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CRL4-DCAF12 Ubiquitin Ligase Controls MOV10 RNA Helicase During Spermatogenesis and T Cell Activation
International Journal of Molecular Sciences Article CRL4-DCAF12 Ubiquitin Ligase Controls MOV10 RNA Helicase during Spermatogenesis and T Cell Activation Tomas Lidak 1,2, Nikol Baloghova 1, Vladimir Korinek 1,3 , Radislav Sedlacek 4, Jana Balounova 4 , Petr Kasparek 4 and Lukas Cermak 1,* 1 Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic; [email protected] (T.L.); [email protected] (N.B.); [email protected] (V.K.) 2 Faculty of Science, Charles University, 128 00 Prague, Czech Republic 3 Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic 4 Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic; [email protected] (R.S.); [email protected] (J.B.); [email protected] (P.K.) * Correspondence: [email protected] Abstract: Multisubunit cullin-RING ubiquitin ligase 4 (CRL4)-DCAF12 recognizes the C-terminal degron containing acidic amino acid residues. However, its physiological roles and substrates are largely unknown. Purification of CRL4-DCAF12 complexes revealed a wide range of potential substrates, including MOV10, an “ancient” RNA-induced silencing complex (RISC) complex RNA helicase. We show that DCAF12 controls the MOV10 protein level via its C-terminal motif in a Citation: Lidak, T.; Baloghova, N.; proteasome- and CRL-dependent manner. Next, we generated Dcaf12 knockout mice and demon- Korinek, V.; Sedlacek, R.; Balounova, strated that the DCAF12-mediated degradation of MOV10 is conserved in mice and humans. -
Grant Application Form Please Complete the Following Form for IETF
©2007 IETF Grant Application Form Please complete the following form for IETF grant applications. This form and all the attachments below must be combined into one document before submitting electronically. Grant submissions will not be accepted otherwise. Attachments Required 1. Specific aims of the proposal (1 page maximum). 2. Rationale of the proposal and relevance to essential tremor (1-2 pages maximum). 3. Preliminary data, if available should be incorporated into the Rationale/Relevance section. Preliminary data are not required for a proposal. However, if preliminary data are referred to in the proposal rationale, or have been used to formulate the hypotheses to be tested, such information must be formally presented in this section. 4. Research methods and procedures (1-2 pages maximum). 5. Anticipated results (half-page maximum). 6. Detailed budget and justification (1 page maximum). 7. Biographic sketch of principal investigator and all professional personnel participating in the project (standard NIH format, including biosketch and other support). 8. Copies of relevant abstracts and/or articles that have been published, are in press, or have been submitted for publication. 9. Completed conflict of interest questionnaire. Project Title: ____________________________________________________________________________ Sponsoring Institution: ____________________________________________________________________ Principal Investigator: Last Name: _______________________________ First Name: ______________________ Middle Initial: __ Degree(s): -
Human Lectins, Their Carbohydrate Affinities and Where to Find Them
biomolecules Review Human Lectins, Their Carbohydrate Affinities and Where to Review HumanFind Them Lectins, Their Carbohydrate Affinities and Where to FindCláudia ThemD. Raposo 1,*, André B. Canelas 2 and M. Teresa Barros 1 1, 2 1 Cláudia D. Raposo * , Andr1 é LAQVB. Canelas‐Requimte,and Department M. Teresa of Chemistry, Barros NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829‐516 Caparica, Portugal; [email protected] 12 GlanbiaLAQV-Requimte,‐AgriChemWhey, Department Lisheen of Chemistry, Mine, Killoran, NOVA Moyne, School E41 of ScienceR622 Co. and Tipperary, Technology, Ireland; canelas‐ [email protected] NOVA de Lisboa, 2829-516 Caparica, Portugal; [email protected] 2* Correspondence:Glanbia-AgriChemWhey, [email protected]; Lisheen Mine, Tel.: Killoran, +351‐212948550 Moyne, E41 R622 Tipperary, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +351-212948550 Abstract: Lectins are a class of proteins responsible for several biological roles such as cell‐cell in‐ Abstract:teractions,Lectins signaling are pathways, a class of and proteins several responsible innate immune for several responses biological against roles pathogens. such as Since cell-cell lec‐ interactions,tins are able signalingto bind to pathways, carbohydrates, and several they can innate be a immuneviable target responses for targeted against drug pathogens. delivery Since sys‐ lectinstems. In are fact, able several to bind lectins to carbohydrates, were approved they by canFood be and a viable Drug targetAdministration for targeted for drugthat purpose. delivery systems.Information In fact, about several specific lectins carbohydrate were approved recognition by Food by andlectin Drug receptors Administration was gathered for that herein, purpose. plus Informationthe specific organs about specific where those carbohydrate lectins can recognition be found by within lectin the receptors human was body. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
Large-Scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers
RESEARCH BRIEF Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers Julie E. Feusier1,2, Sasi Arunachalam1,3,4, Tsewang Tashi3,5,6, Monika J. Baker1, Chad VanSant-Webb1, Amber Ferdig1, Bryan E. Welm3,7, Juan L. Rodriguez-Flores8, Christopher Ours1, Lynn B. Jorde2, Josef T. Prchal3,5,6, and Clinton C. Mason1 ABSTRACT Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by detect- able hematopoietic-associated gene mutations in a person without evidence of hematologic malignancy. We sought to identify additional cancer-presenting mutations usable for CHIP detection by performing a data mining analysis of 48 somatic mutation landscape studies report- ing mutations at diagnoses of 7,430 adult and pediatric patients with leukemia or other hematologic malignancy. Following extraction of 20,141 protein-altering mutations, we identified 434 significantly recurrent mutation hotspots, 364 of which occurred at loci confidently assessable for CHIP. We then performed an additional large-scale analysis of whole-exome sequencing data from 4,538 persons belonging to three noncancer cohorts for clonal mutations. We found the combined cohort prevalence of CHIP with mutations identical to those reported at blood cancer mutation hotspots to be 1.8%, and that some of these CHIP mutations occurred in children. Our findings may help to improve CHIP detec- tion and precancer surveillance for both children and adults. SIGNIFICANCE: This study identifies frequently occurring mutations across several blood cancers that may drive hematologic malignancies and signal increased risk for cancer when detected in healthy persons. We find clonal mutations at these hotspots in a substantial number of individuals from noncan- cer cohorts, including children, showcasing potential for improved precancer surveillance. -
Spatial Localization of Genes Determined by Intranu- Clear DNA Fragmentation with the Fusion Proteins Lamin KRED and Histone
Int. J. Med. Sci. 2013, Vol. 10 1136 Ivyspring International Publisher International Journal of Medical Sciences 2013; 10(9):1136-1148. doi: 10.7150/ijms.6121 Research Paper Spatial Localization of Genes Determined by Intranu- clear DNA Fragmentation with the Fusion Proteins Lamin KRED and Histone KRED und Visible Light Waldemar Waldeck1, Gabriele Mueller1, Karl-Heinz Glatting3, Agnes Hotz-Wagenblatt3, Nicolle Diessl4, Sasithorn Chotewutmonti4, Jörg Langowski1, Wolfhard Semmler2, Manfred Wiessler2 and Klaus Braun2 1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany; 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany; 3. German Cancer Research Center, Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, INF 580, D-69120 Heidelberg, Ger- many; 4. German Cancer Research Center, Genomics and Proteomics Core Facility High Throughput Sequencing, INF 580, D-69120 Heidelberg, Germany. Corresponding author: Dr. Klaus Braun, German Cancer Research Center (DKFZ), Dept. of Medical Physics in Radiology, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. Phone: +49 6221-42 3329 Fax: +49 6221-42 3326 e-mail: [email protected]. © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/ licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. Received: 2013.02.22; Accepted: 2013.06.06; Published: 2013.07.07 Abstract The highly organized DNA architecture inside of the nuclei of cells is accepted in the scientific world. In the human genome about 3 billion nucleotides are organized as chromatin in the cell nucleus. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Novel Extensions of Label Propagation for Biomarker Discovery in Genomic Data
NOVEL EXTENSIONS OF LABEL PROPAGATION FOR BIOMARKER DISCOVERY IN GENOMIC DATA by Matthew E. Stokes B.S. Systems and Control Engineering, Case Western Reserve University, 2008 M.S. Intelligent Systems Program / Biomedical Informatics, University of Pittsburgh 2011 Submitted to the Graduate Faculty of the Kenneth P. Dietrich School of Arts and Sciences in fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2014 UNIVERSITY OF PITTSBURGH DIETRICH SCHOOL OF ARTS AND SCIENCES This dissertation proposal was presented by Matthew E. Stokes on July 17, 2014 and approved by M. Michael Barmada, PhD, Department of Human Genetics Gregory F. Cooper, MD, PhD, Department of Biomedical Informatics and the Intelligent Systems Program Milos Hauskrecht, PhD, Department of Computer Science and the Intelligent Systems Program Dissertation Advisor: Shyam Visweswaran, MD, PhD, Department of Biomedical Informatics and the Intelligent Systems Program ii NOVEL EXTENSIONS OF LABEL PORPAGATION FOR BIOMARKER DISCOVERY IN GENOMIC DATA Matthew E. Stokes, M.S University of Pittsburgh, 2014 Copyright © by Matthew E. Stokes 2014 iii NOVEL EXTENSIONS OF LABEL PROPAGATION FOR BIOMARKER DISCOVERY IN GENOMIC DATA Matthew E. Stokes, PhD University of Pittsburgh, 2014 One primary goal of analyzing genomic data is the identification of biomarkers which may be causative of, correlated with, or otherwise biologically relevant to disease phenotypes. In this work, I implement and extend a multivariate feature ranking algorithm called label propagation (LP) for biomarker discovery in genome-wide single-nucleotide polymorphism (SNP) data. This graph-based algorithm utilizes an iterative propagation method to efficiently compute the strength of association between a SNP and a phenotype. -
Analyses of Long-Term Fine Particulate Air Pollution Exposure, Genetic Variants, and Blood DNA Methylation Age in the Elderly
On Aging: Analyses of Long-Term Fine Particulate Air Pollution Exposure, Genetic Variants, and Blood DNA Methylation Age in the Elderly The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:40050003 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 On Aging: Analyses of Long-term Fine Particulate Air Pollution Exposure, Genetic Variants, and Blood DNA Methylation Age in the Elderly A dissertation presented by Jamaji Chilaka Nwanaji-Enwerem to The Committee on Higher Degrees in Biological Sciences in Public Health in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological Sciences in Public Health Harvard University Cambridge, Massachusetts November, 2017 © 2017 Jamaji Chilaka Nwanaji-Enwerem All rights reserved. Dissertation Advisors: Andrea A. Baccarelli, MD, PhD Jamaji Chilaka Nwanaji-Enwerem & Marc G. Weisskopf, PhD, ScD On Aging: Analyses of Long-term Fine Particulate Air Pollution Exposure, Genetic Variants, and Blood DNA Methylation Age in the Elderly Abstract Human aging is often accompanied by the development of chronic disease. Research has identified molecular processes that are shared by aging-related diseases, and it is widely believed that pre- clinical changes in these aging-related molecular processes (i.e. measures of “biological age”) may be more informative of morbidity and mortality risks than simple chronological age. -
Comparative Analysis of the Ubiquitin-Proteasome System in Homo Sapiens and Saccharomyces Cerevisiae
Comparative Analysis of the Ubiquitin-proteasome system in Homo sapiens and Saccharomyces cerevisiae Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Hartmut Scheel aus Rheinbach Köln, 2005 Berichterstatter: Prof. Dr. R. Jürgen Dohmen Prof. Dr. Thomas Langer Dr. Kay Hofmann Tag der mündlichen Prüfung: 18.07.2005 Zusammenfassung I Zusammenfassung Das Ubiquitin-Proteasom System (UPS) stellt den wichtigsten Abbauweg für intrazelluläre Proteine in eukaryotischen Zellen dar. Das abzubauende Protein wird zunächst über eine Enzym-Kaskade mit einer kovalent gebundenen Ubiquitinkette markiert. Anschließend wird das konjugierte Substrat vom Proteasom erkannt und proteolytisch gespalten. Ubiquitin besitzt eine Reihe von Homologen, die ebenfalls posttranslational an Proteine gekoppelt werden können, wie z.B. SUMO und NEDD8. Die hierbei verwendeten Aktivierungs- und Konjugations-Kaskaden sind vollständig analog zu der des Ubiquitin- Systems. Es ist charakteristisch für das UPS, daß sich die Vielzahl der daran beteiligten Proteine aus nur wenigen Proteinfamilien rekrutiert, die durch gemeinsame, funktionale Homologiedomänen gekennzeichnet sind. Einige dieser funktionalen Domänen sind auch in den Modifikations-Systemen der Ubiquitin-Homologen zu finden, jedoch verfügen diese Systeme zusätzlich über spezifische Domänentypen. Homologiedomänen lassen sich als mathematische Modelle in Form von Domänen- deskriptoren (Profile) beschreiben. Diese Deskriptoren können wiederum dazu verwendet werden, mit Hilfe geeigneter Verfahren eine gegebene Proteinsequenz auf das Vorliegen von entsprechenden Homologiedomänen zu untersuchen. Da die im UPS involvierten Homologie- domänen fast ausschließlich auf dieses System und seine Analoga beschränkt sind, können domänen-spezifische Profile zur Katalogisierung der UPS-relevanten Proteine einer Spezies verwendet werden. Auf dieser Basis können dann die entsprechenden UPS-Repertoires verschiedener Spezies miteinander verglichen werden. -
Toward Understanding the Role of P53 in Cardiovascular Diseases
J. Biomedical Science and Engineering, 2013, 6, 209-212 JBiSE http://dx.doi.org/10.4236/jbise.2013.62A025 Published Online February 2013 (http://www.scirp.org/journal/jbise/) Toward understanding the role of p53 in cardiovascular diseases Mohanalatha Chandrasekharan1, Silvia Vasquez2, Rajesh Kumar Galimudi3, Prashanth Suravajhala1 1Bioclues.org, IKP Knowledge Park, Secunderabad, India 2Instituto Peruano de Energía Nuclear, Centro Nuclear RACSO, Lima, Perú 3Department of Genetics, Osmania University, Hyderabad, India Email: [email protected], [email protected], [email protected], [email protected] Received 14 November 2012; revised 15 December 2012; accepted 22 December 2012 ABSTRACT hypertrophy to heart failure through the suppression of hypoxia inducible factor-1 (HIF-1), which regulates an- Tumour suppressor protein 53 (TP53 or simply p53) giogenesis in the hypertrophied heart. In addition, as p53 is a well known protein linked to apoptosis, cell sig- is known to promote apoptosis, which in turn is involved nalling, cascading and several myriad functions in in heart failure, p53 might be a key molecule in trigger- cells. Many diseases are linked to p53 though analysis ing the development of heart failure from multiple me- show only 216 interaction partners. Whether p53 chanisms [5,6]. While p53 can modulate the activity and plays an important role in cardiovascular diseases expression of some other proteins have been recently (CVD) remains uncertain. Through this bioinfor- studied, whether or not there are potentially beneficial matical analysis, we propose that p53 might play a effects remains to be understood. The actions of the ag- major role in CVD whilst being linked to Hypoxia ing proteins on the CVD have been well studied [7] with and Lupus. -
Integrin Αvβ6-EGFR Crosstalk Regulates Bidirectional Force Transmission and Controls Breast Cancer Invasion
bioRxiv preprint doi: https://doi.org/10.1101/407908; this version posted September 4, 2018. 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. Integrin αVβ6-EGFR crosstalk regulates bidirectional force transmission and controls breast cancer invasion Joanna R. Thomas1#, Kate M. Moore2#, Caroline Sproat2, Horacio J. Maldonado-Lorca1, Stephanie Mo1, Syed Haider3, Dean Hammond1, Gareth J. Thomas5, Ian A. Prior1, Pedro R. Cutillas2, Louise J. Jones2, John F. Marshall2†, Mark R. Morgan1† 1 Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK. 2 Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK. 3 The Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, UK. 4 Cancer Research UK Centre for Epidemiology, Mathematics and Statistics, Wolfson Institute of Preventative Medicine, Queen Mary University London, Charterhouse Square, London EC1M 6BQ, UK. 5 Cancer Sciences Division, Somers Building, Southampton General Hospital, Southampton, SO16 6YA, UK. # Denotes equal contribution † Corresponding author Correspondence to: Dr Mark R. Morgan, PhD, Cellular & Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX,