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Genome Wide Association Mapping Of Root Traits In The Andean Genepool Of Common Bean (Phaseolus Vulgaris L.) Grown With And Without Aluminum Toxicity, Daniel Ambachew, Matthew W. Blair 2021 Tennessee State University

Genome Wide Association Mapping Of Root Traits In The Andean Genepool Of Common Bean (Phaseolus Vulgaris L.) Grown With And Without Aluminum Toxicity, Daniel Ambachew, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity ...


Literature Review Of Human Hdr Syndrome With Gata3 Haplo Insufficiency, Olivia Ambursley-Gries 2021 Western Michigan University

Literature Review Of Human Hdr Syndrome With Gata3 Haplo Insufficiency, Olivia Ambursley-Gries

Honors Theses

This literature mining project is regarding mutations that cause hearing loss in patients with human hypo parathyroid, deafness, and renal dysplasia (HDR) syndrome caused by a mutation in the GATA3 gene. The disease is unique; not all diagnosed individuals present with all symptoms of the triad. Van Esh et al. found that the haploinsufficiency of the GATA3 is found on chromosome 10p14-p15 (ref.1). The focus of this work is to condense the literature on GATA3 haploinsufficiency correlating to human HDR syndrome. Due to the lack of global healthcare access, it can be assumed that many cases remain undiagnosed; 180 ...


Dynamics Of The Soil Microbiome In Ginseng Gardens, Megan E. Lambert 2021 The University of Western Ontario

Dynamics Of The Soil Microbiome In Ginseng Gardens, Megan E. Lambert

Electronic Thesis and Dissertation Repository

Ginseng Replant Disease (GRD) is a syndrome in which ginseng cannot be cultivated in soil previously used to grow ginseng. Since GRD can persist for decades, it severely impacts the Ontario ginseng industry. To better understand the origin of GRD, the impact of ginseng cultivation on the soil microbiome was investigated in bulk soil of three newly planted ginseng gardens in Ontario, from seeding through two years of cultivation. While specific trends in species richness, diversity and composition were unclear, PERMANOVA analyses confirmed that they changed over time. Known GRD-related pathogens, including Ilyonectria mors-panacis and Fusarium oxysporum, were detected in ...


The Rare C9 P167s Risk Variant For Age-Related Macular Degeneration Increases Polymerization Of The Terminal Component Of The Complement Cascade, O. McMahon, S. Patel, Rafael Widjajahakim, Johanna M. Seddon, D. Kavanagh 2021 Newcastle University

The Rare C9 P167s Risk Variant For Age-Related Macular Degeneration Increases Polymerization Of The Terminal Component Of The Complement Cascade, O. Mcmahon, S. Patel, Rafael Widjajahakim, Johanna M. Seddon, D. Kavanagh

Open Access Publications by UMass Chan Authors

Age-related macular degeneration (AMD) is a complex neurodegenerative eye disease with behavioral and genetic etiology and is the leading cause of irreversible vision loss among elderly Caucasians. Functionally significant genetic variants in the alternative pathway of complement have been strongly linked to disease. More recently, a rare variant in the terminal pathway of complement has been associated with increased risk, Complement component 9 (C9) P167S. To assess the functional consequence of this variant, C9 levels were measured in two independent cohorts of AMD patients. In both cohorts, it was demonstrated that the P167S variant was associated with low C9 plasma ...


Successful Atac-Seq From Snap-Frozen Equine Tissues, Sichong Peng, Rebecca Bellone, Jessica L. Petersen, Theodore S. Kalbfleisch, Carrie J. Finno 2021 University of California, Davis

Successful Atac-Seq From Snap-Frozen Equine Tissues, Sichong Peng, Rebecca Bellone, Jessica L. Petersen, Theodore S. Kalbfleisch, Carrie J. Finno

Veterinary Science Faculty Publications

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin ...


Novel Rna Viruses From The Transcriptome Of Pheromone Glands In The Pink Bollworm Moth, Pectinophora Gossypiella, Xiaoyi Dou, Sijun Liu, Victoria Soroker, Ally Harari, Russell Jurenka 2021 Iowa State University

Novel Rna Viruses From The Transcriptome Of Pheromone Glands In The Pink Bollworm Moth, Pectinophora Gossypiella, Xiaoyi Dou, Sijun Liu, Victoria Soroker, Ally Harari, Russell Jurenka

Entomology Publications

In this study, we analyzed the transcriptome obtained from the pheromone gland isolated from two Israeli populations of the pink bollworm Pectinophora gossypiella to identify viral sequences. The lab population and the field samples carried the same viral sequences. We discovered four novel viruses: two positive-sense single-stranded RNA viruses, Pectinophora gossypiella virus 1 (PecgV1, a virus of Iflaviridae) and Pectinophora gossypiella virus 4 (PecgV4, unclassified), and two negative-sense single-stranded RNA viruses, Pectinophora gossypiella virus 2 (PecgV2, a virus of Phasmaviridae) and Pectinophora gossypiella virus 3 (PecgV3, a virus of Phenuiviridae). In addition, sequences derived from two negative-sense single-stranded RNA viruses ...


An Investigation On The Irish Population’S Attitudes And Knowledge Towards Genetic Screening For Cancer, Emer McCarthy, Ada Fleming, Dawn Hannah Cronin 2021 Munster Technological University

An Investigation On The Irish Population’S Attitudes And Knowledge Towards Genetic Screening For Cancer, Emer Mccarthy, Ada Fleming, Dawn Hannah Cronin

International Undergraduate Journal of Health Sciences

Genetic mutations are alterations in DNA that may result in the development of a disease later in life. A BRCA gene is a tumour suppressor gene that helps to prevent the development of some cancers, particularly breast cancer. If a mutation occurs, this gene no longer functions at preventing these cancers. Genetic screening is when a population is tested for a mutation in an attempt to identify a group of people that are positive for the mutation. This can help identify cancer in different populations as well as track their inheritance. This study was conducted online, questioning the Irish populations ...


Full Issue: The International Undergraduate Journal Of Health Sciences, Volume 1, Issue 1, June 2021, 2021 Munster Technological University

Full Issue: The International Undergraduate Journal Of Health Sciences, Volume 1, Issue 1, June 2021

International Undergraduate Journal of Health Sciences

The full June 2021 issue (Volume 1, Issue 1) of the International Undergraduate Journal of Health Sciences


Wormpaths: Caenorhabditis Elegans Metabolic Pathway Annotation And Visualization, Melissa D. Walker, Gabrielle E. Giese, Amy D. Holdorf, Sushila Bhattacharya, Cedric Diot, Aurian Garcia-Gonzalez, Brent Horowitz, Yong-Uk Lee, Thomas Leland, Xuhang Li, Zeynep Mirza, Huimin Na, Shivani Nanda, Olga Ponomarova, Hefei Zhang, Jingyan Zhang, L. Safak Yilmaz, Albertha J. M. Walhout 2021 University of Massachusetts Medical School

Wormpaths: Caenorhabditis Elegans Metabolic Pathway Annotation And Visualization, Melissa D. Walker, Gabrielle E. Giese, Amy D. Holdorf, Sushila Bhattacharya, Cedric Diot, Aurian Garcia-Gonzalez, Brent Horowitz, Yong-Uk Lee, Thomas Leland, Xuhang Li, Zeynep Mirza, Huimin Na, Shivani Nanda, Olga Ponomarova, Hefei Zhang, Jingyan Zhang, L. Safak Yilmaz, Albertha J. M. Walhout

Open Access Publications by UMass Chan Authors

In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology and the response to therapeutic drugs. Visualization of the metabolic pathways that comprise the metabolic network is extremely useful for interpreting a wide variety of experiments. Detailed annotated metabolic pathway maps for C. elegans is mostly limited to pan-organismal maps, many with incomplete or inaccurate pathway and enzyme annotations. Here we present WormPaths, which is composed of two parts: 1) the careful manual annotation of metabolic genes into pathways, categories and levels, and 2) 62 pathway maps that include metabolites ...


Transcriptomic Data Of Bovine Ovarian Granulosa Cells Of Control And High A4 Cows, Alexandria P. Snider, Sarah Romereim, Renee McFee Fee, Adam F. Summers, William E. Pohlmeier, Scott G. Kurz, John S. Davis, Jennifer R. Wood, Andrea S. Cupp 2021 University of Nebraska-Lincoln

Transcriptomic Data Of Bovine Ovarian Granulosa Cells Of Control And High A4 Cows, Alexandria P. Snider, Sarah Romereim, Renee Mcfee Fee, Adam F. Summers, William E. Pohlmeier, Scott G. Kurz, John S. Davis, Jennifer R. Wood, Andrea S. Cupp

Faculty Papers and Publications in Animal Science

Microarray analysis using Affymetrix Bovine GeneChip 1.0 ST Array to determine RNA expression analysis was performed on somatic granulosa cells from two different groups of cows classified based on androstenedione concentration within the follicular fluid (Control vs High A4) of estrogen-active dominant follicles. The normalized linear microarray data was deposited to the NCBI GEO repository (GSE97017 - RNA Expression Data from Bovine Ovarian Granulosa Cells from High or Low Androgen-Content Follicles). Subsequent ANOVA determined genes that were enriched (≥ 1.5 fold more) or decreased (≤ 1.5 fold less) in the High A4 granulosa cells compared to Control granulosa cells and ...


Start Codon Disruption With Crispr/Cas9 Prevents Murine Fuchs' Endothelial Corneal Dystrophy, Hironori Uehara, Guangping Gao, Balamurali K. Ambati 2021 University of Oregon

Start Codon Disruption With Crispr/Cas9 Prevents Murine Fuchs' Endothelial Corneal Dystrophy, Hironori Uehara, Guangping Gao, Balamurali K. Ambati

Open Access Publications by UMass Chan Authors

A missense mutation of collagen type VIII alpha 2 chain (COL8A2) gene leads to early-onset Fuchs' endothelial corneal dystrophy (FECD), which progressively impairs vision through the loss of corneal endothelial cells. We demonstrate that CRISPR/Cas9-based postnatal gene editing achieves structural and functional rescue in a mouse model of FECD. A single intraocular injection of an adenovirus encoding both the Cas9 gene and guide RNA (Ad-Cas9-Col8a2gRNA) efficiently knocked down mutant COL8A2 expression in corneal endothelial cells, prevented endothelial cell loss, and rescued corneal endothelium pumping function in adult Col8a2 mutant mice. There were no adverse sequelae on histology or electroretinography ...


Chromosome-Level Assembly Of The Atlantic Silverside Genome Reveals Extreme Levels Of Sequence Diversity And Structural Genetic Variation, Anna Tigano, Arne Jacobs, Aryn P. Wilder, Ankita Nand, Ye Zhan, Job Dekker, Nina Overgaard Therkildsen 2021 Cornell University

Chromosome-Level Assembly Of The Atlantic Silverside Genome Reveals Extreme Levels Of Sequence Diversity And Structural Genetic Variation, Anna Tigano, Arne Jacobs, Aryn P. Wilder, Ankita Nand, Ye Zhan, Job Dekker, Nina Overgaard Therkildsen

Open Access Publications by UMass Chan Authors

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial ...


Synphilin-1 And Its Effects On Pathogenesis Of Parkinson’S Disease, Mirghani Mohamed 2021 University of Connecticut

Synphilin-1 And Its Effects On Pathogenesis Of Parkinson’S Disease, Mirghani Mohamed

Honors Scholar Theses

Parkinson's Disease (PD) is a progressive neurodegenerative and movement disorder primarily caused by the degradation of dopaminergic neurons. Known markers of neurodegeneration in PD are Lewy Bodies, which are fibrillar aggregates that are found in the brains of PD patients. Lewy Bodies can accumulate from specific mutations in the SNCA gene that codes for alpha-synuclein, a protein enriched in presynaptic neurons. A mutated SNCA gene can cause conformational aggregates of alpha-synuclein to form toxic species mediating neuronal death. Research into alpha-synuclein has led to the discovery of a binding partner known as synphilin-1 that is also found in protein ...


Genetic And Epigenetic Features Of Promoters With Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription Of Cell-Essential Genes, Kaili Fan, Jill E. Moore, Xiao-Ou Zhang, Zhiping Weng 2021 University of Massachusetts Medical School

Genetic And Epigenetic Features Of Promoters With Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription Of Cell-Essential Genes, Kaili Fan, Jill E. Moore, Xiao-Ou Zhang, Zhiping Weng

University of Massachusetts Medical School Faculty Publications

Gene expression is controlled by regulatory elements within accessible chromatin. Although most regulatory elements are cell type-specific, a subset is accessible in nearly all the 517 human and 94 mouse cell and tissue types assayed by the ENCODE consortium. We systematically analyzed 9000 human and 8000 mouse ubiquitously-accessible candidate cis-regulatory elements (cCREs) with promoter-like signatures (PLSs) from ENCODE, which we denote ubi-PLSs. These are more CpG-rich than non-ubi-PLSs and correspond to genes with ubiquitously high transcription, including a majority of cell-essential genes. ubi-PLSs are enriched with motifs of ubiquitously-expressed transcription factors and preferentially bound by transcriptional cofactors regulating ubiquitously-expressed genes ...


Patterns Of Recent Natural Selection On Genetic Loci Associated With Sexually Differentiated Human Body Size And Shape Phenotypes, Audrey M. Arner, Kathleen E. Grogan, Mark Grabowski, Hugo Reyes-Centeno, George H. Perry 2021 Pennsylvania State University

Patterns Of Recent Natural Selection On Genetic Loci Associated With Sexually Differentiated Human Body Size And Shape Phenotypes, Audrey M. Arner, Kathleen E. Grogan, Mark Grabowski, Hugo Reyes-Centeno, George H. Perry

Anthropology Faculty Publications

Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for UK Biobank individuals (~194,000 females and ~167,000 males) to identify a total of 114,199 single nucleotide polymorphisms (SNPs) significantly associated with at ...


Evaluating Toxicity Of Varroa Mite (Varroa Destructor)-Active Dsrna To Monarch Butterfly (Danaus Plexippus) Larvae, Niranjana Krishnan, Maura J. Hall, Richard L. Hellmich, Joel R. Coats, Steven P. Bradbury 2021 Iowa State University

Evaluating Toxicity Of Varroa Mite (Varroa Destructor)-Active Dsrna To Monarch Butterfly (Danaus Plexippus) Larvae, Niranjana Krishnan, Maura J. Hall, Richard L. Hellmich, Joel R. Coats, Steven P. Bradbury

Entomology Publications

Varroa mites (Varroa destructor) are parasitic mites that, combined with other factors, are contributing to high levels of honey bee (Apis mellifera) colony losses. A Varroa-active dsRNA was recently developed to control Varroa mites within honey bee brood cells. This dsRNA has 372 base pairs that are homologous to a sequence region within the Varroa mite calmodulin gene (cam). The Varroa-active dsRNA also shares a 21-base pair match with monarch butterfly (Danaus plexippus) calmodulin mRNA, raising the possibility of non-target effects if there is environmental exposure. We chronically exposed the entire monarch larval stage to common (Asclepias syriaca) and tropical ...


Long-Term Gene–Culture Coevolution And The Human Evolutionary Transition, Timothy M. Waring, Zachary T. Wood 2021 University of Maine

Long-Term Gene–Culture Coevolution And The Human Evolutionary Transition, Timothy M. Waring, Zachary T. Wood

School of Economics Faculty Scholarship

It has been suggested that the human species may be undergoing an evolutionary transition in individuality (ETI). But there is disagreement about how to apply the ETI framework to our species, and whether culture is implicated as either cause or consequence. Long-term gene–culture coevolution (GCC) is also poorly understood. Some have argued that culture steers human evolution, while others proposed that genes hold culture on a leash. We review the literature and evidence on long-term GCC in humans and find a set of common themes. First, culture appears to hold greater adaptive potential than genetic inheritance and is probably ...


Dna Barcoding Of The High-Altitude Artemisia And Nepeta Species, Vyacheslav Dushenkov, Csanad Gurdon, Shukhratdzhon Satorov 2021 CUNY Hostos Community College

Dna Barcoding Of The High-Altitude Artemisia And Nepeta Species, Vyacheslav Dushenkov, Csanad Gurdon, Shukhratdzhon Satorov

Publications and Research

DNA barcoding was performed for four medicinal plant species from the mountain region of Tajikistan. The nucleotide sequences for Artemisia sieberi, Artemisia scoparia, Artemisia vulgaris, and Nepeta glutinosa were deposited into the GenBank at the National Center for Biotechnology Information.


Confronting Sources Of Systematic Error To Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes), Adela Roa-Varón, Rebecca B. Dikow, (...), Eric J. Hilton 2021 Virginia Institute of Marine Science

Confronting Sources Of Systematic Error To Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes), Adela Roa-Varón, Rebecca B. Dikow, (...), Eric J. Hilton

VIMS Articles

Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically ...


T Cell Receptor Genotype And Ubash3a Determine Susceptibility To Rat Autoimmune Diabetes, John P. Mordes, Laura Cort, Zhijun Liu, Ryan Eberwine, Elizabeth P. Blankenhorn, Brian G. Pierce 2021 University of Massachusetts Medical School

T Cell Receptor Genotype And Ubash3a Determine Susceptibility To Rat Autoimmune Diabetes, John P. Mordes, Laura Cort, Zhijun Liu, Ryan Eberwine, Elizabeth P. Blankenhorn, Brian G. Pierce

Open Access Publications by UMass Chan Authors

Genetic analyses of human type 1 diabetes (T1D) have yet to reveal a complete pathophysiologic mechanism. Inbred rats with a high-risk class II major histocompatibility complex (MHC) haplotype (RT1B/D(u)) can illuminate such mechanisms. Using T1D-susceptible LEW.1WR1 rats that express RT1B/D(u) and a susceptible allele of the Ubd promoter, we demonstrate that germline knockout of Tcrb-V13S1A1, which encodes the Vbeta13a T cell receptor beta chain, completely prevents diabetes. Using the RT1B/D(u)-identical LEW.1W rat, which does not develop T1D despite also having the same Tcrb-V13S1A1 beta chain gene but a different allele at ...


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