Human ESCRT-III and VPS4 Proteins Are Required for Centrosome and Spindle Maintenance
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By Submitted in Partial Satisfaction of the Requirements for Degree of in In
Developments of Two Imaging based Technologies for Cell Biology Researches by Xiaowei Yan DISSERTATION Submitted in partial satisfaction of the requirements for degree of DOCTOR OF PHILOSOPHY in Biochemistry and Molecular Biology in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, SAN FRANCISCO Approved: ______________________________________________________________________________Ronald Vale Chair ______________________________________________________________________________Jonathan Weissman ______________________________________________________________________________Orion Weiner ______________________________________________________________________________ ______________________________________________________________________________ Committee Members Copyright 2021 By Xiaowei Yan ii DEDICATION Everything happens for the best. To my family, who supported me with all their love. iii ACKNOWLEDGEMENTS The greatest joy of my PhD has been joining UCSF, working and learning with such a fantastic group of scientists. I am extremely grateful for all the support and mentorship I received and would like to thank: My mentor, Ron Vale, who is such a great and generous person. Thank you for showing me that science is so much fun and thank you for always giving me the freedom in pursuing my interest. I am grateful for all the guidance from you and thank you for always supporting me whenever I needed. You are a person full of wisdom, and I have been learning so much from you and your attitude to science, science community and even life will continue inspire me. Thank you for being my mentor and thank you for being such a great mentor. Everyone else in Vale lab, past and present, for making our lab a sweet home. I would like to give my special thank to Marvin (Marvin Tanenbaum) and Nico (Nico Stuurman), two other mentors for me in the lab. I would like to thank them for helping me adapt to our lab, for all the valuable advice and for all the happiness during the time that we work together. -
Vps4b Heterozygous Mice Do Not Develop Tooth Defects That Replicate
Hu et al. BMC Genetics (2019) 20:7 https://doi.org/10.1186/s12863-018-0699-3 RESEARCH ARTICLE Open Access Vps4b heterozygous mice do not develop tooth defects that replicate human dentin dysplasia I Aiqin Hu1, Ting Lu1,2, Danna Chen1, Jin Huang1, Weiwei Feng1, Yanjun Li1, Dan Guo1, Xiangmin Xu1,3, Dong Chen1,4* and Fu Xiong1,3* Abstract Background: Vacuolar protein sorting-associated protein 4B (VPS4B) is a member of the ATP enzyme AAA protein family, and is mainly involved in protein degradation and cell membrane fusion. Recently, a dominant mutation in this gene was identified in human dentin dysplasia type I (DD-I). Herein, we report the generation of Vps4b knockout (Vps4b KO) mice; however, the homozygous Vps4b KO mutation was embryonic lethal at the early stages of embryo development, and we therefore report the results of heterozygous mutant mice. Results: Mice heterozygous for Vps4b did not develop tooth defects replicating human DD-I. Immunohistochemistry showed that gene KO was successful, as there was decreased expression of Vps4b in heterozygous mice; hematoxylin and eosin (H&E) staining also showed that the width of the pre-dentin zone was increased in heterozygous mice, although the arrangement of the odontoblasts was not significantly different from wild-type (WT) mice. However, H&E staining showed no obvious abnormalities in the bones of heterozygous mice. Moreover, stereomicroscopic and X-ray radiography results indicated no abnormal manifestations in teeth or bones. Furthermore, statistical analysis of the volume and density of dentin and enamel, as well as skeletal analysis, including the volume and separation of trabecular bone analyzed by micro-CT, all showed no differences between Vps4b heterozygotes and WT mice. -
The Endocytic Membrane Trafficking Pathway Plays a Major Role
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Liverpool Repository RESEARCH ARTICLE The Endocytic Membrane Trafficking Pathway Plays a Major Role in the Risk of Parkinson’s Disease Sara Bandres-Ciga, PhD,1,2 Sara Saez-Atienzar, PhD,3 Luis Bonet-Ponce, PhD,4 Kimberley Billingsley, MSc,1,5,6 Dan Vitale, MSc,7 Cornelis Blauwendraat, PhD,1 Jesse Raphael Gibbs, PhD,7 Lasse Pihlstrøm, MD, PhD,8 Ziv Gan-Or, MD, PhD,9,10 The International Parkinson’s Disease Genomics Consortium (IPDGC), Mark R. Cookson, PhD,4 Mike A. Nalls, PhD,1,11 and Andrew B. Singleton, PhD1* 1Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain 3Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 4Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 5Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom 6Department of Pathophysiology, University of Tartu, Tartu, Estonia 7Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 8Department of Neurology, Oslo University Hospital, Oslo, Norway 9Department of Neurology and Neurosurgery, Department of Human Genetics, McGill University, Montréal, Quebec, Canada 10Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada 11Data Tecnica International, Glen Echo, Maryland, USA ABSTRACT studies, summary-data based Mendelian randomization Background: PD is a complex polygenic disorder. -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
The Function and Mechanism of Chmp1a in Tumor Development
Marshall University Marshall Digital Scholar Theses, Dissertations and Capstones 1-1-2008 The uncF tion and Mechanism of Chmp1A in Tumor Development Jing Li [email protected] Follow this and additional works at: http://mds.marshall.edu/etd Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons, and the Oncology Commons Recommended Citation Li, Jing, "The unctF ion and Mechanism of Chmp1A in Tumor Development" (2008). Theses, Dissertations and Capstones. Paper 120. This Thesis is brought to you for free and open access by Marshall Digital Scholar. It has been accepted for inclusion in Theses, Dissertations and Capstones by an authorized administrator of Marshall Digital Scholar. For more information, please contact [email protected]. THE FUNCTION AND MECHANISM OF CHMP1A IN TUMOR DEVELOPMENT Thesis submitted to the Graduate College of Marshall University In partial fulfillment of the requirements for the degree of Master of Science in Biological Sciences by Jing Li Committee Members: Dr. Simon Collier, Committee Chairperson Dr. Maiyon Park Dr. Guozhang Zhu Marshall University May 2008 ABSTRACT THE FUNCTION AND MECHANISM OF CHMP1A IN TUMOR DEVELOPMENT By Jing Li Chmp1A (Chromatin modifying protein 1A/Charged multivesicular protein 1A) is a member of the ESCRT-III (Endosomal Sorting Complex Required for Transport) family. ESCRT complexes play central roles in endosome mediated trafficking via MVB (multivesicular body) formation and sorting. Chmp1A is a potential tumor suppressor, especially in the pancreas. Knockdown of Chmp1A resulted in an increase of anchorage-independent growth of HEK 293T cells. Chmp1A shRNA expressing HEK 293T cells transformed these non-tumorigeneic cells to form tumors in xenograft assays. -
Supp Material.Pdf
Simon et al. Supplementary information: Table of contents p.1 Supplementary material and methods p.2-4 • PoIy(I)-poly(C) Treatment • Flow Cytometry and Immunohistochemistry • Western Blotting • Quantitative RT-PCR • Fluorescence In Situ Hybridization • RNA-Seq • Exome capture • Sequencing Supplementary Figures and Tables Suppl. items Description pages Figure 1 Inactivation of Ezh2 affects normal thymocyte development 5 Figure 2 Ezh2 mouse leukemias express cell surface T cell receptor 6 Figure 3 Expression of EZH2 and Hox genes in T-ALL 7 Figure 4 Additional mutation et deletion of chromatin modifiers in T-ALL 8 Figure 5 PRC2 expression and activity in human lymphoproliferative disease 9 Figure 6 PRC2 regulatory network (String analysis) 10 Table 1 Primers and probes for detection of PRC2 genes 11 Table 2 Patient and T-ALL characteristics 12 Table 3 Statistics of RNA and DNA sequencing 13 Table 4 Mutations found in human T-ALLs (see Fig. 3D and Suppl. Fig. 4) 14 Table 5 SNP populations in analyzed human T-ALL samples 15 Table 6 List of altered genes in T-ALL for DAVID analysis 20 Table 7 List of David functional clusters 31 Table 8 List of acquired SNP tested in normal non leukemic DNA 32 1 Simon et al. Supplementary Material and Methods PoIy(I)-poly(C) Treatment. pIpC (GE Healthcare Lifesciences) was dissolved in endotoxin-free D-PBS (Gibco) at a concentration of 2 mg/ml. Mice received four consecutive injections of 150 μg pIpC every other day. The day of the last pIpC injection was designated as day 0 of experiment. -
Identification and Characterization of Genes Essential for Human Brain Development
Identification and Characterization of Genes Essential for Human Brain Development The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Ganesh, Vijay S. 2012. Identification and Characterization of Genes Essential for Human Brain Development. Doctoral dissertation, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:9773743 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Copyright © 2012 by Vijay S. Ganesh All rights reserved. Dissertation Advisor: Dr. Christopher A. Walsh Author: Vijay S. Ganesh Identification and Characterization of Genes Essential for Human Brain Development Abstract The human brain is a network of ninety billion neurons that allows for many of the behavioral adaptations considered unique to our species. One-fifth of these neurons are layered in an epithelial sheet known as the cerebral cortex, which is exquisitely folded into convolutions called gyri. Defects in neuronal number clinically present with microcephaly (Greek for “small head”), and in inherited cases these defects can be linked to mutations that identify genes essential for neural progenitor proliferation. Most microcephaly genes are characterized to play a role in the centrosome, however rarer presentations of microcephaly have identified different mechanisms. Charged multivesicular body protein/Chromatin modifying protein 1A (CHMP1A) is a member of the ESCRT-III endosomal sorting complex, but is also suggested to localize to the nuclear matrix and regulate chromatin. -
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. -
Anti-VPS4A Antibody (ARG43067)
Product datasheet [email protected] ARG43067 Package: 50 μg anti-VPS4A antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes VPS4A Tested Reactivity Hu, Ms, Rat Tested Application FACS, IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name VPS4A Antigen Species Human Immunogen Recombinant protein corresponding to M1-K71 of Human VPS4A. Conjugation Un-conjugated Alternate Names SKD2; SKD1; hVPS4; Protein SKD2; SKD1A; Vacuolar protein sorting-associated protein 4A; VPS4-1; EC 3.6.4.6; VPS4 Application Instructions Application table Application Dilution FACS 1:150 - 1:500 IHC-P 1:200 - 1:1000 WB 1:500 - 1:2000 Application Note IHC-P: Antigen Retrieval: Heat mediation was performed in EDTA buffer (pH 8.0). * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 49 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer 0.2% Na2HPO4, 0.9% NaCl, 0.05% Sodium azide and 4% Trehalose. Preservative 0.05% Sodium azide Stabilizer 4% Trehalose Concentration 0.5 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed www.arigobio.com 1/3 before use. Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol VPS4A Gene Full Name vacuolar protein sorting 4 homolog A (S. -
Neural Basis of Reward Anticipation and Its Genetic Determinants
Neural basis of reward anticipation and its genetic determinants Tianye Jiaa,b, Christine Macarea,b, Sylvane Desrivièresa,b, Dante A. Gonzalezc, Chenyang Taod, Xiaoxi Jid, Barbara Ruggeria,b, Frauke Neese,f, Tobias Banaschewskie, Gareth J. Barkera, Arun L. W. Bokdeg, Uli Brombergh, Christian Büchelh, Patricia J. Conroda,i, Rachel Dovec, Vincent Frouinj, Jürgen Gallinatk, Hugh Garavanl,m, Penny A. Gowlandn, Andreas Heinzk, Bernd Ittermanno, Mark Lathropp, Hervé Lemaitreq, Jean-Luc Martinotq, Tomáš Pausr,s,t, Zdenka Pausovau, Jean-Baptiste Polinej,v, Marcella Rietschele,w, Trevor Robbinsx, Michael N. Smolkay, Christian P. Müllerz, Jianfeng Fengd,aa, Adrian Rothenfluhc,1, Herta Flore,f,1, Gunter Schumanna,b,1,2, and the IMAGEN Consortium3 aInstitute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, United Kingdom; bMedical Research Council Social, Genetic and Developmental Psychiatry Centre, London SE5 8AF, United Kingdom; cDepartment of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390; dCenter for Computational Systems Biology, Fudan University, Shanghai 200433, People’s Republic of China; eDepartment of Child and Adolescent Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, 68159 Heidelberg, Germany; fDepartment of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Heidelberg, Germany; gTrinity College Institute of Neuroscience and Discipline of Psychiatry, -
CHMP5 Antibody (C-Term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # Ap18536b
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 CHMP5 Antibody (C-term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP18536b Specification CHMP5 Antibody (C-term) - Product Information Application WB,E Primary Accession Q9NZZ3 Other Accession Q4QQV8, Q9D7S9, NP_057494.3 Reactivity Human Predicted Mouse, Rat Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Antigen Region 178-204 CHMP5 Antibody (C-term) - Additional Information CHMP5 Antibody (C-term) (Cat. #AP18536b) western blot analysis in MDA-MB231 cell line Gene ID 51510 lysates (35ug/lane).This demonstrates the Other Names CHMP5 antibody detected the CHMP5 protein Charged multivesicular body protein 5, (arrow). Chromatin-modifying protein 5, SNF7 domain-containing protein 2, Vacuolar protein sorting-associated protein 60, CHMP5 Antibody (C-term) - Background Vps60, hVps60, CHMP5, C9orf83, SNF7DC2 CHMP5 belongs to the chromatin-modifying Target/Specificity protein/charged This CHMP5 antibody is generated from multivesicular body protein (CHMP) family. rabbits immunized with a KLH conjugated These proteins are synthetic peptide between 178-204 amino components of ESCRT-III (endosomal sorting acids from the C-terminal region of human complex required for CHMP5. transport III), a complex involved in degradation of surface Dilution receptor proteins and formation of endocytic WB~~1:1000 multivesicular bodies (MVBs). Some CHMPs have both nuclear and Format cytoplasmic/vesicular Purified polyclonal antibody supplied in PBS distributions, and one such CHMP, CHMP1A with 0.09% (W/V) sodium azide. This (MIM 164010), is required antibody is purified through a protein A for both MVB formation and regulation of cell column, followed by peptide affinity cycle progression purification. -
VPS4B Mutation Impairs the Osteogenic Differentiation of Dental Follicle Cells Derived from a Patient with Dentin Dysplasia Type I
International Journal of Oral Science www.nature.com/ijos ARTICLE OPEN VPS4B mutation impairs the osteogenic differentiation of dental follicle cells derived from a patient with dentin dysplasia type I Qiang Li1,2, Fangli Lu3, Tianxuan Chen4, Ke Zhang4, Yuping Lu1, Xiaocong Li5, Yingying Wang1, Ling Liu1, Qing Tian1, Fu Xiong6 and Dong Chen1 A splicing mutation in VPS4B can cause dentin dysplasia type I (DD-I), a hereditary autosomal-dominant disorder characterized by rootless teeth, the etiology of which is genetically heterogeneous. In our study, dental follicle cells (DFCs) were isolated and cultured from a patient with DD-I and compared with those from an age-matched, healthy control. In a previous study, this DD-I patient was confirmed to have a loss-of-function splicing mutation in VPS4B (IVS7 + 46C > G). The results from this study showed that the isolated DFCs were vimentin-positive and CK14-negative, indicating that the isolated cells were derived from the mesenchyme. DFCs harboring the VPS4B mutation had a significantly higher proliferation rate from day 3 to day 8 than control DFCs, indicating that VPS4B is involved in cell proliferation. The cells were then replenished with osteogenic medium to investigate how the VPS4B mutation affected osteogenic differentiation. Induction of osteogenesis, detected by alizarin red and alkaline phosphatase staining in vitro, was decreased in the DFCs from the DD-I patient compared to the control DFCs. Furthermore, we also found that the VPS4B mutation in the DD-I patient downregulated the expression of osteoblast-related genes, such as ALP, BSP, 1234567890();,: OCN, RUNX2, and their encoded proteins.