique available to the classical guitar. The piece is comprised of various short musical phrases that incorporate a different aspect of the instrument’s many capacities