Molecular And Systemic Epigenetic Inheritance: Integrating Development, Genetics, And Evolution, Robert Lickliter, David S. Moore

Pitzer Faculty Publications and Research

Currently, a central problem for theoretical biology is the integration of development with genetics and evolutionary theory. Through the late 20^th century, biologists held that animals resemble their ancestors strictly because of the transgenerational transmission of DNA. This view effectively wrote development out of evolutionary biology. However, many molecular and developmental biologists now understand that phenotypes—anatomical, physiological, and behavioral traits—are not determined by genes (i.e., DNA segments) alone; instead, they emerge epigenetically from developmental processes involving co-acting genetic factors, environmental factors, molecular epigenetic factors, and other non-genetic factors within organisms’ bodies. This insight forces a rethinking of biological inheritance. …

Effects Of Depth, Distance To Shore, And Water Velocity On Organismal And Extra-Organismal Environmental Dna Concentrations In A Large River, Dylan Keel

Cal Poly Humboldt theses and projects

Environmental DNA (eDNA) is a sensitive tool for detection of aquatic species and concentrations of eDNA in water samples have been useful for estimating abundance. This study evaluated the effects of depth, distance to shore, and water velocity on the concentration of organismal and extra-organismal eDNA concentrations in the Klamath River, California (basin area ≅ 40,000 km²). At each of six river cross sections 32 water samples were collected, including surface samples and depth samples evenly distributed across the cross section, and eDNA concentrations were determined for the parasite Ceratonova shasta and Chinook salmon, Oncorhynchus tshawytscha, using …

Gene-Educational Attainment Interactions In A Multi-Population Genome-Wide Meta-Analysis Identify Novel Lipid Loci, Lisa De Las Fuentes, Karen L Schwander, Michael R Brown, Amy R Bentley, Thomas W Winkler, Yun Ju Sung, Patricia B Munroe, Clint L Miller, Hugo Aschard, Stella Aslibekyan, Traci M Bartz, Lawrence F Bielak, Jin Fang Chai, Ching-Yu Cheng, Rajkumar Dorajoo, Mary F Feitosa, Xiuqing Guo, Fernando P Hartwig, Andrea Horimoto, Ivana Kolčić, Elise Lim, Yongmei Liu, Alisa K Manning, Jonathan Marten, Solomon K Musani, Raymond Noordam, Sandosh Padmanabhan, Tuomo Rankinen, Melissa A Richard, Paul M Ridker, Albert V Smith, Dina Vojinovic, Alan B Zonderman, Maris Alver, Mathilde Boissel, Kaare Christensen, Barry I Freedman, Chuan Gao, Franco Giulianini, Sarah E Harris, Meian He, Fang-Chi Hsu, Brigitte Kühnel, Federica Laguzzi, Xiaoyin Li, Leo-Pekka Lyytikäinen, Ilja M Nolte, Alaitz Poveda, Rainer Rauramaa, Muhammad Riaz, Antonietta Robino, Tamar Sofer, Fumihiko Takeuchi, Bamidele O Tayo, Peter J Van Der Most, Niek Verweij, Erin B Ware, Stefan Weiss, Wanqing Wen, Lisa R Yanek, Yiqiang Zhan, Najaf Amin, Dan E Arking, Christie Ballantyne, Eric Boerwinkle, Jennifer A Brody, Ulrich Broeckel, Archie Campbell, Mickaël Canouil, Xiaoran Chai, Yii-Der Ida Chen, Xu Chen, Kumaraswamy Naidu Chitrala, Maria Pina Concas, Ulf De Faire, Renée De Mutsert, H Janaka De Silva, Paul S De Vries, Ahn Do, Jessica D Faul, Virginia Fisher, James S Floyd, Terrence Forrester, Yechiel Friedlander, Giorgia Girotto, C Charles Gu, Göran Hallmans, Sami Heikkinen, Chew-Kiat Heng, Georg Homuth, Steven Hunt, M Arfan Ikram, David R Jacobs, Maryam Kavousi, Chiea Chuen Khor, Tuomas O Kilpeläinen, Woon-Puay Koh, Pirjo Komulainen, Carl D Langefeld, Jingjing Liang, Kiang Liu, Jianjun Liu, Kurt Lohman, Reedik Mägi, Ani W Manichaikul, Colin A Mckenzie, Thomas Meitinger, Yuri Milaneschi, Matthias Nauck, Christopher P Nelson, Jeffrey R O'Connell, Nicholette D Palmer, Alexandre C Pereira, Thomas Perls, Annette Peters, Ozren Polašek, Olli T Raitakari, Kenneth Rice, Treva K Rice, Stephen S Rich, Charumathi Sabanayagam, Pamela J Schreiner, Xiao-Ou Shu, Stephen Sidney, Mario Sims, Jennifer A Smith, John M Starr, Konstantin Strauch, E Shyong Tai, Kent D Taylor, Michael Y Tsai, André G Uitterlinden, Diana Van Heemst, Melanie Waldenberger, Ya-Xing Wang, Wen-Bin Wei, Gregory Wilson, Deng Xuan, Jie Yao, Caizheng Yu, Jian-Min Yuan, Wei Zhao, Diane M Becker, Amélie Bonnefond, Donald W Bowden, Richard S Cooper, Ian J Deary, Jasmin Divers, Tõnu Esko, Paul W Franks, Philippe Froguel, Christian Gieger, Jost B Jonas, Norihiro Kato, Timo A Lakka, Karin Leander, Terho Lehtimäki, Patrik K E Magnusson, Kari E North, Ioanna Ntalla, Brenda Penninx, Nilesh J Samani, Harold Snieder, Beatrice Spedicati, Pim Van Der Harst, Henry Völzke, Lynne E Wagenknecht, David R Weir, Mary K Wojczynski, Tangchun Wu, Wei Zheng, Xiaofeng Zhu, Claude Bouchard, Daniel I Chasman, Michele K Evans, Ervin R Fox, Vilmundur Gudnason, Caroline Hayward, Bernardo L Horta, Sharon L R Kardia, Jose Eduardo Krieger, Dennis O Mook-Kanamori, Patricia A Peyser, Michael M Province, Bruce M Psaty, Igor Rudan, Xueling Sim, Blair H Smith, Rob M Van Dam, Cornelia M Van Duijn, Tien Yin Wong, Donna K Arnett, Dabeeru C Rao, James Gauderman, Ching-Ti Liu, Alanna C Morrison, Jerome I Rotter, Myriam Fornage

Faculty, Staff and Student Publications

Introduction: Educational attainment, widely used in epidemiologic studies as a surrogate for socioeconomic status, is a predictor of cardiovascular health outcomes.

Methods: A two-stage genome-wide meta-analysis of low-density lipoprotein cholesterol (LDL), high-density lipoprotein cholesterol (HDL), and triglyceride (TG) levels was performed while accounting for gene-educational attainment interactions in up to 226,315 individuals from five population groups. We considered two educational attainment variables: “Some College” (yes/no, for any education beyond high school) and “Graduated College” (yes/no, for completing a 4-year college degree). Genome-wide significant (p < 5 × 10−8) and suggestive (p < 1 × 10−6) variants were identified in Stage 1 (in up to 108,784 individuals) through genome-wide analysis, and those variants were followed up in Stage 2 studies (in up to 117,531 individuals).

Results: In combined analysis of Stages 1 and 2, we identified 18 novel lipid loci (nine …

Whole Genome Sequence Analysis Of Apparent Treatment Resistant Hypertension Status In Participants From The Trans-Omics For Precision Medicine Program, Nicole D Armstrong, Vinodh Srinivasasainagendra, Farah Ammous, Themistocles L Assimes, Amber L Beitelshees, Jennifer Brody, Brian E Cade, Yii-Der Ida Chen, Han Chen, Paul S De Vries, James S Floyd, Nora Franceschini, Xiuqing Guo, Jacklyn N Hellwege, John S House, Chii-Min Hwu, Sharon L R Kardia, Ethan M Lange, Leslie A Lange, Caitrin W Mcdonough, May E Montasser, Jeffrey R O'Connell, Megan M Shuey, Xiao Sun, Rikki M Tanner, Zhe Wang, Wei Zhao, April P Carson, Todd L Edwards, Tanika N Kelly, Eimear E Kenny, Charles Kooperberg, Ruth J F Loos, Alanna C Morrison, Alison Motsinger-Reif, Bruce M Psaty, Dabeeru C Rao, Susan Redline, Stephen S Rich, Jerome I Rotter, Jennifer A Smith, Albert V Smith, Marguerite R Irvin, Donna K Arnett

Faculty, Staff and Student Publications

Introduction: Apparent treatment-resistant hypertension (aTRH) is characterized by the use of four or more antihypertensive (AHT) classes to achieve blood pressure (BP) control. In the current study, we conducted single-variant and gene-based analyses of aTRH among individuals from 12 Trans-Omics for Precision Medicine cohorts with whole-genome sequencing data.

Methods: Cases were defined as individuals treated for hypertension (HTN) taking three different AHT classes, with average systolic BP ≥ 140 or diastolic BP ≥ 90 mmHg, or four or more medications regardless of BP (n = 1,705). A normotensive control group was defined as individuals with BP < 140/90 mmHg (n = 22,079), not on AHT medication. A second control group comprised individuals who were treatment responsive on one AHT medication with BP < 140/ 90 mmHg (n = 5,424). Logistic regression with kinship adjustment using the Scalable and Accurate Implementation of Generalized mixed models (SAIGE) was performed, adjusting for age, sex, and genetic ancestry. We assessed variants using SKAT-O in rare-variant analyses. Single-variant and gene-based tests were conducted in a pooled multi-ethnicity stratum, as well as self-reported ethnic/racial strata (European and African American).

Results: One variant in …

Whole Genome Sequencing Identifies Structural Variants Contributing To Hematologic Traits In The Nhlbi Topmed Program, Marsha M Wheeler, Adrienne M Stilp, Shuquan Rao, Bjarni V Halldórsson, Doruk Beyter, Jia Wen, Anna V Mihkaylova, Caitlin P Mchugh, John Lane, Min-Zhi Jiang, Laura M Raffield, Goo Jun, Fritz J Sedlazeck, Ginger Metcalf, Yao Yao, Joshua B Bis, Nathalie Chami, Paul S De Vries, Pinkal Desai, James S Floyd, Yan Gao, Kai Kammers, Wonji Kim, Jee-Young Moon, Aakrosh Ratan, Lisa R Yanek, Laura Almasy, Lewis C Becker, John Blangero, Michael H Cho, Joanne E Curran, Myriam Fornage, Robert C Kaplan, Joshua P Lewis, Ruth J F Loos, Braxton D Mitchell, Alanna C Morrison, Michael Preuss, Bruce M Psaty, Stephen S Rich, Jerome I Rotter, Hua Tang, Russell P Tracy, Eric Boerwinkle, Goncalo R Abecasis, Thomas W Blackwell, Albert V Smith, Andrew D Johnson, Rasika A Mathias, Deborah A Nickerson, Matthew P Conomos, Yun Li, Unnur Þorsteinsdóttir, Magnús K Magnússon, Kari Stefansson, Nathan D Pankratz, Daniel E Bauer, Paul L Auer, Alex P Reiner

Faculty, Staff and Student Publications

Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits …

A Framework For Detecting Noncoding Rare-Variant Associations Of Large-Scale Whole-Genome Sequencing Studies, Zilin Li, Xihao Li, Hufeng Zhou, Sheila M Gaynor, Margaret Sunitha Selvaraj, Theodore Arapoglou, Corbin Quick, Yaowu Liu, Han Chen, Ryan Sun, Rounak Dey, Donna K Arnett, Paul L Auer, Lawrence F Bielak, Joshua C Bis, Thomas W Blackwell, John Blangero, Eric Boerwinkle, Donald W Bowden, Jennifer A Brody, Brian E Cade, Matthew P Conomos, Adolfo Correa, L Adrienne Cupples, Joanne E Curran, Paul S De Vries, Ravindranath Duggirala, Nora Franceschini, Barry I Freedman, Harald H H Göring, Xiuqing Guo, Rita R Kalyani, Charles Kooperberg, Brian G Kral, Leslie A Lange, Bridget M Lin, Ani Manichaikul, Alisa K Manning, Lisa W Martin, Rasika A Mathias, James B Meigs, Braxton D Mitchell, May E Montasser, Alanna C Morrison, Take Naseri, Jeffrey R O'Connell, Nicholette D Palmer, Patricia A Peyser, Bruce M Psaty, Laura M Raffield, Susan Redline, Alexander P Reiner, Muagututi'a Sefuiva Reupena, Kenneth M Rice, Stephen S Rich, Jennifer A Smith, Kent D Taylor, Margaret A Taub, Ramachandran S Vasan, Daniel E Weeks, James G Wilson, Lisa R Yanek, Wei Zhao, Jerome I Rotter, Cristen J Willer, Pradeep Natarajan, Gina M Peloso, Xihong Lin

Faculty, Staff and Student Publications

Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate …

Data-Driven Biomarker Panel Discovery In Ovarian Cancer Using Heterogenous Data Fusion On Exosomal And Non-Exosomal Microrna Expression Data, Paritra Mandal

All Dissertations

Ovarian cancer (OC) is an aggressive gynecological cancer and is currently the 5th leading cause of deaths due to cancer in women. High mortality rates are attributable to the vague pathogenesis and asymptomatic nature of the early stages. The development of a liquid biopsy for routine OC screening could help identify the disease at an earlier stage, making treatments more likely to be effective thereby increasing survival rates. Exosomes, small (~100nm) extracellular vesicles present in body fluids, have been shown to contain cancer-progression, onset, and related factors, making them good candidates for use in liquid biopsies. However, to date, only …

Leveraging Pleiotropy To Discover And Interpret Gwas Results For Sleep-Associated Traits, Sung Chun, Sebastian Akle, Athanasios Teodosiadis, Brian E Cade, Heming Wang, Tamar Sofer, Daniel S Evans, Katie L Stone, Sina A Gharib, Sutapa Mukherjee, Lyle J Palmer, David Hillman, Jerome I Rotter, Craig L Hanis, John A Stamatoyannopoulos, Susan Redline, Chris Cotsapas, Shamil R Sunyaev

Faculty, Staff and Student Publications

Genetic association studies of many heritable traits resulting from physiological testing often have modest sample sizes due to the cost and burden of the required phenotyping. This reduces statistical power and limits discovery of multiple genetic associations. We present a strategy to leverage pleiotropy between traits to both discover new loci and to provide mechanistic hypotheses of the underlying pathophysiology. Specifically, we combine a colocalization test with a locus-level test of pleiotropy. In simulations, we show that this approach is highly selective for identifying true pleiotropy driven by the same causative variant, thereby improves the chance to replicate the associations …

Identification Of Quantitative Trait Loci (Qtls) For Resistance To Bacterial Leaf Streak: Xanthomonas Translucens Using Qtl And Association Mapping In Three Populations Of Soft Red Winter Wheat, Benjamin Tyler Meritt

LSU Doctoral Dissertations

Bacterial leaf streak (BLS) and black chaff, caused by Xanthomonas translucens pv. undulosa (Xtu), can be a very destructive disease of wheat, especially in the warmer, wetter areas of the Southeastern U.S. Yield losses of up to 40 percent have been recorded in some cases in southern wheat growing regions. With no effective agronomic or chemical method of disease control, identification of genetic resistance is seen as a promising solution. Three soft red winter wheat populations (GAWN, ARK-SNP, and AGS 2060- AGS 2035 DH) representative of soft red winter wheat germplasm in the southeastern U.S. developed by …

Identification And Characterization Of Epicuticular Proteins Of Nematodes Sharing Motifs With Cuticular Proteins Of Arthropods, Bruno Betschart, Marco Bisoffi, Ferial Alaeddine

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Specific collagens and insoluble proteins called cuticlins are major constituents of the nematode cuticles. The epicuticle, which forms the outermost electron-dense layer of the cuticle, is composed of another category of insoluble proteins called epicuticlins. It is distinct from the insoluble cuticlins localized in the cortical layer and the fibrous ribbon underneath lateral alae. Our objective was to identify and characterize genes and their encoded proteins forming the epicuticle. The combination between previously obtained laboratory results and recently made available data through the whole-genome shotgun contigs (WGS) and the transcriptome Shotgun Assembly (TSA) sequencing projects of Ascaris suum allowed us …

Radiation Exposure Determination In A Secure, Cloud-Based Online Environment, Ben C. Shirley, Eliseos J. Mucaki, 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 …

The Effect Of Infection Risk On Female Blood Transcriptomics, Brenna M. G. Gormally, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Defenses against pathogens can take on many forms. For instance, behavioral avoidance of diseased conspecifics is widely documented. Interactions with these infectious conspecifics can also, however, lead to physiological changes in uninfected animals, an effect that is much less well understood. These changes in behavior and physiology are particularly important to study in a reproductive context, where they can impact reproductive decisions and offspring quality. Here, we studied how an acute (3 h) exposure to an immune-challenged male affected female blood transcriptomics and behavior. We predicted that females paired with immune-challenged males would reduce eating and drinking behaviors (as avoidance …

Genetic Variations Mir-10aa>T, Mir-30ca>G, Mir-181at>C, And Mir-499ba>G And The Risk Of Recurrent Pregnancy Loss In Korean Women, Hui-Jeong An, Sung-Hwan Cho, Han-Sung Park, Ji-Hyang Kim, Young-Ran Kim, Woo-Sik Lee, Jung-Ryeol Lee, Seong-Soo Joo, Eun-Hee Ahn, Nam-Keun Kim

Faculty, Staff and Student Publications

This study investigated the genetic association between recurrent pregnancy loss (RPL) and microRNA (miRNA) polymorphisms in miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G in Korean women. Blood samples were collected from 381 RPL patients and 281 control participants, and genotyping of miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G was carried out by TaqMan miRNA RT-Real Time polymerase chain reaction (PCR). Four polymorphisms were identified, including miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G. MiR-10a dominant model (AA vs. AT + TT) and miR-499bGG genotypes were associated with increased RPL risk (adjusted odds ratio [AOR] = …

Comparative Risks Of Initial Aortic Events Associated With Genetic Thoracic Aortic Disease, Ellen S Regalado, Shaine A Morris, Alan C Braverman, Ellen M Hostetler, Julie De Backer, Ruosha Li, Reed E Pyeritz, Anji T Yetman, Elena Cervi, Sherene Shalhub, Richmond Jeremy, Scott Lemaire, Maral Ouzounian, Arturo Evangelista, Catherine Boileau, Guillaume Jondeau, Dianna M Milewicz

Faculty, Staff and Student Publications

BACKGROUND: Pathogenic variants in 11 genes predispose individuals to heritable thoracic aortic disease (HTAD), but limited data are available to stratify the risk for aortic events associated with these genes.

OBJECTIVES: This study sought to compare the risk of first aortic event, specifically thoracic aortic aneurysm surgery or an aortic dissection, among 7 HTAD genes and variant types within each gene.

METHODS: A retrospective cohort of probands and relatives with rare variants in 7 genes for HTAD (n = 1,028) was assessed for the risk of first aortic events based on the gene altered, pathogenic variant type, sex, proband status, …

Prenatal And Pregnancy Loss Evaluation By Noninvasive Screening And Diagnostic Genetic Testing, Abigail Haggerty

Theses & Dissertations

Noninvasive prenatal testing (NIPT) utilizing cell-free fetal DNA (cffDNA) in the maternal blood is the screening test of choice for physicians today. NIPT depends on the amount of cffDNA in the maternal blood, called the fetal fraction (FF). Researchers are investigating the implications of the FF value in reference to multiple variables in pregnancy outcome, including the risk for aneuploidy and maternal factors that influence the FF.

Diagnostic techniques utilized in patient care include cytogenetics, fluorescence in-situ hybridization (FISH), and microarray. Diagnostic testing is critical to confirm or rule out genetic abnormalities among women with abnormal screening results, …

Evaluating Non-Invasive Environmental Methods For Detecting Tropical African Pangolin Species To Inform Conservation Actions, Ichu Godwill Ichu

Theses and Dissertations

Tropical African pangolin species are threatened throughout their range due to habitat loss and illegal take. Limited knowledge on distribution has rendered conservation efforts challenging. Methods commonly used for other wildlife species need to be tested for each pangolin species as each has variable ecologies requiring specific detection and monitoring techniques. This thesis evaluates the efficacy of two non-invasive environmental methods for detecting tropical African pangolin species, and consists of two complementary studies; a proof of concept study using soil sourced eDNA from a white-bellied pangolin enclosure in the Columbus Zoo, Ohio, to detect the species, and a field study …

Clinical And Molecular Characterization Of Key Features Of Phelan-Mcdermid Syndrome And Potential Approaches To Clinical Trials, Bridgette Moffitt

All Dissertations

Phelan-McDermid Syndrome (PMS) is a rare neurodevelopmental disorder that involves chromosomal abnormalities on 22q13.3 and pathogenic variants with the SHANK3 gene. SHANK3 encodes for a critical scaffolding protein that is important in post-synaptic density, function, and maintenance of excitatory synapses. Haploinsufficiency of SHANK3 is considered the major cause of the neurological phenotype of PMS. These studies focused on further characterizing the neurologic phenotype of sleep disturbances in individuals with PMS.

Sleep disturbances are a common feature of PMS, however there is little research available on the subject matter. We reviewed the literature on sleep disturbances and used the Phelan-McDermid Syndrome …

Chromosome Number Evolution, Phylogeography, And The Effects Of Climate Change On Species Distributions In Polyploid Plant Systems, Courtney H. Babin

LSU New Orleans Theses and Dissertations

Polyploidy, a term used to describe organisms with cells having more than two paired sets of chromosomes, is a significant driver of diversification among land plants. Over a century of research has advanced our understanding of polyploidization in some taxa, but polyploid organisms remain understudied. In this dissertation, I investigate chromosome number evolution, phylogeographic structure, genetic differentiation, and the effects of climate change on ploidy level distribution using polyploid plant systems. In the first chapter, I inferred a molecular phylogeny of Allium, an economically important genus that includes cultivated crops and ornamentals, to investigate evolutionary transitions in chromosome number …

Roles Of Oxidative Stress And Dna Methylation In Cigarette Smoking-Induced Accelerated Acute Myeloid Leukemia Progression, Mary Figueroa

Dissertations and Theses (Open Access)

Acute myeloid leukemia (AML) is a commonly diagnosed cancer in smokers. When current or former smokers have AML, they have worse survival compared to never smoking patients. This has been observed clinically for decades, but then it is unknown how smoking leads to worsened AML survival. Smoking causes oxidative stress and altered DNA methylation that persists for decades in peripheral blood mononuclear cells, but these changes from smoking have not been evaluated in the context of AML. We hypothesize that smoking-induced molecular changes, including altered DNA methylation associated with poor AML prognosis, promote AML. We developed a novel model to …

Genetic Protocols For Dna Extraction From White-Tailed Deer Cast Antlers To Confirm Individuality, Zach Carter, Brian C. Peterson, Casey W. Schoenebeck, Kimberly A. Carlson

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

White-tailed deer (Odocoileus virginianus) are the most sought-after deer species in America. The antlers of mammals, such as deer, are one of the fastest regenerative tissues in the world and are grown and naturally cast every year. Research on cast antlers have been used for a variety of purposes including population comparisons and impacts of deer health due to climatic stressors. When investigating cast antlers, it is important to confirm individuality of match sets in addition to antlers of the same individual between years. Therefore, individuality must be confirmed genetically, and protocols must be developed and established to …

Top-Ld: A Tool To Explore Linkage Disequilibrium With Topmed Whole-Genome Sequence Data, Le Huang, Jonathan D Rosen, Quan Sun, Jiawen Chen, Marsha M Wheeler, Ying Zhou, Yuan-I Min, Charles Kooperberg, Matthew P Conomos, Adrienne M Stilp, Stephen S Rich, Jerome I Rotter, Ani Manichaikul, Ruth J F Loos, Eimear E Kenny, Thomas W Blackwell, Albert V Smith, Goo Jun, Fritz J Sedlazeck, Ginger Metcalf, Eric Boerwinkle, Laura M Raffield, Alex P Reiner, Paul L Auer, Yun Li

Faculty, Staff and Student Publications

Current publicly available tools that allow rapid exploration of linkage disequilibrium (LD) between markers (e.g., HaploReg and LDlink) are based on whole-genome sequence (WGS) data from 2,504 individuals in the 1000 Genomes Project. Here, we present toP-LD, an online tool to explore LD inferred with high-coverage (∼30×) WGS data from 15,578 individuals in the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. toP-LD provides a significant upgrade compared to current LD tools, as the toPMed WGS data provide a more comprehensive representation of genetic variation than the 1000 Genomes data, particularly for rare variants and in the specific populations that we …

Association Study Between Mucin 4 (Muc4) Polymorphisms And Idiopathic Recurrent Pregnancy Loss In A Korean Population, Ji-Hyang Kim, Han-Sung Park, Jeong-Yong Lee, Eun-Ju Ko, Young-Ran Kim, Hee-Young Cho, Woo-Sik Lee, Eun-Hee Ahn, Nam-Keun Kim

Faculty, Staff and Student Publications

Recurrent pregnancy loss (RPL) is the loss of two or more consecutive pregnancies before 20 weeks of gestational age. Our study investigated whether mucin 4 (MUC4) polymorphisms are associated with RPL. MUC polymorphisms (rs882605 C>A, rs1104760 A>G, rs2688513 A>G, rs2258447 C>T, and rs2291652 A>G) were genotyped in 374 women with RPL and 239 controls of Korean ethnicity using polymerase chain reaction-restriction fragment length polymorphism analysis and the TaqMan probe SNP genotyping assay. Differences in genotype frequencies between cases of RPL and the controls were compared. MUC4 rs882605 C>A and rs1104760 A>G polymorphisms were …

Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos

Electronic Theses and Dissertations

Given the diversity and complexity within immunoglobulin (IG) loci, effective mouse models first require characterization of intra-strain differences and construction of high-quality reference assemblies for IG loci in several representative strains. To understand light chain germline diversity across biomedically significant mouse strains, we profiled the expressed IGK and IGL repertoires of 18 commonly used laboratory mouse strains using AIRR-seq. Across strains, we observed germline IGKV sequences shared by three different IGK haplotypes and a more conserved IGLV germline repertoire among common laboratory strains. Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing was used to sequence and assemble bacterial artificial chromosomes (BAC) …

Invisible Disabilities, Academic Capital And Competitiveness Of Genetic Counseling Applicants, Natalie E. Stoner, Meagan Choates, Carla Mcgruder, Debra Murray, Theresa Wittman, Sara Wofford, Claire N. Singletary

Dissertations and Theses (Open Access)

The field of genetic counseling has historically lacked diversity. Recent research has begun to explore how visible diversity may present barriers to a genetic counseling applicant becoming competitive, but has not yet characterized potential barriers with invisible diversities, such as being a first-generation college student, or a part of the LBGTQ+ community. Therefore, this study aimed to address this gap among those with invisible diversities, as well as explore their academic capital (AC), a theoretical framework used to identify factors that make students more likely to succeed in post-secondary work including supportive networks, trustworthy information, family uplift, college knowledge, overcoming …

The Synthesis And Purification Methodology Of An Intermolecular Pyrophosphate Sensor: Applications For The Quantitative Polymerase Chain Reaction, Ethan Gevedon

Honors Projects

The optimized synthesis and purification methodology for an intermolecular pyrophosphate sensor scaffold molecule was performed: high performance liquid chromatography afforded the scaffold in excellent purity and yield. The applications of the sensor assembly in the quantitative polymerase chain reaction were discussed, and preliminary results show that

Liquid Biopsies For Type 2 Diabetes Mellitus: Biomarkers For Disease Risk And Diagnosis, Stephanie Chidester

Dissertations

Background: Type 2 diabetes mellitus (T2DM) has reached epidemic proportions in the United States. There is a critical need for earlier and more effective screening and diagnostic tools. Innovative liquid biopsy technologies may play a key role in meeting this need. Liquid biopsies are a non-invasive, adjunctive tool for determining diagnosis, prognosis, and therapeutic response. This dissertation focuses on two potential applications of liquid biopsy technologies to T2DM: (1) epigenome-wide association studies to identify epigenetic markers of risk for T2DM, and (2) extracellular vesicle (EV)-based biomarker studies to identify and detect markers associated with T2DM development and progression. Dissertation studies: …

An Overview Of The Forensic Analysis And Use Of Non-Human Dna, Kaelyn Long

Senior Honors Theses

DNA is present in every living organism on Earth. DNA is also present in a few non-living biological agents such as DNA-containing viruses, and is additionally unique to particular groups of organisms and often even to individuals. This characteristic allows DNA to be quite useful in forensic investigations. This study takes an in-depth look at the forensic use of non-human DNA. DNA analysis is a key component of many forensic investigations, but the majority of these analyses are focused on human DNA. This review examines the ways in which non-human DNA can be useful to forensic investigations. The various unique …

Determining Some Quality Properties Of Oat Genotypes Collected From The Middle And West Black Sea Region, Zeki Mut, Hasan Akay, Ozge Doganay Erbas Kose, Ismail Sezer

The Philippine Agricultural Scientist

Healthy foodstuffs, including functional foods, are the key component of a healthy and prosperous life. Oat grains are rich in protein, soluble dietary fiber, β-glucan, starch, oil, some vitamins and minerals, and thus accepted as a healthy foodstuff. This study was conducted to determine physical and chemical quality traits of many different oat landraces/cultivars. In this study, 251 local oat genotypes, collected from 10 provinces of Western and Middle Black Sea Regions of Turkey and four standard oat cultivars were grown over the experimental fields of the Agricultural Application and Research Center at Samsun Ondokuz Mayıs University for two years …

Cpf1-Based Crispr Genome Editing In The Cyanobacterium N. Punctiforme, Soohan Woo

University of the Pacific Theses and Dissertations

CRISPR systems have been growing in their utility and their application throughout the biological field as researchers continue to grow in their understanding of the relatively novel genome editing technology. However, despite the potential of CRISPR as a genome editing tool, the complexity of applying this technology to a specific organism calls for custom modifications to the system to improve its success rate. In this project, a CRISPR-Cpf1 system that can be effectively employed in the cyanobacterium Nostoc punctiforme was designed, with a focus on the hormogonium development of this species. Multiple plasmids containing the CRISPR system and targeting different …

Characterizing Drought Adaptations, Phenotypic Plasticity, And Fixed Gene Expression Patterns Within Quercus, James K. Rauschendorfer

Dissertations, Master's Theses and Master's Reports

This dissertation was written on topics related to the genus Quercus with a primary focus on Quercus ellipsoidalis (northern pin oak) and Quercus rubra (northern red oak). Within this dissertation are chapters related to the setup of experimental common gardens within the Ford and Kellogg experimental forest, a literature review describing drought adaptations of Quercus sect. Lobatae (red oak group), identification of transcription factors within the Q. robur (English oak) and Q. rubra genomes, a study comparing leaf trait phenotypic plasticity of Q. ellipsoidalis and Q. rubra, and an RNA-seq experiment studying ecological speciation between Q. ellipsoidalis and Q. …