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August 6, 2019 u vol. 116 u no. 32 From the Cover 15973 Cyanobacterial symbionts and cryptic lineage 15861 Neural response to facial emotion 15979 Bacterial interactions and toxic environments 16012 Nunavik Inuit genetic history 16028 Mitochondrial DNA and nuclear epigenome Contents THIS WEEK IN PNAS Cover image: Pictured is a differential 15747 In This Issue interference contrast micrograph of marine dinoflagellate Ornithocercus INNER WORKINGS—An over-the-shoulder look at scientists at work thumii with cyanobacterial symbionts. 15749 How diamonds embedded in meteorites could offer a glimpse into the mantle Takuro Nakayama et al. sequenced the of Mars genome of the cyanobacterium OmCyn, Nola Taylor Redd which is symbiotically associated with single-celled dinoflagellates, and found QNAS that the bacteria represent an underdescribed lineage within an 15752 QnAs with David Reich ecologically important group. Although Beth Azar OmCyn are distributed throughout the world’s oceans, they exist only with PROFILE dinoflagellate hosts, suggesting that there may be other undiscovered cryptic 15754 Profile of Rodolphe Barrangou cyanobacterial lineages. See the article Tinsley H. Davis by Nakayama et al. on pages 15973– See Inaugural Article on page 15774 15978. Image courtesy of Takuro Nakayama. COMMENTARIES 15757 Genomics reveals alga-associated cyanobacteria hiding in plain sight John M. Archibald See companion article on page 15973 15760 Refining the stress gradient hypothesis in a microbial community Sarah P. Hammarlund and William R. Harcombe See companion article on page 15979 15763 Mitochondrial genetics regulate nuclear gene expression through metabolites Jessica L. Fetterman and Scott W. Ballinger See companion article on page 16028 LETTERS 15766 Availability of public databases for triangulation of findings Matthew Lyon, Marcus Munafo, Tom Gaunt, and George Davey Smith 15768 Reply to Lyon et al.: Self-regulation and the foraging gene: From flies to humans Marla B. Sokolowski, Abigail A. Scholer, and James Danckert 15770 The buffering capacity of the brain and optic nerve against spaceflight-associated neuro-ocular syndrome Peter Wostyn, Thomas H. Mader, Charles Robert Gibson, and Peter Paul De Deyn Free online through the PNAS open access option. PNAS u August 6, 2019 u vol. 116 u no. 32 u iii–vi Downloaded by guest on September 29, 2021 15772 Reply to Wostyn et al.: Investigating the 15830 Membraneless polyester microdroplets as primordial spaceflight-associated neuro-ocular syndrome compartments at the origins of life and the human brain in lockstep Tony Z. Jia, Kuhan Chandru, Yayoi Hongo, Rehana Afrin, Angelique Van Ombergen, Steven Jillings, Elena Tomohiro Usui, Kunihiro Myojo, and H. James Cleaves II Tomilovskaya, Floris L. Wuyts, and Peter zu Eulenburg 15836 Exposing the inadequacy of redox formalisms by resolving redox inequivalence within INAUGURAL ARTICLE isovalent clusters Amymarie K. Bartholomew, Justin J. Teesdale, Rau´l Herna´ndez 15774 Genome editing using the endogenous type I Sa´nchez, Brian J. Malbrecht, Cristin E. Juda, Gabriel Me´nard, CRISPR-Cas system in Lactobacillus crispatus Wei Bu, Diana A. Iovan, Alexandre A. Mikhailine, Shao-Liang Claudio Hidalgo-Cantabrana, Yong Jun Goh, Meichen Pan, Zheng, Ritimukta Sarangi, SuYin Grass Wang, Yu-Sheng Chen, Rosemary Sanozky-Dawes, and Rodolphe Barrangou and Theodore A. Betley See Profile on page 15754 15924 Insights into the origin of the high energy-conversion efficiency of F1-ATPase Kwangho Nam and Martin Karplus PHYSICAL SCIENCES ENGINEERING APPLIED PHYSICAL SCIENCES 15842 Label-free chemical imaging flow cytometry by 15784 A stepwise mechanism for aqueous two-phase high-speed multicolor stimulated Raman scattering system formation in concentrated antibody solutions Yuta Suzuki, Koya Kobayashi, Yoshifumi Wakisaka, Dinghuan Bradley A. Rogers, Kelvin B. Rembert, Matthew F. Poyton, Deng, Shunji Tanaka, Chun-Jung Huang, Cheng Lei, Chia-Wei Halil I. Okur, Amanda R. Kale, Tinglu Yang, Jifeng Zhang, Sun, Hanqin Liu, Yasuhiro Fujiwaki, Sangwook Lee, Akihiro and Paul S. Cremer Isozaki, Yusuke Kasai, Takeshi Hayakawa, Shinya Sakuma, 15792 Conformational switching of chiral colloidal rafts Fumihito Arai, Kenichi Koizumi, Hiroshi Tezuka, Mary Inaba, Kei regulates raft–raft attractions and repulsions Hiraki, Takuro Ito, Misa Hase, Satoshi Matsusaka, Kiyotaka Joia M. Miller, Chaitanya Joshi, Prerna Sharma, Arvind Shiba, Kanako Suga, Masako Nishikawa, Masahiro Jona, Baskaran, Aparna Baskaran, Gregory M. Grason, Michael F. Yutaka Yatomi, Yaxiaer Yalikun, Yo Tanaka, Takeaki Sugimura, Hagan, and Zvonimir Dogic Nao Nitta, Keisuke Goda, and Yasuyuki Ozeki BIOPHYSICS AND COMPUTATIONAL BIOLOGY STATISTICS 15895 Perturbation of the interactions of calmodulin with 15849 Reconciling modern machine-learning practice GRK5 using a natural product chemical probe and the classical bias–variance trade-off Tyler S. Beyett, Amy E. Fraley, Emily Labudde, Dhabaleswar Mikhail Belkin, Daniel Hsu, Siyuan Ma, and Soumik Mandal Patra, Ryan C. Coleman, Akito Eguchi, Alisa Glukhova, Qiuyan Chen, Robert M. Williams, Walter J. Koch, David H. Sherman, and John J. G. Tesmer SOCIAL SCIENCES 15930 Assembling multidomain protein structures through PSYCHOLOGICAL AND COGNITIVE SCIENCES analogous global structural alignments 15855 Developmental topography of cortical thickness Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, during infancy and Yang Zhang Fan Wang, Chunfeng Lian, Zhengwang Wu, Han Zhang, Tengfei Li, Yu Meng, Li Wang, Weili Lin, Dinggang Shen, CHEMISTRY and Gang Li 15802 The final steps of [FeFe]-hydrogenase maturation 15861 The neural representation of facial-emotion Oliver Lampret, Julian Esselborn, Rieke Haas, Andreas Rutz, categories reflects conceptual structure Rosalind L. Booth, Leonie Kertess, Florian Wittkamp, Clare F. Megarity, Fraser A. Armstrong, Martin Winkler, Jeffrey A. Brooks, Junichi Chikazoe, Norihiro Sadato, and Thomas Happe and Jonathan B. Freeman 15811 Mapping hole hopping escape routes in proteins 15871 Credit assignment to state-independent task Ruijie D. Teo, Ruobing Wang, Elizabeth R. Smithwick, Agostino representations and its relationship with Migliore, Michael J. Therien, and David N. Beratan model-based decision making Nitzan Shahar, Rani Moran, Tobias U. Hauser, Rogier A. Kievit, 15817 A photostable fluorescent marker for the Daniel McNamee, Michael Moutoussis, NSPN Consortium, superresolution live imaging of the dynamic and Raymond J. Dolan structure of the mitochondrial cristae Chenguang Wang, Masayasu Taki, Yoshikatsu Sato, Yasushi 15877 Officer characteristics and racial disparities in fatal Tamura, Hideyuki Yaginuma, Yasushi Okada, officer-involved shootings and Shigehiro Yamaguchi David J. Johnson, Trevor Tress, Nicole Burkel, Carley Taylor, and Joseph Cesario 15823 Drugging an undruggable pocket on KRAS Dirk Kessler, Michael Gmachl, Andreas Mantoulidis, Laetitia J. 16056 Prestimulus feedback connectivity biases the content Martin, Andreas Zoephel, Moriz Mayer, Andreas Gollner, David of visual experiences Covini, Silke Fischer, Thomas Gerstberger, Teresa Gmaschitz, Elie Rassi, Andreas Wutz, Nadia Mu¨ller-Voggel, Craig Goodwin, Peter Greb, Daniela Ha¨ring, Wolfgang Hela, and Nathan Weisz Johann Hoffmann, Jale Karolyi-Oezguer, Petr Knesl, Stefan Kornigg, Manfred Koegl, Roland Kousek, Lyne Lamarre, SOCIAL SCIENCES Franziska Moser, Silvia Munico-Martinez, Christoph Peinsipp, Jason Phan, Jo¨rg Rinnenthal, Jiqing Sai, Christian Salamon, 15883 Effects of policy-driven hypothetical air pollutant Yvonne Scherbantin, Katharina Schipany, Renate Schnitzer, interventions on childhood asthma incidence in Andreas Schrenk, Bernadette Sharps, Gabriella Siszler, Qi Sun, southern California Alex Waterson, Bernhard Wolkerstorfer, Markus Zeeb, Mark Erika Garcia, Robert Urman, Kiros Berhane, Rob McConnell, Pearson, Stephen W. Fesik, and Darryl B. McConnell and Frank Gilliland iv u www.pnas.org Contents Downloaded by guest on September 29, 2021 BIOLOGICAL SCIENCES 15823 Drugging an undruggable pocket on KRAS Dirk Kessler, Michael Gmachl, Andreas Mantoulidis, Laetitia J. Martin, Andreas Zoephel, Moriz Mayer, Andreas Gollner, David APPLIED BIOLOGICAL SCIENCES Covini, Silke Fischer, Thomas Gerstberger, Teresa Gmaschitz, 15889 A tumor-targeted immune checkpoint blocker Craig Goodwin, Peter Greb, Daniela Ha¨ring, Wolfgang Hela, Yuhan Zhang, Changming Fang, Rongsheng E. Wang, Johann Hoffmann, Jale Karolyi-Oezguer, Petr Knesl, Stefan Ying Wang, Hui Guo, Chao Guo, Lijun Zhao, Shuhong Li, Xia Li, Kornigg, Manfred Koegl, Roland Kousek, Lyne Lamarre, Peter G. Schultz, Yu J. Cao, and Feng Wang Franziska Moser, Silvia Munico-Martinez, Christoph Peinsipp, Jason Phan, Jo¨rg Rinnenthal, Jiqing Sai, Christian Salamon, BIOCHEMISTRY Yvonne Scherbantin, Katharina Schipany, Renate Schnitzer, 15802 The final steps of [FeFe]-hydrogenase maturation Andreas Schrenk, Bernadette Sharps, Gabriella Siszler, Qi Sun, Oliver Lampret, Julian Esselborn, Rieke Haas, Andreas Rutz, Alex Waterson, Bernhard Wolkerstorfer, Markus Zeeb, Mark Rosalind L. Booth, Leonie Kertess, Florian Wittkamp, Clare F. Pearson, Stephen W. Fesik, and Darryl B. McConnell Megarity, Fraser A. Armstrong, Martin Winkler, 15967 OsMTOPVIB is required for meiotic bipolar and Thomas Happe spindle assembly 15895 Perturbation of the interactions of calmodulin with Zhihui Xue, Changzhen Liu, Wenqing Shi, Yongjie Miao, Yi GRK5 using a natural product chemical probe Shen, Ding Tang, Yafei Li, Aiqing You, Yunyuan Xu, Kang Tyler S. Beyett, Amy E. Fraley,
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  • PGC-1Α and Myokines in the Aging Muscle : a Mini-Review

    PGC-1Α and Myokines in the Aging Muscle : a Mini-Review

    Institutional Repository of the University of Basel University Library Schoenbeinstrasse 18-20 CH-4056 Basel, Switzerland http://edoc.unibas.ch/ Year: 2011 PGC-1α and Myokines in the aging muscle : a mini-review Arnold, A. -S. and Egger, A. and Handschin, C. Posted at edoc, University of Basel Official URL: http://edoc.unibas.ch/dok/A6001475 Originally published as: Arnold, A. -S. and Egger, A. and Handschin, C.. (2011) PGC-1α and Myokines in the aging muscle : a mini- review. Gerontology, Vol. 57, H. 1. S. 37-43. PGC-1 and myokines in the aging muscle Anne-Sophie Arnolda,*, Anna Eggera,*, and Christoph Handschina,# aBiozentrum, Division of Pharmacology/Neurobiology, University of Basel, Basel, Switzerland Published in Gerontology. 2011;57(1):37-43. PMID: 20134150. doi: 10.1159/000281883 Copyright © Karger; Gerontology - 1 - PGC-1 and myokines in the aging muscle Anne-Sophie Arnolda,*, Anna Eggera,*, and Christoph Handschina,# aBiozentrum, Division of Pharmacology/Neurobiology, University of Basel, Basel, Switzerland Key words: sarcopenia, skeletal muscle, PGC-1, myokines, transcriptional regulation Footnotes: *equal contribution #Correspondence to: Christoph Handschin, Biozentrum, Division of Pharmacology/Neurobiology, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland, Tel. +41 61 267 2221, Fax +41 61 267 2208, Email [email protected] - 2 - Abstract Aging is associated with far-reaching changes in physiological functions resulting in morbidity and ultimately death. Age-related frailty, insecurity and reduced physical activity contribute to a progressive loss of muscle mass and function, commonly referred to as sarcopenia. Due to the increase in life expectancy in many countries, loss of muscle mass and its consequences gain in relevance for public health.
  • Biozentrum Annual Report Biozentrum Annual Report 2017 Table of Content

    Biozentrum Annual Report Biozentrum Annual Report 2017 Table of Content

    2017 Biozentrum Annual Report Biozentrum Annual Report 2017 Table of content Research at a Glance 3 Core Facilities Biophysics Facility (BF) 99 FACS Core Facility (FCF) 100 Focal Areas Imaging Core Facility (IMCF) 101 Computational & Systems Biology 4 Proteomics Core Facility (PCF) 103 Growth & Development 5 Research IT 106 Infection Biology 6 Neurobiology 7 Structural Biology & Biophysics 8 Associated University Facilities BioEM Lab 109 C-CINA 110 Research Groups Center for Scientific Computing (sciCORE) 111 Prof. Jan Pieter Abrahams 9 Life Sciences Training Facility 112 Prof. Markus Affolter 11 Quantitative Genomics Facility 113 Prof. Silvia Arber 14 Prof. Marek Basler 17 Prof. Attila Becskei 19 Management, Administration & Prof. Petr Broz 21 Services 114 Prof. Dirk Bumann 23 Prof. Christoph Dehio 25 Prof. Fiona Doetsch 28 Prof. Stephan Grzesiek 30 Prof. Michael N. Hall 35 Prof. Christoph Handschin 38 Prof. Sebastian Hiller 41 Prof. Sonja Hofer 44 Prof. Urs Jenal 46 Prof. Roderick Lim 49 Prof. Timm Maier 52 Prof. Thomas Mrsic-Flogel 56 Prof. Richard Neher 58 Prof. Erich A. Nigg 61 Prof. Camilo Perez 64 Prof. Jean Pieters 65 Prof. Markus Rüegg 68 Prof. Peter Scheiffele 71 Prof. Tilman Schirmer 73 Prof. Torsten Schwede 75 Prof. Anne Spang 79 Prof. Martin Spiess 82 Prof. Henning Stahlberg 85 Prof. Kelly Tan 89 Prof. Erik van Nimwegen 91 Prof. Mihaela Zavolan 96 Information on staff as on January 1, 2018 BZ Annual Report 2017 2 Research at a Glance Around 30 topics are the focus of research at the Biozentrum. Research at the Biozentrum embraces a wide range of topics, however one main focus all the research groups share is a The Biozentrum in figures strong interest to understand the molecular organization of living organisms.