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  • A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-16
    Mihajlo Novakovic, Gregory L. Olsen, György Pintér, Daniel Hymon, Boris Fürtig, Harald Schwalbe, Lucio Frydman

    NMR sensitivity-enhancement methods involving hyperpolarized water could be of importance for solution-state biophysical investigations. Hyperpolarized water (HyperW) can enhance the 1H NMR signals of exchangeable sites by orders of magnitude over their thermal counterparts, while providing insight into chemical exchange and solvent accessibility at a site-resolved level. As HyperW’s enhancements are achieved by exploiting fast solvent exchanges associated with minimal interscan delays, possibilities for the rapid monitoring of chemical reactions and biomolecular (re)folding are opened. HyperW NMR can also accommodate heteronuclear transfers, facilitating the rapid acquisition of 2-dimensional (2D) 15N-1H NMR correlations, and thereby combining an enhanced spectral resolution with speed and sensitivity. This work demonstrates how these qualities can come together for the study of nucleic acids. HyperW injections were used to target the guanine-sensing riboswitch aptamer domain (GSRapt) of the xpt-pbuX operon in Bacillus subtilis. Unlike what had been observed in proteins, where residues benefited of HyperW NMR only if/when sufficiently exposed to water, these enhancements applied to every imino resonance throughout the RNA. The >300-fold enhancements observed in the resulting 1H NMR spectra allowed us to monitor in real time the changes that GSRapt undergoes upon binding hypoxanthine, a high-affinity interaction leading to conformational refolding on a ∼1-s timescale at 36 °C. Structural responses could be identified for several nucleotides by 1-dimensional (1D) imino 1H NMR as well as by 2D HyperW NMR spectra acquired upon simultaneous injection of hyperpolarized water and hypoxanthine. The folding landscape revealed by this HyperW strategy for GSRapt, is briefly discussed.

    更新日期:2020-01-17
  • Hepatic neddylation targets and stabilizes electron transfer flavoproteins to facilitate fatty acid {beta}-oxidation [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-15
    Xueying Zhang, Yao-Lin Zhang, Guihua Qiu, Lili Pian, Lu Guo, Huanling Cao, Jian Liu, Yawei Zhao, Xin Li, Zhe Xu, Xiaofeng Huang, Jingru Huang, Jie Dong, Beifen Shen, Hong-Xia Wang, Xiaomin Ying, Weiping J. Zhang, Xuetao Cao, Jiyan Zhang

    Neddylation is a ubiquitination-like pathway that controls cell survival and proliferation by covalently conjugating NEDD8 to lysines in specific substrate proteins. However, the physiological role of neddylation in mammalian metabolism remains elusive, and no mitochondrial targets have been identified. Here, we report that mouse models with liver-specific deficiency of NEDD8 or ubiquitin-like modifier activating enzyme 3 (UBA3), the catalytic subunit of the NEDD8-activating enzyme, exhibit neonatal death with spontaneous fatty liver as well as hepatic cellular senescence. In particular, liver-specific UBA3 deficiency leads to systemic abnormalities similar to glutaric aciduria type II (GA-II), a rare autosomal recessive inherited fatty acid oxidation disorder resulting from defects in mitochondrial electron transfer flavoproteins (ETFs: ETFA and ETFB) or the corresponding ubiquinone oxidoreductase. Neddylation inhibition by various strategies results in decreased protein levels of ETFs in neonatal livers and embryonic hepatocytes. Hepatic neddylation also enhances ETF expression in adult mice and prevents fasting-induced steatosis and mortality. Interestingly, neddylation is active in hepatic mitochondria. ETFs are neddylation substrates, and neddylation stabilizes ETFs by inhibiting their ubiquitination and degradation. Moreover, certain mutations of ETFs found in GA-II patients hinder the neddylation of these substrates. Taken together, our results reveal substrates for neddylation and add insight into GA-II.

    更新日期:2020-01-16
  • Opioid system is necessary but not sufficient for antidepressive actions of ketamine in rodents [Neuroscience]
    PNAS (IF 9.580) Pub Date : 2020-01-15
    Matthew E. Klein, Joshua Chandra, Salma Sheriff, Roberto Malinow

    Slow response to the standard treatment for depression increases suffering and risk of suicide. Ketamine, an N-methyl-d-aspartate (NMDA) receptor antagonist, can rapidly alleviate depressive symptoms and reduce suicidality, possibly by decreasing hyperactivity in the lateral habenula (LHb) brain nucleus. Here we find that in a rat model of human depression, opioid antagonists abolish the ability of ketamine to reduce the depression-like behavioral and LHb hyperactive cellular phenotypes. However, activation of opiate receptors alone is not sufficient to produce ketamine-like effects, nor does ketamine mimic the hedonic effects of an opiate, indicating that the opioid system does not mediate the actions of ketamine but rather is permissive. Thus, ketamine does not act as an opiate but its effects require both NMDA and opiate receptor signaling, suggesting that interactions between these two neurotransmitter systems are necessary to achieve an antidepressant effect.

    更新日期:2020-01-16
  • Near-infrared optogenetic engineering of photothermal nanoCRISPR for programmable genome editing [Applied Biological Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-15
    Xiaohong Chen, Yuxuan Chen, Huhu Xin, Tao Wan, Yuan Ping

    We herein report an optogenetically activatable CRISPR-Cas9 nanosystem for programmable genome editing in the second near-infrared (NIR-II) optical window. The nanosystem, termed nanoCRISPR, is composed of a cationic polymer-coated Au nanorod (APC) and Cas9 plasmid driven by a heat-inducible promoter. The APC not only serves as a carrier for intracellular plasmid delivery but also can harvest external NIR-II photonic energy and convert it into local heat to induce the gene expression of the Cas9 endonuclease. Due to high transfection activity, the APC shows strong ability to induce a significant level of disruption in different genomic loci upon optogenetic activation. Moreover, the precise control of genome-editing activity can be simply programmed by finely tuning exposure time and irradiation time in vitro and in vivo and also enables editing at multiple time points, thus proving the sensitivity and inducibility of such an editing modality. The NIR-II optical feature of nanoCRISPR enables therapeutic genome editing at deep tissue, by which treatment of deep tumor and rescue of fulminant hepatic failure are demonstrated as proof-of-concept therapeutic examples. Importantly, this modality of optogenetic genome editing can significantly minimize the off-target effect of CRISPR-Cas9 in most potential off-target sites. The optogenetically activatable CRISPR-Cas9 nanosystem we have developed offers a useful tool to expand the current applications of CRISPR-Cas9, and also defines a programmable genome-editing strategy toward high precision and spatial specificity.

    更新日期:2020-01-16
  • Algal photosynthesis converts nitric oxide into nitrous oxide [Plant Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-15
    Adrien Burlacot, Pierre Richaud, Arthur Gosset, Yonghua Li-Beisson, Gilles Peltier

    Nitrous oxide (N2O), a potent greenhouse gas in the atmosphere, is produced mostly from aquatic ecosystems, to which algae substantially contribute. However, mechanisms of N2O production by photosynthetic organisms are poorly described. Here we show that the green microalga Chlamydomonas reinhardtii reduces NO into N2O using the photosynthetic electron transport. Through the study of C. reinhardtii mutants deficient in flavodiiron proteins (FLVs) or in a cytochrome p450 (CYP55), we show that FLVs contribute to NO reduction in the light, while CYP55 operates in the dark. Both pathways are active when NO is produced in vivo during the reduction of nitrites and participate in NO homeostasis. Furthermore, NO reduction by both pathways is restricted to chlorophytes, organisms particularly abundant in ocean N2O-producing hot spots. Our results provide a mechanistic understanding of N2O production in eukaryotic phototrophs and represent an important step toward a comprehensive assessment of greenhouse gas emission by aquatic ecosystems.

    更新日期:2020-01-16
  • Nanoscopy through a plasmonic nanolens [Applied Physical Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-15
    Matthew J. Horton, Oluwafemi S. Ojambati, Rohit Chikkaraddy, William M. Deacon, Nuttawut Kongsuwan, Angela Demetriadou, Ortwin Hess, Jeremy J. Baumberg

    Plasmonics now delivers sensors capable of detecting single molecules. The emission enhancements and nanometer-scale optical confinement achieved by these metallic nanostructures vastly increase spectroscopic sensitivity, enabling real-time tracking. However, the interaction of light with such nanostructures typically loses all information about the spatial location of molecules within a plasmonic hot spot. Here, we show that ultrathin plasmonic nanogaps support complete mode sets which strongly influence the far-field emission patterns of embedded emitters and allow the reconstruction of dipole positions with 1-nm precision. Emitters in different locations radiate spots, rings, and askew halo images, arising from interference of 2 radiating antenna modes differently coupling light out of the nanogap, highlighting the imaging potential of these plasmonic “crystal balls.” Emitters at the center are now found to live indefinitely, because they radiate so rapidly.

    更新日期:2020-01-16
  • Correction for Heeger and Mackey, Oscillatory recurrent gated neural integrator circuits (ORGaNICs), a unifying theoretical framework for neural dynamics [Correction]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    National Academy of Sciences

    NEUROSCIENCE, PSYCHOLOGICAL AND COGNITIVE SCIENCES Correction for “Oscillatory recurrent gated neural integrator circuits (ORGaNICs), a unifying theoretical framework for neural dynamics,” by David J. Heeger and Wayne E. …

    更新日期:2020-01-15
  • The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13 [Developmental Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Maria Félix Bastida, Rocío Pérez-Gómez, Anna Trofka, Jianjian Zhu, Alvaro Rada-Iglesias, Rushikesh Sheth, H. Scott Stadler, Susan Mackem, Marian A. Ros

    In the tetrapod limb, the digits (fingers or toes) are the elements most subject to morphological diversification in response to functional adaptations. However, despite their functional importance, the mechanisms controlling digit morphology remain poorly understood. Here we have focused on understanding the special morphology of the thumb (digit 1), the acquisition of which was an important adaptation of the human hand. To this end, we have studied the limbs of the Hoxa13 mouse mutant that specifically fail to form digit 1. We show that, consistent with the role of Hoxa13 in Hoxd transcriptional regulation, the expression of Hoxd13 in Hoxa13 mutant limbs does not extend into the presumptive digit 1 territory, which is therefore devoid of distal Hox transcripts, a circumstance that can explain its agenesis. The loss of Hoxd13 expression, exclusively in digit 1 territory, correlates with increased Gli3 repressor activity, a Hoxd negative regulator, resulting from increased Gli3 transcription that, in turn, is due to the release from the negative modulation exerted by Hox13 paralogs on Gli3 regulatory sequences. Our results indicate that Hoxa13 acts hierarchically to initiate the formation of digit 1 by reducing Gli3 transcription and by enabling expansion of the 5′Hoxd second expression phase, thereby establishing anterior−posterior asymmetry in the handplate. Our work uncovers a mutual antagonism between Gli3 and Hox13 paralogs that has important implications for Hox and Gli3 gene regulation in the context of development and evolution.

    更新日期:2020-01-15
  • Science and Culture: How a conference focused on algorithms balances serious math with computational whimsy [Computer Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Stephen Ornes

    In 1998, a few dozen computer scientists and mathematicians gathered at a picturesque seaside resort on the Tuscan island of Elba off the west coast of Italy. They were there to attend a scientific gathering unlike any other.

    更新日期:2020-01-15
  • Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di-heptamer macromolecular assembly [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Xingjian Xu, Raquel Godoy-Ruiz, Kaylin A. Adipietro, Christopher Peralta, Danya Ben-Hail, Kristen M. Varney, Mary E. Cook, Braden M. Roth, Paul T. Wilder, Thomas Cleveland, Alexander Grishaev, Heather M. Neu, Sarah L. J. Michel, Wenbo Yu, Dorothy Beckett, Richard R. Rustandi, Catherine Lancaster, John W. Loughney, Adam Kristopeit, Sianny Christanti, Jessica W. Olson, Alexander D. MacKerell, Amedee des Georges, Edwin Pozharski, David J. Weber

    Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single-particle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including a symmetric (SymCDTb; 3.14 Å) and an asymmetric form (AsymCDTb; 2.84 Å). Roles played by 2 receptor-binding domains of activated CDTb were of particular interest since the receptor-binding domain 1 lacks sequence homology to any other known toxin, and the receptor-binding domain 2 is completely absent in other well-studied heptameric toxins (i.e., anthrax). For AsymCDTb, a Ca2+ binding site was discovered in the first receptor-binding domain that is important for its stability, and the second receptor-binding domain was found to be critical for host cell toxicity and the di-heptamer fold for both forms of activated CDTb. Together, these studies represent a starting point for developing structure-based drug-design strategies to target the most severe strains of C. difficile.

    更新日期:2020-01-15
  • Profile of James Peebles, Michel Mayor, and Didier Queloz: 2019 Nobel Laureates in Physics [Profiles]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Neta A. Bahcall, Adam Burrows

    Mankind has long been fascinated by the mysteries of our Universe: How old and how big is the Universe? How did the Universe begin and how is it evolving? What is the composition of the Universe and the nature of its dark matter and dark energy? What is our Earth’s place in the cosmos and are there other planets (and life) around other stars?

    更新日期:2020-01-15
  • In This Issue
    PNAS (IF 9.580) Pub Date : 2020-01-14
    National Academy of Sciences

    Music influences rhythmic movement in humans, suggesting a link between the brain’s auditory and motor areas. Understanding chimpanzees’ predisposition to process music could shed light on the evolutionary origins of humans’ response to music. Yuko Hattori and Masaki Tomonaga (pp. 936–942) examined how music affects rhythmic movement, or repetitive movement of the entire body or body parts, in 7 chimpanzees who listened to 6 2-minute piano sounds with different tempos for 6 days. In response to an auditory stimulus, the chimpanzees often swayed and sometimes made rhythmic hand clapping and foot tapping. Compared with female chimpanzees, male chimpanzees were more likely to respond to sound with vocalization and sway rhythmically for longer durations. A separate experiment focused on the chimpanzee most responsive to the auditory stimuli. The chimpanzee was exposed to 4 2-minute sound sessions for 24 days. Both random and regular beats induced rhythmic swaying in the chimpanzee, and beat tempo affected the chimpanzee in a bipedal but …

    更新日期:2020-01-15
  • Further wet-taro evidence from Polynesia’s southernmost Neolithic production margins [Letters (Online Only)]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Ian G. Barber

    For Prebble et al. (1), the cultivation of introduced semiaquatic tropical taro (Colocasia esculenta) on cooler southern Pacific islands during the Polynesian “initial colonization period” (ICP) (1200 to 1500 CE) represents a “striking” Neolithic example of nonoptimal, marginal crop production. In that respect, ICP taro pollen from Ahuahu, a warm-temperate, northern New Zealand (NZ) offshore island, is especially notable (1). However, the suggestion that NZ wet-taro cultivation “may have been confined” to such offshore islands (ref. 1, p. 8828) overlooks important mainland archaeological evidence (Fig. 1).

    更新日期:2020-01-15
  • Reply to Barber: Marginal evidence for taro production in northern New Zealand between 1200 and 1500 CE [Letters (Online Only)]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Matthew Prebble, Atholl J. Anderson, Paul Augustinus, Joshua Emmitt, Stewart J. Fallon, Louise L. Furey, Simon J. Holdaway, Alex Jorgensen, Thegn N. Ladefoged, Peter J. Matthews, Jean-Yves Meyer, Rebecca Phillipps, Rod Wallace, Nicholas Porch

    We welcome Barber’s (1) comments and are grateful for the opportunity to respond. Our study of wetland taro (Colocasia esculenta) gardens during the initial colonization period (ICP) (1200 to 1500 CE) in New Zealand did not overlook the evidence from the Aupouri Peninsula (2–4). We agree that gardens were probably...

    更新日期:2020-01-15
  • Predicting high-risk opioid prescriptions before they are given [Economic Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Justine S. Hastings, Mark Howison, Sarah E. Inman

    Misuse of prescription opioids is a leading cause of premature death in the United States. We use state government administrative data and machine learning methods to examine whether the risk of future opioid dependence, abuse, or poisoning can be predicted in advance of an initial opioid prescription. Our models accurately predict these outcomes and identify particular prior nonopioid prescriptions, medical history, incarceration, and demographics as strong predictors. Using our estimates, we simulate a hypothetical policy which restricts new opioid prescriptions to only those with low predicted risk. The policy’s potential benefits likely outweigh costs across demographic subgroups, even for lenient definitions of “high risk.” Our findings suggest new avenues for prevention using state administrative data, which could aid providers in making better, data-informed decisions when weighing the medical benefits of opioid therapy against the risks.

    更新日期:2020-01-15
  • Predicting research trends with semantic and neural networks with an application in quantum physics [Physics]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Mario Krenn, Anton Zeilinger

    The vast and growing number of publications in all disciplines of science cannot be comprehended by a single human researcher. As a consequence, researchers have to specialize in narrow subdisciplines, which makes it challenging to uncover scientific connections beyond the own field of research. Thus, access to structured knowledge from a large corpus of publications could help push the frontiers of science. Here, we demonstrate a method to build a semantic network from published scientific literature, which we call SemNet. We use SemNet to predict future trends in research and to inspire personalized and surprising seeds of ideas in science. We apply it in the discipline of quantum physics, which has seen an unprecedented growth of activity in recent years. In SemNet, scientific knowledge is represented as an evolving network using the content of 750,000 scientific papers published since 1919. The nodes of the network correspond to physical concepts, and links between two nodes are drawn when two concepts are concurrently studied in research articles. We identify influential and prize-winning research topics from the past inside SemNet, thus confirming that it stores useful semantic knowledge. We train a neural network using states of SemNet of the past to predict future developments in quantum physics and confirm high-quality predictions using historic data. Using network theoretical tools, we can suggest personalized, out-of-the-box ideas by identifying pairs of concepts, which have unique and extremal semantic network properties. Finally, we consider possible future developments and implications of our findings.

    更新日期:2020-01-15
  • Apex structures enhance water drainage on leaves [Applied Biological Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Ting Wang, Yifan Si, Haoyu Dai, Chuxin Li, Can Gao, Zhichao Dong, Lei Jiang

    The rapid removal of rain droplets at the leaf apex is critical for leaves to avoid damage under rainfall conditions, but the general water drainage principle remains unclear. We demonstrate that the apex structure enhances water drainage on the leaf by employing a curvature-controlled mechanism that is based on shaping a balance between reduced capillarity and enhanced gravity components. The leaf apex shape changes from round to triangle to acuminate, and the leaf surface changes from flat to bent, resulting in the increase of the water drainage rate, high-dripping frequencies, and the reduction of retention volumes. For wet tropical plants, such as Alocasia macrorrhiza, Gaussian curvature reconfiguration at the drip tip leads to the capillarity transition from resistance to actuation, further enhancing water drainage to the largest degree possible. The phenomenon is distinct from the widely researched liquid motion control mechanisms, and it offers a specific parametric approach that can be applied to achieve the desired fluidic behavior in a well-controlled way.

    更新日期:2020-01-15
  • Global trends toward urban street-network sprawl [Sustainability Science]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Christopher Barrington-Leigh, Adam Millard-Ball

    We present a global time series of street-network sprawl—that is, sprawl as measured through the local connectivity of the street network. Using high-resolution data from OpenStreetMap and a satellite-derived time series of urbanization, we compute and validate changes over time in multidimensional street connectivity measures based on graph-theoretic and geographic concepts. We report on global, national, and city-level trends since 1975 in the street-network disconnectedness index (SNDi), based on every mapped node and edge in the world. Streets in new developments in 90% of the 134 most populous countries have become less connected since 1975, while just 29% show an improving trend since 2000. The same period saw a near doubling in the relative frequency of a street-network type characterized by high circuity, typical of gated communities. We identify persistence in street-network sprawl, indicative of path-dependent processes. Specifically, cities and countries with low connectivity in recent years also had relatively low preexisting connectivity in our earliest time period. We discuss implications for policy intervention in road building in new and expanding cities as a top priority for sustainable urban development.

    更新日期:2020-01-15
  • Enhancing transport by shaping barriers [Commentaries]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Max Innerbichler, Christoph Dellago

    Many molecular processes of great importance in both nature and technology speed up strongly if temperature is increased. Examples include chemical reactions, biomolecular rearrangements, the diffusion of atoms in solids, and the storage of information on magnetic recording media. In 1889, the Swedish physicist and chemist Svante Arrhenius was the first to give a physical explanation and mathematical description of this phenomenon in the form of the celebrated Arrhenius equation (1). Building on earlier work of the Dutch physical chemist Jacobus Henricus van ’t Hoff, Arrhenius had realized that the particular form of the temperature dependence of reaction rate constants can be understood by assuming that the reaction from reactants to products involves passage through an activated state. As this activated state has a higher energy than the reactants, the reaction must cross an energy barrier and this happens only with assistance from thermal fluctuations of the environment. At higher temperatures, such fluctuations are more intense on average, making it easier for the system to overcome the barrier such that the reaction occurs with higher frequency. At low temperatures, on the other hand, thermal fluctuations of sufficient magnitude become rarer, leading to small reaction rate constants.

    更新日期:2020-01-15
  • CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Elena M. Pugacheva, Naoki Kubo, Dmitri Loukinov, Md Tajmul, Sungyun Kang, Alexander L. Kovalchuk, Alexander V. Strunnikov, Gabriel E. Zentner, Bing Ren, Victor V. Lobanenkov

    The DNA-binding protein CCCTC-binding factor (CTCF) and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. Here, we demonstrate that a 79-aa region within the CTCF N terminus is essential for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N terminus of CTCF fused to artificial zinc fingers was not sufficient to redirect cohesin to non-CTCF binding sites, indicating a lack of an autonomously functioning domain in CTCF responsible for cohesin positioning. BORIS (CTCFL), a germline-specific paralog of CTCF, was unable to anchor cohesin to CTCF DNA binding sites. Furthermore, CTCF–BORIS chimeric constructs provided evidence that, besides the N terminus of CTCF, the first two CTCF zinc fingers, and likely the 3D geometry of CTCF–DNA complexes, are also involved in cohesin retention. Based on this knowledge, we were able to convert BORIS into CTCF with respect to cohesin positioning, thus providing additional molecular details of the ability of CTCF to retain cohesin. Taken together, our data provide insight into the process by which DNA-bound CTCF constrains cohesin movement to shape spatiotemporal genome organization.

    更新日期:2020-01-15
  • Shoot meristem maintenance and immune response signaling converge at the G protein {beta} subunit [Commentaries]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Kevin Rodriguez, G. Venugopala Reddy

    The shoot apical meristem (SAM) harbors a set of pluripotent stem cells that divide continuously to provide cells for the development of all aboveground plant parts (1). A concoction of hormonal and peptide signals and transcription factors, along with mechanical cues, play a role in stem cell maintenance, which requires a delicate balance between cell proliferation rates and rates of differentiation of stem cell daughters (1). The current challenge is to decipher how these signals come together to regulate stem cell maintenance, which requires the functional characterization of regulators in signaling pathways. The same regulators are often utilized for signaling in different contexts, such as development and disease, further complicating the analysis. The study by Wu et al. (2) reveals a role for the G protein β subunit (Gβ) in negatively regulating maize SAM size through the isolation of new alleles that uncouple its function in meristem development and disease resistance.

    更新日期:2020-01-15
  • Brain-wide functional architecture remodeling by alcohol dependence and abstinence [Neuroscience]
    PNAS (IF 9.580) Pub Date : 2020-01-14
    Adam Kimbrough, Daniel J. Lurie, Andres Collazo, Max Kreifeldt, Harpreet Sidhu, Giovana Camila Macedo, Mark D’Esposito, Candice Contet, Olivier George

    Alcohol abuse and alcohol dependence are key factors in the development of alcohol use disorder, which is a pervasive societal problem with substantial economic, medical, and psychiatric consequences. Although our understanding of the neurocircuitry that underlies alcohol use has improved, novel brain regions that are involved in alcohol use and novel biomarkers of alcohol use need to be identified. The present study used a single-cell whole-brain imaging approach to 1) assess whether abstinence from alcohol in an animal model of alcohol dependence alters the functional architecture of brain activity and modularity, 2) validate our current knowledge of the neurocircuitry of alcohol abstinence, and 3) discover brain regions that may be involved in alcohol use. Alcohol abstinence resulted in the whole-brain reorganization of functional architecture in mice and a pronounced decrease in modularity that was not observed in nondependent moderate drinkers. Structuring of the alcohol abstinence network revealed three major brain modules: 1) extended amygdala module, 2) midbrain striatal module, and 3) cortico-hippocampo-thalamic module, reminiscent of the three-stage theory. Many hub brain regions that control this network were identified, including several that have been previously overlooked in alcohol research. These results identify brain targets for future research and demonstrate that alcohol use and dependence remodel brain-wide functional architecture to decrease modularity. Further studies are needed to determine whether the changes in coactivation and modularity that are associated with alcohol abstinence are causal features of alcohol dependence or a consequence of excessive drinking and alcohol exposure.

    更新日期:2020-01-15
  • Correction for Perkins, Core Concept: Albedo is a simple concept that plays complicated roles in climate and astronomy [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    National Academy of Sciences

    CORE CONCEPTS Correction for “Core Concept: Albedo is a simple concept that plays complicated roles in climate and …

    更新日期:2020-01-14
  • Correction for Mann, Core Concept: To improve weather and climate models, researchers are chasing atmospheric gravity waves [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    National Academy of Sciences

    CORE CONCEPTS Correction for “Core Concept: To improve weather and climate models, researchers are chasing atmospheric gravity waves,” by Adam Mann, …

    更新日期:2020-01-14
  • Correction for Gunnar et al., Pubertal stress recalibration reverses the effects of early life stress in postinstitutionalized children [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    National Academy of Sciences

    PSYCHOLOGICAL AND COGNITIVE SCIENCES, PHYSIOLOGY Correction for “Pubertal stress recalibration reverses the effects of early life stress in postinstitutionalized children,” by Megan R. Gunnar, Carrie E. DePasquale, Brie M. Reid, and Bonny Donzella, which was first …

    更新日期:2020-01-14
  • Quantitative detection of iodine in the stratosphere [Environmental Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Theodore K. Koenig, Sunil Baidar, Pedro Campuzano-Jost, Carlos A. Cuevas, Barbara Dix, Rafael P. Fernandez, Hongyu Guo, Samuel R. Hall, Douglas Kinnison, Benjamin A. Nault, Kirk Ullmann, Jose L. Jimenez, Alfonso Saiz-Lopez, Rainer Volkamer

    Oceanic emissions of iodine destroy ozone, modify oxidative capacity, and can form new particles in the troposphere. However, the impact of iodine in the stratosphere is highly uncertain due to the lack of previous quantitative measurements. Here, we report quantitative measurements of iodine monoxide radicals and particulate iodine (Iy,part) from aircraft in the stratosphere. These measurements support that 0.77 ± 0.10 parts per trillion by volume (pptv) total inorganic iodine (Iy) is injected to the stratosphere. These high Iy amounts are indicative of active iodine recycling on ice in the upper troposphere (UT), support the upper end of recent Iy estimates (0 to 0.8 pptv) by the World Meteorological Organization, and are incompatible with zero stratospheric iodine injection. Gas-phase iodine (Iy,gas) in the UT (0.67 ± 0.09 pptv) converts to Iy,part sharply near the tropopause. In the stratosphere, IO radicals remain detectable (0.06 ± 0.03 pptv), indicating persistent Iy,part recycling back to Iy,gas as a result of active multiphase chemistry. At the observed levels, iodine is responsible for 32% of the halogen-induced ozone loss (bromine 40%, chlorine 28%), due primarily to previously unconsidered heterogeneous chemistry. Anthropogenic (pollution) ozone has increased iodine emissions since preindustrial times (ca. factor of 3 since 1950) and could be partly responsible for the continued decrease of ozone in the lower stratosphere. Increasing iodine emissions have implications for ozone radiative forcing and possibly new particle formation near the tropopause.

    更新日期:2020-01-14
  • Polymeric sheet actuators with programmable bioinstructivity [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Zijun Deng, Weiwei Wang, Xun Xu, Oliver E. C. Gould, Karl Kratz, Nan Ma, Andreas Lendlein

    Stem cells are capable of sensing and processing environmental inputs, converting this information to output a specific cell lineage through signaling cascades. Despite the combinatorial nature of mechanical, thermal, and biochemical signals, these stimuli have typically been decoupled and applied independently, requiring continuous regulation by controlling units. We employ a programmable polymer actuator sheet to autonomously synchronize thermal and mechanical signals applied to mesenchymal stem cells (MSCs). Using a grid on its underside, the shape change of polymer sheet, as well as cell morphology, calcium (Ca2+) influx, and focal adhesion assembly, could be visualized and quantified. This paper gives compelling evidence that the temperature sensing and mechanosensing of MSCs are interconnected via intracellular Ca2+. Up-regulated Ca2+ levels lead to a remarkable alteration of histone H3K9 acetylation and activation of osteogenic related genes. The interplay of physical, thermal, and biochemical signaling was utilized to accelerate the cell differentiation toward osteogenic lineage. The approach of programmable bioinstructivity provides a fundamental principle for functional biomaterials exhibiting multifaceted stimuli on differentiation programs. Technological impact is expected in the tissue engineering of periosteum for treating bone defects.

    更新日期:2020-01-14
  • Nociceptin attenuates the escalation of oxycodone self-administration by normalizing CeA-GABA transmission in highly addicted rats [Neuroscience]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Marsida Kallupi, Lieselot L. G. Carrette, Jenni Kononoff, Leah C. Solberg Woods, Abraham A. Palmer, Paul Schweitzer, Olivier George, Giordano de Guglielmo

    Approximately 25% of patients who are prescribed opioids for chronic pain misuse them, and 5 to 10% develop an opioid use disorder. Although the neurobiological target of opioids is well known, the molecular mechanisms that are responsible for the development of addiction-like behaviors in some but not all individuals are poorly known. To address this issue, we used a unique outbred rat population (heterogeneous stock) that better models the behavioral and genetic diversity that is found in humans. We characterized individual differences in addiction-like behaviors using an addiction index that incorporates the key criteria of opioid use disorder: escalated intake, highly motivated responding, and hyperalgesia. Using in vitro electrophysiological recordings in the central nucleus of the amygdala (CeA), we found that rats with high addiction-like behaviors (HA) exhibited a significant increase in γ-aminobutyric acid (GABA) transmission compared with rats with low addiction-like behaviors (LA) and naive rats. The superfusion of CeA slices with nociceptin/orphanin FQ peptide (N/OFQ; 500 nM), an endogenous opioid-like peptide, normalized GABA transmission in HA rats. Intra-CeA levels of N/OFQ were lower in HA rats than in LA rats. Intra-CeA infusions of N/OFQ (1 μg per site) reversed the escalation of oxycodone self-administration in HA rats but not in LA rats. These results demonstrate that the downregulation of N/OFQ levels in the CeA may be responsible for hyper-GABAergic tone in the CeA that is observed in individuals who develop addiction-like behaviors. Based on these results, we hypothesize that small molecules that target the N/OFQ system might be useful for the treatment of opioid use disorder.

    更新日期:2020-01-14
  • Multifeature analyses of vascular cambial cells reveal longevity mechanisms in old Ginkgo biloba trees [Plant Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Li Wang, Jiawen Cui, Biao Jin, Jianguo Zhao, Huimin Xu, Zhaogeng Lu, Weixing Li, Xiaoxia Li, Linling Li, Eryuan Liang, Xiaolan Rao, Shufang Wang, Chunxiang Fu, Fuliang Cao, Richard A. Dixon, Jinxing Lin

    Aging is a universal property of multicellular organisms. Although some tree species can live for centuries or millennia, the molecular and metabolic mechanisms underlying their longevity are unclear. To address this, we investigated age-related changes in the vascular cambium from 15- to 667-y-old Ginkgo biloba trees. The ring width decreased sharply during the first 100 to 200 y, with only a slight change after 200 y of age, accompanied by decreasing numbers of cambial cell layers. In contrast, average basal area increment (BAI) continuously increased with aging, showing that the lateral meristem can retain indeterminacy in old trees. The indole-3-acetic acid (IAA) concentration in cambial cells decreased with age, whereas the content of abscisic acid (ABA) increased significantly. In addition, cell division-, cell expansion-, and differentiation-related genes exhibited significantly lower expression in old trees, especially miR166 and HD-ZIP III interaction networks involved in cambial activity. Disease resistance-associated genes retained high expression in old trees, along with genes associated with synthesis of preformed protective secondary metabolites. Comprehensive evaluation of the expression of genes related to autophagy, senescence, and age-related miRNAs, together with analysis of leaf photosynthetic efficiencies and seed germination rates, demonstrated that the old trees are still in a healthy, mature state, and senescence is not manifested at the whole-plant level. Taken together, our results reveal that long-lived trees have evolved compensatory mechanisms to maintain a balance between growth and aging processes. This involves continued cambial divisions, high expression of resistance-associated genes, and continued synthetic capacity of preformed protective secondary metabolites.

    更新日期:2020-01-14
  • A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo [Microbiology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Evelyn M. Covés-Datson, Steven R. King, Maureen Legendre, Auroni Gupta, Susana M. Chan, Emily Gitlin, Vikram V. Kulkarni, Jezreel Pantaleón García, Donald F. Smee, Elke Lipka, Scott E. Evans, E. Bart Tarbet, Akira Ono, David M. Markovitz

    There is a strong need for a new broad-spectrum antiinfluenza therapeutic, as vaccination and existing treatments are only moderately effective. We previously engineered a lectin, H84T banana lectin (H84T), to retain broad-spectrum activity against multiple influenza strains, including pandemic and avian, while largely eliminating the potentially harmful mitogenicity of the parent compound. The amino acid mutation at position 84 from histidine to threonine minimizes the mitogenicity of the wild-type lectin while maintaining antiinfluenza activity in vitro. We now report that in a lethal mouse model H84T is indeed nonmitogenic, and both early and delayed therapeutic administration of H84T intraperitoneally are highly protective, as is H84T administered subcutaneously. Mechanistically, attachment, which we anticipated to be inhibited by H84T, was only somewhat decreased by the lectin. Instead, H84T is internalized into the late endosomal/lysosomal compartment and inhibits virus–endosome fusion. These studies reveal that H84T is efficacious against influenza virus in vivo, and that the loss of mitogenicity seen previously in tissue culture is also seen in vivo, underscoring the potential utility of H84T as a broad-spectrum antiinfluenza agent.

    更新日期:2020-01-14
  • Generalists are more specialized in low-resource habitats, increasing stability of ecological network structure [Ecology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Moria L. Robinson, Sharon Y. Strauss

    Linking mechanistic processes to the stability of ecological networks is a key frontier in ecology. In trophic networks, “modules”—groups of species that interact more with each other than with other members of the community—confer stability, mitigating effects of species loss or perturbation. Modularity, in turn, is shaped by the interplay between species’ diet breadth traits and environmental influences, which together dictate interaction structure. Despite the importance of network modularity, variation in this emergent property is poorly understood in complex natural systems. Using two years of field data, we quantified interactions between a rich community of lepidopteran herbivores and their host plants across a mosaic of low-resource serpentine and high-resource nonserpentine soils. We used literature and our own observations to categorize herbivore species as generalists (feeding on more than one plant family) or specialists (feeding on one plant family). In both years, the plant-herbivore network was more modular on serpentine than on nonserpentine soils—despite large differences in herbivore assemblage size across years. This structural outcome was primarily driven by reduction in the breadth of host plant use by generalist species, rather than by changes in the composition of species with different fundamental diet breadths. Greater modularity—and thus greater stability—reflects environmental conditions and plastic responses by generalist herbivores to low host plant quality. By considering the dual roles of species traits and ecological processes, we provide a deeper mechanistic understanding of network modularity, and suggest a role for resource availability in shaping network persistence.

    更新日期:2020-01-14
  • Anaerobic peroxisomes in Mastigamoeba balamuthi [Evolution]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Tien Le, Vojtěch Žárský, Eva Nývltová, Petr Rada, Karel Harant, Marie Vancová, Zdeněk Verner, Ivan Hrdý, Jan Tachezy

    The adaptation of eukaryotic cells to anaerobic conditions is reflected by substantial changes to mitochondrial metabolism and functional reduction. Hydrogenosomes belong among the most modified mitochondrial derivative and generate molecular hydrogen concomitant with ATP synthesis. The reduction of mitochondria is frequently associated with loss of peroxisomes, which compartmentalize pathways that generate reactive oxygen species (ROS) and thus protect against cellular damage. The biogenesis and function of peroxisomes are tightly coupled with mitochondria. These organelles share fission machinery components, oxidative metabolism pathways, ROS scavenging activities, and some metabolites. The loss of peroxisomes in eukaryotes with reduced mitochondria is thus not unexpected. Surprisingly, we identified peroxisomes in the anaerobic, hydrogenosome-bearing protist Mastigamoeba balamuthi. We found a conserved set of peroxin (Pex) proteins that are required for protein import, peroxisomal growth, and division. Key membrane-associated Pexs (MbPex3, MbPex11, and MbPex14) were visualized in numerous vesicles distinct from hydrogenosomes, the endoplasmic reticulum (ER), and Golgi complex. Proteomic analysis of cellular fractions and prediction of peroxisomal targeting signals (PTS1/PTS2) identified 51 putative peroxisomal matrix proteins. Expression of selected proteins in Saccharomyces cerevisiae revealed specific targeting to peroxisomes. The matrix proteins identified included components of acyl-CoA and carbohydrate metabolism and pyrimidine and CoA biosynthesis, whereas no components related to either β-oxidation or catalase were present. In conclusion, we identified a subclass of peroxisomes, named “anaerobic” peroxisomes that shift the current paradigm and turn attention to the reductive evolution of peroxisomes in anaerobic organisms.

    更新日期:2020-01-14
  • LINGO1 is a regulatory subunit of large conductance, Ca2+-activated potassium channels [Physiology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Srikanth Dudem, Roddy J. Large, Shruti Kulkarni, Heather McClafferty, Irina G. Tikhonova, Gerard P. Sergeant, Keith D. Thornbury, Michael J. Shipston, Brian A. Perrino, Mark A. Hollywood

    LINGO1 is a transmembrane protein that is up-regulated in the cerebellum of patients with Parkinson’s disease (PD) and Essential Tremor (ET). Patients with additional copies of the LINGO1 gene also present with tremor. Pharmacological or genetic ablation of large conductance Ca2+-activated K+ (BK) channels also result in tremor and motor disorders. We hypothesized that LINGO1 is a regulatory BK channel subunit. We show that 1) LINGO1 coimmunoprecipitated with BK channels in human brain, 2) coexpression of LINGO1 and BK channels resulted in rapidly inactivating BK currents, and 3) LINGO1 reduced the membrane surface expression of BK channels. These results suggest that LINGO1 is a regulator of BK channels, which causes a “functional knockdown” of these currents and may contribute to the tremor associated with increased LINGO1 levels.

    更新日期:2020-01-14
  • CK1{alpha}, CK1{delta}, and CK1ϵ are necrosome components which phosphorylate serine 227 of human RIPK3 to activate necroptosis [Biochemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Sarah Hanna-Addams, Shuzhen Liu, Hua Liu, She Chen, Zhigao Wang

    Necroptosis is a regulated necrotic cell death pathway, mediated by a supermolecular complex called the necrosome, which contains receptor-interacting protein kinase 1 and 3 (RIPK1, RIPK3) and mixed-lineage kinase domain-like protein (MLKL). Phosphorylation of human RIPK3 at serine 227 (S227) has been shown to be required for downstream MLKL binding and necroptosis progression. Tandem immunoprecipitation of RIPK3 reveals that casein kinase 1 (CK1) family proteins associate with the necrosome upon necroptosis induction, and this interaction depends on the kinase activity of RIPK3. In addition, CK1 proteins colocalize with RIPK3 puncta during necroptosis. Importantly, CK1 proteins directly phosphorylate RIPK3 at S227 in vitro and in vivo. Loss of CK1 proteins abolishes S227 phosphorylation and blocks necroptosis. Furthermore, a RIPK3 mutant with mutations in the CK1 recognition motif fails to be phosphorylated at S227, does not bind or phosphorylate MLKL, and is unable to activate necroptosis. These results strongly suggest that CK1 proteins are necrosome components which are responsible for RIPK3-S227 phosphorylation.

    更新日期:2020-01-14
  • Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages [Chemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Huan Peng, Raymond E. Borg, Liam P. Dow, Beth L. Pruitt, Irene A. Chen

    The use of bacteriophages (phages) for antibacterial therapy is under increasing consideration to treat antimicrobial-resistant infections. Phages have evolved multiple mechanisms to target their bacterial hosts, such as high-affinity, environmentally hardy receptor-binding proteins. However, traditional phage therapy suffers from multiple challenges stemming from the use of an exponentially replicating, evolving entity whose biology is not fully characterized (e.g., potential gene transduction). To address this problem, we conjugate the phages to gold nanorods, creating a reagent that can be destroyed upon use (termed “phanorods”). Chimeric phages were engineered to attach specifically to several Gram-negative organisms, including the human pathogens Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae, and the plant pathogen Xanthomonas campestris. The bioconjugated phanorods could selectively target and kill specific bacterial cells using photothermal ablation. Following excitation by near-infrared light, gold nanorods release energy through nonradiative decay pathways, locally generating heat that efficiently kills targeted bacterial cells. Specificity was highlighted in the context of a P. aeruginosa biofilm, in which phanorod irradiation killed bacterial cells while causing minimal damage to epithelial cells. Local temperature and viscosity measurements revealed highly localized and selective ablation of the bacteria. Irradiation of the phanorods also destroyed the phages, preventing replication and reducing potential risks of traditional phage therapy while enabling control over dosing. The phanorod strategy integrates the highly evolved targeting strategies of phages with the photothermal properties of gold nanorods, creating a well-controlled platform for systematic killing of bacterial cells.

    更新日期:2020-01-14
  • Membrane molecular crowding enhances MreB polymerization to shape synthetic cells from spheres to rods [Systems Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    David Garenne, Albert Libchaber, Vincent Noireaux

    Executing gene circuits by cell-free transcription−translation into cell-sized compartments, such as liposomes, is one of the major bottom-up approaches to building minimal cells. The dynamic synthesis and proper self-assembly of macromolecular structures inside liposomes, the cytoskeleton in particular, stands as a central limitation to the development of cell analogs genetically programmed. In this work, we express the Escherichia coli gene mreB inside vesicles with bilayers made of lipid-polyethylene glycol (PEG). We demonstrate that two-dimensional molecular crowding, emulated by the PEG molecules at the lipid bilayer, is enough to promote the polymerization of the protein MreB at the inner membrane into a sturdy cytoskeleton capable of transforming spherical liposomes into elongated shapes, such as rod-like compartments. We quantitatively describe this mechanism with respect to the size of liposomes, lipid composition of the membrane, crowding at the membrane, and strength of MreB synthesis. So far unexplored, molecular crowding at the surface of synthetic cells emerges as an additional development with potential broad applications. The symmetry breaking observed could be an important step toward compartment self-reproduction.

    更新日期:2020-01-14
  • Effective fisheries management instrumental in improving fish stock status [Population Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Ray Hilborn, Ricardo Oscar Amoroso, Christopher M. Anderson, Julia K. Baum, Trevor A. Branch, Christopher Costello, Carryn L. de Moor, Abdelmalek Faraj, Daniel Hively, Olaf P. Jensen, Hiroyuki Kurota, L. Richard Little, Pamela Mace, Tim McClanahan, Michael C. Melnychuk, Cóilín Minto, Giacomo Chato Osio, Ana M. Parma, Maite Pons, Susana Segurado, Cody S. Szuwalski, Jono R. Wilson, Yimin Ye

    Marine fish stocks are an important part of the world food system and are particularly important for many of the poorest people of the world. Most existing analyses suggest overfishing is increasing, and there is widespread concern that fish stocks are decreasing throughout most of the world. We assembled trends in abundance and harvest rate of stocks that are scientifically assessed, constituting half of the reported global marine fish catch. For these stocks, on average, abundance is increasing and is at proposed target levels. Compared with regions that are intensively managed, regions with less-developed fisheries management have, on average, 3-fold greater harvest rates and half the abundance as assessed stocks. Available evidence suggests that the regions without assessments of abundance have little fisheries management, and stocks are in poor shape. Increased application of area-appropriate fisheries science recommendations and management tools are still needed for sustaining fisheries in places where they are lacking.

    更新日期:2020-01-14
  • Probabilistic reanalysis of storm surge extremes in Europe [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Francisco M. Calafat, Marta Marcos

    Extreme sea levels are a significant threat to life, property, and the environment. These threats are managed by coastal planers through the implementation of risk mitigation strategies. Central to such strategies is knowledge of extreme event probabilities. Typically, these probabilities are estimated by fitting a suitable distribution to the observed extreme data. Estimates, however, are often uncertain due to the small number of extreme events in the tide gauge record and are only available at gauged locations. This restricts our ability to implement cost-effective mitigation. A remarkable fact about sea-level extremes is the existence of spatial dependences, yet the vast majority of studies to date have analyzed extremes on a site-by-site basis. Here we demonstrate that spatial dependences can be exploited to address the limitations posed by the spatiotemporal sparseness of the observational record. We achieve this by pooling all of the tide gauge data together through a Bayesian hierarchical model that describes how the distribution of surge extremes varies in time and space. Our approach has two highly desirable advantages: 1) it enables sharing of information across data sites, with a consequent drastic reduction in estimation uncertainty; 2) it permits interpolation of both the extreme values and the extreme distribution parameters at any arbitrary ungauged location. Using our model, we produce an observation-based probabilistic reanalysis of surge extremes covering the entire Atlantic and North Sea coasts of Europe for the period 1960–2013.

    更新日期:2020-01-14
  • A long-distance rRNA base pair impacts the ability of macrolide antibiotics to kill bacteria [Biochemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Maxim S. Svetlov, Sophie Cohen, Nada Alsuhebany, Nora Vázquez-Laslop, Alexander S. Mankin

    While most of the ribosome-targeting antibiotics are bacteriostatic, some members of the macrolide class demonstrate considerable bactericidal activity. We previously showed that an extended alkyl-aryl side chain is the key structural element determining the macrolides’ slow dissociation from the ribosome and likely accounts for the antibiotics’ cidality. In the nontranslating Escherichia coli ribosome, the extended side chain of macrolides interacts with 23S ribosomal RNA (rRNA) nucleotides A752 and U2609, that were proposed to form a base pair. However, the existence of this base pair in the translating ribosome, its possible functional role, and its impact on the binding and cidality of the antibiotic remain unknown. By engineering E. coli cells carrying individual and compensatory mutations at the 752 and 2609 rRNA positions, we show that integrity of the base pair helps to modulate the ribosomal response to regulatory nascent peptides, determines the slow dissociation rate of the extended macrolides from the ribosome, and increases their bactericidal effect. Our findings demonstrate that the ability of antibiotics to kill bacterial cells relies not only on the chemical nature of the inhibitor, but also on structural features of the target.

    更新日期:2020-01-14
  • Single-cell tracking demonstrates copper chaperone Atox1 to be required for breast cancer cell migration [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Stéphanie Blockhuys, Xiaolu Zhang, Pernilla Wittung-Stafshede

    Copper ions are needed for several hallmarks of cancer. However, the involved pathways, mechanisms, and copper-binding proteins are mostly unknown. We recently found that cytoplasmic Antioxidant 1 copper chaperone (Atox1), which is up-regulated in breast cancer, is localized at the lamellipodia edges of aggressive breast cancer cells. To reveal molecular insights into a putative role in cell migration, we here investigated breast cancer cell (MDA-MB-231) migration by video microscopy as a function of Atox1. Tracking of hundreds of individual cells (per condition) over a 9-h time series revealed that cell migration velocity and directionality are significantly reduced upon Atox1 silencing in the cells. Because silencing of the copper transporter ATP7A also reduced cell migration, these proteins appear to be on the same pathway, suggesting that their well-known copper transport activity is involved. In-cell proximity ligation assays demonstrated that Atox1, ATP7A, and the proenzyme of lysyl oxidase (LOX; copper-loaded via ATP7A) are all in close proximity and that LOX activity is reduced upon Atox1 silencing in the cells. Since LOX is an established player in cancer cell migration, our results imply that Atox1 mediates breast cancer cell migration via coordinated copper transport in the ATP7A-LOX axis. Because individual cell migration is an early step in breast cancer metastasis, Atox1 levels in tumor cells may be a predictive measure of metastasis potential and serve as a biomarker for copper depletion therapy.

    更新日期:2020-01-14
  • Climate change and the opportunity cost of conflict [Environmental Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Kevin R. Roche, Michèle Müller-Itten, David N. Dralle, Diogo Bolster, Marc F. Müller

    A growing empirical literature associates climate anomalies with increased risk of violent conflict. This association has been portrayed as a bellwether of future societal instability as the frequency and intensity of extreme weather events are predicted to increase. This paper investigates the theoretical foundation of this claim. A seminal microeconomic model of opportunity costs—a mechanism often thought to drive climate–conflict relationships—is extended by considering realistic changes in the distribution of climate-dependent agricultural income. Results advise caution in using empirical associations between short-run climate anomalies and conflicts to predict the effect of sustained shifts in climate regimes: Although war occurs in bad years, conflict may decrease if agents expect more frequent bad years. Theory suggests a nonmonotonic relation between climate variability and conflict that emerges as agents adapt and adjust their behavior to the new income distribution. We identify 3 measurable statistics of the income distribution that are each unambiguously associated with conflict likelihood. Jointly, these statistics offer a unique signature to distinguish opportunity costs from competing mechanisms that may relate climate anomalies to conflict.

    更新日期:2020-01-14
  • The nutrient sensor OGT regulates Hipk stability and tumorigenic-like activities in Drosophila [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Kenneth Kin Lam Wong, Ta-Wei Liu, Jessica M. Parker, Donald A. R. Sinclair, Yi-Yun Chen, Kay-Hooi Khoo, David J. Vocadlo, Esther M. Verheyen

    Environmental cues such as nutrients alter cellular behaviors by acting on a wide array of molecular sensors inside cells. Of emerging interest is the link observed between effects of dietary sugars on cancer proliferation. Here, we identify the requirements of hexosamine biosynthetic pathway (HBP) and O-GlcNAc transferase (OGT) for Drosophila homeodomain-interacting protein kinase (Hipk)-induced growth abnormalities in response to a high sugar diet. On a normal diet, OGT is both necessary and sufficient for inducing Hipk-mediated tumor-like growth. We further show that OGT maintains Hipk protein stability by blocking its proteasomal degradation and that Hipk is O-GlcNAcylated by OGT. In mammalian cells, human HIPK2 proteins accumulate posttranscriptionally upon OGT overexpression. Mass spectrometry analyses reveal that HIPK2 is at least O-GlcNAc modified at S852, T1009, and S1147 residues. Mutations of these residues reduce HIPK2 O-GlcNAcylation and stability. Together, our data demonstrate a conserved role of OGT in positively regulating the protein stability of HIPKs (fly Hipk and human HIPK2), which likely permits the nutritional responsiveness of HIPKs.

    更新日期:2020-01-14
  • Global warming accelerates uptake of atmospheric mercury in regions experiencing glacier retreat [Environmental Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Xun Wang, Ji Luo, Wei Yuan, Che-Jen Lin, Feiyue Wang, Chen Liu, Genxu Wang, Xinbin Feng

    As global climate continues to warm, melting of glaciers releases a large quantity of mercury (Hg) originally locked in ice into the atmosphere and downstream ecosystems. Here, we show an opposite process that captures atmospheric Hg through glacier-to-vegetation succession. Our study using stable isotope techniques at 3 succession sites on the Tibetan Plateau reveals that evolving vegetation serves as an active “pump” to take up gaseous elemental mercury (Hg0) from the atmosphere. The accelerated uptake enriches the Hg pool size in glacier-retreated areas by a factor of ∼10 compared with the original pool size in the glacier. Through an assessment of Hg source–sink relationship observed in documented glacier-retreated areas in the world (7 sites of tundra/steppe succession and 5 sites of forest succession), we estimate that 400 to 600 Mg of Hg has been accumulated in glacier-retreated areas (5‰ of the global land surface) since the Little Ice Age (∼1850). By 2100, an additional ∼300 Mg of Hg will be sequestered from the atmosphere in glacier-retreated regions globally, which is ∼3 times the total Hg mass loss by meltwater efflux (∼95 Mg) in alpine and subpolar glacier regions. The recapturing of atmospheric Hg by vegetation in glacier-retreated areas is not accounted for in current global Hg models. Similar processes are likely to occur in other regions that experience increased vegetation due to climate or land use changes, which need to be considered in the assessment of global Hg cycling.

    更新日期:2020-01-14
  • Profile of Mary Lou Guerinot [Profiles]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Jennifer Viegas

    On the first Earth Day, April 22, 1970, Mary Lou Guerinot decided that she would major in biology in college in the hope of promoting environmental sustainability. As the 50th anniversary of Earth Day approaches, Guerinot, now a professor of biological sciences at Dartmouth College and a member of the National Academy of Sciences, is well on her way toward achieving that goal through her work on the molecular mechanisms of metal ion uptake and its regulation. Guerinot’s work is laying the foundation for environmentally sustainable, nutrient-dense crops, as well as plant-based solutions for removal of toxic metals from soil. Her Inaugural Article (1) reports the identification of a transcription factor essential for plant growth under iron deficiency. The finding moves her team closer to understanding the iron homeostasis pathway in plants, holding promise for improving agricultural productivity and human health.

    更新日期:2020-01-14
  • Oligodendroglial connexin 47 regulates neuroinflammation upon autoimmune demyelination in a novel mouse model of multiple sclerosis [Neuroscience]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Yinan Zhao, Ryo Yamasaki, Hiroo Yamaguchi, Satoshi Nagata, Hayato Une, Yiwen Cui, Katsuhisa Masaki, Yuko Nakamuta, Kyoko Iinuma, Mitsuru Watanabe, Takuya Matsushita, Noriko Isobe, Jun-ichi Kira

    In multiple sclerosis plaques, oligodendroglial connexin (Cx) 47 constituting main gap junction channels with astroglial Cx43 is persistently lost. As mice with Cx47 single knockout exhibit no demyelination, the roles of Cx47 remain undefined. We aimed to clarify the effects of oligodendroglia-specific Cx47 inducible conditional knockout (icKO) on experimental autoimmune encephalomyelitis (EAE) induced by myelin oligodendrocyte glycoprotein peptide (MOG35-55) in PLP/CreERT;Cx47fl/fl mice at 14 d after tamoxifen injection. Cx47 icKO mice demonstrated exacerbation of acute and chronic relapsing EAE with more pronounced demyelination than Cx47 flox (fl)/fl littermates. CD3+ T cells more abundantly infiltrated the spinal cord in Cx47 icKO than in Cx47 fl/fl mice throughout the acute to chronic phases. CXCR3-CCR6+CD4+ and IL17+IFNγ-CD4+ helper T (Th) 17 cells isolated from spinal cord and brain tissues were significantly increased in Cx47 icKO mice compared with Cx47 fl/fl mice, while MOG35-55-specific proliferation and proinflammatory cytokine production of splenocytes were unaltered. Microarray analysis of isolated microglia revealed stronger microglial activation toward proinflammatory and injury-response phenotypes with increased expressions of chemokines that can attract Th17 cells, including Ccl2, Ccl3, Ccl4, Ccl7, and Ccl8, in Cx47 icKO mice compared with Cx47 fl/fl mice. In Cx47 icKO mice, NOS2+ and MHC class II+ microglia were more enriched immunohistochemically, and A1-specific astroglial gene expressions and astroglia immunostained for C3, a representative A1 astrocyte marker, were significantly increased at the acute phase, compared with Cx47 fl/fl mice. These findings suggest that oligodendroglia-specific Cx47 ablation induces severe inflammation upon autoimmune demyelination, underscoring a critical role for Cx47 in regulating neuroinflammation.

    更新日期:2020-01-14
  • TrkB hyperactivity contributes to brain dysconnectivity, epileptogenesis, and anxiety in zebrafish model of Tuberous Sclerosis Complex [Neuroscience]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Magdalena Kedra, Katarzyna Banasiak, Katarzyna Kisielewska, Lidia Wolinska-Niziol, Jacek Jaworski, Justyna Zmorzynska

    Tuberous Sclerosis Complex (TSC) is a rare genetic disease that manifests with early symptoms, including cortical malformations, childhood epilepsy, and TSC-associated neuropsychiatric disorders (TANDs). Cortical malformations arise during embryonic development and have been linked to childhood epilepsy before, but the underlying mechanisms of this relationship remain insufficiently understood. Zebrafish have emerged as a convenient model to study elementary neurodevelopment; however, without in-depth functional analysis, the Tsc2-deficient zebrafish line cannot be used for studies of TANDs or new drug screening. In this study, we found that the lack of Tsc2 in zebrafish resulted in heterotopias and hyperactivation of the mTorC1 pathway in pallial regions, which are homologous to the mammalian cortex. We observed commissural thinning that was responsible for brain dysconnectivity, recapitulating TSC pathology in human patients. The lack of Tsc2 also delayed axonal development and caused aberrant tract fasciculation, corresponding to the abnormal expression of genes involved in axon navigation. The mutants underwent epileptogenesis that resulted in nonmotor seizures and exhibited increased anxiety-like behavior. We further mapped discrete parameters of locomotor activity to epilepsy-like and anxiety-like behaviors, which were rescued by reducing tyrosine receptor kinase B (TrkB) signaling. Moreover, in contrast to treatment with vigabatrin and rapamycin, TrkB inhibition rescued brain dysconnectivity and anxiety-like behavior. These data reveal that commissural thinning results in the aberrant regulation of anxiety, providing a mechanistic link between brain anatomy and human TANDs. Our findings also implicate TrkB signaling in the complex pathology of TSC and reveal a therapeutic target.

    更新日期:2020-01-14
  • A scalable pipeline for designing reconfigurable organisms [Systems Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Sam Kriegman, Douglas Blackiston, Michael Levin, Josh Bongard

    Living systems are more robust, diverse, complex, and supportive of human life than any technology yet created. However, our ability to create novel lifeforms is currently limited to varying existing organisms or bioengineering organoids in vitro. Here we show a scalable pipeline for creating functional novel lifeforms: AI methods automatically design diverse candidate lifeforms in silico to perform some desired function, and transferable designs are then created using a cell-based construction toolkit to realize living systems with the predicted behaviors. Although some steps in this pipeline still require manual intervention, complete automation in future would pave the way to designing and deploying unique, bespoke living systems for a wide range of functions.

    更新日期:2020-01-14
  • Physiological responses to gravity in an insect [Physiology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Jon F. Harrison, Khaled Adjerid, Anelia Kassi, C. Jaco Klok, John M. VandenBrooks, Meghan E. Duell, Jacob B. Campbell, Stav Talal, Christopher D. Abdo, Kamel Fezzaa, Hodjat Pendar, John J. Socha

    Gravity is one of the most ubiquitous environmental effects on living systems: Cellular and organismal responses to gravity are of central importance to understanding the physiological function of organisms, especially eukaryotes. Gravity has been demonstrated to have strong effects on the closed cardiovascular systems of terrestrial vertebrates, with rapidly responding neural reflexes ensuring proper blood flow despite changes in posture. Invertebrates possess open circulatory systems, which could provide fewer mechanisms to restrict gravity effects on blood flow, suggesting that these species also experience effects of gravity on blood pressure and distribution. However, whether gravity affects the open circulatory systems of invertebrates is unknown, partly due to technical measurement issues associated with small body size. Here we used X-ray imaging, radio-tracing of hemolymph, and micropressure measurements in the American grasshopper, Schistocerca americana, to assess responses to body orientation. Our results show that during changes in body orientation, gravity causes large changes in blood and air distribution, and that body position affects ventilation rate. Remarkably, we also found that insects show similar heart rate responses to body position as vertebrates, and contrasting with the classic understanding of open circulatory systems, have flexible valving systems between thorax and abdomen that can separate pressures. Gravitational effects on invertebrate cardiovascular and respiratory systems are likely to be widely distributed among invertebrates and to have broad influence on morphological and physiological evolution.

    更新日期:2020-01-14
  • Lifetimes of interstellar dust from cosmic ray exposure ages of presolar silicon carbide [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Philipp R. Heck, Jennika Greer, Levke Kööp, Reto Trappitsch, Frank Gyngard, Henner Busemann, Colin Maden, Janaína N. Ávila, Andrew M. Davis, Rainer Wieler

    We determined interstellar cosmic ray exposure ages of 40 large presolar silicon carbide grains extracted from the Murchison CM2 meteorite. Our ages, based on cosmogenic Ne-21, range from 3.9 ± 1.6 Ma to ∼3 ± 2 Ga before the start of the Solar System ∼4.6 Ga ago. A majority of the grains have interstellar lifetimes of <300 Ma, which is shorter than theoretical estimates for large grains. These grains condensed in outflows of asymptotic giant branch stars <4.9 Ga ago that possibly formed during an episode of enhanced star formation ∼7 Ga ago. A minority of the grains have ages >1 Ga. Longer lifetimes are expected for large grains. We determined that at least 12 of the analyzed grains were parts of aggregates in the interstellar medium: The large difference in nuclear recoil loss of cosmic ray spallation products 3He and 21Ne enabled us to estimate that the irradiated objects in the interstellar medium were up to 30 times larger than the analyzed grains. Furthermore, we estimate that the majority of the grains acquired the bulk of their cosmogenic nuclides in the interstellar medium and not by exposure to an enhanced particle flux of the early active sun.

    更新日期:2020-01-14
  • Trop2 is a driver of metastatic prostate cancer with neuroendocrine phenotype via PARP1 [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    En-Chi Hsu, Meghan A. Rice, Abel Bermudez, Fernando Jose Garcia Marques, Merve Aslan, Shiqin Liu, Ali Ghoochani, Chiyuan Amy Zhang, Yun-Sheng Chen, Aimen Zlitni, Sahil Kumar, Rosalie Nolley, Frezghi Habte, Michelle Shen, Kashyap Koul, Donna M. Peehl, Amina Zoubeidi, Sanjiv S. Gambhir, Christian A. Kunder, Sharon J. Pitteri, James D. Brooks, Tanya Stoyanova

    Resistance to androgen deprivation therapy, or castration-resistant prostate cancer (CRPC), is often accompanied by metastasis and is currently the ultimate cause of prostate cancer-associated deaths in men. Recently, secondary hormonal therapies have led to an increase of neuroendocrine prostate cancer (NEPC), a highly aggressive variant of CRPC. Here, we identify that high levels of cell surface receptor Trop2 are predictive of recurrence of localized prostate cancer. Moreover, Trop2 is significantly elevated in CRPC and NEPC, drives prostate cancer growth, and induces neuroendocrine phenotype. Overexpression of Trop2 induces tumor growth and metastasis while loss of Trop2 suppresses these abilities in vivo. Trop2-driven NEPC displays a significant up-regulation of PARP1, and PARP inhibitors significantly delay tumor growth and metastatic colonization and reverse neuroendocrine features in Trop2-driven NEPC. Our findings establish Trop2 as a driver and therapeutic target for metastatic prostate cancer with neuroendocrine phenotype and suggest that high Trop2 levels could identify cancers that are sensitive to Trop2-targeting therapies and PARP1 inhibition.

    更新日期:2020-01-14
  • RAP80 and BRCA1 PARsylation protect chromosome integrity by preventing retention of BRCA1-B/C complexes in DNA repair foci [Medical Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Jekaterina Vohhodina, Kimberly J. Toomire, Sarah A. Petit, Goran Micevic, Geeta Kumari, Vladimir V. Botchkarev, Zhe Li, David M. Livingston, Yiduo Hu

    BRCA1 promotes error-free, homologous recombination-mediated repair (HRR) of DNA double-stranded breaks (DSBs). When excessive and uncontrolled, BRCA1 HRR activity promotes illegitimate recombination and genome disorder. We and others have observed that the BRCA1-associated protein RAP80 recruits BRCA1 to postdamage nuclear foci, and these chromatin structures then restrict the amplitude of BRCA1-driven HRR. What remains unclear is how this process is regulated. Here we report that both BRCA1 poly-ADP ribosylation (PARsylation) and the presence of BRCA1-bound RAP80 are critical for the normal interaction of BRCA1 with some of its partners (e.g., CtIP and BACH1) that are also known components of the aforementioned focal structures. Surprisingly, the simultaneous loss of RAP80 and failure therein of BRCA1 PARsylation results in the dysregulated accumulation in these foci of BRCA1 complexes. This in turn is associated with the intracellular development of a state of hyper-recombination and gross chromosomal disorder. Thus, physiological RAP80-BRCA1 complex formation and BRCA1 PARsylation contribute to the kinetics by which BRCA1 HRR-sustaining complexes normally concentrate in nuclear foci. These events likely contribute to aneuploidy suppression.

    更新日期:2020-01-14
  • HSD3B1 genotype identifies glucocorticoid responsiveness in severe asthma [Physiology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Joe Zein, Benjamin Gaston, Peter Bazeley, Mark D. DeBoer, Robert P. Igo, Eugene R. Bleecker, Deborah Meyers, Suzy Comhair, Nadzeya V. Marozkina, Calvin Cotton, Mona Patel, Mohammad Alyamani, Weiling Xu, William W. Busse, William J. Calhoun, Victor Ortega, Gregory A. Hawkins, Mario Castro, Kian Fan Chung, John V. Fahy, Anne M. Fitzpatrick, Elliot Israel, Nizar N. Jarjour, Bruce Levy, David T. Mauger, Wendy C. Moore, Patricia Noel, Stephen P. Peters, W. Gerald Teague, Sally E. Wenzel, Serpil C. Erzurum, Nima Sharifi

    Asthma resistance to glucocorticoid treatment is a major health problem with unclear etiology. Glucocorticoids inhibit adrenal androgen production. However, androgens have potential benefits in asthma. HSD3B1 encodes for 3β-hydroxysteroid dehydrogenase-1 (3β-HSD1), which catalyzes peripheral conversion from adrenal dehydroepiandrosterone (DHEA) to potent androgens and has a germline missense-encoding polymorphism. The adrenal restrictive HSD3B1(1245A) allele limits conversion, whereas the adrenal permissive HSD3B1(1245C) allele increases DHEA metabolism to potent androgens. In the Severe Asthma Research Program (SARP) III cohort, we determined the association between DHEA-sulfate and percentage predicted forced expiratory volume in 1 s (FEV1PP). HSD3B1(1245) genotypes were assessed, and association between adrenal restrictive and adrenal permissive alleles and FEV1PP in patients with (GC) and without (noGC) daily oral glucocorticoid treatment was determined (n = 318). Validation was performed in a second cohort (SARP I&II; n = 184). DHEA-sulfate is associated with FEV1PP and is suppressed with GC treatment. GC patients homozygous for the adrenal restrictive genotype have lower FEV1PP compared with noGC patients (54.3% vs. 75.1%; P < 0.001). In patients with the homozygous adrenal permissive genotype, there was no FEV1PP difference in GC vs. noGC patients (73.4% vs. 78.9%; P = 0.39). Results were independently confirmed: FEV1PP for homozygous adrenal restrictive genotype in GC vs. noGC is 49.8 vs. 63.4 (P < 0.001), and for homozygous adrenal permissive genotype, it is 66.7 vs. 67.7 (P = 0.92). The adrenal restrictive HSD3B1(1245) genotype is associated with GC resistance. This effect appears to be driven by GC suppression of 3β-HSD1 substrate. Our results suggest opportunities for prediction of GC resistance and pharmacologic intervention.

    更新日期:2020-01-14
  • Genomic insight into the origins and dispersal of the Brazilian coastal natives [Anthropology]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Marcos Araújo Castro e Silva, Kelly Nunes, Renan Barbosa Lemes, Àlex Mas-Sandoval, Carlos Eduardo Guerra Amorim, Jose Eduardo Krieger, José Geraldo Mill, Francisco Mauro Salzano, Maria Cátira Bortolini, Alexandre da Costa Pereira, David Comas, Tábita Hünemeier

    In the 15th century, ∼900,000 Native Americans, mostly Tupí speakers, lived on the Brazilian coast. By the end of the 18th century, the coastal native populations were declared extinct. The Tupí arrived on the east coast after leaving the Amazonian basin ∼2,000 y before present; however, there is no consensus on how this migration occurred: toward the northern Amazon and then directly to the Atlantic coast, or heading south into the continent and then migrating to the coast. Here we leveraged genomic data from one of the last remaining putative representatives of the Tupí coastal branch, a small, admixed, self-reported Tupiniquim community, as well as data of a Guaraní Mbyá native population from Southern Brazil and of three other native populations from the Amazonian region. We demonstrated that the Tupiniquim Native American ancestry is not related to any extant Brazilian Native American population already studied, and thus they could be considered the only living representatives of the extinct Tupí branch that used to settle the Atlantic Coast of Brazil. Furthermore, these data show evidence of a direct migration from Amazon to the Northeast Coast in pre-Columbian time, giving rise to the Tupí Coastal populations, and a single distinct migration southward that originated the Guaraní people from Brazil and Paraguay. This study elucidates the population dynamics and diversification of the Brazilian natives at a genomic level, which was made possible by recovering data from the Brazilian coastal population through the genomes of mestizo individuals.

    更新日期:2020-01-14
  • Ras acts as a molecular switch between two forms of consolidated memory in Drosophila [Neuroscience]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    Nathaniel C. Noyes, Erica Walkinshaw, Ronald L. Davis

    Long-lasting, consolidated memories require not only positive biological processes that facilitate long-term memories (LTM) but also the suppression of inhibitory processes that prevent them. The mushroom body neurons (MBn) in Drosophila melanogaster store protein synthesis-dependent LTM (PSD-LTM) as well as protein synthesis-independent, anesthesia-resistant memory (ARM). The formation of ARM inhibits PSD-LTM but the underlying molecular processes that mediate this interaction remain unknown. Here, we demonstrate that the Ras→Raf→rho kinase (ROCK) pathway in MBn suppresses ARM consolidation, allowing the formation of PSD-LTM. Our initial results revealed that the effects of Ras on memory are due to postacquisition processes. Ras knockdown enhanced memory expression but had no effect on acquisition. Additionally, increasing Ras activity optogenetically after, but not before, acquisition impaired memory performance. The elevated memory produced by Ras knockdown is a result of increased ARM. While Ras knockdown enhanced the consolidation of ARM, it eliminated PSD-LTM. We found that these effects are mediated by the downstream kinase Raf. Similar to Ras, knockdown of Raf enhanced ARM consolidation and impaired PSD-LTM. Surprisingly, knockdown of the canonical downstream extracellular signal-regulated kinase did not reproduce the phenotypes observed with Ras and Raf knockdown. Rather, Ras/Raf inhibition of ROCK was found to be responsible for suppressing ARM. Constitutively active ROCK enhanced ARM and impaired PSD-LTM, while decreasing ROCK activity rescued the enhanced ARM produced by Ras knockdown. We conclude that MBn Ras/Raf inhibition of ROCK suppresses the consolidation of ARM, which permits the formation of PSD-LTM.

    更新日期:2020-01-14
  • Correction for Porter et al., Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinoma [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    National Academy of Sciences

    MEDICAL SCIENCES Correction for “Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinoma,” by Rebecca L. Porter, Neelima K. C. Magnus, Vishal Thapar, Robert Morris, Annamaria Szabolcs, Azfar Neyaz, Anupriya S. Kulkarni, Eric Tai, Abhijit Chougule, Alessandra Hillis, Gabriel Golczer, …

    更新日期:2020-01-14
  • Correction for Hu et al., Structural bases for F plasmid conjugation and F pilus biogenesis in Escherichia coli [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-13
    National Academy of Sciences

    MICROBIOLOGY Correction for “Structural bases for F plasmid conjugation and F pilus biogenesis in Escherichia coli,” …

    更新日期:2020-01-14
  • Resting state structure of the hyperdepolarization activated two-pore channel 3 [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-10
    Miles Sasha Dickinson, Alexander Myasnikov, Jacob Eriksen, Nicole Poweleit, Robert M. Stroud

    Voltage-gated ion channels endow membranes with excitability and the means to propagate action potentials that form the basis of all neuronal signaling. We determined the structure of a voltage-gated sodium channel, two-pore channel 3 (TPC3), which generates ultralong action potentials. TPC3 is distinguished by activation only at extreme membrane depolarization (V50 ∼ +75 mV), in contrast to other TPCs and NaV channels that activate between −20 and 0 mV. We present electrophysiological evidence that TPC3 voltage activation depends only on voltage sensing domain 2 (VSD2) and that each of the three gating arginines in VSD2 reduces the activation threshold. The structure presents a chemical basis for sodium selectivity, and a constricted gate suggests a closed pore consistent with extreme voltage dependence. The structure, confirmed by our electrophysiology, illustrates the configuration of a bona fide resting state voltage sensor, observed without the need for any inhibitory ligand, and independent of any chemical or mutagenic alteration.

    更新日期:2020-01-13
  • Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling [Biochemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-10
    Oleg Klykov, Carmen van der Zwaan, Albert J. R. Heck, Alexander B. Meijer, Richard A. Scheltema

    Upon activation, fibrinogen forms large fibrin biopolymers that coalesce into clots which assist in wound healing. Limited insights into their molecular architecture, due to the sheer size and the insoluble character of fibrin clots, have restricted our ability to develop novel treatments for clotting diseases. The, so far resolved, disparate structural details have provided insights into linear elongation; however, molecular details like the C-terminal domain of the α-chain, the heparin-binding domain on the β-chain, and other functional domains remain elusive. To illuminate these dark areas, we applied cross-linking mass spectrometry (XL-MS) to obtain biochemical evidence in the form of over 300 distance constraints and combined this with structural modeling. These restraints additionally define the interaction network of the clots and provide molecular details for the interaction with human serum albumin (HSA). We were able to construct the structural models of the fibrinogen α-chain (excluding two highly flexible regions) and the N termini of the β-chain, confirm these models with known structural arrangements, and map how the structure laterally aggregates to form intricate lattices together with the γ-chain. We validate the final model by mapping mutations leading to impaired clot formation. From a list of 22 mutations, we uncovered structural features for all, including a crucial role for βArg’169 (UniProt: 196) in lateral aggregation. The resulting model can potentially serve for research on dysfibrinogenemia and amyloidosis as it provides insights into the molecular mechanisms of thrombosis and bleeding disorders related to fibrinogen variants. The structure is provided in the PDB-DEV repository (PDBDEV_00000030).

    更新日期:2020-01-13
  • Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling [Commentaries]
    PNAS (IF 9.580) Pub Date : 2020-01-10
    Ronald M. Levy

    Uncovering mechanisms of protein function is challenging when structural characterization of the functionally relevant states is elusive, for instance for large and flexible proteins which resist crystallization. This is the case for structural maintenance of chromosomes (SMC) proteins and kleisin subunits which are crucial for the segregation of chromosomes during cell division but whose mechanism to organize chromosomes for replication is not known. The two most prominent multisubunit SMC complexes are cohesin and condensin, which form large complexes (more than 650 kDa for condensin) containing long antiparallel coiled coils, making them difficult to study by conventional crystallography or cryoelectron microscopy. Integrative structural biology techniques have arisen in response to these challenges which attempt to solve the puzzle by combining incomplete information from diverse experimental data with computational and theoretical results (1). In PNAS, Krepel et al. (2) use an integrative approach to understanding the mechanism of SMC action which incorporates evolutionary sequence analysis with molecular simulations based on an energy landscape optimized effective potential (AWSEM, associative memory, water-mediated, structure and energy model) along with crystallographic structural information and cross-linking experimental data to map features of the conformational and energy landscapes of SMC proteins. A complete atom-level structural model of …

    更新日期:2020-01-13
  • Metabolic dysregulation in the Atp7b-/- Wilson’s disease mouse model [Medical Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-10
    Clavia Ruth Wooton-Kee, Matthew Robertson, Ying Zhou, Bingning Dong, Zhen Sun, Kang Ho Kim, Hailan Liu, Yong Xu, Nagireddy Putluri, Pradip Saha, Cristian Coarfa, David D. Moore, Alli M. Nuotio-Antar

    Inactivating mutations in the copper transporter Atp7b result in Wilson’s disease. The Atp7b−/− mouse develops hallmarks of Wilson’s disease. The activity of several nuclear receptors decreased in Atp7b−/− mice, and nuclear receptors are critical for maintaining metabolic homeostasis. Therefore, we anticipated that Atp7b−/− mice would exhibit altered progression of diet-induced obesity, fatty liver, and insulin resistance. Following 10 wk on a chow or Western-type diet (40% kcal fat), parameters of glucose and lipid homeostasis were measured. Hepatic metabolites were measured by liquid chromatography–mass spectrometry and correlated with transcriptomic data. Atp7b−/− mice fed a chow diet presented with blunted body-weight gain over time, had lower fat mass, and were more glucose tolerant than wild type (WT) littermate controls. On the Western diet, Atp7b−/− mice exhibited reduced body weight, adiposity, and hepatic steatosis compared with WT controls. Atp7b−/− mice fed either diet were more insulin sensitive than WT controls; however, fasted Atp7b−/− mice exhibited hypoglycemia after administration of insulin due to an impaired glucose counterregulatory response, as evidenced by reduced hepatic glucose production. Coupling gene expression with metabolomic analyses, we observed striking changes in hepatic metabolic profiles in Atp7b−/− mice, including increases in glycolytic intermediates and components of the tricarboxylic acid cycle. In addition, the active phosphorylated form of AMP kinase was significantly increased in Atp7b−/− mice relative to WT controls. Alterations in hepatic metabolic profiles and nuclear receptor signaling were associated with improved glucose tolerance and insulin sensitivity as well as with impaired fasting glucose production in Atp7b−/− mice.

    更新日期:2020-01-13
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