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Articles 1 - 8 of 8
Full-Text Articles in Life Sciences
Activation And Regulation Of The Alkbh3-Ascc Alkylation Repair Pathway, Josh Brickner
Activation And Regulation Of The Alkbh3-Ascc Alkylation Repair Pathway, Josh Brickner
Arts & Sciences Electronic Theses and Dissertations
DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions. These lesions are sensed by distinct pathways to recruit repair factors specific to type of damage. In particular, the ALKBH family of proteins recognizes and repairs specific alkylated lesions, including 1-methyladenine (m1A) and 3-methylcytosine (m3C). A major outstanding question in the field is how the AlkB homologue ALKBH3 and its associated protein partners are recruited to sites of alkylation damage and how this repair activity is regulated. Understanding the upstream signaling events that mediate recognition and repair of DNA alkylation damage is particularly …
Sideromycin Pathway Elucidation: Insights Into Salmycin Biosynthesis, Transport Paradigms, And Drug Release, Gerry Sann Macaraeg Rivera
Sideromycin Pathway Elucidation: Insights Into Salmycin Biosynthesis, Transport Paradigms, And Drug Release, Gerry Sann Macaraeg Rivera
Arts & Sciences Electronic Theses and Dissertations
Antibiotic resistance is an increasing threat in today’s society. In order to overcome resistant bacteria, it is necessary to discover new drugs with novel mechanisms of action. This work focuses on the sideromycin pathway, encompassing the biosynthetic production, mechanism of entry and hydrolysis-mediated drug release. Sideromycins are an interesting approach to combat the rise of antibiotic resistance since they provide a different avenue that overcomes problems that arise when entering the cell. The dissertation is separated into distinct sections dealing with the various areas of interest in the sideromycin pathway, particularly for the sideromycin, salmycin, produced by Streptomyces violaceus. The …
The Impact Of Mrna Structure On Trna Selection And Ribosome Rescue, Erica Nicole Thomas
The Impact Of Mrna Structure On Trna Selection And Ribosome Rescue, Erica Nicole Thomas
Arts & Sciences Electronic Theses and Dissertations
The faithful and rapid translation of proteins from genetic information is an essential feature of the ribosome. The general process of tRNA selection is governed by the ability of the ribosome to select for the aminoacylated tRNA (aa-tRNA) that matches the codon in its A-site. The efficiency and accuracy of this selection depends on the ability of nucleotides to form proper hydrogen bonds. While much is known about how chemical alterations of tRNA and rRNA can impact the fidelity of translation, less is known about how similar changes to mRNA affect decoding. In this work, we describe several studies aimed …
Diverse Far-Red Light Utilization Strategies In Cyanobacteria And Algae, Benjamin Martin Wolf
Diverse Far-Red Light Utilization Strategies In Cyanobacteria And Algae, Benjamin Martin Wolf
Arts & Sciences Electronic Theses and Dissertations
In their natural environments, photosynthetic organisms are often exposed to widely varied light environments. Species adapted to shade light, often found growing in lower layers of photosynthetic biofilms, must survive on filtered light alone. Filtered light is highly enriched in far-red wavelengths, which are normally unavailable for photosynthetic energy production in most oxygenic phototrophs. To overcome light limitations in filtered light environments, some species of algae and cyanobacteria utilize specialized photosynthetic pigments and antenna systems to harvest these far-red wavelengths. By sampling the natural environment and using custom-built far-red light growth chambers, I have isolated several species of oxygenic phototrophs …
Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman
Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman
Arts & Sciences Electronic Theses and Dissertations
Molecular dynamics simulations are a powerful tool to explore conformational landscapes, though limitations in computational hardware commonly thwart observation of biologically relevant events. Since highly specialized or massively parallelized distributed supercomputers are not available to most scientists, there is a strong need for methods that can access long timescale phenomena using commodity hardware. In this thesis, I present the goal-oriented sampling method, Fluctuation Amplification of Specific Traits (FAST), that takes advantage of Markov state models (MSMs) to adaptively explore conformational space using equilibrium-based simulations. This method follows gradients in conformational space to quickly explore relevant conformational transitions with orders of …
Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott
Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott
Arts & Sciences Electronic Theses and Dissertations
This work is focused on iron trafficking through ABC transporters in Staphylococcus aureus and combatting the growing antimicrobial resistance crisis by exploiting virulence factors as therapeutic targets. Specifically, the goal was to understand the role of a siderophore-binding lipoprotein FhuD2 in S. aureus iron trafficking. While S. aureus endogenously produces three metallophores for metal sequestration from the host, FhuD2 is thought to scavenge metals from hydroxamate-based xenosiderophores encountered in the host environment. FhuD2 is a critical virulence factor and vaccine candidate (Novartis) for MRSA. Since xenosiderophore scavenging systems are often dispensable, it was hypothesized that FhuD2 must be playing another …
Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott
Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott
Arts & Sciences Electronic Theses and Dissertations
This work is focused on iron trafficking through ABC transporters in Staphylococcus aureus and combatting the growing antimicrobial resistance crisis by exploiting virulence factors as therapeutic targets. Specifically, the goal was to understand the role of a siderophore-binding lipoprotein FhuD2 in S. aureus iron trafficking. While S. aureus endogenously produces three metallophores for metal sequestration from the host, FhuD2 is thought to scavenge metals from hydroxamate-based xenosiderophores encountered in the host environment. FhuD2 is a critical virulence factor and vaccine candidate (Novartis) for MRSA. Since xenosiderophore scavenging systems are often dispensable, it was hypothesized that FhuD2 must be playing another …
Electron Decoupling With Chirped Microwave Pulses For Magic Angle Spinning Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy, Edward Paul Saliba
Electron Decoupling With Chirped Microwave Pulses For Magic Angle Spinning Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy, Edward Paul Saliba
Arts & Sciences Electronic Theses and Dissertations
Dynamic nuclear polarization (DNP) is a method of generating hyperpolarization of nuclear spins for nuclear magnetic resonance (NMR) spectroscopy. Coherent, time domain techniques make the possibility of DNP directly to spins of interest at room temperature and higher feasible in magic angle spinning (MAS) NMR, allowing for optimal experimental repetition times to be limited by the T_1 of the electron, rather than a much longer T_1DNP, with excellent resolution. The strong hyperfine couplings that make such direct DNP transfers possible, however, can lead to short nuclear relaxation times that result in broadening of nuclear resonances and reduce sensitivity. This dissertation …