@article {69756, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, volume = {188}, year = {2025}, month = {01/2025}, pages = {484-500.e22}, abstract = {

Neuronal dendrites must relay synaptic inputs over long distances, but the mechanisms by which activity-evoked intracellular signals propagate over macroscopic distances remain unclear. Here, we discovered a system of periodically arranged endoplasmic reticulum-plasma membrane (ER-PM) junctions tiling the plasma membrane of dendrites at \~{}1\ μm intervals, interlinked by a meshwork of ER tubules patterned in a ladder-like array. Populated with Junctophilin-linked plasma membrane voltage-gated Ca channels and ER Ca-release channels (ryanodine receptors), ER-PM junctions are hubs for ER-PM crosstalk, fine-tuning of Ca homeostasis, and local activation of the Ca/calmodulin-dependent protein kinase II. Local spine stimulation activates the Ca modulatory machinery, facilitating signal transmission and ryanodine-receptor-dependent Ca release at ER-PM junctions over 20\ μm away. Thus, interconnected ER-PM junctions support signal propagation and Ca release from the spine-adjacent ER. The capacity of this subcellular architecture to modify both local and distant membrane-proximal biochemistry potentially contributes to dendritic computations.

}, keywords = {Animals, Calcium, Calcium Signaling, Calcium-Calmodulin-Dependent Protein Kinase Type 2, Cell Membrane, Dendrites, Endoplasmic Reticulum, Hippocampus, Humans, Male, Mice, Rats, Ryanodine Receptor Calcium Release Channel}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.11.029}, author = {Benedetti, Lorena and Fan, Ruolin and Weigel, Aubrey V and Moore, Andrew S and Houlihan, Patrick R and Kittisopikul, Mark and Park, Grace and Petruncio, Alyson and Hubbard, Philip M and Pang, Song and Xu, C Shan and Hess, Harald F and Saalfeld, Stephan and Rangaraju, Vidhya and Clapham, David E and De Camilli, Pietro and Ryan, Timothy A and Lippincott-Schwartz, Jennifer} } @article {69721, title = {A split-GAL4 driver line resource for Drosophila neuron types}, year = {2025}, month = {01/2025}, doi = {10.7554/elife.98405.3}, url = {http://dx.doi.org/10.7554/eLife.98405.3}, author = {Meissner, Geoffrey W and Vannan, Allison and Jeter, Jennifer and Close, Kari and Depasquale, Gina M and Dorman, Zachary and Forster, Kaitlyn and Beringer, Jaye Anne and Gibney, Theresa V and Hausenfluck, Joanna H and He, Yisheng and Henderson, Kristin and Johnson, Lauren and Johnston, Rebecca M and Ihrke, Gudrun and Iyer, Nirmala and Lazarus, Rachel and Lee, Kelley and Li, Hsing-Hsi and Liaw, Hua-Peng and Melton, Brian and Miller, Scott and Motaher, Reeham and Novak, Alexandra and Ogundeyi, Omotara and Petruncio, Alyson and Price, Jacquelyn and Protopapas, Sophia and Tae, Susana and Taylor, Jennifer and Vorimo, Rebecca and Yarbrough, Brianna and Zeng, Kevin Xiankun and Zugates, Christopher T and Dionne, Heather and Angstadt, Claire and Ashley, Kelly and Cavallaro, Amanda and Dang, Tam and Gonzalez, Guillermo A and Hibbard, Karen L and Huang, Cuizhen and Kao, Jui-Chun and Laverty, Todd and Mercer, Monti and Perez, Brenda and Pitts, Scarlett and Ruiz, Danielle and Vallanadu, Viruthika and Zheng, Grace Zhiyu and Goina, Cristian and Otsuna, Hideo and Rokicki, Konrad and Svirskas, Robert R and Cheong, Han Sj and Dolan, Michael-John and Ehrhardt, Erica and Feng, Kai and El Galfi, Basel and Goldammer, Jens and Huston, Stephen J and Hu, Nan and Ito, Masayoshi and McKellar, Claire and minegishi, ryo and Namiki, Shigehiro and Nern, Aljoscha and Schretter, Catherine E and Sterne, Gabriella R and Venkatasubramanian, Lalanti and Wang, Kaiyu and Wolff, Tanya and Wu, Ming and George, Reed and Malkesman, Oz and Aso, Yoshinori and Card, Gwyneth M and Dickson, Barry J and Korff, Wyatt and Ito, Kei and Truman, James W and Zlatic, Marta and Rubin, Gerald M} } @article {69812, title = {Vimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM}, journal = {Journal of Cell Biology}, volume = {224}, year = {2025}, month = {2025 Apr 03}, pages = {e202406054}, abstract = {

Vimentin intermediate filaments (VIFs) form complex, tightly packed networks; due to this density, traditional imaging approaches cannot discern single-filament behavior. To address this, we developed and validated a sparse vimentin-SunTag labeling strategy, enabling single-particle tracking of individual VIFs and providing a sensitive, unbiased, and quantitative method for measuring global VIF motility. Using this approach, we define the steady-state VIF motility rate, showing a constant \~{}8\% of VIFs undergo directed microtubule-based motion irrespective of subcellular location or local filament density. Significantly, our single-particle tracking approach revealed uncorrelated motion of individual VIFs within bundles, an observation seemingly at odds with conventional models of tightly cross-linked bundles. To address this, we acquired high-resolution focused ion beam scanning electron microscopy volumes of vitreously frozen cells and reconstructed three-dimensional VIF bundles, finding that they form only loosely organized, semi-coherent structures from which single VIFs frequently emerge to locally engage neighboring microtubules. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first time.

bioRxiv Preprint:\ https://doi.org/10.1101/2024.06.10.598346

}, issn = {0021-9525}, doi = {10.1083/jcb.202406054}, url = {https://doi.org/10.1083/jcb.202406054}, author = {Renganathan, Bhuvanasundar and Moore, Andrew S. and Yeo, Wei-Hong and Petruncio, Alyson and Ackerman, David and Weigel, Aubrey V. and Team, The CellMap and Pasolli, H. Amalia and Xu, C. Shan and Shtengel, Gleb and Hess, Harald F. and Serpinskaya, Anna S. and Zhang, Hao F. and Lippincott-Schwartz, Jennifer and Gelfand, Vladimir I.} } @article {69602, title = {Data Release: High-Resolution Imaging and Segmentation of P7 Mouse Tissue Microarchitecture Using FIB-SEM and Machine Learning}, journal = {bioRxiv}, year = {2024}, month = {2024 Sep 07}, abstract = {

This report presents a comprehensive data release exploring the tissue microarchitecture of P7 aged mice using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) combined with machine learning-based segmentations of nuclei. The study includes high-resolution 3D volumes and nucleus segmentations for seven vital tissues{\textemdash}pancreas, liver, kidney, heart, thymus, hippocampus, and skin{\textemdash}from a single mouse. The detailed datasets are openly accessible on OpenOrganelle.org, providing a valuable resource for the scientific community to support further research and collaboration.

}, doi = {10.1101/2024.09.05.611438}, url = {https://www.doi.org/10.1101/2024.09.05.611438}, author = {Ackerman, David and Avetissian, Emma and Bleck, Christopher K. E. and Bogovic, John A. and Innerberger, Michael and Korff, Wyatt and Li, Wei-Ping and Lu, Zhiyuan and Petruncio, Alyson and Preibisch, Stephan and Qiu, Wei and Jeff L Rhoades and Saalfeld, Stephan and Silva, Malan and Trautman, Eric T. and Vorimo, Rebecca and Weigel, Aubrey and Yu, Zhiheng and Zubov, Yurii and ,} } @article {69704, title = {Periodic ER-plasma membrane junctions support long-range Ca signal integration in dendrites.}, journal = {Cell}, year = {2024}, month = {2024 Dec 18}, abstract = {

Neuronal dendrites must relay synaptic inputs over long distances, but the mechanisms by which activity-evoked intracellular signals propagate over macroscopic distances remain unclear. Here, we discovered a system of periodically arranged endoplasmic reticulum-plasma membrane (ER-PM) junctions tiling the plasma membrane of dendrites at \~{}1\ μm intervals, interlinked by a meshwork of ER tubules patterned in a ladder-like array. Populated with Junctophilin-linked plasma membrane voltage-gated Ca channels and ER Ca-release channels (ryanodine receptors), ER-PM junctions are hubs for ER-PM crosstalk, fine-tuning of Ca homeostasis, and local activation of the Ca/calmodulin-dependent protein kinase II. Local spine stimulation activates the Ca modulatory machinery, facilitating signal transmission and ryanodine-receptor-dependent Ca release at ER-PM junctions over 20\ μm away. Thus, interconnected ER-PM junctions support signal propagation and Ca release from the spine-adjacent ER. The capacity of this subcellular architecture to modify both local and distant membrane-proximal biochemistry potentially contributes to dendritic computations.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2024.11.029}, author = {Benedetti, Lorena and Fan, Ruolin and Weigel, Aubrey V and Moore, Andrew S and Houlihan, Patrick R and Kittisopikul, Mark and Park, Grace and Petruncio, Alyson and Hubbard, Philip M and Pang, Song and Xu, C Shan and Hess, Harald F and Saalfeld, Stephan and Rangaraju, Vidhya and Clapham, David E and De Camilli, Pietro and Ryan, Timothy A and Lippincott-Schwartz, Jennifer} } @article {69491, title = {Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM}, journal = {bioRxiv}, year = {2024}, month = {2024 Jun 10}, abstract = {

Vimentin intermediate filaments (VIFs) form complex, tight-packed networks; due to this density, traditional ensemble labeling and imaging approaches cannot accurately discern single filament behavior. To address this, we introduce a sparse vimentin-SunTag labeling strategy to unambiguously visualize individual filament dynamics. This technique confirmed known long-range dynein and kinesin transport of peripheral VIFs and uncovered extensive bidirectional VIF motion within the perinuclear vimentin network, a region we had thought too densely bundled to permit such motility. To examine the nanoscale organization of perinuclear vimentin, we acquired high-resolution electron microscopy volumes of a vitreously frozen cell and reconstructed VIFs and microtubules within a 50 um3 window. Of 583 VIFs identified, most were integrated into long, semi-coherent bundles that fluctuated in width and filament packing density. Unexpectedly, VIFs displayed minimal local co-alignment with microtubules, save for sporadic cross-over sites that we predict facilitate cytoskeletal crosstalk. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first time.

}, doi = {10.1101/2024.06.10.598346}, url = {https://www.biorxiv.org/content/early/2024/06/10/2024.06.10.598346}, author = {Renganathan, Bhuvanasundar and Moore, Andrew S. and Yeo, Wei-Hong and Petruncio, Alyson and Ackerman, David and Wiegel, Aubrey and CellMap Team and Pasolli, H. Amalia and Xu, C. Shan and Hess, Harald F and Serpinskaya, Anna S. and Zhang, Hao F. and Lippincott-Schwartz, Jennifer and Gelfand, Vladimir I.} } @article {68807, title = {Architecture and dynamics of a desmosome-endoplasmic reticulum complex.}, journal = {Nature Cell Biology}, volume = {25}, year = {2023}, month = {2023 Jun 16}, pages = {823-835}, abstract = {

The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signalling and lipid transfer. Here, using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometre proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization, mobility and expression of ER stress transcripts. These findings indicate that desmosomes and the keratin cytoskeleton regulate the distribution, function and dynamics of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.

}, keywords = {Cytoskeleton, Desmosomes, Endoplasmic Reticulum, Intermediate Filaments, Keratins}, issn = {1476-4679}, doi = {10.1038/s41556-023-01154-4}, author = {Bharathan, Navaneetha Krishnan and Giang, William and Hoffman, Coryn L and Aaron, Jesse S and Khuon, Satya and Chew, Teng-Leong and Preibisch, Stephan and Trautman, Eric T and Heinrich, Larissa and Bogovic, John and Bennett, Davis and Ackerman, David and Park, Woohyun and Petruncio, Alyson and Weigel, Aubrey V and Saalfeld, Stephan and Wayne Vogl, A and Stahley, Sara N and Kowalczyk, Andrew P} } @article {68958, title = {Towards Generalizable Organelle Segmentation in Volume Electron Microscopy.}, journal = {Microscopy and Microanalysis}, volume = {29}, year = {2023}, month = {2023 Jul 22}, pages = {975}, keywords = {Organelles, Volume Electron Microscopy}, issn = {1435-8115}, doi = {10.1093/micmic/ozad067.487}, author = {Heinrich, Larissa and Patton, Will and Bennett, Davis and Ackerman, David and Park, Grace and Bogovic, John A and Eckstein, Nils and Petruncio, Alyson and Clements, Jody and Pang, Song and Shan Xu, C and Funke, Jan and Korff, Wyatt and Hess, Harald and Lippincott-Schwartz, Jennifer and Saalfeld, Stephan and Weigel, Aubrey} } @article {67750, title = {Whole-cell organelle segmentation in volume electron microscopy.}, journal = {Nature}, volume = {599}, year = {2021}, month = {2021 Nov 01}, pages = {141-46}, abstract = {

Cells contain hundreds of organelles and macromolecular assemblies. Obtaining a complete understanding of their intricate organization requires the nanometre-level, three-dimensional reconstruction of whole cells, which is only feasible with robust and scalable automatic methods. Here, to support the development of such methods, we annotated up to 35 different cellular organelle classes-ranging from endoplasmic reticulum to microtubules to ribosomes-in diverse sample volumes from multiple cell types imaged at a near-isotropic resolution of 4 nm per voxel with focused ion beam scanning electron microscopy (FIB-SEM). We trained deep learning architectures to segment these structures in 4 nm and 8 nm per voxel FIB-SEM volumes, validated their performance and showed that automatic reconstructions can be used to directly quantify previously inaccessible metrics including spatial interactions between cellular components. We also show that such reconstructions can be used to automatically register light and electron microscopy images for correlative studies. We have created an open data and open-source web repository, {\textquoteright}OpenOrganelle{\textquoteright}, to share the data, computer code and trained models, which will enable scientists everywhere to query and further improve automatic reconstruction of these datasets.

}, issn = {1476-4687}, doi = {10.1038/s41586-021-03977-3}, author = {Heinrich, Larissa and Bennett, Davis and Ackerman, David and Park, Woohyun and Bogovic, John and Eckstein, Nils and Petruncio, Alyson and Clements, Jody and Pang, Song and Xu, C Shan and Funke, Jan and Korff, Wyatt and Hess, Harald F and Lippincott-Schwartz, Jennifer and Saalfeld, Stephan and Weigel, Aubrey V} }