Top 10 Biorxiv Papers Today in Cell Biology


2.143 Mikeys
#1. Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses
Rylie B Walsh, Agata N Becalska, Matthew J Zunitch, Shiyu Wang, Berith Isaac, Anna Yeh, Kate Koles, Avital A Rodal
Neuronal extracellular vesicles (EVs) play critical roles in intercellular communication and in propagation of pathogenic proteins in neurological disease. However, little is known about how cargoes are selectively packaged into neuronal EVs. Here, we examined the intracellular traffic and release of the EV cargoes Amyloid Precursor Protein (APP) and Synaptotagmin-4 (Syt4) at presynaptic nerve terminals of Drosophila motor neurons. We found that loss of the endosomal retromer complex leads to increased EV cargo levels both presynaptically and in EVs, and that this function is separable from previously identified roles of neuronal retromer. Conversely, EV cargo levels are reduced in rab11 mutants, and EV cargo sorting depends on a balance between Rab11-mediated recycling and retromer-dependent removal from the EV pathway. Rab11 and retromer have previously been implicated in Alzheimer's Disease, suggesting that these competing pathways may serve as therapeutic targets for limiting accumulation and release of toxic EV cargoes.
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biorxivpreprint: Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses https://t.co/UiMEOodOFm #bioRxiv
biorxiv_cellbio: Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses https://t.co/w0w2vlKYsL #biorxiv_cellbio
sbotlite: RT @biorxivpreprint: Opposing functions for retromer and Rab11 in extracellular vesicle cargo traffic at synapses https://t.co/UiMEOodOFm…
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Sample Sizes : [8]
Authors: 8
Total Words: 16803
Unqiue Words: 4918

2.088 Mikeys
#2. Changes in the expression of mitochondrial morphology-related genes during the differentiation of murine embryonic stem cells
Jeong Eon Lee, Bong Jong Seo, Min Ji Han, Yean Ju Hong, Kwonho Hong, Hyuk Song, Jeong Woong Lee, Jeong Tae Do
During embryonic development, cells undergo changes in gene expression, signaling pathway activation/inactivation, metabolism, and intracellular organelle structures, which are mediated by mitochondria. Mitochondria continuously switch their morphology between elongated tubular and fragmented globular via mitochondrial fusion and fission. Mitochondrial fusion is mediated by proteins encoded by Mfn1, Mfn2, and Opa1, whereas mitochondrial fission is mediated by proteins encoded by Fis1 and Dmn1L. Here, we investigated the expression patterns of mitochondria-related genes during the differentiation of mouse embryonic stem cells (ESCs) in response to leukemia inhibitory factor (LIF) withdrawal. The expression of Mfn2 and Dnm1L was, as expected, increased and decreased, respectively. By comparing gene expression and mitochondrial morphology, we proposed an index that could precisely represent mitochondrial changes during the differentiation of pluripotent stem cells by analyzing the expression ratios of three fusion- and two...
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biorxivpreprint: Changes in the expression of mitochondrial morphology-related genes during the differentiation of murine embryonic stem cells https://t.co/EOG5ExxcXh #bioRxiv
biorxiv_cellbio: Changes in the expression of mitochondrial morphology-related genes during the differentiation of murine embryonic stem cells https://t.co/55OCTuy7oz #biorxiv_cellbio
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Authors: 8
Total Words: 0
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2.056 Mikeys
#3. Cellular and Molecular Probing of Intact Transparent Human Organs
Shan Zhau, Mihail Ivilinov Todorov, Ruiyao Cai, Hanno Steinke, Elisabeth Kemter, Eckhard Wolf, Jan Lipfert, Ingo Bechmann, Ali Erturk
Optical tissue transparency permits cellular and molecular investigation of complex tissues in 3D, a fundamental need in biomedical sciences. Adult human organs are particularly challenging for this approach, owing to the accumulation of dense and sturdy molecules in decades-aged human tissues. Here, we introduce SHANEL method utilizing a new tissue permeabilization approach to clear and label stiff human organs. We used SHANEL to generate the first intact transparent adult human brain and kidney, and perform 3D histology using antibodies and dyes in centimeters depth. Thereby, we revealed structural details of the sclera, iris and suspensory ligament in the human eye, and the vessels and glomeruli in the human kidney. We also applied SHANEL on transgenic pig organs to map complex structures of EGFP expressing beta cells in >10 cm size pancreas. Overall, SHANEL is a robust and unbiased technology to chart the cellular and molecular architecture of intact large mammalian organs.
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PromPreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/0WZ39Yu5qR
JimJohnsonSci: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
THebertMcGill: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
Astro_Erik: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
MathaCMU: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
MatthiasNahrend: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
ozgungokce: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
aklymchenko: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
KomaToug: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
LipfertLab: RT @PromPreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/0WZ39Yu5qR
cnombela: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
jordanyaron: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
TatsuyaCunshang: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
DenaxaMyrto: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
MarikaRuiyao: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
ssnaka: RT @biorxivpreprint: Cellular and Molecular Probing of Intact Transparent Human Organs https://t.co/2UWna3xCXQ #bioRxiv
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Sample Sizes : None.
Authors: 9
Total Words: 13486
Unqiue Words: 3837

2.023 Mikeys
#4. Dual role of Miro protein clusters in mitochondrial cristae organisation and ER-Mitochondria Contact Sites
Souvik Modi, Guillermo López-Doménech, Elise F Halff, Christian Covill-Cooke, Davor Ivankovic, Daniela Melandri, Lorena Arancibia-Cárcamo, Jemima J Burden, Alan R Lowe, Josef T Kittler
Mitochondrial Rho (Miro) GTPases localize to the outer mitochondrial membrane and are essential machinery for the regulated trafficking of mitochondria to defined subcellular locations. However, their sub-mitochondrial localization and relationship with other critical mitochondrial complexes remains poorly understood. Here, using super-resolution fluorescence microscopy, we report that Miro proteins form nanometer-sized clusters along the mitochondrial outer membrane in association with the Mitochondrial Contact Site and Cristae Organizing System (MICOS). Using knockout mouse embryonic fibroblasts (MEF) we show that Miro1 and Miro2 are required for normal mitochondrial cristae architecture and endoplasmic reticulum-mitochondria contacts sites (ERMCS). Further, we show that Miro couples MICOS to TRAK motor protein adaptors to ensure the concerted transport of the two mitochondrial membranes and the correct distribution of cristae on the mitochondrial membrane. The Miro nanoscale organization, association with MICOS complex and...
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biorxivpreprint: Dual role of Miro protein clusters in mitochondrial cristae organisation and ER-Mitochondria Contact Sites https://t.co/2DgYZNTTrZ #bioRxiv
biorxiv_cellbio: Dual role of Miro protein clusters in mitochondrial cristae organisation and ER-Mitochondria Contact Sites https://t.co/utkHNC2CON #biorxiv_cellbio
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Authors: 10
Total Words: 0
Unqiue Words: 0

2.017 Mikeys
#5. Inheritance of Chromatin Proteins in Budding Yeast: metabolic gene regulators TUP1, FPR4 and Rpd3L are retained in the mother cell.
Pauline Vasseur, Saphia Tonazzini, Francesc Rubert Castro, Iva Sucec, Khadija El Koulali, Serge Urbach, Marta Radman-Livaja
Asymmetric division is a prerequisite for cellular differentiation. Phenotypic transformation during differentiation is a poorly understood epigenetic phenomenon, in which chromatin theoretically plays a role. The assumption that chromatin components segregate asymmetrically in asymmetric divisions has however not been systematically tested. We have developed a live cell imaging method to measure how 18 chromatin proteins are inherited in asymmetric divisions of budding yeast. We show that abundant and moderately abundant maternal proteins segregate stochastically and symmetrically between the two cells with the exception of Rxt3, Fpr4 and Tup1, which are retained in the mother. Mother retention seems to be the norm for low abundance proteins with the exception of Sir2 and the linker histone H1. Our in vivo analysis of chromatin protein behavior in single cells highlights general trends in protein biology during the cell cycle such as coupled protein synthesis and decay, and a correlation between half-lives and cell cycle duration.
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biorxivpreprint: Inheritance of Chromatin Proteins in Budding Yeast: metabolic gene regulators TUP1, FPR4 and Rpd3L are retained in the mother cell. https://t.co/8782IvhpRx #bioRxiv
biorxiv_cellbio: Inheritance of Chromatin Proteins in Budding Yeast: metabolic gene regulators TUP1, FPR4 and Rpd3L are retained in the mother cell. https://t.co/2zClsXayu8 #biorxiv_cellbio
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Sample Sizes : [1000]
Authors: 7
Total Words: 5374
Unqiue Words: 1994

2.001 Mikeys
#6. Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control
Valentina Casa, Macarena Moronta Gines, Eduardo Gade Gusmao, Johan A. Slotman, Anne Zirkel, Natasa Josipovic, Edwin Oole, Wilfred F. J. van IJcken, Adriaan B. Houtsmuller, Argyris Papantonis, Kerstin S. Wendt
Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A and RAD21, cohesin contains in somatic cells one of two orthologous STAG subunits, SA1 or SA2. How these variable subunits affect the function of the cohesin complex is still unclear. SA1- and SA2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of SA1 and SA2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either SA1 or SA2. Following rapid depletion of either subunit, we perform high resolution Hi-C, RNA-sequencing and sequential ChIP studies to show that SA1 and SA2 do not co-occupy individual binding sites and have distinct ways how they affect looping and gene expression. These findings are supported at...
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binki2perdita: “Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control” Our preprint is now online https://t.co/nFbKJwojrv Exciting insights using Hi-C and single molecule localization! Great thanks to the Papantonis lab and all our collaborators!
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Authors: 11
Total Words: 20468
Unqiue Words: 6792

1.996 Mikeys
#7. Stirred Suspension Bioreactor Culture of Porcine Induced Pluripotent Stem Cells
Kyle Burrell, Rkia Dardari, Derek Toms, Taylor Goldsmith, Daniel Villagomez, Alan King, Mark Ungrin, Ina Dobrinski
Induced pluripotent stem cells (iPSCs) are an attractive cell source for regenerative medicine and the development of therapies, as they can proliferate indefinitely under defined conditions and differentiate into any cell type in the body. Large scale expansion of cells is limited in adherent culture, making it difficult to obtain adequate cell numbers for research. It has been previously shown that stirred suspension bioreactors (SSBs) can be used to culture mouse and human stem cells. Pigs are important pre-clinical models for stem cell research. Therefore, this study investigated the use of SSBs as an alternative culture method for the expansion of iPSCs. Using an established porcine iPSC line as well as a new cell line derived and characterized in the current study, we report that porcine iPSCs (piPSCs) can grow in SSB while maintaining characteristics of pluripotency and karyotypic stability similar to cells grown in traditional two-dimensional static culture. This culture method provides a suitable platform for scale up of...
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Sample Sizes : [5, 5, 462, 4, 3, 5, 5, 5, 5, 5, 5, 5, 3]
Authors: 8
Total Words: 9585
Unqiue Words: 3280

1.996 Mikeys
#8. Single-cell RNA-seq analysis reveals the crucial role of Collagen Triplex Helix Repeat Containing 1 (CTHRC1) cardiac fibroblasts for ventricular remodeling after myocardial infarction
Adrian Ruiz-Villalba, Juan P Romero, Silvia C Hernandez, Amaia Vilas-Zornoza, Nikolaus Fortelny, Laura Castro, Patxi San Martin-Uriz, Erika Lorenzo-Vivas, Paula Garcia-Olloqui, Marcel Palacios, Juan Jose Gavira, Gorka Bastarrika, Stefan Janssens, Elena Iglesias, Gloria Abizanda, Xabier Martinez de Morentin, Christoph Bock, Diego Alignani, Gema Medal, David Gomez-Cabrero, Igor Prudovsky, Yong-Ri Jin, Sergey Ryzkov, Haifeng Yin, Beatriz Pelacho, Volkhard Lindner, David Lara-Astiaso, Felipe Prosper
Cardiac fibroblasts have a central role during the ventricular remodeling process associated with different types of cardiac injury. Recent studies have shown that fibroblasts do not respond homogeneously to heart damage, suggesting that the adult myocardium may contain specialized fibroblast subgroups with specific functions. Due to the limited set of bona fide fibroblast markers, a proper characterization of fibroblast population dynamics in response to cardiac damage is still missing. Using single-cell RNA-seq, we identified and characterized a fibroblast subpopulation that emerges in response to myocardial infarction (MI) in a murine model. These activated fibroblasts exhibit a clear pro-fibrotic signature, express high levels of the hormone CTHRC1 and of the immunomodulatory co-receptor CD200 and localize to the injured myocardium. Combining epigenomic profiling with functional assays, we show Sox9 and the non-canonical TGF-β signaling as important regulators mediating their response to cardiac damage. We show that the...
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Authors: 28
Total Words: 11979
Unqiue Words: 3209

1.994 Mikeys
#9. Actin protrusions push on E-cadherin to maintain epithelial cell-cell adhesion
John Xiao He Li, Vivian W. Tang, William M. Brieher
Cadherin mediated cell-cell adhesion is actin dependent, but the precise role of actin in maintaining cell-cell adhesion is not fully understood. Actin polymerization-dependent protrusive activity is required to push distally separated cells close enough together to initiate contact. Whether protrusive activity is required to maintain adhesion in confluent sheets of epithelial cells is not known. By electron microscopy as well as live cell imaging, we have identified a population of protruding actin microspikes that operate continuously near apical junctions of polarized MDCK cells. Live imaging shows that microspikes containing E-cadherin extend into gaps between E-cadherin clusters on neighboring cells while reformation of cadherin clusters across the cell-cell boundary triggers microspike withdrawal. We identify Arp2/3, EVL, and CRMP-1 as three actin assembly factors necessary for microspike formation. Depleting these factors from cells using RNAi results in myosin II-dependent unzipping of cadherin adhesive bonds. Therefore,...
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Authors: 3
Total Words: 10017
Unqiue Words: 2820

1.968 Mikeys
#10. Ferroptosis is programmed by the coordinated regulation of glutathione and iron metabolism by BACH1
Hironari Nishizawa, Mitsuyo Matsumoto, Tomohiko Shindo, Daisuke Saigusa, Hiroki Kato, Katsushi Suzuki, Masaki Sato, Yusho Ishii, Hiroaki Shimokawa, Kazuhiko Igarashi
Ferroptosis is an iron-dependent programmed cell death resulting from alterations of metabolic processes. However, its regulation and physiological significance remain to be elucidated. By analyzing transcriptional responses of murine embryonic fibroblasts exposed to the ferroptosis-inducer erastin, we found that a set of genes related to oxidative stress protection was induced upon ferroptosis. We further showed that the transcription factor BACH1 promoted ferroptosis by repressing the expression of a subset of erastin-inducible genes involved in the synthesis of glutathione or metabolism of intracellular labile iron, including Gclm, Gclc, Slc7a11, Hmox1, Fth1, Ftl1, and Slc40a1. Compared with wild-type mice, Bach1-/- mice showed resistance to myocardial infarction, the seriousness of which was palliated by the iron-chelator deferasirox, which suppressed ferroptosis. Our findings suggest that ferroptosis is programmed at the transcriptional level to induce genes combating labile-iron-induced oxidative stress and executed upon...
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