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Browsing by Author "Montgomery, Taiowa, committee member"

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    The evolution of plasticity in the transcriptome of the Trinidadian guppy
    (Colorado State University. Libraries, 2023) Whedbee, Miles, author; Hoke, Kim, advisor; Sloan, Dan, committee member; Montgomery, Taiowa, committee member; Ben-Hur, Asa, committee member
    Phenotypic plasticity is a ubiquitous feature of all living systems, and there is much interest in how plasticity influences long term evolutionary trajectories. One of the major complications with modeling evolutionary trajectories is that plasticity itself is known to evolve. The evolution of plasticity has mainly been focused on at the level of the whole organism, and it is unclear if plasticity at all levels of biological organization evolve. Models that assume no generational change in plasticity may be overly simplistic; a more nuanced approach could incorporate the evolution of plasticity into the modeling. A first step towards this end is to determine what levels of biological organization plasticity evolves, and then to determine if there are predictable patterns of evolved plasticity. RNA is an intermediate to DNA and protein, that can undergo changes in response to environmental conditions, thereby modifying the genetic information passed on to non-coding RNAs, functional RNAs, and proteins. Responses to environment include both changes in abundance of RNAs, as well as changes to the composition of the molecules. This dissertation focuses on the evolution of plasticity within the transcriptome of Poecilia reticulata (Trinidadian guppy). One of the major known regulators of transcript abundance are small RNAs (sRNAs). Micro RNAs (miRNAs), are a specific type of sRNA that bind transcripts, typically leading to translational silencing. We investigated two forms of plasticity, an abundance measure of plasticity (miRNA differential expression), and a compositional measure of plasticity (A-to-I RNA editing). A-to-I RNA editing is the chemical nucleotide change from adenosine to inosine, catalyzed by the enzyme ADAR. We first produced a set of miRNAs in guppies, and confirmed the presence of key biogenesis pathway components, i.e. argonaute proteins in the genome. Tissue-specific miRNA expression patterns were identified for three tissues in Poecilia reticulata (Trinidadian guppy), brain, ovary and testis. We found most discovered miRNAs were located in intergenic regions of the genome. Some miRNAs matched known miRBase sequences, while others were considered novel guppy miRNAs. We observed miRNAs expressed from tandem clusters and analyzed piRNA distribution in ovary samples. This study provides important insights into guppy small RNA expression, laying the groundwork for future investigations into their regulatory roles. The 3rd chapter of this dissertation revealed many miRNAs with differential expression (DE), including population main effects, rearing condition, and their interactions. Population DE miRNAs showed a wide range of expression levels. Rearing condition main effects were (slightly) less common. We identified miRNAs with evolved expression plasticity, distributed across four categories: reversed, evolved plastic, assimilated, and accommodated. Both populations showed similar numbers of miRNAs exhibiting plasticity. In the final chapter of this dissertation we characterized the "editome" of guppies. The majority of the edits were consistent with A-to-I editing, with a smaller proportion of C-to-U edits. The intragenic edits were distributed among a number of genes. However, there were no significant differences in editing between populations, rearing conditions, or their interaction. This dissertation revealed significant miRNA expression differences and provided insights into A-to-I editing patterns in guppies.
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    The phosphatase PTP-3 regulates AMPA receptor transport in Caenorhabditis elegans
    (Colorado State University. Libraries, 2021) Pierce, Dayton, author; Hoerndli, Frederic, advisor; Kim, Seonil, committee member; Stone-Roy, Leslie, committee member; Montgomery, Taiowa, committee member
    Glutamate mediates the majority of excitatory neurotransmission by activating the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtype of ionotropic glutamate receptors. AMPAR trafficking, which includes local synaptic trafficking and long-distance transport, can be one of many cellular pathways important for cognition. Since the majority of AMPARs are made at the cell body, this exerts a challenge on neurons to correctly transport receptors to often far-reaching synapses. To ensure correct synapse function, the interplay between long-distance AMPAR transport, delivery, removal, and retention need to be tightly regulated. However, how long-distance transport mechanisms communicate with local synaptic delivery and removal is unknown. Previous work has shown a critical role for the receptor-type protein tyrosine phosphatase (RPTP) leukocyte common antigen-related protein (LAR), in regulating AMPAR numbers at synapses. However, these studies have not identified a mechanism for this process. Therefore, my thesis sets out to test how AMPAR transport impacts local synaptic trafficking and the role that the C. elegans homologue of vertebrate LAR, Protein Tyrosine Phosphatase 3A (PTP-3A), has on this regulatory pathway. Chapter 1 is an introduction and its purpose is to provide background knowledge and scientific context for the main questions of my thesis. In Chapter 2, we investigate the question of how does glutamate receptor transport impact local synaptic glutamate receptor numbers. Tyrosine phosphorylation is known to play an important role in glutamate receptor trafficking at the synapse, but not much is known about tyrosine phosphorylation on glutamate receptor transport. The vertebrate phosphatase LAR is known to be important in glutamate receptor transmission in cell culture, but its role in glutamate receptor transport is unknown. Here we investigate the role of the sole C. elegans LAR-RPTP homologue, PTP-3A, on glutamate receptor transport and how this affects local synaptic delivery. We show that PTP-3A mutants display decreased transport as well as decreased delivery of Glutamate Receptor-1 (GLR-1) to synapses. Since PTP-3A is a large structure, 3 IgG domains, 9 fibronectin domains, and 2 phosphatase domains, we sought out to determine what domains were necessary for GLR-1 transport. Domain analysis of LAR revealed that the phosphatase domain is not required for GLR-1 transport but is required to stabilize GLR-1 at synapses. Surprisingly, the Ig-like external domains are sufficient to cell-specifically rescue GLR-1 transport. Interestingly, LAR mutants exhibit decreased short-term and long-term memory whereas mutants lacking the phosphatase domain only show decreased long-term memory. This could be due to a mechanism where efficient GLR-1 transport is sufficient to sustain the synaptic receptor pool during short-term synaptic activity, but stabilization of GLR-1 at synapses is required long-term consolidation. Taken together, our results show a critical role of LAR in long-distance synaptic AMPAR transport. Chapter 3 seeks to identify a role of a known regulator of vertebrate LAR, liprin-α, in glutamate receptor transport. Vertebrate liprin-α is known to bind LAR and correctly localize it to synapses. Previously, the C. elegans sole liprin-α homologue, SYD-2, has only been identified as a regulator of active zone maintenance presynaptically. However, vertebrate liprin-α is known to colocalize with postsynaptic proteins such as PSD-95, GRIP-1, LAR, and GluA2. Since LAR and liprin-α colocalize at the synapse, we reasoned that this interaction might happen in C. elegans as well and that SYD-2 might be in the same regulatory pathway as PTP-3A. Therefore, we asked if loss of SYD-2 would cause a defect in GLR-1 localization in vivo in C. elegans. We show that loss of SYD-2 leads to ~1.5-fold increase in GLR-1 transport but has a ~70% reduction in synaptic and surface GLR-1. This leads to an interesting model where synaptic activity might not be directly correlated with GLR-1 transport. Also, our data suggest that SYD-2 might have additional synaptic roles other than correctly localizing PTP-3A. Finally, Chapter 4 aims to discuss the impact of the data I have generated in my thesis and how experiments from each chapter complement each other and how these have opened new experimental paths. Overall, the work in my dissertation expands on the limited knowledge of how AMPAR transport and synaptic trafficking interact to control synaptic AMPAR numbers. It furthers our knowledge of the role of the phosphatase PTP-3A/LAR in regulating excitatory synaptic maintenance. It also challenges the idea which recent studies have shown that correlates decreased synaptic activity with decreased AMPAR transport. Altogether, it outlines the general importance of understanding how AMPAR transport relates to synaptic plasticity and behavior.
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    ViennaRNA - optimizing a real-world RNA folding program
    (Colorado State University. Libraries, 2023) Save, Vidit V., author; Rajopadhye, Sanjay, advisor; Pallickara, Shrideep, committee member; Montgomery, Taiowa, committee member
    RNA folding is the dynamic process of intra-molecular interactions that makes a linear RNA molecule acquire a secondary structure. Predicting the acquired secondary structure is critical for gene regulation, disease characterization, and improving drug design. ViennaRNA is a highly utilized tool in the synthetic biology community to predict RNA secondary structures. This package is constantly updated to add new features and uses techniques like vectorization to boost its single-core performance. However, reviewing the package revealed that adopting known HPC optimizations to the code base could significantly improve the current performance. Optimizing a program with over 10k lines of code creates several software engineering challenges. Hence, toy kernels that mimic the code's behavior were initially used to explore possible optimizations. These kernels helped save compilation time and boil down the optimization process for the multi-branch loop prediction, a part of RNAfold, to five simple steps. On applying the optimizations described in this thesis, a 2X speedup can be observed for the entire program with a 4.2X speedup for the optimized part of the code. Using Intel's Roofline toolkit shows that applying these optimizations helped achieve cache utilization close to the theoretical L1 bandwidth of the machine. As a part of this thesis, incremental patches were created to integrate optimizations without disrupting the code base while ensuring the program's correctness.