Is Evolution in Response to Extreme Events Good for Population
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Cancer-Milestones December 2020
www.nature.com/collections/cancer-milestones December 2020 Cancer Produced by: With support from: Nature Genetics and Nature Medicine Cancer MILESTONES S2 Foreword S3 Timeline S4 Routes to resistance S5 Tracking cancer in liquid biopsies S6 When cancer prevention went viral S7 A licence to kill S8 Sitting on the fence S9 Not a simple switch S10 Sequencing the secrets of the cancer genome S11 Unleashing the immune system against cancer S12 Engineering armed T cells for the fight S13 Oncohistones: epigenetic drivers of cancer S14 Tumour evolution: from linear paths to branched trees S15 Undruggable? Inconceivable S16 Good bacteria make for good cancer therapy S17 The AI revolution in cancer Credit: S.Fenwick/Springer Nature Limited CITING THE MILESTONES VISIT THE SUPPLEMENT ONLINE SUBSCRIPTIONS AND CUSTOMER SERVICES Nature Milestones in Cancer includes Milestone articles written The Nature Milestones in Cancer supplement can be found at Springer Nature, Subscriptions, by our editors and an online Collection of previously published www.nature.com/collections/cancer-milestones Cromwell Place, Hampshire International Business Park, material. To cite the full project, please use Nature Milestones: Lime Tree Way, Basingstoke, Cancer https://www.nature.com/collections/cancer-milestones CONTRIBUTING JOURNALS Hampshire RG24 8YJ, UK (2020). Should you wish to cite any of the individual Milestones, BMC Cancer, Nature, Nature Cancer, Nature Communications, Tel: +44 (0) 1256 329242 please list Author, A. Title. Nature Milestones: Cancer <Article URL> Nature Genetics, Nature Medicine, Nature Reviews Cancer, [email protected] (2020). For example, Milestone 1 is Valtierra, I. Routes to resistance. Nature Reviews Clinical Oncology, Nature Reviews Drug Discovery, Customer serviCes: www.nature.com/help Nature Milestones: Cancer https://www.nature.com/articles/ Nature Reviews Gastroenterology & Hepatology, d42859-020-00069-6 (2020). -
Understanding Biological Design from Synthetic Circuits
REVIEWS MODELLING Synthetic biology: understanding biological design from synthetic circuits Shankar Mukherji* and Alexander van Oudenaarden‡ Abstract | An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems — from synthetic promoters to the control of cell–cell interactions — has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple biological circuits, such as linear cascades and interlocking feedback loops, as well as to exert control over natural processes, such as gene expression and population dynamics. 10–12 Modularity One of the most astounding findings of the Human potential clinical applications . In this Review, however, A property of a system such Genome Project was that our genome contains as many we focus on how synthetic circuits help us to under- that it can be broken down into genes as that of Drosophila melanogaster. This finding stand how natural biological systems are genetically discrete subparts that perform begged the question: how do you get one organism to assembled and how they operate in organisms from specific tasks independently of look like a fly and another like a human with the same microbes to mammalian cells. In this light, synthetic the other subparts. number of genes? One possibility is that the rich rep- circuits have been crucial as simplified test beds in Bioremediation ertoire of non-protein-coding sequences found in the which to refine our ideas of how similarly structured The treatment of pollution with genomes of complex organisms adds many new parts natural networks function, and they have served as microorganisms. -
Species Extinctions
http://www.iucn.org/about/union/commissions/wcpa/?7695/Multiple-ocean-stresses- threaten-globally-significant-marine-extinction Multiple ocean stresses threaten “globally significant” marine extinction 20 June 2011 | News story An international panel of experts warns in a report released today that marine species are at risk of entering a phase of extinction unprecedented in human history. The preliminary report arises from a ‘State of the Oceans’ workshop co-hosted by IUCN in April, the first ever to consider the cumulative impact of all pressures on the oceans. Considering the latest research across all areas of marine science, the workshop examined the combined effects of pollution, acidification, ocean warming, over-fishing and hypoxia (deoxygenation). The scientific panel concluded that the combination of stresses on the ocean is creating the conditions associated with every previous major extinction of species in Earth’s history. And the speed and rate of degeneration in the ocean is far greater than anyone has predicted. The panel concluded that many of the negative impacts previously identified are greater than the worst predictions. As a result, although difficult to assess, the first steps to globally significant extinction may have begun with a rise in the extinction threat to marine species such as reef- forming corals. “The world’s leading experts on oceans are surprised by the rate and magnitude of changes we are seeing,” says Dan Laffoley, Marine Chair of IUCN’s World Commission on Protected Areas, Senior Advisor on Marine Science and Conservation for IUCN and co-author of the report. “The challenges for the future of the ocean are vast, but unlike previous generations, we know what now needs to happen. -
Michael Lynch
1 Michael Lynch Center for Mechanisms of Evolution, Biodesign Institute Arizona State University Tempe, AZ 85287 Phone: 480-965-0868 Email: [email protected] Birth: 6 December 1951, Auburn, New York Undergraduate education: St. Bonaventure University, Biology - B.S., 1973. Graduate education: University of Minnesota, Ecology and Behavioral Biology - Ph.D., 1977 (advisor: J. Shapiro). Areas of Interest and Research: The integration of molecular and cellular biology, genetics, and evolution; population and quantitative genetics; molecular, genomic, and phenotypic evolution. Select Professional Activities and Service: Director, Biodesign Center for Mechanisms of Evolution, Arizona State University, 2017 – present. Professor, School of Life Sciences, Arizona State University, 2017 – present. Class of 1954 Professor, 2011 – 2017. Distinguished Professor, Indiana University, 2005 – 2017. Professor; Biology, Indiana University, 2001 – 2004. Adjunct Professor, Computer Science, Indiana University, 2014 – 2017. Adjunct Professor, Physics, Indiana University, 2015 – 2017. Professor; Biology, University of Oregon, 1989 – 2001. Director, Ecology and Evolution Program, Univ. of Oregon, 1989 – 1993, 1996 – 2000. Asst., Assoc., Full Professor; Ecology, Ethology, and Evolution; University of Illinois, 1977 – 1989. Co-director, NSF IGERT Training Grant in Evolution, Development, and Genomics, 1999 – 2004. Director, NSF Genetic Mechanisms of Evolution Training Grant, 1990 – 2000. President, Genetics Society of America, 2013. President, Society for Molecular Biology and Evolution, 2009. President, American Genetic Association, 2007. President, Society for the Study of Evolution, 2000. Chair-elect, Section on Biological Sciences American Association for the Advancement of Science, 2017-2020. Vice-president, Genetics Society of America, 2012. Vice-president, Society for the Study of Evolution, 1994. Council Member, Society for the Study of Evolution, 1991 – 1993. -
Towards Population-Scale Long-Read Sequencing
REVIEWS Towards population-scale long-read sequencing Wouter De Coster 1,2,5, Matthias H. Weissensteiner3,5 and Fritz J. Sedlazeck 4 ✉ Abstract | Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale. Genome-wide association Sequencing the DNA or mRNA of multiple individuals These studies highlighted that a substantial proportion studies of one or more species (that is, population-scale sequenc- of hidden variation can be discovered with long-read (GWAS). Studies involving a ing) aims to identify genetic variation at a population sequencing. Indeed, recent long-read sequencing stud- statistical approach in genetics level to address questions in the fields of evolutionary, ies of Icelandic and Chinese populations have already to identify variants that correlate with a certain agricultural and medical research. Previous popula- identified previously undetected variants associated with 11,12 phenotype (for example, a tion studies, including genome-wide association studies height, cholesterol level and anaemia . -
How We Are Evolving New Analyses Suggest That Recent Human Evolution Has Followed a Di!Erent Course Than Biologists Would Have Expected
XXXXXXXX 40 Scientific American, October 2010 Photograph/Illustration by Artist Name © 2010 Scientific American Jonathan K. Pritchard is professor of human genetics at the University of Chicago and a Howard Hughes Medical Institute investigator. He studies genetic variation within and between human populations and the processes that led to this variation. E VO LU T I O N How We Are Evolving New analyses suggest that recent human evolution has followed a di!erent course than biologists would have expected By Jonathan K. Pritchard IN BRIEF As early Homo sapiens spread out from Many scientists thus expected that sur- ural selection—that is, because those nome contains some examples of very Africa starting around 60,000 years ago, veys of our genomes would reveal con- who carry the mutations have greater strong, rapid natural selection, most of they encountered environmental chal- siderable evidence of novel genetic mu- numbers of healthy babies than those the detectable natural selection appears lenges that they could not overcome tations that have recently spread quickly who do not. to have occurred at a far slower pace with prehistoric technology. ïà¹ù¹ùïmyày´ïȹÈù¨Dï¹´åUĂ´Dï- But it turns out that although the ge- than researchers had envisioned. Illustrations by Owen Gildersleeve October 2010, ScientificAmerican.com 41 © 2010 Scientific American !"#$%&'$ "( )*%+$ %," !#-%&$ -".*' ("+ /!* in technologies for studying genetic variation, we were able to first time into the Tibetan plateau, a vast ex- begin to address these questions. panse of steppelands that towers some 14,000 The work is still under way, but the preliminary findings have feet above sea level. -
Simple Stochastic Populations in Habi- Tats with Bounded, and Varying Carry- Ing Capacities
Simple Stochastic Populations in Habi- tats with Bounded, and Varying Carry- ing Capacities Master’s thesis in Complex Adaptive Systems EDWARD KORVEH Department of Mathematical Sciences CHALMERS UNIVERSITY OF TECHNOLOGY Gothenburg, Sweden 2016 Master’s thesis 2016:NN Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology Gothenburg, Sweden 2016 Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH © EDWARD KORVEH, 2016. Supervisor: Peter Jagers, Department of Mathematical Sciences Examiner: Peter Jagers, Department of Mathematical Sciences Master’s Thesis 2016:NN Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology SE-412 96 Gothenburg Gothenburg, Sweden 2016 iv Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH Department of Mathematical Sciences Chalmers University of Technology Abstract A population consisting of one single type of individuals where reproduction is sea- sonal, and by means of asexual binary-splitting with a probability, which depends on the carrying capacity of the habitat, K and the present population is considered. Current models for such binary-splitting populations do not explicitly capture the concepts of early and late extinctions. A new parameter v, called the ‘scaling pa- rameter’ is introduced to scale down the splitting probabilities in the first season, and also in subsequent generations in order to properly observe and record early and late extinctions. The modified model is used to estimate the probabilities of early and late extinctions, and the expected time to extinction in two main cases. -
Measuring the Societal Impact of Open Science – Presentation of a Research Project
InformaatiotutkimusKATSAUS 34(4), 2015 Holmberg et al: Measuring... 1 Holmberg, K.*,1, Didegah, F. 1, Bowman, S. 1, Bowman, T.D. 1, & Kortelainen, T.2 Measuring the societal impact of open science – Presentation of a research project Address: 1Research Unit for the Sociology of Education, University of Turku 2Information Studies, University of Oulu Email: *[email protected] Introduction data, and 2) investigate novel quantitative indica- tors of research impact to incentivize researchers Research assessment has become increasingly in adopting the open science movement. important—especially in these economically challenging times—as funders of research try to Assessing impact of research identify researchers, research groups, and uni- versities that are most deserving of the limited Two approaches have traditionally been used to funds. The goal of any research assessment is to assess research impact: (1) assessments based on discover research that is of the highest quality and citations and (2) assessments based on publica- therefore more deserving of funding. As quality is tion venues. Both approaches have issues that are very difficult and time-consuming to assess and well-documented (e.g., Vanclay, 2012). Citations can be highly subjective, other approaches have have been found to not always reflect quality or been preferred for assessment purposes (especially intellectual debt as they can be created for many when assessing big data). Research assessments different reasons, some of which do not reflect usually focus on evaluating the level of impact a the scientific value of the cited article (Borgman research product has made; impact is therefore & Furner, 2002). In addition citations can take a used as a proxy for quality. -
The Sixth Great Extinction Donations Events "Soon a Millennium Will End
The Rewilding Institute, Dave Foreman, continental conservation Home | Contact | The EcoWild Program | Around the Campfire About Us Fellows The Pleistocene-Holocene Event: Mission Vision The Sixth Great Extinction Donations Events "Soon a millennium will end. With it will pass four billion years of News evolutionary exuberance. Yes, some species will survive, particularly the smaller, tenacious ones living in places far too dry and cold for us to farm or graze. Yet we Resources must face the fact that the Cenozoic, the Age of Mammals which has been in retreat since the catastrophic extinctions of the late Pleistocene is over, and that the Anthropozoic or Catastrophozoic has begun." --Michael Soulè (1996) [Extinction is the gravest conservation problem of our era. Indeed, it is the gravest problem humans face. The following discussion is adapted from Chapters 1, 2, and 4 of Dave Foreman’s Rewilding North America.] Click Here For Full PDF Report... or read report below... Many of our reports are in Adobe Acrobat PDF Format. If you don't already have one, the free Acrobat Reader can be downloaded by clicking this link. The Crisis The most important—and gloomy—scientific discovery of the twentieth century was the extinction crisis. During the 1970s, field biologists grew more and more worried by population drops in thousands of species and by the loss of ecosystems of all kinds around the world. Tropical rainforests were falling to saw and torch. Wetlands were being drained for agriculture. Coral reefs were dying from god knows what. Ocean fish stocks were crashing. Elephants, rhinos, gorillas, tigers, polar bears, and other “charismatic megafauna” were being slaughtered. -
Denkanstöße 5/2021
Denkanstöße 5 aus der Akademie Juli/2021 Eine Schriftenreihe der Berlin-Brandenburgischen Akademie der Wissenschaften Andreas Radbruch und Konrad Reinhart (Hrsg.) NACHHALTIGE MEDIZIN Berlin-Brandenburgische Akademie der Wissenschaften (BBAW) NACHHALTIGE MEDIZIN NACHHALTIGE MEDIZIN Andreas Radbruch und Konrad Reinhart (Hrsg.) Denkanstöße 5/Juli 2021 Herausgeber: Der Präsident der Berlin-Brandenburgischen Akademie der Wissenschaften Redaktion: Elke Luger, Roman Marek und Ute Tintemann Grafik: angenehme gestaltung/Thorsten Probst Druck: PIEREG Druckcenter Berlin GmbH © Berlin-Brandenburgische Akademie der Wissenschaften, 2021 Jägerstraße 22–23, 10117 Berlin, www.bbaw.de Lizenz: CC-BY-NC-SA ISBN: 978-3-949455-00-1 INHALTSVERZEICHNIS Vorwort ....................................................................... 7 Christoph Markschies Einführung in das Thema ...................................................... 9 Britta Siegmund, Max Löhning, Detlev Ganten und Roman M. Marek Einleitung – Wie kann Medizin „nachhaltig“ sein? ............................15 Andreas Radbruch und Konrad Reinhart NACHHALTIGE BIOMEDIZINISCHE FORSCHUNG Nachhaltigkeit in der Medizin: Einzelzellanalysen in Diagnostik und Therapie ................................20 Nikolaus Rajewsky Regenerative Therapien ......................................................26 Hans-Dieter Volk und Petra Reinke ‚genomDE’ – Eine Chance für die deutsche Genommedizin und -forschung ...............................................32 Karl Sperling und Hans-Hilger Ropers Gesundheit neu denken: -
Assessing the Record and Causes of Late Triassic Extinctions
Earth-Science Reviews 65 (2004) 103–139 www.elsevier.com/locate/earscirev Assessing the record and causes of Late Triassic extinctions L.H. Tannera,*, S.G. Lucasb, M.G. Chapmanc a Departments of Geography and Geoscience, Bloomsburg University, Bloomsburg, PA 17815, USA b New Mexico Museum of Natural History, 1801 Mountain Rd. N.W., Albuquerque, NM 87104, USA c Astrogeology Team, U.S. Geological Survey, 2255 N. Gemini Rd., Flagstaff, AZ 86001, USA Abstract Accelerated biotic turnover during the Late Triassic has led to the perception of an end-Triassic mass extinction event, now regarded as one of the ‘‘big five’’ extinctions. Close examination of the fossil record reveals that many groups thought to be affected severely by this event, such as ammonoids, bivalves and conodonts, instead were in decline throughout the Late Triassic, and that other groups were relatively unaffected or subject to only regional effects. Explanations for the biotic turnover have included both gradualistic and catastrophic mechanisms. Regression during the Rhaetian, with consequent habitat loss, is compatible with the disappearance of some marine faunal groups, but may be regional, not global in scale, and cannot explain apparent synchronous decline in the terrestrial realm. Gradual, widespread aridification of the Pangaean supercontinent could explain a decline in terrestrial diversity during the Late Triassic. Although evidence for an impact precisely at the boundary is lacking, the presence of impact structures with Late Triassic ages suggests the possibility of bolide impact-induced environmental degradation prior to the end-Triassic. Widespread eruptions of flood basalts of the Central Atlantic Magmatic Province (CAMP) were synchronous with or slightly postdate the system boundary; emissions of CO2 and SO2 during these eruptions were substantial, but the contradictory evidence for the environmental effects of outgassing of these lavas remains to be resolved. -
Prof. Lori B. Andrews
LORI B. ANDREWS, J.D. IIT Chicago-Kent College of Law • 565 West Adams Street • Chicago, Illinois 60661 312-906-5359 (phone) • 312-906-5388 (fax) • [email protected] EMPLOYMENT: CHICAGO-KENT COLLEGE OF LAW, ILLINOIS INSTITUTE OF TECHNOLOGY, August 1993 – Present Distinguished Professor of Law, 2000 – Present Professor of Law, 1993 – 2000 ILLINOIS INSTITUTE OF TECHNOLOGY INSTITUTE FOR SCIENCE, LAW AND TECHNOLOGY Director, June 1998 – present ILLINOIS INSTITUTE OF TECHNOLOGY Associate Vice President, June 1998 – June 2012 PRINCETON UNIVERSITY, January 2002 – May 2002 Visiting Professor, Public and International Affairs UNIVERSITY OF CHICAGO Senior Scholar, Center for Clinical Medical Ethics, July 1987 – June 2001 Adjunct Professor, School of Law and Graduate School of Business, at various points between 1980 and 1993. CASE WESTERN RESERVE UNIVERSITY SCHOOL OF LAW, January 2000 – June 2000 Ben C. Green Visiting Professor AMERICAN BAR FOUNDATION, April 1980 – September 1997 Research Fellow UNIVERSITY OF HOUSTON LAW CENTER, January 1992 Visiting Professor (taught a three-credit genetics and law course over intersession) AMERICAN BAR ASSOCIATION, September 1978 – April 1980 Assistant Director, Legal Services Group EDUCATION: YALE LAW SCHOOL–Juris Doctor, 1978 Teaching Assistant, Constitutional Law with Professor Eugene Rostow Summer Associate, Cravath, Swaine & Moore, New York YALE UNIVERSITY–Bachelor of Arts, summa cum laude, 1975 Phi Beta Kappa Departmental Honors in Psychology Lori B. Andrews - 2 BOOKS: I Know Who You Are and I Saw What You Did: Social Networks and the Death of Privacy (Simon and Schuster 2012, paperback 2013). Published in Japanese (East Press Co. Ltd., 2013), Arabic (Obeikan Research & Development, 2015), Korean (Youngjin, 2016), and Chinese (Hangzhou Blue Lion Cultural & Creative, 2016).