THE MENDEL NEWSLETTER Archival Resources for the History of Genetics & Allied Sciences
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Models of the Gene Must Inform Data-Mining Strategies in Genomics
entropy Review Models of the Gene Must Inform Data-Mining Strategies in Genomics Łukasz Huminiecki Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, 00-901 Warsaw, Poland; [email protected] Received: 13 July 2020; Accepted: 22 August 2020; Published: 27 August 2020 Abstract: The gene is a fundamental concept of genetics, which emerged with the Mendelian paradigm of heredity at the beginning of the 20th century. However, the concept has since diversified. Somewhat different narratives and models of the gene developed in several sub-disciplines of genetics, that is in classical genetics, population genetics, molecular genetics, genomics, and, recently, also, in systems genetics. Here, I ask how the diversity of the concept impacts data-integration and data-mining strategies for bioinformatics, genomics, statistical genetics, and data science. I also consider theoretical background of the concept of the gene in the ideas of empiricism and experimentalism, as well as reductionist and anti-reductionist narratives on the concept. Finally, a few strategies of analysis from published examples of data-mining projects are discussed. Moreover, the examples are re-interpreted in the light of the theoretical material. I argue that the choice of an optimal level of abstraction for the gene is vital for a successful genome analysis. Keywords: gene concept; scientific method; experimentalism; reductionism; anti-reductionism; data-mining 1. Introduction The gene is one of the most fundamental concepts in genetics (It is as important to biology, as the atom is to physics or the molecule to chemistry.). The concept was born with the Mendelian paradigm of heredity, and fundamentally influenced genetics over 150 years [1]. -
Nature Medicine Essay
COMMENTARY LASKER BASIC MEDICAL RESEARCH AWARD Of maize and men, or peas and people: case histories to justify plants and other model systems David Baulcombe One of the byproducts of molecular biology cork is altogether filled with air, and that air is has been support for the ‘model system’ con- perfectly enclosed in little boxes or cells distinct cept. All living organisms are based on the same from one another.”)2 (Fig. 1). Two hundred fifty genetic code, they have similar subcellular years later, Beijerinck discovered a contagium structures and they use homologous metabolic vivum fluidum in extracts of diseased tobacco pathways. So, mechanisms can be investigated plants that he later referred to as a virus3. using organisms other than those in which In contemporary science, a green alga— the knowledge will be exploited for practical Chlamydomonas reinhardtii—is a useful model benefit. Model systems are particularly use- in the analysis of kidney disease4. However, ful in the early discovery phase of a scientific in this article, I refer to the contribution of endeavor, and recent progress in biomedical plant biology to a family of mechanisms that I science has fully vindicated their use. Jacques refer to as RNA silencing. This topic has been Monod, for example, famously justified his reviewed comprehensively elsewhere5,6, so here work on a bacterial model system by stating I focus on personal experience and my view of that “what is true for Escherichia coli is also future potential from this work. true for elephants.” My fellow laureates, Victor Ambros and Gary Ruvkun, can defend the use The early history of RNA silencing in of the worm Caenorhabditis elegans as a good plants model system and so I will focus on plants. -
Introduction and Historical Perspective
Chapter 1 Introduction and Historical Perspective “ Nothing in biology makes sense except in the light of evolution. ” modified by the developmental history of the organism, Theodosius Dobzhansky its physiology – from cellular to systems levels – and by the social and physical environment. Finally, behaviors are shaped through evolutionary forces of natural selection OVERVIEW that optimize survival and reproduction ( Figure 1.1 ). Truly, the study of behavior provides us with a window through Behavioral genetics aims to understand the genetic which we can view much of biology. mechanisms that enable the nervous system to direct Understanding behaviors requires a multidisciplinary appropriate interactions between organisms and their perspective, with regulation of gene expression at its core. social and physical environments. Early scientific The emerging field of behavioral genetics is still taking explorations of animal behavior defined the fields shape and its boundaries are still being defined. Behavioral of experimental psychology and classical ethology. genetics has evolved through the merger of experimental Behavioral genetics has emerged as an interdisciplin- psychology and classical ethology with evolutionary biol- ary science at the interface of experimental psychology, ogy and genetics, and also incorporates aspects of neuro- classical ethology, genetics, and neuroscience. This science ( Figure 1.2 ). To gain a perspective on the current chapter provides a brief overview of the emergence of definition of this field, it is helpful -
A Short History of DNA Technology 1865 - Gregor Mendel the Father of Genetics
A Short History of DNA Technology 1865 - Gregor Mendel The Father of Genetics The Augustinian monastery in old Brno, Moravia 1865 - Gregor Mendel • Law of Segregation • Law of Independent Assortment • Law of Dominance 1865 1915 - T.H. Morgan Genetics of Drosophila • Short generation time • Easy to maintain • Only 4 pairs of chromosomes 1865 1915 - T.H. Morgan •Genes located on chromosomes •Sex-linked inheritance wild type mutant •Gene linkage 0 •Recombination long aristae short aristae •Genetic mapping gray black body 48.5 body (cross-over maps) 57.5 red eyes cinnabar eyes 67.0 normal wings vestigial wings 104.5 red eyes brown eyes 1865 1928 - Frederick Griffith “Rough” colonies “Smooth” colonies Transformation of Streptococcus pneumoniae Living Living Heat killed Heat killed S cells mixed S cells R cells S cells with living R cells capsule Living S cells in blood Bacterial sample from dead mouse Strain Injection Results 1865 Beadle & Tatum - 1941 One Gene - One Enzyme Hypothesis Neurospora crassa Ascus Ascospores placed X-rays Fruiting on complete body medium All grow Minimal + amino acids No growth Minimal Minimal + vitamins in mutants Fragments placed on minimal medium Minimal plus: Mutant deficient in enzyme that synthesizes arginine Cys Glu Arg Lys His 1865 Beadle & Tatum - 1941 Gene A Gene B Gene C Minimal Medium + Citruline + Arginine + Ornithine Wild type PrecursorEnz A OrnithineEnz B CitrulineEnz C Arginine Metabolic block Class I Precursor OrnithineEnz B CitrulineEnz C Arginine Mutants Class II Mutants PrecursorEnz A Ornithine -
North American Rock Garden Society |
Bulletin of the American Rock Garden Society Vol. 38 Spring 1980 No. 2 The Bulletin Editor Emeritus DR. EDGAR T. WHERRY, Philadelphia, Pa. Editor LAURA LOUISE FOSTER, Falls Village, Conn. 06031 Assistant Editor HARRY DEWEY, 4605 Brandon Lane, Bellsville, Md. 20705 Contributing Editors: Layout Designer: BUFFY PARKER Business Manager ANITA KISTLER, 1421 Ship Rd., West Chester, Pa. 19380 Contents Vol. 38 No. 2 Spring 1980 Erigenia Bulbosa—W. J. Hamilton Jr 53 The Mount Evans Region: Overview—Stanley C. Mahoney 55 Cacti: America's Foremost Rock Plants, Part III—Allan R. Taylor and Panayoti Callas - 59 The Bog—Deanna K. Hagen 66 Not All Plantsmen Are Men: Mary Gibson Henry, Part I— Josephine deN. Henry 68 In a Southwestern Garden—Ray Williams 74 Garden Visits in Czechoslovakia—Hans W. Asmus 80 Seed Preferences, 1978 and 1979—Betty J. Lowry and Ned M. Lowry 82 A Superb Hardhead—Zdenek Zvolanek ~ 86 Book Reviews: Mountain Flower Holidays in Europe by Dr. Lionel J. Bacon 87 Rock Gardening in the South, Part 3—Dwarf and Pygmy Conifers— Elizabeth Lawrence 90 Gardening in Sand—Norman C. Deno 95 Of Cabbages and Kings: Note on Phlox Bifida—Mina Colvin 97 Front Cover Picture—Erigenia bulbosa—William C. Dilger, Freeville, N.Y. Published quarterly by the AMERICAN ROCK GARDEN SOCIETY, incorporated under the laws of the State of New Jersey. You are invited to join. Annual dues (Bulletin included) are: Ordinary Membership, $9.00; Family Membership (two per family), $10.00; Overseas Mem• bership, $8.00 each to be submitted in U.S. funds or International Postal Money Order; Patron's Membership, $25; Life Membership, $250. -
The Population Problem Inherited Evolutio
2000 Earthlearningidea - http://www.earthlearningidea.com/ top edge of Sorting out the evolution of evolution headlines page Lay out your own timeline of how the theory of evolution developed Cut off the left hand edge of these four Earthlearningidea sheets and stick them together to form a timeline. Then stick it down on a bench or table. The ‘Evolution of evolution’ timeline Cut out the milestone boxes in the evolution of evolutionary theory below into strips. Leave the dates attached for less able pupils, but remove them for the more able. Then invite the pupils to sort out the headlines 1975 and place them in the correct places on the timeline – to show how evolutionary theory Photo: Chris King evolved. Species static This image is in the public The early part of the bible is interpreted to show that domain because species are static and there is no evolution. The date of its copyright has expired. 1650 creation of all species is calculated by Archbishop Ussher as 4004BC. Archbishop Ussher Evolution – but how? This image is in the public Early evolutionary ideas are presented by natural domain because 1740 philosophers, Pierre Maupertuis and Erasmus Darwin. its copyright has - expired. 1796 1950 Pierre Maupertuis The population problem This image is in the public Thomas Malthus publishes his idea that populations domain because increase geometrically (2,4,16) whilst food production its copyright has 1798 only increases arithmetically (2,3,4) so there must be expired. population crashes. Thomas Malthus Inherited evolution Permission is granted to copy, Jean-Baptiste Lamarck develops his evolutionary theory distribute and/or – that evolution occurs because offspring change in modify this document under 1800 response to the environment, and these changes are the terms of the inherited from their parents (later shown to be 1925 GNU Free incorrect). -
Florida Women's Heritage Trail Sites 26 Florida "Firsts'' 28 the Florida Women's Club Movement 29 Acknowledgements 32
A Florida Heritag I fii 11 :i rafiM H rtiS ^^I^H ^bIh^^^^^^^Ji ^I^^Bfi^^ Florida Association of Museums The Florida raises the visibility of muse- Women 's ums in the state and serves as Heritage Trail a liaison between museums ^ was pro- and government. '/"'^Vm duced in FAM is managed by a board of cooperation directors elected by the mem- with the bership, which is representa- Florida tive of the spectrum of mu- Association seum disciplines in Florida. of Museums FAM has succeeded in provid- (FAM). The ing numerous economic, Florida educational and informational Association of Museums is a benefits for its members. nonprofit corporation, estab- lished for educational pur- Florida Association of poses. It provides continuing Museums education and networking Post Office Box 10951 opportunities for museum Tallahassee, Florida 32302-2951 professionals, improves the Phone: (850) 222-6028 level of professionalism within FAX: (850) 222-6112 the museum community, www.flamuseums.org Contact the Florida Associa- serves as a resource for infor- tion of Museums for a compli- mation Florida's on museums. mentary copy of "See The World!" Credits Author: Nina McGuire The section on Florida Women's Clubs (pages 29 to 31) is derived from the National Register of Historic Places nomination prepared by DeLand historian Sidney Johnston. Graphic Design: Jonathan Lyons, Lyons Digital Media, Tallahassee. Special thanks to Ann Kozeliski, A Kozeliski Design, Tallahassee, and Steve Little, Division of Historical Resources, Tallahassee. Photography: Ray Stanyard, Tallahassee; Michael Zimny and Phillip M. Pollock, Division of Historical Resources; Pat Canova and Lucy Beebe/ Silver Image; Jim Stokes; Historic Tours of America, Inc., Key West; The Key West Chamber of Commerce; Jacksonville Planning and Development Department; Historic Pensacola Preservation Board. -
Epigenetics Is Normal Science, but Don't Call It Lamarckian
Extended Abstract Volume 6:3, 2020 DOI: 6.2472/imedipce.2020.6.002 Journal of Clinical Epigenetics ISSN: 2472-1158 Open Access Epigenetics is Normal Science, But Don’t Call It Lamarckian David Penny New Zealand Extended Abstract they are general (but not necessarily universal) because they are found in Excavates, which many people consider are ancestral to other eukaryotes [6, 7]. Similarly, an important point is that Epigenetic mechanisms are increasingly being accepted as an integral methylation, phosphorylation, etc. of the DNA and of the histones is a part of normal science. Earlier genetic studies appear to have part of normal evolution (at least in eukaryotes that have the assumed that the only changes were ‘mutations’ as a result of a nucleosome structure) [8]. One of the most interesting aspects is change in the DNA sequence. If any such changes altered the amino methylation (and hydroxymethylation) of cytosine, and this is found in acid sequences then it was effectively a mutation, and if it occurred in many deep branching eukaryotes [9]. Typically there is methylation of a germline cell (including in unicellular organisms) then it could be cytosine molecules, especially in CpG (cytosine followed by guanine) passed on to subsequent generations. However, it is increasingly regions. The role of small RNAs in helping regulate the levels of apparent that other changes are also important, for example, changes protein expression is discussed in [10]. The main point here is that to methylation patterns, and to the histone proteins. Epigenetics was protein expression levels are very variable in all cells – it is not just sometimes consider ‘additional’ to classical genetics, but it is still fully classical genetics that is important; there are many epigenetic dependent on DNA, RNA and protein sequences, and at least since [1] mechanisms affecting the differences in protein expression. -
Using Classical Genetics Simulator (CGS) to Teach Students the Basics of Genetic Research
Tested Studies for Laboratory Teaching Proceedings of the Association for Biology Laboratory Education Vol. 33, 85–94, 2012 Using Classical Genetics Simulator (CGS) to Teach Students the Basics of Genetic Research Jean Heitz1, Mark Wolansky2, and Ben Adamczyk3 1University of Wisconsin, Zoology Department, 250 N. Mills Street, Madison WI 53706 USA 2University of Alberta, Department of Biological Science, Edmonton AB, CAN T6G 2E9 3Genedata, MA, A-1 Cranberry HI, Lexington MA 02421 USA ([email protected];[email protected];[email protected]) Some experiments are not well suited to large introductory labs because of space, time and funding constraints. Among these are classical Mendelian genetics investigations. Cyber labs can overcome these constraints. Classi- cal Genetics Simulator (CGS) gives students the opportunity to perform controlled crosses with model organisms much like a geneticist would do. CGS provides populations of Drosophila, Arabidopsis or mice with unknown patterns of inheritance and gives students the tools to design and perform experiments to discover these patterns. Students require an understanding of the what, why and how of solving genetic problems to successfully complete our cyber genetics lab activities. Keywords: Mendelian genetics, simulator, classical genetics simulator (CGS), linkage, monohybrid, dihybrid Introduction In large introductory biology classes some labs are dif- How can students get practice doing what geneticists ficult to do because of space, time and funding constraints. actually do? Among these are classical Mendelian genetics investiga- An obvious way for students to get practice doing what tions. As a result, we have turned to cyber labs. Working geneticists do is to conduct actual crosses. -
Grassroots Resistance
HUMAN VALUES—INSIGHTS, IMPLICATIONS, APPLICATIONS Grassroots Resistance Marjorie Harris Carr, Ecology, and the Battle to Stop the Cross Florida Barge Canal Leslie Kemp Poole Rollins College n the 1960s the U.S. government began construction of a long-held dream—creating a watery transportation canal I across north Florida to shorten treacherous trade routes. The project promised an infusion of federal dollars and new jobs in this mostly rural area and was considered a “done deal.” That is, until Marjorie Harris Carr (1915–1997) led Florida’s first major grassroots crusade to stop the project from harming the state’s fragile environment. Using facts and the science of ecology, and by engaging the media, Carr and company achieved the seemingly impossible—stopping a major federal public works project in its tracks and setting the stage for future environmental skirmishes across the state and nation. They proved that a skeptical citizenry well-armed with data and determination could overcome the questionable promises of politicians and bureaucrats, leading to a court decision and presidential edict that supported their contention that the potential for environmental damage needs to be assessed before boondoggle projects are undertaken. Since the early days of Spanish occupation in Florida, settlers shared a dream of building a canal across the peninsula to link the Gulf of Mexico with the Atlantic Ocean. This canal would greatly improve the passage of the Spanish treasure fleets that might avoid the treacherous Straits of Florida to the south, an area of shallows, coral reefs, hurricanes, pirates, and “wreckers.” Canal fever continued into the ensuing centuries, and the first U.S. -
Genome As a Multipurpose Structure Built by Evolution Michel Morange
1 Genome as a multipurpose structure built by evolution Michel Morange, Centre Cavaillès, République des savoirs USR 3608, Ecole normale supérieure, 29 rue d’Ulm, 75230 Paris Cedex05, France Email: [email protected] Abstract The publication in 2012 of the results of the ENCODE program generated an acrimonious debate about the role of junk DNA. This debate is a symptom of the difficulties of dovetailing functional and evolutionary descriptions of genomes. My argument is that extant genomes are the result of a progressive evolutionary construction. To the basic function – to give rise to RNA and proteins – have been successively added other functions – regulation by microRNA and epigenetic marks, for instance. This process of complexification was not a regular one, but the result of a complex evolutionary history, different for the different genomes. Better knowledge of the evolutionary history of genomes would help to understand these structures and their functions. Historians and philosophers of biology have amply discussed the difficulty, even the impossibility, of providing a precise definition of a gene (Beurton et al. 2000). The genome no longer appears as a collection of similar genes, but as a multitasking structure formed of different types of genetic elements (Gingeras 2006). Participants in these debates nonetheless often agree on one issue, that the genome is (and has to be) something well defined: a collection of genes, a 2 reservoir of junk DNA, or a structure filled with regulatory sequences. My point of view will be different: the genome is what evolution has progressively made of it. This vision has three important consequences. -
The Sustained Impact of Model Organisms—In Genetics and Epigenetics
| COMMENTARY The Sustained Impact of Model Organisms—in Genetics and Epigenetics Nancy M. Bonini*,†,1 and Shelley L. Berger‡,1 *Department of Cellular and Developmental Biology, Perlman School of Medicine, †Department of Biology, and ‡Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104 KEYWORDS classical genetics; epigenetics; behavior; genomics; human disease Now that DNA sequencing can reveal disease-relevant muta- The Rise of Model Organism Genetics and the tions in humans, it is appropriate to consider the history of Embrace of Molecular Genetics genetic research on model organisms, and whether model Model organism genetics has revealed many fundamental organisms will continue to play an important role. Our view is biological processes. This was achieved by applying unbiased that genetic research in model organisms has had an in- genetic screens to reveal genes and their mechanisms of disputably enormous impact on our understanding of com- action in processes such as cell cycle control (Nasmyth plex biological pathways and their epigenetic regulation, and 2001), basic body plan specification and mechanisms of de- on the development of tools and approaches that have been velopment (Lewis 1978; Nusslein-Volhard and Wieschaus crucial for studies of human biology. We submit that model 1980), and cell death pathways (Ellis and Horvitz 1986; organisms will remain indispensable for interpreting complex Avery and Horvitz 1987), all of which were recognized with genomic data, for testing hypotheses regarding function, and Nobel prizes. for further study of complex behaviors, to reveal not only The sequencing of genomes revealed the breadth of the novel genetic players, but also the profound impact of epige- conservation of genes, and of entire pathways.