Biochemistry, Biophysics, and Structural Biology Commons^™

Investigating Neurite Outgrowth Influenced By Breast Cancer Progression Using In Vitro Models Of Collagen I Hydrogels, Emma Waskom '27, Nikolas Ala-Kokko, Younghye Song

Annual Student Research Poster Session

Through the use of vitro modeling of tumor progression, using collagen I hydrogels and progressing cell lines, a demonstration of the interactions between breast cancer cells and nerve cells can be investigated. With these models, our goal is to compare the measurement of outgrowth of nerve cells through the use of supplemented NGF and co cultures of breast cancer cells. Human MCF-CA1a.cl1, -AneoT, and -10A, adipose-derived stem cells (ASCs), and rat PC-12 cells, were all passaged from 2D cultures and cultured in a collagen I hydrogen at a cell density of 250,000 cells/ml of media. Collagen hydrogels were then made …

Knockdown Of Ketohexokinase Versus Inhibition Of Its Kinase Activity Exert Divergent Effects On Fructose Metabolism, Se-Hyung Park, Taghreed Fadhul, Lindsey R. Conroy, Harrison A. Clarke, Ramon Sun, Kristina Wallenius, Jeremie Boucher, Gavin O'Mahony, Alessandro Boianelli, Marie Persson, Sunhee Jung, Cholsoon Jang, Analia S. Loria, Genesee J. Martinez, Zachary A. Kipp, Evelyn A. Bates, Terry D. Hinds Jr., Senad Divanovic, Samir Softic

Markey Cancer Center Faculty Publications

Excessive fructose intake is a risk factor for the development of obesity and its complications. Targeting ketohexokinase (KHK), the first enzyme of fructose metabolism, has been investigated for the management of metabolic dysfunction–associated steatotic liver disease (MASLD). We compared the effects of systemic, small molecule inhibitor of KHK enzymatic activity with hepatocyte-specific, N-acetylgalactosamine siRNA–mediated knockdown of KHK in mice on an HFD. We measured KHK enzymatic activity, extensively quantified glycogen accumulation, performed RNA-Seq analysis, and enumerated hepatic metabolites using mass spectrometry. Both KHK siRNA and KHK inhibitor led to an improvement in liver steatosis; however, via substantially different mechanisms, KHK …

Predicting The Pathway Involvement Of All Pathway And Associated Compound Entries Defined In The Kyoto Encyclopedia Of Genes And Genomes, Erik D. Huckvale, Hunter Moseley

Markey Cancer Center Faculty Publications

Background/Objectives: Predicting the biochemical pathway involvement of a compound could facilitate the interpretation of biological and biomedical research. Prior prediction approaches have largely focused on metabolism, training machine learning models to solely predict based on metabolic pathways. However, there are many other types of pathways in cells and organisms that are of interest to biologists. Methods: While several publications have made use of the metabolites and metabolic pathways available in the Kyoto Encyclopedia of Genes and Genomes (KEGG), we downloaded all the compound entries with pathway annotations available in the KEGG. From these data, we constructed a dataset where each …

Upregulation Of Fatty Acid Synthase Increases Activity Of Β-Catenin And Expression Of Notum To Enhance Stem-Like Properties Of Colorectal Cancer Cells, Courtney O. Kelson, Josiane Weber Tessmann, Mariah E. Geisen, Daheng He, Chi Wang, Tianyan Gao, B. Mark Evers, Yekaterina Y. Zaytseva

Markey Cancer Center Faculty Publications

Dysregulated fatty acid metabolism is an attractive therapeutic target for colorectal cancer (CRC). We previously reported that fatty acid synthase (FASN), a key enzyme of de novo synthesis, promotes the initiation and progression of CRC. However, the mechanisms of how upregulation of FASN promotes the initiation and progression of CRC are not completely understood. Here, using Apc/VillinCre and ApcMin mouse models, we show that upregulation of FASN is associated with an increase in activity of β-catenin and expression of multiple stem cell markers, including Notum. Genetic and pharmacological downregulation of FASN in mouse adenoma organoids decreases the activation of β-catenin …

Design And Cohort Characteristics Of Track, A Prospective Study Of Hyperkalaemia Management Decision-Making, Judith Hsia, Nitin Shivappa, Ameet Bakhai, Jordi Bover, Javed Butler, Pietro Manuel Ferraro, Linda Fried, Markus P Schneider, Navdeep Tangri, Wolfgang C Winkelmayer, Meredith Bishop, Hungta Chen, Anna-Karin Sundin, Marc P Bonaca

Faculty, Staff and Students Publications

BACKGROUND: Guideline-recommended hyperkalaemia management includes dietary potassium (K

METHODS: This study enrolled participants within 21 days of an episode of hyperkalaemia in four European countries (UK, Spain, Germany, Italy) and the USA. During the 12-month follow up, data collected will include participant and healthcare provider characteristics (specialty and practice setting), hyperkalaemia treatment objectives and strategies, rationale for management decisions and indicators of response and patient-reported perceptions of their hyperkalaemia treatment.

RESULTS: The enrolled cohort includes 1330 participants, mean age 68 years, of whom 31% were women. At baseline, 6% reported heart failure, 55% chronic kidney disease, 29% both and 9% …

A Method For Rapid And Reliable Quantification Of Vegf-Cell Binding Activity, Prabuddha Waduge, Avinash Kaur, Wei Li

Faculty, Staff and Students Publications

Vascular endothelial growth factor (VEGF) is a pleiotropic growth factor that binds a broad spectrum of cell types and regulates diverse cellular processes, including angiogenesis, growth and survival. However, it is technically difficult to quantify VEGF-cell binding activity because of reversible nature of ligand-receptor interactions. Here we used T7 bacteriophage display to quantify and compare binding activity of three human VEGF-A (hVEGF) isoforms, including hVEGF111, 165 and 206. All three isoforms bound equally well to immobilized aflibercept, a decoy VEGF receptor. hVEGF111-Phage exhibited minimal binding to immobilized heparan sulfate, whereas hVEGF206-Phage and hVEGF165-Phage had the highest and intermediate binding to …

Multivalent Protein-Nucleic Acid Interactions Probed By Composition-Gradient Multiangle Light Scattering, Josephine C Ferreon, Natee Kongchan, Phoebe S Tsoi, Kyoung-Jae Choi, Sophia Kenrick, Joel Neilson, Allan Chris M Ferreon

Faculty, Staff and Students Publications

Many RNA-binding proteins, such as TDP-43 or CELF1, interact multivalently with nucleic acid repetitive elements. The molecular stoichiometry of protein to nucleic acid is often difficult to assess, particularly by standard electrophoretic mobility shift assays (EMSAs). Here, we investigate the use of composition-gradient multiangle light scattering (CG-MALS) for quantifying binding affinity and stoichiometry for two RNA-binding proteins with their nucleic acid partners of varied sequence and length: TDP43's N-terminal RNA recognition motifs with both TG/GU-repeat ssDNA and ssRNA, respectively, and CELF1's two N-terminal RNA recognition motifs with (TG/UGUU/GU) repeats and an experimentally defined cognate GU-rich element (GRE). Our CG-MALS data …

Meta-Analysis Comparing Oral Anticoagulant Monotherapy Versus Dual Antithrombotic Therapy In Patients With Atrial Fibrillation And Stable Coronary Artery Disease, Mushood Ahmed, Areeba Ahsan, Aimen Shafiq, Raheel Ahmed, Mahboob Alam, Pierre Sabouret, Jamal S Rana, Gregg C Fonarow

Faculty, Staff and Students Publications

BACKGROUND: Oral anticoagulants (OACs) are routinely used for the management of atrial fibrillation (AF) while antiplatelet agents are used in coronary artery disease (CAD). However, data regarding the comparative clinical outcomes of OAC monotherapy versus dual antithrombotic therapy (anticoagulant plus antiplatelet agent) in patients with AF and stable CAD are limited.

METHODS: A comprehensive search of major databases including PubMed/MEDLINE, Cochrane Library, and Embase was performed from inception to September 1, 2024 to identify randomized control trials (RCTs) that compared OAC monotherapy with dual antithrombotic therapy in patients with AF and stable CAD. The risk ratios (RRs) were estimated with …

Integrated Safety And Efficacy Analyses Of Phase 3 Trials Of A Microbiome Therapeutic For Recurrent Cdi, Colleen S Kraft, Matthew Sims, Michael Silverman, Thomas J Louie, Paul Feuerstadt, Edward S Huang, Sahil Khanna, Charles S Berenson, Elaine E L Wang, Stuart H Cohen, Louis Korman, Christine Lee, Colleen R Kelly, Alberto Odio, Paul P Cook, Bret Lashner, Mayur Ramesh, Princy Kumar, Ananya De, Asli Memisoglu, David A Lombardi, Brooke R Hasson, Barbara H Mcgovern, Lisa Von Moltke, Darrell S Pardi, Ecospor Iii And Ecospor Iv Investigators

Faculty, Staff and Students Publications

INTRODUCTION: Recurrent Clostridioides difficile infection (rCDI) often occurs after standard-of-care antibiotics. VOWST oral spores (VOS, previously SER-109), an FDA-approved orally administered microbiome therapeutic, is indicated to prevent rCDI following antibiotics for rCDI.

OBJECTIVE, DESIGN, AND PATIENTS: To evaluate safety and efficacy of VOS from two phase 3 trials, (randomized, placebo-controlled [ECOSPOR III: NCT03183128] and open-label, single arm [ECOSPOR IV: NCT03183141]) of 349 adults with rCDI and prevalent comorbidities.

METHODS: VOS or placebo [ECOSPOR III only] (4 capsules once daily for 3 days). Integrated analysis of treatment-emergent adverse events (TEAEs) collected through week 8; serious TEAEs and TEAEs of special interest …

Metabolic Crossroads: Gaba Synthesis In Trichomonas Vaginalis Infection, Yesha Dhruv

Biochemistry and Molecular Biology

This study examines the gamma-aminobutyric acid (GABA) synthesis pathway in Trichomonas vaginalis infection of human HCT-8 cells, focusing on key enzymatic processes in glutamate conversion to GABA and metabolic adaptations. The hypothesis tested was that T. vaginalis modulates GABA metabolism to enhance host cell invasion and adaptation. Infection time-point studies, RNA sequencing, and aldehyde dehydrogenase (ALDH) assays were conducted. Comparisons between T. vaginalis strains Casu 2 and Casu 2/MOZ 2 revealed distinct infection dynamics. Casu 2 rapidly attached and replicated within an hour, peaking at 24 hours, while Casu 2/MOZ 2 exhibited delayed replication, peaking at 48 to 72 hours, …

Effect Of Heat Stress On The Expression Of Circulating Cyto(Chemo)Kine And Inflammatory Markers In Broiler Chickens Selected For High- Or Low-Water Efficiency, Elizabeth S. Greene, Travis Tabler, Walter G. Bottje, Sara Orlowski, Sami Dridi

Poultry Science Faculty Publications and Presentations

Background:

Water scarcity is a current, significant global concern that will only increase under the pressure of climate change. Improving water efficiency of poultry is a new and promising area to help temper agriculture's future impact on fresh water availability. Here, we explored the effects of acute heat stress (HS) on circulating stress and inflammatory markers in 2 lines of broilers divergently selected for water efficiency. Methods:

Male chicks from low (LWE) and high water efficient (HWE) lines were raised in 12 environmental chambers (2 pens/chamber, 6 chambers/line, 20 birds/pen) under normal conditions until day 28. On day 29, birds …

Proteomic Analysis Reveals Major Proteins And Pathways That Mediate The Effect Of 17-Β-Estradiol In Cell Division And Apoptosis In Breast Cancer Mcf7 Cells, Zhenqi Zhou, Brihget Sicairos, Jianhong Zhou, Yuchun Du

Biological Sciences Faculty Publications and Presentations

Despite extensive research, the genes/proteins and pathways responsible for the physiological effects of estrogen remain elusive. In this study, we determined the effect of estrogen on global protein expression in breast cancer MCF7 cells using a proteomic method. The expression of 77 cytosolic, 74 nuclear, and 81 membrane/organelle proteins was significantly altered by 17-β-estradiol (E2). Protein enrichment analyses suggest that E2 may stimulate cell division primarily by promoting the G1 to S phase transition and advancing the G2/M checkpoint. The effect of E2 on cell survival was complex, as it could simultaneously enhance and inhibit apoptosis. Bioinformatics analysis suggests that …

The Anaerobic Rose Chamber (Arc): Novel Applications For Probing Clostridioides Difficile Dynamics, Tatiana Zvonareva

Chemistry & Biochemistry Theses & Dissertations

Clostridioides difficile infection (CDI) is an urgent public health threat with a high rate of recurrence and limited treatment options. Caused by the anaerobic intestinal pathogen C. difficile, this disease affects up to 500,000 Americans annually. Despite progress in our understanding of CDI pathophysiology, the lack of effective and accessible experimental platforms compatible with obligate anaerobe physiology hinders the advancement of treatment therapy. The application of in vivo models has been indispensable in understanding CDI pathophysiology, probing the complexity of the host response to the microbe, and establishing treatment protocols, and it continues to be essential in preclinical testing. …

Intercellular Mitochondrial Transfer Contributes To Microenvironmental Fate Redirection Of Mammary Cancer Cells, Julie Sofie Bjerring

Biomedical Sciences Theses & Dissertations

The dynamic cellular microenvironment, made up of resident cells and various macromolecules, differs markedly across tissues in the body. The multidirectional signals that cells receive from this microenvironment, along with the signaling they send back, heavily influence their physiology and behavior. Recent important findings have further validated this notion as the mammary microenvironment has been shown to suppress tumor progression by redirecting cancer cells to adopt a normal mammary epithelial progenitor fate in vivo. However, the mechanism(s) driving changes in metabolic reprogramming and cancer fate redirection is understudied. The work presented in this dissertation focuses on exploring the impact of …

Accurate Crystal Structure Prediction Of New 2d Hybrid Organic–Inorganic Perovskites, Nima Karimitari, William J. Baldwin, Evan W. Muller, Zachary J.L. Bare, W. Joshua Kennedy, Gábor Csányi, Christopher Sutton

Faculty Publications

Low-dimensional hybrid organic–inorganic perovskites (HOIPs) are promising electronically active materials for light absorption and emission. The design space of HOIPs is extremely large, as a variety of organic cations can be combined with different inorganic frameworks. This not only allows for tunable electronic and mechanical properties but also necessitates the development of new tools for in silico high throughput analysis of candidate materials. In this work, we present an accurate, efficient, and widely applicable machine learning interatomic potential (MLIP) trained on 86 diverse experimentally reported HOIP materials. This MLIP was tested on 73 experimentally reported perovskite compositions and achieves a …

Nanopore Signal Deviations From Pseudouridine Modifications In Rna Are Sequence-Specific: Quantification Requires Dedicated Synthetic Controls, Amr Makhamreh, Sepideh Tavakoli, Ali Fallahi, Xinqi Kang, Howard Gamper, Mohammad Nabizadehmashhadtoroghi, Miten Jain, Ya-Ming Hou, Sara H Rouhanifard, Meni Wanunu

Department of Biochemistry and Molecular Biology Faculty Papers

Chemical modifications to mRNA respond dynamically to environmental cues and are important modulators of gene expression. Nanopore direct RNA sequencing has been applied for assessing the presence of pseudouridine (ψ) modifications through basecalling errors and signal analysis. These approaches strongly depend on the sequence context around the modification, and the occupancies derived from these measurements are not quantitative. In this work, we combine direct RNA sequencing of synthetic RNAs bearing site-specific modifications and supervised machine learning models (ModQuant) to achieve near-analytical, site-specific ψ quantification. Our models demonstrate that the ionic current signal features important for accurate ψ classification are sequence …

Inorganic Pyrophosphate Plasma Levels In Patients With Ggcx-Associated Pxe-Like Phenotypes, Qiaoli Li, Catherine Troutman, Mary Peckiconis, Tamara Wurst, Sharon Terry

Department of Biochemistry and Molecular Biology Faculty Papers

ntroduction: Pseudoxanthoma elasticum (PXE) is an autosomal recessive ectopic calcification disorder clinically affecting the skin, eyes, and vascular system. Most cases of PXE are caused by inactivating pathogenic variants in the ABCC6 gene encoding a hepatic transmembrane efflux transporter, which facilitates the extracellular release of ATP, the precursor of inorganic pyrophosphate (PPi), a potent endogenous inhibitor of calcification. Pathogenic variants in GGCX, encoding γ-glutamyl carboxylase required for activation of vitamin K-dependent coagulation factors as well as matrix Gla protein (MGP) and Gla-rich protein (GRP), two inhibitors of ectopic calcification, have also been reported to cause cutaneous changes like those seen …

Characterizing Biomolecular Structure Features Through An Innovative Elliptical Dichroism Spectrometry For Cancer Detection, Yusuf Asad, Keerthi Priya Jangili, Amara Arshad, Maliha Elma, Komila Rasuleva, Alfred Akinlalu, Tommy Gao, Umamaheswara Rao Tida, Wenjie Xia, Dali Sun

Electrical and Computer Engineering: Faculty Scholarship

This research introduces a novel method for evaluating the structural features of biomolecules, utilizing our innovative Elliptical Dichroism (ED) spectrometer specifically designed for stereochemical analysis. By integrating ED spectrometry with autocorrelation (AC) analysis, we investigate the conformational characteristics of biological molecules such as amino acids, proteins, and extracellular vesicles (EVs) induced by elliptically polarized UV absorption. Our streamlined approach offers a cost-effective and portable solution with minimal sample consumption and supports multiple working modes to efficiently characterize biomolecular structures. The insight from this new approach demonstrates potential applications in using biomolecular characterization for cancer detection.

Effects Of Microplastic Biofilms On An Anthropogenically Impacted Suburban Lake, Paris M. Velasquez

Masters Theses

Plastics have been observed in every location on the planet, and their prevalence in the environment is due in part to their strong resistance to degradation. Inland lakes are susceptible to plastic pollution by highway runoff, which contains plastic fragments of brake pads, car tires, litter, and road paint. These plastics eventually enter freshwater environments and degrade into microplastics (

The C-Terminal 4cxxc-Type Zinc Finger Domain Of Cdca7 Recognizes Hemimethylated Dna And Modulates Activities Of Chromatin Remodeling Enzyme Hells, Akeo Shinkai, Hideharu Hashimoto, Chikako Shimura, Hiroaki Fujimoto, Kei Fukuda, Naoki Horikoshi, Masaki Okano, Hitoshi Niwa, Erik W Debler, Hitoshi Kurumizaka, Yoichi Shinkai

Department of Biochemistry and Molecular Biology Faculty Papers

The chromatin-remodeling enzyme helicase lymphoid-specific (HELLS) interacts with cell division cycle-associated 7 (CDCA7) on nucleosomes and is involved in the regulation of DNA methylation in higher organisms. Mutations in these genes cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, which also results in DNA hypomethylation of satellite repeat regions. We investigated the functional domains of human CDCA7 in HELLS using several mutant CDCA7 proteins. The central region is critical for binding to HELLS, activation of ATPase, and nucleosome sliding activities of HELLS-CDCA7. The N-terminal region tends to inhibit ATPase activity. The C-terminal 4CXXC-type zinc finger domain contributes to CpG …

Predicting Mutation-Induced Allosteric Changes In Structures And Conformational Ensembles Of The Abl Kinase Using Alphafold2 Adaptations With Alanine Sequence Scanning, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Despite the success of AlphaFold2 approaches in predicting single protein structures, these methods showed intrinsic limitations in predicting multiple functional conformations of allosteric proteins and have been challenged to accurately capture the effects of single point mutations that induced significant structural changes. We examined several implementations of AlphaFold2 methods to predict conformational ensembles for state-switching mutants of the ABL kinase. The results revealed that a combination of randomized alanine sequence masking with shallow multiple sequence alignment subsampling can significantly expand the conformational diversity of the predicted structural ensembles and capture shifts in populations of the active and inactive ABL states. …

A Preliminary Fuzzy Inference System For Predicting Atmospheric Ozone In An Intermountain Basin, John R. Lawson, Seth N. Lyman

Mathematics and Statistics Faculty Publications

High concentrations of ozone in the Uinta Basin, Utah, can occur after sufficient snowfall and a strong atmospheric anticyclone creates a persistent cold pool that traps emissions from oil and gas operations, where sustained photolysis of the precursors builds ozone to unhealthy concentrations. The basin's winter-ozone system is well understood by domain experts and supported by archives of atmospheric observations. Rules of the system can be formulated in natural language ("sufficient snowfall and high pressure leads to high ozone"), lending itself to analysis with a fuzzy-logic inference system. This method encodes human expertise as machine intelligence in a more prescribed …

Vglut2-Based Glutamatergic Signaling In Central Noradrenergic Neurons Is Dispensable For Normal Breathing And Chemosensory Reflexes, Yuan Chang, Savannah Lusk, Andersen Chang, Christopher S Ward, Russell S Ray

Faculty, Staff and Students Publications

Central noradrenergic (NA) neurons are key constituents of the respiratory homeostatic network. NA dysfunction is implicated in several developmental respiratory disorders including Congenital Central Hyperventilation Syndrome (CCHS), Sudden Infant Death Syndrome (SIDS), and Rett Syndrome. The current unchallenged paradigm in the field, supported by multiple studies, is that glutamate co-transmission in subsets of central NA neurons plays a role in breathing control. If true, NA-glutamate co-transmission may also be mechanistically important in respiratory disorders. However, the requirement of NA-derived glutamate in breathing has not been directly tested and the extent of glutamate co-transmission in the central NA system remains uncharacterized. …

Exploring Biosignatures And Biogeochemical Processes In Lanzarote Lava Tubes: Implications For Martian Analog Research, Vera Palma, Ana Z. Miller, Francesco Sauro, Bogdan P. Onac, José M. De La Rosa, Sara Gutiérrez-Patricio, Beatriz Cubero, José A. Gonzalez-Perez, Jesus Martínez-Frías, A Teresa Caldeira

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Exploring Pristine Microbial Ecosystems From The Uninhabited Volcanic Selvagens Islands, Pedro N. Jiménez-Morillo, Sara Gutiérrez-Patricio, Vera Palma, Ana Teresa Caldeira, Nicasio Tomás Jiménez-Morillo, Ana Z. Miller

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Investigating Therapeutic Activity Of Br-Ormeloxifene (Br-Orm) Against Cervical Cancer, Mohammed Sikander, Shabnam Malik, John Apraku, Sonam Kumari, Parvez Khan, Daniel Zubieta, Hassan Mandil, Aditya Ganju, Bhavin Chauhan, Maria C. Bell, Man Mohan Singh, Sheema Khan, Murali Yallapu, Fathi T. Halaweish, Meena Jaggi, Subhash Chauhan

Research Colloquium

Aberrant activation of β-catenin signaling is strongly associated with cancer proliferation, invasion, migration, and metastasis, thus small molecules that can inhibit this pathway might have great clinical significance. Our molecular modeling studies suggest that Ormeloxifene (ORM), a triphenylethylene molecule docks with β-catenin, and its brominated analogue (Br-ORM) bind more effectively with relatively less energy (-7.6 kcal/mol) to the active site of β-catenin as compared to parent ORM. Herein, we report the synthesis and characterization of a Br-ORM by NMR and FTIR, as well as its anti-cancer potential in cervical cancer models in vitro and in vivo. Br-ORM treatment effectively …

Dissecting The Interplay Of Protein Synthesis And Degradation Pathways In Cellular Adaptation To Stress, Brittany Friedson

Theses and Dissertations

Adaptation to stress requires cells to reprogram transcription, translation, and proteolytic pathways. Although much is known about the response of each program, it remains unclear how they coordinate following stress. My studies in S. cerevisiae identified the Cdk8 kinase module (CKM) of the Mediator complex as a new player in coordinating these processes. It is well established that the CKM consists of four highly conserved proteins (cyclin C, its cognate kinase Cdk8, and two structural proteins Med12 and Med13) and predominantly represses a subset of stress responsive genes in yeast. We demonstrated for the first time that the CKM also …

Non-Redundant Roles For The Human Mrna Decapping Cofactor Paralogs Dcp1a And Dcp1b, Ivana Vukovic, Samantha M. Barnada, Jonathan W. Ruffin, Jon Karlin, Ravi Kumar Lokareddy, Gino Cingolani, Steven B. Mcmahon

Department of Medicine Faculty Papers

Eukaryotic gene expression is regulated at the transcriptional and post-transcriptional levels, with disruption of regulation contributing significantly to human diseases. The 5' m7G mRNA cap is a central node in post-transcriptional regulation, participating in both mRNA stabilization and translation efficiency. In mammals, DCP1a and DCP1b are paralogous cofactor proteins of the mRNA cap hydrolase DCP2. As lower eukaryotes have a single DCP1 cofactor, the functional advantages gained by this evolutionary divergence remain unclear. We report the first functional dissection of DCP1a and DCP1b, demonstrating that they are non-redundant cofactors of DCP2 with unique roles in decapping complex integrity and specificity. …

Engineered Nls-Chimera Downregulates Expression Of Aggregation-Prone Endogenous Fus, Miyuki Hayashi, Amandeep Girdhar, Ying-Hui Ko, Kevin Kim, Jacquelyn Depierro, Joseph R. Buchler, Nikhita Arunprakash, Aditya Bajaj, Gino Cingolani, Lin Guo

Department of Biochemistry and Molecular Biology Faculty Papers

Importin β-superfamily nuclear import receptors (NIRs) mitigate mislocalization and aggregation of RNA-binding proteins (RBPs), like FUS and TDP-43, which are implicated in neurodegenerative diseases. NIRs potently disaggregate RBPs by recognizing their nuclear localization signal (NLS). However, disease-causing mutations in NLS compromise NIR binding and activity. Here, we define features that characterize the anti-aggregation activity of NIR and NLS. We find that high binding affinity between NIR and NLS, and optimal NLS location relative to the aggregating domain plays a role in determining NIR disaggregation activity. A designed FUS chimera (FUS_IBB), carrying the importin β binding (IBB) domain, is …

Malat1 Mediates Tet2 Loss Of Function-Driven Oncogenic Inflammation Via Rna Shielding Of Nf- Kappa B P65, Nana Adjoa Ben-Crentsil

USF Tampa Graduate Theses and Dissertations

TET2 is a dioxygenase that regulates gene expression and hematopoiesis by oxidizing 5-methylcytosine residues on DNA to 5-hydroxymethylcytosine. TET2 mutations are common genetic events in hematological disorders. For example, TET2 is the most frequently mutated gene in Chronic Myelomonocytic Leukemia and occurs in about 33% of other myeloid malignancies. It is also the second commonest mutation in clonal hematopoiesis of indeterminate potential (CHIP), a common premalignant condition in the elderly. TET2 mutations arise in founding clones and are implicated in many non-hematological sequelae seen in CHIP like atherosclerotic disease, chronic liver disease, and severe microbial infections.

The development of TET2-deficient …