Matching Items (109)
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Description
The purpose of this project was to identify proteins associated with the migration and invasion of non-transformed MCF10A mammary epithelial cells with ectopically expressed missense mutations in p53. Because of the prevalence of TP53 missense mutations in basal-like and triple-negative breast cancer tumors, understanding the effect of TP53 mutations on

The purpose of this project was to identify proteins associated with the migration and invasion of non-transformed MCF10A mammary epithelial cells with ectopically expressed missense mutations in p53. Because of the prevalence of TP53 missense mutations in basal-like and triple-negative breast cancer tumors, understanding the effect of TP53 mutations on the phenotypic expression of human mammary epithelial cells may offer new therapeutic targets for those currently lacking in treatment options. As such, MCF10A mammary epithelial cells ectopically overexpressing structural mutations (G245S, H179R, R175H, Y163C, Y220C, and Y234C) and DNA-binding mutations (R248Q, R248W, R273C, and R273H) in the DNA-binding domain were selected for use in this project. Overexpression of p53 in the mutant cell lines was confirmed by western blot and q-PCR analysis targeting the V5 epitope tag present in the pLenti4 vector used to transduce TP53 into the mutant cell lines. Characterization of the invasion and migration phenotypes resulting from the overexpression of p53 in the mutant cell lines was achieved using transwell invasion and migration assays with Boyden chambers. Statistical analysis showed that three cell lines—DNA-contact mutants R248W and R273C and structural mutant Y220C—were consistently more migratory and invasive and demonstrated a relationship between the migration and invasion properties of the mutant cell lines. Two families of proteins were then explored: those involved in the Epithelial-Mesenchymal Transition (EMT) and matrix metalloproteinases (MMPs). Results of q-PCR and immunofluorescence analysis of epithelial marker E-cadherin and mesenchymal proteins Slug and Vimentin did not show a clear relationship between mRNA and protein expression levels with the migration and invasiveness phenotypes observed in the transwell studies. Results of western blotting, q-PCR, and zymography of MMP-2 and MMP-9 also did not show any consistent results indicating a definite relationship between MMPs and the overall invasiveness of the cells. Finally, two drugs were tested as possible treatments inhibiting invasiveness: ebselen and SBI-183. These drugs were tested on only the most invasive of the MCF10A p53 mutant cell lines (R248W, R273C, and Y220C). Results of invasion assay following 30 μM treatment with ebselen and SBI-183 showed that ebselen does not inhibit invasiveness; SBI-183, however, did inhibit invasiveness in all three cell lines tested. As such, SBI-183 will be an important compound to study in the future as a treatment that could potentially serve to benefit triple-negative or basal-like breast cancer patients who currently lack therapeutic treatment options.
ContributorsZhang, Kathie Q (Author) / LaBaer, Joshua (Thesis director) / Anderson, Karen (Committee member) / Gonzalez, Laura (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
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Description

Much is still unknown about dominance hierarchies. Many different species form dominance hierarchies and each species have very different ways of forming these hierarchies. Some engage in various different dominance interactions to establish a dominant position. This experiment aims to use the ant species, Harpegnathos saltator, as a model to

Much is still unknown about dominance hierarchies. Many different species form dominance hierarchies and each species have very different ways of forming these hierarchies. Some engage in various different dominance interactions to establish a dominant position. This experiment aims to use the ant species, Harpegnathos saltator, as a model to explore what sets dominant individuals, or gamergates in this case, apart from non-dominant individuals, or non-gamergates. H. saltator ants perform various different behaviors such as dueling, which is a mutually beneficial behavior, dominance biting, which is an aggressive behavior, and policing which is used to bring down those who are dominant. These behaviors can be used to study the importance of initiation and aggression in hierarchy formation. This experiment will explore how aggression through dominance biting, duel initiation, group size, and time period affect the formation of gamergates. To do so, socially unstable colonies of 15, 30, and 60 ants were video recorded for days until gamergates were established. Then, from the recordings, a period of high activity was selected and observed for dueling, duel initiation, dominance biting, dominance bite downs, and policing. The results showed that gamergates tended to perform dominance biting and dominance bite downs far more than non-gamergates during the period of high activity, but not as clearly with duelling and duel initiations. It was inconclusive whether or not the combination of both dueling and dominance biting was what set gamergates apart from non gamergates as different groups showed different results. Gamergates performed visibly more dominance bite downs than non-gamergates, so aggression may be important in setting gamergates apart from non-gamergates. In terms of group size, the smallest group had the least number of gamergates and the least activity, and the medium and large group had a similar number of gamergates and activity.

ContributorsVarghese, Sarah (Author) / Liebig, Juergen (Thesis director) / Haight, Kevin (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Olfactory discrimination tasks can provide useful information about how olfaction may have evolved by demonstrating which types of compounds animals will detect and respond to. Ants discriminate between nestmates and non-nestmates by using olfaction to detect the cuticular hydrocarbons on other ants, and Camponotus floridanus have particularly clear and aggressive

Olfactory discrimination tasks can provide useful information about how olfaction may have evolved by demonstrating which types of compounds animals will detect and respond to. Ants discriminate between nestmates and non-nestmates by using olfaction to detect the cuticular hydrocarbons on other ants, and Camponotus floridanus have particularly clear and aggressive responses to non-nestmates. A new method of adding hydrocarbons to ants, the “Snow Globe” method was further optimized and tested on C. floridanus. It involves adding hydrocarbons and a solvent to a vial of water, vortexing it, suspending hydrocarbon droplets throughout the solution, and then dipping a narcotized ant in. It is hoped this method can evenly coat ants in hydrocarbon. Ants were treated with heptacosane (C27), nonacosane (C29), hentriacontane (C31), a mixture of C27/C29/C31, 2-methyltriacontane (2MeC30), S-3-methylhentriacontane (SMeC31), and R-3-methylhentriacontane (RMeC31). These were chosen to see how ants reacted in a nestmate recognition context to methyl-branched hydrocarbons, R and S enantiomers, and to multiple added alkanes. Behavior assays were performed on treated ants, as well as two untreated controls, a foreign ant and a nestmate ant. There were 15 replicates of each condition, using 15 different queenright colonies. The Snow Globe method successfully transfers hydrocarbons, as confirmed by solid phase microextraction (SPME) done on treated ants, and the behavior assay data shows the foreign control, SMeC31, and the mixture of C27/29/31 were all statistically significant in their differences from the native control. The multiple alkane mixture received a significant response while single alkanes did not, which supports the idea that larger variations in hydrocarbon profile are needed for an ant to be perceived as foreign. The response to SMeC31 shows C. floridanus can respond during nestmate recognition to hydrocarbons that are not naturally occurring, and it indicates the nestmate recognition process may simply be responding to any compounds not found in the colony profile and rather than detecting particular foreign compounds.

ContributorsNoss, Serena Marie (Author) / Liebig, Juergen (Thesis director) / Pratt, Stephen (Committee member) / Haight, Kevin (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

The membrane proximal region (MPR, residues 649–683) and transmembrane domain (TMD, residues 684–705) of the gp41 subunit of HIV-1’s envelope protein are highly conserved and are important in viral mucosal transmission, virus attachment and membrane fusion with target cells. Several structures of the trimeric membrane proximal external region (residues 662–683)

The membrane proximal region (MPR, residues 649–683) and transmembrane domain (TMD, residues 684–705) of the gp41 subunit of HIV-1’s envelope protein are highly conserved and are important in viral mucosal transmission, virus attachment and membrane fusion with target cells. Several structures of the trimeric membrane proximal external region (residues 662–683) of MPR have been reported at the atomic level; however, the atomic structure of the TMD still remains unknown. To elucidate the structure of both MPR and TMD, we expressed the region spanning both domains, MPR-TM (residues 649–705), in Escherichia coli as a fusion protein with maltose binding protein (MBP). MPR-TM was initially fused to the C-terminus of MBP via a 42 aa-long linker containing a TEV protease recognition site (MBP-linker-MPR-TM).

Biophysical characterization indicated that the purified MBP-linker-MPR-TM protein was a monodisperse and stable candidate for crystallization. However, crystals of the MBP-linker-MPR-TM protein could not be obtained in extensive crystallization screens. It is possible that the 42 residue-long linker between MBP and MPR-TM was interfering with crystal formation. To test this hypothesis, the 42 residue-long linker was replaced with three alanine residues. The fusion protein, MBP-AAA-MPR-TM, was similarly purified and characterized. Significantly, both the MBP-linker-MPR-TM and MBP-AAA-MPR-TM proteins strongly interacted with broadly neutralizing monoclonal antibodies 2F5 and 4E10. With epitopes accessible to the broadly neutralizing antibodies, these MBP/MPR-TM recombinant proteins may be in immunologically relevant conformations that mimic a pre-hairpin intermediate of gp41.

ContributorsGong, Zhen (Author) / Martin Garcia, Jose Manuel (Author) / Daskalova, Sasha (Author) / Craciunescu, Felicia (Author) / Song, Lusheng (Author) / Dorner, Katerina (Author) / Hansen, Debra (Author) / Yang, Jay-How (Author) / LaBaer, Joshua (Author) / Hogue, Brenda (Author) / Mor, Tsafrir (Author) / Fromme, Petra (Author) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Innovations in Medicine (Contributor) / Personalized Diagnostics (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-08-21
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Description
Across the animal kingdom, communication serves a vital purpose. The transfer of information between and among species is often paramount to many behaviors including mating, collaboration, and defense. While research has provided tremendous insight into animal communication and interaction, there is still much that we have yet to understand. Due

Across the animal kingdom, communication serves a vital purpose. The transfer of information between and among species is often paramount to many behaviors including mating, collaboration, and defense. While research has provided tremendous insight into animal communication and interaction, there is still much that we have yet to understand. Due to their reliance on interactions that maximize efficiency within their complicated colony structure and array of member roles, eusocial insects serve as an excellent model for animal communication. Among eusocial insects, ants are some of the most heavily researched, with a tremendous amount of literature focused on their cuticular hydrocarbons. Along with serving as a waterproofing agent, cuticular hydrocarbons also play a major role in recognition and communication in these insects. By studying the importance of hydrocarbons in ant social structure, their tremendously specialized olfactory system, and the use of learning assays in its study, parallels between communication in ants and other animals are revealed, demonstrating how ants serve as a relevant model for animal communication as a whole.
ContributorsSpirek, Benton Forest Ensminger (Author) / Liebig, Juergen (Thesis director) / Pratt, Stephen (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
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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

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
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Description
Insects are small creatures highly susceptible to water loss. A major factor in the prevention of water loss through an insect’s cuticle are their cuticular hydrocarbons (CHC), a lipid layer consisting mostly of long-chain hydrocarbons. CHCs consist of different molecules called alkanes, alkenes, and methyl branched hydrocarbons which all have

Insects are small creatures highly susceptible to water loss. A major factor in the prevention of water loss through an insect’s cuticle are their cuticular hydrocarbons (CHC), a lipid layer consisting mostly of long-chain hydrocarbons. CHCs consist of different molecules called alkanes, alkenes, and methyl branched hydrocarbons which all have varying levels of hydrophobicity. Ants are a massively abundant family of insects with important roles in the ecosystem that also utilize CHCs. Camponotus floridanus isare athe native ant species of the Florida Keys which areis known to have variable environmental temperature. Being exposed to temperatures as high as 35 °C, these ants are expected to have mechanisms that allow them to adapt to their environment. It was hypothesized that CHCs may change in concentration or composition as a means to combat the changes in cuticular permeability due to the variable temperatures that the ants experience. We therefore used C. floridanus worker ants to learn more about CHC plasticity in insects when exposed to elevated temperatures. We found four CHC componentspeaks that showed a statistically significant increase in concentration when comparing the control to treatment colonies: 3,7 dimethyl C31, an underdetermined methyl branched C31, 3,7,11 trimethyl C31, and an undetermined tetramethylbranched C31. These significant changes in concentration occurred on longer chain hydrocarbons. Under further examination, it was found that there was a strong positive correlation between elution time and the differences in medians of peak area between control and treatment colonies. This shows that there was a shift in the CHC profile resulting in an increased concentration of longer chained methyl-branched hydrocarbons. It also suggests that branched hydrocarbons also play some role in the water proofing mechanism of C. floridanus.
ContributorsOn, Thomas (Co-author) / On, Tyler (Co-author) / Liebig, Juergen (Thesis director) / Harrison, Jon (Committee member) / Murdock, Tyler (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
When ants encounter liquid food, they have two options of transporting that food to their nests. The first is the social bucket method in which liquid is carried in the mandibles of the workers back to the nest. The second is trophallaxis in which liquid is imbibed and then transported

When ants encounter liquid food, they have two options of transporting that food to their nests. The first is the social bucket method in which liquid is carried in the mandibles of the workers back to the nest. The second is trophallaxis in which liquid is imbibed and then transported inside the ant back to the nest. The liquid is then regurgitated to fellow nestmates. Ectatomma have been observed using the social bucket method of transport and were considered members of the Ponerine family. However, a new phylogeny created by Borowiec and Rabeling places Ectatomma near to Formecinae and Myrmicinae, both know for practicing trophallaxis. This seems to suggest either Ectatomma is able to utilize trophallaxis as well or that the evolutionary practice of trophallaxis is more plastic than previously believed. The ability of Ectatomma ruidum to utilize trophallaxis was examined in two experiments. The first experiment examined E. ruidum’s ability to practice worker to worker trophallaxis and the second examined E. ruidum’s ability to perform worker to larva trophallaxis. The results of both experiments indicated that E. ruidum cannot utilize trophallaxis but the larva of E. ruidum may be able to regurgitate to the workers. These results in turn seem to suggest that trophallaxis is a bit more plastic than originally thought.
ContributorsCunningham, Cassius Alexander (Author) / Pratt, Stephen (Thesis director) / Liebig, Juergen (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description
Abstract:
Given the incredible variety in ant nest architecture, this experiment sought to evaluate how the nest architecture of Harpegnathos saltator differs from other species’ nests. To achieve the ability to evaluate the structure of H. saltator nest, we created experimental colonies varying in size from 20, 40, 60, 80 workers

Abstract:
Given the incredible variety in ant nest architecture, this experiment sought to evaluate how the nest architecture of Harpegnathos saltator differs from other species’ nests. To achieve the ability to evaluate the structure of H. saltator nest, we created experimental colonies varying in size from 20, 40, 60, 80 workers of Harpegnathos saltator in five-gallon buckets of sand and then allowing the colonies to grow for four months and twelve days. To create the nest casts, we developed a charcoal kiln out of a galvanized trash can and used a ceramic crucible to hold the aluminum being melted. Using molten aluminum to create nest casts of each colony produced, we obtained three poorly developed nests and one decent nest. The decent nest cast, the 80 worker H. saltator nest, was lacking key features of H. saltator nests that have been excavated in the field. However, they do share many of the same structures such as the shaping of the chambers. The ability of the experimental colonies to excavate the soil provided in the buckets to them was likely halted by poor penetration of water into superficial layers of the soil, thus making the soil too difficult to excavate and form the structures that are key elements of the species nest architecture. Despite these key challenges which the colonies faced, the 80-worker colony showed extensive vertical development and did display features associated with natural H. saltator colonies. Thus, given the display of some key features associated with characteristics of the H. saltator nests excavated in the field, it can be said that with some modification to technique that this is a viable avenue for future study of nest architecture and colony structure.
ContributorsAnderson, Clayton Edward (Author) / Liebig, Juergen (Thesis director) / Pratt, Stephen (Committee member) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The purpose of this thesis creative project was to create an educational video to present research findings on the increasingly important issue of human biospecimen preanalytic variables. When a human biospecimen, such as blood, urine, or tissue, is removed from the body, it is subjected to a plethora of variables

The purpose of this thesis creative project was to create an educational video to present research findings on the increasingly important issue of human biospecimen preanalytic variables. When a human biospecimen, such as blood, urine, or tissue, is removed from the body, it is subjected to a plethora of variables that are not recorded or regulated in a vast majority of cases. Frequently, these samples arrive at the research or pathology lab with an unknown history, then undergo analysis for translational research purposes, or to guide clinical management decisions. Thus, compromised specimen quality caused by preanalytic variables has substantial, and potentially devastating, downstream effects. To identify the preanalytic variables with the greatest impact on blood and tissue specimen quality, 45 articles were gathered using PubMed and Google Scholar databases and cited. Based on the articles, the top five variables with the most detrimental effects were identified for both blood and tissue samples. Multiple sets of parameters ensuring specimen fitness were compared for each of the five variables for each specimen type. Then, specific parameters guaranteeing the fitness of the greatest number of analytes were verified. To present the research findings in greater detail, a paper was written that focused on identifying the top variables and key parameters to ensure analyte fitness. To present the overall issue in an easy-to-digest format, a storyboard and script were created as a guideline for a final video project. Ultimately, two alternate versions of the video were created to pertain to the audience of choice (one version for patients, one version for professionals). It is the hope that these videos will be used as educational tools to continue efforts to standardize and enforce human biospecimen preanalytic variable parameters. This is a necessary step to improve the accuracy of our biomedical research data and the healthcare of patients worldwide.
ContributorsAzcarate, Heather (Author) / Compton, Carolyn (Thesis director) / LaBaer, Joshua (Committee member) / Borges, Chad (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2018-12