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Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli, Carson Ercanbrack 2021 University of Arkansas, Fayetteville

Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli, Carson Ercanbrack

Chemistry & Biochemistry Undergraduate Honors Theses

The primary purpose of this project is to evaluate the genes that play a role in the oxidative stress response in Escherichia coli. In doing so, the entire genome of E. coli was subject to throughput in which individual genes were determined to have a role in the bacteria’s oxidative stress response. Moreover, this project focused on the validation of the genes that were able to pass the initial throughput stage. The genes were subject to two forms of validation. In the first validation technique, candidate genes were overexpressed and minimum inhibitory concentrations of hypochlorous acid were taken. Following ...


Using Crispr-Cas9 To Characterize The Role Of Gli-Similar 3 (Glis3) In Insulin Regulation, Pancreatic Development, And Type 2 Diabetes, LilyAnne Grieve 2021 Murray State University

Using Crispr-Cas9 To Characterize The Role Of Gli-Similar 3 (Glis3) In Insulin Regulation, Pancreatic Development, And Type 2 Diabetes, Lilyanne Grieve

Honors College Theses

The prevalence of type 2 diabetes continues to rise nationally and internationally, impacting millions of people worldwide. Type 2 diabetes results from insulin resistance leading to chronic hyperinsulinemia and dysfunction of the insulin producing β cells of the pancreas. While environmental factors can influence the development of type 2 diabetes, research has shown genetics are also involved. Gli-similar 3 (Glis3), a Krüppel-like zinc finger transcription factor, has been identified as a novel regulator of insulin transcription. Evidence has shown that loss-of-function Glis3 mutations decrease insulin expression, implicating Glis3 in the development of type 2 diabetes. However, the distinct role Glis3 ...


Analyzing The Impacts Of Loss Of The Fanca Protein On Chromatin State, Mileena Nguyen 2021 University of Rhode Island

Analyzing The Impacts Of Loss Of The Fanca Protein On Chromatin State, Mileena Nguyen

Senior Honors Projects

No abstract provided.


Interrogating The Functions Of The Histone H2a Repression Domain In Relation To Cell-Cycle Progression In Saccharomyces Cerevisiae, Taylor Nattress 2021 Susquehanna University

Interrogating The Functions Of The Histone H2a Repression Domain In Relation To Cell-Cycle Progression In Saccharomyces Cerevisiae, Taylor Nattress

Senior Scholars Day

In eukaryotic cells, DNA is wrapped around histone proteins to form the basic repeating unit of chromatin, the nucleosome core particle. Most nucleosomes consist of two copies each of histones: H2A and H2B in a heterodimer and histones H3 and H4 in a heterotetramer. Because of their intimate association with DNA, histones regulate all DNA-templated processes such as transcription, DNA replication, and DNA damage response and repair. Several studies have illustrated the importance of a small portion of the histone H2A amino terminal domain which regulates global transcription. This domain is responsible for the repression of ~4% of the yeast ...


The Analysis Of Folate-Dependent Transcription Factor Zinc Finger Protein 410, Feifan Xu 2021 Liberty University

The Analysis Of Folate-Dependent Transcription Factor Zinc Finger Protein 410, Feifan Xu

Senior Honors Theses

A previous study that introduced dietary folate to mice in the form of folic acid to determine if gene activity would be altered based on this biological molecule demonstrated that mice without folic acid had cognition deficits, and this phenomenon was correlated with altered gene expression in their brains. The included bioinformatic analysis revealed two main transcription factors that bind to proteins in the nucleus, and one is known as the Zinc Finger Protein 410 (Zfp410). Due to the lack of literature explaining the function of this transcription factor, this project is intended to analyze Zfp410 in detail from scratch ...


The Effect Of Cadmium On Ovarian Adenocarcinoma Cell Lines: An Investigation Of The Possible Mechanism Of Action, Haley Todd 2021 Bellarmine University

The Effect Of Cadmium On Ovarian Adenocarcinoma Cell Lines: An Investigation Of The Possible Mechanism Of Action, Haley Todd

Undergraduate Theses

Cadmium, a heavy metal and carcinogen, is an environmental and workplace contaminate. As a known endocrine disruptor, it can mimic the proliferative effects of estrogen and is classified as a metalloestrogen. While the proliferative effect of estrogen on cancerous cell growth has been well established, the effects of cadmium have not been fully examined. To determine if cadmium stimulates growth in two human ovarian adenocarcinoma cell lines, OVCAR3 and SKOV3, cells were treated for 48 hours with varying concentrations of cadmium, 0.001 µM – 10 µM, and growth was measured using a cell proliferation assay. Both cell lines showed a ...


Mediation Of The Uncoupled Enos Pathway Following Oxidative Stress Using Tetrahydrobiopterin And Nitric Oxide Donor Drugs To Restore Tetrahydrobiopterin Concentration, Brianna Munnich 2021 Olivet Nazarene University

Mediation Of The Uncoupled Enos Pathway Following Oxidative Stress Using Tetrahydrobiopterin And Nitric Oxide Donor Drugs To Restore Tetrahydrobiopterin Concentration, Brianna Munnich

Scholar Week 2016 - present

Presentation Location: Warming House, Olivet Nazarene University

Abstract

The eNOS pathway, found in the endothelium of blood vessels, is a key regulator of nitric oxide levels in the circulatory system. The pathway is controlled through several positive and negative feedback loops [2]. The cofactor tetrahydrobiopterin (BH4) is a major control point in this pathway and under conditions of stress can be reduced into the dihydrobiopterin (BH2) [2,6,7,8,9]. When the reduced form is predominant, the pathway produces reactive oxygen species (ROS) rather than nitric oxide, causing stress and damage to the vessels [6,7,8,9]. In ...


Coilin Expression During Nucleolar Stress In The Drosophila Brain, Kathryn Rose DeLeo 2021 Louisiana State University

Coilin Expression During Nucleolar Stress In The Drosophila Brain, Kathryn Rose Deleo

LSU Master's Theses

Impairment of ribosome biogenesis disrupts cellular homeostasis and, in the process, causes a state of nucleolar stress in a cell. This triggers human syndromes collectively known as ribosomopathies. One such ribosomopathy is the Treacher Collins syndrome (TCS) which causes congenital craniofacial birth defects and hearing loss in patients. In TCS migration of neural crest cells during development is hindered by the loss of the ribosome assembly factor, treacle, and consequent apoptosis of these progenitor cells. Modeling this disorder in Drosophila was previously accomplished by disruption of Nopp140, treacle’s closest equivalent in Drosophila. During nucleolar stress, the Mushroom Body neuroblast ...


Toward The Discovery Of Biological Functions Associated With The Mechanosensor Mtl1p Of Saccharomyces Cerevisiae Via Integrative Multi-Omics Analysis, Nelson Martínez-Matías, Nataliya Chorna, Sahily González-Crespo, Lilliam Villanueva, Ingrid Montes-Rodríguez, Loyda M. Melendez-Aponte, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ednalise Santiago-Cartagena, Brian C. Rymond, Mohan Babu, Igor Stagljar, José R. Rodríguez-Medina 2021 University of Puerto Rico

Toward The Discovery Of Biological Functions Associated With The Mechanosensor Mtl1p Of Saccharomyces Cerevisiae Via Integrative Multi-Omics Analysis, Nelson Martínez-Matías, Nataliya Chorna, Sahily González-Crespo, Lilliam Villanueva, Ingrid Montes-Rodríguez, Loyda M. Melendez-Aponte, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ednalise Santiago-Cartagena, Brian C. Rymond, Mohan Babu, Igor Stagljar, José R. Rodríguez-Medina

Biology Faculty Publications

Functional analysis of the Mtl1 protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI). We observed upregulation of multiple heat shock proteins (HSPs), proteins associated with the formation of stress granules, and the phosphatase subunit of trehalose 6-phosphate synthase which suggests that mtl1Δ strains undergo intrinsic activation of a non-lethal heat stress response. Furthermore, quantitative global proteomic analysis conducted on TMT-labeled proteins combined with metabolome analysis revealed that mtl1Δ strains exhibit decreased levels of metabolites of carboxylic acid metabolism, decreased ...


Analysis Of Student Learning Gains In A Biochemistry Cure Course During The Mandatory Covid-19 Shift To Online Learning, Ambika Kapil, Santanu De, Arthur Sikora 2021 Nova Southeastern University

Analysis Of Student Learning Gains In A Biochemistry Cure Course During The Mandatory Covid-19 Shift To Online Learning, Ambika Kapil, Santanu De, Arthur Sikora

Biology Faculty Proceedings, Presentations, Speeches, Lectures

Due to the ongoing COVID-19 pandemic, institutions across the world have had to make modifications to existing curricula, especially in the experimental science lab. There is a need to better understand student learning in this environment. Using the Participant Perception Indicator (PPI) survey, we measure the students’ knowledge, experience, and confidence (KEC) growth over the course of a fully online biochemistry course. Using a combination of video explanations, experimental procedure documents and sample data students completed the Biochemistry Authentic Scientific Inquiry Lab (BASIL) Course-based Undergraduate Experience (CURE) in summer 2020. The results and analysis of the survey data gave light ...


Cyclophilin D Is A Sensor Of Nano-Pulse Stimulation, Brittney Ruedlinger, Bani Hani Maisoun, Lucas Potter, Nicola Lai, Stephen J. Beebe 2021 Old Dominion University

Cyclophilin D Is A Sensor Of Nano-Pulse Stimulation, Brittney Ruedlinger, Bani Hani Maisoun, Lucas Potter, Nicola Lai, Stephen J. Beebe

The Graduate School Posters

Nano-Pulse Stimulation (NPS), a pulsed power-derived technology, stimulates structural and functional changes in plasma membranes and cellular organelles. NPS induces a Ca2+ influx and opening of the mitochondrial permeability transition pore (mPTP) that dissipates the mitochondrial membrane potential (ΔΨm) and, when sustained, induces regulated cell death. Here we show that in rat cardiomyoblasts (H9C2) cyclophilin D (CypD) is a mitochondrial sensor for NPS as defined by observations that loss of ΔΨm is Ca2+ and mitochondrial reactive oxygen species (mROS) dependent and cyclosporin A (CsA)-sensitive, which are diagnostic qualities for effects on CypD and the mPTP ...


A Comparison Of Intertidal Metazoan Biodiversity Between Previously Oiled Sheared And Intact Marsh Margins And Between Multiple Salinity Zones In The Coastal Marshes Of Louisiana, Patrick M. Rayle 2021 Louisiana State University and Agricultural and Mechanical College

A Comparison Of Intertidal Metazoan Biodiversity Between Previously Oiled Sheared And Intact Marsh Margins And Between Multiple Salinity Zones In The Coastal Marshes Of Louisiana, Patrick M. Rayle

LSU Master's Theses

Marshes in Louisiana are under threat from numerous natural and anthropogenic sources. A consequence of these threats are sheared marsh margins, which result from the impact of storm surge on previously oiled, weakened marsh. These conditions occurred in Louisiana marshes after Hurricane Isaac in 2012 followed the Deepwater Horizon oil spill in 2010, particularly in the shorelines surrounding Bay Jimmy. The second and third chapters of this thesis focus on the differences in biodiversity between the sheared and intact marsh margins in impacted sites in Bay Jimmy. Metabarcoding methods were used to determine community composition of the sediment within marsh ...


Lung Epithelial Cell Transcriptional Regulation As A Factor In Covid-19 Associated Coagulopathies, Ethan S. FitzGerald, Yongzhi Chen, Katherine A. Fitzgerald, Amanda M. Jamieson 2021 Brown University

Lung Epithelial Cell Transcriptional Regulation As A Factor In Covid-19 Associated Coagulopathies, Ethan S. Fitzgerald, Yongzhi Chen, Katherine A. Fitzgerald, Amanda M. Jamieson

COVID-19 Publications by UMMS Authors

SARS-CoV-2 has rapidly become a global pandemic. In addition to the acute pulmonary symptoms of COVID-19 (the disease associated with SARS-CoV-2 infection), pulmonary and distal coagulopathies have caused morbidity and mortality in many patients. Currently, the molecular pathogenesis underlying COVID-19 associated coagulopathies are unknown. Identifying the molecular basis of how SARS-CoV-2 drives coagulation is essential to mitigating short and long term thrombotic risks of sick and recovered COVID-19 patients. We aimed to perform coagulation focused transcriptome analysis of in vitro infected primary respiratory epithelial cells, patient derived bronchial alveolar lavage (BALF) cells, and circulating immune cells during SARS-CoV-2 infection. Our ...


Swi/Snf Senses Carbon Starvation With A Ph-Sensitive Low Complexity Sequence [Preprint], J. Ignacio Gutiérrez, Gregory P. Brittingham, Yonca Karadeniz, Kathleen D. Tran, Arnob Dutta, Alex S. Holehouse, Craig L. Peterson, Liam J. Holt 2021 University of California - Berkeley

Swi/Snf Senses Carbon Starvation With A Ph-Sensitive Low Complexity Sequence [Preprint], J. Ignacio Gutiérrez, Gregory P. Brittingham, Yonca Karadeniz, Kathleen D. Tran, Arnob Dutta, Alex S. Holehouse, Craig L. Peterson, Liam J. Holt

University of Massachusetts Medical School Faculty Publications

It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in S. cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. We found that a glutamine-rich low complexity sequence (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, were required for efficient transcriptional reprogramming during carbon starvation. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to a model promoter in vitro ...


Relaxed Tarantula Skeletal Muscle Has Two Atp Energy-Saving Mechanisms, Weikang Ma, Sebastian Duno-Miranda, Thomas Irving, Roger W. Craig, Raul A. Padron 2021 Illinois Institute of Technology

Relaxed Tarantula Skeletal Muscle Has Two Atp Energy-Saving Mechanisms, Weikang Ma, Sebastian Duno-Miranda, Thomas Irving, Roger W. Craig, Raul A. Padron

Radiology Publications

Myosin molecules in the relaxed thick filaments of striated muscle have a helical arrangement in which the heads of each molecule interact with each other, forming the interacting-heads motif (IHM). In relaxed mammalian skeletal muscle, this helical ordering occurs only at temperatures > 20 degrees C and is disrupted when temperature is decreased. Recent x-ray diffraction studies of live tarantula skeletal muscle have suggested that the two myosin heads of the IHM (blocked heads [BHs] and free heads [FHs]) have very different roles and dynamics during contraction. Here, we explore temperature-induced changes in the BHs and FHs in relaxed tarantula skeletal ...


Yap And Taz Are Transcriptional Co-Activators Of Ap-1 Proteins And Stat3 During Breast Cellular Transformation [Preprint], Lizhi He, Henry E. Pratt, Fengxiang Wei, Mingshi Gao, Zhiping Weng, Kevin Struhl 2021 Harvard Medical School

Yap And Taz Are Transcriptional Co-Activators Of Ap-1 Proteins And Stat3 During Breast Cellular Transformation [Preprint], Lizhi He, Henry E. Pratt, Fengxiang Wei, Mingshi Gao, Zhiping Weng, Kevin Struhl

University of Massachusetts Medical School Faculty Publications

The YAP and TAZ paralogues are transcriptional co-activators recruited to target sites, primarily by TEAD proteins. Here, we show that YAP and TAZ are also recruited by JUNB and STAT3, key factors that mediate an epigenetic switch linking inflammation to cellular transformation. YAP and TAZ directly interact with JUNB and STAT3 via a WW domain important for transformation, co-occupy many target sites in vivo via AP-1 and (to a lesser extent) STAT3 sequence motifs, and stimulate transcriptional activation by AP-1 proteins. A few target sites are YAP- or TAZ-specific, and they are associated with different sequence motifs and gene classes ...


The N Terminus Of Myosin-Binding Protein C Extends Toward Actin Filaments In Intact Cardiac Muscle, Sheema Rahmanseresht, Kyoung H. Lee, Thomas S. O'Leary, James W. McNamara, Sakthivel Sadayappan, Jeffrey Robbins, David M. Warshaw, Roger W. Craig, Michael J. Previs 2021 University of Vermont

The N Terminus Of Myosin-Binding Protein C Extends Toward Actin Filaments In Intact Cardiac Muscle, Sheema Rahmanseresht, Kyoung H. Lee, Thomas S. O'Leary, James W. Mcnamara, Sakthivel Sadayappan, Jeffrey Robbins, David M. Warshaw, Roger W. Craig, Michael J. Previs

Radiology Publications

Myosin and actin filaments are highly organized within muscle sarcomeres. Myosin-binding protein C (MyBP-C) is a flexible, rod-like protein located within the C-zone of the sarcomere. The C-terminal domain of MyBP-C is tethered to the myosin filament backbone, and the N-terminal domains are postulated to interact with actin and/or the myosin head to modulate filament sliding. To define where the N-terminal domains of MyBP-C are localized in the sarcomere of active and relaxed mouse myocardium, the relative positions of the N terminus of MyBP-C and actin were imaged in fixed muscle samples using super-resolution fluorescence microscopy. The resolution of ...


Direct Recruitment Of Eif4gi And/Dap5 To The 5' Utr Of A Subset Of Human Mrna Drives Their Cap-Independent Translation, Solomon A. Haizel 2021 The Graduate Center, City University of New York

Direct Recruitment Of Eif4gi And/Dap5 To The 5' Utr Of A Subset Of Human Mrna Drives Their Cap-Independent Translation, Solomon A. Haizel

Dissertations, Theses, and Capstone Projects

During unfavorable cellular conditions (e.g., tumor hypoxia, viral infection, nutrient deprivation, etc.), the canonical, cap-dependent translation initiation pathway in human cells is suppressed by sequestration of the cap-binding protein, eukaryotic initiation factor(eIF) 4E, by 4E-binding proteins. Circumvention of cap-dependent translation shutdown has been linked to tumor development and cancer progression. The stress-induced repression of cap-dependent translation has also been correlated with increased eIF4GI and its homolog, Death Associated Protein 5 (DAP5) expression levels, suggesting these factors have a role in cap-independent translation. Despite several evidence pointing towards a link upregulation of eIF4GI and /DAP5 levels during stress conditions ...


Separation And Identification Of Permethylated Glycan Isomers By Reversed Phase Nanolc-Nsi-Ms(N), Simone Kurz, M. Osman Sheikh, Shan Lu, Lance Wells, Michael Tiemeyer 2021 University of Georgia

Separation And Identification Of Permethylated Glycan Isomers By Reversed Phase Nanolc-Nsi-Ms(N), Simone Kurz, M. Osman Sheikh, Shan Lu, Lance Wells, Michael Tiemeyer

Open Access Publications by UMMS Authors

High performance liquid chromatography has been employed for decades to enhance detection sensitivity and quantification of complex analytes within biological mixtures. Among these analytes, glycans released from glycoproteins and glycolipids have been characterized as underivatized or fluorescently tagged derivatives by HPLC coupled to various detection methods. These approaches have proven extremely useful for profiling the structural diversity of glycoprotein and glycolipid glycosylation but require the availability of glycan standards and secondary orthogonal degradation strategies to validate structural assignments. A robust method for HPLC separation of glycans as their permethylated derivatives, coupled with in-line MSn fragmentation to assign structural features independent ...


The Adaptive Potential Of The Middle Domain Of Yeast Hsp90, Pamela A. Cote-Hammarlof, Ines Fragata, Julia M. Flynn, David Mavor, Konstantin B. Zeldovich, Claudia Bank, Daniel N. Bolon 2021 University of Massachusetts Medical School

The Adaptive Potential Of The Middle Domain Of Yeast Hsp90, Pamela A. Cote-Hammarlof, Ines Fragata, Julia M. Flynn, David Mavor, Konstantin B. Zeldovich, Claudia Bank, Daniel N. Bolon

Open Access Publications by UMMS Authors

The distribution of fitness effects (DFEs) of new mutations across different environments quantifies the potential for adaptation in a given environment and its cost in others. So far, results regarding the cost of adaptation across environments have been mixed, and most studies have sampled random mutations across different genes. Here, we quantify systematically how costs of adaptation vary along a large stretch of protein sequence by studying the distribution of fitness effects of the same approximately 2,300 amino-acid changing mutations obtained from deep mutational scanning of 119 amino acids in the middle domain of the heat shock protein Hsp90 ...


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