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Table of Contents: December 2014

COVER

Analyses of the Phlebiopsis gigantea genome reveal enzyme systems involved in the degradation of conifers.

Image Credit: Joel Jurgens and Robert A. Blanchette, University of Minnesota
Issue Image

The wood decay fungus Phlebiopsis gigantea rapidly colonizes conifer wood by metabolizing complex resins as well as the major cell wall polymers cellulose, hemicellulose and lignin. The radial section of pine wood shows extensive erosion of cell walls during hyphal invasion of the ray parenchyma cells and tracheids. See Hori et al.

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Controlling Pre-leukemic Thymocyte Self-Renewal

Steven Goossens, Pieter Van Vlierberghe

Keep on Laying Eggs Mama, RNAi My Reproductive Aging Blues Away

Sandeep Kumar, Zuzana Kocsisova, Kerry Kornfeld

Research Articles

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

Val F. Lanza, María de Toro, M. Pilar Garcillán-Barcia, Azucena Mora, Jorge Blanco, Teresa M. Coque, Fernando de la Cruz

SCL, LMO1 and Notch1 Reprogram Thymocytes into Self-Renewing Cells

Bastien Gerby, Cedric S. Tremblay, Mathieu Tremblay, Shanti Rojas-Sutterlin, Sabine Herblot, Josée Hébert, Guy Sauvageau, Sébastien Lemieux, Eric Lécuyer, Diogo F. T. Veiga, Trang Hoang

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

Mark de Been, Val F. Lanza, María de Toro, Jelle Scharringa, Wietske Dohmen, Yu Du, Juan Hu, Ying Lei, Ning Li, Ave Tooming-Klunderud, Dick J. J. Heederik, Ad C. Fluit, Marc J. M. Bonten, Rob J. L. Willems, Fernando de la Cruz, Willem van Schaik

ABA-Mediated ROS in Mitochondria Regulate Root Meristem Activity by Controlling PLETHORA Expression in Arabidopsis

Li Yang, Jing Zhang, Junna He, Yingying Qin, Deping Hua, Ying Duan, Zhizhong Chen, Zhizhong Gong

Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis

Antoine Claessens, William L. Hamilton, Mihir Kekre, Thomas D. Otto, Adnan Faizullabhoy, Julian C. Rayner, Dominic Kwiatkowski

Mucolipin Co-deficiency Causes Accelerated Endolysosomal Vacuolation of Enterocytes and Failure-to-Thrive from Birth to Weaning

Natalie N. Remis, Teerawat Wiwatpanit, Andrew J. Castiglioni, Emma N. Flores, Jorge A. Cantú, Jaime García-Añoveros

Genome Wide Meta-analysis Highlights the Role of Genetic Variation in RARRES2 in the Regulation of Circulating Serum Chemerin

Anke Tönjes, Markus Scholz, Jana Breitfeld, Carola Marzi, Harald Grallert, Arnd Gross, Claes Ladenvall, Dorit Schleinitz, Kerstin Krause, Holger Kirsten, Esa Laurila, Jennifer Kriebel, Barbara Thorand, Wolfgang Rathmann, Leif Groop, Inga Prokopenko, Bo Isomaa, Frank Beutner, Jürgen Kratzsch, Joachim Thiery, Mathias Fasshauer, Nora Klöting, Christian Gieger, Matthias Blüher, Michael Stumvoll, Peter Kovacs

SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat

Chiara Mizzotti, Ignacio Ezquer, Dario Paolo, Paloma Rueda-Romero, Rosalinda Fiorella Guerra, Raffaella Battaglia, Ilana Rogachev, Asaph Aharoni, Martin M. Kater, Elisabetta Caporali, Lucia Colombo

Enhanced Longevity by Ibuprofen, Conserved in Multiple Species, Occurs in Yeast through Inhibition of Tryptophan Import

Chong He, Scott K. Tsuchiyama, Quynh T. Nguyen, Ekaterina N. Plyusnina, Samuel R. Terrill, Sarah Sahibzada, Bhumil Patel, Alena R. Faulkner, Mikhail V. Shaposhnikov, Ruilin Tian, Mitsuhiro Tsuchiya, Matt Kaeberlein, Alexey A. Moskalev, Brian K. Kennedy, Michael Polymenis

Vangl2-Regulated Polarisation of Second Heart Field-Derived Cells Is Required for Outflow Tract Lengthening during Cardiac Development

Simon A. Ramsbottom, Vipul Sharma, Hong Jun Rhee, Lorraine Eley, Helen M. Phillips, Hannah F. Rigby, Charlotte Dean, Bill Chaudhry, Deborah J. Henderson

Syd/JIP3 and JNK Signaling Are Required for Myonuclear Positioning and Muscle Function

Victoria K. Schulman, Eric S. Folker, Jonathan N. Rosen, Mary K. Baylies

Epistatic Adaptive Evolution of Human Color Vision

Shozo Yokoyama, Jinyi Xing, Yang Liu, Davide Faggionato, Ahmet Altun, William T. Starmer

Notch Signaling Mediates the Age-Associated Decrease in Adhesion of Germline Stem Cells to the Niche

Chen-Yuan Tseng, Shih-Han Kao, Chih-Ling Wan, Yueh Cho, Shu-Yun Tung, Hwei-Jan Hsu

Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation

Jacob C. Ulirsch, Jessica N. Lacy, Xiuli An, Narla Mohandas, Tarjei S. Mikkelsen, Vijay G. Sankaran

Local and Systemic Regulation of Plant Root System Architecture and Symbiotic Nodulation by a Receptor-Like Kinase

Emeline Huault, Carole Laffont, Jiangqi Wen, Kirankumar S. Mysore, Pascal Ratet, Gérard Duc, Florian Frugier

Early Mesozoic Coexistence of Amniotes and Hepadnaviridae

Alexander Suh, Claudia C. Weber, Christian Kehlmaier, Edward L. Braun, Richard E. Green, Uwe Fritz, David A. Ray, Hans Ellegren

Maf1 Is a Novel Target of PTEN and PI3K Signaling That Negatively Regulates Oncogenesis and Lipid Metabolism

Beth M. Palian, Aarti D. Rohira, Sandra A. S. Johnson, Lina He, Ni Zheng, Louis Dubeau, Bangyan L. Stiles, Deborah L. Johnson

Large-scale Metabolomic Profiling Identifies Novel Biomarkers for Incident Coronary Heart Disease

Andrea Ganna, Samira Salihovic, Johan Sundström, Corey D. Broeckling, Åsa K. Hedman, Patrik K. E. Magnusson, Nancy L. Pedersen, Anders Larsson, Agneta Siegbahn, Mihkel Zilmer, Jessica Prenni, Johan Ärnlöv, Lars Lind, Tove Fall, Erik Ingelsson

A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations

Xiaomu Wei, Jishnu Das, Robert Fragoza, Jin Liang, Francisco M. Bastos de Oliveira, Hao Ran Lee, Xiujuan Wang, Matthew Mort, Peter D. Stenson, David N. Cooper, Steven M. Lipkin, Marcus B. Smolka, Haiyuan Yu

Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development

Marcela C. Dotto, Katherine A. Petsch, Milo J. Aukerman, Mary Beatty, Molly Hammell, Marja C. P. Timmermans

Global Analysis of Photosynthesis Transcriptional Regulatory Networks

Saheed Imam, Daniel R. Noguera, Timothy J. Donohue

Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

Xia Shen, Jennifer De Jonge, Simon K. G. Forsberg, Mats E. Pettersson, Zheya Sheng, Lars Hennig, Örjan Carlborg

Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature

Rubén Alcázar, Marcel von Reth, Jaqueline Bautor, Eunyoung Chae, Detlef Weigel, Maarten Koornneef, Jane E. Parker

A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation

Catherine Creppe, Anna Palau, Roberto Malinverni, Vanesa Valero, Marcus Buschbeck

Non-coding roX RNAs Prevent the Binding of the MSL-complex to Heterochromatic Regions

Margarida L. A. Figueiredo, Maria Kim, Philge Philip, Anders Allgardsson, Per Stenberg, Jan Larsson

The nphp-2 and arl-13 Genetic Modules Interact to Regulate Ciliogenesis and Ciliary Microtubule Patterning in C. elegans

Simon R. F. Warburton-Pitt, Malan Silva, Ken C. Q. Nguyen, David H. Hall, Maureen M. Barr

Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development

Hiroaki Okae, Hatsune Chiba, Hitoshi Hiura, Hirotaka Hamada, Akiko Sato, Takafumi Utsunomiya, Hiroyuki Kikuchi, Hiroaki Yoshida, Atsushi Tanaka, Mikita Suyama, Takahiro Arima

Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments

Gerda Saxer, Michael D. Krepps, Eric D. Merkley, Charles Ansong, Brooke L. Deatherage Kaiser, Marie-Thérèse Valovska, Nikola Ristic, Ping T. Yeh, Vittal P. Prakash, Owen P. Leiser, Luay Nakhleh, Henry S. Gibbons, Helen W. Kreuzer, Yousif Shamoo

Detection of Pleiotropy through a Phenome-Wide Association Study (PheWAS) of Epidemiologic Data as Part of the Environmental Architecture for Genes Linked to Environment (EAGLE) Study

Molly A. Hall, Anurag Verma, Kristin D. Brown-Gentry, Robert Goodloe, Jonathan Boston, Sarah Wilson, Bob McClellan, Cara Sutcliffe, Holly H. Dilks, Nila B. Gillani, Hailing Jin, Ping Mayo, Melissa Allen, Nathalie Schnetz-Boutaud, Dana C. Crawford, Marylyn D. Ritchie, Sarah A. Pendergrass

Gene Pathways That Delay Caenorhabditis elegans Reproductive Senescence

Meng C. Wang, Holly D. Oakley, Christopher E. Carr, Jessica N. Sowa, Gary Ruvkun

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

Chiaki Hori, Takuya Ishida, Kiyohiko Igarashi, Masahiro Samejima, Hitoshi Suzuki, Emma Master, Patricia Ferreira, Francisco J. Ruiz-Dueñas, Benjamin Held, Paulo Canessa, Luis F. Larrondo, Monika Schmoll, Irina S. Druzhinina, Christian P. Kubicek, Jill A. Gaskell, Phil Kersten, Franz St. John, Jeremy Glasner, Grzegorz Sabat, Sandra Splinter BonDurant, Khajamohiddin Syed, Jagjit Yadav, Anthony C. Mgbeahuruike, Andriy Kovalchuk, Fred O. Asiegbu, Gerald Lackner, Dirk Hoffmeister, Jorge Rencoret, Ana Gutiérrez, Hui Sun, Erika Lindquist, Kerrie Barry, Robert Riley, Igor V. Grigoriev, Bernard Henrissat, Ursula Kües, Randy M. Berka, Angel T. Martínez, Sarah F. Covert, Robert A. Blanchette, Daniel Cullen

Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in C. elegans

Neda Masoudi, Pablo Ibanez-Cruceyra, Sarah-Lena Offenburger, Alexander Holmes, Anton Gartner

Stratification by Smoking Status Reveals an Association of CHRNA5-A3-B4 Genotype with Body Mass Index in Never Smokers

Amy E. Taylor, Richard W. Morris, Meg E. Fluharty, Johan H. Bjorngaard, Bjørn Olav Åsvold, Maiken E. Gabrielsen, Archie Campbell, Riccardo Marioni, Meena Kumari, Jenni Hällfors, Satu Männistö, Pedro Marques-Vidal, Marika Kaakinen, Alana Cavadino, Iris Postmus, Lise Lotte N. Husemoen, Tea Skaaby, Tarunveer S. Ahluwalia, Jorien L. Treur, Gonneke Willemsen, Caroline Dale, S. Goya Wannamethee, Jari Lahti, Aarno Palotie, Katri Räikkönen, Aliaksei Kisialiou, Alex McConnachie, Sandosh Padmanabhan, Andrew Wong, Christine Dalgård, Lavinia Paternoster, Yoav Ben-Shlomo, Jessica Tyrrell, John Horwood, David M. Fergusson, Martin A. Kennedy, Tim Frayling, Ellen A. Nohr, Lene Christiansen, Kirsten Ohm Kyvik, Diana Kuh, Graham Watt, Johan Eriksson, Peter H. Whincup, Jacqueline M. Vink, Dorret I. Boomsma, George Davey Smith, Debbie Lawlor, Allan Linneberg, Ian Ford, J. Wouter Jukema, Christine Power, Elina Hyppönen, Marjo-Riitta Jarvelin, Martin Preisig, Katja Borodulin, Jaakko Kaprio, Mika Kivimaki, Blair H. Smith, Caroline Hayward, Pål R. Romundstad, Thorkild I. A. Sørensen, Marcus R. Munafò, Naveed Sattar

The Tau Tubulin Kinases TTBK1/2 Promote Accumulation of Pathological TDP-43

Nicole F. Liachko, Pamela J. McMillan, Timothy J. Strovas, Elaine Loomis, Lynne Greenup, Jill R. Murrell, Bernardino Ghetti, Murray A. Raskind, Thomas J. Montine, Thomas D. Bird, James B. Leverenz, Brian C. Kraemer

Genetic Analysis of Circadian Responses to Low Frequency Electromagnetic Fields in Drosophila melanogaster

Giorgio Fedele, Mathew D. Edwards, Supriya Bhutani, John M. Hares, Manuel Murbach, Edward W. Green, Stephane Dissel, Michael H. Hastings, Ezio Rosato, Charalambos P. Kyriacou

Formation of Linear Amplicons with Inverted Duplications in Leishmania Requires the MRE11 Nuclease

Marie-Claude N. Laffitte, Marie-Michelle Genois, Angana Mukherjee, Danielle Légaré, Jean-Yves Masson, Marc Ouellette

Genetic Analysis of the Cardiac Methylome at Single Nucleotide Resolution in a Model of Human Cardiovascular Disease

Michelle D. Johnson, Michael Mueller, Martyna Adamowicz-Brice, Melissa J. Collins, Pascal Gellert, Klio Maratou, Prashant K. Srivastava, Maxime Rotival, Shahena Butt, Laurence Game, Santosh S. Atanur, Nicholas Silver, Penny J. Norsworthy, Sarah R. Langley, Enrico Petretto, Michal Pravenec, Timothy J. Aitman

The Evolution of Fungal Metabolic Pathways

Jennifer H. Wisecaver, Jason C. Slot, Antonis Rokas

Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians

Brandon L. Pierce, Lin Tong, Lin S. Chen, Ronald Rahaman, Maria Argos, Farzana Jasmine, Shantanu Roy, Rachelle Paul-Brutus, Harm-Jan Westra, Lude Franke, Tonu Esko, Rakibuz Zaman, Tariqul Islam, Mahfuzar Rahman, John A. Baron, Muhammad G. Kibriya, Habibul Ahsan

Chondrocytes Transdifferentiate into Osteoblasts in Endochondral Bone during Development, Postnatal Growth and Fracture Healing in Mice

Xin Zhou, Klaus von der Mark, Stephen Henry, William Norton, Henry Adams, Benoit de Crombrugghe

The Evolution of Sex Ratio Distorter Suppression Affects a 25 cM Genomic Region in the Butterfly Hypolimnas bolina

Emily A. Hornett, Bruce Moran, Louise A. Reynolds, Sylvain Charlat, Samuel Tazzyman, Nina Wedell, Chris D. Jiggins, Greg D. D. Hurst

Mutation of Npr2 Leads to Blurred Tonotopic Organization of Central Auditory Circuits in Mice

Cindy C. Lu, Xiao-Jie Cao, Samantha Wright, Le Ma, Donata Oertel, Lisa V. Goodrich

Microevolution of Candida albicans in Macrophages Restores Filamentation in a Nonfilamentous Mutant

Anja Wartenberg, Jörg Linde, Ronny Martin, Maria Schreiner, Fabian Horn, Ilse D. Jacobsen, Sabrina Jenull, Thomas Wolf, Karl Kuchler, Reinhard Guthke, Oliver Kurzai, Anja Forche, Christophe d'Enfert, Sascha Brunke, Bernhard Hube

RAN-Binding Protein 9 is Involved in Alternative Splicing and is Critical for Male Germ Cell Development and Male Fertility

Jianqiang Bao, Chong Tang, Jiachen Li, Ying Zhang, Bhupal P. Bhetwal, Huili Zheng, Wei Yan

The IKAROS Interaction with a Complex Including Chromatin Remodeling and Transcription Elongation Activities Is Required for Hematopoiesis

Stefania Bottardi, Lionel Mavoungou, Helen Pak, Salima Daou, Vincent Bourgoin, Yahia A. Lakehal, El Bachir Affar, Eric Milot

Epigenome-Guided Analysis of the Transcriptome of Plaque Macrophages during Atherosclerosis Regression Reveals Activation of the Wnt Signaling Pathway

Stephen A. Ramsey, Yuliya Vengrenyuk, Prashanthi Menon, Irina Podolsky, Jonathan E. Feig, Alan Aderem, Edward A. Fisher, Elizabeth S. Gold

Germline Signals Deploy NHR-49 to Modulate Fatty-Acid β-Oxidation and Desaturation in Somatic Tissues of C. elegans

Ramesh Ratnappan, Francis R. G. Amrit, Shaw-Wen Chen, Hasreet Gill, Kyle Holden, Jordan Ward, Keith R. Yamamoto, Carissa P. Olsen, Arjumand Ghazi

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

Frédéric J. J. Chain, Philine G. D. Feulner, Mahesh Panchal, Christophe Eizaguirre, Irene E. Samonte, Martin Kalbe, Tobias L. Lenz, Monika Stoll, Erich Bornberg-Bauer, Manfred Milinski, Thorsten B. H. Reusch

In Vivo Occupancy of Mitochondrial Single-Stranded DNA Binding Protein Supports the Strand Displacement Mode of DNA Replication

Javier Miralles Fusté, Yonghong Shi, Sjoerd Wanrooij, Xuefeng Zhu, Elisabeth Jemt, Örjan Persson, Nasim Sabouri, Claes M. Gustafsson, Maria Falkenberg

Genetic Control of Contagious Asexuality in the Pea Aphid

Julie Jaquiéry, Solenn Stoeckel, Chloé Larose, Pierre Nouhaud, Claude Rispe, Lucie Mieuzet, Joël Bonhomme, Frédérique Mahéo, Fabrice Legeai, Jean-Pierre Gauthier, Nathalie Prunier-Leterme, Denis Tagu, Jean-Christophe Simon

Topoisomerase I Plays a Critical Role in Suppressing Genome Instability at a Highly Transcribed G-Quadruplex-Forming Sequence

Puja Yadav, Victoria Harcy, Juan Lucas Argueso, Margaret Dominska, Sue Jinks-Robertson, Nayun Kim

Recurrent Loss of Specific Introns during Angiosperm Evolution

Hao Wang, Katrien M. Devos, Jeffrey L. Bennetzen

A Drosophila ABC Transporter Regulates Lifespan

He Huang, Ying Lu-Bo, Gabriel G. Haddad

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

Jason G. Wallace, Peter J. Bradbury, Nengyi Zhang, Yves Gibon, Mark Stitt, Edward S. Buckler

Increased and Imbalanced dNTP Pools Symmetrically Promote Both Leading and Lagging Strand Replication Infidelity

Robert J. Buckland, Danielle L. Watt, Balasubramanyam Chittoor, Anna Karin Nilsson, Thomas A. Kunkel, Andrei Chabes

Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer

Olga Novikova, Dorie Smith, Ingrid Hahn, Arthur Beauregard, Marlene Belfort

Phosphorylation of Mitochondrial Polyubiquitin by PINK1 Promotes Parkin Mitochondrial Tethering

Kahori Shiba-Fukushima, Taku Arano, Gen Matsumoto, Tsuyoshi Inoshita, Shigeharu Yoshida, Yasushi Ishihama, Kwon-Yul Ryu, Nobuyuki Nukina, Nobutaka Hattori, Yuzuru Imai

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