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Nonsense mediated decay is a pathway that selectively degrades mRNAs that contain premature termination codons (PTCs). The purpose of this study is to research the evolution of NMD in Parabasalia and infer whether they have a normal, functioning nonsense-mediated decay pathway. Parabasalia are single-celled, flagellated protists that have undergone evolutionary

Nonsense mediated decay is a pathway that selectively degrades mRNAs that contain premature termination codons (PTCs). The purpose of this study is to research the evolution of NMD in Parabasalia and infer whether they have a normal, functioning nonsense-mediated decay pathway. Parabasalia are single-celled, flagellated protists that have undergone evolutionary transitions as they become obligate symbionts of termites. The key proteins involved in nonsense-mediated decay, ATM, ATR, UPF1, SMG1, UPF2, UPF3A, UPF3B, were researched and used in order to build phylogenetic trees to analyze what other species of eukaryotes have these same genes and where they branch relative to the nonsense mediated decay proteins present in Parabasalia. The main question being asked in this research is if Parabasalia have enough of the main nonsense mediated decay proteins to have a functional nonsense-mediated decay process and if not, which proteins have been lost over evolutionary history. To carry out this research, phylogenic trees were built using transcriptomes from many different types of eukaryotes that contained the main proteins involved in the nonsense-mediated decay pathway. These transcriptomes were taken from the National Center for Biotechnology Information (NCBI) database using the BLAST algorithm, trimmed using TrimAl, aligned by utilizing AliView which utilizes Muscle. Sequoia was then used to remove redundant species from the trees, and IQ-TREE was used to form the phylogenic trees. This process was repeated four times to create well-rounded trees with various eukaryotic species present. The results of this research found that ATM, ATR, UPF1, SMG1, and UPF2 are present in Parabasalia as well as across many eukaryotic groups, whereas UPF3A and UPF3B were not found in many of the eukaryotes researched. This points to Parabasalia having a normal and functioning nonsense-mediated decay pathway as they have the majority of the essential proteins needed for a functional pathway.

ContributorsHammond, Emma (Author) / Gile, Gillian (Thesis director) / DeVecchio, Duane (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
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The intracellular motility seen in the cytoplasm of angiosperm plant pollen tubes is known as reverse fountain cytoplasmic streaming (i.e., cyclosis). This effect occurs when organelles move anterograde along the cortex of the cell and retrograde down the center of the cell. The result is a displacement of cytoplasmic volume

The intracellular motility seen in the cytoplasm of angiosperm plant pollen tubes is known as reverse fountain cytoplasmic streaming (i.e., cyclosis). This effect occurs when organelles move anterograde along the cortex of the cell and retrograde down the center of the cell. The result is a displacement of cytoplasmic volume causing a cyclic motion of organelles and bulk liquid. Visually, the organelles appear to be traveling in a backwards fountain hence the name. The use of light microscopy bioimaging in this study has documented reverse fountain cytoplasmic streaming for the first time in fungal hyphae of Rhizopus oryzae and other members in the order Mucorales (Mucoromycota). This is a unique characteristic of the mucoralean fungi, with other fungal phyla (e.g., Ascomycota, Basidiomycota) exhibiting unidirectional cytoplasmic behavior that lacks rhythmic streaming (i.e., sleeve-like streaming). The mechanism of reverse fountain cytoplasmic streaming in filamentous fungi is currently unknown. However, in angiosperm plant pollen tubes it’s correlated with the arrangement and activity of the actin cytoskeleton. Thus, the current work assumes that filamentous actin and associated proteins are directly involved with the cytoplasmic behavior in Mucorales hyphae. From an evolutionary perspective, fungi in the Mucorales may have developed reverse fountain cytoplasmic streaming as a method to transport various organelles over long and short distances. In addition, the mechanism is likely to facilitate driving of polarized hyphal growth.
ContributorsShange, Phakade Mdima (Author) / Roberson, Robert W. (Thesis advisor) / Gile, Gillian (Committee member) / Baluch, Debra (Committee member) / Arizona State University (Publisher)
Created2020