Biochemistry, Biophysics, and Structural Biology Commons^™

Sirna Knockdown Of Rptor Alters Gene Expression In Ewing Sarcoma Cells, Sergio Cipriano, David Leavitt, Michael Oliva, Liam Valdez

Posters - 2026

Ewing sarcoma is a highly aggressive cancer that primarily affects children and young adults. Although treatment options exist, many patients do not respond effectively, showing the need for improved targeted therapies¹. RPTOR is a key in mTORC1 complex which regulates cell growth, proliferation, and survival². LY2874455 is a selective pan-FGFR inhibitor that targets growth factor signaling pathways involved in tumor progression³, and FGFR signaling interacts with pathways such as mTOR, making it a potential target for combination therapies. We hypothesized that silencing RPTOR in Ewing sarcoma cells would disrupt mTOR signaling and alter expression of genes linked to cell survival …

Sustainable Mitigation Of Microplastic Pollutants Using Native Plant Species, Antonio Martinez

Posters - 2026

Microplastics (MPs) are defined as small plastic particles that come from the degradation of plastics [Ziani et al. 2023], that hold a regular or irregular shape, ranging from 1μm to 5 mm [Campanale et al. 2025]. This diminutive size makes them virtually impossible to remove once released into the environment[Lee et al. 2023]. Furthermore, biological, chemical, and physical processes break MP's further down in the environment, causing them to exist in nano-level sizes (1nm-1μm) [Lee et al. 2023], further exacerbating their threat to critical habitats. However, recent studies have shown MP contamination expands beyond the natural environment as recent studies …

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 …

Sox18 Unleashed Exploring The Transcriptomic Landscape - Differential Gene Expression Analysis Via Rna Seq In Overexpressed Sox18, Van Nguyen, Kahlie Hernandez, Monabelle Elbayeh

Posters - 2026

Cancer remains a leading cause of death worldwide, and childhood sarcomas such as Rhabdomyosarcoma (RMS) and Ewing Sarcoma (ES) are particularly aggressive with limited targeted treatment options. Despite advancements in cancer therapies, metastatic sarcomas still have a survival rate below 30%, emphasizing the need for new therapeutic targets. SOX18, a transcription factor has played a role in vascular development and endothelial differentiation, functioning as a key driver of angiogenesis. In cancer, increased SOX18 expression has been linked to dysregulated cell migration, invasion, and therapy resistance mechanisms. However, the extent to which SOX18 influences RMS and ES at the transcriptional level …

Discovering Drug-Like Compounds By Targeting Protein-Protein Interactions Using A Yeast-3-Hybrid System, Chesley C. Blake

Senior Theses

Protein-protein interactions are important targets in cancer biology as they can make historically “undruggable” proteins viable drug targets. However, the current approach to targeting protein-protein interactions relies on the use of small molecule drugs, which have low efficiencies as they must cover a large surface area of the interaction. Further, traditional drug therapies often lead to off-target toxicity, limiting therapeutic specificity. The objective of this project is to develop a selection system in yeast to identify short peptide sequences that can disrupt protein-protein interactions specific to cancer cells. Following proof of principle and development of the AH109 yeast strain having …

Glioblastoma Multiforme: A Pathologic Breakdown Of One Of Neuro-Oncology's Greatest Challenges, Rosemary Westphal, Ms

Student Papers, Posters & Projects

Glioblastoma multiforme is the most common adult primary tumor with a grim median survival time of 14.6 months. It is characterized by rapid progression, diffuse infiltration, and rather poor clinical outcomes. The WHO classifies GBM as a grade 4 diffuse astrocytic tumor with distinctive histopathological features including high mitotic activity, marked cellular atypia, microvascular proliferation, and necrosis. Advances in molecular diagnostics have further classified GMB into IDH-wild type and IDH-mutant subtypes, with important therapeutic and prognostic implications. Key genetic alterations, such as EGFR amplification, PTEN loss, TP53 mutations, TERT promoter mutations, and MGMT methylations, have been identified as contributing to …

Investigating The Endogenous & Synthetic Estrogens To The Three Estrogen Receptor Subtypes Of Teleost Fish, Ann Cyril

Posters - 2026

Estrogen and the estrogen receptors are important biological and physiological processes. The various types of estrogen include estrone, estradiol and estriol. Estradiol’s main function is to maintain the reproductive system. Estrone’s main function is to develop the female's reproductive functions. Estriol’s main function is to aid the female's sexual developments but is on the weaker side. The fish, Atlantic Croaker, has three different estrogen receptors: ERα, ERβa, and ERβb. Based on the estrogen receptors, it appears that their binding affinities do differ in strength. Each estrogen receptor has different amino acids involved that could contribute to the difference in their …

An Investigation In The Physiological Effect Of Microplastic And Chemical Mixtures In The Body Length Of C. Elegans, Gregory Guantos, David M. Mares, Jennifer C. Harr Phd

Posters - 2026

• Microplastics (MP) are pieces of plastic less than 5 micrometers (mm). Microplastics are found in our environment and have even been found in the food humans consume, including in drinks from plastic bottles (Hu 2020).

• Di-butyl Phthalate (DBP) is a chemical known as a plasticizer commonly used in PVC applications, ink, fragrances, and adhesives

• Di-butyl Phthalate has been found to have negative effects on the physiological length of C. elegans (Xiyan 2018)

• Microplastics have similarly been found to decrease the physiological length of C. elegans (Schöpfer 2020)

• The combined effects of MPs and DBP include …

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 …

The Role Of Emerin In Myogenic Differentiation, Nicholas Marano

Theses and Dissertations

The nucleus harbors genetic material encapsulated by the nuclear envelope which is composed of an inner and outer nuclear membrane. The establishment and organization of chromatin at the INM is essential for cell fate during the differentiation program. Integral INM proteins are responsible for chromatin organization at the nuclear envelope. Emerin is a highly conserved type II integral INM protein with roles in chromatin organization, cell signaling, and nuclear structure. Mutations in the emerin gene cause Emery Dreifuss Muscular Dystrophy 1 (EDMD1). Emerin is ubiquitously expressed, but loss of emerin function affects specifically skeletal muscle and cardiac tissue. The precise …

Effect Of Novel Antimicrobial Compounds On Fungal And Bacterial Pathogens, Megan Wilderman

Honors Program: Senior Projects (Public)

Antimicrobial resistance is a growing concern in medicine¹ leading to a need for the development of novel compounds. Two compounds were tested in this study, 2-hydroxyethylhydrazine (HEH) and para-nitrophenyl-isocyanide (NPIC). HEH targets phosphatidylcholine (PC) production², and NPIC targets mitochondrial function³. Choline (Cho) is a compound that bypasses the inhibition of HEH through the Kennedy pathway.² Two-fold serial dilutions were conducted in 96-well plates to test the sensitivity of different bacteria to HEH and fungi to HEH and NPIC in different media types. A choline condition was also included in the HEH dilutions to test …

Recombinant Hagfish Intermediate Filament Proteins Enable Neural Culture Substrates That Promote Neurite Extension And Reduce Oxidative Stress, Justin Jones, Kristin Durrant

Browse all Datasets

This dataset supports the production, characterization, and biological validation of a novel recombinant hagfish intermediate filament (rHIF) protein functionalized with spider silk motifs (rHIF-alpha-GRGGL). The data demonstrates a scalable bioprocess resulting in a 7.76 g/L yield, high structural alpha-helicity (77.2%), and significant support for N2a cells.

Tlr3 Mediated Type I Interferon Response In Mammalian Cell Defense Against Cryptosporidium Parvum Infection., Anjelica Matias

Biochemistry and Molecular Biology

Cryptosporidium parvum is a major cause of a diarrheal disease which affects many children in the USA as well as the rest of the world, yet the contribution of its double stranded RNA (dsRNA) viral symbiont, Cryspovirus (CSpV1) to host innate immunity remains unclear. This study investigated whether CSpV1 activates Toll Like Receptor 3 (TLR3) signaling pathways and downstream Interferon type I (IFN I) responses in mammalian intestinal epithelial cells. Confluent Human Ileocecal Colorectal Adenocarcinoma cells (HCT8) were exposed to CSpV1, and the expression levels of Tumor Necrosis Factor Receptor-Associated Factor 3 (TRAF3), Nuclear Factor-𝜅-light chain enhancer of activated B-cells …

Disrupted Nuclear Function And Nucleocytoplasmic Transport In Parkinson’S Disease, Ichiro M. Matoba

The Cardinal Edge

No abstract provided.

Characterization And Advancement Of Molluscan Venom Gland Cell Model Systems, James V. Parziale

Dissertations, Theses, and Capstone Projects

Venomous mollusks, including cone snails and coleoid cephalopods, produce rich repertoires of bioactive peptides with profound effects on cellular physiology, yet there are few tractable experimental systems that exist to study their development, maintenance, and venom secretion. Although therapeutics such as the cone snail peptide Ziconotide demonstrate the biomedical potential of molluscan venoms, progress in understanding how venom glands form, function, and evolve has been hindered by the lack of reliable husbandry and the complete absence of in vitro cell models. Modern comparative genomics has revealed widespread convergent evolution across venomous lineages, but molluscan datasets remain underrepresented, limiting insights into …

Dna Stability In Aqueous Solutions: A Case Study On Poly A - Poly T Duplex Using Molecular Dynamics Simulations, Haripriya Chennuru

Biochemistry and Molecular Biology

This thesis relies on molecular dynamics (MD) simulations, which apply the AMBER software package to analyze the structural stability, energetics, and dynamics of Poly A - Poly T DNA duplexes. This work is mainly concerned with testing configurations of non-bonded interaction cutoffs (12 Å and 15 Å) on the Generalized Born solvation models (IGB1 and IGB2) to determine the most appropriate conditions regarding computation time and physical reliability in DNA molecular dynamics. The solvation models enable effective simulation of solvent effects, facilitating the calculation of simulation parameters to evaluate structural stability within different environmental conditions. Overall, the performance indicates that …

Computational And Functional Characterization Of Terebrid Venom Peptides, Favour T. Achimba

Dissertations, Theses, and Capstone Projects

Venom peptides represent a natural repertoire of bioactive compounds that are potent modulators of ion channels. Teretoxins, venom peptides from terebrid snails, remain underexplored despite their structural and functional diversity. This thesis is the first to comprehensively explore the structure and function of teretoxins using a comparative computational sequence and structure model followed by experimental assays. The majority of the functional focus has been on identifying the ion channel molecular targets of uncharacterized teretoxins. Teretoxins, like other venom peptides, are hypothesized to manipulate the cellular function of a diversity of ion channels. Dysregulation of ion channels leads to several …

4e-Bp1 Differentially Regulates Translation Of A Subset Of Human Mrnas, Mehreen Mahbub

Dissertations, Theses, and Capstone Projects

Elevated levels of eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) influence cap-independent translation by forming a complex with eukaryotic initiation factor 4E (eIF4E) (eIF4E•4E-BP1). Certain mRNAs—including those encoding hypoxia-inducible factor-1α (HIF-1α), fibroblast growth factor-9 (FGF-9), and two isoforms of tumor suppressors, p53 (p53_A, and p53_B)—contain structured 5’untranslated regions (UTRs) that enable translation either via cap-independent translation enhancer (CITE)-like or internal ribosomal entry site (IRES)-like mechanisms. However, how 4E-BP1 modulates these mechanisms remains unclear. Using fluorescence-based anisotropy assays, we showed that the eIF4E•4E-BP1 binds more tightly to the 5’ m⁷G-cap of these mRNAs than eIF4E …

An Antioxidant Cocktail Of Tert-Butylhydroquinone And A Manganese Porphyrin Induces Toxic Levels Of Oxidative Stress In Cancer Cells, Sandra Tamarin, Hannah Jung, Joseph Lamorte, Laura Biesterveld, Gabriel Piñero, Grace Turchetta, Molly Myers, Rebecca Oberley-Deegan, Aimee Eggler

Student Papers, Posters & Projects

Despite significant advancement in cancer treatments, therapies with minimal toxicity to healthy cells are still limited. One targetable weakness of cancer cells is their sensitivity to oxidative stress. We find that the combination of two antioxidants—the common food additive tert-butylhydroquinone (tBHQ) and a manganese porphyrin in clinical trials, MnTnBuOE-2-PyP5+ (MnBuOE)—increases oxidative stress and causes apoptotic death in several cancer cell lines, but not in mouse primary fibroblasts. Investigating the mechanism of cell death, MnBuOE is observed to catalyze the oxidation of tBHQ, producing the electrophilic quinone tert-butylquinone (tBQ). A critical role for tBQ and its electrophilic character was revealed with …

Dapagliflozin Attenuates Cisplatin-Induced Nephrotoxicity In Rats Through Modulation Of Ros/Nf-Κb, Bcl2/Bax And Pink1/Parkin Signaling Pathways, Esraa K. Khallaf, Eman A. Ramadan, Mohey M. Elmazar, Marwa M. Safar

Pharmacy

Dapagliflozin (DPG), an anti-diabetic drug, has gained attention for its renal protective effects through multiple molecular pathways, yet its impact on mitophagy in cisplatin (CIS) nephrotoxicity remains unclear. This study aimed to examine the impact of DPG against CIS-induced nephrotoxicity in rats, targeting mainly PINK1/Parkin-mediated mitophagy and inflammatory/apoptotic pathways. Male Sprague Dawley rats received DPG (10 mg/kg; p.o) daily for 14 consecutive days and AKI was induced by a single injection of CIS (7 mg/kg; i.p) on day 10. Blood glucose, serum levels of creatinine and urea nitrogen, oxidative stress, inflammatory, apoptotic, mitophagy markers, and histological changes were assessed. DPG …

Defining Rna Oligonucleotides That Reverse Deleterious Phase Transitions Of Rna-Binding Proteins With Prion-Like Domains., Lin Guo, Jacob Mann, Jocelyn Mauna, Katie Copley, Hejia Wang, Jack Rubien, Cristian Bergmann, Jenny Carey, Jessica Merjane, Marilyn Ngo, Jiazhen Xu, Hana Odeh, Jiabei Lin, Bo Lim Lee, Laura Ganser, Emma Robinson, Kevin Kim, Anastasia Murthy, Tapas Paul, Bede Portz, Amanda Gleixner, Zamia Diaz, Ashleigh Smirnov, George Padilla, Ellen Lavorando, Carolann Espy, Yulei Shang, Eric Huang, Alessandra Chesi, Nicolas Fawzi, Sua Myong, Christopher Donnelly, James Shorter

Department of Biochemistry and Molecular Biology Faculty Papers

RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs that prevent FUS fibrillization by promoting liquid phases and distinct short RNAs that prevent and reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. We define a short RNA that dissolves cytoplasmic FUS aggregates, restores nuclear FUS, and mitigates FUS toxicity in optogenetic models and ALS …

Generating A Gfp Reporter Via Crispr To Visualize Ssa4 Export, Aara Khairollahi, Rebecca Adams

SPARK Symposium Presentations

In eukaryotic cells, the transport of mRNA from the nucleus to the cytoplasm is a very regulated process controlled by nuclear pore complexes (NPCs). During stress conditions, such as heat shock, most mRNA export is inhibited in Saccharomyces cerevisiae, yet the transcript for SSA4, a gene responsible for refolding denatured essential proteins, is exported. The mechanism behind this selective export remains unknown. To investigate this, we used CRISPR-Cas9 to generate a reporter strain in which the SSA4 open reading frame was replaced or inserted with green fluorescent protein (GFP). This reporter is designed to produce GFP only under conditions that …

Crispr Transgenic Clytia Hemisphaerica As A Vector For Toxin Delivery In A Zebrafish Melanoma Model, Theodore G. Paz

Theses, Dissertations and Culminating Projects

The jellyfish Clytia hemisphaerica has the potential to be used in cancer therapies with the discovery of potential active toxin target regions to be modified for use. The program Venomix is a Uniprot-based database that was utilized in this experiment to generate likely flagged hit regions using Clytia hemisphaerica CDS files run against its database of terrestrial toxins (Furuno et al., 2003; Macrander et al., 2018). By themselves they are indeterminate as to whether they are active toxin region hits (Macrander et al., 2018). With further analysis such as toxin homology in closely related, annotated marine taxa and accounting for …

Fgf Signaling Is Necessary For Newt Lens Regeneration, Leo Alexander Napoleon

Honors Theses and Capstones

The Iberian ribbed newt Pleurodeles waltl can regenerate the lens by transdifferentiating iris pigmented epithelial (IPE) cells into lens epithelial cells (LECs), but the mechanism by which this occurs remains largely uncharacterized. We aim to mechanistically show an early and critical role for FGF signaling by using small molecules to inhibit FGF receptors and observe the histological and intracellular effects. Two inhibitors were found to completely stall lens regeneration. Cell cycle analysis revealed decreased DNA synthesis and uniformly low but unchanged entry to mitosis under signaling inhibition by staining for EdU incorporation and phospho-histone H3 (pH3), respectively. Western blot revealed …

Psr Impacts Chromatin Condensation During Spermatogenesis In Nasonia Vitripennis, Jacqueline R. Solomon

CMC Senior Theses

Paternal Sex Ratio (PSR) is a supernumerary, selfish B chromosome found in the jewel wasp (Nasonia vitripennis). PSR is transmitted strictly paternally to progeny, and when present, it causes paternal genome elimination (PGE) just after fertilization. Due to the haplo-diploid reproduction of N. vitripennis, this PGE event results in all-male broods of progeny, ~90% of which carry and transmit PSR. Thus, PGE is beneficial for PSR’s transmission.  A previous study showed that PSR induces PGE by expressing a gene called haploidizer during spermatogenesis. Although how haploidizer functions in PGE is unknown, this finding suggests two basic models: that (i) the …

Potential Environmental Triggers Of Goodpasture's Disease And The Role Of The Sulfimine Crosslink, Colton S. Miller, Andrea Florian, Elena Pokidysheva

SPARK Symposium Presentations

Goodpasture’s syndrome (GP) is an autoimmune disorder that primarily affects kidneys and lungs. The main issue for patients with Goodpasture's syndrome is the binding of autoantibodies to the glomerular basement membrane (GBM), which hinders the filtration of blood. A key characteristic of Goodpasture's syndrome is the presence of autoantibodies that target the NC1 domain of the α345 isoform of type IV collagen, a crucial component of the GBM that provides structural support and is critical for filtration function. Sulfilimine bonds crosslink the collagen IV NC1 hexamers, contributing to the stabilization of these structures. A recent clinical case of recurring Goodpasture's …

Comparing The Differences Of Hsp90Α And Hsp90Β In Native Protein Complex Incorporation, Daryna Serediuk

Honors Theses and Capstones

Epichaperomes are long-lasting, stable assemblies of chaperones, co-chaperones, and associated factors that facilitate cell survival in maladaptive cellular states. Their inhibition has emerged as an attractive therapeutic strategy for the treatment of cancer and neurodegenerative diseases (Rodina et al., 2016). Epichaperomes are hallmarks of robust proliferation in cancer cell populations across many cancer types and are abundantly present in several stem cell varieties, including induced pluripotent stem cells, human embryonic kidney cells, and cancer stem cells (Kishinevsky et al., 2018).

The core protein of the eukaryotic heat shock protein machinery, Heat Shock Protein 90 (Hsp90), is a central chaperone that …

Design And Advancement Of Analytical Frameworks For In Vivo Single-Photon Calcium Imaging To Characterize Temporal- And Treatment-Dependent Neural Adaptations To Opioid Exposure And Withdrawal In The Medial Prefrontal Cortex, Alexia R. Alsum Dr.

Theses and Dissertations--Pharmacy

Despite the availability of several approved medications for opioid use disorder (OUD), it remains a significant public health concern characterized by persistent neurobiological adaptations that drive relapse and impede successful recovery. The medial prefrontal cortex (mPFC), a region critical for executive control and decision-making, undergoes pronounced functional changes during chronic opioid exposure and withdrawal, yet the cellular mechanisms underlying these adaptations remain poorly understood. This dissertation aims to investigate longitudinal alterations in mPFC neural activity across opioid exposure and withdrawal using in vivo single-photon calcium imaging and newly developed computational frameworks.

Following standard preprocessing to extract and normalize calcium traces, …

Molecular Mechanisms And Metabolic Consequences Of Glucocorticoid Resistance, Genesee J. Martinez

Theses and Dissertations--Pharmacology and Nutritional Sciences

Glucocorticoids are vital steroid hormones that govern metabolism, stress responses, and immune functions through intricate, tissue-specific mechanisms, both genomic and non-genomic. These hormones bind to the glucocorticoid receptor (GR), which then acts as a transcription factor to modulate gene expression. Chronic elevation of glucocorticoid levels may lead to glucocorticoid resistance, resulting in adiposity, inflammation, and insulin resistance, thereby adversely affecting multiple metabolic tissues. Whether produced endogenously or administered exogenously, excessive, chronic glucocorticoid concentrations impair glucocorticoid signaling. Although there are two primary isoforms of the receptor, GR⍺ and GRβ, only GR⍺ interacts with glucocorticoids.Through the research conducted in this dissertation, we …

Fluorescent Protein Imaging Approaches Uncover Dynamic Subcellular Distribution Of Core Clock Proteins In Neurospora Crassa, Ziyan Wang

Dartmouth College Ph.D Dissertations

Circadian clocks are endogenous self-sustained timekeeping systems that allow organisms to anticipate and adapt to daily environmental cycles. Found in diverse forms of life, these molecular clocks regulate the expression of ~ 40% of the genome in animals, fungi, and plants. In animals and fungi, circadian oscillators are built on transcription-translation feedback loops (TTFLs), in which positive regulators drive the expression of negative regulators which, once synthesized and imported into the nucleus, inhibit their own activators. This precisely regulated negative feedback incorporates multiple steps of delays that are essential for generating ~24-hour rhythms. Through these mechanisms, circadian clocks temporally coordinate …