June 2023

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. The emphasis of the BICCN is on the whole mouse brain, with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Hawrylycz et al. provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. The authors illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain. The image shows an example of full neuron morphology mapped to the Allen Common Coordinate System.

Image Credit: Zhixi Yun and Hanchuan Peng

Essay

A biologist’s guide to planning and performing quantitative bioimaging experiments

Rebecca A. Senft, Barbara Diaz-Rohrer, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W. Eliceiri, Beth A. Cimini

PLOS Biology: published June 27, 2023 | https://doi.org/10.1371/journal.pbio.3002167

Consensus View

A guide to the BRAIN Initiative Cell Census Network data ecosystem

Michael Hawrylycz, Maryann E. Martone, Giorgio A. Ascoli, Jan G. Bjaalie, Hong-Wei Dong, Satrajit S. Ghosh, Jesse Gillis, Ronna Hertzano, David R. Haynor, Patrick R. Hof, Yongsoo Kim, Ed Lein, Yufeng Liu, Jeremy A. Miller, Partha P. Mitra, Eran Mukamel, Lydia Ng, David Osumi-Sutherland, Hanchuan Peng, Patrick L. Ray, Raymond Sanchez, Aviv Regev, Alex Ropelewski, Richard H. Scheuermann, Shawn Zheng Kai Tan, Carol L. Thompson, Timothy Tickle, Hagen Tilgner, Merina Varghese, Brock Wester, Owen White, Hongkui Zeng, Brian Aevermann, David Allemang, Seth Ament, Thomas L. Athey, Cody Baker, Katherine S. Baker, Pamela M. Baker, Anita Bandrowski, Samik Banerjee, Prajal Bishwakarma, Ambrose Carr, Min Chen, Roni Choudhury, Jonah Cool, Heather Creasy, Florence D’Orazi, Kylee Degatano, Benjamin Dichter, Song-Lin Ding, Tim Dolbeare, Joseph R. Ecker, Rongxin Fang, Jean-Christophe Fillion-Robin, Timothy P. Fliss, James Gee, Tom Gillespie, Nathan Gouwens, Guo-Qiang Zhang, Yaroslav O. Halchenko, Nomi L. Harris, Brian R. Herb, Houri Hintiryan, Gregory Hood, Sam Horvath, Bingxing Huo, Dorota Jarecka, Shengdian Jiang, Farzaneh Khajouei, Elizabeth A. Kiernan, Huseyin Kir, Lauren Kruse, Changkyu Lee, Boudewijn Lelieveldt, Yang Li, Hanqing Liu, Lijuan Liu, Anup Markuhar, James Mathews, Kaylee L. Mathews, Chris Mezias, Michael I. Miller, Tyler Mollenkopf, Shoaib Mufti, Christopher J. Mungall, Joshua Orvis, Maja A. Puchades, Lei Qu, Joseph P. Receveur, Bing Ren, Nathan Sjoquist, Brian Staats, Daniel Tward, Cindy T. J. van Velthoven, Quanxin Wang, Fangming Xie, Hua Xu, Zizhen Yao, Zhixi Yun, Yun Renee Zhang, W. Jim Zheng, Brian Zingg

PLOS Biology: published June 30, 2023 | https://doi.org/10.1371/journal.pbio.3002133

Perspectives

Is it time for insect researchers to consider their subjects’ welfare?

Andrew Crump, Matilda Gibbons, Meghan Barrett, Jonathan Birch, Lars Chittka

PLOS Biology: published June 1, 2023 | https://doi.org/10.1371/journal.pbio.3002138

PINK1: From Parkinson’s disease to mitophagy and back again

Benjamin O’Callaghan, John Hardy, Helene Plun-Favreau

PLOS Biology: published June 29, 2023 | https://doi.org/10.1371/journal.pbio.3002196

Structural biology: A golden era

Oliviero Carugo, Kristina Djinović-Carugo

PLOS Biology: published June 29, 2023 | https://doi.org/10.1371/journal.pbio.3002187

Primers

How to initiate tissue regeneration by generating mutually exclusive cell states

Tin Tin Su

PLOS Biology: published June 6, 2023 | https://doi.org/10.1371/journal.pbio.3002155

The human embryo selection arena is associated with transposable element activity

Anna Osnato, Vincent Pasque, Laurent David

PLOS Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pbio.3002153

Some flies do not play ping-pong

Arie Fridrich, Yehu Moran

PLOS Biology: published June 7, 2023 | https://doi.org/10.1371/journal.pbio.3002152

Community Page

Learning science alongside peers with intellectual and developmental disabilities

Kaelin N. Rubenzer, Jonathan T. Pierce

PLOS Biology: published June 13, 2023 | https://doi.org/10.1371/journal.pbio.3002147

Research Articles

Distinct neural encoding of glimpsed and masked speech in multitalker situations

Vinay S Raghavan, James O’Sullivan, Stephan Bickel, Ashesh D. Mehta, Nima Mesgarani

PLOS Biology: published June 6, 2023 | https://doi.org/10.1371/journal.pbio.3002128

Dynamic modulation of subthalamic nucleus activity facilitates adaptive behavior

Damian M. Herz, Manuel Bange, Gabriel Gonzalez-Escamilla, Miriam Auer, Muthuraman Muthuraman, Martin Glaser, Rafal Bogacz, Alek Pogosyan, Huiling Tan, Sergiu Groppa, Peter Brown

PLOS Biology: published June 1, 2023 | https://doi.org/10.1371/journal.pbio.3002140

Fear memory recall involves hippocampal somatostatin interneurons

Krisztián Zichó, Katalin E. Sos, Péter Papp, Albert M. Barth, Erik Misák, Áron Orosz, Márton I. Mayer, Réka Z. Sebestény, Gábor Nyiri

PLOS Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pbio.3002154

Sequential involvements of the perirhinal cortex and hippocampus in the recall of item-location associative memory in macaques

Cen Yang, Yuji Naya

PLOS Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pbio.3002145

Preservation of developmental spontaneous activity enables early auditory system maturation in deaf mice

Calvin J. Kersbergen, Travis A. Babola, Patrick O. Kanold, Dwight E. Bergles

PLOS Biology: published June 27, 2023 | https://doi.org/10.1371/journal.pbio.3002160

NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl

Luke A. Simpson, Darren Crowley, Teri Forey, Helena Acosta, Zoltan Ferjentsik, Jodie Chatfield, Alexander Payne, Benjamin S. Simpson, Catherine Redwood, James E. Dixon, Nadine Holmes, Fei Sang, Ramiro Alberio, Matthew Loose, Andrew D. Johnson

PLOS Biology: published June 14, 2023 | https://doi.org/10.1371/journal.pbio.3002121

Constriction imposed by basement membrane regulates developmental cell migration

Ester Molina López, Anna Kabanova, Alexander Winkel, Kristian Franze, Isabel M. Palacios, María D. Martín-Bermudo

PLOS Biology: published June 28, 2023 | https://doi.org/10.1371/journal.pbio.3002172

Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes

Shayan Shamipour, Laura Hofmann, Irene Steccari, Roland Kardos, Carl-Philipp Heisenberg

PLOS Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pbio.3002146

Clade-D auxin response factors regulate auxin signaling and development in the moss Physcomitrium patens

Carlisle Bascom Jr., Michael J. Prigge, Whitnie Szutu, Alexis Bantle, Sophie Irmak, Daniella Tu, Mark Estelle

PLOS Biology: published June 14, 2023 | https://doi.org/10.1371/journal.pbio.3002163

Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans

Jeffrey Vedanayagam, Marion Herbette, Holly Mudgett, Ching-Jung Lin, Chun-Ming Lai, Caitlin McDonough-Goldstein, Stephen Dorus, Benjamin Loppin, Colin Meiklejohn, Raphaëlle Dubruille, Eric C. Lai

PLOS Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pbio.3002136

Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock

Christoph Schmal, Bert Maier, Reut Ashwal-Fluss, Osnat Bartok, Anna-Marie Finger, Tanja Bange, Stella Koutsouli, Maria S. Robles, Sebastian Kadener, Hanspeter Herzel, Achim Kramer

PLOS Biology: published June 28, 2023 | https://doi.org/10.1371/journal.pbio.3002164

Host-specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome

Brian V. Tsu, Rimjhim Agarwal, Nandan S. Gokhale, Jessie Kulsuptrakul, Andrew P. Ryan, Elizabeth J. Fay, Lennice K. Castro, Christopher Beierschmitt, Christina Yap, Elizabeth A. Turcotte, Sofia E. Delgado-Rodriguez, Russell E. Vance, Jennifer L. Hyde, Ram Savan, Patrick S. Mitchell, Matthew D. Daugherty

PLOS Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pbio.3002144

DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner

Madison S. Strine, Wesley L. Cai, Jin Wei, Mia Madel Alfajaro, Renata B. Filler, Scott B. Biering, Sylvia Sarnik, Ryan D. Chow, Ajinkya Patil, Kasey S. Cervantes, Clayton K. Collings, Peter C. DeWeirdt, Ruth E. Hanna, Kevin Schofield, Christopher Hulme, Silvana Konermann, John G. Doench, Patrick D. Hsu, Cigall Kadoch, Qin Yan, Craig B. Wilen

PLOS Biology: published June 13, 2023 | https://doi.org/10.1371/journal.pbio.3002097

Development of an amplicon-based sequencing approach in response to the global emergence of mpox

Nicholas F. G. Chen, Chrispin Chaguza, Luc Gagne, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J. Kapsak, Joel Sevinsky, Kevin Libuit, Daniel J. Park, Peera Hemarajata, Jacob M. Garrigues, Nicole M. Green, Sean Sierra-Patev, Kristin Carpenter-Azevedo, Richard C. Huard, Claire Pearson, Kutluhan Incekara, Christina Nishimura, Jian Ping Huang, Emily Gagnon, Ethan Reever, Jafar Razeq, Anthony Muyombwe, Vítor Borges, Rita Ferreira, Daniel Sobral, Silvia Duarte, Daniela Santos, Luís Vieira, João Paulo Gomes, Carly Aquino, Isabella M. Savino, Karinda Felton, Moneeb Bajwa, Nyjil Hayward, Holly Miller, Allison Naumann, Ria Allman, Neel Greer, Amary Fall, Heba H. Mostafa, Martin P. McHugh, Daniel M. Maloney, Rebecca Dewar, Juliet Kenicer, Abby Parker, Katharine Mathers, Jonathan Wild, Seb Cotton, Kate E. Templeton, George Churchwell, Philip A. Lee, Maria Pedrosa, Brenna McGruder, Sarah Schmedes, Matthew R. Plumb, Xiong Wang, Regina Bones Barcellos, Fernanda M. S. Godinho, Richard Steiner Salvato, Aimee Ceniseros, Mallery I. Breban, Nathan D. Grubaugh, Glen R. Gallagher, Chantal B. F. Vogels

PLOS Biology: published June 13, 2023 | https://doi.org/10.1371/journal.pbio.3002151

Autophagy prevents early proinflammatory responses and neutrophil recruitment during Mycobacterium tuberculosis infection without affecting pathogen burden in macrophages

Rachel L. Kinsella, Jacqueline M. Kimmey, Asya Smirnov, Reilly Woodson, Margaret R. Gaggioli, Sthefany M. Chavez, Darren Kreamalmeyer, Christina L. Stallings

PLOS Biology: published June 15, 2023 | https://doi.org/10.1371/journal.pbio.3002159

Rab26 restricts insulin secretion via sequestering Synaptotagmin-1

Ruijuan Zhuang, Yuxia Zhou, Ziyan Wang, Yating Cao, Jun Chen, Liju Xu, Yandan Ren, Yige Zheng, Ziheng Wei, Hantian Qiu, Liangcheng Li, Yang Han, Ye Yun, Xin Chen, Wanjin Hong, Tuanlao Wang

PLOS Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pbio.3002142

Isoforms of the TAL1 transcription factor have different roles in hematopoiesis and cell growth

Aveksha Sharma, Shani Mistriel-Zerbib, Rauf Ahmad Najar, Eden Engal, Mercedes Bentata, Nadeen Taqatqa, Sara Dahan, Klil Cohen, Shiri Jaffe-Herman, Ophir Geminder, Mai Baker, Yuval Nevo, Inbar Plaschkes, Gillian Kay, Yotam Drier, Michael Berger, Maayan Salton

PLOS Biology: published June 28, 2023 | https://doi.org/10.1371/journal.pbio.3002175

Production of the antidepressant orcinol glucoside in Yarrowia lipolytica with yields over 6,400-fold higher than plant extraction

Bihuan Chen, Xiaonan Liu, Yina Wang, Jie Bai, Xiangyu Liu, Guisheng Xiang, Wei Liu, Xiaoxi Zhu, Jian Cheng, Lina Lu, Guanghui Zhang, Ge Zhang, Zongjie Dai, Shuhui Zi, Shengchao Yang, Huifeng Jiang

PLOS Biology: published June 6, 2023 | https://doi.org/10.1371/journal.pbio.3002131

MLL methyltransferases regulate H3K4 methylation to ensure CENP-A assembly at human centromeres

Kausika Kumar Malik, Sreerama Chaitanya Sridhara, Kaisar Ahmad Lone, Payal Deepakbhai Katariya, Deepshika Pulimamidi, Shweta Tyagi

PLOS Biology: published June 28, 2023 | https://doi.org/10.1371/journal.pbio.3002161

Plant virus movement proteins originated from jelly-roll capsid proteins

Anamarija Butkovic, Valerian V. Dolja, Eugene V. Koonin, Mart Krupovic

PLOS Biology: published June 15, 2023 | https://doi.org/10.1371/journal.pbio.3002157

Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes

Tomohisa Sebastian Tanabe, Martina Grosser, Lea Hahn, Carolin Kümpel, Hanna Hartenfels, Evelyn Vtulkin, Wanda Flegler, Christiane Dahl

PLOS Biology: published June 27, 2023 | https://doi.org/10.1371/journal.pbio.3002177

Structural basis for proapoptotic activation of Bak by the noncanonical BH3-only protein Pxt1

Dahwan Lim, So-Hui Choe, Sein Jin, Seulgi Lee, Younjin Kim, Ho-Chul Shin, Joon Sig Choi, Doo-Byoung Oh, Seung Jun Kim, Jinho Seo, Bonsu Ku

PLOS Biology: published June 14, 2023 | https://doi.org/10.1371/journal.pbio.3002156

Short Reports

Ring neurons in the Drosophila central complex act as a rheostat for sensory modulation of aging

Christi M. Gendron, Tuhin S. Chakraborty, Cathryn Duran, Thomas Dono, Scott D. Pletcher

PLOS Biology: published June 13, 2023 | https://doi.org/10.1371/journal.pbio.3002149

Mechanism of agonist-induced activation of the human itch receptor MRGPRX1

Bing Gan, Leiye Yu, Haifeng Yang, Haizhan Jiao, Bin Pang, Yian Chen, Chen Wang, Rui Lv, Hongli Hu, Zhijian Cao, Ruobing Ren

PLOS Biology: published June 22, 2023 | https://doi.org/10.1371/journal.pbio.3001975

Methods and Resources

The Brain/MINDS Marmoset Connectivity Resource: An open-access platform for cellular-level tracing and tractography in the primate brain

Henrik Skibbe, Muhammad Febrian Rachmadi, Ken Nakae, Carlos Enrique Gutierrez, Junichi Hata, Hiromichi Tsukada, Charissa Poon, Matthias Schlachter, Kenji Doya, Piotr Majka, Marcello G. P. Rosa, Hideyuki Okano, Tetsuo Yamamori, Shin Ishii, Marco Reisert, Akiya Watakabe

PLOS Biology: published June 29, 2023 | https://doi.org/10.1371/journal.pbio.3002158

A single-cell atlas of the sexually dimorphic Drosophila foreleg and its sensory organs during development

Ben R. Hopkins, Olga Barmina, Artyom Kopp

PLOS Biology: published June 28, 2023 | https://doi.org/10.1371/journal.pbio.3002148

Meta-Research Article

Statistical simulations show that scientists need not increase overall sample size by default when including both sexes in in vivo studies

Benjamin Phillips, Timo N. Haschler, Natasha A. Karp

PLOS Biology: published June 8, 2023 | https://doi.org/10.1371/journal.pbio.3002129

Discovery Reports

A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass

Manvendra Singh, Aleksandra M. Kondrashkina, Thomas J. Widmann, Jose L. Cortes, Vikas Bansal, Jichang Wang, Christine Römer, Marta Garcia-Canadas, Jose L. Garcia-Perez, Laurence D. Hurst, Zsuzsanna Izsvák

PLOS Biology: published June 20, 2023 | https://doi.org/10.1371/journal.pbio.3002162