You are hereFeed aggregator

Feed aggregator


With Trump, China Emerges As Global Leader on Climate

Yale Environment 360 - Mon, 11/21/2016 - 07:29

With Donald Trump threatening to withdraw from the Paris Agreement, China is ready to assume leadership of the world’s climate efforts. For China, it is a matter of self-interest – reducing the choking pollution in its cities and seizing the economic opportunities of a low-carbon future. BY ISABEL HILTON

Categories: Environmental News

The genomic basis of circadian and circalunar timing adaptations in a midge

Nature - Mon, 11/21/2016 - 01:00

The genomic basis of circadian and circalunar timing adaptations in a midge

Nature 540, 7631 (2016). doi:10.1038/nature20151

Authors: Tobias S. Kaiser, Birgit Poehn, David Szkiba, Marco Preussner, Fritz J. Sedlazeck, Alexander Zrim, Tobias Neumann, Lam-Tung Nguyen, Andrea J. Betancourt, Thomas Hummel, Heiko Vogel, Silke Dorner, Florian Heyd, Arndt von Haeseler & Kristin Tessmar-Raible

Organisms use endogenous clocks to anticipate regular environmental cycles, such as days and tides. Natural variants resulting in differently timed behaviour or physiology, known as chronotypes in humans, have not been well characterized at the molecular level. We sequenced the genome of Clunio marinus,

Categories: Literature

Brazil’s scientists battle to escape 20-year funding freeze

Nature - Fri, 11/18/2016 - 01:00

Brazil’s scientists battle to escape 20-year funding freeze

Nature 539, 7630 (2016). http://www.nature.com/doifinder/10.1038/nature.2016.21014

Author: Claudio Angelo

Cap at current spending levels could spell ‘end of science in Brazil’, researchers say.

Categories: Literature

Geneticists hope to unlock secrets of bats’ complex sounds

Nature - Fri, 11/18/2016 - 01:00

Geneticists hope to unlock secrets of bats’ complex sounds

Nature 539, 7630 (2016). http://www.nature.com/doifinder/10.1038/nature.2016.20997

Author: Ramin Skibba

Project to sequence the DNA of more than 1,000 species seeks to reveal how bats learn to communicate.

Categories: Literature

Nations Have “Urgent Duty” to Carry Out Paris Accord, UN Conference Says

Yale Environment 360 - Fri, 11/18/2016 - 00:56

As the UN climate conference in Marrakech neared completion, nearly 200 nations, including the United States, reiterated their commitment to the

U.S. Secretary of State John Kerry in Marrakech. Paris agreement, saying that the world has “an urgent duty” to respond to global warming. In the joint statement, known as the Marrakech Action Proclamation, delegates pledged to stand with nations hit hardest by climate change, reduce emissions to meet a 1.5 degree C temperature goal, and mobilize $100 billion for resiliency work. “We welcome the Paris Agreement, its rapid entry into force, with its ambitious goals… in the light of different national circumstances,” the announcement said, “and we affirm our commitment to its full implementation.” Also this week, 47 countries on the front lines of climate change, including Bangladesh, Ethiopia, and Costa Rica, pledged to go 100 percent renewable and carbon neutral in coming decades to “help trigger increased commitments from all countries” to reduce greenhouse gases.

Categories: Environmental News

Full Speed Ahead: Shipping Plans Grow as Arctic Ice Fades

Yale Environment 360 - Thu, 11/17/2016 - 07:31

Russia, China, and other nations are stepping up preparations for the day when large numbers of cargo ships will be traversing a once-icebound Arctic Ocean. But with vessels already plying these waters, experts say the time is now to prepare for the inevitable environmental fallout. BY ED STRUZIK

Categories: Environmental News

Rock core from dinosaur-killing impact reveals how enormous craters form

Nature - Thu, 11/17/2016 - 01:00

Rock core from dinosaur-killing impact reveals how enormous craters form

Nature 539, 7630 (2016). http://www.nature.com/doifinder/10.1038/nature.2016.20994

Author: Alexandra Witze

Drilling into Mexico’s Chicxulub basin also finds shattered rock where underground life could thrive.

Categories: Literature

Hundreds of U.S. Businesses Call For Continued International Climate Action

Yale Environment 360 - Wed, 11/16/2016 - 10:52

More than 360 U.S.-based businesses, including some of the world’s largest multinational corporations, sent a letter to

Delegates at UN climate meetings in Morocco. U.S. and world leaders this week asking them to continue to support the Paris climate agreement and speed up the transition from fossil fuels to renewable energy. "Failure to build a low-carbon economy puts American prosperity at risk,” the group said. “But the right action now will create jobs and boost U.S. competitiveness. We pledge to do our part, in our own operations and beyond.” The statement, presented at United Nations climate meetings in Marrakesh, Morocco this week, was addressed to U.S. President-elect Donald Trump, U.S. President Barack Obama, Congress, and world leaders. Signatories include major conglomerates such as General Mills, Hewlett-Packard, Hilton, Nike, Kellogg, Unilever, Starbucks, and DuPont, as well as more than 50 other companies and investors with annual revenues exceeding $100 million.

Categories: Environmental News

Interview: Are Trees Sentient? Certainly, Says German Forester

Yale Environment 360 - Wed, 11/16/2016 - 07:41

In his bestselling book, The Hidden Life of Trees, German forester Peter Wohlleben argues

Peter Wohlleben that to save the world’s forests from climate change and other threats we must first recognize that trees are “wonderful beings” with innate adaptability, intelligence, and the capacity to communicate with — and heal — other trees. In an interview with Yale Environment 360, Wohlleben discusses how trees live in families, have an inborn memory of events like previous droughts, and possess the capacity to make decisions and fight off predators. Wohlleben has been criticized for anthropomorphizing trees, but he maintains that to succeed in preserving our forests in a rapidly warming world, we must start to look at trees in an entirely different light.
Read the interview.

Categories: Environmental News

Quantum computing: Efficient fault tolerance

Nature - Wed, 11/16/2016 - 01:00

Quantum computing: Efficient fault tolerance

Nature 540, 7631 (2016). doi:10.1038/nature20479

Authors: Daniel Gottesman

Dealing with errors in a quantum computer typically requires complex programming and many additional quantum bits. A technique for controlling errors has been proposed that alleviates both of these problems.

Categories: Literature

Reorientation and faulting of Pluto due to volatile loading within Sputnik Planitia

Nature - Wed, 11/16/2016 - 01:00

Reorientation and faulting of Pluto due to volatile loading within Sputnik Planitia

Nature 540, 7631 (2016). doi:10.1038/nature20120

Authors: James T. Keane, Isamu Matsuyama, Shunichi Kamata & Jordan K. Steckloff

Pluto is an astoundingly diverse, geologically dynamic world. The dominant feature is Sputnik Planitia—a tear-drop-shaped topographic depression approximately 1,000 kilometres in diameter possibly representing an ancient impact basin. The interior of Sputnik Planitia is characterized by a smooth, craterless plain three to four kilometres beneath the surrounding rugged uplands, and represents the surface of a massive unit of actively convecting volatile ices (N2, CH4 and CO) several kilometres thick. This large feature is very near the Pluto–Charon tidal axis. Here we report that the location of Sputnik Planitia is the natural consequence of the sequestration of volatile ices within the basin and the resulting reorientation (true polar wander) of Pluto. Loading of volatile ices within a basin the size of Sputnik Planitia can substantially alter Pluto’s inertia tensor, resulting in a reorientation of the dwarf planet of around 60 degrees with respect to the rotational and tidal axes. The combination of this reorientation, loading and global expansion due to the freezing of a possible subsurface ocean generates stresses within the planet’s lithosphere, resulting in a global network of extensional faults that closely replicate the observed fault networks on Pluto. Sputnik Planitia probably formed northwest of its present location, and was loaded with volatiles over million-year timescales as a result of volatile transport cycles on Pluto. Pluto’s past, present and future orientation is controlled by feedbacks between volatile sublimation and condensation, changing insolation conditions and Pluto’s interior structure.

Categories: Literature

Reorientation of Sputnik Planitia implies a subsurface ocean on Pluto

Nature - Wed, 11/16/2016 - 01:00

Reorientation of Sputnik Planitia implies a subsurface ocean on Pluto

Nature 540, 7631 (2016). doi:10.1038/nature20148

Authors: F. Nimmo, D. P. Hamilton, W. B. McKinnon, P. M. Schenk, R. P. Binzel, C. J. Bierson, R. A. Beyer, J. M. Moore, S. A. Stern, H. A. Weaver, C. B. Olkin, L. A. Young & K. E. Smith

The deep nitrogen-covered basin on Pluto, informally named Sputnik Planitia, is located very close to the longitude of Pluto’s tidal axis and may be an impact feature, by analogy with other large basins in the Solar System. Reorientation of Sputnik Planitia arising from tidal and rotational torques can explain the basin’s present-day location, but requires the feature to be a positive gravity anomaly, despite its negative topography. Here we argue that if Sputnik Planitia did indeed form as a result of an impact and if Pluto possesses a subsurface ocean, the required positive gravity anomaly would naturally result because of shell thinning and ocean uplift, followed by later modest nitrogen deposition. Without a subsurface ocean, a positive gravity anomaly requires an implausibly thick nitrogen layer (exceeding 40 kilometres). To prolong the lifetime of such a subsurface ocean to the present day and to maintain ocean uplift, a rigid, conductive water-ice shell is required. Because nitrogen deposition is latitude-dependent, nitrogen loading and reorientation may have exhibited complex feedbacks.

Categories: Literature

In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration

Nature - Wed, 11/16/2016 - 01:00

In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration

Nature 540, 7631 (2016). doi:10.1038/nature20565

Authors: Keiichiro Suzuki, Yuji Tsunekawa, Reyna Hernandez-Benitez, Jun Wu, Jie Zhu, Euiseok J. Kim, Fumiyuki Hatanaka, Mako Yamamoto, Toshikazu Araoka, Zhe Li, Masakazu Kurita, Tomoaki Hishida, Mo Li, Emi Aizawa, Shicheng Guo, Song Chen, April Goebl, Rupa Devi Soligalla, Jing Qu, Tingshuai Jiang, Xin Fu, Maryam Jafari, Concepcion Rodriguez Esteban, W. Travis Berggren, Jeronimo Lajara, Estrella Nuñez-Delicado, Pedro Guillen, Josep M. Campistol, Fumio Matsuzaki, Guang-Hui Liu, Pierre Magistretti, Kun Zhang, Edward M. Callaway, Kang Zhang & Juan Carlos Izpisua Belmonte

Targeted genome editing via engineered nucleases is an exciting area of biomedical research and holds potential for clinical applications. Despite rapid advances in the field, in vivo targeted transgene integration is still infeasible because current tools are inefficient, especially for non-dividing cells, which compose most adult tissues. This poses a barrier for uncovering fundamental biological principles and developing treatments for a broad range of genetic disorders. Based on clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) technology, here we devise a homology-independent targeted integration (HITI) strategy, which allows for robust DNA knock-in in both dividing and non-dividing cells in vitro and, more importantly, in vivo (for example, in neurons of postnatal mammals). As a proof of concept of its therapeutic potential, we demonstrate the efficacy of HITI in improving visual function using a rat model of the retinal degeneration condition retinitis pigmentosa. The HITI method presented here establishes new avenues for basic research and targeted gene therapies.

Categories: Literature

DNA repair: Clamping down on copy errors

Nature - Wed, 11/16/2016 - 01:00

DNA repair: Clamping down on copy errors

Nature 539, 7630 (2016). doi:10.1038/nature20475

Authors: Neil M. Kad & Bennett Van Houten

Repair enzymes must communicate across hundreds of nucleotides to undo errors made during DNA replication. Imaging reveals that the enzymes do this by forming a series of ring-like clamps that diffuse along the DNA. See Letter p.583

Categories: Literature

Materials science: Improving the image of nanoparticles

Nature - Wed, 11/16/2016 - 01:00

Materials science: Improving the image of nanoparticles

Nature 539, 7630 (2016). doi:10.1038/nature20478

Authors: Christopher S. Wood & Molly M. Stevens

A biocompatible probe that combines fluorescent nanodiamonds and gold nanoparticles allows cells to be imaged using both optical and electron microscopy techniques, opening up fresh opportunities for biological research.

Categories: Literature

Designer matrices for intestinal stem cell and organoid culture

Nature - Wed, 11/16/2016 - 01:00

Designer matrices for intestinal stem cell and organoid culture

Nature 539, 7630 (2016). doi:10.1038/nature20168

Authors: Nikolce Gjorevski, Norman Sachs, Andrea Manfrin, Sonja Giger, Maiia E. Bragina, Paloma Ordóñez-Morán, Hans Clevers & Matthias P. Lutolf

Epithelial organoids recapitulate multiple aspects of real organs, making them promising models of organ development, function and disease. However, the full potential of organoids in research and therapy has remained unrealized, owing to the poorly defined animal-derived matrices in which they are grown. Here we used modular synthetic hydrogel networks to define the key extracellular matrix (ECM) parameters that govern intestinal stem cell (ISC) expansion and organoid formation, and show that separate stages of the process require different mechanical environments and ECM components. In particular, fibronectin-based adhesion was sufficient for ISC survival and proliferation. High matrix stiffness significantly enhanced ISC expansion through a yes-associated protein 1 (YAP)-dependent mechanism. ISC differentiation and organoid formation, on the other hand, required a soft matrix and laminin-based adhesion. We used these insights to build a fully defined culture system for the expansion of mouse and human ISCs. We also produced mechanically dynamic matrices that were initially optimal for ISC expansion and subsequently permissive to differentiation and intestinal organoid formation, thus creating well-defined alternatives to animal-derived matrices for the culture of mouse and human stem-cell-derived organoids. Our approach overcomes multiple limitations of current organoid cultures and greatly expands their applicability in basic and clinical research. The principles presented here can be extended to identify designer matrices that are optimal for long-term culture of other types of stem cells and organoids.

Categories: Literature

Cascading MutS and MutL sliding clamps control DNA diffusion to activate mismatch repair

Nature - Wed, 11/16/2016 - 01:00

Cascading MutS and MutL sliding clamps control DNA diffusion to activate mismatch repair

Nature 539, 7630 (2016). doi:10.1038/nature20562

Authors: Jiaquan Liu, Jeungphill Hanne, Brooke M. Britton, Jared Bennett, Daehyung Kim, Jong-Bong Lee & Richard Fishel

Mismatched nucleotides arise from polymerase misincorporation errors, recombination between heteroallelic parents and chemical or physical DNA damage. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologues initiate mismatch repair and, in higher eukaryotes, act as DNA damage sensors that can trigger apoptosis. Defects in human mismatch repair genes cause Lynch syndrome or hereditary non-polyposis colorectal cancer and 10–40% of related sporadic tumours. However, the collaborative mechanics of MSH and MLH/PMS proteins have not been resolved in any organism. We visualized Escherichia coli (Ec) ensemble mismatch repair and confirmed that EcMutS mismatch recognition results in the formation of stable ATP-bound sliding clamps that randomly diffuse along the DNA with intermittent backbone contact. The EcMutS sliding clamps act as a platform to recruit EcMutL onto the mismatched DNA, forming an EcMutS–EcMutL search complex that then closely follows the DNA backbone. ATP binding by EcMutL establishes a second long-lived DNA clamp that oscillates between the principal EcMutS–EcMutL search complex and unrestricted EcMutS and EcMutL sliding clamps. The EcMutH endonuclease that targets mismatch repair excision only binds clamped EcMutL, increasing its DNA association kinetics by more than 1,000-fold. The assembly of an EcMutS–EcMutL–EcMutH search complex illustrates how sequential stable sliding clamps can modulate one-dimensional diffusion mechanics along the DNA to direct mismatch repair.

Categories: Literature

Genetic and mechanistic diversity of piRNA 3′-end formation

Nature - Wed, 11/16/2016 - 01:00

Genetic and mechanistic diversity of piRNA 3′-end formation

Nature 539, 7630 (2016). doi:10.1038/nature20162

Authors: Rippei Hayashi, Jakob Schnabl, Dominik Handler, Fabio Mohn, Stefan L. Ameres & Julius Brennecke

Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and therefore have important roles in eukaryotic gene silencing. Of the three small RNA classes, microRNAs and short interfering RNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. PIWI-interacting RNAs (piRNAs)—the 22–30-nt-long guides for PIWI-clade Ago proteins that silence transposons in animal gonads—are generated independently of Dicer from single-stranded precursors. piRNA 5′ ends are defined either by Zucchini, the Drosophila homologue of mitoPLD—a mitochondria-anchored endonuclease, or by piRNA-guided target cleavage. Formation of piRNA 3′ ends is poorly understood. Here we report that two genetically and mechanistically distinct pathways generate piRNA 3′ ends in Drosophila. The initiating nucleases are either Zucchini or the PIWI-clade proteins Aubergine (Aub) or Ago3. While Zucchini-mediated cleavages directly define mature piRNA 3′ ends, Aub/Ago3-mediated cleavages liberate pre-piRNAs that require extensive resection by the 3′-to-5′ exoribonuclease Nibbler (Drosophila homologue of Mut-7). The relative activity of these two pathways dictates the extent to which piRNAs are directed to cytoplasmic or nuclear PIWI-clade proteins and thereby sets the balance between post-transcriptional and transcriptional silencing. Notably, loss of both Zucchini and Nibbler reveals a minimal, Argonaute-driven small RNA biogenesis pathway in which piRNA 5′ and 3′ ends are directly produced by closely spaced Aub/Ago3-mediated cleavage events. Our data reveal a coherent model for piRNA biogenesis, and should aid the mechanistic dissection of the processes that govern piRNA 3′-end formation.

Categories: Literature

An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme

Nature - Wed, 11/16/2016 - 01:00

An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme

Nature 539, 7630 (2016). doi:10.1038/nature20159

Authors: Mary Ortmayer, Pierre Lafite, Binuraj R. K. Menon, Tewes Tralau, Karl Fisher, Lukas Denkhaus, Nigel S. Scrutton, Stephen E. J. Rigby, Andrew W. Munro, Sam Hay & David Leys

The universal Per-ARNT-Sim (PAS) domain functions as a signal transduction module involved in sensing diverse stimuli such as small molecules, light, redox state and gases. The highly evolvable PAS scaffold can bind a broad range of ligands, including haem, flavins and metal ions. However, although these ligands can support catalytic activity, to our knowledge no enzymatic PAS domain has been found. Here we report characterization of the first PAS enzyme: a haem-dependent oxidative N-demethylase. Unrelated to other amine oxidases, this enzyme contains haem, flavin mononucleotide, 2Fe-2S and tetrahydrofolic acid cofactors, and specifically catalyses the NADPH-dependent oxidation of dimethylamine. The structure of the α subunit reveals that it is a haem-binding PAS domain, similar in structure to PAS gas sensors. The dimethylamine substrate forms part of a highly polarized oxygen-binding site, and directly assists oxygen activation by acting as both an electron and proton donor. Our data reveal that the ubiquitous PAS domain can make the transition from sensor to enzyme, suggesting that the PAS scaffold can support the development of artificial enzymes.

Categories: Literature

Reality must trump rhetoric after US election shock

Nature - Wed, 11/16/2016 - 01:00

Reality must trump rhetoric after US election shock

Nature 539, 7629 (2016). doi:10.1038/539329a

It is time for scientists and politicians alike to constructively engage with core issues — from climate change and energy independence to social inequality.

Categories: Literature

Secondary Links