Robust Phylogenetic Regression, Richard Adams, Zoe Cain, Raquel Assis, Michael Degiorgio

Entomology and Plant Pathology Faculty Publications and Presentations

Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships. Over the past few decades, the phylogenetic regression framework has become a paradigm of modern comparative biology that has been widely embraced as a remedy for shared ancestry. However, recent evidence has shown doubt over the efficacy of phylogenetic regression, and PCMs more generally, with the suggestion that many of these methods fail to provide an adequate defense against unreplicated evolution—the primary justification for using …

The Influence Of Drd2 Polymorphism Exon 8 C/T (Rs6276) On Manifestations Of Delirium Tremens & Alcohol Withdrawal Seizures, Naomi Schneider

Honors Theses and Capstones

This study explores the correlation between the DRD2 Polymorphism exon 8 C/T (rs6276) and manifestations of delirium tremens (DT). DT is a condition that is clinically diagnosed utilizing two characteristic symptom manifestations: the presence of delirium and severe alcohol withdrawal. It is not entirely understood why DT can occur in some patients, but evidence has suggested that genetic predisposition can play a role. Utilizing the National Institutes of Health (NIH) All of Us Research database and performing a secondary analysis of existing genomic data, this candidate gene association study aims to determine the genotype frequencies within three cohorts: a healthy …

Investigating The Function Of Protein S-Acyltransferase 2 In Arabidopsis Thaliana Using Crispr Mutants, Nicole Benjamin

Honors Theses and Capstones

Arabidopsis thaliana contains 24 Protein Acyl Transferases (PATs). These enzymes are responsible for catalyzing the addition of a palmitate to a target substrate (palmitoylation). However, beyond its broad enzymatic function, it is unknown how PATs interact on a cellular level. This research focuses on identifying the function of PAT2. CRISPR-Cas9 was used to create deletion mutations that would result in a non-functional PAT. Two plants homozygous for a pat2 deletion were identified: pat2-5 and pat2-6. Preliminary results suggest that pollen grains in both pat2 mutants are larger in both length and width. Additionally, it appears that mutant pollen tends to …

Chromatin Regulation By Swi/Snf Remodelers In Somatic Stem Cell Maintenance And Transformation, Luke Thomas Deary

Dartmouth College Ph.D Dissertations

Cell identity is defined by the epigenome, whereby chromatin regulators work in concert to promote gene expression programs that serve a cell’s specialized purpose. Mutations in chromatin regulators are amongst the most frequent drivers of human disease, underscoring the importance of understanding their activities in maintaining cell identity and tissue function. In particular, mutations in subunits of the evolutionarily conserved SWI/SNF chromatin remodeling complexes drive diseases across human tissues in both development and adult tissue maintenance5. Three major SWI/SNF complexes exist: BAF, PBAF, and GBAF, which differ in their composition and genomic targeting but share an ATP-dependent catalytic activity to …

Sccad: Cluster Decomposition-Based Anomaly Detection For Rare Cell Identification In Single-Cell Expression Data, Yunpei Xu, Shaokai Wang, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li, Jianxin Wang

Computer Science Faculty Publications

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate …

Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation

Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited.

Results

Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of …

Hite: A Fast And Accurate Dynamic Boundary Adjustment Approach For Full-Length Transposable Element Detection And Annotation, Kang Hu, Peng Ning, Minghua Xu, You Zou, Jianye Chang, Xin Gao, Yaohang Li, Jue Ruan, Bin Hu, Jianxin Wang

Computer Science Faculty Publications

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, …

Leds For Controlled Environment Agriculture: Leveraging Light To Optimize Crops, Tristan D. Sanders

Graduate Theses, Dissertations, and Problem Reports (ETD)

Indoor agriculture is a growing industry with many of its benefits being recognized. Light emitting diodes (LEDs) reduce production costs compared to traditional light sources. LEDs emit narrow bandwidths of light that allow growers to easily change the wavelengths plants are being grown under by using different combinations of wavelengths. Manipulating the light that plants are grown under is a method to change their physiology which is the basis of this thesis. The goal of the first two studies was to investigate how different light spectra can be used to enhance the nutrition content, growth, and morphology of kale and …

Genetic And Transcriptomic Investigations Of Progressive Ethanol Consumption In The Diversity Outbred Mouse, Zachary Tatom

Theses and Dissertations

As a complex genetic disorder, alcohol use disorder (AUD) is thought to be influenced by many genes each contributing only a small effect to the overall disease liability. Dozens of genes have been implicated as potentially affecting risk for AUD and alcohol consumption. However, understanding the full genetic architecture of AUD – what genes are involved, to what extent, and how these genes are regulated – remains a challenging step in identifying novel treatments. Gene expression studies in humans have attempted to augment GWAS of alcohol consumption but are often confounded by environmental factors; the difficulty of collecting tissue from …

Identification And Characterization Of Two Novel Kcnh2 Mutations Contributing To Long Qt Syndrome, Anthony Owusu-Mensah, Jacqueline Treat, Joyce Bernardi, Ryan Pfeiffer, Robert Goodrow, Bright Tsevi, Victoria Lam, Michel Audette, Jonathan M. Cordeiro, Makarand Deo

Electrical & Computer Engineering Faculty Publications

We identified two different inherited mutations in KCNH2 gene, or human ether-a-go-go related gene (hERG), which are linked to Long QT Syndrome. The first mutation was in a 1-day-old infant, whereas the second was in a 14-year-old girl. The two KCNH2 mutations were transiently transfected into either human embryonic kidney (HEK) cells or human induced pluripotent stem-cell derived cardiomyocytes. We performed associated multiscale computer simulations to elucidate the arrhythmogenic potentials of the KCNH2 mutations. Genetic screening of the first and second index patients revealed a heterozygous missense mutation in KCNH2, resulting in an amino acid change (P632L) in the …

Can Edna Be Used To Locate Shawnee Hills Cavefish Forbesichthys Papilliferus?, Megan Brandt, Timothy Spier Phd, Gary Zeruth Phd

Murray State Theses and Dissertations

Traditional stream fish sampling methods, such as seining and electrofishing, are time consuming, expensive, and limited to short stretches of stream. However, the analysis of environmental DNA (eDNA) from water samples promises to be a quick, inexpensive method for detecting fish. The streams of the Land Between the Lakes Recreational Area (LBL) are unique, undisturbed streams which contain many interesting fish species for which little information exists. One such rare species is the Shawnee Hills Cavefish Forbesichthys papilliferus, which is known to exist in a few LBL streams. However, the complete distribution of the Shawnee Hills Cavefish in LBL …

The Effects Of Early Exposure To Prescription/Illicit Drugs And Drug Metabolites On Larval Zebrafish Behavioral And Motor Function Development, Jacob Thomas, Dena Weinberger, Bikram Subedi, Brandon Capps

Murray State Theses and Dissertations

THE EFFECTS OF EARLY EXPOSURE TO PRESCRIPTION/ILLICIT DRUGS AND DRUG METABOLITES ON LARVAL ZEBRAFISH BEHAVIORAL AND MOTOR FUNCTION DEVELOPMENT

A Thesis Presented to the Faculty of the Department of Biology

Murray State University

Murray, Kentucky

In Partial Fulfillment of the Requirements for the Degree of Masters In Science

By Jacob Thomas, B.S., Murray State University

December 2024

Acknowledgements

Brandon Capps, who pretty much did a whole third of the legwork on this project and saved me lots of headaches;

Chandler Maddox, one of the University of Kentucky’s finest undergrads who came in from the top rope with a folding chair …

Comparing Alternative Developmental Modes: Structure And Gene Expression In The Olfactory System Of Plethodontid Salamanders, Giuseppina S. Lanzilli

Cal Poly Humboldt theses and projects

The olfactory system of extant amphibians changes as the animal transitions from a fully aquatic to a terrestrial lifestyle at metamorphosis. Cellular morphology of the nose and expression patterns of olfactory genes in the nasal cavity have been examined for a variety of frogs and salamanders, but among plethodontid salamanders, molecular data are available only for Plethodon shermani. Using standard histology and micro-CT reconstruction, I investigated the structure of the olfactory organs of larvae, juveniles, and adults of six plethodontid species, with terrestrial, streamside, semiaquatic, and aquatic adults. The overall structure of the olfactory cavity was generally similar across …

Evaluating The Utility Of Tracers To Characterize Environmental Dna Transport And Inform Detection Of Fishes In Small Streams, Gavin B. Bandy

Cal Poly Humboldt theses and projects

This study was motivated by the need to develop a noninvasive and highly sensitive monitoring tool for determining local occupancy of an endangered aquatic species To make inference into the occupancy of fishes within small stream sites, we developed a method to determine whether environmental DNA (eDNA) concentrations from a target species were elevated relative to a tracer, formulated to mimic eDNA and introduced at a single location. We examined patterns in the observed distribution of the tracer to account for the effects of site-specific transport processes and sampling on distributions of naturally occurring eDNA at small spatial scales (400 …

Ai And Ml-Based Risk Assessment Of Chemicals: Predicting Carcinogenic Risk From Chemical-Induced Genomic Instability, Ajay Vikram Singh, Preeti Bhardwaj, Peter Laux, Prachi Pradeep, Madleen Busse, Andreas Luch, Akihiko Hirose, Christopher J. Osgood, Michael W. Stacey

Biological Sciences Faculty Publications

Chemical risk assessment plays a pivotal role in safeguarding public health and environmental safety by evaluating the potential hazards and risks associated with chemical exposures. In recent years, the convergence of artificial intelligence (AI), machine learning (ML), and omics technologies has revolutionized the field of chemical risk assessment, offering new insights into toxicity mechanisms, predictive modeling, and risk management strategies. This perspective review explores the synergistic potential of AI/ML and omics in deciphering clastogen-induced genomic instability for carcinogenic risk prediction. We provide an overview of key findings, challenges, and opportunities in integrating AI/ML and omics technologies for chemical risk assessment, …

Functional Investigation Of Shaggy, An Inhibitor Of Canonical Wnt Signaling, In The Tardigrade Hypsibius Exemplaris, Raul A. Chavarria

UNF Graduate Theses and Dissertations

Tardigrades have a highly simplified anteroposterior (AP) axis. The mechanisms that regulate the development of this secondarily simplified AP axis are not known. In many animals, the canonical Wnt (cWnt) signaling pathway regulates primary axis establishment through antagonistic interactions with inhibitors of cWnt signaling. This study investigated the roles of shaggy, an inhibitor of cWnt signaling, in regulating development in the tardigrade Hypsibius exemplaris. Gene expression patterns of shaggy and other components of the cWnt signaling pathway were analyzed alongside markers of anterior and posterior identity using Hybridization Chain Reaction in situ in H. exemplaris. RNA interference …

Chemical Synthesis Of Sensitive Dna, Komal Chillar

Dissertations, Master's Theses and Master's Reports

Over the past decades, researchers have tried various chemical methods to synthesize modified oligodeoxynucleotides (ODNs, i.e. short segments of DNAs). Traditional ODN synthesis methods require strong basic, and nucleophilic conditions for the deprotection and cleavage of the ODN from the solid support. However, the sensitive ODNs containing labile functionalities are vulnerable to such harsh conditions. Sensitive ODNs have a wide range of applications in research and pharmaceuticals. To synthesize sensitive ODNs, researchers devised different strategies but no practical methods have been developed. To overcome these challenges, we developed alkyl Dim alkyl Dmoc technology. This innovative technology uses weakly basic and …

Assessing Tropical Mammal Diversity And Distribution Using Noninvasive Methods, Tiff L. Degroot

Dissertations, Master's Theses and Master's Reports

Central African tropical forests are rich in biodiversity and home to some of Earth’s most threatened mammals. However, mammals in the region are under increasing threat from habitat loss and degradation, coupled with an increased demand for wild meat. To conserve mammals, wildlife managers and community-led conservation efforts must understand the distribution and diversity of mammal communities. However, funding and logistical challenges make contemporary survey methods, e.g. ground surveys, difficult and expensive. Noninvasive methods allow efficient mammal diversity surveys with minimal field effort. Here, we use camera trapping and invertebrate-derived environmental DNA (“iDNA”) to assess mammal diversity and distribution in …

A Multimolecular Perspective On The Success Of Wolf Recovery And Relocation, Samuel D. Hervey

Dissertations, Master's Theses and Master's Reports

With global biodiversity in decline and many species isolated in fragmented habitats, conservation efforts increasingly rely on natural recolonization and translocation to restore ecosystems. These strategies face challenges such as genetic erosion and habitat limitations, highlighting the need for effective monitoring practices. This research assesses the success of wolf recovery initiatives by examining long-term genetic and genomic health using both traditional and advanced molecular methods. First, we investigated the genetic health of 19 gray wolves (Canis lupus) relocated to Isle Royale National Park to restore ecosystem balance. Initial genetic assessments with microsatellites found that these wolves had genetic diversity metrics …

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 …