Nature Cell Biology contents: January 2014 Volume 16 Number 1, pp 1 - 126

TABLE OF CONTENTS January 2014 Volume 16, Issue 1 Editorials Reviews News and Views Articles Letter Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast series: Drugging the Human Methylome Two independent, but complimentary, webcasts and live Q & A's broadcasting on:  21 January    23 January Sponsored by:     Editorials Top Ending the tyranny of the impact factor   p1 doi:10.1038/ncb2905 The San Francisco Declaration on Research Assessment (DORA), an initiative spearheaded by the American Society for Cell Biology, aims to reform research assessment. Series on Genomic Instability   p1 doi:10.1038/ncb2907 In this issue, we present the first Review in a series covering current knowledge of genomic surveillance mechanisms. Reviews Top Causes and consequences of replication stress   pp2 - 9 Michelle K. Zeman and Karlene A. Cimprich doi:10.1038/ncb2897 Defects in DNA replication, or in the pathways evolved to correct DNA replication problems, can cause genomic instability and disease. Zeman and Cimprich discuss recent advances in our understanding of the cellular responses to replication stress. Stable RNA interference rules for silencing   pp10 - 18 Christof Fellmann and Scott W. Lowe doi:10.1038/ncb2895 Stable RNA interference by shRNA provides a means to study multiple facets of gene function. Fellman and Lowe explore the rules of implementation of this silencing method in the vertebrate system for achieving maximal knockdown with minimal off-target effects. News and Views Top Kidney structures differentiated from stem cells   pp19 - 21 Benjamin D. Humphreys doi:10.1038/ncb2904 Generation of differentiated kidney cell types from pluripotent stem cells would be enormously useful for research and therapeutic purposes, but progress towards this goal has so far been limited. In three recent reports, mature kidney cell types and three-dimensional nephron-like structures were generated from pluripotent cells rapidly and efficiently. A detailed understanding of the signals that drive nephrogenesis proved critical for these achievements. See also: Letter by Takasato et al. Signal integration by GSK3 kinases in the root   pp21 - 23 Carlos S. Galvan-Ampudia and Teva Vernoux doi:10.1038/ncb2898 Signal integration is central to the regulation of patterning during plant development. During lateral root initiation, a signalling pathway controlled by the phloem-secreted TDIF peptide is found to activate the auxin signalling pathway independently of auxin, through phosphorylation of ARF transcription factors by GSK3 (Shaggy-like) kinases. See also: Article by Cho et al. Autophagy chews Fap to promote apoptosis   pp23 - 25 Sanket Joshi and Kevin M. Ryan doi:10.1038/ncb2899 Macroautophagy is a key regulator of cellular integrity and viability, but how the process facilitates apoptosis has remained poorly defined. It has now become clear that autophagy degrades the Fap-1 protein phosphatase, a critical negative regulator of apoptotic cell death signalled by the TNF receptor family member, Fas. See also: Article by Gump et al. Cell Biology JOBS of the week Postdoctoral Associate in Stem Cell Biology State University of New York Postdoc in Stem Cell Biology and Embryogenesis Max Planck Institute for Molecular Genetics Postdoc in skin biolog, molecular biology and cell biology Stony Brook University Assistant or Associate Professor in Pluripotent Stem Cell Biology KU Leuven Interdisciplinary Postdoc Positions in Golgi Cell Biology and Microscopy Yale University More Science jobs from Cell Biology EVENT Translational Control of Brain Function in Health and Disease 7–9 May 2014 London, UK More science events from Articles Top Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages   pp27 - 37 Yusuke Ohnishi, Wolfgang Huber, Akiko Tsumura, Minjung Kang, Panagiotis Xenopoulos et al. doi:10.1038/ncb2881 To delineate the characteristics of lineage emergence in the early mammalian embryo, Hiiragi and colleagues analyse the expression profiles of single cells of the inner cell mass as they differentiate into pluripotent epiblast and primitive endoderm. They observe that cells with initially indistinguishable expression profiles, but exhibiting apparently stochastic differences, resolve into distinct lineages in the late blastocyst through the action of Fgf4. The bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns   pp38 - 46 Martin Loose and Timothy J. Mitchison doi:10.1038/ncb2885 In bacteria, the tubulin-related GTPase FtsZ and the actin-related protein FtsA cooperate to form the Z-ring required for cytokinesis. Loose and Mitchison now show that FtsZ and FtsA can self-organize into dynamic structures in vitro, providing insights into the potential regulatory interplay of the two proteins. Autophagy variation within a cell population determines cell fate through selective degradation of Fap-1   pp47 - 54 Jacob M. Gump, Leah Staskiewicz, Michael J. Morgan, Alison Bamberg, David W. H. Riches et al. doi:10.1038/ncb2886 Data suggest that autophagy, a process normally associated with cell survival, also promotes cell death, depending on the stimulus or cell type. Thorburn and colleagues find that differences in basal autophagy levels in cells determine survival or death in response to death receptor activation, through modulation of Fap-1 degradation. See also: News and Views by Joshi & Ryan Plasma membrane translocation of trimerized MLKL protein is required for TNF-induced necroptosis   pp55 - 65 Zhenyu Cai, Siriporn Jitkaew, Jie Zhao, Hsueh-Cheng Chiang, Swati Choksi et al. doi:10.1038/ncb2883 Liu and colleagues find that MLKL translocates to the plasma membrane to induce TNF-induced necroptosis, possibly through an effect on calcium influx and the action of the cation channel TRPM7. A secreted peptide acts on BIN2-mediated phosphorylation of ARFs to potentiate auxin response during lateral root development   pp66 - 76 Hyunwoo Cho, Hojin Ryu, Sangchul Rho, Kristine Hill, Stephanie Smith et al. doi:10.1038/ncb2893 Auxin signalling controls events in plant development, but it is unclear how auxin sensitivity is regulated. Hwang and colleagues find that phosphorylation of AUXIN RESPONSE FACTORS (ARFs) by BRASSINOSTEROID-INSENSITIVE 2 (BIN2) suppresses their interaction with the repressors AUX/IAA to enhance the transcription of auxin target genes, which is essential for lateral root emergence. See also: News and Views by Galvan-Ampudia & Vernoux Der1 promotes movement of misfolded proteins through the endoplasmic reticulum membrane   pp77 - 86 Martin Mehnert, Thomas Sommer and Ernst Jarosch doi:10.1038/ncb2882 How misfolded proteins are extracted from the endoplasmic reticulum (ER) for degradation remains unclear. Sommer and colleagues demonstrate that following assembly into the HRD ligase complex, Der1 forms oligomers in the ER membrane and enables extraction of proteins from the ER lumen. Calcium-dependent regulation of Rab activation and vesicle fusion by an intracellular P2X ion channel   pp87 - 98 Katie Parkinson, Abigail E. Baines, Thomas Keller, Nicole Gruenheit, Laricia Bragg et al. doi:10.1038/ncb2887 Rab GTPases are important mediators of vesicle trafficking, but how they are regulated is not clear. Thompson and colleagues find that calcium efflux through the ion channel P2XA in the Dictyostelium discoideum contractile vacuole leads to activation of the Rab GTPase-activating protein CnrF, which in turn inactivates Rab11a to allow vacuole fusion. Stem cell quiescence acts as a tumour suppressor in squamous tumours   pp99 - 107 A. C. White, J. K. Khuu, C. Y. Dang, J. Hu, K. V. Tran et al. doi:10.1038/ncb2889 Lowry and colleagues report the potential role of stem cell quiescence as a tumour suppressive mechanism. They show that although hair follicle stem cell activation allows tumour formation in response to oncogenic stimuli, tumours are not initiated during the quiescent phase of the hair cycle. They further find that the presence of Pten is important in maintaining hair follicle stem cell quiescence in this setting. A genetic screen identifies an LKB1–MARK signalling axis controlling the Hippo–YAP pathway   pp108 - 117 Morvarid Mohseni, Jianlong Sun, Allison Lau, Stephen Curtis, Jeffrey Goldsmith et al. doi:10.1038/ncb2884 Camargo and colleagues employed an RNAi screen to identify LKB1 as an upstream regulator of the Hippo pathway. They show that LKB1 regulates SCRIB localization through the MARK kinase, leading to regulation of the activity of YAP through MST1/2 kinases. Letter Top Directing human embryonic stem cell differentiation towards a renal lineage generates a self-organizing kidney   pp118 - 126 M. Takasato, P. X. Er, M. Becroft, J. M. Vanslambrouck, E. G. Stanley et al. doi:10.1038/ncb2894 Differentiation of pluripotent cells into renal lineages has had limited success so far. Melissa Little and colleagues have used defined medium conditions that induce posterior primitive streak and intermediate mesoderm using growth factors used during normal embryogenesis. This results in the synchronous induction of both components of the kidney, the ureteric bud and metanephric mesenchyme, which form a self-organizing nephron structure in vitro. See also: News and Views by Humphreys Top Advertisement Nature Collections TCGA pan-cancer analysis The Cancer Genome Atlas Pan-cancer initiative examines the similarities and differences among the genomic and cellular alterations found in the first dozen tumor types to be profiled by TCGA. 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