Molecular Genetics Commons^™

Characterizing The Role Of Pa5189 Of Pseudomonas Aeruginosa In Deletion And Overexpression Mutants, Seh Na Mellick

Theses/Capstones/Creative Projects

In the context of rising multidrug resistance in biofilm-forming pathogens like Pseudomonas aeruginosa, this study investigates the role of the understudied transcription factor PA5189 in antibiotic resistance and biofilm formation. PA5189 deletion and overexpression mutants were created in a parent P. aeruginosa strain using pEX18Tc-based recombinant suicide vectors, with genotypic verification of putative triparental conjugants achieved through restriction digestion and PCR. The study revealed that PA5189 overexpression significantly increases resistance to commonly used broad spectrum antibiotics such as ciprofloxacin and imipenem. Additionally, differential expression of PA5189 was found to notably affect biofilm formation, with variations contingent on the nutrient …

Towards Understanding The Function Of An Ets-Like Gene In Nematostella Vectensis: Generation Of A Knockout Mutant Line And A Transgenic Reporter Line, Emily Bullock

Biological Sciences Undergraduate Honors Theses

Due to their unique phylogenic position as sister to Bilateria, Cnidaria are often credited with the utility of allowing for reconstruction of ancestral biology based on characteristics shared with bilaterians and other animals. This factor makes investigation into the nervous systems of cnidarians critical in understanding early neural evolution. Wamides, a class of neuropeptides, have been shown to play a regulatory role in life cycle transitions across many different species. The cnidarian specific Wamide neuropeptide, GLWamide, has previously been identified to play an accelerator role in the metamorphic timing of a specific species of sea anemone, Nematostella vectensis. However, …

Elucidation Of The Overexpression Of Taf2 In Eukaryotic Cells, Morgan Osborn

Honors Theses

Through several studies, Taf2 has been found to be upregulated in various cancer cells. However, the mechanism through which this increased expression of Taf2 occurs remains unknown. As evolutionarily conserved ubiquitin-proteasome system (UPS) maintains protein homeostasis for normal cellular function, we hypothesized that stability of Taf2 may be regulated by this UPS and this UPS may be dysregulated in cancer cells causing overexpression of Taf2. To test our hypothesis, we assessed the role of the UPS in the regulation of the stability of Taf2 by 26S proteasome-mediated degradation. To do so, we performed molecular experiments mainly through two steps: 1st …

Examining Population Structure Of Cismontane And Desert Populations Of Zebra-Tailed Lizards (Callisaurus Draconoides) Using Mitochondrial And Nuclear Intron Dna., Lauren Nicole Morrison

Electronic Theses, Projects, and Dissertations

Callisaurus draconoides, also known as the Zebra-Tailed lizard, belongs to the family Phrynosomatidae family (Pianka, et al. 1972). C. draconoides is a widespread desert lizard found western North America. In California, this species can be found in the Mojave and Colorado Deserts. There are currently several populations that reside in the San Bernardino basin on the cismontane side of the Transverse and Peninsular ranges. These mountain ranges have the potential to have isolated the cismontane populations from their typical desert ranges. In addition, geological passes have the potential to serve as migration corridor between the Deserts and cismontane regions. The …

The Role Of B Cell Activation State And Sex In Aryl Hydrocarbon Receptor Mediated Induction Of Chemokine Receptor 9 And Alpha4beta7 Expression In Vitro, Logan Bauerle

Master's Theses

Defense of mucosal tissues from microbial infection and allergy is reliant on continual production of antibodies. The aryl hydrocarbon receptor (AhR) is known to regulate B cell development and is associated with suppression of systemic humoral immunity. Recent attention has been paid to the role of the AhR in altering expression of cell adhesion molecules (CAMs). B cells express CAMs and chemokine receptors to migrate around the body for localized secretion of antibodies. AhR agonists promote B cell migration to the small intestine through upregulation of chemokine receptor 9 (CCR9) and integrin α₄β₇. Both the AhR …

Trna Anticodon Cleavage By Target-Activated Crispr-Cas13a Effector, Ishita Jain, Matvey Kolesnik, Konstantin Kuznedelov, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva, Alexandr Kirillov, Sofia Medvedeva, Alexei Livenskyi, Laura Kazieva, Kira S Makarova, Eugene V Koonin, Sergei Borukhov, Konstantin Severinov, Ekaterina Semenova

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA–guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by Leptotrichia shahii Cas13a expressed in Escherichia coli cells is the cleavage of anticodons in a subset of transfer RNAs (tRNAs) with uridine-rich anticodons. This tRNA cleavage is accompanied by inhibition of protein synthesis, thus …

Annotation Of Hypothetical Genes In Lactococcus Lactis Ssp. Il403, Jennifer A. Tangires

Student Scholar Showcase

The human gastrointestinal tract (GIT) harnesses various microbial organisms involved in almost all processes of physiological homeostasis, among these are lactic acid bacteria (LAB). These bacteria, almost all of which belong to the order Lactobacillales, are able to produce lactic acid, and play an important role in food preservation because they produce bacteriocins. Bacteriocins are antimicrobial proteins that are used to fight off related bacteria in their environment that are competing for the same resources. This study focuses on a specific LAB strain, Lactococcus lactis ssp. IL1403 where 21.9% of its predicted genes have not yet been assigned a function. …

Comparative Genomics Of Selected Lactobacillus Helveticus Strains, Cain Petty

Undergraduate Research Conference

My research is to compare two strains (D76 and H10) of Lactobacillus helveticus and a shared gene between them. I would want to experiment with overexpression to test for any difference in the regulatory function of genes associated with CggR - the central glycolytic genes regulator. The poster I am presenting would outline this and provide a clearer understanding of genes and potential overexpression.

Determining The Effects Of Mistranslating Transfer Rna Variants On Drosophila Melanogaster, Joshua R. Isaacson

Electronic Thesis and Dissertation Repository

Transfer RNAs (tRNAs) play a central role in translation as adaptor molecules between mRNA and protein. Variant tRNAs can cause the misincorporation of an amino acid into a growing polypeptide. Mistranslating tRNA variants are surprisingly common in humans but the effects of mistranslating tRNA variants on eukaryotic biology are poorly understood. My thesis aimed to create a model of tRNA-induced mistranslation using the fruit fly Drosophila melanogaster and characterize the effects of mistranslating tRNA variants on eukaryotic biology.

I first integrated a gene encoding a serine tRNA variant that induced proline-to-serine (P>S) mistranslation into the fly genome. Proteins isolated …

"The Relevant History And Medical And Ethical Future Viability Of Xenotransplantation", Morgan Janes

Augustana Center for the Study of Ethics Essay Contest

Xenotransplantation, the transplantation of organs or tissues from one species to another, presents a complex nexus of medical, ethical, and cultural considerations. In this article, we delve into the multifaceted landscape of xenotransplantation, beginning with a thorough examination of its relevant historical trajectory. From early experiments to recent advancements, we chart the evolution of this field, setting the stage for a nuanced discussion. We then confront the central issue: the true medical viability of xenotransplantation and the looming specter of operative risk. By scrutinizing the ethical dilemmas inherent in xenotransplantation through a multicultural lens, we illuminate the diverse perspectives that …

Hira Gene Mutation In Arabidopsis Via Crispr, Kelly Chen, Claire Shippy, Tara Phelps-Durr

SACAD: John Heinrichs Scholarly and Creative Activity Days

The purpose of this study is to mutate the Histone Repressor A (HIRA) gene in a mustard plant (Arabidopsis) using CRISPR technology. HIRA is a chromatin-remodeling protein that is required for proper development in both plants and animals. Creating new changes (mutations) in HIRA will help us better understand the mechanism of how HIRA regulates transcription, which is important for understanding developmental disorders in animals, as well as how improper development leads to a reduction in crop yields in plants

Documenting The Southern Range Terminus Of The Wood Frog (Lithobates Sylvaticus) In North America, Christian Braswell

Theses

The Wood Frog (Lithobates sylvaticus) holds a remarkable position in North American amphibian biology, with its range extending from the Arctic Circle down to the near sub-tropical southeastern United States. This thesis presents a novel quantitative polymerase chain reaction analysis (qPCR) primer specific to L. sylvaticus and a survey effort regarding the southernmost distribution and detection of this species in Alabama through the application of environmental DNA (eDNA) sampling techniques. By investigating historical data and employing advanced genetic methodologies, this research provides insights into the contemporary status and distribution of the Wood Frog. This research is important to …

Deciphering The Functional Connections Between The Nuclear Paraspeckle And Rad51 Homologous Recombination Proteins Using A Yeast Protein Interaction System, Eric J. Nutz

Senior Theses

Homologous recombination (HR) is a repair pathway for DNA double-stranded breaks. Mutations in HR genes contribute to genomic instability and increase the prevalence of cancer. Exploiting HR deficiency in tumor cells has led to improved synthetic lethality outcomes. RAD51 paralogue protein complexes are known to be involved with HR. Proteomic analysis of RAD51 paralogues reveals a connection to the nuclear paraspeckle. A paraspeckle is a little-known, specialized organelle found in the interchromatin space of the nucleus in mammalian cells. Its three central protein components include SFPQ, NONO, and PSPC1. RAD51D is an HR protein shown previously to interact with SFPQ …

Development Of An In Vitro Model Of Mitochondrial Dna Copy Number Depletion Via Stable Inducible Expression Of D1135a Mutant Dna Polymerase Gamma, Amanda L. Morin

Electronic Thesis and Dissertation Repository

Mitochondria are responsible for several crucial cellular processes and contain their own DNA (mtDNA) that exists in several copies. Variation of mtDNA copy number (mtDNA-CN) alters energy metabolism and can modify the epigenome and transcriptome. We hypothesized that inducible expression of polymerase-deficient D1135A dominant-negative DNA polymerase gamma (DN-POLG) would result in mtDNA-CN depletion. Here, an in vitro model expressing D1135A POLG was created using the Flp-InTM T-RExTM-293 stable inducible expression system. Stable integration was confirmed with PCR amplification and Sanger sequencing of post-integration genomic sequences. D1135A POLG expression was confirmed with Western blot of the FLAG-tag antibody. Induction of D1135A …

Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira S Makarova, Eugene V Koonin, Satish K Nair, Shunsuke Tagami, Konstantin Severinov, Maria L Sokolova

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of …

Investigating Birds As Dispersal Vectors Of Litylenchus Crenatae Subsp. Mccannii (Anguinidae), The Nematode Associated With Beech Leaf Disease, Spencer Rock Parkinson

Graduate Theses, Dissertations, and Problem Reports

Beech leaf disease (BLD) is an emerging forest pathogen primarily affecting American beech (Fagus grandifolia, Ehrh.) in North America and has been attributed to tree mortality of sapling sized trees within five to seven years of infection. Symptoms typically occur in regenerating American beech thickets sprouting from roots of trees killed by beech bark disease. Scientists first observed BLD in Ohio in 2012 and currently has spread to 15 states in the USA and one Canadian province. The nematode Litylenchus crenatae subsp. mccannii (Lcm) is highly associated with BLD symptoms, interveinal chlorosis and defoliation of leaves, and is currently …

Unraveling The Prognostic Significance Of Rgs Gene Family In Gastric Cancer And The Potential Implication Of Rgs4 In Regulating Tumor-Infiltrating Fibroblast, Yalan Yang, Siyuan Xing, Xi Luo, Lulu Guan, Yao Lu, Yiting Wang, Feng Wang

Journal Articles

Regulator of G-protein signaling (RGS) proteins are regulators of signal transduction mediated by G protein-coupled receptors (GPCRs). Current studies have shown that some molecules in the RGS gene family are related to the occurrence, development and poor prognosis of malignant tumors. However, the RGS gene family has been rarely studied in gastric cancer. In this study, we explored the mutation and expression profile of RGS gene family in gastric cancer, and evaluated the prognostic value of RGS expression. Then we established a prognostic model based on RGS gene family and performed functional analysis. Further studies showed that RGS4, as an …

Fused In Sarcoma Regulates Glutamate Signaling And Oxidative Stress Response, Chiong-Hee Wong, Abu Rahat, Howard C Chang

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Mutations in fused in sarcoma (fust-1) are linked to ALS. However, how these ALS causative mutations alter physiological processes and lead to the onset of ALS remains largely unknown. By obtaining humanized fust-1 ALS mutations via CRISPR-CAS9, we generated a C. elegans ALS model. Homozygous fust-1 ALS mutant and fust-1 deletion animals are viable in C. elegans. This allows us to better characterize the molecular mechanisms of fust-1-dependent responses. We found FUST-1 plays a role in regulating superoxide dismutase, glutamate signaling, and oxidative stress. FUST-1 suppresses SOD-1 and VGLUT/EAT-4 in the nervous system. FUST-1 also regulates synaptic AMPA-type glutamate receptor …

Contemporary Vs. Traditional Dna-Based Mutation Testing To Detect Hereditary Breast And Ovarian Cancer Syndrome (Hboc) In Women: A Meta Narrative Review, Hannah Olivia Cantu, Jacob Hipp, Nyela Y. Lopez, Duc Duy Nguyen

Research Methods Poster Session 2024

No abstract provided.

Structural And Functional Consequences Of Pde6 Prenylation In Rod And Cone Photoreceptors, Faezeh Moakedi

Graduate Theses, Dissertations, and Problem Reports

Phosphodiesterase-6 (PDE6) serves as a pivotal component in the phototransduction pathways of both cone and rod photoreceptors. In cones, PDE6 consists of tetrameric subunits: inhibitory (γ') and catalytic (α'). The catalytic subunit, PDE6α', contains a C-terminal prenylation motif. Deletion of this motif is associated with achromatopsia (ACHM), a form of color blindness. The mechanisms underlying the disease and the roles of PDE6 lipidation in vision remain elusive. Meanwhile, rod PDE6 is composed of α and β catalytic subunits and γ inhibitory subunits, with alterations in the C-terminal "prenylation motif" of PDE6β linked to retinitis pigmentosa (RP) pathology. In this comprehensive …