Molecular Genetics Commons^™

Multistrain Hiv-1 Elimination: A Crispr-Cas9 And Theranostics-Based Approach, Jonathan Herskovitz

Theses & Dissertations

A critical barrier to achieving a functional cure for infection by human immunodeficiency virus type one (HIV-1) rests in the presence of latent proviral DNA integrated in the nuclei of host CD4+ T cells and mononuclear phagocytes. Accordingly, HIV-1-infected patients must adhere to lifelong regimens of antiretroviral therapy (ART) to prevent viral rebound, CD4+ T cell decline, and progression to acquired immunodeficiency syndrome (AIDS). Gene editing using clustered regularly interspersed short palindromic repeat (CRISPR)-Cas9 technology stands as one means to inactivate integrated proviral DNA. We devised a mosaic gRNA CRISPR-Cas9 system- TatDE- that targets viral transcriptional regulator genes tat / …

Diagnosis And Distribution Of Florida Sand Darter, Ammocrypta Bifascia (Teleostei; Percidae), In The Flint River, Georgia, Camm C. Swift, Gregory R. Moyer, Christine E. Fallon, Brett Albanese

Southeastern Fishes Council Proceedings

Abstract: In 2013, we observed the presence of an undocumented Ammocrypta species in the lower Flint River, Georgia. The occurrence represents the first record of the genus in Georgia. Subsequent surveys at 24 sites, using seining or snorkeling, documented additional specimens from mainstem sites (n = 3) between Albany and Bainbridge and from Ichawaynochaway Creek (n = 5 sites), a large tributary to the Flint River. We used morphological and genetic data to identify specimens to species. Morphological examination included 23 morphometric and 8 meristic characters from fifteen specimens that were compared to specimens from Williams (1975). For genetic analyses, …

Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff

Honors Scholar Theses

Mechanotransduction is the process by which a mechanical stimulus is converted to a cellular signal. This process is heavily influential of cell morphology, differentiation, and behavior. However, altered levels of mechanical stimuli are also found in many pathological contexts. For example, cancerous cells have stiffer surrounding tissue than healthy cells, and research suggests that this alters cell behavior and promotes metastasis. Despite these findings, the cellular processes behind these signaling alterations remain widely unknown. Understanding these cascades is critical, as involved proteins can give us a deeper understanding of the role of mechanotransduction, and certain proteins can potentially be targeted …

The Deleterious F109s Mutation Disrupts Binding Of Sex-Determining Region Y With Dna, Mohammed Baqur S. Al-Shuhaib Mbsa

Karbala International Journal of Modern Science

Sex-determining region Y (SRY) protein is the master switch in the initiation of male sex differentiation. Mutation in SRY gene results in ambiguous genitalia and abnormalities in reproductive organs. Its function is mainly controlled by its high mobility group (HMG) box. Damage to the HMG box may cause dysfunction of the SRY protein, which may, in turn, lead to sex reversal. This study was conducted to prioritize the deleterious effects of the non-synonymous single nucleotide polymorphisms (nsSNPs) on SRY protein. A series of computational tools were applied to predict nsSNPs with the most harmful effects on protein structure, function, and …

Innate Pathogenic Traits In Oral Yeasts, Ayat Ibrahiem Esmaeel Al-Laaeiby, Adnan A. Al-Mousawi, Inaam M.N. Alrubayae, Abdullah Al-Saadoon, Maysoon Almayahi

Karbala International Journal of Modern Science

The normal flora community plays a significant role in both healthy and patient individual’s bodies. It has improved its ability to change from beneficial to opportunistic organisms causing crucial infections in immunocompromised patients. This study was conducted to identify the community of yeast species, and to investigate potential virulence factors. Saliva samples were collected from healthy individuals, yeast species were isolated and identified using both traditional and advance molecular genetics technique. The results revealed that Candida albicans was the dominant isolate, while Meyerozyma caribbica was the least. The phylogenetic tree was constructed for 13 species using the Neighbour-Joining method, which …

Molecular Identification, Antioxidant Efficacy Of Phenolic Compounds, And Antimicrobial Activity Of Beta-Carotene Isolated From Fruiting Bodies Of Suillus Sp, Shimal Yonuis Abdulhadi, Raghad Nawaf Gergees, Ghazwan Qasim Hasan

Karbala International Journal of Modern Science

Suillus species, in general, are edible mushrooms, and environmentally important that are associated mostly with pine trees in the tropics regions. These fungi considered a remarkable source of phenolic compounds that play a crucial role as antioxidants which may reduce the risk of most human chronic diseases such as cancer, diabetes, asthma, atherosclerosis, Alzheimer, and others. On the other hand, carotenoids (β carotene) are the most popular natural pigments which play an important role to protect the plants from photo-oxidative reactions. In human, these compounds prevent oxidative stress and expects to have antimicrobial activity. Here, the phenolic compounds were …

The Role Of Anti-Inflammatory Cytokine Interleukin-10 (Il-10) In Tauopathies, Lea L. Weston

Biomedical Sciences ETDs

Tauopathies are neurodegenerative diseases, including Alzheimer’s disease, that are associated with pathological accumulation of the microtubule associated protein tau (MAPT, or tau) (Lee et al., 2001). Abnormal hyperphosphorylated tau (pTau) strongly correlate with cognitive impairment (Nelson et al., 2012). Neuroinflammation is also associated with tauopathies (Gerhard et al., 2006b; Edison et al., 2008) and is implicated in driving tau pathology (Yoshiyama et al., 2007, Maphis et al., 2015b). Therefore, it is compelling to understand the role of anti-inflammatory cytokines in limiting neuroinflammation and tau pathology. Interleukin-10 (IL-10) is a well-established anti-inflammatory cytokine with roles in limiting inflammation in the central …

Estimation Of Additive And Dominance Effects Of A Mutant Glutathione S-Transferase Gene On Anthocyanin And Proanthocyanidin Content In Muscadine Grape (Vitis Rotundifolia), Autumn Brown

Horticulture Undergraduate Honors Theses

The skin color of muscadine grapes (Vitis rotundifolia) is typically classified as black or bronze. A glutathione S-transferase, VrunGST4, has been identified as a candidate gene for berry skin color in muscadine grapes. A molecular marker was developed within VrunGST4 to distinguish between muscadine genotypes (cultivars and selections) with bronze (T:T), heterozygote black (C:T), and homozygote black (C:C) berries. The objectives of this study were to determine whether there was a correlation between berry skin color and total anthocyanin content and to calculate additive and dominance effects of VrunGST4 in determining total anthocyanins in the berries and …

Draft Genome Of The Common Snapping Turtle, Chelydra Serpentina, A Model For Phenotypic Plasticity In Reptiles, Debojyoti Das, Sunil Kumar Singh, Jacob Bierstedt, Alyssa Erickson, Gina L. J. Galli, Dane A. Crossley Ii, Turk Rhen

Biology Faculty Publications

Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and molecular genetic studies of …

Population Structure Of A Federally Endangered Plant (Astragalus Jaegerianus Munz, Fabaceae) With Limited Range Using Microsatellites, Sueann Neal

Electronic Theses, Projects, and Dissertations

Studies on population genetics examine the relationship and effects of population structure, migration, gene flow and demographic history, and are therefore important in the conservation of endangered species. Astragalus jaegerianus, a critically federally endangered species found in a geographically restricted range is investigated to determine population structure and genetic variation. Previous research on A. jaegerianus focused on DNA sequence data for cpDNA and nrDNA showed no variation. Further research on A. jaegerianus utilizing AFLP’s on the whole genome indicated substantial gene diversity and population structure consistent with geographically widespread species. AFLP research is a cost-effective process to identify levels …

A Context-Forward In Vivo Functional Genomics Platform For Target Discovery And Establishing Vulnerability Context In Pancreatic Cancer, Johnathon Rose, Johnathon Lynn Rose

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a very poor patient prognosis (5-year survival of ≤ 7%). While transcriptional profiling has aided in the classification of this disease into at least two broader subtypes, this alone has so far been insufficient to inform on more nuanced patterns of oncogenic dependency. We hypothesized that a more comprehensive and granular characterization of PDAC disease diversity is required to establish relevant context for targeted therapy. To this end, we sought to establish an integrated platform to: i) more comprehensively characterize differential oncogenic signaling across our tumor models, and ii) establish …

P53 Drives A Transcriptional Program That Elicits A Non-Cell-Autonomous Response And Alters Cell State In Vivo, Sydney Moyer

Dissertations and Theses (Open Access)

Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene which encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 ChIP-sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes which included Mdm2 but not p21. Global p53 activation …

Novel Polymorphisms Of Zrsr2 And Gpm6b Gene Homologs And Their Use In Sex Identification Of Bovine And Porcine Species, Evan K. Peterson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Accurate and cost-effective PCR based sex identification is important in animal production because it gives producers the ability to determine the sex of embryos prior to transfer, saving time and money. The most efficient PCR sex identification assays work by using a single primer pair to amplify a specific target region located on the Y-chromosome and a second, separate target region on the X-chromosome.

This thesis reports the design of two novel assays. The first assay was designed to target the Zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 (ZRSR2) gene found on the X-chromosome and its Y-chromosome …

Evaluation Of The Xpert Carba-R Nxg Assay For Detection Of Carbapenemase Genes In A Global Challenge Set Of Pseudomonas Aeruginosa Isolates, Fred C. Tenover, Christian M. Gill, Tomefa E. Asempa, Isabella A. Tickler, Caitlin M. Dela Cruz, David P. Nicolau

Biology Faculty Publications

The growing prevalence and diversity of carbapenemase producers among carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates warrants an expansion of detection capabilities. The purpose of this study was to evaluate the performance of the commercially available Xpert Carba-R (Carba-R) and the research-use-only Xpert Carba-R NxG (Carba-R NxG) in a global collection of P. aeruginosa. The challenge set included 123 P. aeruginosa clinical isolates from 12 countries. Isolates were previously categorized via PCR or whole-genome sequencing. Carbapenemase classes tested include VIM, IMP, NDM, SPM, KPC, and GES. Non-carbapenemase (non-CP)-harboring isolates were also tested (negative control). Isolates were tested using the Carba-R NxG and …

Genetic Polymorphism Of Bitter Taste Perception In Tempe, Arizona And Its Association With Nutritional Status, Daniel Woodley, Benjamin Cabrera

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Spatio-Temporal Dynamics Of Fungal Communities And Their Effects On Plants, Kel Cook

Biology ETDs

Fungi perform several critical functions in the environment. Spatiotemporal distributions of fungal communities will mediate when and where these functions happen and how they vary across the landscape. I first explored tropical tree canopy fungal community variation at small spatial scales and documented near total turnover of fungi across sub-meter distances and among adjacent substrates. The second chapter analyzed fungal turnover over the course of three years, where community stability was driven primarily by abundant fungi. In the third chapter, I tested effects of the environment, including host plant and habitat, on canopy fungal communities and found only small effects, …

Identification Of Novel Host Genes Required For Antiviral Immunity And Viral Genome Replication In C. Elegans, Fei Meng

LSU Doctoral Dissertations

RNA interference (RNAi) is a wide-spread gene silencing mechanism that control diverse biological functions and triggered by small interfering RNAs (siRNAs) processed from the viral genome or its replication intermediates. Mechanistic studies of antiviral RNAi in Caenorhabditis elegans has led to the identification of several critical factors involved in the process. As a result, whether antiviral RNAi requires additional novel genes remains to be an open question.

Viruses are intracellular parasites that rely on host products for reproduction. Disrupting their interaction with host factors can significantly compromise their replication and keep them under control. Thus, identification of host genes …

The Impact Of Sample Processing And Media Chemistry On The Culturable Diversity Of Bacteria Isolated From A Cave, Katey E. Bender, Katelyn Glover, Alexander Archey, Hazel A. Barton

International Journal of Speleology

Although molecular approaches can identify members of microbial communities in the environment, genomic information does not necessarily correlate with environmental phenotype. Understanding functional roles can be done by cultivating representative species, yet the culturablility of bacteria from caves remains low, at 0.02%, limiting our understanding of microbial community interactions and processes. We have investigated several factors influencing culturability of bacteria from a single sample location in Maxwelton Sink Cave, WV, USA. Extended incubation of inoculated plates showed a significant increase in colony counts from two to four weeks, indicating that extended incubations increase culturability. There were no significant differences in …

Identification And Characterization Of Novel Genes And Genetic Interactions That Influence Iba Metabolism, Vanessica Jawahir

Dissertations

Indole-3-butyric acid (IBA) is an endogenous storage auxin important for maintaining appropriate indole-3-acetic acid (IAA) levels that influences primary root elongation and lateral root development. IBA is metabolized into free IAA in the peroxisome in a multistep process similar to fatty acid β-oxidation. Although many components specific to IBA metabolism and peroxisome function have been identified, our understanding is incomplete. I sought to identify novel components of IBA metabolism or peroxisome function by conducting a forward genetic screen for Arabidopsis thaliana plants with enhanced resistance to IBA. I identified Long chain acyl-CoA synthetase 4 (LACS4) as a novel gene functioning …

Not Withering On The Evolutionary Vine: Systematic Revision Of The Brown Vine Snake (Reptilia: Squamata: Oxybelis) From Its Northern Distribution, Robert C. Jadin, Christopher Blair, Sarah A. Orlofske, Michael J. Jowers, Gilson A. Rivas, Laurie J. Vitt, Julie M. Ray, Eric N. Smith, John C. Murphy

Publications and Research

The genus Oxybelis currently is composed of four taxa despite numerous studies suggesting and describing multiple taxa within the O. aeneus complex. Here, we utilize a multilocus molecular dataset (i.e. cyt b, ND4, 12S, 16S, cmos, PRLR, 3663 bp) to conduct phylogenetic analyses to assess the evolutionary history of Oxybelis. Our molecular analyses find three major lineages of Oxybelis (i.e. O. aeneus complex, O. brevirostris, O. fulgidus complex) with a sister relationship between O. brevirostris and the O. aeneus complex to the exclusion of the O. fulgidus complex. More specifically, O. aeneus appears to harbor at least …

Herb-Layer Dynamics In An Old-Growth Forest: Vegetation–Environment Relationships And Response To Invasion-Related Perturbations, Taylor M. Buskey, Margaret E. Maloney, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Temperate forests of eastern North America are subject to multiple invasions from non-native species that have the potential to drive long-term dynamics in biodiversity. Garlic mustard (Alliaria petiolata (M. Bieb.) Cavara and Grande) is an invasive plant in many deciduous forests, and management efforts often focus on removing this species to initiate native species restoration. Agrilus planipennis Fairmaire (emerald ash borer; Coleoptera: Buprestidae) is a non-native insect pest that has caused substantial loss of ash trees (Fraxinus spp. L.) in North America. Our goal was to understand how the herbaceous layer in an old-growth forest responded to the removal of …

Mechanistic Insights Into Strigolactone Biosynthesis, Signaling And Regulation During Plant Growth And Development, Kaiser Iqbal Wani, Andleeb Zehra, Sadaf Choudhary, M Naeem, M. Masroor A. Khan, Christian Danve Castroverde, Tariq Aftab

Biology Faculty Publications

Strigolactones (SLs) constitute a group of carotenoid-derived phytohormones with butenolide moieties. These hormones are involved in various functions, including regulation of secondary growth, shoot branching and hypocotyl elongation, and stimulation of seed germination. SLs also control hyphal branching of arbuscular mycorrhizal (AM) fungi, and mediate responses to both abiotic and biotic cues. Most of these functions stem from the interplay of SLs with other hormones, enabling plants to appropriately respond to changing environmental conditions. This dynamic interplay provides opportunities for phytohormones to modulate and augment one another. In this article, we review our current mechanistic understanding of SL biosynthesis, receptors …

Does The Presence Of Multiple Β-Lactamases In Gram-Negative Bacilli Impact The Results Of Antimicrobial Susceptibility Tests And Extended-Spectrum Β-Lactamase And Carbapenemase Confirmation Methods?, Fred C. Tenover, Caitlin M. Dela Cruz, Scott Dewell, Victoria M. Le, Isabella A. Tickler

Biology Faculty Publications

Objectives: Many multidrug-resistant Gram-negative bacilli (MDR-GNB) harbour multiple β-lactamases. The aim of this study was to assess the impact of multiple β-lactamase carriage on the accuracy of susceptibility tests and extended-spectrum β-lactamase (ESBL) and carbapenemase confirmation methods.

Methods: A total of 50 MDR-GNB, of which 29 carried multiple β-lactamases, underwent broth microdilution (BMD) and disk diffusion (DD) testing as well as confirmation tests for ESBLs and carbapenemases. Whole-genome sequencing (WGS) was used for β-lactamase gene identification.

Results: Categorical agreement of BMD and DD testing results ranged from 86.5 to 97.7% for 10 β-lactam agents. BMD and DD algorithms for ESBL …

The Influence Of Riparian Invasion By The Terrestrial Shrub Lonicera Maackii On Aquatic Macroinvertebrates In Temperate Forest Headwater Streams, Michelle N. Little, Kevin W. Custer, Eric B. Borth, Julia I. Chapman, Mitchell J. Kukla, Corey Kuminecz, Margaret E. Maloney, Michaela J. Woods, Ryan Mcewan

Biology Faculty Publications

The ecology of headwater streams is tightly linked to the riparian zone through organic matter subsidies which are highly susceptible to alteration due to biological invasion. Lonicera maackii is a non-native shrub that is a highly successful invader of headwater stream riparian zones in the American Midwest. We assessed effects on benthic macroinvertebrates across a gradient of invasion intensity from references sites with minimal invasion to a site that had a very heavy invasion. Benthic macroinvertebrates were sampled throughout the year and compositional differences were assessed using Non-metric Multidimensional Scaling ordination, and by comparing the prevalence of sensitive (Ephemeroptera, Plectoptera, …

Employing High Probability Gene Choice Elements To Understand Singular Odorant Receptor Expression, Raena Mina

Dissertations, Theses, and Capstone Projects

The ability to detect odorous chemicals in the environment is the oldest of the senses necessary for survival, from escaping danger, finding mates, to locating food. It is said that humans can identify and discriminate up to a trillion different odor mixtures. For chemoreception to have such a high discriminatory power, would require a diverse population of cells dedicated for odor detection. These detector cells are the olfactory sensory neurons (OSNs), which express odorant receptors (ORs) that bind to chemical odors in the environment. In order to increase specificity and sensitivity, an essential property in olfaction is for each OSN …

Regulation Of A Messenger: Raising Oskar, It Takes A Village, Livia V. Bayer

Dissertations, Theses, and Capstone Projects

D. melanogaster oogenesis serves as an excellent system to study the life of an mRNA. Tremendous work has been done to understand the numerous complex mechanisms of mRNA regulation, still there is still so much that is yet to be discovered. In this thesis, I present studies I carried out to address several aspects of oskar mRNA post-transcriptional regulation. Leading me to extend our current understanding of the carefully controlled regulation of oskar mRNA life cycle via a myriad of proteins. I found that a specific NPC component, Nup154 is necessary not only for its export from the nucleus, but …

Genetic Diversity: The Hub Of Plant Breeding, Foster Kangben

International Programs

Agriculture the world over is faced with the threat of food, fiber, and nutrition insecurity especially in the wake of climate change. However, employing two approaches to plant breeding, the molecular and phenotypic methods, can make use of genetic diversity in crop species in order to help surmount these challenges.

Interrelationships Among Monorchiid Trematodes With Special Emphasis On Some Northwestern Atlantic Genera, Apryle Panyi

Master's Theses

The Monorchiidae Odhner, 1911 is a cosmopolitan family of flukes (Trematoda: Digenea) comprising species that parasitize the digestive tract of estuarine and marine fishes as adults. Compared with other oceans, recent morphological or molecular taxonomic work conducted on monorchiid species from the northwestern Atlantic Ocean has been sparse (Manter, 1931; Overstreet, 1969; Andres et al., 2018; Wee et al., 2018, 2019, 2020). Therefore, the present work investigated the interrelationships of some monorchiids from the northwestern Atlantic Ocean with emphasis on several genera and investigated if Lasiotocus minutus (Manter, 1931) Thomas, 1959 constitutes a complex of cryptic species. New morphological and …

Genes Involved In Nitrogen Assimilation In Ustilago Maydis., Sunita Khanal

Electronic Theses and Dissertations

U. maydis can utilize nitrate as a source of nitrogen from its environment, a process requiring a nitrate transporter to bring the nitrate inside the cell. This is followed by a two-step reduction of nitrate to ammonium. At first, nitrate reductase reduces nitrate into nitrite; in the second reaction, nitrite is reduced to ammonium by nitrite reductase. The goal of the study was to identify the nitrate transporter and nitrite reductase genes in U. maydis and characterize them based on their role in mating and virulence. The genes um03848 and um03849 were identified bioinformatically as encoding, respectively, the nitrite reductase …

Comparative Secretomics And Functional Analysis Of Effectors Utilized By The Microbotryum Genus Of Anther-Smut Fungal Pathogens, And Their Role In Host-Specificity., William Christopher Beckerson

Electronic Theses and Dissertations

Understanding how pathogens evolve in response to changes in their host is paramount to combating the spread of emergent strains of disease. This is particularly true for plant pathogens that cause billions of dollars of damages to crops globally, every year. Understanding the molecular interactions between pathogens and their hosts therefore sheds light on the coevolutionary arms race that can result in host-specificity and host-shifts in plant pathogens. This research approaches the question of how fungal pathogens interact with their plant hosts utilizing both unique and shared arsenals of secreted proteins (SPs) during infection, and addresses the question of whether …