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Primary Cilia-Mediated Ventricular Maturation In Congenital Heart Disease: A Role For Erbb Signaling?, Lindsey A. Fitzsimmons, Sergey Ryzhov, Kerry L. Tucker 2020 Maine Medical Center

Primary Cilia-Mediated Ventricular Maturation In Congenital Heart Disease: A Role For Erbb Signaling?, Lindsey A. Fitzsimmons, Sergey Ryzhov, Kerry L. Tucker

Costas T. Lambrew Research Retreat 2020

The embryonic heart requires a unique, and highly-specialized group of progenitor cells called the cardiac neural crest (CNCC), which are known to contribute specifically to the developing valves, the interventricular septum, and the great vessels of the outflow tract. CNCC display primary cilia, which are tiny, plasma-membrane bound organelles that function to modulate cell signaling mechanisms involved in normal heart development as well as congenital heart disease (CHD). Our laboratory has modeled CNCC-specific ciliary loss, using a Wnt1:Cre-2, Ift88-targeted conditional elimination of primary cilia. Loss of cilia in CNCC of Ift88-homozygous mutants (MUT) was characterized by a variety of ...


A "Choose-Your-Own" Classroom-Based Activity That Promotes Scientific Inquiry About Rna Interference, Jeremy L. Hsu 2019 Chapman University

A "Choose-Your-Own" Classroom-Based Activity That Promotes Scientific Inquiry About Rna Interference, Jeremy L. Hsu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

RNA interference (RNAi), the process that results in the degradation of a target gene’s mRNA, is a fundamental part of eukaryotic gene regulation and is also an important molecular technique that allows for experimental manipulation of gene expression without altering DNA sequences. Despite the importance of RNAi, there have been relatively few lecture-based activities designed to teach about the consequences of this process and counter common misconceptions. I present here an inquiry-based activity that is centered around a “choose your own experiment” design where students generate hypotheses and critically evaluate their ideas by choosing several simulated experiments. The activity ...


#8 - Analysis Of Temporal Gene Expression Of Mycobacteriophage Xianyue, Samantha E. Kates 2019 University of North Georgia

#8 - Analysis Of Temporal Gene Expression Of Mycobacteriophage Xianyue, Samantha E. Kates

Georgia Undergraduate Research Conference (GURC)

Analysis of Temporal Gene Expression of Mycobacteriophage XianYue

Samantha Kates

Abstract

Antibiotic resistance has become a prevalent issue in the 21stcentury. The over-prescription and frequent use of antibiotics have allowed host bacteria to escape the effects of antibiotic therapy. An alternative treatment for bacterial infection is bacteriophage (phage) therapy. Phage are viruses that infect and hijack the genetic machinery of its bacterial host which results in host cell death. Mycobacteriophage XianYue was isolated from a soil sample on the campus of the University of North Georgia. Using its bacterial host Mycobacterium smegmatis, a non-infectious mycobacterium, XianYue’s gene ...


Phylogenetic Estimates Of Hiv-1 Gp120 Indel Rates Across The Group M Subtypes, John Palmer, Art Poon 2019 Western University

Phylogenetic Estimates Of Hiv-1 Gp120 Indel Rates Across The Group M Subtypes, John Palmer, Art Poon

Western Research Forum

Insertions and deletions (indels) in the HIV-1 envelope glycoprotein gp120 play a significant role in the evolution of HIV pathogenesis and transmission fitness. While substitution rates in HIV-1 are well characterized by phylogenetic models, there is a lack of quantitative measures of indel rates in HIV-1. Here we use a dated-tip phylogenetic analysis of gp120 sequences to estimate indel rates for 7 subtypes and CRFs of HIV-1 group M.

We obtained and processed 26,359 HIV-1 gp120 sequences from the Los Alamos National Laboratory HIV Sequence database. After filtering these sequences, we extracted the conserved and variable regions from the ...


Integration Of Random Forest Classifiers And Deep Convolutional Neural Networks For Classification And Biomolecular Modeling Of Cancer Driver Mutations, Steve Agajanian, Odeyemi Oluyemi, Gennady M. Verkhivker 2019 Chapman University

Integration Of Random Forest Classifiers And Deep Convolutional Neural Networks For Classification And Biomolecular Modeling Of Cancer Driver Mutations, Steve Agajanian, Odeyemi Oluyemi, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to ...


Yeast Mitochondrial Protein Pet111p Binds Directly To Two Distinct Targets In Cox2 Mrna, Suggesting A Mechanism Of Translational Activation, Julia L Jones, Katharina B Hofmann, Andrew T Cowan, Dmitry Temiakov, Patrick Cramer, Michael Anikin 2019 Rowan University

Yeast Mitochondrial Protein Pet111p Binds Directly To Two Distinct Targets In Cox2 Mrna, Suggesting A Mechanism Of Translational Activation, Julia L Jones, Katharina B Hofmann, Andrew T Cowan, Dmitry Temiakov, Patrick Cramer, Michael Anikin

School of Osteopathic Medicine Faculty Scholarship

The genes in mitochondrial DNA code for essential subunits of the respiratory chain complexes. In yeast, expression of mitochondrial genes is controlled by a group of gene-specific translational activators encoded in the nucleus. These factors appear to be part of a regulatory system that enables concerted expression of the necessary genes from both nuclear and mitochondrial genomes to produce functional respiratory complexes. Many of the translational activators are believed to act on the 5'-untranslated regions of target mRNAs, but the molecular mechanisms involved in this regulation remain obscure. In this study, we used a combination of in vivo and ...


Transcriptional Influence Of Retinoic Acid And Its Effects On Angiogenesis Of Murine Salivary Glands., Isaac Feinn 2019 University of Louisville

Transcriptional Influence Of Retinoic Acid And Its Effects On Angiogenesis Of Murine Salivary Glands., Isaac Feinn

College of Arts & Sciences Senior Honors Theses

Salivary gland hypofunction is a major disorder of salivary glands, and can arise either from diseases such as xerostomia, or from defective epithelial morphogenesis during embryogenesis. Hundreds of thousands of individuals suffer from dry mouth, and there is currently no restorative therapy for these patients. Investigation of salivary gland developmental biology will inform regenerative therapies. Currently it is known that retinoic acid (RA), the biologically active form of Vitamin A, is required for proper development of the salivary gland, but little is known about its cellular mechanism regulating organogenesis. This study sought to analyze salivary gland development in Rdh10 knock ...


Fluorometholone Modulates Gene Expression Of Ocular Surface Mucins, Jonathan Taniguchi, Ajay Sharma 2019 Chapman University

Fluorometholone Modulates Gene Expression Of Ocular Surface Mucins, Jonathan Taniguchi, Ajay Sharma

Pharmacy Faculty Articles and Research

Purpose

Mucins are vital to keep the ocular surface hydrated. Genes encoding for mucins contain a glucocorticoid response element. The purpose of this study was to evaluate the effect of fluorometholone, a glucocorticoid receptor agonist used in the management of dry eye, on the gene expression of conjunctival and corneal epithelial cell mucins.

Methods

Stratified cultures of human conjunctival and corneal epithelial cells were exposed to 25, 50 and 100 nM of fluorometholone alone or in presence of mifepristone, a glucocorticoid receptor antagonist. The mRNA was isolated from the cells and reverse transcribed to cDNA. The cDNA was used for ...


Does Family Communication Matter? Exploring Knowledge Of Breast Cancer Genetics In Cancer Families, Deborah Himes, Sarah H. Davis, Jane Lassetter PhD, RN, Neil E. Peterson, Margaret F. Clayton, Wendy C. Birmingham, Anita Y. Kinney 2019 Brigham Young University - Provo

Does Family Communication Matter? Exploring Knowledge Of Breast Cancer Genetics In Cancer Families, Deborah Himes, Sarah H. Davis, Jane Lassetter Phd, Rn, Neil E. Peterson, Margaret F. Clayton, Wendy C. Birmingham, Anita Y. Kinney

Faculty Publications

Purpose: Knowledge of breast cancer genetics is critical for those at increased hereditary risk who must make decisions about breast cancer screening options. This descriptive study explored theory-based relationships among cognitive and emotional variables related to knowledge of breast cancer genetics in cancer families. Methods: Participants included first-degree relatives of women with breast cancer who had received genetic counseling and testing. Study participants themselves did not have breast cancer and had not received genetic counseling or testing. Data were collected by telephone interviews and surveys. Variables analyzed included numeracy, health literacy, cancer-related distress, age, education, and the reported amount of ...


Estimating Relationships Between Phenotypes And Subjects Drawn From Admixed Families., Elizabeth M. Blue, Lisa A. Brown, Matthew P. Conomos, Jennifer L. Kirk, Alejandro Q. Nato Jr., Alice B. Popejoy, Jesse Raffa, John Ranola, Ellen M. Wijsman, Timothy Thornton 2019 Marshall University

Estimating Relationships Between Phenotypes And Subjects Drawn From Admixed Families., Elizabeth M. Blue, Lisa A. Brown, Matthew P. Conomos, Jennifer L. Kirk, Alejandro Q. Nato Jr., Alice B. Popejoy, Jesse Raffa, John Ranola, Ellen M. Wijsman, Timothy Thornton

Alejandro Nato

Background: Estimating relationships among subjects in a sample, within family structures or caused by population substructure, is complicated in admixed populations. Inaccurate allele frequencies can bias both kinship estimates and tests for association between subjects and a phenotype. We analyzed the simulated and real family data from Genetic Analysis Workshop 19, and were aware of the simulation model.

Results: We found that kinship estimation is more accurate when marker data include common variants whose frequencies are less variable across populations. Estimates of heritability and association vary with age for longitudinally measured traits. Accounting for local ancestry identified different true associations ...


Identity-By-Descent Estimation With Population- And Pedigree-Based Imputation In Admixed Family Data, Mohamad Saad, Alejandro Q. Nato Jr., Fiona L. Grimson, Steven M. Lewis, Lisa A. Brown, Elizabeth M. Blue, Timothy A. Thornton, Elizabeth A. Thompson, Ellen M. Wijsman 2019 Marshall University

Identity-By-Descent Estimation With Population- And Pedigree-Based Imputation In Admixed Family Data, Mohamad Saad, Alejandro Q. Nato Jr., Fiona L. Grimson, Steven M. Lewis, Lisa A. Brown, Elizabeth M. Blue, Timothy A. Thornton, Elizabeth A. Thompson, Ellen M. Wijsman

Alejandro Nato

Background: In the past few years, imputation approaches have been mainly used in population-based designs of genome-wide association studies, although both family- and population-based imputation methods have been proposed. With the recent surge of family-based designs, family-based imputation has become more important. Imputation methods for both designs are based on identity-by-descent (IBD) information. Apart from imputation, the use of IBD information is also common for several types of genetic analysis, including pedigree-based linkage analysis.

Methods: We compared the performance of several family- and population-based imputation methods in large pedigrees provided by Genetic Analysis Workshop 19 (GAW19). We also evaluated the ...


Mapping Genes With Longitudinal Phenotypes Via Bayesian Posterior Probabilities, Anthony Musolf, Alejandro Q. Nato Jr., Douglas Londono, Lisheng Zhou, Tara C. Matise, Derek Gordon 2019 Marshall University

Mapping Genes With Longitudinal Phenotypes Via Bayesian Posterior Probabilities, Anthony Musolf, Alejandro Q. Nato Jr., Douglas Londono, Lisheng Zhou, Tara C. Matise, Derek Gordon

Alejandro Nato

Most association studies focus on disease risk, with less attention paid to disease progression or severity. These phenotypes require longitudinal data. This paper presents a new method for analyzing longitudinal data to map genes in both population-based and family-based studies. Using simulated systolic blood pressure measurements obtained from Genetic Analysis Workshop 18, we cluster the phenotype data into trajectory subgroups. We then use the Bayesian posterior probability of being in the high subgroup as a quantitative trait in an association analysis with genotype data. This method maintains high power (>80%) in locating genes known to affect the simulated phenotype for ...


Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan 2019 Temple University

Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential ...


Hyperautofluorescent Dots Are Characteristic In Ceramide Kinase Like-Associated Retinal Degeneration., Jesse D Sengillo, Galaxy Y Cho, Maarjaliis Paavo, Winston Lee, Eugenia White, Ruben Jauregui, Janet R Sparrow, Rando Allikmets, Stephen H Tsang 2019 Reading Hospital-Tower Health

Hyperautofluorescent Dots Are Characteristic In Ceramide Kinase Like-Associated Retinal Degeneration., Jesse D Sengillo, Galaxy Y Cho, Maarjaliis Paavo, Winston Lee, Eugenia White, Ruben Jauregui, Janet R Sparrow, Rando Allikmets, Stephen H Tsang

Reading Hospital Internal Medicine Residency

There is a lack of studies which seek to discern disease expression in patients with mutations that alter retinal ceramide metabolism, specifically in the ceramide kinase like (CERKL) gene. This cross-sectional case series reports a novel phenotypic manifestation of CERKL-associated retinopathy. Four unrelated patients with homozygous CERKL mutations underwent a complete ocular exam, spectral-domain optical coherence tomography, short-wavelength fundus autofluorescence (SW-AF), quantitative autofluorescence (qAF), and full-field electroretinogram (ffERG). Decreased visual acuity and early-onset maculopathy were present in all patients. All four patients had extensive hyperautofluorescent foci surrounding an area of central atrophy on SW-AF imaging, which has not been previously ...


Cyclin C: The Story Of A Non-Cycling Cyclin., Jan Ježek, Daniel G J Smethurst, David C Stieg, Z A C Kiss, Sara E Hanley, Vidyaramanan Ganesan, Kai-Ti Chang, Katrina F Cooper, Randy Strich 2019 Rowan University

Cyclin C: The Story Of A Non-Cycling Cyclin., Jan Ježek, Daniel G J Smethurst, David C Stieg, Z A C Kiss, Sara E Hanley, Vidyaramanan Ganesan, Kai-Ti Chang, Katrina F Cooper, Randy Strich

School of Osteopathic Medicine Faculty Scholarship

The class I cyclin family is a well-studied group of structurally conserved proteins that interact with their associated cyclin-dependent kinases (Cdks) to regulate different stages of cell cycle progression depending on their oscillating expression levels. However, the role of class II cyclins, which primarily act as transcription factors and whose expression remains constant throughout the cell cycle, is less well understood. As a classic example of a transcriptional cyclin, cyclin C forms a regulatory sub-complex with its partner kinase Cdk8 and two accessory subunits Med12 and Med13 called the Cdk8-dependent kinase module (CKM). The CKM reversibly associates with the multi-subunit ...


Endogenous Antioxidant Overexpression As An Adjuvant To Diet Or Exercise Intervention As Therapy To Counteract Obesity And Beneficially Shift The Gut Microbiome, Deborah Lynn Amos 2019 Marshall University

Endogenous Antioxidant Overexpression As An Adjuvant To Diet Or Exercise Intervention As Therapy To Counteract Obesity And Beneficially Shift The Gut Microbiome, Deborah Lynn Amos

Theses, Dissertations and Capstones

Oxidative stress plays a key role in metabolic syndrome which includes obesity and cardiometabolic diseases. It is implicated that oxygen-derived free radicals generated during the mitochondrial electron transport chain alter the function of specific biological components, thus activating obesogenic pathways such as glucose and lipid signaling. Research on this topic is of vital importance as obesity is a high-risk factor in the development and progression of severe, debilitating, life-threatening maladies such as cardiometabolic diseases, chronic inflammatory pathologies, and cancer. Furthermore, there is no universal effective therapy to combat the rising rates of obesity with over 1.9 billion (39%) adults ...


Epigenetic Changes In Skeletal Muscle: Does Resistance Exercise Protocol Make A Difference?, Jesslyn Hendrickson 2019 Iowa State University

Epigenetic Changes In Skeletal Muscle: Does Resistance Exercise Protocol Make A Difference?, Jesslyn Hendrickson

Creative Components

Performing regular resistance exercise training has been found to improve an individual’s health, including improved metabolism and ability to perform maximal contractile force in skeletal muscle. Certain epigenetic changes are believed to provide a positive impact on individuals and resistance exercise is also known to cause epigenetic changes to occur, including DNA methylation, changes in mRNA expression, differential microRNA expression, and histone modifications. There is debate as to whether these changes are beneficial but with chronic exercise, these changes do appear to provide a benefit to the individual. All these changes play a role in gene expression and the ...


Alternative Splicing In Vertebrate Photoreceptors And Mechanisms Underlying Retinitis Pigmentosa, Jesse C. Sundar 2019 West Virginia University

Alternative Splicing In Vertebrate Photoreceptors And Mechanisms Underlying Retinitis Pigmentosa, Jesse C. Sundar

Graduate Theses, Dissertations, and Problem Reports

RNA binding proteins (RBPs) have emerged as important regulators of gene expression. RBPs typically contain RNA binding domains that recognize a specific sequence and/or structural motifs within the RNA. This allows them to modulate metabolism of RNAs in several possible ways including regulation of alternative splicing and processing, polyadenylation, translocation, localization, modification, stability, or translation. Previous studies have shown the Musashi (MSI) RBP family to be highly expressed in the retina, and more specifically, photoreceptors, but the importance of this expression remains largely unknown. We identified the MSI proteins as potential regulators of alternative exon splicing in murine photoreceptors ...


Correcting Glucose-6-Phosphate Dehydrogenase Deficiency With A Small-Molecule Activator, Sunhee Hwang, Karen Mruk, Simin Rahighi, Andrew G. Raub, Che-Hong Chen, Lisa E. Dorn, Naoki Horikoshi, Soichi Wakatsuki, James K. Chen, Daria Mochly-Rosen 2018 Stanford University

Correcting Glucose-6-Phosphate Dehydrogenase Deficiency With A Small-Molecule Activator, Sunhee Hwang, Karen Mruk, Simin Rahighi, Andrew G. Raub, Che-Hong Chen, Lisa E. Dorn, Naoki Horikoshi, Soichi Wakatsuki, James K. Chen, Daria Mochly-Rosen

Pharmacy Faculty Articles and Research

Glucose-6-phosphate dehydrogenase (G6PD) deficiency, one of the most common human genetic enzymopathies, is caused by over 160 different point mutations and contributes to the severity of many acute and chronic diseases associated with oxidative stress, including hemolytic anemia and bilirubin-induced neurological damage particularly in newborns. As no medications are available to treat G6PD deficiency, here we seek to identify a small molecule that corrects it. Crystallographic study and mutagenesis analysis identify the structural and functional defect of one common mutant (Canton, R459L). Using high-throughput screening, we subsequently identify AG1, a small molecule that increases the activity of the wild-type, the ...


Iron-Dependent Cleavage Of Ribosomal Rna During Oxidative Stress In The Yeast Saccharomyces Cerevisiae, Jessica A Zinskie, Arnab Ghosh, Brandon M Trainor, Daniel Shedlovskiy, Dimitri G Pestov, Natalia Shcherbik 2018 Rowan University

Iron-Dependent Cleavage Of Ribosomal Rna During Oxidative Stress In The Yeast Saccharomyces Cerevisiae, Jessica A Zinskie, Arnab Ghosh, Brandon M Trainor, Daniel Shedlovskiy, Dimitri G Pestov, Natalia Shcherbik

School of Osteopathic Medicine Faculty Scholarship

Stress-induced strand breaks in rRNA have been observed in many organisms, but the mechanisms by which they originate are not well-understood. Here we show that a chemical rather than an enzymatic mechanism initiates rRNA cleavages during oxidative stress in yeast (Saccharomyces cerevisiae). We used cells lacking the mitochondrial glutaredoxin Grx5 to demonstrate that oxidant-induced cleavage formation in 25S rRNA correlates with intracellular iron levels. Sequestering free iron by chemical or genetic means decreased the extent of rRNA degradation and relieved the hypersensitivity of grx5Δ cells to the oxidants. Importantly, subjecting purified ribosomes to an in vitro iron/ascorbate reaction ...


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