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February 27, 2007 ͉ vol. 104 ͉ no. 9 ͉ 3017–3668 Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org Cover image: Three-dimensional atomic level simulations of the absorption of a line defect (screw dislocation) into a nanoscale, coherent internal interface (twin boundary) in copper. The pre-existing partial dislocation (green atoms at far end) in the twin boundary prevents absorption through the long-range elastic interaction with the impinging screw. Atoms are colored by the central symmetry parameter. See the article by Zhu et al. on pages 3031–3036. Image courtesy of Ting Zhu, Ju Li, and Subra Suresh. From the Cover 3031 Engineering nanostructured metals 3095 Parkin protein domain structure 3273 Competition’s minor role in population size 3456 Mechanism of drug-induced weight gain 3651 Rapid early crop spread in Panama Contents PHYSICAL SCIENCES CHEMISTRY THIS WEEK IN PNAS 3026 Effect of carbonates/phosphates as nucleophilic catalysts in dimethylformamide for efficient cyanosilylation of aldehydes and ketones 3017 In This Issue G. K. Surya Prakash, Habiba Vaghoo, Chiradeep Panja, Vijayalakshmi Surampudi, Roman Kultyshev, Thomas Mathew, and George A. Olah COMMENTARIES ENGINEERING 3019 Illuminating the molecular basis for some antipsychotic 3031 Interfacial plasticity governs strain rate sensitivity drug-induced metabolic burden and ductility in nanostructured metals Herbert Y. Meltzer Ting Zhu, Ju Li, Amit Samanta, Hyoung Gyu Kim, ➜ See companion article on page 3456 and Subra Suresh 3021 Small is big: The microfossil perspective on human–plant interaction ENVIRONMENTAL SCIENCES Daniel H. Sandweiss 3037 An estimate of anthropogenic CO2 inventory from ➜ See companion article on page 3651 decadal changes in oceanic carbon content Toste Tanhua, Arne Ko¨rtzinger, Karsten Friis, Darryn W. Waugh, and Douglas W. R. Wallace PROFILE BIOLOGICAL SCIENCES 3023 Profile of Joseph R. Ecker Bijal P. Trivedi ➜ See Inaugural Article on page 13286 in issue 36 ANTHROPOLOGY of volume 103 3043 4,300-Year-old chimpanzee sites and the origins of percussive stone technology Julio Mercader, Huw Barton, Jason Gillespie, Jack Harris, Freely available online through the PNAS open access option. Steven Kuhn, Robert Tyler, and Christophe Boesch PNAS ͉ February 27, 2007 ͉ vol. 104 ͉ no. 9 ͉ iii–x Downloaded by guest on September 25, 2021 APPLIED BIOLOGICAL SCIENCES 3119 Concerted ATP-induced allosteric transitions in GroEL 3049 Biomimetic tissue-engineered anterior cruciate facilitate release of protein substrate domains in an ligament replacement all-or-none manner James A. Cooper, Jr., Janmeet S. Sahota, W. Jay Yakov Kipnis, Niv Papo, Gilad Haran, and Amnon Horovitz Gorum II, Janell Carter, Stephen B. Doty, 3125 Each rhodopsin molecule binds its own arrestin and Cato T. Laurencin Susan M. Hanson, Eugenia V. Gurevich, Sergey A. Vishnivetskiy, Mohamed R. Ahmed, Xiufeng Song, 3055 Targeted gene addition into a specified location in the and Vsevolod V. Gurevich human genome using designed zinc finger nucleases E. A. Moehle, J. M. Rock, Y. L. Lee, Y. Jouvenot, 3129 RNA-binding proteins that inhibit RNA virus infection R. C. DeKelver, P. D. Gregory, F. D. Urnov, Jian Zhu, Kodetham Gopinath, Ayaluru Murali, Guanghui and M. C. Holmes Yi, S. Diane Hayward, Heng Zhu, and Cheng Kao 3135 Regulation of a glutamyl-tRNA synthetase by the BIOCHEMISTRY heme status ´ 3061 Quantifying DNA–protein binding specificities by using Gloria Levican, Assaf Katz, Merly de Armas, Harold ´˜ oligonucleotide mass tags and mass spectroscopy Nunez, and Omar Orellana Lingang Zhang, Simon Kasif, and Charles R. Cantor 3141 Pyrrolysine is not hardwired for cotranslational insertion at UAG codons 3067 In vitro analysis of DNA–protein interactions Alexandre Ambrogelly, Sarath Gundllapalli, by proximity ligation Stephanie Herring, Carla Polycarpo, Carina Sigrun M. Gustafsdottir, Joerg Schlingemann, Frauer, and Dieter So¨ll Alvaro Rada-Iglesias, Edith Schallmeiner, Masood Kamali-Moghaddam, Claes BIOPHYSICS Wadelius, and Ulf Landegren 3147 Determining the stoichiometry of protein 3073 Structure of the non-redox-active tungsten/[4Fe:4S] heterocomplexes in living cells with enzyme acetylene hydratase fluorescence fluctuation spectroscopy Grazyna B. Seiffert, G. Matthias Ullmann, Yan Chen and Joachim D. Mu¨ller Albrecht Messerschmidt, Bernhard Schink, Peter M. H. Kroneck, and Oliver Einsle 3153 Intramolecular domain–domain association/dissociation and phosphoryl transfer in the mannitol transporter 3078 Requirements for DNA hairpin formation by RAG1/2 of Escherichia coli are not coupled Gabrielle J. Grundy, Joanne E. Hesse, and Martin Gellert Jeong-Yong Suh, Junji Iwahara, and G. Marius Clore 3084 Fusicoccins are biosynthesized by an unusual chimera 3159 Establishing the entatic state in folding metallated diterpene synthase in fungi Pseudomonas aeruginosa azurin Tomonobu Toyomasu, Mai Tsukahara, Akane Kaneko, Chenghang Zong, Corey J. Wilson, Tongye Shen, Rie Niida, Wataru Mitsuhashi, Tohru Dairi, Nobuo Pernilla Wittung-Stafshede, Steven L. Mayo, Kato, and Takeshi Sassa and Peter G. Wolynes 3165 Large-scale fluid/fluid phase separation of proteins 3089 Evidence for a dual binding mode of dockerin modules and lipids in giant plasma membrane vesicles to cohesins Tobias Baumgart, Adam T. Hammond, Prabuddha Ana Luísa Carvalho, Fernando M. V. Dias, Tibor Nagy, Sengupta, Samuel T. Hess, David A. Holowka, Jose´ A. M. Prates, Mark R. Proctor, Nicola Barbara A. Baird, and Watt W. Webb Smith, Edward A. Bayer, Gideon J. Davies, Luís M. A. Ferreira, Maria J. Roma˜o, 3171 Extending the absorbing boundary method to fit Carlos M. G. A. Fontes, and Harry J. Gilbert dwell-time distributions of molecular motors with complex kinetic pathways 3095 Structure of the Parkin in-between-ring domain provides Jung-Chi Liao, James A. Spudich, David Parker, insights for E3-ligase dysfunction in autosomal and Scott L. Delp recessive Parkinson’s disease Steven A. Beasley, Ventzislava A. Hristova, and Gary S. Shaw 3177 Near-native structure refinement using in vacuo energy minimization 3101 Trigger Factor can antagonize both SecB and DnaK/DnaJ Christopher M. Summa and Michael Levitt chaperone functions in Escherichia coli 3183 Growth of novel protein structural data ¸ Ronald S. Ullers, Debbie Ang, Francoise Schwager, Michael Levitt Costa Georgopoulos, and Pierre Genevaux 3107 Molecular and structural basis of polo-like kinase 1 CELL BIOLOGY substrate recognition: Implications in 3189 Mitotic retention of gene expression patterns by the centrosomal localization cell fate-determining transcription factor Runx2 ´ Begon˜a García-Alvarez, Guillermo de Ca´rcer, Daniel W. Young, Mohammad Q. Hassan, Xiao-Qing Yang, Sonia Iban˜ez, Elisabeth Bragado-Nilsson, Mario Galindo, Amjad Javed, Sayyed K. Zaidi, Paul and Guillermo Montoya Furcinitti, David Lapointe, Martin Montecino, Jane B. Lian, Janet L. Stein, Andre J. van Wijnen, and Gary S. Stein 3113 Structural basis and evolutionary origin of actin filament capping by twinfilin 3195 Structural characterization of the fission yeast Ville O. Paavilainen, Maarit Hellman, Emmanue`le U5.U2/U6 spliceosome complex Helfer, Miia Bovellan, Arto Annila, Marie-France Melanie D. Ohi, Liping Ren, Joseph S. Wall, Carlier, Perttu Permi, and Pekka Lappalainen Kathleen L. Gould, and Thomas Walz PNAS ͉ February 27, 2007 ͉ vol. 104 ͉ no. 9 ͉ v Downloaded by guest on September 25, 2021 3201 Regulation of brefeldin A-inhibited guanine nucleotide- ECOLOGY exchange protein 1 (BIG1) and BIG2 activity 3267 Complex larval connectivity patterns among marine ␥ via PKA and protein phosphatase 1 invertebrate populations Fuminobu Kuroda, Joel Moss, and Martha Vaughan Bonnie J. Becker, Lisa A. Levin, F. Joel Fodrie, and Pat A. McMillan 3207 Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent 3273 Compensatory dynamics are rare in natural diffuse large B cell lymphomas ecological communities Jose M. Polo, Przemyslaw Juszczynski, Stefano Monti, J. E. Houlahan, D. J. Currie, K. Cottenie, G. S. Cumming, Leandro Cerchietti, Kenny Ye, John M. Greally, S. K. M. Ernest, C. S. Findlay, S. D. Fuhlendorf, Margaret Shipp, and Ari Melnick U. Gaedke, P. Legendre, J. J. Magnuson, B. H. McArdle, E. H. Muldavin, D. Noble, 3213 Loss of ␣-tubulin polyglutamylation in ROSA22 mice R. Russell, R. D. Stevens, T. J. Willis, is associated with abnormal targeting of KIF1A and I. P. Woiwod, and S. M. Wondzell modulated synaptic function Koji Ikegami, Robb L. Heier, Midori Taruishi, Hiroshi Takagi, Masahiro Mukai, Shuichi Shimma, Shu Taira, 3278 Differential contribution of frugivores to complex seed Ken Hatanaka, Nobuhiro Morone, Ikuko Yao, dispersal patterns ˜ Patrick K. Campbell, Shigeki Yuasa, Carsten Janke, P. Jordano, C. García, J. A. Godoy, and J. L. Garcı´a-Castano Grant R. MacGregor, and Mitsutoshi Setou EVOLUTION DEVELOPMENTAL BIOLOGY 3283 Systems-level analysis and evolution of the 3219 Delta-like ligand 4 (Dll4) is induced by VEGF as phototransduction network in Drosophila a negative regulator of angiogenic sprouting Christian R. Landry, Cristian I. Castillo-Davis, I. B. Lobov, R. A. Renard, N. Papadopoulos, Atsushi Ogura, Jun S. Liu, and Daniel L. Hartl N. W. Gale, G. Thurston, G. D. Yancopoulos, and S. J. Wiegand 3289 Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent 3225 The Notch ligand Delta-like 4 negatively regulates Peter L. Morrell and Michael T. Clegg endothelial tip cell formation
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    CV Andreas Sebastian Marquardt Education: 16/7/2010 Ph. D. in Biological Sciences, University of East Anglia, Norwich, UK. 2005 Diplom (M. Sc.) in Biochemistry, Free University Berlin, Berlin, Germany. 2002-2005 Undergraduate studies in Biochemistry at Free University Berlin, Berlin, Germany. 1999-2002 Undergraduate studies in Biochemistry at University of Tübingen, Tübingen, Germany. Employment: Jan. 2018 – Tenured Associate Professor, University of Copenhagen, Copenhagen Plant Science Centre (CPSC), Denmark. Leader of non-coding transcription group. 2015 - 2017 Assistant Professor, University of Copenhagen, Copenhagen Plant Science Centre (CPSC), Denmark. Leader of non-coding transcription group. 2012 - 2014 Visiting Scientist at Whitehead Institute for Biomedical Research, MIT, Cambridge, USA. Topic: Arabidopsis epigenetics & Pol II kinetics, with Prof. Mary Gehring. 2010 - 2014 Postdoc at the Harvard Medical School (HMS), Boston, USA. Topic: chromatin-based lncRNA repression in budding yeast with Prof. Steve Buratowski. 2006 - 2009 Ph. D. thesis research with Prof. Caroline Dean at John Innes Centre (JIC), Norwich, UK. Topic: lncRNA-mediated chromatin regulation of Arabidopsis flowering. 2005-2006 Ph. D. rotation projects with: Prof. David Baulcombe, Dr. Sean Walsh and Prof. Caroline Dean. 2004-2005 Diplom thesis research with Prof. Arp Schnittger at Max-Planck Institute (MPI) for Plant Breeding Research, Cologne, Germany. Summary publication and bibliometric information: Total number of peer-reviewed publications: 15. First author publications: 6 (e.g. Science, Cell, Mol. Cell). Corresponding author publications: 5 (e.g. Nat. Commun, eLife, PLoS Gen). Last author publications: 5 (e.g. Nat. Commun, eLife, PLoS Gen). Citations: 1309 source, H-index: 21: https://scholar.google.com/citations?user=_miZw7oAAAAJ&hl=en ).
  • Natural Variants in C. Elegans Atg-5 3'UTR Uncover Divergent Effects of Autophagy on Polyglutamine Aggregation in Different Tissues

    Natural Variants in C. Elegans Atg-5 3'UTR Uncover Divergent Effects of Autophagy on Polyglutamine Aggregation in Different Tissues

    bioRxiv preprint doi: https://doi.org/10.1101/670042; this version posted June 13, 2019. 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. Natural variants in C. elegans atg-5 3'UTR uncover divergent effects of autophagy on polyglutamine aggregation in different tissues Alexander-Floyd J1, Haroon S2, Ying M1, Entezari AA1,3, Jaeger C1,4, Vermulst M2,5, Gidalevitz T1,#. 1 Biology Department, Drexel University, Philadelphia, PA 19104 2 Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 3Current address: Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107 4Current address: Department of Neuroradiology, Technical University of Munich, Munich, Germany TUM-Neuroimaging Center, Technical University of Munich, Munich, Germany 5Current address: Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089 # Corresponding author. Address correspondence to T.G. ([email protected]) Short title: Divergent effects of autophagy on polyglutamine aggregation in different tissues bioRxiv preprint doi: https://doi.org/10.1101/670042; this version posted June 13, 2019. 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. Abstract Diseases caused by protein misfolding and aggregation, in addition to cell selectivity, often exhibit variation among individuals in the age of onset, progression, and severity of disease.