Microscopy preprints – applications in biology

Posted by FocalPlane, on 3 November 2023

Here is a curated selection of preprints published recently. In this post, we share preprints that use microscopy tools to answer questions in biology.

Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth
Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann

Figure extracted from Spahn, *et al..* The image is made available under a CC-BY 4.0 International license.

Targeting and Imaging Mitochondria with a Novel Cyanine-based Fluorescent Dye and Its Application to Whole Brain Imaging
Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi

Atlas of Plasmodium falciparum intraerythrocytic development using expansion microscopy
Benjamin Liffner, Ana Karla Cepeda Diaz, James Blauwkamp, David Anaguano, Sonja Frölich, Vasant Muralidharan, Danny W. Wilson, Jeffrey Dvorin, Sabrina Absalon

Figure extracted from Liffner, *et al..* The image is made available under a CC-BY 4.0 International license.

Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane
Hauke Winkelmann, Christian P. Richter, Jasper Eising, Jacob Piehler, Rainer Kurre

Correlation of calcium multiphoton with ultrastructural STED imaging of the slit diaphragm in the same glomerulus
Eva Wiesner, Julia Binz-Lotter, Agnes Hackl, David Unnersjö-Jess, Nelli Rutkowski, Thomas Benzing, Matthias J. Hackl

Organelle landscape analysis using a multi-parametric particle-based method
Yoshitaka Kurikawa, Ikuko Koyama-Honda, Keiko Igarashi, Norito Tamura, Seiichi Koike, Noboru Mizushima

Figure extracted from Kurikawa, *et al.* The image is made available under a CC-BY 4.0 International license.

Quantitative Profiling of Lysosomal pH Heterogeneity using Fluorescence Lifetime Imaging Microscopy
Dinghuan Deng, Baiping Wang, Youchen Guan, Hui Zheng, Ayse Sena Mutlu, Meng C. Wang

Structure-preserving fixation allows Scanning Electron Microscopy to reveal biofilm microstructure and interactions with immune cells
Marilyn Wells, Michelle Mikesh, Vernita Gordon

A large-scale volumetric correlated light and electron microscopy study localizes Alzheimer’s disease-related molecules in the hippocampus
Xiaomeng Han, Peter H. Li, Shuohong Wang, Morgan Sanchez, Sneha Aggarwal, Tim Blakely, Richard Schalek, Yaron Meirovitch, Zudi Lin, Yuelong Wu, Fatima Aly, Sylvie Bay, Benoît Delatour, Pierre Lafaye, Hanspeter Pfister, Donglai Wei, Viren Jain, Hidde Ploegh, Jeff Lichtman

Four-dimensional quantitative analysis of cell plate development using lattice light sheet microscopy identifies robust transition points between growth phases
Rosalie Sinclair, Minmin Wang, Zaki Jawaid, Jesse Aaron, Blair Rossetti, Eric Wait, Kent McDonald, Daniel Cox, John Heddleston, Thomas Wilkop, Georgia Drakakaki

Figure extracted from Sinclair, *et al.* The image is made available under a CC-BY-NC 4.0 International license.

Visualisation of gene expression within the context of tissues: an X-ray computed tomography-based multimodal approach
Kristaps Kairišs, Natalia Sokolova, Lucie Zilova, Christina Schlagheck, Robert Reinhardt, Tilo Baumbach, Tomáš Faragó, Thomas van de Kamp, Joachim Wittbrodt, Venera Weinhardt

Unleashing the secrets of plant-fungal interactions using a transformation-free confocal staining technique that supports AI-assisted quantitative analysis
Ashley C. Nelson, Gayan Kariyawasam, Nathan A. Wyatt, Jinling Li, Janine Haueisen, Eva H. Stukenbrock, Pawel Borowicz, Zhaohui Liu, Timothy L. Friesen

Multi-functional ARF1 compartments serve as a hub for short-range cargo transfer to endosomes
Alexander Stockhammer, Petia Adarska, Vini Natalia, Anja Heuhsen, Antonia Klemt, Shelly Harel, Carmen Rodilla-Ramirez, Carissa Spalt, Ece Özsoy, Paula Leupold, Alica Grindel, Eleanor Fox, Joy Orezimena Mejedo, Dmytro Puchkov, Volker Haucke, Francesca Bottanelli

Figure extracted from Stockhammer, *et al.* The image is made available under a CC-BY 4.0 International license.

A Pipeline for a Primate Projectome: mapping every individual myelinated axon across the whole brain
Gregg Wildenberg, Kevin Boergens, Viktor Nikitin, Alex Deriy, Francesco De Carlo, Vincent De Andrade, Xianghui Xiao, Narayan Kasthuri

OSBP-mediated PI(4)P-cholesterol exchange at endoplasmic reticulum-secretory granule contact sites controls insulin secretion
Styliani Panagiotou, Kia Wee Tan, Phuoc My Nguyen, Andreas Müller, Affiong Ika Oqua, Alejandra Tomas, Anna Wendt, Lena Eliasson, Anders Tengholm, Michele Solimena, Olof Idevall-Hagren

ER-to-Golgi trafficking via a dynamic intermediate cis-Golgi tubular network in Arabidopsis
Louise Fougère, Magali Grison, Patricia Laquel, Matheus Montrazi, Fabrice Cordelières, Mónica Fernández-Monreal, Christel Poujol, Tomohiro Uemura, Akihiko Nakano, Yoko Ito, Yohann Boutté

Accurate Automated Segmentation of Autophagic Bodies in Yeast Vacuoles Using Cellpose 2.0
Emily C. Marron, Jonathan Backues, Andrew M. Ross, Steven K. Backues

Long-term in vivo three-photon imaging reveals region-specific differences in healthy and regenerative oligodendrogenesis
Michael A. Thornton, Gregory L. Futia, Michael E. Stockton, Samuel A. Budoff, Alexandra N. Ramirez, Baris Ozbay, Omer Tzang, Karl Kilborn, Alon Poleg-Polsky, Diego Restrepo, Emily A Gibson, Ethan G. Hughes

Super-resolution imaging of potassium channels with genetically encoded EGFP
Isabelle M. Call, Julian L. Bois, Scott B. Hansen

A polarized cell system amenable to subcellular resolution imaging of influenza virus infection
Brault Jean-Baptiste, Thouvenot Catherine, Cannata Serio Magda, Paisant Sylvain, Fernandes Julien, Gény David, Danglot Lydia, Mallet Adeline, Naffakh Nadia

Figure extracted from Jean-Baptiste, *et al.* The image is made available under a CC-BY 4.0 International license.

Super-Resolution Imaging of Fast Morphological Dynamics of Neurons in Behaving Animals
Yujie Zhang, Lu Bai, Xin Wang, Yuchen Zhao, Tianlei Zhang, Lichen Ye, Xufei Du, Zhe Zhang, Jiulin Du, Kai Wang

Nanoscale imaging reveals the mechanisms of ER-to-Golgi transport via a dynamic tubular-vesicular network
Luis Wong-Dilworth, Gresy Bregu, Steffen Restel, Carmen Rodilla-Ramirez, Svenja Ebeling, Shelly Harel, Paula Leupold, Jonathan Grimm, Luke D. Lavis, Jessica Angulo-Capel, Felix Campelo, Francesca Bottanelli

Figure extracted from Wong-Dilworth, *et al.* The image is made available under a CC-BY 4.0 International license.

Unveiling the ultrastructural landscape of native extracellular matrix via lift-out cryo-FIBSEM and cryo-ET
Bettina Zens, Florian Fäßler, Jesse M Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna Alanko, Michael Sixt, Florian KM Schur

The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after open mitosis in mammalian cells
Helena Bragulat-Teixidor, Keisuke Ishihara, Gréta Martina Szücs, Shotaro Otsuka

Figure extracted from Bragulat-Teixidor, *et al.* The image is made available under a CC-BY 4.0 International license.

Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines
Connon I. Thomas, Melissa A. Ryan, Naomi Kamasawa, Benjamin Scholl

Mechanism for Vipp1 spiral formation, ring biogenesis and membrane repair
Souvik Naskar, Andrea Merino, Javier Espadas, Jayanti Singh, Aurelien Roux, Adai Colom, Harry H Low

Neuronal activity modulates the incorporation of newly translated PSD-95 into a robust structure as revealed by STED and MINFLUX
Clara-Marie Gürth, Maria Augusta do Rego Barros Fernandes Lima, Victor Macarrón Palacios, Jasmine Hubrich, Angel Rafael Cereceda Delgado, Nikolaos Mougios, Felipe Opazo, Elisa D’Este

Figure extracted from Gürth, *et al.* The image is made available under a CC-BY-NC 4.0 International license.

Actin-Driven Nanotopography Promotes Stable Integrin Adhesion Formation in Developing Tissue
Tianchi Chen, Cecilia Huertas Fernández-Espartero, Abigail Illand, Ching-Ting Tsai, Yang Yang, Benjamin Klapholz, Pierre Jouchet, Mélanie Fabre, Olivier Rossier, Bianxiao Cui, Sandrine Lévêque-Fort, Nicholas H. Brown, Grégory Giannone

Cryo-EM structure of Alzheimer’s disease tau filaments with PET ligand MK-6240
Peter Kunach, Jaime Vaquer-Alicea, Matthew S. Smith, Robert Hopewell, Jim Monistrol, Luc Moquin, Joseph Therriault, Cecile Tissot, Nesrine Rahmouni, Gassan Massarweh, Jean-Paul Soucy, Marie-Christine Guiot, Brian K. Shoichet, Pedro Rosa-Neto, Marc I. Diamond, Sarah H. Shahmoradian

T cells Use Focal Adhesions to Pull Themselves Through Confined Environments
Alexia Caillier, David Oleksyn, Deborah J. Fowell, Jim Miller, Patrick W. Oakes

Cryo-EM structures of Tau filaments from the brains of mice transgenic for human mutant P301S Tau
Manuel Schweighauser, Alexey G. Murzin, Jennifer Macdonald, Isabelle L. Lavenir, R. Anthony Crowther, Sjors H.W. Scheres, Michel Goedert

Three-dimensional visualization of blood vessels in human gliomas based on tissue clearing and deep learning
Xinyue Wang, Xiaodu Yang, Dian He, Yunhao Luo, Qiyuan Huang, Ting Li, Zhaoyu Ye, Chun Ye, Minglin Zhang, Heiming Lai, Yingying Xu, Haitao Sun

Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover
Carolyn M Ott, Russel Torres, Tung-Sheng Kuan, Aaron T Kuan, JoAnn Buchanan, Leila Elabbady, Sharmishtaa Seshamani, Agnes L Bodor, Forrest C Collman, Davi D Bock, Wei-Chung Allen Lee, Nuno Macarico da Costa, Jennifer Lippincott-Schwartz

Visualization of cristae and mtDNA dynamics and interactions with super-resolution microscopy
Peng Xi, Wei Ren, Xichuan Ge, Meiqi Li, Jing Sun, Shiyi Li, Chunyan Shan, Baoxiang Gao