This Week in Science

Science  13 Jul 2018:
Vol. 361, Issue 6398, pp. 141
  1. Plant Science

    How rice defeats the floodwaters

    1. Pamela J. Hines

    A farmer tends flooded deepwater rice fields in Bangladesh.

    CREDIT: RICHARD I'ANSON/GETTY IMAGES

    Deepwater rice varieties grow taller when flooded, in a growth response driven by the plant hormones gibberellin and ethylene. This keeps the leaves above the water. Kuroha et al. identified the genes underlying this phenotype, which encode a component of the gibberellin biosynthetic pathway and its regulatory ethylene-responsive transcription factor. This genetic relay drives growth of the plant stem internodes in response to flooding. Modern cultivated deepwater rice, which has been domesticated for adaptation to the monsoon season of Bangladesh, emerged from the genetic variation found in wild rice strains over a broader geographic region.

    Science, this issue p. 181

  2. Physics

    Simulating correlated electron systems

    1. Ian S. Osborne

    Correlated electron systems are generally difficult to simulate because of limited capabilities of computational resources. Harris et al. used a D-Wave chip based on a large array of superconducting elements to simulate the phases of a complex magnetic system. They tuned the amount of frustration within the lattice and varied the effective transverse magnetic field, which revealed phase transitions between a paramagnetic, an ordered antiferromagnetic, and a spin-glass phase. The results compare well to theory for this spin-glass problem, validating the approach for simulating problems in materials physics.

    Science, this issue p. 162

  3. Geodetic Monitoring

    Nuclear testing under the radar

    1. Brent Grocholski

    North Korea conducted its sixth underground nuclear weapons test in September 2017. The seismic waves generated from the test allow for triangulation and explosive yield estimates. However, Wang et al. show that synthetic aperture radar (SAR) should be added to the arsenal of techniques used to detect and characterize nuclear tests. SAR tracks deformation from space, which resulted in a better constraint of source parameters by using deformation from the nuclear test and the subsequent collapse of Mount Mantap. The test occurred at a depth of about half a kilometer, with an explosive yield around 10 times that of the Hiroshima explosion.

    Science, this issue p. 166

  4. Greenhouse Gases

    A leaky endeavor

    1. H. Jesse Smith

    Considerable amounts of the greenhouse gas methane leak from the U.S. oil and natural gas supply chain. Alvarez et al. reassessed the magnitude of this leakage and found that in 2015, supply chain emissions were ∼60% higher than the U.S. Environmental Protection Agency inventory estimate. They suggest that this discrepancy exists because current inventory methods miss emissions that occur during abnormal operating conditions. These data, and the methodology used to obtain them, could improve and verify international inventories of greenhouse gases and provide a better understanding of mitigation efforts outlined by the Paris Agreement.

    Science, this issue p. 186

  5. Evolutionary Cognition

    The impact of time wasted

    1. Sacha Vignieri

    The amount of time already spent on a task influences human choice about whether to continue. This dedicated time, known as the “sunk cost,” reduces the likelihood of giving up the pursuit of a reward, even when there is no indication of likely success. Sweis et al. show that this sensitivity to time invested occurs similarly in mice, rats, and humans (see the Perspective by Brosnan). All three display a resistance to giving up their pursuit of a reward in a foraging context, but only after they have made the decision to pursue the reward.

    Science, this issue p. 178; see also p. 124

  6. Early Development

    It takes two to tango

    1. Stella M. Hurtley

    Dual spindles separate maternal and paternal chromosomes in parallel.

    CREDIT: ARTASIOVA/HOSSAIN/REICHMANN/ELLENBERG/EMBL

    Fusion of egg and sperm combines the genetic material of both parents in one cell. In mammals, including humans, each parental genome is initially confined in a separate pronucleus. For the new organism to develop, the two genomes must be spatially coordinated so that the first embryonic division can create two cells that combine both genomes in one nucleus. Reichmann et al. found that at the beginning of the first division, two microtubule spindles organize the maternal and paternal chromosomes and subsequently align to segregate the parental genomes in parallel (see the Perspective by Zielinska and Schuh). Failure of spindle alignment led to two-celled embryos with more than one nucleus per cell. Dual-spindle assembly in the zygote thus offers a potential mechanistic explanation for division errors frequently observed in human embryos in the fertility clinic.

    Science, this issue p. 189; see also p. 128

  7. Hepatitis C Virus

    Hampering HCV transmission

    1. Catherine A. Charneski

    No hepatitis C virus (HCV) vaccine is currently available. Furthermore, evidence from studies in nonhuman primates suggests that any future human HCV vaccine would be unlikely to induce complete immunity. Major et al. examined whether lowered HCV titers potentially resulting from an imperfect vaccine might still stem HCV transmission in people who inject drugs. They measured the HCV RNA from infected human plasma retained in contaminated needles and syringes. Their mathematical model combining these measurements with published data on HCV viral kinetics suggested that a partially effective vaccine could reduce the HCV transmission risk from sharing contaminated needles and syringes.

    Sci. Transl. Med. 10, eaao4496 (2018).

  8. Cell Biology

    An inflammatory way to activate AMPK

    1. Wei Wong

    In its role as a sensor of energy status, the kinase AMPK is activated by phosphorylation mediated by the tumor suppressor LKB1. Antonia and Baldwin found that AMPK activation could also be mediated by a pathway involving TAK1, a kinase associated with inflammatory pathways, and its target, IKK. IKK phosphorylated AMPK independently of LKB1. Combining an IKK inhibitor with the cancer drug phenformin improved the drug's ability to kill LKB1-deficient cancer cells, highlighting a potential treatment for cancers lacking this tumor suppressor.

    Sci. Signal. 11, eaan5850 (2018).

  9. Plant Science

    Genomic traces of symbiosis loss

    1. Pamela J. Hines

    A symbiosis between certain bacteria and their plant hosts delivers fixed nitrogen to the plants. Griesmann et al. sequenced several plant genomes to analyze why nitrogen-fixing symbiosis is irregularly scattered through the evolutionary tree (see the Perspective by Nagy). Various genomes carried traces of lost pathways that could have supported nitrogen-fixing symbiosis. It seems that this symbiosis, which relies on multiple pathways and complex interorganismal signaling, is susceptible to selection and prone to being lost over evolutionary time.

    Science, this issue p. eaat1743; see also p. 125

  10. Neutrino Astrophysics

    Neutrino emission from a flaring blazar

    1. Keith T. Smith

    Neutrinos interact only very weakly with matter, but giant detectors have succeeded in detecting small numbers of astrophysical neutrinos. Aside from a diffuse background, only two individual sources have been identified: the Sun and a nearby supernova in 1987. A multiteam collaboration detected a high-energy neutrino event whose arrival direction was consistent with a known blazar—a type of quasar with a relativistic jet oriented directly along our line of sight. The blazar, TXS 0506+056, was found to be undergoing a gamma-ray flare, prompting an extensive multiwavelength campaign. Motivated by this discovery, the IceCube collaboration examined lower-energy neutrinos detected over the previous several years, finding an excess emission at the location of the blazar. Thus, blazars are a source of astrophysical neutrinos.

    Science, this issue p. 147, p. eaat1378

  11. Synthetic Biology

    Engineering multilayered cellular structures

    1. L. Bryan Ray

    The ability to program the manufacture of biological structures may yield new biomaterials or synthetic tissues and organs. Toda et al. engineered mammalian “sender” and “receiver” cells with synthetic cell surface ligands and receptors that controlled gene regulatory circuits based on Notch signaling. Programming the cells to express cell adhesion molecules and other regulatory molecules enabled spontaneous formation of multilayered structures, like those that form during embryonic development. The three-layered structures even showed regeneration after injury.

    Science, this issue p. 156

  12. Ferroelectricity

    Perovskites go organic

    1. Brent Grocholski

    The perovskite structure accommodates many different combinations of elements, making it attractive for use in a wide variety of applications. Building perovskites out of only organic compounds is appealing because these materials tend to be flexible, fracture-resistant, and potentially easier to synthesize than their inorganic counterparts. Ye et al. describe a previously unknown family of all-organic perovskites, of which they synthesized 23 different family members (see the Perspective by Li and Ji). The compounds are attractive as ferroelectrics, including one compound with properties close to the well-known inorganic ferroelectric BaTiO3.

    Science, this issue p. 151; see also p. 132

  13. Organic Chemistry

    A silver cleaver splits cyclic amines

    1. Jake Yeston

    Carbon-carbon single bonds are fairly unreactive when they are not strained in a tight ring. Roque et al. now report that a silver salt can cleave C–C bonds in unstrained cyclic amines such as pyrrolidines and piperidines. Paired with an electrophilic fluorine source in aqueous solution, the silver first oxidizes the α carbon adjacent to the nitrogen. Ring-opening fluorination of the β carbon then proceeds by an apparent radical mechanism. The reaction offers a versatile means of introducing fluorine to structural motifs common in pharmaceutical research.

    Science, this issue p. 171

  14. Early Ocean

    The rise of oxygen

    1. H. Jesse Smith

    To understand the evolution of the biosphere, we need to know how much oxygen was present in Earth's atmosphere during most of the past 2.5 billion years. However, there are few proxies sensitive enough to quantify O2 at the low levels present until slightly less than 1 billion years ago. Lu et al. measured iodine/calcium ratios in marine carbonates, which are a proxy for dissolved oxygen concentrations in the upper ocean. They found that a major, but temporary, rise in atmospheric O2 occurred at around 400 million years ago and that O2 levels underwent a step change to near-modern values around 200 million years ago.

    Science, this issue p. 174

  15. Infectious Diseases

    Tracking parasite decline

    1. Gemma Alderton

    Neglected tropical diseases, such as malaria, are often caused by parasites, the population dynamics of which are difficult to track. Control programs that are aimed at eradicating these diseases would benefit from an ability to monitor parasite populations to assess efficacy and tailor responses. In a Perspective, Cotton et al. discuss the use of genomics to track parasite populations and their evolution in the context of control programs. They also discuss how conservation genomics can inform us about the dynamics of extinction.

    Science, this issue p. 130

  16. Human Genetics

    Methylation patterns in early embryos

    1. Philippa J. Benson

    The methylation state of an embryo can be influenced by its environment, although whether this affects a person's health later in life is unclear. A mother's diet can influence genomic regions that vary greatly in methylation state, known as metastable epialleles (MEs). Kessler et al. performed genome-wide screening on 687 candidate MEs in preimplantation embryos of North American Caucasians. Compared with ME patterns previously observed in a Gambian population and in Chinese embryos, regions of the embryonic genome that are sensitive to season of conception harbored many MEs and atypical methylation patterns. Thus, MEs are sensitive to genetic and environmental features.

    Sci. Adv. 10.1126/sciadv.aat2624 (2018).

  17. Thymus

    Metabolic signaling circuits in thymocytes

    1. Anand Balasubramani

    Cell differentiation is often accompanied by metabolic changes. Yang et al. report that generation of double-positive (DP) thymocytes, which have both CD4 and CD8 antigens on their surface, from double-negative (DN) thymocytes coincides with dynamic regulation of glycolytic and oxidative metabolism. Given the central role of mTORC1 (mechanistic target of rapamycin complex 1) signaling in regulating metabolic changes, the authors examined the role of the mTORC1 pathway in thymocyte development. They conditionally deleted RAPTOR, a key component of the mTORC1 complex. Loss of RAPTOR impaired the DN-to-DP transition, but unexpectedly also perturbed the balance between αβ and γδ T cells.

    Sci. Immunol. 3, eaas9818 (2018).

  18. Structural Dynamics

    Look fast

    1. Michael A. Funk

    Organisms from bacteria to humans sense and react to light. Proteins that contain the light-sensitive molecule retinal couple absorption of light to conformational changes that produce a signal or move ions across a membrane. Nogly et al. used an x-ray laser to probe the earliest structural changes to the retinal chromophore within microcrystals of the ion pump bacteriorhodopsin (see the Perspective by Moffat). The excited-state retinal wiggles but is held in place so that only one double bond of retinal is capable of isomerizing. A water molecule adjacent to the proton-pumping Schiff base responds to changes in charge distribution in the chromophore even before the movement of atoms begins.

    Science, this issue p. eaat0094; see also p. 127

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