Characterization of Long Non-Coding Rnas in Systemic Sclerosis Monocytes: a Potential Role for PSMB8-AS1 in Altered Cytokine Secretion
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
An Integrative Analysis of Gene Expression and Molecular
Muraro and Simmons BMC Bioinformatics (2016) 17:42 DOI 10.1186/s12859-016-0886-z RESEARCH ARTICLE Open Access An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease Daniele Muraro* and Alison Simmons Abstract Background: Inflammatory bowel disease (IBD) consists of two main disease-subtypes, Crohn’s disease (CD) and ulcerative colitis (UC); these subtypes share overlapping genetic and clinical features. Genome-wide microarray data enable unbiased documentation of alterations in gene expression that may be disease-specific. As genetic diseases are believed to be caused by genetic alterations affecting the function of signalling pathways, module-centric optimisation algorithms, whose aim is to identify sub-networks that are dys-regulated in disease, are emerging as promising approaches. Results: In order to account for the topological structure of molecular interaction networks, we developed an optimisation algorithm that integrates databases of known molecular interactions with gene expression data; such integration enables identification of differentially regulated network modules. We verified the performance of our algorithm by testing it on simulated networks; we then applied the same method to study experimental data derived from microarray analysis of CD and UC biopsies and human interactome databases. This analysis allowed the extraction of dys-regulated subnetworks under different experimental conditions (inflamed and uninflamed tissues in CD and UC). Optimisation was performed to highlight differentially expressed network modules that may be common or specific to the disease subtype. Conclusions: We show that the selected subnetworks include genes and pathways of known relevance for IBD; in particular, the solutions found highlight cross-talk among enriched pathways, mainly the JAK/STAT signalling pathway and the EGF receptor signalling pathway. -
Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics
GBE Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics Marisa C.W. Lim1,*, Christopher C. Witt2, Catherine H. Graham1,3,andLilianaM.Davalos 1,4 1Department of Ecology and Evolution, Stony Brook University 2 Museum of Southwestern Biology and Department of Biology, University of New Mexico Downloaded from https://academic.oup.com/gbe/article-abstract/11/6/1552/5494706 by guest on 08 June 2019 3Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland 4Consortium for Inter-Disciplinary Environmental Research, Stony Brook University *Corresponding author: E-mail: [email protected]. Accepted: May 12, 2019 Data deposition: The raw read data have been deposited in the NCBI Sequence Read Archive under BioProject: PRJNA543673, BioSample: SAMN11774663-SAMN11774674, SRA Study: SRP198856. All scripts used for analyses are available on Dryad: doi:10.5061/dryad.v961mb4. Abstract High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. -
Protein Expression Analysis of an in Vitro Murine Model of Prostate Cancer Progression: Towards Identification of High-Potential Therapeutic Targets
Journal of Personalized Medicine Article Protein Expression Analysis of an In Vitro Murine Model of Prostate Cancer Progression: Towards Identification of High-Potential Therapeutic Targets Hisham F. Bahmad 1,2,3 , Wenjing Peng 4, Rui Zhu 4, Farah Ballout 1, Alissar Monzer 1, 1,5 6, , 1, , 4, , Mohamad K. Elajami , Firas Kobeissy * y , Wassim Abou-Kheir * y and Yehia Mechref * y 1 Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon; [email protected] (H.F.B.); [email protected] (F.B.); [email protected] (A.M.); [email protected] (M.K.E.) 2 Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA 3 Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA 4 Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; [email protected] (W.P.); [email protected] (R.Z.) 5 Department of Internal Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA 6 Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon * Correspondence: [email protected] (F.K.); [email protected] (W.A.-K.); [email protected] (Y.M.); Tel.: +961-1-350000 (ext. 4805) (F.K.); +961-1-350000 (ext. 4778) (W.A.K.); +1-806-834-8246 (Y.M.); Fax: +1-806-742-1289 (Y.M.); 961-1-744464 (W.A.K.) These authors have contributed equally to this work as joint senior authors. -
PDF Datasheet
Product Datasheet Cactin Overexpression Lysate NBP2-06542 Unit Size: 0.1 mg Store at -80C. Avoid freeze-thaw cycles. Protocols, Publications, Related Products, Reviews, Research Tools and Images at: www.novusbio.com/NBP2-06542 Updated 3/17/2020 v.20.1 Earn rewards for product reviews and publications. Submit a publication at www.novusbio.com/publications Submit a review at www.novusbio.com/reviews/destination/NBP2-06542 Page 1 of 2 v.20.1 Updated 3/17/2020 NBP2-06542 Cactin Overexpression Lysate Product Information Unit Size 0.1 mg Concentration The exact concentration of the protein of interest cannot be determined for overexpression lysates. Please contact technical support for more information. Storage Store at -80C. Avoid freeze-thaw cycles. Buffer RIPA buffer Target Molecular Weight 88.5 kDa Product Description Description Transient overexpression lysate of chromosome 19 open reading frame 29 (C19orf29), transcript variant 2 The lysate was created in HEK293T cells, using Plasmid ID RC213573 and based on accession number NM_021231. The protein contains a C-MYC/DDK Tag. Gene ID 58509 Gene Symbol CACTIN Species Human Notes HEK293T cells in 10-cm dishes were transiently transfected with a non-lipid polymer transfection reagent specially designed and manufactured for large volume DNA transfection. Transfected cells were cultured for 48hrs before collection. The cells were lysed in modified RIPA buffer (25mM Tris-HCl pH7.6, 150mM NaCl, 1% NP-40, 1mM EDTA, 1xProteinase inhibitor cocktail mix, 1mM PMSF and 1mM Na3VO4, and then centrifuged to clarify the lysate. Protein concentration was measured by BCA protein assay kit.This product is manufactured by and sold under license from OriGene Technologies and its use is limited solely for research purposes. -
Characterisation of Expression Patterns and Functional Role of Cactin in Early Zebrafish Development
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by MURAL - Maynooth University Research Archive Library Gene Expression Patterns 10 (2010) 199–206 Contents lists available at ScienceDirect Gene Expression Patterns journal homepage: www.elsevier.com/locate/gep Characterisation of expression patterns and functional role of Cactin in early zebrafish development Paola Atzei a, Fan Yang b, Ross Collery b, Breandan N. Kennedy b,1, Paul N. Moynagh a,*,1 a Institute of Immunology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland b UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland article info abstract Article history: The immune system of teleost zebrafish (Danio rerio) shows high similarity to mammalian counterparts Received 21 December 2009 sharing many innate immune components including Toll-Like Receptors (TLRs), cytokines, chemokines Received in revised form 12 March 2010 and complement molecules. As in mammals, zebrafish also contains the transcription factor NF-jB that Accepted 19 March 2010 plays dualist roles in innate immunity and early development. Indeed NF-jB members are expressed in Available online 27 March 2010 different temporal patterns during the early stages of zebrafish embryogenesis indicating that each mol- ecule is involved in specific developmental events. In the present study we employ zebrafish as a model Keywords: to characterise the expression pattern and role of a novel NF-jB regulator, termed Cactin, in early devel- Toll-like receptors opment. Cactin was first characterised in Drosophila as a new member of the Rel pathway that could NF-jB Cactin affect the generation of dorsal–ventral polarity. -
Molecular Pathology and Novel Clinical Therapy for Uterine
ANTICANCER RESEARCH 36 : 4997-5008 (2016) doi:10.21873/anticanres.11068 Review Molecular Pathology and Novel Clinical Therapy for Uterine Leiomyosarcoma TAKUMA HAYASHI 1,2 , MIKI KAWANO 2,3 , TOMOYUKI ICHIMURA 4, KOICHI IDA 1, HIROFUMI ANDO 1, DORIT ZHARHARY 5, YAE KANAI 6, HIROYUKI ABURATANI 7, SUSUMU TONEGAWA 8, TANRI SHIOZAWA 1, NOBUO YAEGASHI 9 and IKUO KONISHI 10 1Department of Obstetrics and Gynecology, Shinshu University School of Medicine, Nagano, Japan; 2Department of Medical Technology, International University of Health and Welfare, Chiba, Japan; 3Department of Health Science, Kyushu University Graduate School of Medicine, Fukuoka, Japan; 4Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka, Japan; 5SIGMA-Aldrich Israel, Rehovot, Israel; 6Pathology Division, Keio University School of Medicine, Tokyo, Japan; 7The Cancer System Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan; 8Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, U.S.A.; 9Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Miyagi, Japan; 10 National Hospital Organization Kyoto Medical Centre, Kyoto, Japan Abstract. Patients with uterine leiomyosarcoma (LMS) disease prevalence of ~37% by 12 months of age. Furthermore, typically present with vaginal bleeding, pain, and a pelvic a recent report showed the loss of ability to induce PSMB9/ β1 i mass, with atypical presentations of hypercalcemia and expression, -
Datasheet: VPA00155 Product Details
Datasheet: VPA00155 Description: GOAT ANTI PSMB8 Specificity: PSMB8 Format: Purified Product Type: PrecisionAb™ Polyclonal Isotype: Polyclonal IgG Quantity: 100 µl Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Species Cross Reacts with: Rat Reactivity N.B. Antibody reactivity and working conditions may vary between species. Product Form Purified IgG - liquid Preparation Goat polyclonal antibody purified by affinity chromatography Buffer Solution TRIS buffered saline Preservative 0.02% Sodium Azide (NaN ) 0.5 % BSA Stabilisers 3 Immunogen Peptide with the sequence C-DVSDLLHQYREANQ, from the C terminus of the protein sequence External Database Links UniProt: P28062 Related reagents Entrez Gene: 5696 PSMB8 Related reagents Synonyms LMP7, PSMB5i, RING10, Y2 Page 1 of 2 Specificity Goat anti Human PSMB8 antibody recognizes proteasome subunit beta type-8, also known as Low molecular mass protein 7, macropain subunit C13, multicatalytic endopeptidase complex subunit C13, proteasome component C13, and proteasome subunit beta-5i. The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. -
Downloaded the “Top Edge” Version
bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 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 4.0 International license. 1 Drosophila models of pathogenic copy-number variant genes show global and 2 non-neuronal defects during development 3 Short title: Non-neuronal defects of fly homologs of CNV genes 4 Tanzeen Yusuff1,4, Matthew Jensen1,4, Sneha Yennawar1,4, Lucilla Pizzo1, Siddharth 5 Karthikeyan1, Dagny J. Gould1, Avik Sarker1, Yurika Matsui1,2, Janani Iyer1, Zhi-Chun Lai1,2, 6 and Santhosh Girirajan1,3* 7 8 1. Department of Biochemistry and Molecular Biology, Pennsylvania State University, 9 University Park, PA 16802 10 2. Department of Biology, Pennsylvania State University, University Park, PA 16802 11 3. Department of Anthropology, Pennsylvania State University, University Park, PA 16802 12 4 contributed equally to work 13 14 *Correspondence: 15 Santhosh Girirajan, MBBS, PhD 16 205A Life Sciences Building 17 Pennsylvania State University 18 University Park, PA 16802 19 E-mail: [email protected] 20 Phone: 814-865-0674 21 1 bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 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 4.0 International license. 22 ABSTRACT 23 While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non- 24 neuronal phenotypes, functional studies evaluating these regions have focused on the molecular 25 basis of neuronal defects. -
A Genome-Wide Rnai Screen for Modifiers of Polyglutamine-Induced Neurotoxicity in Drosophila
A Genome-Wide RNAi Screen for Modifiers of Polyglutamine-Induced Neurotoxicity in Drosophila Doctoral Thesis In partial fulfilment of the requirements for the degree “Doctor rerum naturalium (Dr. rer. nat.)” in the Molecular Medicine Study Programme at the Georg-August University Göttingen submitted by Hannes Voßfeldt born in Zerbst/Anhalt, Germany Göttingen, January 2012 FÜR MEINE FAMILIE - IM GEDENKEN AN NADINE DU FEHLST. … IT MATTERS NOT HOW STRAIT THE GATE, HOW CHARGED WITH PUNISHMENTS THE SCROLL, I AM THE MASTER OF MY FATE: I AM THE CAPTAIN OF MY SOUL. … Invictus – William Ernest Henley Members of the Thesis Committee: Supervisor Prof. Dr. med. Jörg B. Schulz Head of Department of Neurology University Medical Centre RWTH Aachen University Pauwelsstrasse 30 52074 Aachen Second member of the Thesis Committee Prof. Dr. rer. nat. Ernst A. Wimmer Head of Department of Developmental Biology Johann Friedrich Blumenbach Institute of Zoology and Anthropology Georg-August University Göttingen Justus-von-Liebig-Weg 11 37077 Göttingen Third member of the Thesis Committee Dr. rer. nat. Till Marquardt Research Group Developmental Neurobiology European Neuroscience Institute Göttingen Grisebachstrasse 5 37077 Göttingen Date of Disputation: 2 April 2012 Affidavit I hereby declare that my doctoral thesis entitled “A Genome-Wide RNAi Screen for Modifiers of Polyglutamine-Induced Neurotoxicity in Drosophila” has been written independently with no other sources and aids than quoted. Göttingen, January 2012 Hannes Voßfeldt LIST OF PUBLICATIONS IV List of Publications Parts of this work have already been published with authorisation of Prof. Jörg B. Schulz, Head of the Department of Neurology, University Medical Centre of the RWTH Aachen University, on behalf of the thesis committee. -
Proteasome Immunosubunits Protect Against the Development of CD8 T Cell-Mediated Autoimmune Diseases
Proteasome Immunosubunits Protect against the Development of CD8 T Cell-Mediated Autoimmune Diseases This information is current as Dietmar M. W. Zaiss, Cornelis P. J. Bekker, Andrea Gröne, of September 29, 2021. Benedicte A. Lie and Alice J. A. M. Sijts J Immunol published online 29 July 2011 http://www.jimmunol.org/content/early/2011/07/29/jimmun ol.1101003 Downloaded from Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision http://www.jimmunol.org/ • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: by guest on September 29, 2021 http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2011 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published July 29, 2011, doi:10.4049/jimmunol.1101003 The Journal of Immunology Proteasome Immunosubunits Protect against the Development of CD8 T Cell-Mediated Autoimmune Diseases Dietmar M. W. Zaiss,* Cornelis P. J. Bekker,* Andrea Gro¨ne,† Benedicte A. Lie,‡ and Alice J. A. M. Sijts* Exposure of cells to inflammatory cytokines induces the expression of three proteasome immunosubunits, two of which are encoded in the MHC class II region. -
Intratumoral Injection of SYNB1891, a Synthetic Biotic Medicine Designed
Intratumoral injection of SYNB1891 A Synthetic Biotic medicine designed to activate the innate immune system. Therapy demonstrates target engagement in humans including intratumoral STING activation. Janku F, MD Anderson Cancer Center; Luke JJ, UPMC Hillman Cancer Center; Brennan AM, Synlogic; Riese RJ, Synlogic; Varterasian M, Pharmaceutical Consultant; Kuhn K, Synlogic; Sokolovska A, Synlogic; Strauss J, Mary Crowley Cancer Research Presented by Filip Janku, MD, PhD Study supported by Synlogic, Inc American Association for Cancer Research (AACR) April 2021 Introduction and Methods SYNB1891 Strain Phase 1 First-in-Human Clinical Trial • Live, modified strain of the probiotic E. coli • Enrolling patients with refractory advanced solid Nissle engineered to produce cyclic tumors or lymphoma dinucleotides (CDN) under hypoxia leading to stimulator of interferon genes (STING)- • Intratumoral (IT) injection of SYNB1891 on Days activation 1, 8 and 15 of the first 21-day cycle and then on Day 1 of each subsequent cycle. • Preferentially taken up by phagocytic antigen- presenting cells in tumors, activating • Dose escalation planned across 7 cohorts (1x106 complementary innate immune pathways – 1x109 live cells) with Arm 1 consisting of (direct CDN STING activation; cGAS-mediated SYNB1891 as monotherapy, and Arm 2 in STING activation and TLR4/MyD88 activation by combination with atezolizumab the bacterial chassis) SYNB1891 was safe and well-tolerated in heterogenous population Nov 2020: Interim Analysis IA Updated through 15 Mar 2021 15 Mar 2021: -
Biological Models of Colorectal Cancer Metastasis and Tumor Suppression
BIOLOGICAL MODELS OF COLORECTAL CANCER METASTASIS AND TUMOR SUPPRESSION PROVIDE MECHANISTIC INSIGHTS TO GUIDE PERSONALIZED CARE OF THE COLORECTAL CANCER PATIENT By Jesse Joshua Smith Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University In partial fulfillment of the requirements For the degree of DOCTOR OF PHILOSOPHY In Cell and Developmental Biology May, 2010 Nashville, Tennessee Approved: Professor R. Daniel Beauchamp Professor Robert J. Coffey Professor Mark deCaestecker Professor Ethan Lee Professor Steven K. Hanks Copyright 2010 by Jesse Joshua Smith All Rights Reserved To my grandparents, Gladys and A.L. Lyth and Juanda Ruth and J.E. Smith, fully supportive and never in doubt. To my amazing and enduring parents, Rebecca Lyth and Jesse E. Smith, Jr., always there for me. .my sure foundation. To Jeannine, Bill and Reagan for encouragement, patience, love, trust and a solid backing. To Granny George and Shawn for loving support and care. And To my beautiful wife, Kelly, My heart, soul and great love, Infinitely supportive, patient and graceful. ii ACKNOWLEDGEMENTS This work would not have been possible without the financial support of the Vanderbilt Medical Scientist Training Program through the Clinical and Translational Science Award (Clinical Investigator Track), the Society of University Surgeons-Ethicon Scholarship Fund and the Surgical Oncology T32 grant and the Vanderbilt Medical Center Section of Surgical Sciences and the Department of Surgical Oncology. I am especially indebted to Drs. R. Daniel Beauchamp, Chairman of the Section of Surgical Sciences, Dr. James R. Goldenring, Vice Chairman of Research of the Department of Surgery, Dr. Naji N.