The Science of Malaria Eradication
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Challenges Across Large-Scale Biomolecular and Polymer Simulations
Challenges across Large-Scale Biomolecular and Polymer Simulations February 21, 2017 - February 24, 2017 CECAM-AT Ivan Coluzza University of Vienna, Austria Samuela Pasquali Paris Descartes University, France Barbara Capone University of Vienna, Austria Christoph Dellago University of Vienna, Austria Tamar Schlick New York University, USA 1 Description The goal of this workshop is to bring together scientists who study large scale molecular systems both in the biological world and those from the polymer science community. This workshop aims to bring broad-minded scientists interested in these challenges to discuss state-of-the-art approaches and issues with the goal of advancing structural biophysics and applied fields. By discussing various approaches and ways to integrate knowledge on multiple scales, we hope to build a community to advance this important field. The increase in computer power in tandem with algorithmic and force-field improvements are opening opportunities for modeling large biomolecular systems as never before. Yet, many challenges in modeling and simulations of such complex systems, in realistic environments, require innovations to make the necessary experimental connections and develop new theories and mechanistic details of the associated processes. The workshop that we propose will follow and build upon the first workshop organized in Telluride (June 14-18, 2015) by Tamar Schlick and Klaus Schulten entitled "Challenges in Simulating Large-Scale Biomolecular Complexes", by focusing on the following subjects: - Large scale simulations with respect to time and system size. We will include recent advances in atomistic force-fields and technological advances in algorithms and hardware that make possible simulations on the millisecond time scales for systems composed of millions of atoms, such as large solvated biomolecules. -
Study Unveils Hidden Molecular Machinery in RNA Processes 21 September 2016
Study unveils hidden molecular machinery in RNA processes 21 September 2016 In epigenetics, the environment can produce a physiological change that gets passed down from generation to generation; however, the cells' DNA sequence is never changed and remains exactly the same. Plants are ideal model systems, Sanbonmatsu pointed out, allowing the study of epigenetic memory (where one generation of cells remembers what happened to the previous generation of cells) in slow motion. For this paper, the focus was on an RNA string known as COOLAIR that controls the timing of flowering of plants in the springtime, in that it Artist's impression of a long, non-coding RNA system. senses how long a plant has been exposed to cold. Grey/blue/red indicates main long non-coding RNA. When these RNAs are turned off or removed, Green, showing a second RNA interacting with long- plants simply do not flower. noncoding RNA. Magenta ribbons and blue barrels indicated RNA-interacting proteins. Credit: Los Alamos "Flowers may seem frivolous, compared with the National Laboratory, Kara Fischer and Karissa Sanbonmatsu working structure of the rest of the plant's leaves, stems and roots, but they actually hold the keys to survival for flowering plants," Sanbonmatsu said. A special stretch of ribonucleic acid (RNA) called "In fact, the plant's reproductive success depends COOLAIR is revealing its inner structure and critically on the precise timing of flowering in the function to scientists, displaying a striking springtime. Our discovery, finding mechanical resemblance to an RNA molecular machine, substructures inside COOLAIR, is a big piece of territory previously understood to be limited to the evidence that the RNAs may be more like cells' protein factory (the 'ribosome') and not a skill machines, and they assist in this implementation of set given to mere strings of RNA. -
˜ Ü Proceedings
ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ The 2nd International Symposium on Large-scale Computational Science and Engineering ਫ਼Ňो̸ႏ Proceedings Ȳ ̵ 4 Nov. 8, 2012, Thursday ̵7SUએਫ਼ɝ Science Council of Japan, Tokyo, Japan ΪŮ Sponsor Science Council of Japan Japan Science and Technology Agency ȁŮ Co-sponsor ̵7̺µ˨SU (The Japan Society for Industrial and Applied Mathematics) ̵7̴SUThe Chemical Society of Japan ̵7ɝļSU (The Japan Society of Mechanical Engineers) ̵7ওÜǜSU (The Japan Society for Computational Engineering and Science) ̵7ওÜ˨ǜSU (Japan Society for Computational Methods in Engineering) ̵7ওÜ˒SೳϤ JACM (Japan Association for Computational Mechanics) ̵7ÙāćĎĞÙĉĕSU (Japan Society for Simulation Technology) ̵7̀SU (The Physical Society of Japan) ͨଦ Support Ҝ˿తğU (Society of Automotive Engineers of Japan) ÙĕÿÚÈĂ୳̸ ಶȲÕĕöćĞáͬ೯ͮЏΆ]h:ŃĝwɰBĝฎBΡS: ǜS:ǥĝ̓˵ΡS:%Ư¦ͼƯ¦ĀčãÛÓĞč:o: ̈sï¯̀o¯Āčã÷ÅÚåÑÛϧ¶È{ʢ"pΑÒΠ ¥°n®:̒{hÒ p˨̈s̋°f®¢}; 7ÙĕÿÚÈĂ:w°ʢ"ɰญΠo:ìðĝòÆÌΚǥႸ ȏ:izΡS¬āÑď:f¯hĀÑďϧ¶ॾz}¯ɰญ¶È {:Ąéč̴¨˨ĕওÜýϚ¬ÙāćĎĞÙĉĕçȷ³¯Åᆏ h:ƼȎ̅1{h¯êåùÑċÛʢ"͵¶ŝΨ{ਫ਼Ňóïčখ ਭ¶ࢌh¢};w°¬®:ϣʢ"ᆏ̉ਭĝğ:ࣽ˨ʢ" ᆏȁ೫¦p͒o®:ʢ"ᆏ¶୨l¬®̑qÒ p̋ °¯wp/˽y°¢};¢:ͽӑ̙>¦̈˨xί˕hq:w̙ ჳÕĕöćĞáÙāćĎĞÙĉĕʢ"˲ʵÒ ¶ͽӑ̓Uȁ{h ͳlh¢}; ― 3 ― ùďÒċĂ ࿔UƅŬ ÙĕÿÚÈĂએ࿇ƅŬ ʆǕ Ǟɖ̵7SUએ f̑S ˝Dž ȁŮ͵.ࢢƅŬ ǯΨ ç͂ΡSğƊҶɝǻãæʢ"Ǟൺ ΆȅΪ=ਚÅ 78 ùĎìČਫ਼Ňìð ϞUᜨÑŦ Ïͽ̴Sʢ"ôওÜiz̀ʢ" ࿇ ĀÈď þÊďƼÛêċÛøčÒ̑SŃ̴̀Sʢ"ô ˝Dž ÚĉÝ÷ āÑčůƼÕďċë̑SþĞčâĞ× ˝Dž Πญ 1ͽ൫ůƼͩÍČ÷ËčíÄ̑S ˝Dž 78]78 O£ ]787] ùĎìČਫ਼ŇᜠòÆÌ ϞUᜨİ7 ͐ȶϊÿ̑S ˝Dž ĂĞĕ Ï ÏĂᅁƼÒDzᇻ̑S ɀ˝Dž ÍČĞ× ×ĕþĕĀæůƼďÛÄċĄÛƼWʢ"ô -
FINDING FUNCTION in MYSTERY TRANSCRIPTS Little Is Known About the Function of Most Long Non-Coding Rnas
TECHNOLOGY FEATURE FINDING FUNCTION IN MYSTERY TRANSCRIPTS Little is known about the function of most long non-coding RNAs. But a suite of new tools might change that. KARISSA Y. SANBONMATSU KARISSA Y. Conceptual model of a long non-coding RNA that provides structural scaffolding (grey) while binding to proteins (magenta) using highly structured domains (green, pink and orange). BY KELLY RAE CHI because they contain repetitive stretches of code pluripotent cells that develop into a human that sequence analysers had tended to filter out. fetus: those that comprise the ‘inner cell mass’ of n 2013, a group of researchers decided to dig It was a big blind spot. Other labs had uncov- an embryo that has yet to implant in the uterus2. deeper into a human embryonic stem-cell ered early evidence of RNAs that are rich in These RNA stretches are examples of long line called H1 — and uncovered some sur- repetitive codes and important in human stem non-coding RNAs (lncRNAs) — sequences at Iprises. H1 is one of the best known stem-cell cells. As the researchers, who were based mostly least 200 bases long that do not encode proteins. lines, yet the team managed to unearth more at California’s Stanford University, examined lncRNAs are present in many different kinds than 2,000 previously uncharacterized stretches their haul, they realized that they had hit on of tissue and are often found in specific spots of RNA1. What is more, 146 of those were exclu- exactly these kinds of RNA. Among their list inside a cell. But most lack a defined function sive to human embryonic stem cells, offering of 146 RNA sequences, says team member Vit- and, until recently, were thought to be little more tantalizing leads into pluripotency — the ability torio Sebastiano, three of the most abundant — than transcriptional noise. -
Program Information
RNA 2021 The 26th Annual Meeting of the RNA Society On-line May 25–June 4, 2021 RNA 2021 On-Line The 26th Annual Meeting of the RNA Society CORRECT THE MESSAGE CHANGE A LIFETM Locanabio’s CORRECTXTM platform is pioneering a new class of gene therapies by correcting the th th May 25 – June 4 , 2021 dysfunctional RNA that causes a broad range of neurodegenerative, neuromuscular and retinal diseases Gene Yeo – University of California San Diego, USA Katrin Karbstein – Scripps Research Institute, Florida, USA V. Narry Kim – Seoul National University, South Korea Anna Marie Pyle – Yale University, USA Xavier Roca – Nanyang Technological University, Singapore Jörg Vogel – University of Würzburg, Germany RNA 2021 • On-line GENERAL INFORMATION Citation of abstracts presented during RNA 2021 On-line (in bibliographies or other) is strictly prohibited. Material should be treated as personal communication and is to be cited only with the expressed written ® consent of the author(s). The Sequel IIe System NO UNAUTHORIZED PHOTOGRAPHY OF ANY MATTER PRESENTED DURING THE ON-LINE MEETING: To encourage sharing of unpublished data at the RNA Society Annual Meeting, taking of photographs, screenshots, videos, and/or downloading or saving Reveal the functional e ects any material is strictly prohibited. of alternative splicing with USE OF SOCIAL MEDIA: The official hash tag of the 26th Annual Meeting of the RNA Society is full-length transcript sequencing #RNA2021. The organizers encourage attendees to tweet about the amazing science they experience during the meeting. However, please respect these few simple rules when using the #RNA2021 hash tag, or when talking about the meeting on Twitter and other social media platforms: 1. -
Tumor Therapy in Mice Via Antigen Targeting to a Novel, DC- Restricted C-Type Lectin
Tumor therapy in mice via antigen targeting to a novel, DC- restricted C-type lectin David Sancho, … , James R. Carlyle, Caetano Reis e Sousa J Clin Invest. 2008;118(6):2098-2110. https://doi.org/10.1172/JCI34584. Research Article Immunology The mouse CD8α+ DC subset excels at cross-presentation of antigen, which can elicit robust CTL responses. A receptor allowing specific antigen targeting to this subset and its equivalent in humans would therefore be useful for the induction of antitumor CTLs. Here, we have characterized a C-type lectin of the NK cell receptor group that we named DC, NK lectin group receptor-1 (DNGR-1). DNGR-1 was found to be expressed in mice at high levels by CD8+ DCs and at low levels by plasmacytoid DCs but not by other hematopoietic cells. Human DNGR-1 was also restricted in expression to a small subset of blood DCs that bear similarities to mouse CD8α+ DCs. The selective expression pattern and observed endocytic activity of DNGR-1 suggested that it could be used for antigen targeting to DCs. Consistent with this notion, antigen epitopes covalently coupled to an antibody specific for mouse DNGR-1 were selectively cross-presented by CD8α+ DCs in vivo and, when given with adjuvants, induced potent CTL responses. When the antigens corresponded to tumor-expressed peptides, treatment with the antibody conjugate and adjuvant could prevent development or mediate eradication of B16 melanoma lung pseudometastases. We conclude that DNGR-1 is a novel, highly specific marker of mouse and human DC subsets that can be exploited for CTL cross-priming and tumor therapy. -
BIOLOGY 639 SCIENCE ONLINE the Unexpected Brains Behind Blood Vessel Growth 641 THIS WEEK in SCIENCE 668 U.K
4 February 2005 Vol. 307 No. 5710 Pages 629–796 $10 07%.'+%#%+& 2416'+0(70%6+10 37#06+6#6+8' 51(69#4' #/2.+(+%#6+10 %'..$+1.1); %.10+0) /+%41#44#;5 #0#.;5+5 #0#.;5+5 2%4 51.76+105 Finish first with a superior species. 50% faster real-time results with FullVelocity™ QPCR Kits! Our FullVelocity™ master mixes use a novel enzyme species to deliver Superior Performance vs. Taq -Based Reagents FullVelocity™ Taq -Based real-time results faster than conventional reagents. With a simple change Reagent Kits Reagent Kits Enzyme species High-speed Thermus to the thermal profile on your existing real-time PCR system, the archaeal Fast time to results FullVelocity technology provides you high-speed amplification without Enzyme thermostability dUTP incorporation requiring any special equipment or re-optimization. SYBR® Green tolerance Price per reaction $$$ • Fast, economical • Efficient, specific and • Probe and SYBR® results sensitive Green chemistries Need More Information? Give Us A Call: Ask Us About These Great Products: Stratagene USA and Canada Stratagene Europe FullVelocity™ QPCR Master Mix* 600561 Order: (800) 424-5444 x3 Order: 00800-7000-7000 FullVelocity™ QRT-PCR Master Mix* 600562 Technical Services: (800) 894-1304 Technical Services: 00800-7400-7400 FullVelocity™ SYBR® Green QPCR Master Mix 600581 FullVelocity™ SYBR® Green QRT-PCR Master Mix 600582 Stratagene Japan K.K. *U.S. Patent Nos. 6,528,254, 6,548,250, and patents pending. Order: 03-5159-2060 Purchase of these products is accompanied by a license to use them in the Polymerase Chain Reaction (PCR) Technical Services: 03-5159-2070 process in conjunction with a thermal cycler whose use in the automated performance of the PCR process is YYYUVTCVCIGPGEQO covered by the up-front license fee, either by payment to Applied Biosystems or as purchased, i.e., an authorized thermal cycler. -
Green Biotechnology: Kill Or Cure?
issue 11 winter 2008|2009 promoting excellence in the molecular life sciences in europe Dear Reader, Green biotechnology: kill or cure? Recognising excellence is core to EMBO – the member- ship has been doing just that since nomination of the fi rst 200 EMBO Members in the 1960’s. This year again we welcome newly elected members to EMBO (see page 4). And we congratulate Luc Montagnier, Roger Tsien and Harald zur Hausen – EMBO Members awarded The Nobel Prize this year. The discipli- nary breadth of molecular life sciences is much broader today than it was some 40 years ago. For this reason, a modifi ed member election procedure was adopted – see page 5. You may have noticed some changes to format in this issue of EMBOencounters: fi rst, you are hearing from me as Deputy Director – a role I share with EMBO Fellowships Programme Manager Jan Taplick. Secondly, we plan a lead story for each issue to highlight © www.goldenrice.org topics relevant to EMBO activities. Golden Rice could help prevent vitamin A defi ciency in the developing world. This issue’s lead story investigates today’s Soaring grain prices, high energy costs and increasingly louder riots on the streets of perceptions of the green revolution – the focus famine-stricken countries such as Haiti or Somalia are forcing politicians and the public of the next EMBO/EMBL Science & Society to reconsider their opposition to modern agriculture and crops created through breed- Conference. EMBO Science & Society aims to ing techniques that employ methods of molecular genetics. Will the fi erce opposition of create dialogue between policy makers and western countries to so-called genetically modifi ed (GM) crops eventually give way to the public and complements our numerous the acceptance that they might help tackle the global food crisis and even prevent some activities that share knowledge addressing the diseases? challenges of our changing world. -
Poster Session 10: Translation 21:00 - 22:00 Friday, 29Th May, 2020 Poster
Poster Session 10: Translation 21:00 - 22:00 Friday, 29th May, 2020 Poster 66 Translational fidelity is maintained through precise aminoacyl-tRNA accommodation dynamics gated by Elongation Factor Tu Dylan Girodat1, Scott Blanchard2, Hans-Joachim Wieden3, Karissa Sanbonmatsu1 1Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA. 2Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. 3Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada Abstract The fidelity of translation is enigmatic, as the efficiency of cognate aminoacyl(aa)-tRNA selection by the ribosome is greater than what can be predicted from Watson-Crick base-pairing between the codon in the mRNA and the anticodon in the tRNA. The complexity of this process arises from the fact that aa-tRNA selection is a multistep process aided by auxiliary proteins such as the GTPase elongation factor (EF)-Tu, responsible for delivery of aa-tRNA to the ribosome. As such, the precise structural mechanism of how the ribosome in complex with EF-Tu selects for cognate aa-tRNA remains to be fully resolved. Here, using all-atom molecular dynamics (MD) simulations, we identify subtle differences between cognate and near-cognate aa-tRNA movement into the ribosome and how conformational rearrangements of EF-Tu aid in tRNA selection. Near-cognate aa-tRNA accommodation follows an alternative trajectory, compared to cognate aa-tRNA, leading to a misaligned position within the A-site. The origins of the alternative trajectory originate from the perturbed base-pairing between the codon and anticodon of the mRNA and tRNA, respectively. -
The Fourth AICS International Symposium
The Fourth AICS International Symposium Computer and Computational Sciences for Exascale Computing December 2—3, 2013, Kobe, JAPAN Organized and Sponsored by RIKEN AICS This Symposium is a part of RIKEN Symposium Series. Supported by: RIKEN HPCI Program for Computational Life Sciences Computational Materials Science Initiative JAMSTEC: Japan Agency for Marine-Earth Science and Technology Institute of Industrial Science, the University of Tokyo Japan Atomic Energy Agency Japan Aerospace Exploration Agency Joint Institute for Computational Fundamental Science (JICFuS) Information Initiative Center, Hokkaido University Cyberscience Center, Tohoku University Center for Computational Sciences, University of Tsukuba Information Technology Center, the University of Tokyo Global Scientific Information and Computing Center, Tokyo Institute of Technology Information Technology Center, Nagoya University Academic Center for Computing and Media Studies, Kyoto University Cybermedia Center, Osaka University Research Institute for Information Technology, Kyushu University National Institute of Informatics The Fourth AICS International Symposium Computer and Computational Sciences for Exascale Computing Program Invited Lecture Program December 2 (Monday) Opening Remarks 09:30 – 09:45 Kimihiko Hirao (RIKEN Advanced Institute for Computational Science) HPC in Computational Disaster Mitigation and Reduction 09:45 – 10:25 Seismic damage simulation of buildings in urban areas based on GPU and a physics engine Xinzheng Lu 10 (Department of Civil Engineering, -
Myosin II Synergizes with F-Actin to Promote DNGR-1-Dependent Cross-Presentation of Dead Cell-Associated Antigens
Article Myosin II Synergizes with F-Actin to Promote DNGR- 1-Dependent Cross-Presentation of Dead Cell- Associated Antigens Graphical Abstract Authors Oliver Schulz, Pavel Hanc, Jan P. Bo¨ ttcher, Robbert Hoogeboom, Sandra S. Diebold, Pavel Tolar, Caetano Reis e Sousa Correspondence [email protected] In Brief Schulz et al. show that dead cells lacking myosin II have a diminished capacity to serve as antigen donors for dendritic cells that express the DNGR-1 receptor. DNGR-1 binds to F-actin exposed on cell corpses, and myosin II organizes actin filaments into bundles that cross-link the receptor more efficiently. Highlights d Myosin II amplifies the activity of the DNGR-1 ligand F-actin d Lack of myosin II in donor cells reduces DNGR-1-dependent cross-presentation d Beads with F-actin and myosin II can target antigens to cDC1 for CD8 T cell priming Schulz et al., 2018, Cell Reports 24, 419–428 July 10, 2018 ª 2018 The Francis Crick Institute. https://doi.org/10.1016/j.celrep.2018.06.038 Cell Reports Article Myosin II Synergizes with F-Actin to Promote DNGR-1-Dependent Cross-Presentation of Dead Cell-Associated Antigens Oliver Schulz,1 Pavel Hanc, 1,5 Jan P. Bo¨ ttcher,1 Robbert Hoogeboom,2,6 Sandra S. Diebold,3 Pavel Tolar,2,4 and Caetano Reis e Sousa1,7,* 1Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK 2Immune Receptor Activation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK 3Biotherapeutics Division, National Institute for Biological Standards and Control, Potters -
Actin Is an Evolutionarily-Conserved Damage-Associated Molecular
RESEARCH ARTICLE Actin is an evolutionarily-conserved damage-associated molecular pattern that signals tissue injury in Drosophila melanogaster Naren Srinivasan1†, Oliver Gordon1†, Susan Ahrens1‡, Anna Franz2, Safia Deddouche1§, Probir Chakravarty3, David Phillips4, Ali A Yunus5, Michael K Rosen5, Rita S Valente6, Luis Teixeira6, Barry Thompson7, Marc S Dionne8, Will Wood9, Caetano Reis e Sousa1* 1Immunobiology Laboratory, The Francis Crick Institute, London, United Kingdom; 2Department of Biochemistry, Biomedical Sciences, University Walk, University of Bristol, Bristol, United Kingdom; 3Bioinformatics, The Francis Crick Institute, London, United Kingdom; 4Genomics-Equipment Park, The Francis Crick Institute, London, United Kingdom; 5Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States; 6Instituto Gulbenkian de Cieˆncia, Oeiras, Portugal; 7Epithelial Biology Laboratory, The Francis Crick Institute, *For correspondence: caetano@ London, United Kingdom; 8Department of Life Sciences and MRC Centre for crick.ac.uk Molecular Bacteriology and Infection, South Kensington Campus, Imperial College 9 †These authors contributed London, London, United Kingdom; Department of Cellular and Molecular Medicine, equally to this work Biomedical Sciences, University of Bristol, Bristol, United Kingdom Present address: ‡Voisin Consulting Life Sciences, Surrey, United Kingdom; §Open Innovation Access Platform, Abstract Damage-associated molecular patterns (DAMPs) are molecules released by dead cells Sanofi Strasbourg, Strasbourg, that trigger sterile inflammation and, in vertebrates, adaptive immunity. Actin is a DAMP detected France in mammals by the receptor, DNGR-1, expressed by dendritic cells (DCs). DNGR-1 is phosphorylated by Src-family kinases and recruits the tyrosine kinase Syk to promote DC cross- Competing interests: The presentation of dead cell-associated antigens. Here we report that actin is also a DAMP in authors declare that no invertebrates that lack DCs and adaptive immunity.