Digital Commons Network^™

Upregulation Of Coilin Mrna Upon Nopp140-/- In Drosophila Melanogaster., Sara Grace Hubacek

Honors Capstones

No abstract provided.

Unintended Consequences For Tanf: An Incubator For Domestic Violence?, Kathryn Rose Deleo

Honors Capstones

No abstract provided.

The Tensile Root Strength Of Emergent Coastal Macrophytes, Lauris Olivia Hollis

LSU Doctoral Dissertations

Spartina patens is a dominant emergent macrophyte in fresh, intermediate, and brackish marshes along the Atlantic and Gulf coasts of United States where its biomechanical properties are a key component of wetland health and resilience. Its root biomass and tensile root strength are essential for anchorage, erosion protection, and are important determinants of soil strength. Nutrients and the herbicide atrazine are suspected of negatively impacting this wetland plant and others. The objectives of this study were to: 1) ascertain the tensile root strength of five emergent coastal macrophytes in coastal estuaries, and 2) test the effects of nutrient addition, atrazine …

Identifying Apparent Local Stable Isotope Equilibrium In A Complex Non-Equilibrium System, Yuyang He, Xiaobin Cao, Jianwei Wang, Huiming Bao

Faculty Publications

Copyright © 2017 John Wiley & Sons, Ltd. Rationale: Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Methods: Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) …

Identifying Apparent Local Stable Isotope Equilibrium In A Complex Non-Equilibrium System, Yuyang He, Xiaobin Cao, Jianwei Wang, Huiming Bao

Faculty Publications

Copyright © 2017 John Wiley & Sons, Ltd. Rationale: Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Methods: Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) …

Copper Complex For Capturing Carbon Dioxide, Andrew W. Maverick, Uttam R. Pokharel, Frank R. Fronczek

College of Science Patents

A composition and method are disclosed for capturing CO₂. A pollutant/greenhouse gas can be converted into a valuable organic compound using a nontoxic reducing agent. CO₂ may be economically captured from the atmosphere, from products of combustion, or from byproducts of various chemical processes. The method reduces CO₂ in a three-step reaction cycle, in which a binuclear metal-organic compound converts CO₂ to oxalate in a redox cycle under mild conditions.

Assessing Changes In Self-Reported Driving Ability After Mild Traumatic Brain Injury, John Philip Kelly Bernstein

LSU Master's Theses

The ability to safely drive a car requires intact cognitive functioning across a variety of domains, many of which are adversely affected following a moderate-to-severe traumatic brain injury (TBI). Mild traumatic brain injury (mTBI) impacts similar cognitive facets, albeit to a less severe extent, and preliminary evidence suggests that mTBI may also have a deleterious effect on driving abilities immediately following injury. However, changes in driving ability over the course of recovery from mTBI have not been adequately examined. The present study addressed this dearth in the literature through examination of self-reported driving ability in 18 participants with a recent …

Microfluidic Technology And Application In Urinal Analysis, Jiwen Xiang

LSU Doctoral Dissertations

Microfluidic technology offers numerous advantages in minimizing and integrating the traditional assays. However, the lack of efficient control components of the microfluidic systems has been hindering the widely commercialization of the technology. The research work in this dissertation focused on the development of effective control components for microfluidic applications.

A linear peristaltic pump was firstly designed, fabricated, and tested for conventional microfluidics by synchronously compressing the microfluidic channel with a miniature cam-follower system in Chapter 2. The miniature cam-follower system and microfluidic chip was prototyped using three-dimensional (3D) printing technology and soft lithography technology. Results from experimental test showed that …

Hypertension, Genes, And Environment: Challenges For Prevention And Risk Prediction, Richard Cooper

Faculty Publications

No abstract provided.

Recently Integrated Alu Insertions In The Squirrel Monkey (Saimiri) Lineage And Application For Population Analyses, Jasmine N. Baker, Jerilyn A. Walker, Michael W. Denham, Charles D. Loupe, Mark A. Batzer

Faculty Publications

© 2018 The Author(s). Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus …

Innovative Monte Carlo Methods For Sampling Molecular Conformations, Aliasghar Sepehri

LSU Doctoral Dissertations

Sampling molecular conformations is an important step in evaluating physical, mechanical, hydrodynamic, and optical properties of flexible molecules especially polymers. One powerful method for this purpose is configurational-bias Monte Carlo in which one random segment of a molecule is chosen, all segments toward one random end are removed, and then regrown segment by segment to produce a new geometry to be accepted/rejected according to probability laws. The advantage of this method is the ability to generate acceptable conformations that are favorable for intra- and intermolecular energies to save computational costs. However, when there are several interdependent energetic terms, trial generation …

Assessment Of Hydrologic Connectivity In An Ungauged Wetland With Insar Observations, Fernando Jaramillo, Ian Brown, Pascal Castellazzi, Luisa Espinosa, Alice Guittard, Sang Hoon Hong, Victor H. Rivera-Monroy, Shimon Wdowinski

Faculty Publications

The Ciénaga Grande de Santa Marta (CGSM) is one of the world's most productive tropical wetlands and one that has witnessed some of the greatest recorded dieback of mangroves. Human-driven loss of hydrologic connectivity by roads, artificial channels and water flow regulation appears to be the reason behind mangrove mortality in this ungauged wetland. In this study, we determined the CGSM's current state of hydrologic connectivity by combining a remote sensing technique, termed as Wetland Interferometric Synthetic Aperture Radar (InSAR), with a hydrologic study of river water discharge. For this research, we processed 29 ALOS-PALSAR acquisitions taken during the period …

The Absence Of Dhhc3 Affects Primary And Latent Herpes Simplex Virus 1 Infection, Shaohui Wang, Kevin R. Mott, Marianne Cilluffo, Casey L. Kilpatrick, Shoko Murakami, Alexander V. Ljubimov, Konstantin G. Kousoulas, Sita Awasthi, Bernhard Luscher, Homayon Ghiasi

Faculty Publications

© 2018 American Society for Microbiology. UL20, an essential herpes simplex virus 1 (HSV-1) protein, is involved in cytoplasmic envelopment of virions and virus egress. We reported recently that UL20 can bind to a host protein encoded by the zinc finger DHHC-type containing 3 (ZDHHC3) gene (also known as Golgi-specific DHHC zinc finger protein [GODZ]). Here, we show for the first time that HSV-1 replication is compromised in murine embryonic fibroblasts (MEFs) isolated from GODZ-/- mice. The absence of GODZ resulted in blocking palmitoylation of UL20 and altered localization and expression of UL20 and glycoprotein K (gK); the expression of …

Ecological Drivers Of Song Evolution In Birds: Disentangling The Effects Of Habitat And Morphology, Elizabeth Perrault Derryberry, Nathalie Seddon, Graham Earnest Derryberry, Santiago Claramunt, Glenn Fairbanks Seeholzer, Robb Thomas Brumfield, Joseph Andrew Tobias

Faculty Publications

© 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Environmental differences influence the evolutionary divergence of mating signals through selection acting either directly on signal transmission (“sensory drive”) or because morphological adaptation to different foraging niches causes divergence in “magic traits” associated with signal production, thus indirectly driving signal evolution. Sensory drive and magic traits both contribute to variation in signal structure, yet we have limited understanding of the relative role of these direct and indirect processes during signal evolution. Using phylogenetic analyses across 276 species of ovenbirds (Aves: Furnariidae), we compared the extent to …

Peptide Ligands For Targeting The Extracellular Domain Of Egfr: Comparison Between Linear And Cyclic Peptides, Tyrslai M. Williams, Rushikesh Sable, Sitanshu Singh, Maria Graca H. Vicente, Seetharama D. Jois

Faculty Publications

© 2017 John Wiley & Sons A/S Colorectal cancer (CRC) is the third most common solid internal malignancy among cancers. Early detection of cancer is key to increasing the survival rate of colorectal cancer patients. Overexpression of the EGFR protein is associated with CRC. We have designed a series of peptides that are highly specific for the extracellular domain of EGFR, based on our earlier studies on linear peptides. The previously reported linear peptide LARLLT, known to bind to EGFR, was modified with the goals of increasing its stability and its specificity toward EGFR. Peptide modifications, including D-amino acid substitution, …

Hidden Endemism, Deep Polyphyly, And Repeated Dispersal Across The Isthmus Of Tehuantepec: Diversification Of The White-Collared Seedeater Complex (Thraupidae: Sporophila Torqueola), Nicholas A. Mason, Arturo Olvera-Vital, Irby J. Lovette, Adolfo G. Navarro-Sigüenza

Faculty Publications

© 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White-collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements …

Optimal Data Partitioning, Multispecies Coalescent And Bayesian Concordance Analyses Resolve Early Divergences Of The Grape Family (Vitaceae), Limin Lu, Cymon J. Cox, Sarah Mathews, Wei Wang, Jun Wen, Zhiduan Chen

Faculty Publications

© The Willi Hennig Society 2017 Evolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep-level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep-level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned …

Cambial Phenology Informs Tree-Ring Analysis Of Fire Seasonality In Coastal Plain Pine Savannas, Monica T. Rother, Jean M. Huffman, Grant L. Harley, William J. Platt, Neil Jones, Kevin M. Robertson, Steve L. Orzell

Faculty Publications

© 2018, The Author(s). Understanding of historical fire seasonality should facilitate development of concepts regarding fire as an ecological and evolutionary process. In tree-ring based fire-history studies, the seasonality of fire scars can be classified based on the position of the fire scar within or between growth rings. Cambial phenology studies are needed to precisely relate a fire-scar position to months within a year because the timing of dormancy, earlywood production, and latewood production varies by species and location. We examined cambial phenology patterns of longleaf pine (Pinus palustris Mill.), slash pine (P. elliottii Engelm.), and South Florida slash pine …

Aromatic Interactions At The Ligand–Protein Interface: Implications For The Development Of Docking Scoring Functions, Michal Brylinski

Faculty Publications

© 2017 John Wiley & Sons A/S The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand–protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experimental and computer-generated structures of ligand–protein complexes, considering various combinations of aromatic amino acid residues and ligand rings. The geometry of interfacial π–π stacking in crystal structures accords with experimental and theoretical data collected for simple systems, such as …

Reference Quality Genome Assemblies Of Three Parastagonospora Nodorum Isolates Differing In Virulence On Wheat, Jonathan K. Richards, Nathan A. Wyatt, Zhaohui Liu, Justin D. Faris, Timothy L. Friesen

Faculty Publications

Parastagonospora nodorum, the causal agent of Septoria nodorum blotch in wheat, has emerged as a model necrotrophic fungal organism for the study of host-microbe interactions. To date, three necrotrophic effectors have been identified and characterized from this pathogen, including SnToxA, SnTox1, and SnTox3. Necrotrophic effector identification was greatly aided by the development of a draft genome of Australian isolate SN15 via Sanger sequencing, yet it remained largely fragmented. This research presents the development of nearly finished genomes of P. nodorum isolates Sn4, Sn2000, and Sn79-1087 using long-read sequencing technology. RNAseq analysis of isolate Sn4, consisting of eight time points covering …

Insect Effects On Ecosystem Services—Introduction, T. D. Schowalter, J. A. Noriega, T. Tscharntke

Faculty Publications

Natural ecosystems provide a variety of services on which humans, and other organisms, depend for survival and well-being. These ecosystem services can be categorized as provisioning (production of food, fiber, water and other resources), cultural (non-material benefits, such as recreation, spiritual and other aesthetic values), supporting (primary production, pollination, decomposition and soil formation necessary for resource production) and regulating (biological control and other feedback mechanisms that maintain relatively consistent delivery of services). Ecosystems also have been viewed as producing “disservices” such as pests, litter, biological hazards such as diseases, animal attacks, allergenic and poisonous organisms, and geophysical hazards such as …

Recently Integrated Alu Insertions In The Squirrel Monkey (Saimiri) Lineage And Application For Population Analyses, Mark Batzer, Jasmine N. Baker, Jerilyn A. Walker, Michael W. Denham, Charles D. Loupe

Faculty Publications

Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups. …

An Ancient Estuarine-Circulation Nutrient Trap: The Late Pennsylvanian Midcontinent Sea Of North America, Thomas J. Algeo, Achim D. Herrmann

Faculty Publications

© 2018 Geological Society of America. The Late Pennsylvanian Midcontinent Sea (LPMS) of North America, which existed during glacioeustatic highstands of the late Paleozoic ice age, was an immense ( > 1 × 106 km2) cratonic interior sea exhibiting large-scale estuarine circulation, with a low-salinity surface plume overlying a high-salinity, anoxic, deep water mass. As in river estuaries, these conditions resulted in trapping and recycling of nutrients and organic-reactive elements (e.g., trace metals such as Mo, U, and Zn) in the subpycnoclinal water mass, leading to total organic carbon (TOC) to 40% and peak trace metal enrichment factors (EFs) of 540 …

A Strategy For Sperm Cryopreservation Of Atlantic Salmon, Salmo Salar, For Remote Commercial-Scale High-Throughput Processing, Huiping Yang, E. Hu, John T. Buchanan, Terrence R. Tiersch

Faculty Publications

Sperm cryopreservation is an essential tool for long-term storage of genetic resources for aquaculture fishes. The goal of this study was to develop an efficient and streamlined protocol for high-throughput processing for sperm cryopreservation in Atlantic salmon, Salmo salar. The objectives were to evaluate: (1) osmolality of blood serum for determining extender osmolality, (2) effects of extenders for fresh sperm dilution and refrigerated storage, (3) effects of methanol and dimethyl sulfoxide (DMSO) on fresh sperm motility, and (4) motility and fertility after thawing. In this study, sperm samples were collected at a hatchery site in Canada and shipped to a …

Spatial Rice Yield Estimation Based On Modis And Sentinel-1 Sar Data And Oryza Crop Growth Model, Tri D. Setiyono, Emma D. Quicho, Luca Gatti, Manuel Campos-Taberner, Lorenzo Busetto, Francesco Collivignarelli, Francisco Javier García-Haro, Mirco Boschetti, Nasreen Islam Khan, Francesco Holecz

Faculty Publications

Crop insurance is a viable solution to reduce the vulnerability of smallholder farmers to risks from pest and disease outbreaks, extreme weather events, and market shocks that threaten their household food and income security. In developing and emerging countries, the implementation of area yield-based insurance, the form of crop insurance preferred by clients and industry, is constrained by the limited availability of detailed historical yield records. Remote-sensing technology can help to fill this gap by providing an unbiased and replicable source of the needed data. This study is dedicated to demonstrating and validating the methodology of remote sensing and crop …

A Three Year Study Of Metal Levels In Skin Biopsies Of Whales In The Gulf Of Mexico After The Deepwater Horizon Oil Crisis, John Pierce Wise, James T.F. Wise, Catherine F. Wise, Sandra S. Wise, Christy Gianios, Hong Xie, Ron Walter, Mikki Boswell, Cairong Zhu, Tongzhang Zheng, Christopher Perkins, John Pierce Wise

Faculty Publications

In response to the explosion of the Deepwater Horizon and the massive release of oil that followed, we conducted three annual research voyages to investigate how the oil spill would impact the marine offshore environment. Most investigations into the ecological and toxicological impacts of the Deepwater Horizon Oil crisis have mainly focused on the fate of the oil and dispersants, but few have considered the release of metals into the environment. From studies of previous oil spills, other marine oil industries, and analyses of oil compositions, it is evident that metals are frequently encountered. Several metals have been reported in …

Preparation And Characterization Of Nanocellulose And Its Application In Composite Materials, Xiuxuan Sun

LSU Doctoral Dissertations

Transparent cellulose films from 2,2,6,6-tetramethylpiperidine-1-oxyl radical oxidized cellulose nanocrystals (TOCNs) and 64 wt% sulfuric acid treated cellulose nanocrystals (SACNs) were prepared from bleached wood pulps. Film morphology, optical, mechanical, thermal, and surface wettability properties were characterized and compared. The results showed that TOCNs and SACNs had different average length, diameter, and aspect ratio.

The effect of cellulose nanofibers (CNFs) on flow, hydration, morphology, and strength of oil well cement (OWC) was investigated using a range of spectroscopic methods coupled with rheological modeling and strength analysis. The Vom-Berg model showed the best fitting result of the rheology data. The addition of …

Rice Nucleosome Patterns Undergo Remodeling Coincident With Stress-Induced Gene Expression, Qi Zhang, Dong Ha Oh, Sandra Feuer Ditusa, Mangu V. Ramanarao, Niranjan Baisakh, Maheshi Dassanayake, Aaron P. Smith

Faculty Publications

© 2018 The Author(s). Background: Formation of nucleosomes along eukaryotic DNA has an impact on transcription. Major transcriptional changes occur in response to low external phosphate (Pi) in plants, but the involvement of chromatin-level mechanisms in Pi starvation responses have not been investigated. Results: We mapped nucleosomes along with transcriptional changes after 24-h of Pi starvation in rice (Oryza sativa) by deep sequencing of micrococcal nuclease digested chromatin and ribosome-depleted RNA. We demonstrated that nucleosome patterns at rice genes were affected by both cis- and trans-determinants, including GC content and transcription. Also, categorizing rice genes by nucleosome patterns across the …

First Record Of The Non-Native Pacu, Piaractus Brachypomus, In Lago Petén-Itzá, Guatemala, Central America, Diego J. Elias, Susan F. Mochel, Prosanta Chakrabarty, Caleb D. Mcmahan

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

We documented the first record of the non-native species Piaractus brachypomus (Characiformes: Serrasalmidae) in Lago Petén-Itzá, Petén, Guatemala. One brined specimen was donated by a local fisherman in San Benito, El Petén. The captured specimen was reportedly collected in the southern basin of the lake. We used the mitochondrial gene cytochrome oxidase I (COI) to validate identity of the specimen. We hypothesize that the local aquarium trade is the most likely source of introduction of the non-native Pacu in Lago Petén-Itzá.

Documentamos el primer registro de la especie no nativa Piaractus brachypomus (Characiformes: Serrasalmidae) en el lago Petén Itzá, Petén, …

Experimental Evidence Of A Pathogen Invasion Threshold, Tad A. Dallas, Martin Krkošek, John M. Drake

Faculty Publications

© 2018 The Authors. Host density thresholds to pathogen invasion separate regions of parameter space corresponding to endemic and diseasefree states. The host density threshold is a central concept in theoretical epidemiology and a common target of human and wildlife disease control programmes, but there is mixed evidence supporting the existence of thresholds, especially in wildlife populations or for pathogens with complex transmission modes (e.g. environmental transmission). Here, we demonstrate the existence of a host density threshold for an environmentally transmitted pathogen by combining an epidemiological model with a microcosm experiment. Experimental epidemics consisted of replicate populations of naive crustacean …