Table of Contents

Biological Sciences

• Biochemistry

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    Basis for substrate recognition and distinction by matrix metalloproteinases

    Boris I. Ratnikov, Piotr Cieplak, Kosi Gramatikoff, James Pierce, Alexey Eroshkin, Yoshinobu Igarashi, Marat Kazanov, Qing Sun, Adam Godzik, Andrei Osterman, Boguslaw Stec, Alex Strongin, and Jeffrey W. Smith

    PNAS October 7, 2014 111 (40) E4148-E4155; first published September 22, 2014. https://doi.org/10.1073/pnas.1406134111
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    Structural insights into the role of iron–histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins

    Mark A. Herzik Jr., Rohan Jonnalagadda, John Kuriyan, and Michael A. Marletta

    PNAS October 7, 2014 111 (40) E4156-E4164; first published September 24, 2014. https://doi.org/10.1073/pnas.1416936111
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    Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity

    • Inaugural Article

    Na An, Aaron M. Fleming, Eric G. Middleton, and Cynthia J. Burrows

    PNAS October 7, 2014 111 (40) 14325-14331; first published September 15, 2014. https://doi.org/10.1073/pnas.1415944111

    See companion article:

    • QnAs with Cynthia J. Burrows

      - Oct 27, 2014
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    Pharmacologic rescue of an enzyme-trafficking defect in primary hyperoxaluria 1

    Non Miyata, Janos Steffen, Meghan E. Johnson, Sonia Fargue, Christopher J. Danpure, and Carla M. Koehler

    PNAS October 7, 2014 111 (40) 14406-14411; first published September 18, 2014. https://doi.org/10.1073/pnas.1408401111
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    The cardiac-specific N-terminal region of troponin I positions the regulatory domain of troponin C

    Peter M. Hwang, Fangze Cai, Sandra E. Pineda-Sanabria, David C. Corson, and Brian D. Sykes

    PNAS October 7, 2014 111 (40) 14412-14417; first published September 22, 2014. https://doi.org/10.1073/pnas.1410775111
  • Open Access

    Ribosome-induced tuning of GTP hydrolysis by a translational GTPase

    Cristina Maracci, Frank Peske, Ev Dannies, Corinna Pohl, and Marina V. Rodnina

    PNAS October 7, 2014 111 (40) 14418-14423; first published September 22, 2014. https://doi.org/10.1073/pnas.1412676111

• Biophysics and Computational Biology

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    Modeling putative therapeutic implications of exosome exchange between tumor and immune cells

    Mingyang Lu, Bin Huang, Samir M. Hanash, José N. Onuchic, and Eshel Ben-Jacob

    PNAS October 7, 2014 111 (40) E4165-E4174; first published September 22, 2014. https://doi.org/10.1073/pnas.1416745111
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    Structural and energetic determinants of adhesive binding specificity in type I cadherins

    Jeremie Vendome, Klara Felsovalyi, Hang Song, Zhongyu Yang, Xiangshu Jin, Julia Brasch, Oliver J. Harrison, Goran Ahlsen, Fabiana Bahna, Anna Kaczynska, Phinikoula S. Katsamba, Darwin Edmond, Wayne L. Hubbell, Lawrence Shapiro, and Barry Honig

    PNAS October 7, 2014 111 (40) E4175-E4184; first published September 24, 2014. https://doi.org/10.1073/pnas.1416737111
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    Dominance of misfolded intermediates in the dynamics of α-helix folding

    Milo M. Lin, Dmitry Shorokhov, and Ahmed H. Zewail

    PNAS October 7, 2014 111 (40) 14424-14429; first published September 22, 2014. https://doi.org/10.1073/pnas.1416300111

• Cell Biology

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    Bimodal activation of BubR1 by Bub3 sustains mitotic checkpoint signaling

    Joo Seok Han, Benjamin Vitre, Daniele Fachinetti, and Don W. Cleveland

    PNAS October 7, 2014 111 (40) E4185-E4193; first published September 22, 2014. https://doi.org/10.1073/pnas.1416277111
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    Platelet mechanosensing of substrate stiffness during clot formation mediates adhesion, spreading, and activation

    Yongzhi Qiu, Ashley C. Brown, David R. Myers, Yumiko Sakurai, Robert G. Mannino, Reginald Tran, Byungwook Ahn, Elaissa T. Hardy, Matthew F. Kee, Sanjay Kumar, Gang Bao, Thomas H. Barker, and Wilbur A. Lam

    PNAS October 7, 2014 111 (40) 14430-14435; first published September 22, 2014. https://doi.org/10.1073/pnas.1322917111
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    Hematopoietic RIPK1 deficiency results in bone marrow failure caused by apoptosis and RIPK3-mediated necroptosis

    Justine E. Roderick, Nicole Hermance, Matija Zelic, Matthew J. Simmons, Apostolos Polykratis, Manolis Pasparakis, and Michelle A. Kelliher

    PNAS October 7, 2014 111 (40) 14436-14441; first published September 22, 2014. https://doi.org/10.1073/pnas.1409389111
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    Cell fate regulation by gelsolin in human gynecologic cancers

    Mohammad R. Abedini, Pei-Wen Wang, Yu-Fang Huang, Mingju Cao, Cheng-Yang Chou, Dar-Bin Shieh, and Benjamin K. Tsang

    PNAS October 7, 2014 111 (40) 14442-14447; first published September 22, 2014. https://doi.org/10.1073/pnas.1401166111
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    Cellular memory in eukaryotic chemotaxis

    Monica Skoge, Haicen Yue, Michael Erickstad, Albert Bae, Herbert Levine, Alex Groisman, William F. Loomis, and Wouter-Jan Rappel

    PNAS October 7, 2014 111 (40) 14448-14453; first published September 23, 2014. https://doi.org/10.1073/pnas.1412197111

    See companion article:

    • Cell memory and adaptation in chemotaxis

      - Oct 15, 2014
  • Open Access

    Dysregulation of gene expression as a cause of Cockayne syndrome neurological disease

    Yuming Wang, Probir Chakravarty, Michael Ranes, Gavin Kelly, Philip J. Brooks, Edward Neilan, Aengus Stewart, Giampietro Schiavo, and Jesper Q. Svejstrup

    PNAS October 7, 2014 111 (40) 14454-14459; first published September 23, 2014. https://doi.org/10.1073/pnas.1412569111

• Developmental Biology

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    Beclin-1 deficiency in the murine ovary results in the reduction of progesterone production to promote preterm labor

    Thomas R. Gawriluk, CheMyong Ko, Xiaoman Hong, Lane K. Christenson, and Edmund B. Rucker III

    PNAS October 7, 2014 111 (40) E4194-E4203; first published September 22, 2014. https://doi.org/10.1073/pnas.1409323111
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    Mechanochemical actuators of embryonic epithelial contractility

    YongTae Kim, Melis Hazar, Deepthi S. Vijayraghavan, Jiho Song, Timothy R. Jackson, Sagar D. Joshi, William C. Messner, Lance A. Davidson, and Philip R. LeDuc

    PNAS October 7, 2014 111 (40) 14366-14371; first published September 22, 2014. https://doi.org/10.1073/pnas.1405209111
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    Mosquito-specific microRNA-1174 targets serine hydroxymethyltransferase to control key functions in the gut

    Shiping Liu, Keira J. Lucas, Sourav Roy, Jisu Ha, and Alexander S. Raikhel

    PNAS October 7, 2014 111 (40) 14460-14465; first published September 22, 2014. https://doi.org/10.1073/pnas.1416278111
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    Ebf2 is a selective marker of brown and beige adipogenic precursor cells

    • From the Cover

    Wenshan Wang, Megan Kissig, Sona Rajakumari, Li Huang, Hee-woong Lim, Kyoung-Jae Won, and Patrick Seale

    PNAS October 7, 2014 111 (40) 14466-14471; first published September 2, 2014. https://doi.org/10.1073/pnas.1412685111

    See companion article:

    • Unwiring the transcriptional heat circuit

      - Sep 26, 2014

• Ecology

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    Collapse of an ecological network in Ancient Egypt

    Justin D. Yeakel, Mathias M. Pires, Lars Rudolf, Nathaniel J. Dominy, Paul L. Koch, Paulo R. Guimarães Jr., and Thilo Gross

    PNAS October 7, 2014 111 (40) 14472-14477; first published September 8, 2014. https://doi.org/10.1073/pnas.1408471111

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    • Recovering ecological pattern in Ancient Egypt

      - Jan 13, 2015
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    Discontinuity in the responses of ecosystem processes and multifunctionality to altered soil community composition

    Mark A. Bradford, Stephen A. Wood, Richard D. Bardgett, Helaina I. J. Black, Michael Bonkowski, Till Eggers, Susan J. Grayston, Ellen Kandeler, Peter Manning, Heikki Setälä, and T. Hefin Jones

    PNAS October 7, 2014 111 (40) 14478-14483; first published September 22, 2014. https://doi.org/10.1073/pnas.1413707111

    See companion article:

    • Aggregation obscures inference

      - Dec 05, 2014

• Environmental Sciences

  • Open Access

    Reforestation as a novel abatement and compliance measure for ground-level ozone

    Timm Kroeger, Francisco J. Escobedo, José L. Hernandez, Sebastián Varela, Sonia Delphin, Jonathan R. B. Fisher, and Janice Waldron

    PNAS October 7, 2014 111 (40) E4204-E4213; first published September 8, 2014. https://doi.org/10.1073/pnas.1409785111

• Evolution

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    Structural adaptations to diverse fighting styles in sexually selected weapons

    • From the Cover

    Erin L. McCullough, Bret W. Tobalske, and Douglas J. Emlen

    PNAS October 7, 2014 111 (40) 14484-14488; first published September 8, 2014. https://doi.org/10.1073/pnas.1409585111
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    Conifer species adapt to low-rainfall climates by following one of two divergent pathways

    Timothy J. Brodribb, Scott A.M. McAdam, Gregory J. Jordan, and Samuel C.V. Martins

    PNAS October 7, 2014 111 (40) 14489-14493; first published September 22, 2014. https://doi.org/10.1073/pnas.1407930111
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    Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance

    Seungsoo Kim, Tami D. Lieberman, and Roy Kishony

    PNAS October 7, 2014 111 (40) 14494-14499; first published September 22, 2014. https://doi.org/10.1073/pnas.1409800111
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    Complementary symbiont contributions to plant decomposition in a fungus-farming termite

    Michael Poulsen, Haofu Hu, Cai Li, Zhensheng Chen, Luohao Xu, Saria Otani, Sanne Nygaard, Tania Nobre, Sylvia Klaubauf, Philipp M. Schindler, Frank Hauser, Hailin Pan, Zhikai Yang, Anton S. M. Sonnenberg, Z. Wilhelm de Beer, Yong Zhang, Michael J. Wingfield, Cornelis J. P. Grimmelikhuijzen, Ronald P. de Vries, Judith Korb, Duur K. Aanen, Jun Wang, Jacobus J. Boomsma, and Guojie Zhang

    PNAS October 7, 2014 111 (40) 14500-14505; first published September 22, 2014. https://doi.org/10.1073/pnas.1319718111

• Genetics

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    Transformation of quiescent adult oligodendrocyte precursor cells into malignant glioma through a multistep reactivation process

    Rui Pedro Galvao, Anita Kasina, Robert S. McNeill, Jordan E. Harbin, Oded Foreman, Roel G. W. Verhaak, Akiko Nishiyama, C. Ryan Miller, and Hui Zong

    PNAS October 7, 2014 111 (40) E4214-E4223; first published September 22, 2014. https://doi.org/10.1073/pnas.1414389111
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    An extended Shine–Dalgarno sequence in mRNA functionally bypasses a vital defect in initiator tRNA

    Sunil Shetty, HimaPriyanka Nadimpalli, Riyaz Ahmad Shah, Smriti Arora, Gautam Das, and Umesh Varshney

    PNAS October 7, 2014 111 (40) E4224-E4233; first published September 22, 2014. https://doi.org/10.1073/pnas.1411637111
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    Chromatin reader L(3)mbt requires the Myb–MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment

    Daniel P. Blanchard, Daphne Georlette, Lisa Antoszewski, and Michael R. Botchan

    PNAS October 7, 2014 111 (40) E4234-E4243; first published September 23, 2014. https://doi.org/10.1073/pnas.1416321111

• Immunology and Inflammation

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    Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy

    Alexander W. Kay, Julia Fukuyama, Natali Aziz, Cornelia L. Dekker, Sally Mackey, Gary E. Swan, Mark M. Davis, Susan Holmes, and Catherine A. Blish

    PNAS October 7, 2014 111 (40) 14506-14511; first published September 22, 2014. https://doi.org/10.1073/pnas.1416569111

• Medical Sciences

  • Open Access

    Insulin and insulin-like growth factor 1 receptors are required for normal expression of imprinted genes

    Jeremie Boucher, Marika Charalambous, Kim Zarse, Marcelo A. Mori, Andre Kleinridders, Michael Ristow, Anne C. Ferguson-Smith, and C. Ronald Kahn

    PNAS October 7, 2014 111 (40) 14512-14517; first published September 22, 2014. https://doi.org/10.1073/pnas.1415475111
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    MicroRNA-223 coordinates cholesterol homeostasis

    Kasey C. Vickers, Stuart R. Landstreet, Michael G. Levin, Bassem M. Shoucri, Cynthia L. Toth, Robert C. Taylor, Brian T. Palmisano, Fatiha Tabet, Huanhuan L. Cui, Kerry-Anne Rye, Praveen Sethupathy, and Alan T. Remaley

    PNAS October 7, 2014 111 (40) 14518-14523; first published September 22, 2014. https://doi.org/10.1073/pnas.1215767111
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    Dendritic spinopathy in transgenic mice expressing ALS/dementia-linked mutant UBQLN2

    George H. Gorrie, Faisal Fecto, Daniel Radzicki, Craig Weiss, Yong Shi, Hongxin Dong, Hong Zhai, Ronggen Fu, Erdong Liu, Sisi Li, Hasan Arrat, Eileen H. Bigio, John F. Disterhoft, Marco Martina, Enrico Mugnaini, Teepu Siddique, and Han-Xiang Deng

    PNAS October 7, 2014 111 (40) 14524-14529; first published September 22, 2014. https://doi.org/10.1073/pnas.1405741111
  • Open Access

    Resolvin D1 limits 5-lipoxygenase nuclear localization and leukotriene B₄ synthesis by inhibiting a calcium-activated kinase pathway

    Gabrielle Fredman, Lale Ozcan, Stefano Spolitu, Jason Hellmann, Matthew Spite, Johannes Backs, and Ira Tabas

    PNAS October 7, 2014 111 (40) 14530-14535; first published September 22, 2014. https://doi.org/10.1073/pnas.1410851111

• Microbiology

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    Involvement of the host DNA-repair enzyme TDP2 in formation of the covalently closed circular DNA persistence reservoir of hepatitis B viruses

    Christian Königer, Ida Wingert, Moritz Marsmann, Christine Rösler, Jürgen Beck, and Michael Nassal

    PNAS October 7, 2014 111 (40) E4244-E4253; first published September 8, 2014. https://doi.org/10.1073/pnas.1409986111
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    Shigella IpaH7.8 E3 ubiquitin ligase targets glomulin and activates inflammasomes to demolish macrophages

    Shiho Suzuki, Hitomi Mimuro, Minsoo Kim, Michinaga Ogawa, Hiroshi Ashida, Takahito Toyotome, Luigi Franchi, Masato Suzuki, Takahito Sanada, Toshihiko Suzuki, Hiroko Tsutsui, Gabriel Núñez, and Chihiro Sasakawa

    PNAS October 7, 2014 111 (40) E4254-E4263; first published September 22, 2014. https://doi.org/10.1073/pnas.1324021111
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    Precisely modulated pathogenicity island interference with late phage gene transcription

    Geeta Ram, John Chen, Hope F. Ross, and Richard P. Novick

    PNAS October 7, 2014 111 (40) 14536-14541; first published September 22, 2014. https://doi.org/10.1073/pnas.1406749111
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    Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt

    Mounir Georges AbouHaidar, Srividhya Venkataraman, Ashkan Golshani, Bolin Liu, and Tauqeer Ahmad

    PNAS October 7, 2014 111 (40) 14542-14547; first published September 24, 2014. https://doi.org/10.1073/pnas.1402814111

• Neuroscience

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    Object and spatial mnemonic interference differentially engage lateral and medial entorhinal cortex in humans

    Zachariah M. Reagh and Michael A. Yassa

    PNAS October 7, 2014 111 (40) E4264-E4273; first published September 22, 2014. https://doi.org/10.1073/pnas.1411250111
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    α-Synuclein assembles into higher-order multimers upon membrane binding to promote SNARE complex formation

    Jacqueline Burré, Manu Sharma, and Thomas C. Südhof

    PNAS October 7, 2014 111 (40) E4274-E4283; first published September 22, 2014. https://doi.org/10.1073/pnas.1416598111
  • Open Access

    Alpha and gamma oscillations characterize feedback and feedforward processing in monkey visual cortex

    • From the Cover

    Timo van Kerkoerle, Matthew W. Self, Bruno Dagnino, Marie-Alice Gariel-Mathis, Jasper Poort, Chris van der Togt, and Pieter R. Roelfsema

    PNAS October 7, 2014 111 (40) 14332-14341; first published September 9, 2014. https://doi.org/10.1073/pnas.1402773111

    See companion article:

    • Frequencies mark the direction of communication

      - Sep 29, 2014
  • Open Access

    Frequency selectivity without resonance in a fluid waveguide

    Marcel van der Heijden

    PNAS October 7, 2014 111 (40) 14548-14552; first published September 18, 2014. https://doi.org/10.1073/pnas.1412412111
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    Statistical learning of recurring sound patterns encodes auditory objects in songbird forebrain

    Kai Lu and David S. Vicario

    PNAS October 7, 2014 111 (40) 14553-14558; first published September 22, 2014. https://doi.org/10.1073/pnas.1412109111
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    Beat synchronization predicts neural speech encoding and reading readiness in preschoolers

    Kali Woodruff Carr, Travis White-Schwoch, Adam T. Tierney, Dana L. Strait, and Nina Kraus

    PNAS October 7, 2014 111 (40) 14559-14564; first published September 22, 2014. https://doi.org/10.1073/pnas.1406219111
  • Open Access

    Unique semantic space in the brain of each beholder predicts perceived similarity

    Ian Charest, Rogier A. Kievit, Taylor W. Schmitz, Diana Deca, and Nikolaus Kriegeskorte

    PNAS October 7, 2014 111 (40) 14565-14570; first published September 22, 2014. https://doi.org/10.1073/pnas.1402594111

• Pharmacology

  • Open Access

    Molecular matchmaking between the popular weight-loss herb Hoodia gordonii and GPR119, a potential drug target for metabolic disorder

    Shuyong Zhang, Yuyong Ma, Jing Li, Junjun Ma, Biao Yu, and Xin Xie

    PNAS October 7, 2014 111 (40) 14571-14576; first published September 22, 2014. https://doi.org/10.1073/pnas.1324130111

• Physiology

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    Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function

    • From the Cover

    Andrea Saponaro, Sofia R. Pauleta, Francesca Cantini, Manolis Matzapetakis, Christian Hammann, Chiara Donadoni, Lei Hu, Gerhard Thiel, Lucia Banci, Bina Santoro, and Anna Moroni

    PNAS October 7, 2014 111 (40) 14577-14582; first published September 2, 2014. https://doi.org/10.1073/pnas.1410389111

    See companion article:

    • HCN channel gating

      - Sep 23, 2014
  • Open Access

    Antifreeze protein-induced superheating of ice inside Antarctic notothenioid fishes inhibits melting during summer warming

    Paul A. Cziko, Arthur L. DeVries, Clive W. Evans, and Chi-Hing Christina Cheng

    PNAS October 7, 2014 111 (40) 14583-14588; first published September 22, 2014. https://doi.org/10.1073/pnas.1410256111
  • Open Access

    Deleting titin’s I-band/A-band junction reveals critical roles for titin in biomechanical sensing and cardiac function

    Henk L. Granzier, Kirk R. Hutchinson, Paola Tonino, Mei Methawasin, Frank W. Li, Rebecca E. Slater, Mathew M. Bull, Chandra Saripalli, Christopher T. Pappas, Carol C. Gregorio, and John E. Smith III

    PNAS October 7, 2014 111 (40) 14589-14594; first published September 22, 2014. https://doi.org/10.1073/pnas.1411493111

    See companion article:

    • IA junction does not control filament length

      - Feb 18, 2015

• Plant Biology

  • Open Access

    FBH1 affects warm temperature responses in the Arabidopsis circadian clock

    Dawn H. Nagel, Jose L. Pruneda-Paz, and Steve A. Kay

    PNAS October 7, 2014 111 (40) 14595-14600; first published September 22, 2014. https://doi.org/10.1073/pnas.1416666111
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    Range of cell-wall alterations enhance saccharification in Brachypodium distachyon mutants

    Poppy E. Marriott, Richard Sibout, Catherine Lapierre, Jonatan U. Fangel, William G. T. Willats, Herman Hofte, Leonardo D. Gómez, and Simon J. McQueen-Mason

    PNAS October 7, 2014 111 (40) 14601-14606; first published September 22, 2014. https://doi.org/10.1073/pnas.1414020111
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    NODULE INCEPTION creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production

    Takashi Soyano, Hideki Hirakawa, Shusei Sato, Makoto Hayashi, and Masayoshi Kawaguchi

    PNAS October 7, 2014 111 (40) 14607-14612; first published September 22, 2014. https://doi.org/10.1073/pnas.1412716111
  • Open Access

    Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis

    Mengji Cao, Peng Du, Xianbing Wang, Yun-Qi Yu, Yan-Hong Qiu, Wanxiang Li, Amit Gal-On, Changyong Zhou, Yi Li, and Shou-Wei Ding

    PNAS October 7, 2014 111 (40) 14613-14618; first published September 8, 2014. https://doi.org/10.1073/pnas.1407131111
  • Open Access

    A mechanistic framework for noncell autonomous stem cell induction in Arabidopsis

    Gabor Daum, Anna Medzihradszky, Takuya Suzaki, and Jan U. Lohmann

    PNAS October 7, 2014 111 (40) 14619-14624; first published September 22, 2014. https://doi.org/10.1073/pnas.1406446111

• Psychological and Cognitive Sciences

  • Open Access

    Human preferences for sexually dimorphic faces may be evolutionarily novel

    Isabel M. Scott, Andrew P. Clark, Steven C. Josephson, Adam H. Boyette, Innes C. Cuthill, Ruby L. Fried, Mhairi A. Gibson, Barry S. Hewlett, Mark Jamieson, William Jankowiak, P. Lynne Honey, Zejun Huang, Melissa A. Liebert, Benjamin G. Purzycki, John H. Shaver, J. Josh Snodgrass, Richard Sosis, Lawrence S. Sugiyama, Viren Swami, Douglas W. Yu, Yangke Zhao, and Ian S. Penton-Voak

    PNAS October 7, 2014 111 (40) 14388-14393; first published September 22, 2014. https://doi.org/10.1073/pnas.1409643111

• Sustainability Science

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    Toward a theory of resilience for international development applications

    Christopher B. Barrett and Mark A. Constas

    PNAS October 7, 2014 111 (40) 14625-14630; first published September 22, 2014. https://doi.org/10.1073/pnas.1320880111

• Systems Biology

  • Open Access

    Epigenetic dysregulation by nickel through repressive chromatin domain disruption

    Cynthia C. Jose, Beisi Xu, Lakshmanan Jagannathan, Candi Trac, Ramya K. Mallela, Takamitsu Hattori, Darson Lai, Shohei Koide, Dustin E. Schones, and Suresh Cuddapah

    PNAS October 7, 2014 111 (40) 14631-14636; first published September 22, 2014. https://doi.org/10.1073/pnas.1406923111