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Biology Things to Do
Post 16 Biology things to do: Competition: The Royal Society of Biology has a photography competition with the theme ‘our changing world’ more information can be found by following the link. https://www.rsb.org.uk/get-involved/rsb-competitions/photography-competition The prize for the winner of the under 18 competition is £500 Reading: We have split these reading lists into 3 categories, this is to give you an idea of how ‘easy’ the reading is – for example Bill Bryson’s ‘The Body’ whilst very factual and interesting is designed for the general population to read. On the other hand ‘Evolution in 4 dimensions’ is designed with a biologist in mind – if evolution is your thing – give it a go! Category 1 are the easiest reads and category 3 are the most difficult – but all worthwhile. Category 1 Category 2 Category 3 ‘The Body’ https://thebiologist.rsb.org.uk/biologist ‘Evolution in 4 dimensions’ Bill Bryson Eva Jablonka & Marion J.Lamb ‘A short history of nearly ‘Darwin comes to Town’ ‘The Epigenetics everything’ Memo Schilthuizen Revolution’ Bill Bryson Nessa Carey ‘Sapiens’ ‘The immortal life of Henrietta Lacks’ ‘The Cell: Discovering the Yuval Noah Harari Rebecca Skloot microscopic World that Determines our Health, Consciousness, and Our Future’ Joshua Z.Rappoport PhD, Barry Abrams et al. ‘Homo Deus’ ‘Evolution: The Human Story, 2nd ‘Life: an unauthorized Yuval Noah Harari edition’ biography’ Alice Roberts Richard Fortey ‘The Selfish Gene’ ‘The soul of an octopus’ Richard Dawkins Sy Montgomery ‘The Ancestor’s Tale’ ‘The Gene: An intimate history’ Richard Dawkins and Yan Siddhartha Mukherjee Wong ‘This is going to hurt’ ‘In the shadow of man’ Adam Kay Jane Goodall ‘Human Universe’ ‘The Book of Humans’ Brian Cox Adam Rutherford ‘Life on Earth’ David Attenborough ‘Anatomy and physiology for dummies’ Tasks Option 1: https://pbiol.rsb.org.uk/cells-to-systems/support-and-movement/observing-earthworm-locomotion The idea is to find Earthworms and compare their movement on different surfaces. -
A Multiscale Tool to Explore Genomic Conservation
SynVisio: A Multiscale Tool to Explore Genomic Conservation A Thesis Submitted to the College of Graduate and Postdoctoral Studies in Partial Fulfillment of the Requirements for the degree of Master of Science in the Department of Computer Science University of Saskatchewan Saskatoon By Venkat Kiran Bandi ©Venkat Kiran Bandi, May/2020. All rights reserved. Permission to Use In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Computer Science 176 Thorvaldson Building 110 Science Place University of Saskatchewan Saskatoon, Saskatchewan Canada S7N 5C9 Or Dean College of Graduate and Postdoctoral Studies University of Saskatchewan 116 Thorvaldson Building, 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada i Abstract Comparative analysis of genomes is an important area in biological research that can shed light on an organism's internal functions and evolutionary history. -
A Zebrafish Reporter Line Reveals Immune and Neuronal Expression of Endogenous Retrovirus
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427598; this version posted January 21, 2021. 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. A zebrafish reporter line reveals immune and neuronal expression of endogenous retrovirus. Noémie Hamilton1,2*, Amy Clarke1, Hannah Isles1, Euan Carson1, Jean-Pierre Levraud3, Stephen A Renshaw1 1. The Bateson Centre, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK 2. The Institute of Neuroscience, University of Sheffield, Sheffield, UK 3. Macrophages et Développement de l’Immunité, Institut Pasteur, CNRS UMR3738, 25 rue du docteur Roux, 75015 Paris *Corresponding author: [email protected] Abstract Endogenous retroviruses (ERVs) are fossils left in our genome from retrovirus infections of the past. Their sequences are part of every vertebrate genome and their random integrations are thought to have contributed to evolution. Although ERVs are mainly kept silenced by the host genome, they are found activated in multiple disease states such as auto-inflammatory disorders and neurological diseases. What makes defining their role in health and diseases challenging is the numerous copies in mammalian genomes and the lack of tools to study them. In this study, we identified 8 copies of the zebrafish endogenous retrovirus (zferv). We created and characterised the first in vivo ERV reporter line in any species. Using a combination of live imaging, flow cytometry and single cell RNA sequencing, we mapped zferv expression to early T cells and neurons. -
Evolution and Function of Drososphila Melanogaster Cis-Regulatory Sequences
Evolution and Function of Drososphila melanogaster cis-regulatory Sequences By Aaron Hardin A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michael Eisen, Chair Professor Doris Bachtrog Professor Gary Karpen Professor Lior Pachter Fall 2013 Evolution and Function of Drososphila melanogaster cis-regulatory Sequences This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License 2013 by Aaron Hardin 1 Abstract Evolution and Function of Drososphila melanogaster cis-regulatory Sequences by Aaron Hardin Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Michael Eisen, Chair In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods on the natural genetic variation in a population. This works integrates an investigation of the consequences of polymorphisms at three stages of gene regulation in the developing fly embryo: the diversity at cis-regulatory modules, the integration of transcription factor binding into changes in chromatin state and the effects of these inputs on the final phenotype of embryonic gene expression. i I dedicate this dissertation to Mela Hardin who has been here for me at all times, even when we were apart. ii Contents List of Figures iv List of Tables vi Acknowledgments vii 1 Introduction1 2 Within Species Diversity in cis-Regulatory Modules6 2.1 Introduction....................................6 2.2 Results.......................................8 2.2.1 Genome wide diversity in transcription factor binding sites......8 2.2.2 Genome wide purifying selection on cis-regulatory modules......9 2.3 Discussion.....................................9 2.4 Methods for finding polymorphisms...................... -
A Burst of Protein Sequence Evolution and a Prolonged Period of Asymmetric Evolution Follow Gene Duplication in Yeast
Downloaded from genome.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Letter A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast Devin R. Scannell1,2 and Kenneth H. Wolfe Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whether it applies to both gene copies or just one. We provide initial answers to these questions by comparing the rate of protein sequence evolution among eight yeast species, between a large set of duplicate gene pairs that were created by a whole-genome duplication (WGD) and a set of genes that were returned to single-copy after this event. Importantly, we use a new method that takes into account the tendency for slowly evolving genes to be retained preferentially in duplicate. We show that, on average, proteins encoded by duplicate gene pairs evolved at least three times faster immediately after the WGD than single-copy genes to which they behave identically in non-WGD lineages. Although the high rate in duplicated genes subsequently declined rapidly, it has not yet returned to the typical rate for single-copy genes. In addition, we show that although duplicate gene pairs often have highly asymmetric rates of evolution, even the slower members of pairs show evidence of a burst of protein sequence evolution immediately after duplication. -
A Phd Position Is Available in the Research Group of Aoife Mclysaght
A PhD position is available in the research group of Aoife McLysaght in Trinity College Dublin to work on comparative genomics of vertebrates with a focus on understanding dosage sensitive genes in terms of evolution and disease. The execution of the project will involve bioinformatics and computer programming as well as statistical analysis of data. For examples of the kinds of things we work on, look up our papers on PubMed: https://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=mclysaght+a[au]&dispmax=50 Applicants should be in the final year of, or hold, a bachelor's degree in molecular biology with an interest and aptitude for programming and bioinformatics; or vice versa (computer science bachelor's with an interest in molecular biology). Interest and enthusiasm for molecular evolution is essential. Students will be expected to be self-motivated and creative and to work closely with other members of the team. This is a four-year position and comes with a tax-free stipend of 18000euro and covers fees up to EU level (non-EU students may apply, but fees are only covered up to EU rates). TCD is Ireland’s top ranked University and a member of the League of European Research Universities (LERU). The McLysaght lab is funded by a European Research Council (ERC) Starting Grant. Lab: http://www.gen.tcd.ie/molevol/ Applications including a cover letter, CV, summary of scientific interests and reasons for being interested in our research group, and contact details for two referees should be made to [email protected]. -
Even Scientists Can't Predict the Future – Or Can They? Edited by Jim Al
EVEN SCIEntists can’t prEDICT THE FUTURE – OR CAN THEY? Edited by Jim Al-Khalili PROFILE BOOKS What's Next?.indd 3 30/08/2017 16:25 First published in Great Britain in 2017 by Profile Books Ltd 3 Holford Yard Bevin Way London wc1x 9hd www.profilebooks.com 10 9 8 7 6 5 4 3 2 1 Selection, introduction and Chapter 18 (‘Teleportation and Time Travel’) copyright © Jim Al-Khalili 2017 Other chapters copyright of the author in each case © Philip Ball, Margaret A. Boden, Naomi Climer, Lewis Dartnell, Jeff Hardy, Winfried K. Hensinger, Adam Kucharski, John Miles, Anna Ploszajski, Aarathi Prasad, Louisa Preston, Adam Rutherford, Noel Sharkey, Julia Slingo, Gaia Vince, Mark Walker, Alan Woodward 2017 The moral right of the authors has been asserted. All rights reserved. Without limiting the rights under copyright reserved above, no part of this publication may be reproduced, stored or introduced into a retrieval system, or transmitted, in any form or by any means (electronic, mechanical, photocopying, recording or otherwise), without the prior written permission of both the copyright owner and the publisher of this book. All reasonable efforts have been made to obtain copyright permissions where required. Any omissions and errors of attribution are unintentional and will, if notified in writing to the publisher, be corrected in future printings. A CIP catalogue record for this book is available from the British Library. ISBN 978 1 78125 895 8 eISBN 978 1 78283 376 5 Text design by Sue Lamble Typeset in Sabon by MacGuru Ltd Printed and bound in Britain -
Applied Science (Equivalent to One a Level)
Applied Science (equivalent to one A Level) This is a programme of activities and resources to prepare you to start BTEC Applied Science in September. It is aimed to be used throughout the remainder of the Summer term and over the Summer Holidays to ensure you are ready to start your course in September. Book Recommendations The books below are all popular science books and great for extending your understanding of Science. Bryson and Goldacre are available as ebooks from Hampshire library service. https://www.hants.gov.uk/librariesandarchives/library/whatyoucanborrow/ebooksaudi obooks A Short History of Nearly Everything A whistle-stop tour through many aspects of history from the Big Bang to now. This is a really accessible read that will re-familiarise you with common concepts and introduce you to some of the more colourful characters from the history of science! Available at amazon.co.uk Periodic Tales: The Curious Lives of the Elements (Paperback) Hugh AlderseyWilliams ISBN-10: 0141041455 http://bit.ly/pixlchembook1 This book covers the chemical elements, where they come from and how they are used. There are loads of fascinating insights into uses for chemicals you would have never even thought about. Bad Science (Paperback) Ben Goldacre ISBN-10: 000728487X http://bit.ly/pixlchembook3 Here Ben Goldacre takes apart anyone who published bad / misleading or dodgy science – this book will make you think about everything the advertising industry tries to sell you by making it sound ‘sciency’. TV and film Recommendations You won’t find Jurassic Park on this list, but they are all great watching for a rainy day. -
Hell on Earth
01 CHAPTER 3 02 03 04 Hell on Earth 05 06 07 08 09 10 11 12 “Long is the way, and hard, that out of hell leads up to 13 light.” 14 John Milton, Paradise Lost 15 16 17 f you want to construct a picture of the earth on which life first 18 emerged, think about how we’ve named it. There are four geo- 19 logical eons spanning the earth’s 4, 540-million-year existence. 20 IThe most recent three names reflect our planet’s propensity for liv- 21 ing things, all referring to stages of life. The second eon is called the 22 Archean, which rather confusingly translates as “origins.” The third 23 eon is the Proterozoic, roughly translating from Greek as “earlier 24 life”; the current eon, the Phanerozoic, started around 542 million 25 years ago and means “visible life.” 26 But the first eon, the period from the formation of the earth up 27 to 3. 8 billion years ago, is called the Hadean, derived from Hades, 28 the ancient Greek version of hell. 29 Life does not merely inhabit this planet; it has shaped it and is 30 part of it. Not just in the current era of man-made climate change, S31 but all through life’s history on Earth, life has affected the rocks N32 9781617230059_Creation_TX_p1-278.indd 61 26/02/13 7:51 PM 62 CREATION 01 below our feet and the sky above us. And necessarily, the origin of 02 life is inseparable from the fury of the formation of the earth in the 03 first place. -
SYNTHETIC LIFE: How Far Could It Go? How Far Should It Go? WELCOME
SYNTHETIC LIFE: How far could it go? How far should it go? WELCOME Synthetic biology is a revolutionary technology that could have a huge impact on humans and our environment. The potential impact of this area of science is astonishing; from bacteria that could generate energy, to creating food without the need for large organisms. Synthetic biology is dividing opinion. Today’s speakers Professor Paul Freemont, Dr Louise Horsfall, Professor Robert Edwards, Dr Susan Molyneux-Hodgson and Chair Dr Adam Rutherford will discuss and debate this exciting topic and its possible applications. This event has been organised by the Biochemical Society and the Royal Society of Biology, as part of Biology Week 2015. We hope you enjoy the lively talks and thought-provoking debate. #BiologyWeek WHAT IS SYNTHETIC BIOLOGY? Synthetic biology is so new there isn’t one singular definition for it. It is based on the idea that engineering approaches can be used to study biological systems, manipulate them and to produce new ones that do not exist in nature. All living things contain DNA (deoxyribonucleic acid), and it is found in every cell in our bodies. It is a unique code, made up of a sequence of chemicals. This sequence, called our genetic code or genome, determines how an organism is made; the same way the letters in the alphabet form words or sentences. Humans have been manipulating the genetic code for thousands of years, by selectively breeding plants and animals with desired characteristics. As we have learned how to read and manipulate the genetic code, we have started to take genetic information from one organism and transfer it to another. -
Review 2015–16 Review
Review 2015–16 Review 2015–16 AR cover 1.indd 1 3/2/2017 3:00:03 PM TO PRINT.indd 82 3/2/2017 1:56:30 PM Inside A year in view 4 A note from the President 11 A note from the Executive Secretary 13 We explore 17 We award 27 We engage 31 We advise 49 We support 55 New members 61 Donations 73 Bereavements 78 Accounts 80 This report covers the period from March 2015 to December 2016 TO PRINT.indd 1 3/2/2017 1:53:07 PM 156 new entries added to the Dictionary of Irish Biography 61 maps from Irish Historic Towns Atlas now available online 10 volumes of Documents on Irish Foreign Policy to date 6 US-Ireland Research Innovation Award winners 1 prehistoric bear bone excavated with RIA grants TO PRINT.indd 2 3/2/2017 1:53:08 PM 19 1,400 visits on 1,500 events and meetings Culture Night 2016 13,300 followers on Twitter 20,100 books sold 100,000,000 stamps inspired by A History of Ireland in 100 Objects 38,500 visitors 70,000 441,900 in research grants awarded downloads € of 1916 Portraits and Lives TO PRINT.indd 3 3/2/2017 1:53:09 PM US-Ireland Research Innovation Awards 2016: L–R Eddie Cullen, Ulster Bank; Minister for Jobs, Enterprise and Innovation, Mary Mitchell O’Connor, TD; Shaun Murphy, KPMG and James O’Connor, American Chamber of Commerce. Participant at Inspiring Ireland London Collection Day, organised by the Digital Repository of Ireland in March 2016. -
SG Stories004-President-Of-Ireland
COMMUNITY SYNTHETIC BIOLOGY EVENT LAUNCHES PRESIDENT OF IRELAND ETHICS INITIATIVE WHO? ▶ Science Gallery Dublin ▶ President of Ireland Ethics Initiative ▶ Drew Endy, Associate Professor of Stanford University Professor of Bioengineering, Stanford University Bioengineering Drew Endy came Hugh Whittall, Director of Nuffield to Science Gallery Dublin in Council on Bioethics, UK 2014 as the inaugural event of the ▶ Aoife McLysaght, Professor of Genetics, President of Ireland Ethics Initiative, Trinity College Dublin leading to awareness and ▶ Celsius Research Cluster, Dublin City discussion of critical ethical issues University around synthetic biology. ▶ President of Ireland Ethics Initiative WHAT? The President of Ireland Ethics Initiative is a series of discussions on prominent ethical issues headed by Irish President Michael D Higgins, and the inaugural event was held in Science Gallery Dublin in January 2014. Synthetic Biology pioneer Drew Endy, from Stanford University, spoke about synthetic biology and engaged in a discussion with audience members, geneticist Aoife McLysaght and Nuffield Council on Bioethics Director Hugh Whittall, exploring the nature and ethics of synthetic biology. The event tied in with Science Gallery Dublin’s synthetic biology themed GROW YOUR OWN... exhibition. Evaluation of the event was carried out by the Celsius Research Cluster in Dublin City University. Event attendees were asked questions about synthetic biology before and after the event, and the results showed an increase in awareness of synthetic biology