Life Sciences Commons^™

The Normative Problem Of Shame, Timothy James Oakberg

Arts & Sciences Graduate Student Theses and Dissertations

What role should shame play in our lives? This is the normative problem of shame, and it is the focus of this dissertation. Through an examination of empirical research on shame and shame-proneness, I argue that shame should have only a very limited role in our lives. More specifically, we ought not cultivate shame, because a substantial amount of empirical literature points to the conclusion that shame-proneness is counterproductive at both an individual and a societal level. Expanding on this general answer to the normative problem of shame, I discuss in detail three proposals regarding shame from the realms of …

Use Of Proteomics To Probe Dynamic Changes In Cyanobacteria, Amelia Yen Nguyen

Arts & Sciences Graduate Student Theses and Dissertations

Cyanobacteria are unicellular photosynthetic microorganisms that capture and convert light energy to chemical energy, which is the precursor for feed, fuel, and food. These oxygenic phototrophs appear blue-green in color due to the blue bilin pigments in their phycobilisomes and green chlorophyll pigments in their photosystems. They also have diverse morphologies, and thrive in terrestrial, marine water, fresh water, as well as extreme environments. Cyanobacteria have developed a number of protective mechanisms and adaptive responses that allow the photosynthetic process to operate optimally under diverse and extreme conditions. Prolonged deprivation of essential nutrients, such as nitrogen and sulfur, commonly found …

Infantile Batten Disease: Effective Therapy And Novel Model, Charles Shyng

Arts & Sciences Graduate Student Theses and Dissertations

Infantile neuronal ceroid lipofuscinosis (INCL, Infantile Batten) is typically an early onset, neurodegenerative lysosomal storage disorder. INCL is caused by mutations to the gene CLN1 which codes for the lysosomal enzyme palmitoyl-protein thioesterase-1 (PPT1). PPT1 is a soluble lysosomal enzyme that functions to cleave fatty acyl chains from proteins destined for degradation. Deficiency in PPT1 leads to the accumulation of autofluorescent storage material, a hallmark of the NCLs. The storage material has been implicated in progressive histopathological changes in the brain such as neuronal loss, astrocytosis, microgliosis, and immune cell infiltration. These histopathological changes result in a progression of clinical …

Gene Association Mapping In The Era Of Next-Generation Sequencing And Systems Biology, Tianxiao Zhang

Arts & Sciences Graduate Student Theses and Dissertations

In the past decade, advancement of genotyping technology, first microarray then “next-generation” sequencing, has enabled scientists to examine the susceptible genes that contribute to the risk of complex disorders using a genome-wide, “hypothesis free” strategy. However, despite this “hypothesis free” label, these genome-wide approaches (including genome-wide association and whole genome sequencing studies) depend on two implicit assumptions. The first assumption is that the genetic risk of complex traits is contributed by independent genes/variants (assumption of independence).The second assumption is that different genes have equal potentiality to confer to the genetic predisposition of the complex traits (assumption of equality). Despite the …

Systematics And Evolution Of The Arundinoideae And Micrairoideae (Poaceae), Jordan Kinsley Teisher

Arts & Sciences Graduate Student Theses and Dissertations

The grass family, Poaceae, is one of the most ecologically and economically important plant groups on Earth. However, the large size (over 11,000 species) and geographic range of the family makes complete resolution of the evolutionary relationships in Poaceae challenging, with some significant groups remaining neglected. Two such understudied clades, subfamilies Arundinoideae and Micrairoideae, possess an incredible amount of morphological and ecological diversity for their sizes, making them a potentially rewarding system in which to study evolution of a wide range of grass features. In this dissertation, I resolved many of the long-standing systematic issues in Arundinoideae and Micrairoideae and …

Functions Of The Dna Polymerase Delta Replicase In Lagging Strand Replication, Joseph L. Stodola

Arts & Sciences Graduate Student Theses and Dissertations

The work described in this dissertation focuses on several aspects of DNA replication in the model organism Saccharomyces cerevisiae, with particular attention paid to the function of the replicative DNA polymerase delta (Pol ), and its functions in Okazaki fragment synthesis and maturation. The first major theme of this dissertation is investigating the role that metal binding motifs play in the structure and function of Pol and other budding yeast polymerases. First, I discuss the role that two metal binding motifs within the catalytic subunit of Pol play in creating the multi-subunit polymerase complex and in promoting crucial interactions with …

Effects Of An Electronic, Motion-Activated Scarecrow On Foraging Time In Nocturnal Vertebrate Crop Pets In South Africa, Mallory Clouse

Mahurin Honors College Capstone Experience/Thesis Projects

The normal behaviors of animals can disrupt human activities, resulting in human wildlifeconflict. In South Africa, nocturnal crop raiders are a significant source of human wildlifeconflict for farmers. Major nocturnal pest animals are Cape porcupine (Hystrix africaeaustralis) and bushpig (Potamochoerus larvatus). Although methods of deterring animals from agricultural areas have been explored, nocturnal crop raiding remains difficult to mitigate. Most research studies focus on deterring non-human primates and elephants, but methods that may be successful in deterring such larger mammals are not necessarily effective at discouraging smaller, nocturnal crop raiders. This study examined the efficacy of …

An Assessment Of Scholastic Basketball Programs: Administration, Facilities, And Support, Leah Cannady

Mahurin Honors College Capstone Experience/Thesis Projects

The main purpose of this study was to validate the survey insturement created to evaluate various aspects of scholastic basketball programs—including but not limited to administration, facilities, and support. All boys and girls head basketball coaches in South Dakota were administered an electronic survey created for the study. To incentivize participation, respondents could choose to be entered to win a monetary donation of $250 to their basketball program. Descriptive statstics were used to summarize respondent demographics and other statistical measures were used to indicate reliability and validity of the survey instrument. Cronbach’s alpha was calculated at .711 and Pearson’s correlation …

Maternal Sleep Loss During Fetal Development Alters Offspring Endocrine Responses To Stress Throughout Life, Audrey Brown

Mahurin Honors College Capstone Experience/Thesis Projects

The hypothalamic-pituitary-adrenal (HPA) axis releases glucocorticoids, including corticosterone (CORT), in response to stress. CORT then negatively feeds back to inhibit its own production by binding to glucocorticoid receptors (GRs) in the hypothalamus and pituitary gland. The HPA axis is subject to “programming” by abnormal stimuli during early development, which may permanently alter how the HPA axis responds to stress. These altered responses have been linked to an increased risk for human psychiatric and metabolic disorders in later life, but the mechanism by which this happens is not fully understood. This study tests the hypothesis that changes to GR expression patterns …

Natural Establishment Of Earthworms On Reclaimed Lignite Mine Soils, Lacey Russell, Kenneth Farrish, Jerry Leon Young, George Damoff, Brian Oswald

Student Publications

This two-year field study surveyed earthworm community characteristics on a chronosequence under afforested pine and hardwood lignite mine soils at the Beckville and Oak Hill lignite coal mines in east Texas. The following were used as indicators of earthworm community characteristics: reclamation type, forest cover type, age since reclamation and physical and chemical soil properties. The Beckville mine was sampled from February 2012 through March 2013; the Oak Hill mine was sampled from April 2013 through March 2014. The study was a 2x2x3 factorial design with reclamation type (mixed overburden vs. haul back), cover-type ((pine plantation (pp) and mixed pine …

Investment Appraisal Of Automatic Milking And Conventional Milking Technologies In A Pasture-Based Dairy System, John Shortall, Laurence Shalloo, Cathriona Foley, Roy D. Sleator, Bernadette O'Brien

Department of Biological Sciences Publications

The successful integration of automatic milking (AM) systems and grazing has resulted in AM becoming a feasible alternative to conventional milking (CM) in pasture-based systems. The objective of this study was to identify the profitability of AM in a pasture-based system, relative to CM herringbone parlors with 2 different levels of automation, across 2 farm sizes, over a 10-yr period following initial investment. The scenarios which were evaluated were (1) a medium farm milking 70 cows twice daily, with 1 AM unit, a 12-unit CM medium-specification (MS) parlor and a 12-unit CM high-specification (HS) parlor, and (2) a large farm …

Physical Separation From The Mate Diminishes Male’S Attentiveness Towards Other Females: A Study In Monogamous Prairie Voles Microtus Ochrogaster, Christine J. Delevan, Natalia A. Rodriguez, Karine M. Legzim, Fayeza Aliou, Jamie T. Parker, Maryam Bashad

Publications and Research

We tested whether continuous cohabitation in monogamous voles affects the mated male’s attentiveness to his breeding partner versus another female. Each male was housed in a 3-chamber apparatus with a Focal female (FF) and a Control female (CF) for 13 days then placed in a T-maze to assess his attentiveness to and memory of those females. The Distal male remained physically separated from both females, but received their distal cues. The Separate male cohabited with the FF for 3 days then remained physically separated from both females. The Disrupt male’s continuous cohabitation with the FF was disrupted by having him …

Interleukin-6 Increases Matrix Metalloproteinase-14 (Mmp-14) Levels Via Down-Regulation Of P53 To Drive Cancer Progression, Jillian Cathcart, Anna Banach, Alice Liu, Jun Chen, Michael S. Goligorsky, Jian Cao

NYMC Faculty Publications

Matrix metalloproteinases (MMPs) play critical roles in cancer invasion and metastasis by digesting basement membrane and extracellular matrix (ECM). Much attention has focused on the enzymatic activities of MMPs; however, the regulatory mechanism of MMP expression remains elusive. By employing bioinformatics analysis, we identified a potential p53 response element within the MMP-14 promoter. Experimentally, we found that p53 can repress MMP-14 promoter activity, whereas deletion of this p53 response element abrogated this effect. Furthermore, we found that p53 expression decreases MMP-14 mRNA and protein levels and attenuates MMP-14-mediated cellular functions. Additional promoter analysis and chromatin immunoprecipitation studies identified a mechanism …

Low Florida Coral Calcification Rates In The Plio-Pleistocene, Thomas C. Brachert, Markus Reuter, Stefan Kruger, James S. Klaus, Kevin P. Helmle, Janice M. Lough

Marine & Environmental Sciences Faculty Articles

In geological outcrops and drill cores from reef frameworks, the skeletons of scleractinian corals are usually leached and more or less completely transformed into sparry calcite because the highly porous skeletons formed of metastable aragonite (CaCO3) undergo rapid diagenetic alteration. Upon alteration, ghost structures of the distinct annual growth bands often allow for reconstructions of annual extension ( =  growth) rates, but information on skeletal density needed for reconstructions of calcification rates is invariably lost. This report presents the bulk density, extension rates and calcification rates of fossil reef corals which underwent minor diagenetic alteration only. The corals derive from …

Itar: A Web Server For Identifying Target Genes Of Transcription Factors Using Chip-Seq Or Chip-Chip Data, Chia-Chun Yang, Erik H. Andrews, Min-Hsuan Chen, Wan-Yu Wang

Dartmouth Scholarship

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP’s output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the …

Plasmid Dna Bind And Elute Chromatography Using Borosilicate Filters And Filter Holders, Stacey D. Floyd, Camille S. Baird, Jordan Finnell, Tsz Ming Tsang, Robert C. Davis, Kenneth A. Christensen

Student Works

This research has been completed to determine whether plasmid DNA will bind to a simple borosilicate filter in a reusable filter holder, and whether it can be released in a controlled procedure after a wash has been done to eliminate impurities.

The motivation for this is to help small research groups, both in educational settings as well as in other small research settings be able to study isolated DNA without much of the expense generally associated with purification kits and to remove the limitations on trial numbers imposed by the expense of each individual isolation kit.

Medical research, forensics, and …

Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.

McKelvey School of Engineering Graduate Student Theses & Dissertations

In human stool, a large population of bacterial genes and transcripts from hundreds of genera coexist with host genes and transcripts. Assessments of the metagenome and transcriptome are particularly challenging, since there is a great deal of sequence overlap among related species and related genes. We sequenced the total RNA content from stool samples in a neonate using previously-described methods. We then performed stepwise alignment of different populations of RNA sequence reads to different indices, including ribosomal databases, the human genome, and all sequenced bacterial genomes. Each pool of RNA at each alignment step was subjected to compression to assess …

Universal Modes Of Awareness? A “Pre-Reflective” Premise, Uta M. Jürgens

Animal Sentience

Mark Rowlands holds that creatures endowed with pre-reflective awareness may qualify as persons: In pre-reflective awareness, the self and the unity of mental life are implicit in the stream of experience. Rowlands generalizes from an introspective analysis of pre-reflective consciousness in humans to pre-reflective awareness in general. I describe three examples of empirical findings that corroborate the assumption that animal minds have some of the same basic modes of pre-reflective awareness as human minds.

Does Cognitive Impairment Affect Rehabilitation Outcome In Parkinson’S Disease?, Davide Ferrazzoli, Paola Ortelli, Roberto Maestri, Rossana Bera, Nir Giladi, Maria Felice Ghilardi, Gianni Pezzoli, Giusseppe Frazzitta

Publications and Research

Background: The cognitive status is generally considered as a major determinant of rehabilitation outcome in Parkinson’s disease (PD). No studies about the effect of cognitive impairment on motor rehabilitation outcomes in PD have been performed before.

Objective: This study is aimed to evaluate the impact of cognitive decline on rehabilitation outcomes in patients with PD.

Methods: We retrospectively identified 485 patients with PD hospitalized for a 4-week Multidisciplinary Intensive Rehabilitation Treatment (MIRT) between January 2014 and September 2015. According to Mini Mental State Examination (MMSE), patients were divided into: group 1—normal cognition (score 27–30), group 2—mild cognitive …

The Design Of The Mosquito And Its Dangers, Alan L. Gillen, Frank Sherwin

Faculty Publications and Presentations

Mosquitoes (Family Culicidae) have been the scourge of mankind since the Fall. Although seemingly designed to inflict suffering and pain via rapid reproduction and formidable mouthparts, evidence mounts that this creature was not always the deadly vector it is today. Mosquitoes are currently and have always been pollinators. The majority of their lives they feed on plants, nectar, pollen, and microbes even in today's world. The Zika virus is but the latest of a significant list of pathogens spread by “the world’s most dangerous animal.” In the past, Christians have been involved in key discoveries linking mosquitoes to diseases.

Interactions Of Nucleic Acid Bases With Temozolomide. Stacked, Perpendicular, And Coplanar Heterodimers, Okuma Emile Kasende, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson–Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a …

Theory Of Inclusive Fitness, David C. Queller

Biology Faculty Research

A review of Social Evolution and Inclusive Fitness Theory: An Introduction. By James A. R. Marshall. Princeton (New Jersey): Princeton University Press. $39.95. xix + 195 p.; ill.; index. ISBN: 978-0-691-16156-3. 2015.

Contrasting Origin Of B Chromosomes In Two Cervids (Siberian Roe Deer And Grey Brocket Deer) Unravelled By Chromosome-Specific Dna Sequencing, Alexey I. Makunin, Ilya G. Kichigin, Denis M. Larkin, Patricia C. M. O'Brien, Malcolm A. Ferguson-Smith, Fengtang Yang, Anastasiya A. Proskuryakova, Nadezhda V. Vorobieva, Ekaterina N. Chernyaeva, Stephen J. O'Brien, Alexander S. Graphodatsky, Vladimir Trifonov

Biology Faculty Articles

Background

B chromosomes are dispensable and variable karyotypic elements found in some species of animals, plants and fungi. They often originate from duplications and translocations of host genomic regions or result from hybridization. In most species, little is known about their DNA content. Here we perform high-throughput sequencing and analysis of B chromosomes of roe deer and brocket deer, the only representatives of Cetartiodactyla known to have B chromosomes.

Results

In this study we developed an approach to identify genomic regions present on chromosomes by high-throughput sequencing of DNA generated from flow-sorted chromosomes using degenerate-oligonucleotide-primed PCR. Application of this method …

What If Klein & Barron Are Right About Insect Sentience?, Bob Fischer

Animal Sentience

If Klein & Barron are right, then insects may well be able to feel pain. If they can, then the standard approach to animal ethics generates some implausible results. Philosophers need to develop alternatives to this framework to avoid them.

Subjective Experience And Moral Standing, Andy Lamey

Animal Sentience

Klein & Barron’s analysis focuses on the capacity for any subjective experience at all. It does not seek to demonstrate that insects can experience pleasure and pain in particular. This would be something of which insects have not traditionally been thought capable. If further research were to demonstrate that one or more insect species turn out to be conscious, yet incapable of experiencing pleasure and pain, it would give rise to a philosophical question that ethicists have yet to answer: Would a creature that is conscious, but lacks the capacity to feel pain, have moral standing?

Investigations Of Storage Root Development In Cassava (Manihot Esculenta Crantz), Yeetoh Chaweewan

Dissertations

The tropical root crop cassava is cultivated for its large starchy storage roots. Understanding critical processes in root tuberization is essential if improvement programs are to secure future yields for farmers. Studies were undertaken to identify critical components of storage root development at the anatomical and gene expression levels. Two types of roots were identified from greenhouse-grown stem cuttings: basal roots, which develop from the stem cut end and are prolific in nature, and nodal roots, which originate from the region of the buried axillary bud. Only nodal roots develop to produce storage organs. Anatomical sectioning was performed to determine …

Lipophosphoglycans From Leishmania Amazonensis Strains Display Immunomodulatory Properties Via Tlr4 And Do Not Affect Sand Fly Infection, Paula M. Nogueira, Rafael R. Assis, Ana C. Torrecilhas, Elvira M. Saraiva, Natália L. Pessoa, Marco A. Campos, Eric F. Marialva, Cláudia M. Ríos-Velasquez, Felipe A. Pessoa, Nágila F. Secundino, Jerônimo N. Rugani, Elsa Nieves, Salvatore J. Turco, Maria N. Melo, Rodrigo P. Soares

Molecular and Cellular Biochemistry Faculty Publications

The immunomodulatory properties of lipophosphoglycans (LPG) from New World species of Leishmania have been assessed in Leishmania infantum and Leishmania braziliensis, the causative agents of visceral and cutaneous leishmaniasis, respectively. This glycoconjugate is highly polymorphic among species with variation in sugars that branch off the conserved Gal(β1,4)Man(α1)-PO₄ backbone of repeat units. Here, the immunomodulatory activity of LPGs from Leishmania amazonensis, the causative agent of diffuse cutaneous leishmaniasis, was evaluated in two strains from Brazil. One strain (PH8) was originally isolated from the sand fly and the other (Josefa) was isolated from a human case. The ability of …

Habitat Suitability Modeling For The Mississippi Sandhill Crane, Grus Canadensis Pulla, Linda C. Salande

LSU New Orleans Theses and Dissertations

In this study, I modeled the suitability of habitat on the Mississippi Sandhill Crane National Wildlife Refuge for the federally endangered Mississippi Sandhill Crane (Grus Canadensis pulla). Habitat type and suitability changed over time due to seasonality of vegetation and succession in the absence of burning. Cranes used highly suitable habitat more in the non-growing than in the growing season, and may have been more constrained by resource availability during winter months. Cranes used some less-suitable areas including cypress drains, which provide roosting sites, and supplemental food plots. The mismatch between predicted quality and crane use suggests that …

Phylogenetic Relationships And Evolution Of Snakes, Alex Figueroa

LSU New Orleans Theses and Dissertations

Snakes represent an impressive evolutionary radiation of over 3,500 widely-distributed species, categorized into 515 genera, encompassing a diverse range of morphologies and ecologies. This diversity is likely attributable to their distinctive morphology, which has allowed them to populate a wide range of habitat types within most major ecosystems. In my first chapter, I provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). I then …

Comparing Methods Of Euthanasia And Gill Culture For Hypoxia Research On The Gulf Killifish, Fundulus Grandis, Kristina M. Farragut

LSU New Orleans Theses and Dissertations

Aquatic hypoxia, or low dissolved oxygen, is a growing environmental concern and has detrimental effects on many fishes. Research on fish responses to hypoxia includes whole animal studies as well as organ culture systems. In this thesis, the gulf killifish, Fundulus grandis, was used to determine the interaction between hypoxic exposure and four common euthanasia techniques on selected blood and gill variables and to develop an in vitro gill incubation system. Euthanasia techniques had differential effects on blood and gill, with the common fish anesthetic MS-222 having the greatest effects, but none altered the response to hypoxia. During the …