Matching Items (52)
Description
Hundreds of thousands of people die annually from malaria; a protozoan of the genus Plasmodium is responsible for this mortality. The Plasmodium parasite undergoes several life stages within the mosquito vector, the transition between which require passage across the lumen of the mosquito midgut. It has been observed that in about 15% of parasites that develop ookinetes in the mosquito abdomen, sporozoites never develop in the salivary glands, indicating that passage across the midgut lumen is a significant barrier in parasite development (Gamage-Mendis et al., 1993). We aim to investigate a possible correlation between passage through the midgut lumen and drug-resistance trends in Plasmodium falciparum parasites. This study contains a total of 1024 Anopheles mosquitoes: 187 Anopheles gambiae and 837 Anopheles funestus samples collected in high malaria transmission areas of Mozambique between March and June of 2016. Sanger sequencing will be used to determine the prevalence of known resistance alleles for anti-malarial drugs: chloroquine resistance transporter (pfcrt), multidrug resistance (pfmdr1) gene, dihydropteroate synthase (pfdhps) and dihydrofolate reductase (pfdhfr). We compare prevalence of resistance between abdomen and head/thorax in order to determine whether drug resistant parasites are disproportionately hindered during their passage through the midgut lumen. A statistically significant difference between resistance alleles in the two studied body sections supports the efficacy of new anti-malarial gene surveillance strategies in areas of high malaria transmission.
ContributorsPhillips, Keeley Isabella (Author) / Huijben, Silvie (Thesis director) / Gile, Gillian (Committee member) / Young, Steven (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Single molecule FRET experiments are important for studying processes that happen on the molecular scale. By using pulsed illumination and collecting single photons, it is possible to use information gained from the fluorescence lifetime of the chromophores in the FRET pair to gain more accurate estimates of the underlying FRET rate which is used to determine information about the distance between the chromophores of the FRET pair. In this paper, we outline a method that utilizes Bayesian inference to learn parameter values for a model informed by the physics of a immobilized single-molecule FRET experiment. This method is unique in that it combines a rigorous look at the photophysics of the FRET pair and a nonparametric treatment of the molecular conformational statespace, allowing the method to learn not just relevant photophysical rates (such as relaxation rates and FRET rates), but also the number of molecular conformational states.
ContributorsSafar, Matthew Matej (Author) / Presse, Steve (Thesis director) / Sgouralis, Ioannis (Committee member) / Department of Physics (Contributor) / School of Mathematical and Statistical Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
A statistical method is proposed to learn what the diffusion coefficient is at any point in space of a cell membrane. The method used bayesian non-parametrics to learn this value. Learning the diffusion coefficient might be useful for understanding more about cellular dynamics.
ContributorsGallimore, Austin Lee (Author) / Presse, Steve (Thesis director) / Armbruster, Dieter (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
The 18S ribosomal RNA gene is ubiquitous across eukaryotes as it encodes the RNA component of the ribosomal small subunit. It is the most commonly used marker in molecular studies of unicellular eukaryotes (protists) due to its species specificity and high copy number in the protist genome. Recent studies have revealed the widespread occurrence of intragenomic (intra-individual) polymorphism in many protists, an understudied phenomenon which contradicts the assumed homogeneity of the 18S throughout an individual genome. This thesis quantifies and analyzes the level of intragenomic and intraspecific 18S sequence variability in three Trichonympha species (T. campanula, T. collaris, T. postcylindrica) from Zootermopsis termites. Single-cell DNA extractions, PCR, cloning, and sequencing were performed to obtain 18S rRNA sequence reads, which were then analyzed to determine levels of sequence divergence among individuals and among species. Intragenomic variability was encountered in all three species. However, excluding singleton mutations, sequence divergence was less than 1% in 53 of the 56 compared individuals. T. collaris exhibited the most substantial intragenomic variability, with sequence divergence ranging from 0 to 3.4%. Further studies with more clones per cell are needed to elucidate the true extent of intragenomic variability in Trichonympha.
ContributorsBobbett, Bradley (Author) / Gile, Gillian (Thesis director) / Liebig, Juergen (Committee member) / School of International Letters and Cultures (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
OP50 Esherichia coli is a Gram-negative bacterium with a fast replication rate and can be easily manipulated, making it a model species for many science disciplines. To probe this bacterium’s search strategy, cultures were starved and the cell velocity was probed at various points later in time after perturbing the buffer in which the bacteria were located. To start, we added E.coli OP50 filtrate. In yet another experiment filtrate from a Bdellovibrio bacteriovorus (Gram-negative predator) culture was added to monitor the OP50’s differential response to cues from its environment. Using MATLAB code, thousands of E.coli tracks were measured.
ContributorsSanchez, Alec Jesus (Author) / Presse, Steve (Thesis director) / Gile, Gillian (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Lower termites are classified as termites that require a symbiotic relationship with their hindgut community of single-celled protozoa in order to gather nutrients to survive. The class Spirotrichonymphea is one of the six classes of protists that make up the Phylum Parabasalia. Within the class Spirotrichonymphea, there are 3 families and 11 genera. In this study, the Spirotrichonympha, Spironympha, and Microjoenia genera (family Spirotrichonymphidae), Holomastigotes genus (family Holomastigotidae), along with a new genus Brugerollea were targeted for molecular analysis. Protist cells were collected from Reticulitermes tibialis (Rhinotermitidae), Hodotermopsis sjostedti (Archotermopsidae), and Paraneotermes simplicornis (Kalotermidiae). Most molecular phylogenetic studies of termite-associated protists have used the 18S rRNA gene, however, there have been some ambiguities in the phylogeny of this gene. EF1-α, also known as EF1A, is a protein whose sequence can additionally be used to study the evolution of protists. EF1-α gene sequences were obtained from isolated protist cells by reverse transcription PCR (RT-PCR). Additionally, the 18S rRNA gene was amplified to confirm the isolated cells’ identity and compare the two phylogenetic methods, to see which would better resolve phylogenetic ambiguities. Sequences were compiled into an alignment for each target gene, and then a maximum likelihood tree was created for each using RAxML. Results from both trees supports the monophyly of Spirotrichonymphea and the polyphyly of genus Spirotrichonympha. However, neither gene fully resolves the phylogeny of Spirotrichonymphea.
ContributorsNguyen, Keana (Author) / Gile, Gillian (Thesis director) / De Martini, Francesca (Committee member) / Taerum, Stephen Joshua (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The gut microbiome of many termites consists of a diverse range of protists that aid in the digestion of food particles. One of these families of protists is Oxymonadida. This project focuses on finding the evolutionary relationship between oxymonads and their most recent common ancestor, Trimastigidae, by building phylogenetic trees. This project was important because there is a large amount of species of oxymonads. This is because oxymonads adapt to the particular termite it lives in, and there are many species of termites. Understanding each species relationship helps give more knowledge and insight as to where some of the unknown species may go, even though they may not have DNA sequences yet. One unpublished sequence for Microrhopalodina was used in this paper, which previously had no molecular data available. The trees retrieved in this project had some discrepancies compared to previous studies and found an interesting relationship for Microrhopalodina. Microrhopalodina was included in the Oxymonas clade, indicating a very close relationship between the two species. It may even suggest that Microrhopalodina should be considered part of the species Oxymonas. Furthermore, Streblomastix branched in between Monocercomonoides and Trimastigidae, which is a different result than previous papers have found. Streblomastix was previously found to branch between Blattamonas and Monocercomonoides. The most recent paper on Blattamonas stated that they were unsure what family this species belongs to due to its molecular diversity, but its appearance resembles Monocercomonoides which is part of the family Polymastigidae. The trees produced in this project may indicate that Blattamonas belongs in the Polymastigidae family after all.
ContributorsStotts, Cherise (Co-author, Co-author) / Jasso-Selles, Daniel E. (Co-author) / Gile, Gillian H. (Thesis director) / DeMartini, Francesca (Committee member) / Mee, Evan D. (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The objective of this study was to compare the effectiveness of a newly developed DJO Global cervical collar with the previously studied Össur Americas Miami J collar in restricting cervical spine movement and reducing tissue interface pressure. 3D kinematic data were obtained for twelve healthy participants volunteers (6 female, 6 male) using a 10 camera infrared motion capture system (Motion Analysis Corp.). Cervical range of motion (CROM) in each plane was calculated as the angle between the head and thorax rigid-body axes. CROM was calculated using custom-written Matlab (MathWorks, Natick, MA) scripts. Tissue interface pressure (TIP) was measured between the head and the collar with three flexible pressure sensor pads over the anterior mandibles and occiput. The distribution of interface pressures was obtained in both the seated and supine positions. Both collars significantly restricted range of motion in all movement directions (p < 0.001) compared to no collar. There were no statistically significant differences in restrictiveness nor tissue interface pressures between the collars. Both collars exhibited similar CROM restriction in all planes and similar interface pressures in both positions. The newly developed DJO collar properly functioned as it markedly restricted spinal movement and produced low contact pressures. The Miami J collar has long been scientifically recognized as an effective collar; however, our data shows that the latest DJO collar was able to exhibit comparable contact pressures and decreases in cervical motion. As manufacturers produce improved collar designs, continued scientific testing should be executed in search of a collar capable of enhanced CROM restriction and the diminution of TIP.
ContributorsAraghi, Kasra (Author) / Gile, Gillian (Thesis director) / McCamley, John (Committee member) / Jacofsky, Marc (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Bdellovibrio bacteriovorus is a predatory bacterium that may serve as a living antibiotic by destroying biofilms and invading gram-negative bacteria. Swimming at over 100μm s-1, these predators collide into their prey and invade them to complete their life cycle. While previous experiments have investigated B. bacteriovorus’ motility, no study has yet collected swim speed variations over the lifespan of B. bacteriovorus. In this study, we used state-of-the-art bacterial tracking methods to record the speed of tens of thousands of bacteria. These results were used to describe their metabolic state under starvation conditions in which they lose energy in a dissipative manner by propelling themselves at high speeds through solution. In particular, we investigated the metabolic response of starved predators to the addition of prey-lysate.
ContributorsCarlson, Mikayla Lynn (Co-author) / David, Rowland (Co-author) / Presse, Steve (Thesis director) / Gile, Gillian (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The termite Coptotermes gestroi is a small subterranean termite originating from Southeast Asia. The hindgut of C. gestroi contains five distinct species of parabasalid: Pseudotrichonympha leei, two undescribed species from the genus Holomastigotoides, and two undescribed species from the genus Cononympha. This study investigates the protist symbionts in C. gestroi and the relationship between their relative abundance as inferred by Illumina sequence reads and the directly observed abundances for each protist genus. Illumina amplicon sequencing as a means of DNA analysis is a proven method for identification and diversity analysis, although the specific ratios of sequence reads to cell abundance in protists is not well known. In this study, protist communities were observed under light microscopy; cells were counted under hemocytometer and characterized at the molecular level using Illumina amplicon sequencing. When comparing sequence read abundances to cell abundances, some general trends were found in both analysis methods. Cononmypha repeatedly formed the majority of the community, while Holomastigotoides and Pseudotrichonympha were responsible for a smaller yet similar portion of the population. Cell counts and sequence reads were also compared using an assumed linear model, with R2 values generated to quantify the relationship between both. The results suggest that Illumina sequencing can be used to obtain rough estimates of community diversity, but the high variability within the data suggest that the read abundances should be treated with caution.
ContributorsAvilucea, Erin L. (Author) / Gile, Gillian (Thesis director) / DeMartini, Francesca (Committee member) / Taerum, Stephen Joshua (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05