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Table of Contents

May 2019

Cover

High-resolution mapping reveals that microniches in the gastric glands control Helicobacter pylori colonization of the stomach
Issue Image

Lifelong infection of the gastric mucosa by Helicobacter pylori can lead to peptic ulcers and gastric cancer. However, how the bacteria maintain chronic colonization in the face of constant mucus and epithelial cell turnover in the stomach is unclear. Fung et al. present a new model of how H. pylori establish and persist in stomach, which involves the colonization of a specialized microenvironment, or microniche, deep in the gastric glands. Using quantitative three-dimensional confocal microscopy and passive CLARITY technique, which renders tissues optically transparent, the authors analyzed intact stomachs from mice infected with a mixture of isogenic, fluorescent H. pylori strains with unprecedented spatial resolution. The image shows mouse gastric glands infected with H. pylori expressing tdTomato (red, left panel), green fluorescent protein (green, right panel), or a mixture of both bacterial strains (red and green, middle panel). In each panel, host nuclei are stained blue and host actin white.

Image Credit: Fung et al.

Editorial

Caveat Pre-Emptor: Contextualising peer review and publication

The PLOS Biology Staff Editors

PLOS Biology: published May 22, 2019 | https://doi.org/10.1371/journal.pbio.3000234

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Perspective

Open science challenges, benefits and tips in early career and beyond

Christopher Allen, David M. A. Mehler

PLOS Biology: published May 1, 2019 | https://doi.org/10.1371/journal.pbio.3000246

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Primers

Evolution, development, and organization of the cortical connectome

Miguel Ángel García-Cabezas, Basilis Zikopoulos

PLOS Biology: published May 10, 2019 | https://doi.org/10.1371/journal.pbio.3000259

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Feminizer and doublesex knock-outs cause honey bees to switch sexes

Alison McAfee, Jeffery S. Pettis, David R. Tarpy, Leonard J. Foster

PLOS Biology: published May 6, 2019 | https://doi.org/10.1371/journal.pbio.3000256

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Community Pages

AccessLab: Workshops to broaden access to scientific research

Amber G. F. Griffiths, Ivvet Modinou, Clio Heslop, Charlotte Brand, Aidan Weatherill, Kate Baker, Anna E. Hughes, Jen Lewis, Lee de Mora, Sara Mynott, Katherine E. Roberts, David J. Griffiths

PLOS Biology: published May 28, 2019 | https://doi.org/10.1371/journal.pbio.3000258

A 3D-printed hand-powered centrifuge for molecular biology

Gaurav Byagathvalli, Aaron Pomerantz, Soham Sinha, Janet Standeven, M. Saad Bhamla

PLOS Biology: published May 21, 2019 | https://doi.org/10.1371/journal.pbio.3000251

Research Articles

Intact but empty forests? Patterns of hunting-induced mammal defaunation in the tropics

Ana Benítez-López, Luca Santini, Aafke M. Schipper, Michela Busana, Mark A. J. Huijbregts

PLOS Biology: published May 14, 2019 | https://doi.org/10.1371/journal.pbio.3000247

Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation

David McAdams, Kristofer Wollein Waldetoft, Christine Tedijanto, Marc Lipsitch, Sam P. Brown

PLOS Biology: published May 16, 2019 | https://doi.org/10.1371/journal.pbio.3000250

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

Jacob L. Steenwyk, Dana A. Opulente, Jacek Kominek, Xing-Xing Shen, Xiaofan Zhou, Abigail L. Labella, Noah P. Bradley, Brandt F. Eichman, Neža Čadež, Diego Libkind, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas

PLOS Biology: published May 21, 2019 | https://doi.org/10.1371/journal.pbio.3000255

High-resolution mapping reveals that microniches in the gastric glands control Helicobacter pylori colonization of the stomach

Connie Fung, Shumin Tan, Mifuyu Nakajima, Emma C. Skoog, Luis Fernando Camarillo-Guerrero, Jessica A. Klein, Trevor D. Lawley, Jay V. Solnick, Tadashi Fukami, Manuel R. Amieva

PLOS Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pbio.3000231

Entorhinal transformations in abstract frames of reference

Raphael Kaplan, Karl J. Friston

PLOS Biology: published May 2, 2019 | https://doi.org/10.1371/journal.pbio.3000230

Microstructural and functional gradients are increasingly dissociated in transmodal cortices

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PLOS Biology: published May 20, 2019 | https://doi.org/10.1371/journal.pbio.3000284

Amot and Yap1 regulate neuronal dendritic tree complexity and locomotor coordination in mice

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PLOS Biology: published May 1, 2019 | https://doi.org/10.1371/journal.pbio.3000253

Chemosensory sensilla of the Drosophila wing express a candidate ionotropic pheromone receptor

Zhe He, Yichen Luo, Xueying Shang, Jennifer S. Sun, John R. Carlson

PLOS Biology: published May 21, 2019 | https://doi.org/10.1371/journal.pbio.2006619

Fat body–specific vitellogenin expression regulates host-seeking behaviour in the mosquito Aedes albopictus

Jessica Dittmer, Ayad Alafndi, Paolo Gabrieli

PLOS Biology: published May 9, 2019 | https://doi.org/10.1371/journal.pbio.3000238

Dysfunctional peripheral T follicular helper cells dominate in people with impaired influenza vaccine responses: Results from the FLORAH study

Suresh Pallikkuth, Lesley R. de Armas, Stefano Rinaldi, Varghese K. George, Li Pan, Kristopher L. Arheart, Rajendra Pahwa, Savita Pahwa

PLOS Biology: published May 17, 2019 | https://doi.org/10.1371/journal.pbio.3000257

Foxp1 is critical for the maintenance of regulatory T-cell homeostasis and suppressive function

Jiazi Ren, Lei Han, Jinyi Tang, Yuanhua Liu, Xiaoxue Deng, Qiuyue Liu, Pei Hao, Xiaoming Feng, Bin Li, Hui Hu, Haikun Wang

PLOS Biology: published May 24, 2019 | https://doi.org/10.1371/journal.pbio.3000270

Simu-dependent clearance of dying cells regulates macrophage function and inflammation resolution

Hannah Grace Roddie, Emma Louise Armitage, Jonathon Alexis Coates, Simon Andrew Johnston, Iwan Robert Evans

PLOS Biology: published May 14, 2019 | https://doi.org/10.1371/journal.pbio.2006741

Regulation of membrane phospholipid asymmetry by Notch-mediated flippase expression controls the number of intraepithelial TCRαβ+CD8αα+ T cells

Chieko Ishifune, Shin-ichi Tsukumo, Yoichi Maekawa, Katsuto Hozumi, Doo Hyun Chung, Chihiro Motozono, Sho Yamasaki, Hiroyasu Nakano, Koji Yasutomo

PLOS Biology: published May 9, 2019 | https://doi.org/10.1371/journal.pbio.3000262

Islands of retroelements are major components of Drosophila centromeres

Ching-Ho Chang, Ankita Chavan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-Ting Wu, Amanda M. Larracuente, Barbara G. Mellone

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Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature

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PLOS Biology: published May 8, 2019 | https://doi.org/10.1371/journal.pbio.3000263

Rapid antigen diversification through mitotic recombination in the human malaria parasite Plasmodium falciparum

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Cell aging preserves cellular immortality in the presence of lethal levels of damage

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PLOS Biology: published May 23, 2019 | https://doi.org/10.1371/journal.pbio.3000266

Simple nutrients bypass the requirement for HLH-30 in coupling lysosomal nutrient sensing to survival

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mRNA association by aminoacyl tRNA synthetase occurs at a putative anticodon mimic and autoregulates translation in response to tRNA levels

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PLOS Biology: published May 13, 2019 | https://doi.org/10.1371/journal.pbio.3000260

Short Reports

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

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PLOS Biology: published May 13, 2019 | https://doi.org/10.1371/journal.pbio.3000265

Methods and Resources

Reversible association with motor proteins (RAMP): A streptavidin-based method to manipulate organelle positioning

Carlos M. Guardia, Raffaella De Pace, Aritra Sen, Amra Saric, Michal Jarnik, David A. Kolin, Ambarish Kunwar, Juan S. Bonifacino

PLOS Biology: published May 17, 2019 | https://doi.org/10.1371/journal.pbio.3000279

Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies

Yung-Heng Chang, Richard M. Keegan, Lisa Prazak, Josh Dubnau

PLOS Biology: published May 16, 2019 | https://doi.org/10.1371/journal.pbio.3000278

Systematically improved in vitro culture conditions reveal new insights into the reproductive biology of the human parasite Schistosoma mansoni

Jipeng Wang, Rui Chen, James J. Collins III

PLOS Biology: published May 8, 2019 | https://doi.org/10.1371/journal.pbio.3000254

Meta-Research Article

Animal models of chemotherapy-induced peripheral neuropathy: A machine-assisted systematic review and meta-analysis

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PLOS Biology: published May 20, 2019 | https://doi.org/10.1371/journal.pbio.3000243