The Chemistry of Genome Editing and Imaging
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[email protected] (609) 258-5981 Jonikaslab.Princeton.Edu Updated 3/10/2021
Martin Casimir Jonikas, Ph.D. Assistant Professor, Department of Molecular Biology Princeton University, Princeton, NJ 08544 [email protected] (609) 258-5981 jonikaslab.princeton.edu updated 3/10/2021 VISION My group seeks to advance the basic understanding of cell biology. We study the pyrenoid, a fascinating phase-separated organelle that enhances CO2 capture in nearly all eukaryotic algae. Understanding the pyrenoid is important for three reasons: (1) the pyrenoid plays a central role in our planet’s carbon cycle, (2) the pyrenoid embodies fundamental questions in organelle biogenesis, and (3) engineering a pyrenoid into land plants could dramatically increase crop yields. To accelerate progress, we are developing community resources for the unicellular green alga Chlamydomonas reinhardtii as a model system for photosynthetic organisms. My group also seeks to nurture and train future world-leading scientists. EDUCATION 2004 B.S., Aerospace Engineering, Massachusetts Institute of Technology 2009 Ph.D., Biochemistry and Molecular Biology, University of California, San Francisco. Research advisors: Dr. Jonathan Weissman and Dr. Peter Walter PROFESSIONAL POSITIONS 2010-2016 Young Investigator (faculty position equivalent to Assistant Professor), Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 2011-2016 Assistant Professor by courtesy, Department of Biology, Stanford University, Stanford, CA 2016-present Assistant Professor, Department of Molecular Biology, Princeton University, Princeton, NJ 2019-present Affiliated Faculty, Princeton Quantitative and Computational Biology Program AWARDS AND HONORS 2002 1st place, MIT 2.007 Robotics Competition 2005 National Science Foundation Graduate Research Fellowship 2009 Harvard Bauer Fellowship (declined) 2010 Air Force Office of Scientific Research Young Investigator Award 2015 National Institutes of Health Director's New Innovator Award 2016 HHMI-Simons Faculty Scholar Award 2020 Vilcek Prize for Creative Promise in Biomedical Science Martin Casimir Jonikas, Ph.D. -
Xiaowei Zhuang Harvard University, Howard Hughes Medical Institute Xiaowei Zhuang Is the David B
Xiaowei Zhuang Harvard University, Howard Hughes Medical Institute Xiaowei Zhuang is the David B. Arnold Professor of Science at Harvard University and an investigator of Howard Hughes Medical Institute. Her laboratory has developed single-molecule, super-resolution and genomic- scale imaging methods, including STORM and MERFISH, and has used these methods to discover novel molecular structures in cells and cell organizations in tissues. Zhuang received her BS in physics from the University of Science and Technology of China, her PhD in physics in the lab of Prof. Y. R. Shen at University of California, Berkeley, and her postdoctoral training in biophysics in the lab of Prof. Steven Chu at Stanford University. She joined the faculty of Harvard University in 2001 and became a Howard Hughes Medical Institute investigator in 2005. Zhuang is a member of the US National Academy of Sciences and the American Academy of Arts and Sciences, a foreign member of the Chinese Academy of Sciences and the European Molecular Biology Organization, a fellow of the American Association of the Advancement of Science and the American Physical Society. She received honorary doctorate degrees from the Stockholm University in Sweden and the Delft University of Technology in the Netherlands. She has received a number of awards, including the Breakthrough Prize in Life Sciences, National Academy of Sciences Award in Scientific Discovery, Dr. H.P. Heineken Prize for Biochemistry and Biophysics, National Academy of Sciences Award in Molecular Biology, Raymond and Beverly Sackler International Prize in Biophysics, Max Delbruck Prize in Biological Physics, American Chemical Society Pure Chemistry Award, MacArthur Fellowship, etc. -
Quantifying Nucleation in Vivo Reveals the Physical Basis of Prion-Like Phase Behavior
bioRxiv preprint doi: https://doi.org/10.1101/205690; this version posted March 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Quantifying nucleation in vivo reveals the physical basis of prion-like phase behavior 1,3 1,3 1,2,3 1,3 1,3 Tarique Khan , Tejbir S. Kandola , Jianzheng Wu , Shriram Venkatesan , Ellen Ketter , 1 1 1 1 1 Jeffrey J. Lange , Alejandro Rodríguez Gama , Andrew Box , Jay R. Unruh , Malcolm Cook , 1,2, and Randal Halfmann * 1 Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110 2 Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA 3 These authors contributed equally *Corresponding author: [email protected] Highlights ● Distributed Amphifluoric FRET (DAmFRET) quantifies nucleation in living cells ● DAmFRET rapidly distinguishes prion-like from non-prion phase transitions ● Nucleation barriers allow switch-like temporal control of protein activity ● Sequence-intrinsic features determine the concentration-dependence of nucleation barriers Summary Protein self-assemblies modulate protein activities over biological time scales that can exceed the lifetimes of the proteins or even the cells that harbor them. We hypothesized that these time scales relate to kinetic barriers inherent to the nucleation of ordered phases. To investigate nucleation barriers in living cells, we developed Distributed Amphifluoric FRET (DAmFRET). DAmFRET exploits a photoconvertible fluorophore, heterogeneous expression, and large cell numbers to quantify via flow cytometry the extent of a protein’s self-assembly as a function of cellular concentration. -
Molecular Chaperones & Stress Responses
Abstracts of papers presented at the 2010 meeting on MOLECULAR CHAPERONES & STRESS RESPONSES May 4–May 8, 2010 CORE Metadata, citation and similar papers at core.ac.uk Provided by Cold Spring Harbor Laboratory Institutional Repository Cold Spring Harbor Laboratory Cold Spring Harbor, New York Abstracts of papers presented at the 2010 meeting on MOLECULAR CHAPERONES & STRESS RESPONSES May 4–May 8, 2010 Arranged by F. Ulrich Hartl, Max Planck Institute for Biochemistry, Germany David Ron, New York University School of Medicine Jonathan Weissman, HHMI/University of California, San Francisco Cold Spring Harbor Laboratory Cold Spring Harbor, New York This meeting was funded in part by the National Institute on Aging; the National Heart, Lung and Blood Institute; and the National Institute of General Medical Sciences; branches of the National Institutes of Health; and Enzo Life Sciences, Inc. Contributions from the following companies provide core support for the Cold Spring Harbor meetings program. Corporate Sponsors Agilent Technologies Life Technologies (Invitrogen & AstraZeneca Applied Biosystems) BioVentures, Inc. Merck (Schering-Plough) Research Bristol-Myers Squibb Company Laboratories Genentech, Inc. New England BioLabs, Inc. GlaxoSmithKline OSI Pharmaceuticals, Inc. Hoffmann-La Roche Inc. Sanofi-Aventis Plant Corporate Associates Monsanto Company Pioneer Hi-Bred International, Inc. Foundations Hudson-Alpha Institute for Biotechnology Front cover, top: HSP90, a regulator of cell survival. Inhibition of HSP90 activity by drugs like geldanamycin (GA) destabilizes client proteins which ultimately lead to the onset of apoptosis. Dana Haley-Vicente, Assay Designs (an Enzo Life Sciences company). Front cover, bottom: C. elegans expressing a proteotoxic polyglutamine- expansion protein. Richard Morimoto, Northwestern University. -
The Titans of the Cosmos
FALL 2018 Titans of the Cosmos Exploring the Mysteries of Neutron Star Mergers & Supermassive Black Holes 10 | Educating the next generation of innovators in science and industry 16 | Berkeley leads the way in data science education Research Highlights, Department News & More CONTENTS CHAIR’SLETTER RESEARCH HIGHLIGHTS2 Recent breakthroughs in faculty-led investigations PHOTO: BEN AILES PHOTO: TITANS OF THE COSMOS Fall classes are underway, our introductory courses ON THE COVER: Exploring the Mysteries of are packed, and we have good news on several fronts. Berkeley astrophysicist Daniel Kasen's research group uses Neutron Star Mergers and On July 1 we welcomed our newest faculty member, supercomputers at the National Supermassive Black Holes condensed matter theorist Mike Zalatel. In August the Energy Research Scientific Com- puting Center at LBNL to model 2018 Academic Rankings of World Universities were cosmic explosions. See page 4. announced, with Berkeley Physics second, between MIT CHAIR and Stanford – fine company. In September we learned Wick Haxton 4 that Professor Barbara Jacak will be awarded the 2019 MANAGING EDITOR & Tom Bonner Prize of the American Physical Society for DIRECTOR OF DEVELOPMENT her leadership of the PHENIX detector at Brookhaven’s Rachel Schafer Relativistic Heavy Ion Collider, and new graduate stu- CONTRIBUTING EDITOR & dent Nick Sherman will receive the LeRoy Apker Award SCIENCE WRITER for outstanding undergraduate research in theoretical Devi Mathieu PHYSICS INNOVATORS condensed matter and mathematical physics. Most re- DESIGN 10INITIATIVE cently, Assistant Professor Norman Yao has been named Sarah Wittmer Educating the Next a Packard Fellow, one of the most prestigious awards CONTRIBUTORS Generation of Innovators available in STEM disciplines. -
11/05/09 Agenda Attachment 6
Bioinformatics @ UCSF: Faculty Multidisciplinary graduate study in biological composition, structure, David Agard function and evolution at the [email protected] molecular and systems levels Professor, Biochemistry & Biophysics Apply Now Structure, function, and folding of proteins, chromosomes, and About the Program centrosomes Training Program: Program Overview Core Curriculum Nadav Ahituv Electives [email protected] Seminars & Journal Club Assistant Professor, Bioengineering and Therapeutic Sciences Academic Progression & Procedures Deciphering the role of gene regulatory sequences in human People: biology and disease Students Faculty Alumni Patricia Babbitt Current Events [email protected] Admission Information Professor, Bioengineering and Therapeutic Sciences and Links Pharmaceutical Chemistry Contact Computational and experimental analysis of protein NEWS: UCSF wins HHMI Award for its superfamilies for functional inference and enzyme design Integrative Program in Complex Biological Systems Bruce Conklin [email protected] Associate Professor, Gladstone Institute of Cardiovascular Disease, Medicine & Pharmacology Combining the tools of molecular biology, genetics, bioinformatics, and physiology to answer fundamental issues in pharmacology. Joe DeRisi [email protected] Hughes Investigator, Associate Professor, Biochemistry & Biophysics Malaria gene expression profiling, functional genomics, microarrays Ken Dill [email protected] Professor, Pharmaceutical Chemistry Statistical mechanics of biomolecules, protein -
The Life of Proteins: the Good, the Mostly Good and the Ugly
MEETING REPORT The life of proteins: the good, the mostly good and the ugly Richard I Morimoto, Arnold J M Driessen, Ramanujan S Hegde & Thomas Langer The health of the proteome in the face of multiple and diverse challenges directly influences the health of the cell and the lifespan of the organism. A recent meeting held in Nara, Japan, provided an exciting platform for scientific exchange and provocative discussions on the biology of proteins and protein homeostasis across multiple scales of analysis and model systems. The International Conference on Protein Community brought together nearly 300 scientists in Japan to exchange ideas on how proteins in healthy humans are expressed, folded, translocated, assembled and disassembled, and on how such events can go awry, leading to a myriad of protein conformational diseases. The meeting, held in Nara, Japan, in September 2010, coincided with the 1,300th birthday of Nara, Japan’s ancient capital, and provided a meditative setting for reflecting on the impact of advances in Nature America, Inc. All rights reserved. All rights Inc. America, Nature protein community research on biology and 1 1 medicine. It also provided an opportunity to consider the success of the protein community © 20 program in Japan since meetings on the stress response (Kyoto, 1989) and on the life of proteins (Awaji Island, 2005). The highlights and poster presentations. During these socials, and accessory factors. Considerable effort has of the Nara meeting were, without question, graduate and postdoctoral students and all of been and continues to be devoted toward the social periods held after long days of talks the speakers sat together on tatami mats at low understanding the mechanistic basis of protein tables replete with refreshments and enjoyed maturation and chaperone function. -
Spring 2011 Prizes and Awards
Spring 2011 Prizes and Awards APS Announces Spring 2011 Prize and Award Recipients Forty-three prizes and awards will be presented during special sessions at three spring meetings of the Society: the 2011 March Meeting, March 21-25, in Dallas, TX, the 2011 April Meeting, April 30-May 3, in Anaheim, CA, and the 2011 Atomic, Molecular and Optical Physics Meeting, June 13-14, in Atlanta, GA. Citations and biographical information for each recipient follow. The Apker Award recipients appeared in the December 2010 issue of APS News (http://www.aps.org/programs/honors/ awards/apker.cfm). Additional biographical information and appropriate web links can be found at the APS website (http://www.aps.org/programs/honors/index.cfm). Nominations for most of next year’s prizes and awards are now being accepted. For details, see page 8 of this insert. Will Allis Prize for the joined the University of Illinois at Hughes Medical Institute. Her Physik Department of the Technical University at Study of Ionized Gases Chicago, and Argonne National lab develops advanced optical Munchen. Herbert Spohn is most widely known Laboratory in 1987. Research imaging techniques, in particular through his work on interacting stochastic particle Frank Isakson Prize for contributions include the observa- single-molecule and super-reso- systems. He strived for a deeper understanding of Optical Effects in Solids tion of conformal invariance at the lution imaging methods, to study how macroscopic laws emerge from the underly- Ising critical point, the Luttinger problems of biomedical interest. ing motion of atoms. Andrei Sakharov Prize scaling of the Fermi volume in Zhuang received her B.S. -
Vierzig Jahre Fachverband Atomphysik
DEUTSCHE PHYSIKALISCHE GESELLSCHAFT E.V. Vierzig Jahre Fachverband Atomphysik 1972 - 2012 Herausgegeben von Uwe Becker, Rainer Hentges, Bernd Lohmann, Burkhard Langer Please help us to improve this document by mailing your corrections to Rainer Hentges, Schönhauser Allee 68, 10437 Berlin, [email protected]. In particular it would be nice to get all the names correctly spelled. t Inhalt v06 [ i \ 23. Mai 2013 t Register Vorwort Vor 40 Jahren fanden die ersten Sitzungen des neugegründeten Fachverbands Atomphysik auf der Frühjahrstagung der Deutschen Physikalischen Gesellschaft in Hannover statt. In den davorliegenden Tagungen wurden die Bereiche Atom-, Kern- und Teilchenphysik noch in ge- meinsamen Sitzungen behandelt. Die Gründungsperiode des Fachverbands Atomphysik fand in einer Zeit statt, in der sich das spezifische Fachgebiet in keiner besonders guten Position im Hinblick auf seinen Bei- trag zum Fortschritt der Physik im Allgemeinen befand. Dieser Fortschritt wurde in zuneh- mendem Maße in Fachkreisen mit den faszinierenden Entdeckungen in der Hochenergie- Physik gleichgesetzt. Dass Atomphysik in der breiteren Öffentlichkeit immer noch als Syn- onym für Atom-, Kern- und Elementarteilchenphysik stand, der Titel eines Buches meines Doktorvaters Hans Bucka, ein Schüler von Hans Kopfermann, war in Fachkreisen längst ver- gessen und das Gesamtgebiet in seine jeweiligen Unterdisziplinen aufgeteilt. Hier stand die Hochenergie-Physik, welche die klassische Kernphysik bereits in atemberaubendem Tempo überholt hatte, eineindeutig als Speerspitze der Physik im Vordergrund des Interesses. Es war eine Zeit, in der ich mich manchmal entschuldigen musste, meine Doktorarbeit noch auf ei- nem Gebiet durchzuführen, von dem viele meinten, dies sei doch die „Physik der Frühphase der Quantenphysik“ also die Physik der zwanziger Jahre. -
《中国学术期刊文摘》赠阅 《中国学术期刊文摘》赠阅 CHINESE SCIENCE ABSTRACTS (Monthly, Established in 2006) Vol
《中国学术期刊文摘》赠阅 《中国学术期刊文摘》赠阅 CHINESE SCIENCE ABSTRACTS (Monthly, Established in 2006) Vol. 10 No. 3, 2015 (Sum No. 105) Published on March 15, 2015 Chinese Science Abstracts Competent Authority: Contents China Association for Science and Technology Hot Topic Supporting Organization: Department of Society Affa irs and Academic Activities 2014 Nobel Prize in Chemistry——Super-resolved Fluorescence China Association for Science and Technology Microscopy…………………………………………………………………1 Sponsor: 2014 Nobel Prize in Physiology or Medicine——Positioning Science and Technology Review Publishing House System in the Brain……………………………………………………………12 Publisher: High Impact Papers Science and Technology Review Publishing House Highly Cited Papers TOP5……………………………………………………26 Editor-in-chief: CHEN Zhangliang Materials Science Coatings Films (26) Materials Science Composites (27) Chief of the Staff/Deputy Editor-in-chief: Materials Science Multidisciplinary (29) Materials Science Paper Wood (30) SU Qing [email protected] Materials Science Textiles (32) Mathematical Computational Biology (33) Deputy Chief of the Staff/Deputy Editor-in-chief: Mathematics Applied (35) Mathematics Interdisciplinary Applications (36) SHI Yongchao [email protected] Mathematics (37) Mechanics (38) Medical Informatics (40) Deputy Editor-in-chief: SONG Jun Medical Laboratory Technology (41) Medicine General Internal (44) Deputy Director of Editorial Department: Medicine Legal (46) Medicine Research Experimental (48) WANG Shuaishuai [email protected] Metallurgy Metallurgical Engineering -
Ceapins Block the Unfolded Protein Response Sensor Atf6a by Inducing a Neomorphic Inter-Organelle Tether
RESEARCH ARTICLE Ceapins block the unfolded protein response sensor ATF6a by inducing a neomorphic inter-organelle tether Sandra Elizabeth Torres1,2,3, Ciara M Gallagher2,3†‡, Lars Plate4,5†, Meghna Gupta2, Christina R Liem1,3, Xiaoyan Guo6,7, Ruilin Tian6,7, Robert M Stroud2, Martin Kampmann6,7, Jonathan S Weissman1,3*, Peter Walter2,3* 1Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States; 2Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States; 3Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States; 4Department of Chemistry, Vanderbilt University, Nashville, United States; 5Department of Biological Sciences, Vanderbilt University, Nashville, United States; 6Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, United States; 7Chan Zuckerberg Biohub, San Francisco, United States *For correspondence: [email protected] Abstract The unfolded protein response (UPR) detects and restores deficits in the endoplasmic (JSW); a [email protected] (PW) reticulum (ER) protein folding capacity. Ceapins specifically inhibit the UPR sensor ATF6 , an ER- tethered transcription factor, by retaining it at the ER through an unknown mechanism. Our † These authors contributed genome-wide CRISPR interference (CRISPRi) screen reveals that Ceapins function is completely equally to this work dependent on the ABCD3 peroxisomal transporter. Proteomics studies establish that ABCD3 Present address: ‡Cairn physically associates with ER-resident ATF6a in cells and in vitro in a Ceapin-dependent manner. Biosciences, San Francisco, Ceapins induce the neomorphic association of ER and peroxisomes by directly tethering the United States cytosolic domain of ATF6a to ABCD3’s transmembrane regions without inhibiting or depending on Competing interests: The ABCD3 transporter activity. -
Physics in the Time of Coronavirus
Harvard University Department of Physics Newsletter FALL 2020 Physics In The Time Of Coronavirus also in this issue: Radioastronomy’s First Spectral Line John Doyle: Trapping and Cooling Molecules Christopher Stubbs: A Dean for All Seasons Cora Dvorkin: Digging into the History of the Cosmos A Tribute to Carol Davis ON THE COVER: The Department Hundreds of boxes CONTENTS of lab kits are ready Today: for shipment at the Instructional Physics Labs Letter from the Chair ....................................................................................................................2 Inset: Lab kit for Physics 16 176 FACULTY HIGHLIGHTS Undergraduate concentrators Promotions and New Faculty......................................................................................................3 Faculty Prizes, Awards, and Acknowledgments ......................................................................6 Books by Faculty ...........................................................................................................................7 248 COVER STORY Graduate students Physics in the Time of Coronavirus .............................................................................................8 78 HISTORICAL FOCUS Radioastronomy’s First Spectral Line: A Glimpse of the Handiwork of Creation ..............14 Postdoctoral fellows FEATURED 125 -RKQ'R\OH7UDSSLQJDQG&RROLQJ0ROHFXOHVDVD3DWKWR6FLHQWLÀF$GYDQFHPHQW .....20 Christopher Stubbs: A Dean for All Seasons ...........................................................................27