This Week in Science

Science  30 Apr 2021:
Vol. 372, Issue 6541, pp. 476
  1. Island Ecology

    Accelerating ecosystem disruption

    1. Andrew M. Sugden

    Human arrival on islands and subsequent activities, such as pineapple farming in Hawai'i pictured here, have accelerated vegetation turnover in these isolated ecosystems.

    PHOTO: GREG BALFOUR EVANS/ALAMY STOCK PHOTO

    Oceanic islands are among the most recent areas on Earth to have been colonized by humans, in many cases in just the past few thousand years. Therefore, they are important laboratories for the study of human impacts on natural vegetation and biodiversity. Nogué et al. provide a quantitative palaeoecological study of 27 islands around the world, focusing on pollen records of vegetation composition before and after human arrival. The authors found a consistent pattern of acceleration of vegetation turnover after human invasion, with median rates of change increasing by a factor of six. These changes occurred regardless of geographical and ecological features of the island and show how rapidly ecosystems can change and how island ecosystems are set on new trajectories.

    Science, this issue p. 488

  2. Induced Seismicity

    Varying the stop lights

    1. Brent Grocholski

    Traffic light protocols can help to mitigate induced earthquakes from unconventional oil production. However, they are not geographically tuned to account for how shaking may actually translate to structural damage. Schultz et al. incorporated damage tolerance into a traffic light protocol for the Eagle Ford shale play. They found that shut-off may be necessary more quickly in populated regions, whereas sparsely populated areas of the play can take up to a magnitude 5 earthquake without issue. This risk-based strategy provides a more nuanced approach to regulating induced seismicity.

    Science, this issue p. 504

  3. Paleoecology

    Pre-Columbian reforestation in Amazonia

    1. Andrew M. Sugden

    An early 17th-century temporary reduction in global atmospheric carbon dioxide (CO2) levels has now been attributed to reforestation in Amazonia after the catastrophic loss of life of the indigenous population caused by diseases brought by European invaders. Using fossil pollen data from Amazonian lake sediments with temporal resolution over the past millennium, Bush et al. found that forest recovery began 300 to 600 years before the population crash. The more recent nadir in atmospheric CO2 was not associated with rapid reforestation at that time. The vegetation changes appear to be the result of changing patterns of land use in the centuries preceding the European arrival and the resulting devastation, whereas the cause of the CO2 decline remains enigmatic.

    Science, this issue p. 484

  4. Multiferroics

    An optically active spiral

    1. Jelena Stajic

    The material cupric oxide exhibits magnetoelectric coupling, meaning that its magnetic properties can be controlled by electric fields. In its spin spiral phase, cupric oxide has a spiral magnetic ordering that can be right- or left-handed. Masuda et al. used electric fields to create purely left- or right-handed samples and then studied their optical activity. The samples exhibited natural optical activity, which the researchers were then able to control with electric fields.

    Science, this issue p. 496

  5. Nanofluidics

    Gated ion flow in graphene oxide membranes

    1. Marc S. Lavine

    Cells are adept at fast, gated ion flow through tailored channels, which is key to many biological processes. Xue et al. developed ion transistors from reduced graphene oxide membranes and observed a field-enhanced diffusivity of the ions (see the Perspective by Hinds). By applying electrical gating, the average surface potential on the graphene layer could be controlled, thus altering the energy barrier for ion intercalation into the channel and leading to very high diffusion rates. The authors observed selective ion transport two orders of magnitude faster than the ion diffusion in bulk water.

    Science, this issue p. 501; see also p. 459

  6. Acute Lung Injury

    ROS-mediated lung protection

    1. Mattia Maroso

    Neutrophils accumulate in the lung after acute lung injury (ALI) and play a role in the innate immune response through multiple mechanisms, including the production of reactive oxygen species (ROS). Yuan et al. investigated the mechanisms regulating ROS production during ALI and developed a therapeutic intervention. The authors found that the kinases MAP3K2 and MAP3K3 inhibited ROS production from neutrophils. Pazopanib, a specific MAP3K2/3 inhibitor, ameliorated ALI in mice by modulating phosphorylation of p47, a subunit of the NADPH oxidase 2 complex. This treatment was effective in reducing pulmonary edema in a pilot study in patients who underwent lung transplantation.

    Sci. Transl. Med. 13, eabc2499 (2021).

  7. Ecosystem Engineers

    Digging for water

    1. Sacha Vignieri

    Horses and donkeys dig shallow wells that are used by many species.

    IMAGE: PETRA KACZENSKY

    Water is scarce in dryland ecosystems. Some larger animals in these regions dig wells that may provide water to other species. This behavior may have been common among megafauna that are now extinct, especially in North and South America, where megafaunal extinctions were the most severe. Lundgren et al. tested whether feral equids (horses and donkeys) reintroduced to desert regions in the North American southwest dig wells that provide ecosystem-level benefits. They found that equid-dug wells increased water availability, were used by a large number of species, and decreased distance between water sources. Abandoned wells also led to increased germination in key riparian tree species. Such equid-dug wells improve water availability, perhaps replacing a lost megafaunal function.

    Science, this issue p. 491

  8. Immunology

    Putting DCs into overdrive

    1. Leslie K. Ferrarelli

    When dendritic cells (DCs) detect signals indicative of infection, cell death, or cancer, they respond by activating a signaling complex known as the inflammasome, which results in proinflammatory cytokine secretion but usually leads to the death of the DCs. By analyzing human primary DCs from the blood, spleen, and bone marrow, Hatscher et al. found that type 2 conventional DCs, in an unusual turn, did not die after inflammasome-induced cytokine secretion. Instead, these cells entered a hyperactive state that elicited more effective responses from certain T helper cell subsets.

    Sci. Signal. 14, eabe1757 (2021).

  9. Microbiology

    The gut microbiota in industrialization

    1. Gemma Alderton

    The gut microbiota has evolved with humans to perform important functions that contribute to human health. However, this community of microbes has changed with industrialization and exposure to factors that affect composition, such as processed foods and antibiotics. Growing awareness of these changes has prompted proposals to restore the gut microbiota to preindustrialized states to reduce the burden of noncommunicable disease. In a Perspective, Carmody et al. discuss why this approach requires more consideration of gut microbial evolution with industrialization. For example, it remains unknown whether changes in the gut microbiota reflect adaptation to industrial lifestyles; if so, then “rewilding” may be problematic or ineffective. The authors argue that we need a better understanding of what defines a health-promoting gut microbiota that is matched to the lifestyle and environment of industrialized people.

    Science, this issue p. 462

  10. Transcription

    Assembling for transcription initiation

    1. Di Jiang

    Eukaryotic transcription initiation by RNA polymerase II (Pol II) requires the assembly of a preinitiation complex (PIC) on core promoters. The binding of TATA box–binding protein (TBP) to the TATA box promoter has been thought to be a general rule in PIC assembly and transcription initiation. However, most coding genes lack a TATA box, and nearly all Pol II–mediated gene transcription requires the TBP-containing multisubunit complex transcription factor IID (TFIID). Chen et al. determined the structures of human TFIID-based PIC in sequential assembly states and revealed that TFIID supports distinct PIC assembly on TATA-containing and TATA-lacking promoters. The finding resolves the long-standing mystery of how one set of general transcription machinery initiates transcription on diverse promoters.

    Science, this issue p. eaba8490

  11. Plant Science

    The daily rhythms of agriculture

    1. Pamela J. Hines

    Sunlight drives agriculture, and plant circadian rhythms tune the plant's response to daily light-dark cycles. Steed et al. discuss how agricultural productivity might be improved by consideration of how the plant's circadian rhythm alters plant responses to the challenges posed by its environment.

    Science, this issue p. eabc9141

  12. CRISPR

    Small RNAs guard CRISPR-Cas

    1. Di Jiang

    The microbial adaptive immunity system CRISPR-Cas benefits microbes by warding off genetic invaders, but it also inflicts a fitness cost because of occasional autoimmune reactions, rendering CRISPR loci evolutionarily unstable. Li et al. identified previously unnoticed toxin-antitoxin RNA pairs embedded within diverse CRISPR-Cas loci. The antitoxin RNA mimics a CRISPR RNA and repurposes the CRISPR immunity effector to transcriptionally repress a toxin RNA that would otherwise arrest cell growth by sequestering a rare transfer RNA. These small RNAs thus form a symbiosis with CRISPR, rendering CRISPR addictive to the host despite its fitness cost. These findings reveal how CRISPR-Cas can operate as a selfish genetic element.

    Science, this issue p. eabe5601

  13. Vaccines

    Viral peptide is key to T cell priming

    1. Seth Thomas Scanlon

    Simian immunodeficiency virus (SIV) vaccines containing a strain 68-1 rhesus cytomegalovirus (RhCMV) vector elicit strong CD8+ T cell responses that can control and clear SIV infections. The SIV peptides targeted by these T cells are presented on major histocompatibility complex (MHC) II and the nonclassical MHC-Ib molecule MHC-E rather than the more typical MHC-Ia. Verweij et al. show that the 68-1 RhCMV–encoded peptide VL9 drives intracellular transport of MHC-E and recognition of RhCMV-infected targets by MHC-E–restricted CD8+ T cells. Rhesus macaques vaccinated with a mutant 68-1 RhCMV lacking VL9 showed no priming of MHC-E–restricted CD8+ T cells and no protection against SIV. This work strongly suggests that future effective CMV-based HIV vaccines in humans will also require MHC-E–restricted CD8+ T cell priming.

    Science, this issue p. eabe9233

  14. Pathogen Evolution

    Jump starting pathogen evolution

    1. Caroline Ash

    Mycobacteria are mostly environmental saprotrophs, but during human history, some have become our pathogens. In the past 50 years or so, intractable and virulent infections of Mycobacterium abscessus have emerged in people with cystic fibrosis. Bryant et al. investigated how these mycobacteria have evolved into human pathogens so quickly (see the Perspective by Brugha and Spencer). Chronic infections in the lung offer plenty of evolutionary scope for the emergence of virulent clones after horizontal gene transfer and hypermutation. Pathogens are acquired by environmental contamination, which leaves open a window for clinical control because the most virulent clones survive poorly outside the body. Therefore, immediate treatment and enhanced infection-control measures for M. abscessus cases could reduce opportunities for the evolution of direct person-to-person transmission.

    Science, this issue p. eabb8699; see also p. 465

  15. Quantum Computing

    Move aside, aluminum

    1. Jelena Stajic

    Some of the most promising schemes for quantum information processing involve superconductors. In addition to the established superconducting qubits, topological qubits may one day be realized in semiconductor-superconductor heterostructures. The superconductor most widely used in this context is aluminum, in which processes that cause decoherence are suppressed. Pendharkar et al. go beyond this paradigm to show that superconducting tin can be used in place of aluminum (see the Perspective by Fatemi and Devoret). The authors grew nanowires of indium antimonide, which is a semiconductor, and coated them with a thin layer of tin without using cumbersome epitaxial growth techniques. This process creates a well-defined, “hard” superconducting gap in the nanowires, which is a prerequisite for using them as the basis for a potential topological qubit.

    Science, this issue p. 508; see also p. 464

  16. Noncanonical Genome

    Biosynthesis and replication, from A to Z

    1. Di Jiang

    Four nucleobases. adenine (A), cytosine (C), guanine (G), and thymine (T), are usually thought to be invariable in DNA. In bacterial viruses, however, each of the DNA bases have variations that help them to escape degradation by bacterial restriction enzymes. In the genome of cyanophage S-2L, A is completely replaced by diaminopurine (Z), which forms three hydrogen bonds with T and thus creates non–Watson-Crick base pairing in the DNA of this virus (see the Perspective by Grome and Isaacs). Zhou et al. and Sleiman et al. determined the biochemical pathway that produces Z, which revealed more Z genomes in viruses hosted in bacteria distributed widely in the environment and phylogeny. Pezo et al. identified a DNA polymerase that incorporates Z into DNA while rejecting A. These findings enrich our understanding of biodiversity and expand the genetic palette for synthetic biology.

    Science, this issue p. 512, 516, 520; see also p. 460

  17. T Cells

    Early emergence

    1. Christiana N. Fogg

    γδ T cells are an innate-like subset of T cells that can recognize and respond to microbes. Tan et al. studied the activation and differentiation of γδ T cells to better understand their development and persistence. They used single-cell RNA sequencing and paired γδ T cell receptor (TCR) analysis from neonatal cord blood or adult peripheral blood, and observed a high level of heterogeneity that correlated with TCR usage in immature and differentiated γδ T cell clusters. The authors detected type 1– and type 3–like Vγ9Vδ2+ T cell subsets with distinct sets of TCR clonotypes. Similar type 3 Vγ9Vδ2+ T cells were found in neonatal cord blood and the early fetal thymus, suggesting that these cells emerge early in fetal development and can persist into adulthood.

    Sci. Immunol. 6, eabf0125 (2021).

  18. Coronavirus

    How an early variant got ahead

    1. Valda Vinson

    Throughout the COVID-19 pandemic, epidemiologists have monitored the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with particular focus on the spike protein. An early variant with an aspartic acid (D) to glycine (G) mutation at position 614, D614G, rapidly became dominant and is maintained in current variants of concern. Zhang et al. investigated the structural basis for the increased spread of this variant, which does so even though it binds less tightly to the host receptor (see the Perspective by Choe and Farzan). Structural and biochemical studies on a full-length G614 spike trimer showed that there are interactions not present in D614 that prevent premature loss of the S1 subunit that binds angiotensin-converting enzyme 2. This stabilization effectively increases the number of spikes that can facilitate infection.

    Science, this issue p. 525; see also p. 466

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