Subfamily Clustering Using Label Uncertainty (For Transposable Element Families),
2022
University of Montana, Missoula
Subfamily Clustering Using Label Uncertainty (For Transposable Element Families), Audrey M. Shingleton
Graduate Student Theses, Dissertations, & Professional Papers
Biological sequence annotation is typically performed by aligning a sequence to a database of known sequence elements. For transposable elements, these known sequences represent subfamily consensus sequences. When many of the subfamily models in the database are highly similar to each other, a sequence belonging to one subfamily can easily be mistaken as belonging to another, causing non-reproducible subfamily annotation. Because annotation with subfamilies is expected to give some amount of insight into a sequence’s evolutionary history, it is important that such annotation be reproducible. Here, we present our software tool, SCULU, which builds upon our previously-described methods for computing …
Improving Molecular Diagnosis Of Suspected Mendelian Disorders With Rna Splicing Analysis,
2022
University of Pennsylvania
Improving Molecular Diagnosis Of Suspected Mendelian Disorders With Rna Splicing Analysis, Joseph Krittameth Aicher
Publicly Accessible Penn Dissertations
Exome sequencing is the most advanced standard-of-care genetic test for people with suspected Mendelian disorders. Yet, the diagnostic rate of exome sequencing is only 31%. RNA sequencing (RNA-seq) is a promising molecular test for detecting potentially pathogenic changes in RNA splicing as part of obtaining a molecular diagnosis. In this dissertation, I develop new computational tools and perform analyses towards improving how we detect these potentially pathogenic changes in RNA splicing with the goal of improving the molecular diagnostic rate. First, in Chapter 1, I review background on how we diagnose patients and how RNA splicing and RNA-seq could be …
Evaluación De La Posible Existencia Biológica De Proteínas A Partir De Secuencias De Arns Generados Por Modelamiento Computacional Pseudoaleatorio,
2022
Universidad de La Salle, Bogotá
Evaluación De La Posible Existencia Biológica De Proteínas A Partir De Secuencias De Arns Generados Por Modelamiento Computacional Pseudoaleatorio, Joan Sebastián Gutiérrez Sánchez, Andrés Reinaldo Chacón Prada
Biología
Las proteínas son biomoléculas fundamentales para el funcionamiento de los sistemas biológicos, por lo que entender como surgen y evolucionan es de gran interés teórico. Algunos autores consideran que el origen de las proteínas se dio por el ordenamiento aleatorio de secuencias polipeptídicas; por este motivo el objetivo de este trabajo es inferir si el proceso de creación de secuencias de ARN mensajeros es de carácter estocástico, mediante el diseño y programación de un código computacional en Python que genera secuencias de ARN de manera pseudoaleatoria; posteriormente, se tradujeron las secuencias de ARN obtenidas a aminoácidos para poder realizar un …
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy,
2022
University of Montana, Missoula
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont
Graduate Student Theses, Dissertations, & Professional Papers
Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …
Estimating Weighted Panel Sizes For Primary Care Providers: An Assessment Of Clustering And Novel Methods Of Panel Size Estimation On Electronic Medical Records,
2022
Virginia Commonwealth University
Estimating Weighted Panel Sizes For Primary Care Providers: An Assessment Of Clustering And Novel Methods Of Panel Size Estimation On Electronic Medical Records, Martin A. Lavallee
Theses and Dissertations
Primary Care is on the frontlines of healthcare, thus they see the most diverse set of patients. In order to achieve high functioning primary care, a practice must establish empanelment, the pairing of patients to providers. Enumeration of empanelment, or estimating panel sizes, helps ensure that the demands of the patients demand the supply of providers and optimize the balance of primary care resources to improve quality of care. Further we can adjust panel sizes by using patient-level data on healthcare utilization and complexity extracted from the electronic medial record to determine the amount of care or burden of work …
Bioinformatic Pipeline For Determining Terminal Repeats In The Human Cytomegalovirus Genome Assembled With Pacbio Long Read Sequences,
2022
Virginia Commonwealth University
Bioinformatic Pipeline For Determining Terminal Repeats In The Human Cytomegalovirus Genome Assembled With Pacbio Long Read Sequences, Ahmed Al Qaffas
Theses and Dissertations
Human Cytomegalovirus (HCMV) is a member of the betaherpesvirinae subfamily of the Herpesvirus family. HCMV infection is common among adults worldwide, with an estimated seroprevalence of 66 to 95%, depending on the geographic region (Zuhair et al., 2019). Although most of the virus genomic content has been studied extensively, the terminal repeating region sequences remain understudied. Two main challenges hindered the study of the region: a) limitations of sequencing technologies; and b) misassembly of the repeats due to its complex nature. Here I show a novel bioinformatics pipeline that takes advantage of PacBio's long reads to resolve the challenges mentioned …
Identifying The Human Homologs Of Yeast Rab Proteins Ypt10 & Ypt11 And A Global-Scale Louse Endosymbiont Genome Variation,
2022
Virginia Commonwealth University
Identifying The Human Homologs Of Yeast Rab Proteins Ypt10 & Ypt11 And A Global-Scale Louse Endosymbiont Genome Variation, Nathaniel P. Smith
Theses and Dissertations
Amyotrophic lateral sclerosis (ALS) is a late-onset fatal neurodegenerative disease that causes loss of upper and/or lower motor neurons, and currently has no treatment or cure available. Over 90% of cases occur spontaneously with unknown causes, highlighting the complexity of the disease, and only 10% of cases are linked to heritable genetic mutations. Numerous ALS-linked genes are conserved through evolution, and model organisms may therefore provide opportunities to understand disease pathology at a molecular or cellular level, proving instrumental in identifying therapeutic targets. ALS subtype 8 (ALS8) is caused by an autosomal dominant P56S mutation in the VAPB gene that …
The Isolation And Characterization Of Bacteriophage Hasitha,
2022
Western Kentucky University
The Isolation And Characterization Of Bacteriophage Hasitha, Gillian Brown
Mahurin Honors College Capstone Experience/Thesis Projects
Microbacteriophage Hasitha is a virus that infects Microbacterium foliorum, a bacterium associated with grasses that was first discovered in Germany. Hasitha was isolated from an enriched compost sample and is of particular interest due to its unusual growth pattern. Most bacteriophages require actively growing host cells to produce new phage progeny. However, Hasitha can infect and kill stationary (non-replicating) bacterial cells. We discovered this unusual characteristic through a fortuitous observation of infected lawns that were allowed to incubate in the lab workspace for approximately one month. During this time, a noticeable “halo” grew around the initial site of infection …
Bone Marrow Stroma-Induced Transcriptome Signatures Of Multiple Myeloma As Modulated By Junb,
2022
West Virginia University
Bone Marrow Stroma-Induced Transcriptome Signatures Of Multiple Myeloma As Modulated By Junb, Jasleen Kaur Gandhi
Graduate Theses, Dissertations, and Problem Reports
The bone marrow (BM) microenvironment acts as a breeding ground for drug resistance in multiple myeloma (MM). The interaction with bone marrow stromal cells (BMSCs) confer environment-mediated drug resistance (EMDR) to multiple myeloma. We investigated BM stroma-induced transcriptome signatures of MM cells through a sophisticated analysis of gene expression. In particular, we defined transcription program modulated by JunB, an emerging regulator of MM pathogenesis and a member of the transcription factor superfamily activator protein 1 (AP-1), in response to BM stimulation. The data and results lay down a foundation for future studies to illustrate the regulatory role of JunB in …
Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum,
2022
West Virginia University
Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith
Graduate Theses, Dissertations, and Problem Reports
Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …
Prevotella Phylogeny: Genomic And Molecular Insights Into The Role Of The Human Commensal Prevotella In Cystic Fibrosis,
2022
University of Pennsylvania
Prevotella Phylogeny: Genomic And Molecular Insights Into The Role Of The Human Commensal Prevotella In Cystic Fibrosis, Prioty Ferheen Sarwar
Publicly Accessible Penn Dissertations
The genus Prevotella comprises of a diverse set of gram-negative anaerobes that are implicated in both health and disease. Prevotella is a common human commensal of various anatomic sites but can also be associated with the dysbiotic microbiomes of various chronic inflammatory diseases. Due to it’s association with both commensalism and disease, the role of Prevotella in disease progression is unclear. However, Prevotella has shown immunomodulatory potential, the ability to change the metabolic microenvironment and other cytotoxic phenotypes in both in vitro and in vivo studies. Despite this, Prevotella remains understudied both at the genomic and phenotypic levels. In this …
Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published Papers,
2022
University of Pennsylvania
Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published Papers, David Nicholson
Publicly Accessible Penn Dissertations
Scientific communication is essential for science as it enables the field to grow. This task is often accomplished through a written form such as preprints and published papers. We can obtain a high-level understanding of science and how scientific trends adapt over time by analyzing these resources. This thesis focuses on conducting multiple analyses using biomedical preprints and published papers. In Chapter 2, we explore the language contained within preprints and examine how this language changes due to the peer-review process. We find that token differences between published papers and preprints are stylistically based, suggesting that peer-review results in modest …
Predicting Gene Function Of Unknown Yeast Orfs Through Phylogenetic Comparative Analysis,
2022
Georgia College
Predicting Gene Function Of Unknown Yeast Orfs Through Phylogenetic Comparative Analysis, Lewis Barr
Graduate Research Showcase
Yeast (Saccharomyces cerevisiae) has been an instrumental model system for an extraordinary diverse array of research applications for over a century now. The S. cerevisiae genome was fully sequenced in 1996, and, as a result, 6,753 potential proteins were identified. These putative proteins were established by investigating likely open reading frames within the genome. Over the past few decades, nearly 5,000 open reading frames (ORFs) and their expressed proteins have been described, and the remaining undefined open reading frames are labeled as open reading frames of unknown function (ORFans). To better understand the remaining gaps within the S. …
Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea),
2022
Virginia Commonwealth University
Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea), Tyler A. Hohenstein
Theses and Dissertations
In this study I attempted to further resolve the population genetic structure in the Prothonotary Warbler (Protonotaria citrea), and conducted an outlier SNP analysis and exploratory gene ontology analysis to investigate potential ongoing natural selection in the species. This analysis of population structure confirms previous work by DeSaix et al. (2019), where weak population structure was observed between eastern sites along the Atlantic Coastal Plain, and western sites in the Mississippi Alluvial Valley, possibly due to a genetic discontinuity across the Appalachian Mountains. I conducted two forms of outlier SNP analyses, a principal component analysis (PCA)-based approach to identify SNPs …
Proteome Database,
2022
SUNY Stony Brook
Proteome Database, Mariana Rius, Jackie L. Collier, Joshua Rest
SoMAS Research Data
No abstract provided.
Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy,
2022
South Dakota State University
Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy, Michael Robben
Electronic Theses and Dissertations
Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in …
Radiation Exposure Determination In A Secure, Cloudbased Online Environment,
2022
Cytognomix Inc
Radiation Exposure Determination In A Secure, Cloudbased Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Joan H.M. Knoll, Peter Rogan
Biochemistry Publications
Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI …
From Thermal Springs To Subway Benches: Exploring The Diversity Of Carbon Monoxide Dehydrogenases Through Metagenomes, Phylogenetics, And Machine Learning,
2022
Michigan Technological University
From Thermal Springs To Subway Benches: Exploring The Diversity Of Carbon Monoxide Dehydrogenases Through Metagenomes, Phylogenetics, And Machine Learning, Isaac Bigcraft
Dissertations, Master's Theses and Master's Reports
Carbon monoxide is well known as a toxic gas but can also be an important input and intermediary for microbial metabolisms. Carbon monoxide dehydrogenases (CODHs) serve as key enzyme complexes for a variety of microbial carbon monoxide (CO) utilization pathways. Such pathways include the Wood-Ljungdahl pathway, which is important in methanogenesis and acetogenesis, metal and sulfate reduction pathways, hydrogen production, and others. The CODH enzymes allow microbes to turn the traditionally toxic waste gas of CO into a useful carbon and energy source. Despite the flexibility of CODH enzymes, the use of carbon monoxide is still believed to be a …
Comparative Transcriptomic Analysis Of Cancer Testis Genes In Ovarian Cancer,
2022
Michigan Technological University
Comparative Transcriptomic Analysis Of Cancer Testis Genes In Ovarian Cancer, Zayne Knuth
Dissertations, Master's Theses and Master's Reports
Cancer testis genes are common targets for the development of immunotherapy for cancer treatment. Ovarian cancer is one of the leading causes of death in women cancer patients. Cancer testis genes play a role in tumorigenesis, but it is not clear how these genes are activated. This study utilized differential expression analysis between The Cancer Genome Atlas (TCGA) ovarian cancer data, Genotype-Tissue Expression (GTEx) non-cancerous ovary and testis data, and cell line data to identify a list of cancer testis genes that have a novel expression profile. To identify ovarian cancer testis genes, we obtained normal ovary tissue data and …
Evolutionary Conservation Of The Dream Subcomplex Muvb,
2022
Michigan Technological University
Evolutionary Conservation Of The Dream Subcomplex Muvb, Spencer Snider
Dissertations, Master's Theses and Master's Reports
As the publications of annotated genomes from species representing most domains of life continue to grow exponentially, we are gaining more insight into how proteins, cellular pathways, and protein complexes evolved. We are interested in understanding how each protein in the 8-subunit transcriptional repressor complex called DREAM interacts with each other. DREAM is comprised of 3 main components: an E2F-DP transcription factor heterodimer, a pocket protein, and the highly conserved 5-subunit subcomplex called MuvB. We hypothesize that the mechanism of DREAM’s formation on chromatin dictates how DREAM functions to turn off target gene expression. Unfortunately, many interaction surfaces remain unknown, …
