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- Creators: Barrett, The Honors College
Description
Cancer remains one of the leading killers throughout the world. Death and disability due to lung cancer in particular accounts for one of the largest global economic burdens a disease presents. The burden on third-world countries is especially large due to the unusually large financial stress that comes from late tumor detection and expensive treatment options. Early detection using inexpensive techniques may relieve much of the burden throughout the world, not just in more developed countries. I examined the immune responses of lung cancer patients using immunosignatures – patterns of reactivity between host serum antibodies and random peptides. Immunosignatures reveal disease-specific patterns that are very reproducible. Immunosignaturing is a chip-based method that has the ability to display the antibody diversity from individual sera sample with low cost. Immunosignaturing is a medical diagnostic test that has many applications in current medical research and in diagnosis. From a previous clinical study, patients diagnosed for lung cancer were tested for their immunosignature vs. healthy non-cancer volunteers. The pattern of reactivity against the random peptides (the ‘immunosignature’) revealed common signals in cancer patients, absent from healthy controls. My study involved the search for common amino acid motifs in the cancer-specific peptides. My search through the hundreds of ‘hits’ revealed certain motifs that were repeated more times than expected by random chance. The amino acids that were the most conserved in each set include tryptophan, aspartic acid, glutamic acid, proline, alanine, serine, and lysine. The most overall conserved amino acid observed between each set was D - aspartic acid. The motifs were short (no more than 5-6 amino acids in a row), but the total number of motifs I identified was large enough to assure significance. I utilized Excel to organize the large peptide sequence libraries, then CLUSTALW to cluster similar-sequence peptides, then GLAM2 to find common themes in groups of peptides. In so doing, I found sequences that were also present in translated cancer expression libraries (RNA) that matched my motifs, suggesting that immunosignatures can find cancer-specific antigens that can be both diagnostic and potentially therapeutic.
ContributorsShiehzadegan, Shima (Author) / Johnston, Stephen (Thesis director) / Stafford, Phillip (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
The purpose of this project is to create a useful tool for musicians that utilizes the harmonic content of their playing to recommend new, relevant chords to play. This is done by training various Long Short-Term Memory (LSTM) Recurrent Neural Networks (RNNs) on the lead sheets of 100 different jazz standards. A total of 200 unique datasets were produced and tested, resulting in the prediction of nearly 51 million chords. A note-prediction accuracy of 82.1% and a chord-prediction accuracy of 34.5% were achieved across all datasets. Methods of data representation that were rooted in valid music theory frameworks were found to increase the efficacy of harmonic prediction by up to 6%. Optimal LSTM input sizes were also determined for each method of data representation.
ContributorsRangaswami, Sriram Madhav (Author) / Lalitha, Sankar (Thesis director) / Jayasuriya, Suren (Committee member) / Electrical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Malignant Pleural Mesothelioma is a type of lung cancer usually discovered at an advanced stage at which point there is no cure. Six primary MPM cell lines were used to conduct in vitro research to make conclusions about specific gene mutations associated with Mesothelioma. DNA exome sequencing, a time efficient and inexpensive technique, was used for identifying specific DNA mutations. Computational analysis of exome sequencing data was used to make conclusions about copy number variation among common MPM genes. Results show a CDKN2A gene heterozygous deletion in Meso24 cell line. This data is validated by a previous CRISPR-Cas9 outgrowth screen for Meso24 where the knocked-out gene caused increased Meso24 growth.
ContributorsKrdi, Ghena (Author) / Plaisier, Christopher (Thesis director) / Wilson, Melissa (Committee member) / School of Life Sciences (Contributor) / Hugh Downs School of Human Communication (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Analyzing human DNA sequence data allows researchers to identify variants associated with disease, reconstruct the demographic histories of human populations, and further understand the structure and function of the genome. Identifying variants in whole genome sequences is a crucial bioinformatics step in sequence data processing and can be performed using multiple approaches. To investigate the consistency between different bioinformatics methods, we compared the accuracy and sensitivity of two genotyping strategies, joint variant calling and single-sample variant calling. Autosomal and sex chromosome variant call sets were produced by joint and single-sample calling variants for 10 female individuals. The accuracy of variant calls was assessed using SNP array genotype data collected from each individual. To compare the ability of joint and single-sample calling to capture low-frequency variants, folded site frequency spectra were constructed from variant call sets. To investigate the potential for these different variant calling methods to impact downstream analyses, we estimated nucleotide diversity for call sets produced using each approach. We found that while both methods were equally accurate when validated by SNP array sites, single-sample calling identified a greater number of singletons. However, estimates of nucleotide diversity were robust to these differences in the site frequency spectrum between call sets. Our results suggest that despite single-sample calling’s greater sensitivity for low-frequency variants, the differences between approaches have a minimal effect on downstream analyses. While joint calling may be a more efficient approach for genotyping many samples, in situations that preclude large sample sizes, our study suggests that single-sample calling is a suitable alternative.
ContributorsHowell, Emma (Co-author) / Wilson, Melissa (Thesis director) / Stone, Anne (Committee member) / Phung, Tanya (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
In most bird species, females disperse prior to their first breeding attempt, while males remain close to the place they were hatched for their entire lives (Greenwood and Harvey (1982)). Explanations for such female bias in natal dispersal have focused on the potential benefits that males derive from knowing the local environment to establish territories, while females search for suitable mates (Greenwood (1980)). However, the variables shaping dispersal decisions appear more complex (Mabry et al. (2013), Végvári et al. (2018)). There are a number of different variables that could act as a driving force behind dispersal including the social mating system, food competition, inbreeding avoidance, predation, and others. Here, we investigate whether females are the dispersing sex in great-tailed grackles, which have a mating system where the males hold territories and the females choose which territory to place their nest in (Johnson et al. (2000)). We used genetic approaches to identify sex biases in the propensity to disperse. In the experiment, we found that the male grackles were less related to each other while the female grackles were more related to each other. Building on that, the average distance between closely related individuals of the male group was longer than the average distance of closely related females. But, the mantel correlograms for the males and females both lack a consistent trend. Overall, the results indicated suggest that the males are the dispersing sex while the females are potentially philopatric and that the average dispersal distance for the grackle is greater than 2000 meters, the size of the sampling range used in the experiment. These results will inform our long-term study on the relationship between behavioral flexibility and rapid geographic range expansion by elucidating which individuals are likely to experience similar conditions across their lives, and which are likely to face new conditions when they become breeders.
ContributorsSevchik, August L (Author) / Langergraber, Kevin (Thesis director) / Logan, Corina (Committee member) / College of Integrative Sciences and Arts (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05