Electrospray Photochemical Oxidation Of Proteins, Remilekun O. Lawal, Fabrizio Donnarumma, Kermit K. Murray

Faculty Publications

© 2019, American Society for Mass Spectrometry. Photooxidation of peptides and proteins by pulsed ultraviolet laser irradiation of an electrospray in the ion source of a mass spectrometer was demonstrated. A 193-nm excimer laser at 1.5-mJ pulse energy was focused with a cylindrical lens at the exit of a nanoelectrospray capillary and ions were sampled into a quadrupole time-of-flight mass spectrometer. A solution containing a peptide or protein and hydrogen peroxide was infused into the spray at a flow rate of 1 μL/min using a syringe pump. The laser creates OH radicals directly in the spray which modify biomolecules within …

Binding Site Matching In Rational Drug Design: Algorithms And Applications, Misagh Naderi, Jeffrey Mitchell Lemoine, Rajiv Gandhi Govindaraj, Omar Zade Kana, Wei Pan Feinstein, Michal Brylinski

Faculty Publications

© 2018 The Author(s) 2018. Published by Oxford University Press. All rights reserved. Interactions between proteins and small molecules are critical for biological functions. These interactions often occur in small cavities within protein structures, known as ligand-binding pockets. Understanding the physicochemical qualities of binding pockets is essential to improve not only our basic knowledge of biological systems, but also drug development procedures. In order to quantify similarities among pockets in terms of their geometries and chemical properties, either bound ligands can be compared to one another or binding sites can be matched directly. Both perspectives routinely take advantage of computational …

Haplotype Characterization Of The Sd1 Semidwarf Gene In United States Rice, Brijesh Angira, Christopher K. Addison, Tommaso Cerioli, Democrito B. Rebong, Diane R. Wang, Nathan Pumplin, Jong H. Ham, James H. Oard, Steven D. Linscombe, Adam N. Famoso

Faculty Publications

Plant height is an important target in US rice (Oryza sativa L.) breeding programs and the large effect of the sd1 semidwarf gene makes it a suitable target for marker-assisted selection. Although the deletion underlying the semidwarf allele is known and a gel-based DNA marker is available, this marker is not ideal for applied breeding because of throughput and cost constraints. The objectives of this study were to characterize the haplotype diversity at the SD1 locus within US rice germplasm and develop a single nucleotide polymorphism (SNP) assay for breeding applications. The International Rice Research Institute (IRRI) SNP-Seek database was …

A Bayesian Adaptive Phase Ii Clinical Trial Design Accounting For Spatial Variation, Beibei Guo, Yong Zang

Faculty Publications

Conventional phase II clinical trials evaluate the treatment effects under the assumption of patient homogeneity. However, due to inter-patient heterogeneity, the effect of a treatment may differ remarkably among subgroups of patients. Besides patient’s individual characteristics such as age, gender, and biomarker status, a substantial amount of this heterogeneity could be due to the spatial variation across geographic regions because of unmeasured or unknown spatially varying environmental and social exposures. In this article, we propose a hierarchical Bayesian adaptive design for two-arm randomized phase II clinical trials that accounts for the spatial variation as well as patient’s individual characteristics. We …

Avian Ecological Succession In The Amazon: A Long-Term Case Study Following Experimental Deforestation, Cameron L. Rutt, Vitek Jirinec

Faculty Publications

Approximately 20% of the Brazilian Amazon has now been deforested, and the Amazon is currently experiencing the highest rates of deforestation in a decade, leading to large-scale land-use changes. Roads have consistently been implicated as drivers of ongoing Amazon deforestation and may act as corridors to facilitate species invasions. Long-term data, however, are necessary to determine how ecological succession alters avian communities following deforestation and whether established roads lead to a constant influx of new species. We used data across nearly 40 years from a large-scale deforestation experiment in the central Amazon to examine the avian colonization process in a …

Is Iodine Deficiency Still A Problem In Sub-Saharan Africa?: A Review, Sanjoy Saha, Brenda A.Z. Abu, Yasaman Jamshidi-Naeini, Upasana Mukherjee, Makenzie Miller, Li Ling Peng, Wilna Oldewage-Theron

Faculty Publications

Iodine is an essential trace mineral, vital for its functions in many physiological processes in the human body. Both iodine deficiency (ID) and excess are associated with adverse health effects; ID and excess iodine intake have both been identified in sub-Saharan Africa (SSA). The review aims to (1) review the iodine status among populations in SSA until October 2018, and (2) identify populations at risk of excess or inadequate iodine intakes. A systematic search of relevant articles was carried out by a seven-member research team using PubMed, Science Direct and Scopus. A total of twenty-two articles was included for data …

Expected Genotype Quality And Diploidized Marker Data From Genotyping-By-Sequencing Of Urochloa Spp. Tetraploids, Filipe Inácio Matias, Karem Guimarães Xavier Meireles, Sheila Tiemi Nagamatsu, Sanzio Carvalho Lima Barrios, Cacilda Borges Do Valle, Marcelo Falsarella Carazzolle, Roberto Fritsche-Neto, Jeffrey B. Endelman

Faculty Publications

Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized …

Scheduling Optimization Of Parallel Linear Algebra Algorithms Using Supervised Learning, Gabriel Laberge, Shahrzad Shirzad, Patrick Diehl, Hartmut Kaiser, Serge Prudhomme, Adrian S. Lemoine

Faculty Publications

Linear algebra algorithms are used widely in a variety of domains, e.g machine learning, numerical physics and video games graphics. For all these applications, loop-level parallelism is required to achieve high performance. However, finding the optimal way to schedule the workload between threads is a non-trivial problem because it depends on the structure of the algorithm being parallelized and the hardware the executable is run on. In the realm of Asynchronous Many Task runtime systems, a key aspect of the scheduling problem is predicting the proper chunk-size, where the chunk-size is defined as the number of iterations of a for-loop …

Review Of Naturally Occurring Ammonia In Groundwater And Its Effect On Using Chloramines For Drinking Water Disinfection In Louisiana, Athena Lindsay

Honors Capstones

No abstract provided.

Neogene Chemical Weathering And Provenance Records Of The Western Himalaya Preserved In The Arabian Sea, Peng Zhou

LSU Doctoral Dissertations

Some tectonic models for the Himalaya emphasize the importance of surface processes in controlling the structural evolution. To investigate this tectonic–climatic interactions, and the weathering and erosion of the western Himalaya, International Ocean Discovery Program (IODP) Expedition 355 drilled two sites (site U1456 and U1457) in Laxmi Basin, which located in the Eastern Arabian Sea. In my research project, I plan to use a series of geochemical and geochronological methods on the sediment samples from the cores of these two sites, and sediments from an industrial borehole Indus Marine A-1, which near the Indus river mouth, to reconstruct a climatic …

Evaluating Feline Release Criteria Following Iodine-131 Therapy For Hyperthyroidism, Anthony Davila

LSU Master's Theses

Hyperthyroidism is a very common endocrine disorder in both humans and cats. Radioactive iodine ablation therapy is considered the gold standard; however, the patient becomes a radiation source and poses a potential radiological risk to others. The regulations governing when the patient can be released differ between human medicine and veterinary medicine. A human patient can receive up to 33 mCi of I-131 and be discharged the same day; yet a feline patient can receive a dose as low as 2 mCi and require multiple days of hospitalization. This discrepancy has not been satisfactorily addressed; and overly restrictive release criteria …

Coupled Pore-To-Continuum Multiscale Modeling Of Dynamic Particle Filtration Processes In Porous Media, John Rayner Blears

LSU Doctoral Dissertations

Modeling particle transport and retention in porous media is important in fields such as hydrocarbon extraction, groundwater filtration, and membrane separation. While the continuum-scale (>1 m) is usually of practical interest, pore-scale (1-100 μm) dynamics govern the transport and retention of particles. Therefore, accurate modeling of continuum-scale behavior requires an effective incorporation of pore-scale dynamics. Due to current computational limits however, the large spatial and temporal discrepancies of these scales prohibit modeling an entire continuum-scale system as a single pore-scale model. Even if a pore-scale model could incorporate every pore contained in a continuum-scale system, an upscaling scheme that …

Factors Influencing Retirement Decision Making For Louisiana State Government Employees, Osama A. Amous

LSU Doctoral Dissertations

ABSTRACT

Public pension members continually face factors affecting their decision to retire in the changing American society. Workers are living longer and need more medical care with better retirement benefits. For Louisiana public employees specifically, no prior studies have examined the factors affecting workers’ decision to retire nor evaluated the factors impacting workers’ decision.

This multiphase study aimed to identify factors and evaluate the decision-making process that enables Louisianans to retire happily and satisfied with a guaranteed income, and to examine millennials’ decision-making process. In the initial phase, ten active and retired male and female participants answered questions in-person, leading …

Exploring Queer Space In Marsden Hartley's Late Work, William Corey Stout

LSU Master's Theses

Most scholars agree on the attraction men held for the artist Marsden Hartley. However, much of the discussion revolves around debates on Hartley’s sexual identity, mainly in the readings of the male subjects in his paintings. Speculating on the nature of Hartley’s sexual practice puts a narrow focus on his work as either evidence for or against Hartley’s homosexuality. The fixed lens of an unspoken homosexual identity waiting to be read into his paintings overlooks important aspects that define queer experience outside of sexual acts. How can we think about queerness in Hartley’s work outside of sexual identity? This thesis …

Relating Individual Characteristics And Task Complexity To Performance Effectiveness In Individual And Collaborative Problem Solving, Kaveh Sheikhrezaei

LSU Doctoral Dissertations

The objective of this research is to examine the variables that influence performance effectiveness on individual and collaborative problem solving. The last few years have seen renewed interest in how team member personal characteristics and team composition characteristics impact team effectiveness.

Even with a growing quantity of organizations performing jobs by using groups, little is understood how people included in a team impact intragroup interaction and results. Most research investigates group’s performance based on a single characteristic which causes much confusion and contradictory results of the variables that impact overall group performance. Most research typically does not analyze the composition …

Mechanism Of Neutrophil Homeostasis And Immunity In Pneumonia And Sepsis, Sagar Paudel

LSU Doctoral Dissertations

Severe bacterial pneumonia and septicemia are pressing health problems. A better understanding of cellular and molecular players of neutrophil immunity and homeostasis in bacterial pneumonia and sepsis is critical for inspiring novel therapeutics. Chemokine CXCL1 is a widely secreted neutrophil attractant and Nod-like receptor (NLRC4) is commonly expressed cytoplasmic pathogen sensor in hematopoietic compartments. How these innate mediators convert pathogen signals into molecular cues of immune response in context of Gram-positive bacterial pneumonia and septicemia largely remain unknown. Utilizing Cxcl1 gene deficient mice, we demonstrate CXCL1 regulates neutrophil influx, bacterial clearance, and host survival in pneumococcal pneumonia-derived sepsis. Furthermore, Cxcl1 …

The Impact Of Bridge Program Participation On The Academic Success And Retention Of Freshman Music Majors, Allie Celeste Prest

LSU Doctoral Dissertations

The bridge program for incoming music majors at Louisiana State University, run by the School of Music, is a program in its sixth year of existence (2014-2019). The program is a 5 day pre-college orientation that seeks to “bridge the gaps” for incoming music majors through a variety of programming, including sessions on note taking and lectures (given by current music faculty), peer-led integration sessions, financial and time-management workshops presented by university staff, and panels with alumni and community arts leaders. This program was developed as a departmental response to the call to increase the academic success and retention of …

The Value Of Benevolence: Wealth, Philanthropy, And Police Power Before The Civil War, Thomas Ewing Barber

LSU Doctoral Dissertations

Americans before the Civil War (regardless of race, creed, class, or gender) were not strangers to the complexities involved with charitable giving, and the obligations they entailed. They, like other societies over time and space, sought charitable actions that enhanced corporate identity in public or private life, or as Benjamin Franklin later identified those gifts that enhanced the “public good.” Pursuit of the public good, however, resulted in a myriad of negative outcomes that constrained personal liberty through institutional confinement, degrading labor, and physical punishment. By the eve of the Civil War many Americans were just as divided about the …

From Preparation To Practice: A Qualitative Study Examining The Perceptions Of General Education Teachers, Kemba Ayanna Allen

LSU Doctoral Dissertations

ABSTRACT

Teachers are certified either by a traditional university-based program or an alternative route to certification program. Graduates transition into teaching from diverse backgrounds and bring with them various experiences and predetermined expectations and visions of the profession. Teacher education preparation curriculum traditionally has included exposure to pedagogy and theory. These programs amass many underprepared students, which results in graduates who are underexposed to pedagogical best practices.

The scholarship of teaching and learning (SoTL) approach to teaching views learning spaces as sites for knowledge-building, innovation, and inquiry. According to the SoTL, the educator looks carefully and critically at students’ learning …

Investigation Of Subsurface Stratigraphy And Groundwater Dynamics In The Mississippi River Delta, An Li

LSU Doctoral Dissertations

The Mississippi River Delta (MRD) is socioeconomically important to the state of Louisiana and the United States. Various types of land-water system data have been collected in the MRD. However, very few efforts have been made to utilize these datasets in modeling regional stratigraphy and groundwater dynamics in the MRD, especially for the upper 50 m of the depth. In this interval of depth, the Mississippi River and surrounding interdistributary bays intensively interact with the groundwater system. The lack of knowledge in regional stratigraphy and groundwater dynamics hinder an understanding of how hydrogeological setting affects processes such as surface-groundwater interaction, …

Visualization And Quantitation Of Radioiodine Distribution In Silver Zeolite Cartridges, Daniel Dimarco

LSU Master's Theses

Iodine 131 is a major fission product released during a nuclear incident. This isotope provides a serious health hazard for humans and the environment, therefore nuclear power plants must monitor releases using air sampling. The air sampling is accomplished using air filter cartridges using silver zeolite as a filter media. During an emergency situation, silver zeolite is useful for its affinity to I-131 without adsorbing other radioactive gases. After leaving the plume, these cartridges are counted in a low background area. This measurement does not take into account the distribution of radioiodine in the cartridge. This study explores two methods …

Inside Voice: Charlotte Smith, (In)Sensibility, And Emotional Cadences In Lyric Silence, Christie Marie Cognevich

LSU Doctoral Dissertations

This dissertation is an investigation into lyric poetry and the sonnet’s emotional-sensory qualities demonstrated by Charlotte Turner Smith, a late eighteenth-century poet and novelist best known for her mournful “elegiac sonnets.” While Smith’s sonnets have been largely read as sensibility poetry through a materialist lens, I suggest Smith demonstrates an insensible lyrical mode through distinctly troubled mind/body connections. Much of Smith’s poetry is characterized by melancholy as it attempts to express a complicated grief. This attempt leads Smith to the thematics of insensibility, both as a literal and as a figurative concept. Thus, the conventional poetic tradition linking the oracular …

An Integration Of East And West: History, Analysis And Reception Of The Yellow River Piano Concerto, Lin Tao

LSU Doctoral Dissertations

The Yellow River Piano Concerto remains as one of a few representative and major instrumental compositions within the Chinese repertoire since it was composed in 1969. Thanks to the devoted work of Chinese pianists, the Yellow River Piano Concerto has disseminated around the world and has become a musical symbol of Chinese culture in recent years. This piano concerto serves as a tool for the cultural communication between China and the world. The Yellow River Piano Concerto has a unique ability to depict Chinese culture and history through the language of music. Its exotic pentatonic melodies and eastern orchestrations make …

Characterization And Amplification Of Retrotransposable Elements Platy-1 And Alu In The Cebidae Lineage Of Platyrrhine Primates, Jessica Storer

LSU Doctoral Dissertations

Alu mobile elements are much more than “junk DNA”. Inherent properties such as high copy number, small ~300 bp size, and their nearly homoplasy-free nature make these elements particularly useful in resolving primate phylogenies. In addition, shared sequence features and identity with the Alu element allow for discovery of new SINE retrotransposons, such as the Platyrrhine-limited Platy-1 element. Building on previous research of subfamily analysis, the Platy-1 and Alu elements can be used not only to explore the controversial New World monkey (NWM) phylogeny, but also the mode and tempo of their amplification in different primate genera and species.

Chapter …

Environmentally Persistent Free Radicals: Linking Air Pollution And Poor Respiratory Health?, Peter D. Sly, Stephania A. Cormier, Slawomir Lomnicki, Jeffrey N. Harding, Keith Grimwood, Griffith University

Faculty Publications

No abstract provided.

How Protein - Protein Interactions Contribute To Pyrenoid Formation In Chlamydomonas, Ananya Mukherjee, James V. Moroney

Faculty Publications

© The Author(s) 2019. The chloroplast pyrenoid, an important component of the CO2 concentrating mechanism of algae, is a structure composed primarily of Rubisco. In Chlamydomonas, Rubisco in the pyrenoid is held together by the linker protein EPYC1. Atkinson et al., (2019) determined the regions of the Rubisco small subunit and EPYC1 that are important for the protein-protein interaction, thus making progress towards reconstruction of a pyrenoid in higher plants. Why is a protein soluble in one organism while its homologue in another species becomes part of a liquidlike cell structure? That is the question being addressed by Atkinson et …

Short- And Intermediate-Range Structure And Dynamics Of Fe-Ni-C Liquid Under Compression, Jianwei Wang

Faculty Publications

Properties of liquid Fe alloys under high-pressure conditions are crucial for understanding the composition, thermal state, and dynamics of Earth's core. Experiments on such liquids, however, are often performed under pressures far below those of the outer core, necessitating long extrapolations of experimental results to core conditions. Such estimates can be complicated by light elements possibly forming pressure-dependent molecular clusters that can significantly affect the physical properties of liquids as core conditions are approached. First-principles molecular dynamics simulations were employed to compute the properties of an Fe-Ni-C liquid with a composition of Fe3.7Ni0.37C at 1673 K and pressures from 0 …

Short- And Intermediate-Range Structure And Dynamics Of Fe-Ni-C Liquid Under Compression, Jianwei Wang

Faculty Publications

Properties of liquid Fe alloys under high-pressure conditions are crucial for understanding the composition, thermal state, and dynamics of Earth's core. Experiments on such liquids, however, are often performed under pressures far below those of the outer core, necessitating long extrapolations of experimental results to core conditions. Such estimates can be complicated by light elements possibly forming pressure-dependent molecular clusters that can significantly affect the physical properties of liquids as core conditions are approached. First-principles molecular dynamics simulations were employed to compute the properties of an Fe-Ni-C liquid with a composition of Fe3.7Ni0.37C at 1673 K and pressures from 0 …

Accumulation Over Evolutionary Time As A Major Cause Of Biodiversity Hotspots In Conifers, Mekala Sundaram, Michael J. Donoghue, Aljos Farjon, Denis Filer, Sarah Mathews, Walter Jetz, Andrew B. Leslie

Faculty Publications

© 2019 The Author(s) Published by the Royal Society. All rights reserved. Biodiversity hotspots are important for understanding how areas of high species richness form, but disentangling the processes that produce them is difficult. We combine geographical ranges, phylogenetic relationships and trait data for 606 conifer species in order to explore the mechanisms underlying richness hotspot formation. We identify eight richness hotspots that overlap known centres of plant endemism and diversity, and find that conifer richness hotspots occur in mountainous areas within broader regions of long-term climate stability. Conifer hotspots are not unique in their species composition, traits or phylogenetic …

Detecting Parasite Associations Within Multi-Species Host And Parasite Communities, Tad A. Dallas, Anna Liisa Laine, Otso Ovaskainen

Faculty Publications

© 2019 The Author(s) Published by the Royal Society. All rights reserved. Understanding the role of biotic interactions in shaping natural communities is a long-standing challenge in ecology. It is particularly pertinent to parasite communities sharing the same host communities and individuals, as the interactions among parasites—both competition and facilitation—may have far-reaching implications for parasite transmission and evolution. Aggregated parasite burdens may suggest that infected host individuals are either more prone to infection, or that infection by a parasite species facilitates another, leading to a positive parasite–parasite interaction. However, parasite species may also compete for host resources, leading to the …