Genomics Commons^™

Genomic Characterization Of Enterococcus Spp Infecting Chicken Embryo, Aishat Olaoluwa Lawal

Graduate Theses and Dissertations

Chicken embryo mortality has been attributed to bacterial infections and can lead to a decline in hatchability, posing potential losses in the broiler industry. This study aims to investigate the vertical transmission of specific bacterial pathogens from breeder hens to subsequent broiler flocks through MGEs and their association with host specificity. In our sampling of 360 eggs from a broiler flock, we isolated various Enterococcus species, including E. gallinarum and E. faecalis, from incubated egg yolks or aborted embryos. E. avium was found in unincubated bad yolks. Other species like Streptococcus, Lactobacillus, and Bacillus were observed but presumed to be …

The Genomics Of Champ1: Insights Into Their Cell-Type Specificity And Developmental Trajectories, Zoe Marie Van Caugherty

MUSC Theses and Dissertations

Chromosome alignment maintaining phosphoprotein 1(CHAMP1) is a gene that encodes a zinc finger protein that is involved in in the maintenance of kinetochore-microtubule attachment and regulating chromosome segregation in mitosis. (Itoh et al., 2011) CHAMP1 mutations have been shown to be major risk factors for neurodevelopmental disorders (NDDs) and autism spectrum disorder (ASD).(Asakura et al., 2021; Isidor et al., 2016; Levy et al., 2022) Although there is information on the link between CHAMP1 mutations and NDD, the role of CHAMP1 in regulating processes of human cortical development, namely, neurogenesis, proliferation, and electrophysiological properties of newly born neurons, is unknown. This …

Edna Metabarcoding And The Construction Of Primers For The Identification Of Gulf Of Mexico Elasmobranchs And Selachii, Isabella Lima

Honors Projects

eDNA, or environmental DNA, is found free-existing in any environment. It can be extracted from its environment and used to identify organisms that were recently in the area. In recent years, eDNA metabarcoding has been used to help examine communities for overall species presence and biodiversity. This capstone sought to create a mock proposal for an eDNA survey of Gulf of Mexico elasmobranch and Selachii species due to their overall decline in numbers. Additionally, general and discriminatory PCR primers were created in-silico and assessed for initial quality. This capstone documents the feasibility of an eDNA study, constructing the necessary primers, …

Tissue-Specific Atlas Of Trans-Models For Gene Regulation Elucidates Complex Regulation Patterns, Robert Dagostino, Assaf Gottlieb

Faculty, Staff and Student Publications

BACKGROUND: Deciphering gene regulation is essential for understanding the underlying mechanisms of healthy and disease states. While the regulatory networks formed by transcription factors (TFs) and their target genes has been mostly studied with relation to cis effects such as in TF binding sites, we focused on trans effects of TFs on the expression of their transcribed genes and their potential mechanisms.

RESULTS: We provide a comprehensive tissue-specific atlas, spanning 49 tissues of TF variations affecting gene expression through computational models considering two potential mechanisms, including combinatorial regulation by the expression of the TFs, and by genetic variants within the …

Enhancement Of Applied Rice Breeding Programs: Exploring Factors Impacting Genomic Selection Accuracy And Discovery Of A Novel Gene For Grain Shape, Maria G. Montiel

LSU Doctoral Dissertations

Plant breeding is a crucial tool in addressing global challenges such as climate change, population growth, and the need for more resilient crops. Rice serves as a staple food for a significant portion of the global population and has served as a model crop for genetic and genomic studies. Genomic selection (GS) has become valuable tool in plant breeding, allowing breeders to predict breeding lines’ performance based on their genotypes. The training (TS) set is a central component of genomic selection and the optimization of the training set is crucial for efficient implementation of genomic selection. The first two objectives …

"The Relevant History And Medical And Ethical Future Viability Of Xenotransplantation", Morgan Janes

Augustana Center for the Study of Ethics Essay Contest

Xenotransplantation, the transplantation of organs or tissues from one species to another, presents a complex nexus of medical, ethical, and cultural considerations. In this article, we delve into the multifaceted landscape of xenotransplantation, beginning with a thorough examination of its relevant historical trajectory. From early experiments to recent advancements, we chart the evolution of this field, setting the stage for a nuanced discussion. We then confront the central issue: the true medical viability of xenotransplantation and the looming specter of operative risk. By scrutinizing the ethical dilemmas inherent in xenotransplantation through a multicultural lens, we illuminate the diverse perspectives that …

Nodal Variants Are Associated With A Continuum Of Laterality Defects From Simple D-Transposition Of The Great Arteries To Heterotaxy, Zain Dardas, Jawid M Fatih, Angad Jolly, Moez Dawood, Haowei Du, Christopher M Grochowski, Edward G Jones, Shalini N Jhangiani, Xander H T Wehrens, Pengfei Liu, Weimin Bi, Eric Boerwinkle, Jennifer E Posey, Donna M Muzny, Richard A Gibbs, James R Lupski, Zeynep Coban-Akdemir, Shaine A Morris

Faculty, Staff and Student Publications

BACKGROUND: NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects.

METHODS: We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with …

Rainwater Harvesting Systems Metagenomics, Jade Riddle, Julia Parsons

Spring Showcase for Research and Creative Inquiry

Climate change induced water scarcity has led to an increasing interest in non-traditional water sources such as rainwater. However, there are lingering health and safety concerns due to the lack of research into the microbial communities contained within collection systems. To address this gap, water samples were collected from rain barrels around northern Virginia for microbial analysis. Each microbe within the sample has a unique genome subject to DNA testing. Environmental DNA was prepared from the collected water samples. To characterize the microbial community, both targeted sequencing and whole genome sequencing approaches were used. Using targeted sequencing of the 16s …

Population Genomics Provide Insight Into Ancestral Relationships And Diversity Of The Feral Horses Of Theodore Roosevelt National Park, Melissa A. Thompson, Blake E. Mccann, Turk Rhen, Rebecca Simmons

Biology Faculty Publications

Theodore Roosevelt National Park (TRNP) manages a herd of feral horses (Equus caballus) which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, …

Genome-Wide Crispr Screen Reveals The Synthetic Lethality Between Bcl2l1 Inhibition And Radiotherapy, Ling Yin, Xiaoding Hu, Guangsheng Pei, Mengfan Tang, You Zhou, Huimin Zhang, Min Huang, Siting Li, Jie Zhang, Citu Citu, Zhongming Zhao, Bisrat G Debeb, Xu Feng, Junjie Chen

Faculty, Staff and Student Publications

Radiation therapy (RT) is one of the most commonly used anticancer therapies. However, the landscape of cellular response to irradiation, especially to a single high-dose irradiation, remains largely unknown. In this study, we performed a whole-genome CRISPR loss-of-function screen and revealed temporal inherent and acquired responses to RT. Specifically, we found that loss of the IL1R1 pathway led to cellular resistance to RT. This is in part because of the involvement of radiation-induced IL1R1-dependent transcriptional regulation, which relies on the NF-κB pathway. Moreover, the mitochondrial anti-apoptotic pathway, particularly the BCL2L1 gene, is crucially important for cell survival after radiation. BCL2L1 …

Grb2 Stabilizes Rad51 At Reversed Replication Forks Suppressing Genomic Instability And Innate Immunity Against Cancer, Zu Ye, Shengfeng Xu, Yin Shi, Xueqian Cheng, Yuan Zhang, Sunetra Roy, Sarita Namjoshi, Michael A Longo, Todd M Link, Katharina Schlacher, Guang Peng, Dihua Yu, Bin Wang, John A Tainer, Zamal Ahmed

Faculty, Staff and Student Publications

Growth factor receptor-bound protein 2 (GRB2) is a cytoplasmic adapter for tyrosine kinase signaling and a nuclear adapter for homology-directed-DNA repair. Here we find nuclear GRB2 protects DNA at stalled replication forks from MRE11-mediated degradation in the BRCA2 replication fork protection axis. Mechanistically, GRB2 binds and inhibits RAD51 ATPase activity to stabilize RAD51 on stalled replication forks. In GRB2-depleted cells, PARP inhibitor (PARPi) treatment releases DNA fragments from stalled forks into the cytoplasm that activate the cGAS-STING pathway to trigger pro-inflammatory cytokine production. Moreover in a syngeneic mouse metastatic ovarian cancer model, GRB2 depletion in the context of PARPi treatment …

Identifying Environmental And Genetic Risk Factors Of Diseases In Case-Control Studies, Siting Li

Dartmouth College Ph.D Dissertations

In response to the increasing efforts in disease prevention and treatment, this thesis applies statistical methods to investigate environmental and genetic risk factors associated with two diseases: bladder cancer and amyotrophic lateral sclerosis (ALS). For bladder cancer, we investigated the association between toenail metal mixture and bladder cancer risk, along with gene expression levels associated with bladder cancer risk. For ALS, our investigation involves identifying genetic variants and gene expression levels associated with ALS risk and exploring gene-smoking interactions linked to ALS risk.

In chapter two, we developed an adaptive-mixture-categorization (AMC)-based g-computation method combining g-computation with optimized exposure categorization. We …

Sox On Tumors, A Comfort Or A Constraint?, Junqing Jiang, Yufei Wang, Mengyu Sun, Xiangyuan Luo, Zerui Zhang, Yijun Wang, Siwen Li, Dian Hu, Jiaqian Zhang, Zhangfan Wu, Xiaoping Chen, Bixiang Zhang, Xiao Xu, Shuai Wang, Shengjun Xu, Wenjie Huang, Limin Xia

Faculty, Staff and Student Publications

The sex-determining region Y (SRY)-related high-mobility group (HMG) box (SOX) family, composed of 20 transcription factors, is a conserved family with a highly homologous HMG domain. Due to their crucial role in determining cell fate, the dysregulation of SOX family members is closely associated with tumorigenesis, including tumor invasion, metastasis, proliferation, apoptosis, epithelial-mesenchymal transition, stemness and drug resistance. Despite considerable research to investigate the mechanisms and functions of the SOX family, confusion remains regarding aspects such as the role of the SOX family in tumor immune microenvironment (TIME) and contradictory impacts the SOX family exerts on tumors. This review summarizes …

The Hsp90-Myc-Cdk9 Network Drives Therapeutic Resistance In Mantle Cell Lymphoma, Fangfang Yan, Vivian Jiang, Alexa Jordan, Yuxuan Che, Yang Liu, Qingsong Cai, Yu Xue, Yijing Li, Joseph Mcintosh, Zhihong Chen, Jovanny Vargas, Lei Nie, Yixin Yao, Heng-Huan Lee, Wei Wang, Johnnelson R Bigcal, Maria Badillo, Jitendra Meena, Christopher Flowers, Jia Zhou, Zhongming Zhao, Lukas M Simon, Michael Wang

Faculty, Staff and Student Publications

Brexucabtagene autoleucel CAR-T therapy is highly efficacious in overcoming resistance to Bruton's tyrosine kinase inhibitors (BTKi) in mantle cell lymphoma. However, many patients relapse post CAR-T therapy with dismal outcomes. To dissect the underlying mechanisms of sequential resistance to BTKi and CAR-T therapy, we performed single-cell RNA sequencing analysis for 66 samples from 25 patients treated with BTKi and/or CAR-T therapy and conducted in-depth bioinformatics™ analysis. Our analysis revealed that MYC activity progressively increased with sequential resistance. HSP90AB1 (Heat shock protein 90 alpha family class B member 1), a MYC target, was identified as early driver of CAR-T resistance. CDK9 …

Recent Progress And Perspectives On Development Of Gene Editing Tools, Zixian Liu, Chengping Li, Gogo Jun-Jie Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

The gene editing field has witnessed remarkable advancements in recent years, leading to the establishment and refinement of multidimensional gene editing platforms. These innovations have enabled precise targeted gene knockout, repair, and insertion. These tools have stimulated significant progress in fundamental research, therapeutics, agriculture, environment protection, and industrial applications. In this review, we provide a comprehensive overview of the milestones in gene editing tool development and offer perspectives on potential future directions for this rapidly evolving field.

Research On Innovative Development Path And Policy Guarantee Of China’S Synthetic Biology Industry, Hongjun Geng, Chang Wang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Synthetic biology is hailed as the third revolution in life sciences after the discovery of the DNA double helix structure and genomic technology, and is the core driving force for the leapfrog development of next-generation biomanufacturing and the future bioeconomy, opening up an opportunity window for the reshaping of the global manufacturing map. How to strategically position the synthesis biology industry and seize the strategic high ground in the industry is a core topic of interest for global science and technology powers and manufacturing powers. Based on the identification of problems in the development of China’s synthesis biology industry, this …

Delineating The Mechanism Of Fragility At Bcl6 Breakpoint Region Associated With Translocations In Diffuse Large B Cell Lymphoma, Vidya Gopalakrishnan, Urbi Roy, Shikha Srivastava, Khyati M Kariya, Shivangi Sharma, Saniya M Javedakar, Bibha Choudhary, Sathees C Raghavan

Faculty, Staff and Student Publications

BCL6 translocation is one of the most common chromosomal translocations in cancer and results in its enhanced expression in germinal center B cells. It involves the fusion of BCL6 with any of its twenty-six Ig and non-Ig translocation partners associated with diffuse large B cell lymphoma (DLBCL). Despite being discovered long back, the mechanism of BCL6 fragility is largely unknown. Analysis of the translocation breakpoints in 5' UTR of BCL6 reveals the clustering of most of the breakpoints around a region termed Cluster II. In silico analysis of the breakpoint cluster sequence identified sequence motifs that could potentially fold into …

Computational Analysis Of Cas Proteins Unlocks New Potential In Hiv-1 Targeted Gene Therapy, Will Dampier, Rachel Berman, Michael Nonnemacher, Brian Wigdahl

Kimmel Cancer Center Faculty Papers

Introduction: The human immunodeficiency virus type 1 (HIV-1) pandemic has been slowed with the advent of anti-retroviral therapy (ART). However, ART is not a cure and as such has pushed the disease into a chronic infection. One potential cure strategy that has shown promise is the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas gene editing system. It has recently been shown to successfully edit and/or excise the integrated provirus from infected cells and inhibit HIV-1 in vitro, ex vivo, and in vivo. These studies have primarily been conducted with SpCas9 or SaCas9. However, additional Cas proteins are …

Whole Genome Sequencing For The Millipede Cherokia Georgiana, Elena Cruz, Will Wittstock, Daniel Hastings, Arnab Sengupta, Bruce A. Snyder

Graduate Research Showcase

Out of thousands of known millipede species, only five sequenced genomes of species (in four of sixteen orders) are publicly available. No whole genomes and limited genetic information are available for incredibly diverse families such as Xystodesmidae. Our research goal is to sequence the whole genome of the millipede Cherokia georgiana. A de novo sequence of the complete genome of a North American species will facilitate future research in understanding gene expression under a variety of conditions. Many interesting biological processes in millipedes are poorly described, such as the production of a defensive hydrogen cyanide secretion found in the …

Understanding The Origin Of Parthenogenesis Via Crossing And Crispr Gene Editing In Daphnia Pulex, Thinh Pham

Biology Dissertations - Archive

Daphnia has been used as a key model system for studying ecological changes, evolution, and genomics for the past few decades due to its rapid turnover time in reproduction. The organism possesses two fascinating modes of reproduction: obligate parthenogenesis and cyclical parthenogenesis. This dissertation delves into the intricate reproductive strategies of Daphnia pulex, focusing on hybrid F1s from different reproductive modes. The first aim is to investigate 31 hybrid F1s generated from obligate parthenogenesis (OP) and cyclical parthenogenesis (CP) parental lines. Transcriptomic analysis reveals misexpression patterns and regulatory divergences, highlighting meiosis-related genes like CDC6 as potential parthenogenesis regulators. The …