| | | Volume 511 Number 7507 | | | | nature | | The science that matters. Every week. | | | | | | | | | | | Jump to the content that matters to you | | | | | | | | | | | | | | | New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers | | The discovery of numerous feathered dinosaurs and early birds has set the iconic Urvogel (or 'first bird') Archaeopteryx in a broader context. But this venerable taxon still has the capacity to surprise. A newly discovered specimen — only the eleventh found since 1861 — shows a generous covering of feathers all over the body. Of particular note is a hind-limb covering resembling feathered 'trousers' . The discovery suggests that pennaceous feathers — the type we are familiar with on birds today — evolved for reasons other than flight, perhaps for display. | | | | | | | | | | | | | A close-pair binary in a distant triple supermassive black hole system | | The discovery of a triple supermassive black hole system in a distant galaxy provides a rare opportunity to observe what may be the result of galactic mergers. Of the four known triple black-hole systems, the closest pair of black holes are 2.4 kiloparsecs (1 parsec is around 3.26 light years) apart. In the newly discovered triple supermassive black-hole system, the closest pair is separated by around 140 parsecs, and is described as a tight pair. The presence of the tight pair is imprinted onto the properties of the large-scale radio jets generated by black holes, which provides a useful way to search for other tight pairs without needing extremely high resolution observations. | | | | | | | | | | | | | Abrupt pre-Bølling–Allerød warming and circulation changes in the deep ocean | | The Bølling–Allerød (B/A) warm phase, which occurred about 14,700 years ago, was one of the more prominent climate events punctuating the end of the last glaciation, but the underlying physical mechanisms driving it remain unclear. Nivedita Thiagarajan and colleagues use a coral dataset to examine the intermediate depth circulation of the ocean at the time. The data suggest that a layer of warm water, possibly of southern origin, lay in the deep North Atlantic during the Heinrich stadial 1 cool period that preceded the Bølling–Allerød interstadial. This warm water served as a heat reservoir that kick-started the resumption of vigorous ocean circulation. | | | | | | | | | | | | | | | | | | | | | In this week's podcast: a new Archaeopteryx skeleton wears feathered trousers, predicting teenage binge drinkers, and how the First World War liberated women in science, but not for long. In our latest video feature, California is home to an unusual stem cell agency; it’s funded by the state. We asked baseball fans if they’d vote for more funding. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Academic freedom under threat ▶ | | | | The human rights of academics in Egypt are being eroded by the military regime that has taken control of the country. The Arab Spring is on hold. | | | | | | | | | | | | STAP retracted ▶ | | | | Two retractions highlight long-standing issues of trust and sloppiness that must be addressed. | | | | | | | | | | | | Science and war ▶ | | | | As the centenary of its outbreak approaches, Nature looks back on the First World War. | | | | | | | | | | | | | | | | | | | | | | | | Seven days: 27 June–3 July 2014 ▶ | | | | The week in science: Retracted GM study republished; Mars landing gear passes first test; and UK public votes for antibiotics research in Longitude Prize. | | | | | | | | | | | | | | | | | | | | | | | | GM maize splits Mexico ▶ | | | | Legal challenge to transgenic crops has created a rift in the country’s scientific community. | | | | | | | | | | | | | | | | | | | | Astronomy: Planets in chaos ▶ | | | | The discovery of thousands of star systems wildly different from our own has demolished ideas about how planets form. Astronomers are searching for a whole new theory. | | | | Stem cells: Hope on the line ▶ | | | | A decade ago, voters in California changed the biomedical research landscape by directly funding embryonic stem-cell research. Now the organization they created needs a hit to survive. | | | | | | | | | | | | | | | | Women in science: A temporary liberation ▶ | | | | The First World War ushered women into laboratories and factories. In Britain, it may have won them the vote, argues Patricia Fara, but not the battle for equality. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |  | | | Grants competition:
Advancing the Science of Imagination: Toward an "Imagination Quotient" Award amounts up to $200k. The Imagination Institute announces an international grants competition for research and intervention projects on the measurement and improvement of imagination. Deadline: September 30, 2014 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Reprogramming human endothelial cells to haematopoietic cells requires vascular induction ▶ | | | | Vladislav M. Sandler, Raphael Lis, Ying Liu et al. | | | | This study describes the conversion of human fetal and adult vascular endothelial cells into engraftable haematopoietic progenitors by transduction with some transcription factors and then culture on a vascular niche feeder layer; the haematopoietic progenitors may be useful for the generation of engraftable healthy and long-lasting haematopoietic cells for treatment of inherited and acquired blood disorders. | | | | | | | | | | | | Abnormalities in human pluripotent cells due to reprogramming mechanisms ▶ | | | | Hong Ma, Robert Morey, Ryan C. O'Neil et al. | | | | Genome-wide analysis of matched human IVF embryonic stem cells (IVF ES cells), induced pluripotent stem cells (iPS cells) and nuclear transfer ES cells (NT ES cells) derived by somatic cell nuclear transfer (SCNT) reveals that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT; NT ES cells and iPS cells derived from the same somatic cells contain comparable numbers of de novo copy number variations, but whereas DNA methylation and transcriptome profiles of NT ES cells and IVF ES cells are similar, iPS cells have residual patterns typical of parental somatic cells. | | | | | | | | | | | | Three-dimensional structure of human γ-secretase ▶ | | | | Peilong Lu, Xiao-chen Bai, Dan Ma et al. | | | | The three-dimensional structure of intact human γ-secretase complex at 4.5 Å resolution is revealed by cryo-electron-microscopy single-particle analysis; the complex comprises a horseshoe-shaped transmembrane domain containing 19 transmembrane segments, and a large extracellular domain from nicastrin, which sits immediately above the hollow space formed by the horseshoe. | | | | | | | | | | | | | | | | | | | | Neuropsychosocial profiles of current and future adolescent alcohol misusers ▶ | | | | Robert Whelan, Richard Watts, Catherine A. Orr et al. | | | | Many factors have been proposed as contributors to risk of alcohol abuse, but quantifying their influence has been difficult; here a longitudinal study of a large sample of adolescents and machine learning are used to generate models of predictors of current and future alcohol abuse, assessing the relative contribution of many factors, including life history, individual personality differences, brain structure and genotype. | | | | | | | | | | | | Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA ▶ | | | | Emilia Huerta-Sánchez, Xin Jin, Asan et al. | | | | Admixture with other hominin species helped humans to adapt to high-altitude environments; the EPAS1 gene in Tibetan individuals has an unusual haplotype structure that probably resulted from introgression of DNA from Denisovan or Denisovan-related individuals into humans, and this haplotype is only found in Denisovans and Tibetans, and at low frequency among Han Chinese. | | | | | | | | | | | | Enhancer loops appear stable during development and are associated with paused polymerase ▶ | | | | Yad Ghavi-Helm, Felix A. Klein, Tibor Pakozdi et al. | | | | A high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis shows that although local regulatory interactions are frequent, long-range interactions are also very common; unexpectedly, most interactions appear unchanged between tissues and across development and are formed prior to gene expression, indicating that transcription initiates from preformed enhancer–promoter loops, which are associated with paused polymerase. | | | | | | | | | | | | ABCB5 is a limbal stem cell gene required for corneal development and repair ▶ | | | | Bruce R. Ksander, Paraskevi E. Kolovou, Brian J. Wilson et al. | | | | The loss of limbal stem cells (LSCs) due to injury or disease is one of the leading causes of blindness; here, the ABCB5 protein is identified as a marker of LSCs in mouse and human eye, and shown to be functionally required for LSC maintenance, corneal development and repair. | | | | | | | | | | | | Mutant IDH inhibits HNF-4α to block hepatocyte differentiation and promote biliary cancer ▶ | | | | Supriya K. Saha, Christine A. Parachoniak, Krishna S. Ghanta et al. | | | | Gain-of-function mutations in isocitrate dehydrogenase (IDH) are among the most common genetic alterations in intrahepatic cholangiocarcinoma (IHCC), a deadly cancer of the liver bile ducts; now mutant IDH is shown to block liver cell differentiation through the suppression of HNF-4α, a master regulator of hepatocyte identity and quiescence, leading to expansion of liver progenitor cells primed for progression to IHCC. | | | | | | | | | | | | | | | | WNT7A and PAX6 define corneal epithelium homeostasis and pathogenesis ▶ | | | | Hong Ouyang, Yuanchao Xue, Ying Lin et al. | | | | p63 and PAX6 act to specify limbal stem or progenitor cells (LSCs), and WNT7A controls corneal epithelium differentiation through PAX6; loss of WNT7A or PAX6 induces LSCs into epithelium, and transduction of PAX6 in skin epithelial stem cells converts them to LSC-like cells and transplantation in a rabbit corneal injury model can replenish corneal epithelial cells and repair damaged corneal surface. | | | | | | | | | | | | | | | | A dynamic model of bovine tuberculosis spread and control in Great Britain ▶ | | | | Ellen Brooks-Pollock, Gareth O. Roberts, Matt J. Keeling | | | | Bovine tuberculosis is a major economic burden on the cattle industry, and attempts to control it have been politically controversial; here farm movement and bovine tuberculosis incidence data are used to construct a mechanistic model and tease apart the factors contributing to epidemic bovine tuberculosis spread. | | | | | | | | | | | | | | | | Patterning and post-patterning modes of evolutionary digit loss in mammals ▶ | | | | Kimberly L. Cooper, Karen E. Sears, Aysu Uygur et al. | | | | A study of limb development in multiple mammals reveals that evolutionary digit loss has occured in many different ways—at different stages and by different mechanisms, such as regulation of Shh in initial digit specification events or by removal of digits through cell death. | | | | | | | | | | | | Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs ▶ | | | | Javier Lopez-Rios, Amandine Duchesne, Dario Speziale et al. | | | | The basic five-digit limb of tetrapods has been altered many times during evolution, usually by the progressive loss of digits — this study tracks the molecular underpinnings of this change, showing that in comparison to mouse, the polarized gene expression in the bovine limb bud is progressively lost due to evolutionary alteration of the cis-regulatory sequences that control Ptch1 expression in response to SHH signalling in the digit-forming handplate. | | | | | | | | | | | | Structural basis for outer membrane lipopolysaccharide insertion ▶ | | | | Haohao Dong, Quanju Xiang, Yinghong Gu et al. | | | | Lipopolysaccharide, an essential component of the outer membranes of Gram-negative bacteria, is inserted by LptD–LptE, a protein complex with a unique ‘barrel and plug’ architecture; the structure, molecular dynamics simulations and functional assays of the LptD–LptE complex of Salmonella typhimurium suggest that lipopolysaccharide may pass through the barrel and is then inserted into the outer leaflet of the outer membrane through a lateral opening between two β-strands of LptD. | | | | | | | | | | | | | | | | Genomic divergence in a ring species complex ▶ | | | | Miguel Alcaide, Elizabeth S. C. Scordato, Trevor D. Price et al. | | | | Two species may be fully reproductively isolated at the point they meet, but be connected by continuous gene flow by a longer route around the back of a geographical barrier; such a ring species complex exists for the greenish warbler, and genomics shows that there have been several historical breaks in gene flow along the continuum, as well as some introgression between the end forms. | | | | | | | | | | | | RLIM is dispensable for X-chromosome inactivation in the mouse embryonic epiblast ▶ | | | | JongDae Shin, Mary C. Wallingford, Judith Gallant et al. | | | | The ubiquitin ligase RLIM is known to activate the long non-coding RNA Xist, which is crucial for X-chromosome inactivation in female mice; however, unlike imprinted X-chromosome inactivation that requires RLIM for Xist expression, evidence is now provided that during random X-chromosome inactivation Xist expression is regulated by an RLIM-independent pathway in vivo. | | | | | | | | | | | | The sonic hedgehog factor GLI1 imparts drug resistance through inducible glucuronidation ▶ | | | | Hiba Ahmad Zahreddine, Biljana Culjkovic-Kraljacic, Sarit Assouline et al. | | | | A new mechanism by which acute myeloid leukaemia patients become resistant to Ara-C and a newer treatment, ribavirin, is uncovered; these drugs can be glucuronidated and thereby inactivated by members of the UDP glucuronosyltransferase family of enzymes activated through GLI1 signalling. | | | | | | | | | | | | | | | | | | | | | | | | Structural basis for lipopolysaccharide insertion in the bacterial outer membrane ▶ | | | | Shuai Qiao, Qingshan Luo, Yan Zhao et al. | | | | Lipopolysaccharide, an essential component of the Gram-negative bacteria outer membrane, is inserted by LptD–LptE, a protein complex with a unique ‘barrel and plug’ architecture; the structure of the LptD–LptE complex of Shigella flexneri determined here shows LptD forming a 26-stranded β-barrel with LptE located inside the barrel of LptD, the first two β-strands are distorted by two proline residues, creating a potential portal in the barrel wall that might allow lateral diffusion of lipopolysaccharide into the outer membrane. | | | | Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars ▶ | | | | Margaret Pallotta, Thorsten Schnurbusch, Julie Hayes, Alison Hay, Ute Baumann, Jeff Paull, Peter Langridge, Tim Sutton | | | | Adaptation of wheat to environments where growth is limited by boron toxicity has resulted from multiple genomic changes and selection for functionally diverse alleles. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Brief Communications Arising | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Launching in January 2015, Nature Plants will be a new monthly journal concerned with all aspects of plants be it their evolution, genetics, development or metabolism, their interactions with the environment, or their societal significance.
Visit the site to find out more, register for updates and to submit your paper! | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Three-dimensional structure of human γ-secretase ▶ | | | | Peilong Lu, Xiao-chen Bai, Dan Ma et al. | | | | The three-dimensional structure of intact human γ-secretase complex at 4.5 Å resolution is revealed by cryo-electron-microscopy single-particle analysis; the complex comprises a horseshoe-shaped transmembrane domain containing 19 transmembrane segments, and a large extracellular domain from nicastrin, which sits immediately above the hollow space formed by the horseshoe. | | | | | | | | | | | | Neuropsychosocial profiles of current and future adolescent alcohol misusers ▶ | | | | Robert Whelan, Richard Watts, Catherine A. Orr et al. | | | | Many factors have been proposed as contributors to risk of alcohol abuse, but quantifying their influence has been difficult; here a longitudinal study of a large sample of adolescents and machine learning are used to generate models of predictors of current and future alcohol abuse, assessing the relative contribution of many factors, including life history, individual personality differences, brain structure and genotype. | | | | | | | | | | | | ABCB5 is a limbal stem cell gene required for corneal development and repair ▶ | | | | Bruce R. Ksander, Paraskevi E. Kolovou, Brian J. Wilson et al. | | | | The loss of limbal stem cells (LSCs) due to injury or disease is one of the leading causes of blindness; here, the ABCB5 protein is identified as a marker of LSCs in mouse and human eye, and shown to be functionally required for LSC maintenance, corneal development and repair. | | | | | | | | | | | | Mutant IDH inhibits HNF-4α to block hepatocyte differentiation and promote biliary cancer ▶ | | | | Supriya K. Saha, Christine A. Parachoniak, Krishna S. Ghanta et al. | | | | Gain-of-function mutations in isocitrate dehydrogenase (IDH) are among the most common genetic alterations in intrahepatic cholangiocarcinoma (IHCC), a deadly cancer of the liver bile ducts; now mutant IDH is shown to block liver cell differentiation through the suppression of HNF-4α, a master regulator of hepatocyte identity and quiescence, leading to expansion of liver progenitor cells primed for progression to IHCC. | | | | | | | | | | | | A dynamic model of bovine tuberculosis spread and control in Great Britain ▶ | | | | Ellen Brooks-Pollock, Gareth O. Roberts, Matt J. Keeling | | | | Bovine tuberculosis is a major economic burden on the cattle industry, and attempts to control it have been politically controversial; here farm movement and bovine tuberculosis incidence data are used to construct a mechanistic model and tease apart the factors contributing to epidemic bovine tuberculosis spread. | | | | | | | | | | | | | | | | The sonic hedgehog factor GLI1 imparts drug resistance through inducible glucuronidation ▶ | | | | Hiba Ahmad Zahreddine, Biljana Culjkovic-Kraljacic, Sarit Assouline et al. | | | | A new mechanism by which acute myeloid leukaemia patients become resistant to Ara-C and a newer treatment, ribavirin, is uncovered; these drugs can be glucuronidated and thereby inactivated by members of the UDP glucuronosyltransferase family of enzymes activated through GLI1 signalling. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Normal-state nodal electronic structure in underdoped high-Tc copper oxides ▶ | | | | Suchitra E. Sebastian, N. Harrison, F. F. Balakirev et al. | | | | Quantum oscillation measurements in the underdoped copper oxide YBa2Cu3O6 + x reveal a nodal electronic structure from charge order, which helps to characterize the normal state out of which superconductivity emerges in the underdoped regime. | | | | | | | | | | | | Giant nonlinear response from plasmonic metasurfaces coupled to intersubband transitions ▶ | | | | Jongwon Lee, Mykhailo Tymchenko, Christos Argyropoulos et al. | | | | Multiple-quantum-well semiconductors can provide one of the largest known nonlinear material responses, which is, however, geometrically limited to light beams polarized perpendicular to the semiconductor layers; by coupling a plasmonic metasurface to the semiconductor heterostructure, this limitation can be lifted, opening a new path towards ultrathin planarized components with large nonlinear response. | | | | | | | | | | | | Quantum control and process tomography of a semiconductor quantum dot hybrid qubit ▶ | | | | Dohun Kim, Zhan Shi, C. B. Simmons et al. | | | | A simply prepared quantum bit that is a hybrid of spin and charge enables full control on the Bloch sphere with π-rotation times of less than 100 picoseconds in two orthogonal directions; the speed arises from the charge-like characteristics, and the spin-like features result in increased quantum coherence. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Quantification of dissolved iron sources to the North Atlantic Ocean ▶ | | | | Tim M. Conway, Seth G. John | | | | A high-resolution oceanic section of dissolved iron stable isotope ratios reveals that the primary source of dissolved iron to the North Atlantic is atmospheric dust, while seafloor sediments and submarine volcanic vents also contribute significantly. | | | | | | | | | | | | | | | | Abrupt pre-Bølling–Allerød warming and circulation changes in the deep ocean ▶ | | | | Nivedita Thiagarajan, Adam V. Subhas, John R. Southon et al. | | | | Analysis of radiocarbon and uranium-series dates and clumped isotope temperature estimates from water column profiles of fossil deep-sea corals in the North Atlantic shows that the release of heat from warm waters in the deep North Atlantic Ocean probably triggered the Bølling–Allerød warming and reinvigoration of the Atlantic meridional overturning circulation 14,700 years ago. | | | | | | | | | | | | | | | | | | | | | | | | Brief Communications Arising | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Scientific Reports
Fast and simple publishing! nature.com/scientificreports | | | | | | | | | | | | | | | | | | | | | | | | Media consulting: Entertaining science ▶ | | | | Scientific advisers for films and television help to bring credibility to the screen — and take some tangible and intangible benefits back to the lab. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Careers related news & comment | | | | | | | | | | | | | | | | | | | | | | 
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