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Novel Polymorphisms Of Zrsr2 And Gpm6b Gene Homologs And Their Use In Sex Identification Of Bovine And Porcine Species, Evan K. Peterson 2020 Utah State University

Novel Polymorphisms Of Zrsr2 And Gpm6b Gene Homologs And Their Use In Sex Identification Of Bovine And Porcine Species, Evan K. Peterson

All Graduate Theses and Dissertations

Accurate and cost-effective PCR based sex identification is important in animal production because it gives producers the ability to determine the sex of embryos prior to transfer, saving time and money. The most efficient PCR sex identification assays work by using a single primer pair to amplify a specific target region located on the Y-chromosome and a second, separate target region on the X-chromosome.

This thesis reports the design of two novel assays. The first assay was designed to target the Zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 (ZRSR2) gene found on the X-chromosome and its ...


Molecular Taxonomy And Phylogenetic Analysis Of Dove And Pigeon Species (Aves: Columbidae) Of Pakistan, Based On Coi Region Of Mitochondrial Dna, Hina Rafiq, Fakhar -i-Abbas, Fakhra Nazir, Fida Muhammad Khan 2020 Institute of Natural and Management Sciences (INAM), Rawalpindi

Molecular Taxonomy And Phylogenetic Analysis Of Dove And Pigeon Species (Aves: Columbidae) Of Pakistan, Based On Coi Region Of Mitochondrial Dna, Hina Rafiq, Fakhar -I-Abbas, Fakhra Nazir, Fida Muhammad Khan

Journal of Bioresource Management

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining ...


Estimating Partial Body Ionizing Radiation Exposure By Automated Cytogenetic Biodosimetry, Peter Rogan 2020 The University of Western Ontario

Estimating Partial Body Ionizing Radiation Exposure By Automated Cytogenetic Biodosimetry, Peter Rogan

Biochemistry Publications

Purpose: Inhomogeneous exposures to ionizing radiation can be detected and quantified with the Dicentric Chromosome Assay (DCA) of metaphase cells. Complete automation of interpretation of the DCA for whole body irradiation has significantly improved throughput without compromising accuracy, however low levels of residual false positive dicentric chromosomes (DCs) have confounded its application for partial body exposure determination.

Materials and Methods: We describe a method of estimating and correcting for false positive DCs in digitally processed images of metaphase cells. Nearly all DCs detected in unirradiated calibration samples are introduced by digital image processing. DC frequencies of irradiated calibration samples and ...


Whole Genome Sequence Data Provides Novel Insights Into The Genetic Architecture Of Meat Quality Traits In Beef, Joel D. Leal-Gutiérrez, Fernanda M. Rezende, James M. Reecy, Luke M. Kramer, Francisco Peñagaricano, Raluca G. Mateescu 2020 University of Florida

Whole Genome Sequence Data Provides Novel Insights Into The Genetic Architecture Of Meat Quality Traits In Beef, Joel D. Leal-Gutiérrez, Fernanda M. Rezende, James M. Reecy, Luke M. Kramer, Francisco Peñagaricano, Raluca G. Mateescu

Animal Science Publications

Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue using whole-genome data in an Angus population, (2) identify enriched pathways in each GWA analysis; (3) construct a protein–protein interaction network using the associated genes and (4) perform a μ-calpain proteolysis assessment for associated structural proteins. An Angus-sired population of 2,285 individuals was assessed. Animals were transported to ...


Genome Scan Detection Of Selective Sweeps Among Biotypes Of The Soybean Aphid, Aphis Glycines, With Differing Virulence To Resistance To A. Glycines (Rag) Traits In Soybean, Glycine Max, Brad S. Coates, Jessica D. Hohenstein, Rosanna Giordano, Ravi Kiran Donthu, Andrew P. Michel, Erin W. Hodgson, Matthew E. O'Neal 2020 U.S. Department of Agriculture

Genome Scan Detection Of Selective Sweeps Among Biotypes Of The Soybean Aphid, Aphis Glycines, With Differing Virulence To Resistance To A. Glycines (Rag) Traits In Soybean, Glycine Max, Brad S. Coates, Jessica D. Hohenstein, Rosanna Giordano, Ravi Kiran Donthu, Andrew P. Michel, Erin W. Hodgson, Matthew E. O'Neal

Entomology Publications

Multiple biotypes of soybean aphid, Aphis glycines, occur in North America adapted for survival (virulence) on soybean, Glycine max, with one or more different resistance to A. glycines (Rag) traits. The degree of genome-wide variance between biotypes and the basis of virulence remains unknown, but the latter is hypothesized to involve secreted effector proteins. Between 167,249 and 217,750 single nucleotide polymorphisms (SNPs) were predicted from whole genome re-sequencing of A. glycines avirulent biotype 1 (B1) and virulent B2, B3 and B4 colony-derived iso-female lines when compared to the draft B1 genome assembly, Ag_bt1_v6.0. Differences in nucleotide diversity ...


Machine Learning Applications For Drug Repurposing, Hansaim Lim 2020 The Graduate Center, City University of New York

Machine Learning Applications For Drug Repurposing, Hansaim Lim

Dissertations, Theses, and Capstone Projects

The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected ...


Pfred: A Computational Platform For Sirna And Antisense Oligonucleotides Design, Simone Sciabola, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert Stanton 2020 Biogen

Pfred: A Computational Platform For Sirna And Antisense Oligonucleotides Design, Simone Sciabola, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert Stanton

University of Massachusetts Medical School Faculty Publications

PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred ...


Phylogenetic Analysis Of Sars-Cov-2 In The Boston Area Highlights The Role Of Recurrent Importation And Superspreading Events, Jacob Lemieux, Katherine J. Siddle, Jeremy Luban, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia M. Pierce, Eric Rosenberg, Pardis C. Sabeti, Daniel J. Park, Bronwyn L. MacInnis 2020 Broad Institute

Phylogenetic Analysis Of Sars-Cov-2 In The Boston Area Highlights The Role Of Recurrent Importation And Superspreading Events, Jacob Lemieux, Katherine J. Siddle, Jeremy Luban, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia M. Pierce, Eric Rosenberg, Pardis C. Sabeti, Daniel J. Park, Bronwyn L. Macinnis

COVID-19 Publications by UMMS Authors

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe ...


Genome-Wide Mapping Of Human Dna Replication By Optical Replication Mapping Supports A Stochastic Model Of Eukaryotic Replication Timing, Weitao Wang, Kyle Klein, Karel Proesmans, Northwestern University, Claire Marchal, Xiaopeng Zhu, Tyler M. Borrman, Alex Hastie, Zhiping Weng, Simon Fraser University, Paris Sciences et Lettres University, Florida State University, Nicholas R. Rhind 2020 Paris Sciences et Lettres University

Genome-Wide Mapping Of Human Dna Replication By Optical Replication Mapping Supports A Stochastic Model Of Eukaryotic Replication Timing, Weitao Wang, Kyle Klein, Karel Proesmans, Northwestern University, Claire Marchal, Xiaopeng Zhu, Tyler M. Borrman, Alex Hastie, Zhiping Weng, Simon Fraser University, Paris Sciences Et Lettres University, Florida State University, Nicholas R. Rhind

University of Massachusetts Medical School Faculty Publications

DNA replication is regulated by the location and timing of replication initiation. Therefore, much effort has been invested in identifying and analyzing the sites of human replication initiation. However, the heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual initiation site utilization in metazoans has made mapping the location and timing of replication initiation in human cells difficult. A potential solution to the problem of human replication mapping is single-molecule analysis. However, current approaches do not provide the throughput required for genome-wide experiments. To address this challenge, we have developed Optical Replication Mapping (ORM), a high-throughput single-molecule ...


Genome-Wide Characterization Of The Grf Family And Their Roles In Response To Salt Stress In Gossypium, Jun-Feng Cao, Jin-Quan Huang, Xia Liu, Chao-Chen Huang, Zi-Shou Zheng, Xiu-Fang Zhang, Xiao-Xia Shangguan, Ling-Jian Wang, Yu-Gao Zhang, Jonathan F. Wendel, Corrinne E. Grover, Zhi-Wen Chen 2020 Chinese Academy of Sciences

Genome-Wide Characterization Of The Grf Family And Their Roles In Response To Salt Stress In Gossypium, Jun-Feng Cao, Jin-Quan Huang, Xia Liu, Chao-Chen Huang, Zi-Shou Zheng, Xiu-Fang Zhang, Xiao-Xia Shangguan, Ling-Jian Wang, Yu-Gao Zhang, Jonathan F. Wendel, Corrinne E. Grover, Zhi-Wen Chen

Ecology, Evolution and Organismal Biology Publications

Background: Cotton (Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt stress, but their roles have not been studied in cotton under salt stress.

Results: We identified 19 GRF genes in G. raimondii, 18 in G. arboreum, 34 in G. hirsutum and 45 in G. barbadense, respectively. These GRF genes were phylogenetically analyzed leading to the recognition of seven GRF clades. GRF genes from diploid cottons (G. raimondii and G. arboreum) were largely retained in allopolyploid cotton, with ...


Broad Host Range Of Sars-Cov-2 Predicted By Comparative And Structural Analysis Of Ace2 In Vertebrates, Joana Damas, Elinor K. Karlsson, Harris A. Lewin 2020 University of California, Davis

Broad Host Range Of Sars-Cov-2 Predicted By Comparative And Structural Analysis Of Ace2 In Vertebrates, Joana Damas, Elinor K. Karlsson, Harris A. Lewin

COVID-19 Publications by UMMS Authors

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike ...


From Phocine Distemper To Avian Influenza: A Study Of Immunogenetic Diversity In Two Sympatric Pinniped Species, Alayna K. Gigliotti 2020 University of Maine

From Phocine Distemper To Avian Influenza: A Study Of Immunogenetic Diversity In Two Sympatric Pinniped Species, Alayna K. Gigliotti

Electronic Theses and Dissertations

Gray (Halichoerus grypus) and harbor (Phoca vitulina) seals are sympatric species that inhabit the North Atlantic and have been subject to mortality events from disease outbreaks, particularly phocine distemper and avian influenza virus. Across mortality events, gray seals tend to exhibit a higher survival rate, which could be explained by various ecological factors impacting rates or direction of selection in parts of the genome related to the immune system. These factors could include haul-out site density, habitat, and degree of inter/intraspecies interaction. This research aims to compare genetic diversity within the Major Histocompatibility Complex (MHC) class I gene complex ...


Rates And Patterns Of Indels In Hiv-1 Gp120 Within And Among Hosts, John Lawrence Palmer 2020 The University of Western Ontario

Rates And Patterns Of Indels In Hiv-1 Gp120 Within And Among Hosts, John Lawrence Palmer

Electronic Thesis and Dissertation Repository

Insertions and deletions (indels) in the HIV-1 gp120 variable loops modulate sensitivity to neutralizing antibodies and are therefore implicated in HIV-1 immune escape. However, the rates and characteristics of variable loop indels have not been investigated within hosts. Here, I report a within-host phylogenetic analysis of gp120 variable loop indels, with mentions to my preceding study on these indels among hosts.

We processed longitudinally-sampled gp120 sequences collected from a public database (n = 11,265) and the Novitsky Lab (n=2,541). I generated time-scaled within-host phylogenies using BEAST, extracted indels by reconstructing ancestral sequences in Historian, and estimated variable loop ...


Inherent Regulatory Asymmetry Emanating From Network Architecture In A Prevalent Autoregulatory Motif, Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster 2020 University of Massachusetts Medical School

Inherent Regulatory Asymmetry Emanating From Network Architecture In A Prevalent Autoregulatory Motif, Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster

Open Access Articles

Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its target genes have inherent asymmetry in regulation, even when their promoters are identical; the TF gene being more repressed than its targets. The magnitude of ...


Atlas Of Transcription Factor Binding Sites From Encode Dnase Hypersensitivity Data Across 27 Tissue Types., Cory C Funk, Alex M Casella, Segun Jung, Matthew A Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner, Todd E Golde, Arthur Toga, Leroy Hood, John D Van Horn, Carl Kesselman, Ian Foster, Ravi Madduri, Nathan D Price, Seth A Ament 2020 Institute for Systems Biology, Seattle, WA, 98109-5263, USA.

Atlas Of Transcription Factor Binding Sites From Encode Dnase Hypersensitivity Data Across 27 Tissue Types., Cory C Funk, Alex M Casella, Segun Jung, Matthew A Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner, Todd E Golde, Arthur Toga, Leroy Hood, John D Van Horn, Carl Kesselman, Ian Foster, Ravi Madduri, Nathan D Price, Seth A Ament

Articles, Abstracts, and Reports

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human ...


Reduced Neurog3 Gene Dosage Shifts Enteroendocrine Progenitor Toward Goblet Cell Lineage In The Mouse Intestine, Joyce H. Li, Subir Ray, Alper Kucukural, Gerard Gradwohl, Andrew B. Leiter 2020 University of Massachusetts Medical School

Reduced Neurog3 Gene Dosage Shifts Enteroendocrine Progenitor Toward Goblet Cell Lineage In The Mouse Intestine, Joyce H. Li, Subir Ray, Alper Kucukural, Gerard Gradwohl, Andrew B. Leiter

University of Massachusetts Medical School Faculty Publications

BACKGROUND and AIMS: Transient expression of Neurog3 commits intestinal secretory progenitors to become enteroendocrine-biased progenitors and hence drive enteroendocrine differentiation. Loss of Neurog3 in mouse resulted in the depletion of intestinal enteroendocrine cells (EECs) and an increase in goblet cells. Earlier studies in developing mouse pancreas showed Neurog3 gene dosage in endocrine and exocrine cell fate allocation. We aimed to determine whether Neurog3 gene dosage controls fate choice of enteroendocrine progenitors.

METHODS: We acquired mutant Neurog3 reporter mice carrying 2, 1, or null Neurog3 alleles to study Neurog3 gene dosage effect by lineage tracing. Cell types arising from Neurog3+ progenitors ...


The P-Glycoprotein Repertoire Of The Equine Parasitic Nematode Parascaris Univalens, Alexander P. Gerhard, Jürgen Krücken, Emanuel Heitlinger, I. Jana I. Janssen, Marta Basiaga, Sławomir Kornaś, Céline Beier, Martin K. Nielsen, Richard E. Davis, Jianbin Wang, Georg von Samson-Himmelstjerna 2020 Freie Universität Berlin, Germany

The P-Glycoprotein Repertoire Of The Equine Parasitic Nematode Parascaris Univalens, Alexander P. Gerhard, Jürgen Krücken, Emanuel Heitlinger, I. Jana I. Janssen, Marta Basiaga, Sławomir Kornaś, Céline Beier, Martin K. Nielsen, Richard E. Davis, Jianbin Wang, Georg Von Samson-Himmelstjerna

Maxwell H. Gluck Equine Research Center Faculty Publications

P-glycoproteins (Pgp) have been proposed as contributors to the widespread macrocyclic lactone (ML) resistance in several nematode species including a major pathogen of foals, Parascaris univalens. Using new and available RNA-seq data, ten different genomic loci encoding Pgps were identified and characterized by transcriptome-guided RT-PCRs and Sanger sequencing. Phylogenetic analysis revealed an ascarid-specific Pgp lineage, Pgp-18, as well as two paralogues of Pgp-11 and Pgp-16. Comparative gene expression analyses in P. univalens and Caenorhabditis elegans show that the intestine is the major site of expression but individual gene expression patterns were not conserved between the two nematodes. In P. univalens ...


A Shark Conservationists Toolbox: Current Dna Methods And Techniques Aiding In The Conservation Of Sharks, Arianna N. Nixon 2020 Nova Southeastern University

A Shark Conservationists Toolbox: Current Dna Methods And Techniques Aiding In The Conservation Of Sharks, Arianna N. Nixon

All HCAS Student Capstones, Theses, and Dissertations

Elasmobranchs are important members of their community. Many sharks are important apex predators that help maintain the health of their ecosystem. However, shark populations are globally declining. This is partially due to the fact that sharks are highly targeted for their fins, meat, liver oil, teeth, and skin. However, they are also killed from anthropogenic effects such as habitat destruction and pollution. Most shark species have life history characteristics that also make them more vulnerable to overfishing. Sharks are also difficult to study due to their elusive nature and identification issues. That is why molecular tools are increasingly becoming important ...


Transcriptome Analysis Reveals Inhibitory Effects Of Lentogenic Newcastle Disease Virus On Cell Survival And Immune Function In Spleen Of Commercial Layer Chicks, Jibin Zhang, Michael G. Kaiser, Rodrigo A. Gallardo, Terra R. Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont 2020 Iowa State University

Transcriptome Analysis Reveals Inhibitory Effects Of Lentogenic Newcastle Disease Virus On Cell Survival And Immune Function In Spleen Of Commercial Layer Chicks, Jibin Zhang, Michael G. Kaiser, Rodrigo A. Gallardo, Terra R. Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont

Animal Science Publications

As a major infectious disease in chickens, Newcastle disease causes considerable economic losses in the poultry industry, especially in developing countries where there is limited access to effective vaccination. Therefore, enhancing resistance to the virus in commercial chickens through breeding is a promising way to promote poultry production. In this study, we investigated gene expression changes at 2 and 6 dpi after infection at day21 with a lentogenic Newcastle disease virus in a commercial egg-laying chicken hybrid using RNA sequencing analysis. By comparing NDV challenged and nonchallenged groups, 526 differentially expressed genes (DEGs) (FDR < 0.05) were identified at 2 dpi, and only 36 at 6 dpi. For the DEGs at 2 dpi, IPA analysis predicted inhibition of multiple signaling pathways in response to NDV that regulate immune cell development and activity, neurogenesis and angiogenesis. Upregulation of Interferon Induced Protein with Tetratricopeptide Repeats 5 (IFIT5) in response to NDV was consistent between the current and most previous studies. Sprouty RTK Signaling Antagonist 1 (SPRY1), a DEG in the current study is located in a significant QTL associated with virus load at 6 dpi in the same population. These identified pathways and DEGs provide potential targets to further study breeding strategy to enhance NDV resistance in chickens.


Melting Dsdna Donor Molecules Potentiates Precision Genome Editing In C. Elegans, Krishna S. Ghanta, Craig C. Mello 2020 University of Massachusetts Medical School

Melting Dsdna Donor Molecules Potentiates Precision Genome Editing In C. Elegans, Krishna S. Ghanta, Craig C. Mello

University of Massachusetts Medical School Faculty Publications

CRISPR genome editing has revolutionized genetics in many organisms. In the nematode Caenorhabditis elegans one injection into each of the two gonad arms of an adult hermaphrodite exposes hundreds of meiotic germ cells to editing mixtures, permitting the recovery of multiple indels or small precision edits from each successfully injected animal. Unfortunately, particularly for long insertions, editing efficiencies can vary widely, necessitating multiple injections, and often requiring co-selection strategies. Here we show that melting double stranded DNA (dsDNA) donor molecules prior to injection increases the frequency of precise homology-directed repair (HDR) by several fold for longer edits. We describe troubleshooting ...


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