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End date: 2016 × Has files: Yes × search.filters.applied.f.isOrgUnitOfPublicationTitle: College of Sciences × search.filters.applied.f.resourcesubtype: Undergraduate Thesis ×

Publication Search Results

Now showing 1 - 10 of 79
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Aggressive Phenotypes in Malawi Cichlids Associated with V1AR Variant

2016-12 , Schappaugh, Nicholas A.

The cichlid model provides a great opportunity to explore diversity in behavioral phenotypes. Different groups of Malawi cichlids exhibit distinct patterns of behavior for a variety of scenarios, including aggressive encounters. These cichlids, characterized by the rocky or sandy habitats they occupy, exhibit strong genetic divergence, possessing large numbers of alternatively fixed variants between them. One such variant exists in the gene avpr1a, also known as V1aR, a major receptor for vasopressin in humans. This gene has been linked to behavioral effects across a variety of animal species, with this specific variant likely to have significant structural implications for the receptor product. Here we investigate the aggressive behaviors of a set of rock and sand hybrid fish for their association with the variant observed in V1aR. While specific metrics of aggression showed similar trends in these hybrids compared to those observed in the parental rock and sand species, ultimately these trends were not significant and were inconclusive. However, these results serve as a preliminary investigation of this gene’s involvement in cichlid aggressive behavior. In future work, further examination of the locus will be conducted utilizing more precise and powerful methods in order to draw stronger conclusions.

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Establishing a Working Protocol for Plasmid Cloning and shRNA Design in Endogenous Brachionus manjavacas Gene TRP7

2016-07-18 , Krishnappan, Sharadha

Current transfection protocol in rotifers only allows for temporary transfection within rotifers and does not allow for the continuous knockdown of endogenous genes, thereby inhibiting the possibility of observing long-term biological effects in response to specific perpetual gene knockdowns. This study aims to address this particular issue by establishing a working protocol for plasmid cloning and shRNA design within an endogenous gene of B. manjavacas with known biological effects, allowing for the exploration into the optimization of a transfection protocol and demonstration of RNAi knockdown of the known gene within the rotifers as subsequent studies. Manipulation of gene expression in rotifers could occur through plasmid vector insertions, which induce silencing of a gene’s expression with short hairpin RNA (shRNA), via RNAi. This would effectively stimulate gene knockdown, allowing for the observation of biological effects such as changes in fecundity and lifespan. With the establishment of a working protocol for plasmid cloning and shRNA design, as a result of this study, the optimization of a transfection protocol for rotifers is explored. With increased efficiency in the transfection of rotifers, populations of rotifers expressing the plasmid can be amassed, allowing for experimental design that examine the varying aging mechanisms and effects that are stimulated due to permanent changes in target gene expression through RNAi. This, in turn, could give rise to the identification of evolutionarily conserved genes that regulate organismal aging, which could lead to further implications in the field of pharmacological intervention in mammalian aging as well as in the field of biogerontology overall.

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Changes in Nutrient Dynamics in the Gulf of Mexico due to Increase in Mississippi River Flow

2016-01-25 , Taylor, Anna

The Gulf of Mexico underwent multiple environmental changes in 2010 and 2011, including the Deepwater Horizon oil spill and a large in increase of freshwater input from the Mississippi River. Both of these events had the potential to change nutrient dynamics. In this study, I focused on the changes of nutrient dynamics in surface water in the northern Gulf of Mexico and what brought about those changes. It was found that surface water nutrient concentrations of nitrate, nitrite, and phosphate were much higher in the year 2011. This change was found to be due to the freshwater input from the Mississippi River through geographical location and relation to salinity.

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Finding Food in an Aquatic Desert: How cruising copepods detect their next phytoplankton meal

2016-01-25 , Taylor, Jazmyne Z. C.

Copepods exist in an aquatic food desert where finding food is difficult given the constraints of their environment. They live in a three dimensional world and must filter 106 times their own body volume to cover their nutritional needs (Kiorboe, 2011). Copepods sense chemical, hydromechanical or both cues for prey and mate detection. Hydromechanoreception is the dominant sensory mechanism used to locate nearby prey (Legier-Visser,et al. 1986, Goncalves et al. 2014)). However, it is relatively unknown how copepods detect their prey from a distance. This study focused on the sensory mechanism and behavior of an abundant pelagic copepod, Temora longicornis, tracking a co-occurring phytoplankton prey, Tetraselmis suecica. The wake of a mobile prey was mimicked in the form of a trail-like cue and scented with either the smell of T. suecica, female T. longicornis, or remained scentless. Males were exposed to all three treatments, whereas females only to T. suecica and a scentless trail. Preliminary results indicate that male and female T. longicornis copepods may rely on chemical and hydromechanical cues for prey detection. Why it is important to determine the mechanism copepods use for remote detection of prey? The ocean contains numerous tiny trails scented with the smell of phytoplankton which leak from the source prey patch. It has been suggested that trail-sensing copepods will be more successful at finding mates and food than those who do not follow trails (Yen et al., 2010). Results from this study may open a new avenue of research for the success of trail-sensing organisms.

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Generalizing Disease Associations to Non-Studied Populations

2016-12 , Patel, Kane

This study determines whether risk allele frequencies (RAFs) for common diseases can be generalized in genome wide association surveys (GWAS) that are done in different populations other than the original study population. To test this, the study compares RAFs gathered from the NHRI-EBI GWAS Catalog and 1000 Genomes Project by study population and checks if there is bias towards the study population. If the trend is present, the study looks to answer the question of whether or not this is due to an inherent bias from the study population, or a pre-ascertained bias in the genotyping single nucleotide polymorphism (SNP) chip array. To test bias in the technology, the study compares allele frequencies for disease SNPs and non-disease SNPs on Illumina1M and Affymetrix 6.0 genotyping arrays. If the bias still persists, then there is an inherent bias due to the study population alone. At this point, the study will examine the role of other contributing factors to differences in disease allele frequencies across populations. These include: type of disease, number of participants in the GWAS, whether alleles have a large effect, etc. This study potentially contributes the overall field of population genetics and personalized medicine. Essentially, the goal is to ensure that the information attained can be used to create models that could correct potential bias in GWAS studies.

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Morphological Variation in Hemiphractus Fasciatus (Anura: Hylidae: Hemiphractinae)

2016-07-18 , Martin, Kathryn G.

We describe morphological variation within the species Hemiphractus fasciatus, with special focus on populations in Panama, and determined the two allopatric populations are morphologically distinct, suggesting that there are at least two species involved in this system... The distinct groups are from eastern and western Panama, with the Panama Canal as the divider. Recent genetic analysis suggested there are three genetically distinct groups within H. fasciatus. The western specimens can be distinguished by cranial morphology, the texture of the skin under the throat.

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The Effect of Environmental Factors on Bacteria Associated with Sphagnum Mosses

2016-01-25 , Sexton, William Kyle

Sphagnum peat mosses play an important role in the global carbon cycle by sequestering carbon as biomass thorough photosynthesis. Biodegradation in the northern peatlands is slow in part due to acidic and nutrient-poor soil conditions, so biomass accumulates over time as peat. Sphagnum mosses partner with bacteria that fix atmospheric nitrogen to supplement their nitrogen intake in these nutrient-poor soils. Climate change is altering temperatures, precipitation, and nitrogen deposition rates in the northern peatlands. These changes are accompanied by an increased release of greenhouse gases and a decline in Sphagnum ground coverage. The nitrogen-fixing bacteria associated with Sphagnum mosses need to be studied in order to understand how their relationship will be impacted by climate change. In this study I show that higher pH levels and nutrient concentrations can negatively impact the growth of potential nitrogen-fixing bacteria associated with two species of Sphagnum mosses. I also demonstrate that bacteria associated with these mosses overall are adapted to low-nitrogen conditions and a wide pH range.

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Catalytic abilities of the Schistosoma mansoni hammerhead ribozyme with mutated substrates in ice

2016-12 , Calvird, Audrey

The synthesis of biomolecules in an environment similar to a pre-biotic Earth within the field of evolutionary chemistry has applications in understanding abiogenesis and the evolution of early biological systems on Earth. The RNA world is a prebiotic environment proposed and subsequently heavily studied in effort to better understand how biochemical reactions started on Earth. This study proposes to assess the catalytic ability of a Hammerhead Ribozyme (HHRz) isolated from the protozoa Schistosoma mansoni (Schist HHRz). It has been previously shown that the Schist HHRz can catalyze the synthesis of extended sequences of ribonucleic acid (RNA) by ligating two RNA substrates in ice, as well as cleave the same substrate back to the original separate substrates in the presence of Mg2+ (Lie et al. 2016). The same study showed that the Schist HHRz is able to catalyze the ligation with mutated substrates (Lie et al. 2016). This study aims to evaluate Schist HHRz’s ability to ligate a mutated substrate in comparison to the wild type substrate in ice, as well as compare the kinetics of the Schist HHRz to cleave the mutated and wild type substrates in the presence of Mg2+. This study will utilize the techniques specified by Lie et al. (2016) to further investigate the extent of the ligation of a mutated substrate catalyzed by the Schist HHRz compared to that of the wild type substrate. This study also assays the kinetics of the cleavage reaction catalyzed by the same Schist HHRz of both the wild type substrate and mutated substrate. This study hopes to improve the understanding of pre-biotic biochemistry in efforts to identify possible mechanisms or models for RNA polymerization by ribozymes on early Earth.

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Effects on the Pocillopora verrucosa microbiome when in contact with macroalgae under ocean acidification

2016-07-18 , Gantt, Shelby

Hard coral cover is in decline and this decline has generally coincided with macroalgal proliferation in coral reefs. Coral degradation can be caused by many variables but this study is focused on potential degradation due to direct competition with allelopathic macroalgae under the effects of future ocean acidification. Allelopathy is the use of chemicals for protection or competitive purposes. It has previously been shown that algae compete with corals through allelopathy, but not if allelopathy causes the microbiome of the coral to enter a diseased state, though there have been several cases of diseased microbiome states observed. As such, it is of interest to determine if the allelopathic competition from algae affects the coral microbiome, leading to a diseased state, and whether these interactions are exaggerated or effected by ocean acidification. We hypothesize that macroalgal allelopathy effects the microbiome of the reef-building coral Pocillopora verrucosa and that these competitive interactions will be affected by the stressor of ocean acidification. We expect the latter because of previous evidence that increased pH causes stress to some species of corals. To test this, we used a pre-established scale of algal allelopathy demonstrated in Rasher et al. (2011) and placed corals and algae in contact under ocean acidification conditions for 3 weeks before samples were processed for microbial taxonomy. The initial analyses have demonstrated no significant differences in the abundances of major microbial taxa compositions for the sampled coral microbiomes when in the presence of the various allelopathic macroalgae, but these are preliminary findings. The data will require finer microbial analysis to determine whether or not there are any significant effects on the coral microbiomes.

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Factors that Increase the Efficiency of DNA Repair when Using Transcript RNA as a Template

2016-01-25 , Skulskaya, Olexandra

Interaction with various chemicals and environmental agents can cause damages to DNA. In this study, we particularly focus on double stranded breaks (DSBs) and a repair mechanism that uses transcript RNA to repair the break. A previous study has shown that the frequency of DSB repair by transcript RNA in the cis system is increased in cells with a genotype of spt3 rnh1 rnh201. This research focuses on determining factors that increase the efficiency of DSB repair when using transcript RNA as a template. Cells with the genotype of spt3 rnh1 rnh201 in a cis-system were mutated and transformed with gene over expression library in two separate experiments. We have found 13 candidates from 20,000 mutated cells that can improve the efficiency of repair using transcript RNA, as well as 58 potential candidates out of 3,784 cells transformed with the yeast gene over expression library.

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