DOCSLIB.ORG

Advances in Bioinformatics and Computational Biology

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Advances in Bioinformatics and Computational Biology João C. Setubal Nalvo F. Almeida (Eds.) Advances in Bioinformatics and LNBI 8213 Computational Biology 8th Brazilian Symposium on Bioinformatics, BSB 2013 Recife, Brazil, November 2013 Proceedings 123 Lecture Notes in Bioinformatics 8213 Edited by S. Istrail, P. Pevzner, and M. Waterman Editorial Board: A. Apostolico S. Brunak M. Gelfand T. Lengauer S. Miyano G. Myers M.-F. Sagot D. Sankoff R. Shamir T. Speed M. Vingron W. Wong Subseries of Lecture Notes in Computer Science João C. Setubal Nalvo F. Almeida (Eds.) Advances in Bioinformatics and Computational Biology 8th Brazilian Symposium on Bioinformatics, BSB 2013 Recife, Brazil, November 3-7, 2013 Proceedings 13 Volume Editors João C. Setubal University of São Paulo, Institute of Chemistry Avenida Prof. Lineu Prestes, 748 sala 911, 05508-000 São Paulo, SP, Brazil E-mail: [email protected] Nalvo F. Almeida Federal University of Mato Grosso do Sul, School of Computing Facom-UFMS, CP 549, 79070-900 Campo Grande, MS, Brazil E-mail: [email protected] ISSN 0302-9743 e-ISSN 1611-3349 ISBN 978-3-319-02623-7 e-ISBN 978-3-319-02624-4 DOI 10.1007/978-3-319-02624-4 Springer Cham Heidelberg New York Dordrecht London Library of Congress Control Number: 2013949541 CR Subject Classification (1998): J.3, F.2, H.2, I.5, I.2, F.1, I.5 LNCS Sublibrary: SL 8 – Bioinformatics © Springer International Publishing Switzerland 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Typesetting: Camera-ready by author, data conversion by Scientific Publishing Services, Chennai, India Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface This volume contains the papers selected for presentation at the 8th Brazilian Symposium on Bioinformatics (BSB 2013), held during November 3–6, 2013, in Recife, Brazil. BSB is an international conference that covers all aspects of bioin- formatics and computational biology. This year the event was jointly organized by the special interest group in Computational Biology of the Brazilian Com- puter Society (SBC), which has been the organizer of BSB for the past several years, and by the Brazilian Association for Bioinformatics and Computational Biology (AB3C), which has been the organizer of another event, the X-Meeeting, also for the past several years. This year for the first time the two events were co-located. As in previous editions, BSB 2013 had an international Program Committee (PC) of 46 members. After a rigorous review process by the PC, 18 papers were accepted to be orally presented at the event, and are printed in this volume. In addition to the technical presentations, BSB 2013 featured keynote talks from David Roos (University of Pennsylvania), Peter Stadler (University of Leipzig), and Martin Tompa (University of Washington). Peter Stadler graciously con- tributed an invited paper to these proceedings (“The Trouble with Long-Range Base Pairs in RNA Folding”). BSB 2013 was made possible by the dedication and work of many people and organizations. We would like to express our sincere thanks to all PC members, as well as to the external reviewers. Their names are listed in the pages that follow. We are also grateful to the local organizers and volunteers for their valuable help; the sponsors for making the event financially viable; Guilherme P. Telles and Peter Stadler for assisting in the preparation of the proceedings; and Springer for agreeing to publish this volume. Finally, we would like to thank all authors for their time and effort in submitting their work and the invited speakers for having accepted our invitation. This year selected BSB 2013 papers were invited for submission in expanded format to a special issue of the IEEE/ACM Transactions on Computational Biology and Bioinformatics. We thank Ying Xu (Editor-in-Chief) and Dong Xu (Associate Editor-in-Chief) for this opportunity. November 2013 Jo˜ao C. Setubal Nalvo F. Almeida Organization BSB 2013 was organized by Universidade Federal de Pernambuco. Conference Chairs Katia S. Guimar˜aes Universidade Federal de Pernambuco, Brazil Paulo Gustavo S. Fonseca Universidade Federal de Pernambuco, Brazil Ana Benko Iseppon Universidade Federal de Pernambuco, Brazil Valdir Balbino Universidade Federal de Pernambuco, Brazil Program Chairs Jo˜ao C. Setubal Universidade de S˜ao Paulo, Brazil Nalvo F. Almeida Universidade Federal de Mato Grosso do Sul, Brazil Steering Comittee Guilherme P. Telles (President) Universidade Estadual de Campinas, Brazil Ivan G. Costa Filho Universidade Federal de Pernambuco, Brazil Luis Antonio Kowada Universidade Federal Fluminense, Brazil Marcelo de Macedo Br´ıgido Universidade de Bras´ılia, Brazil Marcilio C.P. de Souto Universit´e d’Orl´eans, France Osmar Norberto de Souza PUC Rio Grande do Sul, Brazil S´ergio Vale Aguiar Campos Universidade Federal de Minas Gerais, Brazil Sponsors Sociedade Brasileira de Computa¸c˜ao (SBC) Associa¸c˜ao Brasileira de Bioinform´atica e Biologia Computacional (AB3C) Funding Conselho Nacional de Desenvolvimento Cient´ıfico e Tecnol´ogico (CNPq) Coordena¸c˜ao de Aperfei¸coamento de Pessoal de N´ıvel Superior (CAPES) Funda¸c˜ao de Amparo `aCiˆencia e Tecnologia de Pernambuco (FACEPE) VIII Organization Program Committee Said S. Adi Universidade Federal de Mato Grosso do Sul, Brazil Nalvo F. Almeida Universidade Federal de Mato Grosso do Sul, Brazil Fernando Alvarez-Val´´ ın Universidad de la Republica, Uruguay Ana L.C. Bazzan Universidade Federal do Rio Grande do Sul, Brazil Ana M. Benko-Iseppon Universidade Federal de Pernambuco, Brazil Mar´ılia D.V. Braga Inmetro, Brazil Marcelo de Macedo Br´ıgido Universidade de Bras´ılia, Brazil Sergio Campos Universidade Federal de Minas Gerais, Brazil Alessandra Carbone Pierre and Marie Curie University, France Ivan Gesteira Costa Universidade Federal de Pernambuco, Brazil Andr´e C.P.L.F. de Carvalho Universidade de S˜ao Paulo/S˜ao Carlos, Brazil Marcilio de Souto Universit´e d’Orl´eans, France Emanuel Maltempi de Souza Universidade Federal do Paran´a, Brazil Osmar Norberto de Souza PUC Rio Grande do Sul, Brazil Luciano Digiampietri Universidade de S˜ao Paulo, Brazil Alan Durham Universidade de S˜ao Paulo, Brazil Carlos E. Ferreira Universidade de S˜ao Paulo, Brazil Andr´e Fujita Universidade de S˜ao Paulo, Brazil Katia S. Guimar˜aes Universidade Federal de Pernambuco, Brazil Lenny Heath Virginia Tech, USA Dirk Husmeier University of Glasgow, UK Andre Kashiwabara Universidade Tecnol´ogica Federal do Paran´a, Brazil Ney Lemke Universidade Est. Paulista J´ulio Mesquita Filho, Brazil Sergio Lifschitz PUC Rio de Janeiro, Brazil Ana Carolina Lorena Universidade Federal do ABC, Brazil Wellington Martins Universidade Federal de Goi´as, Brazil Marta Mattoso Universidade Federal do Rio de Janeiro, Brazil Satoru Miyano University of Tokyo, Japan Houtan Noushmehr Universidade de S˜ao Paulo, Brazil Guilherme Oliveira Funda¸c˜ao Oswaldo Cruz, Minas Gerais, Brazil Alexey Onufriev Virginia Tech, USA Miguel Ortega Universidade Federal de Minas Gerais, Brazil Sergio Pantano Instituto Pasteur de Montevideo, Uruguay Alexandre Rossi Paschoal Universidade Tecnol´ogica Federal do Paran´a, Brazil Duncan Ruiz PUC Rio Grande do Sul, Brazil Marie-France Sagot Inria, France Alexander Schliep Rutgers University, USA Organization IX Jo˜ao Setubal Universidade de S˜ao Paulo, Brazil Peter F. Stadler University of Leipzig, Germany Jens Stoye University of Bielefeld, Germany Guilherme P. Telles Universidade Estadual de Campinas, Brazil Thiago Venancio Universidade Federal Fluminense, Brazil Maria Emilia T. Walter Universidade de Bras´ılia, Brazil Additional Reviewers Poly Hannah Da Silva Universidade Federal Fluminense, Brazil Marcelo Henriques de Carvalho Universidade Federal de Mato Grosso do Sul, Brazil Zanoni Dias Universidade Estadual de Campinas, Brazil Marcio Dorn Universidade Federal do Rio Grande do Sul, Brazil Alessandra Faria-Campos
Load more

Recommended publications
  • Analysis of Trans Esnps Infers Regulatory Network Architecture
    Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation.
    [Show full text]
  • Identification of the Binding Partners for Hspb2 and Cryab Reveals
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity.
    [Show full text]
  • 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.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Circular RNA Hsa Circ 0005114‑Mir‑142‑3P/Mir‑590‑5P‑ Adenomatous
    ONCOLOGY LETTERS 21: 58, 2021 Circular RNA hsa_circ_0005114‑miR‑142‑3p/miR‑590‑5p‑ adenomatous polyposis coli protein axis as a potential target for treatment of glioma BO WEI1*, LE WANG2* and JINGWEI ZHAO1 1Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033; 2Department of Ophthalmology, The First Hospital of Jilin University, Jilin University, Changchun, Jilin 130021, P.R. China Received September 12, 2019; Accepted October 22, 2020 DOI: 10.3892/ol.2020.12320 Abstract. Glioma is the most common type of brain tumor APC expression with a good overall survival rate. UALCAN and is associated with a high mortality rate. Despite recent analysis using TCGA data of glioblastoma multiforme and the advances in treatment options, the overall prognosis in patients GSE25632 and GSE103229 microarray datasets showed that with glioma remains poor. Studies have suggested that circular hsa‑miR‑142‑3p/hsa‑miR‑590‑5p was upregulated and APC (circ)RNAs serve important roles in the development and was downregulated. Thus, hsa‑miR‑142‑3p/hsa‑miR‑590‑5p‑ progression of glioma and may have potential as therapeutic APC‑related circ/ceRNA axes may be important in glioma, targets. However, the expression profiles of circRNAs and their and hsa_circ_0005114 interacted with both of these miRNAs. functions in glioma have rarely been studied. The present study Functional analysis showed that hsa_circ_0005114 was aimed to screen differentially expressed circRNAs (DECs) involved in insulin secretion, while APC was associated with between glioma and normal brain tissues using sequencing the Wnt signaling pathway. In conclusion, hsa_circ_0005114‑ data collected from the Gene Expression Omnibus database miR‑142‑3p/miR‑590‑5p‑APC ceRNA axes may be potential (GSE86202 and GSE92322 datasets) and explain their mecha‑ targets for the treatment of glioma.
    [Show full text]
  • Evolution of the DAN Gene Family in Vertebrates
    bioRxiv preprint doi: https://doi.org/10.1101/794404; this version posted June 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-NC 4.0 International license. RESEARCH ARTICLE Evolution of the DAN gene family in vertebrates Juan C. Opazo1,2,3, Federico G. Hoffmann4,5, Kattina Zavala1, Scott V. Edwards6 1Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. 2David Rockefeller Center for Latin American Studies, Harvard University, Cambridge, MA 02138, USA. 3Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD). 4 Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, 39762, USA. Cite as: Opazo JC, Hoffmann FG, 5 Zavala K, Edwards SV (2020) Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State Evolution of the DAN gene family in University, Mississippi State, 39762, USA. vertebrates. bioRxiv, 794404, ver. 3 peer-reviewed and recommended by 6 PCI Evolutionary Biology. doi: Department of Organismic and Evolutionary Biology, Harvard University, 10.1101/794404 Cambridge, MA 02138, USA. This article has been peer-reviewed and recommended by Peer Community in Evolutionary Biology Posted: 29 June 2020 doi: 10.24072/pci.evolbiol.100104 ABSTRACT Recommender: Kateryna Makova The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification.
    [Show full text]
  • Multivariate Analysis Reveals Differentially Expressed Genes
    www.nature.com/scientificreports OPEN Multivariate analysis reveals diferentially expressed genes among distinct subtypes of difuse astrocytic gliomas: diagnostic implications Nerea González‑García1,2, Ana Belén Nieto‑Librero1,2, Ana Luisa Vital3, Herminio José Tao4, María González‑Tablas2,5,6, Álvaro Otero2, Purifcación Galindo‑Villardón1,2, Alberto Orfao2,5,6 & María Dolores Tabernero2,5,6,7* Diagnosis and classifcation of gliomas mostly relies on histopathology and a few genetic markers. Here we interrogated microarray gene expression profles (GEP) of 268 difuse astrocytic gliomas—33 difuse astrocytomas (DA), 52 anaplastic astrocytomas (AA) and 183 primary glioblastoma (GBM)—based on multivariate analysis, to identify discriminatory GEP that might support precise histopathological tumor stratifcation, particularly among inconclusive cases with II–III grade diagnosed, which have diferent prognosis and treatment strategies. Microarrays based GEP was analyzed on 155 difuse astrocytic gliomas (discovery cohort) and validated in another 113 tumors (validation set) via sequential univariate analysis (pairwise comparison) for discriminatory gene selection, followed by nonnegative matrix factorization and canonical biplot for identifcation of discriminatory GEP among the distinct histological tumor subtypes. GEP data analysis identifed a set of 27 genes capable of diferentiating among distinct subtypes of gliomas that might support current histological classifcation. DA + AA showed similar molecular profles with only a few discriminatory genes
    [Show full text]
  • Rabbit Anti-ADAM9/FITC Conjugated Antibody-SL20104R-FITC
    SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-ADAM9/FITC Conjugated antibody SL20104R-FITC Product Name: Anti-ADAM9/FITC Chinese Name: FITC标记的去整合素样金属蛋白酶9抗体 A disintegrin and metalloproteinase domain 9; A disintegrin and metalloproteinase domain 9; ADAM 9 antibody ADAM metallopeptidase domain 9; Cellular disintegrin Alias: related protein; Disintegrin and metalloproteinase domain 9; MCMP; MDC9; Meltrin gamma; Metalloprotease disintegrin cysteine rich protein 9; Mltng; Myeloma cell metalloproteinase; ADAM9_HUMAN. Organism Species: Rabbit Clonality: Polyclonal React Species: Human,Mouse,Rat,Dog,Cow,Rabbit,Sheep, ICC=1:50-200IF=1:50-200 Applications: not yet tested in other applications. optimal dilutions/concentrations should be determined by the end user. Molecular weight: 88kDa Form: Lyophilized or Liquid Concentration: 2mg/1ml immunogen: KLH conjugated synthetic peptide derived from human ADAM9 Lsotype: IgGwww.sunlongbiotech.com Purification: affinity purified by Protein A Storage Buffer: 0.01M TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Store at -20 °C for one year. Avoid repeated freeze/thaw cycles. The lyophilized antibody is stable at room temperature for at least one month and for greater than a year Storage: when kept at -20°C. When reconstituted in sterile pH 7.4 0.01M PBS or diluent of antibody the antibody is stable for at least two weeks at 2-4 °C. background: This gene encodes a member of the ADAM (a disintegrin and metalloprotease domain) family. Members of this family are membrane-anchored proteins structurally related to Product Detail: snake venom disintegrins, and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis.
    [Show full text]
  • RET Gene Fusions in Malignancies of the Thyroid and Other Tissues
    G C A T T A C G G C A T genes Review RET Gene Fusions in Malignancies of the Thyroid and Other Tissues Massimo Santoro 1,*, Marialuisa Moccia 1, Giorgia Federico 1 and Francesca Carlomagno 1,2 1 Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy; [email protected] (M.M.); [email protected] (G.F.); [email protected] (F.C.) 2 Institute of Endocrinology and Experimental Oncology of the CNR, 80131 Naples, Italy * Correspondence: [email protected] Received: 10 March 2020; Accepted: 12 April 2020; Published: 15 April 2020 Abstract: Following the identification of the BCR-ABL1 (Breakpoint Cluster Region-ABelson murine Leukemia) fusion in chronic myelogenous leukemia, gene fusions generating chimeric oncoproteins have been recognized as common genomic structural variations in human malignancies. This is, in particular, a frequent mechanism in the oncogenic conversion of protein kinases. Gene fusion was the first mechanism identified for the oncogenic activation of the receptor tyrosine kinase RET (REarranged during Transfection), initially discovered in papillary thyroid carcinoma (PTC). More recently, the advent of highly sensitive massive parallel (next generation sequencing, NGS) sequencing of tumor DNA or cell-free (cfDNA) circulating tumor DNA, allowed for the detection of RET fusions in many other solid and hematopoietic malignancies. This review summarizes the role of RET fusions in the pathogenesis of human cancer. Keywords: kinase; tyrosine kinase inhibitor; targeted therapy; thyroid cancer 1. The RET Receptor RET (REarranged during Transfection) was initially isolated as a rearranged oncoprotein upon the transfection of a human lymphoma DNA [1].
    [Show full text]
  • Identification of Differentially Expressed Genes Between Primary Lung Cancer and Lymph Node Metastasis Via Bioinformatic Analysis
    3754 ONCOLOGY LETTERS 18: 3754-3768, 2019 Identification of differentially expressed genes between primary lung cancer and lymph node metastasis via bioinformatic analysis NAN ZHANG and SHAO-WEI ZHANG Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China Received January 10, 2019; Accepted July 12, 2019 DOI: 10.3892/ol.2019.10723 Abstract. Lung cancer (LC), with its high morbidity and cBioPortal. A total of 308 DEGs were identified in the two mortality rates, is one of the most widespread and malignant microarray datasets, which were mainly enriched during neoplasms. Mediastinal lymph node metastasis (MLNM) cellular processes, including the Gene Ontology terms ‘cell’, severely affects postoperative survival of patients with LC. ‘catalytic activity’, ‘molecular function regulator’, ‘signal trans- Additionally, the molecular mechanisms of LC with MLNM ducer activity’ and ‘binding’. The PPI network was composed (MM LC) remain not well understood. To identify the key of 315 edges and 167 nodes. Its significant module had 11 hub biomarkers in its carcinogenesis and development, the data- genes, and high expression of actin β, MYC, arginine vaso- sets GSE23822 and GSE13213 were obtained from the Gene pressin, vesicle associated membrane protein 2 and integrin Expression Omnibus database. The differentially expressed subunit β1, and low expression of NOTCH1, synaptojanin 2 genes (DEGs) were identified, and the Database for Annotation, and intersectin 2 were significantly associated with poor OS. Visualization and Integrated Discovery was used to perform In summary, hub genes and DEGs presented in the present functional annotations of DEGs. Search Tool for the Retrieval study may help identify underlying targets for diagnostic and of Interacting Genes and Cytoscape were utilized to obtain the therapeutic methods for MM LC.
    [Show full text]
  • 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.
    [Show full text]
  • CDC123 Antibody (RQ6088)
    CDC123 Antibody (RQ6088) Catalog No. Formulation Size RQ6088 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Affinity purified Buffer Lyophilized from 1X PBS with 2% Trehalose and 0.025% sodium azide UniProt O75794 Localization Cytoplasmic Applications Western blot : 1-2ug/ml Immunohistochemistry (FFPE) : 2-5ug/ml Immunofluorescence : 5ug/ml Flow cytometry : 1-3ug/million cells Direct ELISA : 0.1-0.5ug/ml Limitations This CDC123 antibody is available for research use only. Immunofluorescent staining of FFPE human A431 cells with CDC123 antibody (green) and DAPI nuclear stain (blue). HIER: steam section in pH6 citrate buffer for 20 min. IHC staining of FFPE human pancreatic cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human bladder cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human appendicitis tissue with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human ovarian cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human liver cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human gastric cancer with CDC123 antibody.
    [Show full text]