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Multi-Omics Integration Through Single-Cell Copy Number Analysis In Cancer, Chi-Yun Wu 2022 University of Pennsylvania

Multi-Omics Integration Through Single-Cell Copy Number Analysis In Cancer, Chi-Yun Wu

Publicly Accessible Penn Dissertations

Genetic and epigenetic alterations combine to drive cancer progression. Heterogeneous cell populations within tumors are associated with poor prognosis and outcomes. Copy number aberrations (CNAs), a genetic variant commonly occurring in tumors, are used as markers to detect subclones and reconstruct tumor phylogeny. Multi-omics integration between CNAs and other modalities on tumor subclones facilitates studying the interplay between genome and epigenome, and their effects on transcriptome. So far, there is still a lack of computational methods for the multi-omics integration of different types of single-cell and ST tumor sequencing data. Therefore, the aim of this thesis is to extract (allele-specific) …


Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, Keaun Amani, Vanessa Shivnauth, Christian Castroverde 2022 Wilfrid Laurier University

Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, Keaun Amani, Vanessa Shivnauth, Christian Castroverde

Biology Faculty Publications

Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CAM-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation and diversification in most species remain unclear. Here we have created CBP60-DB, a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs …


Bone Marrow Stroma-Induced Transcriptome Signatures Of Multiple Myeloma As Modulated By Junb, Jasleen Kaur Gandhi 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 …


Identifying The Human Homologs Of Yeast Rab Proteins Ypt10 & Ypt11 And A Global-Scale Louse Endosymbiont Genome Variation, Nathaniel P. Smith 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 …


Environmental Effects On Constructed Wetland Microbial Diversity And Function In The Context Of Wastewater Management, Sandrine Grandmont-Lemire 2022 Cal Poly Humboldt

Environmental Effects On Constructed Wetland Microbial Diversity And Function In The Context Of Wastewater Management, Sandrine Grandmont-Lemire

Cal Poly Humboldt theses and projects

Microbial communities play a crucial role in ecosystems, yet we know little about how microbial diversity influences ecosystem functioning. An important gap in our understanding is how environmental change affects microbial Biodiversity-Ecosystem Function relationships (BEF). These complex interactions between microbial biodiversity and ecosystem function can influence major biogeochemical processes, such as the nitrogen cycle in wetland ecosystems, which play an important role in managing wastewater. To address the effect of biodiversity on function, my study investigates the BEF relationships between microbial diversity and the function in terms of ammonia removal from wastewater at the Arcata Wastewater Treatment Facility (AWTF) both …


Determining Haplotype Specific X Chromosome Inactivation State And Related Epigenetic Features In Female X-Linked Genes, Ariah Dawn Mackie 2022 Cal Poly Humboldt

Determining Haplotype Specific X Chromosome Inactivation State And Related Epigenetic Features In Female X-Linked Genes, Ariah Dawn Mackie

Cal Poly Humboldt theses and projects

Females with heterozygous X-linked mutations are prone to pseudo-haploinsufficiency because random X chromosome inactivation (XCI) silences one of their two X chromosomes. A prior study explored the theory that reactivating the silenced healthy allele could be a treatment for pseudo-haploinsufficient females. The next step was to evaluate this approach in a clinically relevant stem cell model of the rare neurological disease CDKL5 Deficiency Disorder (CDD). It was necessary to validate X-inactivation state with respect to CDKL5 allele expression in one of these models. We explored CDKL5 allele expression in two populations of CDD female patient-derived induced pluripotent stem cells (iPSCs) …


Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith 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 …


Bioinformatic Pipeline For Determining Terminal Repeats In The Human Cytomegalovirus Genome Assembled With Pacbio Long Read Sequences, Ahmed Al Qaffas 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 …


Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea), Tyler A. Hohenstein 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 …


Differential Gene Expression Analysis Of Zebrafish Embryos Exposed To Simulated Microgravity And Insights Into Cellular Effects, Nicholas Lien 2022 San Jose State University

Differential Gene Expression Analysis Of Zebrafish Embryos Exposed To Simulated Microgravity And Insights Into Cellular Effects, Nicholas Lien

Master's Projects

Spaceflight consists of many dangers which adversely affects the health of astronauts through hazards such as microgravity and cosmic radiation. One area that is still poorly understood is how spaceflight impacts human reproductive health. This study aims to shed insight into how microgravity may impact the development of embryos. Differential gene expression analysis was performed via Jupyter Notebook and SLURM scripts and run on SJSU’s HPC server as a method of implementing NASA GeneLab’s RNA-Seq Consensus Pipeline. Data for this project utilized RNA-Seq files for early-stage embryonic zebrafish (Danio rerio), stored under GLDS-373. Gene Set Enrichment Analysis was performed to …


Metagenomic Analysis Of Microbial 18s Eukaryotes Communities And Environmental Factors In The Western Antarctic Peninsula Waters During Austral Summers, Idan Siman-Tov 2022 San Jose State University

Metagenomic Analysis Of Microbial 18s Eukaryotes Communities And Environmental Factors In The Western Antarctic Peninsula Waters During Austral Summers, Idan Siman-Tov

Master's Projects

Little is known about the environmental factors that impact eukaryotic microbial populations in the Western Antarctic Peninsula. Metagenomic and environmental data have been collected over the course of three consecutive austral summers in the Western Antarctic Peninsula off Palmer Station. More than 13 million 18S rRNA eukaryotic sequences have been taxonomically identified and categorized from the Antarctic water samples collected. Here we will investigate the environmental factors that affect eukaryotic organism populations, as well as possible indicator species that could provide insight as to the status of other eukaryotic species. Due to climate change, understanding these factors and identifying status …


Conservation And Prevalence Of Sequence Paired Sites In Humans, Punit Sundar 2022 San Jose State University

Conservation And Prevalence Of Sequence Paired Sites In Humans, Punit Sundar

Master's Projects

The completion of the Human Genome Project in 2003 made it possible to leverage the power of computers to quicken biological discoveries. The human genome contains rich information relevant to the proper functions of cells that is computationally arduous and costly to investigate in a laboratory setting. Specifically, gene expression levels in cells can be impacted when functionally relevant motifs in the DNA are mutated preventing proper transcription factor binding. To study the consequences of such mutations, it is necessary to first identify such functionally relevant regions of the genome using computational approaches. A signaling pathway that is of particular …


A Lims-Less System For Genotyping Data In Marker-Assisted Selection, Alex Rios 2022 San Jose State University

A Lims-Less System For Genotyping Data In Marker-Assisted Selection, Alex Rios

Master's Projects

Climate change and feeding the growing human population are two tightly intertwined problems we face now. Innovations across several agricultural sectors are needed to meet these challenges as we proceed into the future. Seed companies and plant breeders are at the forefront of producing new plant varieties that must survive under the unique stresses of extreme weather patterns caused by changing climates. This project aims to provide breeders with faster marker results by streamlining the data process of marker-assisted selection (MAS). Manually managing genotyping data in MAS can take several hours or days to compile results for breeders. Although some …


The Impact Of Bisphenol A And Its Analogues On Neurodevelopmental Transcriptomes In Drosophila Melanogaster, An Nguyen 2022 San Jose State University

The Impact Of Bisphenol A And Its Analogues On Neurodevelopmental Transcriptomes In Drosophila Melanogaster, An Nguyen

Master's Projects

No abstract provided.


Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published Papers, David Nicholson 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 …


Understanding How The Relative Abundance Of Candida Species Impacts Transcriptional Regulation In Coculture Biofilms, Diksha Kool 2022 San Jose State University

Understanding How The Relative Abundance Of Candida Species Impacts Transcriptional Regulation In Coculture Biofilms, Diksha Kool

Master's Projects

ABSTRACT Candida albicans and Candida glabrata are common fungal species that can change from commensal to pathogen due to their ability to form robust biofilms. Candida species are the leading cause of life-threatening conditions like Candidemia, and the existing treatments for biofilm-related infections are suboptimal. Research shows that the relative abundance of the two Candida species promotes biofilm formation, enhances pathogenicity, and increases antibiotic resistance. Thus, focusing on the importance of coculture, this paper utilizes RNA sequencing to investigate the gene expression leading to biofilm development in coculture through a time-series study.


Mirna-Seq Analysis Pipeline And R Shiny App, Alexis Torres 2022 San Jose State University

Mirna-Seq Analysis Pipeline And R Shiny App, Alexis Torres

Master's Projects

ABSTRACT Thrombosis in the internal jugular vein (IJV) has been identified as a risk factor for astronauts undergoing spaceflight, following a 2019 study in which one astronaut developed a thrombus, and several others experienced stagnant or retrograde blood flow. To better understand this phenomenon, a model that simulates the effects of microgravity on blood flow in the IJV is being developed. mRNA and microRNA NGS sequencing will be used to study the transcriptome of human umbilical vein endothelial cells (HUVEC) in simulated microgravity conditions. A microRNA sequencing (miRNA-seq) pipeline has been developed to quantify the miRNA sequencing results. A graphical …


Comparison Of An Oxford Nanopore Technologies Sequencing Platform To Existing Sequencing Methods For Differential Expression Studies, Nikola Klier 2022 San Jose State University

Comparison Of An Oxford Nanopore Technologies Sequencing Platform To Existing Sequencing Methods For Differential Expression Studies, Nikola Klier

Master's Projects

As the genomics revolution continues, there is constant pressure to make sequencing technology more accessible and practical for a growing series of applications. Existing sequencing technologies are often prohibitively expensive, limiting their use for novel diagnostic and research applications. Additionally, existing technologies are often limited by short read lengths, which may present problems to certain quantitative sequencing applications. One such application is Differential Expression Analysis, in which RNA-Seq is performed in paired samples under different experimental conditions to identify differences in gene expression. In this study, an Oxford Nanopore Technologies sequencing platform was used to conduct a differential expression study …


Mrna-Sequencing Pipeline And Pathway Analysis To Determine The Effects Of Bisphenol A On Fragile X Syndrome In Drosophila Melanogaster, Rashi Raghulan 2022 San Jose State University

Mrna-Sequencing Pipeline And Pathway Analysis To Determine The Effects Of Bisphenol A On Fragile X Syndrome In Drosophila Melanogaster, Rashi Raghulan

Master's Projects

Neurological disorders (NDDs), like Fragile X Syndrome (FXS), are becoming more prevalent. One outstanding question in the field is how genetic risk factors for NDDs, like Fmr1, converge with environmental risk factors like bisphenol A (BPA). Our research compares and contrasts the different molecular impacts of BPA exposure in wild-type and FXS flies using mRNA-sequencing analysis. This analysis identifies the mutation in the Fmr1 gene is shown to have a stronger effect on the Drosophila than the presence of BPA, resulting in significant differential gene expression that perturbed several neurological pathways. Moreover, numerous genes responsible for genetic human diseases have …


An Investigation Of Segmental Duplications Across Topologically Associating Domains, Sara Bell 2022 San Jose State University

An Investigation Of Segmental Duplications Across Topologically Associating Domains, Sara Bell

Master's Projects

High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data. TADs have boundaries disrupted by structural variants (SVs), hypothesized to form due to recombination that occurs between segmental duplications (SDs). Little research is available about the effects of SDs at TAD boundaries. This project aimed to understand the distribution of SDs near TADs and determine any overlap between the two features. We analyzed public data and found SDs to have low breakpoint frequency and coverage at TAD boundaries. We then processed a …


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