December 2020

Correlative light, electron, and ion microscopy (CLEIM) offers huge potential to track the intracellular fate of antibiotics, with organelle-level resolution. However, a correlative approach that enables subcellular antibiotic visualisation in pathogen-infected tissue is lacking. Here, Fearns et al. developed correlative light, electron, and ion microscopy in tissue (CLEIMiT) and used it to identify the cell type-specific accumulation of an antibiotic in lung lesions of mice infected with Mycobacterium tuberculosis. Using CLEIMiT, the authors found that the anti-tuberculosis drug bedaquiline is localised not only in foamy macrophages in the lungs during infection but also accumulates in polymorphonuclear cells. The image shows a photomontage in four different pseudo-colors of micro-computed tomography of whole lung from a mouse aerosol-infected with Mycobacterium tuberculosis.

Image Credit: Antony Fearns and Angela Rodgers

Primer

TNF-α signaling: TACE inhibition to put out the burning heart

Gesine M. Dittrich, Joerg Heineke

PLOS Biology: published December 9, 2020 | https://doi.org/10.1371/journal.pbio.3001037

Research Articles

Patterns of smallpox mortality in London, England, over three centuries

Olga Krylova, David J. D. Earn

PLOS Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pbio.3000506

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Dan Vanderpool, Bui Quang Minh, Robert Lanfear, Daniel Hughes, Shwetha Murali, R. Alan Harris, Muthuswamy Raveendran, Donna M. Muzny, Mark S. Hibbins, Robert J. Williamson, Richard A. Gibbs, Kim C. Worley, Jeffrey Rogers, Matthew W. Hahn

PLOS Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pbio.3000954

Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history

Eva Bons, Christine Leemann, Karin J. Metzner, Roland R. Regoes

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3001010

Daptomycin treatment impacts resistance in off-target populations of vancomycin-resistant Enterococcus faecium

Clare L. Kinnear, Elsa Hansen, Valerie J. Morley, Kevin C. Tracy, Meghan Forstchen, Andrew F. Read, Robert J. Woods

PLOS Biology: published December 17, 2020 | https://doi.org/10.1371/journal.pbio.3000987

Diagnosis of latent tuberculosis infection is associated with reduced HIV viral load and lower risk for opportunistic infections in people living with HIV

Katharina Kusejko, Huldrych F. Günthard, Gregory S. Olson, Kyra Zens, Katharine Darling, Nina Khanna, Hansjakob Furrer, Pauline Vetter, Enos Bernasconi, Pietro Vernazza, Matthias Hoffmann, Roger D. Kouyos, Johannes Nemeth, the Swiss HIV Cohort Study

PLOS Biology: published December 7, 2020 | https://doi.org/10.1371/journal.pbio.3000963

The actions of others act as a pseudo-reward to drive imitation in the context of social reinforcement learning

Anis Najar, Emmanuelle Bonnet, Bahador Bahrami, Stefano Palminteri

PLOS Biology: published December 8, 2020 | https://doi.org/10.1371/journal.pbio.3001028

Decoding the neural dynamics of free choice in humans

Thomas Thiery, Anne-Lise Saive, Etienne Combrisson, Arthur Dehgan, Julien Bastin, Philippe Kahane, Alain Berthoz, Jean-Philippe Lachaux, Karim Jerbi

PLOS Biology: published December 10, 2020 | https://doi.org/10.1371/journal.pbio.3000864

Generalizable brain network markers of major depressive disorder across multiple imaging sites

Ayumu Yamashita, Yuki Sakai, Takashi Yamada, Noriaki Yahata, Akira Kunimatsu, Naohiro Okada, Takashi Itahashi, Ryuichiro Hashimoto, Hiroto Mizuta, Naho Ichikawa, Masahiro Takamura, Go Okada, Hirotaka Yamagata, Kenichiro Harada, Koji Matsuo, Saori C. Tanaka, Mitsuo Kawato, Kiyoto Kasai, Nobumasa Kato, Hidehiko Takahashi, Yasumasa Okamoto, Okito Yamashita, Hiroshi Imamizu

PLOS Biology: published December 7, 2020 | https://doi.org/10.1371/journal.pbio.3000966

Prediction error signaling explains neuronal mismatch responses in the medial prefrontal cortex

Lorena Casado-Román, Guillermo V. Carbajal, David Pérez-González, Manuel S. Malmierca

PLOS Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pbio.3001019

Neuroinflammation in the normal-appearing white matter (NAWM) of the multiple sclerosis brain causes abnormalities at the nodes of Ranvier

Patricia Gallego-Delgado, Rachel James, Eleanor Browne, Joanna Meng, Swetha Umashankar, Li Tan, Carmen Picon, Nicholas D. Mazarakis, A. Aldo Faisal, Owain W. Howell, Richard Reynolds

PLOS Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pbio.3001008

Biparental contributions of the H2A.B histone variant control embryonic development in mice

Antoine Molaro, Anna J. Wood, Derek Janssens, Selina M. Kindelay, Michael T. Eickbush, Steven Wu, Priti Singh, Charles H. Muller, Steven Henikoff, Harmit S. Malik

PLOS Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pbio.3001001

Transmembrane tumor necrosis factor alpha attenuates pressure-overload cardiac hypertrophy via tumor necrosis factor receptor 2

Kun Miao, Ling Zhou, Hongping Ba, Chenxi Li, Haiyan Gu, Bingjiao Yin, Jing Wang, Xiang-ping Yang, Zhuoya Li, Dao Wen Wang

PLOS Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pbio.3000967

Absence of nuclear receptors LXRs impairs immune response to androgen deprivation and leads to prostate neoplasia

Laura Bousset, Amandine Septier, Julio Bunay, Allison Voisin, Rachel Guiton, Christelle Damon-Soubeyrant, Yoan Renaud, Angélique De Haze, Vincent Sapin, Anne Fogli, Amandine Rambur, Cyrille De Joussineau, Ayhan Kocer, Amalia Trousson, Joëlle Henry-Berger, Marcus Höring, Gerhard Liebisch, Silke Matysik, Jean-Marc A. Lobaccaro, Laurent Morel, Silvère Baron

PLOS Biology: published December 7, 2020 | https://doi.org/10.1371/journal.pbio.3000948

YAP/TAZ deficiency reprograms macrophage phenotype and improves infarct healing and cardiac function after myocardial infarction

Masum M. Mia, Dasan Mary Cibi, Siti Aishah Binte Abdul Ghani, Weihua Song, Nicole Tee, Sujoy Ghosh, Junhao Mao, Eric N. Olson, Manvendra K. Singh

PLOS Biology: published December 2, 2020 | https://doi.org/10.1371/journal.pbio.3000941

The Drosophila amyloid precursor protein homologue mediates neuronal survival and neuroglial interactions

Irini A. Kessissoglou, Dominique Langui, Amr Hasan, Maral Maral, Suchetana B. Dutta, Peter Robin Hiesinger, Bassem A. Hassan

PLOS Biology: published December 8, 2020 | https://doi.org/10.1371/journal.pbio.3000703

Increased prostaglandin-D₂ in male STAT3-deficient hearts shifts cardiac progenitor cells from endothelial to white adipocyte differentiation

Elisabeth Stelling, Melanie Ricke-Hoch, Sergej Erschow, Steve Hoffmann, Anke Katharina Bergmann, Maren Heimerl, Stefan Pietzsch, Karin Battmer, Alexandra Haase, Britta Stapel, Michaela Scherr, Jean-Luc Balligand, Ofer Binah, Denise Hilfiker-Kleiner

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3000739

Oligodendrocytes support axonal transport and maintenance via exosome secretion

Carsten Frühbeis, Wen Ping Kuo-Elsner, Christina Müller, Kerstin Barth, Leticia Peris, Stefan Tenzer, Wiebke Möbius, Hauke B. Werner, Klaus-Armin Nave, Dominik Fröhlich, Eva-Maria Krämer-Albers

PLOS Biology: published December 22, 2020 | https://doi.org/10.1371/journal.pbio.3000621

Regulation of glial size by eicosapentaenoic acid through a novel Golgi apparatus mechanism

Albert Zhang, Ziqiang Guan, Kyle Ockerman, Pengyuan Dong, Jiansheng Guo, Zhiping Wang, Dong Yan

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3001051

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

Thomas Julou, Ludovit Zweifel, Diana Blank, Athos Fiori, Erik van Nimwegen

PLOS Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pbio.3000952

Clustering of Tir during enteropathogenic E. coli infection triggers calcium influx–dependent pyroptosis in intestinal epithelial cells

Qiyun Zhong, Theodoros I. Roumeliotis, Zuza Kozik, Massiel Cepeda-Molero, Luis Ángel Fernández, Avinash R. Shenoy, Chris Bakal, Gad Frankel, Jyoti S. Choudhary

PLOS Biology: published December 30, 2020 | https://doi.org/10.1371/journal.pbio.3000986

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Chaoyi Xu, Douglas K. Fischer, Sanela Rankovic, Wen Li, Robert A. Dick, Brent Runge, Roman Zadorozhnyi, Jinwoo Ahn, Christopher Aiken, Tatyana Polenova, Alan N. Engelman, Zandrea Ambrose, Itay Rousso, Juan R. Perilla

PLOS Biology: published December 17, 2020 | https://doi.org/10.1371/journal.pbio.3001015

Glycosylation generates an efficacious and immunogenic vaccine against H7N9 influenza virus

Jin Il Kim, Sehee Park, Joon-Yong Bae, Sunmi Lee, Jeonghun Kim, Gayeong Kim, Kirim Yoo, Jun Heo, Yong Seok Kim, Jae Soo Shin, Mee Sook Park, Man-Seong Park

PLOS Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pbio.3001024

Telomeric TART elements target the piRNA machinery in Drosophila

Christopher E. Ellison, Meenakshi S. Kagda, Weihuan Cao

PLOS Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pbio.3000689

Phosphorylation of seryl-tRNA synthetase by ATM/ATR is essential for hypoxia-induced angiogenesis

Yi Shi, Ze Liu, Qian Zhang, Ingrid Vallee, Zhongying Mo, Shuji Kishi, Xiang-Lei Yang

PLOS Biology: published December 22, 2020 | https://doi.org/10.1371/journal.pbio.3000991

Mitochondrial dysfunction induces RNA interference in C. elegans through a pathway homologous to the mammalian RIG-I antiviral response

Kai Mao, Peter Breen, Gary Ruvkun

PLOS Biology: published December 2, 2020 | https://doi.org/10.1371/journal.pbio.3000996

Loss of hepatic aldolase B activates Akt and promotes hepatocellular carcinogenesis by destabilizing the Aldob/Akt/PP2A protein complex

Xuxiao He, Min Li, Hongming Yu, Guijun Liu, Ningning Wang, Chunzhao Yin, Qiaochu Tu, Goutham Narla, Yongzhen Tao, Shuqun Cheng, Huiyong Yin

PLOS Biology: published December 4, 2020 | https://doi.org/10.1371/journal.pbio.3000803

Infection-induced 5′-half molecules of tRNA^HisGUG activate Toll-like receptor 7

Kamlesh Pawar, Megumi Shigematsu, Soroush Sharbati, Yohei Kirino

PLOS Biology: published December 17, 2020 | https://doi.org/10.1371/journal.pbio.3000982

The Venus flytrap trigger hair–specific potassium channel KDM1 can reestablish the K⁺ gradient required for hapto-electric signaling

Anda L. Iosip, Jennifer Böhm, Sönke Scherzer, Khaled A. S. Al-Rasheid, Ingo Dreyer, Jörg Schultz, Dirk Becker, Ines Kreuzer, Rainer Hedrich

PLOS Biology: published December 9, 2020 | https://doi.org/10.1371/journal.pbio.3000964

LSM12-EPAC1 defines a neuroprotective pathway that sustains the nucleocytoplasmic RAN gradient

Jongbo Lee, Jumin Park, Ji-hyung Kim, Giwook Lee, Tae-Eun Park, Ki-Jun Yoon, Yoon Ki Kim, Chunghun Lim

PLOS Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pbio.3001002

Signatures of host–pathogen evolutionary conflict reveal MISTR—A conserved MItochondrial STress Response network

Mahsa Sorouri, Tyron Chang, Palmy Jesudhasan, Chelsea Pinkham, Nels C. Elde, Dustin C. Hancks

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3001045

In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators

Jennifer L. Franks, Raquel C. Martinez-Chacin, Xianxi Wang, Rochelle L. Tiedemann, Thomas Bonacci, Rajarshi Choudhury, Derek L. Bolhuis, Taylor P. Enrico, Ryan D. Mouery, Jeffrey S. Damrauer, Feng Yan, Joseph S. Harrison, M. Ben Major, Katherine A. Hoadley, Aussie Suzuki, Scott B. Rothbart, Nicholas G. Brown, Michael J. Emanuele

PLOS Biology: published December 11, 2020 | https://doi.org/10.1371/journal.pbio.3000975

CEP290 is essential for the initiation of ciliary transition zone assembly

Zhimao Wu, Nan Pang, Yingying Zhang, Huicheng Chen, Ying Peng, Jingyan Fu, Qing Wei

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3001034

The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins

Carina Conceicao, Nazia Thakur, Stacey Human, James T. Kelly, Leanne Logan, Dagmara Bialy, Sushant Bhat, Phoebe Stevenson-Leggett, Adrian K. Zagrajek, Philippa Hollinghurst, Michal Varga, Christina Tsirigoti, Matthew Tully, Chris Chiu, Katy Moffat, Adrian Paul Silesian, John A. Hammond, Helena J. Maier, Erica Bickerton, Holly Shelton, Isabelle Dietrich, Stephen C. Graham, Dalan Bailey

PLOS Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pbio.3001016

Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma

Tsan-Wen Lu, Phillip C. Aoto, Jui-Hung Weng, Cole Nielsen, Jennifer N. Cash, James Hall, Ping Zhang, Sanford M. Simon, Michael A. Cianfrocco, Susan S. Taylor

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3001018

Short Reports

Prior expectations evoke stimulus-specific activity in the deep layers of the primary visual cortex

Fraser Aitken, Georgios Menelaou, Oliver Warrington, Renée S. Koolschijn, Nadège Corbin, Martina F. Callaghan, Peter Kok

PLOS Biology: published December 7, 2020 | https://doi.org/10.1371/journal.pbio.3001023

Reoccurring neural stem cell divisions in the adult zebrafish telencephalon are sufficient for the emergence of aggregated spatiotemporal patterns

Valerio Lupperger, Carsten Marr, Prisca Chapouton

PLOS Biology: published December 8, 2020 | https://doi.org/10.1371/journal.pbio.3000708

Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis

Michael David Brügger, Tomas Valenta, Hassan Fazilaty, George Hausmann, Konrad Basler

PLOS Biology: published December 11, 2020 | https://doi.org/10.1371/journal.pbio.3001032

Self-limiting stem-cell niche signaling through degradation of a stem-cell receptor

Sophia Ladyzhets, Matthew Antel, Taylor Simao, Nathan Gasek, Ann E. Cowan, Mayu Inaba

PLOS Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pbio.3001003

Methods and Resources

Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny

Valeriano Parravicini, Jordan M. Casey, Nina M. D. Schiettekatte, Simon J. Brandl, Chloé Pozas-Schacre, Jérémy Carlot, Graham J. Edgar, Nicholas A. J. Graham, Mireille Harmelin-Vivien, Michel Kulbicki, Giovanni Strona, Rick D. Stuart-Smith

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3000702

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

Jacob L. Steenwyk, Thomas J. Buida III, Yuanning Li, Xing-Xing Shen, Antonis Rokas

PLOS Biology: published December 2, 2020 | https://doi.org/10.1371/journal.pbio.3001007

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides

Alexander M. Kloosterman, Peter Cimermancic, Somayah S. Elsayed, Chao Du, Michalis Hadjithomas, Mohamed S. Donia, Michael A. Fischbach, Gilles P. van Wezel, Marnix H. Medema

PLOS Biology: published December 22, 2020 | https://doi.org/10.1371/journal.pbio.3001026

A comprehensive atlas of white matter tracts in the chimpanzee

Katherine L. Bryant, Longchuan Li, Nicole Eichert, Rogier B. Mars

PLOS Biology: published December 31, 2020 | https://doi.org/10.1371/journal.pbio.3000971

Correlative light electron ion microscopy reveals in vivo localisation of bedaquiline in Mycobacterium tuberculosis–infected lungs

Antony Fearns, Daniel J. Greenwood, Angela Rodgers, Haibo Jiang, Maximiliano G. Gutierrez

PLOS Biology: published December 31, 2020 | https://doi.org/10.1371/journal.pbio.3000879

Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing

Xiaoying Fan, Dong Tang, Yuhan Liao, Pidong Li, Yu Zhang, Minxia Wang, Fan Liang, Xiao Wang, Yun Gao, Lu Wen, Depeng Wang, Yang Wang, Fuchou Tang

PLOS Biology: published December 30, 2020 | https://doi.org/10.1371/journal.pbio.3001017

Single-cell transcriptome landscape of ovarian cells during primordial follicle assembly in mice

Jun-Jie Wang, Wei Ge, Qiu-Yue Zhai, Jing-Cai Liu, Xiao-Wen Sun, Wen-Xiang Liu, Lan Li, Chu-Zhao Lei, Paul W. Dyce, Massimo De Felici, Wei Shen

PLOS Biology: published December 22, 2020 | https://doi.org/10.1371/journal.pbio.3001025

A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection

Martin A. M. Reijns, Louise Thompson, Juan Carlos Acosta, Holly A. Black, Francisco J. Sanchez-Luque, Austin Diamond, David A. Parry, Alison Daniels, Marie O'Shea, Carolina Uggenti, Maria C. Sanchez, Alan O'Callaghan, Michelle L. L. McNab, Martyna Adamowicz, Elias T. Friman, Toby Hurd, Edward J. Jarman, Frederic Li Mow Chee, Jacqueline K. Rainger, Marion Walker, Camilla Drake, Dasa Longman, Christine Mordstein, Sophie J. Warlow, Stewart McKay, Louise Slater, Morad Ansari, Ian P. M. Tomlinson, David Moore, Nadine Wilkinson, Jill Shepherd, Kate Templeton, Ingolfur Johannessen, Christine Tait-Burkard, Jürgen G. Haas, Nick Gilbert, Ian R. Adams, Andrew P. Jackson

PLOS Biology: published December 15, 2020 | https://doi.org/10.1371/journal.pbio.3001030

Rapid detection of SARS-CoV-2 with CRISPR-Cas12a

Dan Xiong, Wenjun Dai, Jiaojiao Gong, Guande Li, Nansong Liu, Wei Wu, Jiaqiang Pan, Chen Chen, Yingzhen Jiao, Huina Deng, Junwei Ye, Xuanxuan Zhang, Huiling Huang, Qianyun Li, Liang Xue, Xiuming Zhang, Guanghui Tang

PLOS Biology: published December 15, 2020 | https://doi.org/10.1371/journal.pbio.3000978

Design of novel granulopoietic proteins by topological rescaffolding

Birte Hernandez Alvarez, Julia Skokowa, Murray Coles, Perihan Mir, Masoud Nasri, Kateryna Maksymenko, Laura Weidmann, Katherine W. Rogers, Karl Welte, Andrei N. Lupas, Patrick Müller, Mohammad ElGamacy

PLOS Biology: published December 22, 2020 | https://doi.org/10.1371/journal.pbio.3000919

Meta-Research Article

Ensuring the quality and specificity of preregistrations

Marjan Bakker, Coosje L. S. Veldkamp, Marcel A. L. M. van Assen, Elise A. V. Crompvoets, How Hwee Ong, Brian A. Nosek, Courtney K. Soderberg, David Mellor, Jelte M. Wicherts

PLOS Biology: published December 9, 2020 | https://doi.org/10.1371/journal.pbio.3000937

Discovery Reports

Convergent evolution of diverse Bacillus anthracis outbreak strains toward altered surface oligosaccharides that modulate anthrax pathogenesis

Michael H. Norris, Alexander Kirpich, Andrew P. Bluhm, Diansy Zincke, Ted Hadfield, Jose Miguel Ponciano, Jason K. Blackburn

PLOS Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pbio.3001052

Pseudomonas aeruginosa cleaves the decoding center of Caenorhabditis elegans ribosomes

Alejandro Vasquez-Rifo, Emiliano P. Ricci, Victor Ambros

PLOS Biology: published December 1, 2020 | https://doi.org/10.1371/journal.pbio.3000969

Cover

Correlative light electron ion microscopy reveals in vivo localisation of bedaquiline in Mycobacterium tuberculosis-infected lungs

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**Correlative light electron ion microscopy reveals in vivo localisation of bedaquiline in Mycobacterium tuberculosis-infected lungs**