Ancient DNA: a History of the Science Before Jurassic Park
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A Novel SERRS Sandwich-Hybridization Assay To
A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target Cecile Feuillie, Maxime Mohamad Merheb, Benjamin Gillet, Gilles Montagnac, Isabelle Daniel, Catherine Haenni To cite this version: Cecile Feuillie, Maxime Mohamad Merheb, Benjamin Gillet, Gilles Montagnac, Isabelle Daniel, et al.. A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target. PLoS ONE, Public Library of Science, 2011, 6 (5), pp.e17847. 10.1371/journal.pone.0017847. hal-00659271 HAL Id: hal-00659271 https://hal.archives-ouvertes.fr/hal-00659271 Submitted on 12 Jan 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target Ce´cile Feuillie1., Maxime Mohamad Merheb2., Benjamin Gillet3, Gilles Montagnac1, Isabelle Daniel1, Catherine Ha¨nni2* 1 Laboratoire de Ge´ologie de Lyon - Terre Plane`tes Environnement, ENS Lyon, Universite´ Lyon 1, CNRS, Ecole Normale Supe´rieure de Lyon, Lyon, France, 2 Institut de Ge´nomique Fonctionnelle de Lyon, Universite´ Lyon 1, CNRS, INRA, Ecole Normale Supe´rieure de Lyon, Lyon, France, 3 Plateforme nationale de Pale´oge´ne´tique UMS PALGENE, CNRS - ENS de Lyon, Lyon, France Abstract In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. -
"Paleogenomics" In
Rev. Cell Biol. Mol. Medicine Paleogenomics 243 Paleogenomics Peter D. Heintzman*, André E. R. Soares*, Dan Chang, and Beth Shapiro Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA 1 Reconstructing Paleogenomes 245 1.1 Ancient DNA 245 1.1.1 The Nature of Ancient DNA 245 1.1.2 The Common Effects of DNA Damage 246 1.2 The Recovery and Sequencing of Ancient DNA 246 1.2.1 Ancient DNA Extraction 246 1.2.2 DNA Library Preparation 247 1.2.3 Capture-Based Target Enrichment 248 1.2.4 Quantification of aDNA and Sequencing 249 1.3 Assembly and Analysis of a Paleogenome 250 1.3.1 Initial Data Processing 251 1.3.2 Mapping and Quality Control 252 1.3.3 Paleogenomic Analysis 253 2 Case Studies 253 2.1 Hominin Paleogenomics 253 2.1.1 The Origin of Hominin Paleogenetics 253 2.1.2 Entering the Paleogenomics Era 254 2.1.3 The First Complete Human Paleogenome 255 2.1.4 Human and Neandertal Paleogenomics 255 2.2 The Black Death and Insights into Ancient Plagues 257 2.3 Reconstruction and Selection of Ancient Phenotypes 258 2.4 Epigenetics of Ancient Species 260 3 Conclusions 261 Acknowledgments 261 References 261 ∗These authors contributed equally to this study. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA Vol 1 | No 3 | 2015 244 Paleogenomics Rev. Cell Biol. Mol. Medicine Keywords Paleogenomics The science of reconstructing and analyzing the genomes of organisms that are not alive in the present day. Ancient DNA (aDNA) Ancient DNA is DNA that is extracted and characterized from degraded biological spec- imens, including preserved bones, teeth, hair, seeds, or other tissues. -
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. -
Mapping Our Genes—Genome Projects: How Big? How Fast?
Mapping Our Genes—Genome Projects: How Big? How Fast? April 1988 NTIS order #PB88-212402 Recommended Citation: U.S. Congress, Office of Technology Assessment, Mapping Our Genes-The Genmne Projects.’ How Big, How Fast? OTA-BA-373 (Washington, DC: U.S. Government Printing Office, April 1988). Library of Congress Catalog Card Number 87-619898 For sale by the Superintendent of Documents U.S. Government Printing Office, Washington, DC 20402-9325 (order form can be found in the back of this report) Foreword For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technol- ogy, and politics. Congress is responsible for ‘(writing the rules” of what various Federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the U.S. Congress, The House Committee on Energy and Commerce requested that OTA undertake the project. The House Committee on Science, Space, and Technology, the Senate Com- mittee on Labor and Human Resources, and the Senate Committee on Energy and Natu- ral Resources also asked OTA to address specific points of concern to them. Congres- sional interest focused on several issues: ● how to assess the rationales for conducting human genome projects, ● how to fund human genome projects (at what level and through which mech- anisms), ● how to coordinate the scientific and technical programs of the several Federal agencies and private interests already supporting various genome projects, and ● how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. -
Curriculum Vitae Johannes Krause
Curriculum vitae Johannes Krause Born 1980 in Leinefelde, Thuringia, Germany Contact Max Planck Institute for Evolutionary Anthropology Department of Archaeogenetics Deutscher Platz 6 04103 Leipzig, GERMANY E-mail [email protected] Webpage https://www.eva.mpg.de/archaeogenetics/staff.html Research Focus • Ancient DNA • Archaeogenetics • Human Evolution • Ancient Pathogen Genomics • Comparative and Evolutionary Genomics • Human Immunogenetics Present Positions since 2020 Director, Max Planck Institute for Evolutionary Anthropology, Leipzig, Department of Archaeogenetics since 2018 Full Professor for Archaeogenetics, Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena since 2016 Director, Max-Planck – Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM) since 2015 Honorary Professor for Archaeo- and Paleogenetics, Institute for Archaeological Sciences, Eberhard Karls University Tuebingen Professional Career 2014 - 2020 Director, Max Planck Institute for the Science of Human History, Jena, Department of Archaeogenetics 2013 - 2015 Full Professor (W3) for Archaeo- and Paleogenetics, Institute for Archaeological Sciences, Eberhard Karls University Tuebingen 2010 - 2013 Junior Professor (W1) for Palaeogenetics, Institute for Archaeological Sciences, Eberhard Karls University Tuebingen 2008 - 2010 Postdoctoral Fellow at the Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany. Research: Ancient human genetics and genomics 2005 - -
1 Constructing the Scientific Population in the Human Genome Diversity and 1000 Genome Projects Joseph Vitti I. Introduction: P
Constructing the Scientific Population in the Human Genome Diversity and 1000 Genome Projects Joseph Vitti I. Introduction: Populations Coming into Focus In November 2012, some eleven years after the publication of the first draft sequence of a human genome, an article published in Nature reported a new ‘map’ of the human genome – created from not one, but 1,092 individuals. For many researchers, however, what was compelling was not the number of individuals sequenced, but rather the fourteen worldwide populations they represented. Comparisons that could be made within and among these populations represented new possibilities for the scientific study of human genetic variation. The paper – which has been cited over 400 times in the subsequent year – was the output of the first phase of the 1000 Genomes Project, one of several international research consortia launched with the intent of identifying and cataloguing such variation. With the project’s phase three data release, anticipated in early spring 2014, the sample size will rise to over 2500 individuals representing twenty-six populations. Each individual’s full sequence data is made publicly available online, and is also preserved through the establishment of immortal cell lines, from which DNA can be extracted and distributed. With these developments, population-based science has been made genomic, and scientific conceptions of human populations have begun to crystallize (see appendix). Such extensive biobanking and databasing of human populations is remarkable for a number of reasons, not least among them the socially charged terrain that such an enterprise inevitably must navigate. While the 1000 Genomes Project (1000G) has been relatively uncontroversial in its reception, predecessors such as the Human Genome Diversity Project (HGDP), first conceived in 1991, faced greater difficulty. -
Commencement Program 1977 Whitworth University
Whitworth Digital Commons Whitworth University Commencement Programs University Archives 1977 Commencement Program 1977 Whitworth University Follow this and additional works at: https://digitalcommons.whitworth.edu/commencement- programs Recommended Citation Whitworth University , "Commencement Program 1977" Whitworth University (1977). Commencement Programs. Paper 45. https://digitalcommons.whitworth.edu/commencement-programs/45 This Book is brought to you for free and open access by the University Archives at Whitworth University. It has been accepted for inclusion in Commencement Programs by an authorized administrator of Whitworth University. EIGHTY-SEVENTH SPRING COMMENCEMENT SUNDAY, MAY 15, 1977 Spokane, Washington "Friends, Iwill remember you, think of you, pray for you. And when another day is through I'll still be friends with you." THE PRELUDE THE CONFERRING OF THE GRADUATE DEGREES The Whitworth College Concert Band Edward B. Lindaman, L.H.D., Sc.D., President Richard V. Evans, DMA., Director Duncan S. Ferguson, Ph.D., Vice-President for Academic Affairs Jack W. Hatch, Vice-Chairman of the Board of Trustees Alvin B. Quail, Ed.D., Professor of Education, Director of Graduate THE PROCESSIONAL Studies March Processional Clare E. Grundman Ronald R. Short, Ph.D., Professor of Psychology, Director of M.A.A.B.S. The Whitworth College Concert Band Program Richard V. Evans, DMA., Director Glenn E. Fehler, M.Ed., Registrar THE INVOCATION A HYMN Ronald C. White, Ph.D., Chaplain Joyful, Joyful, We Adore Thee Joyful, joyful, we adore Thee, God of glory, Lord of love; Hearts unfold like flowers before Thee, Opening to the sun above. SCRIPTURE Melt the clouds of sin and sadness, Drive the dark of doubt away; Giver of immortal gladness, Fill us with the light of day. -
How to Resurrect Ancestral Proteins As Proxies for Ancient Biogeochemistry T ∗ Amanda K
Free Radical Biology and Medicine 140 (2019) 260–269 Contents lists available at ScienceDirect Free Radical Biology and Medicine journal homepage: www.elsevier.com/locate/freeradbiomed How to resurrect ancestral proteins as proxies for ancient biogeochemistry T ∗ Amanda K. Garciaa, Betül Kaçara,b, a Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA b Department of Astronomy and Steward Observatory, University of Arizona, Tucson, AZ, 85721, USA ARTICLE INFO ABSTRACT Keywords: Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical Ancestral sequence reconstruction cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of en- Great oxidation event zymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, Nitrogenase interpretations of these signatures are limited by the assumption that such enzymes have remained functionally Paleophenotype conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in con- Phylogenetic uncertainty junction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to RuBisCO Biosignatures experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within mo- lecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme -
CURRENT TECHNOLOGY and RESOURCE NEEDS the Specific and Primary Agouronpurposes Are to Perform Research in the Sciences
The Agouron Institute GEOBIOLOGY CURRENT TECHNOLOGY and RESOURCE NEEDS The specific and primary AGOURONpurposes are to perform research in the sciences INSTITUTEand in mathematics, to disseminate the results obtained therefrom, all to benefit mankind. Cover photo: Phototrophic sulfur and non-sulfur bacteria in an enrichment from a microbial mat reveal part of the enormous diversity of microorganisms. © 2001 The Agouron Institute 45 GEOBIOLOGY CURRENT TECHNOLOGY and RESOURCE NEEDS The Agouron Institute INTRODUCTION 3 GEOBIOLOGY: 5 Current Research General Overview 5 Advances in Probing The Rock Record 6 Advances in Molecular Biology and Genomics 9 Current Research Directions 11 Questions of What and When: Detecting Life in the Geologic Record 12 Molecular Fossils 12 Morphological Fossils 14 Isotopic Signatures 16 Question of Who and How: Deciphering the Mechanisms of Evolution 18 Genetic Diversity 18 Microbial Physiology 20 Eukaryotic Systems 23 Experimental Paleogenetics 25 GEOBIOLOGY: Resource Needs 29 An Intensive Training Course in Geobiology 30 A Postdoctoral Fellowship Program in Geobiology 31 Support for Specific Research Projects 32 REFERENCES 34 2 Agouron Institute had expanded considerably and had obtained additional funding from the NSF and the NIH. A group of molecular biologists and chemists were collaborating to exploit new technology in which synthetic oligonucleotides were used to direct specific mutations in genes. A crystallography group had been INTRODUCTION formed and they were collaborating with the molecular biologists to study the properties of the altered proteins. These were among the very first applications of the new technology to form what is now the very ith the discovery of recombi- large field of protein engineering. -
Multiple Substitutions Create Biased Estimates of Divergence Times and Small Increases in the Variance to Mean Ratio
Heredity 58 (1987) 331-339 The Genetical Society of Great Britain Received 30 May 1986 Multiple substitutions create biased estimates of divergence times and small increases in the variance to mean ratio G. Brian GoJding Department of Biology, 4700 Keele St., York University, North York, Ontario, Canada M3J 1P3. Analysis of mutational processes has demonstrated that mutations usually occur as non-random events with many factors that influence the fidelity of DNA replication. One such unusual pattern of mutation shows that some mutational events will create more than one sequence alteration. This possibility is not generally considered in estimates of sequence divergence and yet affects both the mean and variance of these estimates. Theoretical results and simulation results are presented to examine how extensive the effects of multiple alterations resulting from single mutational events may be on sequence divergence. It is shown that estimates of the divergence times are biased but that this bias is not large unless the number of sequence alterations per event are unrealistically large. The number of alterations per event required to achieve a given bias is determined. The variance is increased by multiple alterations above the variance expected for the same mean number of single alterations, but not up to the levels that are observed in nature. The resulting increase in the variance to mean ratio changes with the amount of divergence, from an initially high ratio followed by a slow decline to one. INTRODUCTION nucleotides (Kimura, 1981; Aoki et aL, 1980; Sequencecomparisons among homologous genes Takahata and Kimura, 1981; Kaplan and Risko, allow differences between species to be measured 1982; Aquadro et a!., 1984). -
Allan Wilson Centre Key OUTREACH Achievements
underscopethe ALLAN WILSON CENTRE KEY OUTREACH ACHIEVEMENTS HAMISH SPENCER BREEDING SHEEP IN NEW ZEALAND AND CHINA, LINKING CHARLES DARWIN, BEER ADVERTISING AND GENETICS At the first Joint Research Centre workshop on Sheep Breeding and Development Biology Hamish spoke at the Chinese Academy of Sciences in Beijing about the connections between his theoretical work on evolution and recent research showing how the environment in the broadest sense affects gene function. What’s the link between Charles Darwin, beer advertising and genetics? Hamish revealed the relationship between these seeming disparate elements in two presentations, one to Invercargill’s University of the Third Age and one to the local community and senior students at Tolaga Bay Area School. WENDY NEWPORT-SMITH COMMEMORATING ALLAN WILSON, SUPPORTING BIOLOGY EDUCATION, BUILDING SUSTAINABLE COMMUNITIES The Allan Wilson Centre organised Out of Africa, the successful lecture series commemorating Allan Wilson’s life and work delivered by Rebecca Cann, Professor of Cell and Molecular Biology at the University of Hawaii. A former graduate of Allan’s, Professor Cann shared with capacity audiences in Dunedin, Nelson, Auckland, Wellington and Palmerston North her experiences of working with Allan and the changes in evolutionary biology since his death 20 years ago. Allan Wilson’s contribution to science was the topic of a keynote address delivered by Allan Wilson Centre Director Charles Daugherty at The Biology Educators’ Association of New Zealand BioLive conference as part of our sponsorship of the event. Our sponsorship included hosting an event for educators and the launch of a powerpoint presentation to introduce evolutionary concepts to Year 10 students, using the story of human evolution as an example. -
Nature November 1984.Pdf
to@ ANrn\ :,Ar( I\LVVJAI\U^,r,^/. ViLtiJ fossil evolutionar.v s1'nthesis by studying DNA, stiil look like nothing more tnan.a Palaeomolecular !t"lggJ too early tr'1 nlorious dream. Hou ever, it is far io nitl"up. and it nright just be possible.that buneo fossilized Raising the dead and ;SA ;;t ,ur" i' ed in some ^"materlal. point: DNA can easily be from Alec J. JeffreYs One final iare outiii.a ito* animals that have died' and Not press) and my oun (unpublished) survive for the quagga as dead as a dodo? of DNA [".. J.i.a it is stable and should Is ;;;;; ih;, suLstanrialquantities It is there- i"tit.'rtl""iior indeed might be the dodo' .i"*i.t rvithout degradation' Russell can be recor ered fronr Prcserveo or museums should ii";;';;;;rkable findinss of almost fore viral thar zoos co-workers rn"*rnotft tissue' Unfortunately' to store DNA from as iii-".rti, Allan wilson and microbial con- siart sysrematically of this issue are it comes from recent as possible' and certainly ;;;-ili on Page 282 "ii"i probably introduced after .uny'rp..i.t go Because even though the iu-i"urion, any that face exrinction' Friedrich ;'";;t;;,o uv;. Elephant-like DNA sequences froni chimaera of horse and excavation. *ho discovered nucleic acid in ouunnu. u curious at vanishingli' low levels (less tnli.r.t't.i, ,.bii b..urn. extinct just over a century "."1*i.", ;;;.-;"t. of its DNA has survived in a ;;;.;; ip.cimen in a state suitable for TE "';;;moiecular cloning' start, Higuchi et al' managed to & irofut.