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Rare And Low Frequency Genomic Variants Impacting Neuronal Functions Modify The Dup7q11.23 Phenotype, Farah Qaiser, Yue Yin, Carolyn B. Mervis, Colleen A. Morris, Bonita P. Klein-Tasman, Elaine Tam, Lucy R. Osborne, Ryan K.C. Yuen 2021 University of Toronto

Rare And Low Frequency Genomic Variants Impacting Neuronal Functions Modify The Dup7q11.23 Phenotype, Farah Qaiser, Yue Yin, Carolyn B. Mervis, Colleen A. Morris, Bonita P. Klein-Tasman, Elaine Tam, Lucy R. Osborne, Ryan K.C. Yuen

School of Medicine Faculty Publications

© 2021, The Author(s). Background: 7q11.23 duplication (Dup7) is one of the most frequent recurrent copy number variants (CNVs) in individuals with autism spectrum disorder (ASD), but based on gold-standard assessments, only 19% of Dup7 carriers have ASD, suggesting that additional genetic factors are necessary to manifest the ASD phenotype. To assess the contribution of additional genetic variants to the Dup7 phenotype, we conducted whole-genome sequencing analysis of 20 Dup7 carriers: nine with ASD (Dup7-ASD) and 11 without ASD (Dup7-non-ASD). Results: We identified three rare variants of potential clinical relevance for ASD: a 1q21.1 microdeletion (Dup7-non-ASD) and two ...


A Tissue Specific Transcriptomic, Proteomic And Phospho-Proteomic Atlas Of The Translational Machinery Of Arabidopsis Thaliana, Abdullah Salim 2021 University of Tennessee, Knoxville

A Tissue Specific Transcriptomic, Proteomic And Phospho-Proteomic Atlas Of The Translational Machinery Of Arabidopsis Thaliana, Abdullah Salim

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Gene expression encompasses the flow of genetic information from DNA to mRNA (transcription) and from mRNA to protein (translation) along with the regulatory mechanisms underlying these processes. Omics technologies offer a powerful toolset with which to study gene expression at each of these stages. A recently published dataset integrating transcriptomic, proteomic and phospho-proteomic measurements from 30 Arabidopsis thaliana tissues provides a unique resource to explore gene expression.1 The translational machinery (the ribosome, and its initiation, elongation, and termination factors) are a core component in gene expression. Defects in translation can be lethal or lead to major developmental defects and ...


Has Maize Overtaken Our Reality? A Personal Briefing, Biochemical Comparison, Agrigenomics, And History Of Maize, Nader Pahlevan 2021 University of Mississippi

Has Maize Overtaken Our Reality? A Personal Briefing, Biochemical Comparison, Agrigenomics, And History Of Maize, Nader Pahlevan

Honors Theses

Maize (Zea mays ssp. Mays) is a revolutionary cereal grain that has raced to the world’s most popular staple crop, transforming societies and impacting history. This paper aims to build and portray the story maize has created through its journey to world domination. The important details that encompass this literature are maize’s cultural significance in my life’s story, the comparison of various starches broken down into amylose and amylopectin ratios, a summative historical account on maize’s spread throughout numerous parts of the old world, and the genetical analysis of maize that explains the key features that ...


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 ...


Involvement Of The Ino80 Chromatin Remodeling Complex In Cell Division And Genomic Stability, Ethan Chen 2021 University of Arkansas, Fayetteville

Involvement Of The Ino80 Chromatin Remodeling Complex In Cell Division And Genomic Stability, Ethan Chen

Biomedical Engineering Undergraduate Honors Theses

Cell division is a vital biological process for growth and development in both single and multi-cellular organisms—whereby the cell must duplicate its organelles and genome in entirety and appropriately distribute the copied contents to the daughter cells. Cells undergo a cycle of two distinct phases: interphase and mitosis. During interphase, the cell replicates its genomic DNA (in the form of chromosomes) located within the nucleus. DNA replication is carried out in a euchromatin state, where the chromosome structure is loose and easily accessible by DNA polymerase and other replication enzymes. Upon the completion of replication, chromatin is condensed into ...


Understanding The Genetics Of Schizophrenia, Matthew Toohey 2021 Southern Maine Community College

Understanding The Genetics Of Schizophrenia, Matthew Toohey

Thinking Matters Symposium

Schizophrenia has been considered heritable for a long time, but only with the advent of new technologies such as whole-genome sequencing and genome-wide association studies can we begin to identify specific molecular causes of schizophrenia. This poster will review some of the genetic variants that research groups have associated with schizophrenia. Current research has indicated that schizophrenia is a polygenic disease and has been linked to many genes. Some of these common risk variants are in protein coding sections of the DNA. These proteins are often linked to neurological development or immune system function. Other variants that have been associated ...


307— Cooperation Of Selfish Genetic Elements In Stalk-Eyed Flies, Suhani Patel, Ben McPherson 2021 SUNY Geneseo

307— Cooperation Of Selfish Genetic Elements In Stalk-Eyed Flies, Suhani Patel, Ben Mcpherson

GREAT Day

SGEs are selfish genetic elements that increase the likelihood of their own transmission regardless of the host’s best interest. Transposable elements (TEs) and meiotic drivers are both types of SGEs. SGEs subsequently result in genetic conflict as they disrupt functional elements in the genome. We are working to better understand the cooperation of selfish genetic elements in Stalk-Eyed flies. Transposable elements are counteracted by small non-coding RNA molecules called piRNA. These RNA molecules work by reducing the expression of TEs by degrading TE RNA transcripts. Prior work in stalk-eyed flies has shown that TEs are expressed at a higher ...


Annotation Of The Genome Of Drosophilia Ananassae, Landon Kehr 2021 Taylor University

Annotation Of The Genome Of Drosophilia Ananassae, Landon Kehr

Celebration of Scholarship 2021

This project involves the use of software to annotate the genome of D. ananassae in collaboration with the Genomics Education Partnership. Annotations include coding regions and transcription start sites for specific genes that are homologous to D. melanogaster genes.


Comparative Genomics For D. Ananassae, Hailey Chang, Tia Watkins 2021 Taylor University

Comparative Genomics For D. Ananassae, Hailey Chang, Tia Watkins

Celebration of Scholarship 2021

The purpose of this project is to utilize comparative genomics tools to characterize specific genes in D. Ananassae. This is done in collaboration with the Genomics Education Partnership.


An Ensemble Of The Icluster Method To Analyze Longitudinal Lncrna Expression Data For Psoriasis Patients, Suyan Tian, Chi Wang 2021 The First Hospital of Jilin University, China

An Ensemble Of The Icluster Method To Analyze Longitudinal Lncrna Expression Data For Psoriasis Patients, Suyan Tian, Chi Wang

Internal Medicine Faculty Publications

BACKGROUND: Psoriasis is an immune-mediated, inflammatory disorder of the skin with chronic inflammation and hyper-proliferation of the epidermis. Since psoriasis has genetic components and the diseased tissue of psoriasis is very easily accessible, it is natural to use high-throughput technologies to characterize psoriasis and thus seek targeted therapies. Transcriptional profiles change correspondingly after an intervention. Unlike cross-sectional gene expression data, longitudinal gene expression data can capture the dynamic changes and thus facilitate causal inference.

METHODS: Using the iCluster method as a building block, an ensemble method was proposed and applied to a longitudinal gene expression dataset for psoriasis, with the ...


The Giant Axolotl Genome Uncovers The Evolution, Scaling, And Transcriptional Control Of Complex Gene Loci, Siegfried Schloissnig, Akane Kawaguchi, Sergej Nowoshilow, Francisco Falcon, Leo Otsuki, Pietro Tardivo, Nataliya Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith, S. Randal Voss, Elly M. Tanaka 2021 Institute of Molecular Pathology, Austria

The Giant Axolotl Genome Uncovers The Evolution, Scaling, And Transcriptional Control Of Complex Gene Loci, Siegfried Schloissnig, Akane Kawaguchi, Sergej Nowoshilow, Francisco Falcon, Leo Otsuki, Pietro Tardivo, Nataliya Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith, S. Randal Voss, Elly M. Tanaka

Biology Faculty Publications

Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, we describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth ...


Variation In The Genome And Transcriptome Associated With Beef Cattle Production And Investigation Of The Metabolic Consequences Of Beta-Adrenergic Agonist Supplementation, Renae L. Sieck 2021 University of Nebraska - Lincoln

Variation In The Genome And Transcriptome Associated With Beef Cattle Production And Investigation Of The Metabolic Consequences Of Beta-Adrenergic Agonist Supplementation, Renae L. Sieck

Theses and Dissertations in Animal Science

Beta-adrenergic agonists (β-AA) are widely used supplements in livestock production to improve feed efficiency and increase lean muscle mass. Heat stress is one of the largest economic burdens to the livestock industry due to production efficiency losses and morbidity and mortality of animals. Both β-AA and catecholamines released in response to heat stress bind to β-adrenoceptors on the skeletal muscle cell surface to activate downstream signaling pathways. The purpose of this study was to determine if β-AA supplementation and heat stress have an additive effect on the skeletal muscle transcriptome. 3’ RNA sequencing of samples of the longissimus dorsiwas ...


Nanopore Guided Regional Assembly, Eleni Adam, Desh Ranjan, Harold Riethman 2021 Old Dominion University

Nanopore Guided Regional Assembly, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are the “caps” of the chromosomes and their vital role is to protect them. Possible telomere dysfunction caused by telomere rearrangements can be fatal for the cell and result in age-related diseases, including cancer. The telomeres and subtelomeres are regions that are hard to investigate. The current technology cannot provide their complete sequence, instead the DNA is given in multiple pieces. Current methods of assembling the pieces of these regions are not accurate enough due to the region’s high variability and complex repeated patterns. We propose a hybrid assembly method, the NPGREAT, which utilizes two of the ...


Genomics Of Response To Prrsv In Purebred And Crossbred Sows: Antibody Response And Performance Following Natural Infection Versus Vaccination, Leticia P. Sanglard, Felipe M. W. Hickmann, Yijian Huang, Kent A. Gray, Daniel C. L. Linhares, Jack C. M. Dekkers, Megan C. Niederwerder, Rohan L. Fernando, Joseph Braccini Neto, Nick V. L. Serão 2021 Iowa State University

Genomics Of Response To Prrsv In Purebred And Crossbred Sows: Antibody Response And Performance Following Natural Infection Versus Vaccination, Leticia P. Sanglard, Felipe M. W. Hickmann, Yijian Huang, Kent A. Gray, Daniel C. L. Linhares, Jack C. M. Dekkers, Megan C. Niederwerder, Rohan L. Fernando, Joseph Braccini Neto, Nick V. L. Serão

Veterinary Diagnostic and Production Animal Medicine Publications

Antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) following a PRRSV-outbreak (S/POutbreak) in a purebred nucleus and following a PRRSV-vaccination (S/PVx) in commercial crossbred herds have been proposed as genetic indicator traits for improved reproductive performance in PRRSV-infected purebred and PRRSV-vaccinated crossbred sows, respectively. In this study, we investigated the genetic relationships of S/POutbreak and S/PVx with performance at the commercial (vaccinated crossbred sows) and nucleus level (non-infected and PRRSV-infected purebred sows), respectively, and tested the effect of previously identified SNP for these indicator traits. Antibody response was ...


Stategra: Multi-Omics Data Integration - A Conceptual Scheme With A Bioinformatics Pipeline, Nuria Planell, Vincenzo Lagani, Patricia Sebastian-Leon, Frans van der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegner, David Gomez-Cabrero 2021 Universidad Pública de Navarra (UPNA)

Stategra: Multi-Omics Data Integration - A Conceptual Scheme With A Bioinformatics Pipeline, Nuria Planell, Vincenzo Lagani, Patricia Sebastian-Leon, Frans Van Der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegner, David Gomez-Cabrero

Computational Medicine Center Faculty Papers

Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of deciphering different regulatory layers. Yet, while there is a myriad of bioinformatics tools, each multi-omics analysis appears to start from scratch with an arbitrary decision over which tools to use and how to combine them. Therefore, it is an unmet need to conceptualize how to integrate such data and implement and validate pipelines in different cases. We have designed a conceptual framework (STATegra), aiming it to be as generic as possible for multi-omics analysis, combining ...


Sociality Sculpts Similar Patterns Of Molecular Evolution In Two Independently Evolved Lineages Of Eusocial Bees, Wyatt A. Shell, Michael A. Steffen, Hannah K. Pare, Arun S. Seetharam, Andrew J. Severin, Amy L. Toth, Sandra M. Rehan 2021 York University

Sociality Sculpts Similar Patterns Of Molecular Evolution In Two Independently Evolved Lineages Of Eusocial Bees, Wyatt A. Shell, Michael A. Steffen, Hannah K. Pare, Arun S. Seetharam, Andrew J. Severin, Amy L. Toth, Sandra M. Rehan

Genome Informatics Facility Publications

While it is well known that the genome can affect social behavior, recent models posit that social lifestyles can, in turn, influence genome evolution. Here, we perform the most phylogenetically comprehensive comparative analysis of 16 bee genomes to date: incorporating two published and four new carpenter bee genomes (Apidae: Xylocopinae) for a first-ever genomic comparison with a monophyletic clade containing solitary through advanced eusocial taxa. We find that eusocial lineages have undergone more gene family expansions, feature more signatures of positive selection, and have higher counts of taxonomically restricted genes than solitary and weakly social lineages. Transcriptomic data reveal that ...


Complete Genome Sequence Of Campylobacter Hepaticus Usa52, Associated With Chicken Spotty Liver Disease, Zuowei Wu, Orhan Sahin, Qijing Zhang 2021 Iowa State University

Complete Genome Sequence Of Campylobacter Hepaticus Usa52, Associated With Chicken Spotty Liver Disease, Zuowei Wu, Orhan Sahin, Qijing Zhang

Veterinary Microbiology and Preventive Medicine Publications

Campylobacter hepaticus was recently identified as the etiological agent of chicken spotty liver disease. Here, we report the complete genome sequence of C. hepaticus strain USA52 from the United States. The genome comprises a chromosome of 1,509,100 bp with an average GC content of 28.02%.


Annotation Of Chromatin States In 66 Complete Mouse Epigenomes During Development, Arjan van der Velde, Kaili Fan, Junko Tsuji, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Zhiping Weng 2021 University of Massachusetts Medical School

Annotation Of Chromatin States In 66 Complete Mouse Epigenomes During Development, Arjan Van Der Velde, Kaili Fan, Junko Tsuji, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Zhiping Weng

Open Access Publications by UMMS Authors

The morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors ...


The Look Ahead Trace Back Optimizer For Genomic Selection Under Transparent And Opaque Simulators, Fatemeh Amini, Felipe Restrepo Franco, Guiping Hu, Lizhi Wang 2021 Iowa State University

The Look Ahead Trace Back Optimizer For Genomic Selection Under Transparent And Opaque Simulators, Fatemeh Amini, Felipe Restrepo Franco, Guiping Hu, Lizhi Wang

Industrial and Manufacturing Systems Engineering Publications

Recent advances in genomic selection (GS) have demonstrated the importance of not only the accuracy of genomic prediction but also the intelligence of selection strategies. The look ahead selection algorithm, for example, has been found to significantly outperform the widely used truncation selection approach in terms of genetic gain, thanks to its strategy of selecting breeding parents that may not necessarily be elite themselves but have the best chance of producing elite progeny in the future. This paper presents the look ahead trace back algorithm as a new variant of the look ahead approach, which introduces several improvements to further ...


The Genomics Of Ecological Flexibility, Large Brains, And Long Lives In Capuchin Monkeys Revealed With Fecalfacs., Joseph D Orkin, Michael J Montague, Daniela Tejada-Martinez, Marc de Manuel, Javier Del Campo, Saul Cheves Hernandez, Anthony Di Fiore, Claudia Fontsere, Jason A Hodgson, Mareike C Janiak, Lukas F K Kuderna, Esther Lizano, Maria Pia Martin, Yoshihito Niimura, George H Perry, Carmen Soto Valverde, Jia Tang, Wesley C Warren, João Pedro de Magalhães, Shoji Kawamura, Tomàs Marquès-Bonet, Roman Krawetz, Amanda D Melin 2021 University of Calgary

The Genomics Of Ecological Flexibility, Large Brains, And Long Lives In Capuchin Monkeys Revealed With Fecalfacs., Joseph D Orkin, Michael J Montague, Daniela Tejada-Martinez, Marc De Manuel, Javier Del Campo, Saul Cheves Hernandez, Anthony Di Fiore, Claudia Fontsere, Jason A Hodgson, Mareike C Janiak, Lukas F K Kuderna, Esther Lizano, Maria Pia Martin, Yoshihito Niimura, George H Perry, Carmen Soto Valverde, Jia Tang, Wesley C Warren, João Pedro De Magalhães, Shoji Kawamura, Tomàs Marquès-Bonet, Roman Krawetz, Amanda D Melin

Department of Biochemistry and Molecular Biology Faculty Papers

Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to ...


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