Matching Items (28)
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
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 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
Description
The termite Zootermopsis nevadensis nuttingi, which is located in coastal forests of the western United States, plays an important ecological role in the breakdown and digestion of wood. Vital to this role are symbiotic protists residing in the termite's hindgut. Five protist genera of varying size and morphology make up this gut community. Despite years of study on this termite species, little was known about the spatial organization of the protist community within Zootermopsis nevadensis nuttingi. To resolve this issue, a study was conducted in which the distribution of protist genera among gut segments was observed and elucidated. This was done by separating hindgut segments, then counting the protists using a hemocytometer at a magnification of 200x. 60 segments from 20 termites were examined, and the total number of protists counted was 69,560. Images were also taken using a scanning electron microscope. Statistically significant, distinct distribution patterns were found for Trichonympha, Trichomitopsis and Streblomastix, while the small genera of Hexamastix and Tricercomitus appeared to have no special distribution. Trichomitopsis was more abundant in the posterior hindgut, Streblomastix was more abundant anteriorly, while the distribution of Trichonympha varied by colony. Hexamastix and Tricercomitus make up a large majority of the protists observed in any segment, followed by Streblomastix, Trichomitopsis and Trichonympha. Understanding the distribution of different protists within the hindgut may improve our understanding of the ecological relationships among protists as well as their individual roles in lignocellulose digestion, contributing to a better understanding of the hindgut system as a whole.
ContributorsPiarowski, Christina Marie (Author) / Gile, Gillian (Thesis director) / DeMartini, Francesca (Committee member) / Taerum, Stephen (Committee member) / School of International Letters and Cultures (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Antibiotic resistance in the modern era has reached near-epidemic levels, resulting in much more difficult treatment of previously well-managed pathogens. Previous understandings of how antibiotic resistance emerges failed to account for the function of the environment. Over the past 15 years, new research has provided a link between the environmental and clinical spheres of antibiotic use. This data suggests that environmental bacteria, particularly those found in livestock farming ecosystems, may significantly contribute to the overall flow of antibiotic resistance genes into human populations. The main force behind this is the utilization of antibiotics as growth promoters in animal feed supplements, seeding individual animals and their surroundings with low doses of antibiotics. Notable increases in resistance have been observed within areas that utilize these supplements, as well as in connected but unrelated systems. Waste management strategies are poorly implemented, leading to the dispersal of contaminated runoff into groundwater and riverine environments. Furthermore, existing waste processing is limited in efficacy, often releasing large amounts of unprocessed antibiotics as well as a concentrated population of resistant bacteria. Within these resistant populations, horizontal gene transfer has emerged as a vehicle for the distribution of resistance genes into other populations of bacteria. Due to the prevalence of these transfer events, a new role for the environment as a reservoir and incubator of resistance genes is proposed. Current strategies for managing the spread of antibiotic resistance are woefully inadequate, and the continued emergence of new resistance mechanisms due to negligence highlights the need for global, multidisciplinary solutions. To corral the spread of antibiotic resistance, a system is proposed that utilizes metagenomic monitoring and the enforcement of core global policies to slow the advance of resistance while waiting for novel treatment strategies to bear fruit.
ContributorsHrkal, Jacob (Author) / Gile, Gillian (Thesis director) / Shi, Yixin (Committee member) / Sarno, Analissa (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Parabasalia is a phylum of flagellated protists with a large range of cell sizes, spanning from as little as 7 µm in length (e.g. Pentatrichomonas hominis) to well over 300 µm (e.g. Pseudotrichonympha grassii). Many Parabasalia are associated with animals in mutualistic, parasitic, or commensal relationships. The largest Parabasalia species are obligate mutualists of termites, which help to digest lignocellulose. While the specific digestive roles of different protist species are mostly unknown, Parabasalia with different cell sizes are known to inhabit different regions of the termite hindgut. It is currently unclear whether these size differences are driven by selection or drift, but it is well known that cell size correlates with genome size in eukaryotes. Therefore, in order to gain insight into possible selection pressures or mechanisms for cell size increase, genome sizes were estimated for the five Parabasalia species that inhabit the hindgut of Coptotermes formosanus Shiraki. The cell volumes and C-values for the five protist species are 89,190 µm3 and 147 pg in Pseudotrichonympha grassii, 26,679 µm3 and 56 pg in Holomastigotoides hartmanni, 8,985 µm3 and 29 pg in Holomastigotoides minor, 1,996 µm3 and 12 pg in Cononympha leidyi , and 386 µm3 and 6 pg in Cononympha koidzumii. The positive correlation between genome size and cell size was maintained in this group (R2 = 0.76). These genome sizes are much larger than the previously estimated genome sizes of non-termite associated Parabasalia, which spanned 2-fold ranging from 0.088 pg (in Tetratrichomonas gallinarum) to 0.181 pg (in Trichomonas foetus). With these new estimates, the range now spans over 1,500-fold from 0.088 pg to 147 pg in P. grassii, implying potential differences in the level of selective pressures for genome size in termite-associated Parabasalia compared to other protists.
ContributorsMontoya, Samantha (Author) / Gile, Gillian (Thesis advisor) / Wideman, Jeremy (Committee member) / Chouvenc, Thomas (Committee member) / Arizona State University (Publisher)
Created2021