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`Volume 33 Number 22 | 18 November 2014
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`JOURNAL
`
`THE
`EMBO
`
`The EMBOJournal VOL 33|NO22|2014
`emboj.embopress.org
`
`Table of contents
`
`Editorial
`
`2597 Transparent, Reproducible Data
`Bernd Pulverer
`
`Have you seen?
`
`2598
`
`Shigella hacks host immune responses by reprogramming the host
`epigenome
`Hiroshi Ashida & Chihiro Sasakawa
`
`2601=Splicing together sister chromatids
`Have you seen? 2598
`Juan Valcarcel & Marcos Malumbres
`
`2604 Old dog, newtricks: Arfl required for mitochondria homeostasis
`Catherine Rabouille
`
`Articles
`
`Chromatin, Epigenetics, Genomics &
`2606_Shigella flexneri targets the HP1y subcode through the
`Functional Genomics; Microbiology,
`i “> phosphothreonine lyase OspF
`Virology & Host Pathogen Interaction
`Habiba Harouz, Christophe Rachez, Benoit M Meijer, Benoit Marteyn,
`Francoise Donnadieu, Flarence Cammas, Christian Muchardt,
`Philippe Sansonetti & Laurence Arbibe
`
`Functional genomicsidentifies a requirement of pre-mRNAsplicing
`2623
`“Pa factorsfor sister chromatid cohesion
`Sriramkumar Sundaramoorthy, Maria Dolores Vazquez-Novelle,
`Sergey Lekomtsev, Michael Howell & Mark Petronczki
`
`DNA Replication, Repair & Recombination;
`RNA Biology
`
`DNA Replication, Repair & Recombination;
`SNW1enables sister chromatid cohesion by mediating the splicing of
`2643
`RNA Biology
`“»—sororin and APC2 pre-mRNAs
`Petra van der Lelij, Roman R Stocsits, Rene Ladurner, Georg Petzold,
`Emanuel Kreidl, Birgit Koch, Julia Schmitz, Beate Neumann, Jan Ellenberg
`& Jan-Michael Peters
`
`2659 Thesmall GTPase Arfl modulates mitochondrial morphology
`“> and function
`Karin B Ackema, JUrgen Hench, Stefan Béckler, Shyi Chyi Wang,
`Ursula Sauder, Heidi Mergentaler, Benedikt Westermann, Frédéric Bard,
`Stephan Frank & Anne Spang
`
`2676 OPA1-dependent cristae modulation is essential for cellular adaptation
`"Pte metabolic demand
`David A Patten, Jacob Wong, Mireille Khacho, Vincent Soubannier,
`Ryan| Mailloux, Karine Pilon-Larose, Jason G MacLaurin, David S Park,
`Heidi M McBride, Laura Trinkle-Mulcahy, Mary-Ellen Harper,
`Marc Germain & Ruth $ Slack
`
`Membrane & Intracellular Transport
`
`Membrane & Intracellular Transport;
`Metabolism
`
`

`

`The EMBOJournal VOL33|NO22| 2014
`embo)j.embopress.org
`
`2692 Crystal structure of a c-di-AMP riboswitch reveals an internally
`“ pseudo-dimeric RNA
`Christopher P Jones & Adrian R Ferré-D'Amaré
`
`RNA Biology; Structural Biology
`
`Cell Cycle; Post-translational Modifications,
`2704=Inhibitor-3 ensures bipolar mitotic spindle attachmentby limiting
`Proteolysis & Proteomics
`1, “P association ofSDS22 with kinetochore-bound protein phosphatase-1
`Annika Eiteneuer, Jonas Seiler, Matthias Weith, Monique Beullens, Bart Lesage,
`Veronica Krenn, Andrea Musacchio, Mathieu Bollen & Hemmo Meyer
`
`Immunology; Transcription
`
`Peripheral naturalkiller cell maturation depends on the transcription
`2721
`“factor Aiolos
`Melissa L Holmes, Nicholas D Huntington, Rebecca PL Thong,Jason Brady,
`Yoshihiro Hayakawa, Christopher E Andoniou, Peter Fleming, Wei Shi, Gordon
`K Smyth, Mariapia A Degli-Esposti, Gabrielle T Belz, Axel Kallies, Sebastian
`Carotta, Mark J Smyth & Stephen L Nutt
`
`Corrigendum
`
`2735
`
`Tubulin glycylases are required for primary cilia, controlof cell
`proliferation and tumor developmentin colon
`Cecilia Rocha, Laura Papon, Wulfran Cacheux, Patricia Marques Sousa, Valeria
`Lascano,Olivia Tort, Tiziana Giordano, Sophie Vacher, Benedicte Lemmers,
`Pascale Mariani, Didier Meseure, Jan Paul Medema, lvan Biéche, Michael
`Hahne & Carsten Janke
`
`Fi
`
`Open-access article distributed under the termsof a Creative Commons Atrribution License
`“| Source Data: figures are complemented by pr imary data
`i? Transparent Process: anonymousreferee reports and editonal/author correspondenceare
`published alongsidethe researcharticle
`
`Cover, The Mechanicsof Bactenophage 14—The artist, Janice Wong,isa medical/scientific
`illustrator and animator (steampunk_medical@bhotmail.com). Her passionsinclude combining
`creativity, iMagination, and science to create engaging images. Janice writes about this image,
`“Initially when| started composingthis piece in 3D, | wanted a more ‘natural’ environment
`that is more typical of medical art. However, | was so captivated by the ‘mechanical’ natureof
`the bacteriophage T4 that| just ran with the idea and created something more original with
`a steampunk look and feel. | wantedit to lookas if someone sat at his/her desk and worked
`meticulously in constructing an actual bacteriophage, fashioned frambits and pieces of scraps
`salvaged from all different sources. Despite the steampunk look,| took care in ensuring that the
`bacteriophageis accurately represented,eg, its head is icosahedral withall the surface proteins
`(gp24, Hoc, etc) represented, albeitin scrap metal.”
`
`

`

`This material may be protected by Copyright law (Title 17 U.S. Code)
`
`Editorial
`
`OO) NE
`
`THE
`EMBO
`
`Transparent, Reproducible Data
`
`Bernd Pulverer
`
`reporting of
`the
`for
`New guidelines
`research and source data enhance the
`
`and
`interpretation
`published research.
`
`reproducibility
`
`of
`
`Source Data—a new dimension for
`
`research papers
`
`he scientific research paper remains
`the main mode of sharing scientific
`Two
`aspects
`information.
`key
`contribute to the unabated success of this
`
`Source Data provides a foundation toa
`paper that affords a much richer view ofthe
`findings discussed and enables reanalysis
`and reuse by the interested reader, as well
`(The data
`
`are
`access.
`as computational
`Ht also
`a CC-0 license.)
`published under
`provides an efficient means to archive data
`in close juxtaposition with the paper that
`discusses the findings.
`A central tenet of publishing is to ensure
`reproducibility, This requires the transparent
`and detailed reporting and sharing not only
`of the data, but also the underlying methods
`and reagents. Our goal is ta develop method
`sections that satisfy these conditions, includ-
`ing detailed experimental protocols
`and
`reagents that can be identified unambigu-
`ously, and which link directly to the relevant
`figure panels and data. We are conscious
`that these enhancements will need to tie into
`the
`
`development
`tools
`management
`of
`this
`information
`
`of
`laboratory
`digital
`that
`allow) submission
`without
`unreasonably
`
`burdening the authors.
`
`likely
`
`at) The EMBO Journal
`
`(Pulverer,
`
`require-
`2014a). The checklist’ highlights
`nents fram the journal's guide to authors
`that are often overlooked,
`including key
`information for figure panels and captions,
`Appropriate statistical weatment for data, the
`reporting of
`reagents, animal models and
`human subject-derived data, as well as guid-
`ance to optimize data accessibility. The
`focus is on the molecular and cell biological
`research typically reported in) The EMBO
`Journal,
`
`to guidance
`similar
`is)
`checklist
`The
`issued by a number other journals, including
`Nature and Science.
`It is consistent with the
`Guidelines
`for
`and
`Principles
`Preclinical Research
`
`Reporting
`published this month
`by a group of journals including the four
`EMBO Press journals. The principles were
`agreed at
`a workshop held) under
`the
`auspices of
`the NIH earlier this summer,
`where it was agreed that
`journals have a
`responsibility to act as gatekeepers for a reli
`able literature.
`
`format, despite the myriad possibilities for
`hew Ways to share research in an online
`validation
`by
`peer
`world:
`Independent
`review and the juxtaposition of
`research
`results—presented in figures,
`tables, and
`videos with the authors’ textual
`interpre-
`tation of
`these results, For many years,
`publishers have focused largely on rendering
`text
`for publication and search engines are
`limited to indexing the tithe, abstract, intro-
`duction,
`results, methods and) discussion
`Please review the checklist even if you
`sections of a paper. Yet, the claims made in
`are not preparing a manuscript
`for publica-
`Checklist for reporting life sciences
`a paper rely on data selected by the authors
`research
`tion at this ime—the points highlighted will
`and synthesized into figures that
`illustrate
`help inform the planning of a successful
`the findings for the human reader. Figures
`research
`wherever
`you
`plan
`to
`project
`are the heart of the paper and should open a
`submit your results, Please also regard: this
`vista on the research data, Unfortunately,
`as a
`living document we hope to obtain
`that view is currently often limited to data
`your feedback to add to and revise the intor
`vistalizations
`and
`illustrations. As we
`mation periodically, The list
`is
`intended to
`help our authors publish transparent and
`reproducible research papers; it
`is emphati
`cally not
`to make the publication process
`more cumbersome.
`
`and
`
`EMBO
`
`Press
`
`This
`journal
`its
`three
`for
`siblings have introduced a Cheeklist
`Authors in order to enhance and standardize
`the reporting of key information in research
`papers and to support reanalysis and repet-
`tion of experiments
`by
`the community.
`Reporting standards are well established in
`clinical research; the aim of this checklist
`is
`
`have reported previously (Lemberger, 2010;
`2014a,b), we
`the
`Pulverer,
`encourage
`presentation of Source Data, and indeed
`links to Source Data are already available in
`to consistently Capture essential information
`many figures in the journal. Source Data
`in preclinical
`research and to ensure that
`provides
`access
`to minimally processed
`authors, editors, and referees can cross
`References
`versions of
`the data underlying figures such
`
`check these—basicefficiently whether
`
`Lemberger T (2010) From bench to website, Mal
`as data files used to plot graphs and experi-
`Syst Biol 6; 410
`mental replicates or less cropped versions of
`Pulverer B (2014a) EMBOPress
`representative data shown ina figure panel.
`publish, EMBO J 33:
`1-
`2
`source Data can also include higher resolu-
`lian
`data
`Pulverer B (2014b) STAP dance. EMBO | 33:
`require completion upon revision of a manu
`renderings
`of
`compressed in
`1285-1286
`script—a stage when publication is highly
`ligures far efficient downloading.
`
`requirements for reporting reliable research
`have been met. While completion of thelist
`at
`initial submission is welcome, we only
`
`a new way to
`
`EMBO, Hedelbero, Germany E mail Bernd Pulverer@embojournalorg
`DO! 10:152752/emby 201490278
`
`2014 The Author
`
`This material was copied
`at the NLM and may be
`Subject US Copyright Laws
`
`The EMBO Journal Vol 34 | No 22 | 2014
`
`