Cell Biology Commons^™

Identifying The Role Of Human Dna Polymerase Delta During Human Cytomegalovirus Genome Synthesis, Rachel Laree Dansereau

Dartmouth College Master’s Theses

Human cytomegalovirus (HCMV) is a large double stranded DNA virus and member of the Herpesviridae family. Like all herpesviruses, HCMV presents with characteristics of persistent, lifelong infections that transition between lytic and latent states. The replication of the viral genome is traditionally thought to occur by a rolling circle mechanism, but this model is supported by little evidence. It is known that HCMV actively recruits several host proteins to viral replication compartments (RCs), including proteins involved in the DNA damage response (DDR). The exact mechanisms of how these proteins are used and in what ways they help the virus remain …

Untangling G-Quadruplexes In Dna: The Effects Of Nucleotide Excision Repair, Jaidelin Alvardo, Abiageal Riley, Erick Morales Orrante, Raynne Malik

Posters - 2026

Nucleotide Excision Repair (NER) remo ves bulky DNA lesions that are attributed to UV irradiation, environmental mutagens, and chemo-therapeutic agents (Schärer, CSH Perspectives Biology, 2013). G4- quadruplexes are formed by four guanines hydrogen bonded together to form a planar ring, and stacking of the hydrophobic G quartets stabilizes the quadruplex structure Capra et al.,PLoS Computational Biology, 2010). A surplus of this structure is linked to genomic Instability and cancer development.

Prior studies indicate that because NER eliminates large lesions of DNA, there may be a link to the removal of G4-quadruplexes through Nucleotide Excision Repair (De Magis et al, Nature,2020). …

Exploring Base Excision Repair Using Gene Knockout, Gregory Guantos, Cailyn Brock, Kamily Visser, Dylan Vargas

Posters - 2026

•             Base Excision Repair (BER) fixes damaged 3DNA bases throughout the cell cycle by removing damaged bases and replacing either one nucleotide in short-patch BER or a short stretch of nucleotides in long-patch BER. (Hindi, 2021, Cellular and Molecular Life Sciences:CMLS)

•             4G-quadruplexes (G4s) are 4 stranded secondary DNA structures formed in guanine rich areas of DNA and RNA. (Rhodes, 2015, Nucleic Acids Research)

The URA3 plasmid was used as a PCR template to make a gene deletion construct, then yeast were transformed so APN1 was replaced by URA3. 2APN1 encodes a major DNA repair enzyme in yeast, and strains …

Nucleotide Excision Repair In Yeast, Kinleigh Mines, Larry Ramirez, Jacob Rodriguez, Delynda Gonzalez

Posters - 2026

DNA damage occurs constantly in cells due to environmental factors and normal cellular processes, making DNA repair pathways essential for maintaining genomic stability (Hindi et al., 2021). One major repair mechanism is Nucleotide Excision Repair (NER), which is responsible for recognizing and removing bulky DNA lesions that distort the double helix structure (Scharer, 2013). In Saccharomyces cerevisiae (yeast), the RAD14 gene plays a critical role in this pathway by helping identify and initiate repair of damaged DNA (Scharer, 2013). Another source of instability comes from the formation of G-quadruplex (G4) structures, which are secondary DNA configurations that can interfere with …

Investigating The Role And Expression Of Aquaporin 10 Paralogs In Spiny Dogfish (Squalus Acanthias), Esosa Omoregie

College of Graduate Studies: Theses & Dissertations

Aquaporins (AQPs) are integral membrane proteins that facilitate the selective transport of water and small solutes across cell membranes, playing essential roles in maintaining osmotic balance in vertebrates. Among them, aquaglyceroporins such as AQP10 are capable of transporting water, glycerol, and urea, contributing to osmoregulatory and metabolic processes. This study investigated the expression, localization, and potential physiological roles of two AQP10 paralogs, AQP10C1 and AQP10C2, in the spiny dogfish (Squalus acanthias), a marine elasmobranch that maintains osmotic equilibrium through urea retention and ion regulation. Using RT-PCR, quantitative PCR, Western blotting and immunohistochemistry the study identified tissue-specific expression patterns of …

The Effects Of Ewing Sarcoma Through The Overexpression And Knockdown Of Transcription Factors Sox18 And Stat1, Victoria Castillo, Melany Cervantes, Nicole Robles, Terry Jo Shackleford

Cell and Molecular Methods

SOX18, a transcription factor with a DNA-binding HMG domain, plays a critical role in regulatory processes linked to cancer progression. Exhibiting oncogenic properties, SOX18 has been linked to various cancers, where it promotes tumor growth by enhancing cell invasion, uncontrolled proliferation, and resistance to apoptosis through dysregulated signaling pathways. STAT1, a protein crucial for immune system regulation, is prominently expressed in immune-associated tissues like the lymph nodes, and bone marrow, suggesting it could play a role in tumor growth. Ewing Sarcoma (EWS), an aggressive cancer that targets bone and soft tissue, carries a high mortality rate of 90% without treatment …

Opa1 And Disease-Causing Mutants Perturb Mitochondrial Nucleoid Distribution, J. Macuada, I. Molina-Riquelme, G. Vidal, N. Pérez-Bravo, C. Vásquez-Trincado, G. Aedo, D. Lagos, P. Yu-Wai-Man, R. Horvath, T. J. Rudge, B. Cartes-Saavedra, V. Eisner

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Optic atrophy protein 1 (OPA1) mediates inner mitochondrial membrane (IMM) fusion and cristae organization. Mutations in OPA1 cause autosomal dominant optic atrophy (ADOA), a leading cause of blindness. Cells from ADOA patients show impaired mitochondrial fusion, cristae structure, bioenergetic function, and mitochondrial DNA (mtDNA) integrity. The mtDNA encodes electron transport chain subunits and is packaged into nucleoids spread within the mitochondrial population. Nucleoids interact with the IMM, and their distribution is tightly linked to mitochondrial fusion and cristae shaping. Yet, little is known about the physio-pathological relevance of nucleoid distribution. We studied the effect of OPA1 and ADOA-associated mutants on …

Manipulation Of Cellular Proliferating Cell Nuclear Antigen (Pcna) During Herpes Simplex Virus Type 1 Infection, Jessica Packard, Jill A. Dembowski

Electronic Theses and Dissertations

Herpes simplex virus type 1 (HSV-1) is a double stranded DNA virus that replicates within the nucleus of host cells. Using accelerated native isolation of proteins on nascent DNA (aniPOND), cellular proteins were found to associate with HSV-1 replication forks. One host factor of interest is proliferating cell nuclear antigen (PCNA), the DNA sliding clamp that tethers DNA polymerases and DNA damage response proteins to replicating cellular DNA. Although HSV-1 encodes its own DNA polymerase processivity factor (UL42), PCNA plays a key role in HSV-1 infection. We used commercially available PCNA inhibitors and short hairpin RNAs (shRNA) to investigate how …

The Effect Of The Oncometabolite Fumarate In The Response To Dna Damage: An Analysis Of The Role Of Fumarate In The Response Of Cells A2780 To Dna Damage Induced By Cisplatin, Gillian Luczyk, Luisa María Sierra, Enol Álvarez González

DU Undergraduate Research Journal Archive

Previous research has been conducted on the effect of oncometabolites on DNA damage repair; however, these studies have traditionally focused on the response to damage caused by DNA double-strand breaks, whereas this study involves cisplatin-induced damage that creates DNA cross-links. This study reports on the effect of the oncometabolite fumarate on the response of A2780 cells to DNA damage produced by cisplatin. Three assays were used to complete this study: comet assay, cell cycle assay and apoptosis assay. The comet assay revealed that fumarate influenced the response of cells to DNA damage and, at a lower 1mM concentration, appeared to …

Generating A Colorimetric Ssa4 Transcript Export Reporter For Multicopy Suppression Screen In S. Cerevisiae, Zaid Hatem

[Archive] Belmont University Research Symposium (BURS)

The export of mRNA from the nucleus to the cytoplasm is a regulatory point that is essential to the pathway of gene expression in eukaryotic cells. The export of mRNA transcripts is mediated through selective doorways called the nuclear pore complexes (NPC). Additionally, there are proteins associated with the nuclear pore complex that assist in facilitating the export. This includes association with the export receptor, Mex67, which binds to the transcript and ferries it through NPCs. During cellular stress, such as heat shock, the export of housekeeping mRNA transcripts is halted, forcing these transcripts to remain inside the nucleus and …

Involvement Of The Ino80 Chromatin Remodeling Complex In Cell Division And Genomic Stability, Ethan Chen

Biomedical Engineering Undergraduate Honors Theses

Cell division is a vital biological process for growth and development in both single and multi-cellular organisms—whereby the cell must duplicate its organelles and genome in entirety and appropriately distribute the copied contents to the daughter cells. Cells undergo a cycle of two distinct phases: interphase and mitosis. During interphase, the cell replicates its genomic DNA (in the form of chromosomes) located within the nucleus. DNA replication is carried out in a euchromatin state, where the chromosome structure is loose and easily accessible by DNA polymerase and other replication enzymes. Upon the completion of replication, chromatin is condensed into highly …

Science, But Not Fiction: Colby Researchers Consider How "Extreme-Ophiles" Survive And Thrive In The World's Toughest Places, Gerry Boyle

Colby Magazine

"We're exploring how the cell makes the decision to do this," said Assistant Professor of Biology Ron Peck.

Sensing Ribonuclease H Activity With Dna Nanoswitches, Ruju Trivedi

Biological Sciences

Ribonuclease H (RNase H) is a damage-repair protein and ribonuclease that specifically catalyzes the hydrolysis of RNA in an RNA/DNA duplex and breaks down RNA/DNA junctions. It plays an important role in a variety of biological processes including DNA replication, DNA repair, and transcription. It is also pivotal in anti-HIV drug development and the analysis of cellular processes and has been shown to be a potential therapeutic target for various neoplastic diseases. This thesis discusses a unique assay based on DNA nanoswitches to detect RNase H levels and activity. The assay is based on conformational changes of DNA nanoswitches in …

Analyzing The Effect On Ligand Sensitivity For Xenopus Tropicalis Mc1r, Mc3r, Mc4r, And Mc5r As A Result Of Coexpression With Gallus Gallus Mrap1 In Chinese Hamster Ovary Cells, Avery Niemann, Robert Dores

DU Undergraduate Research Journal Archive

Some melanocortin receptors and the accessory protein MRAP1 have been found to interact in novel ways when co-expressed in the same cells following stimulation with either ACTH (1-24) or αMSH. These interactions have been seen for mammalian, bird, and some bony fish melanocortin receptors. Such analysis has not been done yet on the amphibian melanocortin receptors, MC1R, MC3R, MC4R, and MC5R. To this end, this study was done on the effects regarding ligand sensitivity for ACTH (1-24) and αMSH, when the MC1R, MC3R, MC4R, and MC5R paralogs of the amphibian, Xenopus tropicalis were expressed in Chinese Hamster Ovary cells either …

Pcr Cloning: New Parameters For Managing Alzheimer’S Dementia, Asra Khan, Rehana Rehman, Saara Ahmad

Department of Biological & Biomedical Sciences

No abstract provided.

Spatial Reorganization Of Histone-Like Nucleoid Structuring Proteins Caused By Silver Nanoparticles, Meaad Alqahtany

Graduate Theses and Dissertations

Silver nanoparticles (AgNPs) and ions (Ag+) can be the new generation of antibiotics due to their antimicrobial effects against bacteria and other microbes. Many studies have shown that AgNPs and suppress the growth of bacteria and damage the cell walls of the microbes; therefore, treating bacterial cells with AgNPs may be a promising method to terminate multi-resistant bacteria. In this work, the effect of AgNPs with two different surface coatings on the spatial reorganization of histone-like nucleoid structuring (H-NS) proteins in Escherichia coli bacteria was investigated using quantitative super-resolution fluorescence microscopy to understand the toxicity and antimicrobial mechanism of AgNPs. …

X-Inactivation And Epigenetics, Serena Weston

Thinking Matters Symposium Archive

To prevent abnormal development caused by expressing both X chromosomes, female mammals inactivate one of their X chromosomes using an epigenetic process called dosage compensation. This literature review examines how X chromosome inactivation (XCI) occurs during the formation and development of an embryo. This condensation of DNA is marked by histone tail modifications, DNA methylation, and the arrival of structural proteins resulting in extraordinarily stable heterochromatin. X-inactivation is regulated in cis by the X-inactivation center (Xic) that contains the Xist gene and its antisense gene, Tsix. On one X chromosome, Xist RNA is expressed and coats the center of the …

N-Terminal Domain Of Human Uracil Dna Glycosylase (Hung2) Promotes Targeting To Uracil Sites Adjacent To Ssdna-Dsdna Junctions, Brian P Weiser, Gaddiel Rodriguez, Philip A Cole, James T Stivers

Rowan-Virtua School of Osteopathic Medicine Departmental Research

The N-terminal domain (NTD) of nuclear human uracil DNA glycosylase (hUNG2) assists in targeting hUNG2 to replication forks through specific interactions with replication protein A (RPA). Here, we explored hUNG2 activity in the presence and absence of RPA using substrates with ssDNA-dsDNA junctions that mimic structural features of the replication fork and transcriptional R-loops. We find that when RPA is tightly bound to the ssDNA overhang of junction DNA substrates, base excision by hUNG2 is strongly biased toward uracils located 21 bp or less from the ssDNA-dsDNA junction. In the absence of RPA, hUNG2 still showed an 8-fold excision bias …

Mechanism Of Transcription Anti-Termination In Human Mitochondria., Hauke S Hillen, Andrey V Parshin, Karen Agaronyan, Yaroslav I Morozov, James J Graber, Aleksandar Chernev, Kathrin Schwinghammer, Henning Urlaub, Michael Anikin, Patrick Cramer, Dmitry Temiakov

Rowan-Virtua School of Osteopathic Medicine Departmental Research

In human mitochondria, transcription termination events at a G-quadruplex region near the replication origin are thought to drive replication of mtDNA by generation of an RNA primer. This process is suppressed by a key regulator of mtDNA-the transcription factor TEFM. We determined the structure of an anti-termination complex in which TEFM is bound to transcribing mtRNAP. The structure reveals interactions of the dimeric pseudonuclease core of TEFM with mobile structural elements in mtRNAP and the nucleic acid components of the elongation complex (EC). Binding of TEFM to the DNA forms a downstream "sliding clamp," providing high processivity to the EC. …

Epigenetic Regulation Of Gene Expression During Spermatogenesis, Karishma Nayak

Senior Honors Projects

In the US livestock production industry, improving reproductive efficiency will improve animal welfare and maintain reasonable costs of meat and milk for consumers. In recent research, abnormalities in epigenetic markers in sperm during spermatogenesis, has been linked to male subfertility in many species. Epigenetics is the study of changes in organisms caused by modifications of gene expression, including DNA methylation, rather than alteration of the genetic code itself. When this process is disturbed, it can negatively impact semen therefore decreasing its fertility. Through further research on how DNA methylation influences gene expression during spermatogenesis and its impact on sperm quality, …

Detection Of Viable Microorganisms Using Propidium Monoazide, Erik J. Mcfarland, Adrian Ponce Dr.

STAR Program Research Presentations

Propidium monoazide (PMA) is a molecular tool used to assess viability of microorganisms. Currently, PMA is thought to discern viability through membrane permeability; PMA enters only membrane compromised cells, irreversibly crosslinks to theirDNAand precipitates theDNAout of solution, preventing it from being amplified during polymerase chain reaction (PCR). Using PMA on a sample of live and dead microorganisms results in only theDNAof living organisms being amplified and identified. Therefore, a comparison ofPCRresults with and without PMA allows one to determine the live fraction and total population, respectively.

Current literature provides conflicting evidence as to the effectiveness of the technique. Our research …

Immune Recognition Of Self Nucleic Acids Driven By Endogenous Antimicrobial Peptides: Role In Autoimmunity, Dipyaman Ganguly

Dissertations and Theses (Open Access)

Innate immune recognition of extracellular host-derived self-DNA and self-RNA is prevented by endosomal seclusion of the Toll-like receptors (TLRs) in the dendritic cells (DCs). However, in psoriasis plasmacytoid dendritic cells have been found to be able to sense self-DNA molecules in complex with the endogenous cationic antimicrobial peptide LL37, which are internalized into the endosomal compartments and thus can access TLR9. We investigated whether this endogenous peptide can also interact with extracellular self-RNA and lead to DC activation. We found that LL37 binds self-RNA as well as self-DNA going into an electrostatic interaction; forms micro-aggregates of nano-scale particles protected from …

Water. New Waters And New Life, Juan Enriquez

New England Journal of Public Policy

An excerpt from an article about life sciences taken from the proceedings of the Education for Public Inquiry and International Citizenship (EPIIC) Symposium held at Tufts University in Massachusetts in February 2005 is presented.

The Drosophila Melanogaster Rad54 Homolog, Dmrad54, Is Involved In The Repair Of Radiation Damage And Recombination, Rolf Kooistra, José B. M. Zonneveld, Anja De Jong, Jan C. J. Eeken, Chris J. Osgood, Jean-Marie Buerstedde, Paul H. M. Lohman, Albert Pastink

Biological Sciences Faculty Publications

The RAD54 gene of Saccharomyces cerevisiae plays a crucial role in recombinational repair of double-strand breaks in DNA. Here the isolation and functional characterization of the RAD54 homolog of the fruit fly Drosophila melanogaster, DmRAD54, are described. The putative Dmrad54 protein displays 46 to 57% identity to its homologs from yeast and mammals. DmRAD54 RNA was detected at all stages of fly development, but an increased level was observed in early embryos and ovarian tissue. To determine the function of DmRAD54, a null mutant was isolated by random mutagenesis. DmRAD54-deficient flies develop normally, but the females …

Unusual Structure Of A Human Middle Repetitive Dna, Duminda D. Ratnasinghe

Electronic Theses and Dissertations

The L2Hs sequences are a polymorphic, interspersed, middle repetitive DNA family unique to human genomes. Genomic fingerprinting indicates that these DNAs vary from one individual to another and between tissues of the same individual. Sequence analysis reveals that they are AT-rich (76%) and contain many unusual sequence arrangements (palindromes, inverted and direct repeats). These sequence properties confer on the L2Hs elements the potential to fold into non-B-form structures, a characteristic of recombination hot spots. To test this hypothesis carbodiimide, osmium tetroxide and S$\sb1$ nuclease were used as single-strand specific probes to study a recombinant plasmid, pN6.4.39, containing a single L2Hs …

Characterization Of The Dna And Chromosonal Analysis Of Embryonic Dermacentor Variabilis (Say) Cells In Culture, Stanley Nicholas Mason

Biological Sciences Theses & Dissertations

Cultured embryonic Dermacentor variabilis cells were examined by spectrophotometric techniques to determine total cellular DNA concentration and guanine-cytosine content of the DNA and by differential staining procedures to define the karyotype further. The cells were found to have a mean DNA content of 16.98 pg and a DNA guanine-cytosine content of 49%. Chromosome banding attempts resulted in the specific characterization of four chromosomes and differential grouping of the seven remaining chromosomes. A previously unreported submetacentric chromosome was identified.