Genetics and Genomics Commons^™

The Role Of The Bps Immunity Repressor In The Regulation Of Pathogenic Mycobacterium Chelonae Gene Expression, Emma Freeman

Honors College

Mycobacterium tuberculosis is the leading cause of death by an infectious disease (MacNeil, 2019). In 2018, 10 million people developed tuberculosis and half a million infections were resistant to antibiotics (WHO, 2019). Nearly all members of the M. tuberculosis complex are lysogens, meaning they carry prophage, or integrated viral genomes within the host genome (Fan et al., 2016). The non-pathogenic vaccine strain (M. bovis Bacillus Calmette–Guérin (BCG)) is the exception, which suggests prophage play a role in virulence (Fan et al., 2016). Because not all prophage encode obvious virulence genes, we hypothesize that prophage impact bacterial virulence by altering ...

Construction Of A Target-Specific Crispr-Cas9 Vector For The Purpose Of Introducing Mutations Into The Fum1 Gene Of Fusarium Verticillioides, Jennifer Petsche

Honors Program Theses

In molecular biology, CRISPR-Cas9 is a useful gene editing tool that takes advantage of a powerful cleaving enzyme and DNA sequences found in prokaryotes. In this study, a target-specific CRISPR-Cas9 vector containing an RNA-guided Cas9 nuclease specific for the FUM1 gene was constructed for the purpose of introducing mutations into the FUM1 gene of Fusarium verticillioides. Plasmids pFC332 and pFC334 were isolated. A guide RNA sequence was designed and amplified using Polymerase Chain Reaction (PCR) with pFC334 as the template. Sticky ends were created through restriction enzyme digestion of pFC332. These pieces were combined using Uracil-Specific Excision Reagent (USER) fusion ...

Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster

University Scholar Projects

Flower color plays an important role in pollinator discrimination and speciation. Understanding the genetic contributions to flower color differences between two closely related species, Mimulus cardinalis and Mimulus parishii, can improve understanding of how they developed different pollination syndromes and diverged from a recent common ancestor. M. cardinalis is hummingbird-pollinated and has large, bright red flowers while M. parishii is self-pollinated and has small, pale pink flowers. An F2 hybrid population between these two species was created to establish a platform for analysis of the genetic architecture controlling the differences in anthocyanin pigmentation. Statistical analysis of anthocyanin concentration distribution in ...

Liver Transcriptomic Analysis After Short- And Long-Term Feeding Of Soy Protein Isolate And Its Ability To Reduce Liver Steatosis In Obese Zucker Rats, Melisa Kozaczek

Theses and Dissertations

According to the Centers for Disease Control and Prevention (CDC) the prevalence of obesity in adults in the United States during 2017-2018 was a 42.4%, a high number considering all the risks factors associated with this disorder, such as cardiovascular disease, insulin resistance, diabetes type 2, and fatty liver disease, among others. Fatty liver disease is the accumulation of lipids in the liver that can account for more than 5 to 10% of the liver’s weight. There are two types of fatty liver disease, alcoholic fatty liver disease (AFLD), and non-alcoholic fatty liver disease (NAFLD). AFLD is the ...

Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin

Theses and Dissertations

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population ...

Haplotype-Based Genome-Wide Association Studies For Carcass And Growth Traits In Chicken, Hui Zhang, Lin-Yong Shen, Zi-Chun Xu, Luke M. Kramer, Jia-Qiang Yu, Xin-Yang Zhang, Wei Na, Li-Li Yang, Zhi-Ping Cao, Peng Luan, James M. Reecy, Hui Li

Animal Science Publications

There have been several genome-wide association study (GWAS) reported for carcass, growth, and meat traits in chickens. Most of these studies have been based on single SNPs GWAS. In contrast, haplotype-based GWAS reports have been limited. In the present study, 2 Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) and genotyped with the chicken 60K SNP chip were used to perform a haplotype-based GWAS. The lean and fat chicken lines were selected for abdominal fat content for 11 yr. Abdominal fat weight was significantly different between the 2 lines; however, there was no difference for body ...

Optimization Of Rt-Qpcr Protocols To Quantify Chua Gene Expression In Campylobacter Jejuni Mutants Under Iron-Limited Conditions, Jacob D. Wilbert

Chancellor’s Honors Program Projects

No abstract provided.

Identifying The Link Between Non-Coding Regulatory Rnas And Phenotypic Severity In A Zebrafish Model Of Gmppb Dystroglycanopathy, Grace Smith

Honors College

Muscular Dystrophy (MD) is characterized by varying severity and time-of-onset by individuals afflicted with the same forms of MD, a phenomenon that is not well understood. MD affects 250,000 individuals in the United States and is characterized by mutations in the dystroglycan complex. gmppb encodes an enzyme that glycosylates dystroglycan, making it functionally active; thus, mutations in gmppb cause dystroglycanopathic MD1 . The zebrafish (Danio rerio) is a powerful vertebrate model for musculoskeletal development and disease. Like human patients, gmppb mutant zebrafish present both mild and severe phenotypes. In order to understand the molecular mechanisms involved, we performed high-throughput RNA ...

Phenotypic Variability Among Patients With D4z4 Reduced Allele Facioscapulohumeral Muscular Dystrophy, Lucia Ruggiero, Rossella Tupler

Open Access Articles

Importance: Facioscapulohumeral muscular dystrophy (FSHD) is considered an autosomal dominant disorder, associated with the deletion of tandemly arrayed D4Z4 repetitive elements. The extensive use of molecular analysis of the D4Z4 locus for FSHD diagnosis has revealed wide clinical variability, suggesting that subgroups of patients exist among carriers of the D4Z4 reduced allele (DRA).

Objective: To investigate the clinical expression of FSHD in the genetic subgroup of carriers of a DRA with 7 to 8 repeat units (RUs).

Design, Setting, and Participants: This multicenter cross-sectional study included 422 carriers of DRA with 7 to 8 RUs (187 unrelated probands and 235 ...

Evolutionary And Ecological Determinism Of Host Specificity In Arthropod Parasites, Joseph Levey

UCARE Research Products

Understanding why some diseases infect more species than others is crucial for predicting where and when disease will spread, which can inform the management of wildlife, agriculture, and human health. Currently, large scale patterns of host-parasite dynamics are being studied to understand where to look for and how to manage emerging human diseases (Leroy 2005; Benelli 2018). Previous research has used the Global Mammal Parasite Database (GMPD) to look at host breadth—the number and diversity of species a pathogen can infect—for various groups of parasites, e.g. helminths, arthropods, fungi, etc., from a host-centric perspective (Stephens et al ...

An Analysis Of Crispr-Cas Gene Editing In Agriculture, Ashley Laliberte

Honors Scholar Theses

The CRISPR-Cas system is a promising form of gene editing, especially for the agriculture industry. The ability to make single-nucleotide edits within a gene of interest, without the need to introduce foreign DNA, is a powerful tool for designing healthier and more efficient crops and food animals. This system provides opportunity for increased nutritional value, decreased food waste, and more economically and environmentally sustainable food production. Though this biotechnology is facing mechanistic limitations due to off-target effects and inefficient homology-directed repair, vast improvements have already been made to improve its efficacy. The CRISPR-Cas system is already the most advanced form ...

The Coordinate Actions Of Calcineurin And Hog1 Mediate The Stress Response Through Multiple Nodes Of The Cell Cycle Network, Cassandra M. Leech, Mackenzie J. Flynn, Heather E. Arsenault, Jianhong Ou, Haibo Liu, Lihua Julie Zhu, Jennifer A. Benanti

Open Access Articles

Upon exposure to environmental stressors, cells transiently arrest the cell cycle while they adapt and restore homeostasis. A challenge for all cells is to distinguish between stress signals and coordinate the appropriate adaptive response with cell cycle arrest. Here we investigate the role of the phosphatase calcineurin (CN) in the stress response and demonstrate that CN activates the Hog1/p38 pathway in both yeast and human cells. In yeast, the MAPK Hog1 is transiently activated in response to several well-studied osmostressors. We show that when a stressor simultaneously activates CN and Hog1, CN disrupts Hog1-stimulated negative feedback to prolong Hog1 ...

Sars-Cov-2 Receptor Ace2 Is An Interferon-Stimulated Gene In Human Airway Epithelial Cells And Is Detected In Specific Cell Subsets Across Tissues, Carly G. K. Ziegler, Yuming Cao, Zhiru Guo, Jennifer P. Wang, Robert W. Finberg, Manuel Garber, Alex K. Shalek, Jose Ordovas-Montanes, Hca Lung Biological Network

COVID-19 Publications by UMMS Authors

There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung ...

Transcriptomic Profiling Reveals Extraordinary Diversity Of Venom Peptides In Unexplored Predatory Gastropods Of The Genus Clavus, Aiping Lu, Maren Watkins, Qing Li, Samuel D. Robinson, Gisela P. Concepcion, Mark Yandell, Zhiping Weng, Baldomero M. Olivera, Helena Safavi-Hemami, Alexander E. Fedosov

Open Access Articles

Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis, and two specimens of Cv. davidgilmouri were analyzed, leading to ...

Genetic Studies Of Wildlife, Brittaney L. Buchanan

Dissertations & Theses in Natural Resources

Genetic techniques are being more frequently used to understand the biology and management of wildlife species. The wild turkey is one species of genetic interest because the correct identification of individuals to the subspecies level is difficult using traditional methods. Currently phenotypic differences in plumage, especially the upper tail coverts, are used to assign individuals to subspecies. To hunters wanting to complete a “grand slam,” identification of birds’ subspecies is important. This study focuses on the five extant subspecies: Eastern (M. g. silvestris), Osceola (M. g. osceola), Rio Grande (M. g. intermedia), Merriam’s (M. g. merriami), and Gould’s ...

Chemical Modifications Of Adenine Base Editor Mrna And Guide Rna Expand Its Application Scope, Tingting Jiang, Xiao-Ou Zhang, Yueying Cao, Zhiping Weng, Wen Xue

Open Access Articles

CRISPR-Cas9-associated base editing is a promising tool to correct pathogenic single nucleotide mutations in research or therapeutic settings. Efficient base editing requires cellular exposure to levels of base editors that can be difficult to attain in hard-to-transfect cells or in vivo. Here we engineer a chemically modified mRNA-encoded adenine base editor that mediates robust editing at various cellular genomic sites together with moderately modified guide RNA, and show its therapeutic potential in correcting pathogenic single nucleotide mutations in cell and animal models of diseases. The optimized chemical modifications of adenine base editor mRNA and guide RNA expand the applicability of ...

The Covid-19 Pandemic: A Comprehensive Review Of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, And Control, Yosra A. Helmy, Mohamed Fawzy, Ahmed Elaswad, Ahmed Sobieh, Scott P. Kenney, Awad A. Shehata

COVID-19 Publications by UMMS Authors

A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global ...

A Basic Ddradseq Two‐Enzyme Protocol Performs Well With Herbarium And Silica‐Dried Tissues Across Four Genera, Ingrid E. Jordon-Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels

Faculty Journal Articles

Premise

The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica‐dried and herbarium tissue.

Methods

DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed.

Results

Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically ...

Genetic Variance In Flocculin Protein Family, Sarah Dooley, Dale Beach

Student Showcase for Research and Creative Inquiry

Yeast fermentation produces a number of commercially important products, most typically represented by alcoholic beverages. In craft breweries that do not use expensive filtration systems, selecting a yeast variety for fermentation can determine the clarity of the product from hazy Belgian pilsner to a crisp, clear American lager. Flocculation refers to a stress response behavior in yeast to group together (flocculate) in conditions like low sugar or high alcohol content as experienced at the end of fermentation. Higher levels of flocculation increase the clarity. The process of flocculation is genetically controlled through a series of complicated interactions and depends on ...

454— Effects Of Meiotic Drive On Developing Eyestalks In Stalk-Eyed Flies, Karissa Garbarini, Olivia Smith

GREAT Day

Teleopsis dalmanni, commonly known as Stalk-Eyed flies, are known for their sexually dimorphic eye-stalks which females use to pick mates. In the wild, some individuals contain meiotic drive which is known to influence eye-stalk length and sex ratios. Our goal was to identify genes in developing eye tissue that are affected by meiotic drive. We are studying males with drive because they tend to have shorter eye stalks, then we will determine what genes are being disrupted or changed due to meiotic drive being present in that individual. We want to study this because males with shorter eye stalks have ...