Geonomics & Science News

Geonomics & Science News

GENOMEWEB

See Orig3N at the Game - 30 Jun 2016


Start From Scratch - 30 Jun 2016


Promising Trial - 30 Jun 2016


This Week in Nature - 30 Jun 2016


Moonshot Booster - 29 Jun 2016


Unseen Bugs of the T - 29 Jun 2016


This Week in Cell - 29 Jun 2016


Know Thy Genes. Or Not. - 28 Jun 2016


Not the Right Genotype - 28 Jun 2016


New Name, Wider Focus - 28 Jun 2016


SCIENCENOW

[This Week in Science] Making and maintaining a healthy proteome - 1 Jul 2016

Author: Stella M. Hurtley


[Review] In vivo aspects of protein folding and quality control - 1 Jul 2016

Most proteins must fold into unique three-dimensional structures to perform their biological functions. In the crowded cellular environment, newly synthesized proteins are at risk of misfolding and forming toxic aggregate species. To ensure efficient folding, different classes of molecular chaperones receive the nascent protein chain emerging from the ribosome and guide it along a productive folding pathway. Because proteins are structurally dynamic, constant surveillance of the proteome by an integrated network of chaperones and protein degradation machineries is required to maintain protein homeostasis (proteostasis). The capacity of this proteostasis network declines during aging, facilitating neurodegeneration and other chronic diseases associated with protein aggregation. Understanding the proteostasis network holds the promise of identifying targets for pharmacological intervention in these pathologies. Authors: David Balchin, Manajit Hayer-Hartl, F. Ulrich Hartl


[Report] Catalytic, asymmetric difluorination of alkenes to generate difluoromethylated stereocenters - 1 Jul 2016

Difluoromethyl groups possess specific steric and electronic properties that invite their use as chemically inert surrogates of alcohols, thiols, and other polar functional groups important in a wide assortment of molecular recognition processes. We report here a method for the catalytic, asymmetric, migratory geminal difluorination of β-substituted styrenes to access a variety of products bearing difluoromethylated tertiary or quaternary stereocenters. The reaction uses commercially available reagents (m-chloroperbenzoic acid and hydrogen fluoride pyridine) and a simple chiral aryl iodide catalyst and is carried out readily on a gram scale. Substituent effects and temperature-dependent variations in enantioselectivity suggest that cation-π interactions play an important role in stereodifferentiation by the catalyst. Authors: Steven M. Banik, Jonathan William Medley, Eric N. Jacobsen


[Research Article] A mechanism for the elimination of the female gamete centrosome in Drosophila melanogaster - 1 Jul 2016

An important feature of fertilization is the asymmetric inheritance of centrioles. In most species it is the sperm that contributes the initial centriole, which builds the first centrosome that is essential for early development. However, given that centrioles are thought to be exceptionally stable structures, the mechanism behind centriole disappearance in the female germ line remains elusive and paradoxical. We elucidated a program for centriole maintenance in fruit flies, led by Polo kinase and the pericentriolar matrix (PCM): The PCM is down-regulated in the female germ line during oogenesis, which results in centriole loss. Perturbing this program prevents centriole loss, leading to abnormal meiotic and mitotic divisions, and thus to female sterility. This mechanism challenges the view that centrioles are intrinsically stable structures and reveals general functions for Polo kinase and the PCM in centriole maintenance. We propose that regulation of this maintenance program is essential for successful sexual reproduction and defines centriole life span in different tissues in homeostasis and disease, thereby shaping the cytoskeleton. Authors: A. Pimenta-Marques, I. Bento, C. A. M. Lopes, P. Duarte, S. C. Jana, M. Bettencourt-Dias


[Editors' Choice] Inducing potential voters to go the polls - 1 Jul 2016

Author: Gilbert Chin


[Editorial] Science and Brexit - 1 Jul 2016

Last week's dramatic vote by the United Kingdom (UK) to leave the European Union (EU) was the culmination of a heated referendum campaign that questioned the value of partnerships between the UK and the EU. Now, with many bridges burned—or at least charred—where do political leaders go next? Politicians in the UK and EU are going to need every available foundation on which to rebuild trust and mutual interests. They will need to discover once again how to work in partnership. It will be a long and difficult process; one in which science should play a crucial role. Author: Graeme Reid


[Report] Visualization and analysis of gene expression in tissue sections by spatial transcriptomics - 1 Jul 2016

Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call “spatial transcriptomics,” that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics. Authors: Patrik L. Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O. Westholm, Mikael Huss, Annelie Mollbrink, Sten Linnarsson, Simone Codeluppi, Åke Borg, Fredrik Pontén, Paul Igor Costea, Pelin Sahlén, Jan Mulder, Olaf Bergmann, Joakim Lundeberg, Jonas Frisén


[In Brief] News at a glance - 1 Jul 2016

In science news around the world, new U.S. rules on drone operations get a general thumbs up from researchers, a rare and perilous rescue mission of sick workers from the National Science Foundation's South Pole station succeeds, the World Anti-Doping Agency suspends Brazil's Doping Control Laboratory just weeks before the Olympics are set to begin in Rio de Janeiro, the European Commission extends the license of the controversial herbicide glyphosate for another 18 months, and more. Also, Science chats with conservationist Mike Sutton about a November ballot item to legalize the cultivation and sale of marijuana in California. And the International Energy Agency reports that a relatively modest global investment of $4.8 trillion in cleaner energy sources would help prevent millions of deaths due to air pollution in the coming decades.


[This Week in Science] Female-fatal product of the Yob gene - 1 Jul 2016

Author: Caroline Ash


[In Depth] ‘Brexit’ casts pall on future of U.K. science - 1 Jul 2016

Days after the United Kingdom's momentous vote in favor of leaving the European Union, the U.K. science community is seething with anxiety. No one knows whether U.K. science will struggle or thrive when the divorce goes ahead. Neither the U.K. government nor the European Commission had thought through beforehand how U.K. research could untangle itself from the European enterprise—or whether it even needs to. Scientists have pressing and practical questions: Can U.K. researchers continue to apply for E.U. grants? Will reviewers looking at a proposal involving U.K. scientists wonder about their commitment? Will U.K. postdocs have trouble taking up positions on the continent? What is the future for E.U. facilities on U.K. soil? Author: Daniel Clery


[Editors' Choice] On the origin of the achievement gap - 1 Jul 2016

Author: Melissa McCartney


[In Depth] Fighting autoimmunity with immune cells - 1 Jul 2016

Autoimmune diseases share a grim similarity with cancer: People's own cells become their enemies. But a study published online in Science reveals a happier parallel, suggesting that a therapy designed to harness the immune system to attack cancer cells may also cull the turncoat immune cells behind certain autoimmune diseases. The approach relies on chimeric antigen receptor T cells, or CAR T cells: immune cells genetically modified to home in on a desired target on cancer cells or—in this case—on rogue B cells, another immune cell type. The new study only gauged the CAR T cells' capabilities in the lab dish and in mouse models of pemphigus vulgaris, an autoimmune condition in which B cells secrete antibodies that attack a protein in skin and mucous membrane. But some scientists are already calling the approach, which specifically targets the errant B cells, a breakthrough. Author: Mitch Leslie


[Report] A maleness gene in the malaria mosquito Anopheles gambiae - 1 Jul 2016

The molecular pathways controlling gender are highly variable and have been identified in only a few nonmammalian model species. In many insects, maleness is conferred by a Y chromosome–linked M factor of unknown nature. We have isolated and characterized a gene, Yob, for the M factor in the malaria mosquito Anopheles gambiae. Yob, activated at the beginning of zygotic transcription and expressed throughout a male’s life, controls male-specific splicing of the doublesex gene. Silencing embryonic Yob expression is male-lethal, whereas ectopic embryonic delivery of Yob transcripts yields male-only broods. This female-killing property may be an invaluable tool for creation of conditional male-only transgenic Anopheles strains for malaria control programs. Authors: Elzbieta Krzywinska, Nathan J. Dennison, Gareth J. Lycett, Jaroslaw Krzywinski


[In Depth] Researchers rise to challenge of replacing helium-3 - 1 Jul 2016

U.S. researchers have finally overcome a little-known legacy of the 11 September 2001 terrorist attacks: a dire shortage of helium-3 (He-3). The rare isotope has unique properties that make it invaluable for applications from cryogenics to detecting hidden nuclear bomb material. But in 2008, experts feared that the U.S. stockpile, managed by the Department of Energy's (DOE's) Isotope Program, would run out as early as 2010, as terrorism fears drove up demand for detectors of nuclear material. DOE curtailed He-3 sales while it and other agencies raced to find He-3 alternatives. Observers hail the effort as a remarkable success. A dozen alternatives are in the pipeline or already on the market, and the He-3 stockpile is out of danger. DOE's reserves will top 160,000 liters by 2040, according to a new projection the department provided to Science. Author: Richard Stone


[Research Article] Immune modulation by MANF promotes tissue repair and regenerative success in the retina - 1 Jul 2016

Regenerative therapies are limited by unfavorable environments in aging and diseased tissues. A promising strategy to improve success is to balance inflammatory and anti-inflammatory signals and enhance endogenous tissue repair mechanisms. Here, we identified a conserved immune modulatory mechanism that governs the interaction between damaged retinal cells and immune cells to promote tissue repair. In damaged retina of flies and mice, platelet-derived growth factor (PDGF)–like signaling induced mesencephalic astrocyte-derived neurotrophic factor (MANF) in innate immune cells. MANF promoted alternative activation of innate immune cells, enhanced neuroprotection and tissue repair, and improved the success of photoreceptor replacement therapies. Thus, immune modulation is required during tissue repair and regeneration. This approach may improve the efficacy of stem-cell–based regenerative therapies. Authors: Joana Neves, Jie Zhu, Pedro Sousa-Victor, Mia Konjikusic, Rebeccah Riley, Shereen Chew, Yanyan Qi, Heinrich Jasper, Deepak A. Lamba


[In Depth] CFC bans pay off as Antarctic ozone layer starts to mend - 1 Jul 2016

Ever since its discovery in 1985, the springtime ozone hole over Antarctica has been an insistent reminder of humankind's ability to cause environmental harm. But the wound has begun to heal: There is now evidence that the hole is shrinking. The 1987 Montreal Protocol phased out ozone-destroying chemicals. And measurements have shown that atmospheric concentrations of those chemicals are declining. Now, researchers have found evidence of the intended consequence: a less holy ozone layer. Using satellites, ground-based instruments, and ozone-measuring weather balloons, they showed that since 2000, the September hole shrunk by 4 million square kilometers—an area bigger than India. An extra challenge was demonstrating that the shrinkage was due to the drop in chemicals. Using a 3D atmospheric model, the researchers separated the effect of the chemicals from those of weather and volcanic emissions, which can also destroy ozone. The model helped explain anomalously large ozone holes like the one in October 2015—which was largely due to the eruption earlier that year of the Calbuco volcano in southern Chile. Although the hole has begun to heal, the ozone-destroying chemicals have long atmospheric lifetimes. So scientists don't expect the hole to close up completely until 2050, at the earliest. Author: Eric Hand


[This Week in Science] Clocking electrons as they exit a metal - 1 Jul 2016

Author: Jake Yeston


[In Depth] Scientists cheer Senate bill - 1 Jul 2016

It may not show U.S. scientists the money, but it definitely shows them the love. This week the Senate commerce and science committee marked up a long-awaited bill governing programs at the National Science Foundation (NSF) and the National Institute of Standards and Technology as well as government-wide policies on science education and innovation. In sharp contrast to a sheaf of related legislation adopted by the U.S. House of Representatives in the past year that has infuriated many researchers, the Senate bill aligns with the science community's view on several key issues. It endorses NSF's current approach to choosing what research to fund, proposes ways to reduce the amount of time that universities and scientists spend complying with rules governing recipients of federal research dollars, and calls for the spread of NSF's wildly popular Innovation Corps program to train budding academic entrepreneurs. Author: Jeffrey Mervis


[This Week in Science] Stargazin and the AMPA receptor - 1 Jul 2016

Author: Stella M. Hurtley


[Feature] South Africa's bid to end AIDS - 1 Jul 2016

South Africa has more people living with HIV, an estimated 6.6 million, than any country in the world. About half are now receiving antiretroviral (ARV) treatment, which has greatly stressed the country's health care system. Now, South Africa plans to encourage all infected people to learn their status and start treatment as part of the drive to end its epidemic. The cornerstone of the campaign is the fact that HIV-infected people who take ARVs and fully suppress their virus rarely transmit to others. Mathematical models suggest that 73% of the infected population has to achieve this to slow spread and start the epidemic's downward spiral. South Africa has pledged to hit this target by 2020, in keeping with a global goal set by the Joint United Nations Programme on HIV/AIDS, but many experts doubt it can succeed by then—and others question the model itself. When the biannual International AIDS Conference takes place in Durban, South Africa, later this month, these issues likely will be in center stage. Author: Jon Cohen


[Editors' Choice] A special brain network for mathematics - 1 Jul 2016

Author: Peter Stern


[Letter] Science in brief - 1 Jul 2016


[Editors' Choice] Neural tube on a chip - 1 Jul 2016

Author: Pamela J. Hines


[Perspective] How frigate birds soar around the doldrums - 1 Jul 2016

In 1492, Columbus encountered frigate birds while en route to the New World and noted that the bird “does not alight on the sea nor depart from land 20 leagues” (1). Columbus observed correctly that frigate birds do not land on the sea, but he severely underestimated how far some frigate birds fly from land. On page 74 of this issue, Weimerskirch et al. (2) show that great frigate birds (Fregata minor) reduce transit costs by riding strong thermal updrafts beneath or inside cumulus clouds and then gliding long distances to another thermal, searching for food along the way. By exploiting cumulus clouds and trade winds in the Indian Ocean, the birds forage around the doldrums, a largely windless zone. Authors: Raymond B. Huey, Curtis Deutsch


[Report] A vacuum flash–assisted solution process for high-efficiency large-area perovskite solar cells - 1 Jul 2016

Metal halide perovskite solar cells (PSCs) currently attract enormous research interest because of their high solar-to-electric power conversion efficiency (PCE) and low fabrication costs, but their practical development is hampered by difficulties in achieving high performance with large-size devices. We devised a simple vacuum flash–assisted solution processing method to obtain shiny, smooth, crystalline perovskite films of high electronic quality over large areas. This enabled us to fabricate solar cells with an aperture area exceeding 1 square centimeter, a maximum efficiency of 20.5%, and a certified PCE of 19.6%. By contrast, the best certified PCE to date is 15.6% for PSCs of similar size. We demonstrate that the reproducibility of the method is excellent and that the cells show virtually no hysteresis. Our approach enables the realization of highly efficient large-area PSCs for practical deployment. Authors: Xiong Li, Dongqin Bi, Chenyi Yi, Jean-David Décoppet, Jingshan Luo, Shaik Mohammed Zakeeruddin, Anders Hagfeldt, Michael Grätzel


[Perspective] Timing photoemission—Final state matters - 1 Jul 2016

The photoemission of electrons from atoms, molecules, and condensed matter provides the experimental basis of our understanding of electronic structure. During the process of photoemission, a sufficiently large quantum of electromagnetic radiation (a photon) is absorbed by matter and converted into an electronic excitation, promoting a bound electron into a final state above the vacuum energy Evac. In photoemission spectroscopy, the kinetic energy and momentum of electrons in such final states are analyzed after their propagation to a distant detector. To determine the electronic structure of the sample, the “sudden approximation” has to be fulfilled, whereby the photoelectron leaves the sample fast enough, without further interaction with the remaining electronic structure. On page 62 of this issue, Tao et al. (1) provide unprecedented insight into final-state dynamics by measuring the time a photoelectron takes to leave a solid material for characteristically different final states. By comparing an electron excited to a final state of a nickel solid Ψ Nif with one excited to a state of vacuum Ψ vacf, they establish that a photoelectron resides in the final state for 200 attoseconds (as) (2 × 10−16 s) before it leaves the nickel (see the figure). Such time scales would still allow for the electron to interact with its surroundings and, thus, are relevant for the validity of the sudden approximation. Authors: Uwe Bovensiepen, Manuel Ligges


[Report] Mycorrhizal association as a primary control of the CO2 fertilization effect - 1 Jul 2016

Plants buffer increasing atmospheric carbon dioxide (CO2) concentrations through enhanced growth, but the question whether nitrogen availability constrains the magnitude of this ecosystem service remains unresolved. Synthesizing experiments from around the world, we show that CO2 fertilization is best explained by a simple interaction between nitrogen availability and mycorrhizal association. Plant species that associate with ectomycorrhizal fungi show a strong biomass increase (30 ± 3%, P < 0.001) in response to elevated CO2 regardless of nitrogen availability, whereas low nitrogen availability limits CO2 fertilization (0 ± 5%, P = 0.946) in plants that associate with arbuscular mycorrhizal fungi. The incorporation of mycorrhizae in global carbon cycle models is feasible, and crucial if we are to accurately project ecosystem responses and feedbacks to climate change. Authors: César Terrer, Sara Vicca, Bruce A. Hungate, Richard P. Phillips, I. Colin Prentice


[Perspective] The evolutionary path of least resistance - 1 Jul 2016

Paleontologists typically reconstruct past behavior by assuming that function follows form. But there can be more than one function for a given form, and different forms can serve the same function. Deconstructing these relationships can be complicated. Here, we use an example from human evolution—markedly different tooth morphologies in early hominins—to show that insights about the underlying genetic architecture of form can help us to better infer function and deepen our understanding of evolution. Authors: P. S. Ungar, L. J. Hlusko


[New Products] New Products - 1 Jul 2016

A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.


[Perspective] Promoting CNS repair - 1 Jul 2016

A developmental loss of intrinsic reparative capacity and the inhibitory environment in injury and disease contribute to regenerative failure in the central nervous system (CNS). The same factors are thought to hinder endogenous and exogenous regenerative therapies, including cell-based replacement (1, 2). In neurodegenerative disorders, the contributions of microglia, astrocytes, and peripheral immune cells may be both harmful and beneficial. For example, resident microglia and peripheral cells of the innate immune system promote inflammation and cell death (apoptosis) in response to CNS injury, but immune cell activation also has been associated with neuroprotection and repair (3). This duality suggests that stimulating protective functions while minimizing proapoptotic and inhibitory signals could prove critical in treating neurodegenerative disease. On page 43 of this issue, Neves et al. (4) show that a neurotrophic signaling pathway in microglia and innate immune cells that is activated in disease or injury can be leveraged to promote neuroprotection and tissue repair. Authors: Evan G. Cameron, Jeffrey L. Goldberg


[This Week in Science] Evolutionary lessons from hominin teeth - 1 Jul 2016

Author: Julia Fahrenkamp-Uppenbrink


[Perspective] How climate change affects plants' sex lives - 1 Jul 2016

Climate change affects wild plant species across their geographical ranges. Studies at the margins of species' ranges reveal upslope expansion, low-elevation range contraction, and, in some cases, a lack of geographic response to climate change (1). However, all populations, including those in the core of species' ranges, are subject to climate-driven natural selection that promotes adaptation to a warmer world (2). Theoretical models show that coupled spatial and temporal responses of populations can mediate the negative effects of climate change (3, 4), but it remains unclear whether these processes can occur fast enough to rescue populations from extinction (5). On page 69 of this issue, Petry et al. (6) report rapid spatial and temporal change in plant sex ratios in response to changing climatic conditions. These changes could facilitate geographic range shifts in the montane perennial herb valerian (Valeriana edulis). Authors: Julie R. Etterson, Susan J. Mazer


[This Week in Science] MANF enough for tissue repair - 1 Jul 2016

Author: Stella M. Hurtley


[Perspective] Yob makes mosquitoes male - 1 Jul 2016

Most developmental processes show deep conservation across great phylogenetic distances. In contrast, the signal that triggers the primary genetic switch between the sexes has evolved with remarkable rapidity—entirely lacking the “respectable antiquity” (1) seen in other comparable systems. Coupled with the repeat-rich structure of Y chromosomes, this has made the identification of genetically dominant “M” male-determining factors especially challenging. On page 67 of this issue, Krzywinska et al. (2) compared gene transcript sequences from male and female embryos of the malaria mosquito Anopheles gambiae and identified an early-expressed gene on the Y chromosome, designated Yob. Crucially, they show that it controls sex-specific splicing of dsx (double-sex), the conserved binary switch between male and female development (3), fulfilling the criteria for M. Yob partly overlaps, and probably is a better-annotated version of, a previously identified gene called YG2 (4), recently shown to be conserved across the An. gambiae species complex (5). Author: Steven P. Sinkins


[This Week in Science] Kicking out an unwanted centrosome - 1 Jul 2016

Author: Stella M. Hurtley


[Policy Forum] Reforms to improve U.S. government accountability - 1 Jul 2016

Five decades after the United States first enacted the Freedom of Information Act (FOIA), Congress has voted to make the first major reforms to the statute since 2007. President Lyndon Johnson signed the first FOIA on 4 July 1966, enshrining in law the public's right to access to information from executive branch government agencies. Scientists and others around the world can use the FOIA to learn what the U.S. government has done in its policies and practices. Proposed reforms should be a net benefit to public understanding of the scientific process and knowledge, by increasing the access of scientists to archival materials and reducing the likelihood of science and scientists being suppressed by official secrecy or bureaucracy. Authors: Alexander B. Howard, Patrice McDermott


[This Week in Science] Changing sex ratios - 1 Jul 2016

Author: Sacha Vignieri


[Book Review] Envisioning a different future - 1 Jul 2016

Nearly 40 years after Rachel Carson highlighted the dangers of DDT to wildlife, its use and that of a range of other organic pollutants became tightly restricted through the ratification of the Stockholm Convention. But as George Woodwell argues in his latest book, A World to Live In, key lessons that might have been gleaned from the DDT story have not been learned, with devastating consequencesfor life on our planet. A leading ecologist with decades of experience in the effects of disturbance on ecosystems, Woodwell shows that diverse industrial activities—from nuclear power production to fossil-fuel burning to contemporary agricultural practices—are affecting the chemical processes that underpin all life on Earth. Author: Julia Fahrenkamp-Uppenbrink


[This Week in Science] A new type of cancer cluster - 1 Jul 2016

Author: Megan Frisk


[Book Review] The battle lines are drawn - 1 Jul 2016

In his new book, The War on Science, Shawn Otto documents the modern clash between what he calls the "authoritarians" (governments, large corporations, and religious groups) and the "antiauthoritarians" (scientists and other liberal thinkers). Drawing on recent examples ranging from the evolution debate to vaccine skepticism, Otto describes the emergence of an antiscience movement whose focus is to disrupt the creation of evidence-based policy for the sake of preserving profitable business models or entrenched religious dogma. Author: Peter R. Reczek


[Editors' Choice] Drinking straws for the stomach - 1 Jul 2016

Author: Marc S. Lavine


[This Week in Science] Fungi relieve nitrogen limitation - 1 Jul 2016

Author: H. Jesse Smith


[Editors' Choice] Activating Inflammation - 1 Jul 2016

Author: Stella M. Hurtley


[This Week in Science] Mapping ADP-ribosylation by PARPs - 1 Jul 2016

Author: Beverly A. Purnell


[Editors' Choice] Induction is the key to production - 1 Jul 2016

Author: Nicholas S. Wigginton


[This Week in Science] Scales, feathers, and hair have a lot in common - 1 Jul 2016

Author: Shahid Naeem


[Research Article] Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation - 1 Jul 2016

Poly[adenosine diphosphate (ADP)–ribose] polymerases (PARPs) are a family of enzymes that modulate diverse biological processes through covalent transfer of ADP-ribose from the oxidized form of nicotinamide adenine dinucleotide (NAD+) onto substrate proteins. Here we report a robust NAD+ analog–sensitive approach for PARPs, which allows PARP-specific ADP-ribosylation of substrates that is suitable for subsequent copper-catalyzed azide-alkyne cycloaddition reactions. Using this approach, we mapped hundreds of sites of ADP-ribosylation for PARPs 1, 2, and 3 across the proteome, as well as thousands of PARP-1–mediated ADP-ribosylation sites across the genome. We found that PARP-1 ADP-ribosylates and inhibits negative elongation factor (NELF), a protein complex that regulates promoter-proximal pausing by RNA polymerase II (Pol II). Depletion or inhibition of PARP-1 or mutation of the ADP-ribosylation sites on NELF-E promotes Pol II pausing, providing a clear functional link between PARP-1, ADP-ribosylation, and NELF. This analog-sensitive approach should be broadly applicable across the PARP family and has the potential to illuminate the ADP-ribosylated proteome and the molecular mechanisms used by individual PARPs to mediate their responses to cellular signals. Authors: Bryan A. Gibson, Yajie Zhang, Hong Jiang, Kristine M. Hussey, Jonathan H. Shrimp, Hening Lin, Frank Schwede, Yonghao Yu, W. Lee Kraus


[This Week in Science] Better in a flash of perovskite - 1 Jul 2016

Author: Phil Szuromi


[Report] Large wind ripples on Mars: A record of atmospheric evolution - 1 Jul 2016

Wind blowing over sand on Earth produces decimeter-wavelength ripples and hundred-meter– to kilometer-wavelength dunes: bedforms of two distinct size modes. Observations from the Mars Science Laboratory Curiosity rover and the Mars Reconnaissance Orbiter reveal that Mars hosts a third stable wind-driven bedform, with meter-scale wavelengths. These bedforms are spatially uniform in size and typically have asymmetric profiles with angle-of-repose lee slopes and sinuous crest lines, making them unlike terrestrial wind ripples. Rather, these structures resemble fluid-drag ripples, which on Earth include water-worked current ripples, but on Mars instead form by wind because of the higher kinematic viscosity of the low-density atmosphere. A reevaluation of the wind-deposited strata in the Burns formation (about 3.7 billion years old or younger) identifies potential wind-drag ripple stratification formed under a thin atmosphere. Authors: M. G. A. Lapotre, R. C. Ewing, M. P. Lamb, W. W. Fischer, J. P. Grotzinger, D. M. Rubin, K. W. Lewis, M. J. Ballard, M. Day, S. Gupta, S. G. Banham, N. T. Bridges, D. J. Des Marais, A. A. Fraeman, J. A. Grant, K. E. Herkenhoff, D. W. Ming, M. A. Mischna, M. S. Rice, D. A. Sumner, A. R. Vasavada, R. A. Yingst


[This Week in Science] Adding two fluorines to just one carbon - 1 Jul 2016

Author: Jake Yeston


[Report] Direct time-domain observation of attosecond final-state lifetimes in photoemission from solids - 1 Jul 2016

Attosecond spectroscopic techniques have made it possible to measure differences in transport times for photoelectrons from localized core levels and delocalized valence bands in solids. We report the application of attosecond pulse trains to directly and unambiguously measure the difference in lifetimes between photoelectrons born into free electron–like states and those excited into unoccupied excited states in the band structure of nickel (111). An enormous increase in lifetime of 212 ± 30 attoseconds occurs when the final state coincides with a short-lived excited state. Moreover, a strong dependence of this lifetime on emission angle is directly related to the final-state band dispersion as a function of electron transverse momentum. This finding underscores the importance of the material band structure in determining photoelectron lifetimes and corresponding electron escape depths. Authors: Zhensheng Tao, Cong Chen, Tibor Szilvási, Mark Keller, Manos Mavrikakis, Henry Kapteyn, Margaret Murnane


[This Week in Science] Unexpected forms of sand dunes on Mars - 1 Jul 2016

Author: Keith T. Smith


[Report] Sex-specific responses to climate change in plants alter population sex ratio and performance - 1 Jul 2016

Males and females are ecologically distinct in many species, but whether responses to climate change are sex-specific is unknown. We document sex-specific responses to climate change in the plant Valeriana edulis (valerian) over four decades and across its 1800-meter elevation range. Increased elevation was associated with increased water availability and female frequency, likely owing to sex-specific water use efficiency and survival. Recent aridification caused male frequency to move upslope at 175 meters per decade, a rate of trait shift outpacing reported species’ range shifts by an order of magnitude. This increase in male frequency reduced pollen limitation and increased seedset. Coupled with previous studies reporting sex-specific arthropod communities, these results underscore the importance of ecological differences between the sexes in mediating biological responses to climate change. Authors: William K. Petry, Judith D. Soule, Amy M. Iler, Ana Chicas-Mosier, David W. Inouye, Tom E. X. Miller, Kailen A. Mooney


[This Week in Science] Spatial structure of RNA expression - 1 Jul 2016

Author: Laura M. Zahn


[Report] Frigate birds track atmospheric conditions over months-long transoceanic flights - 1 Jul 2016

Understanding how animals respond to atmospheric conditions across space is critical for understanding the evolution of flight strategies and long-distance migrations. We studied the three-dimensional movements and energetics of great frigate birds (Fregata minor) and showed that they can stay aloft for months during transoceanic flights. To do this, birds track the edge of the doldrums to take advantage of favorable winds and strong convection. Locally, they use a roller-coaster flight, relying on thermals and wind to soar within a 50- to 600-meter altitude band under cumulus clouds and then glide over kilometers at low energy costs. To deal with the local scarcity of clouds and gain longer gliding distances, birds regularly soar inside cumulus clouds to use their strong updraft, and they can reach altitudes of 4000 meters, where freezing conditions occur. Authors: Henri Weimerskirch, Charles Bishop, Tiphaine Jeanniard-du-Dot, Aurélien Prudor, Gottfried Sachs


[This Week in Science] Cloud-gliding frigate birds - 1 Jul 2016

Author: Sacha Vignieri


[Report] Elucidation of AMPA receptor–stargazin complexes by cryo–electron microscopy - 1 Jul 2016

AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate fast excitatory neurotransmission and contribute to high cognitive processes such as learning and memory. In the brain, AMPAR trafficking, gating, and pharmacology is tightly controlled by transmembrane AMPAR regulatory proteins (TARPs). Here, we used cryo–electron microscopy to elucidate the structural basis of AMPAR regulation by one of these auxiliary proteins, TARP γ2, or stargazin (STZ). Our structures illuminate the variable interaction stoichiometry of the AMPAR-TARP complex, with one or two TARP molecules binding one tetrameric AMPAR. Analysis of the AMPAR-STZ binding interfaces suggests that electrostatic interactions between the extracellular domains of AMPAR and STZ play an important role in modulating AMPAR function through contact surfaces that are conserved across AMPARs and TARPs. We propose a model explaining how TARPs stabilize the activated state of AMPARs and how the interactions between AMPARs and their auxiliary proteins control fast excitatory synaptic transmission. Authors: Edward C. Twomey, Maria V. Yelshanskaya, Robert A. Grassucci, Joachim Frank, Alexander I. Sobolevsky


[This Week in Science] Building the route to metastasis - 1 Jul 2016

Author: Leslie K. Ferrarelli


[Working Life] The measure of success - 1 Jul 2016

Author: Melanie L. Blanchette


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