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3. Investigating the Folding of the Class I Type II PreQ1 Riboswitch in Cellular Conditions

open_access
Open Access
Author:
Luteran, Emily Michelle
Title:
Investigating the Folding of the Class I Type II PreQ1 Riboswitch in Cellular Conditions
Area of Honors:
Chemistry
Keywords:
preQ1
riboswitch
RNA
folding
cellular conditions
File:
Download Emily_Luteran_Thesis_Final.pdf
Thesis Supervisors:
Philip C. Bevilacqua, Thesis Supervisor
Raymond Lee Funk, Thesis Honors Advisor
Scott A Showalter, Faculty Reader
Xin Zhang, Faculty Reader

5. Investigation and Structural Analysis of Innate Immune Sensor PKR Activation by the Clostridia Bolteae Twister Ribozyme

open_access
Open Access
Author:
Anmangandla, Ananya
Title:
Investigation and Structural Analysis of Innate Immune Sensor PKR Activation by the Clostridia Bolteae Twister Ribozyme
Area of Honors:
Chemistry
Keywords:
RNA
Ribozyme
PKR
Protein Kinase R
Innate Immunity
Biochemistry
Chemistry
Functional RNAs
Twister Ribozyme
File:
Download AAnmangandla_UGThesis2017__1_.pdf
Thesis Supervisors:
Philip C. Bevilacqua, Thesis Supervisor
Raymond Lee Funk, Thesis Honors Advisor

6. THE IMPACT OF ENDOGENOUS RETROVIRUS S2220 ON MULE DEER ISY1 GENE EXPRESSION

open_access
Open Access
Author:
Bogale, Kaleb Tadesse
Title:
THE IMPACT OF ENDOGENOUS RETROVIRUS S2220 ON MULE DEER ISY1 GENE EXPRESSION
Area of Honors:
Biology
Keywords:
Endogenous retrovirus
ERV
LTR
long terminal repeat
solo LTR
solo long terminal repeat
gene expression
mule deer
Odocoileus hemionus
RNA
Splicing
retrovirus
pre-mrna splicing gene
ISY1 gene
isy1
gene regulation
hardy-weinberg equilibrium
population genetics
Bos taurus
domestic cow
Ovis aris
sheep
File:
Download KalebBogale_ThesisFinal.pdf
Thesis Supervisors:
Dr. Mary Poss, Thesis Supervisor
Dr. Bernhard Lüscher, Thesis Honors Advisor

13. 1. Characterization of Twisters Ribozymes at Splice Sites 2. Development of a Computational Pipeline to Discover Small Self-cleaving Ribozymes with Helical Imperfections

restricted_to_institution
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:
RNA
Ribozymes
Splicing
High-throughput Pipeline
File:
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Thesis Supervisors:
Philip C Bevilacqua, Thesis Supervisor
Joseph C. Reese, Thesis Honors Advisor

14. Exploring the Specialization of Expansion Segments in Stage-Specific Plasmodium Ribosomes

open_access
Open Access
Author:
Wardeh, Leena
Title:
Exploring the Specialization of Expansion Segments in Stage-Specific Plasmodium Ribosomes
Area of Honors:
Biology
Keywords:
malaria
parasites
parasitology
molecular biology
ribosomes
ribosomal specialization
expansion segments
Leena Wardeh
Scott Lindner
James McGee
Allen Minns
RNA
DNA
RNA probes
polyacrylamide gel
transcription
translation
electroelution
biotinylation
sequencing
EMSA
File:
Download Exploring_the_Specialization_of_Expansion_Segments_in___Temporally_Expressed_Plasmodium_Ribosomes_-_Leena_Wardeh_s_Schreyer_Honors_College_Thesis_Spring_2024.pdf
Thesis Supervisors:
Scott E. Lindner, Thesis Supervisor
Timothy J Jegla, Thesis Honors Advisor

16. Thermodynamic Parameters of Non-Watson-Crick Base Paired Structures in In-vitro and In-Vivo-Like Conditions

restricted_to_institution
Restricted (Penn State Only)
Author:
Winemiller, Atlas
Title:
Thermodynamic Parameters of Non-Watson-Crick Base Paired Structures in In-vitro and In-Vivo-Like Conditions
Area of Honors:
Chemistry
Keywords:
RNA
thermodynamics
non-Watson-Crick
in vivo-like
File:
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Thesis Supervisors:
Philip C Bevilacqua, Thesis Supervisor
Stewart Anthony Mallory, Thesis Honors Advisor
Elizabeth A Jolley, Faculty Reader

17. Development of a Functional RNA-Identifying Computational Pipeline and its Application to SARS-CoV-2

open_access
Open Access
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-2
RNA
pseudoknots
SNPs
RNA structure conservation
frameshifting element
FSE
File:
Download Forstmeier_Thesis_2022_final_revised.pdf
Thesis Supervisors:
Philip C Bevilacqua, Thesis Supervisor
Teh-Hui Kao, Thesis Honors Advisor

18. Advancing RNA Duplex Kinetics: Modeling One-Step and Two-Step Pathways through Computation and Experimentation

restricted_to_institution
Restricted (Penn State Only)
Author:
Guerin, Gracie
Title:
Advancing RNA Duplex Kinetics: Modeling One-Step and Two-Step Pathways through Computation and Experimentation
Area of Honors:
Chemistry
Keywords:
RNA
kinetics
modeling
File:
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Thesis Supervisors:
Philip C Bevilacqua, Thesis Supervisor
Benjamin James Lear, Thesis Honors Advisor
Elizabeth A Jolley, Faculty Reader