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Drug development: A chance of survival

Nature - Wed, 11/19/2014 - 01:00

Drug development: A chance of survival

Nature. doi:10.1038/515S118a

Author: Hannah Hoag

People with advanced melanoma are living longer thanks to treatments that target cancerous cells or encourage the immune system to wipe out the tumour.

Categories: Literature

Skin colour: No hiding in the dark

Nature - Wed, 11/19/2014 - 01:00

Skin colour: No hiding in the dark

Nature. doi:10.1038/515S121a

Author: Sujata Gupta

Melanoma is most common in light-skinned people, but it can also afflict those with darker pigment. Finding out why would help to explain the disease's origins.

Categories: Literature

Protection: The sunscreen pill

Nature - Wed, 11/19/2014 - 01:00

Protection: The sunscreen pill

Nature. doi:10.1038/515S124a

Author: Erin Biba

A tablet that protects against sunburn is an attractive idea, but the science is patchy.

Categories: Literature

Perspective: Protect the USA from UVA

Nature - Wed, 11/19/2014 - 01:00

Perspective: Protect the USA from UVA

Nature. doi:10.1038/515S126a

Author: Michael J. Werner

The United States does not have access to the latest sunscreens. The Sunscreen Innovation Act could set that right, says Michael J. Werner.

Categories: Literature

Correction

Nature - Wed, 11/19/2014 - 01:00

Correction

Nature 515, 7527 (2014). http://www.nature.com/doifinder/10.1038/515324b

The News story '“Forgotten” NIH smallpox virus languishes on death row' (Nature514, 544; 2014) wrongly said that the WHO Advisory Committee on Variola Virus Research agreed to commission a report on the bioterror threat from synthesized smallpox — that report was

Categories: Literature

Genomics: Mice in the ENCODE spotlight

Nature - Wed, 11/19/2014 - 01:00

Genomics: Mice in the ENCODE spotlight

Nature 515, 7527 (2014). doi:10.1038/515346a

Authors: Piero Carninci

Following on from affiliated projects in humans and model invertebrates, the Mouse ENCODE Project presents comprehensive data sets on genome regulation in this key mammalian model. See Articles p.355, p.365, p.371 & Letter p.402

Categories: Literature

Materials physics: Reactive walls

Nature - Wed, 11/19/2014 - 01:00

Materials physics: Reactive walls

Nature 515, 7527 (2014). doi:10.1038/515348a

Authors: Philippe Ghosez & Jean-Marc Triscone

Domain walls are natural borders in ferromagnetic, ferroelectric or ferroelastic materials. It seems that they can also be reactive areas that produce crystallographic phases never before observed in bulk materials. See Letter p.379

Categories: Literature

Biogeochemistry: Agriculture and the global carbon cycle

Nature - Wed, 11/19/2014 - 01:00

Biogeochemistry: Agriculture and the global carbon cycle

Nature 515, 7527 (2014). doi:10.1038/515351a

Authors: Natasha MacBean & Philippe Peylin

Evolving agricultural practices dramatically increased crop production in the twentieth century. Two studies now find that this has altered the seasonal flux of atmospheric carbon dioxide. See Letters p.394 & p.398

Categories: Literature

A comparative encyclopedia of DNA elements in the mouse genome

Nature - Wed, 11/19/2014 - 01:00

A comparative encyclopedia of DNA elements in the mouse genome

Nature 515, 7527 (2014). doi:10.1038/nature13992

Authors: Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba, Richard Sandstrom, Zhihai Ma, Carrie Davis, Benjamin D. Pope, Yin Shen, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman, Rajinder Kaul, Eric Rynes, Anthony Kirilusha, Georgi K. Marinov, Brian A. Williams, Diane Trout, Henry Amrhein, Katherine Fisher-Aylor, Igor Antoshechkin, Gilberto DeSalvo, Lei-Hoon See, Meagan Fastuca, Jorg Drenkow, Chris Zaleski, Alex Dobin, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer, Olgert Denas, Kanwei Li, M. A. Bender, Miaohua Zhang, Rachel Byron, Mark T. Groudine, David McCleary, Long Pham, Zhen Ye, Samantha Kuan, Lee Edsall, Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis, Cheryl A. Keller, Christapher S. Morrissey, Tejaswini Mishra, Deepti Jain, Nergiz Dogan, Robert S. Harris, Philip Cayting, Trupti Kawli, Alan P. Boyle, Ghia Euskirchen, Anshul Kundaje, Shin Lin, Yiing Lin, Camden Jansen, Venkat S. Malladi, Melissa S. Cline, Drew T. Erickson, Vanessa M. Kirkup, Katrina Learned, Cricket A. Sloan, Kate R. Rosenbloom, Beatriz Lacerda de Sousa, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian, Tamer Kahveci, Dongwon Lee, W. James Kent, Miguel Ramalho Santos, Javier Herrero, Cedric Notredame, Audra Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Theresa Canfield, Peter J. Sabo, Matthew S. Wilken, Thomas A. Reh, Erika Giste, Anthony Shafer, Tanya Kutyavin, Eric Haugen, Douglas Dunn, Alex P. Reynolds, Shane Neph, Richard Humbert, R. Scott Hansen, Marella De Bruijn, Licia Selleri, Alexander Rudensky, Steven Josefowicz, Robert Samstein, Evan E. Eichler, Stuart H. Orkin, Dana Levasseur, Thalia Papayannopoulou, Kai-Hsin Chang, Arthur Skoultchi, Srikanta Gosh, Christine Disteche, Piper Treuting, Yanli Wang, Mitchell J. Weiss, Gerd A. Blobel, Xiaoyi Cao, Sheng Zhong, Ting Wang, Peter J. Good, Rebecca F. Lowdon, Leslie B. Adams, Xiao-Qiao Zhou, Michael J. Pazin, Elise A. Feingold, Barbara Wold, James Taylor, Ali Mortazavi, Sherman M. Weissman, John A. Stamatoyannopoulos, Michael P. Snyder, Roderic Guigo, Thomas R. Gingeras, David M. Gilbert, Ross C. Hardison, Michael A. Beer & Bing Ren

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the

Categories: Literature

Conservation of trans-acting circuitry during mammalian regulatory evolution

Nature - Wed, 11/19/2014 - 01:00

Conservation of trans-acting circuitry during mammalian regulatory evolution

Nature 515, 7527 (2014). doi:10.1038/nature13972

Authors: Andrew B. Stergachis, Shane Neph, Richard Sandstrom, Eric Haugen, Alex P. Reynolds, Miaohua Zhang, Rachel Byron, Theresa Canfield, Sandra Stelhing-Sun, Kristen Lee, Robert E. Thurman, Shinny Vong, Daniel Bates, Fidencio Neri, Morgan Diegel, Erika Giste, Douglas Dunn, Jeff Vierstra, R. Scott Hansen, Audra K. Johnson, Peter J. Sabo, Matthew S. Wilken, Thomas A. Reh, Piper M. Treuting, Rajinder Kaul, Mark Groudine, M. A. Bender, Elhanan Borenstein & John A. Stamatoyannopoulos

The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic

Categories: Literature

Principles of regulatory information conservation between mouse and human

Nature - Wed, 11/19/2014 - 01:00

Principles of regulatory information conservation between mouse and human

Nature 515, 7527 (2014). doi:10.1038/nature13985

Authors: Yong Cheng, Zhihai Ma, Bong-Hyun Kim, Weisheng Wu, Philip Cayting, Alan P. Boyle, Vasavi Sundaram, Xiaoyun Xing, Nergiz Dogan, Jingjing Li, Ghia Euskirchen, Shin Lin, Yiing Lin, Axel Visel, Trupti Kawli, Xinqiong Yang, Dorrelyn Patacsil, Cheryl A. Keller, Belinda Giardine, The Mouse ENCODE Consortium, Anshul Kundaje, Ting Wang, Len A. Pennacchio, Zhiping Weng, Ross C. Hardison & Michael P. Snyder

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human–mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here

Categories: Literature

The power of relativistic jets is larger than the luminosity of their accretion disks

Nature - Wed, 11/19/2014 - 01:00

The power of relativistic jets is larger than the luminosity of their accretion disks

Nature 515, 7527 (2014). doi:10.1038/nature13856

Authors: G. Ghisellini, F. Tavecchio, L. Maraschi, A. Celotti & T. Sbarrato

Theoretical models for the production of relativistic jets from active galactic nuclei predict that jet power arises from the spin and mass of the central supermassive black hole, as well as from the magnetic field near the event horizon. The physical mechanism underlying the contribution from the magnetic field is the torque exerted on the rotating black hole by the field amplified by the accreting material. If the squared magnetic field is proportional to the accretion rate, then there will be a correlation between jet power and accretion luminosity. There is evidence for such a correlation, but inadequate knowledge of the accretion luminosity of the limited and inhomogeneous samples used prevented a firm conclusion. Here we report an analysis of archival observations of a sample of blazars (quasars whose jets point towards Earth) that overcomes previous limitations. We find a clear correlation between jet power, as measured through the γ-ray luminosity, and accretion luminosity, as measured by the broad emission lines, with the jet power dominating the disk luminosity, in agreement with numerical simulations. This implies that the magnetic field threading the black hole horizon reaches the maximum value sustainable by the accreting matter.

Categories: Literature

Artificial chemical and magnetic structure at the domain walls of an epitaxial oxide

Nature - Wed, 11/19/2014 - 01:00

Artificial chemical and magnetic structure at the domain walls of an epitaxial oxide

Nature 515, 7527 (2014). doi:10.1038/nature13918

Authors: S. Farokhipoor, C. Magén, S. Venkatesan, J. Íñiguez, C. J. M. Daumont, D. Rubi, E. Snoeck, M. Mostovoy, C. de Graaf, A. Müller, M. Döblinger, C. Scheu & B. Noheda

Progress in nanotechnology requires new approaches to materials synthesis that make it possible to control material functionality down to the smallest scales. An objective of materials research is to achieve enhanced control over the physical properties of materials such as ferromagnets, ferroelectrics and superconductors. In this context, complex oxides and inorganic perovskites are attractive because slight adjustments of their atomic structures can produce large physical responses and result in multiple functionalities. In addition, these materials often contain ferroelastic domains. The intrinsic symmetry breaking that takes place at the domain walls can induce properties absent from the domains themselves, such as magnetic or ferroelectric order and other functionalities, as well as coupling between them. Moreover, large domain wall densities create intense strain gradients, which can also affect the material’s properties. Here we show that, owing to large local stresses, domain walls can promote the formation of unusual phases. In this sense, the domain walls can function as nanoscale chemical reactors. We synthesize a two-dimensional ferromagnetic phase at the domain walls of the orthorhombic perovskite terbium manganite (TbMnO3), which was grown in thin layers under epitaxial strain on strontium titanate (SrTiO3) substrates. This phase is yet to be created by standard chemical routes. The density of the two-dimensional sheets can be tuned by changing the film thickness or the substrate lattice parameter (that is, the epitaxial strain), and the distance between sheets can be made as small as 5 nanometres in ultrathin films, such that the new phase at domain walls represents up to 25 per cent of the film volume. The general concept of using domain walls of epitaxial oxides to promote the formation of unusual phases may be applicable to other materials systems, thus giving access to new classes of nanoscale materials for applications in nanoelectronics and spintronics.

Categories: Literature

Agricultural Green Revolution as a driver of increasing atmospheric CO2 seasonal amplitude

Nature - Wed, 11/19/2014 - 01:00

Agricultural Green Revolution as a driver of increasing atmospheric CO2 seasonal amplitude

Nature 515, 7527 (2014). doi:10.1038/nature13893

Authors: Ning Zeng, Fang Zhao, George J. Collatz, Eugenia Kalnay, Ross J. Salawitch, Tristram O. West & Luis Guanter

The atmospheric carbon dioxide (CO2) record displays a prominent seasonal cycle that arises mainly from changes in vegetation growth and the corresponding CO2 uptake during the boreal spring and summer growing seasons and CO2 release during the autumn and winter seasons. The CO2 seasonal amplitude has increased over the past five decades, suggesting an increase in Northern Hemisphere biospheric activity. It has been proposed that vegetation growth may have been stimulated by higher concentrations of CO2 as well as by warming in recent decades, but such mechanisms have been unable to explain the full range and magnitude of the observed increase in CO2 seasonal amplitude. Here we suggest that the intensification of agriculture (the Green Revolution, in which much greater crop yield per unit area was achieved by hybridization, irrigation and fertilization) during the past five decades is a driver of changes in the seasonal characteristics of the global carbon cycle. Our analysis of CO2 data and atmospheric inversions shows a robust 15 per cent long-term increase in CO2 seasonal amplitude from 1961 to 2010, punctuated by large decadal and interannual variations. Using a terrestrial carbon cycle model that takes into account high-yield cultivars, fertilizer use and irrigation, we find that the long-term increase in CO2 seasonal amplitude arises from two major regions: the mid-latitude cropland between 25° N and 60° N and the high-latitude natural vegetation between 50° N and 70° N. The long-term trend of seasonal amplitude increase is 0.311 ± 0.027 per cent per year, of which sensitivity experiments attribute 45, 29 and 26 per cent to land-use change, climate variability and change, and increased productivity due to CO2 fertilization, respectively. Vegetation growth was earlier by one to two weeks, as measured by the mid-point of vegetation carbon uptake, and took up 0.5 petagrams more carbon in July, the height of the growing season, during 2001–2010 than in 1961–1970, suggesting that human land use and management contribute to seasonal changes in the CO2 exchange between the biosphere and the atmosphere.

Categories: Literature

Direct human influence on atmospheric CO2 seasonality from increased cropland productivity

Nature - Wed, 11/19/2014 - 01:00

Direct human influence on atmospheric CO2 seasonality from increased cropland productivity

Nature 515, 7527 (2014). doi:10.1038/nature13957

Authors: Josh M. Gray, Steve Frolking, Eric A. Kort, Deepak K. Ray, Christopher J. Kucharik, Navin Ramankutty & Mark A. Friedl

Ground- and aircraft-based measurements show that the seasonal amplitude of Northern Hemisphere atmospheric carbon dioxide (CO2) concentrations has increased by as much as 50 per cent over the past 50 years. This increase has been linked to changes in temperate, boreal and arctic ecosystem properties and processes such as enhanced photosynthesis, increased heterotrophic respiration, and expansion of woody vegetation. However, the precise causal mechanisms behind the observed changes in atmospheric CO2 seasonality remain unclear. Here we use production statistics and a carbon accounting model to show that increases in agricultural productivity, which have been largely overlooked in previous investigations, explain as much as a quarter of the observed changes in atmospheric CO2 seasonality. Specifically, Northern Hemisphere extratropical maize, wheat, rice, and soybean production grew by 240 per cent between 1961 and 2008, thereby increasing the amount of net carbon uptake by croplands during the Northern Hemisphere growing season by 0.33 petagrams. Maize alone accounts for two-thirds of this change, owing mostly to agricultural intensification within concentrated production zones in the midwestern United States and northern China. Maize, wheat, rice, and soybeans account for about 68 per cent of extratropical dry biomass production, so it is likely that the total impact of increased agricultural production exceeds the amount quantified here.

Categories: Literature

Topologically associating domains are stable units of replication-timing regulation

Nature - Wed, 11/19/2014 - 01:00

Topologically associating domains are stable units of replication-timing regulation

Nature 515, 7527 (2014). doi:10.1038/nature13986

Authors: Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Weisheng Wu, Olgert Denas, Daniel L. Vera, Yanli Wang, R. Scott Hansen, Theresa K. Canfield, Robert E. Thurman, Yong Cheng, Günhan Gülsoy, Jonathan H. Dennis, Michael P. Snyder, John A. Stamatoyannopoulos, James Taylor, Ross C. Hardison, Tamer Kahveci, Bing Ren & David M. Gilbert

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400–800 kilobases (‘replication domains’), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

Categories: Literature

Social Media Can Help Track Severity of Air Pollution, Researchers Say

Yale Environment 360 - Tue, 11/18/2014 - 10:48

Social media posts can help researchers estimate air pollution levels with significant accuracy, according to a team of computer scientists from the University of Wisconsin. The researchers analyzed posts on Weibo — a Twitter-like site that is China's most popular social media outlet — from 108 Chinese cities over 30 days, tracking how often people complained about the air and the words they used to describe air quality. The study showed that the process can provide accurate, real-time information on the air quality index, a widely used measure of common air pollutants. Large Chinese cities sometimes have physical monitoring stations to gauge pollution levels, but smaller cities generally do not because monitors are expensive to install and maintain. The researchers hope these findings will help residents of smaller towns and less affluent areas understand the severity of their local air pollution. Between 350,000 and 500,000 Chinese citizens die prematurely each year because of air pollution, a former Chinese health minister estimated in the journal The Lancet.

Categories: Environmental News

A global vision

Nature - Tue, 11/18/2014 - 01:00

A global vision

Nature 515, 7527 (2014). doi:10.1038/515311a

The International Council for Science needs to define its mission and show its members that it is worth their membership fees.

Categories: Literature

Philae’s 64 hours of comet science yield rich data

Nature - Tue, 11/18/2014 - 01:00

Philae’s 64 hours of comet science yield rich data

Nature 515, 7527 (2014). http://www.nature.com/doifinder/10.1038/515319a

Author: Elizabeth Gibney

Comet lander is now hibernating, but has already altered our understanding of these objects.

Categories: Literature

‘Platinum’ genome takes on disease

Nature - Tue, 11/18/2014 - 01:00

‘Platinum’ genome takes on disease

Nature 515, 7527 (2014). http://www.nature.com/doifinder/10.1038/515323a

Author: Ewen Callaway

Disease sites targeted in assembly of more-complete version of the human genome sequence.

Categories: Literature

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