November 2020

Using mRNA sequencing and de novo transcriptome assembly, Lambert et al. identified, cloned, and characterized nine previously undiscovered fluorescent protein homologs from Aequorea victoria and a related Aequorea species, finding that most sequences were highly divergent from the well-known and widely used A. victoria green fluorescent protein (GFP). Among these fluorescent proteins are the brightest GFP homolog yet characterized and a reversibly photochromic fluorescent protein that responds to UV and blue light. Beyond green emitters, Aequorea species express purple- and blue-pigmented chromoproteins with absorbances ranging from green to far-red, including two that are photoconvertible. X-ray crystallography revealed that Aequorea chromoproteins contain a chemically novel chromophore with an unexpected crosslink to the main polypeptide chain. Because of the unique attributes of several of these newly discovered fluorescent proteins, the authors expect that Aequorea will, once again, give rise to an entirely new generation of useful probes for bioimaging and biosensing. The image shows solutions of five purified recombinant proteins from Aequorea species, illuminated with 480-nm LED (top) and white light (bottom).

Image Credit: pbio.3000936

Editorial

Epidemics on the move: Climate change and infectious disease

Matthew B. Thomas

PLOS Biology: published November 24, 2020 | https://doi.org/10.1371/journal.pbio.3001013

Essays

Effects of climate change on parasites and disease in estuarine and nearshore environments

James E. Byers

PLOS Biology: published November 24, 2020 | https://doi.org/10.1371/journal.pbio.3000743

Understanding how temperature shifts could impact infectious disease

Jason R. Rohr, Jeremy M. Cohen

PLOS Biology: published November 24, 2020 | https://doi.org/10.1371/journal.pbio.3000938

Building resilience to mosquito-borne diseases in the Caribbean

Rachel Lowe, Sadie J. Ryan, Roché Mahon, Cedric J. Van Meerbeeck, Adrian R. Trotman, Laura-Lee G. Boodram, Mercy J. Borbor-Cordova, Anna M. Stewart-Ibarra

PLOS Biology: published November 24, 2020 | https://doi.org/10.1371/journal.pbio.3000791

Climate change and disease in plant communities

Jeremy J. Burdon, Jiasui Zhan

PLOS Biology: published November 24, 2020 | https://doi.org/10.1371/journal.pbio.3000949

We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data

Simon Kasif, Richard J. Roberts

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000999

Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control

Benjamin M. Althouse, Edward A. Wenger, Joel C. Miller, Samuel V. Scarpino, Antoine Allard, Laurent Hébert-Dufresne, Hao Hu

PLOS Biology: published November 12, 2020 | https://doi.org/10.1371/journal.pbio.3000897

Unsolved Mystery

Find and fuse: Unsolved mysteries in sperm–egg recognition

Enrica Bianchi, Gavin J. Wright

PLOS Biology: published November 13, 2020 | https://doi.org/10.1371/journal.pbio.3000953

Perspectives

Monitor for COVID-19 vaccine resistance evolution during clinical trials

David A. Kennedy, Andrew F. Read

PLOS Biology: published November 9, 2020 | https://doi.org/10.1371/journal.pbio.3001000

Common ground: The foundation of interdisciplinary research on bat disease emergence

Rebekah C. Kading, Tigga Kingston

PLOS Biology: published November 9, 2020 | https://doi.org/10.1371/journal.pbio.3000947

Research Articles

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

Young Mi Kwon, Kevin Gori, Naomi Park, Nicole Potts, Kate Swift, Jinhong Wang, Maximilian R. Stammnitz, Naomi Cannell, Adrian Baez-Ortega, Sebastien Comte, Samantha Fox, Colette Harmsen, Stewart Huxtable, Menna Jones, Alexandre Kreiss, Clare Lawrence, Billie Lazenby, Sarah Peck, Ruth Pye, Gregory Woods, Mona Zimmermann, David C. Wedge, David Pemberton, Michael R. Stratton, Rodrigo Hamede, Elizabeth P. Murchison

PLOS Biology: published November 24, 2020 | https://doi.org/10.1371/journal.pbio.3000926

Many, but not all, lineage-specific genes can be explained by homology detection failure

Caroline M. Weisman, Andrew W. Murray, Sean R. Eddy

PLOS Biology: published November 2, 2020 | https://doi.org/10.1371/journal.pbio.3000862

The noncoding small RNA SsrA is released by Vibrio fischeri and modulates critical host responses

Silvia Moriano-Gutierrez, Clotilde Bongrand, Tara Essock-Burns, Leo Wu, Margaret J. McFall-Ngai, Edward G. Ruby

PLOS Biology: published November 3, 2020 | https://doi.org/10.1371/journal.pbio.3000934

Rules warp feature encoding in decision-making circuits

R. Becket Ebitz, Jiaxin Cindy Tu, Benjamin Y. Hayden

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000951

Integrating when and what information in the left parietal lobe allows language rule generalization

Joan Orpella, Pablo Ripollés, Manuela Ruzzoli, Julià L. Amengual, Alicia Callejas, Anna Martinez-Alvarez, Salvador Soto-Faraco, Ruth de Diego-Balaguer

PLOS Biology: published November 2, 2020 | https://doi.org/10.1371/journal.pbio.3000895

Computational imaging during video game playing shows dynamic synchronization of cortical and subcortical networks of emotions

Joana Leitão, Ben Meuleman, Dimitri Van De Ville, Patrik Vuilleumier

PLOS Biology: published November 12, 2020 | https://doi.org/10.1371/journal.pbio.3000900

A multi-scale cortical wiring space links cellular architecture and functional dynamics in the human brain

Casey Paquola, Jakob Seidlitz, Oualid Benkarim, Jessica Royer, Petr Klimes, Richard A. I. Bethlehem, Sara Larivière, Reinder Vos de Wael, Raul Rodríguez-Cruces, Jeffery A. Hall, Birgit Frauscher, Jonathan Smallwood, Boris C. Bernhardt

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000979

Cortical morphology at birth reflects spatiotemporal patterns of gene expression in the fetal human brain

Gareth Ball, Jakob Seidlitz, Jonathan O’Muircheartaigh, Ralica Dimitrova, Daphna Fenchel, Antonios Makropoulos, Daan Christiaens, Andreas Schuh, Jonathan Passerat-Palmbach, Jana Hutter, Lucilio Cordero-Grande, Emer Hughes, Anthony Price, Jo V. Hajnal, Daniel Rueckert, Emma C. Robinson, A David Edwards

PLOS Biology: published November 23, 2020 | https://doi.org/10.1371/journal.pbio.3000976

Task-related activity in human visual cortex

Zvi N. Roth, Minyoung Ryoo, Elisha P. Merriam

PLOS Biology: published November 6, 2020 | https://doi.org/10.1371/journal.pbio.3000921

Independent representations of self-motion and object location in barrel cortex output

Jonathan Andrew Cheung, Phillip Maire, Jinho Kim, Kiana Lee, Garrett Flynn, Samuel Andrew Hires

PLOS Biology: published November 3, 2020 | https://doi.org/10.1371/journal.pbio.3000882

Temporal coding of echo spectral shape in the bat auditory cortex

Silvio Macias, Kushal Bakshi, Francisco Garcia-Rosales, Julio C. Hechavarria, Michael Smotherman

PLOS Biology: published November 10, 2020 | https://doi.org/10.1371/journal.pbio.3000831

Budgerigars have complex sleep structure similar to that of mammals

Sofija V. Canavan, Daniel Margoliash

PLOS Biology: published November 17, 2020 | https://doi.org/10.1371/journal.pbio.3000929

Hippocampal neurons with stable excitatory connectivity become part of neuronal representations

Tim P. Castello-Waldow, Ghabiba Weston, Alessandro F. Ulivi, Alireza Chenani, Yonatan Loewenstein, Alon Chen, Alessio Attardo

PLOS Biology: published November 3, 2020 | https://doi.org/10.1371/journal.pbio.3000928

Hippocampal cells integrate past memory and present perception for the future

Cen Yang, Yuji Naya

PLOS Biology: published November 18, 2020 | https://doi.org/10.1371/journal.pbio.3000876

The M-current works in tandem with the persistent sodium current to set the speed of locomotion

Jérémy Verneuil, Cécile Brocard, Virginie Trouplin, Laurent Villard, Julie Peyronnet-Roux, Frédéric Brocard

PLOS Biology: published November 13, 2020 | https://doi.org/10.1371/journal.pbio.3000738

Gradient in cytoplasmic pressure in germline cells controls overlying epithelial cell morphogenesis

Laurie-Anne Lamiré, Pascale Milani, Gaël Runel, Annamaria Kiss, Leticia Arias, Blandine Vergier, Stève de Bossoreille, Pradeep Das, David Cluet, Arezki Boudaoud, Muriel Grammont

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000940

Local retinoic acid signaling directs emergence of the extraocular muscle functional unit

Glenda Evangelina Comai, Markéta Tesařová, Valérie Dupé, Muriel Rhinn, Pedro Vallecillo-García, Fabio da Silva, Betty Feret, Katherine Exelby, Pascal Dollé, Leif Carlsson, Brian Pryce, François Spitz, Sigmar Stricker, Tomáš Zikmund, Jozef Kaiser, James Briscoe, Andreas Schedl, Norbert B. Ghyselinck, Ronen Schweitzer, Shahragim Tajbakhsh

PLOS Biology: published November 17, 2020 | https://doi.org/10.1371/journal.pbio.3000902

Structural myelin defects are associated with low axonal ATP levels but rapid recovery from energy deprivation in a mouse model of spastic paraplegia

Andrea Trevisiol, Kathrin Kusch, Anna M. Steyer, Ingo Gregor, Christos Nardis, Ulrike Winkler, Susanne Köhler, Alejandro Restrepo, Wiebke Möbius, Hauke B. Werner, Klaus-Armin Nave, Johannes Hirrlinger

PLOS Biology: published November 16, 2020 | https://doi.org/10.1371/journal.pbio.3000943

Blood–brain barrier genetic disruption leads to protective barrier formation at the Glia Limitans

Pierre Mora, Pierre-Louis Hollier, Sarah Guimbal, Alice Abelanet, Aïssata Diop, Lauriane Cornuault, Thierry Couffinhal, Sam Horng, Alain-Pierre Gadeau, Marie-Ange Renault, Candice Chapouly

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000946

TOP1α, UPF1, and TTG2 regulate seed size in a parental dosage–dependent manner

Chengxiang Li, Ximing Gong, Bin Zhang, Zhe Liang, Chui Eng Wong, Benjamin Yen How See, Hao Yu

PLOS Biology: published November 6, 2020 | https://doi.org/10.1371/journal.pbio.3000930

Nucleotide de novo synthesis increases breast cancer stemness and metastasis via cGMP-PKG-MAPK signaling pathway

Yajing Lv, Xiaoshuang Wang, Xiaoyu Li, Guangwei Xu, Yuting Bai, Jiayi Wu, Yongjun Piao, Yi Shi, Rong Xiang, Longlong Wang

PLOS Biology: published November 13, 2020 | https://doi.org/10.1371/journal.pbio.3000872

EphrinB1 modulates glutamatergic inputs into POMC-expressing progenitors and controls glucose homeostasis

Manon Gervais, Gwenaël Labouèbe, Alexandre Picard, Bernard Thorens, Sophie Croizier

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000680

NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype

Mahmoud H. Elbatreek, Sepideh Sadegh, Elisa Anastasi, Emre Guney, Cristian Nogales, Tim Kacprowski, Ahmed A. Hassan, Andreas Teubner, Po-Hsun Huang, Chien-Yi Hsu, Paul M. H. Schiffers, Ger M. Janssen, Pamela W. M. Kleikers, Anil Wipat, Jan Baumbach, Jo G. R. De Mey, Harald H. H. W. Schmidt

PLOS Biology: published November 10, 2020 | https://doi.org/10.1371/journal.pbio.3000885

Membrane progesterone receptor induces meiosis in Xenopus oocytes through endocytosis into signaling endosomes and interaction with APPL1 and Akt2

Nancy Nader, Maya Dib, Rawad Hodeify, Raphael Courjaret, Asha Elmi, Ayat S. Hammad, Raja Dey, Xin-Yun Huang, Khaled Machaca

PLOS Biology: published November 2, 2020 | https://doi.org/10.1371/journal.pbio.3000901

Unifying the mechanism of mitotic exit control in a spatiotemporal logical model

Rowan S. M. Howell, Cinzia Klemm, Peter H. Thorpe, Attila Csikász-Nagy

PLOS Biology: published November 12, 2020 | https://doi.org/10.1371/journal.pbio.3000917

Ribosome biogenesis is a downstream effector of the oncogenic U2AF1-S34F mutation

Abdalla Akef, Kathy McGraw, Steven D. Cappell, Daniel R. Larson

PLOS Biology: published November 2, 2020 | https://doi.org/10.1371/journal.pbio.3000920

A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19

Yadi Zhou, Yuan Hou, Jiayu Shen, Reena Mehra, Asha Kallianpur, Daniel A. Culver, Michaela U. Gack, Samar Farha, Joe Zein, Suzy Comhair, Claudio Fiocchi, Thaddeus Stappenbeck, Timothy Chan, Charis Eng, Jae U. Jung, Lara Jehi, Serpil Erzurum, Feixiong Cheng

PLOS Biology: published November 6, 2020 | https://doi.org/10.1371/journal.pbio.3000970

Rational design of highly potent broad-spectrum enterovirus inhibitors targeting the nonstructural protein 2C

Lisa Bauer, Roberto Manganaro, Birgit Zonsics, Daniel L. Hurdiss, Marleen Zwaagstra, Tim Donselaar, Naemi G. E. Welter, Regina G. D. M. van Kleef, Moira Lorenzo Lopez, Federica Bevilacqua, Thamidur Raman, Salvatore Ferla, Marcella Bassetto, Johan Neyts, Jeroen R. P. M. Strating, Remco H. S. Westerink, Andrea Brancale, Frank J. M. van Kuppeveld

PLOS Biology: published November 6, 2020 | https://doi.org/10.1371/journal.pbio.3000904

Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses

Ryan Houston, Shiori Sekine, Michael J. Calderon, Fayaz Seifuddin, Guanghui Wang, Hiroyuki Kawagishi, Daniela A. Malide, Yuesheng Li, Marjan Gucek, Mehdi Pirooznia, Alissa J. Nelson, Matthew P. Stokes, Jacob Stewart-Ornstein, Steven J. Mullett, Stacy G. Wendell, Simon C. Watkins, Toren Finkel, Yusuke Sekine

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000981

Structure of the Lifeact–F-actin complex

Alexander Belyy, Felipe Merino, Oleg Sitsel, Stefan Raunser

PLOS Biology: published November 20, 2020 | https://doi.org/10.1371/journal.pbio.3000925

Short Reports

Transmissible cancers and the evolution of sex under the Red Queen hypothesis

Thomas G. Aubier, Matthias Galipaud, E. Yagmur Erten, Hanna Kokko

PLOS Biology: published November 19, 2020 | https://doi.org/10.1371/journal.pbio.3000916

Little evidence for an effect of smoking on multiple sclerosis risk: A Mendelian Randomization study

Ruth E. Mitchell, Kirsty Bates, Robyn E. Wootton, Adil Harroud, J. Brent Richards, George Davey Smith, Marcus R. Munafò

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000973

Methods and Resources

Generation and validation of versatile inducible CRISPRi embryonic stem cell and mouse model

Rui Li, Xianyou Xia, Xing Wang, Xiaoyu Sun, Zhongye Dai, Dawei Huo, Huimin Zheng, Haiqing Xiong, Aibin He, Xudong Wu

PLOS Biology: published November 30, 2020 | https://doi.org/10.1371/journal.pbio.3000749

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis

PLOS Biology: published November 20, 2020 | https://doi.org/10.1371/journal.pbio.3000675

SiCTeC: An inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging

Benjamin D. Knapp, Lillian Zhu, Kerwyn Casey Huang

PLOS Biology: published November 6, 2020 | https://doi.org/10.1371/journal.pbio.3000786

Aequorea’s secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing

Gerard G. Lambert, Hadrien Depernet, Guillaume Gotthard, Darrin T. Schultz, Isabelle Navizet, Talley Lambert, Stephen R. Adams, Albertina Torreblanca-Zanca, Meihua Chu, Daphne S. Bindels, Vincent Levesque, Jennifer Nero Moffatt, Anya Salih, Antoine Royant, Nathan C. Shaner

PLOS Biology: published November 2, 2020 | https://doi.org/10.1371/journal.pbio.3000936

Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging

Yong Qian, Danielle M. Orozco Cosio, Kiryl D. Piatkevich, Sarah Aufmkolk, Wan-Chi Su, Orhan T. Celiker, Anne Schohl, Mitchell H. Murdock, Abhi Aggarwal, Yu-Fen Chang, Paul W. Wiseman, Edward S. Ruthazer, Edward S. Boyden, Robert E. Campbell

PLOS Biology: published November 24, 2020 | https://doi.org/10.1371/journal.pbio.3000965

Cover

Aequorea's secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing