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Publicly Accessible Penn Dissertations

Sequencing

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Full-Text Articles in Molecular Biology

Genome-Wide Approaches To Study Rna Secondary Structure, Nathan Daniel Berkowitz Jan 2016

Genome-Wide Approaches To Study Rna Secondary Structure, Nathan Daniel Berkowitz

Publicly Accessible Penn Dissertations

The central hypothesis of molecular biology depicts RNA as an intermediary conveyor of genetic information. RNA is transcribed from DNA and translated to proteins, the molecular machines of the cell. However, many RNAs do not encode protein and instead function as molecular machines themselves. The most famous examples are ribosomal RNAs and transfer RNAs, which together form the core translational machinery of the cell. Many other non-coding RNAs have been discovered including catalytic and regulatory RNAs. In many cases RNA function is tightly linked to its secondary structure, which is the collection of hydrogen bonds between complimentary RNA sequences that ...


Telomere And Proximal Sequence Analysis Using High-Throughput Sequencing Reads, Nick Stong Jan 2014

Telomere And Proximal Sequence Analysis Using High-Throughput Sequencing Reads, Nick Stong

Publicly Accessible Penn Dissertations

The telomere is a specialized simple sequence repeat found at the end of all linear chromosomes. It acts as a substrate for telomere binding factors that in coordination with other interacting elements form what is known as the shelterin complex to protect the end of the chromosome from the DNA damage repair machinery. The telomere shortens with each cell division, and once critically short is no longer able to perform this role. Short dysfunctional telomeres result in cellular senescence, apoptosis, or genome instability. Telomere length is regulated by many factors including cis-acting elements in the proximal sequence which is known ...


Methods In And Applications Of The Sequencing Of Short Non-Coding Rnas, Paul Ryvkin Jan 2013

Methods In And Applications Of The Sequencing Of Short Non-Coding Rnas, Paul Ryvkin

Publicly Accessible Penn Dissertations

Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields ranging from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non-coding RNAs, as well as a study in which they are applied to Alzheimer ...