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Thinking Beyond Association Tests: Using Mathematical Models To Identify Genes Influencing Exceptional Longevity, Sandeep Acharya

McKelvey School of Engineering Graduate Student Theses & Dissertations

The main goal in the genetic study of trait biology is to identify genetic factors, such as variants and genes, that causally influence traits and to understand the downstream mechanisms through which they exert their effects. This dissertation improves our understanding of trait biology by building on widely applied omics-wide association studies (omics-WAS), such as GWAS and TWAS, and proposing methods that (1) combine association statistics from multiple omics modalities and (2) systematically incorporate prior knowledge from biological networks and functional annotations with omics-WAS summary statistics. First, we apply meta-analysis to integrate gene-level p-values from GWAS, TWAS, and rare-variant analyses …

Exploring Ddr2’S Role In Caf Extracellular Matrix Production And Tumor Progression, Favour Ayomide Akinjiyan

Arts & Sciences Graduate Student Theses and Dissertations

Ovarian cancer has poor survival outcomes particularly for advanced stage, metastatic disease. Metastasis is promoted by interactions of stromal cells, such as cancer-associated fibroblasts (CAFs) in the tumor microenvironment (TME), with tumor cells. CAFs play a key role in tumor progression by remodeling the TME and extracellular matrix (ECM) to result in a more permissive environment for tumor progression. It has been shown that fibroblasts, in particular myofibroblasts, utilize metabolism to support ECM remodeling. However, the intricate mechanisms by which CAFs support collagen production and tumor progression are poorly understood. In this study, we show that the fibrillar collagen receptor, …

Functional And Comparative Genomics Of The C.Sojina- Soybean Interaction, Alejandra Maria Vargas Oyuela

LSU Master's Theses

Frogeye leaf spot (FLS), caused by Cercospora sojina, is a significant foliar disease of soybean (Glycine max) and is responsible for substantial yield losses worldwide. While management strategies rely on host resistance and fungicide applications, the emergence of new virulent races and fungicide-resistant isolates necessitates a deeper understanding of C. sojina host interactions and genomic variability. Here, we employed comparative and functional genomic approaches to decipher the molecular mechanisms underlying the C. sojina-soybean interaction. A dual RNA sequencing approach was used to identify transcriptomic changes in G. max cultivars Blackhawk (susceptible) and Davis (resistant) across multiple …

A Natural Short Sleep Mutation Promotes Longevity Through Mitochondrial Respiration In Drosophila, Pritika Pandey

LSU Doctoral Dissertations

Aging is an irreversible process characterized by progressive physiological decline and an increased risk of metabolic disorders, cognitive impairment, cardiovascular diseases, and neurodegeneration. Disruptions to the circadian clock—whether due to genetic mutations or behavioral factors—accelerate aging and age-related pathologies, highlighting a strong link between circadian regulation and longevity. However, certain individuals harbor a dec2^P384R mutation, which enables natural short sleep without the detrimental effects of chronic sleep deprivation. This suggests that these individuals have evolved adaptations that activate pro-health pathways, allowing them to function optimally with reduced sleep. To investigate the genetic mechanisms underlying these changes, we developed a …

Passive Integrated Transponders: An Effective Marking Technique For Individual Identification Of Anaxyrus Fowleri?, Emily Haner

Steeplechase: An ORCA Student Journal

With the rise of fungal disease such as Chytridiomycosis causing massive population declines for many species of frogs and toads (order Anura), specific conservation strategies are needed now more than ever. In many cases, being able to mark and identify individuals is a necessary step in developing an effective conservation plan. Individual identification allows researchers to obtain accurate population estimates, which are needed to test the progress and validity of conservation management decisions. However, due to their unique life history, including cutaneous respiration, Anurans are among the most difficult wildlife species to effectively mark for individual identification. In a mesocosm …

Crossword: Test Your Biology!, Sukie Weinger

Osmosis Magazine

Biology themed Crossword Puzzle.

Intelligence Without An 'I': "I Think, Therefore I Am", Darshan Shah

Osmosis Magazine

From Billie Eilish hits to corny Pinterest tattoos, Rene Descartes’ famous dictum is embedded in modern Western consciousness. But, like all philosophy, it operates within a paradigm of assumptions about the world that remain open to challenge. Over centuries of Cartesian influence, these assumptions have become invisible in our philosophies and sciences, informing the very questions we ask about intelligence and where we search for it in the world.

Zealandan Interview With Dr.Kristine Grayson From Aotearoa New Zealand, Paxton Mills

Osmosis Magazine

ZealandDr. Kristine Grayson, Associate Professor of Biology, has been passionate about science and travel, particularly toAotearoa New Zealand, for some time.

The Science Behind Covid Testing, Zion Kim

Osmosis Magazine

On March 11, 2020, the World Health Organization (WHO) officially declared a COVID-19 pandemic (“CDC…”, 2024). We all remember the days we had to wear masks, shove cotton swabs into our noses and mouths, and quarantine ourselves from others after being infected by the COVID-19 virus. We take this test all the time and trust their accuracy, but we never stop to ask how they work. We all know that a double line indicates an infection of COVID-19, but why?

Arsenic & The Princess Bride: How Your Body Handles Poison, Martin Jara

Osmosis Magazine

It’s a simply iconic scene from a simply iconic movie; in the cult classic film The Princess Bride, the protagonist Westley faces off against the scoundrel Vizzini in a battle of wits to rescue his true love. The challenge is simple: each man is given a chalice, one of them containing poisonous iocane powder. Colorless, odorless, tasteless, and soluble in water, Vizzini must choose the unpoisoned chalice off wits alone. However, he chooses wrong, dying instantly.

Not Human Enough: The Origins Of The Uncanny Valley, Franklin Young

Osmosis Magazine

Why do we feel creeped out when we see something almost human—like a lifelike robot or a bad CGI character? This phenomenon, known as the uncanny valley, describes the uncomfortable emotional response humans experience when encountering entities that appear nearly, but not quite, human. First introduced by Japanese robotics professor Masahiro Mori in 1970, the concept suggests that as objects become more humanlike in appearance, our emotional response to them becomes increasingly positive —until reaching a point where subtle imperfections trigger strong feelings of revulsion.

The Neurobiology Of Schizophrenia: Reduced Brain Volume And Its Implications, Erlinda Sali

Osmosis Magazine

Schizophrenia is a neurological disorder that is highly complex and often misunderstood. Characterized by hallucinations and delusions, disorders of thought and speech, behavior, and emotions, schizophrenia is more complex than how the media portrays it.

Osmosis Magazine - Science Magazine

Osmosis Magazine

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Cutting Waste In Tupper's Restaurant, Logan Salvator, Christien Merritt, Lily Amaral, Erik Dukes

Earth Day Symposium on Climate and Sustainablity

No abstract provided.

A New Centruroides Species And First Record Of C. Tapachulaensis Hoffmann, 1932 (Scorpiones: Buthidae) From Honduras, Luis F. De Armas, Alex M. Cubas-Rodríguez

Euscorpius

A new species of striped bark scorpions, Centruroides lenca sp. n. is described, based on both sexes, from the Pacayita Volcano Biological Reserve (2,385 m a. s. l.), Ocotepeque Department, in the southwestern Honduras. By its general pattern, the new species resembles C. thorellii (Kraepelin, 1891), from which it clearly differs by having stronger and very darker pedipalp chelae, minute subaculear tubercle and basal pectinal plate with a large central pit in the female, among other diagnostic characters. Also, Centruroides tapachulaensis Hoffmann, 1932 is recorded for the first time from Honduras, on the basis of two observed or collected specimens …

Developing An Unfolding-Incorporated Coarse-Grained Polymer Model For Fibrinogen To Study The Mechanical Behaviour, Vivek Sharma, Poulomi Sadhukhan

Northeast Journal of Complex Systems (NEJCS)

Fibrinogen is a protein found in blood that forms Fibrin polymer network to build a clot during wound healing process when there is a cut in the blood vessel. The fibrin fiber is highly stretchable and shows a complex mechanical properties. The fibrin monomer, Fibrinogen, has a very complex structure which is responsible for its unusual elastic behaviour. In this work, we focus on mechanism of unfolding of D-domain of Fibrinogen, and study its effect in the mechanical behaviour. We develop a coarse-grained (CG) bead-spring model for Fibrinogen which captures the unfolding of folded D-domains along with other necessary structural …

Biallelic Fgf4 Variants Linked To Thoracic Dystrophy And Respiratory Insufficiency, Laura M. Watts, Esther Kinning, Donald R. Latner, Marla Johnston, Jessica Patrick-Esteve, Gregory M. Cooper, Stephen R.F. Twigg, Alistair T. Pagnamenta, Jenny C. Taylor

School of Medicine Faculty Publications

The thoracic dystrophies are inherited skeletal conditions where abnormal embryonic development of the thoracic skeleton results in a narrow chest, pulmonary hypoplasia, and respiratory insufficiency, which can be severe or lethal. The majority of thoracic dystrophies are due to biallelic alterations in genes needed for normal ciliary function. However, despite the identification of over 20 genes as causal for the thoracic dystrophy phenotype, around 20% of patients remain without a molecular diagnosis. We present two unrelated families with a clinical diagnosis of thoracic dystrophy with associated respiratory insufficiency without a molecular diagnosis on previous genetic testing. Both harbor rare biallelic …

Ensemble Learning With Explainable Ai For Improved Heart Disease Prediction Based On Multiple Datasets, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Zhongming Zhao

Faculty, Staff and Student Publications

Heart disease is one of the leading causes of death worldwide. Predicting and detecting heart disease early is crucial, as it allows medical professionals to take appropriate and necessary actions at earlier stages. Healthcare professionals can diagnose cardiac conditions more accurately by applying machine learning technology. This study aimed to enhance heart disease prediction using stacking and voting ensemble methods. Fifteen base models were trained on two different heart disease datasets. After evaluating various combinations, six base models were pipelined to develop ensemble models employing a meta-model (stacking) and a majority vote (voting). The performance of the stacking and voting …

Maximizing Germination Of Three Native Plants For Rangeland Restoration And Urban Landscapes Through Seed Enhancements, Janetta Teichert

Theses and Dissertations

Native plants offer numerous ecological benefits and opportunities for both rangeland restoration and urban landscaping, making their integration essential for building sustainable ecosystems. They enhance soil health, promote pollinator activity, increase microbial diversity, and support both wildlife and livestock, all of which contribute to overall ecosystem resilience. A promising strategy to improve the use of native plants is the application of seed enhancement technologies, which can optimize seed germination, improve seedling establishment, and enhance overall plant success in challenging environments. These post-harvest seed treatments incorporate materials that improve seed performance, often through coatings composed of binders, fillers, and active ingredients. …

Trenching And Compost Sustain Grain Yield Increases Over Nine Years On Deep Sands But At A Cost, David J.M. Hall, Tom J. Edwards

Grain and Other Field Crops Research Articles

Context. Crops grown on deep sands on the south coast of WA are limited by soil physical and chemical properties including compaction and poor nutrition. Aims. Crops grown on deep sands on the south coast of Western Australia are limited by soil physical and chemical properties including compaction and poor nutrition. Our aim was to determine what effects deep-placed organic amendments have on soil properties and crop production in a deep sand and whether such amendments are profitable. Methods. A long-term field trial was conducted over nine years (2015–2023) to investigate soil amendments including lime (0 and …

Phytochemistry, Antioxidant And Cytotoxic Activities Of Hibiscus (Hibiscus Rosa-Sinensis) Extract On Mcf-7 Breast Cancer Cells, Ade Arsianti, Isma Zahira Suhaima, Steven Gill, Ajeng Megawati Fajrin, Lince Dameria Nadapdap, Norma Nur Azizah, Hiroki Tanimoto, Shun Hirota

Indonesian Journal of Medical Chemistry and Bioinformatics

Background: Breast cancer is the most common type of cancer in women with a very high mortality rate. This cancer is caused by uncontrolled growth of breast cells. Treatments for this malignancy are surgery, chemotherapy, and radiotherapy, however those methods can cause adverse effects and quite expensive. Complementary and alternative medicines (CAMs) are also used to support those main treatments, one of them is herbal medicine. Hibiscus rosa-sinensis is known to have various phytochemical components with antioxidant, antibacterial, anticancer, and analgesic activities. This study is aimed to determine the phytochemical composition, antioxidant activity and cytotoxicity of Hibiscus rosa-sinensis extract towards …

Can The Discovery Of High-Impact Diagnostics Be Improved By Matching The Sampling Rate Of Clinical Diagnostics To The Frequency Domain Of Diagnostic Information?, Steven W Millward, Peng Wei, David Piwnica-Worms, Seth T Gammon

Faculty, Staff and Student Publications

Over the past 30 years, academic and industrial research investigators have developed molecular reporters to visualize cell death in complex biological systems. In parallel, clinical researchers, chemists, biochemists, and molecular biologists have endeavored to translate these molecular tools into clinical imaging agents. Despite these efforts, there are no clinically approved imaging methodologies with which to image cell death consistently and quantitatively. One reason may reside in the intrinsic mismatch between the sampling frequency of translational molecular imaging and the biochemical kinetics that define cell death. Beyond cell death imaging, many active research programs are now attempting to create translational diagnostic …

Swi/Snf Complex-Mediated Znf410 Cooperative Binding Maintains Chromatin Accessibility And Enhancer Activity, Siyuan Xu, Chuxuan Peng, Ren Ren, Haowen Lu, Han Zhao, Sijian Xia, Yijie Shen, Bin Xu, Haoyue Zhang, Xiaodong Cheng, Gerd A Blobel, Xianjiang Lan

Faculty, Staff and Student Publications

The clustering of multiple transcription factor binding sites (TFBSs) for the same TF has proved to be a pervasive feature of cis-regulatory elements in the eukaryotic genome. However, the contribution of binding sites within the homotypic clusters of TFBSs (HCTs) to TF binding and target gene expression remains to be understood. Here, we characterize the CHD4 enhancers that harbor unique functional ZNF410 HCTs genome wide. We uncover that ZNF410 controls chromatin accessibility and activity of the CHD4 enhancer regions. We demonstrate that ZNF410 binds to the HCTs in a collaborative fashion, further conferring transcriptional activation. In particular, three ZNF410 motifs …

Impacts Of Climate Change On Cannibalism And Disease Transmission In The Fall Armyworm, Kale Rougeau

LSU Master's Theses

Climate change may alter host-pathogen dynamics in terrestrial ecosystems due to rising global temperatures and carbon dioxide levels. Here, we examined cannibalism and disease transmission using the fall armyworm (Spodoptera frugiperda), an invasive agricultural pest, and its species-specific lethal baculovirus, Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV), under various potential challenges of climate change. We used three temperature treatments (cooler, optimal, warmer) based on the fall armyworm’s thermal performance curve to simulate a changing climate and four artificial diets with various protein-to-carbohydrate ratios (low, equal, high, standard) to manipulate resource quality from altered carbon dioxide levels. We found that higher …

A Geospatial Livestock-Carrying Capacity Model (Glcc) In The Akmola Oblast, Kazakhstan, Jiaguo Qi, Zihan Lin, Mark A. Weltz, Kenneth Spaeth, Gulnaz Iskakova

Biological, Geological, and Environmental Faculty Publications

Spatial disparities in rangeland conditions across Kazakhstan complicate field-based assessments of livestock-carrying capacity (LCC), a critical metric for the country's food security and economic planning. This study developed a geospatial livestock-carrying capacity (GLCC) modeling framework to quantify LCC spatio-temporal dynamics at the Oblast level, by integrating satellite-derived data on vegetation, water resources, and terrain with in situ measurements. By providing ground-truth observations and contextual detail, field-based measurements complement remote sensing data and help to validate estimates and improve the reliability of the GLCC model. The modeling framework was successfully applied and validated in a case study in the Akmola Oblast, …

Genetic Regulation Of Anthocyanin Biosynthesis In Flower Color In Gilia, Veronica Mosquera

Theses and Dissertations

Gilia was the model species in this research to study the genetic regulation of flower color. I generated an F2 population from a cross of two closely related leafy-stemmed Gilia: G. capitata with blue and G. yorkii with white flowers, to obtain the fertile F1, which was selfed. The F2 population showed a segregation ratio between pigmented versus white flowers 3:1, suggesting a single locus with a major effect on the regulation of flower color. Then, the G. yorkii genome was assembled and annotated to become the reference genome to genotype-by-sequencing (GBS) 189 F2 individuals. The Quantitative Trait Loci (QTL) …

Sustainable Forage Yield Improvement Through Perennial Grass–Legume Intercropping In Degraded Grasslands, Alina-Ștefania Stanciu

Turkish Journal of Agriculture and Forestry

Grasslands constitute one of the largest terrestrial biomes, providing essential ecosystem services such as biodiversity preservation, food production, and climate change mitigation. Globally, the desertification and degradation of grasslands have been accelerated by intensified land use and climate change. It is crucial to conserve and restore grasslands to address climate and biodiversity challenges. However, due to their diverse nature and undervalued benefits for humans, grasslands have often been overlooked in terms of preservation, conservation, and restoration compared to forests. In sustainable agriculture, intercropping grasses with legumes can enhance crop nutritional quality, increase productivity, and impact soil microbiological activity, ultimately leading …

Effect Of Different Mulch Materials Applications On Weed Control, Plant Characteristics, And Yield In Garlic (Allium Sativum L.), Ayşe Usanmaz Bozhüyük

Turkish Journal of Agriculture and Forestry

This study was conducted in plots under controlled conditions in the Silvan district of Diyarbakır Province in 2023. The local garlic genotype (Allium sativum L.) from Diyarbakır was used as the plant material. Three different organic mulching materials (sawdust, pine, and straw) were applied at a thickness of 5 cm. The effects of these mulching materials on leaf number, root length, plant height, number of cloves per plant, plant density, bulb diameter, dry and fresh weight of garlic, dry and fresh weight of weeds, weed density, and yield were analysed. A total of 34 weed species from 15 families were …

Appraisal Of Germination Behavior And Activity In Newly Developed Rice Lines, Muhammad Usman Akbar, Muhammad Aqeel, Maryam M. Alomran, Ijaz Haider, Omar Mahmoud Al-Zoubi, Ali Noman

Turkish Journal of Agriculture and Forestry

Rice is a fundamental food source for more than half of the global population. This study evaluated the germination capacity of four rice lines [Sakh (V1), Campena (V2), Kharamana (V3), and Binicol (V5)] and one local variety, KSK-282 (V5). The findings revealed significant differences in the germination attributes among the rice lines. V1 and V3 showed superior germination performance, while V5 consistently exhibited the lowest values. The one-way analysis of variance (ANOVA) showed significant differences (p ≤ 0.05) across multiple parameters, including the coefficient of velocity of germination (CVG), germination index, mean germination rate (MGR), and synchronization index. A significant …

Digital Image Processing In Determining The Degree Of Turnip Yellows Virus Infection In Oilseed Rape, Alina-Ștefania Stanciu, Teodor Rusu, Alin Cristian Teușdea, Olimpia Smaranda Mintaș, Mihai Marcel Cărbunar, Cristian Oneț

Turkish Journal of Agriculture and Forestry

In agricultural crops, leaves play crucial roles in plant physiology, providing information on both the quantity and quality of future production. They also serve as indicators for diagnosing foliar diseases. Detecting plant diseases through image reading and computer vision in a specific format allows for both quantitative and qualitative studies, which is a key step in diagnosing diseases using images of leaves exhibiting symptoms specific to a pathogen. In this study, we present an approach that integrates digital image processing to assess the extent of turnip yellows virus (genus Polerovirus, family Solemoviridae) infection in oilseed rape. This study focuses on …