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Table of Contents: September 2017

Wild primates are now recognised as important reservoirs of malaria parasites that can infect humans. Diez Benavente et al. studied the macaque parasite Plasmodium knowlesi. They used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Their analysis reveals genetic regions that have been recently exchanged between long-tailed and pig-tailed macaques, which contain genes with signals indicative of rapid contemporary ecological change, including deforestation. The image shows a long-tailed macaque (Macaca fascicularis), one of two simian hosts known to carry the zoonotic malaria parasite P. knowlesi in Malaysia. See Diez Benavente et al.

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Image Credit: Shankar S. (flickr; CC BY 2.0)

Editorial

Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology

Leah E. Mechanic, Sara Lindström, Kenneth M. Daily, Solveig K. Sieberts, Christopher I. Amos, Huann-Sheng Chen, Nancy J. Cox, Marina Dathe, Eric J. Feuer, Michael J. Guertin, Joshua Hoffman, Yunxian Liu, Jason H. Moore, Chad L. Myers, Marylyn D. Ritchie, Joellen Schildkraut, Fredrick Schumacher, John S. Witte, Wen Wang, Scott M. Williams, U4C Challenge Participants, U4C Challenge Data Contributors, Elizabeth M. Gillanders

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Perspective

"T-bet"-ing on autoimmunity variants

Michelle L. T. Nguyen, Dimitre R. Simeonov, Alexander Marson

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Review

Forensic genetics and genomics: Much more than just a human affair

Miguel Arenas, Filipe Pereira, Manuela Oliveira, Nadia Pinto, Alexandra M. Lopes, Veronica Gomes, Angel Carracedo, Antonio Amorim

Research Articles

Functional divergence of chloroplast Cpn60α subunits during Arabidopsis embryo development

Xiaolong Ke, Wenxuan Zou, Yafang Ren, Zhiqin Wang, Jin Li, Xuan Wu, Jie Zhao

Widespread epistasis regulates glucose homeostasis and gene expression

Anlu Chen, Yang Liu, Scott M. Williams, Nathan Morris, David A. Buchner

Estimation of kinship coefficient in structured and admixed populations using sparse sequencing data

Jinzhuang Dou, Baoluo Sun, Xueling Sim, Jason D. Hughes, Dermot F. Reilly, E. Shyong Tai, Jianjun Liu, Chaolong Wang

Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States

Le Shu, Kei Hang K. Chan, Guanglin Zhang, Tianxiao Huan, Zeyneb Kurt, Yuqi Zhao, Veronica Codoni, David-Alexandre Trégouët, Cardiogenics Consortium, Jun Yang, James G. Wilson, Xi Luo, Daniel Levy, Aldons J. Lusis, Simin Liu, Xia Yang

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites

Emily R. Ebel, Natalie Telis, Sandeep Venkataram, Dmitri A. Petrov, David Enard

The population genetics of human disease: The case of recessive, lethal mutations

Carlos Eduardo G. Amorim, Ziyue Gao, Zachary Baker, José Francisco Diesel, Yuval B. Simons, Imran S. Haque, Joseph Pickrell, Molly Przeworski

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Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

Jinliang Yang, Sofiane Mezmouk, Andy Baumgarten, Edward S. Buckler, Katherine E. Guill, Michael D. McMullen, Rita H. Mumm, Jeffrey Ross-Ibarra

Rescuing the aberrant sex development of H3K9 demethylase Jmjd1a-deficient mice by modulating H3K9 methylation balance

Shunsuke Kuroki, Naoki Okashita, Shoko Baba, Ryo Maeda, Shingo Miyawaki, Masashi Yano, Miyoko Yamaguchi, Satsuki Kitano, Hitoshi Miyachi, Akihiro Itoh, Minoru Yoshida, Makoto Tachibana

p53-dependent programmed necrosis controls germ cell homeostasis during spermatogenesis

Francesco Napoletano, Benjamin Gibert, Keren Yacobi-Sharon, Stéphane Vincent, Clémentine Favrot, Patrick Mehlen, Victor Girard, Margaux Teil, Gilles Chatelain, Ludivine Walter, Eli Arama, Bertrand Mollereau

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

Mario López-Pérez, Jose M. Haro-Moreno, Rafael Gonzalez-Serrano, Marcos Parras-Moltó, Francisco Rodriguez-Valera

A two-step transport pathway allows the mother cell to nurture the developing spore in Bacillus subtilis

Fernando H. Ramírez-Guadiana, Alexander J. Meeske, Christopher D. A. Rodrigues, Rocío del Carmen Barajas-Ornelas, Andrew C. Kruse, David Z. Rudner

Formation of a TBX20-CASZ1 protein complex is protective against dilated cardiomyopathy and critical for cardiac homeostasis

Leslie Kennedy, Erin Kaltenbrun, Todd M. Greco, Brenda Temple, Laura E. Herring, Ileana M. Cristea, Frank L. Conlon

Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model

Edward B. Li, Dawn Truong, Shawn A. Hallett, Kusumika Mukherjee, Brian C. Schutte, Eric C. Liao

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

Niedzica Camacho, Peter Van Loo, Sandra Edwards, Jonathan D. Kay, Lucy Matthews, Kerstin Haase, Jeremy Clark, Nening Dennis, Sarah Thomas, Barbara Kremeyer, Jorge Zamora, Adam P. Butler, Gunes Gundem, Sue Merson, Hayley Luxton, Steve Hawkins, Mohammed Ghori, Luke Marsden, Adam Lambert, Katalin Karaszi, Gill Pelvender, Charlie E. Massie, Zsofia Kote-Jarai, Keiran Raine, David Jones, William J. Howat, Steven Hazell, Naomi Livni, Cyril Fisher, Christopher Ogden, Pardeep Kumar, Alan Thompson, David Nicol, Erik Mayer, Tim Dudderidge, Yongwei Yu, Hongwei Zhang, Nimish C. Shah, Vincent J. Gnanapragasam, The CRUK-ICGC Prostate Group, William Isaacs, Tapio Visakorpi, Freddie Hamdy, Dan Berney, Clare Verrill, Anne Y. Warren, David C. Wedge, Andrew G. Lynch, Christopher S. Foster, Yong Jie Lu, G. Steven Bova, Hayley C. Whitaker, Ultan McDermott, David E. Neal, Rosalind Eeles, Colin S. Cooper, Daniel S. Brewer

A Rab5 GTPase module is important for autophagosome closure

Fan Zhou, Shenshen Zou, Yong Chen, Zhanna Lipatova, Dan Sun, Xiaolong Zhu, Rui Li, Zulin Wu, Weiming You, Xiaoxia Cong, Yiting Zhou, Zhiping Xie, Valeriya Gyurkovska, Yutao Liu, Qunli Li, Wenjing Li, Jie Cheng, Yongheng Liang, Nava Segev

Dynein light chain regulates adaptive and innate B cell development by distinctive genetic mechanisms

Ashleigh King, Lingli Li, David M. Wong, Rui Liu, Rebecca Bamford, Andreas Strasser, David M. Tarlinton, Jörg Heierhorst

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

Ernest Diez Benavente, Paola Florez de Sessions, Robert W. Moon, Anthony A. Holder, Michael J. Blackman, Cally Roper, Christopher J. Drakeley, Arnab Pain, Colin J. Sutherland, Martin L. Hibberd, Susana Campino, Taane G. Clark

DNA replication stress restricts ribosomal DNA copy number

Devika Salim, William D. Bradford, Amy Freeland, Gillian Cady, Jianmin Wang, Steven C. Pruitt, Jennifer L. Gerton

The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases

Muhammad Ahsan, Weronica E. Ek, Mathias Rask-Andersen, Torgny Karlsson, Allan Lind-Thomsen, Stefan Enroth, Ulf Gyllensten, Åsa Johansson

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

Emily L. Clark, Stephen J. Bush, Mary E. B. McCulloch, Iseabail L. Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu G. Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, C. Bruce Whitelaw, Tom C. Freeman, Kim M. Summers, Alan L. Archibald, David A. Hume

Genomics-enabled analysis of the emergent disease cotton bacterial blight

Anne Z. Phillips, Jeffrey C. Berry, Mark C. Wilson, Anupama Vijayaraghavan, Jillian Burke, J. Imani Bunn, Tom W. Allen, Terry Wheeler, Rebecca S. Bart

Defective erythropoiesis caused by mutations of the thyroid hormone receptor α gene

Sunmi Park, Cho Rong Han, Jeong Won Park, Li Zhao, Xuguang Zhu, Mark Willingham, David M. Bodine, Sheue-yann Cheng

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis

Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret R. Crawford, Konrad Paszkiewicz, Nicholas A. Kent, James A. H. Murray

Glucosamine stimulates pheromone-independent dimorphic transition in Cryptococcus neoformans by promoting Crz1 nuclear translocation

Xinping Xu, Jianfeng Lin, Youbao Zhao, Elyssa Kirkman, Yee-Seul So, Yong-Sun Bahn, Xiaorong Lin

Chlamydomonas DYX1C1/PF23 is essential for axonemal assembly and proper morphology of inner dynein arms

Ryosuke Yamamoto, Jagan M. Obbineni, Lea M. Alford, Takahiro Ide, Mikito Owa, Juyeon Hwang, Takahide Kon, Kazuo Inaba, Noliyanda James, Stephen M. King, Takashi Ishikawa, Winfield S. Sale, Susan K. Dutcher

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Six1 is essential for differentiation and patterning of the mammalian auditory sensory epithelium

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The adiponectin receptor AdipoR2 and its Caenorhabditis elegans homolog PAQR-2 prevent membrane rigidification by exogenous saturated fatty acids

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FtsEX-mediated regulation of the final stages of cell division reveals morphogenetic plasticity in Caulobacter crescentus

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Microtubule-actin crosslinking factor 1 (Macf1) domain function in Balbiani body dissociation and nuclear positioning

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5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells

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