October 2019

Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. While much progress has been made in understanding the mechanisms of planar leaf development, it remains unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. This study by Lee et al. uses 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. The study shows that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. The image shows a U. gibba trap (about 1 mm across) imaged by confocal microscopy about 10 days after initiation; the green areas indicate clones of cells in which expression of green fluorescent protein has been induced by heat-shock (against a red mCherry background).

Image Credit: Karen Lee, Yohei Koide, John Fozard and Claire Bushell

Perspectives

An ecosystem-wide reproductive failure with more snow in the Arctic

Niels Martin Schmidt, Jeroen Reneerkens, Jens Hesselbjerg Christensen, Martin Olesen, Tomas Roslin

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000392

The NIH public access policy did not harm biomedical journals

A. Townsend Peterson, Paul E. Johnson, Narayani Barve, Ada Emmett, Marc L. Greenberg, Josh Bolick, Huijie Qiao

PLOS Biology: published October 23, 2019 | https://doi.org/10.1371/journal.pbio.3000352

Primer

Waves of prediction

Karl J. Friston

PLOS Biology: published October 3, 2019 | https://doi.org/10.1371/journal.pbio.3000426

Community Pages

The NIH Open Citation Collection: A public access, broad coverage resource

B. Ian Hutchins, Kirk L. Baker, Matthew T. Davis, Mario A. Diwersy, Ehsanul Haque, Robert M. Harriman, Travis A. Hoppe, Stephen A. Leicht, Payam Meyer, George M. Santangelo

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000385

Refining animal research: The Animal Study Registry

Bettina Bert, Céline Heinl, Justyna Chmielewska, Franziska Schwarz, Barbara Grune, Andreas Hensel, Matthias Greiner, Gilbert Schönfelder

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000463

Research Articles

Combinatorial mutagenesis of rapidly evolving residues yields super-restrictor antiviral proteins

Rossana Colón-Thillet, Emily Hsieh, Laura Graf, Richard N. McLaughlin Jr, Janet M. Young, Georg Kochs, Michael Emerman, Harmit S. Malik

PLOS Biology: published October 1, 2019 | https://doi.org/10.1371/journal.pbio.3000181

A neural ensemble correlation code for sound category identification

Mina Sadeghi, Xiu Zhai, Ian H. Stevenson, Monty A. Escabí

PLOS Biology: published October 1, 2019 | https://doi.org/10.1371/journal.pbio.3000449

Symmetry breaking in the embryonic skin triggers directional and sequential plumage patterning

Richard Bailleul, Camille Curantz, Carole Desmarquet-Trin Dinh, Magdalena Hidalgo, Jonathan Touboul, Marie Manceau

PLOS Biology: published October 2, 2019 | https://doi.org/10.1371/journal.pbio.3000448

Alpha oscillations and traveling waves: Signatures of predictive coding?

Andrea Alamia, Rufin VanRullen

PLOS Biology: published October 3, 2019 | https://doi.org/10.1371/journal.pbio.3000487

Human motor cortical beta bursts relate to movement planning and response errors

Simon Little, James Bonaiuto, Gareth Barnes, Sven Bestmann

PLOS Biology: published October 4, 2019 | https://doi.org/10.1371/journal.pbio.3000479

A photoactivatable crosslinking system reveals protein interactions in the Toxoplasma gondii inner membrane complex

Charles Paul Choi, Andy Seong Moon, Peter Sungmin Back, Yasaman Jami‐Alahmadi, Ajay Amar Vashisht, James Akira Wohlschlegel, Peter John Bradley

PLOS Biology: published October 4, 2019 | https://doi.org/10.1371/journal.pbio.3000475

A hormone receptor pathway cell-autonomously delays neuron morphological aging by suppressing endocytosis

Claire E. Richardson, Callista Yee, Kang Shen

PLOS Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pbio.3000452

The developmental Wnt signaling pathway effector β-catenin/TCF mediates hepatic functions of the sex hormone estradiol in regulating lipid metabolism

Lili Tian, Weijuan Shao, Wilfred Ip, Zhuolun Song, Yasaman Badakhshi, Tianru Jin

PLOS Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pbio.3000444

Mating induces switch from hormone-dependent to hormone-independent steroid receptor–mediated growth in Drosophila secondary cells

Aaron Leiblich, Josephine E. E. U. Hellberg, Aashika Sekar, Carina Gandy, Claudia C. Mendes, Siamak Redhai, John Mason, Mark Wainwright, Pauline Marie, Deborah C. I. Goberdhan, Freddie C. Hamdy, Clive Wilson

PLOS Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pbio.3000145

Cisd2 is essential to delaying cardiac aging and to maintaining heart functions

Chi-Hsiao Yeh, Zhao-Qing Shen, Shao-Yu Hsiung, Pei-Chun Wu, Yuan-Chi Teng, Yi-Ju Chou, Su-Wen Fang, Chian-Feng Chen, Yu-Ting Yan, Lung-Sen Kao, Cheng-Heng Kao, Ting-Fen Tsai

PLOS Biology: published October 8, 2019 | https://doi.org/10.1371/journal.pbio.3000508

Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses

Bo Lv, Qin An, Qiao Zeng, Xunyi Zhang, Ping Lu, Yanqiu Wang, Xianmin Zhu, Yazhong Ji, Guoping Fan, Zhigang Xue

PLOS Biology: published October 9, 2019 | https://doi.org/10.1371/journal.pbio.3000187

Autism candidate gene DIP2A regulates spine morphogenesis via acetylation of cortactin

Jun Ma, Lu-Qing Zhang, Zi-Xuan He, Xiao-Xiao He, Ya-Jun Wang, You-Li Jian, Xin Wang, Bin-Bin Zhang, Ce Su, Jun Lu, Bai-Qu Huang, Yu Zhang, Gui-Yun Wang, Wei-Xiang Guo, De-Lai Qiu, Lin Mei, Wen-Cheng Xiong, Yao-Wu Zheng, Xiao-Juan Zhu

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000461

Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism

Karen J. I. Lee, Claire Bushell, Yohei Koide, John A. Fozard, Chunlan Piao, Man Yu, Jacob Newman, Christopher Whitewoods, Jerome Avondo, Richard Kennaway, Athanasius F. M. Marée, Minlong Cui, Enrico Coen

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000427

NF1-cAMP signaling dissociates cell type–specific contributions of striatal medium spiny neurons to reward valuation and motor control

Laurie P. Sutton, Brian S. Muntean, Olga Ostrovskaya, Stefano Zucca, Maria Dao, Cesare Orlandi, Chenghui Song, Keqiang Xie, Kirill A. Martemyanov

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000477

Development of neural specialization for print: Evidence for predictive coding in visual word recognition

Jing Zhao, Urs Maurer, Sheng He, Xuchu Weng

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000474

Sex chromosomes control vertical transmission of feminizing Wolbachia symbionts in an isopod

Thomas Becking, Mohamed Amine Chebbi, Isabelle Giraud, Bouziane Moumen, Tiffany Laverré, Yves Caubet, Jean Peccoud, Clément Gilbert, Richard Cordaux

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000438

Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing

Cathleen M. Green, Zhong Li, Aaron D. Smith, Olga Novikova, Valjean R. Bacot-Davis, Fengshan Gao, Saiyang Hu, Nilesh K. Banavali, Dennis J. Thiele, Hongmin Li, Marlene Belfort

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000104

Cell confinement reveals a branched-actin independent circuit for neutrophil polarity

Brian R. Graziano, Jason P. Town, Ewa Sitarska, Tamas L. Nagy, Miha Fošnarič, Samo Penič, Aleš Iglič, Veronika Kralj-Iglič, Nir S. Gov, Alba Diz-Muñoz, Orion D. Weiner

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000457

Dynamic evolution in the key honey bee pathogen deformed wing virus: Novel insights into virulence and competition using reverse genetics

Eugene V. Ryabov, Anna K. Childers, Dawn Lopez, Kyle Grubbs, Francisco Posada-Florez, Daniel Weaver, William Girten, Dennis vanEngelsdorp, Yanping Chen, Jay D. Evans

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000502

Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease

Weizhong Chen, Hongyuan Zhang, Yifei Zhang, Yu Wang, Jianhua Gan, Quanjiang Ji

PLOS Biology: published October 11, 2019 | https://doi.org/10.1371/journal.pbio.3000496

Walking enhances peripheral visual processing in humans

Liyu Cao, Barbara Händel

PLOS Biology: published October 11, 2019 | https://doi.org/10.1371/journal.pbio.3000511

KHDC3L mutation causes recurrent pregnancy loss by inducing genomic instability of human early embryonic cells

Weidao Zhang, Zhongliang Chen, Dengfeng Zhang, Bo Zhao, Lu Liu, Zhengyuan Xie, Yonggang Yao, Ping Zheng

PLOS Biology: published October 14, 2019 | https://doi.org/10.1371/journal.pbio.3000468

Prepontine non-giant neurons drive flexible escape behavior in zebrafish

Gregory D. Marquart, Kathryn M. Tabor, Sadie A. Bergeron, Kevin L. Briggman, Harold A. Burgess

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000480

Resurrection of the ancestral RH5 invasion ligand provides a molecular explanation for the origin of P. falciparum malaria in humans

Francis Galaway, Ryan Yu, Anastasia Constantinou, Franck Prugnolle, Gavin J. Wright

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000490

Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids

Sapna Chhabra, Lizhong Liu, Ryan Goh, Xiangyu Kong, Aryeh Warmflash

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000498

Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering

Shu-Ting You, Yu-Ting Jhou, Cheng-Fu Kao, Jun-Yi Leu

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000433

The Hippo pathway integrates PI3K–Akt signals with mechanical and polarity cues to control tissue growth

Nerea Borreguero-Muñoz, Georgina C. Fletcher, Mario Aguilar-Aragon, Ahmed Elbediwy, Zoé I. Vincent-Mistiaen, Barry J. Thompson

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000509

Ratiometric GPCR signaling enables directional sensing in yeast

Nicholas T. Henderson, Michael Pablo, Debraj Ghose, Manuella R. Clark-Cotton, Trevin R. Zyla, James Nolen, Timothy C. Elston, Daniel J. Lew

PLOS Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pbio.3000484

Machine learning of human plasma lipidomes for obesity estimation in a large population cohort

Mathias J. Gerl, Christian Klose, Michal A. Surma, Celine Fernandez, Olle Melander, Satu Männistö, Katja Borodulin, Aki S. Havulinna, Veikko Salomaa, Elina Ikonen, Carlo V. Cannistraci, Kai Simons

PLOS Biology: published October 18, 2019 | https://doi.org/10.1371/journal.pbio.3000443

Large-scale death of retinal astrocytes during normal development is non-apoptotic and implemented by microglia

Vanessa M. Puñal, Caitlin E. Paisley, Federica S. Brecha, Monica A. Lee, Robin M. Perelli, Jingjing Wang, Emily G. O’Koren, Caroline R. Ackley, Daniel R. Saban, Benjamin E. Reese, Jeremy N. Kay

PLOS Biology: published October 18, 2019 | https://doi.org/10.1371/journal.pbio.3000492

High-throughput micropatterning platform reveals Nodal-dependent bisection of peri-gastrulation–associated versus preneurulation-associated fate patterning

Mukul Tewary, Dominika Dziedzicka, Joel Ostblom, Laura Prochazka, Nika Shakiba, Tiam Heydari, Daniel Aguilar-Hidalgo, Curtis Woodford, Elia Piccinini, David Becerra-Alonso, Alice Vickers, Blaise Louis, Nafees Rahman, Davide Danovi, Mieke Geens, Fiona M. Watt, Peter W. Zandstra

PLOS Biology: published October 21, 2019 | https://doi.org/10.1371/journal.pbio.3000081

Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance

Jeff Maltas, Kevin B. Wood

PLOS Biology: published October 25, 2019 | https://doi.org/10.1371/journal.pbio.3000515

Yeast α-arrestin Art2 is the key regulator of ubiquitylation-dependent endocytosis of plasma membrane vitamin B1 transporters

Jérôme Savocco, Sylvain Nootens, Wilhelmine Afokpa, Mathilde Bausart, Xiaoqian Chen, Jennifer Villers, Henri-François Renard, Martine Prévost, Ruddy Wattiez, Pierre Morsomme

PLOS Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pbio.3000512

Phase variation of a signal transduction system controls Clostridioides difficile colony morphology, motility, and virulence

Elizabeth M. Garrett, Ognjen Sekulovic, Daniela Wetzel, Joshua B. Jones, Adrianne N. Edwards, Germán Vargas-Cuebas, Shonna M. McBride, Rita Tamayo

PLOS Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pbio.3000379

SorCS1-mediated sorting in dendrites maintains neurexin axonal surface polarization required for synaptic function

Luís F. Ribeiro, Ben Verpoort, Julie Nys, Kristel M. Vennekens, Keimpe D. Wierda, Joris de Wit

PLOS Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pbio.3000466

Cell generation dynamics underlying naive T-cell homeostasis in adult humans

Jeff E. Mold, Pedro Réu, Axel Olin, Samuel Bernard, Jakob Michaëlsson, Sanket Rane, Andrew Yates, Azadeh Khosravi, Mehran Salehpour, Göran Possnert, Petter Brodin, Jonas Frisén

PLOS Biology: published October 29, 2019 | https://doi.org/10.1371/journal.pbio.3000383

Short Reports

Somatosensory cortex participates in the consolidation of human motor memory

Neeraj Kumar, Timothy F. Manning, David J. Ostry

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000469

The lunar cycle drives migration of a nocturnal bird

Gabriel Norevik, Susanne Åkesson, Arne Andersson, Johan Bäckman, Anders Hedenström

PLOS Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pbio.3000456

A rotifer-derived paralytic compound prevents transmission of schistosomiasis to a mammalian host

Jiarong Gao, Ning Yang, Fred A. Lewis, Peter Yau, James J. Collins III, Jonathan V. Sweedler, Phillip A. Newmark

PLOS Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pbio.3000485

Song playbacks demonstrate slower evolution of song discrimination in birds from Amazonia than from temperate North America

Jason T. Weir, Trevor D. Price

PLOS Biology: published October 22, 2019 | https://doi.org/10.1371/journal.pbio.3000478

Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection

Kyle J. Card, Thomas LaBar, Jasper B. Gomez, Richard E. Lenski

PLOS Biology: published October 23, 2019 | https://doi.org/10.1371/journal.pbio.3000397

Mechanical stiffness of reconstituted actin patches correlates tightly with endocytosis efficiency

Jessica Planade, Reda Belbahri, Micaela Boiero Sanders, Audrey Guillotin, Olivia du Roure, Alphée Michelot, Julien Heuvingh

PLOS Biology: published October 25, 2019 | https://doi.org/10.1371/journal.pbio.3000500

Methods and Resources

Dynamic enhancers control skeletal muscle identity and reprogramming

Krithika Ramachandran, Madhavi D. Senagolage, Meredith A. Sommars, Christopher R. Futtner, Yasuhiro Omura, Amanda L. Allred, Grant D. Barish

PLOS Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pbio.3000467

Mechanically resolved imaging of bacteria using expansion microscopy

Youngbin Lim, Anthony L. Shiver, Margarita Khariton, Keara M. Lane, Katharine M. Ng, Samuel R. Bray, Jian Qin, Kerwyn Casey Huang, Bo Wang

PLOS Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pbio.3000268

Meta-Research Article

Predicting translational progress in biomedical research

B. Ian Hutchins, Matthew T. Davis, Rebecca A. Meseroll, George M. Santangelo

PLOS Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pbio.3000416

Corrections

Correction: Environmental pollution is associated with increased risk of psychiatric disorders in the US and Denmark

The PLOS Biology Staff

PLOS Biology: published October 2, 2019 | https://doi.org/10.1371/journal.pbio.3000513

Correction: Selection and characterization of ultrahigh potency designed ankyrin repeat protein inhibitors of C. difficile toxin B

Rudo Simeon, Mengqiu Jiang, Ana M. Chamoun-Emanuelli, Hua Yu, Yongrong Zhang, Ran Meng, Zeyu Peng, Joanita Jakana, Junjie Zhang, Hanping Feng, Zhilei Chen

PLOS Biology: published October 4, 2019 | https://doi.org/10.1371/journal.pbio.3000514

Correction: Loss of Bardet-Biedl syndrome proteins causes synaptic aberrations in principal neurons

Naila Haq, Christoph Schmidt-Hieber, Fernando J. Sialana, Lorenza Ciani, Janosch P. Heller, Michelle Stewart, Liz Bentley, Sara Wells, Richard J. Rodenburg, Patrick M. Nolan, Elizabeth Forsythe, Michael C. Wu, Gert Lubec, Patricia C. Salinas, Michael Häusser, Philip L. Beales, Sofia Christou-Savina

PLOS Biology: published October 8, 2019 | https://doi.org/10.1371/journal.pbio.3000520

Correction: The Naturally Processed CD95L Elicits a c-Yes/Calcium/PI3K-Driven Cell Migration Pathway

Sébastien Tauzin, Benjamin Chaigne-Delalande, Eric Selva, Nadine Khadra, Sophie Daburon, Cécile Contin-Bordes, Patrick Blanco, Jacques Le Seyec, Thomas Ducret, Laurent Counillon, Jean-François Moreau, Paul Hofman, Pierre Vacher, Patrick Legembre

PLOS Biology: published October 8, 2019 | https://doi.org/10.1371/journal.pbio.3000521

Correction: MCC950/CRID3 potently targets the NACHT domain of wild-type NLRP3 but not disease-associated mutants for inflammasome inhibition

Lieselotte Vande Walle, Irma B. Stowe, Pavel Šácha, Bettina L. Lee, Dieter Demon, Amelie Fossoul, Filip Van Hauwermeiren, Pedro H. V. Saavedra, Petr Šimon, Vladimír Šubr, Libor Kostka, Craig E. Stivala, Victoria C. Pham, Steven T. Staben, Sayumi Yamazoe, Jan Konvalinka, Nobuhiko Kayagaki, Mohamed Lamkanfi

PLOS Biology: published October 16, 2019 | https://doi.org/10.1371/journal.pbio.3000529

Expression of Concern

Expression of Concern: Brain–Computer Interface–Based Communication in the Completely Locked-In State

The PLOS Biology Staff

PLOS Biology: published October 16, 2019 | https://doi.org/10.1371/journal.pbio.3000527

Cover

Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism

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