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Proceedings of the National Academy of Sciences
Journal Prestige (SJR): 6.092
Citation Impact (citeScore): 9
Number of Followers: 1014  
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ISSN (Print) 0027-8424 - ISSN (Online) 1091-6490
Published by PNAS Homepage  [1 journal]
  • Photoreceptive retinal ganglion cells control the information rate of the
           optic nerve [Neuroscience]
    • Authors: Nina Milosavljevic; Riccardo Storchi, Cyril G. Eleftheriou, Andrea Colins, Rasmus S. Petersen, Robert J. Lucas
      Abstract: Information transfer in the brain relies upon energetically expensive spiking activity of neurons. Rates of information flow should therefore be carefully optimized, but mechanisms to control this parameter are poorly understood. We address this deficit in the visual system, where ambient light (irradiance) is predictive of the amount of information...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1810701115
      Issue No: Vol. 115, No. 50 (2018)
  • Interplay of the Norrin and Wnt7a/Wnt7b signaling systems in blood-brain
           barrier and blood-retina barrier development and maintenance
    • Authors: Yanshu Wang; Chris Cho, John Williams, Philip M. Smallwood, Chi Zhang, Harald J. Junge, Jeremy Nathans
      Abstract: β-Catenin signaling controls the development and maintenance of the blood–brain barrier (BBB) and the blood–retina barrier (BRB), but the division of labor and degree of redundancy between the two principal ligand–receptor systems—the Norrin and Wnt7a/Wnt7b systems—are incompletely defined. Here, we present a loss-of-function genetic analysis of postnatal BBB and BRB...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1813217115
      Issue No: Vol. 115, No. 50 (2018)
  • TRPV1 pore turret dictates distinct DkTx and capsaicin gating
    • Authors: Matan Geron; Rakesh Kumar, Wenchang Zhou, Jose D. Faraldo–Gomez, Valeria Vasquez, Avi Priel
      Abstract: Many neurotoxins inflict pain by targeting receptors expressed on nociceptors, such as the polymodal cationic channel TRPV1. The tarantula double-knot toxin (DkTx) is a peptide with an atypical bivalent structure, providing it with the unique capability to lock TRPV1 in its open state and evoke an irreversible channel activation. Here,...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1809662115
      Issue No: Vol. 115, No. 50 (2018)
  • Role of human Hv1 channels in sperm capacitation and white blood cell
           respiratory burst established by a designed peptide inhibitor [Physiology]
    • Authors: Ruiming Zhao; Kelleigh Kennedy, Gerardo A. De Blas, Gerardo Orta, Martin A. Pavarotti, Rodolfo J. Arias, Jose Luis de la Vega–Beltran, Qufei Li, Hui Dai, Eduardo Perozo, Luis S. Mayorga, Alberto Darszon, Steve A. N. Goldstein
      Abstract: Using a de novo peptide inhibitor, Corza6 (C6), we demonstrate that the human voltage-gated proton channel (hHv1) is the main pathway for H+ efflux that allows capacitation in sperm and permits sustained reactive oxygen species (ROS) production in white blood cells (WBCs). C6 was identified by a phage-display strategy whereby...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1816189115
      Issue No: Vol. 115, No. 50 (2018)
  • PYL8 mediates ABA perception in the root through non-cell-autonomous and
           ligand-stabilization-based mechanisms [Plant Biology]
    • Authors: Borȷa Belda–Palazon; Mary–Paz Gonzalez–Garcia, Jorge Lozano–Juste, Alberto Coego, Regina Antoni, Jose Julian, Marta Peirats–Llobet, Lesia Rodriguez, Ana Berbel, Daniela Dietrich, Maria A. Fernandez, Francisco Madueno, Malcolm J. Bennett, Pedro L. Rodriguez
      Abstract: The phytohormone abscisic acid (ABA) plays a key role regulating root growth, root system architecture, and root adaptive responses, such as hydrotropism. The molecular and cellular mechanisms that regulate the action of core ABA signaling components in roots are not fully understood. ABA is perceived through receptors from the PYR/PYL/RCAR...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1815410115
      Issue No: Vol. 115, No. 50 (2018)
  • Hinge region of Arabidopsis phyA plays an important role in regulating
           phyA function [Plant Biology]
    • Authors: Yangyang Zhou; Li Yang, Jie Duan, Jinkui Cheng, Yunping Shen, Xiaoji Wang, Run Han, Hong Li, Zhen Li, Lihong Wang, William Terzaghi, Danmeng Zhu, Haodong Chen, Xing Wang Deng, Jigang Li
      Abstract: Phytochrome A (phyA) is the only plant photoreceptor that perceives far-red light and then mediates various responses to this signal. Phosphorylation and dephosphorylation of oat phyA have been extensively studied, and it was shown that phosphorylation of a serine residue in the hinge region of oat phyA could regulate the...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1813162115
      Issue No: Vol. 115, No. 50 (2018)
  • Metabolic network-based stratification of hepatocellular carcinoma reveals
           three distinct tumor subtypes [Systems Biology]
    • Authors: Gholamreza Bidkhori; Rui Benfeitas, Martina Klevstig, Cheng Zhang, Jens Nielsen, Mathias Uhlen, Jan Boren, Adil Mardinoglu
      Abstract: Hepatocellular carcinoma (HCC) is one of the most frequent forms of liver cancer, and effective treatment methods are limited due to tumor heterogeneity. There is a great need for comprehensive approaches to stratify HCC patients, gain biological insights into subtypes, and ultimately identify effective therapeutic targets. We stratified HCC patients...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1807305115
      Issue No: Vol. 115, No. 50 (2018)
  • Correction for Yoon et al., Control of movement vigor and decision making
           during foraging [Corrections]
    • Abstract: NEUROSCIENCE, PSYCHOLOGICAL AND COGNITIVE SCIENCES Correction for “Control of movement vigor and decision making during foraging,” by Tehrim Yoon, Robert B. Geary, Alaa A. Ahmed, and Reza Shadmehr, which was first published October 15, 2018; 10.1073/pnas.1812979115 (Proc Natl Acad Sci USA 115:E10476–E10485). The authors note that, due to a printer’s...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1818731115
      Issue No: Vol. 115, No. 50 (2018)
  • Retraction for Baradaran-Heravi et al., Gentamicin B1 is a minor
           gentamicin component with major nonsense mutation suppression activity
    • Abstract: GENETICS Retraction for “Gentamicin B1 is a minor gentamicin component with major nonsense mutation suppression activity,” by Alireza Baradaran-Heravi, Jürgen Niesser, Aruna D. Balgi, Kunho Choi, Carla Zimmerman, Andrew P. South, Hilary J. Anderson, Natalie C. Strynadka, Marcel B. Bally, and Michel Roberge, which was first published March 13, 2017;...
      PubDate: 2018-12-11T10:16:38-08:00
      DOI: 10.1073/pnas.1818172115
      Issue No: Vol. 115, No. 50 (2018)
  • There is no evidence that pupil mimicry is a social phenomenon [Social
    • Authors: Sebastiaan Mathot; Marnix Naber
      Abstract: When you look at someone with large pupils, your own pupils dilate as well; when you look at someone with small pupils, your own pupils constrict. This phenomenon is referred to as pupil mimicry. Recently, in PNAS, Prochazkova et al. (1) claim that pupil mimicry reflects trust and theory of...
      Keywords: Letters
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1814429115
      Issue No: Vol. 115, No. 50 (2018)
  • Reply to Mathot and Naber: Neuroimaging shows that pupil mimicry is a
           social phenomenon [Social Sciences]
    • Authors: Eliska Prochazkova; Luisa Prochazkova, Michael Rojek Giffin, H. Steven Scholte, Carsten K. W. De Dreu, Mariska E. Kret
      Abstract: We recently reported that an individual’s pupils mimic changes in the pupils of his or her interaction partner, that mimicking dilating pupils associates with more trust in economic games, and that such pupil mimicry-related trust tracked neural activation in brain areas associated with theory of mind (1). Our findings confirm...
      Keywords: Letters
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1815545115
      Issue No: Vol. 115, No. 50 (2018)
  • Intrinsic cellular chirality regulates left-right symmetry breaking during
           cardiac looping [Biophysics and Computational Biology]
    • Authors: Poulomi Ray; Amanda S. Chin, Kathryn E. Worley, Jie Fan, Gurleen Kaur, Mingfu Wu, Leo Q. Wan
      Abstract: The vertebrate body plan is overall symmetrical but left–right (LR) asymmetric in the shape and positioning of internal organs. Although several theories have been proposed, the biophysical mechanisms underlying LR asymmetry are still unclear, especially the role of cell chirality, the LR asymmetry at the cellular level, on organ asymmetry....
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1808052115
      Issue No: Vol. 115, No. 50 (2018)
  • Visualizing atomic sizes and molecular shapes with the classical turning
           surface of the Kohn-Sham potential [Chemistry]
    • Authors: Egor Ospadov; Jianmin Tao, Viktor N. Staroverov, John P. Perdew
      Abstract: The Kohn–Sham potential veff(r) is the effective multiplicative operator in a noninteracting Schrödinger equation that reproduces the ground-state density of a real (interacting) system. The sizes and shapes of atoms, molecules, and solids can be defined in terms of Kohn–Sham potentials in a nonarbitrary way that accords with chemical intuition...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1814300115
      Issue No: Vol. 115, No. 50 (2018)
  • Eurasian river spring flood observations support net Arctic Ocean mercury
           export to the atmosphere and Atlantic Ocean [Earth, Atmospheric, and
           Planetary Sciences]
    • Authors: Jeroen E. Sonke; Roman Teisserenc, Lars–Eric Heimburger–Boavida, Mariia V. Petrova, Nicolas Marusczak, Theo Le Dantec, Artem V. Chupakov, Chuxian Li, Colin P. Thackray, Elsie M. Sunderland, Nikita Tananaev, Oleg S. Pokrovsky
      Abstract: Midlatitude anthropogenic mercury (Hg) emissions and discharge reach the Arctic Ocean (AO) by atmospheric and oceanic transport. Recent studies suggest that Arctic river Hg inputs have been a potentially overlooked source of Hg to the AO. Observations on Hg in Eurasian rivers, which represent 80% of freshwater inputs to the...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811957115
      Issue No: Vol. 115, No. 50 (2018)
  • Strong impact of wildfires on the abundance and aging of black carbon in
           the lowermost stratosphere [Environmental Sciences]
    • Authors: Jeannine Ditas; Nan Ma, Yuxuan Zhang, Denise Assmann, Marco Neumaier, Hella Riede, Einar Karu, Jonathan Williams, Dieter Scharffe, Qiaoqiao Wang, Jorge Saturno, Joshua P. Schwarz, Joseph M. Katich, Gavin R. McMeeking, Andreas Zahn, Markus Hermann, Carl A. M. Brenninkmeiȷer, Meinrat O. Andreae, Ulrich Poschl, Hang Su, Yafang Cheng
      Abstract: Wildfires inject large amounts of black carbon (BC) particles into the atmosphere, which can reach the lowermost stratosphere (LMS) and cause strong radiative forcing. During a 14-month period of observations on board a passenger aircraft flying between Europe and North America, we found frequent and widespread biomass burning (BB) plumes,...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1806868115
      Issue No: Vol. 115, No. 50 (2018)
  • The calculation of transcript flux ratios reveals single regulatory
           mechanisms capable of activation and repression [Biochemistry]
    • Authors: Eric A. Galburt
      Abstract: The regulation of transcription allows cells to adjust the rate of RNA polymerases (RNAPs) initiated in a promoter-specific manner. Classically, transcription factors are directed to a subset of promoters via the recognition of DNA sequence motifs. However, a unique class of regulators is recruited directly through interactions with RNAP. Surprisingly,...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1809454115
      Issue No: Vol. 115, No. 50 (2018)
  • Phage Mu Gam protein promotes NHEJ in concert with Escherichia coli ligase
    • Authors: Sudipta Bhattacharyya; Michael M. Soniat, David Walker, Sooin Jang, Ilya J. Finkelstein, Rasika M. Harshey
      Abstract: The Gam protein of transposable phage Mu is an ortholog of eukaryotic and bacterial Ku proteins, which carry out nonhomologous DNA end joining (NHEJ) with the help of dedicated ATP-dependent ligases. Many bacteria carry Gam homologs associated with either complete or defective Mu-like prophages, but the role of Gam in...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1816606115
      Issue No: Vol. 115, No. 50 (2018)
  • Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2
           sensing [Biochemistry]
    • Authors: Brandan Pedre; David Young, Daniel Charlier, Alvaro Mourenza, Leonardo Astolfi Rosado, Laura Marcos–Pascual, Khadiȷa Wahni, Edo Martens, Alfonso G. de la Rubia, Vsevolod V. Belousov, Luis M. Mateos, Joris Messens
      Abstract: Hydrogen peroxide (H2O2) is a strong oxidant capable of oxidizing cysteinyl thiolates, yet only a few cysteine-containing proteins have exceptional reactivity toward H2O2. One such example is the prokaryotic transcription factor OxyR, which controls the antioxidant response in bacteria, and which specifically and rapidly reduces H2O2. In this study, we...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1807954115
      Issue No: Vol. 115, No. 50 (2018)
  • NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I
    • Authors: Andrew M. Clarke; Krysta L. Engel, Keith E. Giles, Chad M. Petit, David A. Schneider
      Abstract: DNA sequence motifs that affect RNA polymerase transcription elongation are well studied in prokaryotic organisms and contribute directly to regulation of gene expression. Despite significant work on the regulation of eukaryotic transcription, the effect of DNA template sequence on RNA polymerase I (Pol I) transcription elongation remains unknown. In this...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1809421115
      Issue No: Vol. 115, No. 50 (2018)
  • UBL domain of Usp14 and other proteins stimulates proteasome activities
           and protein degradation in cells [Biochemistry]
    • Authors: Hyoung Tae Kim; Alfred L. Goldberg
      Abstract: The best-known function of ubiquitin-like (UBL) domains in proteins is to enable their binding to 26S proteasomes. The proteasome-associated deubiquitinating enzyme Usp14/UBP6 contains an N-terminal UBL domain and is an important regulator of proteasomal activity. Usp14 by itself represses multiple proteasomal activities but, upon binding a ubiquitin chain, Usp14 stimulates...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1808731115
      Issue No: Vol. 115, No. 50 (2018)
  • Mechanistic insights into the interactions of NAP1 with the SKICH domains
           of NDP52 and TAX1BP1 [Biophysics and Computational Biology]
    • Authors: Tao Fu; Jianping Liu, Yingli Wang, Xingqiao Xie, Shichen Hu, Lifeng Pan
      Abstract: NDP52 and TAX1BP1, two SKIP carboxyl homology (SKICH) domain-containing autophagy receptors, play crucial roles in selective autophagy. The autophagic functions of NDP52 and TAX1BP1 are regulated by TANK-binding kinase 1 (TBK1), which may associate with them through the adaptor NAP1. However, the molecular mechanism governing the interactions of NAP1 with...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811421115
      Issue No: Vol. 115, No. 50 (2018)
  • Dual functions for OVAAL in initiation of RAF/MEK/ERK prosurvival signals
           and evasion of p27-mediated cellular senescence [Cell Biology]
    • Authors: Ben Sang; Yuan Yuan Zhang, Su Tang Guo, Ling Fei Kong, Qiong Cheng, Guang Zhi Liu, Rick F. Thorne, Xu Dong Zhang, Lei Jin, Mian Wu
      Abstract: Long noncoding RNAs (lncRNAs) function through a diverse array of mechanisms that are not presently fully understood. Here, we sought to find lncRNAs differentially regulated in cancer cells resistant to either TNF-related apoptosis-inducing ligand (TRAIL) or the Mcl-1 inhibitor UMI-77, agents that act through the extrinsic and intrinsic apoptotic pathways,...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1805950115
      Issue No: Vol. 115, No. 50 (2018)
  • Cancer-associated fibroblasts suppress SOX2-induced dysplasia in a lung
           squamous cancer coculture [Cell Biology]
    • Authors: Shuang Chen; Andreas Giannakou, Sarah Wyman, Janet Gruzas, Jonathon Golas, Wenyan Zhong, Christine Loreth, Latha Sridharan, Ting-Ting Yamin, Marc Damelin, Kenneth G. Geles
      Abstract: Tumorigenesis depends on intricate interactions between genetically altered tumor cells and their surrounding microenvironment. While oncogenic drivers in lung squamous carcinoma (LUSC) have been described, the role of stroma in modulating tissue architecture, particularly cell polarity, remains unclear. Here, we report the establishment of a 3D coculture system of LUSC...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1803718115
      Issue No: Vol. 115, No. 50 (2018)
  • Coordinated histone modifications and chromatin reorganization in a single
           cell revealed by FRET biosensors [Cell Biology]
    • Authors: Qin Peng; Shaoying Lu, Yuxin Shi, Yijia Pan, Praopim Limsakul, Andrei V. Chernov, Juhui Qiu, Xiaoqi Chai, Yiwen Shi, Pengzhi Wang, Yanmin Ji, Yi-Shuan J. Li, Alex Y. Strongin, Vladislav V. Verkhusha, Juan Carlos Izpisua Belmonte, Bing Ren, Yuanliang Wang, Shu Chien, Yingxiao Wang
      Abstract: The dramatic reorganization of chromatin during mitosis is perhaps one of the most fundamental of all cell processes. It remains unclear how epigenetic histone modifications, despite their crucial roles in regulating chromatin architectures, are dynamically coordinated with chromatin reorganization in controlling this process. We have developed and characterized biosensors with...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811818115
      Issue No: Vol. 115, No. 50 (2018)
  • Evolution of host support for two ancient bacterial symbionts with
           differentially degraded genomes in a leafhopper host [Evolution]
    • Authors: Meng Mao; Xiushuai Yang, Gordon M. Bennett
      Abstract: Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811932115
      Issue No: Vol. 115, No. 50 (2018)
  • Germline genetic polymorphisms influence tumor gene expression and immune
           cell infiltration [Genetics]
    • Authors: Yoong Wearn Lim; Haiyin Chen-Harris, Oleg Mayba, Steve Lianoglou, Arthur Wuster, Tushar Bhangale, Zia Khan, Sanjeev Mariathasan, Anneleen Daemen, Jens Reeder, Peter M. Haverty, William F. Forrest, Matthew Brauer, Ira Mellman, Matthew L. Albert
      Abstract: Cancer immunotherapy has emerged as an effective therapy in a variety of cancers. However, a key challenge in the field is that only a subset of patients who receive immunotherapy exhibit durable response. It has been hypothesized that host genetics influences the inherent immune profiles of patients and may underlie...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1804506115
      Issue No: Vol. 115, No. 50 (2018)
  • Transcriptional landscape of B cell precursor acute lymphoblastic leukemia
           based on an international study of 1,223 cases [Genetics]
    • Authors: Jian–Feng Li; Yu–Ting Dai, Henrik Lillȷebȷorn, Shu–Hong Shen, Bo–Wen Cui, Ling Bai, Yuan–Fang Liu, Mao–Xiang Qian, Yasuo Kubota, Hitoshi Kiyoi, Itaru Matsumura, Yasushi Miyazaki, Linda Olsson, Ah Moy Tan, Hany Ariffin, Jing Chen, Junko Takita, Takahiko Yasuda, Hiroyuki Mano, Bertil Johansson, Jun J. Yang, Allen Eng–Juh Yeoh, Fumihiko Hayakawa, Zhu Chen, Ching–Hon Pui, Thoas Fioretos, Sai–Juan Chen, Jin–Yan Huang
      Abstract: Most B cell precursor acute lymphoblastic leukemia (BCP ALL) can be classified into known major genetic subtypes, while a substantial proportion of BCP ALL remains poorly characterized in relation to its underlying genomic abnormalities. We therefore initiated a large-scale international study to reanalyze and delineate the transcriptome landscape of 1,223...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1814397115
      Issue No: Vol. 115, No. 50 (2018)
  • Molecular mechanisms of biogenesis of apoptotic exosome-like vesicles and
           their roles as damage-associated molecular patterns [Immunology and
    • Authors: Soo Jeong Park; Jeong Mi Kim, Jihyo Kim, Jaehark Hur, Sun Park, Kyongmin Kim, Ho-Joon Shin, Yong-Joon Chwae
      Abstract: Recent research has led to contradictory notions regarding the conventional theory that apoptotic cell death can evoke inflammatory or immunogenic responses orchestrated by released damage-associated patterns (DAMPs). By inducing IL-1β from bone marrow-derived macrophages in an effort to determine the inflammatory mediators released from apoptotic cells, we found that exosomal...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811432115
      Issue No: Vol. 115, No. 50 (2018)
  • CD226 regulates natural killer cell antitumor responses via
           phosphorylation-mediated inactivation of transcription factor FOXO1
           [Immunology and Inflammation]
    • Authors: Xiangnan Du; Patricia de Almeida, Nick Manieri, Denise de Almeida Nagata, Thomas D. Wu, Kristin Harden Bowles, Vidhyalakshmi Arumugam, Jill Schartner, Rafael Cubas, Stephanie Mittman, Vincent Javinal, Keith R. Anderson, Soren Warming, Jane L. Grogan, Eugene Y. Chiang
      Abstract: Natural killer (NK) cell recognition of tumor cells is mediated through activating receptors such as CD226, with suppression of effector functions often controlled by negative regulatory transcription factors such as FOXO1. Here we show that CD226 regulation of NK cell cytotoxicity is facilitated through inactivation of FOXO1. Gene-expression analysis of...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1814052115
      Issue No: Vol. 115, No. 50 (2018)
  • Citrate-based materials fuel human stem cells by metabonegenic regulation
           [Medical Sciences]
    • Authors: Chuying Ma; Xinggui Tian, Jimin P. Kim, Denghui Xie, Xiang Ao, Dingying Shan, Qiaoling Lin, Maria R. Hudock, Xiaochun Bai, Jian Yang
      Abstract: A comprehensive understanding of the key microenvironmental signals regulating bone regeneration is pivotal for the effective design of bioinspired orthopedic materials. Here, we identified citrate as an osteopromotive factor and revealed its metabonegenic role in mediating citrate metabolism and its downstream effects on the osteogenic differentiation of human mesenchymal stem...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1813000115
      Issue No: Vol. 115, No. 50 (2018)
  • Structure and architecture of immature and mature murine leukemia virus
           capsids [Microbiology]
    • Authors: Kun Qu; Barbel Glass, Michal Doležal, Florian K. M. Schur, Brice Murciano, Alan Rein, Michaela Rumlova, Tomaš Ruml, Hans–Georg Krausslich, John A. G. Briggs
      Abstract: Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811580115
      Issue No: Vol. 115, No. 50 (2018)
  • Comparative genomics reveals the molecular determinants of rapid growth of
           the cyanobacterium Synechococcus elongatus UTEX 2973 [Microbiology]
    • Authors: Justin Ungerer; Kristen E. Wendt, John I. Hendry, Costas D. Maranas, Himadri B. Pakrasi
      Abstract: Cyanobacteria are emerging as attractive organisms for sustainable bioproduction. We previously described Synechococcus elongatus UTEX 2973 as the fastest growing cyanobacterium known. Synechococcus 2973 exhibits high light tolerance and an increased photosynthetic rate and produces biomass at three times the rate of its close relative, the model strain Synechococcus elongatus...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1814912115
      Issue No: Vol. 115, No. 50 (2018)
  • Staphylococcus aureus coagulases are exploitable yet stable public goods
           in clinically relevant conditions [Microbiology]
    • Authors: Urvish Trivedi; Jonas S. Madsen, Jake Everett, Cody Fell, Jakob Russel, Jakob Haaber, Heidi A. Crosby, Alexander R. Horswill, Mette Burmolle, Kendra P. Rumbaugh, Soren J. Sorensen
      Abstract: Coagulation is an innate defense mechanism intended to limit blood loss and trap invading pathogens during infection. However, Staphylococcus aureus has the ability to hijack the coagulation cascade and generate clots via secretion of coagulases. Although many S. aureus have this characteristic, some do not. The population dynamics regarding this...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1804850115
      Issue No: Vol. 115, No. 50 (2018)
  • DksA-DnaJ redox interactions provide a signal for the activation of
           bacterial RNA polymerase [Microbiology]
    • Authors: Ju–Sim Kim; Lin Liu, Liam F. Fitzsimmons, Yang Wang, Matthew A. Crawford, Mauricio Mastrogiovanni, Madia Truȷillo, James Karl A. Till, Rafael Radi, Shaodong Dai, Andres Vazquez–Torres
      Abstract: RNA polymerase is the only known protein partner of the transcriptional regulator DksA. Herein, we demonstrate that the chaperone DnaJ establishes direct, redox-based interactions with oxidized DksA. Cysteine residues in the zinc finger of DksA become oxidized in Salmonella exposed to low concentrations of hydrogen peroxide (H2O2). The resulting disulfide...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1813572115
      Issue No: Vol. 115, No. 50 (2018)
  • Integrative approach using Yersinia pestis genomes to revisit the
           historical landscape of plague during the Medieval Period [Microbiology]
    • Authors: Amine Namouchi, Meriam Guellil, Oliver Kersten, Stephanie Hansch, Claudio Ottoni, Boris V. Schmid, Elsa Pacciani, Luisa Quaglia, Marco Vermunt, Egil L. Bauer, Michael Derrick, Anne O. Jensen, Sacha Kacki, Samuel K. Cohn Jr; Nils C. Stenseth, Barbara Bramanti
      Abstract: Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1812865115
      Issue No: Vol. 115, No. 50 (2018)
  • Emergent elasticity in the neural code for space [Neuroscience]
    • Authors: Samuel A. Ocko; Kiah Hardcastle, Lisa M. Giocomo, Surya Ganguli
      Abstract: Upon encountering a novel environment, an animal must construct a consistent environmental map, as well as an internal estimate of its position within that map, by combining information from two distinct sources: self-motion cues and sensory landmark cues. How do known aspects of neural circuit dynamics and synaptic plasticity conspire...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1805959115
      Issue No: Vol. 115, No. 50 (2018)
  • The adult oligodendrocyte can participate in remyelination [Neuroscience]
    • Authors: Ian D. Duncan; Abigail B. Radcliff, Moones Heidari, Grahame Kidd, Benjamin K. August, Lauren A. Wierenga
      Abstract: Endogenous remyelination of the CNS can be robust and restore function, yet in multiple sclerosis it becomes less complete with time. Promoting remyelination is a major therapeutic goal, both to restore function and to protect axons from degeneration. Remyelination is thought to depend on oligodendrocyte progenitor cells, giving rise to...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1808064115
      Issue No: Vol. 115, No. 50 (2018)
  • In This Issue [This Week in PNAS]
    • Pages: 12537 - 12538
      Abstract: Commuting patterns influence housing and job choices Beijing subway map. Image courtesy of iStock/LordRunar. Few longitudinal studies have examined links between job and housing dynamics and commuting patterns of urban residents. Jie Huang et al. (pp. 12710–12715) conducted a 7-year study that tracked transit smartcards of 4,248 commuters in Beijing,...
      Keywords: In This Issue
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/iti5018115
      Issue No: Vol. 115, No. 50 (2018)
  • News Feature: Targeting metastasis to halt cancer’s spread [Medical
    • Authors: Carolyn Beans
      Pages: 12539 - 12543
      Abstract: Studies reveal the mechanisms behind tumor metastasis and how to stymie it. But primary tumors still get the lion’s share of researchers’ attention. When a cancer cell spreads from a primary tumor to the brain, it immediately meets a formidable opponent: the astrocyte. These stalwart defenders protect against any would-be...
      Keywords: News Features, Front Matter
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1818892115
      Issue No: Vol. 115, No. 50 (2018)
  • Profile of Akiko Iwasaki [Profiles]
    • Authors: Jennifer Viegas
      Pages: 12544 - 12546
      Abstract: Akiko Iwasaki, an immunologist at the Yale School of Medicine and a Howard Hughes Medical Institute Investigator, has made significant contributions toward understanding innate and adaptive immunity. Her achievements include the demonstration of tissue-specific properties of dendritic cells (DCs), discovery of a pathway by which immune responses to viruses can...
      Keywords: PNAS Profiles
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1818903115
      Issue No: Vol. 115, No. 50 (2018)
  • Navigating the fitness landscape using multiallele genome editing
    • Authors: Neil T. Miller; Robert L. Burnap
      Pages: 12547 - 12549
      Abstract: What are the cellular limits that constrain the maximal rate of microbial cell duplication' What are the genetic determinants conferring maximal microbial growth rates' In the case of Cyanobacteria—an ecologically ubiquitous and diverse phylum of prokaryotes capable of oxygenic photosynthesis—these have increasingly become questions of both applied and fundamental significance....
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1818285115
      Issue No: Vol. 115, No. 50 (2018)
  • Puzzling conformational changes affecting proteins binding to the RNA
           polymerase [Microbiology]
    • Authors: Llorenc Fernandez–Coll; Katarzyna Potrykus, Michael Cashel
      Pages: 12550 - 12552
      Abstract: RNA polymerase (RNAP) secondary-channel binding proteins have similar structures and directly bind to RNAP itself, unlike many transcriptional factors that instead interact with DNA. Since these proteins have different functions yet bind to the same site on RNAP, competition for binding determines the ensuing regulatory effects (1–5). In PNAS, Kim...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1818361115
      Issue No: Vol. 115, No. 50 (2018)
  • Temperature throws a developmental switch [Developmental Biology]
    • Authors: Christoph Englert
      Pages: 12553 - 12555
      Abstract: A tantalizing task in the postgenomic era is to decipher the basis of gene–environment interactions or, to phrase it more explicitly, How do environmental cues regulate decisions on organismal developmental fate' In PNAS, Romney et al. (1) shine some light on how a developmental decision can be influenced by external...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1818216115
      Issue No: Vol. 115, No. 50 (2018)
  • Alternative pathway to reduced artemisinin susceptibility in Plasmodium
           falciparum [Microbiology]
    • Authors: Ryan C. Henrici; Colin J. Sutherland
      Pages: 12556 - 12558
      Abstract: Malaria case management across endemic regions of the globe relies on artemisinin (ART) combination therapies for the rapid treatment of acute Plasmodium infection and prevention of severe disease. However, the efficacy of combination therapy is threatened by reduced sensitivity of Plasmodium falciparum to ART and partner drugs, which, in turn,...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1818287115
      Issue No: Vol. 115, No. 50 (2018)
  • ERVmap analysis reveals genome-wide transcription of human endogenous
           retroviruses [Immunology and Inflammation]
    • Authors: Maria Tokuyama; Yong Kong, Eric Song, Teshika Jayewickreme, Insoo Kang, Akiko Iwasaki
      Pages: 12565 - 12572
      Abstract: Endogenous retroviruses (ERVs) are integrated retroviral elements that make up 8% of the human genome. However, the impact of ERVs on human health and disease is not well understood. While select ERVs have been implicated in diseases, including autoimmune disease and cancer, the lack of tools to analyze genome-wide, locus-specific...
      Keywords: Inaugural Articles
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1814589115
      Issue No: Vol. 115, No. 50 (2018)
  • Forecasting innovations in science, technology, and education
    • Authors: Katy Borner; William B. Rouse, Paul Trunfio, H. Eugene Stanley
      Pages: 12573 - 12581
      Abstract: Human survival depends on our ability to predict future outcomes so that we can make informed decisions. Human cognition and perception are optimized for local, short-term decision-making, such as deciding when to fight or flight, whom to mate, or what to eat. For more elaborate decisions (e.g., when to harvest,...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1818750115
      Issue No: Vol. 115, No. 50 (2018)
  • Modeling research universities: Predicting probable futures of public vs.
           private and large vs. small research universities [Colloquium Paper]
    • Authors: William B. Rouse; John V. Lombardi, Diane D. Craig
      Pages: 12582 - 12589
      Abstract: The future of the American academic research enterprise is considered. Data are presented that characterize the resources available for the 160 best-resourced research universities, a small subset of the 2,285 4-year, nonprofit, higher education institutions. A computational model of research universities was extended and used to simulate three strategic scenarios:...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1807174115
      Issue No: Vol. 115, No. 50 (2018)
  • Twin-Win Model: A human-centered approach to research success [Colloquium
    • Authors: Ben Shneiderman
      Pages: 12590 - 12594
      Abstract: A 70-year-old simmering debate has erupted into vigorous battles over the most effective ways to conduct research. Well-established beliefs are being forcefully challenged by advocates of new research models. While there can be no final resolution to this battle, this paper offers the Twin-Win Model to guide teams of researchers,...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1802918115
      Issue No: Vol. 115, No. 50 (2018)
  • Vision for a systems architecture to integrate and transform population
           health [Colloquium Paper]
    • Authors: Guruprasad Madhavan; Charles E. Phelps, William B. Rouse, Rino Rappuoli
      Pages: 12595 - 12602
      Abstract: Entities involved in population health often share a common mission while acting independently of one another and perhaps redundantly. Population health is in everybody’s interest, but nobody is really in charge of promoting it. Across governments, corporations, and frontline operations, lack of coordination, lack of resources, and lack of reliable,...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1809919115
      Issue No: Vol. 115, No. 50 (2018)
  • The chaperone effect in scientific publishing [Colloquium Paper]
    • Authors: Vedran Sekara; Pierre Deville, Sebastian E. Ahnert, Albert–Laszlo Barabasi, Roberta Sinatra, Sune Lehmann
      Pages: 12603 - 12607
      Abstract: Experience plays a critical role in crafting high-impact scientific work. This is particularly evident in top multidisciplinary journals, where a scientist is unlikely to appear as senior author if he or she has not previously published within the same journal. Here, we develop a quantitative understanding of author order by...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1800471115
      Issue No: Vol. 115, No. 50 (2018)
  • Scientific prize network predicts who pushes the boundaries of science
           [Colloquium Paper]
    • Authors: Yifang Ma; Brian Uzzi
      Pages: 12608 - 12615
      Abstract: Scientific prizes confer credibility to persons, ideas, and disciplines, provide financial incentives, and promote community-building celebrations. We examine the growth dynamics and interlocking relationships found in the worldwide scientific prize network. We focus on understanding how the knowledge linkages among prizes and scientists’ propensities for prizewinning relate to knowledge pathways...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1800485115
      Issue No: Vol. 115, No. 50 (2018)
  • Changing demographics of scientific careers: The rise of the temporary
           workforce [Colloquium Paper]
    • Authors: Staša Miloȷević; Filippo Radicchi, John P. Walsh
      Pages: 12616 - 12623
      Abstract: Contemporary science has been characterized by an exponential growth in publications and a rise of team science. At the same time, there has been an increase in the number of awarded PhD degrees, which has not been accompanied by a similar expansion in the number of academic positions. In such...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1800478115
      Issue No: Vol. 115, No. 50 (2018)
  • How science and technology developments impact employment and education
           [Colloquium Paper]
    • Authors: Wendy Martinez
      Pages: 12624 - 12629
      Abstract: A better understanding of how developments in science and technology influence the creation of new occupations and subsequent changes in educational programs can help decision makers at all levels of our society. As a result of research and development efforts, innovations are achieved, resulting in the creation of new occupations...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1803216115
      Issue No: Vol. 115, No. 50 (2018)
  • Skill discrepancies between research, education, and jobs reveal the
           critical need to supply soft skills for the data economy [Colloquium
    • Authors: Katy Borner; Olga Scrivner, Mike Gallant, Shutian Ma, Xiaozhong Liu, Keith Chewning, Lingfei Wu, James A. Evans
      Pages: 12630 - 12637
      Abstract: Rapid research progress in science and technology (S&T) and continuously shifting workforce needs exert pressure on each other and on the educational and training systems that link them. Higher education institutions aim to equip new generations of students with skills and expertise relevant to workforce participation for decades to come,...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1804247115
      Issue No: Vol. 115, No. 50 (2018)
  • Opportunities to observe and measure intangible inputs to innovation:
           Definitions, operationalization, and examples [Colloquium Paper]
    • Authors: Sallie Keller; Gizem Korkmaz, Carol Robbins, Stephanie Shipp
      Pages: 12638 - 12645
      Abstract: Measuring the value of intangibles is not easy, because they are critical but usually invisible components of the innovation process. Today, access to nonsurvey data sources, such as administrative data and repositories captured on web pages, opens opportunities to create intangibles based on new sources of information and capture intangible...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1800467115
      Issue No: Vol. 115, No. 50 (2018)
  • The role of industry-specific, occupation-specific, and location-specific
           knowledge in the growth and survival of new firms [Colloquium Paper]
    • Authors: C. Jara-Figueroa; Bogang Jun, Edward L. Glaeser, Cesar A. Hidalgo
      Pages: 12646 - 12653
      Abstract: How do regions acquire the knowledge they need to diversify their economic activities' How does the migration of workers among firms and industries contribute to the diffusion of that knowledge' Here we measure the industry-, occupation-, and location-specific knowledge carried by workers from one establishment to the next, using a...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1800475115
      Issue No: Vol. 115, No. 50 (2018)
  • Macroscopic dynamics and the collapse of urban traffic [Colloquium Paper]
    • Authors: Luis E. Olmos; Serdar Colak, Saȷȷad Shafiei, Meead Saberi, Marta C. Gonzalez
      Pages: 12654 - 12661
      Abstract: Stories of mega-jams that last tens of hours or even days appear not only in fiction but also in reality. In this context, it is important to characterize the collapse of the network, defined as the transition from a characteristic travel time to orders of magnitude longer for the same...
      Keywords: Sackler Colloquium on Modeling and Visualizing Science and Technology Developments
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1800474115
      Issue No: Vol. 115, No. 50 (2018)
  • Intrinsically ultrastrong plasmon-exciton interactions in crystallized
           films of carbon nanotubes [Applied Physical Sciences]
    • Authors: Po-Hsun Ho; Damon B. Farmer, George S. Tulevski, Shu-Jen Han, Douglas M. Bishop, Lynne M. Gignac, Jim Bucchignano, Phaedon Avouris, Abram L. Falk
      Pages: 12662 - 12667
      Abstract: In cavity quantum electrodynamics, optical emitters that are strongly coupled to cavities give rise to polaritons with characteristics of both the emitters and the cavity excitations. We show that carbon nanotubes can be crystallized into chip-scale, two-dimensionally ordered films and that this material enables intrinsically ultrastrong emitter–cavity interactions: Rather than...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1816251115
      Issue No: Vol. 115, No. 50 (2018)
  • Contact mechanics between the human finger and a touchscreen under
           electroadhesion [Applied Physical Sciences]
    • Authors: Mehmet Ayyildiz; Michele Scaraggi, Omer Sirin, Cagatay Basdogan, Bo N. J. Persson
      Pages: 12668 - 12673
      Abstract: The understanding and control of human skin contact against technological substrates is the key aspect behind the design of several electromechanical devices. Among these, surface haptic displays that modulate the friction between the human finger and touch surface are emerging as user interfaces. One such modulation can be achieved by...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811750115
      Issue No: Vol. 115, No. 50 (2018)
  • Jump rope vortex in liquid metal convection [Applied Physical Sciences]
    • Authors: Tobias Vogt; Susanne Horn, Alexander M. Grannan, Jonathan M. Aurnou
      Pages: 12674 - 12679
      Abstract: Understanding large-scale circulations (LSCs) in turbulent convective systems is important for the study of stars, planets, and in many industrial applications. The canonical model of the LSC is quasi-planar with additional horizontal sloshing and torsional modes [Brown E, Ahlers G (2009) J Fluid Mech 638:383–400; Funfschilling D, Ahlers G (2004)...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1812260115
      Issue No: Vol. 115, No. 50 (2018)
  • Measurability of the epidemic reproduction number in data-driven contact
           networks [Population Biology]
    • Authors: Quan-Hui Liu; Marco Ajelli, Alberto Aleta, Stefano Merler, Yamir Moreno, Alessandro Vespignani
      Pages: 12680 - 12685
      Abstract: The basic reproduction number is one of the conceptual cornerstones of mathematical epidemiology. Its classical definition as the number of secondary cases generated by a typical infected individual in a fully susceptible population finds a clear analytical expression in homogeneous and stratified mixing models. Along with the generation time (the...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811115115
      Issue No: Vol. 115, No. 50 (2018)
  • Directing the reactivity of metal hydrides for selective CO2 reduction
    • Authors: Bianca M. Ceballos; Jenny Y. Yang
      Pages: 12686 - 12691
      Abstract: A critical challenge in electrocatalytic CO2 reduction to renewable fuels is product selectivity. Desirable products of CO2 reduction require proton equivalents, but key catalytic intermediates can also be competent for direct proton reduction to H2. Understanding how to manage divergent reaction pathways at these shared intermediates is essential to achieving...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811396115
      Issue No: Vol. 115, No. 50 (2018)
  • Single-atomic cobalt sites embedded in hierarchically ordered porous
           nitrogen-doped carbon as a superior bifunctional electrocatalyst
    • Authors: Tingting Sun; Shu Zhao, Wenxing Chen, Dong Zhai, Juncai Dong, Yu Wang, Shaolong Zhang, Aijuan Han, Lin Gu, Rong Yu, Xiaodong Wen, Hanlin Ren, Lianbin Xu, Chen Chen, Qing Peng, Dingsheng Wang, Yadong Li
      Pages: 12692 - 12697
      Abstract: Exploring efficient and cost-effective catalysts to replace precious metal catalysts, such as Pt, for electrocatalytic oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER) holds great promise for renewable energy technologies. Herein, we prepare a type of Co catalyst with single-atomic Co sites embedded in hierarchically ordered porous N-doped carbon...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1813605115
      Issue No: Vol. 115, No. 50 (2018)
  • Quantifying the role of mineral bridges on the fracture resistance of
           nacre-like composites [Engineering]
    • Authors: Madeleine Grossman; Florian Bouville, Kunal Masania, Andre R. Studart
      Pages: 12698 - 12703
      Abstract: The nacreous layer of mollusk shells holds design concepts that can effectively enhance the fracture resistance of lightweight brittle materials. Mineral bridges are known to increase the fracture resistance of nacre-inspired materials, but their role is difficult to quantify due to the lack of experimental systems where only this parameter...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1805094115
      Issue No: Vol. 115, No. 50 (2018)
  • Precise tracking of vaccine-responding T cell clones reveals convergent
           and personalized response in identical twins [Immunology and Inflammation]
    • Authors: Mikhail V. Pogorelyy; Anastasia A. Minervina, Maximilian Puelma Touzel, Anastasiia L. Sycheva, Ekaterina A. Komech, Elena I. Kovalenko, Galina G. Karganova, Evgeniy S. Egorov, Alexander Yu. Komkov, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Thierry Mora, Aleksandra M. Walczak, Yuri B. Lebedev
      Pages: 12704 - 12709
      Abstract: T cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1809642115
      Issue No: Vol. 115, No. 50 (2018)
  • Tracking job and housing dynamics with smartcard data [Social Sciences]
    • Authors: Jie Huang; David Levinson, Jiaoe Wang, Jiangping Zhou, Zi-jia Wang
      Pages: 12710 - 12715
      Abstract: Residential locations, the jobs–housing relationship, and commuting patterns are key elements to understand urban spatial structure and how city dwellers live. Their successive interaction is important for various fields including urban planning, transport, intraurban migration studies, and social science. However, understanding of the long-term trajectories of workplace and home location,...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1815928115
      Issue No: Vol. 115, No. 50 (2018)
  • Engineered occluded apo-intermediate of LacY [Biochemistry]
    • Authors: Irina Smirnova; Vladimir Kasho, H. Ronald Kaback
      Pages: 12716 - 12721
      Abstract: The lactose permease of Escherichia coli (LacY) utilizes an alternating access symport mechanism with multiple conformational intermediates, but only inward (cytoplasmic)- or outward (periplasmic)-open structures have been characterized by X-ray crystallography. It is demonstrated here with sugar-binding studies that cross-linking paired-Cys replacements across the closed cytoplasmic cavity stabilize an occluded...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1816267115
      Issue No: Vol. 115, No. 50 (2018)
  • Mechanism of the E2 to E1 transition in Ca2+ pump revealed by crystal
           structures of gating residue mutants [Biochemistry]
    • Authors: Naoki Tsunekawa; Haruo Ogawa, Junko Tsueda, Toshihiko Akiba, Chikashi Toyoshima
      Pages: 12722 - 12727
      Abstract: Ca2+-ATPase of sarcoplasmic reticulum (SERCA1a) pumps two Ca2+ per ATP hydrolyzed from the cytoplasm and two or three protons in the opposite direction. In the E2 state, after transferring Ca2+ into the lumen of sarcoplasmic reticulum, all of the acidic residues that coordinate Ca2+ are thought to be protonated, including...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1815472115
      Issue No: Vol. 115, No. 50 (2018)
  • Genetically encodable bioluminescent system from fungi [Biochemistry]
    • Authors: Alexey A. Kotlobay; Karen S. Sarkisyan, Yuliana A. Mokrushina, Marina Marcet–Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Andrey Y. Gorokhovatsky, Andrey Vvedensky, Konstantin V. Purtov, Valentin N. Petushkov, Natalȷa S. Rodionova, Tatiana V. Chepurnyh, Liliia I. Fakhranurova, Elena B. Guglya, Rustam Ziganshin, Aleksandra S. Tsarkova, Zinaida M. Kaskova, Victoria Shender, Maxim Abakumov, Tatiana O. Abakumova, Inna S. Povolotskaya, Fedor M. Eroshkin, Andrey G. Zaraisky, Alexander S. Mishin, Sergey V. Dolgov, Tatiana Y. Mitiouchkina, Eugene P. Kopantzev, Hans E. Waldenmaier, Anderson G. Oliveira, Yuichi Oba, Ekaterina Barsova, Ekaterina A. Bogdanova, Toni Gabaldon, Cassius V. Stevani, Sergey Lukyanov, Ivan V. Smirnov, Josef I. Gitelson, Fyodor A. Kondrashov, Ilia V. Yampolsky
      Pages: 12728 - 12732
      Abstract: Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1803615115
      Issue No: Vol. 115, No. 50 (2018)
  • A2A adenosine receptor functional states characterized by 19F-NMR
           [Biophysics and Computational Biology]
    • Authors: Lukas Sušac; Matthew T. Eddy, Tatiana Didenko, Raymond C. Stevens, Kurt Wuthrich
      Pages: 12733 - 12738
      Abstract: The human proteome contains 826 G protein-coupled receptors (GPCR), which control a wide array of key physiological functions, making them important drug targets. GPCR functions are based on allosteric coupling from the extracellular orthosteric drug binding site across the cell membrane to intracellular binding sites for partners such as G...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1813649115
      Issue No: Vol. 115, No. 50 (2018)
  • Bottom-up modeling of chromatin segregation due to epigenetic
           modifications [Biophysics and Computational Biology]
    • Authors: Quinn MacPherson; Bruno Beltran, Andrew J. Spakowitz
      Pages: 12739 - 12744
      Abstract: We use a chromosome-scale simulation to show that the preferential binding of heterochromatin protein 1 (HP1) to regions high in histone methylation (specifically H3K9me3) results in phase segregation and reproduces features of the observed Hi-C contact map. Specifically, we perform Monte Carlo simulations with one computational bead per nucleosome and...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1812268115
      Issue No: Vol. 115, No. 50 (2018)
  • Benefits of phenotypic plasticity for population growth in varying
           environments [Biophysics and Computational Biology]
    • Authors: BingKan Xue; Stanislas Leibler
      Pages: 12745 - 12750
      Abstract: Phenotypic plasticity refers to the capacity of the same organisms to exhibit different characteristics under varied environmental conditions. A plastic developmental program allows organisms to sense environmental cues in early stages of life and express phenotypes that are better fitted to environments encountered later in life. This is often considered...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1813447115
      Issue No: Vol. 115, No. 50 (2018)
  • Molecular mechanism of fusion pore formation driven by the neuronal SNARE
           complex [Biophysics and Computational Biology]
    • Authors: Satyan Sharma; Manfred Lindau
      Pages: 12751 - 12756
      Abstract: Release of neurotransmitters from synaptic vesicles begins with a narrow fusion pore, the structure of which remains unresolved. To obtain a structural model of the fusion pore, we performed coarse-grained molecular dynamics simulations of fusion between a nanodisc and a planar bilayer bridged by four partially unzipped SNARE complexes. The...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1816495115
      Issue No: Vol. 115, No. 50 (2018)
  • Molecular structure of the ATP-bound, phosphorylated human CFTR
           [Biophysics and Computational Biology]
    • Authors: Zhe Zhang; Fangyu Liu, Jue Chen
      Pages: 12757 - 12762
      Abstract: The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel important in maintaining proper functions of the lung, pancreas, and intestine. The activity of CFTR is regulated by ATP and protein kinase A-dependent phosphorylation. To understand the conformational changes elicited by phosphorylation and ATP binding, we present here the...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1815287115
      Issue No: Vol. 115, No. 50 (2018)
  • Temperature-dependent vitamin D signaling regulates developmental
           trajectory associated with diapause in an annual killifish [Developmental
    • Authors: Amie L. T. Romney; Erin M. Davis, Meranda M. Corona, Josiah T. Wagner, Jason E. Podrabsky
      Pages: 12763 - 12768
      Abstract: The mechanisms that integrate environmental signals into developmental programs remain largely uncharacterized. Nuclear receptors (NRs) are ligand-regulated transcription factors that orchestrate the expression of complex phenotypes. The vitamin D receptor (VDR) is an NR activated by 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3], a hormone derived from 7-dehydrocholesterol (7-DHC). VDR signaling is best known...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1804590115
      Issue No: Vol. 115, No. 50 (2018)
  • Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme
           insular change within a morphologically conservative radiation [Evolution]
    • Authors: Roseina Woods; Samuel T. Turvey, Selina Brace, Ross D. E. MacPhee, Ian Barnes
      Pages: 12769 - 12774
      Abstract: The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1808603115
      Issue No: Vol. 115, No. 50 (2018)
  • Phylogenomics and the evolution of hemipteroid insects [Evolution]
    • Authors: Kevin P. Johnson; Christopher H. Dietrich, Frank Friedrich, Rolf G. Beutel, Benjamin Wipfler, Ralph S. Peters, Julie M. Allen, Malte Petersen, Alexander Donath, Kimberly K. O. Walden, Alexey M. Kozlov, Lars Podsiadlowski, Christoph Mayer, Karen Meusemann, Alexandros Vasilikopoulos, Robert M. Waterhouse, Stephen L. Cameron, Christiane Weirauch, Daniel R. Swanson, Diana M. Percy, Nate B. Hardy, Irene Terry, Shanlin Liu, Xin Zhou, Bernhard Misof, Hugh M. Robertson, Kazunori Yoshizawa
      Pages: 12775 - 12780
      Abstract: Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1815820115
      Issue No: Vol. 115, No. 50 (2018)
  • The unusual rainbow trout sex determination gene hijacked the canonical
           vertebrate gonadal differentiation pathway [Evolution]
    • Authors: Sylvain Bertho; Amaury Herpin, Adele Branthonne, Elodie Jouanno, Ayaka Yano, Barbara Nicol, Thomas Muller, Maelle Pannetier, Eric Pailhoux, Misako Miwa, Goro Yoshizaki, Manfred Schartl, Yann Guiguen
      Pages: 12781 - 12786
      Abstract: Evolutionary novelties require rewiring of transcriptional networks and/or the evolution of new gene functions. Sex determination (SD), one of the most plastic evolutionary processes, requires such novelties. Studies on the evolution of vertebrate SD revealed that new master SD genes are generally recruited from genes involved in the downstream SD...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1803826115
      Issue No: Vol. 115, No. 50 (2018)
  • Quantifying the risk of hemiplasy in phylogenetic inference [Evolution]
    • Authors: Rafael F. Guerrero; Matthew W. Hahn
      Pages: 12787 - 12792
      Abstract: Convergent evolution—the appearance of the same character state in apparently unrelated organisms—is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811268115
      Issue No: Vol. 115, No. 50 (2018)
  • SUMOylation of PCNA by PIAS1 and PIAS4 promotes template switch in the
           chicken and human B cell lines [Genetics]
    • Authors: Mohiuddin Mohiuddin; Terry John Evans, Md Maminur Rahman, Islam Shamima Keka, Masataka Tsuda, Hiroyuki Sasanuma, Shunichi Takeda
      Pages: 12793 - 12798
      Abstract: DNA damage tolerance (DDT) releases replication blockage caused by damaged nucleotides on template strands employing two alternative pathways, error-prone translesion DNA synthesis (TLS) and error-free template switch (TS). Lys164 of proliferating cell nuclear antigen (PCNA) is SUMOylated during the physiological cell cycle. To explore the role for SUMOylation of PCNA...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1716349115
      Issue No: Vol. 115, No. 50 (2018)
  • Mutations in Plasmodium falciparum actin-binding protein coronin confer
           reduced artemisinin susceptibility [Microbiology]
    • Authors: Allison R. Demas; Aabha I. Sharma, Wesley Wong, Angela M. Early, Seth Redmond, Selina Bopp, Daniel E. Neafsey, Sarah K. Volkman, Daniel L. Hartl, Dyann F. Wirth
      Pages: 12799 - 12804
      Abstract: Drug resistance is an obstacle to global malaria control, as evidenced by the recent emergence and rapid spread of delayed artemisinin (ART) clearance by mutant forms of the PfKelch13 protein in Southeast Asia. Identifying genetic determinants of ART resistance in African-derived parasites is important for surveillance and for understanding the...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1812317115
      Issue No: Vol. 115, No. 50 (2018)
  • Discovery of Kaposi‚Äôs sarcoma herpesvirus-encoded circular RNAs and a
           human antiviral circular RNA [Microbiology]
    • Authors: Takanobu Tagawa; Shaoȷian Gao, Vishal N. Koparde, Mileidy Gonzalez, John L. Spouge, Anna P. Serquina, Kathryn Lurain, Ramya Ramaswami, Thomas S. Uldrick, Robert Yarchoan, Joseph M. Ziegelbauer
      Pages: 12805 - 12810
      Abstract: Noncoding RNAs have substantial effects in host–virus interactions. Circular RNAs (circRNAs) are novel single-stranded noncoding RNAs which can decoy other RNAs or RNA-binding proteins to inhibit their functions. The role of circRNAs is largely unknown in the context of Kaposi’s sarcoma herpesvirus (KSHV). We hypothesized that circRNAs influence viral infection...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1816183115
      Issue No: Vol. 115, No. 50 (2018)
  • Individual synaptic vesicles mediate stimulated exocytosis from cochlear
           inner hair cells [Neuroscience]
    • Authors: Chad Paul Grabner; Tobias Moser
      Pages: 12811 - 12816
      Abstract: Spontaneous excitatory postsynaptic currents (sEPSCs) measured from the first synapse in the mammalian auditory pathway reach a large mean amplitude with a high level of variance (CV between 0.3 and 1). This has led some to propose that each inner hair cell (IHC) ribbon-type active zone (AZ), on average, releases...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1811814115
      Issue No: Vol. 115, No. 50 (2018)
  • Mechanically activated ion channel PIEZO1 is required for lymphatic valve
           formation [Physiology]
    • Authors: Keiko Nonomura; Viktor Lukacs, Daniel T. Sweet, Lauren M. Goddard, Akemi Kanie, Tess Whitwam, Sanjeev S. Ranade, Toshihiko Fujimori, Mark L. Kahn, Ardem Patapoutian
      Pages: 12817 - 12822
      Abstract: PIEZO1 is a cation channel that is activated by mechanical forces such as fluid shear stress or membrane stretch. PIEZO1 loss-of-function mutations in patients are associated with congenital lymphedema with pleural effusion. However, the mechanistic link between PIEZO1 function and the development or function of the lymphatic system is currently...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1817070115
      Issue No: Vol. 115, No. 50 (2018)
  • TOR and RPS6 transmit light signals to enhance protein translation in
           deetiolating Arabidopsis seedlings [Plant Biology]
    • Authors: Guan-Hong Chen; Ming-Jung Liu, Yan Xiong, Jen Sheen, Shu-Hsing Wu
      Pages: 12823 - 12828
      Abstract: Deetiolation is an essential developmental process transforming young plant seedlings into the vegetative phase with photosynthetic activities. Light signals initiate this important developmental process by triggering massive reprogramming of the transcriptome and translatome. Compared with the wealth of knowledge of transcriptional regulation, the molecular mechanism underlying this light-triggered translational enhancement...
      PubDate: 2018-12-11T10:16:37-08:00
      DOI: 10.1073/pnas.1809526115
      Issue No: Vol. 115, No. 50 (2018)
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