Epigenesys: Epigenetics Meets Systems Biology
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Epigenetics Landscape (Fig
© 2015. Published by The Company of Biologists Ltd | The Journal of Experimental Biology (2015) 218, 816-818 doi:10.1242/jeb.120071 CLASSICS Conrad Waddington and ‘decisions’ that could be represented as exploited plasticity that is already ‘valleys’ and ‘forks’ in a developmental present in the population. That strongly the origin of epigenetics landscape (Fig. 1). He knew from his suggests that all the alleles (gene developmental studies that embryo fruit variants) necessary for the inheritance of flies could be persuaded to show different the characteristic were already present in thorax and wing structures, simply by the population, but not initially in any changing the environmental temperature or particular individuals in the correct by a chemical stimulus. In his landscape combination. The experiment simply diagram, this could be represented as a brings them together. This is a small manipulation in slope that would lead modification of the pattern of the genome to one channel in the landscape being in response to the environmental change, favoured over another, so that the adult but not in a way that requires any new could show a different phenotype starting mutations. I came to this conclusion from the same genotype. before reading Waddington’s (1957) Epigenetics book, The Strategy of the Genes. But it is Denis Noble discusses Conrad The next step in his experiment was to in fact one of Waddington’s own ideas! Waddington’s classic paper, ‘The genetic select for and breed from the animals that He writes ‘There is no … reason which ’ assimilation of the bithorax phenotype , displayed the new characteristic. -
The for Report 07-08
THE CENTER FOR INTEGRATIVE GENOMICS REPORT 07-08 www.unil.ch/cig Table of Contents INTRODUCTION 2 The CIG at a glance 2 The CIG Scientific Advisory Committee 3 Message from the Director 4 RESEARCH 6 Richard Benton Chemosensory perception in Drosophila: from genes to behaviour 8 Béatrice Desvergne Networking activity of PPARs during development and in adult metabolic homeostasis 10 Christian Fankhauser The effects of light on plant growth and development 12 Paul Franken Genetics and energetics of sleep homeostasis and circadian rhythms 14 Nouria Hernandez Mechanisms of basal and regulated RNA polymerase II and III transcription of ncRNA in mammalian cells 16 Winship Herr Regulation of cell proliferation 18 Henrik Kaessmann Mammalian evolutionary genomics 20 Sophie Martin Molecular mechanisms of cell polarization 22 Liliane Michalik Transcriptional control of tissue repair and angiogenesis 24 Alexandre Reymond Genome structure and expression 26 Andrzej Stasiak Functional transitions of DNA structure 28 Mehdi Tafti Genetics of sleep and the sleep EEG 30 Bernard Thorens Molecular and physiological analysis of energy homeostasis in health and disease 32 Walter Wahli The multifaceted roles of PPARs 34 Other groups at the Génopode 37 CORE FACILITIES 40 Lausanne DNA Array Facility (DAFL) 42 Protein Analysis Facility (PAF) 44 Core facilities associated with the CIG 46 EDUCATION 48 Courses and lectures given by CIG members 50 Doing a PhD at the CIG 52 Seminars and symposia 54 The CIG annual retreat 62 The CIG and the public 63 Artist in residence at the CIG 63 PEOPLE 64 1 Introduction The Center for IntegratiVE Genomics (CIG) at A glance The Center for Integrative Genomics (CIG) is the newest depart- ment of the Faculty of Biology and Medicine of the University of Lausanne (UNIL). -
Unusual Activity of a Chlamydomonas TET/JBP Family Enzyme ,† ,‡ ,§,∥ 2 L
1 Unusual Activity of a Chlamydomonas TET/JBP Family Enzyme ,† ,‡ ,§,∥ 2 L. Aravind,* Shankar Balasubramanian,* and Anjana Rao* † 3 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 4 20894, United States ‡ 5 Department of Chemistry and Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, U.K. § 6 La Jolla Institute for Immunology and Sanford Consortium for Regenerative Medicine, La Jolla, California 92037, United States ∥ 7 Department of Pharmacology and Moores Cancer Center, University of California, San Diego, California 92093, United States 8 he Great Oxygenation Event, which occurred on earth to 5mC. 5hmC and 5caC are produced in minor amounts, 55 9 T around 2.45 billion years ago, opened up the niche for through a mechanism that apparently does not require 2OG 56 10 enzymes that could directly oxidize substrates using molecular but needs ascorbate. 57 11 oxygen (O2), including the 2-oxoglutarate (2OG) and Fe(II)- Ascorbate (>1 mM) is believed to help reduce Fe(III) at the 58 12 dependent dioxygenases. 2OGFe-dioxygenases possess a active site of 2OGFe-dioxygenases back to Fe(II), thereby 59 13 double-stranded b-helix fold, with an iron center chelated by “resetting” the active site for catalysis. Addition of ascorbate 60 1 14 two histidines and an aspartate. 2OGFe-dioxygenases catalyze results in a dose-dependent improvement in catalysis by 61 4 15 the incorporation of one atom of O2 into 2-oxoglutarate, mammalian TET1 and an increased amount of 5hmC in cells. 62 16 oxidizing it to succinate, and the second atom into an organic Thus, instead of the usual 2OG substrate, C. -
AI and Bioinformatics
AI Magazine Volume 25 Number 1 (2004) (© AAAI) Articles Editorial Introduction AI and Bioinformatics Janice Glasgow, Igor Jurisica, and Burkhard Rost ■ This article is an editorial introduction to the re- modern-day biology is far more complex than search discipline of bioinformatics and to the articles suggested by the simplified sketch presented in this special issue. In particular, we address the issue here. In fact, researchers in life sciences live off of how techniques from AI can be applied to many of the introduction of new concepts; the discov- the open and complex problems of modern-day mol- ecular biology. ery of exceptions; and the addition of details that usually complicate, rather than simplify, his special issue of AI Magazine focuses the overall understanding of the field. on some areas of research in bioinfor- Possibly the most rapidly growing area of re- Tmatics that have benefited from applying cent activity in bioinformatics is the analysis AI techniques. Undoubtedly, bioinformatics is of microarray data. The article by Michael Mol- a truly interdisciplinary field: Although some la, Michael Waddell, David Page, and Jude researchers continuously affect wet labs in life Shavlik (“Using Machine Learning to Design science through collaborations or provision of and Interpret Gene-Expression Microarrays”) tools, others are rooted in the theory depart- introduces some background information and ments of exact sciences (physics, chemistry, or provides a comprehensive description of how engineering) or computer sciences. This wide techniques from machine learning can be used variety creates many different perspectives and to help understand this high-dimensional and terminologies. One result of this Babel of lan- prolific gene-expression data. -
EMBC Annual Report 2007
EMBO | EMBC annual report 2007 EUROPEAN MOLECULAR BIOLOGY ORGANIZATION | EUROPEAN MOLECULAR BIOLOGY CONFERENCE EMBO | EMBC table of contents introduction preface by Hermann Bujard, EMBO 4 preface by Tim Hunt and Christiane Nüsslein-Volhard, EMBO Council 6 preface by Marja Makarow and Isabella Beretta, EMBC 7 past & present timeline 10 brief history 11 EMBO | EMBC | EMBL aims 12 EMBO actions 2007 15 EMBC actions 2007 17 EMBO & EMBC programmes and activities fellowship programme 20 courses & workshops programme 21 young investigator programme 22 installation grants 23 science & society programme 24 electronic information programme 25 EMBO activities The EMBO Journal 28 EMBO reports 29 Molecular Systems Biology 30 journal subject categories 31 national science reviews 32 women in science 33 gold medal 34 award for communication in the life sciences 35 plenary lectures 36 communications 37 European Life Sciences Forum (ELSF) 38 ➔ 2 table of contents appendix EMBC delegates and advisers 42 EMBC scale of contributions 49 EMBO council members 2007 50 EMBO committee members & auditors 2007 51 EMBO council members 2008 52 EMBO committee members & auditors 2008 53 EMBO members elected in 2007 54 advisory editorial boards & senior editors 2007 64 long-term fellowship awards 2007 66 long-term fellowships: statistics 82 long-term fellowships 2007: geographical distribution 84 short-term fellowship awards 2007 86 short-term fellowships: statistics 104 short-term fellowships 2007: geographical distribution 106 young investigators 2007 108 installation -
ANNUAL REPORT 2010 Contents
ANNUAL REPORT 2010 Contents I. Overviews ...............................................................................................................3 Year 2010 in review, Director of FIMM ............................................................................. 3 Views from the former and current Chair of the Board ...................................................5 II. FIMM Launch Event ................................................................................................ 6 III. How is the Nordic EMBL Partnership build-up progressing in Oslo and Umeå? ..........7 IV. Academician of Science, Professor Leena Peltonen-Palotie in memoriam .............. 8 V. Research ................................................................................................................ 10 Human Genomics ..........................................................................................................10 Medical Systems Biology and Translational Research ..................................................... 14 Research collaborations and highlights ..........................................................................21 Personalized medicine of cancer becoming a reality.......................................................25 Doctoral Training ...........................................................................................................26 VI. Technology Centre .................................................................................................28 Genomics Unit ..............................................................................................................28 -
The Evolution of Universal Adaptations of Life Is Driven by Universal Properties of Matter: Energy, Entropy, and Interaction [Version 2; Peer Review: 3 Approved]
F1000Research 2020, 9:626 Last updated: 23 SEP 2021 OPINION ARTICLE The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction [version 2; peer review: 3 approved] Irun R. Cohen 1, Assaf Marron 2 1Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel 2Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel v2 First published: 18 Jun 2020, 9:626 Open Peer Review https://doi.org/10.12688/f1000research.24447.1 Second version: 30 Jul 2020, 9:626 https://doi.org/10.12688/f1000research.24447.2 Reviewer Status Latest published: 02 Sep 2020, 9:626 https://doi.org/10.12688/f1000research.24447.3 Invited Reviewers 1 2 3 Abstract The evolution of multicellular eukaryotes expresses two sorts of version 3 adaptations: local adaptations like fur or feathers, which characterize (revision) species in particular environments, and universal adaptations like 02 Sep 2020 microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms version 2 driving the universal adaptations of multicellulars should themselves (revision) report report be universal, and propose a mechanism based on properties of matter 30 Jul 2020 and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. version 1 Metabolic networks channel some of this energy to form cooperating, 18 Jun 2020 report report interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it 1. -
IST Annual Report 2019
Annual Report 2019 IST Austria administrative and The people of IST Austria technical support staff by nationality Austria 59.4% Nationalities on campus Germany 5.6% Hungary 3.1% Poland 2.5% Romania 2.5% Scientists as well as administrative and technical support staff come Italy 2.1% Russia 1.7% from all over the world to conduct and back research at IST Austria. Czech Republic 1.4% As of December 31, 2019, a total of 72 nationalities were represented India 1.4% Slovakia 1.4% on campus. Spain 1.4% UK 1.4% Other 16.1% North America Europe Asia Canada Albania Italy Afghanistan Cuba Andorra Latvia Bangladesh El Salvador Armenia Lithuania China Mexico Austria Luxembourg South Korea USA Belarus Macedonia India Belgium Malta Iran Bosnia and Netherlands Israel Herzegovina Norway Japan Bulgaria Poland Jordan Croatia Portugal Kazakhstan Cyprus Romania Lebanon Czech Republic Serbia Mongolia Denmark Slovakia Philippines Finland Slovenia Russia France Spain Singapore Georgia Sweden Syria Germany Switzerland Vietnam Greece Turkey Hungary UK Ireland Ukraine Africa Egypt Kenya IST Austria scientists by nationality Libya Austria 14.7% Nigeria Germany 10.9% South America Italy 7.4% Argentina India 5.9% Russia 4.7% Brazil Slovakia 4.1% Chile China 4.1% Colombia Hungary 3.7% Peru Spain 3.3% Uruguay USA 3.1% Czech Republic 2.9% UK 2.4% Oceania Other 32.8% Australia Content 2 HAPPY BIRTHDAY! 40 RESEARCH 4 Foreword by the president 42 Biology 5 Board member voices 44 Computer science 6 “An Austrian miracle” 46 Mathematics A year of celebration 48 Neuroscience -
EMBO Facts & Figures
excellence in life sciences Reykjavik Helsinki Oslo Stockholm Tallinn EMBO facts & figures & EMBO facts Copenhagen Dublin Amsterdam Berlin Warsaw London Brussels Prague Luxembourg Paris Vienna Bratislava Budapest Bern Ljubljana Zagreb Rome Madrid Ankara Lisbon Athens Jerusalem EMBO facts & figures HIGHLIGHTS CONTACT EMBO & EMBC EMBO Long-Term Fellowships Five Advanced Fellows are selected (page ). Long-Term and Short-Term Fellowships are awarded. The Fellows’ EMBO Young Investigators Meeting is held in Heidelberg in June . EMBO Installation Grants New EMBO Members & EMBO elects new members (page ), selects Young EMBO Women in Science Young Investigators Investigators (page ) and eight Installation Grantees Gerlind Wallon EMBO Scientific Publications (page ). Programme Manager Bernd Pulverer S Maria Leptin Deputy Director Head A EMBO Science Policy Issues report on quotas in academia to assure gender balance. R EMBO Director + + A Conducts workshops on emerging biotechnologies and on H T cognitive genomics. Gives invited talks at US National Academy E IC of Sciences, International Summit on Human Genome Editing, I H 5 D MAN 201 O N Washington, DC.; World Congress on Research Integrity, Rio de A M Janeiro; International Scienti c Advisory Board for the Centre for Eilish Craddock IT 2 015 Mammalian Synthetic Biology, Edinburgh. Personal Assistant to EMBO Fellowships EMBO Scientific Publications EMBO Gold Medal Sarah Teichmann and Ido Amit receive the EMBO Gold the EMBO Director David del Álamo Thomas Lemberger Medal (page ). + Programme Manager Deputy Head EMBO Global Activities India and Singapore sign agreements to become EMBC Associate + + Member States. EMBO Courses & Workshops More than , participants from countries attend 6th scienti c events (page ); participants attend EMBO Laboratory Management Courses (page ); rst online course EMBO Courses & Workshops recorded in collaboration with iBiology. -
Wellcome Investigators March 2011
Wellcome Trust Investigator Awards Feedback from Expert Review Group members 28 March 2011 1 Roughly 7 months between application and final outcome The Expert Review Groups 1. Cell and Developmental Biology 2. Cellular and Molecular Neuroscience (Zaf Bashir) 3. Cognitive Neuroscience and Mental Health 4. Genetics, Genomics and Population Research (George Davey Smith) 5. Immune Systems in Health and Disease (David Wraith) 6. Molecular Basis of Cell Function 7. Pathogen Biology and Disease Transmission 8. Physiology in Health and Disease (Paul Martin) 9. Population and Public Health (Rona Campbell) 2 Summary Feedback from ERG Panels • The bar is very high across all nine panels • Track record led - CV must demonstrate a substantial impact of your research (e.g. high impact journals, record of ground breaking research, clear upward trajectory etc) To paraphrase Walport ‘to support scientists with the best track records, obviously appropriate to the stage in their career’ • Notable esteem factors (but note ‘several FRSs were not shortlisted’) • Your novelty of your research vision is CRUCIAL. Don’t just carry on doing more of the same • The Trust is not averse to risk (but what about ERG panel members?) • Success rate for short-listing for interview is ~15-25% at Senior Investigator level (3-5 proposals shortlisted from each ERG) • Fewer New Investigator than Senior Investigator applications – an opportunity? • There are fewer applications overall for the second round, but ‘the bar will not be lowered’ The Challenge UoB has roughly 45 existing -
Conference Ontyph Id
10th INTERNATIONAL CONFERENCE ON TYPH ID & OTHER INVASIVE SALMONELLOSES April 4–6, 2017 | Kampala, Uganda 10th INTERNATIONAL CONFERENCE ON TYPH ID & OTHER INVASIVE SALMONELLOSES WELCOME April 4–6, 2017 | Kampala, Uganda THE WORLD NEEDS ACTION ON TYPHOID — BUILDING EVIDENCE AND REFINING STRATEGIES The Coalition against Typhoid, housed at the Sabin Vaccine Institute, welcomes you to the 10th International Conference on Typhoid and Other Invasive Salmonelloses. We are pleased to provide a forum for more than 300 researchers, policy makers, immunization managers and advocates to come together to share the latest developments and best strategies to reduce the burden of typhoid, paratyphoid and nontyphoidal salmonelloses (NTS) on communities around the world. The conference theme, “From Evidence to Action,” is timely as we prepare for the introduction of new typhoid conjugate vaccines. The research, evidence and ideas shared this week in Kampala will provide the foundation for global action against typhoid, paratyphoid and NTS. Together, we will review crucial developments to reduce the global burden of these diseases, including results from major surveillance projects in Africa and Asia, the potential of human infection models and strategies for countering antibiotic resistance. The program will also highlight outbreak control methods, exciting innovations in diagnostics, water, sanitation and hygiene strategies for prevention, and policy measures aimed at accelerating the implementation of these interventions. The coming availability of a new generation of typhoid conjugate vaccines makes this a pivotal moment for global action on typhoid. These promising new vaccines offer important advantages over prior vaccines, including longer duration of protection, the ability to protect young children, and the potential for administration with other vaccines in routine immunization of infants. -
Snakemake As a Workflow Engine for Reciprocal BLAST Analyses
Snakemake as a workflow engine for reciprocal BLAST analyses Lukas Becker A thesis presented for the degree of Bachelor of Science Supervisor: Prof. Dr. Gunnar Klau Second Assessor: Dr. Nicolas Schmelling Algorithmic Bioinformatics Heinrich Heine University Düsseldorf Germany 25th February, 2021 Acknowledgments I would like to express my gratitude for Prof. Gunnar Klau whose encouragement and guidance throughout this study has been a great support. Furthermore, I owe special thanks to Dr. Nicolas Schmelling for his invaluable support, constructive feedback and continued assistance in my various questions. Thanks for the opportunity to work on this thesis and the experience to work on this cooperative topic. In addition, I would like to thank Philipp Spohr for his patience with my many questions and his advice and valuable guidance. Thanks. ii Abstract In modern genomic analysis, homology describes the evolutionary relationship between two sequences. In addition to a diverse classification of homology, the key concept for evolutionary and comparative genomics is the dichotomous differentiation of homology into orthologous and paralogous sequences. Sets of orthologous genes are used to obtain information regarding gene functions and phylogenetic relationships because orthologs tend to retain their biolog- ical function. Various methods have been developed in order to identify orthologous genes. Typically, orthologous and paralogous gene relationships are disentangled by measuring and comparing sequence similarities within sequences of interest. More precisely, when search- ing orthologous sequences in different genomes, those sequences will most likely match each other as best hits when performing sequence similarity searches. The resulting sequences are called reciprocal best hits (RBHs). The identification of RBHs is the most common method to infer putative orthologs in comparative genomic studies.