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Table of Contents: August 2014

COVER

The silky contour feather from a Chinese Silkie chicken.

Image Credit: Chungang Feng, China Agricultural University, Beijing, China
Issue Image

The feather is an excellent model for evolution and development. The Silkie chicken breed is fixed for the silky-feather mutation, and is named based on the fascinating silky-feather phenotype. In contrast to the closed pennaceous feathers in the wild-type, the silky-feathers lack hooklets on the distal barbules and fail to form the vane. In this issue, Feng et al. report the identification of the silky-feather mutation located in the promoter of PDSS2. This is the first report of a feather structure variation associated with PDSS2 and provides new insight into the feather morphogenesis.

Review

Human Social Genomics

Steven W. Cole

Research Articles

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

Miguel Carneiro, Frank W. Albert, Sandra Afonso, Ricardo J. Pereira, Hernan Burbano, Rita Campos, José Melo-Ferreira, Jose A. Blanco-Aguiar, Rafael Villafuerte, Michael W. Nachman, Jeffrey M. Good, Nuno Ferrand

Sp6 and Sp8 Transcription Factors Control AER Formation and Dorsal-Ventral Patterning in Limb Development

Endika Haro, Irene Delgado, Marisa Junco, Yoshihiko Yamada, Ahmed Mansouri, Kerby C. Oberg, Marian A. Ros

The TRIM-NHL Protein LIN-41 Controls the Onset of Developmental Plasticity in Caenorhabditis elegans

Cristina Tocchini, Jeremy J. Keusch, Sarah B. Miller, Susanne Finger, Heinz Gut, Michael B. Stadler, Rafal Ciosk

Multiple Regulation of Rad51-Mediated Homologous Recombination by Fission Yeast Fbh1

Yasuhiro Tsutsui, Yumiko Kurokawa, Kentaro Ito, Md. Shahjahan P. Siddique, Yumiko Kawano, Fumiaki Yamao, Hiroshi Iwasaki

Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome

Jutta Vogelmann, Antoine Le Gall, Stephanie Dejardin, Frederic Allemand, Adrien Gamot, Gilles Labesse, Olivier Cuvier, Nicolas Nègre, Martin Cohen-Gonsaud, Emmanuel Margeat, Marcelo Nöllmann

Ku-Mediated Coupling of DNA Cleavage and Repair during Programmed Genome Rearrangements in the Ciliate Paramecium tetraurelia

Antoine Marmignon, Julien Bischerour, Aude Silve, Clémentine Fojcik, Emeline Dubois, Olivier Arnaiz, Aurélie Kapusta, Sophie Malinsky, Mireille Bétermier

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways

Bode A. Olukolu, Guan-Feng Wang, Vijay Vontimitta, Bala P. Venkata, Sandeep Marla, Jiabing Ji, Emma Gachomo, Kevin Chu, Adisu Negeri, Jacqueline Benson, Rebecca Nelson, Peter Bradbury, Dahlia Nielsen, James B. Holland, Peter J. Balint-Kurti, Gurmukh Johal

A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

Chungang Feng, Yu Gao, Ben Dorshorst, Chi Song, Xiaorong Gu, Qingyuan Li, Jinxiu Li, Tongxin Liu, Carl-Johan Rubin, Yiqiang Zhao, Yanqiang Wang, Jing Fei, Huifang Li, Kuanwei Chen, Hao Qu, Dingming Shu, Chris Ashwell, Yang Da, Leif Andersson, Xiaoxiang Hu, Ning Li

A Conserved Dopamine-Cholecystokinin Signaling Pathway Shapes Context–Dependent Caenorhabditis elegans Behavior

Raja Bhattacharya, Denis Touroutine, Belinda Barbagallo, Jason Climer, Christopher M. Lambert, Christopher M. Clark, Mark J. Alkema, Michael M. Francis

SMA-Causing Missense Mutations in Survival motor neuron (Smn) Display a Wide Range of Phenotypes When Modeled in Drosophila

Kavita Praveen, Ying Wen, Kelsey M. Gray, John J. Noto, Akash R. Patlolla, Gregory D. Van Duyne, A. Gregory Matera

Wnt-Mediated Repression via Bipartite DNA Recognition by TCF in the Drosophila Hematopoietic System

Chen U. Zhang, Timothy A. Blauwkamp, Peter E. Burby, Ken M. Cadigan

Functional Specialization Among Members Of Knickkopf Family Of Proteins In Insect Cuticle Organization

Sujata S. Chaudhari, Bernard Moussian, Charles A. Specht, Yasuyuki Arakane, Karl J. Kramer, Richard W. Beeman, Subbaratnam Muthukrishnan

EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation

Sara Elgamal, Assaf Katz, Steven J. Hersch, David Newsom, Peter White, William Wiley Navarre, Michael Ibba

The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in Arabidopsis thaliana

Heike Lange, Hélène Zuber, François M. Sement, Johana Chicher, Lauriane Kuhn, Philippe Hammann, Véronique Brunaud, Caroline Bérard, Nathalie Bouteiller, Sandrine Balzergue, Sébastien Aubourg, Marie-Laure Martin-Magniette, Hervé Vaucheret, Dominique Gagliardi

The MAP Kinase p38 Is Part of Drosophila melanogaster's Circadian Clock

Verena Dusik, Pingkalai R. Senthilan, Benjamin Mentzel, Heiko Hartlieb, Corinna Wülbeck, Taishi Yoshii, Thomas Raabe, Charlotte Helfrich-Förster

Pooled Segregant Sequencing Reveals Genetic Determinants of Yeast Pseudohyphal Growth

Qingxuan Song, Cole Johnson, Thomas E. Wilson, Anuj Kumar

Inference of Transposable Element Ancestry

Aaron C. Wacholder, Corey Cox, Thomas J. Meyer, Robert P. Ruggiero, Vijetha Vemulapalli, Annette Damert, Lucia Carbone, David D. Pollock

Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)

Volker U. Schwartze, Sascha Winter, Ekaterina Shelest, Marina Marcet-Houben, Fabian Horn, Stefanie Wehner, Jörg Linde, Vito Valiante, Michael Sammeth, Konstantin Riege, Minou Nowrousian, Kerstin Kaerger, Ilse D. Jacobsen, Manja Marz, Axel A. Brakhage, Toni Gabaldón, Sebastian Böcker, Kerstin Voigt

Conditional Inactivation of Upstream Binding Factor Reveals Its Epigenetic Functions and the Existence of a Somatic Nucleolar Precursor Body

Nourdine Hamdane, Victor Y. Stefanovsky, Michel G. Tremblay, Attila Németh, Eric Paquet, Frédéric Lessard, Elaine Sanij, Ross Hannan, Tom Moss

EVA-1 Functions as an UNC-40 Co-receptor to Enhance Attraction to the MADD-4 Guidance Cue in Caenorhabditis elegans

Kevin Ka Ming Chan, Ashwin Seetharaman, Rachel Bagg, Guillermo Selman, Yuqian Zhang, Joowan Kim, Peter J. Roy

Global Genetic Variations Predict Brain Response to Faces

Erin W. Dickie, Amir Tahmasebi, Leon French, Natasa Kovacevic, Tobias Banaschewski, Gareth J. Barker, Arun Bokde, Christian Büchel, Patricia Conrod, Herta Flor, Hugh Garavan, Juergen Gallinat, Penny Gowland, Andreas Heinz, Bernd Ittermann, Claire Lawrence, Karl Mann, Jean-Luc Martinot, Frauke Nees, Thomas Nichols, Mark Lathrop, Eva Loth, Zdenka Pausova, Marcela Rietschel, Michal N. Smolka, Andreas Ströhle, Roberto Toro, Gunter Schumann, Tomáš Paus , the IMAGEN consortium

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

Paul Verdu, Trevor J. Pemberton, Romain Laurent, Brian M. Kemp, Angelica Gonzalez-Oliver, Clara Gorodezky, Cris E. Hughes, Milena R. Shattuck, Barbara Petzelt, Joycelynn Mitchell, Harold Harry, Theresa William, Rosita Worl, Jerome S. Cybulski, Noah A. Rosenberg, Ripan S. Malhi

Phosphorylation of a Central Clock Transcription Factor Is Required for Thermal but Not Photic Entrainment

Euna Lee, Eun Hee Jeong, Hyun-Jeong Jeong, Evrim Yildirim, Jens T. Vanselow, Fanny Ng, Yixiao Liu, Guruswamy Mahesh, Achim Kramer, Paul E. Hardin, Isaac Edery, Eun Young Kim

Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture

Alicia R. Martin, Helio A. Costa, Tuuli Lappalainen, Brenna M. Henn, Jeffrey M. Kidd, Muh-Ching Yee, Fabian Grubert, Howard M. Cann, Michael Snyder, Stephen B. Montgomery, Carlos D. Bustamante

The Population Genetics of Evolutionary Rescue

H. Allen Orr, Robert L. Unckless

Genetic Deletion of SEPT7 Reveals a Cell Type-Specific Role of Septins in Microtubule Destabilization for the Completion of Cytokinesis

Manoj B. Menon, Akihiro Sawada, Anuhar Chaturvedi, Pooja Mishra, Karin Schuster-Gossler, Melanie Galla, Axel Schambach, Achim Gossler, Reinhold Förster, Michael Heuser, Alexey Kotlyarov, Makoto Kinoshita, Matthias Gaestel

Evidence for Divisome Localization Mechanisms Independent of the Min System and SlmA in Escherichia coli

Matthew W. Bailey, Paola Bisicchia, Boyd T. Warren, David J. Sherratt, Jaan Männik

KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development

Karl B. Shpargel, Joshua Starmer, Della Yee, Michael Pohlers, Terry Magnuson

Syndecan-1 Is Required to Maintain Intradermal Fat and Prevent Cold Stress

Ildiko Kasza, Yewseok Suh, Damian Wollny, Rod J. Clark, Avtar Roopra, Ricki J. Colman, Ormond A. MacDougald, Timothy A. Shedd, David W. Nelson, Mei-I Yen, Chi-Liang Eric Yen, Caroline M. Alexander

A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters

Ozlem Yildirim, Jui-Hung Hung, Ryan J. Cedeno, Zhiping Weng, Christopher J. Lengner, Oliver J. Rando

Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes

Maggie C. Y. Ng, Daniel Shriner, Brian H. Chen, Jiang Li, Wei-Min Chen, Xiuqing Guo, Jiankang Liu, Suzette J. Bielinski, Lisa R. Yanek, Michael A. Nalls, Mary E. Comeau, Laura J. Rasmussen-Torvik, Richard A. Jensen, Daniel S. Evans, Yan V. Sun, Ping An, Sanjay R. Patel, Yingchang Lu, Jirong Long, Loren L. Armstrong, Lynne Wagenknecht, Lingyao Yang, Beverly M. Snively, Nicholette D. Palmer, Poorva Mudgal, Carl D. Langefeld, Keith L. Keene, Barry I. Freedman, Josyf C. Mychaleckyj, Uma Nayak, Leslie J. Raffel, Mark O. Goodarzi, Y-D Ida Chen, Herman A. Taylor Jr., Adolfo Correa, Mario Sims, David Couper, James S. Pankow, Eric Boerwinkle, Adebowale Adeyemo, Ayo Doumatey, Guanjie Chen, Rasika A. Mathias, Dhananjay Vaidya, Andrew B. Singleton, Alan B. Zonderman, Robert P. Igo Jr., John R. Sedor, Edmond K. Kabagambe, David S. Siscovick, Barbara McKnight, Kenneth Rice, Yongmei Liu, Wen-Chi Hsueh, Wei Zhao, Lawrence F. Bielak, Aldi Kraja, Michael A. Province, Erwin P. Bottinger, Omri Gottesman, Qiuyin Cai, Wei Zheng, William J. Blot, William L. Lowe, Jennifer A. Pacheco, Dana C. Crawford, Elin Grundberg, Stephen S. Rich, M. Geoffrey Hayes, Xiao-Ou Shu, Ruth J. F. Loos, Ingrid B. Borecki, Patricia A. Peyser, Steven R. Cummings, Bruce M. Psaty, Myriam Fornage, Sudha K. Iyengar, Michele K. Evans, Diane M. Becker, W. H. Linda Kao, James G. Wilson, Jerome I. Rotter, Michèle M. Sale, Simin Liu, Charles N. Rotimi, Donald W. Bowden , the FIND Consortium, the eMERGE Consortium, the DIAGRAM Consortium, the MuTHER Consortium, for the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium

Arabidopsis miR171-Targeted Scarecrow-Like Proteins Bind to GT cis-Elements and Mediate Gibberellin-Regulated Chlorophyll Biosynthesis under Light Conditions

Zhaoxue Ma, Xupeng Hu, Wenjuan Cai, Weihua Huang, Xin Zhou, Qian Luo, Hongquan Yang, Jiawei Wang, Jirong Huang

Asymmetric Division and Differential Gene Expression during a Bacterial Developmental Program Requires DivIVA

Prahathees Eswaramoorthy, Peter W. Winter, Peter Wawrzusin, Andrew G. York, Hari Shroff, Kumaran S. Ramamurthi

Demography and the Age of Rare Variants

Iain Mathieson, Gil McVean

The Response to High CO2 Levels Requires the Neuropeptide Secretion Component HID-1 to Promote Pumping Inhibition

Kfir Sharabi, Chayki Charar, Nurit Friedman, Inbar Mizrahi, Alon Zaslaver, Jacob I. Sznajder, Yosef Gruenbaum

Retinoic Acid Activates Two Pathways Required for Meiosis in Mice

Jana Koubova, Yueh-Chiang Hu, Tanmoy Bhattacharyya, Y. Q. Shirleen Soh, Mark E. Gill, Mary L. Goodheart, Cathryn A. Hogarth, Michael D. Griswold, David C. Page

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

Claire Chewapreecha, Pekka Marttinen, Nicholas J. Croucher, Susannah J. Salter, Simon R. Harris, Alison E. Mather, William P. Hanage, David Goldblatt, Francois H. Nosten, Claudia Turner, Paul Turner, Stephen D. Bentley, Julian Parkhill

Dysfunction of the CNS-Heart Axis in Mouse Models of Huntington's Disease

Michal Mielcarek, Linda Inuabasi, Marie K. Bondulich, Thomas Muller, Georgina F. Osborne, Sophie A. Franklin, Donna L. Smith, Andreas Neueder, Jim Rosinski, Ivan Rattray, Andrea Protti, Gillian P. Bates

Response Regulator Heterodimer Formation Controls a Key Stage in Streptomyces Development

Mahmoud M. Al-Bassam, Maureen J. Bibb, Matthew J. Bush, Govind Chandra, Mark J. Buttner

A Genetic Strategy to Measure Circulating Drosophila Insulin Reveals Genes Regulating Insulin Production and Secretion

Sangbin Park, Ronald W. Alfa, Sydni M. Topper, Grace E. S. Kim, Lutz Kockel, Seung K. Kim

Corrections