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Journal Cover
Proceedings of the National Academy of Sciences
Journal Prestige (SJR): 6.092
Citation Impact (citeScore): 9
Number of Followers: 1044  
  Full-text available via subscription Subscription journal
ISSN (Print) 0027-8424 - ISSN (Online) 1091-6490
Published by PNAS Homepage  [1 journal]
  • In This Issue [This Week in PNAS]
    • Pages: 2389 - 2389
      Abstract: Visualizing flu virus uncoating in infected cells Transmission electron micrograph of IAV virions encapsulating quantum dots. The genome of influenza A virus (IAV) comprises eight segmented RNA strands enclosed in a coat. During infection, the virus is uncoated in the cytoplasm of host cells, viral RNA is imported into the...
      Keywords: In This Issue
      PubDate: 2019-02-12T09:46:13-08:00
      DOI: 10.1073/iti0719116
      Issue No: Vol. 116, No. 7 (2019)
  • Ontogenetic deepening of Northeast Atlantic fish stocks is not driven by
           fishing exploitation [Biological Sciences]
    • Authors: Alan R. Baudron; Gretta Pecl, Caleb Gardner, Paul G. Fernandes, Asta Audzijonyte
      Pages: 2390 - 2392
      Abstract: For many marine fish species, the average size of individuals increases with depth. This phenomenon, first described a century ago, is known as ontogenetic deepening (1, 2). Several mechanisms have been proposed to explain it: optimal foraging; predation avoidance; and different optimal growth temperature for larger individuals, causing them to...
      Keywords: Letters
      PubDate: 2019-02-12T09:46:13-08:00
      DOI: 10.1073/pnas.1817295116
      Issue No: Vol. 116, No. 7 (2019)
  • Reply to Baudron et al.: Fishing matters: Age-specific deepening is driven
           by exploitation [Biological Sciences]
    • Authors: Kenneth T. Frank; Brian Petrie, William C. Leggett, Daniel G. Boyce
      Pages: 2393 - 2394
      Abstract: In their response to our paper “Exploitation drives an ontogenetic-like deepening in marine fish” (1), Baudron et al. (2) unfairly characterize our result as an alternative explanation. Throughout our paper, and in the closing remark, we explicitly state that additional factors must be considered: “Ontogenetic factors, fisheries exploitation, and climate...
      Keywords: Letters
      PubDate: 2019-02-12T09:46:13-08:00
      DOI: 10.1073/pnas.1819288116
      Issue No: Vol. 116, No. 7 (2019)
  • Zinc depletion does not necessarily induce ribosome hibernation in
           mycobacteria [Biological Sciences]
    • Authors: Victor Tobiasson; Allexa Dow, Sladjana Prisic, A. Amunts
      Pages: 2395 - 2397
      Abstract: In PNAS, Li et al. (1) recently reported analysis of Mycobacterium smegmatis ribosomes formed under zinc-limited conditions. A zinc chelator [N,N,N′,N′-tetrakis(2-pyridylmethyl)-ethylenediamine] was added to growth medium and an extended purification procedure was employed to obtain zinc-depleted (C−) ribosomes for cryo-EM. The structure was solved at 3.5-Å resolution and showed five...
      Keywords: Letters
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1817490116
      Issue No: Vol. 116, No. 7 (2019)
  • Reply to Tobiasson et al.: Zinc depletion is a specific signal for
           induction of ribosome hibernation in mycobacteria [Biological Sciences]
    • Authors: Yunlong Li; Manjuli R. Sharma, Ravi K. Koripella, Joseph T. Wade, Todd A. Gray, Keith M. Derbyshire, Rajendra K. Agrawal, Anil K. Ojha
      Pages: 2398 - 2399
      Abstract: We previously reported (1) in PNAS that zinc depletion in Mycobacterium smegmatis leads to reprogramming of ribosomes in which five ribosomal proteins (r-proteins) with a conserved zinc-finger CXXC motif (C+) are replaced by their paralogs lacking the motif (C−). Notably, the reprogrammed ribosomes enter into a hibernating state by binding...
      Keywords: Letters
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1821103116
      Issue No: Vol. 116, No. 7 (2019)
  • Opinion: “Plan S” falls short for society publishers—and for the
           researchers they serve [Physics]
    • Authors: Marcia McNutt
      Pages: 2400 - 2403
      Abstract: Over the course of my long scientific career, I have had experience with academic publishing from several perspectives: as an author, as an associate editor of both academic and for-profit journals, as chair of a society’s journals board, as editor-in-chief of a major society journal (Science), and now as the...
      Keywords: Opinions, Front Matter
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1900359116
      Issue No: Vol. 116, No. 7 (2019)
  • Quantum dots crack the influenza uncoating puzzle [Biophysics and
           Computational Biology]
    • Authors: Yohei Yamauchi
      Pages: 2404 - 2406
      Abstract: One hundred years ago, the devastating 1918–1919 Spanish influenza pandemic took the lives of 50 to 100 million people, or 3 to 5% of the world population (1). Influenza A virus (IAV) pandemics occur when an animal IAV crosses the species barrier, usually by acquiring a new genetic trait by...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1822089116
      Issue No: Vol. 116, No. 7 (2019)
  • Species coexistence through competition and rapid evolution [Ecology]
    • Authors: Malin L. Pinsky
      Pages: 2407 - 2409
      Abstract: With nature “red in tooth and claw” (1), how do so many species coexist' Why do some species not outcompete the others to extinction' This is a question that has long fascinated ecologists and evolutionary biologists (2), especially given the incredible diversity of seemingly similar species in tropical forests or...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1822091116
      Issue No: Vol. 116, No. 7 (2019)
  • Biodiversity conservation of Morlocks in west-central Texas [Evolution]
    • Authors: C. Richard Tracy
      Pages: 2410 - 2412
      Abstract: In PNAS, Devitt et al. (1) present a profoundly interesting and important report of phylogeographic and phylogenetic analyses of a group of salamanders in the genus Eurycea in the Edwards and Trinity aquifers in west-central Texas. These analyses led the authors to extend the scope of their study to analyze...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1821145116
      Issue No: Vol. 116, No. 7 (2019)
  • Thickness scaling of ferroelectricity in BiFeO3 by tomographic atomic
           force microscopy [Applied Physical Sciences]
    • Authors: James J. Steffes; Roger A. Ristau, Ramamoorthy Ramesh, Bryan D. Huey
      Pages: 2413 - 2418
      Abstract: Nanometer-scale 3D imaging of materials properties is critical for understanding equilibrium states in electronic materials, as well as for optimization of device performance and reliability, even though such capabilities remain a substantial experimental challenge. Tomographic atomic force microscopy (TAFM) is presented as a subtractive scanning probe technique for high-resolution, 3D...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1806074116
      Issue No: Vol. 116, No. 7 (2019)
  • Flow interactions between uncoordinated flapping swimmers give rise to
           group cohesion [Applied Physical Sciences]
    • Authors: Joel W. Newbolt; Jun Zhang, Leif Ristroph
      Pages: 2419 - 2424
      Abstract: Many species of fish and birds travel in groups, yet the role of fluid-mediated interactions in schools and flocks is not fully understood. Previous fluid-dynamical models of these collective behaviors assume that all individuals flap identically, whereas animal groups involve variations across members as well as active modifications of wing...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1816098116
      Issue No: Vol. 116, No. 7 (2019)
  • Magnetic control of graphitic microparticles in aqueous solutions [Applied
           Physical Sciences]
    • Authors: Johnny Nguyen; Dario Valter Conca, Johannes Stein, Laura Bovo, Chris A. Howard, Isabel Llorente Garcia
      Pages: 2425 - 2434
      Abstract: Graphite is an inexpensive material with useful electrical, magnetic, thermal, and optical properties. It is also biocompatible and used universally as a substrate. Micrometer-sized graphitic particles in solution are therefore ideal candidates for novel lab-on-a-chip and remote manipulation applications in biomedicine, biophysics, chemistry, and condensed-matter physics. However, submerged graphite is...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1817989116
      Issue No: Vol. 116, No. 7 (2019)
  • SNARE machinery is optimized for ultrafast fusion [Biophysics and
           Computational Biology]
    • Authors: Fabio Manca; Frederic Pincet, Lev Truskinovsky, James E. Rothman, Lionel Foret, Matthieu Caruel
      Pages: 2435 - 2442
      Abstract: SNARE proteins zipper to form complexes (SNAREpins) that power vesicle fusion with target membranes in a variety of biological processes. A single SNAREpin takes about 1 s to fuse two bilayers, yet a handful can ensure release of neurotransmitters from synaptic vesicles much faster: in a 10th of a millisecond....
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1820394116
      Issue No: Vol. 116, No. 7 (2019)
  • Exploring fast proton transfer events associated with lateral proton
           diffusion on the surface of membranes [Chemistry]
    • Authors: Nadav Amdursky; Yiyang Lin, Noora Aho, Gerrit Groenhof
      Pages: 2443 - 2451
      Abstract: Proton diffusion (PD) across biological membranes is a fundamental process in many biological systems, and much experimental and theoretical effort has been employed for deciphering it. Here, we report on a spectroscopic probe, which can be tightly tethered to the membrane, for following fast (nanosecond) proton transfer events on the...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1812351116
      Issue No: Vol. 116, No. 7 (2019)
  • Effects of knot tightness at the molecular level [Chemistry]
    • Authors: Liang Zhang; Jean–Francois Lemonnier, Angela Acocella, Matteo Calvaresi, Francesco Zerbetto, David A. Leigh
      Pages: 2452 - 2457
      Abstract: Three 819 knots in closed-loop strands of different lengths (∼20, 23, and 26 nm) were used to experimentally assess the consequences of knot tightness at the molecular level. Through the use of 1H NMR, diffusion-ordered spectroscopy (DOSY), circular dichroism (CD), collision-induced dissociation mass spectrometry (CID-MS) and molecular dynamics (MD) simulations...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1815570116
      Issue No: Vol. 116, No. 7 (2019)
  • Impact of nuclear quantum effects on the structural inhomogeneity of
           liquid water [Chemistry]
    • Authors: Arian Berger; Gustavo Ciardi, David Sidler, Peter Hamm, Andrey Shalit
      Pages: 2458 - 2463
      Abstract: The 2D Raman–terahertz (THz) response of liquid water is studied in dependence of temperature and isotope substitution (H2O, D2O, and H218O). In either case, a very short-lived (i.e., between 75 and 95 fs) echo is observed that reports on the inhomogeneity of the low-frequency intermolecular modes and hence, on the...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1818182116
      Issue No: Vol. 116, No. 7 (2019)
  • Dynamics of geologic CO2 storage and plume motion revealed by seismic coda
           waves [Earth, Atmospheric, and Planetary Sciences]
    • Authors: Tieyuan Zhu; Jonathan Ajo-Franklin, Thomas M. Daley, Chris Marone
      Pages: 2464 - 2469
      Abstract: Quantifying the dynamics of sequestered CO2 plumes is critical for safe long-term storage, providing guidance on plume extent, and detecting stratigraphic seal failure. However, existing seismic monitoring methods based on wave reflection or transmission probe a limited rock volume and their sensitivity decreases as CO2 saturation increases, decreasing their utility...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1810903116
      Issue No: Vol. 116, No. 7 (2019)
  • Influences of light and humidity on carbonyl sulfide-based estimates of
           photosynthesis [Earth, Atmospheric, and Planetary Sciences]
    • Authors: Linda M. J. Kooiȷmans; Wu Sun, Juho Aalto, Kukka–Maaria Erkkila, Kadmiel Maseyk, Ulrike Seibt, Timo Vesala, Ivan Mammarella, Huilin Chen
      Pages: 2470 - 2475
      Abstract: Understanding climate controls on gross primary productivity (GPP) is crucial for accurate projections of the future land carbon cycle. Major uncertainties exist due to the challenge in separating GPP and respiration from observations of the carbon dioxide (CO2) flux. Carbonyl sulfide (COS) has a dominant vegetative sink, and plant COS...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1807600116
      Issue No: Vol. 116, No. 7 (2019)
  • Realizing the potential of dielectric elastomer artificial muscles
    • Authors: Mihai Duduta; Ehsan Hajiesmaili, Huichan Zhao, Robert J. Wood, David R. Clarke
      Pages: 2476 - 2481
      Abstract: Soft robotics represents a new set of technologies aimed at operating in natural environments and near the human body. To interact with their environment, soft robots require artificial muscles to actuate movement. These artificial muscles need to be as strong, fast, and robust as their natural counterparts. Dielectric elastomer actuators...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1815053116
      Issue No: Vol. 116, No. 7 (2019)
  • Directional pumping of water and oil microdroplets on slippery surface
    • Authors: Jieke Jiang; Jun Gao, Hengdi Zhang, Wenqing He, Jianqiang Zhang, Dan Daniel, Xi Yao
      Pages: 2482 - 2487
      Abstract: Transporting water and oil microdroplets is important for applications ranging from water harvesting to biomedical analysis but remains a great challenge. This is due to the amplified contact angle hysteresis and insufficient driving force in the micrometer scale, especially for low-surface energy oil droplets. Coalescence of neighboring droplets, which releases...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1817172116
      Issue No: Vol. 116, No. 7 (2019)
  • Fluorescent reconstitution on deposition of PM2.5 in lung and
           extrapulmonary organs [Applied Biological Sciences]
    • Authors: Donghai Li; Yongjian Li, Guiling Li, Yu Zhang, Jiang Li, Haosheng Chen
      Pages: 2488 - 2493
      Abstract: The deposition of PM2.5 (fine particulate matter in air with diameter smaller than 2.5 μm) in lungs is harmful to human health. However, real-time observation on the deposition of particles in the acinar area of the lung is still a challenge in experiments. Here, a fluorescent imaging method is developed...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1818134116
      Issue No: Vol. 116, No. 7 (2019)
  • Stratification of reactivity determines nitrate removal in groundwater
           [Environmental Sciences]
    • Authors: Tamara Kolbe; Jean–Raynald de Dreuzy, Benȷamin W. Abbott, Luc Aquilina, Tristan Babey, Christopher T. Green, Jan H. Fleckenstein, Thierry Labasque, Anniet M. Laverman, Jean Marcais, Stefan Peiffer, Zahra Thomas, Gilles Pinay
      Pages: 2494 - 2499
      Abstract: Biogeochemical reactions occur unevenly in space and time, but this heterogeneity is often simplified as a linear average due to sparse data, especially in subsurface environments where access is limited. For example, little is known about the spatial variability of groundwater denitrification, an important process in removing nitrate originating from...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1816892116
      Issue No: Vol. 116, No. 7 (2019)
  • Actuation of magnetoelastic membranes in precessing magnetic fields
    • Authors: Chase Austyn Brisbois; Mykola Tasinkevych, Pablo Vazquez–Monteȷo, Monica Olvera de la Cruz
      Pages: 2500 - 2505
      Abstract: Superparamagnetic nanoparticles incorporated into elastic media offer the possibility of creating actuators driven by external fields in a multitude of environments. Here, magnetoelastic membranes are studied through a combination of continuum mechanics and molecular dynamics simulations. We show how induced magnetic interactions affect the buckling and the configuration of magnetoelastic...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1816731116
      Issue No: Vol. 116, No. 7 (2019)
  • Limits of multifunctionality in tunable networks [Physics]
    • Authors: Jason W. Rocks; Henrik Ronellenfitsch, Andrea J. Liu, Sidney R. Nagel, Eleni Katifori
      Pages: 2506 - 2511
      Abstract: Nature is rife with networks that are functionally optimized to propagate inputs to perform specific tasks. Whether via genetic evolution or dynamic adaptation, many networks create functionality by locally tuning interactions between nodes. Here we explore this behavior in two contexts: strain propagation in mechanical networks and pressure redistribution in...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1806790116
      Issue No: Vol. 116, No. 7 (2019)
  • Dynamics of frequency-swept nuclear spin optical pumping in powdered
           diamond at low magnetic fields [Physics]
    • Authors: Pablo R. Zangara; Siddharth Dhomkar, Ashok Ajoy, Kristina Liu, Raffi Nazaryan, Daniela Pagliero, Dieter Suter, Jeffrey A. Reimer, Alexander Pines, Carlos A. Meriles
      Pages: 2512 - 2520
      Abstract: A broad effort is underway to improve the sensitivity of NMR through the use of dynamic nuclear polarization. Nitrogen vacancy (NV) centers in diamond offer an appealing platform because these paramagnetic defects can be optically polarized efficiently at room temperature. However, work thus far has been mainly limited to single...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1811994116
      Issue No: Vol. 116, No. 7 (2019)
  • Fighting misinformation on social media using crowdsourced judgments of
           news source quality [Psychological and Cognitive Sciences]
    • Authors: Gordon Pennycook; David G. Rand
      Pages: 2521 - 2526
      Abstract: Reducing the spread of misinformation, especially on social media, is a major challenge. We investigate one potential approach: having social media platform algorithms preferentially display content from news sources that users rate as trustworthy. To do so, we ask whether crowdsourced trust ratings can effectively differentiate more versus less reliable...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1806781116
      Issue No: Vol. 116, No. 7 (2019)
  • The impact of income, land, and wealth inequality on agricultural
           expansion in Latin America [Sustainability Science]
    • Authors: M. Graziano Ceddia
      Pages: 2527 - 2532
      Abstract: Agricultural expansion remains the most prominent proximate cause of tropical deforestation in Latin America, a region characterized by deforestation rates substantially above the world average and extremely high inequality. This paper deploys several multivariate statistical models to test whether different aspects of inequality, within a context of increasing agricultural productivity,...
      Keywords: Sustainability Science
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1814894116
      Issue No: Vol. 116, No. 7 (2019)
  • Zn-dependent bifunctional proteases are responsible for leader peptide
           processing of class III lanthipeptides [Chemistry]
    • Authors: Shaoming Chen; Bing Xu, Erquan Chen, Jiaqi Wang, Jingxia Lu, Stefano Donadio, Huiming Ge, Huan Wang
      Pages: 2533 - 2538
      Abstract: Lanthipeptides are an important subfamily of ribosomally synthesized and posttranslationally modified peptides, and the removal of their N-terminal leader peptides by a designated protease(s) is a key step during maturation. Whereas proteases for class I and II lanthipeptides are well-characterized, the identity of the protease(s) responsible for class III leader...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1815594116
      Issue No: Vol. 116, No. 7 (2019)
  • Peptidic degron for IMiD-induced degradation of heterologous proteins
    • Authors: Vidyasagar Koduri; Samuel K. McBrayer, Ella Liberzon, Adam C. Wang, Kimberly J. Briggs, Hyejin Cho, William G. Kaelin Jr.
      Pages: 2539 - 2544
      Abstract: Current systems for modulating the abundance of proteins of interest in living cells are powerful tools for studying protein function but differ in terms of their complexity and ease of use. Moreover, no one system is ideal for all applications, and the best system for a given protein of interest...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1818109116
      Issue No: Vol. 116, No. 7 (2019)
  • Structure-based development of new RAS-effector inhibitors from a
           combination of active and inactive RAS-binding compounds [Biochemistry]
    • Authors: Abimael Cruz-Migoni; Peter Canning, Camilo E. Quevedo, Carole J. R. Bataille, Nicolas Bery, Ami Miller, Angela J. Russell, Simon E. V. Phillips, Stephen B. Carr, Terence H. Rabbitts
      Pages: 2545 - 2550
      Abstract: The RAS gene family is frequently mutated in human cancers, and the quest for compounds that bind to mutant RAS remains a major goal, as it also does for inhibitors of protein–protein interactions. We have refined crystallization conditions for KRAS169Q61H-yielding crystals suitable for soaking with compounds and exploited this to...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1811360116
      Issue No: Vol. 116, No. 7 (2019)
  • Discovery of potent SOS1 inhibitors that block RAS activation via
           disruption of the RAS-SOS1 interaction [Biochemistry]
    • Authors: Roman C. Hillig; Brice Sautier, Jens Schroeder, Dieter Moosmayer, Andre Hilpmann, Christian M. Stegmann, Nicolas D. Werbeck, Hans Briem, Ulf Boemer, Joerg Weiske, Volker Badock, Julia Mastouri, Kirstin Petersen, Gerhard Siemeister, Jan D. Kahmann, Dennis Wegener, Niels Bohnke, Knut Eis, Keith Graham, Lars Wortmann, Franz von Nussbaum, Benȷamin Bader
      Pages: 2551 - 2560
      Abstract: Since the late 1980s, mutations in the RAS genes have been recognized as major oncogenes with a high occurrence rate in human cancers. Such mutations reduce the ability of the small GTPase RAS to hydrolyze GTP, keeping this molecular switch in a constitutively active GTP-bound form that drives, unchecked, oncogenic...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1812963116
      Issue No: Vol. 116, No. 7 (2019)
  • Fanconi anemia protein FANCI functions in ribosome biogenesis
    • Authors: Samuel B. Sondalle; Simonne Longerich, Lisa M. Ogawa, Patrick Sung, Susan J. Baserga
      Pages: 2561 - 2570
      Abstract: Fanconi anemia (FA) is a disease of DNA repair characterized by bone marrow failure and a reduced ability to remove DNA interstrand cross-links. Here, we provide evidence that the FA protein FANCI also functions in ribosome biogenesis, the process of making ribosomes that initiates in the nucleolus. We show that...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1811557116
      Issue No: Vol. 116, No. 7 (2019)
  • Thermodynamically reversible paths of the first fusion intermediate reveal
           an important role for membrane anchors of fusion proteins [Biophysics and
           Computational Biology]
    • Authors: Yuliya G. Smirnova; Herre Jelger Risselada, Marcus Muller
      Pages: 2571 - 2576
      Abstract: Biological membrane fusion proceeds via an essential topological transition of the two membranes involved. Known players such as certain lipid species and fusion proteins are generally believed to alter the free energy and thus the rate of the fusion reaction. Quantifying these effects by theory poses a major challenge since...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1818200116
      Issue No: Vol. 116, No. 7 (2019)
  • Real-time dissection of dynamic uncoating of individual influenza viruses
           [Biophysics and Computational Biology]
    • Authors: Chong Qin; Wei Li, Qin Li, Wen Yin, Xiaowei Zhang, Zhiping Zhang, Xian-En Zhang, Zongqiang Cui
      Pages: 2577 - 2582
      Abstract: Uncoating is an obligatory step in the virus life cycle that serves as an antiviral target. Unfortunately, it is challenging to study viral uncoating due to methodology limitations for detecting this transient and dynamic event. The uncoating of influenza A virus (IAV), which contains an unusual genome of eight segmented...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1812632116
      Issue No: Vol. 116, No. 7 (2019)
  • Transcription factor regulation of RNA polymerase’s torque generation
           capacity [Biophysics and Computational Biology]
    • Authors: Jie Ma, Chuang Tan, Xiang Gao, Robert M. Fulbright Jr; Jeffrey W. Roberts, Michelle D. Wang
      Pages: 2583 - 2588
      Abstract: During transcription, RNA polymerase (RNAP) supercoils DNA as it translocates. The resulting torsional stress in DNA can accumulate and, in the absence of regulatory mechanisms, becomes a barrier to RNAP elongation, causing RNAP stalling, backtracking, and transcriptional arrest. Here we investigate whether and how a transcription factor may regulate both...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1807031116
      Issue No: Vol. 116, No. 7 (2019)
  • Quantification of reaction cycle parameters for an essential molecular
           switch in an auxin-responsive transcription circuit in rice [Biophysics
           and Computational Biology]
    • Authors: Lucila Andrea Acevedo; Jeahoo Kwon, Linda K. Nicholson
      Pages: 2589 - 2594
      Abstract: Protein-based molecular switches play critical roles in biological processes. The importance of the prolyl cis−trans switch is underscored by the ubiquitous presence of peptidyl prolyl isomerases such as cyclophilins that accelerate the intrinsically slow isomerization rate. In rice, a tryptophan−proline (W-P) cis−trans switch in transcription repressor protein OsIAA11 along with...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1817038116
      Issue No: Vol. 116, No. 7 (2019)
  • Torsional stress generated by ADF/cofilin on cross-linked actin filaments
           boosts their severing [Biophysics and Computational Biology]
    • Authors: Hugo Wioland; Antoine Jegou, Guillaume Romet-Lemonne
      Pages: 2595 - 2602
      Abstract: Proteins of the actin depolymerizing factor (ADF)/cofilin family are the central regulators of actin filament disassembly. A key function of ADF/cofilin is to sever actin filaments. However, how it does so in a physiological context, where filaments are interconnected and under mechanical stress, remains unclear. Here, we monitor and quantify...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1812053116
      Issue No: Vol. 116, No. 7 (2019)
  • Cells exhibiting strong p16INK4a promoter activation in vivo display
           features of senescence [Cell Biology]
    • Authors: Jie-Yu Liu; George P. Souroullas, Brian O. Diekman, Janakiraman Krishnamurthy, Brandon M. Hall, Jessica A. Sorrentino, Joel S. Parker, Garrett A. Sessions, Andrei V. Gudkov, Norman E. Sharpless
      Pages: 2603 - 2611
      Abstract: The activation of cellular senescence throughout the lifespan promotes tumor suppression, whereas the persistence of senescent cells contributes to aspects of aging. This theory has been limited, however, by an inability to identify and isolate individual senescent cells within an intact organism. Toward that end, we generated a murine reporter...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1818313116
      Issue No: Vol. 116, No. 7 (2019)
  • Regional neutrality evolves through local adaptive niche evolution
    • Authors: Mathew A. Leibold; Mark C. Urban, Luc De Meester, Christopher A. Klausmeier, Joost Vanoverbeke
      Pages: 2612 - 2617
      Abstract: Biodiversity in natural systems can be maintained either because niche differentiation among competitors facilitates stable coexistence or because equal fitness among neutral species allows for their long-term cooccurrence despite a slow drift toward extinction. Whereas the relative importance of these two ecological mechanisms has been well-studied in the absence of...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1808615116
      Issue No: Vol. 116, No. 7 (2019)
  • Transitions between foot postures are associated with elevated rates of
           body size evolution in mammals [Evolution]
    • Authors: Tai Kubo; Manabu Sakamoto, Andrew Meade, Chris Venditti
      Pages: 2618 - 2623
      Abstract: Terrestrial mammals have evolved various foot postures: flat-footed (plantigrady), tiptoed (digitigrady), and hooved (unguligrady) postures. Although the importance of foot posture on ecology and body size of mammalian species has been widely recognized, its evolutionary trajectory and influence on body size evolution across mammalian phylogeny remain untested. Taking a Bayesian...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1814329116
      Issue No: Vol. 116, No. 7 (2019)
  • Species delimitation in endangered groundwater salamanders: Implications
           for aquifer management and biodiversity conservation [Evolution]
    • Authors: Thomas J. Devitt; April M. Wright, David C. Cannatella, David M. Hillis
      Pages: 2624 - 2633
      Abstract: Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards–Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1815014116
      Issue No: Vol. 116, No. 7 (2019)
  • Genetically modified hematopoietic stem/progenitor cells that produce
           IL-10-secreting regulatory T cells [Immunology and Inflammation]
    • Authors: Sze-Ling Ng; Ester Leno-Duran, Dibyendu Samanta, Steven C. Almo, Jack L. Strominger
      Pages: 2634 - 2639
      Abstract: Random amino acid copolymers used in the treatment of multiple sclerosis in man or experimental autoimmune encephalomyelitis (EAE) in mice [poly(Y,E,A,K)n, known as Copaxone, and poly(Y,F,A,K)n] function at least in part by generation of IL-10–secreting regulatory T cells that mediate bystander immunosuppression. The mechanism through which these copolymers induce Tregs...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1811984116
      Issue No: Vol. 116, No. 7 (2019)
  • Reprogramming responsiveness to checkpoint blockade in dysfunctional CD8 T
           cells [Immunology and Inflammation]
    • Authors: Christine E. Nelson; Lauren J. Mills, Jennifer L. McCurtain, Emily A. Thompson, Davis M. Seelig, Siddheshvar Bhela, Clare F. Quarnstrom, Brian T. Fife, Vaiva Vezys
      Pages: 2640 - 2645
      Abstract: Established T cell dysfunction is a barrier to antitumor responses, and checkpoint blockade presumably reverses this. Many patients fail to respond to treatment and/or develop autoimmune adverse events. The underlying reason for T cell responsiveness remains elusive. Here, we show that susceptibility to checkpoint blockade is dependent on the activation...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1810326116
      Issue No: Vol. 116, No. 7 (2019)
  • IL-33/regulatory T cell axis triggers the development of a tumor-promoting
           immune environment in chronic inflammation [Immunology and Inflammation]
    • Authors: Amir H. Ameri; Sara Moradi Tuchayi, Anniek Zaalberg, Jong Ho Park, Kenneth H. Ngo, Tiancheng Li, Elena Lopez, Marco Colonna, Richard T. Lee, Mari Mino-Kenudson, Shadmehr Demehri
      Pages: 2646 - 2651
      Abstract: Chronic inflammation’s tumor-promoting potential is well-recognized; however, the mechanism underlying the development of this immune environment is unknown. Studying the transition from acute, tumor-suppressive to chronic, tumor-promoting allergic contact dermatitis (ACD) revealed how tumor-promoting chronic inflammation develops. Epidermis-derived interleukin (IL)-33 up-regulation and its induction of regulatory T cell (Treg) accumulation...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1815016116
      Issue No: Vol. 116, No. 7 (2019)
  • Mutual interplay between IL-17-producing {gamma}{delta}T cells and
           microbiota orchestrates oral mucosal homeostasis [Immunology and
    • Authors: Anneke Wilharm; Yaara Tabib, Maria Nassar, Annika Reinhardt, Gabriel Mizraȷi, Inga Sandrock, Oded Heyman, Joana Barros–Martins, Yuval Aizenbud, Abed Khalaileh, Luba Eli–Berchoer, Eran Elinav, Asaf Wilensky, Reinhold Forster, Herve Bercovier, Immo Prinz, Avi–Hai Hovav
      Pages: 2652 - 2661
      Abstract: γδT cells are a major component of epithelial tissues and play a role in tissue homeostasis and host defense. γδT cells also reside in the gingiva, an oral tissue covered with specialized epithelium that continuously monitors the challenging dental biofilm. Whereas most research on intraepithelial γδT cells focuses on the...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1818812116
      Issue No: Vol. 116, No. 7 (2019)
  • Experimental and computational analyses reveal dynamics of tumor vessel
           cooption and optimal treatment strategies [Medical Sciences]
    • Authors: Chrysovalantis Voutouri; Nathaniel D. Kirkpatrick, Euiheon Chung, Fotios Mpekris, James W. Baish, Lance L. Munn, Dai Fukumura, Triantafyllos Stylianopoulos, Rakesh K. Jain
      Pages: 2662 - 2671
      Abstract: Cooption of the host vasculature is a strategy that some cancers use to sustain tumor progression without—or before—angiogenesis or in response to antiangiogenic therapy. Facilitated by certain growth factors, cooption can mediate tumor infiltration and confer resistance to antiangiogenic drugs. Unfortunately, this mode of tumor progression is difficult to target...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1818322116
      Issue No: Vol. 116, No. 7 (2019)
  • Ferroptosis as a target for protection against cardiomyopathy [Medical
    • Authors: Xuexian Fang; Hao Wang, Dan Han, Enjun Xie, Xiang Yang, Jiayu Wei, Shanshan Gu, Feng Gao, Nali Zhu, Xiangju Yin, Qi Cheng, Pan Zhang, Wei Dai, Jinghai Chen, Fuquan Yang, Huang-Tian Yang, Andreas Linkermann, Wei Gu, Junxia Min, Fudi Wang
      Pages: 2672 - 2680
      Abstract: Heart disease is the leading cause of death worldwide. A key pathogenic factor in the development of lethal heart failure is loss of terminally differentiated cardiomyocytes. However, mechanisms of cardiomyocyte death remain unclear. Here, we discovered and demonstrated that ferroptosis, a programmed iron-dependent cell death, as a mechanism in murine...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1821022116
      Issue No: Vol. 116, No. 7 (2019)
  • Human coronaviruses OC43 and HKU1 bind to 9-O-acetylated sialic acids via
           a conserved receptor-binding site in spike protein domain A [Microbiology]
    • Authors: Ruben J. G. Hulswit; Yifei Lang, Mark J. G. Bakkers, Wentao Li, Zeshi Li, Arie Schouten, Bram Ophorst, Frank J. M. van Kuppeveld, Geert-Jan Boons, Berend-Jan Bosch, Eric G. Huizinga, Raoul J. de Groot
      Pages: 2681 - 2690
      Abstract: Human betacoronaviruses OC43 and HKU1 are endemic respiratory pathogens and, while related, originated from independent zoonotic introductions. OC43 is in fact a host-range variant of the species Betacoronavirus-1, and more closely related to bovine coronavirus (BCoV)—its presumptive ancestor—and porcine hemagglutinating encephalomyelitis virus (PHEV). The β1-coronaviruses (β1CoVs) and HKU1 employ glycan-based...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1809667116
      Issue No: Vol. 116, No. 7 (2019)
  • Agent-based representations of objects and actions in the monkey
           pre-supplementary motor area [Neuroscience]
    • Authors: Alessandro Livi; Marco Lanzilotto, Monica Maranesi, Leonardo Fogassi, Giacomo Rizzolatti, Luca Bonini
      Pages: 2691 - 2700
      Abstract: Information about objects around us is essential for planning actions and for predicting those of others. Here, we studied pre-supplementary motor area F6 neurons with a task in which monkeys viewed and grasped (or refrained from grasping) objects, and then observed a human doing the same task. We found “action-related...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1810890116
      Issue No: Vol. 116, No. 7 (2019)
  • The glutathione cycle shapes synaptic glutamate activity [Neuroscience]
    • Authors: Thomas W. Sedlak; Bindu D. Paul, Gregory M. Parker, Lynda D. Hester, Adele M. Snowman, Yu Taniguchi, Atsushi Kamiya, Solomon H. Snyder, Akira Sawa
      Pages: 2701 - 2706
      Abstract: Glutamate is the most abundant excitatory neurotransmitter, present at the bulk of cortical synapses, and participating in many physiologic and pathologic processes ranging from learning and memory to stroke. The tripeptide, glutathione, is one-third glutamate and present at up to low millimolar intracellular concentrations in brain, mediating antioxidant defenses and...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1817885116
      Issue No: Vol. 116, No. 7 (2019)
  • Inositol polyphosphate multikinase mediates extinction of fear memory
    • Authors: Jina Park; Francesco Longo, Seung Ju Park, Seulgi Lee, Mihyun Bae, Richa Tyagi, Jin-Hee Han, Seyun Kim, Emanuela Santini, Eric Klann, Solomon H. Snyder
      Pages: 2707 - 2712
      Abstract: Inositol polyphosphate multikinase (IPMK), the key enzyme for the biosynthesis of higher inositol polyphosphates and phosphatidylinositol 3,4,5-trisphosphate, also acts as a versatile signaling player in regulating tissue growth and metabolism. To elucidate neurobehavioral functions of IPMK, we generated mice in which IPMK was deleted from the excitatory neurons of the...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1812771116
      Issue No: Vol. 116, No. 7 (2019)
  • Developmental trajectory of social influence integration into perceptual
           decisions in children [Neuroscience]
    • Authors: Imogen Large; Elizabeth Pellicano, Andreas Mojzisch, Kristine Krug
      Pages: 2713 - 2722
      Abstract: The opinions of others have a profound influence on decision making in adults. The impact of social influence appears to change during childhood, but the underlying mechanisms and their development remain unclear. We tested 125 neurotypical children between the ages of 6 and 14 years on a perceptual decision task...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1808153116
      Issue No: Vol. 116, No. 7 (2019)
  • Stimulus complexity shapes response correlations in primary visual cortex
    • Authors: Mihaly Banyai; Andreea Lazar, Liane Klein, Johanna Klon–Lipok, Marcell Stippinger, Wolf Singer, Gergő Orban
      Pages: 2723 - 2732
      Abstract: Spike count correlations (SCCs) are ubiquitous in sensory cortices, are characterized by rich structure, and arise from structured internal dynamics. However, most theories of visual perception treat contributions of neurons to the representation of stimuli independently and focus on mean responses. Here, we argue that, in a functional model of...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1816766116
      Issue No: Vol. 116, No. 7 (2019)
  • REM sleep’s unique associations with corticosterone regulation,
    • Authors: Mathieu Nollet; Harriet Hicks, Andrew P. McCarthy, Huihai Wu, Carla S. Moller–Levet, Emma E. Laing, Karim Malki, Nathan Lawless, Keith A. Wafford, Derk–Jan Diȷk, Raphaelle Winsky–Sommerer
      Pages: 2733 - 2742
      Abstract: One of sleep’s putative functions is mediation of adaptation to waking experiences. Chronic stress is a common waking experience; however, which specific aspect of sleep is most responsive, and how sleep changes relate to behavioral disturbances and molecular correlates remain unknown. We quantified sleep, physical, endocrine, and behavioral variables, as...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1816456116
      Issue No: Vol. 116, No. 7 (2019)
  • Effective connectivity changes in LSD-induced altered states of
           consciousness in humans [Pharmacology]
    • Authors: Katrin H. Preller; Adeel Razi, Peter Zeidman, Philipp Stampfli, Karl J. Friston, Franz X. Vollenweider
      Pages: 2743 - 2748
      Abstract: Psychedelics exert unique effects on human consciousness. The thalamic filter model suggests that core effects of psychedelics may result from gating deficits, based on a disintegration of information processing within cortico–striato–thalamo-cortical (CSTC) feedback loops. To test this hypothesis, we characterized changes in directed (effective) connectivity between selected CTSC regions after...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1815129116
      Issue No: Vol. 116, No. 7 (2019)
  • North America’s oldest boreal trees are more efficient water users due
           to increased [CO2], but do not grow faster [Earth, Atmospheric, and
           Planetary Sciences]
    • Authors: Claudie Giguere–Croteau; Etienne Boucher, Yves Bergeron, Martin P. Girardin, Igor Drobyshev, Lucas C. R. Silva, Jean–Francois Helie, Michelle Garneau
      Pages: 2749 - 2754
      Abstract: Due to anthropogenic emissions and changes in land use, trees are now exposed to atmospheric levels of [CO2] that are unprecedented for 650,000 y [Lüthi et al. (2008) Nature 453:379–382] (thousands of tree generations). Trees are expected to acclimate by modulating leaf–gas exchanges and alter water use efficiency which may...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1816686116
      Issue No: Vol. 116, No. 7 (2019)
  • Enhanced resistance to bacterial and oomycete pathogens by short tandem
           target mimic RNAs in tomato [Plant Biology]
    • Authors: Alex Canto-Pastor; Bruno A. M. C. Santos, Adrian A. Valli, William Summers, Sebastian Schornack, David C. Baulcombe
      Pages: 2755 - 2760
      Abstract: Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family miRNAs that are in a distinct 22-nt class of miRNAs with a double mode of action. First, they cleave the target RNA, as with the canonical 21-nt miRNAs, and second,...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1814380116
      Issue No: Vol. 116, No. 7 (2019)
  • Maternal small RNAs mediate spatial-temporal regulation of gene
           expression, imprinting, and seed development in Arabidopsis [Plant
    • Authors: Ryan C. Kirkbride; Jie Lu, Changqing Zhang, Rebecca A. Mosher, David C. Baulcombe, Z. Jeffrey Chen
      Pages: 2761 - 2766
      Abstract: Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1-mediated pathway. To investigate their biological functions, we characterized siRNAs in the endosperm and seed coat that were separated by laser-capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1807621116
      Issue No: Vol. 116, No. 7 (2019)
  • Transgressive segregation reveals mechanisms of Arabidopsis immunity to
           Brassica-infecting races of white rust (Albugo candida) [Plant Biology]
    • Authors: Volkan Cevik; Freddy Boutrot, Wiebke Apel, Alexandre Robert-Seilaniantz, Oliver J. Furzer, Amey Redkar, Baptiste Castel, Paula X. Kover, David C. Prince, Eric B. Holub, Jonathan D. G. Jones
      Pages: 2767 - 2773
      Abstract: Arabidopsis thaliana accessions are universally resistant at the adult leaf stage to white rust (Albugo candida) races that infect the crop species Brassica juncea and Brassica oleracea. We used transgressive segregation in recombinant inbred lines to test if this apparent species-wide (nonhost) resistance in A. thaliana is due to natural...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1812911116
      Issue No: Vol. 116, No. 7 (2019)
  • Correction for Su et al., Pyruvate cycle increases aminoglycoside efficacy
           and provides respiratory energy in bacteria [Corrections]
    • Pages: 2774 - 2775
      Abstract: MICROBIOLOGY Correction for “Pyruvate cycle increases aminoglycoside efficacy and provides respiratory energy in bacteria,” by Yu-bin Su, Bo Peng, Hui Li, Zhi-xue Cheng, Tian-tuo Zhang, Jia-xin Zhu, Dan Li, Min-yi Li, Jin-zhou Ye, Chao-chao Du, Song Zhang, Xian-liang Zhao, Man-jun Yang, and Xuan-xian Peng, which was first published January 30,...
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1816299115
      Issue No: Vol. 116, No. 7 (2019)
  • Correction to Supporting Information for Griscom et al., Natural climate
           solutions [SI Correction]
    • Pages: 2776 - 2776
      Abstract: EARTH, ATMOSPHERIC, AND PLANETARY SCIENCES, SUSTAINABILITY SCIENCE Correction to Supporting Information for “Natural climate solutions,” by Bronson W. Griscom, Justin Adams, Peter W. Ellis, Richard A. Houghton, Guy Lomax, Daniela A. Miteva, William H. Schlesinger, David Shoch, Juha V. Siikamäki, Pete Smith, Peter Woodbury, Chris Zganjar, Allen Blackman, João Campari,...
      Keywords: Sustainability Science
      PubDate: 2019-02-12T09:46:14-08:00
      DOI: 10.1073/pnas.1900868116
      Issue No: Vol. 116, No. 7 (2019)
School of Mathematical and Computer Sciences
Heriot-Watt University
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