Genetics Commons^™

The Role Of Mitochondrial Pyruvate Carrier 1 (Mpc1) In Heart Failure And Its Implications For Cardiac Recovery, Obadiah Issachar Kirk

Mahurin Honors College Capstone Experience/Thesis Projects

Heart failure (HF) is a complex syndrome with high mortality rates around the world. HF also has diverse etiology as many things contribute such as hypertension, obesity, coronary artery disease, inflammation, and cardiac arrhythmias. Studies have shown that unloading of a failing heart with a left ventricular assist device (LVAD) can lead to cardiac recovery in a subpopulation of individuals with advanced HF. RNA-sequencing and protein expression analysis of myocardial tissue from HF patients who underwent the LVAD implant and heart transplant indicated that subpopulation of HF patients who responded to LVAD unloading had significantly lower levels of mitochondrial pyruvate …

Using Cuda To Enhance Data Processing Of Variant Call Format Files For Statistical Genetic Analysis, Heather Mckinnon

All Graduate Projects

Utilizing the power of GPU parallel processing with CUDA can speed up the processing of Variant Call Format (VCF) files and statistical analysis of genomic data. A software package designed toward this purpose would be beneficial to genetic researchers by saving them time which they could spend on other aspects of their research. A data set containing genetics from a study of trichome production in Mimulus guttatus, or yellow monkey flower, was used to develop a package to test the effectiveness of GPU parallel processing versus serial executions. After a serial version of the code was generated and benchmarked, OpenACC …

Machine Learning Methods For The Analysis Of Metagenomes, Vito Adrian Cantu Alessio Robles

CGU Theses & Dissertations

As of October 2020, there are 18.6 × 1015 DNA base pairs publicly available in the Sequence Read Archive and this number is growing at an exponential rate. As DNA sequencing prices continue to drop, many research groups around the world have incorporated high throughput sequencing in their research, giving us access to sequences from many distinct ecosystems. This has revolutionized the field of metagenomics, which aims to fully characterize all organisms and their interactions in a particular system. Nevertheless, the plethora of available data has made its analysis difficult as traditional techniques such as genome assembly or sequence alignment …

Single Nucleotide Polymorphism (Snps) Study On X-Chromosome In Thai Sle Populations, Krisana Jaiwan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Systemic Lupus Erythematosus (SLE) is common autoimmune disease in Thailand which dominantly in females in ratio 9:1 of patients. Previous study has shown that the genetic components especially in X chromosome contributed a lot to the disease development. However, the susceptibility loci in Thai population have not been fully examined. Here, we conducted genome-wide association study (GWAS) on X chromosome using the data from two independent cohorts: primary dataset (controls = 1,683, SLE = 487) and secondary dataset (controls = 1,711, SLE = 455). Through meta-analyzing and imputation base on 1 KGP the two data set, SNP rs1059702 in IRAK1- …

Functional Analysis Of Squamosa-Promoter Binding Protein Like 13 In Controlling Flowering Time, Plant Architecture, Grain Size, And Grain Number In Wheat, Ajay Gupta

Electronic Theses and Dissertations

Higher and stable yield is always a major objective of wheat genetic improvement programs. The SQUAMOSA-promoter binding protein-like (SPL) genes constitute a small family of plant-specific transcription factors with diverse functions in plant development and growth and have great potential in improving yield and other major agronomic traits. However, the functional characterization of the SPL gene family in wheat is far behind other cereal crops such as rice. Using phylogenetic analysis, we identified 56 wheat orthologues of rice SPL genes belonging to 19 homoeologous groups. Among these 19 orthologous TaSPL genes, nine harbor the micro RNA 156 recognition element (MRE) …

Development And Validation Of Gene Delivery Methods For ​Crassostrea Virginica, Adrienne N. Tracy

Honors Theses

The Eastern oyster (Crassostrea virginica) is an important part of the East Coastal USA economy because aquaculture creates jobs. Sadly, the oysters are under constant threat due to increasing pollution, red tides, and diseases. Bivalves, and oysters in particular, are also becoming potential model organisms in medical research. With the sequencing of the oyster genome, scientists are focusing on deciphering the function of the predicted genes. However, the limited number of molecular and cellular tools available makes functional annotation of the genome challenging. A consistent, replicable gene delivery system needs to be developed to assess gene function and understand the …

The Origin And Evolution Of Flower Characters In Angiosperms With A Case Study On The Genetic Basis Of Zygomorphic Corolla Development In Bee And Hummingbird Pollinated Species Of Schizanthus (Solanaceae), Ghadeer Bukhari

Theses and Dissertations

This Ph.D. dissertation investigates two main projects separated into two chapters, one for each. The first chapter explores the evolution of flowering plants (angiosperms), a macro-scale study. The second project is on a micro-scale that focus on exploring the genes that regulate the similarities and the differences of flower morphology reflecting their different pollination syndromes in two species of Schizanthus (Solanaceae), i.e., S. pinnatus, a bee-pollinated flower, and S. grahamii, a hummingbird- pollinated flower.

In the first chapter, I used floral diagrams to study the origin and the evolution of floral traits in angiosperms, a new set of morphological data …

Novel Strategies To Overcome Carboplatin Resistance In Triple Negative Breast Cancer Using Patient Derived Xenografts, Mohammad A. Al Zubi

Theses and Dissertations

Triple-negative breast cancer (TNBC) patients have a poor prognosis and rely on chemotherapeutic treatment as standard of care. Often, they develop chemotherapy resistance, which leaves them without more therapeutic options, like targeted therapy. New models have been developed to test targeted inhibitors in human tumors, and they are known as patient-derived xenografts (PDX). These tumors are obtained from patients, then established and maintained in mice where they areused for tumor studies. In this work, we characterized 14 PDXs for their primary tumor growth rate and investigated metastatic propensity using spontaneous and experiment metastasis models. We utilized RNA-sequencing to characterize contributions …

Analysis Of Genetic Structure And Pathogen Dynamics Of Ixodes Scapularis In Southwestern Virginia, Leemu Jackson

Undergraduate Honors Theses

Ixodes scapularis, or the blacklegged tick, is the primary vector of Borrelia burgdorferi. This pathogen is the causative agent of Lyme disease, the most common vector-transmitted disease in the United States. Although I. scapularis is distributed throughout the eastern U.S., Lyme disease is only considered endemic in the northeastern region of the country. Prior to 2007, Lyme disease was uncommon in Virginia, but since then cases of Lyme disease have increased dramatically with a hotspot forming in the Roanoke-Blacksburg area. The purpose of the current study was to determine whether B. burgdorferi prevalence and the genetic structure of I. …

Dispelling The Mirage Of C4-Driven Drought Tolerance In Poaceae: A Phylogenomic Study, Matthew P. Nissenbaum

Graduate Research Theses & Dissertations

Climate change has been considered a key driver for adaptations in water usage efficiency (WUE) in plants. Perceptions persist that C4 photosynthesis is indicative of some level of WUE. Here, we examined the interaction and evolution of WUE within the grass family, Poaceae, as it pertains to photosynthetic pathway. Unique to this study is the magnitude of taxa sampled, presence of intrageneric sampling, and use of complete plastid genomes (plastomes) for phylogenomic analyses.

310 species were sampled, including 26 with newly sequenced plastomes, which were assembled de novo from next-generation sequencing data. Additional plastomes were downloaded from the National Center …

The Effects Of Parental Factors And Personal Attributes On Birth Control Use Under The Genetic Influences Of 5-Httlpr Among Adolescents, Hyun-Jin Cho

Legacy Theses & Dissertations (2009 - 2024)

The purpose of this study was (a) to examine relationships between parental influences and personal attributes on birth control use and (b) to identify genetic influences on such relationships by comparing the frequencies of common genetic variants—short allele vs. long allele—in 5-HTTLPR among adolescents (N = 5,852). Data from the Wave 1 and Wave 4 of the National Longitudinal Study of Adolescent Health were used to examine the birth control use of adolescents who were in 7th through 12th grade in 1994–1995. Multi-group Structural Equation Modeling analyses were used to identify the relationship among factors. Results did not find significant …

Role Of Microrna-483 In Pancreatic Β-Cells, Jackson Waugh

Dissertations, Master's Theses and Master's Reports

Insulin is an essential hormone produced by β-cells in the pancreas. The release of insulin is tightly regulated in healthy people in order to control blood sugar level in our body. However, people with Type 2 Diabetes have insufficient insulin secretion from pancreatic β-cells, leaving to high blood sugar (hyperglycemia) and β-cell failure. microRNAs (miRNAs or miR) are newly discovered small regulatory molecules and have emerged as important regulator of cell growth, differentiation, and organ function. Altered miRNA function has been implicated in the pathogenesis of a variety of human disease, including diabetes. In this report, we focus on dissecting …

การพัฒนาแถบตรวจ Mtb Strip แบบอ่านผลด้วยตาเปล่าอย่างรวดเร็ว สำหรับวินิจฉัยวัณโรคจากปฏิกิริยา Multiplex-Recombinase Polymerase Amplification, วิลาณี เดชขจร

Chulalongkorn University Theses and Dissertations (Chula ETD)

วัณโรคเป็นโรคติดต่อที่มีการระบาดทั่วโลก และยังคงเป็นปัญหาสาธารณสุขที่สำคัญของประเทศไทย วัณโรคยังเป็นสาเหตุของการเสียชีวิตจากโรคติดต่อสูงเป็นอันดับสองรองจากโรคเอดส์ โดยมีสาเหตุมาจากเชื้อแบคทีเรีย Mycobacterium tuberculosis complex (MTBC) การตรวจวินิจฉัยวัณโรคทางห้องปฏิบัติการ เป็นหนึ่งปัจจัยที่สำคัญในการควบคุมการแพร่ระบาดของโรค การนำเทคนิคทางอณูชีววิทยาเข้ามาใช้วินิจฉัยทางห้องปฏิบัติการ ซึ่งมีความรวดเร็วมากกว่าการเพาะเลี้ยงเชื้อด้วยวิธีดั้งเดิมและสามารถวินิจฉัยโรคได้ภายใน 1 วัน มีบทบาทที่สำคัญในการวินิจวัณโรคในปัจจุบัน การศึกษานี้มีวัตถุประสงค์ในการพัฒนาแถบตรวจ MTB Strip แบบอ่านผลด้วยตาเปล่าอย่างรวดเร็ว สำหรับวินิจฉัยวัณโรคจากปฏิกิริยา Multiplex-recombinase polymerase amplification (M-RPA) โดยใช้ไพรเมอร์ที่จำเพาะต่อ IS1081 และ IS6110 ซึ่งมีความจำเพาะต่อเชื้อ MTBC และตรวจสอบผลผลิตของทั้งสอง IS ร่วมกัน เพื่อเพิ่มความไวของเทคนิคในการวินิจฉัยวัณโรค การทดสอบเบื้องต้นกับดีเอ็นเอที่สกัดจากโคโลนีของเชื้อ แสดงให้เห็นว่าเทคนิค M-RPA ร่วมกับแถบตรวจ MTB Strip สามารถจำแนกเชื้อ MTBC ออกจาก NTM ได้อย่างถูกต้อง เมื่อนำเทคนิค M-RPA ร่วมกับแถบตรวจ MTB Strip มาวินิจฉัยกับดีเอ็นเอที่สกัดจากสิ่งส่งตรวจเสมหะจำนวน 131 ตัวอย่าง พบว่ามีความไวและความจำเพาะ เท่ากับ 91.03% และ 84.91% ตามลำดับ โดยมีค่าความสอดคล้องในเกณฑ์ดี (κ=0.762) เมื่อเปรียบเทียบกับการย้อมสีทนกรด ในขณะที่มีความไวและความจำเพาะเท่ากับ 100.0% และ 94.55% ตามลำดับ และมีค่าความสอดคล้องในเกณฑ์ดีมาก (κ=0.953) เมื่อเปรียบเทียบกับเทคนิค Real-time PCR เทคนิค M-RPA ร่วมกับแถบตรวจ MTB Strip ใช้ระยะเวลาทำปฏิกิริยาเพียง 25 นาที ภายใต้อุณหภูมิ 37 องศาเซลเซียส และตรวจสอบผลผลิตด้วยแถบตรวจ MTB Strip ภายในเวลา 15 นาที โดยตรวจสอบความเข้มข้นดีเอ็นเอตั้งต้นน้อยที่สุดได้เท่ากับ 0.1 ng/µl และไม่เกิดปฏิกิริยาข้ามกลุ่มเชื้อแบคทีเรียสายพันธุ์อื่นที่มักก่อโรคในระบบทางเดินหายใจ ดังนั้นเทคนิค M-RPA ร่วมกับแถบตรวจ MTB Strip จึงเป็นเทคนิคที่มีความรวดเร็ว ไม่ซับซ้อน …

Investigation Into The Roles Of Her9 And Capn5 During Retinal Development And Regeneration, Cagney Coomer

Theses and Dissertations--Biology

The formation of a healthy and functioning eye requires coordinated interactions between numerous signaling pathways and gene regulatory networks within the developing neural retina. Tight regulation of gene expression is required for cell specification and differentiation in this multilayered, light sensitive tissue. The photoreceptors are the light detecting cells of the retina, capable of functioning in both intense sunlight and dim light at night. When pigment cells of the photoreceptor outer segment are activated by light, a complex chain of events called phototransduction leads to the electrical signal cascade that is transmitted through the retina and ultimately to the brain …

Effects Of Thinning Regimes On Genetic Variation Of White Oak (Quercus Alba L.) In Upland Oak Forests Of Eastern Kentucky, Rachel Gayle Thunder

Theses and Dissertations--Forestry and Natural Resources

This research assesses the effects of silvicultural thinnings, varying in residual basal area and number of thinnings, on genetic diversity and relatedness of white oak (Quercus alba L.). The objectives were to (1) develop microsatellite DNA markers (simple sequence repeats, SSRs) for assessing the genetic diversity of white oak and (2) determine if thinnings significantly change the degree of diversity and relatedness in white oak stands. For objective 1, 84 primer pairs from previously predicted genomic SSRs of white oak were evaluated for consistent PCR amplification and polymorphism. Twenty of the 84 primer pairs amplified consistently and were confirmed …

Investigation Of The Phenotypic Effect Of Mutating A Highly-Conserved Cysteine Residue In The Rna Polymerase Beta Prime Subunit Of E. Coli Rna Polymerase, Meg Dillingham

Mahurin Honors College Capstone Experience/Thesis Projects

All bacteria contain a multi-subunit RNA polymerase (RNAPs) that is essential for gene expression. Because of the centrality of these enzymes in cellular life, the structure and function of the various subunits is intensely studied. The primary sequence of the RNAP β’ subunit contains five cysteine residues that are highly conserved. Four of the cysteines coordinate a zinc atom and form the beta prime subunit zinc binding domain (ZBD). Mutation of any one of the ZBD cysteines is lethal to the cell. However, the role of the fifth residue (C58), which is located upstream of the ZBD cysteines, has not …

Sampling The Local Fare: Fishes At The Sam Israel House Pit (45gr76), Soap Lake, Washington, Adam Fruge

All Master's Theses

The Sam Israel site is a precontact archaeological complex with numerous fish bones at the north end of Soap Lake, Washington. Excavated in 1976, the fish remains recovered from there were never fully analyzed prior to this research. Since this inland Columbia Plateau site had thousands of fish bones, it contained untapped potential for our understanding of ancient local fish procurement. As such, I conducted a detailed analysis of 2,862 fish bone specimens from the Sam Israel House Pit locus to: study a larger sample of fish bones in greater detail than was done before; compare the distribution of fishes …

Ecological And Genetic Connectivity Of Shrews (Sorex Spp.) Across Interstate-90 In The Washington Cascade Range, Jordan Ryckman

All Master's Theses

Roads negatively affect wildlife by degrading and fragmenting habitat. The I-90 Snoqualmie Pass East project was established to improve traffic safety for both humans and wildlife. Here, the Washington State Department of Transportation is constructing wildlife crossing structures to increase ecosystem connectivity as part of this project. The goal of my study was to investigate shrews – very small mammals with presumably low mobility and dispersal capacity – at sites on the eastern slopes of the Cascade Range where wildlife crossing structures will be built in the future. My main objectives were to verify shrew species composition, assess population genetic …

The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio

Graduate Theses, Dissertations, and Problem Reports (ETD)

The acquisition of microbial partners is a strategy used by a diverse group of arthropods to overcome ecological barriers that might normally make certain niches uninhabitable. The unique phylogenetic opportunities attainable from the natural experiment of the Sodalis-allied clade allow for better understanding of how molecular structures evolve through time. Here, we focus on the evolution of the flagellar synthesis pathway, due to its complexity and ability to diverge in response to ecological pressures. We used this molecular pathway and natural experiment to show that normal evolutionary outcomes associated with symbiosis (i.e., genome reduction) do not explain the predicted conservation …

Trees, Fungi, Insects: How Host Plant Genetics Builds A Community, Sandra Jeanne Simon

Graduate Theses, Dissertations, and Problem Reports (ETD)

Organisms, such as fungi and insects, can cause millions of acres of agricultural and forest damage, while others provide billions of dollars in ecological services such as education, aesthetic enjoyment, pollination, and gardening. Plant breeding and biotechnology can potentially help establish a balance between the proliferation of detrimental pests and attraction of beneficial insects. Variation in plant physiological and morphological characteristics are extremely important in the ability of host tissues to support many different types of organisms. When that variation is genetically heritable in a plant population, shifts in the underlying genes can have predictable consequences in structuring entire ecosystems. …