This Week in Science

Science  06 Sep 2019:
Vol. 365, Issue 6457, pp. 995
  1. Nanophotonics

    Miniaturizing spectrometers

    1. Ian S. Osborne

    Artistic interpretation of a nanowire spectrometer

    CREDIT: ELLA MARU STUDIO

    Spectroscopy is a ubiquitous characterization tool spanning most scientific and many industrial disciplines. Most handheld spectrometers are based on tabletop optical components, which limits the scale to which these spectrometers can be shrunk. To address the desire for miniaturized spectrometers with a micrometer-scale (and smaller) footprint, Yang et al. developed such a microspectrometer based on single, compositionally engineered nanowire. This result is a practical step forward for the use of other light-sensitive nanomaterials for such ultra-miniaturized spectroscopy platforms.

    Science, this issue p. 1017

  2. Atomic Physics

    Unraveling the proton puzzle

    1. Jelena Stajic

    The discrepancy between the proton size deduced from the Lamb shift in muonic hydrogen and the average, textbook value based on regular (electronic) hydrogen has puzzled physicists for nearly a decade. One possible resolution could be that electrons interact with protons in a different way than muons do, which would require “new physics.” Bezginov et al. measured the Lamb shift in electronic hydrogen, which allowed for a direct comparison to the Lamb shift measured in muonic hydrogen. The two results agreed, but the discrepancy with the averaged value remains.

    Science, this issue p. 1007

  3. Coral Reefs

    Invisible threat

    1. Sacha Vignieri

    Our changing climate is a threat to corals, causing disfiguring bleaching and mortality to reefs that once teemed with life. Shlesinger and Loya alert us to an equally dangerous yet nearly invisible hazard to coral: loss of breeding synchrony (see the Perspective by Fogarty and Marhaver). They found that environmental changes have resulted in shifts in the timing of gamete release in several species of broadcast-spawning corals in the Red Sea. Similar changes are likely occurring globally. Such a loss of spawning synchrony could result in reproductive failure, a much less obvious but no less insidious threat to coral reefs.

    Science, this issue p. 1002; see also p. 987

  4. Radio Astronomy

    General relativity reveals pulsar beams

    1. Keith T. Smith

    Pulsars are rotating neutron stars that emit beams of radio waves along their magnetic poles, seen as regular pulses if the beam points toward Earth. Desvignes et al. monitored a pulsar for more than a decade, observing how its radio pulses vary. General relativity causes precession of the rotation axis, because of the influence of a binary companion. In 2005, two pulses per rotation were visible, one from each magnetic pole, but by 2018 one had precessed out of our line of sight and disappeared. Mapping the radio emission across the magnetic pole determines the beaming angle, the angular region in which a radio observer can detect a pulsar.

    Science, this issue p. 1013

  5. Nanomaterials

    Precisely folding nanographene

    1. Phil Szuromi

    Graphene nanostructures that would result from folding or rolling graphene monolayers or bilayers have been predicted to have a number of interesting electronic properties, but control over such folding processes has been limited. Chen et al. used a scanning tunneling microscope tip to fold and unfold graphene nanoislands etched on graphite surfaces at low temperatures (4 kelvin). The fold angle could be precisely controlled to create different twist angles in bilayer graphene and a tubelike edge in folded graphene. They also folded 5 ring–7 ring defects and explored this heterojunction with scanning tunneling spectroscopy.

    Science, this issue p. 1036

  6. Marine Science

    Ocean greening off Hawai'i

    1. Caroline Ash

    From June to August 2018, the eruption of Kīlauea volcano triggered a diatom-dominated phytoplankton bloom. Wilson et al. set sail to sample the plume, deploying subsea gliders and using satellite monitoring to measure the dynamics of this rare event in the nutrient-poor Pacific (see the Perspective by Ducklow and Plank). They found subsurface chlorophyll maxima not visible by remote sensing, performed transcriptome and N isotope marker analysis, and measured nutrients, partitioning of biomass into different organisms, and primary production. Much of the data are corroborated by physical modeling of the ocean dynamics. The authors conclude that the plume was fed by the lava heating subsurface water and triggering upwelling of deepwater nutrients to the surface rather than by direct injection of micronutrients from lava.

    Science, this issue p. 1040; see also p. 978

  7. Autoimmunity

    Early insulin recognition by T cells

    1. Ifor Williams

    Type 1 diabetes is initiated by loss of T cell tolerance to pancreatic islet autoantigens, including insulin. Gioia et al. developed major histocompatibility complex (MHC)–peptide conjugates capable of distinguishing populations of insulin-reactive CD4+ T cells from diabetes-prone mice. These reagents differ in the register used for insulin peptide binding to class II MHC. Analysis of pancreatic islet tissue revealed that the earliest phase of the anti-insulin T cell response in islets is dominated by T cells that recognize an insulin12–20 peptide–MHC class II complex. Identification of the primary mode of peptide recognition used by the early anti-insulin T cells opens the door to designing inhibitors capable of selectively blocking activation of these rogue T cells.

    Sci. Immunol. 4, eaaw6329 (2019).

  8. Research Methods

    Animal behavior analysis at scale

    1. Aaron Clauset

    Video data provides insights into the social dynamics of wild animals, but processing large video datasets can be expensive and labor intensive. Using a deep convolutional neural network, Schofield et al. developed an automated pipeline to detect, track, and recognize individual animals from video in the wild. They demonstrate and evaluate this approach using a multiyear chimpanzee dataset. This system allowed researchers to monitor individual animals and automatically extract behavioral and social dynamics of individuals and groups directly from video.

    Sci. Adv. 10.1126/sciadv.aaw0736 (2019).

  9. Molecular Biology

    Heterogeneity in genome organization

    1. Steve Mao

    How the genome is organized in the three-dimensional space of the cell nucleus influences the activity of gene expression. Finn and Misteli review features of genome architecture and cell- and allele-specific variability in spatial genome organization. They also connect stochasticity in gene transcription and variability in genome organization and discuss the functional consequences of genome variability at the cell and population levels in development and disease.

    Science, this issue p. eaaw9498

  10. Human Evolution

    Ancient human movements through Asia

    1. Laura M. Zahn

    Ancient DNA has allowed us to begin tracing the history of human movements across the globe. Narasimhan et al. identify a complex pattern of human migrations and admixture events in South and Central Asia by performing genetic analysis of more than 500 people who lived over the past 8000 years (see the Perspective by Schaefer and Shapiro). They establish key phases in the population prehistory of Eurasia, including the spread of farming peoples from the Near East, with movements both westward and eastward. The people known as the Yamnaya in the Bronze Age also moved both westward and eastward from a focal area located north of the Black Sea. The overall patterns of genetic clines reflect similar and parallel patterns in South Asia and Europe.

    Science, this issue p. eaat7487; see also p. 981

  11. Natural Products

    Double warhead does DNA damage

    1. Michael A. Funk

    Strains of the human gut bacterium Escherichia coli carrying the clb gene cluster produce a secondary metabolite dubbed colibactin and have been provocatively linked to colorectal cancer in some models. Colibactin has been difficult to isolate in full, but pieces of the structure have been worked out, including an electrophilic warhead. Xue et al. found that colibactin contains two conjoined warheads, which is consistent with its ability to alkylate and cross-link DNA. Chemical synthesis and comparison to cell coculture confirm the structure and properties of this unstable and potentially carcinogenic metabolite.

    Science, this issue p. eaax2685

  12. Machine Learning

    Efficient sampling of equilibrium states

    1. Marc S. Lavine

    Molecular dynamics or Monte Carlo methods can be used to sample equilibrium states, but these methods become computationally expensive for complex systems, where the transition from one equilibrium state to another may only occur through rare events. Noé et al. used neural networks and deep learning to generate distributions of independent soft condensed-matter samples at equilibrium (see the Perspective by Tuckerman). Supervised training is used to construct invertible transformations between the coordinates of the complex system of interest and simple Gaussian coordinates of the same dimensionality. Thus, configurations can be sampled in this simpler coordinate system and then transformed back into the complex one using the correct statistical weighting.

    Science, this issue p. eaaw1147; see also p. 982

  13. Topological Optics

    An optical contortionist

    1. Ian S. Osborne

    The development of gauge fields is fundamental to our theoretical understanding of interactions in physical systems. There are two kinds of fields: Abelian, in which the measured effects on an observable parameter are commutative; and non-Abelian (noncommutative), where the sequence in which the field is applied matters. The latter are more difficult to realize in solid-state systems, but recent theoretical work has suggested that these could be synthesized optically. Yang et al. generated non-Abelian gauge fields by cascading multiple nonreciprocal optical elements and verified this accomplishment by the observed interference patterns in a Sagnac interferometer. Having a system that is tunable between Abelian and non-Abelian regimes will be important for studying complex topological states in photonic platforms.

    Science, this issue p. 1021

  14. HIV Treatment

    An antibody is not the antidote

    1. Valda Vinson

    An HIV therapeutic that would give long-term remission without sustained antiretroviral therapy (ART) is a long-term goal. Byrareddy et al. [Science 354, 197 (2016)] reported that treating simian immunodeficiency virus (SIV)–positive macaques with an antibody against integrin α4β7 during and after ART results in sustained virologic control after stopping all treatment. Three studies in this issue question the reproducibility of that result. Di Mascio et al. sequenced the virus used in the 2016 study and found that it was a variant with a stop codon in the nef gene rather than a wild-type virus. Abbink et al. used the same antibody for α4β7 as before but tested control of a more commonly used pathogenic virus. Iwamato et al. used the same nef-stop virus as in the earlier paper but combined the antibody against the integrin with an antibody against the SIV envelope glycoprotein, which also blocks viral binding of the integrin. None of these three new studies found that treating with the antibody had any effect on virologic control after stopping ART treatment.

    Science, this issue p. 1025, p. 1029, p. 1033

  15. Synthetic Biology

    Stabilizing synthetic gene circuits

    1. L. Bryan Ray

    Making synthetic gene circuits in bacteria is one thing, but making them stable under selective pressure with high mutation rates is another. Liao et al. addressed this problem with an ecological strategy in which they created three strains of bacteria, each of which could kill or be killed by one of the other strains (see the Perspective by Johnston and Collins). Once the first strain of bacteria hosting the engineered circuit underwent mutations that decreased function, the system could be “rebooted” by addition of another strain that killed the first but also contained the desired synthetic circuit, allowing its function to proceed unperturbed. This strategy provides a way to control synthetic ecosystems and maintain synthetic gene circuits without using traditional selection to maintain plasmids with antibiotics.

    Science, this issue p. 1045; see also p. 986

  16. Microbiology

    Microbial colonization in early life

    1. Gemma Alderton

    Accumulating evidence suggests that microbial colonization of tissues in early life, especially the gastrointestinal tract, may have long-term effects on health, potentially including the development of obesity and neuropsychiatric disorders. In a Perspective, McDonald and McCoy explain when infants are exposed to the maternal microbiota and how this might affect development and future health. They also discuss the idea of vertical transmission of disease risk from mother to offspring through microbiota colonization and whether this can be improved therapeutically.

    Science, this issue p. 984

  17. Cancer

    Two pathways hit with one inhibitor

    1. Yevgeniya Nusinovich

    Acute myeloid leukemia is an aggressive cancer that can be difficult to treat because of rapidly evolving therapeutic resistance. Melgar et al. focused on a subtype of acute myeloid leukemia characterized by mutations in a receptor gene FLT3. Although FLT3 inhibitors can target oncogenic signaling pathways in this cancer, their effects do not last. The authors identified a pathway involved in the innate immune stress response whose activation promoted resistance to drugs targeting the FLT3 pathway, then they developed an inhibitor that targets both pathways at once. This multikinase inhibitor showed promising results in vitro and in animals.

    Sci. Transl. Med. 11, eaaw8828 (2019).

  18. Metabolism

    Resisting a metabolic poison

    1. Wei Wong

    Once imported into cells and phosphorylated, the glucose analog 2-deoxyglucose (2DG) inhibits glycolysis. As glycolysis is up-regulated in many cancers, 2DG has been proposed as a treatment. Using yeast as a model, Defenouillère et al. investigated how cells become resistant to 2DG. Exposure to 2DG activated several signaling pathways, resulting in the increased expression of the gene encoding the phosphatase Dog2. When overexpressed, a human homolog of Dog2 conferred 2DG resistance to human cells, suggesting that cancer cells with increased abundance of this phosphatase could escape the toxic effects of 2DG.

    Sci. Signal. 12, eaaw8000 (2019).

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