The Genomic Organization and Expression Pattern of the Low-Affinity Fc Gamma Receptors (Fcγr) in the Göttingen Minipig
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Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
Chain Locus Heavy Genomic Organization of the Variable
Antibody Repertoire Development in Fetal and Neonatal Piglets. XI. The Relationship of Variable Heavy Chain Gene Usage and the Genomic Organization of the Variable Heavy This information is current as Chain Locus of September 27, 2021. Tomoko Eguchi-Ogawa, Nancy Wertz, Xiu-Zhu Sun, Francois Puimi, Hirohide Uenishi, Kevin Wells, Patrick Chardon, Gregory J. Tobin and John E. Butler J Immunol published online 5 March 2010 Downloaded from http://www.jimmunol.org/content/early/2010/03/05/jimmun ol.0903616 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2010/03/05/jimmunol.090361 Material 6.DC1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 27, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts Errata An erratum has been published regarding this article. Please see next page or: /content/190/3/1383.full.pdf The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published March 5, 2010, doi:10.4049/jimmunol.0903616 The Journal of Immunology Antibody Repertoire Development in Fetal and Neonatal Piglets. -
Mouse Fcrla Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Fcrla Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Fcrla conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Fcrla gene (NCBI Reference Sequence: NM_001160215 ; Ensembl: ENSMUSG00000038421 ) is located on Mouse chromosome 1. 5 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 5 (Transcript: ENSMUST00000046322). Exon 2~4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Fcrla gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-100H5 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for a targeted allele exhibit largely normal T-dependent and T-independent antibody responses with an increase in IgG1 after secondary challenge with sheep red blood cells. Exon 2~4 is not frameshift exon, and covers 69.69% of the coding region. The size of intron 1 for 5'-loxP site insertion: 5054 bp, and the size of intron 4 for 3'-loxP site insertion: 2439 bp. The size of effective cKO region: ~2074 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Fcrla Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. -
Genomic Insights Into Drug Resistance Determinants in Cedecea Neteri, a Rare Opportunistic Pathogen
microorganisms Article Genomic Insights into Drug Resistance Determinants in Cedecea neteri, A Rare Opportunistic Pathogen Dorothea K. Thompson * and Stephen M. Sharkady Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Campbell University, Buies Creek, NC 27506, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-910-893-7463 Abstract: Cedecea, a genus in the Enterobacteriaceae family, includes several opportunistic pathogens reported to cause an array of sporadic acute infections, most notably of the lung and bloodstream. One species, Cedecea neteri, is associated with cases of bacteremia in immunocompromised hosts and has documented resistance to different antibiotics, including β-lactams and colistin. Despite the potential to inflict serious infections, knowledge about drug resistance determinants in Cedecea is limited. In this study, we utilized whole-genome sequence data available for three environmental strains (SSMD04, M006, ND14a) of C. neteri and various bioinformatics tools to analyze drug resistance genes in this bacterium. All three genomes harbor multiple chromosome-encoded β-lactamase genes. A deeper analysis of β-lactamase genes in SSMD04 revealed four metallo-β-lactamases, a novel variant, and a CMY/ACT-type AmpC putatively regulated by a divergently transcribed AmpR. Homologs of known resistance-nodulation-cell division (RND)-type multidrug efflux pumps such as OqxB, AcrB, AcrD, and MdtBC were also identified. Genomic island prediction for SSMD04 indicated that tolC, involved in drug and toxin export across the outer membrane of Gram-negative bacteria, Citation: Thompson, D.K.; Sharkady, was acquired by a transposase-mediated genetic transfer mechanism. Our study provides new S.M. Genomic Insights into Drug insights into drug resistance mechanisms of an environmental microorganism capable of behaving as Resistance Determinants in Cedecea a clinically relevant opportunistic pathogen. -
Genomic Organization of Mouse Fcy Receptor Genes
Proc. Nail. Acad. Sci. USA Vol. 87, pp. 2856-2860, April 1990 Immunology Genomic organization of mouse Fcy receptor genes (Fc receptors/exon-ntron junctions/protein domains/immunoglobulin gene superfamily) ANTHONY KULCZYCKI, JR.*t, JENNIFER WEBBER*, HAUNANI A. SOARES*, MICHAEL D. ONKEN*, JAMES A. THOMPSON*, DAVID D. CHAPLIN*t, DENNIS Y. LOH*t, AND JEFFREY P. TILLINGHAST* *Department of Medicine and tHoward Hughes Medical Institute, Washington University School of Medicine, Saint Louis, MO 63110 Communicated by David M. Kipnis, January 16, 1990 ABSTRACT We have isolated and characterized the gene responsible for intrathymic deletion of a large fraction of coding for the mouse Fc receptor that is termed Fc,,RHa. The potentially self-reactive T-cell clones (11-13). gene contains five exons and spans approximately 9 kilobases. An understanding of the relationship of the various Fc Unlike most members of the immunoglobulin gene superfam- receptor genes to each other, the factors influencing their ily, this gene utilizes multiple exons to encode its leader peptide. evolution, and molecular mechanisms regulating their The first exon encodes the hydrophobic region of the signal expression requires a detailed analysis of the structures of sequence; the second exon, which contains only 21 base pairs, their genes. Here we report the characterization of two encodes a segment of the signal peptidase recognition site; and members of this gene family. the beginning of the third exon encodes the predicted site of peptidase cleavage. The third and fourth exons each code for immunoglobulin-like extracellular domains. The fifth exon MATERIALS AND METHODS encodes the hydrophobic transmembrane domain and the Screening of Mouse cDNA and Genomic Libraries. -
Human J3 Satellite
Proc. Nati. Acad. Sci. USA Vol. 86, pp. 6250-6254, August 1989 Genetics Human j3 satellite DNA: Genomic organization and sequence definition of a class of highly repetitive tandem DNA (human genome/concerted evolution/acrocentric chromosomes) JOHN S. WAYE AND HUNTINGTON F. WILLARD* Department of Medical Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada Communicated by Charles R. Cantor, May 15, 1989 (receivedfor review August 23, 1988) ABSTRACT We describe a class ofhuman repetitive DNA, In this report, we describe the isolation and characteriza- called (3 satellite, that, at a most fundamental level, exists as tion of a human satellite DNA family, f satellitet which is tandem arrays of diverged -68-base-pair monomer repeat unrelated in structure or sequence to any previously de- units. The monomer units are organized as distinct subsets, scribed human satellite DNAs. These sequences comprise a each characterized by a multimeric higher-order repeat unit minimum of several million base pairs of DNA in the human that is tandemly reiterated and represents a recent unit of genome and are organized, at a fundamental level, as tandem amplification. We have cloned, characterized, and determined arrays of diverged -68-bp monomer repeat units. The P the sequence of two (3 satellite higher-order repeat units: one satellite DNA family is subdivided into two or more distinct located on chromosome 9, the other on the acrocentric chro- subsets, at least one of which is shared by the five pairs of mosomes (13, 14, 15, 21, and 22) and perhaps other sites in the acrocentric chromosomes. genome. Analysis by pulsed-field gel electrophoresis reveals that these tandem arrays are localized in large domains (50-300 MATERIALS AND METHODS kilobase pairs) that are marked by restriction fragment length polymorphisms. -
The Genomic Organization of Plant Pathogenicity in Fusarium Species Martijn Rep1 and H Corby Kistler2
Available online at www.sciencedirect.com The genomic organization of plant pathogenicity in Fusarium species Martijn Rep1 and H Corby Kistler2 Comparative genomics is a powerful tool to infer the molecular cation and genetic transmission. We here highlight recent basis of fungal pathogenicity and its evolution by identifying insights into the evolution of disease-causing ability differences in gene content and genomic organization between among plant pathogenic fungi, focusing on the compara- fungi with different hosts or modes of infection. Through tive genomic analysis of Fusarium species with additional comparative analysis, pathogenicity-related chromosomes reference to other fungi. have been identified in Fusarium oxysporum and Fusarium solani that contain genes for host-specific virulence. Lateral Comparative genomics transfer of pathogenicity chromosomes, inferred from genomic In 2007 the Broad Institute released its first Fusarium data, now has been experimentally confirmed. Likewise, comparativegenomicswebsite(http://www.broadinstitute. comparative genomics reveals the evolutionary relationships org/annotation/genome/fusarium_group/MultiHome. among toxin gene clusters whereby the loss and gain of genes html), which brought together high quality sequence from the cluster may be understood in an evolutionary context assemblies of the plant pathogenic fungus Fusarium grami- of toxin diversification. The genomic milieu of effector genes, nearum, sequenced previously [1] and two new WGS for encoding small secreted proteins, also suggests mechanisms the species Fusarium verticillioides and Fusarium oxysporum. that promote genetic diversification for the benefit of the At the sametime,theJoint Genome Institute (JGI) released pathogen. a WGS for Fusarium solani (Nectria haematococca)(http:// Addresses genome.jgi-psf.org/Necha2/Necha2.home.html). The four 1 Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of genomes share considerable sequence similarity as well as Science, University of Amsterdam, P.O. -
Laboratory Genetics and Genomics Learning Guide
American Board of Medical Genetics and Genomics Learning Guide for Laboratory Genetics and Genomics May 2016 INTRODUCTION: These learning guides have been developed by the ABMGG to assist training program directors and trainees as they design, implement, monitor and evaluate the educational content of their ABMGG accredited training programs. The format of these learning guides reflects the common areas of knowledge and training that have been developed by the medical profession across the training spectra and that are often referred to as the “Six Competencies.” The ABMGG has taken these areas of knowledge and experience and translated them into more specific content areas for ABMGG accredited programs. These learning guides are not presumed to be inclusive or exclusive. Thus you will find that they mirror many other guiding principle documents from within the genetics community. Similarly, while they attempt to cover as many specific areas of training as possible, they cannot be viewed as the only areas of knowledge and expertise that are required to become a successful medical genetics professional. They are, as indicated, learning guides; and are not rules or testing outlines. These guides are offered to the medical genetics educational community as one source of information concerning knowledge areas that may be useful in developing and evaluating the educational content of training programs. Domain Objectives Skills 1. Patient care Pre-analytic laboratory Identify appropriate specimens for Select appropriate containers, anticoagulants, collection media, antibiotics, and skills study, and methods of collection, preservatives for validated specimen type. preservation, and transport Identify factors important for the transport of specimens, such as overnight delivery, transport media and containers, recommended temperatures. -
Precision Medicine Informatics: Principles, Prospects, and Challenges
Received October 22, 2019, accepted December 26, 2019, date of publication January 13, 2020, date of current version January 23, 2020. Digital Object Identifier 10.1109/ACCESS.2020.2965955 Precision Medicine Informatics: Principles, Prospects, and Challenges MUHAMMAD AFZAL 1, (Member, IEEE), S. M. RIAZUL ISLAM 2, (Member, IEEE), MAQBOOL HUSSAIN 1, AND SUNGYOUNG LEE 3, (Member, IEEE) 1Department of Software, Sejong University, Seoul 05006, South Korea 2Department of Computer Science and Engineering, Sejong University, Seoul 05006, South Korea 3Department of Computer Science and Engineering, Kyung Hee University, Yongin 17104, South Korea Corresponding author: Sungyoung Lee ([email protected]) This work was supported in part by the Ministry of Science and ICT (MSIT), South Korea, through the Information Technology Research Center (ITRC) Support Program under Grant IITP-2017-0-01629, and in part by the Institute for Information & Communications Technology Promotion (IITP), through the Korea Government (MSIT) under Grant 2017-0-00655 and Grant NRF-2019R1A2C2090504. ABSTRACT Precision medicine (PM) is an emerging approach that appears with the impression of changing the existing paradigm of medical practice. Recent advances in technological innovations and genetics and the growing availability of health data have set a new pace of the research and impose a set of new requirements on the different stakeholders. Some studies are available that discuss about the different aspects of PM. Nevertheless, a holistic representation of those aspects deemed to confer with the technological perspective, in relation to the applications and challenges, have been mostly ignored. In this context, this paper surveys the advances in PM from the informatics viewpoint and reviews the enabling tools and techniques in a categorized manner. -
Genomic Organization
Proc. Nati. Acad. Sci. USA Vol. 85, pp. 4218-4222, June 1988 Biochemistry Primary structure of the human follistatin precursor and its genomic organization (ovary/testis/pituitary/prehormone/alternative splicing) SHUNICHI SHIMASAKI*, MAKOTO KOGA*, FREDERICK ESCHt, KAREN COOKSEY*, MALUZ MERCADO*, ANN KOBA*, NAOTO UENO*, SHAO-YAO YING*, NICHOLAS LING*, AND ROGER GUILLEMIN* *Laboratories for Neuroendocrinology, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037; and tAthena Neurosciences, Inc., 887-D Industrial Road, San Carlos, CA 94070 Contributed by Roger Guillemin, February 23, 1988 ABSTRACT Follistatin is a single-chain gonadal protein characterized porcine inhibins A and B. By use ofthe porcine that specifically inhibits follicle-stimulating hormone release. cDNA as a probe, we report herein the cloning and sequenc- By use ofthe recently characterized porcine follistatin cDNA as ing of the human follistatin precursor as well as the deter- a probe to screen a human testis cDNA library and a genomic mination of its genomic organizationA library, the structure of the complete human follistatin pre- cursor as well as its genomic organization have been deter- mined. Three of eight cDNA clones that were sequenced MATERIALS AND METHODS predicted a precursor with 344 amino acids, whereas the Cloning and DNA Sequencing. An oligo(dT)-primed human remaining five cDNA clones encoded a 317 amino acid precur- testicular cDNA library constructed with the vector Agtll sor, resulting from alternative splicing ofthe precursor mRNA. was purchased from Clontech (Palo Alto, CA). The mRNA Mature follistatins contain four contiguous domains that are used to produce the library was derived from the testis of a encoded by precisely separated exons; three of the domains are healthy 50-year-old man. -
Fc Receptor-Like Proteins in Pathophysiology of B-Cell Disorder
C al & ellu ic la n r li Im C m f u Journal of o n l o a l n o r Capone et al., J Clin Cell Immunol 2016, 7:3 g u y o J DOI: 10.4172/2155-9899.1000427 ISSN: 2155-9899 Clinical & Cellular Immunology Review Article Open Access Fc Receptor-Like Proteins in Pathophysiology of B-cell Disorder Mollie Capone, John Matthew Bryant, Natalie Sutkowski and Azizul Haque* Department of Microbiology and Immunology, and Hollings Cancer Center, Medical University of South Carolina, 173 Ashley Avenue, BSB-201, Charleston, SC 29425, USA *Corresponding author: Azizul Haque, Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, BSB-201, Charleston, SC 29425, USA, Tel: 843-792-9466; Fax: 843-792-2464; E-mail: [email protected] Received date: November 17, 2015; Accepted date: June 08, 2016; Published date: June 17, 2016 Copyright: © 2016 Capone M, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Members of the family of Fc receptor-like (FcRL) proteins, homologous to FcγRI, have been identified by multiple research groups. Consequently, they have been described using multiple nomenclatures including Fc receptor homologs (FcRH), immunoglobulin superfamily receptor translocation-associated genes (IRTA), immunoglobulin-Fc- gp42-related genes (IFGP), Src homology 2 domain-containing phosphatase anchor proteins (SPAP), and B cell cross-linked by anti-immunoglobulin M-activating sequences (BXMAS). They are now referred to under a unified nomenclature as FCRL. -
A Genetic Revolution in Rare-Disease Medicine
News & views These large swathes of repetitive DNA come Karen H. Miga is at the UC Santa Cruz 8. Koren, S. et al. Nature Biotechnol. 30, 693–700 with different sets of rules, in terms of their Genomics Institute, University of California, (2012). 9. Jain, M. et al. Nature Biotechnol. 36, 338–345 (2018). genomic organization and evolution. They are Santa Cruz, California 95064, USA. 10. Jain, M. et al. Nature Biotechnol. 36, 321–323 (2018). also subject to different epigenetic regulation e-mail: [email protected] 11. Chaisson, M. J. P. et al. Nature 517, 608–611 (2015). (molecular modifications to DNA and associ- 12. Wenger, A. M. et al. Nature Biotechnol. 37, 1155–1162 (2019). ated proteins that do not alter the underlying 13. Nurk, S. et al. Genome Res. 30, 1291–1305 (2020). DNA sequence), which leads repetitive DNA to 14. Bzikadze, A. V. & Pevzner, P. A. Nature Biotechnol. 38, 1. International Human Genome Sequencing Consortium. differ from euchromatin in terms of its organ- 1309–1316 (2020). Nature 409, 860–921 (2001). 15. Zentner, G. E., Saiakhova, A., Manaenkov, P., Adams, M. D. ization, replication timing and transcriptional 2. Venter, J. C. et al. Science 291, 1304–1351 (2001). & Scacheri, P. C. Nucleic Acids Res. 39, 4949–4960 activity17–19. Many genome-wide tools and data 3. Schneider, V. A. et al. Genome Res. 27, 849–864 (2017). (2011). 4. Miga, K. H. et al. Nature 585, 79–84 (2020). 16. Schueler, M. G., Higgins, A. W., Rudd, M. K., Gustashaw, K. sets cannot yet fully capture all this informa- 5.