Genetics and Genomics Commons^™

Microsatellites Reveal The Population Genetic Structure Of Yellow Perch In Minnesota, Megan Boche

Journal of Earth and Life Science

When analyzing a population’s genetic makeup, looking at variation of individuals and populations is a crucial factor. The management of yellow perch will be aided by this information particularly in regard to stocking or relocation. Microsatellite loci were used to analyze the genetic population structure of yellow perch Perca flavescens within and among 29 sampling areas throughout Minnesota’s basins. Seven microsatellite DNA loci were evaluated, with heterozygosities ranging from 0.41 to 0.78. The Lower Mississippi basin samples showed higher numbers of alleles per locus and greater expected heterozygosities compared to other basins, with Lake Pepin (PEP) exhibiting the highest average …

Marine Heatwave Response Plan For Western Australia’S Wild Capture Fisheries And Aquaculture, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

The purpose of the Western Australian wild capture fisheries and aquaculture marine heatwave response plan (the Plan) is to document the Department’s approach for identifying and responding to the hazard of a marine heatwave on wild catch fisheries (commercial, recreational, charter and customary) and aquaculture resources within the geographic boundaries of WA. It provides risk reduction strategies and establishes best-practice processes for each stage of the hazard management and response continuum, ensuring that DPIRD is able to adequately prepare for, respond to, and recover from marine heatwave events. This Plan operates in conjunction with WA’s existing aquatic resource management framework, …

Snake Venoms As Models For Understanding The Origins And Evolution Of Gene Regulatory Networks, Siddharth S. Gopalan

Biology Dissertations - Archive

Understanding the relationship between genotype and phenotype is a fundamental goal of biology. However, the vastly complex nature of eukaryotic gene regulation can make deriving precise relationships between genotype and phenotype challenging. The gene regulatory architecture of snake venom systems provide an opportunity to study this problem in a phenotypic system with immense variation in phenotypes and the underlying genetics. Using a set of integrated functional genomic approaches with snake venoms as a central model, in this dissertation, I provide several examples of the regulatory mechanisms by which diversity in phenotypes arises. Specifically, I identify how gene expression heterogeneity between …

Genetic Analysis Of Methionine Restriction-Associated Mitochondrial Unfolded Protein Response Signaling., Josh D. Dodge

Biology Dissertations - Archive

The lifespan of an organism is dictated by various genetic and environmental factors. One such determinant is the health of mitochondria which are organelles that mediate various critical cell functions including a significant role in generating the vast supply of cellular energy. Indeed, the gradual decline of mitochondrial function is believed to be a hallmark and possible cause of aging. Paradoxically, mild mitochondrial dysfunction early in life extends lifespan in various model organisms. Cells use diverse approaches to promote mitochondrial homeostasis, including the transcriptional reprogramming of cells by mitochondrial unfolded protein response (UPRmt) to mitigate mitochondrial stress. Consistently, UPRmt activation …

Utilizing Β-Gal To Visualize Selective Transport Of The Ssa4 Gene In S.Cerevisiae, Ian M. Staertow, Rebecca L. Adams Phd

Science University Research Symposium (SURS)

In eukaryotic cells such as Saccharomyces cerevisiae, protein synthesis begins with the transport of mRNA from the nucleus to the cytoplasm. In order for mRNA to leave the nucleus, it must first bind to specific transport proteins which can then facilitate transport via the nuclear pore complex (NPC), a selectively permeable membrane within the cell's nuclear envelope. Under environmental stress, such as heat shock, S. cerevisiae cells modulate transport rates. In this case, in heat stress or “heat shock” most mRNA transcripts will remain in the nucleus. The SSA4 transcript encodes for a chaperone protein which facilitates the subsequent export …

Influence Of Multi-Species Data On Gene-Disease Associations In Substance Use Disorder Using Random Walk With Restart Models, Erich J. Baker, Everest U. Castaneda, Sharon Moore, Jason A. Bubier, Stephen K. Grady, Michael A. Langston, Elissa J. Chessler

Funded Scholarship

A major challenge lies in discovering, emphasizing, and characterizing human gene-disease and gene-gene associations. The limitations of data on the role of human gene products in substance use disorder (SUD) makes it challenging to transition from genetic associations to actionable insights. The integration of data from multiple diverse sources, including information-dense studies in model organisms, has the potential to address this gap. We demonstrate a modified performance of the Random Walk with Restart algorithm when multi-species data is integrated in the heterogeneous network within the context of SUD. Additionally, our approach distinguishes among disparate pathways derived from the Kyoto Encyclopedia …

Derivation Of The Maintenance Energy Requirements In Growing Jersey Heifers: Supplementary Table S1, Addison L. Carroll, Michael J. Vandehaar, Paul J. Kononoff

Department of Animal Science: Faculty Publications

Supplemental table for Addison L. Carroll, Michael J. VandeHaar, and Paul J. Kononoff. Derivation of the maintenance energy requirements in growing Jersey heifers. Journal of Dairy Science (2025).

Beyond Homogeneity: Exploring Causal Heterogeneity In Psychopathology, Philip B. Vinh

Theses and Dissertations

Traditional models in psychiatric research often impose assumptions of causal homogeneity, treating population-level associations as reflective of uniform underlying mechanisms. This dissertation challenges that assumption by introducing statistical and machine learning frameworks designed to detect and model causal heterogeneity in the development of psychopathology. Central to this approach is the advancement of finite mixture structural equation modeling (FM-SEM) to identify latent subgroups characterized by distinct, and sometimes opposing, causal pathways.

The dissertation comprises three integrated empirical studies. The first introduces mixDoC, a finite mixture extension of the classical Direction of Causation (DoC) model applied to twin data, enabling the detection …

The Role Of Horizontal Gene Transfer In Antibiotic Resistance Amidst Prevalent Community And Healthcare-Associated Mrsa Rates, Gabrielle Nascimento

Honors College Theses

In recent decades, cases of community-acquired MRSA (CA-MRSA) and healthcare-associated MRSA (HA-MRSA) have been on the rise. The ability of antibiotic resistance to transfer between microorganisms greatly expands its threat to the effective treatment and containment of bacterial infections. The mecA gene is found on a mobile cassette within the Staphylococcal cell and encodes for PBP2a, an alternate version of penicillin-binding protein (PBP) with less binding affinity for β-lactam antibiotics, increasing resistance to the effects of antibiotics. The goal of this research is to investigate the horizontal transfer of the mecA gene between various Staphylococcus species as well as to …

Using Abandoned Model Systems And Historical Literature To Teach Modern Concepts And Techniques In Cell Biology, Leocadia V. Paliulis, Gunar Fabig, Sandra Stein, Silke Tulok, Anja Nobst, Chukwuebuka William Okafornta, Thomas Kurth, Thomas Müller-Reichert

Faculty Journal Articles

The cell biology literature of the 19th and early-to-mid 20th centuries is full of the seminal works that were critical for the development of our current understanding of biology but were done using model systems that are no longer commonly used. We argue that these historical papers are ideal for the development of course-based research experiences, both because the background work is conceptually and technically straightforward, and because the study of the abandoned systems stopped prior to the availability of modern techniques. These abandoned systems offer outstanding opportunities for teaching modern light and electron microscopy techniques, thus providing students with …

General Kernel Machine Methods For Multi-Omics Integration And Genome-Wide Association Testing With Related Individuals, Amarise Little, Ni Zhao, Anna Mikhaylova, Angela Zhang, Wodan Ling, Florian Thibord, Andrew D. Johnson, Laura M. Raffield, Joanne E. Curran, John Blangero

School of Medicine Publications

Integrating multi-omics data may help researchers understand the genetic underpinnings of complex traits and diseases. However, the best ways to integrate multi-omics data and use them to address pressing scientific questions remain a challenge. One important and topical problem is how to assess the aggregate effect of multiple genomic data types (e.g. genotypes and gene expression levels) on a phenotype, particularly while accommodating routine issues, such as having related subjects' data in analyses. In this paper, we extend an existing composite kernel machine regression model to integrate two multi-omics data types, while accommodating for general correlation structures amongst outcomes. Due …

Functional Characterization Of The Hdt5 Gene In Aspergillus Flavus Morphogenesis, Mycotoxin Production, And Fungal Phytopathogenicity, Brenda Omburo

Graduate Research Theses & Dissertations

The present study aimed at elucidating the role of hdt5 in fungal morphology, mycotoxin production and in plant virulence in Aspergillus flavus. Currently, methodologies to prevent the negative impact of A. flavus are insufficient. It is known that expression of the hdt5 gene is dependent on hbx1, a master regulatory gene that affects expression of hundreds of genes in the A. flavus genome, controlling both development and secondary metabolism. However, while the aflatoxin gene cluster has been elucidated, the genetic regulatory mechanisms controlled by hdt5 are not fully understood. For this study, therefore, a complete strain set composed of a …

Gadd34 And Crep Regulation In The Unfolded Protein Response, Comparing Molecular Mechanisms In Humans And Zebrafish, Angela Adams

University of the Pacific Theses and Dissertations

In eukaryotic cells, many newly synthesized proteins are sent to the endoplasmic reticulum (ER) of a cell to be folded into the proper conformation for functionality. When proteins get misfolded, or cannot be folded fast enough, these proteins accumulate in the ER which causes the cell to become stressed. This leads to a process known as the Unfolded Protein Response (UPR). Once UPR has been initiated, the α subunit of eukaryotic initiation factor 2 (eIF2α) becomes phosphorylated to inhibit global protein synthesis within the cell, while simultaneously activating the expression of several genes to either aid in cell recovery or …

History, Annotated Gazetteer, And Bibliography Of Ornithology In Kalimantan, Indonesian Borneo, Frederick H. Sheldon, Mohammad Irham, Daisy G. S. Kho, Erik Meijaard, Subir B. Shakya, Dewi M. Prawiradilaga, Sebastianus (Bas) Van Balen

Occasional Papers of the Museum of Natural Science, Louisiana State University

Kalimantan comprises nearly three quarters of the island of Borneo and is the place where scientific study of Bornean birds began. We describe the history of bird research in Kalimantan from its beginning, highlighting the ornithologists who explored the region and how their interests and methods changed over time, from a concentration on specimen collection, to examinations of community ecology, to conservation in the face of habitat change and species depletion, to the latest investigations using satellite, genetic, and digital technology. We also highlight some future directions for research, especially the need for more work on basic ecology and biogeography. …

Potential Of Using Trembling Aspen To Make Structural Engineered Wood Products, Dawei Wang

Aspen Bibliography

Trembling aspen (Populus tremuloides) is abundant in Canada but is widely considered an underutilized species. This study was aimed at evaluating the potential of using aspen lumber to produce cross-laminated timber (CLT), glued-laminated timber (glulam), and wood I-joists. The key mechanical properties of these engineered wood products, which were fabricated using a modified grading criterion, were examined. It was found that 1) The mean effective bending stiffness and characteristic bending moment resistance of 5-layer CLT specimens in the major-strength direction were 5,069x10⁹ N·mm²/m and 97.65x10⁶ N·mm/m; 2) The mean apparent MOE and characteristic modulus …

Borreliosis And Doxycycline Treatment Disrupt Gut Microbiota And Immune Responses In Nonhuman Primates, Ethan G. Napier, Isaac R. Cinco, Sheridan B. Wagner, Ethan V. Stuart, Qi Qiao, Joshua Taylor, Brian Stevenson, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Borrelia burgdorferi (Bb) is the spirochete that causes Lyme disease (LD). Transmission to humans occurs via bites of infected Ixodes spp. ticks. Doxycycline is often used to treat LD patients, which is sometimes delayed due to current diagnostic challenges. Recently, several lines of evidence show dysbiosis of the gut microbiome in LD patients, which may be a host factor contributing to pathogenesis and symp tomology but is still an understudied area in the field. To address this knowledge gap, we longitudinally compared the immune response and gut microbial composi tion of Japanese macaques after intradermal infection with Bb strain 297 …

Periconceptual Nutrition And The Preimplantation Embryo: Approaches For Intervention And Generational Health, Abigail Klein

Dissertations and Theses

The typical American diet exceeds dietary fat recommendations, contributing to the rising rates of obesity. This negatively impacts fertility, pregnancy and fetal growth, and lifelong offspring health. During pregnancy, this also increases risk of co-morbidities like gestational diabetes. Despite this, lipids are not screened during pregnancy and limited research exists evaluating these co-exposures on offspring health. Our lab used a rat model of maternal high fat (HF) diet with late-gestation diabetes (DM) to demonstrate that mitochondrial dysfunction and oxidative stress incite lifelong cardiometabolic disease risk in offspring. To determine the timing of damage, we hypothesized that maternal overnutrition incites mitochondrial …

Gramseq-Dta: A Grammar-Based Drug-Target Affinity Prediction Approach Fusing Gene Expression Information, Kasul Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug–target affinity (DTA) prediction is a critical aspect of drug discovery. The meaningful representation of drugs and targets is crucial for accurate prediction. Using 1D string-based representations for drugs and targets is a common approach that has demonstrated good results in drug–target affinity prediction. However, these approach lacks information on the relative position of the atoms and bonds. To address this limitation, graph-based representations have been used to some extent. However, solely considering the structural aspect of drugs and targets may be insufficient for accurate DTA prediction. Integrating the functional aspect of these drugs at the genetic level can enhance …

Characterizing Somatic Variants In Nanopore Data With Machine Learning, Shwethal Sayeeram Trikannad

Master's Projects

Oxford Nanopore Technology (ONT) is a popular long-read sequencer in genomics. However, its high base-calling error rate produces several sequencing artifacts. Detection of somatic variants in ONT sequenced tumor-normal samples remains challenging due to low frequencies. In this study, machine learning was applied to a dataset created by benchmarking ClairS output against HCC1395 and colo829 truth sets to classify variants and artifacts. Relevant features were engineered from sequence context and variant site characteristics to model artifact profiles. HistGradientBoostingClassifier achieved 0.876950 accuracy, outperforming all other models. Variant quality was the top predictor with an aggregate accuracy of over 85%. This work …

Determination Of Structural Factors Contributing To Protection Of Zinc Fingers In Estrogen Receptor Α Through Molecular Dynamic Simulations, Patricia B. Lutz, Wesley R. Coombs, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

The ERα transcription factor that induces tumor growth is a potential target for breast cancer treatment. Each monomer of the ERα DNA-binding domain (ERαDBD) homodimer has two conserved (Cys)₄-type zinc fingers, ZF1 (N-terminal) and ZF2 (C-terminal). Electrophilic agents release Zn²⁺ by oxidizing the coordinating Cys of the more labile ZF2 to inhibit dimerization and DNA binding. Microsecond-length molecular dynamics (MD) simulations show that greater flexibility of ZF2 in the ERαDBD monomer leaves its Cys more solvent accessible and less shielded from electrophilic attack by sulfur-centered hydrogen bonds than ZF1 which is buried in the protein. In the …