Insights Into Calcium-Sensing Receptor Trafficking and Biased Signalling by Studies of Calcium Homeostasis
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The Wnt Pathway Scaffold Protein Axin Promotes Signaling Specificity by Suppressing Competing Kinase Reactions
bioRxiv preprint doi: https://doi.org/10.1101/768242; this version posted September 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The Wnt pathway scaffold protein Axin promotes signaling specificity by suppressing competing kinase reactions Maire Gavagan1,2, Erin Fagnan1,2, Elizabeth B. Speltz1, and Jesse G. Zalatan1,* 1Department of Chemistry, University of Washington, Seattle, WA 98195, USA 2These authors contributed equally to this work *Correspondence: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/768242; this version posted September 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract GSK3β is a multifunctional kinase that phosphorylates β-catenin in the Wnt signaling network and also acts on other protein targets in response to distinct cellular signals. To test the long-standing hypothesis that the scaffold protein Axin specifically accelerates β-catenin phosphorylation, we measured GSK3β reaction rates with multiple substrates in a minimal, biochemically-reconstituted system. We observed an unexpectedly small, ~2-fold Axin-mediated rate increase for the β-catenin reaction. The much larger effects reported previously may have arisen because Axin can rescue GSK3β from an inactive state that occurs only under highly specific conditions. -
CK1 Is Required for a Mitotic Checkpoint That Delays Cytokinesis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Current Biology 23, 1920–1926, October 7, 2013 ª2013 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2013.07.077 Report CK1 Is Required for a Mitotic Checkpoint that Delays Cytokinesis Alyssa E. Johnson,1 Jun-Song Chen,1 isoforms were detected, which collapsed into a discrete ladder and Kathleen L. Gould1,* upon phosphatase treatment (Figure 1A, lanes 1 and 2). These 1Department of Cell and Developmental Biology, Vanderbilt bands are ubiquitinated isoforms because they collapse into a University School of Medicine, Nashville, TN 37232, USA single band in the absence of dma1+ (Figure 1A, lane 4) and Dma1 is required for Sid4 ubiquitination [6]. In dma1D cells, a single slower-migrating form of Sid4 was detected, which Summary was collapsed by phosphatase treatment, indicating that Sid4 is phosphorylated in vivo (Figure 1A, lanes 3 and 4). In vivo Failure to accurately partition genetic material during cell radiolabeling experiments validated Sid4 as a phosphoprotein division causes aneuploidy and drives tumorigenesis [1]. and revealed that Sid4 is phosphorylated on serines and thre- Cell-cycle checkpoints safeguard cells from such catastro- onines (see Figures S1A–S1C available online). The constitu- phes by impeding cell-cycle progression when mistakes tive presence of an unmodified Sid4 isoform indicates that arise. FHA-RING E3 ligases, including human RNF8 [2] and only a subpopulation of Sid4 is modified (Figure 1A). Collec- CHFR [3] and fission yeast Dma1 [4], relay checkpoint signals tively, these data indicate that Sid4 is ubiquitinated and phos- by binding phosphorylated proteins via their FHA domains phorylated in vivo. -
Seq2pathway Vignette
seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway. -
Calcium Signaling at the Endoplasmic Reticulum Fine-Tuning Stress
Cell Calcium 70 (2018) 24–31 Contents lists available at ScienceDirect Cell Calcium journal homepage: www.elsevier.com/locate/ceca Review Calcium signaling at the endoplasmic reticulum: fine-tuning stress responses T ⁎ Amado Carreras-Suredaa,b,c, Philippe Pihána,b,c, Claudio Hetza,b,c,d,e, a Center for Geroscience, Brain Health and Metabolism, Faculty of Medicine, University of Chile, Chile b Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile c Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile d Buck Institute for Research on Aging, Novato, CA, 94945, USA e Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA ARTICLE INFO ABSTRACT Keywords: Endoplasmic reticulum (ER) calcium signaling is implicated in a myriad of coordinated cellular processes. The ER homeostasis ER calcium content is tightly regulated as it allows a favorable environment for protein folding, in addition to ER stress operate as a major reservoir for fast and specific release of calcium. Altered ER homeostasis impacts protein Calcium handling mechanisms folding, activating the unfolded protein response (UPR) as a rescue mechanism to restore proteostasis. ER cal- Calcium homeostasis cium release impacts mitochondrial metabolism and also fine-tunes the threshold to undergo apoptosis under Unfolded protein response chronic stress. The global coordination between UPR signaling and energetic demands takes place at mi- Mitochondrial associated membranes Mitochondria biology tochondrial associated membranes (MAMs), specialized subdomains mediating interorganelle communication. Here we discuss current models explaining the functional relationship between ER homeostasis and various cellular responses to coordinate proteostasis and metabolic maintenance. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Impact of Digestive Inflammatory Environment and Genipin
International Journal of Molecular Sciences Article Impact of Digestive Inflammatory Environment and Genipin Crosslinking on Immunomodulatory Capacity of Injectable Musculoskeletal Tissue Scaffold Colin Shortridge 1, Ehsan Akbari Fakhrabadi 2 , Leah M. Wuescher 3 , Randall G. Worth 3, Matthew W. Liberatore 2 and Eda Yildirim-Ayan 1,4,* 1 Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH 43606, USA; [email protected] 2 Department of Chemical Engineering, College of Engineering, University of Toledo, Toledo, OH 43606, USA; [email protected] (E.A.F.); [email protected] (M.W.L.) 3 Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH 43614, USA; [email protected] (L.M.W.); [email protected] (R.G.W.) 4 Department of Orthopaedic Surgery, University of Toledo Medical Center, Toledo, OH 43614, USA * Correspondence: [email protected]; Tel.: +1-419-530-8257; Fax: +1-419-530-8030 Abstract: The paracrine and autocrine processes of the host response play an integral role in the success of scaffold-based tissue regeneration. Recently, the immunomodulatory scaffolds have received huge attention for modulating inflammation around the host tissue through releasing anti- inflammatory cytokine. However, controlling the inflammation and providing a sustained release of anti-inflammatory cytokine from the scaffold in the digestive inflammatory environment are predicated upon a comprehensive understanding of three fundamental questions. (1) How does the Citation: Shortridge, C.; Akbari release rate of cytokine from the scaffold change in the digestive inflammatory environment? (2) Fakhrabadi, E.; Wuescher, L.M.; Can we prevent the premature scaffold degradation and burst release of the loaded cytokine in the Worth, R.G.; Liberatore, M.W.; digestive inflammatory environment? (3) How does the scaffold degradation prevention technique Yildirim-Ayan, E. -
Calcium Signaling in Aging and Neurodegenerative Diseases 2019
International Journal of Molecular Sciences Meeting Report Calcium Signaling in Aging and Neurodegenerative Diseases 2019 Luísa Cortes 1,2 , João Malva 2,3,4, Ana Cristina Rego 1,2,3 and Cláudia F. Pereira 1,2,3,* 1 Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Rua Larga, Faculty of Medicine, Polo I, 1st floor, 3004-504 Coimbra, Portugal; [email protected] (L.C.); [email protected] (A.C.R.) 2 CIBB-Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Rua Larga, Faculty of Medicine, Polo I, 1st floor, 3004-504 Coimbra, Portugal; [email protected] 3 Faculty of Medicine, Azinhaga de Santa Comba, Celas, 3000-548 Coimbra, Portugal 4 iCRB- Coimbra Institute for Clinical and Biomedical Research; Azinhaga de Santa Comba, Celas, 3000-548 Coimbra, Portugal * Correspondence: [email protected] Received: 28 December 2019; Accepted: 4 February 2020; Published: 7 February 2020 Abstract: The European Calcium Society (ECS) workshop, which is held every 2 years, is a dedicated meeting of scientists interested in the elucidation of the action of calcium binding, calcium signaling and the study of proteins and organelles, such as mitochondria and endoplasmic reticulum, thereby involved, either in health and disease conditions. The 8th edition of the ECS workshop was organized by a group of researchers from the University of Coimbra, Portugal, in close collaboration with ECS board members. Thanks to the central role of “Calcium Signaling in Aging and Neurodegenerative Disorders”, the ECS 2019 workshop was attended by 62 experts who presented their results in a plenary lecture and five regular symposia, two oral communication sessions and two poster sessions, followed by a hands-on session on calcium imaging. -
Table S2.Up Or Down Regulated Genes in Tcof1 Knockdown Neuroblastoma N1E-115 Cells Involved in Differentbiological Process Anal
Table S2.Up or down regulated genes in Tcof1 knockdown neuroblastoma N1E-115 cells involved in differentbiological process analysed by DAVID database Pop Pop Fold Term PValue Genes Bonferroni Benjamini FDR Hits Total Enrichment GO:0044257~cellular protein catabolic 2.77E-10 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 537 13588 1.944851 8.64E-07 8.64E-07 5.02E-07 process ISG15, ATG7, PSENEN, LOC100046898, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, ASB8, DCUN1D1, PSMA6, SIAH1A, TRIM32, RNF138, GM12396, RNF20, USP17L5, FBXO11, RAD23B, NEDD8, UBE2V2, RFFL, CDC GO:0051603~proteolysis involved in 4.52E-10 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 534 13588 1.93519 1.41E-06 7.04E-07 8.18E-07 cellular protein catabolic process ISG15, ATG7, PSENEN, LOC100046898, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, ASB8, DCUN1D1, PSMA6, SIAH1A, TRIM32, RNF138, GM12396, RNF20, USP17L5, FBXO11, RAD23B, NEDD8, UBE2V2, RFFL, CDC GO:0044265~cellular macromolecule 6.09E-10 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 609 13588 1.859332 1.90E-06 6.32E-07 1.10E-06 catabolic process ISG15, RBM8A, ATG7, LOC100046898, PSENEN, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, ASB8, DCUN1D1, PSMA6, SIAH1A, TRIM32, RNF138, GM12396, RNF20, XRN2, USP17L5, FBXO11, RAD23B, UBE2V2, NED GO:0030163~protein catabolic process 1.81E-09 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 556 13588 1.87839 5.64E-06 1.41E-06 3.27E-06 ISG15, ATG7, PSENEN, LOC100046898, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, -
Crosstalk Between Casein Kinase II and Ste20-Related Kinase Nak1
University of Massachusetts Medical School eScholarship@UMMS GSBS Student Publications Graduate School of Biomedical Sciences 2013-03-05 Crosstalk between casein kinase II and Ste20-related kinase Nak1 Lubos Cipak University of Vienna Et al. Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_sp Part of the Biochemistry Commons, Cell Biology Commons, Cellular and Molecular Physiology Commons, and the Molecular Biology Commons Repository Citation Cipak L, Gupta S, Rajovic I, Jin Q, Anrather D, Ammerer G, McCollum D, Gregan J. (2013). Crosstalk between casein kinase II and Ste20-related kinase Nak1. GSBS Student Publications. https://doi.org/ 10.4161/cc.24095. Retrieved from https://escholarship.umassmed.edu/gsbs_sp/1850 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Student Publications by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. EXTRA VIEW Cell Cycle 12:6, 884–888; March 15, 2013; © 2013 Landes Bioscience Crosstalk between casein kinase II and Ste20-related kinase Nak1 Lubos Cipak,1,2,† Sneha Gupta,3,† Iva Rajovic,1 Quan-Wen Jin,3,4 Dorothea Anrather,1 Gustav Ammerer,1 Dannel McCollum3,* and Juraj Gregan1,5,* 1Max F. Perutz Laboratories; Department of Chromosome Biology; University of Vienna; Vienna, Austria; 2Cancer Research Institute; Slovak Academy of Sciences; Bratislava, Slovak Republic; 3Department of Microbiology and Physiological Systems and Program in Cell Dynamics; University of Massachusetts Medical School; Worcester, MA USA; 4Department of Biological Medicine; School of Life Sciences; Xiamen University; Xiamen, China; 5Department of Genetics; Comenius University; Bratislava, Slovak Republic †These authors contributed equally to this work. -
Electrical Synaptic Transmission Requires a Postsynaptic Scaffolding Protein
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.03.410696; this version posted December 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. TITLE: Electrical synaptic transmission requires a postsynaptic scaffolding protein Abagael M. Lasseigne1*, Fabio A. Echeverry2*, Sundas Ijaz2*, Jennifer Carlisle Michel1*, E. Anne Martin1, Audrey J. Marsh1, Elisa Trujillo1, Kurt C. Marsden3, Alberto E. Pereda2#, Adam C. Miller1#@ * denotes co-first author # denotes co-corresponding author @ denotes lead contact Affiliations: 1 Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA 2 Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA 3 Department of Biological Sciences, NC State University, Raleigh, NC 27695, USA Correspondence: [email protected] [email protected] Keywords: gap junction; connexin; ZO1 ZO-1; synaptic development; electrical coupling 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.03.410696; this version posted December 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. SUMMARY Electrical synaptic transmission relies on neuronal gap junctions containing channels constructed by Connexins. While at chemical synapses neurotransmitter-gated ion channels are critically supported by scaffolding proteins, it is unknown if channels at electrical synapses require similar scaffold support. -
Ykt6 Membrane-To-Cytosol Cycling Regulates Exosomal Wnt Secretion
bioRxiv preprint doi: https://doi.org/10.1101/485565; this version posted December 3, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Ykt6 membrane-to-cytosol cycling regulates exosomal Wnt secretion Karen Linnemannstöns1,2, Pradhipa Karuna1,2, Leonie Witte1,2, Jeanette Kittel1,2, Adi Danieli1,2, Denise Müller1,2, Lena Nitsch1,2, Mona Honemann-Capito1,2, Ferdinand Grawe3,4, Andreas Wodarz3,4 and Julia Christina Gross1,2* Affiliations: 1Hematology and Oncology, University Medical Center Goettingen, Goettingen, Germany. 2Developmental Biochemistry, University Medical Center Goettingen, Goettingen, Germany. 3Molecular Cell Biology, Institute I for Anatomy, University of Cologne Medical School, Cologne, Germany 4Cluster of Excellence-Cellular Stress Response in Aging-Associated Diseases (CECAD), Cologne, Germany *Correspondence: Dr. Julia Christina Gross, Hematology and Oncology/Developmental Biochemistry, University Medical Center Goettingen, Justus-von-Liebig Weg 11, 37077 Goettingen Germany Abstract Protein trafficking in the secretory pathway, for example the secretion of Wnt proteins, requires tight regulation. These ligands activate Wnt signaling pathways and are crucially involved in development and disease. Wnt is transported to the plasma membrane by its cargo receptor Evi, where Wnt/Evi complexes are endocytosed and sorted onto exosomes for long-range secretion. However, the trafficking steps within the endosomal compartment are not fully understood. The promiscuous SNARE Ykt6 folds into an auto-inhibiting conformation in the cytosol, but a portion associates with membranes by its farnesylated and palmitoylated C-terminus. Here, we demonstrate that membrane detachment of Ykt6 is essential for exosomal Wnt secretion. -
Integrating Protein Copy Numbers with Interaction Networks to Quantify Stoichiometry in Mammalian Endocytosis
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis Daisy Duan1, Meretta Hanson1, David O. Holland2, Margaret E Johnson1* 1TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218. 2NIH, Bethesda, MD, 20892. *Corresponding Author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at various copy numbers within a cell, from hundreds (e.g. auxilin) to millions (e.g. clathrin). Between cell types with identical genomes, copy numbers further vary significantly both in absolute and relative abundance. These variations contain essential information about each protein’s function, but how significant are these variations and how can they be quantified to infer useful functional behavior? Here, we address this by quantifying the stoichiometry of proteins involved in the CME network. We find robust trends across three cell types in proteins that are sub- vs super-stoichiometric in terms of protein function, network topology (e.g.