(APOCI, -C2, and -E and LDLR) and the Genes C3, PEPD, and GPI (Whole-Arm Translocation/Somatic Cell Hybrids/Genomic Clones/Gene Family/Atherosclerosis) A

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Harnessing the Power of Epigenetics for Targeted Nutrition

SPONSOR FEATURE SPONSOR FEATURE NESTLÉ RESEARCH: Harnessing the power of epigenetics for targeted nutrition Authors Diet and genomes interact. Because of its contin- products that are nutritious, safe, promote and Martin Kussmann*, Jennifer Dean*, uous and lifelong impact, nutrition might be the maintain health, and prevent disease. With the Rondo P. Middleton†, Peter J. van most important environmental factor for human advent and development of many new technolo- Bladeren* & Johannes le Coutre* health. Molecular nutrition research strives gies, molecular nutrition research has opened to understand this interaction. Nutrigenetics up new doors of understanding – not only con- *Nestlé Research Center, addresses how an individual’s genetic make-up cerning which dietary components may impact 1000 Lausanne 26, Switzerland. leads to a predisposition for nutritional health; an organism’s health, but also how. These new †Nestlé Purina Research, St. Louis, MO, nutrigenomics (encompassing transcriptomics, insights have allowed a greater understanding 63164 USA. proteomics and metabonomics) asks how nutri- of the systems involved at multiple levels, from tion modulates gene expression; and epigenetics whole animal to the cellular and molecular lev- provides insights into a new level of regulation els. Although challenges in this area still remain, involving mechanisms of development, parental the main focus continues to be the improvement gene imprinting and metabolic programming that of health through diet. Modern molecular nutri- are beyond genetic control. tional research aims at health promotion, dis- Tailoring diets and nutrient compositions to the ease prevention, performance improvement and needs of consumer groups that share the same benefit-risk assessment1. health state, life stage or life style is a main goal Nutrition has conventionally been considered of current nutritional research.
Human Chromosome‐Specific Aneuploidy Is Influenced by DNA

Article Human chromosome-specific aneuploidy is influenced by DNA-dependent centromeric features Marie Dumont1,†, Riccardo Gamba1,†, Pierre Gestraud1,2,3, Sjoerd Klaasen4, Joseph T Worrall5, Sippe G De Vries6, Vincent Boudreau7, Catalina Salinas-Luypaert1, Paul S Maddox7, Susanne MA Lens6, Geert JPL Kops4 , Sarah E McClelland5, Karen H Miga8 & Daniele Fachinetti1,* Abstract Introduction Intrinsic genomic features of individual chromosomes can contri- Defects during cell division can lead to loss or gain of chromosomes bute to chromosome-specific aneuploidy. Centromeres are key in the daughter cells, a phenomenon called aneuploidy. This alters elements for the maintenance of chromosome segregation fidelity gene copy number and cell homeostasis, leading to genomic instabil- via a specialized chromatin marked by CENP-A wrapped by repeti- ity and pathological conditions including genetic diseases and various tive DNA. These long stretches of repetitive DNA vary in length types of cancers (Gordon et al, 2012; Santaguida & Amon, 2015). among human chromosomes. Using CENP-A genetic inactivation in While it is known that selection is a key process in maintaining aneu- human cells, we directly interrogate if differences in the centro- ploidy in cancer, a preceding mis-segregation event is required. It was mere length reflect the heterogeneity of centromeric DNA-depen- shown that chromosome-specific aneuploidy occurs under conditions dent features and whether this, in turn, affects the genesis of that compromise genome stability, such as treatments with micro- chromosome-specific aneuploidy. Using three distinct approaches, tubule poisons (Caria et al, 1996; Worrall et al, 2018), heterochro- we show that mis-segregation rates vary among different chromo- matin hypomethylation (Fauth & Scherthan, 1998), or following somes under conditions that compromise centromere function.
GENOME GENERATION Glossary

GENOME GENERATION Glossary Chromosome An organism’s DNA is packaged into chromosomes. Humans have 23 pairs of chromosomesincluding one pair of sex chromosomes. Women have two X chromosomes and men have one X and one Y chromosome. Dominant (see also recessive) Genes come in pairs. A dominant form of a gene is the “stronger” version that will be expressed. Therefore if someone has one dominant and one recessive form of a gene, only the characteristics of the dominant form will appear. DNA DNA is the long molecule that contains the genetic instructions for nearly all living things. Two strands of DNA are twisted together into a double helix. The DNA code is made up of four chemical letters (A, C, G and T) which are commonly referred to as bases or nucleotides. Gene A gene is a section of DNA that is the code for a specific biological component, usually a protein. Each gene may have several alternative forms. Each of us has two copies of most of our genes, one copy inherited from each parent. Most of our traits are the result of the combined effects of a number of different genes. Very few traits are the result of just one gene. Genetic sequence The precise order of letters (bases) in a section of DNA. Genome A genome is the complete DNA instructions for an organism. The human genome contains 3 billion DNA letters and approximately 23,000 genes. Genomics Genomics is the study of genomes. This includes not only the DNA sequence itself, but also an understanding of the function and regulation of genes both individually and in combination.
The Circular Genetic Map of Phage 813 by Ron Baker and Irwin Tessman

THE CIRCULAR GENETIC MAP OF PHAGE 813 BY RON BAKER AND IRWIN TESSMAN DEPARTMENT OF BIOLOGICAL SCIENCES, PURDUE UNIVERSITY, LAFAYETTE, INDIANA Communicated by S. E. Luria, July 24, 1967 Because of its small size1 phage S13 is suitable for a study of all its genes and their functions. With this aim, conditionally lethal mutants of the suppressible (su) and temperature-sensitive (t) type have been isolated and classified into seven complementation groups, and the general function of five of the genes implicitly defined by these complementation groups has been determined.8-10 This paper is concerned with the mapping of the seven known phage genes, with the ultimate aim of understanding both the organization of the phage genome and the mechanism by which it undergoes genetic recombination. Although the DNA molecule of S13, as shown for the closely related phage ,X174, is physically circular both in the single-stranded form of the mature virus11 and in the double-stranded replicative form,12' 13 this does not necessarily imply that the genetic map should also be circular since circular DNA is neither necessary nor sufficient for genetic circularity. On the one hand, a linear DNA molecule can give rise to a circular genetic map if the nucleotide sequences are circularly permuted;14 an example is the T2-T4 phage system.'5-17 On the other hand, a circular DNA can yield a linear map if recombination involves opening of the ring at a unique site, as seems to occur for phage X, which forms a closed DNA molecule after infections yet has a linear vegetative and prophage genetic map.19 In this report it will be shown that the genetic map of S13, as determined entirely by 3-factor crosses, is indeed circular, and, as might be expected for a circular genome, the occurrence of double recombination events appears to be the rule.
An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial Chromosome

The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 133-151 Article 7 2018 An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial chromosome Robert W. Carter Stephen Lee University of Idaho John C. Sanford Cornell University, Cornell University College of Agriculture and Life Sciences School of Integrative Plant Science,Follow this Plant and Biology additional Section works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y- chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H.
Expression-Based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project

Downloaded from genome.cshlp.org on October 11, 2021 - Published by Cold Spring Harbor Laboratory Press Resource Expression-based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project Robert Clifford, Michael Edmonson, Ying Hu, Cu Nguyen, Titia Scherpbier, and Kenneth H. Buetow1 Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 USA SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute’s CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/).
Alzheimer's Disease Genetics Fact Sheet

Alzheimer’s Disease Genetics FACT SHEET cientists don’t yet fully In other diseases, a genetic variant understand what causes may occur. This change in a gene can SAlzheimer’s disease. How- sometimes cause a disease directly. ever, the more they learn about More often, it acts to increase or this devastating disease, the more decrease a person’s risk of develop- they realize that genes* play an ing a disease or condition. When a important role in its development. genetic variant increases disease risk Research conducted and funded but does not directly cause a disease, by the National Institute on Aging it is called a genetic risk factor. (NIA) at the National Institutes of Health and others is advancing Alzheimer’s Disease Genetics the field of Alzheimer’s disease genetics. Alzheimer’s disease is an irreversible, progressive brain disease. It is charac- terized by the development of amyloid The Genetics of Disease plaques and neurofibrillary tangles, the loss of connections between nerve Some diseases are caused by a cells, or neurons, in the brain, and genetic mutation, or permanent the death of these nerve cells. There change in one or more specific are two types of Alzheimer’s—early- genes. If a person inherits from onset and late-onset. Both types have a parent a genetic mutation that a genetic component. causes a certain disease, then he or she will usually get the disease. Early-Onset Alzheimer’s Disease Sickle cell anemia, cystic fibrosis, and early-onset familial Alzheimer’s Early-onset Alzheimer’s disease disease are examples of inherited occurs in people age 30 to 60.
HUMAN GENE MAPPING WORKSHOPS C.1973–C.1991

HUMAN GENE MAPPING WORKSHOPS c.1973–c.1991 The transcript of a Witness Seminar held by the History of Modern Biomedicine Research Group, Queen Mary University of London, on 25 March 2014 Edited by E M Jones and E M Tansey Volume 54 2015 ©The Trustee of the Wellcome Trust, London, 2015 First published by Queen Mary University of London, 2015 The History of Modern Biomedicine Research Group is funded by the Wellcome Trust, which is a registered charity, no. 210183. ISBN 978 1 91019 5031 All volumes are freely available online at www.histmodbiomed.org Please cite as: Jones E M, Tansey E M. (eds) (2015) Human Gene Mapping Workshops c.1973–c.1991. Wellcome Witnesses to Contemporary Medicine, vol. 54. London: Queen Mary University of London. CONTENTS What is a Witness Seminar? v Acknowledgements E M Tansey and E M Jones vii Illustrations and credits ix Abbreviations and ancillary guides xi Introduction Professor Peter Goodfellow xiii Transcript Edited by E M Jones and E M Tansey 1 Appendix 1 Photographs of participants at HGM1, Yale; ‘New Haven Conference 1973: First International Workshop on Human Gene Mapping’ 90 Appendix 2 Photograph of (EMBO) workshop on ‘Cell Hybridization and Somatic Cell Genetics’, 1973 96 Biographical notes 99 References 109 Index 129 Witness Seminars: Meetings and publications 141 WHAT IS A WITNESS SEMINAR? The Witness Seminar is a specialized form of oral history, where several individuals associated with a particular set of circumstances or events are invited to meet together to discuss, debate, and agree or disagree about their memories. The meeting is recorded, transcribed, and edited for publication.
Cell Growth and Reproduction Lesson 6.2: Chromosomes and DNA Replication

Chapter 6: Cell Growth and Reproduction Lesson 6.2: Chromosomes and DNA Replication Cell reproduction involves a series of steps that always begin with the processes of interphase. During interphase the cell’s genetic information which is stored in its nucleus in the form of chromatin, composed of both mitotic and interphase chromosomes molecules of protein complexes and DNA strands that are loosely coiled winds tightly to be replicated. It is estimated that the DNA in human cells consists of approximately three billion nucleotides. If a DNA molecule was stretched out it would measure over 20 miles in length and all of it is stored in the microscopic nuclei of human cells. This lesson will help you to understand how such an enormous amount of DNA is coiled and packed in a complicated yet organized manner. During cell reproduction as a cell gets ready to divide the DNA coils even more into tightly compact structures. Lesson Objectives • Describe the coiled structure of chromosomes. • Understand that chromosomes are coiled structures made of DNA and proteins. They form after DNA replicates and are the form in which the genetic material goes through cell division. • Discover that DNA replication is semi-conservative; half of the parent DNA molecule is conserved in each of the two daughter DNA molecules. • Outline discoveries that led to knowledge of DNA’s structure and function. • Examine the processes of DNA replication. Vocabulary • centromere • double helix • Chargaff’s rules • histones • chromatid • nucleosomes • chromatin • semi-conservative DNA replication • chromosome • sister chromatids • DNA replication • transformation Introduction In eukaryotic cells, the nucleus divides before the cell itself divides.
Metabolism As Related to Chromosome Structure and the Duration of Life by John W

METABOLISM AS RELATED TO CHROMOSOME STRUCTURE AND THE DURATION OF LIFE BY JOHN W. GOWEN (From the Department of Animal Pathology of The Rockefeller Institute for Medical Research, Princeton, N. ].) (Received for publication, December 16, 1930) In this paper it is proposed to measure the katabollsm of four fundamentally distinct groups of animals all within the same species and having closely similar genetic constitutions. These groups differ in what are perhaps the most significant elements of life. The chromosome structure of the first group is that of the type female, diploid; the second group is that of the type male, diploid but having one X and Y instead of the two X-chromosomes of the type female; the third group of flies are triploid, three sex chromosomes and three sets of autosomes; the fourth group, sex-intergrades has two X-chromo- somes and three sets of autosomes. Katabolism is a direct function of the cells composing the bodies of all animals. The cells of these four groups differ in size; the type male cells are the smallest; the females are somewhat, possibly a tenth, larger; the sex-intergrades and triploid cells are a half larger. The larger cell size suggests that any function within the cell would be performed in a larger way. The carbon dioxide production should enable us to measure physiologically the extent of this activity and present us with data on that fundamental point the relation of cell size to metabolic activity. The durations of life of these different groups have been measured. The forms with the balanced chromosome complexes within their cells live the longest time, the unbalanced groups the least.
Genetic Variation in Chromosome Y Regulates Susceptibility to Influenza a Virus Infection

Genetic variation in chromosome Y regulates susceptibility to influenza A virus infection Dimitry N. Krementsova, Laure K. Casea, Oliver Dienzb, Abbas Razaa, Qian Fanga, Jennifer L. Athera, Matthew E. Poyntera, Jonathan E. Boysonb, Janice Y. Bunnc, and Cory Teuschera,d,1 aDepartment of Medicine, University of Vermont, Burlington, VT 05405; bDepartment of Surgery, University of Vermont, Burlington, VT 05405; cDepartment of Medical Biostatistics, University of Vermont, Burlington, VT 05405; and dDepartment of Pathology, University of Vermont, Burlington, VT 05405 Edited by Sabra Klein, Johns Hopkins University, Baltimore, MD, and accepted by Editorial Board Member Peter Palese January 23, 2017 (received for review December 20, 2016) Males of many species, ranging from humans to insects, are more encephalomyelitis (EAE) in SJL/J mice, which are controlled by susceptible than females to parasitic, fungal, bacterial, and viral genetic variation in ChrY (23–25). Moreover, with respect to infections. One mechanism that has been proposed to account for viral infections, we reported that genetic variation in ChrY this difference is the immunocompetence handicap model, which influences both survival following infection with Coxsackie- posits that the greater infectious disease burden in males is due to virus B3 virus (CVB3) (26) and susceptibility to CVB3-induced testosterone, which drives the development of secondary male sex autoimmune myocarditis (27). To address whether genetic vari- characteristics at the expense of suppressing immunity. However, ation in ChrY is capable of influencing susceptibility to IAV and emerging data suggest that cell-intrinsic (chromosome X and Y) the associated sex differences, we studied the susceptibility of a sex-specific factors also may contribute to the sex differences in panel of ChrY consomic strains on the C57BL/6J background infectious disease burden.
Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time

non-coding RNA Perspective Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time Nicholas Delihas Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, NY 11794-5222, USA; [email protected] Received: 16 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Abstract: A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, and the long noncoding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionarily conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin-specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it is presented. Keywords: de novo gene birth; gene evolution; protogene; long noncoding RNA genes; pseudogenes; USP18; GGT5; Alu sequences 1. Introduction The genesis of genes has been a major topic of interest for several decades [1,2]. One mechanism of gene formation is by duplication of existing genes [1,3].