Genetics and Genomics Commons^™

Paternal Ages And Genetic Diseases And Congenital Anomalies, Neda Hamood

Honors Undergraduate Theses

The purpose of this thesis 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 advanced paternal ages and genetic diseases and congenital anomalies remains unclear. However, there is room for improvement to systematically investigate the relationship between specific congenital anomalies in newborns and advanced paternal ages. More recently, the link between advanced paternal age (as opposed to existing studies analyzing advanced maternal age alone) and genetic diseases has been recognized by researchers, epidemiologists, and various health experts. Thus, …

We Achieved Efficient Gene Editing In Zebrafish Using A Two-Part Rna Crispr-Cas9 System, Kyrian Carley, Daniel Sculley, Emma Pastoor, Valeria Lacroix, Ashley Meyer, Brianna Jansen, Joshua Deyoung, Rachael Baker, Amy Wilstermann

Summer Research

• Establish effective protocols for using CRISPR-Cas9 technology with the equipment we have in our lab.
• Create a zebrafish model of BCS1L mutations to better elucidate genotype-phenotype connections.

Molecular Dynamics Of Bcs1l: A New Homology Model And The Structural Impact Of Pathogenic Mutations, Josh Deyoung, Sadie Heeringa, Rachael Baker, Amy Wilstermann

Summer Research

• Mutations to BCS1L can lead to one of three distinct rare diseases: Björnstad syndrome, BCS1L mitopathy, GRACILE syndrome
• These diseases cause a variety of symptoms in patients that range from mild (hearing loss and brittle hair) to severe and fatal (iron overload, failure to thrive, lactic acidosis, aminoaciduria, early death)

Viropana (Vna) 2, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 2

• ID – vna 2
• Details – Gene from a novel protein family belonging to the regeneration tool kit of Notophthalmus viridescens
• Base pairs – 396

Viropana (Vna) 4, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 4

• ID – vna 4
• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens
• Base pairs – 501

Awareness Of Genetic Predispositions That Increase The Risk Of Breast Cancer, Carly Huber

Honors Undergraduate Theses

Breast cancer is the most commonly diagnosed cancer in women in the United States and is the leading cause of cancer-related death among women worldwide. Certain demographics, such as racial/ethnic, age, and gender groups, are underrepresented in breast cancer studies. This lack of representation results in issues with creating genetic tests, as variants associated with those groups are not being detected. Furthermore, these underrepresented demographics are receiving a worse prognosis than those that are overrepresented in research. This study aimed to understand how informed the understudied racial/ethnic, gender, and age populations are regarding breast cancer and genetic testing compared to …

The Study Of Ppal And Its Role In The Development Of Physcomitrella Patens, Susana Perez-Martinez, Christine Chen, Mark P. Running

Undergraduate Arts and Research Showcase

Protein Prenylation is the addition of lipids to select proteins that play a key role during the development of plants. There are three enzymes that play a role in protein prenylation: protein farnesyltransferase (PFT), protein geranylgeranyl-transferase-I (PGGT), and Rab geranylgeranyltransferase (Rab-GGT). However, there is a protein called PPAL that has a similar alpha subunit of PFT, PGGT, and RAB-GGT but its biochemical function is unknown. Physconmitrella patens, a type of moss, was chosen to explore the role of PpPPAL in the development process. There are two copies of PPAL found in moss. PPAL1 and PPAL2. To study the role …

Genetic Diversity & Connectivity Of Chasmanthium Latifolium (Poaceae) In Pennsylvania & The Effect On Conservation Status Of A Rare Species, Jonathan D. Hayes

Honors Theses

Chasmanthium latifolium (Michx.) Yates (Poaceae) is a loosely colonial, rhizomatous, perennial grass species that lives in riparian habitats, making it fittingly referred to as river oats. Native to the southern Midwest and the eastern half of the United States, C. latifolium reaches the northeastern edge of its range in Pennsylvania. Within Pennsylvania, eleven extant C. latifolium populations are found along four waterways: the Monongahela River, the Susquehanna River, and two tributaries to the Susquehanna River. This limited state distribution exhibits an east-west disjunct distribution, where western populations are largely separated from eastern populations with one centrally located population. Between the …

Disease Prevalence And The Population Genetic Structure Of Crassostrea Virginica Along The Georgia Coast, Sarah Batchelor

College of Graduate Studies: Theses & Dissertations

The Eastern Oyster, Crassostrea virginica, is an ecologically important species that plays a role in protecting shorelines, water filtration, and providing habitat and food for various fish species. Perkinsus marinus and Haplosporidium nesloni are two pathogens currently affecting oyster populations. These pathogens have both been documented as causes of mass mortality events along the East coast. They greatly diminish the health of oysters, resulting in the degradation of oyster tissue, reduction in growth and reproductive ability, and may cause death. In this study, wild oysters were collected from eleven locations along the Georgia coast to investigate the presence, intensity, …

Discovering Genes Involved In The Synthesis Of Secondary Metabolites From The Seeds Of Moringa Oleifera Through Transcriptome Analysis, Vivian A. Panes, Ma. Divina Kristi A. Discar

Biology Faculty Publications

Moringa oleifera is a widely used crop that produces seeds with a plethora of benefits encompassing health and nutrition. Secondary metabolite compounds were determined in the seeds of Moringa oleifera that possess nutritional and pharmacological benefits. Although various phytochemical researchers reported the presence of secondary metabolites in M. oleifera seeds, there is a lack of research on the genes encoding for enzymes that catalyze the synthesis of secondary metabolites in the seeds of M. oleifera. In the present study, RNA sequencing was used to analyze the transcriptome of the mature seed embryos of M. oleifera. Biological pathway analysis …

Investigation Into The Genetic Provenance Of Three Rare Plants With East-West Disjunction Patterns In Pennsylvania., Scott Schuette, Christopher T. Martine

Other Faculty Research and Publications

Rare plant conservation relies on an understanding of the natural history, biology and ecology, and real and potential threats to their populations to inform state regulations that serve to protect the species from extirpation. This work often involves extensive field surveys over several years to determine population sizes and whether those populations are seeing reductions in number of individuals necessary to maintain the genetic diversity within and between those populations. Species and populations with high genetic diversity are better equipped to withstand sudden changes to their habitats that derive from land use changes and changing climate. There are a variety …

Vasculogenic Mimicry: Role Of Melanoma Differentiation Associated Gene-9/Syntenin, Jinkal Modi, Anjan Pradhan, Luni Emdad, Swadesh Das, Paul Fisher

Graduate Research Posters

Malignant melanoma (MM) is the most aggressive skin cancer and the most frequent skin disorder in Caucasians. MM is associated with aggressive and progressive disease states, leading to major cancer-related morbidity and mortality. Recent investigations identify a new non-angiogenesis-dependent pathway vasculogenic mimicry (VM), which is considered a cancer hallmark that can independently facilitate tumor neovascularization by the formation of fluid-conducting and vascular endothelial cells. MM cells undergoing VM can dedifferentiate into numerous cellular phenotypes and acquire endothelial-like features, resulting in the formation of the de novo matrix-rich vascular-like network, such as plasma and red blood cells. The co-generation of endothelial …

Attitudes And Opinions About Direct-To-Consumer Genetic Testing In Undergraduate Science Students, Morgan N. Driver, Sally I-Chun Kuo, Olivia Nayeri, Chloe J. Walker, Chelsea Derlan Willians, Tricia Smith, Amy E. Adkins, Danielle M. Dick

Graduate Research Posters

Background: There has been exponential growth in the number of direct-to-consumer genetic testing kits sold in the past decade. Consumers utilize direct-to-consumer genetic tests for a number of reasons which include learning about one’s ancestry and potential ways to manage health. Emerging adults tend to be early adopters of new technologies; however, there has been little research regarding the opinions about direct-to-consumer genetic testing in emerging adults.

Methods: Data came from a study conducted in an upper-level biology course focusing on understanding undergraduate science students’ overall experiences with receiving personalized genetic testing results from 23andMe. The present study used data …

Principal Components Analysis Corrects Collider Bias In Polygenic Risk Score Effect Size Estimation, Nathaniel S. Thomas, Peter B. Barr, Fazil Aliev, Sally I. Kuo, Danielle M. Dick, Jessica E. Salvatore

Graduate Research Posters

BACKGROUND: Genome-wide polygenic scoring has emerged as a way to predict psychiatric and behavioral outcomes and identify environments that promote the expression of genetic risks. An increasing number of studies demonstrate that the effects of polygenic risk scores (PRS) may be biased by the inclusion of heritable environments as covariates when the environment is influenced by unmeasured confounding variables, an example of collider bias. Inclusion of the principal components of observed confounders as covariates may correct for the effect of unmeasured confounders.

METHODS: A simulation study was conducted to test principal components analysis (PCA) as a correction for collider bias. …

Transcriptional Repressor Protein Based Macrolide Biosensor Development With Improved Sensitivity, Jayani A. Christopher

Graduate Research Posters

Macrolide antibiotics are in high demand for clinical applications. Macrolides are biosynthesized via giant assembly line polyketide synthases (PKS) which are arranged in a modular fashion. Combinatorial biosynthetic methods have been used to produce diversified macrolides by reprograming these modules and modifying tailoring enzymes required for post synthetic modifications. However it is challenging due to the size and complexity of PKSs. To overcome this challenge, new enzymes for macrolide diversification could be obtained by directed evolution where a large number of enzyme variants need to be screened. Therefore it is important to develop high throughput screening methods to identify the …

Pharmacogenomics And Ssris Appropriateness In Older Community Dwelling African Americans, Wint War Phyo, Lana Sargent, Elvin T. Price

Graduate Research Posters

Background: Depressive and anxiety disorders are among the most common illnesses experienced by older adults (age > 60). The selective serotonin reuptake inhibitors (SSRIs) are preferred class of antidepressants for these disorders due to their high efficacy and safety profiles among older adults. However, SSRIs are metabolized by highly polymorphic cytochrome P450 enzymes, specifically CYP2D6 and CYP2C19. This can lead to variable dose-response outcomes, especially among older African American population.

Objective: Analyze the frequency of CYP2D6 and CYP2C19 polymorphisms in African American older adults who are taking SSRIs and identify potential inappropriate use of SSRIs in these older adults using the …

Mechanisms Of Cadmium-Induced And Epidermal Growth Factor Receptor Mutation-Driven Lung Tumorigenesis, Hsuan-Pei Lin

Theses and Dissertations--Toxicology and Cancer Biology

Cadmium (Cd) is a ubiquitous pollutant in the environment and a known carcinogen for lung cancer. Cd has been shown to act as a weak mutagen, which suggests that it may exert tumorigenic effect through non-genotoxic ways, such as epigenetic mechanisms. The goal of this project is to investigate the mechanisms of Cd carcinogenesis focusing on the role of lncRNA dysregulations. The Cd-exposed cells formed significantly more colonies in soft agar, displayed cancer stem cell (CSC)-like property and formed tumors in nude mice. Mechanistically, the lncRNA microarray analysis revealed that chronic Cd exposure dysregulates lncRNA expressions. Q-PCR analysis confirmed the …

The Ethical Controversy Around Gene-Editing Technology, Katrina Powers

A with Honors Projects

In this honors project, the author discusses the risks and benefits of using CRISPR to edit genetics.

Lettuce (Lactuca Sativa) Productivity Influenced By Microbial Inocula Under Nitrogen-Limited Conditions In Aquaponics., Jessica A Day, Christian Diener, Anne E Otwell, Kourtney E Tams, Brad Bebout, Angela M Detweiler, Michael D Lee, Madeline T Scott, Wilson Ta, Monica Ha, Shienna A Carreon, Kenny Tong, Abdirizak A Ali, Sean M Gibbons, Nitin S Baliga

Articles, Abstracts, and Reports

The demand for food will outpace productivity of conventional agriculture due to projected growth of the human population, concomitant with shrinkage of arable land, increasing scarcity of freshwater, and a rapidly changing climate. While aquaponics has potential to sustainably supplement food production with minimal environmental impact, there is a need to better characterize the complex interplay between the various components (fish, plant, microbiome) of these systems to optimize scale up and productivity. Here, we investigated how the commonly-implemented practice of continued microbial community transfer from pre-existing systems might promote or impede productivity of aquaponics. Specifically, we monitored plant growth phenotypes, …

A Multispecies Perspective Into Dietary Genetic Adaptations And Ancient Migration In The Peruvian Andes, Kelsey Jorgensen

Wayne State University Dissertations

Successful adaptation to the high-elevation Andes would have required both cultural and biological adaptations by early human populations. These past adaptations continue to shape the evolutionary outcomes of both humans and non-human species today. A multispecies perspective was used to examine how humans and non-human creatures, specifically insects, were shaped by past human adaptations. This dissertation asked two primary questions: 1) Given the importance and evolutionary history of potato consumption in the Peruvian Andes, is a genetic adaptation to better digest potato starch detectable in present-day Peruvians? and 2) Using the Andean Potato Weevil (APW) phylogeny as a proxy, what …

Haplotype Network Branch Diversity, A New Metric Combining Genetic And Topological Diversity To Compare The Complexity Of Haplotype Networks, Eric Garcia, Daniel Wright, Remy Gatkins, May B. Roberts, Hudson T. Pinheiro, Eva Salas, Jei-Ying Chen, Jacob R. Winnikoff, Giacomo Bernardi

Biological Sciences Faculty Publications

A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published metric haplotype network diversity (HNd). However, unlike HNd which uses a combination of network …

Psxii-19 Urine Metabolomics Analysis Associated With Feed Efficiency On Crossbred Steers During The Growing And Finishing Period On Forage- And Concentrate- Based Diets., Virginia M. Artegoitia, John Newman, Ronald M. Lewis, Andrew P. Foote, Harvey C. Freetly

Department of Animal Science: Faculty Publications

A discovery project to identify non‐invasive biomarkers that can detect subtle metabolic discrepancies for cattle feed efficiency was performed using untargeted and targeted urine metabolomics by ultra-performance liquid chromatography-mass spectrometry. Individual feed intake and body weight gain were measured in crossbred steers (n = 80) on a forage-based growing ration (stage-1) followed by a high-concentrate diet finishing ration (stage- 2). Urine was collected on study days 0, 21, 42, 63, and 83 for each dietary stage. In total, 28 steers with the greatest and the least average daily-gain (ADG) within 0.32 SD of the mean of dry-matter-intake (DMI) were used. …

Epigenetic Clock And Methylation Study Of Oocytes From A Bovine Model Of Reproductive Aging, Pawel Kordowitzki, Amin Haghani, Joseph A. Zoller, Caesar Z. Li, Ken Raj, Matthew L. Spangler, Steve Horvath

Department of Animal Science: Faculty Publications

Cattle are an attractive animal model of fertility in women due to their high degree of similarity relative to follicle selection, embryo cleavage, blastocyst formation, and gestation length. To facilitate future studies of the epigenetic underpinnings of aging effects in the female reproductive axis, several DNA methylation-based biomarkers of aging (epigenetic clocks) for bovine oocytes are presented. One such clock was germane to only oocytes, while a dual-tissue clock was highly predictive of age in both oocytes and blood. Dual species clocks that apply to both humans and cattle were also developed and evaluated. These epigenetic clocks can be used …

Relationship Between Urinary Energy And Urinary Nitrogen Or Carbon Excretion In Lactating Jersey Cows, D. L. Morris, Jeffrey L. Firkins, C. Lee, W. P. Weiss, Paul J. Kononoff

Department of Animal Science: Faculty Publications

Measurement of urinary energy (UE) excretion is essential to determine metabolizable energy (ME) supply. Our objectives were to evaluate the accuracy of using urinary N (UN) or C (UC) to estimate UE and ultimately improve the accuracy of estimating ME. Individual animal data (n = 433) were used from 11 studies with Jersey cows at the University of Nebraska–Lincoln, where samples were analyzed after drying (n = 299) or on an as-is basis (n = 134). Dried samples resulted in greater estimated error variance compared with as-is samples, and thus only as-is samples were used for final models. The as-is …

Computational Study Of Target Gene Interactions - Enhancers And Micrornas, Amlan Talukder

Electronic Theses and Dissertations, 2020-2023

Gene expression is an essential mechanism for physical and mental development of human. Aberrant regulation of gene expression creates abnormality in human body than can lead to complicated diseases. Gene expression can be regulated at any stage from the chromatin unfolding stage to post-translation stage of protein. In this study, we focused on two important factors of gene expression regulation that participate in the gene expression process at the transcription and the post-transcriptional stages; enhancer-promoter interactions and miRNA-mRNA interactions. The enhancer-promoter interactions are difficult to detect due to the large distance between the enhancer and promoter region and cell-specific activity …

A Hybrid Gene Selection Strategy Based On Fisher And Ant Colony Optimization Algorithm For Breast Cancer Classification, Mohammed Hamim, Ismail El Moudden, Mohan D. Pant, Hicham Moutachaouik, Mustapha Hain

EVMS School of Health Professions Faculty Publications

Breast cancer poses the greatest threat to human life and especially to women's life. Despite the progress made in data mining technology in recent years, the ability to predict and diagnose such fatal diseases based on gene expression data still reveals a limited prediction performance, which may not be surprising since most of the genes in expression data are believed to be irrelevant or redundant. The dimensionality reduction process may be considered as a crucial step to analyze gene expression data, as it can reduce the high dimensionality of the breast cancer datasets, which may result into a better prediction …

An Evaluation Of The Bighorn Sheep Population In Badlands National Park, Austin J. Wieseler

Electronic Theses and Dissertations

Within the last century, bighorn sheep (Ovis canadensis) in the badlands ecosystem of western South Dakota have been subjected to complete extirpation, reintroduction, disease die-offs, genetic bottlenecking, and population augmentation. Subsequently, the population in Badlands National Park (BNP) appears to have recovered, but it was unknown to what degree past events had influenced the population. From 2017-2019, we conducted research on 5 subherds within 2 management units in BNP to 1) survey for the presence of respiratory pathogens and estimate the prevalence of other potentially infectious diseases; 2) assess adult and lamb survival and cause-specific mortality; 3) estimate population size …

Functional Analysis Of Folate Biosynthesis Genes Of Rickettsia Monacensis Str. Humboldt Via Complementation Assay, Brandon James Hill

Cal Poly Humboldt theses and projects

Nutritive symbiosis between bacteria and ticks is observed across a range of microbes and hosts, however, little characterization on the molecular components responsible for these symbioses has been done. Previous studies in our lab demonstrated that Rickettsia monacensis str. Humboldt (RMSH) can synthesize folate de novo via folA, folC, folE, folKP, and ptpS pathway. In this study expression of RMSH folate genes within a folate gene mutant E. coli K-12 strain BW25113 was used to functionally characterize RMSH folate genes in vivo. RMSH folate genes were subcloned into TransBac vector and transformed into folA, …

Microbiome Community And Parasitic Infections In Wild Bees, Mark G. Young

Honors Theses

The microbiome is increasingly recognized for its complex relationship with host fitness. Akin to primates and other social animals, bumblebees harbor a specific microbiome derived from social contact. The bumblebee microbiome is characteristically species poor, with just a few “core” phylotypes accounting for the majority of total abundance. Genomic analyses reveal phylogenetic congruence and adaptation of the core endosymbionts to the bumblebee gut, indicating a shared evolutionary history. Prior investigations reveal that the relative abundance of core microbes is negatively associated with infection by a trypanosome, Crithidia bombi, and that the microbiome has a mechanistic role in immunity. As …

ผลของสารสกัดเห็ดกระถินพิมาน Phellinus Linteus ต่อความเป็นพิษของเซลล์และการแสดงออกของยีนในเซลล์มะเร็งปากมดลูก, ธนวิชญ์ แสงคีรีพัฒน์

Chulalongkorn University Theses and Dissertations (Chula ETD)

มะเร็งปากมดลูกเป็นหนึ่งในมะเร็งที่มีจำนวนผู้ป่วยและอัตราการเสียชีวิตที่สูง ถึงแม้ว่าจะมีการฉีดวัคซีนป้องกันการติดเชื้อไวรัส human papilloma virus ซึ่งเป็นหนึ่งในสาเหตุสำคัญของการเกิดมะเร็งปากมดลูกแต่ประชากรบางกลุ่มโดยเฉพาะอย่างยิ่งในกลุ่มประเทศที่มีรายได้ระดับน้อยถึงปานกลางนั้นไม่สามารถเข้าถึงได้ โดยปัจจุบันนี้ได้มีการศึกษาพบว่ามีสมุนไพรบางชนิดที่มีฤทธิ์ในการรักษาและป้องกันการเกิดมะเร็งได้โดยเฉพาะอย่างยิ่งเห็ดกระถินพิมาน ในการศึกษานี้ได้ทำการศึกษาถึงความสามารถในการยับยั้งการเจริญเติบโตของเซลล์มะเร็งปากมดลูกด้วยสารสกัด 3 สูตรด้วยกันได้แก่ สารสกัดเห็ดกระถินพิมาน และสารสกัดสูตรตำรับอีก 2 สูตร (สูตรตำรับ A และ B) ที่มีองค์ประกอบของเห็ดกระถินพิมานและสมุนไพรอื่น ๆ ที่ต่างกัน จากการศึกษาพบว่าสารสกัดทั้ง 3 สูตรนั้นมีความสามารถในการลดอัตราการมีชีวิตของเซลล์มะเร็งปากมดลูก C33a SiHa และ HeLa ในระยะเวลา 2 วัน แต่ยังคงมีความเป็นพิษต่อเซลล์ไตที่ได้จากตัวอ่อนของมนุษย์ HEK293 ในระดับที่สูง ยิ่งไปกว่านั้นพบว่าสารสกัดสูตรตำรับ B นั้นมีความสามารถในการลดการเจริญเจริญเติบโตของเซลล์ SiHa อย่างมีนัยสำคัญทางสถิติ (p = 0.005) เมื่อเปรียบเทียบกับชุดการทดลองควบคุม และส่งผลให้การแสดงออกของยีน CDK7 และ MKI67 ลดลงอย่างมีนัยสำคัญทางสถิติ ในทำนองเดียวกันสารสกัดเห็ดกระถินพิมานก็มีความสามารถในการลดการเจริญเติบโตของเซลล์ C33a อย่างมีนัยสำคัญทางสถิติ (p = 0.025) เมื่อเปรียบเทียบกับชุดการทดลองควบคุม และส่งผลให้การแสดงออกของยีนทั้งสองลดลงอย่างมีนัยสำคัญทางสถิติเช่นเดียวกัน