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Evaluating Soil Health And Crop Yield In Louisiana Agricultural Systems: Impacts Of Best Management Practices And Prediction Models, Hector J. Mendoza Lagos

LSU Doctoral Dissertations

The adoption of conservation management practices is critical for improving soil health, enhancing nutrient use efficiency, and sustaining crop productivity in row crop systems in Louisiana. This study evaluated the role of conservation agronomic practices, soil biochemical indicators, and machine learning predictive models to improve soil nutrient dynamics, soil health indicators, microbial communities (MC), and crop productivity on a corn (Zea mays L.) research plot scale and in a commercial forty-hectare cotton (Gassypium hirsutum L.)-corn-soybean (Glycine max L.) rotation system in northeast Louisiana. The objectives of the study were to evaluate soil nutrient dynamics and MCs under …

Mitochondria-Er Contact Sites (Mercs) In The Cell Cycle: Molecular Architecture And Functional Remodeling Across Cellular States, Eduardo Silva-Pavez, Bruno Torres-Gonzalez, Michelle Sotomayor, Benjamín Cartes-Saavedra, Dorian V. Ziegler, Yessia Hidalgo-Fadic, Ulises Ahumada-Castro

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Mitochondria–endoplasmic reticulum (ER) contact sites (MERCS) are nanoscopic, dynamic platforms integrating metabolism, signaling, and stress responses to regulate cell fate. These nanoscopic interfaces remodel continuously to meet the demands of proliferating, quiescent, and senescent cells. We synthesize evidence that MERCS actively coordinate local Ca2+ signaling, non-vesicular lipid transfer, and proteostasis to shape mitochondrial function and cellular homeostasis. We discuss how MERCS architecture changes across the cell cycle and during arrest, distinguishing adaptive from maladaptive remodeling, and consider therapeutic potential in aging and age-related disease.

Planting Oak Seedlings For Forest Regeneration, Ryan Bohannon

Forestry and Natural Resources

Oaks are an important component of forests across the Southeast and are favored for a variety of objectives, including the provision of wildlife habitat and timber. Planting oak seedlings can be an effective practice for promoting successful oak regeneration in managed forests. This publication provides forest landowners and managers with practical recommendations for oak enrichment planting, including species and seedling selection, seedling care, planting techniques, and post-planting practices to promote survival and growth.

Host Range And Characterization Of Phytophthora Species That Cause Plant Diseases In California, Dinh Hieu Pham

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Phytophthora is one of the most destructive genera of plant pathogens in California, posing significant threats to both nursery production and natural ecosystems. Phytophthora ramorum, the causal agent of Sudden Oak Death (SOD), has expanded its host range to include more than 100 plant species. In addition, Phytophthora elongata, previously isolated in Western Australia from Eucalyptus marginata in 2013, has recently been detected for the first time in the United States on Rhododendron species. This naturally raises concern that a new etiological species has entered the country. Therefore, the goal of this thesis study was three-fold:  i) to …

Early Life Exposure To Antibiotics Increases The Risk Of Myopia: A Retrospective Cohort Study, Peng-Tai Tien, Chang-Ching Wei, Sheng-Chun Lin, Ping Ping Meng, Yu-Te Huang, Jamie Jiin-Yi Chen, Ming-Yen Wu, Ying-Hsiu Shih, Tzu-Ju Hsu, Fuu-Jen Tsai, Yao-Chien Wang, Hui-Ju Lin, Lei Wan

BioMedicine

Background

Myopia is a growing health issue, expected to affect nearly half of the global population by 2050. Genetic predisposition and early environmental influences both play crucial roles in the development of myopia. Identifying modifiable risks and early interventions is critical. Antibiotics, commonly given to young children, may disrupt gut microbiota, which has been linked to ocular diseases in humans and animals.

Aim We aimed to investigate the association between antibiotic use in early life and the risk of developing myopia.

Methods Retrospective cohort study using data from a national health insurance database examined children aged three years or younger, …

Unveiling Immune-Related Gene Signatures In Triple Negative Breast Cancer Through Integrated Transcriptomic Analysis, Priyanga Paranthaman, Ramanathan Karuppasamy, Shanthi Veerappapillai

BioMedicine

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and poor prognosis. Understanding the underlying molecular mechanisms, particularly immune-related gene networks, is critical for identifying novel therapeutic targets. Aim: This study aimed to identify immune-related hub genes involved in TNBC progression by integrating microarray and RNA sequencing data. Methods: We integrated microarray and RNA sequencing datasets from five Gene Expression Omnibus (GEO) studies (GSE36295, GSE37751, GSE61724, GSE38959, and GSE58135) to identify differentially expressed genes (DEGs). Protein–protein interaction (PPI) networks were constructed using the STRING database. Key modules and hub genes were identified through network analysis. …

Evaluation Of Bai-Zhu (Atractylodes Macrocephala)-Based Herbal Formulae In Breast Cancer: Implications For Metastasis Via Zeb1 And Slug Modulation, Yen Shen Lu, Pei Yen Yeh, Ling-Chun Yeh, Chia-Lin Lee, Ying-Chyi Song

BioMedicine

Background: Bai-Zhu (Atractylodes macrocephala Koidz. [Asteraceae]) is classified in traditional Chinese medicine (TCM) as an herb that targets the gastric and pancreatic meridians to support normal nutrient uptake. As such, Bai-Zhu is commonly included in herbal formulations for treating gastrointestinal dysfunction and alleviating pain and swelling. Formulae containing Bai-Zhu are also frequently used as complementary or alternative therapies to mitigate the side effects of tumor treatments. However, their direct effects on cancer cells remain inadequately understood in modern biomedical science. This study aims to characterize the impact of Bai-Zhu-containing formulae on breast cancer cells using contemporary molecular and cellular …

Impacts Of Dna Ligase I Genotypes On Taiwan Parkinson’S Disease, Chao-Hsuan Chen, Wen-Shin Chang, Chia-Wen Tsai, Da-Tian Bau, Shih-Wei Hsu, Kun-Ting Hong, Chon-Haw Tsai, Fuu-Jen Tsai, Ming-Kuei Lu, Jai-Sing Yang

BioMedicine

Introduction: Genetic polymorphisms in DNA repair pathways can modulate

DNA repair capacity and influence susceptibility to aging-related disorders, including Parkinson’s disease (PD). This study evaluated the association between the DNA ligase I rs20579 polymorphism and PD risk.

Materials and Methods: Genotyping of DNA ligase I rs20579 was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in

123 PD patients and 492 age- and sex-matched controls of Taiwanese Han ethnicity.

Associations between rs20579 genotypes and PD risk were analyzed.

Results: Among controls, the genotype distribution of rs20579 was 78.7% GG, 19.3% AG, and 2.0% AA, compared with 75.6%, 21.1%, and …

Hepatoprotective Evaluation Of Benzoylated Emodin Derivatives: Integrating Bioinformatics And In Vitro Studies, Firdayani Firdayani, Putri Hawa Syaifie, Siska Andrina Kusumastuti, Muthia Rahayu Iresha, Wirawan Adikusuma, Dhecella Winy Cintya Ningrum, Etik Mardliyati, Ayu Masyita, Ariza Yandwiputra Besari, Fathir Azzaki Iradata, Lucy Arianie

BioMedicine

Background: Emodin exhibits various pharmacological activities, including hepatoprotective effects. However, its clinical application is limited by poor absorption and low oral bioavailability. This study aimed to optimize emodin through benzoylation and to assess the hepatoprotective potential of the resulting derivatives integrating bioinformatics and in vitro methods.

Methods: We conducted network pharmacology, molecular docking and molecular dynamics (MD) simulations to predict potential targets and interactions of benzoylated emodin derivatives. The derivatives were synthesized and evaluated for cytotoxicity using the MTT assay. The hepatoprotective effects were assessed in vitro using a paracetamol-induced HepG2 cell injury model.

Results: Network pharmacology analysis and gene …

High-Throughput Robotic Ethanol Inhibition Assays For Engineered Thermophilic Biofuel Strains, Kevin He, Daniel Olson, Marybeth Maloney, Anthony Lanahan

Wetterhahn Science Symposium Posters

Ethanol stress assays are commonly used to evaluate microbial tolerance, metabolic adaptation, and fermentation performance. However, manual liquid handling introduces variability across replicate wells and small-volume pipetting steps, limiting reproducibility and throughput. This study developed an automated OT-2 robotic workflow to generate replicated ethanol concentration gradients for high-throughput inhibition assays in engineered thermophilic biofuel strains. Kinetic plate-reader measurements were used to quantify ethanol-dependent growth responses under anaerobic fermentation conditions. The reasearch question is: How do engineered thermophilic biofuel strains differ in ethanol-dependent growth inhibition under anaerobic fermentation conditions, and can automated robotic assays improve the reproducibility of these measurements? Can …

Rethinking Functional Groupings In Basketball Wings Through Ecological Trait Frameworks, Dhruv Mehrotra

Theses and Dissertations

This paper starts with a review about Plant Functional Types and then goes deeper into the conceptual foundations of Plant Functional Types (PFT's) with detailed discussion of global trait spectra such as the leaf economics spectrum and the fast-slow continuum. Using concepts like response and effect traits, the review then talks about how a trait based ecological framework can provide a more robust guideline to classify plants. The review then talks about how players in basketball have been classified in the past along with some of the newer typologies. The review starts to draw some parallels between the ecological framework …

Wake-On-Anomaly Federated Architecture For Privacy-Preserving Poultry Health Early Warning, Mahmoud Aziz Louati

Masters Theses

Highly pathogenic avian influenza outbreaks, respiratory disease, heat stress, and silent equipment failures share one operational reality: they are detected too late because today’s poultry-health workflow is reactive, manual, and dependent on producers volunteering commercially sensitive data. This thesis presents a wake-on-anomaly federated architecture that addresses both the detection-latency problem and the privacy–adoption deadlock that has so far prevented cross-farm collaboration. The architecture is organized in two tiers. Tier 1 is a lightweight LSTM autoencoder that continuously screens four routine telemetry channels (water, feed, house temperature, activity proxy) and emits a per-window reconstruction-error score. A debounced k-of-m trigger with cooldown …

Seed Endophyte Bacillus Atrophaeus Colonizes Root And Shoot Tissues Providing Antifungal Activity During Wheat Seedling Establishment, Anagha Wankhade, Zhiting Xu, Ashlynn Clark, David Britt

Biological Engineering Student Research

Seed-associated endophytes become active during germination, playing important roles as early colonizers of plant tissues and contributing to plant health while residing in a protective niche. In this study, we characterized a wheat-derived bacterial isolate, JunSE1L, to determine its functional traits and ecological role in the plant microbiome. The isolate was identified as Bacillus atrophaeus based on 16S rRNA analysis. JunSE1L exhibited nutrient-dependent plasticity in colony architecture, forming robust hydrophobic biofilms and pellicles under rich nutrient availability while swarming and forming thin, often dendritic colonies under defined nutrition. JunSE1L produced highly surface-active compounds that lowered the surface tension of water …

A Disorder-Aware Computational Framework To Identify Structurally Tractable Targets In Proliferative Vitreoretinopathy, Mak B. Djulbegovic, Nedym Hadzijahic, David J. Taylor Gonzalez, Michael Antonietti, Sidra Zafar, Ajay E. Kuriyan

Wills Eye Hospital Papers

OBJECTIVE: Proliferative vitreoretinopathy (PVR) remains a major cause of failure after rhegmatogenous retinal detachment repair and lacks effective pharmacologic therapies. Although epithelial-mesenchymal transition (EMT) is central to PVR pathogenesis, the structural determinants governing the tractability of EMT regulators, particularly those involving intrinsic disorder, remain poorly defined. We developed a disorder-aware, artificial intelligence-enabled computational framework to evaluate EMT-associated proteins in PVR and prioritize structurally tractable regulators for structure-based targeting.

DESIGN: A computational, hypothesis-generating study employing an in silico screening and structural modeling pipeline.

SUBJECTS: No human subjects or biological specimens were included. The dataset comprised 25 EMT-associated proteins implicated in PVR, …

Popgenhelpr: An R Package To Streamline And Facilitate Informed Population Genomic Analyses And Visualization Of Genetic Ancestry, Diversity And Differentiation, Keaka Farleigh, Mason O. Murphy, Christopher Marie Blair, Tereza Jezkova

Publications and Research

Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and FST. PopGenHelpR also provides five …

Phytochemical Composition And Bioactivities Of Roselle (Hibiscus Sabdariffa L.) Extracts Obtained By Infusion, Ethanolic Maceration, And Maltodextrin-Assisted Drying, Risna Silvianti, Warsito Warsito, Elok Zubaidah, Zubaidah Ningsih, Aqidatul Izza

Karbala International Journal of Modern Science

Roselle (Hibiscus sabdariffa L.) is rich in phenolic compounds and anthocyanins, but the extraction method may influence its chemical composition and biological activity. This study compared hot-water infusion, ethanolic maceration, and maltodextrin-assisted drying. It aimed to examine the relationship between the extraction method, chemical profile, and bioactivity. The resulting extracts (EI, EM, and EP) were analyzed for total phenolic, flavonoid, and anthocyanin, LC-HRMS profiles, and antioxidant capacity by the FRAP assay. Antibacterial analysis was conducted against Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 25923) using agar well diffusion. Cytotoxicity tests (MTT, 24 h) were performed against HT-29, 4T1, …

Effects Of Warming On Growth And Leaf Colonization By Litter Mat-Forming Fungi In A Wet Tropical Forest In Puerto Rico, Ari E. Puentes, D. Jean Lodge, Deyaneira A. Ortiz-Iglesias, Tatiana Barreto-Vélez, Laura C. Rubio-Lebrón, Hieu Chu, Christine S. O'Connell, Sasha C. Reed, Tana E. Wood

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Wet tropical forests are experiencing rising temperatures and increased frequency and intensity of extreme climatic events, such as cyclones, which can increase rates of soil erosion and surface runoff. Fungal litter mats, formed by agaric decomposer fungi, play a crucial role in stabilizing slopes, preventing erosion, and aiding nutrient cycling; however, little is known about how warming affects litter mat growth and function. We investigated two litter mat-forming fungi, Gymnopus johnstonii and Marasmius aff. crinis-equi, in warmed (+4°C above ambient) and control plots in the Luquillo Experimental Forest, Puerto Rico. Growth and time-to-leaf colonization were monitored over 6 weeks …

Lowland Tropical Forests Remain A Methane Sink Under Warming And Long-Term Hurricane Disturbance Recovery, Gabriele Larocca Conte, Lucia Zuvela, Rachel Cruz-Pérez, Tatiana Barreto-Vélez, Nibia Becerra-Santillan, Sophia F. Campbell, Hieu P. Chu, Trung Dam, Iana F. Grullón-Penkova, Miriam Kleit, Deyaneira A. Ortiz-Iglesias, Laura C. Rubio-Lebrón, Molly A. Cavaleri, Sasha C. Reed, Debjani Sihi, Tana E. Wood, Christine S. O'Connell

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Methane (CH₄) is a potent greenhouse gas, and tropical forests account for roughly one–third of global atmospheric CH₄ uptake by soils. Projected warming and more frequent hurricanes in these ecosystems may alter soil CH₄ sink strength, as warmer and wetter soils enhance methanogenesis activity. We measured soil CH₄ and CO₂ efflux during the calendar summer months of 2023 and 2024 alongside continuous records of soil moisture, soil and air temperature, and precipitation in an in–situ warming experiment (TRACE) located in a lowland tropical forest in Puerto Rico, six to seven years after Hurricanes Irma …

Structure And Diversity Of Play Behavior In Juvenile Belding's Ground Squirrels, Paul O'Driscoll Ii

Master's Theses

Play behavior is ubiquitous among juvenile mammals and can promote motor, social, and cognitive development, providing multiple adaptive benefits to young animals in some cases. The structure of play can be linked to the benefits it confers on individuals. I evaluated the structure of play in juvenile Belding’s ground squirrels (Urocitellus beldingi), a species for which multiple adaptive benefits of play have been identified. I compared juvenile play in U. beldingi to adult sexual and aggressive behavior to determine and classify similarities between juvenile play and adult behavior. I evaluated diversity in the behaviors expressed during play interactions and diversity …

Improving Human-Wildlife Coexistence: An Ecological And Educational Approach To Rewilding Grizzly Bears (Ursus Arctos Horribilis) In California, Amanda C. D. Rosales

Master's Projects and Capstones

Megafauna extinction during the Holocene has been both caused and amplified by climatic changes and human influence. By the last half century, large carnivores were diminished in Europe and the United States, but policies increasingly addressed species decline and their territories expanded. This research examined large carnivore rewilding across the European Union and United States, specifically for rewilding brown bears, Ursus arctos, in historic habitat. Next, case studies for the health status of climate-impacted whitebark pine, Pinus albicaulis, a high energy food for bears, was assessed. Ultimately, research case studies, human perspective surveys, and the California Department of Education content …

Examining The Ligands, Location, And Function Of Toll-Like Receptor 10, Kiefer Keanu Tam

Master's Theses

Toll-like receptors are a class of innate immune pattern recognition receptors that detect pathogen-associated molecular patterns and regulate downstream inflammatory responses. Toll-like receptor 10 remains the only human TLR whose ligand specificity, cellular localization, and immunological function are not fully defined. Emerging evidence suggests that TLR10 may play an anti-inflammatory role and can heterodimerize with TLR2 to modulate immune signaling. Previous studies from our laboratory demonstrated that stimulation with heat-killed Mycobacterium tuberculosis promotes TLR2-TLR10 heterodimerization and trafficking to the cell surface. In this study, we expanded our ligand panel to include additional gram-positive bacteria, particularly anti-inflammatory probiotic species, to further …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Kev's Dinghy Boat Workshops, Ruiyang Xiao

Masters Theses

In a culture where convenience replaces process, this project argues that making — even when inefficient, imperfect, or unnecessary — enables forms of engagement that buying cannot.

Technologies and Services nowadays are able to fulfill human’s desire to travel and explore at ease. However, this convenience proposes a mode of engagement based only in deeper knowledge of context and thus our experience with the world around us is hence diminished. Our engagement with the world becomes heavily mediated, regulated and controlled.

This project investigates how hands-on engagement with water can reintroduce + restore our sense of joy, curiosity, consequence, and …

Insects And Arthropods And Their Role In Human Society, Emily Marie Perez-Medina

Whittier Scholars Program

With brightly colored exoskeletons, an excess of both eyes and legs, and seemingly  unpredictable behaviors, insects and arthropods come across as unusual and strange to general audiences. For this reason, they are often classified as “gross,” “ugly,” or “scary,” antagonists  in popular culture. What is not recognized when being represented to the masses is how much human society depends on their presence, and how a world without insects would be a world without most things humans know and love. In order to help reduce the stigma of these tiny, yet mighty creatures, this project serves as a call to action …

Coenzyme Q10 Improves Functional And Structural Parameters Of Dairy Goat Sperm During Cooling And Cryopreservation, Ranadheer Narlagiri, Abdallah M. Shahat, Courtney Henry, Ashvini Pawar, Niki C. Whitley, Iman B. Shaheed, Mahipal Singh, Brou Kouakou, Irina A. Polejaeva, Adel R. Moawad

Animal, Dairy, and Veterinary Science Faculty Publications

Cryopreservation of gametes is crucial for conserving genetic diversity in livestock and endangered species, but the process can significantly impair sperm quality due to oxidative stress. Our aim was to evaluate the impacts of coenzyme Q10 (CoQ10) supplementation on the in vitro quality of cooled and cryopreserved goat semen. Semen samples collected from six mature Saanen bucks were pooled then diluted with AndroMed^® semen extender to a final concentration of 800 × 10⁶ sperm/mL. Diluted semen was supplemented with 0, 1, 2, 5, 10, and 20 µM CoQ10. Extended semen was either cooled at 4 °C for 72 …

Bat Species Acoustic Detections And Mist Net Captures 2017, 2018, 2019, 2022, 2023, 2025., Laroy Brandt

Faculty Peer-Reviewed Publications

No abstract provided.

Foveate, Dahlia Aggarwal

Masters Theses

This thesis investigates how textiles can unsettle visual assumptions, encouraging a perceptual shift. Through weaving, upholstery, and spatial installation, the work stages a tension between what a surface appears to be and how it is encountered by the body. Through woven pattern, tactile texture, and trompe l’oeil textile surfaces, perception is something negotiated rather than fixed: the eye anticipates one reality while the hand discovers another.

Drawing on a range of sensations gathered from observing landscape formations and textures, it translates enduring scale and material qualities into an interior landscape of woven surfaces and textile-based furniture. Rather than serving as …

Colonization Of Southern Flying Squirrels (Glaucomys Volans) To Urban Nebraska: Range Expansion Or Human Assisted Translocation?, Jennifer Wettschreck, James Wilson, Robert E. Wilson, Abby May, Megan Cary, Jeffrey Huebschman, Sarah A. Sonsthagen

Biology Faculty Publications

Southern flying squirrels (Glaucomys volans; Linnaeus 1758) were first observed in Lincoln, Nebraska, in 2018, 80 km north of their described range. Given that southern flying squirrels are a species of concern within Nebraska, determining the origin of this new population (natural expansion or pet-trade) garnered interest from state biologists. Further, the recent colonization of Lincoln by southern flying squirrels presents a unique opportunity to investigate the genetic implications of a founding event on a small arboreal mammal. The Lincoln population had genetic characteristics suggestive of a single-event colonization with fewer rare alleles and lower genetic diversity than potential …

Watershed Amendments: Assembling New Pervious Ground From Landscape Waste, Sophie Kaplan-Bucciarelli

Masters Theses

In Providence, Rhode Island, much of the downtown area is built over a vast historic tidal estuary. Though we no longer see the salt marshes, wooded bluffs, or meadows that once characterized this landscape, we recognize their absence in contemporary crises of urban heat, flooding, polluted soils and stormwater runoff, and habitat loss. These conditions are particularly acute along the city’s industrialized river corridors, where vacant lots and parking areas sit idle, their history paved over and potential constrained by limited imagination and resources.

These lots - already experiments in fill and land building after centuries of disturbance - can …

Somatic Prosthetics For Planetary Resonance, Disha Dharesh Kumar R

Masters Theses

This thesis investigates how industrial design can transcend extractive technological paradigms in favor of relational interfaces that foster planetary attunement. Framing the climate crisis as a 'crisis of imagination', the research challenges the Western bifurcation of nature and culture by drawing on Indic cosmologies- which recognize stones, plants, and ecosystems as conscious at different levels and participants in a shared cosmic field. By synthesizing research in Biosemiotics, Quantum Information Pansycishm, and Neuroscience, the project redefines intelligence as a distributed, more-than-human phenomenon.

The research materializes as a speculative design artifact: a device that functions as a somatic prosthetic for planetary resonance. …