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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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]. -
Gerry Roche "A Memoir"
A Survivor’s Story: a memoir of a life lived in the shadow of a youthful brush with psychiatry by Gerry Roche And the end of all our exploring Will be to arrive where we started And know the place for the first time. TS Eliot: Four Quartets Contents Introduction 4 Chapter 1 : Ground Zero 7 1971: Lecturing, Depression, Drinking, John of Gods, … Chapter 2 : Zero minus one 21 1945-71: Childhood, School, University … Chapter 3 : Zero’s aftermath: destination ‘cold turkey’ 41 1971-81: MSc., Lecturing, Sculpting, Medication-free, Building Restoration, …… Chapter 4 : After ‘cold turkey’: the cake 68 1981-92: Tibet, India, Log Cabin Building, … Chapter 5 : And then the icing on the cake 105 1992-96: China, Karakoram, more Building, Ethiopia, ... Chapter 6 : And then the cognac … (and the bitter 150 lemon) 1996-2012: MPhil, Iran, Japan, PhD, more Building, Syria ... (and prostate cancer) … Chapter 7 : A Coda 201 2012-15: award of PhD … Armenia, Korea, … Postscript : Stigma: an inerasable, unexpungeable, 215 indestructible, indelible stain. Appendix: : Medical interventions on the grounds of 226 ‘best interests’ Endnotes 233 2 I wish to dedicate this memoir to my sons Philip and Peter and to their mother (and my-ex-wife) Mette, with love and thanks. I wish to give a special word of thanks to Ms. Maureen Cronin, Mr. Brian McDonnell, Mr. Charles O’Brien and Ms. Jill Breivik who assisted me in editing this memoir. 3 Introduction A cure is not overcoming anything, a cure is learning to live with what your are, and with what the past has made you, with what you've made of yourself with your own past .1 The story that I tell is of a journey, or perhaps more of an enforced wandering or a detour occasioned by what, at the time, seemed as inconsequential as the taking of a short break. -
R I2009 2010
cover to print_Layout 1 10/12/2010 11:04 Page 1 ANNUAL REVIEW rANNUAL i 20092010 2009 Future paths / 2010 Nicholas Canny reflects on the Academy’s evolving role Innovation Ireland Tom Brazil assesses the Report of the Innovation Taskforce Eurosciences Biennale Open Forum R O Peter Mitchell looks to opportunities ahead as Dublin YAL becomes European City of Science in 2012 IRISH Quote/unquote Michael Cronin argues for critical thinking A vision for astronomy and ACADEMY astrophysics in Ireland David Fegan traces the journey of the cosmos from the ‘Big Bang’ On the shelf 9-volume Dictionary of Irish Biography ACADAMH R ÍOG A N A H É IREA NN RIA RIA ROYAL IRISH ACADEMY • ACADAMH RÍOGA NA HÉIREANN RIA cover to print_Layout 1 10/12/2010 11:04 Page 2 ContentS } Key Achievements 2009–10 p2 } President’s Report—Future paths: on the Academy’s evolving role p4 } Secretary’s Report—Innovation Ireland: the Report of the Innovation Taskforce p8 } Science Secretary’s Report—Eurosciences Biennale Open Forum—Dublin’s opportunity p11 } PL&A Secretary’s Report—Quote/unquote—on critical thinking p16 } Senior Vice-President’s Report—A vision for astronomy and astrophysics in Ireland p20 } New Members p24 } Distinctions conferred on Members p31 } Bereavements p32 } Academy Committees Report p38 } Competitive measures—on Craig Barrett’s Academy address p42 } ‘The Future Role of the University in a Changing World’ p45 } A Year in View p47 } Research Projects p54 } Art and Architecture of Ireland (AAI) p54 } Dictionary of Irish Biography (DIB) p56 } Dictionary -
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 -
Reports of Sponsored Meetings
Reports of Sponsored Meetings Women in Mathematics Day Ireland 2018 29 August 2018, O'Brien Centre for Science, UCD Organisers School of Mathematics and Statistics, University College Dublin Co-Chairs: Isabella Gollini, Aoibhinn N´ıSh´uilleabh´ain Committee members: Michelle Carey, Vasiliki Dimitrakopoulou, Mark Dukes, Claire Gormley, Gabrielle Kelly, Pauline Mellon, Neil O'Connell, Adamaria Perrotta, Michael Salter-Townshend, John Sheekey, Helena Smigoc. The Women in Mathematics Day Ireland (WIMDI) has become an annual conference since its inauguration in 2010. The conference is a multi-faceted event that includes plenary talks, academic and indus- trial research talks, poster sessions for students, and the centrepiece of this year's event has been the celebration and acknowledgement of Sheila Tinney's work in the mathematical sciences and marks the centenary of her birth. Dr. Sheila Tinney was the first Irish woman to receive a PhD in Mathematics, was the first female fellow of DIAS (Dublin Institute of Advanced Studies), was one of the first four women to be admitted to the Royal Irish Academy and also lectured at UCD. This year's event attracted almost 150 people from all over Ireland, and the audience at the event included girls from St Mark's Commu- nity School, students, lecturers and general public from around the country. 22 23 The day was opened by Minister for Higher Education Mary Mitchell O'Connor and the UCD Vice-President for Research, Inno- vation & Impact Prof. Orla Feely. In celebration of the centenary of Sheila Tinney's birth, an Irish Scientist plaque was unveiled in her honour. -
An Open Letter to the Government of Ireland
An Open Letter to the Government of Ireland As scientists in Ireland and Irish scientists abroad, we are committed to making our contribution to Ireland’s recovery by doing the best and most innovative research possible. However, we are deeply concerned about the research policies implemented by the current government. The policy of sustained investment in scientific excellence that helped build a vibrant scientific community in Ireland over the past fifteen years has given way to a short- sighted drive for commercialisable research in a very limited set of prescribed areas. Along with an investment in research that is below the EU average, steadily decreasing core grants to universities, and a constant demand to increase student numbers, these policies are creating a perfect storm for scientific research and education in Ireland and are undermining our abilities to carry out worldclass research, to retain scientific talent in the country and also to educate future scientists and build a real and sustainable knowledge economy. Innovation needs a strong core in basic research A wealth of economic research shows that sustained investment in basic research pays huge dividends economically, not just through the generation of intellectual property and the development of new companies, but also by building human capital and by attracting companies that hope to benefit from a vibrant research community. Countries with long- established and functional research systems that successfully underpin economic development rely on a well-balanced mix between basic and applied research. The Irish Government’s current investment in applied research is welcome and forms an essential part of an overall strategy to generate economic return from scientific research. -
Irish Mathematics Calendar 2016 Maths Calendar Layout 1 14/12/2015 18:09 Page 2
Maths Calendar_Layout 1 14/12/2015 18:09 Page 1 Irish Mathematics Calendar 2016 Maths Calendar_Layout 1 14/12/2015 18:09 Page 2 Des MacHale Annette Pilkington was born 28 January in Castlebar, Mayo, and was educated at UCG and the was born 16 January in Daingean, Offaly. She University of Keele. He has spent his entire career at UCC, working in group was educated at UCD and at the University of and ring theory. He wrote the definitive biography of George Boole, the first Notre Dame, where she now teaches. She is an Prof of Maths at what was then Queen's College Cork. He has also authored algebraist whose research interests are in a large number of books on puzzles and humour. classical groups, K-theory, and representation theory. Mathematical physicist Sheila Tinney (née Power, 1918-2010) Ken Houston was born 15 January in Galway, where her father was professor was born 13 January in Belfast, and was educated at of maths. She was educated at UCD and the University of QUB. He taught at UU Jordanstown for over 3 Edinburgh, becoming the first Irish woman to get a doctorate in decades, where he aimed to encourage in mathematics mathematical science. She worked at UCD, introducing undergrads the art of mathematical modelling and to generations of students to quantum physics. adopt this as their professional "Way of Life," and he published a lot in this area. His book Creators of Mathematics: The Irish Connection is essential reading. Robert Boyle (1627-1691) Brendan Goldsmith was born 22 January in Belfast, was born 25 January in Lismore, Waterford, and as a child was and was educated at QUB and Oxford. -
Video Transcript: Women Walls at RIA | Accenture
WOMEN WALLS AT RIA: THE DOCUMENTARY VIDEO TRANSCRIPT Women have made huge progress in Ireland I’ve worked in the Academy for over 20 years I’d over the last century, but just how equal is the forgotten and it annoyed me you know I was society we’ve created today? Have women been annoyed and irritated myself and because I have recognised enough in our history and in our been conscious of the fact that it’s not public spaces? With an increase in spotlight on acceptable but it does give a bad impression of gender issues and gender equality, the Royal the Academy and it just gave a bad impression Irish academy on Dublin’s Dawson Street has of Irish intellectual life arch tells us so much chosen to commemorate and celebrate amazing about what we value as a society about who is Irish women at the home of academic excellence welcome about who fits in Irish communicates for some of our greatest minds both male and our expectations of our gender so in a very female, but a walk public forum if we’re leaving women out of them Around Academy house tells a different story. actually were perpetuating women being less The Royal Irish Academy was formed in 1785 visible and indeed their work being less known at the learner’s society promoting the sciences that’s carried on to future generations and in and the humanities. It’s a remarkable selection many ways less valued it’s not only in the of some of Ireland’s best academics committing Academy that we don’t see female faces you go their lives to finding answers to questions that to any public building