Jeffrey Evan Barrick
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Carnival of Evolution #58: Visions of the Evolutionary Future Bradly Alicea Michigan State University
Carnival of Evolution #58: visions of the evolutionary future Bradly Alicea Michigan State University Originally published at: http://syntheticdaisies.blogspot.com on April 1, 2013 (http://syntheticdaisies.blogspot.com/2013/04/carnival-of-evolution-58-visions-of.html) Welcome to Carnival of Evolution! Now with albedo! Introduction What does the future look like? For some, the future is the place of constant progress and a place where dreams become reality. For others, the future is a scary, dystopian place. When actualized, however, future worlds fall somewhere in between these two visions. Can we make accurate projections about the future? As I pointed out in a Synthetic Daisies post from February [1], futurists and technologists have a pretty dismal track record at projecting future scenarios, and often get things notoriously wrong. UPPER LEFT: Ad from the 1982 opening of EPCOT Center, Florida. UPPER RIGHT: Dystopic future city from the movie "Idiocracy" (Inset is the cover of "Future Shock" by Alvin Toffler). BOTTOM LEFT: Bank of England Economic Forecast (circa 2011). BOTTOM RIGHT: New New York, circa 3000 (from the TV show "Futurama"). With visions of the future in mind, this month's Carnival of Evolution (#58) theme is the future of evolution. While a significant component of evolutionary biology involves reconstructing the past [2], we are actually (with error, of course) also predicting the future. Yet can we do any better than futurists or technologists? It is hard to say, and if you have opinions on this I would be glad to hear them. However, this month's CoE will address five themes that may (or may not) help us understand where the complexity of life is headed. -
Science in School the European Journal for Science Teachers Autumn 2017 | Issue 41 | Issue 2017 Autumn
Subscribe free in Europe: FREE www.scienceinschool.org Science in School The European journal for science teachers Autumn 2017 | Issue 41 2017 Autumn DesignDesign inspirationinspiration TheThe secretssecrets ofof sharkshark skinskin ISSN: 1818-0353 www.scienceinschool.org ISSN: 1818-0353 www.scienceinschool.org INSPIREINSPIRE SupportingSupporting AfricanAfrican science:science: the role of fruit flies Published and funded by EIROforum by funded and Published the role of fruit flies TEACHTEACH AA particleparticle acceleratoraccelerator inin youryour saladsalad bowlbowl Image courtesy of Ariane Böhm / Grunwald Kadow lab Kadow of Ariane Böhm / Grunwald Image courtesy Image courtesy of Andrew Burgess / shutterstock.com Burgess of Andrew Image courtesy SUPPORTING AFRICAN SCIENCE: 35 HOW DO BIRDS FLY? 38 THE ROLE OF FRUIT FLIES A HANDS-ON DEMONSTRATION Not only is the fruit fly a valuable model Dissect a chicken from the supermarket organism, but it is also helping to put Africa to discover the unusual pulley system that on the scientific world map. enables birds to fly. Image courtesy of Stefan Pircher / Shutterstock Pircher of Stefan Image courtesy DESIGN INSPIRATION: THE SECRETS OF SHARK SKIN 19 Shark skin is adapted for energy-efficient swimming in remarkable ways, some of which are now being copied by designers and engineers. UNDERSTAND INSPIRE 4 News from the EIROs: Exotic particles, 35 Supporting African science: fusion-device ashtrays and lunar missions the role of fruit flies 8 Cellulose: from trees to treats TEACH 13 Gravitational -
A Systematic, Label-Free Method for Identifying RNA-Associated Proteins in Vivo Provides Insights Into Vertebrate Ciliary Beatin
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.966754; this version posted March 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 A systematic, label-free method for identifying RNA- associated proteins in vivo provides insights into vertebrate ciliary beating Kevin Drew*, Chanjae Lee*, Rachael M. Cox, Vy Dang, Caitlin C. Devitt, Ophelia Papoulas, Ryan L. Huizar, Edward M. Marcotte** and John B. Wallingford** Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712 *These authors contributed equally **To whom correspondence should be addressed: John Wallingford Patterson Labs 2401 Speedway Austin, Texas 78712 [email protected] 512-232-2784 Edward Marcotte 2500 Speedway, MBB 3.148BA Austin, Texas 78712 [email protected] 512-471-5435 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.966754; this version posted March 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 2 Abstract: Cell-type specific RNA-associated proteins (RAPs) are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RAPs, we currently have few comprehensive rosters of cell-type specific RAPs in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-interacting proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. -
Experimental Evolution of Escherichia Coli Harboring an Ancient Translation Protein
J Mol Evol DOI 10.1007/s00239-017-9781-0 ORIGINAL ARTICLE Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein Betül Kacar1,2 · Xueliang Ge3 · Suparna Sanyal3 · Eric A. Gaucher4,5 Received: 8 October 2016 / Accepted: 30 January 2017 © The Author(s) 2017. This article is published with open access at Springerlink.com Abstract The ability to design synthetic genes and engi- We subsequently evolved replicate hybrid bacterial popula- neer biological systems at the genome scale opens new tions for 2000 generations in the laboratory and examined means by which to characterize phenotypic states and the adaptive response via fitness assays, whole genome the responses of biological systems to perturbations. One sequencing, proteomics, and biochemical assays. Hybrid emerging method involves inserting artificial genes into lineages exhibit a general adaptive strategy in which the bacterial genomes and examining how the genome and its fitness cost of the ancient gene was ameliorated in part by new genes adapt to each other. Here we report the devel- upregulation of protein production. Our results suggest that opment and implementation of a modified approach to an ancient–modern recombinant method may pave the way this method, in which phylogenetically inferred genes are for the synthesis of organisms that exhibit ancient pheno- inserted into a microbial genome, and laboratory evolu- types, and that laboratory evolution of these organisms may tion is then used to examine the adaptive potential of the prove useful in elucidating insights into historical adaptive resulting hybrid genome. Specifically, we engineered an processes. approximately 700-million-year-old inferred ancestral vari- ant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in Background place of the native tufB gene. -
Trouble with Testosterone Test
Trouble with testosterone test Annual Meeting Special Section CONTENTS NEWS FEATURES PERSPECTIVES 2 14 36 EDITOR’S NOTE THE TROUBLE WITH PUBLIC AFFAIRS It’s time THE TESTOSTERONE TEST Are postdocs still invisible? 3 18 38 PRESIDENT’S MESSAGE MASTERS OF PHYSIOLOGY MINORITY AFFAIRS Celebrating serendipity 38 Exemplifying Sewer’s commitment to diversity 22 40 Diversifying the scientic 4 THE 2017 ANNUAL MEETING NEWS FROM THE HILL workforce with IMAGE 23 Expand your scientic horizons A lot at stake 42 Cultivating a focus on diversity 29 e spotlight is on you as a community 30 Promoting lifelong learning 5 34 Advance your careers, grad students MEMBER UPDATE 44 and postdocs! TRANSITIONS 35 Reminders for the 2017 ASBMB 7 Undergraduate Poster Competition Wrestling with life RETROSPECTIVE 7 Roscoe Owen Brady (1923–2016) 14 48 9 Roger Tsien (1952–2016) Experts are OPEN CHANNELS grappling with what constitutes 10 high testosterone 42 blood levels in elite NEWS track and eld Blind wins Tabor award women athletes. for work on nuclear lipids 11 JOURNAL NEWS 11 Blocking potato blight’s ability 22 to set up shop 12 Infant gut microbes’ thirst for milk proteins 13 How a single-cell marine organism makes fatty acids 12 44 TRANSITION STATES NOVEMBER 2016 ASBMB TODAY 1 EDITOR’S NOTE THE MEMBER MAGAZINE OF THE AMERICAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY It’s time By Angela Hopp OFFICERS COUNCIL MEMBERS Natalie Ahn Squire J. Booker President Victoria J. DeRose Wayne Fairbrother. recently saw a documen- Ben Corb, in his “News Steven McKnight Karen G. Fleming tary on Netix about from the Hill” column, Past President Rachel Green uncontacted tribes in writes about the count- Jennifer DuBois Susan Marqusee I Secretary Jared Rutter the rainforest on the border down to a new American Celia A. -
MICROBIOLOGY Graduate Program
MICROBIOLOGY Graduate Program Student Handbook 2020-21 THE UNIVERSITY OF TEXAS AT AUSTIN Welcome! .............................................................................................................................................................. 4 Responsibilities of a Microbiology Graduate Student ........................................................................................ 4 The Graduate School ......................................................................................................................................... 4 The College of Natural Sciences (CNS) ............................................................................................................ 5 The Institute for Cell and Molecular Biology (ICMB) ......................................................................................... 5 The Microbiology Graduate Program (MIC) ...................................................................................................... 5 Microbiology Graduate Program Administration ................................................................................................ 6 The Microbiology Graduate Studies Committee (GSC) .................................................................................... 6 Degrees Offered ................................................................................................................................................... 7 Doctor of Philosophy (Ph.D.) ............................................................................................................................ -
The Man Who Bottled Evolution
NEWSFOCUS EAST LANSING, MICHIGAN—When most biologists want to understand how evolu- tion unfolds, they look for clues in the fossil The Man Who record or the natural world. Richard Lenski simply walks across his Michigan State Uni- versity lab to his freezers. There, stored in Bottled Evolution 4000 vials, are bacteria dating back to 1988. That was the year Lenski started a simple but radical experiment. He put samples of Richard Lenski’s 25-year experiment in bacterial evolution Escherichia coli into a sugar solution, stop- shows no signs of running out of surprises about how pered the flasks, and waited to see what mutation and selection shape living things would happen. It was a study with no defi ned endpoint, so risky that he didn’t try very hard to get outside funding for it. After 25 years and 58,000 bacterial generations, Lenski’s bacteria are still growing, mutating, and evolving. They are proving as critical to understanding the workings of evolution as classic paleontology studies such as Stephen Jay Gould’s research on the pace of change in mollusks. Lenski’s humble E. coli have shown, among other things, how multiple small mutations can prepare the ground for a major change; how new species can arise and diverge; and that Gould was mistaken on November 24, 2013 when he claimed that, given a second chance, evolution would likely take a completely different course. Most recently, the colonies have demonstrated that, contrary to what many biologists thought, evolution never comes to a stop, even in an unchanging environment. -
An Aging-Independent Replicative Lifespan in a Symmetrically Dividing
TOOLS AND RESOURCES An aging-independent replicative lifespan in a symmetrically dividing eukaryote Eric C Spivey1,2†, Stephen K Jones Jr1,2†, James R Rybarski1, Fatema A Saifuddin1, Ilya J Finkelstein1,2,3* 1Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States; 2Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, United States; 3Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, United States Abstract The replicative lifespan (RLS) of a cell—defined as the number of cell divisions before death—has informed our understanding of the mechanisms of cellular aging. However, little is known about aging and longevity in symmetrically dividing eukaryotic cells because most prior studies have used budding yeast for RLS studies. Here, we describe a multiplexed fission yeast lifespan micro-dissector (multFYLM) and an associated image processing pipeline for performing high-throughput and automated single-cell micro-dissection. Using the multFYLM, we observe continuous replication of hundreds of individual fission yeast cells for over seventy-five generations. Surprisingly, cells die without the classic hallmarks of cellular aging, such as progressive changes in size, doubling time, or sibling health. Genetic perturbations and drugs can extend the RLS via an aging-independent mechanism. Using a quantitative model to analyze these results, we conclude that fission yeast does not age and that cellular aging and replicative lifespan can be uncoupled in a eukaryotic cell. DOI: 10.7554/eLife.20340.001 *For correspondence: [email protected] †These authors contributed Introduction equally to this work Aging is the progressive decrease of an organism’s fitness over time. -
The International Conference on Intelligent Biology
The Author(s) BMC Genomics 2017, 18(Suppl 6):703 DOI 10.1186/s12864-017-4018-6 INTRODUCTION Open Access The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics Zhongming Zhao1,2*, Zhandong Liu3, Ken Chen4, Yan Guo5, Genevera I. Allen3,6, Jiajie Zhang7, W. Jim Zheng7 and Jianhua Ruan8* From The International Conference on Intelligent Biology and Medicine (ICIBM) 2016 Houston, TX, USA. 08-10 December 2016 Abstract In this editorial, we first summarize the 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) that was held on December 8–10, 2016 in Houston, Texas, USA, and then briefly introduce the ten research articles included in this supplement issue. ICIBM 2016 included four workshops or tutorials, four keynote lectures, four conference invited talks, eight concurrent scientific sessions and a poster session for 53 accepted abstracts, covering current topics in bioinformatics, systems biology, intelligent computing, and biomedical informatics. Through our call for papers, a total of 77 original manuscripts were submitted to ICIBM 2016. After peer review, 11 articles were selected in this special issue, covering topics such as single cell RNA-seq analysis method, genome sequence and variation analysis, bioinformatics method for vaccine development, and cancer genomics. Introduction more than 150 scientists or trainees across the world with The 2016 International Conference on Intelligent Biology diverse backgrounds and training ranging from biology, and Medicine (ICIBM 2016) was held from December 8th medicine, computer science, bioengineering, bioinformat- to 10th, 2016 in Houston, Texas, USA. This is the fifth ics, statistics, mathematics, and genomics, among others. -
Downloaded From
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.02.130138; this version posted June 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Maintenance of Metabolic Plasticity Despite Relaxed Selection in a Long-Term Evolution Experiment with Escherichia coli Nkrumah A. Grant,1,2,3* Rohan Maddamsetti,4 and Richard E. Lenski1,2,3 1. BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan 48824; 2. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824; 3. Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing 48824; 4. Department of Biomedical Engineering, DuKe University, Durham, North Carolina 27708. * Corresponding author; e-mail: [email protected] 1 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.02.130138; this version posted June 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 2 ABSTRACT: Traits that are unused in a given environment are subject to processes that tend to erode 3 them, leading to reduced fitness in other environments. Although this general tendency is clear, 4 we know much less about why some traits are lost while others are retained, and about the roles of 5 mutation and selection in generating different responses. -
Front Matter Template
Copyright by Erik Michael Quandt 2014 The Dissertation Committee for Erik Michael Quandt Certifies that this is the approved version of the following dissertation: Genetic and Biochemical Dissection of Complex Evolved Traits in Bacteria Committee: George Georgiou, Supervisor Andrew D. Ellington, Co-Supervisor Jeffrey E. Barrick Ian Molineux Hal Alper Genetic and Biochemical Dissection of Complex Evolved Traits in Bacteria by Erik Michael Quandt, B.S. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August 2014 Acknowledgements First and foremost, I would like to thank my advisors Dr. George Georgiou and Dr. Andrew Ellington who gave me the opportunity to work in their labs and who have supported and guided me through my studies. I owe a huge debt of gratitude to Dr. Jeffrey Barrick who I learned a great deal from and whose advice helped me stay on track. I value the time we spent working together and thank him for always being available for brainstorming and entertaining my often crazy ideas. I would like to thank the members of the Georgiou, Ellington, and Barrick labs for their partnership over the past 5 years. I would especially like to thank Dr. Tomohiro Makino for helping me get started in the lab as well as my labmates: Kam Hon Hoi, Dr. William Kelton, Dr. Costas Chrysostomou, and Dr. Li Yi whose friendship and comradery made this endeavor enjoyable. I would also like to thank my many collaborators that I had the privilege to work with: Dr. -
Program Book
The Genetics Society of America Conferences 15th International Xenopus Conference August 24-28, 2014 • Pacific Grove, CA PROGRAM GUIDE LEGEND Information/Guest Check-In Disabled Parking E EV Charging Station V Beverage Vending Machine N S Ice Machine Julia Morgan Historic Building W Roadway Pedestrian Pathway Outdoor Group Activity Area Program and Abstracts Meeting Organizers Carole LaBonne, Northwestern University John Wallingford, University of Texas at Austin Organizing Committee: Julie Baker, Stanford Univ Chris Field, Harvard Medical School Carmen Domingo, San Francisco State Univ Anna Philpott, Univ of Cambridge 9650 Rockville Pike, Bethesda, Maryland 20814-3998 Telephone: (301) 634-7300 • Fax: (301) 634-7079 E-mail: [email protected] • Web site: genetics-gsa.org Thank You to the Following Companies for their Generous Support Platinum Sponsor Gold Sponsors Additional Support Provided by: Carl Zeiss Microscopy, LLC Monterey Convention & Gene Tools, LLC Visitors Bureau Leica Microsystems Xenopus Express 2 Table of Contents General Information ........................................................................................................................... 5 Schedule of Events ............................................................................................................................. 6 Exhibitors ........................................................................................................................................... 8 Opening Session and Plenary/Platform Sessions ............................................................................