Genetics and Genomics Commons^™

Bison Influences On Composition And Diversity Of Riparian Plant Communities In Yellowstone National Park, J. Boone Kauffman, Dian Lyn Cummings, Cimarron Kauffman, Robert L. Beschta, Jeremy Brooks, Keeley Macneill, William J. Ripple

Aspen Bibliography

Riparian zones are among the most biologically diverse ecosystems in the Intermountain West, USA, and provide valuable ecosystem services, including high rates of biotic productivity, nutrient processing, and carbon storage. Thus, their sustainability is a high priority for land managers. Large ungulates affect composition and structure of riparian/stream ecosystems through herbivory and physical effects, via trailing and trampling. Bison (Bison bison) in Yellowstone National Park (YNP) have been characterized as "ecosystem engineers" because of their demonstrated effects on phenology, aboveground productivity of grasses, and woody vegetation structure. Bison have greatly increased in numbers during the last two decades …

Molecular Diagnosis Of Non X-Linked Ectodermal Dysplasias Using Next Generation Sequencing, Eman Abdelalim Rabie

Theses and Dissertations

Ectodermal Dysplasias (EDs) are rare heterogenous monogenic developmental disorders sharing the impairment of at least two surface ectoderm-derived organs. Symptoms characteristically manifest developmental abnormalities of the teeth, and three skin derivatives: hair follicles, nails, and sweat glands. The disease-causing gene was identified for only fewer than half of 160 characterized ED phenotypes. Expectedly, ED-causing genes regulate or function in ectodermal-developmental processes. The most common phenotype is hypohidrotic ED featuring teeth agenesis, and diminished or complete absence of hair and sweat production. Disease-causing variants of EDA, EDAR, EDARADD and WNT10A genes were identified in 60-90% of ED patients in …

Neuroprotective Effects Of Green Tea (Camellia Sinensis) And Broccoli (Brassica Oleracea) Extracts In An In Vitro Model Of Multiple Sclerosis, Sara Taha Fathallah

Theses and Dissertations

Multiple Sclerosis (MS) is a neurodegenerative autoimmune disease in which the immune system attacks the central nervous system (CNS) resulting in demyelination. Currently, there is no specific treatment for MS. Here, we propose testing the neuroprotective potential of Green tea (Camellia sinensis), and Broccoli (Brassica oleracea) extracts in an in vitro model of multiple sclerosis.

Methods and Results: Green tea and Broccoli plant extracts were analyzed with GC-MS and tested for their neuroprotective effects in an in vitro MS model using Cuprizone (CPZ) on the Human neuroblastoma SH-SY5Y cell line. Cell viability assays proved the safety of the extracts …

Directed Carbapenemase Testing Is No Longer Just For Enterobacterales: Cost, Labor, And Workflow Assessment Of Expanding Carbapenemase Testing To Carbapenem-Resistant P. Aeruginosa, Fred C. Tenover, Christian M. Gill, Poonam Rajkotia, Amity L. Roberts, David P. Nicolau

Biology Faculty Publications

Molecular carbapenem-resistance testing, such as for the presence of carbapenemases genes, is commonly implemented for the detection of carbapenemase-producing Enterobacterales. Carbapenemase-producing P. aeruginosa is also associated with significant morbidity and mortality, although; prevalence may be underappreciated in the United States due to a lack of carbapenemase testing. The present study sought to compare hands-on time, cost and workflow implementation of carbapenemase gene testing in Enterobacterales and P. aeruginosa isolates versus sending out isolates to a public health laboratory (PHL) for testing to assess if in-house can provide actionable results. The time to carbapenemase gene results were compared. Differences in cost …

Paternal Ages And Genetic Diseases And Congenital Anomalies, Neda Hamood

The Pegasus Review: UCF Undergraduate Research Journal

he purpose of this research is to investigate the link between Advanced Paternal Ages (APA) (i.e., APA ≥ 35 years and APA ≥ 50 years) and genetic diseases and congenital anomalies. Currently, the relationship between both APA and genetic diseases and congenital anomalies remains unclear. There is room for improvement, however, to investigate systematically the relationship between specific congenital anomalies in newborns and APA. More recently, the link between APA (as opposed to existing studies analyzing Advanced Maternal Age alone) and genetic diseases has been recognized by researchers, epidemiologists, and various health experts. Thus, this study serves to examine the …

Novel Data-Driven Approaches To Elucidate Interactions Between Soybean And Phytopthora Sojae, Thivanka Sandaruwan Ratnayake

Student Theses and Dissertations

Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora stem and root rot (PSR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PSR has entailed host genetic resistance (i.e., vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes complicated by climate instability necessitates the development of novel technologies for the attenuation of PSR in field environments. Therefore, the objective of the present study was …

Periconceptual Maternal Nutrition Affects Fetal Liver Programming Of Energy- And Lipid-Related Genes, Wellison J. S. Diniz, Alison K. Ward, Kacie L. Mccathy, Cierrah J. Kassetas, Friederike Baumgaertner, Lawrence P. Reynolds, Pawel P. Borowicz, Kevin K. Sedivec, James D. Kirsch, Sheri T. Dorsam, Tammi L. Neville, J. Chris Forcherio, Ronald Scott, Joel S. Caton, Carl R. Dahlen

Department of Animal Science: Faculty Publications

During pregnancy, the fetus relies on the dam for its nutrient supply. Nutritional stimuli during fetal organ development can program hepatic metabolism and function. Herein, we investigated the role of vitamin and mineral supplementation (VTM or NoVTM—at least 71 days pre-breeding to day 83 of gestation) and rate of weight gain (low (LG) or moderate (MG)—from breeding to day 83) on the fetal liver transcriptome and the underlying biological pathways. Crossbred Angus beef heifers (n = 35) were randomly assigned to one of four treatments in a 2 × 2 factorial design (VTM_LG, VTM_MG, NoVTM_LG, and NoVTM_MG). Gene expression …

The Clinical And Genetic Spectrum Of Autosomal-Recessive Tor1a-Related Disorders, Afshin Saffari, Tracy Lau, Homa Tajsharghi, Ehsan Ghayoor Karimiani, Ariana Kariminejad, Stephanie Efthymiou, Giovanni Zifarelli, Tipu Sultan, Mehran Beiraghi Toosi, Shahnaz Ibrahim

Department of Paediatrics and Child Health

In the field of rare diseases, progress in molecular diagnostics led to the recognition that variants linked to autosomal-dominant neurodegenerative diseases of later onset can, in the context of biallelic inheritance, cause devastating neurodevelopmental disorders and infantile or childhood-onset neurodegeneration. TOR1A-associated arthrogryposis multiplex congenita 5 (AMC5) is a rare neurodevelopmental disorder arising from biallelic variants in TOR1A, a gene that in the heterozygous state is associated to torsion dystonia-1 (DYT1 or DYT-TOR1A), an early-onset dystonia with reduced penetrance. While 15 individuals with TOR1A-AMC5 have been reported (less than 10 in detail), a systematic investigation of the full disease-associated spectrum has …

Standing Genetic Variation As A Potential Mechanism Of Novel Cave Phenotype Evolution In The Freshwater Isopod, Asellus Aquaticus, Lizet R. Rodas, Serban M. Sarbu, Raluca Bancila, Devon Price, Žiga Fišer, Meredith E. Protas

Natural Sciences and Mathematics | Faculty Scholarship

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F2 crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the …

Population Dynamics Of A Long-Term Selection Experiment In White Plymouth Rock Chickens Selected For Low Or High Body Weight, S. J. Harrison, P. B. Siegel, C. F. Honaker, Ronald M. Lewis

Department of Animal Science: Faculty Publications

The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selection horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 individuals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was available. Inbreeding (F …

Additional Taxonomic Refinements Suggested By Genomic Analysis Of Butterflies, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Paul A. Opler, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Comparative analyses of genomic data reveal further insights into the phylogeny and taxonomic classification of butterflies presented here. As a result, 2 new subgenera and 2 new species of Hesperiidae are described: Borna Grishin, subgen. n. (type species Godmania borincona Watson, 1937) and Lilla Grishin, subgen. n. (type species Choranthus lilliae Bell, 1931) of Choranthus Scudder, 1872, Cecropterus (Murgaria) markwalkeri Grishin, sp. n. (type locality in Mexico: Sonora), and Hedone yunga Grishin, sp. n. (type locality in Bolivia: Yungas, La Paz). The lectotype is designated for Aethilla toxeus Plötz, 1882. The type locality of Dion uza (Hewitson, 1877) is likely …

Evaluation Of Gross Energy Concentration Of Neutral Detergent Fiber Contained In Feed And Fecal Samples, J. D. Stypinski, Paul J. Kononoff, W. P. Weiss

Department of Animal Science: Faculty Publications

Starch and NDF are usually assumed to contain the same concentration of gross energy (GE), but NDF is more variable in chemical composition and varies more in the extent of digestion. The variable chemical composition of NDF may have direct implications on dairy nutrition models that predict dietary GE and use this estimate for also predicting digestible energy. For example, when NDF is enriched in lignin and protein, the concentration of GE would increase, whereas NDF enriched in ash would have the opposite effect. Current nutritional models, such as the NASEM (2021) and CNCPS (6.55), assume a GE coefficient of …

Gasdermin D Deficiency In Vascular Smooth Muscle Cells Ameliorates Abdominal Aortic Aneurysm Through Reducing Putrescine Synthesis, Jianing Gao, Yanghui Chen, Huiqing Wang, Xin Li, Ke Li, Yangkai Xu, Xianwei Xie, Yansong Guo, Nana Yang, Xinhua Zhang, Dong Ma, Hong S. Lu, Ying H. Shen, Yong Liu, Jifeng Zhang, Y. Eugene Chen, Alan Daugherty, Dao Wen Wang, Lemin Zheng

Saha Cardiovascular Research Center Faculty Publications

Abdominal aortic aneurysm (AAA) is a common vascular disease associated with significant phenotypic alterations in vascular smooth muscle cells (VSMCs). Gasdermin D (GSDMD) is a pore-forming effector of pyroptosis. In this study, the role of VSMC-specific GSDMD in the phenotypic alteration of VSMCs and AAA formation is determined. Single-cell transcriptome analyses reveal Gsdmd upregulation in aortic VSMCs in angiotensin (Ang) II-induced AAA. VSMC-specific Gsdmd deletion ameliorates Ang II-induced AAA in apolipoprotein E (ApoE)−/− mice. Using untargeted metabolomic analysis, it is found that putrescine is significantly reduced in the plasma and aortic tissues of VSMC-specific GSDMD deficient mice. High putrescine levels …

De Novo Transcriptome Assembly From The Nodal Root Growth Zone Of Hydrated And Water-Deficit Stressed Maize Inbred Line Fr697, Sidharth Sen, Shannon K. King, Tyler Mccubbin, Laura A. Greeley, Rachel A. Mertz, Cheyenne Becker, Nicole Niehues, Shuai Zeng, Jonathan T. Stemmle, Scott C. Peck, Melvin J. Oliver, Felix B. Fritschi, David M. Braun, Robert E. Sharp, Trupti Joshi

Biomedical Sciences

Certain cultivars of maize show increased tolerance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaptation, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697‑specific RNA‑Seq datasets were generated and used for a de novo transcriptome assembly to characterize any genotype‑specific genetic features. The assembly was aided by an Iso‑Seq library of transcripts …

Clic And Membrane Wound Repair Pathways Enable Pandemic Norovirus Entry And Infection, B. Vijayalakshmi Ayyar, Khalil Ettayebi, Wilhelm Salmen, Umesh C. Karandikar, Frederick H. Neill, Victoria R. Tenge, Sue E. Crawford, Erhard Bieberich, B. V. Venkataram Prasad, Robert L. Atmar, Mary K. Estes

Markey Cancer Center Faculty Publications

Globally, most cases of gastroenteritis are caused by pandemic GII.4 human norovirus (HuNoV) strains with no approved therapies or vaccines available. The cellular pathways that these strains exploit for cell entry and internalization are unknown. Here, using nontransformed human jejunal enteroids (HIEs) that recapitulate the physiology of the gastrointestinal tract, we show that infectious GII.4 virions and virus-like particles are endocytosed using a unique combination of endosomal acidification-dependent clathrin-independent carriers (CLIC), acid sphingomyelinase (ASM)-mediated lysosomal exocytosis, and membrane wound repair pathways. We found that besides the known interaction of the viral capsid Protruding (P) domain with host glycans, the Shell …

Genetic Effect On Body Mass Index And Cardiovascular Disease Across Generations, Josée Dupuis

Faculty, Staff and Student Publications

BACKGROUND: Whether genetics contribute to the rising prevalence of obesity or its cardiovascular consequences in today's obesogenic environment remains unclear. We sought to determine whether the effects of a higher aggregate genetic burden of obesity risk on body mass index (BMI) or cardiovascular disease (CVD) differed by birth year.

METHODS: We split the FHS (Framingham Heart Study) into 4 equally sized birth cohorts (birth year before 1932, 1932 to 1946, 1947 to 1959, and after 1960). We modeled a genetic predisposition to obesity using an additive genetic risk score (GRS) of 941 BMI-associated variants and tested for GRS-birth year interaction …

Genetic Determinants Involved In Acquisition Of Iron In The Opportunistic Pathogen Mycobacterium Abscessus, Manal F. Farhat

Dissertations, Theses, and Capstone Projects

The opportunistic pathogen Mycobacterium abscessus subsp. abscessus (Mab) has become an emerging public health threat due to the increasing number of Mab-associated chronic pulmonary disease cases. Infection cure rates are only 50% due to the complex resistance of Mab to most antimicrobial drugs and chemotherapy.

Deeper knowledge of Mab biology is needed to illuminate potential candidates for development of improved therapeutics against Mab infections. The ESX-3 type VII protein secretion system of Mab plays an important role in host inflammatory and pathological responses during infection.

In this study, we demonstrate a functional link between the ESX-3 secretion …

American Eel (Anguilla Rostrata) And Other Fishes As Surveyed By Environmental Dna In The Bronx River And Hudson River Watershed, Sam C. Chin

Dissertations, Theses, and Capstone Projects

Mounting an effective response to the threats faced by freshwater fish may require expansions to aquatic biomonitoring in excess of what is feasible using the capture-based survey techniques currently relied upon by natural resource managers. Methods for analyzing environmental DNA (eDNA) are emerging as a minimally invasive and cost-effective approach for surveying fish and other organisms. By detecting taxon-specific DNA sequences recovered from environmental samples (e.g. water, sediment), eDNA methods are able to infer species presence from samples that can be collected rapidly with simple equipment. In many cases, eDNA detection rates of fish species have been shown to meet …

Displaying And Delivering Viral Membrane Antigens Via Ww Domain–Activated Extracellular Vesicles, Sengjin Choi, Zhiping Yang, Qiyu Wang, Zhi Qiao, Maoyun Sun, Joshua Wiggins, Shi-Hua Xiang, Quan Lu

Nebraska Center for Virology: Faculty Publications

Membrane proteins expressed on the surface of enveloped viruses are conformational antigens readily recognized by B cells of the immune system. An effective vaccine would require the synthesis and delivery of these native conformational antigens in lipid membranes that preserve specific epitope structures. We have created an extracellular vesicle–based technology that allows viral membrane antigens to be selectively recruited onto the surface of WW domain–activated extracellular vesicles (WAEVs). Budding of WAEVs requires secretory carrier-associated membrane protein 3, which through its proline-proline-alanine-tyrosine motif interacts with WW domains to recruit fused viral membrane antigens onto WAEVs. Immunization with influenza and HIV viral …

Displaying And Delivering Viral Membrane Antigens Via Ww Domain–Activated Extracellular Vesicles, Sengjin Choi, Zhiping Yang, Qiyu Wang, Zhi Qiao, Maoyun Sun, Joshua Wiggins, Shi-Hua Xiang, Quan Lu

Nebraska Center for Virology: Faculty Publications

Membrane proteins expressed on the surface of enveloped viruses are conformational antigens readily recognized by B cells of the immune system. An effective vaccine would require the synthesis and delivery of these native conformational antigens in lipid membranes that preserve specific epitope structures. We have created an extracellular vesicle–based technology that allows viral membrane antigens to be selectively recruited onto the surface of WW domain–activated extracellular vesicles (WAEVs). Budding of WAEVs requires secretory carrier-associated membrane protein 3, which through its proline-proline-alanine-tyrosine motif interacts with WW domains to recruit fused viral membrane antigens onto WAEVs. Immunization with influenza and HIV viral …