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Mitochondria drive microglial NRLP3 inflammasome activation via TSPO bioRxiv. Cell Biol. Pub Date : 2024-03-18 Aarti Singh, Manuel Rigon, Marta Caldeira, Danilo Faccenda, Dong Xia, Jordi Lopez-Tremoleda, Zahra Falah Hassan Al-Khateeb, Tong Guo, Rosella Abeti, Paola Giunti, Michelangelo Campanella
Uncontrolled microglial response is core to neuroinflammatory brain diseases. The correlation between the mitochondrial protein TSPO and inflammation has so far failed to explain whether TSPO positively or negatively regulates microglial function. The recent evidence on the species specificity of TSPO in microglia demands a deeper understanding of the protein biology in these brain-resident macrophages
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Endosomal sorting protein SNX4 limits synaptic vesicle docking and release bioRxiv. Cell Biol. Pub Date : 2024-03-18 Josse Poppinga, Nolan J. Barret, L. Niels Cornelisse, Matthijs Verhage, Jan R.T. van Weering
Sortin-Nexin 4 (SNX4) is an evolutionary conserved organizer of membrane recycling. In neurons, SNX4 accumulates in synapses, but how SNX4 affects synapse function remains unknown. We generated a conditional SNX4 knock-out mouse model and report that SNX4 cKO synapses show enhanced neurotransmission during train stimulation, while the first evoked EPSC was normal. SNX4 depletion did not affect vesicle
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Cell intrinsic mechanical regulation of plasma membrane accumulation at the cytokinetic furrow bioRxiv. Cell Biol. Pub Date : 2024-03-18 Roberto Alonso-Matilla, Alice Lam, Teemu P Miettinen
Cytokinesis is the process where the mother cell's cytoplasm separates into daughter cells. This is driven by an actomyosin contractile ring that produces cortical contractility and drives cleavage furrow ingression, resulting in the formation of a thin intercellular bridge. While cytoskeletal reorganization during cytokinesis has been extensively studied, little is known about the spatiotemporal dynamics
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A progeria-associated BAF-1 mutation modulates gene expression and accelerates aging in C. elegans bioRxiv. Cell Biol. Pub Date : 2024-03-17 Raquel Romero-Bueno, Adrian Fragoso-Luna, Cristina Ayuso, Alan Kavsek, Christian G. Riedel, Jordan D Ward, Peter Askjaer
Alterations in the nuclear envelope are linked to a variety of rare diseases termed laminopathies. These include both tissue specific and systemic diseases. A single amino acid substitution in human barrier to autointegration factor (BAF) at position 12 (A12T) causes Néstor-Guillermo Progeria Syndrome (NGPS). This premature ageing condition affects a variety of tissues, leading to growth retardation
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A consensus motif in ASH1 and further transcripts unifies several RNA motifs required for interaction with the She2p/She3p transport machinery and mRNA localization in yeast bioRxiv. Cell Biol. Pub Date : 2024-03-17 Markus Seiler, Annika Niedner, Simone Heber, Michael Feldbruegge, Ralf-Peter Jansen, Dierk Niessing, Kathi Zarnack
Asymmetric localization of the ASH1 transcript is a central step in the regulation of mating type switching in Saccharomyces cerevisae and a paradigm for localized mRNAs specifically recognized by the She2p/3p transport machinery. Four RNA elements in ASH1 are known to mediate bud localization, but it remained unclear what a consensus motif of all four She2p/3p recognition sites (SRS) might look like
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Tuft cells act as regenerative stem cells in the human intestine bioRxiv. Cell Biol. Pub Date : 2024-03-17 Lulu Huang, Jochem H. Bernink, Amir Giladi, Daniel Krueger, Gijs J.F. van Son, Maarten H. Geurts, Georg Busslinger, Lin Lin, Maurice Zandvliet, Peter J. Peters, Carmen Lopez-Iglesias, Christianne J. Buskens, Willem A. Bemelman, Harry Begthel, Hans Clevers
In mice, intestinal tuft cells have been described as a long-lived, post-mitotic cell type of which two distinct subsets have been identified, named tuft-1 and tuft-21. By combining analysis of primary human intestinal resection material and intestinal organoids, we identify four distinct human tuft cell states, two of which overlap with their murine counterparts. We show that tuft cell development
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Multi-omics discovery of hallmark protein and lipid features of circulating small extracellular vesicles in humans bioRxiv. Cell Biol. Pub Date : 2024-03-17 Alin Rai, Kevin Huynh, Qi Hui Poh, Haoyun Fang, Bethany Claridge, Jonathon Cross, Thy Duong, Carla Duarte, Thomas Marwick, Peter Meikle, David W Greening
Extracellular vesicles (EVs) are now being increasingly recognized as an essential signalling entity in human plasma, linking them to health and various diseases. Still, their core protein and lipid componentry, which lie at the centre of EV form and function, remains poorly defined. Achieving this unmet milestone remains greatly hindered by abundant non-vesicular extracellular plasma components (non-EVs)
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Cell culture differentiation and proliferation conditions influence the in vitro regeneration of the human airway epithelium bioRxiv. Cell Biol. Pub Date : 2024-03-17 Elisa Redman, Morgane Fierville, Amélie Cavard, Magali Plaisant, Marie-Jeanne Arguel, Sandra Ruiz Garcia, Eamon Martin McAndrew, Cédric Girard-Riboulleau, Kévin Lebrigand, Virginie Magnone, Gilles Ponzio, Delphine Gras, Pascal Chanez, Sophie Abélanet, Pascal Barbry, Brice Marcet, Laure-Emmanuelle Zaragosi
The human airway mucociliary epithelium can be recapitulated in vitro using primary cells cultured in an Air-Liquid Interface (ALI), a reliable surrogate to perform pathophysiological studies. As tremendous variations exist between media used for ALI-cultured human airway epithelial cells, our study aimed to evaluate the impact of several media (BEGM, PneumaCult, "Half&Half" and "Clancy") on cell type
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Nuclear compression-mediated DNA damage drives ATR-dependent Lamin expression and mouse ESC differentiation bioRxiv. Cell Biol. Pub Date : 2024-03-17 Tanusri Roy, Niyati Piplani, Lakshmi Kavitha Sthanam, Swetlana Ghosh, Niharika Tiwary, Sayak Dhar, W. Chingmei Wangsa Konyak, Santosh Surendra Panigrahi, Priya Singh, Divya Tej Sowpati, Sreelaja Nair, Sushil Kumar, P Chandra Shekar, Shamik Sen
Embryonic stem cells (ESCs) which are susceptible to DNA damage depend on a robust and highly efficient DNA damage response (DDR) mechanism for their survival. However, the implications of physical force-mediated DNA damage on ESC fate remains unclear. We show that stiffness-dependent spreading of mouse ESCs (mESCs) induces DNA damage through nuclear compression, with DNA damage causing differentiation
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Physiologic media renders human iPSC-derived macrophages permissive for M. tuberculosis by rewiring organelle function and metabolism bioRxiv. Cell Biol. Pub Date : 2024-03-17 Claudio Bussi, Rachel Lai, Natalia Athanasiadi, Maximiliano G Gutierrez
In vitro studies are crucial for our understanding of the human macrophage immune functions. However, traditional in vitro culture media poorly reflect the metabolic composition of blood, potentially affecting the outcomes of these studies. Here, we analysed the impact of a physiological medium on human induced pluripotent stem cell (iPSC)-derived macrophages (iPSDM) function. Macrophages cultured
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Caskin2 is a novel talin and Abi1-binding protein that promotes cell motility bioRxiv. Cell Biol. Pub Date : 2024-03-17 Wei Wang, Paul Atherton, Maaike Kreft, Lisa te Molder, Sabine van der Poel, Liesbeth Hoekman, Patrick Celie, Robbie P Joosten, Reinhard Faessler, Anastassis Perrakis, Arnoud Sonnenberg
Talin couples the actomyosin cytoskeleton to integrins and transmits tension to the extracellular matrix. Talin also interacts with numerous additional proteins capable of modulating the actin-integrin linkage and thus downstream mechanosignaling cascades. Here, we demonstrate that the scaffold protein Caskin2 interacts directly with the R8 domain of talin through its C-terminal LD motif. Caskin2 also
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Wee1 inhibition decouples Cdk1 and Plk1 activities: a role for gradual Cdk1 activation throughout G2 phase. bioRxiv. Cell Biol. Pub Date : 2024-03-17 Karen Akopyan, Arne Lindqvist
At completion of DNA replication, the mitotic kinases CDK1 and PLK1 are activated. Their activities increase slowly through early G2 phase, but the reason for this low-level activity before mitotic entry is not clear. Using a combination of experiments and mathematical modelling, we find that gradual CDK1 activation through G2 phase stimulates production of mitotic factors and coordinates activation
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Myocardin-related transcription factor drives epithelial fibrogenesis in polycystic kidney disease bioRxiv. Cell Biol. Pub Date : 2024-03-17 Zsuzsanna Lichner, Mei Ding, Tarang Khare, Qinghong Dan, Raquel Benitez, Mercedesz Praszner, Xuewen Song, Rola Saleeb, Boris Hinz, York Pei, Katalin Szaszi, Andras Kapus
Polycystic kidney disease (PKD) is characterized by extensive cyst formation and progressive fibrosis. However, the molecular mechanisms whereby the loss/loss-of-function of Polycystin 1 or 2 (PC1/2) provokes fibrosis are largely unknown. The small GTPase RhoA has been recently implicated in cystogenesis, and we have shown that the RhoA/cytoskeleton/myocardin-related transcription factor (MRTF) pathway
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Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging bioRxiv. Cell Biol. Pub Date : 2024-03-16 Shovik Bandyopadhyay, Michael Duffy, Kyung Jin Ahn, Minxing Pang, David Smith, Gwendolyn Duncan, Jonathan Sussman, Jihan Zhang, Jeffrey Huang, Yu Lieh Lin, Barbara Xiong, Tamjid Imtiaz, Chia-hui Chen, Anusha Thadi, Changya Chen, Jason Xu, Melissa Reichart, Vinodh Pillai, Oraine Snaith, Derek Oldridge, Siddharth Bhattacharyya, Ivan H Maillard, Martin Carroll, Charles Nelson, Ling Qin, Kai Tan
The bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNASeq) to profile 29,325 enriched
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cGAS-STING is responsible for aging of telomerase deficient zebrafish bioRxiv. Cell Biol. Pub Date : 2024-03-16 Naz Serifoglu, Giulia Allavena, Bruno Bastos-Lopes, Marta Marzullo, Pavlos Bousounis, Eirini Trompouki, Miguel Godinho Ferreira
Telomere shortening occurs in multiple tissues throughout aging. When telomeres become critically short, they trigger DNA damage responses and p53 stabilization, leading to apoptosis or replicative senescence. In vitro, cells with short telomeres activate the cGAS-STING innate immune pathway resulting in type I interferon inflammation and senescence. However, the consequences of these events to the
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Inhibition of Proteasome Activity Facilitates Definitive Endodermal Specification of pluripotent Stem Cells by influencing YAP signaling bioRxiv. Cell Biol. Pub Date : 2024-03-16 Akshaya Ashok, Ashwini Ashwatnarayan, Smitha Bhaskar, Spandana Shekar, Jyothi Prasanna, ANUJITH KUMAR
Understanding the molecular players that control the specification of definitive endoderm is imperative to obtain the homogenous population of pancreatic β-cells from stem cells. Though the Ubiquitin proteasome system (UPS) has been envisaged as a crucial intracellular protein degradation system, its role in germ layer specification remains elusive. In this study, using a mouse embryonic stem cells
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Redefining the role of Hypoxia-inducible factors (HIFs) in oxygen homeostasis bioRxiv. Cell Biol. Pub Date : 2024-03-16 Clemente Fernández Arias, Franciso J Acosta, Federica Bertocchini, Cristina Fernández-Arias
Hypoxia-inducible factors (HIFs) are key regulators of intracellular oxygen homeostasis. The marked increase in HIFs activity in hypoxia as compared to normoxia, together with their transcriptional control of primary metabolic pathways, motivated the widespread view of HIFs as responsible for the cell's metabolic adaptation to hypoxic stress. In this work, we suggest that this prevailing model of HIFs
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Development of the 12-base short dimeric myogenetic oligodeoxynucleotide that induces myogenic differentiation bioRxiv. Cell Biol. Pub Date : 2024-03-16 Koji Umezawa, Rena Ikeda, Taiichi Sakamoto, Yuya Enomoto, Yuma Nihashi, Sayaka Shinji, Takeshi Shimosato, Hiroshi Kagami, Tomohide Takaya
A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5'-AGA TTA GGG TGA GGG TGA-3'), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining
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Abnormal global longitudinal strain and reduced serum inflammatory markers in cardiac AL amyloidosis patients without significant amyloid fibril deposition bioRxiv. Cell Biol. Pub Date : 2024-03-16 Camille Vanessa Edwards, Grace M Ferri, Josue Villegas-Galaviz, Sabrina Ghosh, Pushpinder Singh Bawa, Feiya Wang, Elena Klimtchuk, Tinuola B Ajayi, Gareth J Morgan, Tatiana Prokaeva, Andrew Staron, Frederick L Ruberg, Vaishali Sanchorawala, Richard M Giadone, George J Murphy
Background: Cardiac dysfunction in AL amyloidosis is thought to be partly related to the direct impact of AL LCs on cardiomyocyte function, with the degree of dysfunction at diagnosis as a major determinant of clinical outcomes. Nonetheless, mechanisms underlying LC-induced myocardial toxicity are not well understood. We identified gene expression changes correlating with human cardiac cells exposed
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Construction and Application of a Technical Platform for Determining Cell Cycle- and Autophagy-Associated Cellular Uptake of Lipid-Based Nanoparticles bioRxiv. Cell Biol. Pub Date : 2024-03-16 Yisha Wang, Gan Luo, Haiyang Wang, Yue Zheng, Xiao Xu, Wenbin Zhou, Junrong Lin, Baocheng Chen, Meihua Sui
Cellular uptake of biomedical nanoparticles has been shown to be affected by key cellular biological properties. However, very little is known about the influence of cell cycle and autophagy on nanoparticle uptake. What's even more tough is that several long-lasting methodological barriers hamper the experimental performance and restrict the research and development. Herein, a multi functional platform
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Real-time TIRF imaging of single adiponectin vesicle exocytosis in 3T3-L1 adipocytes stably expressing mCherry fused to human adiponectin bioRxiv. Cell Biol. Pub Date : 2024-03-16 Man Mohan Shrestha, Sebastian Barg, Charlotta S Olofsson
Adiponectin is a peptide hormone abundantly released from adipocytes, and reduced circulating levels are associated with obesity-related diseases, such as type 2 diabetes, insulin resistance and cardiovascular disease. Adiponectin is released by regulated exocytosis of secretory vesicles, but traditional molecular biology and imaging techniques lack the specificity and time resolution to adequately
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Measuring integrin force loading rates using a two-step DNA tension sensor bioRxiv. Cell Biol. Pub Date : 2024-03-15 J. Dale Combs, Alexander K Foote, Hiroaki Ogasawara, Arventh Velusamy, Sk Aysha Rashid, Joseph Nicholas Mancuso, Khalid Salaita
Cells apply forces to extracellular matrix (ECM) ligands through transmembrane integrin receptors: an interaction which is intimately involved in cell motility, wound healing, cancer invasion and metastasis. These small (pN) forces exerted by cells have been studied by molecular tension fluorescence microscopy (MTFM), which utilizes a force-induced conformational change of a probe to detect mechanical
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Generation of densely labeled oligonucleotides for the detection of small genomic elements bioRxiv. Cell Biol. Pub Date : 2024-03-15 Clemens Steinek, Miguel Guirao Ortiz, Gabriela Stumberger, Annika J. Toelke, David Hoerl, Thomas Carell, Hartmann Harz, Heinrich Leonhardt
The genome contains numerous regulatory elements that may undergo complex interactions and contribute to the establishment, maintenance, and change of cellular identity. Three-dimensional genome organization can be explored with fluorescence in situ hybridization (FISH) at the single-cell level, but the detection of small genomic loci remains challenging. Here, we provide a rapid and simple protocol
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Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability bioRxiv. Cell Biol. Pub Date : 2024-03-15 Ken Ishikawa, Saeko Soejima, Takashi Nishimura, Shigeaki Saitoh
The fission yeast, Schizosaccharomyces pombe, is an excellent eukaryote model organism to study essential biological processes. Its genome contains ~1200 genes essential for cell viability, most of which are evolutionarily conserved. To study these essential genes, resources enabling conditional perturbation of target genes are required. Here, we constructed comprehensive arrayed libraries of plasmids
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SARS-CoV-2 remodels the Golgi apparatus to facilitate viral assembly and secretion bioRxiv. Cell Biol. Pub Date : 2024-03-15 Jianchao Zhang, Andrew Kennedy, Daniel Macedo de Melo Jorge, Lijuan Xing, Whitney Reid, Sarah Bui, Joseph Joppich, Molly Rose, Sevval Ercan, Qiyi Tang, Andrew W. Tai, Yanzhuang Wang
The COVID-19 pandemic is caused by SARS-CoV-2, an enveloped RNA virus. Despite extensive investigation, the molecular mechanisms for its assembly and secretion remain largely elusive. Here, we show that SARS-CoV-2 infection induces global alterations of the host endomembrane system, including dramatic Golgi fragmentation. SARS-CoV-2 virions are enriched in the fragmented Golgi. Disrupting Golgi function
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Deep super-resolution imaging of thick tissue using structured illumination with adaptive optics bioRxiv. Cell Biol. Pub Date : 2024-03-15 Jingyu Wang, Danail Stoychev, Mick Phillips, David Miguel Susano Pinto, Richard M Parton, Nick Hall, Josh Titlow, Ana Rita Faria, Matthew Wincott, Dalia Gala, Andreas Gerondopoulos, Niloufer Irani, Ian Dobbie, Lothar Schermelleh, Martin Booth, Ilan Davis
3D structured illumination microscopy (3D-SIM) doubles the resolution of fluorescence imaging in lateral and axial directions and increases contrast in both fixed and live specimens. However, 3D-SIM has so far not been widely applied to imaging deep in thick tissues due to its sensitivity to specimen-induced aberrations, making the method difficult to apply beyond 10 μm in depth. Furthermore, 3D-SIM
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Heparan sulfate dependent phase separation of CCL5 and its chemotactic activity bioRxiv. Cell Biol. Pub Date : 2024-03-15 Xiaolin Yu, Guangfei Duan, Pengfei Pei, Long Chen, Renji Gu, Wenrui Hu, Hongli Zhang, Yan-Dong Wang, LiLi Gong, Lihong Liu, Ting-Ting Chu, Jin-Ping Li, Shi-Zhong Luo
Secreted chemokines form concentration gradients in target tissues to control migratory directions and patterns of immune cells in response to inflammatory stimulation; however, how the gradients are formed is much debated. Heparan sulfate (HS) binds to chemokines and modulates their activities. In this study, we investigated the roles of HS in the gradient formation and chemoattractant activity of
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Systematic mutagenesis assay promotes comprehension of the strand-bias laws for mutations induced by oxidative DNA damage bioRxiv. Cell Biol. Pub Date : 2024-03-15 Hidehiko Kawai, Shungo Ebi, Ryusei Sugihara, Chiho Fujiwara, Yoshihiro Fujikawa, Shingo Kimura, Hiroyuki Kamiya
We have recently developed an efficient and sensitive method for analyzing mutations caused by various environmental and endogenous factors which utilizes nucleotide-barcoded supF shuttle vector libraries with a multiplexed NGS assay, referred to hereafter as supF NGS assay. Ionizing-radiation-induced cancer is known to be difficult to distinguish from spontaneous cancer, especially in the case of
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Transdifferentiation of fibroblasts into muscle cells to constitute cultured meat with tunable intramuscular fat deposition bioRxiv. Cell Biol. Pub Date : 2024-03-15 Tongtong Ma, Ruimin Ren, Jianqi Lv, Ruipeng Yang, Xinyi Zheng, Yang Hu, Guiyu Zhu, Heng Wang
Current studies on cultured meat mainly focused on the muscle tissue reconstruction in vitro, but lack the formation of intramuscular fat which is a crucial factor in determining taste, texture and nutritional contents. Therefore, incorporating fat into cultured meat is of superior value. In this study, we employed the myogenic/lipogenic transdifferentiation of chicken fibroblasts in 3D to produce
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Computational Tools for the Analysis of Meiotic Prophase I Images bioRxiv. Cell Biol. Pub Date : 2024-03-15 James Hugh Crichton, Ian R Adams
Prophase I is a remarkable stage of meiotic division during which homologous chromosomes pair together and exchange DNA by meiotic recombination. Fluorescence microscopy of meiotic chromosome spreads is a central tool in the study of this process, with chromosome axis proteins being visualised as extended filaments upon which recombination proteins localise in focal patterns. Chromosome pairing and
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The polarity protein Yurt associates with the plasma membrane via basic and hydrophobic motifs embedded in its FERM domain bioRxiv. Cell Biol. Pub Date : 2024-03-15 Clemence L. Gamblin, Charles Alende, Francois Corriveau, Alexandra Jette, Frederique Parent-Prevost, Cornelia Biehler, Nathalie Majeau, Melanie Laurin, Patrick Laprise
The subcellular distribution of the polarity protein Yrt is subjected to a spatio-temporal regulation in D. melanogaster embryonic epithelia. After cellularization, Yrt binds to the lateral membrane of ectodermal cells and maintains this localization throughout embryogenesis. During terminal differentiation of the epidermis, Yrt accumulates to septate junctions and is also recruited to the apical domain
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FHOD-1/profilin-mediated actin assembly protects sarcomeres against contraction-induced deformation in C. elegans bioRxiv. Cell Biol. Pub Date : 2024-03-15 Michael J. Kimmich, Sumana Sundaramurthy, Meaghan A. Geary, Leila Lesanpezeshki, Curtis V. Yingling, Siva A. Vanapalli, Ryan S. Littlefield, David Pruyne
Formin HOmology Domain 2-containing (FHOD) proteins are a subfamily of actin-organizing formins that are important for proper striated muscle development in many animals. We had shown previously that absence of the sole FHOD protein, FHOD-1, in C. elegans results in thin body-wall muscles with misshapen dense bodies, structures that serve as sarcomere Z-lines in body-wall muscle. However, the mechanism
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The Dystrophin-Dystroglycan complex ensures cytokinesis efficiency in Drosophila epithelia bioRxiv. Cell Biol. Pub Date : 2024-03-14 Margarida Goncalves, Catarina Lopes, Herve Alegot, Mariana Osswald, Floris Bosveld, Carolina Ramos, Graziella Richard, Yohanns Bellaiche, Vincent Mirouse, Eurico Morais-de-Sa
Cytokinesis physically separates daughter cells at the end of cell division. This step is particularly challenging for epithelial cells, which are connected to their neighbors and to the extracellular matrix by transmembrane protein complexes. To systematically evaluate the impact of the cell adhesion machinery on epithelial cytokinesis efficiency, we performed an RNAi-based modifier screen in the
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Regulation of Versican Expression in Macrophages is Mediated by Canonical Type I Interferon Signaling via ISGF3 bioRxiv. Cell Biol. Pub Date : 2024-03-14 Mary Y. Chang, Christina K. Chan, Jourdan E. Brune, Anne Manicone, Karol Bomsztyk, Charles W. Frevert, William A. Altemeier
Growing evidence supports a role for versican as an important component of the inflammatory response, with both pro- and anti-inflammatory roles depending on the specific context of the system or disease under investigation. Our goal is to understand the regulation of macrophage-derived versican and the role it plays in innate immunity. In previous work, we showed that LPS triggers a signaling cascade
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DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2 bioRxiv. Cell Biol. Pub Date : 2024-03-14 Csenge K Rezi, Mariam Aslanyan, Gaurav D Diwan, Tao Cheng, Mohamed Chamlali, Katrin Junger, Zeinab Anvarian, esben lorentzen, Kleo B Pauly, Yasmin Bahadori, Eduardo FA Fernandes, Feng Qian, Sebastien Tosi, Soren T Christensen, Stine F Pedersen, Kristian Stromgaard, Robert B Russell, Jeffrey H Miner, Moe R Mahjoub, Karsten Boldt, Ronald Roepman, Lotte B Pedersen
Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney caused ciliary elongation and cystogenesis, and cell-based proximity
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Multivalent 28S rRNA Is the Organizer of the Nucleolus's Multi-layered Architecture bioRxiv. Cell Biol. Pub Date : 2024-03-14 Jieli Wei, Yize Zhang, Bingcheng Ye, Xueyuan Fan, Yucen Hu, ShengQ Xiang, Weirui Ma
The nucleolus widely exists in all eukaryotic species. Throughout evolution, two types of nucleoli have emerged: bipartite, which has two-layered subcompartments, and tripartite, which features three nested sub-compartments: granular component (GC), dense fibrillar component (DFC), and fibrillar center (FC). FC and DFC form a core-shell architecture and are immersed by a large GC. However, factors
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SuperResNET single molecule localization microscopy model-free network analysis of Nup96 achieves molecular resolution bioRxiv. Cell Biol. Pub Date : 2024-03-13 Y. Lydia Li, Ismail M Khater, Christian Hallgrimson, Ben Cardoen, Timothy H Wong, Ghassan Hamarneh, Ivan R Nabi
SuperResNET is an integrated machine learning-based image analysis software for visualizing and quantifying 3D point cloud localization data acquired by single molecule localization microscopy (SMLM). The computational modules of SuperResNET include correction for multiple blinking of a single fluorophore, followed by denoising, segmentation (clustering), and feature extraction, which are then used
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Bacterial RNA promotes proteostasis through inter-tissue communication in C. elegans bioRxiv. Cell Biol. Pub Date : 2024-03-13 Emmanouil Kyriakakis, Chiara Medde, Danilo Ritz, Geoffrey Fucile, Alexander Schmidt, Anne Spang
Life expectancy has been increasing over the last decades, which is not matched by an increase in healthspan. Besides genetic composition, environmental and nutritional factors influence both health- and lifespan. Diet is thought to be a major factor for healthy ageing. Here, we show that dietary RNA species extend healthspan in C. elegans. Inherent bacterial-derived double stranded RNA reduces protein
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Chemical inhibition of the integrated stress response impairs the ubiquitin-proteasome system bioRxiv. Cell Biol. Pub Date : 2024-03-13 Shanshan Xu, Maria E Gierisch, Enrica Barchi, Ina Poser, Simon Alberti, Florian A Salomons, Nico P Dantuma
The Integrated Stress Response Inhibitor (ISRIB) is an experimental compound that has been used to explore the potential beneficial effects of reducing the activation of the integrated stress response (ISR). As the ISR is a protective response, there is, however, a risk that its inhibition may compromise the cell's ability to restore protein homeostasis. Here, we show that ISRIB treatment impairs degradation
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Engineered Migrasomes: A Robust, Thermally Stable Vaccination Platform bioRxiv. Cell Biol. Pub Date : 2024-03-14 Dongju Wang, Haifang Wang, Wei Wan, Zihui Zhu, Takami Sho, Yi Zheng, Xing Zhang, Longyu Dou, Qiang Ding, Li Yu, Zhihua Liu
The burgeoning abilities of pathogens and tumor cells to evade immune responses underscore the urgent need for innovative vaccination platforms based on a variety of biological mechanisms. The current logistical challenges associated with cold-chain (i.e. low-temperature) transportation particularly impacts access to vaccines in the global south. We recently discovered organelles called migrasomes
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Visualizing histone H4K20me1 in knock-in mice expressing the mCherry-tagged modification-specific intracellular antibody bioRxiv. Cell Biol. Pub Date : 2024-03-14 Yuko Sato, Maoko Takenoshita, Miku Ueoka, Jun Ueda, Kazuo Yamagata, Hiroshi Kimura
During development and differentiation, histone modifications dynamically change locally and globally, associated with transcriptional regulation, DNA replication and repair, and chromosome condensation. The level of histone H4 Lys20 monomethylation (H4K20me1) increases during the G2 to M phases of the cell cycle and is enriched in facultative heterochromatin, such as inactive X chromosomes in cycling
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Cell surface morphology mimicking nano-bio platform for immune cell stimulation bioRxiv. Cell Biol. Pub Date : 2024-03-13 Beena Varghese, Jose Alfredo Gonzalez-Navarro, Valentino Libero Pio Guerra, Margarita Faizulina, Daria Artemieva, Tomas Chum, Tejaswini Rama Bangalore Ramakrishna, Marek Cebecauer, Petr Kovaricek
Studying the complex realm of cellular communication and interactions by fluorescence microscopy requires sample fixation on a transparent substrate. To activate T cells, which are pivotal in controlling the immune system, it is important to present the activating antigen in a spatial arrangement similar to the nature of the antigen-presenting cell, including the presence of ligands on microvilli.
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Toward generalizable phenotype prediction from single-cell morphology representations bioRxiv. Cell Biol. Pub Date : 2024-03-13 Jenna Tomkinson, Roshan Kern, Cameron Mattson, Gregory P Way
Functional cell processes (e.g., molecular signaling, response to environmental stimuli, mitosis, etc.) impact cell phenotypes, which scientists can easily and robustly measure with cell morphology. However, linking these morphology measurements with phenotypes remains challenging because biologically interpretable phenotypes require manually annotated labels. Automatic phenotype annotation from cell
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Phosphoproteomic analysis reveals the diversity of signaling behind ErbB inhibitor-induced phenotypes bioRxiv. Cell Biol. Pub Date : 2024-03-13 Katri Mataleena Vaparanta, Anne Jokilammi, Johannes Merilahti, Johanna Orling, Noora Virtanen, Cecilia Sahlgren, Klaus Elenius, Ilkka Paatero
The impact of kinase inhibitors on the phosphoproteome has been rarely investigated at a whole organism level. Here we performed a phosphoproteomic analysis in embryonic zebrafish to identify the signaling pathways perturbed by ErbB receptor tyrosine kinase inhibitors at the organism level. The phosphorylation of proteins associated with the PI3K/Akt, p38 MAPK, Notch, Hippo/Yap and beta-catenin signaling
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Border-zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration bioRxiv. Cell Biol. Pub Date : 2024-03-13 Florian Constanty, Bailin Wu, Ke-Hsuan Wei, I-Ting Lin, Julia Dallmann, Stefan Guenther, Till Lautenschlaeger, Rashmi Priya, Shih-Lei Lai, Didier Y.R. Stainier, Arica Beisaw
Despite numerous advances in our understanding of zebrafish cardiac regeneration, an aspect that remains less studied is how regenerating cardiomyocytes invade, and eventually replace, the collagen-containing fibrotic tissue following injury. Here, we provide an in-depth analysis of the process of cardiomyocyte invasion using live-imaging and histological approaches. We observed close interactions
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Autophagosome turnover requires Arp2/3 complex-mediated maintenance of lysosomal integrity bioRxiv. Cell Biol. Pub Date : 2024-03-13 Corey Theodore, Lianna Wagner, Ken Campellone
Autophagy is an intracellular degradation process that maintains homeostasis, responds to stress, and plays key roles in the prevention of aging and disease. Autophagosome biogenesis, vesicle rocketing, and autolysosome tubulation are controlled by multiple actin nucleation factors, but the impact of actin assembly on completion of the autophagic pathway is not well understood. Here we studied autophagosome
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Katanin, kinesin-13 and ataxin-2 inhibit premature interaction between maternal and paternal genomes in C. elegans zygotes bioRxiv. Cell Biol. Pub Date : 2024-03-13 Elizabeth A Beath, Cynthia Bailey, Meghana Mahantesh Magadam, Shuyan Qiu, Karen Perry L McNally, Francis J McNally
Fertilization occurs before completion of oocyte meiosis in the majority of animal species and sperm contents move long distances within zygotes of mouse and C. elegans. If incorporated into the meiotic spindle, paternal chromosomes could be expelled into a polar body resulting in lethal monosomy. Through live imaging of fertilization in C. elegans, we found that the microtubule disassembling enzymes
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Mesenchymal stromal cell chondrogenesis under ALK1/2/3-specific BMP inhibition: A revision of the prohypertrophic signalling network concept bioRxiv. Cell Biol. Pub Date : 2024-03-13 Solvig Diederichs, Simon I Dreher, Sarah-Anna Nueesch, Sven Schmidt, Christian Merle, Wiltrud Richter
Background: In vitro chondrogenesis of mesenchymal stromal cells (MSCs) driven by the essential chondro-inducer transforming growth factor (TGF)-β is instable and yields undesired hypertrophic cartilage predisposed to bone formation in vivo. TGF-β can non-canonically activate bone morphogenetic protein-associated ALK1/2/3 receptors. These have been accused of driving hypertrophic MSC misdifferentiation
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Functional genetics reveals modulators of anti-microtubule drug sensitivity bioRxiv. Cell Biol. Pub Date : 2024-03-13 Kuan-Chung Su, Elena Radul, Nolan K Maier, Mary-Jane Tsang, Claire S Goul, Brittania Moodie, Heather R Keys, Iain M Cheeseman
Microtubules play essential roles in diverse cellular processes and are important pharmacological targets for treating human disease. Here, we sought to identify cellular factors that modulate the sensitivity of cells to anti-microtubule drugs. We conducted a genome-wide CRISPR/Cas9-based functional genetics screen in human cells treated with the microtubule-destabilizing drug nocodazole or the mi
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A Novel Cell Culture Scratch Assay Platform Generates Reproducible Gaps for Quantitative Cell Movement-Based Studies bioRxiv. Cell Biol. Pub Date : 2024-03-12 Nicholas Wolpert, Lauren S Gollahon
Scratch assays are routinely performed for multiple research applications in cell biology (i.e., migration, metastasis, repair mechanisms, etc.). Conventional scratches are usually generated with pipette tips. User inconsistencies and varying pipette tips are major obstacles to reproducibility and quantitative power. Here, we present a novel, scratch/gap generating, cell culture plate-based, platform
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A Microphysiological HHT-on-a-Chip Platform Recapitulates Patient Vascular Lesions bioRxiv. Cell Biol. Pub Date : 2024-03-12 Jennifer Fang, Christopher J. Hatch, Jillian Andrejecsk, William Van Trigt, Damie J. Juat, Yu-Hsi Chen, Satomi Matsumoto, Abraham P. Lee, Christopher C Hughes
Hereditary Hemorrhagic Telangiectasia (HHT) is a rare congenital disease in which fragile vascular malformations focally develop in multiple organs. These can be small (telangiectasias) or large (arteriovenous malformations, AVMs) and may rupture leading to frequent, uncontrolled bleeding. There are few treatment options and no cure for HHT. Most HHT patients are heterozygous for loss-of-function mutations
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Effect of Electroacupuncture Pretreatment on Cognitive Impairment and Mitophagy in Aging Model Rats and its mechanism bioRxiv. Cell Biol. Pub Date : 2024-03-12 Biyong Liu, Tiantian Tan, Jianmin Liu, Zhijie Li, Su Qiu, Chengkai Xiong, Qing Liu, Jialin Li, Yihong Li, Qunhu Feng
Abstract: Objective Investigate the effects of "Shuanggu Yitong" EA pretreatment on cognitive impairment, mitochondrial function, and mitophagy in aging model rats, and to analyze the related mechanisms. Methods: Forty 3-month-old male SD rats were randomly divided into a blank group, a model group, an EA group, and a sham EA group, with 10 rats in each group. And the Morris water maze test was performed
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Regulation of Interstitial Lung Diseases by Pulmonary Endothelial Cells via PLVAP bioRxiv. Cell Biol. Pub Date : 2024-03-12 Xin Zhang, Liping Jia, Ruijie Hou, Yue-an Zhao, Liangliang Zhang, Xia Tong, Yan Mo, Lanlan Zhang
The lack of standardized treatments for Idiopathic Pulmonary Fibrosis (IPF) and non-IPF progressive fibrotic interstitial lung diseases (non-IPF-PF) highlights the need for identifying common therapeutic targets. We utilize single-cell RNA sequencing data from six disease groups, including IPF and non-IPF-PF such as Sarcoidosis, Systemic Sclerosis (SSc), Non-Specific Interstitial Pneumonitis (NSIP)
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Establishing a method for the cryopreservation of viable peripheral blood mononuclear cells in the International Space Station bioRxiv. Cell Biol. Pub Date : 2024-03-12 Hiroto Ishii, Rin Endo, Sanae Hamanaka, Nobuyuki Hidaka, Maki Miyauchi, Naho Hagiwara, Takahisa Miyao, Tohru Yamamori, Tatsuya Aiba, Nobuko Akiyama, Taishin Akiyama
The analysis of cells frozen within the International Space Station (ISS) will provide crucial insights into the impact of the space environment on cellular functions and properties. The objective of this study was to develop a method for cryopreserving blood cells under the specific constraints of the ISS. In a ground experiment, mouse blood was directly mixed with a cryoprotectant and gradually frozen
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Regulatory Dynamics of Sch9 in Response to Cytosolic Acidification: From Spatial Reconfiguration to Cellular Adaptation to Stresses bioRxiv. Cell Biol. Pub Date : 2024-03-12 Rui Fujii, Eigo Takeda, Eisuke Itakura, Akira Matsuura
The regulation of cellular metabolism in response to intracellular and extracellular conditions is critical for cell survival. In Saccharomyces cerevisiae, Sch9 is a well-established substrate of the target of rapamycin complex 1 (TORC1) and regulates metabolic pathways and stress responses. Sch9 is enriched on the vacuolar membrane through binding to PI(3,5)P2, and this localization is essential for
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Requirement of Nek2a and cyclin A2 for Wapl-dependent removal of cohesin from prophase chromatin bioRxiv. Cell Biol. Pub Date : 2024-03-12 Susanne Hellmuth, Olaf Stemmann
Sister chromatid cohesion is mediated by the cohesin complex. In mitotic prophase cohesin is removed from chromosome arms in a Wapl- and phosphorylation-dependent manner. Sgo1-PP2A protects pericentromeric cohesion by dephosphorylation of cohesin and its associated Wapl antagonist sororin. However, Sgo1-PP2A relocates to inner kinetochores well before sister chromatids are separated by separase, leaving
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A Fully-Automated Senescence Test (FAST) for the high-throughput quantification of senescence-associated markers bioRxiv. Cell Biol. Pub Date : 2024-03-12 Francesco Neri, Selma N Takajjart, Chad A Lerner, Pierre-Yves Desprez, Birgit Schilling, Judith Campisi, Akos A Gerencser
Cellular senescence is a major driver of aging and age-related diseases. Quantification of senescent cells remains challenging due to the lack of senescence-specific markers and generalist, unbiased methodology. Here, we describe the Fully-Automated Senescence Test (FAST), an image-based method for the high-throughput, single-cell assessment of senescence in cultured cells. FAST quantifies three of
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DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS bioRxiv. Cell Biol. Pub Date : 2024-03-12 Evan Michael Appleton, Kyunghee Hong, Cristina Rodriguez-Caycedo, Yoshiaki Tanaka, Asaf Ashkenazy-Titelman, Ketaki Bhide, Cody Rasmussen-Ivey, Xochitl Ambriz-Pena, Nataly Korover, Hao Bai, Ana Quieroz, Jorgen Nelson, Grishma Rathod, Gregory Knox, Miles Morgan, Nandini Malviya, Kairui Zhang, Brody McNutt, James Kehler, Amanda Kowalczyk, Austin Bow, Bryan McLendon, Brandi L Cantarel, Matt James, Christopher
The crisis of biodiversity loss in the anthropogenic era requires new tools for studying non-model organisms. Elephants, for example, are both an endangered species and excellent models studying complex phenotypes like size, social behavior, and longevity, but they remain severely understudied. Here we report the first derivation of elephant (Elephas maximus) induced pluripotent stem cells (emiPSCs)
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Novel Ser74 of NF-kappaB/CgIkappaBalpha Phosphorylated by MAPK/ERK Regulates Temperature Adaptation in Oysters bioRxiv. Cell Biol. Pub Date : 2024-03-12 Li Li, Chaogang Wang, Zhuxiang Jiang, Mingyang Du, Rihao Cong, Wei Wang, Taiping Zhang, Jincheng Chen, Guofan Zhang
Phosphorylation of IkappaBalpha at Ser32 and Ser36 by IKKs during biotic stress triggers its ubiquitin-proteasome degradation, causing to the nuclear translocation of REL, representing a key cascade mechanism in metazoans conserved and immune core signaling pathway, NF-kappaB. However, studies on its response to abiotic stress and signal transduction by phosphorylation in mollusks are lacking. Here
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Cytokine and Chemokine Receptor Profiles in Adipose Tissue Vasculature Unravel Endothelial Cell Responses in HIV bioRxiv. Cell Biol. Pub Date : 2024-03-12 Laventa M. Obare, Stephen Priest, Anas Ismael, Mona Mashayekhi, Xiuqi Zhang, Lindsey Stolze, Quanhu Sheng, Zer Vue, Kit Neikirk, Heather Beasley, Curtis Gabriel, Tecla Temu, Sara Gianella, Simon Mallal, John Koethe, Antentor Hinton, Samuel Bailin, Celestine N Wanjalla
Chronic systemic inflammation contributes to a substantially elevated risk of myocardial infarction in people living with HIV (PLWH). Endothelial cell dysfunction disrupts vascular homeostasis regulation, increasing the risk of vasoconstriction, inflammation, and thrombosis that contribute to cardiovascular disease. Our objective was to study the effects of plasma from PLWH on endothelial cell (EC)