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Clinical Validation And Diagnostic Rate/Outcomes Of A Dual Molecular Diagnostic Assay For Myotonic Dystrophy 1., Maxime Cadieux-Dion, Isabelle Thiffault, Midhat S. Farooqi, Joseph Alaimo 2020 Children's Mercy Hospital

Clinical Validation And Diagnostic Rate/Outcomes Of A Dual Molecular Diagnostic Assay For Myotonic Dystrophy 1., Maxime Cadieux-Dion, Isabelle Thiffault, Midhat S. Farooqi, Joseph Alaimo

Research Days

No abstract provided.


-Synuclein And Mitochondrial Dysfunction Induced Er Stress Leading To Parkinson’S Disease, Sony Hoang 2020 Iowa State University

-Synuclein And Mitochondrial Dysfunction Induced Er Stress Leading To Parkinson’S Disease, Sony Hoang

Creative Components

Parkinson’s disease is, at the neuropathological level, characterized by the death of dopaminergic neurons. PD pathogenesis is multifactorial, there are several mechanisms that malfunction leading to the death of dopaminergic neurons. The mitochondria are vital for the normal functioning of a cell, they are the primary energy generator for the cell. In addition to their energy metabolism role, mitochondria are involved in many cellular processes, such as the stress response and cell death pathways. As a result, mitochondrial impairment and the genes that are related to its functionality are linked to progressive neurodegeneration. Considering parkin, PINK1, DJ-1, and LRRK2 ...


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 ...


Eugenics In The 21st Century, Jessica Linn Chin 2019 The Graduate Center, City University of New York

Eugenics In The 21st Century, Jessica Linn Chin

All Dissertations, Theses, and Capstone Projects

Eugenics is the science of enhancing the human population through the management of breeding and hereditary traits. This thesis explores the history of eugenics and shows how eugenic practices continue in the 21st century with advancements in technology and positive eugenic goals that can result in adverse effects on the human body and society. When Sir Francis Galton coined the term eugenics in 1883, he intended to improve British society with the use of positive eugenics. Galton used positive eugenics to encourage people with good mental and physical qualities to produce more children. He avoided negative eugenics, which involved ...


Altering Entry Angles In A Jump Landing Task Modifies Biomechanical Risk Factors Of Acl Injury, Shekoofe Saadat, Mitchell L. Stephenson, Jason C. Gillette 2019 Iowa State University

Altering Entry Angles In A Jump Landing Task Modifies Biomechanical Risk Factors Of Acl Injury, Shekoofe Saadat, Mitchell L. Stephenson, Jason C. Gillette

Kinesiology Presentations, Posters and Proceedings

This study investigated the effects of changing the entry-angle of a jump landing movement on ACL injury risk factors. Eight female recreational athletes performed 21 trials of a jump landing task. The direction of the first jump varied from -90° to 90° from the anterior axis in 30-degree increments. As the entry angle increased to the left, peak knee flexion and valgus angles as well as external valgus moments remained the same. In conditions where participants jumped more to their right, knee flexion angles were smaller and knee external valgus moments were greater. It can be concluded that kinematic analyses ...


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 ...


Isolating And Quantifying The Role Of Developmental Noise In Generating Phenotypic Variation, Maria Kiskowski, Tilmann Glimm, Nickolas Moreno, Tony Gamble, Ylenia Chiari 2019 University of South Alabama

Isolating And Quantifying The Role Of Developmental Noise In Generating Phenotypic Variation, Maria Kiskowski, Tilmann Glimm, Nickolas Moreno, Tony Gamble, Ylenia Chiari

Mathematics

Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic variation. While evolutionary biology has long focused on teasing apart the relative contribution of genes and environment to phenotypic variation, our understanding of the role of developmental noise has lagged due to technical difficulties in directly measuring the contribution of developmental noise. The influence of developmental noise is likely underestimated in studies of phenotypic variation due to ...


Prefrontal Corticotropin-Releasing Factor (Crf) Neurons Act Locally To Modulate Frontostriatal Cognition And Circuit Function., Sofiya Hupalo, Andrea J Martin, Rebecca K Green, David M Devilbiss, Craig W Berridge 2019 University of Wisconsin - Madison

Prefrontal Corticotropin-Releasing Factor (Crf) Neurons Act Locally To Modulate Frontostriatal Cognition And Circuit Function., Sofiya Hupalo, Andrea J Martin, Rebecca K Green, David M Devilbiss, Craig W Berridge

School of Osteopathic Medicine Faculty Scholarship

The PFC and extended frontostriatal circuitry support higher cognitive processes that guide goal-directed behavior. PFC-dependent cognitive dysfunction is a core feature of multiple psychiatric disorders. Unfortunately, a major limiting factor in the development of treatments for PFC cognitive dysfunction is our limited understanding of the neural mechanisms underlying PFC-dependent cognition. We recently demonstrated that activation of corticotropin-releasing factor (CRF) receptors in the caudal dorsomedial PFC (dmPFC) impairs higher cognitive function, as measured in a working memory task. Currently, there remains much unknown about CRF-dependent regulation of cognition, including the source of CRF for cognition-modulating receptors and the output pathways modulated ...


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 ...


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 ...


Kinetics Of Dextromethorphan-O-Demethylase Activity And Distribution Of Cyp2d In Four Commonly-Used Subcellular Fractions Of Rat Brain, Barent N. Dubois, Farideh Amirrad, Reza Mehvar 2018 Chapman University

Kinetics Of Dextromethorphan-O-Demethylase Activity And Distribution Of Cyp2d In Four Commonly-Used Subcellular Fractions Of Rat Brain, Barent N. Dubois, Farideh Amirrad, Reza Mehvar

Pharmacy Faculty Articles and Research

The purpose of this study was to compare the enzymatic kinetics and distribution of cytochrome P450 2D (CYP2D) among different rat brain subcellular fractions.

Rat brains were used to prepare total membrane, crude mitochondrial, purified mitochondrial, and microsomal fractions, in addition to total homogenate. Michaelis–Menten kinetics of the brain CYP2D activity was estimated based on the conversion of dextromethorphan (DXM) to dextrorphan using UPLC-MS/MS. Protein levels of CYP2D and subcellular markers were determined by Western blot.

Microsomal CYP2D exhibited high affinity and low capacity, compared with the mitochondrial CYP2D that had a much lower (∼50-fold) affinity but a ...


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 ...


Genetic Candidate Variants In Two Multigenerational Families With Childhood Apraxia Of Speech, Peter Beate, Ellen M. Wijsman, Alejandro Q. Nato Jr., Mark M. Matsushita, Kathy L. Chapman, Ian B. Stanaway, John Wolff, Kaori Oda, Virginia B. Gabo, Wendy H. Raskind 2018 Marshall University

Genetic Candidate Variants In Two Multigenerational Families With Childhood Apraxia Of Speech, Peter Beate, Ellen M. Wijsman, Alejandro Q. Nato Jr., Mark M. Matsushita, Kathy L. Chapman, Ian B. Stanaway, John Wolff, Kaori Oda, Virginia B. Gabo, Wendy H. Raskind

Alejandro Nato

Childhood apraxia of speech (CAS) is a severe and socially debilitating form of speech sound disorder with suspected genetic involvement, but the genetic etiology is not yet well understood. Very few known or putative causal genes have been identified to date, e.g., FOXP2 and BCL11A. Building a knowledge base of the genetic etiology of CAS will make it possible to identify infants at genetic risk and motivate the development of effective very early intervention programs. We investigated the genetic etiology of CAS in two large multigenerational families with familial CAS. Complementary genomic methods included Markov chain Monte Carlo linkage ...


Multipoint Genome-Wide Linkage Scan For Nonword Repetition In A Multigenerational Family Further Supports Chromosome 13q As A Locus For Verbal Trait Disorders, D. T. Truong, L. D. Shriberg, S. D. Smith, K. L. Chapman, A. R. Scheer-Cohen, M. M.C. DeMille, A. K. Adams, Alejandro Q. Nato Jr., E. M. Wijsman, J. D. Eicher, J. R. Gruen 2018 Marshall University

Multipoint Genome-Wide Linkage Scan For Nonword Repetition In A Multigenerational Family Further Supports Chromosome 13q As A Locus For Verbal Trait Disorders, D. T. Truong, L. D. Shriberg, S. D. Smith, K. L. Chapman, A. R. Scheer-Cohen, M. M.C. Demille, A. K. Adams, Alejandro Q. Nato Jr., E. M. Wijsman, J. D. Eicher, J. R. Gruen

Alejandro Nato

Verbal trait disorders encompass a wide range of conditions and are marked by deficits in five domains that impair a person’s ability to communicate: speech, language, reading, spelling, and writing. Nonword repetition is a robust endophenotype for verbal trait disorders that is sensitive to cognitive processes critical to verbal development, including auditory processing, phonological working memory, and motor planning and programming. In the present study, we present a six-generation extended pedigree with a history of verbal trait disorders. Using genome-wide multipoint variance component linkage analysis of nonword repetition, we identified a region spanning chromosome 13q14–q21 with LOD = 4 ...


N-Terminal Domain Of Human Uracil Dna Glycosylase (Hung2) Promotes Targeting To Uracil Sites Adjacent To Ssdna-Dsdna Junctions, Brian P Weiser, Gaddiel Rodriguez, Philip A Cole, James T Stivers 2018 Rowan University

N-Terminal Domain Of Human Uracil Dna Glycosylase (Hung2) Promotes Targeting To Uracil Sites Adjacent To Ssdna-Dsdna Junctions, Brian P Weiser, Gaddiel Rodriguez, Philip A Cole, James T Stivers

School of Osteopathic Medicine Faculty Scholarship

The N-terminal domain (NTD) of nuclear human uracil DNA glycosylase (hUNG2) assists in targeting hUNG2 to replication forks through specific interactions with replication protein A (RPA). Here, we explored hUNG2 activity in the presence and absence of RPA using substrates with ssDNA-dsDNA junctions that mimic structural features of the replication fork and transcriptional R-loops. We find that when RPA is tightly bound to the ssDNA overhang of junction DNA substrates, base excision by hUNG2 is strongly biased toward uracils located 21 bp or less from the ssDNA-dsDNA junction. In the absence of RPA, hUNG2 still showed an 8-fold excision bias ...


Foki Vitamin D Receptor Gene Polymorphisms And Metabolic Health In Pregnant Saudi Women, Maysa Alzaim 2018 University of Massachusetts Amherst

Foki Vitamin D Receptor Gene Polymorphisms And Metabolic Health In Pregnant Saudi Women, Maysa Alzaim

Doctoral Dissertations

Lifestyles have been dynamically changing in the past few years in Saudi Arabia, and the prevalence of non-communicable diseases (NCDs), such as obesity, diabetes, hypertension, high cholesterol, and other cardiovascular diseases (CVD), is notably increasing. In fact, NCDs are affecting a growing number of people in SA, especially women of childbearing age. Vitamin D deficiency has also become pandemic and a major public health concern among the Saudi population despite the abundance of sunlight. The most vulnerable groups are pregnant women and their newborns. Previous studies have correlated low vitamin D status with a higher risk of adverse short- and ...


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