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Bayesmotif: De Novo Protein Sorting Motif Discovery From Impure Datasets, Jianjun Hu, F. Zhang

Faculty Publications

Background

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms.

Methods

We formulated the protein sorting motif discovery problem as a classification problem …

Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang

Faculty Publications

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to …

Physical Work Exposures: Comparing Self-Reported, Observer-Rated And O*Net Ratings, Bethany T. Gardner, David A. Lombardi, Ann Marie Dale, Alfred Franzblau, Bradley Evanoff

Occupational and Health Faculty Publications

No abstract provided.

History Of Latter-Day Saint Education In Nauvoo 1839-1845, Marnie Hopkins

Student Works

Understanding the history of education within The Church of Jesus Christ of Latter-day Saints is essential in order to comprehend the full history of the Church, its people and culture. As the records of the Church have continued to be explored, members and non- members alike have been enriched by the lives of the early saints. Historians have made wonderful progress to provide the common reader with access to the records and history of the Church. However, there is still a substantial amount of research to be performed. One major gap in the research can be found during the Nauvoo …

Increased Weed Diversity, Density And Above-Ground Biomass In Long-Term Organic Crop Rotations, Samuel E. Wortman, John L. Lindquist, Milton J. Haar, Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

While weed management is consistently a top priority among farmers, there is also growing concern for the conservation of biodiversity. Maintaining diverse weed communities below bioeconomic thresholds may provide ecosystem services for the crop and the surrounding ecosystem. This study was conducted to determine if weed diversity, density and biomass differ within and among organic and conventional crop rotations. In 2007 and 2008, we sampled weed communities in four long-term crop rotations near Mead, Nebraska, United States using seedbank analyses (elutriation and greenhouse emergence) and above-ground biomass sampling. Two conventional crop rotations consisted of a corn (Zea mays) …

Structural Analysis Of Affect In The Pre-Purchase Context, Rosemary R. Seva, Henry Been Lirn Duh, Martin G. Helander

DLSU Business & Economics Review

Previous studies on consumption related affect did not identify specific components in the pre-purchase context. This article reviewed theoretical bases of affect and its relationship to product judgment and determined the components and structure of pre-purchase affect. Field studies were conducted to gather an initial list of affect experienced before purchasing “highinvolvement” products. An initial list of 94 pre-purchase affect was identified and trimmed down to 18 after further statistical analysis. A second study was conducted to determine the structure of the pre-purchase emotion set (PES) derived from the first study. Multidimensional scaling was used and four clusters of emotion …

Taking Stock: The Magnuson-Stevens Act Revisited. Background Materials On The Msa, Jacqueline Rolleri

Sea Grant Law Fellow Publications

No abstract provided.

Impacts Of The Spotted Spiny Lobster (Panulirus Guttatus) On The Long-Spined Sea Urchin (Diadema Antillarum) And Patch Reef Communities In The Florida Keys, Meredith D. Kintzing

Biological Sciences Theses & Dissertations

Caribbean coral reefs have undergone a phase shift from a system dominated by corals to one where algae are pervasive. This shift was precipitated by the loss of herbivores, including the mass mortality of the long spined sea urchin (Diadema antillarum), coupled with disease and the recruitment failure of hermatypic corals. Diadema populations have recovered in some areas of the Caribbean, but are still below historical levels in the Florida Keys, likely due to low larval supply coupled with predation on juveniles. Lobsters are sea urchin predators in other systems and the spotted spiny lobster (Panulirus guttatus …

The Effects Of Expressive Writing On Stress, Mood, And Perception Of Self-Efficacy And Of Instructor, Sophia S. Tailor

Counseling & Human Services Theses & Dissertations

The purpose of this study was to determine if emotional disclosure through expressive writing would have an effect on stress, mood, self-efficacy, and perception of instructor in a population of undergraduate human services students. This study used a randomized control-group pretest-posttest design with three experimental conditions. There were 32 participants with (N = 10) emotional disclosure group, (N = 11) factual disclosure group, and (N = 11) the control group. The study was conducted over three consecutive days following a variation of Pennebaker's (1986) expressive writing protocol. Study measures and writing samples were collected via a web-based interface. The data …

Questions Of Transfer: Writers' Perspective On Familiar/Unfamiliar Writing Tasks In A Capstone Writing Course, Heather G. Lettner-Rust

English Theses & Dissertations

Understanding what students bring from one writing context to another may the central concern for teachers of writing from elementary school to adult learning. Research from the field of composition studies offers knowledge about writing as process(es) (Emig, 1971; Shaughnessy, 1979; Russell, 1999), as socially constructed performances (Flower & Hayes, 1980; Bartholomae, 1985; Bloom, 1985), and as part of a larger activity system (Russell, 1997). This dissertation ties together theories of writing as an activity in a broader system of tools and outcomes and current research on transfer in writing in order to illustrate writers' perspectives on particular writing tasks. …

Active Control Of Shocks And Sonic Boom Ground Signal, Bedri Yagiz

Mechanical & Aerospace Engineering Theses & Dissertations

The manipulation of a flow field to obtain a desired change is a much heightened subject. Active flow control has been the subject of the major research areas in fluid mechanics for the past two decades. It offers new solutions for mitigation of shock strength, sonic boom alleviation, drag minimization, reducing blade-vortex interaction noise in helicopters, stall control and the performance maximization of existing designs to meet the increasing requirements of the aircraft industries. Despite the wide variety of the potential applications of active flow control, the majority of studies have been performed at subsonic speeds. The active flow control …

Experimental And Numerical Analysis Of Fuel Cells, Abul Bashar Mahmud Hasan

LSU Doctoral Dissertations

Fuel Cells are attractive power source for use in electronic applications. Physical phenomena (water generation, saturation effect in fuel cell, poisoning, and thermal stress) are studied that governs the operation of a Proton Exchange Membrane Fuel Cell (PEMFC) and Solid Oxide Fuel cell (SOFC). Additionally, experimental studies and numerical simulations on PEMFC gas flow channel, the determination of the impact of the single channel fuel cell are presented. Furthermore, preliminary study is done for the application of APS (Air Plasma Spray) to SOFC and adhesion of anode and cathode with electrolytes for the determination of parameters involved in manufacturing the …

Connections Between Individual Dispersal Behavior And The Multi-Scale Distribution Of A Saproxylic Beetle, Heather Bird Jackson

LSU Doctoral Dissertations

Species incidence results from a complex interaction among species traits (e.g., mobility and behavior), intra- and inter-specific interactions, quality and configuration of the landscape, and historical events. Determining which factors are most important to incidence is difficult because the multiple processes affecting incidence operate at different temporal and spatial scales. I conducted an empirically-based study relating individual behavior (dispersal, habitat selection, and intra-specific interactions) with hierarchically-organized environmental filters to predict the incidence of Odontotaenius disjunctus (Passalidae), a saproxylic (=decayed wood dependent) beetle common to eastern North American forests, at multiple spatial scales. In dispersal experiments, O. disjunctus movement was faster …

Ecological Assembly Of High-Diversity Plant Communities: Dispersal, Competition, And Environmental Filtering In Longleaf Pine Savannas, Jonathan Andrew Myers

LSU Doctoral Dissertations

Ecological mechanisms proposed to explain community assembly and the maintenance of biodiversity are hypothesized to fall along a theoretical continuum bounded at one extreme by deterministic processes (“niche assembly”) and at the other extreme by stochastic processes (“dispersal assembly”). In this dissertation, I explore the idea that the position of ecological communities along the niche-dispersal assembly continuum is dynamic in space and time. Using field experiments in a high-diversity longleaf pine savanna, I test the general hypothesis that “ecological filters” (competition, disturbance, and resource availability) contribute to niche assembly through their effects on established plant species and recruitment from the …

Antioxidant Nanoparticles As Delivery Systems, Carlos Ernesto Astete R.

LSU Doctoral Dissertations

The goal of the study was to develop antioxidant polymeric nanoparticles as a new delivery system for food and pharmaceutical applications. Natural antioxidants like alpha-tocopherol, vitamin C, and carnosine, are responsible to protect biological systems against free radicals attack. The conjugation of vitamin C-vitamin E (EC) and alpha-tocopherol-carnosine (VECAR) were performed to obtain antioxidant surfactants which were used for polymeric nanoparticle synthesis. The surfactant made of á-tocopherol (vitamin E) and ascorbic acid (vitamin C) of antioxidant properties dubbed as EC was used to make poly(lactic-co-glycolic) acid (PLGA) nanoparticles. Self-assembled EC nanostructures and PLGA-EC nanoparticles were made by nanoprecipitation, and the …

Monstrous Bodies: Femininity And Agency In Young Adult Horror Fiction, June Pulliam

LSU Doctoral Dissertations

Young Adult horror fiction with female protagonists presents sympathetically the untenable situation of adolescent girls within society whereby they are increasingly pressured to embody a doll-like feminine ideal that deprives them of voice and agency. In Young Adult horror fiction, the monstrous Other problematizes what is presented to girls as “normal” and “natural” feminine behavior. As a double with a difference, the monstrous Other is an iteration of femininity whose similarity to the original implies the possibility of resisting restrictive gender roles. Because in Young Adult horror fiction the monstrous Other is nearly always a sympathetic character, it is fairly …

Demography, Health Status, And Mortuary Rituals Of The Late Woodland Poole-Rose Ossuary, Ontario, Canada: A Study Of The Clavicles, Nicole Elizabeth Smith

LSU Master's Theses

This thesis is an analysis of the clavicles from a pre-contact (1550 A.D. ±50 years) native ossuary burial from Ontario, Canada. The Poole-Rose ossuary clavicles were analyzed for demography, pathological processes, trauma, and cultural modifications. Demographic markers on the clavicles are derived from the minimum number of individuals (MNI) estimation, medial epiphyseal age, and sex. Pathological processes are indicated by the presence of degenerative joint disease (DJD), periosteal reactions, and lytic lesions. Trauma includes healed fractures and cuts from defleshing of the clavicles. The presence of pre-burial cut marks is an indication of cultural modifications that were likely part of …

Point-Of-Care Immunoassay System Using Carbon Nanotube Labels, Adeyabeba Abera

LSU Doctoral Dissertations

The goal of this research was to develop enhanced signal detection mechanisms for immunosensing using carbon nanotubes (CNTs). The utilization of CNT labels for direct electrical measurement was implemented on lateral flow system and microfluidic integrated interdigitated array microelectrodes. These sensing mechanisms in simple and miniaturized system provided higher sensitivity and autonomous flow control for rapid detection aimed at point-of-care diagnostics. Specific functionalization protocols were carried out to chemically modify the surface of the CNTs for uniform dispersion and antibody conjugation in aqueous solution. Surfactant assisted dispersion of the CNTs was studied using PVP and PEG. Covalent conjugation of antibodies …

Application Of Anti-H Monoclonal Antibodies To Develop Rapid Immunoassay For Vibrio Vulnificus, Ravirajsinh Jadeja

LSU Doctoral Dissertations

In the US there are about 76 million foodborne illness cases reported every year, in spite of initiatives by federal agencies. This emphasizes the need for the development of novel detection techniques which are sensitive, specific and rapid. A detection technique should be rapid enough to give results same day, allowing companies to release food lots without delay and decreasing storage costs. This kind of screening would also allow immediate measures, if needed, before releasing the lots. In the case of Vibrio vulnificus (V. vulnificus), conventional methods are available to identify and enumerate this pathogen in oysters, but they are …

Cross-Talk-Free Dual-Color Fluorescence Cross-Correlation Spectroscopy For High-Throughtput Screening, Wonbae Lee

LSU Doctoral Dissertations

High throughput processing of chemical/biochemical information is critical in many areas, such as genome sequencing, drug discovery and clinical diagnostics. Integral to collecting information at high rates with the necessary throughput is the development of systems that can not only monitor the results with high precision and accuracy, but also prepare and process samples prior to the analytical measurement. To achieve the required throughput, we have conducted work directed toward developing a system that provides detection sensitivity at the single-molecule detection (SMD) level. The research was first focused on the development of a sensitive strategy for the detection of proteins …

Analysis And Modeling Of Hurricane Impacts On A Coastal Louisiana Lake Bottom, Angelina Freeman

LSU Doctoral Dissertations

Tropical cyclone impacts on wetland, terrestrial, and shelf systems have been previously studied and reasonably delineated, but little is known about the response of coastal lakes to storm events. For the first time, tropical cyclone impacts on a shallow coastal lake in the Louisiana coastal plain have been studied using direct lines of evidence and numerical modeling. Using side-scan sonar, CHIRP subbottom and echo sounder bathymetric profiles, the lake bottom and shallow subsurface of Sister Lake was imaged pre- and post-Hurricanes Katrina and Rita to provide a geologic framework for assessing the effects of these storms. Box cores were collected …

A Four-Cysteine Zinc Finger In Carboxyltransferase Structurally Links The Functions Of Enzymatic Activity And Negative Feedback Regulation Of Translation, Glen D. Meades

LSU Doctoral Dissertations

Acetyl-CoA carboxylase is the first and committed step of de novo fatty acid synthesis in all organisms. In Escherichia coli, the enzyme is expressed as separate proteins for the three functional components: a biotin carboxylase, a biotin carboxyl carrier protein, and a carboxyltransferase. The carboxyltransferase enzyme has an α2β2 heterotetrameric quaternary arrangement. The crystal structure of the β subunit revealed a zinc-binding domain, a feature common among nucleic acid-binding proteins. Carboxyltransferase preferentially binds mRNA coding for its two subunits over other nucleic acids, suggesting a means by which the enzyme can regulate its own expression. In the first study, the …

Optimization And Toxocologic Effects Of Cancer Immuno-Electrogene Therapy Using A Tumor-Targeted Interleukin-12 Gene Construct, Scott Douglas Reed

LSU Doctoral Dissertations

This dissertation includes a comprehensive current review of reversible electroporation (EP) and other related physical gene transfection techniques; an overview of results of electrochemogene therapy (ECGT) used to treat naturally occurring spontaneous neoplasms in dogs; and the results of comprehensive, pre-clinical toxicology testing of electrogene therapy (EGT) of a tumor-targeted version of interleukin-12 (IL-12) in mice. Intralesional bleomycin (BLM) and feline interleukin-12 (fIL-12) DNA injection combined with trans-lesional EP resulted in complete cure of two recurrent oral squamous cell carcinomas and an acanthomatous ameloblastoma in a series of six cases of spontaneous neoplasia in pet dogs. The three remaining dogs, …

Pregnancy Rates In Beef Cattle Artifically Inseminated With Frozen-Thawed Aged Beef Semen, David Barry Carwell

LSU Master's Theses

The duration of frozen semen storage had no effect on pregnancy rates (60%, 61% and 61%, respectively) in Angus females inseminated with semen from 25 Angus bulls from Time Frames 1 (1960-1975), 2 (1976-1991) and 3 (1992-2006). Pregnancy rates were not different for beef females inseminated with semen from Time Frames 1, 2 and 3 (55%, 62% and 55%, respectively). There were no differences for total and progressive sperm motility across Time Frames 1 (42% and 29%), Time Frame 2 (51% and 38%) and Time Frame 3 (55% and 41%) and percentage of normal and abnormal sperm from bulls in …

Communication Deficits In Babies With Autism And Pervasive Developmental Disorder - Not Otherwise Specified (Pdd-Nos), Max Horovitz

LSU Master's Theses

Autism Spectrum Disorders (ASDs) are characterized by pervasive impairments in communication, socialization, and repetitive behaviors or interests. While there is a growing interest in early ASDs, very few studies have looked at the nature of these impairments before age 3. In order to better strengthen early assessment and intervention for ASDs, more knowledge is needed in this area. The current studies aimed to determine if, and in what ways, communication impairments are present in infants and toddlers (17-37 months) diagnosed with autism and Pervasive Developmental Disorder – Not Otherwise Specified (PDD-NOS). In the first study, infants with autism and PDD-NOS …

The Influence Of Self-Esteem And Selected Demographic Characteristics On The Academic Achievement Of Freshman Students In The College Of Agriculture At A Research-Extensive University, Mae Blanchard Gaspard

LSU Doctoral Dissertations

The primary purpose of this study was to determine if a relationship existed between self-esteem and academic achievement among students at the freshman level in the College of Agriculture at a Research-Extensive University in the Southern Region of the United States. The sample of the study was all students at one selected Research-Extensive University enrolled in the Introduction to Agriculture course which was a requirement for agriculture students at the freshman level. Three instruments were used for data collection. The Adult Form of the Coopersmith Inventory was administered at two data collection points at the beginning and end of the …

A Qualitative Exploration Of Christian, Native American Families, Mandy Lynn Swanson

LSU Doctoral Dissertations

Research on Native American families is limited and emphasizes the deficits of families and overlooks those Native American families that are thriving. This study seeks to illuminate the strengths of highly religious, Christian, Native American, married couples. The study employs a strengths-based perspective to examine how and why religious coping is meaningful and influential for these Native American couples’ enduring marriages and in their efforts to be responsive parents. From interviews of fifteen heterosexual, Native American, married couples (n=30), five themes emerged from the coding and analysis: 1) Faith and Culture: “They go hand in hand”, 2) Influence of Faith …

Genetic And Cytological Investigation Of Nucleostemin-1 In Drosophila Melanogaster, Raphyel Ojomo Rosby

LSU Doctoral Dissertations

Mammalian nucleostemin (NS) is a nucleolar GTP-binding protein implicated in cell cycle progression, stem cell proliferation, and ribosome assembly. Drosophila melanogaster contains a four-member nucleostemin family (NS1-4). Nucleostemin 1 (NS1) is the closest orthologue to human NS; it shares 33% identity and 67% similarity with human NS. We show that NS1 has intrinsic GTPase and ATPase activity, and that it is present within nucleoli of most larval and adult cells. Endogenous NS1 and lightly expressed GFP-NS1 enrich within the nucleolar granular regions as expected, while over-expressed GFP-NS1 localizes throughout the nucleolus and nucleoplasm, and to several transcriptionally active inter-bands of …

The Evolution Of Freeze Tolerance In A Historically Tropical Snail, Alice B. Dennis

LSU Doctoral Dissertations

Geographic range differences among species may result from differences in their physiological tolerances. In the intertidal zone, marine and terrestrial environments intersect to create a unique habitat, across which physiological tolerance strongly influences range. The snail Melampus bidentatus occurs in coastal salt marshes in the western Atlantic and Gulf of Mexico. I have used sequence data from one mitochondrial (CO1) and two nuclear markers (histone H3 and a mitochondrial carrier protein, MCP) to identify three cryptic species within Melampus bidentatus, and to infer their relationships to other Melampus. To identify microhabitat differences between two cryptic species, I modeled their distributions …

Exercise-Induced Alterations In Melanocortin Receptor Expression And Inflammation, Tara Michelle Henagan

LSU Doctoral Dissertations

Inflammatory cytokines play a significant role in the pathogenesis of obesity-related diseases and have been implicated as integral factors in both early and late phases of atherosclerosis. Lifestyle modifications such as increasing physical activity and making dietary changes to induce weight loss are part of the primary prescription for the treatment of metabolic syndrome. Additionally, physical activity has been implicated as a potentially effective regimen for the control of inflammation, yet little is known about the anti-inflammatory mechanistic alterations induced by physical activity.

Exercise training causes acute changes in inflammation immediately post exercise, evidenced by upregulation of inflammatory cytokines and …