Biochemistry Commons^™

The Role Of Secondary And Tertiary Structure In The Cap-Independent Translation Of Fgf-9 And Hif-1-Alpha, Amanda Michelle Whittaker

Dissertations, Theses, and Capstone Projects

Under normoxic conditions, eukaryotes initiate translation of RNA through eIF4E recognition of the 5’ cap. However, under cellular stress, eukaryotic translation must be initiated through a 4E-independent, or “cap-independent” mechanism, involving eukaryotic initiation factor 4G (eIF4G) binding directly to the 5’ untranslated regions (5’ UTR) of the RNA. eIF4G binding then recruits the ribosome to the transcript. While this mechanism is useful for translation of apoptotic transcripts and transcripts involved in cell survival, cap-independent translation is also utilized by oncogenic RNA for tumorigenesis. Previous work by our lab and others has categorized this recruitment and initiation mechanism as either internal-ribosome-entry-site …

Solvation Thermodynamic Mapping Approaches For Computer-Aided Drug Discovery, Vjay Molino

Dissertations, Theses, and Capstone Projects

The drug discovery process is inherently long and costly, prompting the development and integration of computational tools to mitigate these challenges. One of area explored in computer-aided drug discovery is to understand the role of solvation in protein-drug binding and to develop computational tools and methods that can be integrated in the drug discovery process. Grid Inhomogeneous Solvation Theory (GIST) is a tool that provides a framework for mapping solvation thermodynamiproperties of water molecules on the protein surface.This thesis explores the use of GIST in generating pharmacophore models and elucidates the role of solvation in protein structural fluctuations.

One of …

A Microrna-Regulated Transcriptional State Defines Intratumoral Cd8+ T Cells That Respond To Immunotherapy, William W. Tang, Ben Battistone, Kaylyn M. Bauer, Allison M. Weis, Cindy Barba, Muhammad Zaki Hidayatullah Fadlullah, Arevik Ghazaryan, Van B. Tran, Soh-Hyun Lee, Z. Busra Agir, Morgan C. Nelson, Emmanuel Stephen Victor, Amber Thibeaux, Colton Hernandez, Jacob Tantalla, Aik C. Tan, Dinesh Rao, Matthew Williams, Micah J. Drummond, Ellen J. Beswick, June L. Round, H. Atakan Ekiz, Warren P/ Voth, Ryan M. O’Connell

Markey Cancer Center Faculty Publications

The rising incidence of advanced-stage colorectal cancer (CRC) and poor survival outcomes necessitate new and effective therapies. Immune checkpoint inhibitors (ICIs), specifically anti-PD-1 therapy, show promise, yet clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8 + T cell-infiltrated tumors through an unbiased in vivo CRISPR-Cas9 screen identifying functional tumor antigen-specific CD8+ T cell-expressed microRNAs. T cell miR-155 is required for anti-PD-1 responses and for a vital intratumor CD8 + T cell differentiation cascade by repressing Ship-1, inhibiting Tcf-1 and stemness, and subsequently enhancing Cxcr6 expression, anti-tumor immunity, and effector functions. Based …

Staying Sane In The Membrane: Neutral Sphingomyelinase 2 As A Master Regulator Of Plasma Membrane Ceramide, Zainuddin Quadri, Erhard Bieberich

Markey Cancer Center Faculty Publications

Ceramide, a key signaling sphingolipid in the plasma membrane, plays a pivotal role in fundamental cellular processes such as adhesion, polarity, and programmed cell death. The generation of plasma membrane ceramide is largely attributed to the activity of two types of sphingomyelinases: neutral sphingomyelinase 2 (nSMase2, Smpd3) and acid sphingomyelinase (aSMase, Smpd1). While many studies have explored ceramide generation following experimental activation of these enzymes, the mechanisms governing basal or steady- state ceramide levels have remained poorly understood. Using an innovative mass spectrometry approach developed in the Canals’ lab, the team has quantified the distinct contributions of nSMase2 and aSMase …

Genome-Wide Profiling Of Trna Modifications By Induro-Trnaseq Reveals Coordinated Changes, Yuko Nakano, Howard Gamper, Henri Mcguigan, Sunita Maharjan, Jiatong Li, Zhiyi Sun, Erbay Yigit, Sebastian Grünberg, Keerthana Krishnan, Nan-Sheng Li, Joseph Piccirilli, Ralph Kleiner, Nicole Nichols, Brian Gregory, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro-a new group-II intron-encoded RT-to map and quantify genome-wide tRNA modifications in Induro-tRNAseq. We show that Induro progressively increases readthrough over time by selectively overcoming RT stops without altering the misincorporation frequency. In a parallel analysis of Induro vs. a related RT, we provide comparative datasets to facilitate the prediction of each modification. We assess tRNA modifications across five human cell lines and …

Retracted: Conserved Domains In Promoters Of Differentially Expressed Genes: How To Find Them And What Can They Tell Us?, Emalynn E. Tobias

Mako: NSU Undergraduate Student Journal

THIS ARTICLE HAS BEEN RETRACTED DUE TO THE FOLLOWING REASON: inadvertent errors in several citations.

The complex process of regulating gene expression involves a large number of cis- and trans-acting components. The cis elements also referred to as cis regulatory elements (CREs) are highly conserved across species, and are often referred to as conserved domains mainly located in the promoters of genes. The trans acting sequences such as enhancers, moderators and insulators are also crucial in the regulation of gene expression. With an increased influx of genomic and transcriptomic data, study of differentially expressed genes (DEGs) is highly effective in …

Associations Between Social Determinants Of Health And Mental Health Disorders Among U.S. Population: A Cross-Sectional Study, S. Tanarsuwongkul

Faculty Publications

Aims

The impact of social determinants of health (SDOH) on mental health is increasingly realized. A comprehensive study examining the associations of SDOH with mental health disorders has yet to be accomplished. This study evaluated the associations between five domains of SDOH and the SDOH summary score and mental health disorders in the United States.

Methods

We analyzed data from a diverse group of participants enrolled in the All of Us research programme, a research programme to gather data from one million people living in the United States, in a cross-sectional design. The primary exposure was SDOH based on Healthy …

Characterizing The Molecular Complexities Of Iga1 By Serum Proteomics In The Context Of Iga Nephropathy, Mary A. Cunningham

All ETDs from UAB

Immunoglobulin A1 (IgA1) is the second most abundantly produced immunoglobulin in circulation per day and plays a key role in human immunity. Two molecular complexities of IgA1 make accurately studying the protein challenging. The first is that IgA1 exists in three main molecular forms in the serum of humans: monomeric (mIgA1, 80-90% of serum IgA1), polymeric (pIgA1, 10-20% of serum IgA1), and IgA1-containing immune complexes (IgA1-IC, <0.5% of serum IgA1). The second complexity is that the hinge-region of IgA1 is extensively O-glycosylated and exhibits a high level of variation in its O-glycans, particularly in the degree of sialylation. In context of the autoimmune disease IgA nephropathy (IgAN), patients have elevated levels of IgA1 that has reduced levels of galactose (Gal) in the IgA1 hinge-region (Gal-deficient IgA1). This Gal-deficient IgA1 forms immune complexes with IgG autoantibodies (IgA1-IC), deposits in the glomeruli, and induces kidney injury. While it is established that these large IgA1-IC (>700 kDa) formed in the circulation are pathogenic, there remains a gap in knowledge about other blood proteins that may be associating with IgA1 in complexes. It is also necessary to understand the native …

Nls-Binding Deficient Kapβ2 Reduces Neurotoxicity Via Selective Interaction With C9orf72-Als/Ftd Dipeptide Repeats, Kevin Kim, Amandeep Girdhar, Maria Elena Cicardi, V. Kankate, Miyuki Hayashi, Ruoyu Yang, Jenny Carey, Charlotte M Fare, James Shorter, Gino Cingolani, Davide Trotti, Lin Guo

Department of Biochemistry and Molecular Biology Faculty Papers

Arginine-rich dipeptide repeat proteins (R-DPRs) are highly toxic proteins found in patients with C9orf72-linked amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). R-DPRs can cause toxicity by disrupting the natural phase behavior of RNA-binding proteins (RBPs). Mitigating this abnormal phase behavior is, therefore, crucial to reduce R-DPR-induced toxicity. Here, we use FUS as a model RBP to investigate the mechanism of R-DPR-induced aberrant RBP phase transition. We find that this phase transition can be mitigated by Kapβ2. However, as a nuclear import receptor and phase modifier for PY-NLS-containing RBPs, the function of WT Kapβ2 could lead to undesired interaction with its …

Protein-Metal Interactions Of A-Synuclein And Bioactive Transition Metals Via Molecular Dynamics, Gonzalo R. Vazquez

Theses and Dissertations

Parkinson’s Disease (PD) is a neurodegenerative movement disorder which has been found to target the dopaminergic neurons of the substantia nigra. It is characterized by the formation of masses known as Lewy Bodies, formed by aggregates of the intrinsically disordered protein (IDP) -synuclein (asyn). Research suggests that alpha synuclein can undergo aggregation in the presence of heavy metals, which may accumulate in the body through a variety of mechanisms. To study how metals may play a role in wildtype (WT) asyn aggregation, MD simulation of the protein was performed in the presence of bioactive transition metals including Fe2+, Fe3+, Cu+, …

Anti-Cancer Compounds Based On Natural Imidazole Compounds, Autumn Forsythe, Victoria Hardy, Kerri L. Shelton

CSU Tower Day

We are developing a comprehensive review on imidazole-based compounds of natural origin, the most common groups of compounds, and their properties, such as the imidazole ring. The intent of this presentation is to learn about the compound’s occurrence, general/predicted properties, and advantages. The review will be a fluid development comparing imidazole derivatives of natural origin with antinociceptive/lethal properties from the last 5 years. This review would include both purely extracted products but also those modified by synthesis.

Biological And Chemical Evaluation Of Amide-Based Cjoc42 Derivatives As Potential Gankyrin-Inhibitors For The Treatment Of Breast, Lung, And Liver Cancer, Benita Britton-George

Theses and Dissertations

Gankyrin is an ankyrin-repeat protein overexpressed in certain cancers and is responsible for cell growth and proliferation. Gankyrin is important to the development of many types of cancer, including breast, lung, and liver cancer. Consequently, gankyrin and its various protein-protein interactions, are prospective therapeutic targets for inhibiting the progression of certain cancers. In 2016, the first small molecule inhibitor of gankyrin, cjoc42, was discovered and subsequently demonstrated modest antiproliferative activity against liver cancer cells. Previous work from our lab demonstrated that replacing the sulfonate ester of cjoc42 with an amide group significantly improved gankyrin binding while enhancing antiproliferative activity against …

Structural Impacts Of Canonical And Non-Canonical Oligonucleotide Modifications, Deepak Shrestha

Wayne State University Dissertations

Nucleic acids, including DNA (deoxyribonucleic acid) and RNA (ribonucleic acids), are the fundamental building blocks of living organisms. The events that cause modification of DNA/RNA are of interest because they impact the nucleic acid function. Targeting DNA is important for treating diseases such as cancer. Cisplatin (cisPt) is a well-studied drug that targets DNA and blocks replication, but its use is limited by adverse side effects and cellular resistance. Prevoius research addressed some of these challenges through development of platinum analogues such as carboplatin and oxaliplatin. Amino acid-linked platinum analogues (AAPt) are the focus of this thesis work. AAPt complexes …

Mass Spectrometry Combined With Chemical Biology To Study Human Ailments, Eric Thomas Jacquerio Davis

Wayne State University Dissertations

Post-translational modifications (PTMs) are essential as chemical changes that regulate protein function, activity, stability, interactions, and localization after protein synthesis. PTMs, such as phosphorylation, acetylation, and ubiquitination, can activate or deactivate proteins, influence their interactions with other molecules, and determine their cellular location. This regulation is vital for numerous biological processes, such as cell cycle control, signal transduction, and gene expression. Abnormal PTMs are linked to various diseases in humans, including parasitic infection, blood disorders, cancers, and neurodegenerative diseases, making their study crucial for understanding disease mechanisms and developing targeted therapies. In the Pflum lab, we are interested in the …

Identifying The Constituents Of Pyrolysis Oil Using Supercritical Fluid Chromatography- Fraction Collection (Sfc-Fc) And Gas Chromatography- Mass Spectrometry/Vacuum Ultraviolet Spectroscopy (Gc-Ms/Vuv), Sadid Morshed

2025 Fall Honors Capstones Projects - Archive

Plastic waste continues to accumulate as production increases and disposal methods remain insufficient. Even with recycling programs in place, much of the discarded plastic still ends up in landfills or waterways, eventually breaking down into harmful microplastics. One promising solution is the conversion of plastic waste into pyrolysis oil, which can also serve as an alternative feedstock for chemicals. Pyrolysis oil is produced by heating plastics to approximately 800 °C in the absence of oxygen, resulting in a complex mixture of hydrocarbons that includes paraffins, isoparaffins, olefins, naphthenes, and aromatics. Analyzing the amount of oxygen, nitrogen, and sulfur in these …

Resveratrol Exerts Anti-Inflammatory Effects On Human Thp-1 Macrophages, Valeria B. Martinez

Chemistry & Biochemistry Theses - Archive

Inflammation is a natural biological response to harmful stimuli. It initiates a series of reactions that prompt defensive and curative mechanisms, ridding the body of offending agents and healing remaining injuries. Inflammation involves the intricate communication between cells, requiring complex signaling that mediates various pathways. This acute form of inflammation is vital for our survival, promoting a myriad of mechanisms that function to defend and heal. However, if this inflammatory response is not resolved, it results in a prolonged condition referred to as chronic inflammation. This persistent inflammatory state is incredibly harmful, damaging the host's healthy cells, tissues, and organs. …

The Role Of Sodium Butyrate As An Inflammatory Regulator And Its Effect On Long Noncoding Rnas In Neuroinflammation, Angel Covarrubias

Chemistry & Biochemistry Theses - Archive

Inflammation is a crucial homeostatic process that contributes to both the elimination of foreign invaders and tissue repair. Inflammation at sites of tissue injury or infection is initiated by the detection of a harmful stimulus, triggering vital inflammatory immune signaling pathways and a cascade of cytokines and inflammatory mediators. The dysregulation of this process, however, can result in inappropriate inflammatory responses manifesting in tissue damage and compromised cell function. Dysregulation of the inflammatory response is seen frequently in many human diseases such as Diabetes, Cancer, cardiovascular disease, and neurodegenerative diseases.

In the context of the Central Nervous system, inflammation is …

Characterizing And Targeting The Non-Catalytic Functions Of Phosphatase Of Regenerating Liver 3 (Prl-3) In Oncogenesis And Cancer Progression, Jeffery T. Jolly

Theses and Dissertations--Molecular and Cellular Biochemistry

Phosphatase of Regenerating Liver 3 (PRL-3) is frequently upregulated in various cancers and is associated with poor patient prognosis. Although traditionally studied for its phosphatase activity, PRL-3 also interacts with the CNNM family of magnesium transporters through its catalytic site, and these two functions are mutually exclusive at any given time. Most previous studies relied on a commonly used PRL-3 mutation that disrupts both phosphatase activity and CNNM binding, making it challenging to determine which function drives its oncogenic effects. To address this gap in the field, I utilized a panel of PRL-3 mutants that selectively disrupt either phosphatase activity …

Traction Force Microscopy Using An Epifluorescence Microscope: Experimental Considerations And Caveats, Zaria Booth, Mazen Mezher, Rudra Patel, Venkat Maruthamuthu

Mechanical & Aerospace Engineering Faculty Publications

Forces exerted by cells due to their internal contractility play fundamental roles in a host of processes, including adhesion, migration, survival and differentiation. Traction force microscopy (TFM) enables the determination of forces exerted by cells or cell collectives on their environment, which is typically taken to be an extra-cellular matrix (ECM)-coated substrate. Sample preparation for TFM involves the plating of cells onto an environment embedded with fiducial markers. The imaging of these fiducial markers in the presence and absence of the cells then enables calculation of the displacement of localized regions of the environment, and, consequently, the spatial distribution of …

Transient Transmembrane-Electrostatically Localized Protons And Transmembrane Potential In A Laser Flashed Bacteriorhodopsin Purple Membrane Open Flat Sheet - Summary, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The transmembrane-electrostatically localized protons/cations charges (TELCs, also known as TELPs) model may serve as a unified framework to explain a wide range of bioenergetic phenomena. Transient transmembrane-electrostatically localized protons (TELPs) and transmembrane potential in a laser flash-energized bacteriorhodopsin (bR) purple membrane (PM) open flat sheet are now better analyzed. Under the Heberle et al. (1994) experimental conditions, the number of bR molecules is now calculated to be 8200 per PM open flat sheet with a diameter of 600 nm. With a single-turnover laser flash intensity of 3 mJ/cm² to photoexcite 10% of the bR molecules, the laser flash-induced peak TELCs …

Identification Of A Serine Protease Involved In Spinosad Degradation In The Yellow Fever Mosquito, Aedes Aegypti, Hongxiao Yu, Caixia Peng, Zhaohui Chen, Jie Li, Yunqi Li, Xiaojing Zhu, Yuqi Huang, Linlong Jiang, Pablo Sobrado, Jianqiang Lan, Yingying Guo, Qian Han

Chemistry Faculty Research & Creative Works

Spinosad is a widely used insecticide effective in controlling Aedes aegypti populations, but the molecular mechanisms underlying resistance remain poorly understood. This study explores the role of a serine protease, AeaSP (AAEL002624), in the potential detoxification ability of spinosad. Our results showed the crude protein of Ae. aegypti degraded approximately 48% of spinosad in vitro within 1 h; based on our previous research, AeaSP was believed to be potentially involved in the degradation of spinosad. Subsequently, AeaSP was recombinantly expressed in vitro, and its enzymatic activity was tested using BAEE as a substrate, with a Michaelis constant (KM) of 0.88 …

Durable Oxyfluoride Waste Forms For Salt Wastes From Molten Salt Reactors, Alevtina A. Maksimova, Jake W. Amoroso, Matthew Page, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Molten salt reactors (MSRs) are promising technology to replace traditional light and heavy water reactors in the near future. Waste management for MSRs, however, remains a pressing concern that needs to be resolved prior to realizing deployment of MSRs. Specifically, the generated salt waste needs to be safely sequestered, a task made difficult by the high solubility of the salt waste that can cause the release of radionuclides into the environment. This work demonstrates a new approach to immobilize multiple fluoride salts into a single waste form by converting highly-soluble fluorides to durable and stable oxyfluorides. Notably, we report a …

Optimization Of Small-Scale Bioreactors For Increased Pdna Production And Yield, Laura M. Hills

Honors Theses and Capstones

No abstract provided.

The Relevance Of Dnajb1 Protein Dimerization Against The Human Neurodegenerative Diseases, Erina Kotreli, Trang Le, Szymon Ciesielski

Dean's Leadership Council Library Research Prize

All biological functions in living organisms depend on the activity of proteins, long molecules that must twist and fold into specific shapes to become functional. A subset of proteins known as molecular chaperones is essential for maintaining cellular health by assisting other proteins in folding correctly and refolding those damaged by stress. When proteins misfold and clump together, they can form toxic aggregates linked to many neurodegenerative diseases, including Alzheimer’s disease (AD), one of the leading causes of death in the United States. In AD, these protein aggregates form organized, elongated structures referred to as amyloid-like fibrils, which damage neurons …

Functional Characterization Of Vago In Black Tiger Shrimp Penaeus Monodon Ikk-Nf-Κb Signaling Pathway Against Viral Infection, Zittipong Nanakorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cytokines serve as key regulators in innate antiviral defense. In crustaceans, research on cytokine-mediated immunity remains limited. A previous study in Penaeus monodon has demonstrated that PmVago proteins exhibit cytokine-like function by acting through the inhibitor of kappa B kinase-nuclear factor κB (IKK-NF-κB) cascade to defend against white spot syndrome virus (WSSV). In this study, five PmVago isoforms were identified, each showing differential transcriptional responses to pathogen challenges. Among them, PmVago1 and PmVago4 exhibited strong antiviral responses against WSSV infection. RNA interference of PmVago1 and PmVago4 increased shrimp susceptibility to WSSV infection with enhanced viral replication. Their suppression also disrupted …

Electrochemical Detection Of Prostate Cancer—Associated Mirna-141 Using A Low-Cost Disposable Biosensor, Alexander Hunt, Gymama Slaughter

Center for Bioelectronics Publications

Prostate cancer is the second leading cause of cancer-related deaths among men in the United States. The early detection of aggressive forms is critical. Current diagnostic methods, including PSA testing and biopsies, are invasive and often yield false results. MicroRNA-141 (miRNA-141) has emerged as a promising non-invasive biomarker due to its elevated levels in the urine of patients with metastatic prostate cancer. Here, a low-cost, paper-based electrochemical biosensor for the sensitive detection of miRNA-141 in synthetic urine is reported. The device employs inkjet-printed gold electrodes on photopaper, functionalized with thiolated single-stranded DNA-141 capture probes for specific target recognition. The biosensor …

Characterization Of The Erv41-Erv46 Complex As A Retrograde Receptor For Misfolded Secretory Proteins, John Andrew Fuesler

Dartmouth College Ph.D Dissertations

The Endoplasmic Reticulum (ER), the site of secretory protein biosynthesis

provides a favorable environment to promote polypeptide folding, protein

oligomerization and export. Although the ER contains many chaperones and other

factors that assist in protein folding, this process is error prone. Eukaryotes have

evolved protein quality control checkpoints to maintain homeostasis in the secretory

pathway, however these processes are imperfect and may result in proteotoxicity

when toxic levels or aggregates of proteins arise. Mutations in proteins involved in

trafficking in the early secretory pathway are closely associated with disease states.

Therefore, it is of great interest to further understand how …

Investigating The Lyoprotective Properties Of An Antifreeze Protein From A Broadleaf Desert Shrub, Alexzandria Sheppard

Honors Theses and Capstones

Lyophilization, or freeze-drying, is an important preservation method for protein-based products, such as protein pharmaceuticals. However, the process introduces both freezing and drying stresses that can harm proteins. Here, we have studied the efficacy of AnAFP, a dehydrin-like antifreeze protein isolated from the broadleaf desert shrub Ammopiptanthus nanus, in reducing enzyme damage during freeze-drying, or lyophilization. We have shown that AnAFP can protect the model enzyme lactate dehydrogenase (LDH) from both freezing and dehydration damages during lyophilization with similar or better efficacy than 10% w/v sucrose and superior to that of another known antifreeze protein.

Site-Specific Modification Of Antibodies Utilizing Microbial Transglutaminase For Improved Immunoassay Performance, Emily Beitello

Theses and Dissertations

Immobilization strategies used for fixing antibodies to solid phase surfaces significantly contribute to the antigen capture capacity and influences the performance and sensitivity of immunoassays. Traditional methodologies result in the random orientation and/or the weak attachment of immobilized antibodies. Different formats of immunoassays scope in applicability to many fields of research and everyday use. Improving the efficiency of immobilizing antibodies in immunoassays is a beneficial endeavor to increase assay sensitivity. Here, we investigated the use of enzyme-mediated conjugation of antibodies to facilitate a highly oriented immobilization. Microbial transglutaminase (mTG) catalyzes the covalent bond formation between a plethora of primary amine …

Open Path Spectroscopic Detection Of The Hydroxyl Radical: A Comparison Between Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) And Bbceas Coupled With A Fabry-Pérot Interferometer (Bbceas-Fp), Callum Flowerday, Ryan Thalman, Matthew C. Asplund, Samuel A. Badstubner, Adam K. Cook, Philip Lundrigan, Jaron C. Hansen

ScholarsArchive Data

Data collected by the BBCEAS and BBCEAS-FP instruments described in the paper "Open Path Spectroscopic Detection of the Hydroxyl Radical: A Comparison Between Broadband Cavity-Enhanced Absorption Spectroscopy (BBCEAS) and BBCEAS coupled with a Fabry-Pérot Interferometer (BBCEAS-FP)"