Genetics Commons^™

Mutating Lysine 336 In Msh6 Does Not Appear To Affect Dna Mismatch Repair In Saccharomyces Cerevisiae, Anthony Thompson, Daniel Reese, Noa Bennafield, Kalila Daveron, Christopher Bolden, Joanna E. Haye-Bertolozzi

XULAneXUS

Defects in the DNA mismatch repair process results in the accumulation of mutations and disease. Mutations in MSH6 and MSH2, encoding for the subunits of the MutSα complex, are often responsible for Constitutional Mismatch Repair Deficiency (CMMRD) and Lynch Syndrome (LS), respectively. This work focused on DNA mismatch repair through analysis of the MSH6 missense variant msh6-K336T. The mutation examined in this study is msh6-K336T in Saccharomyces cerevisiae, which is equivalent to msh6-K431T in humans. The mutation results in the replacement of lysine with threonine, an amino acid with different properties. It was therefore hypothesized that the mutation …

Genetic Diversity Analysis Of Greater Yam (Dioscorea Alata L.) Collections Using Tuber Morphology And Simple Sequence Repeats (Ssr) Markers, Junelyn Ravelo, Lara Jaaziel Batalon, Antonio Lalusin

The Philippine Agricultural Scientist

The diversity of 148 greater yam (Dioscorea alata L.) accessions from the collections of the National Plant Genetics Resources Laboratory (NPGRL), Visayas State University (VSU), and the Institute of Crop Science - University of the Philippines Los Baños (ICROPS-UPLB) was evaluated using 54 Dioscorea-based SSR markers. Out of 54 SSR markers, polymorphic bands were amplified in 50 SSR markers with Polymorphic Information Content (PIC) values ranging from 0.65 to 0.89. Subsequent cluster analysis generated nine distinct clusters with a Jaccard’s distance index of 0.85, implying 85% dissimilarity among the greater yam accessions. Each formed cluster from the analysis comprised …

Caprin1 And Fmr1 Genetically Interact To Regulate The Development Of The Larval Drosophila Neuromuscular Junction, Seraphina Loukas, Scott Barbee

DU Undergraduate Research Journal Archive

Fragile X Syndrome (FXS) is the most prevalent inherited neurodevelopmental disorder and the most common single-gene cause of autism (Richter and Zhao 2021). FXS occurs due to the loss of the Fmr1 gene, and its respective protein, the Fragile X Messenger Ribonucleoprotein (FMRP). FMRP is an RNA-binding protein (RBP) with notable functions in synaptic development.  Given that cellular processes often entail the collaborative actions of multiple proteins acting as binding partners to regulate mRNA metabolism, identifying FMRP's associates is essential for comprehending FXS mechanisms. Caprin1 was identified as a high-confidence interactor via its co-immunoprecipitation with FMRP in an IP/LC experiment …

The Tissue-Specific Role Of Smn-1 In C. Elegans, Lindsey Philips

Biological Sciences Theses and Dissertations

Spinal muscular atrophy (SMA) is an autosomal recessive disease that results from mutations in the Survival Motor Neuron (SMN-1) gene. Although SMN is a ubiquitously expressed protein that acts as an RNA-binding protein (RBP), SMA is characterized by the selective degeneration of motor neurons of the lower spinal cord. Despite a clear understanding of the genetic causes underlying SMA, the mechanisms associated with low SMN levels to disease pathogenesis remains unclear. Here, we investigate the role SMN-1 has in different tissues to begin understanding possible mechanisms. This project has three aims that has guided our experiments. The first aim is …

Unveiling The Nexus Of Cellular Quality Control: Exploring The Interplay Between Ribosome-Associated Protein Quality Control And Mitochondrial Quality Control Pathways, Foozhan Tahmasebinia

Biological Sciences Theses and Dissertations

In eukaryotic cells, the intricate interplay between cellular quality control mechanisms is crucial for maintaining homeostasis and safeguarding the integrity of vital processes, spanning from macromolecule synthesis to the renewal of entire cellular organelles.

Disruption of these networks can lead to severe diseases such as metabolic disorders, underscoring the interconnected nature and feedback control mechanisms inherent in biological systems, including cellular quality control systems. This interconnectedness extends to the intricate communication between organelles, enabling coordinated functioning and adaptation to changing cellular conditions, particularly in response to stressors.

While the exact mechanisms governing these communications within cellular quality control systems remain …

Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali

Electronic Theses and Dissertations

The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …

Identifying Key Evolving Residues That Drive Cid/Cal1 Incompatibility In Drosophila Species, Hayden Yuan, Barbara Mellone

Honors Scholar Theses

The centromere, an essential locus on the chromosome critically important for faithful chromosome segregation during cell division, requires the incorporation of centromere protein A (CENP-A/CID) orchestrated by the chaperone CAL1. This thesis investigates the structural requirements governing the interaction between CAL1 and CID, with a focus on two diverged Drosophila species. Using a combination of structural analysis prediction and cellular assays, I explored the compatibility between the N-terminal region of CAL1 and the L1 domain of CID. Previous results demonstrate species specific interactions between CAL1 and CID, with endogenous Drosophila melanogaster (mel) CAL1 efficiently depositing Drosophila melanogaster CID …

Characterizing The Role Of Pa5189 Of Pseudomonas Aeruginosa In Deletion And Overexpression Mutants, Seh Na Mellick

Theses/Capstones/Creative Projects

In the context of rising multidrug resistance in biofilm-forming pathogens like Pseudomonas aeruginosa, this study investigates the role of the understudied transcription factor PA5189 in antibiotic resistance and biofilm formation. PA5189 deletion and overexpression mutants were created in a parent P. aeruginosa strain using pEX18Tc-based recombinant suicide vectors, with genotypic verification of putative triparental conjugants achieved through restriction digestion and PCR. The study revealed that PA5189 overexpression significantly increases resistance to commonly used broad spectrum antibiotics such as ciprofloxacin and imipenem. Additionally, differential expression of PA5189 was found to notably affect biofilm formation, with variations contingent on the nutrient …

Annotation Of Hypothetical Genes In Lactococcus Lactis Ssp. Il403, Jennifer A. Tangires

Student Scholar Showcase

The human gastrointestinal tract (GIT) harnesses various microbial organisms involved in almost all processes of physiological homeostasis, among these are lactic acid bacteria (LAB). These bacteria, almost all of which belong to the order Lactobacillales, are able to produce lactic acid, and play an important role in food preservation because they produce bacteriocins. Bacteriocins are antimicrobial proteins that are used to fight off related bacteria in their environment that are competing for the same resources. This study focuses on a specific LAB strain, Lactococcus lactis ssp. IL1403 where 21.9% of its predicted genes have not yet been assigned a function. …

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

Augustana Center for the Study of Ethics Essay Contest

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

Documenting The Southern Range Terminus Of The Wood Frog (Lithobates Sylvaticus) In North America, Christian Braswell

Theses

The Wood Frog (Lithobates sylvaticus) holds a remarkable position in North American amphibian biology, with its range extending from the Arctic Circle down to the near sub-tropical southeastern United States. This thesis presents a novel quantitative polymerase chain reaction analysis (qPCR) primer specific to L. sylvaticus and a survey effort regarding the southernmost distribution and detection of this species in Alabama through the application of environmental DNA (eDNA) sampling techniques. By investigating historical data and employing advanced genetic methodologies, this research provides insights into the contemporary status and distribution of the Wood Frog. This research is important to …

Exploring The Role Of Calcineurin In Filamentation Across Inducing Conditions In The Fungal Pathogen Candida Albicans, Patricia Harte-Maxwell, Jill R. Blankenship

UNO Student Research and Creative Activity Fair

Candida albicans is an opportunistic human pathogenic fungus affecting millions of people globally; high mortality rates are possible in systemic infection. Filamentation or a filamentous growth pattern is a primary virulence mechanism of C. albicans underlying other virulent behaviour....

Agrobacterium-Mediated Genetic Transformation And Plant Regeneration From Cotyledons In Philippine Eggplant (Solanum Melongena L.) Acc. ‘Ph 11424’, Mark Gabriel Sagarbarria, John Albert Caraan, Patrick Lipio, Ian Bien Oloc-Oloc, Kazuo Watanabe, Desiree Hautea

The Philippine Agricultural Scientist

Eggplant (Solanum melongena L.) is one of the most important vegetables grown and consumed in the Philippines hence, continuous breeding programs are vital to maintain the supply of this economically important crop. This study demonstrates the first successful Agrobacterium-mediated genetic transformation and plant regeneration of the Philippine eggplant cultivar ‘PH 11424’, also known as ‘Mistisa’. Cotyledons from 2-wk-old seedlings were used as explants, which were transformed with disarmed Agrobacterium tumefaciens strain LBA4404 harboring a binary vector for CRISPR/Cas9 expression and hygromycin phosphotransferase (HPT), an antibiotic selection marker. Growth of shoot primordia from the agro-infected explants was observed during selective culture …

Plk1 Overexpression Drives Tumorigenesis In A Prostate Cancer Mouse Model, Emile Kachouh

Theses and Dissertations

Prostate cancer is the leading cause of cancer-related deaths among men worldwide, and the development of resistance to existing treatments necessitates the exploration of new therapeutic strategies, including combination therapies. This study investigates the role of Polo-like kinase 1 (PLK1), located on chromosome 16p12.2, as an oncogene in prostate cancer. We generated a transgenic mouse model with prostate-specific overexpression of PLK1 to closely mimic human prostate cancer progression. Quantitative PCR (qPCR) analysis was employed to characterize the molecular profile of PLK1, revealing its implication in multiple pathways. To further elucidate the functional consequences of PLK1 overexpression, we confirmed phenotypic progression …

The Splice Index As A Prognostic Biomarker Of Strength And Function In Myotonic Dystrophy Type 1, Marina Provenzano

Theses and Dissertations

Myotonic dystrophy type 1 (DM1) is a slowly progressive, multisystem disorder caused by a CTG repeat expansion in the DMPK 3’UTR that leads to global dysregulation of alternative splicing. The resulting decline in physical function is slow, and no reliable biomarkers exist for predicting disease progression; however, an RNA mis-splicing biomarker associated with weakness may have utility in predicting functional outcomes. Here we validate the Splice Index (SI) as a potential biomarker of DM1-associated strength and function. Muscle biopsies of the tibialis anterior were collected from DM1-affected individuals at baseline (n = 46) and 3-months (n = 34), along with …

Quantitative Trait Loci Influencing Elemental Content In Grapevine Leaves, Jesse L. Krokower

Graduate Theses/Dissertations

In grapevine, the influence of the plant’s elemental composition (the ionome) on fruit and wine quality is well established, but its genetic underpinnings have received limited scientific attention. In this study, I analyzed the leaf ionome of 131 interspecific F1 hybrid progeny plants from a cross between a Vitis rupestris Scheele (♀) and a Vitis riparia Michx (♂) parents, which were replicated in four different environments: Southwest Missouri, Central Missouri, South Dakota, and New York. I sampled leaves at three different times during the growing season at all four locations and had the concentration of 20 elements measured using ICP-MS. …

Exploring 3d Genome Interaction And Epigenetic Regulation Via Swi/Snf Complex And Deep Learning Models, Ruoyun Wang

Dartmouth College Ph.D Dissertations

The three-dimensional organization of the genome is fundamental in regulating gene expression and maintaining cellular function. This organization's complexities, influenced by epigenetic marks and chromatin remodeling complexes, are crucial for understanding genomic regulation. Among these, the SWI/SNF complexes are key, facilitating chromatin accessibility and regulating gene activity across cell types. The first part of my dissertation focuses on SWI/SNF complexes, exploring their role in chromatin remodeling and their impact on 3D genome architecture. Utilizing next-generation sequencing (NGS) techniques, this section investigates the interplay between these complexes and chromatin structure. During my research on the SWI/SNF complex, I was intrigued by …

Contemporary Vs. Traditional Dna-Based Mutation Testing To Detect Hereditary Breast And Ovarian Cancer Syndrome (Hboc) In Women: A Meta Narrative Review, Hannah Olivia Cantu, Jacob Hipp, Nyela Y. Lopez, Duc Duy Nguyen

Research Methods Poster Session 2024

No abstract provided.

Re-Programming Transcription Factor Function For Neuroscience Research Of Addiction: Investigating The Role Of Zinc Finger Proteins In Driving Cocaine Reinforcement In Mice, Joseph A. Picone

Theses and Dissertations

Administration of addictive drugs like cocaine or morphine initiates aberrant gene transcription within brain reward circuitry neurons, which contributes to the lasting behavioral maladaptations that define addiction. The drug-induced expression and function of key brain transcription factors (TFs) is one major mechanism through which these drugs are able to regulate transcription, and as a consequence, lasting damaging drug-related behaviors including compulsive drug use. The goal of this dissertation is to more fully understand the molecular mechanistic drug-specific actions of TFs within the rodent nucleus accumbens (NAc). The findings from these studies could serve as the basis to identify novel candidate …

Transcription And Translation Regulation Of Germ Cell To Maternal Transition, Noor Kotb

Electronic Theses & Dissertations (2024 - present)

In sexually reproducing organisms, the process of gametogenesis produces mature eggs and sperms required for fertilization to occur. The egg's quality is crucial for the healthy development of the next generation, making oogenesis a tightly regulated process with multiple benchmarks. To investigate the intricacies of oogenesis, we utilized the Drosophila oogenesis system as our primary model. This choice was motivated by several factors. Firstly, the process of egg development in Drosophila is conserved across species, making it a valuable proxy for understanding oogenesis in other organisms, including humans. Secondly, Drosophila melanogaster has long been established as a powerhouse in genetic …

Ribosome Hibernation Factor Induces Antibiotic Persisters Of Mycobacterium Tuberculosis In Neutrophil-Rich Lung Lesions, Jamie Corro

Electronic Theses & Dissertations (2024 - present)

Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is a prescient global health threat and the leading cause of death by an infectious agent. Treatment of Mtb infection involves administering 2-4 antibiotics for a minimum of 6 months. This extended drug regimen is required to target a subpopulation of persistent bacilli. As their name implies, these bacteria can “persist” by acquiring nonhereditary and transient antibiotic tolerance. Although the precise mechanism is unknown, it’s often attributed to slowing cellular growth and metabolic processes. During zinc deprivation, bacteria can remodel their ribosomes by replacing their zinc-binding paralogues containing the CXXC motif (C+) …

Developing Cellular Systems To Elucidate Rna Structural Dynamics Of Cag Expansion Transcripts In Spinocerebellar Ataxias, Victoria Demeo

Electronic Theses & Dissertations (2024 - present)

Spinocerebellar ataxias (SCAs) are a diverse group of over 40 genetically heterogeneous neurodegenerative disorders, many of which are caused by a trinucleotide CAG repeat expansion in the coding region of specific genes. These expansions lead to the production of polyglutamine (polyQ) tracts that interfere with normal protein function, triggering cellular dysfunction and contributing to disease pathogenesis. The most well-known of these SCAs, such as SCA1, SCA2, and SCA3, exhibit progressive neurodegeneration, yet the precise mechanisms through which these mutations cause disease remain poorly understood.

A significant challenge in studying CAG repeat expansion disorders lies in the complexity of the disease …

Structural And Functional Consequences Of Pde6 Prenylation In Rod And Cone Photoreceptors, Faezeh Moakedi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Phosphodiesterase-6 (PDE6) serves as a pivotal component in the phototransduction pathways of both cone and rod photoreceptors. In cones, PDE6 consists of tetrameric subunits: inhibitory (γ') and catalytic (α'). The catalytic subunit, PDE6α', contains a C-terminal prenylation motif. Deletion of this motif is associated with achromatopsia (ACHM), a form of color blindness. The mechanisms underlying the disease and the roles of PDE6 lipidation in vision remain elusive. Meanwhile, rod PDE6 is composed of α and β catalytic subunits and γ inhibitory subunits, with alterations in the C-terminal "prenylation motif" of PDE6β linked to retinitis pigmentosa (RP) pathology. In this comprehensive …

ฤทธิ์ของสารสกัดจากมะกรูดต่อภาวะเครียด Oxidative Stress ในหนอน Caenorhabditis Elegans, ณัฐพงศ์ นพโลหะ

Chulalongkorn University Theses and Dissertations (Chula ETD)

ภาวะโรคไม่ติดต่อเรื้อรัง หรือ Non-Communicable Disease (NCDs) เป็นภาวะโรคที่ไม่ได้ติดต่อจากคนสู่คนได้รวมถึงไม่ได้เกิดจากการติดเชื้อโรค โดยสาเหตุหนึ่งของภาวะกลุ่มโรคนี้คือการเกิดภาวะ oxidative stress ที่ทำให้ร่างกายมีปริมาณของสารอนุมูลอิสระไม่สมดุล โดยที่ผ่านมาจำนวนผู้ป่วยในโรคนี้มีจำนวนเพิ่มขึ้นอย่างต่อเนื่อง ซึ่งแนวทางการรักษาส่วนใหญ่มักจะมาจากการรักษาตามอาการ ดังนั้นการแก้ปัญหาโรคนี้ให้ได้ผลมากที่สุดคือการป้องกันการเกิดโรคมากกว่าการรักษา ผู้วิจัยจึงสนใจที่จะนำมะกรูดที่มีสรรพคุณต้านอนุมูลอิสระมาทดสอบ โดยมีวัตถุประสงค์เพื่อศึกษาฤทธิ์ของสารสกัดจากใบมะกรูดและผิวมะกรูด ในการช่วยลดการเกิดภาวะ oxidative stress สำหรับการช่วยยืดอายุของ C. elegans ที่ถูกชักนำให้เกิดภาวะ oxidative stress โดยแบ่งการศึกษาออกเป็น 4 ขั้นตอน ได้แก่ ตอนที่ 1 ศึกษาฤทธิ์ของสารสกัดจากมะกรูดต่อ E.coli OP50 ที่เป็นอาหารของ C. elegans พบว่าสารสกัดจากใบมะกรูดและผิวมะกรูดไม่มีผลในการยับยั้งการเจริญของ E.coli OP50 เมื่อเทียบกับการยับยั้งการเจริญเติบโตของยา Penicillin-Streptomycin ที่ใช้เป็นกลุ่มควบคุม จึงสามารถใช้สารสกัดจากใบมะกรูดและผิวมะกรูดในการทดสอบได้ โดยที่ไม่มีผลต่อ E.coli OP50 ที่ใช้เป็นอาหารของ C. elegans ตอนที่ 2 การศึกษาฤทธิ์ของสารสกัดจากใบมะกรูดและผิวมะกรูดที่มีผลต่อการรอดชีวิตของ C. elegans ที่ถูกชักนำให้เกิดภาวะ oxidative stress พบว่าสารสกัดจากใบมะกรูดและผิวมะกรูดที่ความเข้มข้น 50 , 100 และ 200 ug/ml มีอัตราการรอดชีวิตของ C. elegans เมื่อเทียบกับ C. elegans ที่ไม่ได้ให้สารสกัดจากใบมะกรูดและผิวมะกรูด แตกต่างกันอย่างมีนัยสำคัญทางสถิติ 0.05 และตอนที่ 3 การศึกษาฤทธิ์ของสารสกัดจากใบมะกรูดและผิวมะกรูดต่อการยับยั้งปริมาณ ROS ของ C. elegans ที่ถูกชักนำให้เกิดภาวะ oxidative stress โดยพบว่าใบมะกรูดและผิวมะกรูดที่ความเข้มข้น 50 , 100 และ 200 ug/ml มีค่าปริมาณสาร ROS ของ C. elegans ที่ให้สารสกัดจากใบมะกรูดและผิวมะกรูด เมื่อเทียบกับ C. elegans ที่ไม่ให้สารสกัดจากใบมะกรูดและผิวมะกรูด …

การปรับสมดุลไมโครไบโอมในลำไส้ด้วยเชื้อ Lactobacillus Rhamnosus Gg ช่วยบรรเทาความรุนแรงจากการติดเชื้อในกระแสเลือด ในหนูที่ถูกเหนี่ยวนำให้เกิดความชราโดยน้ำตาล D-Galactose และกระตุ้นภาวะติดเชื้อในกระแสเลือดโดยวิธีการผูกและเจาะลำไส้ใหญ่ส่วนต้น, ชาลิสา พินิจจันทร์

Chulalongkorn University Theses and Dissertations (Chula ETD)

การเสียสมดุลของจุลินทรีย์ในลำไส้อาจทำให้เกิดภาวะลำไส้รั่ว เกิดการติดเชื้อในกระแสเลือดตามมาได้ ซึ่งสภาวะดังกล่าวมักพบมากในผู้สูงอายุ การศึกษาก่อนหน้านี้พบว่าโพรไบโอติกสามารถลดการเสียสมดุลของจุลินทรีย์ในลำไส้ แต่การศึกษาเรื่องผลของการรับประทานเชื้อโพรไบโอติดต่อของการลดความรุนแรงจากการติดเชื้อในกระแสเลือด รวมทั้งภาวะ Sepsis-associated encephalopathy (SAE) ในผู้สูงอายุนั้นยังไม่มีการศึกษาที่ชัดเจน วัตถุประสงค์ของการศึกษา เพื่อทดสอบความสามารถของเชื้อโพรไบโอติกสายพันธุ์ Lacticaseibacillus rhamnosus GG (LGG) ในการช่วยลดความรุนแรงของการติดเชื้อในกระแสเลือดในหนูที่ถูกเหนี่ยวนำให้เกิดสภาวะชราโดยการใช้น้ำตาลกาแลคโตส ผู้วิจัยทำการให้เชื้อ LGG ทางปากกับหนูทดลอง เปรียบเทียบกับกลุ่มควบคุม และทดสอบความแตกต่างของจุลินทรีย์ในลำไส้ในอุจจาระของหนูด้วยวิธี 16S RNA sequencing พร้อมวัดสภาวะความชราของหนูด้วยเทคนิค Histochemistry ในอวัยวะภายใน จากนั้นหนูทั้ง 2 กลุ่มจะถูกกระตุ้นให้เกิดการติดเชื้อในกระแสเลือดโดยวิธีการผูกและเจาะลำไส้ใหญ่ส่วนต้น (CLP) และวัดความรุนแรงของการติดเชื้อในกระแสเลือดโดยการวัดอัตราการตาย ระดับ creatinine (Scr), Alanine transaminase (ALT), cytokines (IL-6 TNF-α IL-10 และ IL-1ß) ในซีรัมโดยเทคนิค Enzyme-linked immunosorbent assay (ELISA) การตรวจวัด Sepsis encephalopathy ผู้วิจัยใช้ค่ามาตรฐาน SHIRPA เพื่อช่วยในการวัด นอกจากนี้เพื่อหาสาเหตุของการลดความรุนแรงจากการติดเชื้อในกระแสเลือดด้วยเชื้อโพรไบโอติก ผู้วิจัยนำ Lactobacillus condition media (LCM) ร่วมกับ Lipopolysaccharide (LPS) มาใช้ในการกระตุ้นเซลล์ RAW 264.7 , เซลล์ BV-2 และเซลล์ HT-22 จากนั้นทำการวัดปริมาณ Inflammatory cytokines ด้วยเทคนิค ELISA และวัดการแสดงออกของยีน IL-6 TNF-α IL-10 IL-1ß Fizz Arg-1 NF-kB TLR-4 และยีน iNOS ด้วยเทคนิค Quantitative real-time PCR (qPCR) จากผลการวิเคราะห์จุลินทรีย์ในอุจจาระ แสดงให้เห็นว่าหนูชรามีการสูญเสียสมดุลของจุลินทรีย์ในลำไส้ และพบการเกิดพังผืดในปอด ไต และตับ ซึ่งเชื้อ …

Consequences Of Spatial Structure In Soil–Geomorphic Data On The Results Of Machine Learning Models, Daehyun Kim, Insang Song, Lorrayne Miralha, Daniel R. Hirmas, Ryan W. Mcewan, Tom G. Mueller, Pavel Samonil

Biology Faculty Publications

In this paper, we examined the degree to which inherent spatial structure in soil properties influences the outcomes of machine learning (ML) approaches to predicting soil spatial variability. We compared the performances of four ML algorithms (support vector machine, artificial neural network, random forest, and random forest for spatial data) against two non-ML algorithms (ordinary least squares regression and spatial filtering regression). None of the ML algorithms produced residuals that had lower mean values or were less autocorrelated over space compared with the non-ML approaches. We recommend the use of random forest when a soil variable of interest is weakly …

Increased Coding Potential Of Bovine Herpesvirus 1, Victoria Jefferson

Theses and Dissertations

Bovine respiratory disease (BRD) costs the cattle industry millions of dollars in costs in treatment and loss every year in the United States. A significant pathogen often contributes to BRD is Bovine Herpesvirus 1 (BoHV-1), a double stranded DNA virus with the ability to establish latency in the trigeminal ganglia and neurons. Primary infection with BoHV-1 results in immunosuppression that increases the risk of secondary bacterial infection and pneumonia. Because herpesviruses infect their hosts for life and can be reactivated in times of stress, BoHV-1 can present a recurring risk of BRD. The following research aims to expand the knowledge …

A Study Of The Snd1/Prmt5 Axis In Liver Cancer By Genetic Mouse Models, Tanner Wright, Tanner Wright

Dissertations and Theses (Open Access)

Arginine methylation is an essential post-translational modification (PTM) in cells. Protein arginine methyltransferase 5 (PRMT5) is the primary enzyme that catalyzes symmetric dimethyl arginine (SDMA) and requires methylosome protein 50 (MEP50) for stability and enzymatic activity which are necessary for life and development. Effector proteins bind different types of PTM’s to facilitate signaling. Staphylococcal nuclease Tudor domain containing 1 (SND1) is an effector that specifically binds SDMA via its single C-terminal Tudor domain. Both SND1 and PRMT5 have been implicated in hepatocellular carcinoma (HCC). SND1 has been confirmed as a driver of HCC using genetically engineered mouse models (GEMMs), though, …

Single-Cell Multiomics Of The Human Retina Reveals Hierarchical Transcription Factor Collaboration In Mediating Cell Type-Specific Effects Of Genetic Variants On Gene Regulation, Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M Deangelis, Yumei Li, Rui Chen

Faculty, Staff and Students Publications

BACKGROUND: Systematic characterization of how genetic variation modulates gene regulation in a cell type-specific context is essential for understanding complex traits. To address this question, we profile gene expression and chromatin accessibility in cells from healthy retinae of 20 human donors through single-cell multiomics and genomic sequencing.

RESULTS: We map eQTL, caQTL, allelic-specific expression, and allelic-specific chromatin accessibility in major retinal cell types. By integrating these results, we identify and characterize regulatory elements and genetic variants effective on gene regulation in individual cell types. The majority of identified sc-eQTLs and sc-caQTLs display cell type-specific effects, while the cis-elements containing genetic …

Engaging Students In A Genetics Course-Based Undergraduate Research Experience Utilizing Caenorhabditis Elegans In Hybrid Learning To Explore Human Disease Gene Variants, Natalie Forte, Virginia Veasey, Bethany Christie, Amira Carter, Marli Hanks, Alan Holderfield, Taylor Houston, Anil Challa, Ashley Turner

Research, Publications & Creative Work

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment—the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams …