Image Data Resource: a Bioimage Data Integration and Publication Platform
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A Call for Public Archives for Biological Image Data Public Data Archives Are the Backbone of Modern Biological Research
comment A call for public archives for biological image data Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus enabling the creation of the frst public bioimage datasets. We present the rationale for the construction of bioimage archives and their associated databases to underpin the next revolution in bioinformatics discovery. Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook, Ugis Sarkans, Ardan Patwardhan, Alvis Brazma and Ewan Birney ince the mid-1970s it has been possible image data to encourage both reuse and in automation and throughput allow this to analyze the molecular composition extraction of knowledge. to be done in a systematic manner. We Sof living organisms, from the individual Despite the long history of biological expect that, for example, super-resolution units (nucleotides, amino acids, and imaging, the tools and resources for imaging will be applied across biological metabolites) to the macromolecules they collecting, managing, and sharing image and biomedical imaging; examples in are part of (DNA, RNA, and proteins), data are immature compared with those multidimensional imaging8 and high- as well as the interactions among available for sequence and 3D structure content screening9 have recently been these components1–3. The cost of such data. In the following sections we reported. It is very likely that imaging data measurements has decreased remarkably outline the current barriers to progress, volume and complexity will continue to over time, and technological development the technological developments that grow. Second, the emergence of powerful has widened their scope from investigations could provide solutions, and how those computer-based approaches for image of gene and transcript sequences (genomics/ infrastructure solutions can meet the interpretation, quantification, and modeling transcriptomics) to proteins (proteomics) outlined need. -
A Network Propagation Approach to Prioritize Long Tail Genes in Cancer
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.05.429983; this version posted February 8, 2021. 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. A Network Propagation Approach to Prioritize Long Tail Genes in Cancer Hussein Mohsen1,*, Vignesh Gunasekharan2, Tao Qing2, Sahand Negahban3, Zoltan Szallasi4, Lajos Pusztai2,*, Mark B. Gerstein1,5,6,3,* 1 Computational Biology & Bioinformatics Program, Yale University, New Haven, CT 06511, USA 2 Breast Medical Oncology, Yale School of Medicine, New Haven, CT 06511, USA 3 Department of Statistics & Data Science, Yale University, New Haven, CT 06511, USA 4 Children’s Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA 5 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA 6 Department of Computer Science, Yale University, New Haven, CT 06511, USA * Corresponding author Abstract Introduction. The diversity of genomic alterations in cancer pose challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the “long tail” of the mutational distribution, uncovered new genes with significant implication in cancer development. The study of these genes often requires integrative approaches with multiple types of biological data. Network propagation methods have demonstrated high efficacy in uncovering genomic patterns underlying cancer using biological interaction networks. Yet, the majority of these analyses have focused their assessment on detecting known cancer genes or identifying altered subnetworks. -
3 on the Nature of Biological Data
ON THE NATURE OF BIOLOGICAL DATA 35 3 On the Nature of Biological Data Twenty-first century biology will be a data-intensive enterprise. Laboratory data will continue to underpin biology’s tradition of being empirical and descriptive. In addition, they will provide confirming or disconfirming evidence for the various theories and models of biological phenomena that researchers build. Also, because 21st century biology will be a collective effort, it is critical that data be widely shareable and interoperable among diverse laboratories and computer systems. This chapter describes the nature of biological data and the requirements that scientists place on data so that they are useful. 3.1 DATA HETEROGENEITY An immense challenge—one of the most central facing 21st century biology—is that of managing the variety and complexity of data types, the hierarchy of biology, and the inevitable need to acquire data by a wide variety of modalities. Biological data come in many types. For instance, biological data may consist of the following:1 • Sequences. Sequence data, such as those associated with the DNA of various species, have grown enormously with the development of automated sequencing technology. In addition to the human genome, a variety of other genomes have been collected, covering organisms including bacteria, yeast, chicken, fruit flies, and mice.2 Other projects seek to characterize the genomes of all of the organisms living in a given ecosystem even without knowing all of them beforehand.3 Sequence data generally 1This discussion of data types draws heavily on H.V. Jagadish and F. Olken, eds., Data Management for the Biosciences, Report of the NSF/NLM Workshop of Data Management for Molecular and Cell Biology, February 2-3, 2003, Available at http:// www.eecs.umich.edu/~jag/wdmbio/wdmb_rpt.pdf. -
Characterization of Genomic Copy Number Variation in Mus Musculus Associated with the Germline of Inbred and Wild Mouse Populations, Normal Development, and Cancer
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 4-18-2019 2:00 PM Characterization of genomic copy number variation in Mus musculus associated with the germline of inbred and wild mouse populations, normal development, and cancer Maja Milojevic The University of Western Ontario Supervisor Hill, Kathleen A. The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Doctor of Philosophy © Maja Milojevic 2019 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Genetics and Genomics Commons Recommended Citation Milojevic, Maja, "Characterization of genomic copy number variation in Mus musculus associated with the germline of inbred and wild mouse populations, normal development, and cancer" (2019). Electronic Thesis and Dissertation Repository. 6146. https://ir.lib.uwo.ca/etd/6146 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract Mus musculus is a human commensal species and an important model of human development and disease with a need for approaches to determine the contribution of copy number variants (CNVs) to genetic variation in laboratory and wild mice, and arising with normal mouse development and disease. Here, the Mouse Diversity Genotyping array (MDGA)-approach to CNV detection is developed to characterize CNV differences between laboratory and wild mice, between multiple normal tissues of the same mouse, and between primary mammary gland tumours and metastatic lung tissue. -
Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces Cerevisiae Received: 26 October 2016 Henriette Uthe, Jens T
www.nature.com/scientificreports OPEN Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae Received: 26 October 2016 Henriette Uthe, Jens T. Vanselow & Andreas Schlosser Accepted: 25 January 2017 Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Published: 27 February 2017 Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis. The Mediator complex is an essential coactivator of eukaryotic transcription. Its major function is to communi- cate regulatory signals from gene-specific transcription factors upstream of the transcription start site to RNA Polymerase II (Pol II) and to promote activator-dependent assembly and stabilization of the preinitiation complex (PIC)1–3. The yeast Mediator complex is composed of 25 subunits and forms four distinct modules: the head, the middle, and the tail module, in addition to the four-subunit CDK8 kinase module (CKM), which can reversibly associate with the 21-subunit Mediator complex. -
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Supplementary Figure S1. Results of flow cytometry analysis, performed to estimate CD34 positivity, after immunomagnetic separation in two different experiments. As monoclonal antibody for labeling the sample, the fluorescein isothiocyanate (FITC)- conjugated mouse anti-human CD34 MoAb (Mylteni) was used. Briefly, cell samples were incubated in the presence of the indicated MoAbs, at the proper dilution, in PBS containing 5% FCS and 1% Fc receptor (FcR) blocking reagent (Miltenyi) for 30 min at 4 C. Cells were then washed twice, resuspended with PBS and analyzed by a Coulter Epics XL (Coulter Electronics Inc., Hialeah, FL, USA) flow cytometer. only use Non-commercial 1 Supplementary Table S1. Complete list of the datasets used in this study and their sources. GEO Total samples Geo selected GEO accession of used Platform Reference series in series samples samples GSM142565 GSM142566 GSM142567 GSM142568 GSE6146 HG-U133A 14 8 - GSM142569 GSM142571 GSM142572 GSM142574 GSM51391 GSM51392 GSE2666 HG-U133A 36 4 1 GSM51393 GSM51394 only GSM321583 GSE12803 HG-U133A 20 3 GSM321584 2 GSM321585 use Promyelocytes_1 Promyelocytes_2 Promyelocytes_3 Promyelocytes_4 HG-U133A 8 8 3 GSE64282 Promyelocytes_5 Promyelocytes_6 Promyelocytes_7 Promyelocytes_8 Non-commercial 2 Supplementary Table S2. Chromosomal regions up-regulated in CD34+ samples as identified by the LAP procedure with the two-class statistics coded in the PREDA R package and an FDR threshold of 0.5. Functional enrichment analysis has been performed using DAVID (http://david.abcc.ncifcrf.gov/) -
Molecular and Cellular Mechanisms of the Angiogenic Effect of Poly(Methacrylic Acid-Co-Methyl Methacrylate) Beads
Molecular and Cellular Mechanisms of the Angiogenic Effect of Poly(methacrylic acid-co-methyl methacrylate) Beads by Lindsay Elizabeth Fitzpatrick A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Institute of Biomaterials and Biomedical Engineering University of Toronto © Copyright by Lindsay Elizabeth Fitzpatrick 2012 Molecular and Cellular Mechanisms of the Angiogenic Effect of Poly(methacrylic acid-co-methyl methacrylate) Beads Lindsay Elizabeth Fitzpatrick Doctorate of Philosophy Institute of Biomaterials and Biomedical Engineering University of Toronto 2012 Abstract Poly(methacrylic acid -co- methyl methacrylate) beads were previously shown to have a therapeutic effect on wound closure through the promotion of angiogenesis. However, it was unclear how this polymer elicited its beneficial properties. The goal of this thesis was to characterize the host response to MAA beads by identifying molecules of interest involved in MAA-mediated angiogenesis (in comparison to poly(methyl methacrylate) beads, PMMA). Using a model of diabetic wound healing and a macrophage-like cell line (dTHP-1), eight molecules of interest were identified in the host response to MAA beads. Gene and/or protein expression analysis showed that MAA beads increased the expression of Shh, IL-1β, IL-6, TNF- α and Spry2, but decreased the expression of CXCL10 and CXCL12, compared to PMMA and no beads. MAA beads also appeared to modulate the expression of OPN. In vivo, the global gene expression of OPN was increased in wounds treated with MAA beads, compared to PMMA and no beads. In contrast, dTHP-1 decreased OPN gene expression compared to PMMA and no beads, but expressed the same amount of secreted OPN, suggesting that the cells decreased the expression of the intracellular isoform of OPN. -
Anti-MED30 (Aa 1-100) Polyclonal Antibody (CABT- BL5153) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Anti-MED30 (aa 1-100) polyclonal antibody (CABT- BL5153) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Product Overview Rabbit polyclonal antibody to Human MED30. Antigen Description The multiprotein TRAP/Mediator complex facilitates gene expression through a wide variety of transcriptional activators. MED30 is a component of this complex that appears to be metazoan specific (Baek et al., 2002 Immunogen Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human MED30 / TRAP25. Isotype IgG Source/Host Rabbit Species Reactivity Human Purification Immunogen affinity purified Conjugate Unconjugated Cellular Localization Nuclear Format Liquid Size 100 μg Buffer 1% BSA, PBS, pH 7.4 Preservative 0.02% Sodium Azide Storage Store at 4°C short term (1-2 weeks). Aliquot and store at -20°C or -80°C. Avoid repeated freeze/thaw cycles. BACKGROUND Introduction The multiprotein TRAP/Mediator complex facilitates gene expression through a wide variety of transcriptional activators. MED30 is a component of this complex that appears to be metazoan specific (Baek et al., 2002 [PubMed 11909976]).[supplied by OMIM, Nov 2010] 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved GENE INFORMATION Entrez Gene ID 90390 Protein Refseq NP_542382 UniProt ID Q96HR3 Chromosome Location 8q24.11 Pathway Developmental Biology, organism-specific biosystem; Gene Expression, organism-specific -
Identification of Protein Complexes Associated with Myocardial Infarction Using a Bioinformatics Approach
MOLECULAR MEDICINE REPORTS 18: 3569-3576, 2018 Identification of protein complexes associated with myocardial infarction using a bioinformatics approach NIANHUI JIAO1, YONGJIE QI1, CHANGLI LV2, HONGJUN LI3 and FENGYONG YANG1 1Intensive Care Unit; 2Emergency Department, Laiwu People's Hospital, Laiwu, Shandong 271199; 3Emergency Department, The Central Hospital of Tai'an, Tai'an, Shandong 271000, P.R. China Received November 3, 2016; Accepted January 3, 2018 DOI: 10.3892/mmr.2018.9414 Abstract. Myocardial infarction (MI) is a leading cause of clinical outcomes regarding high-risk MI. For example, muta- mortality and disability worldwide. Determination of the tions in the myocardial infarction-associated transcript have molecular mechanisms underlying the disease is crucial for been reported to cause susceptibility to MI (5). In addition, it identifying possible therapeutic targets and designing effective was demonstrated that mutations in the oxidized low-density treatments. On the basis that MI may be caused by dysfunc- lipoprotein receptor 1 gene may significantly increase the tional protein complexes rather than single genes, the present risk of MI (6). Although some MI-related genes have been study aimed to use a bioinformatics approach to identifying detected, many were identified independently and functional complexes that may serve important roles in the develop- associations among the genes have rarely been explored. ment of MI. By investigating the proteins involved in these Therefore, it is necessary to investigate MI from a systematic identified complexes, numerous proteins have been reported perspective, as the complex disease was reported to occur due that are related to MI, whereas other proteins interacted to the dysregulation of functional gene sets (7). -
Protein Purification Protein Localization in Vivo Fluorescent Imaging Protein Arrays Real Time Imaging Protein Interactions Protein Trafficking Protein Turnover
Overcoming Challenges of Protein Analysis in Mammalian Systems Danette L. Daniels, Ph.D. Current Technologies for Protein Analysis Biochemical/ In Vivo Proteomic Cell Based Animal Analysis Analysis Models Fluorescent proteins Affinity tags Antibodies How about a system applicable to the all approaches that also addresses limitations of current methods? • Minimal interference with protein of interest • Efficient capture/isolation • Detection/real-time imaging • Differential labeling • High Signal/background HaloTag Platform Biochemical/ In Vivo Proteomic Cell Based Animal Analysis Analysis Models Protein purification Protein localization In vivo fluorescent imaging Protein arrays Real time imaging Protein interactions Protein trafficking Protein turnover HaloTag® HaloCHIP™ HaloLink™ HaloTag® Fluorescent Purification Protein:DNA Protein Arrays Pull-Down Ligands HaloTag is a Genetically Engineered Protein Fusion Tag O Functional Protein of Cl O Interest HT + group Protein of Functional HT O O Interest group . A monomeric , 34 kDa, modified bacterial dehalogenase genetically engineered to covalently bind specific, synthetic HaloTag® ligands . Irreversible, covalent attachment of chemical functionalities . Suitable as either N- or C- terminal fusion Mutagenized HaloTag® Protein Enables Covalent HaloTag®-Ligand Complex Hydrolase (DhaA) HaloTag® Catalytic process Facilitated bond formation T r p 1 0 7 T r p 1 0 7 HaloTag®: • 34kDa protein • Monomeric N N H N 4 1 H N A s n - H H • Single change: C l 4 1 A s n C l 2 1 His272Phe for covalent O R O O - C C bond. 3 R O 1 0 6 A s p 1 0 6 A s p O H O H Covalent bond: H H O O • Stable after N C G l u 1 3 0 C G l u 1 3 0 N - O denaturation. -
Functional Diversification of the Nleg Effector Family in Enterohemorrhagic Escherichia Coli
Functional diversification of the NleG effector family in enterohemorrhagic Escherichia coli Dylan Valleaua, Dustin J. Littleb, Dominika Borekc,d, Tatiana Skarinaa, Andrew T. Quailea, Rosa Di Leoa, Scott Houlistone,f, Alexander Lemake,f, Cheryl H. Arrowsmithe,f, Brian K. Coombesb, and Alexei Savchenkoa,g,1 aDepartment of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada; bDepartment of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; cDepartment of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390; dDepartment of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; ePrincess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; fDepartment of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; and gDepartment of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada Edited by Ralph R. Isberg, Howard Hughes Medical Institute and Tufts University School of Medicine, Boston, MA, and approved August 15, 2018 (receivedfor review November 6, 2017) The pathogenic strategy of Escherichia coli and many other gram- chains. Depending on the length and nature of the polyubiquitin negative pathogens relies on the translocation of a specific set of chain, it posttranslationally regulates the target protein’s locali- proteins, called effectors, into the eukaryotic host cell during in- zation, activation, or degradation. Ubiquitination is a multistep fection. These effectors act in concert to modulate host cell pro- process which begins with the ubiquitin-activating enzyme (E1) cesses in favor of the invading pathogen. Injected by the type III using ATP to “charge” ubiquitin, covalently binding the ubiquitin secretion system (T3SS), the effector arsenal of enterohemorrhagic C terminus by a thioester linkage. -
Visualization of Biomedical Data
Visualization of Biomedical Data Corresponding author: Seán I. O’Donoghue; email: [email protected] • Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia • Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia • School of Biotechnology and Biomolecular Sciences, UNSW, Kensington NSW 2033, Australia Benedetta Frida Baldi; email: [email protected] • Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia Susan J Clark; email: [email protected] • Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia Aaron E. Darling; email: [email protected] • The ithree institute, University of Technology Sydney, Ultimo NSW 2007, Australia James M. Hogan; email: [email protected] • School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane QLD, 4000, Australia Sandeep Kaur; email: [email protected] • School of Computer Science and Engineering, UNSW, Kensington NSW 2033, Australia Lena Maier-Hein; email: [email protected] • Div. Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany Davis J. McCarthy; email: [email protected] • European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD, Hinxton, Cambridge, UK • St. Vincent’s Institute of Medical Research, Fitzroy VIC 3065, Australia William