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Table of Contents: April 2015

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Clonal polymorphism mainly results from somatic mutations that occur naturally during plant growth. In grapevine, arrays of clones have been selected within varieties as a valuable source of diversity, among them clones showing berry color polymorphism. To identify mutations responsible for this color polymorphism, we studied a collection of 33 clones of Pinot noir, Pinot gris, and Pinot blanc. See Pelsy et al.

Perspective

Research Articles

Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis

Bin Tu, Li Liu, Chi Xu, Jixian Zhai, Shengben Li, Miguel A. Lopez, Yuanyuan Zhao, Yu Yu, Vanitharani Ramachandran, Guodong Ren, Bin Yu, Shigui Li, Blake C. Meyers, Beixin Mo, Xuemei Chen

Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites

Hanif Samad, Francesc Coll, Mark D. Preston, Harold Ocholla, Rick M. Fairhurst, Taane G. Clark

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression

Marta Robledo, Benjamin Frage, Patrick R. Wright, Anke Becker

Windpipe Controls Drosophila Intestinal Homeostasis by Regulating JAK/STAT Pathway via Promoting Receptor Endocytosis and Lysosomal Degradation

Wenyan Ren, Yan Zhang, Min Li, Longfei Wu, Guolun Wang, Gyeong-Hun Baeg, Jia You, Zhouhua Li, Xinhua Lin

Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana

Norma Fàbregas, Pau Formosa-Jordan, Ana Confraria, Riccardo Siligato, Jose M. Alonso, Ranjan Swarup, Malcolm J. Bennett, Ari Pekka Mähönen, Ana I. Caño-Delgado, Marta Ibañes

The Functional Interplay Between the t(9;22)-Associated Fusion Proteins BCR/ABL and ABL/BCR in Philadelphia Chromosome-Positive Acute Lymphatic Leukemia

Anahita Rafiei, Afsar Ali Mian, Claudia Döring, Anna Metodieva, Claudia Oancea, Frederic B. Thalheimer, Martin Leo Hansmann, Oliver Gerhard Ottmann, Martin Ruthardt

The Protein Quality Control Machinery Regulates Its Misassembled Proteasome Subunits

Lee Zeev Peters, Ofri Karmon, Galit David-Kadoch, Rotem Hazan, Tzenlin Yu, Michael H. Glickman, Shay Ben-Aroya

Spatio-temporal Remodeling of Functional Membrane Microdomains Organizes the Signaling Networks of a Bacterium

Johannes Schneider, Teresa Klein, Benjamin Mielich-Süss, Gudrun Koch, Christian Franke, Oscar P. Kuipers, Ákos T. Kovács, Markus Sauer, Daniel Lopez

The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease

Loukas Moutsianas, Vineeta Agarwala, Christian Fuchsberger, Jason Flannick, Manuel A. Rivas, Kyle J. Gaulton, Patrick K. Albers, Gil McVean, Michael Boehnke, David Altshuler, Mark I. McCarthy , GoT2D Consortium

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

Wencheng Li, Bei You, Mainul Hoque, Dinghai Zheng, Wenting Luo, Zhe Ji, Ji Yeon Park, Samuel I. Gunderson, Auinash Kalsotra, James L. Manley, Bin Tian

The Pif1 Helicase, a Negative Regulator of Telomerase, Acts Preferentially at Long Telomeres

Jane A. Phillips, Angela Chan, Katrin Paeschke, Virginia A. Zakian

Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis

Tasuku Ito, Yoshiaki Tarutani, Taiko Kim To, Mohamed Kassam, Evelyne Duvernois-Berthet, Sandra Cortijo, Kazuya Takashima, Hidetoshi Saze, Atsushi Toyoda, Asao Fujiyama, Vincent Colot, Tetsuji Kakutani

Ataxin-2 Regulates RGS8 Translation in a New BAC-SCA2 Transgenic Mouse Model

Warunee Dansithong, Sharan Paul, Karla P. Figueroa, Marc D. Rinehart, Shaina Wiest, Lance T. Pflieger, Daniel R. Scoles, Stefan M. Pulst

The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia

Bayazit Yunusbayev, Mait Metspalu, Ene Metspalu, Albert Valeev, Sergei Litvinov, Ruslan Valiev, Vita Akhmetova, Elena Balanovska, Oleg Balanovsky, Shahlo Turdikulova, Dilbar Dalimova, Pagbajabyn Nymadawa, Ardeshir Bahmanimehr, Hovhannes Sahakyan, Kristiina Tambets, Sardana Fedorova, Nikolay Barashkov, Irina Khidiyatova, Evelin Mihailov, Rita Khusainova, Larisa Damba, Miroslava Derenko, Boris Malyarchuk, Ludmila Osipova, Mikhail Voevoda, Levon Yepiskoposyan, Toomas Kivisild, Elza Khusnutdinova, Richard Villems

The Chromatin Remodeler CHD8 Is Required for Activation of Progesterone Receptor-Dependent Enhancers

María Ceballos-Chávez, Alicia Subtil-Rodríguez, Eugenia G. Giannopoulou, Daniel Soronellas, Elena Vázquez-Chávez, Guillermo P. Vicent, Olivier Elemento, Miguel Beato, José C. Reyes

Genome-Wide Association Study Identifies Nox3 as a Critical Gene for Susceptibility to Noise-Induced Hearing Loss

Joel Lavinsky, Amanda L. Crow, Calvin Pan, Juemei Wang, Ksenia A. Aaron, Maria K. Ho, Qingzhong Li, Pehzman Salehide, Anthony Myint, Maya Monges-Hernadez, Eleazar Eskin, Hooman Allayee, Aldons J. Lusis, Rick A. Friedman

Experimental Swap of Anopheles gambiae's Assortative Mating Preferences Demonstrates Key Role of X-Chromosome Divergence Island in Incipient Sympatric Speciation

Fred Aboagye-Antwi, Nahla Alhafez, Gareth D. Weedall, Jessica Brothwood, Sharanjit Kandola, Doug Paton, Abrahamane Fofana, Lisa Olohan, Mauro Pazmiño Betancourth, Nkiru E. Ekechukwu, Rowida Baeshen, Sékou F. Traorè, Abdoulaye Diabate, Frédéric Tripet

Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling

Kazunari Nozue, An V. Tat, Upendra Kumar Devisetty, Matthew Robinson, Maxwell R. Mumbach, Yasunori Ichihashi, Saradadevi Lekkala, Julin N. Maloof

Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

Ophir Shalem, Eilon Sharon, Shai Lubliner, Ifat Regev, Maya Lotan-Pompan, Zohar Yakhini, Eran Segal

A Single Nucleotide Polymorphism Uncovers a Novel Function for the Transcription Factor Ace2 during Candida albicans Hyphal Development

Diana M. Calderón-Noreña, Alberto González-Novo, Sara Orellana-Muñoz, Pilar Gutiérrez-Escribano, Yolanda Arnáiz-Pita, Encarnación Dueñas-Santero, M. Belén Suárez, Marie-Elisabeth Bougnoux, Francisco del Rey, Gavin Sherlock, Christophe d’Enfert, Jaime Correa-Bordes, Carlos R. Vázquez de Aldana

A Missense Change in the ATG4D Gene Links Aberrant Autophagy to a Neurodegenerative Vacuolar Storage Disease

Kaisa Kyöstilä, Pernilla Syrjä, Vidhya Jagannathan, Gayathri Chandrasekar, Tarja S. Jokinen, Eija H. Seppälä, Doreen Becker, Michaela Drögemüller, Elisabeth Dietschi, Cord Drögemüller, Johann Lang, Frank Steffen, Cecilia Rohdin, Karin H. Jäderlund, Anu K. Lappalainen, Kerstin Hahn, Peter Wohlsein, Wolfgang Baumgärtner, Diana Henke, Anna Oevermann, Juha Kere, Hannes Lohi, Tosso Leeb

Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection

Minal Çalışkan, Samuel W. Baker, Yoav Gilad, Carole Ober

SERPINB11 Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies

Carrie J. Finno, Carlynn Stevens, Amy Young, Verena Affolter, Nikhil A. Joshi, Sheila Ramsay, Danika L. Bannasch

MAPK Signaling Pathway Alters Expression of Midgut ALP and ABCC Genes and Causes Resistance to Bacillus thuringiensis Cry1Ac Toxin in Diamondback Moth

Zhaojiang Guo, Shi Kang, Defeng Chen, Qingjun Wu, Shaoli Wang, Wen Xie, Xun Zhu, Simon W. Baxter, Xuguo Zhou, Juan Luis Jurat-Fuentes, Youjun Zhang

Spastin Binds to Lipid Droplets and Affects Lipid Metabolism

Chrisovalantis Papadopoulos, Genny Orso, Giuseppe Mancuso, Marija Herholz, Sentiljana Gumeni, Nimesha Tadepalle, Christian Jüngst, Anne Tzschichholz, Astrid Schauss, Stefan Höning, Aleksandra Trifunovic, Andrea Daga, Elena I. Rugarli

Volatility of Mutator Phenotypes at Single Cell Resolution

Scott R. Kennedy, Eric M. Schultz, Thomas M. Chappell, Brendan Kohrn, Gary M. Knowels, Alan J. Herr

Genomic Location of the Major Ribosomal Protein Gene Locus Determines Vibrio cholerae Global Growth and Infectivity

Alfonso Soler-Bistué, Juan A. Mondotte, Michael Jason Bland, Marie-Eve Val, María-Carla Saleh, Didier Mazel

A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi

Trung Anh Trieu, Silvia Calo, Francisco E. Nicolás, Ana Vila, Simon Moxon, Tamas Dalmay, Santiago Torres-Martínez, Victoriano Garre, Rosa M. Ruiz-Vázquez

Lack of GDAP1 Induces Neuronal Calcium and Mitochondrial Defects in a Knockout Mouse Model of Charcot-Marie-Tooth Neuropathy

Manuela Barneo-Muñoz, Paula Juárez, Azahara Civera-Tregón, Laura Yndriago, David Pla-Martin, Jennifer Zenker, Carmen Cuevas-Martín, Anna Estela, María Sánchez-Aragó, Jerónimo Forteza-Vila, José M. Cuezva, Roman Chrast, Francesc Palau

The Cryptococcus neoformans Alkaline Response Pathway: Identification of a Novel Rim Pathway Activator

Kyla S. Ost, Teresa R. O’Meara, Naureen Huda, Shannon K. Esher, J. Andrew Alspaugh

The DNA Helicase Recql4 Is Required for Normal Osteoblast Expansion and Osteosarcoma Formation

Alvin J. M. Ng, Mannu K. Walia, Monique F. Smeets, Anthony J. Mutsaers, Natalie A. Sims, Louise E. Purton, Nicole C. Walsh, T. John Martin, Carl R. Walkley

Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model

Gerhard Moser, Sang Hong Lee, Ben J. Hayes, Michael E. Goddard, Naomi R. Wray, Peter M. Visscher

Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution

Jonathan Terhorst, Christian Schlötterer, Yun S. Song

A Multi-layered Protein Network Stabilizes the Escherichia coli FtsZ-ring and Modulates Constriction Dynamics

Jackson Buss, Carla Coltharp, Gleb Shtengel, Xinxing Yang, Harald Hess, Jie Xiao

Proteolysis of Virulence Regulator ToxR Is Associated with Entry of Vibrio cholerae into a Dormant State

Salvador Almagro-Moreno, Tae K. Kim, Karen Skorupski, Ronald K. Taylor

Comprehensive Profiling of Amino Acid Response Uncovers Unique Methionine-Deprived Response Dependent on Intact Creatine Biosynthesis

Xiaohu Tang, Melissa M. Keenan, Jianli Wu, Chih-An Lin, Laura Dubois, J. Will Thompson, Stephen J. Freedland, Susan K. Murphy, Jen-Tsan Chi

The Lowe Syndrome Protein OCRL1 Is Required for Endocytosis in the Zebrafish Pronephric Tubule

Francesca Oltrabella, Grzegorz Pietka, Irene Barinaga-Rementeria Ramirez, Aleksandr Mironov, Toby Starborg, Iain A. Drummond, Katherine A. Hinchliffe, Martin Lowe

Lipid-Induced Epigenomic Changes in Human Macrophages Identify a Coronary Artery Disease-Associated Variant that Regulates PPAP2B Expression through Altered C/EBP-Beta Binding

Michael E. Reschen, Kyle J. Gaulton, Da Lin, Elizabeth J. Soilleux, Andrew J. Morris, Susan S. Smyth, Christopher A. O'Callaghan

Viable Neuronopathic Gaucher Disease Model in Medaka (Oryzias latipes) Displays Axonal Accumulation of Alpha-Synuclein

Norihito Uemura, Masato Koike, Satoshi Ansai, Masato Kinoshita, Tomoko Ishikawa-Fujiwara, Hideaki Matsui, Kiyoshi Naruse, Naoaki Sakamoto, Yasuo Uchiyama, Takeshi Todo, Shunichi Takeda, Hodaka Yamakado, Ryosuke Takahashi

Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Color in Grapevine

Frédérique Pelsy, Vincent Dumas, Lucie Bévilacqua, Stéphanie Hocquigny, Didier Merdinoglu

Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in Bacillus subtilis

Mónica Serrano, JinXin Gao, João Bota, Ashley R. Bate, Jeffrey Meisner, Patrick Eichenberger, Charles P. Moran Jr., Adriano O. Henriques

Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

Jingqun Ao, Yinnan Mu, Li-Xin Xiang, DingDing Fan, MingJi Feng, Shicui Zhang, Qiong Shi, Lv-Yun Zhu, Ting Li, Yang Ding, Li Nie, Qiuhua Li, Wei-ren Dong, Liang Jiang, Bing Sun, XinHui Zhang, Mingyu Li, Hai-Qi Zhang, ShangBo Xie, YaBing Zhu, XuanTing Jiang, Xianhui Wang, Pengfei Mu, Wei Chen, Zhen Yue, Zhuo Wang, Jun Wang, Jian-Zhong Shao, Xinhua Chen

Nxf1 Natural Variant E610G Is a Semi-dominant Suppressor of IAP-Induced RNA Processing Defects

Dorothy Concepcion, Kevin D. Ross, Kasey R. Hutt, Gene W. Yeo, Bruce A. Hamilton

The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in cis and trans

Eric M. Camino, John C. Butts, Alison Ordway, Jordan E. Vellky, Mark Rebeiz, Thomas M. Williams

Co-chaperone p23 Regulates C. elegans Lifespan in Response to Temperature

Makoto Horikawa, Surojit Sural, Ao-Lin Hsu, Adam Antebi

Spatial Fluctuations in Expression of the Heterocyst Differentiation Regulatory Gene hetR in Anabaena Filaments

Laura Corrales-Guerrero, Asaf Tal, Rinat Arbel-Goren, Vicente Mariscal, Enrique Flores, Antonia Herrero, Joel Stavans

Genome-Destabilizing Effects Associated with Top1 Loss or Accumulation of Top1 Cleavage Complexes in Yeast

Sabrina L. Andersen, Roketa S. Sloan, Thomas D. Petes, Sue Jinks-Robertson

CAPER Is Vital for Energy and Redox Homeostasis by Integrating Glucose-Induced Mitochondrial Functions via ERR-α-Gabpa and Stress-Induced Adaptive Responses via NF-κB-cMYC

Yun Kyoung Kang, Nagireddy Putluri, Suman Maity, Anna Tsimelzon, Olga Ilkayeva, Qianxing Mo, David Lonard, George Michailidis, Arun Sreekumar, Christopher B. Newgard, Meng Wang, Sophia Y. Tsai, Ming-Jer Tsai, Bert W. O'Malley

Retraction

Retraction: Astakine 2—the Dark Knight Linking Melatonin to Circadian Regulation in Crustaceans

Apiruck Watthanasurorot, Netnapa Saelee, Amornrat Phongdara, Sittiruk Roytrakul, Pikul Jiravanichpaisal, Kenneth Söderhäll, Irene Söderhäll