Table of Contents

Volume 508 Number 7497 pp432-560

24 April 2014

About the cover

Mammalian Y chromosomes, known for their roles in sex determination and male fertility, often contain repetitive sequences that make them harder to assemble than the rest of the genome. To counter this problem Henrik Kaessmann and colleagues have developed a new transcript assembly approach based on male-specific RNA/genomic sequencing data to explore Y evolution across 15 species representing all major mammalian lineages. They find evidence for two independent sex chromosome originations in mammals and one in birds. Their analysis of the Y/W gene repertoires suggests that although some genes evolved novel functions in sex determination/spermatogenesis as a result of temporal/spatial expression changes, most Y genes probably persisted, at least initially, as a result of dosage constraints. In a parallel study, Daniel Bellott and colleagues reconstructed the evolution of the Y chromosome, using a comprehensive comparative analysis of the genomic sequence of X–Y gene pairs from seven placental mammals and one marsupial. They conclude that evolution streamlined the gene content of the human Y chromosome through selection to maintain the ancestral dosage of homologous X–Y gene pairs that regulate gene expression throughout the body. They propose that these genes make the Y chromosome essential for male viability and contribute to differences between the sexes in health and disease. Cover: Daren Newman

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World View


Seven Days

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News in Focus




Books and Arts

  • Medicine: The commodified body

    Scott Carney assesses a study of banked human blood, sperm and milk.

    • Review of Banking on the Body: The Market in Blood, Milk, and Sperm in Modern America
      Kara W. Swanson
  • Climate science: Stratospheric folly

    Tim Kruger examines an argument against injecting aerosols into the atmosphere to counter climate change.

    • Review of Can Science Fix Climate Change? A Case Against Climate Engineering
      Mike Hulme



  • Grants: Funder storm

    A confluence of budget disappointments has confounded US scientists and left many uncertain about their future.

    • Helen Shen



Career Briefs

  • Burnout predictors

    A greater total workload makes women more vulnerable to burnout, finds study.

  • Science 2.0

    Study concludes that more scientists should use social media in their work.

naturejobs job listings and advertising features


  • Pop-ups

    Captive audience.

    • Robert Dawson



  • Guidelines for investigating causality of sequence variants in human diseaseOpen

    • D. G. MacArthur
    • T. A. Manolio
    • D. P. Dimmock
    • H. L. Rehm
    • J. Shendure
    • G. R. Abecasis
    • D. R. Adams
    • R. B. Altman
    • S. E. Antonarakis
    • E. A. Ashley
    • J. C. Barrett
    • L. G. Biesecker
    • D. F. Conrad
    • G. M. Cooper
    • N. J. Cox
    • M. J. Daly
    • M. B. Gerstein
    • D. B. Goldstein
    • J. N. Hirschhorn
    • S. M. Leal
    • L. A. Pennacchio
    • J. A. Stamatoyannopoulos
    • S. R. Sunyaev
    • D. Valle
    • B. F. Voight
    • W. Winckler
    • C. Gunter

    Acceleration in discovery of rare genetic variants possibly linked with disease may mean an increased risk of false-positive reports of causality; this Perspective proposes guidelines to distinguish disease-causing sequence variants from the many potentially functional variants in a human genome, and to assess confidence in their pathogenicity, and highlights priority areas for development.


  • Sea-level and deep-sea-temperature variability over the past 5.3 million years

    • E. J. Rohling
    • G. L. Foster
    • K. M. Grant
    • G. Marino
    • A. P. Roberts
    • M. E. Tamisiea
    • F. Williams

    A novel approach to the estimation of sea level and deep-sea temperature has been used to determine these quantities over the past 5.3 million years; this approach, based on oxygen isotope records from the eastern Mediterranean, shows that temperature and sea-level histories are broadly correlated but also show intriguing temporal offsets.

    See also
  • Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

    • Daniel W. Bellott
    • Jennifer F. Hughes
    • Helen Skaletsky
    • Laura G. Brown
    • Tatyana Pyntikova
    • Ting-Jan Cho
    • Natalia Koutseva
    • Sara Zaghlul
    • Tina Graves
    • Susie Rock
    • Colin Kremitzki
    • Robert S. Fulton
    • Shannon Dugan
    • Yan Ding
    • Donna Morton
    • Ziad Khan
    • Lora Lewis
    • Christian Buhay
    • Qiaoyan Wang
    • Jennifer Watt
    • Michael Holder
    • Sandy Lee
    • Lynne Nazareth
    • Steve Rozen
    • Donna M. Muzny
    • Wesley C. Warren
    • Richard A. Gibbs
    • Richard K. Wilson
    • David C. Page

    A study comparing the Y chromosome across mammalian species reveals that selection to maintain the ancestral dosage of homologous X–Y gene pairs preserved a handful of genes on the Y chromosome while the rest were lost; the survival of broadly expressed dosage-sensitive regulators of gene expression suggest that the human Y chromosome is essential for male viability.

    See also
    See also


  • Superconducting quantum circuits at the surface code threshold for fault tolerance

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    • J. Kelly
    • A. Megrant
    • A. Veitia
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    • E. Jeffrey
    • T. C. White
    • J. Mutus
    • A. G. Fowler
    • B. Campbell
    • Y. Chen
    • Z. Chen
    • B. Chiaro
    • A. Dunsworth
    • C. Neill
    • P. O’Malley
    • P. Roushan
    • A. Vainsencher
    • J. Wenner
    • A. N. Korotkov
    • A. N. Cleland
    • John M. Martinis

    A universal set of logic gates in a superconducting quantum circuit is shown to have gate fidelities at the threshold for fault-tolerant quantum computing by the surface code approach, in which the quantum bits are distributed in an array of planar topology and have only nearest-neighbour couplings.

  • Hybrid shallow on-axis and deep off-axis hydrothermal circulation at fast-spreading ridges

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    • Sonja Theissen-Krah
    • Lars H. Rüpke
    • Jason P. Morgan
    • Karthik Iyer
    • Sven Petersen
    • Colin W. Devey

    High-resolution three-dimensional simulations of hydrothermal flow beneath fast-spreading ridges predict two interacting flow components — shallow on-axis flow and deeper off-axis flow — that merge to feed axial vent sites, reconciling previously incompatible models favouring only one flow component.

  • Plate tectonics, damage and inheritance

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    • Yanick Ricard

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  • Herbivores and nutrients control grassland plant diversity via light limitation

    • Elizabeth T. Borer
    • Eric W. Seabloom
    • Daniel S. Gruner
    • W. Stanley Harpole
    • Helmut Hillebrand
    • Eric M. Lind
    • Peter B. Adler
    • Juan Alberti
    • T. Michael Anderson
    • Jonathan D. Bakker
    • Lori Biederman
    • Dana Blumenthal
    • Cynthia S. Brown
    • Lars A. Brudvig
    • Yvonne M. Buckley
    • Marc Cadotte
    • Chengjin Chu
    • Elsa E. Cleland
    • Michael J. Crawley
    • Pedro Daleo
    • Ellen I. Damschen
    • Kendi F. Davies
    • Nicole M. DeCrappeo
    • Guozhen Du
    • Jennifer Firn
    • Yann Hautier
    • Robert W. Heckman
    • Andy Hector
    • Janneke HilleRisLambers
    • Oscar Iribarne
    • Julia A. Klein
    • Johannes M. H. Knops
    • Kimberly J. La Pierre
    • Andrew D. B. Leakey
    • Wei Li
    • Andrew S. MacDougall
    • Rebecca L. McCulley
    • Brett A. Melbourne
    • Charles E. Mitchell
    • Joslin L. Moore
    • Brent Mortensen
    • Lydia R. O'Halloran
    • John L. Orrock
    • Jesús Pascual
    • Suzanne M. Prober
    • David A. Pyke
    • Anita C. Risch
    • Martin Schuetz
    • Melinda D. Smith
    • Carly J. Stevens
    • Lauren L. Sullivan
    • Ryan J. Williams
    • Peter D. Wragg
    • Justin P. Wright
    • Louie H. Yang

    Experimental data collected from 40 grasslands on 6 continents show that nutrients and herbivores can serve as counteracting forces to control local plant diversity; nutrient addition reduces local diversity through light limitation, and herbivory rescues diversity at sites where it alleviates light limitation.

  • Eutrophication weakens stabilizing effects of diversity in natural grasslands

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    • Elizabeth T. Borer
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    • Helmut Hillebrand
    • Eric M. Lind
    • Andrew S. MacDougall
    • Carly J. Stevens
    • Jonathan D. Bakker
    • Yvonne M. Buckley
    • Chengjin Chu
    • Scott L. Collins
    • Pedro Daleo
    • Ellen I. Damschen
    • Kendi F. Davies
    • Philip A. Fay
    • Jennifer Firn
    • Daniel S. Gruner
    • Virginia L. Jin
    • Julia A. Klein
    • Johannes M. H. Knops
    • Kimberly J. La Pierre
    • Wei Li
    • Rebecca L. McCulley
    • Brett A. Melbourne
    • Joslin L. Moore
    • Lydia R. O’Halloran
    • Suzanne M. Prober
    • Anita C. Risch
    • Mahesh Sankaran
    • Martin Schuetz
    • Andy Hector

    Experimental eutrophication weakens the stabilizing effects of plant diversity on the productivity of natural grasslands.

  • Trogocytosis by Entamoeba histolytica contributes to cell killing and tissue invasion

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    • Michael D. Solga
    • Nicole M. Mackey-Lawrence
    • Somlata
    • Alok Bhattacharya
    • William A. Petri Jr

    Entamoeba histolytica, the causative agent of fatal diarrhoeal disease in children in the developing world, is shown here to kill human cells by biting off and ingesting pieces of cells, in a process reminiscent of the trogocytosis seen between immune cells; ingestion of bites is required for killing and this mechanism is used both in tissue culture and during invasion of intestinal explants.

    See also
  • Inhibition of miR-25 improves cardiac contractility in the failing heart

    • Christine Wahlquist
    • Dongtak Jeong
    • Agustin Rojas-Muñoz
    • Changwon Kho
    • Ahyoung Lee
    • Shinichi Mitsuyama
    • Alain van Mil
    • Woo Jin Park
    • Joost P. G. Sluijter
    • Pieter A. F. Doevendans
    • Roger J. Hajjar
    • Mark Mercola

    Reduced activity of the calcium-transporting ATPase SERCA2a is a hallmark of heart failure; here, microRNAs that downregulate SERCA2a function are identified, and antagonism of one, miR-25, is shown to halt heart failure in mice.

  • Cell-cycle-regulated activation of Akt kinase by phosphorylation at its carboxyl terminus

    • Pengda Liu
    • Michael Begley
    • Wojciech Michowski
    • Hiroyuki Inuzuka
    • Miriam Ginzberg
    • Daming Gao
    • Peiling Tsou
    • Wenjian Gan
    • Antonella Papa
    • Byeong Mo Kim
    • Lixin Wan
    • Amrik Singh
    • Bo Zhai
    • Min Yuan
    • Zhiwei Wang
    • Steven P. Gygi
    • Tae Ho Lee
    • Kun-Ping Lu
    • Alex Toker
    • Pier Paolo Pandolfi
    • John M. Asara
    • Marc W. Kirschner
    • Piotr Sicinski
    • Lewis Cantley
    • Wenyi Wei

    Phosphorylation of Akt at its carboxy-terminal tail is an essential layer of Akt activation to regulate its physiological functions.

  • Nectar secretion requires sucrose phosphate synthases and the sugar transporter SWEET9

    • I Winnie Lin
    • Davide Sosso
    • Li-Qing Chen
    • Klaus Gase
    • Sang-Gyu Kim
    • Danny Kessler
    • Peter M. Klinkenberg
    • Molly K. Gorder
    • Bi-Huei Hou
    • Xiao-Qing Qu
    • Clay J. Carter
    • Ian T. Baldwin
    • Wolf B. Frommer

    Although nectar is known to be important, for example in plant–insect interactions, little has been known about the mechanism of its secretion; sucrose phosphate synthases are now reported to be essential for the synthesis of the sucrose component of nectar and the transporter protein SWEET9 is shown to mediate sucrose export into the extracellular space of the nectary.

  • Structure of a type IV secretion system

    • Harry H. Low
    • Francesca Gubellini
    • Angel Rivera-Calzada
    • Nathalie Braun
    • Sarah Connery
    • Annick Dujeancourt
    • Fang Lu
    • Adam Redzej
    • Rémi Fronzes
    • Elena V. Orlova
    • Gabriel Waksman

    The three-dimensional structure of the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid.


  • Corrigendum: C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma

    • Matthew Parker
    • Kumarasamypet M. Mohankumar
    • Chandanamali Punchihewa
    • Ricardo Weinlich
    • James D. Dalton
    • Yongjin Li
    • Ryan Lee
    • Ruth G. Tatevossian
    • Timothy N. Phoenix
    • Radhika Thiruvenkatam
    • Elsie White
    • Bo Tang
    • Wilda Orisme
    • Kirti Gupta
    • Michael Rusch
    • Xiang Chen
    • Yuxin Li
    • Panduka Nagahawhatte
    • Erin Hedlund
    • David Finkelstein
    • Gang Wu
    • Sheila Shurtleff
    • John Easton
    • Kristy Boggs
    • Donald Yergeau
    • Bhavin Vadodaria
    • Heather L. Mulder
    • Jared Becksfort
    • Pankaj Gupta
    • Robert Huether
    • Jing Ma
    • Guangchun Song
    • Amar Gajjar
    • Thomas Merchant
    • Frederick Boop
    • Amy A. Smith
    • Li Ding
    • Charles Lu
    • Kerri Ochoa
    • David Zhao
    • Robert S. Fulton
    • Lucinda L. Fulton
    • Elaine R. Mardis
    • Richard K. Wilson
    • James R. Downing
    • Douglas R. Green
    • Jinghui Zhang
    • David W. Ellison
    • Richard J. Gilbertson