1. The Mechanism of NELF Recruitment by DSIF in Promoter-proximal Pausing of RNA Polymerase II Restricted (Penn State Only) Author: Deng, Eilene Title: The Mechanism of NELF Recruitment by DSIF in Promoter-proximal Pausing of RNA Polymerase II Area of Honors: Biochemistry and Molecular Biology Keywords: promoter-proximal pausingtranscription factorsgene regulationDSIFNELFRNA Polymerase II File: Login to Download Thesis Supervisors: David Scott Gilmour, Thesis SupervisorLorraine C Santy, Thesis Honors Advisor
2. Investigation of the Behavior of RNA G-quadruplexes from the Human Genome under Physiological Conditions Restricted (Penn State Only) Author: Veglia, Karleigh Title: Investigation of the Behavior of RNA G-quadruplexes from the Human Genome under Physiological Conditions Area of Honors: Biochemistry and Molecular Biology Keywords: G-QuadruplexesRNA Folding File: Login to Download Thesis Supervisors: Philip C Bevilacqua, Thesis SupervisorTeh-Hui Kao, Thesis Honors Advisor
3. The Effect of the Small RNA RyhB on the Structure of its mRNA Targets Restricted (Penn State Only) Author: Grecco, Samantha Title: The Effect of the Small RNA RyhB on the Structure of its mRNA Targets Area of Honors: Biochemistry and Molecular Biology Keywords: sRNARyhBgene expression profilingin vivo chemical structure probingpulldown assayantibiotic resistancestructure-function relationship File: Login to Download Thesis Supervisors: Philip C Bevilacqua, Thesis SupervisorYing Gu, Thesis Honors Advisor
4. Characterization of the Injury Response of Ciliated Neurons in Drosophila Restricted (Penn State Only) Author: Mauger, Abigail Title: Characterization of the Injury Response of Ciliated Neurons in Drosophila Area of Honors: Biochemistry and Molecular Biology Keywords: axon injuryciliated neuronschordotonalDLKaxon regenerationDrosophilaneuronaxon File: Login to Download Thesis Supervisors: Melissa Rolls, Thesis SupervisorSanthosh Girirajan, Thesis Honors Advisor
5. The Chemotherapeutic Agent CX-5461 Affects Cell Viability Through a Topoisomerase II Poison-Like Mechanism Restricted (Penn State Only) Author: Dennis, Kady Title: The Chemotherapeutic Agent CX-5461 Affects Cell Viability Through a Topoisomerase II Poison-Like Mechanism Area of Honors: Biochemistry and Molecular Biology Keywords: CX-5461mechanism of actionRNA Polymerase I inhibitorTopoisomerase II poison File: Login to Download Thesis Supervisors: Justin R Pritchard, Thesis SupervisorJoseph C. Reese, Thesis Honors Advisor
6. Understanding the Mechanisms Controlling the Localization of Microtubule Organization Proteins in Drosophila Neurons Restricted (Penn State Only) Author: Long, Melissa Title: Understanding the Mechanisms Controlling the Localization of Microtubule Organization Proteins in Drosophila Neurons Area of Honors: Biochemistry and Molecular Biology Keywords: DrosophilaNeuroscienceMicrotubule NucleationClathrin-Mediated EndocytosisWnt SignalingDendrite File: Login to Download Thesis Supervisors: Melissa Rolls, Thesis SupervisorDavid Scott Gilmour, Thesis Honors Advisor
7. Development of a Functional RNA-Identifying Computational Pipeline and its Application to SARS-CoV-2 Restricted (Penn State Only) Author: Forstmeier, Peter Title: Development of a Functional RNA-Identifying Computational Pipeline and its Application to SARS-CoV-2 Area of Honors: Biochemistry and Molecular Biology Keywords: SARS-CoV-2RNApseudoknotsSNPsRNA structure conservationframeshifting elementFSE File: Login to Download Thesis Supervisors: Philip C Bevilacqua, Thesis SupervisorTeh-Hui Kao, Thesis Honors Advisor
8. Mechanistic Study of Halogenation by Iron(II) and 2-Oxoglutarate-Dependent Oxygenases Restricted (Penn State Only) Author: Katch, Bryce Title: Mechanistic Study of Halogenation by Iron(II) and 2-Oxoglutarate-Dependent Oxygenases Area of Honors: Biochemistry and Molecular Biology Keywords: EnzymologyStructural BiologyC-H ActivationSadABesD File: Login to Download Thesis Supervisors: Amie Kathleen Boal, Thesis SupervisorTimothy Charles Meredith, Thesis Honors Advisor
9. Identifying an MNase Sensitive Particle associated with Rap1 Restricted (Penn State Only) Author: Pitts, Cass Title: Identifying an MNase Sensitive Particle associated with Rap1 Area of Honors: Biochemistry and Molecular Biology Keywords: ChromatinNucleosome displacing factorsRap1SAGABudding yeastGene regulation File: Login to Download Thesis Supervisors: Lu Bai, Thesis SupervisorJoseph C. Reese, Thesis Honors Advisor
10. High Resolution Structure and Neutralization Mechanism of 1G1 Fab Bound to Poliovirus Type 3 Restricted (Penn State Only) Author: Faust, Julia Title: High Resolution Structure and Neutralization Mechanism of 1G1 Fab Bound to Poliovirus Type 3 Area of Honors: Biochemistry and Molecular Biology Keywords: CryoEMpoliovirusSPV3virologyneutralizing antibody1G1 Fabstructural biology File: Login to Download Thesis Supervisors: Susan Hafenstein, Thesis SupervisorTimothy Charles Meredith, Thesis Honors Advisor
11. Cost-effective Molecular Weight Standards for Protein Size-exclusion Chromatography: HISftnA and HISDps Expression and Purification Restricted (Penn State Only) Author: Howells, Joshua Title: Cost-effective Molecular Weight Standards for Protein Size-exclusion Chromatography: HISftnA and HISDps Expression and Purification Area of Honors: Biochemistry and Molecular Biology Keywords: Size-exclusion chromatographymolecular weight standardsEscherichia coli bacterial ferritinEscherichia coli DNA-binding protein from starved cells File: Login to Download Thesis Supervisors: Song Tan, Thesis SupervisorSong Tan, Thesis Honors AdvisorJean-Paul Armache, Faculty Reader
12. Engineering Mitochondrial Transport Control Using Miro1 Restricted (Penn State Only) Author: Litvak, Michelle Title: Engineering Mitochondrial Transport Control Using Miro1 Area of Honors: Biochemistry and Molecular Biology Keywords: miro1proteinmitochondrial File: Login to Download Thesis Supervisors: Nikolay Dokholyan, Thesis SupervisorSanthosh Girirajan, Thesis Honors AdvisorJean-Paul Armache, Faculty Reader
13. Investigating Regeneration, Function, and Shape of Drosophila Sensory Dendrites Restricted (Penn State Only) Author: Bernard, Annabelle Title: Investigating Regeneration, Function, and Shape of Drosophila Sensory Dendrites Area of Honors: Biochemistry and Molecular Biology Keywords: Dendrite regenerationDrosophila melanogasterNociceptionFunctional recoveryPruning File: Login to Download Thesis Supervisors: Melissa Rolls, Thesis SupervisorTimothy Charles Meredith, Thesis Honors Advisor
14. Optimization of Size Exclusion Chromatography Protein Standards Restricted (Penn State Only) Author: Mongia, Advay Title: Optimization of Size Exclusion Chromatography Protein Standards Area of Honors: Biochemistry and Molecular Biology Keywords: Size Exclusion ChromatographyProtein Standardsprotein expressionprotein purificationgel filtration chromatographybacterioferritin File: Login to Download Thesis Supervisors: Song Tan, Thesis SupervisorJoseph C. Reese, Thesis Honors Advisor
15. Mechanisms of FXR Activation by Synthetic Ligands Restricted (Penn State Only) Author: Meinert, Emily Title: Mechanisms of FXR Activation by Synthetic Ligands Area of Honors: Biochemistry and Molecular Biology Keywords: nuclear receptorssite-directed mutagenesisdual luciferasetransformationmammalian cell culturesynthetic ligandbile acid File: Login to Download Thesis Supervisors: C Denise Okafor, Thesis SupervisorTeh-Hui Kao, Thesis Honors Advisor
16. Chemogenetically Induced Activation of Cortical Somatostatin Interneurons Results in Enhanced Pyramidal Neuron Activity in Rodent Models Restricted (Penn State Only) Author: Hutsell, Alexander Title: Chemogenetically Induced Activation of Cortical Somatostatin Interneurons Results in Enhanced Pyramidal Neuron Activity in Rodent Models Area of Honors: Biochemistry and Molecular Biology Keywords: Chronic StressChemogenetic ManipulationPrelimbic Cortexmedial prefrontal cortexSomatostatin InterneuronsPyramidal CellsInhibition and Excitation in the brain File: Login to Download Thesis Supervisors: Bernhard Luscher, Thesis SupervisorTimothy Charles Meredith, Thesis Honors Advisor
17. Engineering of an Aptamer Tagged Dengue Virus for RNA Imaging Restricted (Penn State Only) Author: Lombard, Clair Title: Engineering of an Aptamer Tagged Dengue Virus for RNA Imaging Area of Honors: Biochemistry and Molecular Biology Keywords: Dengue VirusFlavivirus Life CycleRNA Imaging Techniques File: Login to Download Thesis Supervisors: Joyce Jose, Thesis SupervisorTimothy Charles Meredith, Thesis Honors Advisor
18. Associations Between Child Environmental Enteric Dysfunction And Stress Restricted (Penn State Only) Author: Bialek, Lexie Title: Associations Between Child Environmental Enteric Dysfunction And Stress Area of Honors: Biochemistry and Molecular Biology Keywords: Environmental Enteric DysfunctionOxidative stressBiomarkerGut-Brain Axis File: Login to Download Thesis Supervisors: Timothy Charles Meredith, Thesis SupervisorTeh-Hui Kao, Thesis Honors AdvisorAudrie Lin, Thesis Supervisor
19. 1. Characterization of Twisters Ribozymes at Splice Sites 2. Development of a Computational Pipeline to Discover Small Self-cleaving Ribozymes with Helical Imperfections Restricted (Penn State Only) Author: Chang, Benjamin Title: 1. Characterization of Twisters Ribozymes at Splice Sites 2. Development of a Computational Pipeline to Discover Small Self-cleaving Ribozymes with Helical Imperfections Area of Honors: Biochemistry and Molecular Biology Keywords: RNARibozymesSplicingHigh-throughput Pipeline File: Login to Download Thesis Supervisors: Philip C Bevilacqua, Thesis SupervisorJoseph C. Reese, Thesis Honors Advisor
20. Resilience of the Symbiosis Between Vibrio fischeri and Euprymna scolopes Restricted (Penn State Only) Author: Cook, Rachel Title: Resilience of the Symbiosis Between Vibrio fischeri and Euprymna scolopes Area of Honors: Biochemistry and Molecular Biology Keywords: SymbiosisTransgenerational effectDietReproductionEuprymna scolopesVibrio fischeri File: Login to Download Thesis Supervisors: Wendy Hanna-Rose, Thesis Honors AdvisorTimothy Iwao Miyashiro, Thesis Supervisor
21. Cost-effective Molecular Weight Standards for Protein Size Exclusion Chromatography Restricted (Penn State Only) Author: Sokol, Joshua Title: Cost-effective Molecular Weight Standards for Protein Size Exclusion Chromatography Area of Honors: Biochemistry and Molecular Biology Keywords: Size exclusion chromatographyGel filtration chromatographyGlobularLiquid chromatographyProteinRecombinant DNASEC-MALSAnalytical UltracentrifugationSedimentation equilibriumMetal affinity chromatographyIon-exchange chromatographyMolecular weight File: Login to Download Thesis Supervisors: Song Tan, Thesis SupervisorYing Gu, Thesis Honors Advisor
22. Understanding the Role of Envelope Protein of Tick-borne Flaviviruses in Vector Specificity Restricted (Penn State Only) Author: Wang, Anqi Title: Understanding the Role of Envelope Protein of Tick-borne Flaviviruses in Vector Specificity Area of Honors: Biochemistry and Molecular Biology Keywords: Virologybiochemistryflaviviruschimera File: Login to Download Thesis Supervisors: Joyce Jose, Thesis SupervisorSong Tan, Thesis Honors Advisor
23. Investigating Strain Level Diversity Among Natural Co-Isolated Vibrio Fischeri Restricted (Penn State Only) Author: Harter, Rachel Title: Investigating Strain Level Diversity Among Natural Co-Isolated Vibrio Fischeri Area of Honors: Biochemistry and Molecular Biology Keywords: transformationbacteriastrain diversitygenomicgeneticvibrio fischerisymbiosismutualismeuprymna scolopesmicrobiologymolecular biologybiochemistryquorum sensing File: Login to Download Thesis Supervisors: Timothy Iwao Miyashiro, Thesis SupervisorWendy Hanna-Rose, Thesis Honors Advisor
24. Neural Networks for Regulatory Element Analysis at Repetitive Genomic Regions Restricted (Penn State Only) Author: Shi, Jeff Title: Neural Networks for Regulatory Element Analysis at Repetitive Genomic Regions Area of Honors: Biochemistry and Molecular Biology Keywords: Neural NetworksENCODEDomain AdaptationTransposable ElementsRepetitive Regions File: Login to Download Thesis Supervisors: Shaun Mahony, Thesis SupervisorYing Gu, Thesis Honors Advisor
25. Purification and Characterization of Chromatin Remodeler SNF2L Restricted (Penn State Only) Author: Waldt, Hannah Title: Purification and Characterization of Chromatin Remodeler SNF2L Area of Honors: Biochemistry and Molecular Biology Keywords: BiochemistryStructural BiologyChromatinISWISNF2LNegative Stain EMCryo-EM File: Login to Download Thesis Supervisors: Jean-Paul Armache, Thesis SupervisorSanthosh Girirajan, Thesis Honors Advisor