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Infrared Laser Ablation Of Biomolecules From Formalin-Fixed Tissue, Blessing Chisom Egbejiogu Mar 2025

Infrared Laser Ablation Of Biomolecules From Formalin-Fixed Tissue, Blessing Chisom Egbejiogu

LSU Doctoral Dissertations

In the research described in this dissertation, a high-precision infrared laser ablation microsampling method was utilized for spatially resolved proteomic and lipidomic analyses of formalin fixed paraffin embedded (FFPE) tissue, a widely used archival sample in biomedical research. Despite its extensive use, FFPE tissue presents challenges for proteomic analysis due to protein cross-linking and modifications introduced during fixation, which can hinder extraction and identification. Developing a streamlined high-resolution method to recover biomolecules from FFPE samples is critical for advancing biomarker discovery, retrospective studies, and multi-omics research. To address these challenges, this study employs an infrared (IR) laser ablation microdissection system …

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Trans-Arg: Predicting Antibiotic Resistance Genes With A Transformer-Based Model And Pretrained Protein Language Model, Mohd Manzar Abbas, Amit Ranjan, Aixin Hou, Supratik Mukhopadhyay Mar 2025

Trans-Arg: Predicting Antibiotic Resistance Genes With A Transformer-Based Model And Pretrained Protein Language Model, Mohd Manzar Abbas, Amit Ranjan, Aixin Hou, Supratik Mukhopadhyay

Faculty Publications

Antibiotic resistance presents an emerging challenge to global health by reducing the efficacy of antibiotics administered to treat bacterial infections. Traditional approaches for detecting antibiotic resistance genes (ARGs) involve alignment-based sequence similarity techniques, which are time-consuming and resource-intensive. This signifies the necessity for developing advanced computational methods to detect ARGs early. To address this challenge, we introduce Trans-ARG, a novel multi-head attention transformer-based model designed to predict potential ARGs. Our approach leverages the pretrained ESMFold model to extract embeddings from protein sequences, capturing intricate structural and functional information. Protein sequences labelled as ARG or non-ARG were used as the dataset. …

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Kg-Dta: A Knowledge Graph-Based Meta-Path Learning Framework To Predict Drug-Target Binding Affinity, Amit Ranjan, Adam Bess, Md Saiful Islam Sajol, Magesh Rajasekaran, Chris Alvin, Supratik Mukhopadhyay Mar 2025

Kg-Dta: A Knowledge Graph-Based Meta-Path Learning Framework To Predict Drug-Target Binding Affinity, Amit Ranjan, Adam Bess, Md Saiful Islam Sajol, Magesh Rajasekaran, Chris Alvin, Supratik Mukhopadhyay

Faculty Publications

Drug target affinity (DTA) prediction is essential at different phases of drug discovery and virtual drug screening. However, traditional wet lab experiments are time and resource-intensive owing to the complex interactions within the vast biological and chemical spaces. Computational methods have proven their potential to predict DTA, but none have considered the association of drugs and proteins to capture the complex interactions in the biological network between drugs and proteins. To address this, we propose a novel framework leveraging knowledge graph-based meta-path learning (KG-DTA) to enhance DTA prediction. First, we construct a weighted heterogeneous network of drugs and proteins that …

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Developing A Southern Ocean Marine Ecosystem Model Ensemble To Assess Climate Risks And Uncertainties, Kieran Murphy, Denisse Fierro-Arcos, Tyler Rohr, David Green, Camilla Novaglio, Katherine Baker, Kelly Ortega-Cisneros, Tyler D. Eddy, Cheryl S. Harrison, Simeon L. Hill, Patrick Eskuche-Keith, Camila Cataldo-Mendez, Colleen M. Petrik, Matthew Pinkerton, Paul Spence, Ilaria Stollberg, Roshni C. Subramaniam, Rowan Trebilco, Vivitskaia Tulloch, Juliano Palacios-Abrantes, Sophie Bestley, Daniele Bianchi, Philip Boyd, Pearse J. Buchanan, Andrea Bryndum-Buchholz, Marta Coll, Stuart Corney, Samik Datta, Jason D. Everett, Romain Forestier, Elizabeth A. Fulton, Vianney Guibourd De Luzinais, Ryan Heneghan Mar 2025

Developing A Southern Ocean Marine Ecosystem Model Ensemble To Assess Climate Risks And Uncertainties, Kieran Murphy, Denisse Fierro-Arcos, Tyler Rohr, David Green, Camilla Novaglio, Katherine Baker, Kelly Ortega-Cisneros, Tyler D. Eddy, Cheryl S. Harrison, Simeon L. Hill, Patrick Eskuche-Keith, Camila Cataldo-Mendez, Colleen M. Petrik, Matthew Pinkerton, Paul Spence, Ilaria Stollberg, Roshni C. Subramaniam, Rowan Trebilco, Vivitskaia Tulloch, Juliano Palacios-Abrantes, Sophie Bestley, Daniele Bianchi, Philip Boyd, Pearse J. Buchanan, Andrea Bryndum-Buchholz, Marta Coll, Stuart Corney, Samik Datta, Jason D. Everett, Romain Forestier, Elizabeth A. Fulton, Vianney Guibourd De Luzinais, Ryan Heneghan

Faculty Publications

Climate change could irreversibly modify Southern Ocean ecosystems. Marine ecosystem model (MEM) ensembles can assist policy making by projecting future changes and allowing the evaluation and assessment of alternative management approaches. However, projected changes in total consumer biomass from the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) global MEM ensemble highlight an uncertain future for the Southern Ocean, indicating the need for a region-specific ensemble. A large source of model uncertainty originates from the Earth system models used to force FishMIP models, particularly future changes to lower trophic level biomass and sea-ice coverage. To build confidence in regional MEMs …

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Global And Regional Marine Ecosystem Models Reveal Key Uncertainties In Climate Change Projections, Tyler D. Eddy, Ryan F. Heneghan, Andrea Bryndum-Buchholz, Elizabeth A. Fulton, Cheryl S. Harrison, Derek P. Tittensor, Heike K. Lotze, Kelly Ortega-Cisneros, Camilla Novaglio, Daniele Bianchi, Matthias Büchner, Catherine Bulman, William W.L. Cheung, Villy Christensen, Marta Coll, Jason D. Everett, Denisse Fierro-Arcos, Eric D. Galbraith, Didier Gascuel, Jerome Guiet, Steve Mackinson, Olivier Maury, Susa Niiranen, Ricardo Oliveros-Ramos, Juliano Palacios-Abrantes, Chiara Piroddi, Hubert Du Pontavice, Jonathan Reum, Anthony J. Richardson, Jacob Schewe, Lynne Shannon, Yunne Jai Shin, Jeroen Steenbeek Mar 2025

Global And Regional Marine Ecosystem Models Reveal Key Uncertainties In Climate Change Projections, Tyler D. Eddy, Ryan F. Heneghan, Andrea Bryndum-Buchholz, Elizabeth A. Fulton, Cheryl S. Harrison, Derek P. Tittensor, Heike K. Lotze, Kelly Ortega-Cisneros, Camilla Novaglio, Daniele Bianchi, Matthias Büchner, Catherine Bulman, William W.L. Cheung, Villy Christensen, Marta Coll, Jason D. Everett, Denisse Fierro-Arcos, Eric D. Galbraith, Didier Gascuel, Jerome Guiet, Steve Mackinson, Olivier Maury, Susa Niiranen, Ricardo Oliveros-Ramos, Juliano Palacios-Abrantes, Chiara Piroddi, Hubert Du Pontavice, Jonathan Reum, Anthony J. Richardson, Jacob Schewe, Lynne Shannon, Yunne Jai Shin, Jeroen Steenbeek

Faculty Publications

Climate change is affecting ocean temperature, acidity, currents, and primary production, causing shifts in species distributions, marine ecosystems, and ultimately fisheries. Earth system models simulate climate change impacts on physical and biogeochemical properties of future oceans under varying emissions scenarios. Coupling these simulations with an ensemble of global marine ecosystem models has indicated broad decreases of fish biomass with warming. However, regional details of these impacts remain much more uncertain. Here, we employ CMIP5 and CMIP6 climate change impact projections using two Earth system models coupled with four regional and nine global marine ecosystem models in 10 ocean regions to …

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Modulators Of Energy Expenditure Accuracy In Adults With Overweight Or Obesity: E-Mechanic Secondary Analyses, Rachel Matthews, Christoph Höchsmann, Melissa L. Erickson, James L. Dorling, Guillaume Spielmann, Neil M. Johannsen, Timothy S. Church, Corby K. Martin Mar 2025

Modulators Of Energy Expenditure Accuracy In Adults With Overweight Or Obesity: E-Mechanic Secondary Analyses, Rachel Matthews, Christoph Höchsmann, Melissa L. Erickson, James L. Dorling, Guillaume Spielmann, Neil M. Johannsen, Timothy S. Church, Corby K. Martin

Faculty Publications

Purpose American College of Sports Medicine (ACSM) metabolic equations are used to estimate energy expenditure (EE) of physical activity and prescribe aerobic exercise to meet EE requirements. Limited evidence supports their accuracy in sedentary adults with overweight or obesity during controlled exercise interventions. The purpose of this study was to compare EE estimated by the ACSM walking equation versus EE measured by indirect calorimetry during a 24-wk aerobic exercise intervention, and identify potential modulators for their accuracy. Methods Data from the exercising groups (8 or 20 kcal·kg body weight-1·wk-1) of the E-MECHANIC study were utilized in this ancillary analysis (N …

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From The Mountains To The Beach: Water Purification Ecosystem Services And Recreational Beach Use In Puerto Rico, Maya Corridore, Rebeca De Jesús Crespo, Mariam Valladares-Castellanos, Thomas Douthat Mar 2025

From The Mountains To The Beach: Water Purification Ecosystem Services And Recreational Beach Use In Puerto Rico, Maya Corridore, Rebeca De Jesús Crespo, Mariam Valladares-Castellanos, Thomas Douthat

Faculty Publications

Recreational beach use is important for coastal economies and is influenced by water clarity, a trait that may be maintained by water purification ecosystem services (ESs). However, few studies have addressed these linkages. In this study, we ask the following questions: (1) Do watershed-scale water purification ecosystem services influence coastal water quality? (2) Does coastal water quality help explain beach visitation rates? To address these questions, we focused on Puerto Rico (PR), where coastal tourism has economic and cultural importance. We estimated water purification ESs using the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST), coastal water quality using long-term …

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A 3d Superposition Approximation For Gamma Knife Dose Calculation, Payton H. Stone, Lam M. Lay, Raymi Ramirez, Daniel Neck, Connel Chu, Joyoni Dey, David Solis Mar 2025

A 3d Superposition Approximation For Gamma Knife Dose Calculation, Payton H. Stone, Lam M. Lay, Raymi Ramirez, Daniel Neck, Connel Chu, Joyoni Dey, David Solis

Faculty Publications

Effective dose calculation is essential for optimizing Gamma Knife (GK) stereotactic radiosurgery (SRS) treatment plans. Modern GK systems allow independent sector activation, enabling complex dose distributions per shot. This study presents a dose approximation method designed to account for shot flexibility and generate 3D doses external to GammaPlan. A treatment plan was created with the TMR10 calculation for individual sector activations using a Radiosurgery Head Phantom. The resulting dose arrays established a basis set of sector-specific distributions, which were then referenced by shot parameters from the plan, allowing dose accumulation through superposition. This superposition approximation (SA) was compared to the …

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The Contemporary Distribution Of Scincine Lizards Does Not Reflect Their Biogeographic Origin, Aniruddha Datta-Roy, Matthew C. Brandley, Christopher C. Austin, Aaron M. Bauer, David James Harris, Salvador Carranza, Kanishka D.B. Ukuwela, Anslem De Silva, Krystal A. Tolley, K. Praveen Karanth, Maitreya Sil Mar 2025

The Contemporary Distribution Of Scincine Lizards Does Not Reflect Their Biogeographic Origin, Aniruddha Datta-Roy, Matthew C. Brandley, Christopher C. Austin, Aaron M. Bauer, David James Harris, Salvador Carranza, Kanishka D.B. Ukuwela, Anslem De Silva, Krystal A. Tolley, K. Praveen Karanth, Maitreya Sil

Faculty Publications

Aim: We assess the systematic relationships and historical biogeographic patterns in the subfamily Scincinae, a group of lizards that primarily inhabits the Afro-Madagascan and Saharo-Arabian regions with isolated lineages in Europe, North America, East Asia, India and Sri Lanka. The contemporary distribution of these lineages on the historical Laurasian and Gondwanan landmasses make scincines an ideal system to study the roles of vicariance and dispersal on a geologic scale of tens of millions of years. Location: Global. Taxon: Subfamily Scincinae (Family Scincidae). Methods: We conducted biogeographic analyses on a reconstructed, time-calibrated species tree of scincine genera, including members of the …

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Modulating The Aqueous Micellar Reorganization Of Sequence-Defined Ionic Peptoid Block Copolymers By Ionizable Monomer Position And Solution Ph, Bailee N. Barrett, Pedram Azizihariri, Vijay T. John, Donghui Zhang Feb 2025

Modulating The Aqueous Micellar Reorganization Of Sequence-Defined Ionic Peptoid Block Copolymers By Ionizable Monomer Position And Solution Ph, Bailee N. Barrett, Pedram Azizihariri, Vijay T. John, Donghui Zhang

Faculty Publications

The micellar aggregation of singly charged sequence-defined ionic peptoid block copolymers can be finely tuned by adjusting the position of the ionizable monomer along the chain and varying the solution pH. The pH-induced structural reorganization of these micelles was found to depend on the position of the ionizable monomer along the chain, influencing the balance of the hydrophobic interactions, excluded volume effect, and electrostatic forces (i.e., charge repulsion, solvation of the ionic monomers, counterion association) that govern the micellar structure. As the solution pH increases, positioning the ionizable monomer closer to the junction of the hydrophobic and hydrophilic blocks causes …

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Impact Of Voluntary Exercise On Systemic Inflammation In A 2? Hit Model Of Heart Failure With Preserved Ejection Fraction, Heather Quiriarte, Eunhan Cho, Youyoung Kim, Jake E. Doiron, Gregory Davis, James Stampley, Robert C. Noland, Zhen Li, Sanjiv J. Shah, Brian A. Irving, Guillaume Spielmann, David J. Lefer, Timothy D. Allerton Feb 2025

Impact Of Voluntary Exercise On Systemic Inflammation In A 2? Hit Model Of Heart Failure With Preserved Ejection Fraction, Heather Quiriarte, Eunhan Cho, Youyoung Kim, Jake E. Doiron, Gregory Davis, James Stampley, Robert C. Noland, Zhen Li, Sanjiv J. Shah, Brian A. Irving, Guillaume Spielmann, David J. Lefer, Timothy D. Allerton

Faculty Publications

No abstract provided.

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Soil Contamination By Environmentally Persistent Free Radicals And Dioxins Following Train Derailment In East Palestine, Oh, Myron L. Lard, Sarah E. Eichler, Peng Gao, Kuldeep Singh, Joseph D. Ortiz, Robert L. Cook, Slawomir Lomnicki, Stephania A. Cormier, Jennifer Richmond-Bryant Feb 2025

Soil Contamination By Environmentally Persistent Free Radicals And Dioxins Following Train Derailment In East Palestine, Oh, Myron L. Lard, Sarah E. Eichler, Peng Gao, Kuldeep Singh, Joseph D. Ortiz, Robert L. Cook, Slawomir Lomnicki, Stephania A. Cormier, Jennifer Richmond-Bryant

Division of Basic Science Faculty Publications

The Norfolk Southern train derailment on February 3, 2023, in East Palestine, Ohio, prompted concerns about the health impacts from the chemical spills and open-air combustion. We hypothesize that the combustion of chemicals, including vinyl chloride, in the presence of transition-metal oxides from the train, tracks, and soil minerals were conducive to the formation of hazardous byproducts including environmentally persistent free radicals (EPFRs), dioxins, and furans. We also hypothesize that these harmful byproducts of combustion have a shared origin and thus will have elevated concentrations in soil samples collected close to the derailment site when compared to concentrations in background …

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A Numerical Assessment Of Ocean Alkalinity Enhancement Efficiency On A River-Dominated Continental Shelf—A Case Study In The Northern Gulf Of Mexico, Yanda Ou, Z. George Xue, Xinping Hu Feb 2025

A Numerical Assessment Of Ocean Alkalinity Enhancement Efficiency On A River-Dominated Continental Shelf—A Case Study In The Northern Gulf Of Mexico, Yanda Ou, Z. George Xue, Xinping Hu

Faculty Publications

A robust high-resolution coupled hydrodynamic-biogeochemical model was applied to the northern Gulf of Mexico to assess the efficiency of river- and ocean-sourced ocean alkalinity enhancement (OAE). Sensitivity tests indicate that the effectiveness of OAE-induced CO2 uptake is primarily influenced by the amount of alkalinity introduced and local wind-driven mixing, with the former determining the overall uptake and the latter affecting short-term variability. Compared to ocean-sourced OAE (direct ocean release), river-sourced OAE (elevated river alkalinity) is more effective and sustainable. River-sourced OAE has higher CO2 uptake efficiency with reduced spatial and temporal uncertainty and greater overall CO2 uptake. For river-sourced OAE, …

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An Integrated Global-To-Regional Scale Workflow For Simulating Climate Change Impacts On Marine Ecosystems, Kelly Ortega-Cisneros, Denisse Fierros-Arcos, Max Lindmark, Camilla Novaglio, Phoebe Woodworth-Jefcoats, Tyler D. Eddy, Marta Coll, Elizabeth Fulton, Ricardo Oliveros-Ramos, Jonathan Reum, Yunne Jai Shin, Cathy Bulman, Leonardo Capitani, Samik Datta, Kieran Murphy, Alice Rogers, Lynne Shannon, George A. Whitehouse, Ezekiel Adekoya, Beatriz S. Dias, Alba Fuster-Alonso, Cecilie Hansen, Bérengère Husson, Vidette Mcgregor, Alaia Morell, Hem Nalini Morzaria Luna, Jazel Ouled-Cheikh, James Ruzicka, Jeroen Steenbeek, Ilaria Stollberg, Roshni C. Subramaniam, Vivitskaia Tulloch, Andrea Bryndum-Buchholz Feb 2025

An Integrated Global-To-Regional Scale Workflow For Simulating Climate Change Impacts On Marine Ecosystems, Kelly Ortega-Cisneros, Denisse Fierros-Arcos, Max Lindmark, Camilla Novaglio, Phoebe Woodworth-Jefcoats, Tyler D. Eddy, Marta Coll, Elizabeth Fulton, Ricardo Oliveros-Ramos, Jonathan Reum, Yunne Jai Shin, Cathy Bulman, Leonardo Capitani, Samik Datta, Kieran Murphy, Alice Rogers, Lynne Shannon, George A. Whitehouse, Ezekiel Adekoya, Beatriz S. Dias, Alba Fuster-Alonso, Cecilie Hansen, Bérengère Husson, Vidette Mcgregor, Alaia Morell, Hem Nalini Morzaria Luna, Jazel Ouled-Cheikh, James Ruzicka, Jeroen Steenbeek, Ilaria Stollberg, Roshni C. Subramaniam, Vivitskaia Tulloch, Andrea Bryndum-Buchholz

Faculty Publications

As the urgency to evaluate the impacts of climate change on marine ecosystems increases, there is a need to develop robust projections and improve the uptake of ecosystem model outputs in policy and planning. Standardizing input and output data is a crucial step in evaluating and communicating results, but can be challenging when using models with diverse structures, assumptions, and outputs that address region-specific issues. We developed an implementation framework and workflow to standardize the climate and fishing forcings used by regional models contributing to the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) and to facilitate comparative analyses across …

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Empowering Citizens Through The Development And Deployment Of A Community-Based Environmental Health Reporting Tool, Willow Sauermilch, Jennifer Irving, Margaret Reams, Chuqi Guo, Stephania Cormier, Jennifer Richmond-Bryant Feb 2025

Empowering Citizens Through The Development And Deployment Of A Community-Based Environmental Health Reporting Tool, Willow Sauermilch, Jennifer Irving, Margaret Reams, Chuqi Guo, Stephania Cormier, Jennifer Richmond-Bryant

Division of Basic Science Faculty Publications

Community-based participatory research provides communities with an avenue to actively collaborate with environmental researchers. The research aims to gain insight into critical problems of concern to community members while maintaining community autonomy over the research and its outcomes. This article describes the development and implementation of an environmental health communication tool designed to meet the needs of residents of Colfax, Louisiana, a rural community with limited technological access, which is engaging in advocacy with federal and state regulatory agencies to prohibit open burning and open detonation of military and Superfund wastes at a nearby thermal treatment site. We discuss how …

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A Data-Driven Approach To Enhance The Prediction Of Bacteria–Metabolite Interactions In The Human Gut Microbiome Using Enzyme Encodings And Metabolite Structural Embeddings, Gopal Srivastava, Michal Brylinski Feb 2025

A Data-Driven Approach To Enhance The Prediction Of Bacteria–Metabolite Interactions In The Human Gut Microbiome Using Enzyme Encodings And Metabolite Structural Embeddings, Gopal Srivastava, Michal Brylinski

Faculty Publications

Background: The human gut microbiome is critical for host health by facilitating essential metabolic processes. Our study presents a data-driven analysis across 312 bacterial species and 154 unique metabolites to enhance the understanding of underlying metabolic processes in gut bacteria. The focus of the study was to create a strategy to generate a theoretical (negative) set for binary classification models to predict the consumption and production of metabolites in the human gut microbiome. Results: Our models achieved median balanced accuracies of 0.74 for consumption predictions and 0.95 for production predictions, highlighting the effectiveness of this approach in generating reliable negative …

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Interactive Effects Of Co2, Temperature, And Nitrate Limitation On The Growth And Physiology Of Strain Ccmp 1334 Of The Marine Cyanobacterium Synechococcus (Cyanophyceae), Alyssa K. Sharbaugh, Edward A. Laws Feb 2025

Interactive Effects Of Co2, Temperature, And Nitrate Limitation On The Growth And Physiology Of Strain Ccmp 1334 Of The Marine Cyanobacterium Synechococcus (Cyanophyceae), Alyssa K. Sharbaugh, Edward A. Laws

Faculty Publications

The marine cyanobacterium Synecococcus sp. (CCMP 1334) was grown in a continuous culture system on a 12:12 h light:dark cycle at all combinations of low and high pCO2 (400 and 1000 ppmv, respectively), nutrient availability (nitrate-limited and nutrient-replete conditions), and temperatures of 21, 24, 28, 32, and 35°C. The maximum nutrient-replete growth rate was ~1.15 day−1 at 32–35°C. Median nutrient-replete growth rates were higher at 1000 ppmv than at 400 ppmv pCO2 at all temperatures. Carbon:nitrogen ratios were independent of pCO2 at a fixed relative growth rate (i.e., growth rate ÷ nutrient-replete growth rate) but decreased with increasing temperature. …

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Butterfly Species Vary In Sex-Specific Sodium Accumulation From Larval Diets, Luis Y. Santiago-Rosario, Alexander M. Shephard, Emilie Snell-Rood, Achim D. Herrmann, Kyle E. Harms Feb 2025

Butterfly Species Vary In Sex-Specific Sodium Accumulation From Larval Diets, Luis Y. Santiago-Rosario, Alexander M. Shephard, Emilie Snell-Rood, Achim D. Herrmann, Kyle E. Harms

Faculty Publications

Sodium is essential for animals, and its heterogeneous distribution can cause a range of phenomena, from sodium-seeking behaviours to impacting their performance. Although sodium content in soils and plants is relatively well documented, data for higher trophic levels are limited. Knowledge of the variation in sodium in lower trophic levels could have implications for understanding the behaviour and physiology of species at higher levels. We investigated the variation in tissue sodium concentration between males and females of four butterfly species. Puddling behaviour of Lepidoptera suggests sodium needs of males are generally greater than females, thus, we predicted males would accumulate …

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Increased Expression Of The Small Lysosomal Gene Svip In The Drosophila Gut Suppresses Pathophysiological Features Associated With A High-Fat Diet, Brennan M. Mercola, Tatiana V. Villalobos, Jocelyn E. Wood, Ankita Basu, Alyssa E. Johnson Feb 2025

Increased Expression Of The Small Lysosomal Gene Svip In The Drosophila Gut Suppresses Pathophysiological Features Associated With A High-Fat Diet, Brennan M. Mercola, Tatiana V. Villalobos, Jocelyn E. Wood, Ankita Basu, Alyssa E. Johnson

Faculty Publications

Lysosomes are digestive organelles that are crucial for nutrient sensing and metabolism. Lysosome impairment is linked to a broad spectrum of metabolic disorders, underscoring their importance to human health. Thus, lysosomes are an attractive target for metabolic disease therapies. In previous work, we discovered a novel class of tubular lysosomes that are morphologically and functionally distinct from traditionally described vesicular lysosomes. Tubular lysosomes are present in multiple tissues, are broadly conserved from invertebrates to mammals, are more proficient at degrading autophagic cargo than vesicular lysosomes, and delay signs of tissue aging when induced ectopically. Thus, triggering tubular lysosome formation presents …

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Earliest Ancient Maya Salt Production In Southern Belize: Excavations At Jay-Yi Nah, Heather Mckillop, E. Cory Sills Feb 2025

Earliest Ancient Maya Salt Production In Southern Belize: Excavations At Jay-Yi Nah, Heather Mckillop, E. Cory Sills

Faculty Publications

Salt works along the Yucatan coasts of Mexico and Belize provide a record of salt production for inland trade during the height of Late Classic Maya civilisation (AD 550-800). At the Paynes Creek Salt Works in Belize, production focused on the creation of salt cakes by boiling brine in pots supported over fires in dedicated salt kitchens. Underwater excavations at the Early Classic (AD 250-550) site of Jay-yi Nah now indicate there was a longer and evolving tradition of salt making in the area, one that initially employed large, incurved bowls to meet local or down-the-line trade needs before inland …

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The Eastern Oyster Behavioral Response To Low Salinity And Hypoxia In Controlled And Natural Settings, Siyah Yongue Jan 2025

The Eastern Oyster Behavioral Response To Low Salinity And Hypoxia In Controlled And Natural Settings, Siyah Yongue

LSU Master's Theses

Oyster aquaculture is expanding in the northern Gulf of Mexico, but climate change may challenge the sustainability of this industry. Projected increases in the frequency and intensity of low salinity and low dissolved oxygen (DO) periods could impact the behavior, metabolism, growth, and survival of oysters. Characterizing how oyster behavior links to environmental stressors could help better identify thresholds in their tolerance and inform predictive tools for aquaculture professionals. In this research, the effect of separate and concomitant exposures to low salinity and DO on the behavioral response of oysters was examined in the lab. The impact of other environmental …

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Spin Caloritronics As A Probe Of Nonunitary Superconductors, Taiki Matsushita, Takeshi Mizushima, Yusuke Masaki, Satoshi Fujimoto, Ilya Vekhter Jan 2025

Spin Caloritronics As A Probe Of Nonunitary Superconductors, Taiki Matsushita, Takeshi Mizushima, Yusuke Masaki, Satoshi Fujimoto, Ilya Vekhter

Faculty Publications

Superconducting spintronics explores the interplay between superconductivity and magnetism, sparking substantial interest in nonunitary superconductors as a platform for magneto-superconducting phenomena. However, identifying nonunitary superconductors remains challenging. We demonstrate that spin current driven by thermal gradients sensitively probes the nature of the condensate in nonunitary superconductors. Spin polarization of the condensate in momentum space induces the superconducting spin Seebeck effect, where a spin current is generated along thermal gradients without a thermoelectric charge current. Notably, the nonvanishing superconducting spin Seebeck effect provides a smoking gun evidence of nonunitary superconductivity because it reflects the spin polarization of the condensate in momentum …

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Ghost Fishing Due To Derelict Crab Traps In Louisiana’S Barataria Basin, Emma C. Villemarette Jan 2025

Ghost Fishing Due To Derelict Crab Traps In Louisiana’S Barataria Basin, Emma C. Villemarette

LSU Master's Theses

Ghost fishing, the unintentional entrapment of sea life by derelict fishing gear, is an ecologic and socioeconomic concern in Louisiana's crabbing industry (blue crab, Callinectes sapidus). These ghost fishing traps cause unknown and unaccounted for mortality in blue crab and bycatch species. I aimed to track changes to derelict crab trap catch and trap deterioration over seasons and between habitats. I set and monitored 33 simulated derelict crab traps over 367 soak days in three varying habitats along Barataria Bay, Louisiana. Traps were checked once every two weeks and an additional daily check for five days per season. Blue …

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Using Phylogenetics And Floral Evolution Of Sicklebill Hummingbird-Pollinated Centropogon Subgenus Centropogon To Support Undergraduate Research, Janet Mansaray Jan 2025

Using Phylogenetics And Floral Evolution Of Sicklebill Hummingbird-Pollinated Centropogon Subgenus Centropogon To Support Undergraduate Research, Janet Mansaray

LSU Doctoral Dissertations

The genus Centropogon subgenus Centropogon, offers an ideal system for studying macroevolutionary patterns due to its diverse floral morphologies and specialized pollinator interactions. This subgenus comprises 55 species, mostly found in mid-elevation Andean forests, where many species exhibit abruptly curved flowers, often associated with pollination by sicklebill hummingbirds. Using phylogenomic approaches, we conducted the first densely sampled analysis of this group, confirming the monophyly of two sections. Our study highlighted extensive gene tree discordance, likely driven by incomplete lineage sorting. Floral curvature and inflorescence structure evolved in a correlated fashion, leading to multiple independent losses of traits linked to …

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Synthesis And Characterization Of Bimetallic Plasmonic Nanoparticles Using Linear And Nonlinear Spectroscopy, Daniel Babayode Jan 2025

Synthesis And Characterization Of Bimetallic Plasmonic Nanoparticles Using Linear And Nonlinear Spectroscopy, Daniel Babayode

LSU Doctoral Dissertations

Recent exploration in the field of nanomaterials has led to the investigation of noble metal nanoparticles for various nanomedical applications. The spectroscopy of these nanoparticles is studied using both linear and nonlinear optical processes such as second harmonic generation (SHG), two-photon fluorescence (TPF), and extinction spectroscopy. Details pertaining to the growth dynamics of silver-gold core-shell (Ag@Au CS) nanoparticles (NPs) and gold-silver-gold core-shell-shell (Au@Ag@Au CSS) nanoparticles (NPs) are currently being investigated in order to obtain better control and optimization of the nanoparticle size and surface morphology. Transmission electron microscopy (TEM) images show that the nanoparticles have tunable core and shell sizes …

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The Importance Of Fauna-Mediated Sediment O2 Consumption In The Ngom Hypoxic Zone, Hannah Beck, Kanchan Maiti Jan 2025

The Importance Of Fauna-Mediated Sediment O2 Consumption In The Ngom Hypoxic Zone, Hannah Beck, Kanchan Maiti

Faculty Publications

The northern Gulf of Mexico (NGOM) coastal shelf adjacent to the Mississippi and Atchafalaya rivers system experiences strong seasonal hypoxia in the late summer and coupled physical-biological models suggest that hypoxia formation in the NGOM is sensitive to benthic biogeochemical processes. However, the processes driving sediment oxygen consumption and their relationship to bottom oxygen concentration remain enigmatic. This study for the first time concurrently measured in situ total oxygen uptake (TOU) and diffusive oxygen uptake (DOU) during two different hypoxia seasons. The relatively large DOU: TOU ratio of 0.33 ± 0.07 observed during this study suggests more significant benthic infauna …

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Indirect Effects And Context Dependency In Stream Fish Invasions, William K. Annis, Lily M. Thompson, Stephen R. Midway, Julian D. Olden, Brandon K. Peoples Jan 2025

Indirect Effects And Context Dependency In Stream Fish Invasions, William K. Annis, Lily M. Thompson, Stephen R. Midway, Julian D. Olden, Brandon K. Peoples

Faculty Publications

Aim: Invasion ecology is replete with a body of well-supported yet contradictory evidence for numerous invasion hypotheses, likely as a result of context dependency. Context dependency in invasion studies can arise in two ways: (1) apparent, when results differ between studies solely due to methodical differences, or (2) mechanistic, when results truly differ due to ecological processes. One form of apparent context dependency occurs when causally linked factors associated with invasion success (hereafter, invasion drivers) either mask or enhance each other's effect on invasion success. Mechanistic context dependency can occur when regional scale processes modify the influence of local scale …

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Flood Risk And Mitigation Calculator Tool To Support Decision-Making For Enhancing Community Resilience: A Case Study Of The U.S.A. Gulf Coastal Region, Rubayet Bin Mostafiz, Ayat Al Assi, Arash Taghinezhad, Carol J. Friedland, Robert V. Rohli, Md Adilur Rahim, Christopher T. Emrich, Melanie Gall, Eric Johnson Jan 2025

Flood Risk And Mitigation Calculator Tool To Support Decision-Making For Enhancing Community Resilience: A Case Study Of The U.S.A. Gulf Coastal Region, Rubayet Bin Mostafiz, Ayat Al Assi, Arash Taghinezhad, Carol J. Friedland, Robert V. Rohli, Md Adilur Rahim, Christopher T. Emrich, Melanie Gall, Eric Johnson

Faculty Publications

Real-estate websites make it easy to find and access information about a home. Information on property value, square footage, number of rooms, quality of schools, crime rates, and more is readily available. Some of these platforms have begun integrating climate-related risks in generic ways. However, this information provides limited if any actionable value and is unlikely to guide people’s decision-making on buying or renting a home, deciding where to vacation, or investing in a property. Making residents aware of the natural hazard risks to which their homes may be exposed is an important component of making communities more resilient. Both …

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The Impact Of Seasonal Hydrological Disturbances On The Presence And Formation Of Toxic Cyanobacteria Blooms In Coastal Louisiana, Courtney Nicole Hammond, Sibel Bargu, Caitlin R.R. Turner, Matthew Hiatt, John R. White Jan 2025

The Impact Of Seasonal Hydrological Disturbances On The Presence And Formation Of Toxic Cyanobacteria Blooms In Coastal Louisiana, Courtney Nicole Hammond, Sibel Bargu, Caitlin R.R. Turner, Matthew Hiatt, John R. White

Faculty Publications

Estuaries in the Gulf, especially Lake Pontchartrain Estuary in southeastern Louisiana, USA, are experiencing significant changes due to climate change and coastal restoration efforts. Lake Pontchartrain Estuary receives nutrient-rich Mississippi River water through a controlled diversion called Bonnet Carré Spillway (BCS), which has been associated with toxic cyanobacterial blooms (cyanoHABs). This study examines the seasonal factors influencing cyanoHABs in the Lake Pontchartrain Estuary when the BCS is closed, addressing gaps in the understanding of HABs related to other physical drivers. Field samples collected in 2021, during the closure of the spillway, revealed significant evidence of seasonal variations in cyanoHAB formation. …

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Corrigendum: Diatom Transcriptional And Physiological Responses To Changes In Iron Bioavailability Across Ocean Provinces (Frontiers In Marine Science, (2017), 4, (360), 10.3389/Fmars.2017.00360), Natalie R. Cohen, Kelsey A. Ellis, Robert H. Lampe, Heather Mcnair, Benjamin S. Twining, Maria T. Maldonado, Mark A. Brzezinski, Fedor I. Kuzminov, Kimberlee Thamatrakoln, Claire P. Till, Kenneth W. Bruland, William G. Sunda, Sibel Bargu, Adrian Marchetti Jan 2025

Corrigendum: Diatom Transcriptional And Physiological Responses To Changes In Iron Bioavailability Across Ocean Provinces (Frontiers In Marine Science, (2017), 4, (360), 10.3389/Fmars.2017.00360), Natalie R. Cohen, Kelsey A. Ellis, Robert H. Lampe, Heather Mcnair, Benjamin S. Twining, Maria T. Maldonado, Mark A. Brzezinski, Fedor I. Kuzminov, Kimberlee Thamatrakoln, Claire P. Till, Kenneth W. Bruland, William G. Sunda, Sibel Bargu, Adrian Marchetti

Faculty Publications

In the published article, there was an error in Figure 3 as published. The initial (T0) phytoplankton community composition at site C2 was incorrectly displayed, with prasinophytes erroneously appearing as relatively abundant taxa. The corrected Figure 3 appears below. The average transcript proportions of phytoplankton taxa (outer charts) and diatom genera (inner charts) from initial seawater (T0) and during the first time point (T1; see Supplementary Table 1) within the Fe addition (Fe) and DFB addition (DFB) treatments at each site. Note that for site O5, the T2 control (Ctl) treatment is provided as the Fe-limited comparison. A text correction …

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