Genetics and Genomics Commons^™

Transcriptomics Of Learning, Pablo Iturralde

Theses

Learning is a basic and important component of behavior yet we have very little empirical information about the interaction between mechanisms of learning and evolution. In our work, we are testing hypotheses about the neurogenetic mechanisms through which animal learning abilities evolve. We are able to test this directly by using experimentally evolved populations of flies, which differ in learning ability. These populations were previously evolved within the lab by creating worlds with different patterns of change following theoretically predicted effects on which enhanced learning will evolve. How has evolution acted to modulate genes and gene expression in the brain …

Species Distribution And Conservation Genetics Of The Upland And Midland Chorus Frogs (Pseudacris) In Kentucky, Tucker Cambridge

Masters Theses & Specialist Projects

The upland (Pseudacris feriarum) and midland (P. triseriata) chorus frogs are closely related cryptic species that are best distinguished genetically. The distribution of these species within the Commonwealth of Kentucky has previously been defined by only a handful of genetic samples, making delineation of range limits for each species difficult. Accurate understanding of species distributions, and the genetic structure within them, are vitally important for conservation management of amphibian species. In this study, I have collected genetic samples from across the putative ranges of P. triseriata and P. feriarum in Kentucky and used next-generation sequencing technology to generate more fine-scale …

Identifying Kif Subtype That Mediates Axonal Targeting Of Kv7 Channels, Allison Houghton, Jennifer Walters, Mary Hong, Dhruv Joshi, Hee Jung Chung

PRECS 2018

Early-onset Benign Familial Neonatal Epilepsy (BFNE) and Epileptic Encephalopathy (EE), are associated with mutations in neuronal KCNQ/Kv7 channel subunits Kv7.2 and Kv7.3. Kv7 channels are voltage-dependent potassium channels. Enriched at the axonal plasma membrane, they pump potassium ions out of the neurons and inhibit repetitive or burst firing of action potentials. A single neuronal Kv7 channel is a heterotetramer composed of two Kv7.2 and two Kv7.3 subunits. BFNE and EE mutations in Kv7.2 and Kv7.3 lead to decreased surface expression along the axon, which means less potassium ions are moved across the axonal membrane where action potentials are generated and …

Production Of Bioactive Isothiocyanates By Bacterial Myrosinase, Juan Isaiz, Xiaoji Liu, Michael J. Miller

PRECS student projects

Isothiocyanates (ITCs) are bioactive products found in several plants belonging to the Brassicaceae family, and are produced as defense upon disruption of the tissue by herbivores or pathogens, but in humans they have shown anti-cancer and anti-inflammatory properties.

Although we know gut microbes can hydrolyze GSL into ITC, the mechanism is not known. With improved detection methods, the aim of this experiment is to explore whether the gut microbial myrosinase β-glucosidase found within the genome of E. coli Nissle 1917 can hydrolyze glucosinolates (GSLs) into detectable ITCs.

Sperm-Mediated Effects Of Predation Risk On Reproduction In Male Threespined Sticklebacks, Shayne Kempfer, Erika Carlson, Jennifer Hellmann, Jason Keagy, Alison Bell

PRECS student projects

Threespined sticklebacks, Gasterosteus aculeatus, exhibit male-only parental care, but will decrease paternal care if exposed to predators while given care or if their mate has had prior experiences with predators. The offspring will experience lasting effects based on the experience of their parents (behavior-mediated transgenerational plasticity). While other studies have concluded that male exposure to predators prior to fertilization (sperm-mediated transgenerational plasticity) impacts offspring, whether sperm-mediated effects exist in sticklebacks, and for how many generations the effects persist is unknown. Courtship trials with both predator exposed and predator unexposed females with six male treatment groups shows significant impact of maternal …

How Does Climate Change Affect Endophytic Fungi?, Amber Toussaint, Natalie Christian, Katy Heath

PRECS student projects

Plant-associated microorganisms can have major effects on plant health, but climate change can affect plant microbiomes. While it is unknown how climate change will affect aboveground plant-associated microorganisms, such as foliar endophytic fungi, we hypothesize that increased CO₂ concentrations will increase species richness and diversity in endophytic fungal communities, because increased plant photosynthesis under elevated CO₂ will increase the resources available to the fungi.

The Effect Of Imidacloprid On Honey Bee Queen Fecundity, Jamilyn Martin, Julia D. Fine, Amy Cash-Ahmed, Gene E. Robinson

PRECS 2018

Imidacloprid is a neonicotinoid insecticide commonly used in agricultural settings to control insect pests by acting as an agonist of acetylcholine receptors and inducing paralysis and mortality. In small doses, imidacloprid can cause loss of memory and foraging ability along with impaired learning and a lowered immune response in western honey bees (Apis mellifera). Effects of neonicotinoid insecticides on colony reproduction have been documented including decreased colony expansion, queen failure and replacement, and decreased queen egg laying.

For this study, we examined the effects of imidacloprid on the fecundity of queen bees when their worker attendants were exposed to low …

Development Of A Rapid Diagnostic Assay For The Colorimetric Detection Of Bacterial And Viral Pathogens Using Loop-Mediated Isothermal Amplification Coupled With A Peptide Nucleic Acid And Gold Nanoparticle Reporter System, William Brown

All NMU Master's Theses

Detection of pathogenic agents remains pivotal to the control and prevention of infectious disease. While diagnostic methods continue to break barriers, the need for accurate, sensitive, and rapid methods persists. Current methods for pathogen detection, including culture, immunochemical, or molecular-based techniques, are subject to significant limitations that restrict their clinical utility. Point-of-care (POC) tests have received attention for the diagnostic screening of infectious disease, with benefits of simplicity, affordability, and convenience. This study describes the development of a novel loop-mediated isothermal amplification (LAMP) reaction followed by a peptide nucleic acid (PNA) probe and gold nanoparticle (AuNP) detection system that results …

Abrf Proteome Informatics Research Group (Iprg) 2016 Study: Inferring Proteoforms From Bottom-Up Proteomics Data., Joon-Yong Lee, Hyungwon Choi, Christopher M Colangelo, Darryl Davis, Michael R Hoopmann, Lukas Käll, Henry Lam, Samuel H Payne, Yasset Perez-Riverol, Matthew The, Ryan Wilson, Susan T Weintraub, Magnus Palmblad

Articles, Abstracts, and Reports

This report presents the results from the 2016 Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG) study on proteoform inference and false discovery rate (FDR) estimation from bottom-up proteomics data. For this study, 3 replicate Q Exactive Orbitrap liquid chromatography-tandom mass spectrometry datasets were generated from each of 4

Methamphetamine Effects On Adolescent Brain Development In Both Sexes, Jessica Alvarez, Sarah Westbrook, Joshua Gulley

PRECS 2018

Vulnerability to drug addiction in adolescents (ADOLs) may lead to faster rates of addiction and higher rates of relapse. The brain is developing in adolescence, including the prefrontal cortex (PFC) and the nucleus accumbens (NAc), which are regions involved in self-control and reward systems, respectively. Further, females, both human and rat models, often exhibit faster rates of addiction than males. Research from this lab has found previously that adult rats of both sexes exposed to amphetamine during ADOL had reduced expression of dopamine D₁ receptors (D₁R) in the medial PFC but no change in the NAc. The …

Finding Dex-1 Phenotype Suppressing Components, Matthew Barnum, Kristen Flatt, Nathan E. Schroeder

PRECS 2018

Caenorhabditis elegans is a species of microscopic round worm that has been used as a genetic model for over forty years. When in an adverse environment, C. elegans larvae cease reproductive development and enter the stress-resistant dauer stage.

dex-1 mutants of C. elegans are deficient in this protein, resulting in shortened dendrites and a sensitivity to sodium dodecyl sulfate (SDS). SDS will kill any non-dauer C. elegans, but wild type dauers will survive well past the standard concentration of 1% SDS. Thus, treatment with SDS is commonly how labs isolate dauers. By contrast, dex-1 dauers (Fig.3) will …

Phosphorus Vs. Mycorrhiza: Mitigation Of Lead Uptake In Tomatoes, Helen Senerchia, Liz Miernicki, Andrew Margenot

PRECS 2018

This study seeks to understand how the mutualist relationship between arbuscular mycorrhizal fungi (AM) and Solanum lycopersicum (tomato) affects the uptake and distribution of iron (Pb) found in soil by tomatoes and how the effects of phosphorous (P) application may pose a trade-off between AM and P mitigation of bioavailability of Pb.

Functional Polymorphisms Of Alcohol Metabolism Genes And Their Protection Against Alcoholism Via Gene Therapy: A Systematic Review, Olivia Tzeng

Psychological Science Undergraduate Honors Theses

Around 45% of East Asians are unable to fully metabolize ethanol due to functional

polymorphisms of alcohol metabolism genes, specifically alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH). These individuals display high levels of toxic blood acetaldehyde when consuming alcohol, causing symptoms such as tachycardia, vomiting, and flushing. The studies included in this review examine how functional polymorphisms of ADH and ALDH protect against alcoholism in addition to how polymorphisms can be utilized as protection against alcoholism via gene therapy. The studies included found that carriers of the ADH and ALDH polymorphisms were 66 to 99% genetically protected against alcoholism. Through …

Small Non-Coding Rna Expression And Vertebrate Anoxia Tolerance, Claire L. Riggs, Amanda Summers, Daniel E. Warren, Göran E. Nilsson, Sjannie Lefevre, W. W. Dowd, Sarah Milton, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Background: Extreme anoxia tolerance requires a metabolic depression whose modulation could involve small non-coding RNAs (small ncRNAs), which are specific, rapid, and reversible regulators of gene expression. A previous study of small ncRNA expression in embryos of the annual killifish Austrofundulus limnaeus, the most anoxiatolerant vertebrate known, revealed a specific expression pattern of small ncRNAs that could play important roles in anoxia tolerance. Here, we conduct a comparative study on the presence and expression of small ncRNAs in the most anoxia-tolerant representatives of several major vertebrate lineages, to investigate the evolution of and mechanisms supporting extreme anoxia tolerance. The epaulette …

Water Flow And Biofilm Cover Influence Environmental Dna Detection In Recirculating Streams, Arial Shogren, Jennifer L. Tank, Scott P. Egan, Olivia August, Emma J. Rosi, Brittany R. Hanrahan, Mark A. Renshaw, Crysta A. Gantz, Diogo Bolster

Environmental Science and Management Faculty Publications and Presentations

The increasing use of environmental DNA (eDNA) for determination of species presence in aquatic ecosystems is an invaluable technique for both ecology as a field and for the management of aquatic ecosystems. We examined the degradation dynamics of fish eDNA using an experimental array of recirculating streams, also using a “nested” primer assay to estimate degradation among eDNA fragment sizes. We introduced eDNA into streams with a range of water velocities (0.1–0.8 m s–1) and substrate biofilm coverage (0–100%) and monitored eDNA concentrations over time (∼10 d) to assess how biophysical conditions influence eDNA persistence. We found that the presence …

Arthropod Transcriptional Activator Protein-1 (Ap-1) Aids Tick-Rickettsial Pathogen Survival In The Cold, Supreet Khanal, Vikas Taank, John F. Anderson, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Ixodes scapularis ticks transmit several pathogens to humans including rickettsial bacterium, Anaplasma phagocytophilum. Here, we report that A. phagocytophilum uses tick transcriptional activator protein-1 (AP-1) as a molecular switch in the regulation of arthropod antifreeze gene, iafgp. RNAi-mediated silencing of ap-1 expression significantly affected iafgp gene expression and A. phagocytophilum burden in ticks upon acquisition from the murine host. Gel shift assays provide evidence that both the bacterium and AP-1 influences iafgp promoter and expression. The luciferase assays revealed that a region of approximately 700 bp upstream of the antifreeze gene is sufficient for AP-1 binding to promote …

Self-Reported Oral Health Assessment And Attitudes Toward Oral Health For Adults With Cystic Fibrosis, Ahmed Ali Almuntashiri

Dental Hygiene Theses & Dissertations

Purpose: Cystic fibrosis (CF) is a chronic genetic disorder that an individual has at birth. Cystic fibrosis impacts equally all races, gender and becomes worse over time. The aim of this current study was to evaluate oral health status, interaction with the oral health system, and oral health awareness in adults with cystic fibrosis. Methods: A validated survey consisting of 27 questions was distributed online through cystic fibrosis Facebook pages. Individuals with CF who were 18 years old or older, residing in the U.S. and having English as their primary language were asked to respond to the survey. Independent variables …

Genomic And Physiological Characterization Of The Verrucomicrobia Isolate Geminisphaera Colitermitum Gen, John T. Wertz, Eunji Kim, John A. Breznak, Thomas M. Schmidt

University Faculty Publications and Creative Works

The name Diplosphaera, the proposed genus name for Verrucomicrobia strain TAV2, was previously used for a microalga. Subsequently, we corrected the genus name to Didymococcus. Although we consulted with nomenclature authorities before the original publication, we learned recently that this corrected name also is not appropriate. In order to maintain the correct taxonomy in the literature, the revised genus and species names for the organism in our paper are described below.

Viral Recombination: Ecology, Evolution, And Pathogenesis, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Recombination between and within virus genomes is being increasingly recognized as a major driver of virus evolution. Virus evolution can lead to changes in virus pathogenesis and virus ecology. The ubiquity of high-throughput sequencing of multiple virus isolates has revolutionized data acquisition, thus the editors of Viruses decided that a Special Issue on viral recombination was appropriate.

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses—which infect members of the order Sulfolobales, growing optimally at 80 C and pH 3—are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. Nonetheless, much remains to be learned about these viruses. In order to investigate fusellovirus evolution, we have isolated and characterized a novel fusellovirus, Sulfolobus spindle-shaped virus 10 (formerly SSV-L1). Comparative genomic analyses highlight significant similarity with both SSV8 and SSV9, as well as conservation of promoter elements within the Fuselloviridae. SSV10 encodes five ORFs with no …

Epigenetic Alterations Mediate Ipsc Normalization Of Dna-Repair Expression And Tnr Stability In Huntington's Disease, Peter A. Mollica, Martina Zamponi, John Reid, Deepak Sharma, Alyson E. White, Roy C. Ogle, Robert D. Bruno, Patrick C. Sachs

School of Medical Diagnostics & Translational Sciences Publications

Huntington's disease (HD) is a rare autosomal dominant neurodegenerative disorder caused by a cytosine-adenine-guanine (CAG) trinucleotide repeat (TNR) expansion within the HTT gene. The mechanisms underlying HD-associated cellular dysfunction in pluripotency and neurodevelopment are poorly understood. We had previously identified downregulation of selected DNA repair genes in HD fibroblasts relative to wild-type fibroblasts, as a result of promoter hypermethylation. Here, we tested the hypothesis that hypomethylation during cellular reprogramming to the induced pluripotent stem cell (iPSC) state leads to upregulation of DNA repair genes and stabilization of TNRs in HD cells. We sought to determine how the HD TNR region …

Inference And Analysis Of Multilayered Mirna-Mediated Networks In Cancer, Duc Do

Dissertations (1934 -)

MicroRNAs (miRNAs) are small noncoding transcripts that can regulate gene expression, thereby controlling diverse biological processes. Aberrant disruptions of miRNA expression and their interactions with other biological agents (e.g., coding and noncoding transcripts) have been associated with several types of cancer. The goal of this dissertation is to use multidimensional genomic data to model two different gene regulation mechanisms by miRNAs in cancer. This dissertation results from two research projects. The first project investigates a miRNA-mediated gene regulation mechanism called competing endogenous RNA (ceRNA) interactions, which suggests that some transcripts can indirectly regulate one another's activity through their interactions with …

Detecting, Quantifying, And Discriminating The Mechanism Of Mosaic Chromosomal Aneuploidies Using Mad-Seq, Yu Kong, Esther R. Berko, Anthony Marcketta, Shahina B. Maqbool, Claudia A. Simoes-Pires, David F. Kronn, John M. Greally

NYMC Faculty Publications

Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost, or the need to culture cells. We describe the mosaic aneuploidy detection by massively parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (

The Effect Of Sweeteners In Drosophila Melanogaster's Locomotion., Araceli Francisco

The International Student Science Fair 2018

This research aims to measure how much locomotion is affected in Drosophila melanogaster considering the alimentation. The experiment was divided in a control group, a group fed with natural sugar and another fed with artificial sugar. The diets were prepared based on standard laboratory food (SLF) by varying the sugar. Several generations were grown. The locomotion was measured through monitors with infrared lasers which calculated the number of times the fly passed through it. They were accustomed to a day and night cycle and were kept under observation for a period of 13 days. As a result, the group that …

A Humanized Hypertrophic Cardiomyopathy Model To Elucidate Molecular Mechanism In Disease Pathology, Ragavi Vijayakumar, Maxine Hong

The International Student Science Fair 2018

Hypertrophic cardiomyopathy (HCM), that clinically manifests as an enlarged heart is a highly prevalent cardiac disorder with propensity towards arrhythmia-induced sudden cardiac death. The mechanism of HCM remains poorly defined, necessitating further understanding of the disease for improved therapeutic strategies. As it is challenging to obtain cardiac biopsies from human subjects, using induced pluripotent stem cells technology, we generated cardiomyocytes (CMs) in a dish from HCM patients. These HCM-CMs presented the clinical manifestation in that they were significantly larger in size in comparison to control (healthy)-CMs. Furthermore, gene expression profiling of cardiac ion channels revealed increased transcripts encoding for calcium …

Exploring The Role Of Rna Polymerase Iii Complex Assembly On Ribosomal Dna Silencing In Saccharomyces Cerevisiae, Kyle Thomas Kern

LSU Doctoral Dissertations

The yeast rDNA region is host to a number of transcriptional regulatory elements, which work in conjunction to generate essential RNA subunits of ribosomes, as well as protecting the region from DNA damage. The role of RNA polymerase III complex binding at the 5S gene on rDNA silencing in the NTS2 region was investigated, both by use of a TY1:MET15 reporter insert and a MET15 gene integration at an endogenous SphI site. It was discovered that Pol III complexes do have an effect on reporter expression in the NTS2 region, though the specific effect was different based on the method …

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Biology Faculty Articles

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is …

Novel Role Of Prostate Apoptosis Response-4 Tumor Suppressor In B-Cell Chronic Lymphocytic Leukemia, Mary Kathryn Mckenna, Sunil K. Noothi, Sara S. Alhakeem, Karine Z. Oben, Joseph T. Greene, Rajeswaran Mani, Kathryn L. Perry, James P. Collard, Jacqueline R. Rivas, Gerhard C. Hildebrandt, Roger A. Fleischman, Eric B. Durbin, John C. Byrd, Chi Wang, Natarajan Muthusamy, Vivek M. Rangnekar, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Prostate apoptosis response-4 (Par-4), a proapoptotic tumor suppressor protein, is downregulated in many cancers including renal cell carcinoma, glioblastoma, endometrial, and breast cancer. Par-4 induces apoptosis selectively in various types of cancer cells but not normal cells. We found that chronic lymphocytic leukemia (CLL) cells from human patients and from Eµ-Tcl1 mice constitutively express Par-4 in greater amounts than normal B-1 or B-2 cells. Interestingly, knockdown of Par-4 in human CLL-derived Mec-1 cells results in a robust increase in p21/WAF1 expression and decreased growth due to delayed G1-to-S cell-cycle transition. Lack of Par-4 also increased the expression of p21 and …

Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii

LSU Doctoral Dissertations

Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates.

The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an …

Epidermal-Specific Deletion Of Tc-Ptp Promotes Uvb-Induced Epidermal Cell Survival Through The Regulation Of Flk-1/Jnk Signaling, Minwoo Baek, Mihwa Kim, Jae Sung Lim, Liza D. Morales, Joselin Hernandez, Srinivas Mummidi, Sarah Williams-Blangero, Ik-Soon Jang, Andrew Tsin, Dae Joon Kim

School of Medicine Publications

UVB exposure can contribute to the development of skin cancer by modulating protein tyrosine kinase (PTK) signaling. It has been suggested that UVB radiation increases the ligand-dependent activation of PTKs and induces PTP inactivation. Our recent studies have shown that T-cell protein tyrosine phosphatase (TC-PTP) attenuates skin carcinogenesis induced by chemical regimens, which indicates its critical role in the prevention of skin cancer. In the current work, we report that TC-PTP increases keratinocyte susceptibility to UVB-induced apoptosis via the downregulation of Flk-1/JNK signaling. We showed that loss of TC-PTP led to resistance to UVB-induced apoptosis in vivo epidermis. We established …