2020-2021 Senior Honors Theses
Permanent URI for this collectionhttps://hdl.handle.net/10657/8168
This collection contains theses produced by Class of 2021 Honors students
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Browsing 2020-2021 Senior Honors Theses by Department "Biology and Biochemistry, Department of"
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Item A Study of Cis-Regulatory Sequences Of Wnt1 in the Disease Osteogenesis Imperfecta(2021-05) Dalibalta, Maria SaadWnt1 is known to be mutated in the inherited cases of the disease Osteogenesis Imperfecta, a bone genetic disorder also known as the brittle bone disease. The canonical Wnt signaling pathway has a known role in bone homeostasis and development and studies have shown that wnt1, an evolutionarily conserved member of the Wnt signaling pathway, is particularly important for the Wnt canonical pathway in osteoblast differentiation. This suggests a potential role of wnt1 in bone homeostasis. Understanding the regulation of wnt1 expression by cis-regulatory elements during development is important to understand the role it plays in bone development and homeostasis. This project uses ATAC seq (Assay for Transposase-Accessible Chromatin) datasets available to the public to study regions within and surrounding the wnt1 gene to find open chromatin regions, as this is associated with enhancer activity. The enhancers that are shown to be active are studied closely using the ENCODE project to obtain information on the expression profiles of the enhancers and the tissue in which they may be active. The activity of the enhancers was compared in tissues where wnt1-signaling is known to be important: hindbrain tissue, adipose tissue, and bone marrow macrophage and two enhancers with the highest activity were identified. By knowing these cis-regulatory sequences of wnt1, now it could be easier to possibly use wnt1 expression as a therapeutic target in the disease Osteogenesis Imperfecta.Item An Analysis of Errors and Discrepenices in Analyzing Single Cell RNA Sequence Data(2021-05) Modi, Paulomi SanjaykumarSingle-cell RNA sequencing (scRNA-seq) is an extremely vital sequencing technology that has enabled High-throughput mapping of cellular differentiation hierarchies. scRNA-seq has excellent sequencing potential with a wide range of applications beyond regular transcriptome profiling. scRNA-seq process involves analyzing data using 3' end counting technology, which involves sample composition and analytical processing including pre-processing, normalization, alignment and clustering. In order to accomplish this task bioinformaticians around the world have developed many computational tools. As of 2019, there exist 385 different tools that can be used to analyze scRNA-seq data, and that number is growing. Although this continuous addition of new features to single-cell data analysis confronts technical gaps with bulk RNA-seq, there have been very few attempts to standardize these practices. This study explores the various approaches to re-analyze previously published single cell RNA-cell sequencing data and discusses subsequent challenges to utilize publicly available data sets to conduct a multicenter study. Considering the differences in data publication formats, there are several methods that can be employed. 1) Analyzing BCL files 2) Analyzing FASTQ files 3) Analyzing matrix files 4) Analyzing Seurat or ScanPy objects. This thesis provides a concise overview of some of the steps, algorithms, and approaches that are currently used in the analysis of single-cell RNA-sequencing data, with an emphasis on recent developments. Hence, I propose that in order to develop reproducible algorithms and analysis software for scRNA-seq data sets, it is vital that standardization across all analysis platform exist and the software developers recognize and understand the computational challenges posed by the analysis tasks.Item Sex Determination in Xenopus laevis Tadpoles and Effects of Sexual Dimorphism on Traumatic Brain Injury(2021-05) Khan, DaniaThis paper aims to create a standard sex determination method of Xenopus laevis tadpoles at a stage in which gonadogenesis is not yet complete however, sexual differentiation is ongoing. The methods are comprised of using tadpole tail snips, isolating DNA, conducting PCR based on six different sex-related gene identified in this paper, and then using gel electrophoresis to observe the presence of each gene within the Xenopus laevis tadpoles by observing presence of correlating band patterns on the gel. This project is meant to be utilized in terms of identifying the sex of the tadpole subjects later used in Traumatic Brain Injury experiments (courtesy of Sydnee Spruiell) to be able to observe sexual dimorphism of tadpoles upon experiencing traumatic brain injuries. Of the six sex related genes: dmrt1.L, dmrt1.S, dmw, capn5Z, ccdc69W, and scanW, the results convey that ccdc69W and scanW are the most reliable indicators of sex determination. Both genes are highly likely (r=0.80) to be present together and if expression is tested and presence is observed then the corresponding tadpole can be identified as a female. The Edema Accumulation Experiment is conducted by measuring brain water content of tadpoles after a traumatic brain injury. The results implied that while both male and female tadpoles had undergone similar percentages of water content gain, the male tadpoles had a higher level of water accumulation because their water content levels at baseline are higher to begin with than in females.