Knock-Out of the Neural Death Effector Domain Protein PEA-15 Demonstrates That Its Expression Protects Astrocytes from TNF␣-Induced Apoptosis
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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
DEDD (NM 001039712) Human Untagged Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for SC310813 DEDD (NM_001039712) Human Untagged Clone Product data: Product Type: Expression Plasmids Product Name: DEDD (NM_001039712) Human Untagged Clone Tag: Tag Free Symbol: DEDD Synonyms: CASP8IP1; DEDD1; DEFT; FLDED1; KE05 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin Fully Sequenced ORF: >NCBI ORF sequence for NM_001039712, the custom clone sequence may differ by one or more nucleotides ATGGCGGGCCTAAAGCGGCGGGCAAGCCAGGTGTGGCCAGAAGAGCATGGTGAGCAGGAACATGGGCTGT ACAGCCTGCACCGCATGTTTGACATCGTGGGCACTCATCTGACACACAGAGATGTGCGCGTGCTTTCTTT CCTCTTTGTTGATGTCATTGATGACCACGAGCGTGGACTCATCCGAAATGGACGTGACTTCTTATTGGCA CTGGAGCGCCAGGGCCGCTGTGATGAAAGTAACTTTCGCCAGGTGCTGCAGCTGCTGCGCATCATCACTC GCCACGACCTGCTGCCCTACGTCACCCTCAAGAGGAGACGGGCTGTGTGCCCTGATCTTGTAGACAAGTA TCTGGAGGAGACATCAATTCGCTATGTGACCCCCAGAGCCCTCAGTGATCCAGAACCAAGGCCTCCCCAG CCCTCTAAAACAGTGCCTCCCCACTATCCTGTGGTGTGTTGCCCCACTTCGGGTCCTCAGATGTGTAGCA AGCGGCCAGCCCGAGGGAGAGCCACACTTGGGAGCCAGCGAAAACGCCGGAAGTCAGTGACACCAGATCC CAAGGAGAAGCAGACATGTGACATCAGACTGCGGGTTCGGGCTGAATACTGCCAGCATGAGACTGCTCTG CAGGGCAATGTCTTCTCTAACAAGCAGGACCCACTTGAGCGCCAGTTTGAGCGCTTTAACCAGGCCAACA CCATCCTCAAGTCCCGGGACCTGGGCTCCATCATCTGTGACATCAAGTTCTCTGAGCTCACCTACCTCGA TGCATTCTGGCGTGACTACATCAATGGCTCTTTATTAGAGGCACTTAAAGGTGTCTTCATCACAGACTCC CTCAAGCAAGCTGTGGGCCATGAAGCCATCAAGCTGCTGGTAAATGTAGACGAGGAGGACTATGAGCTGG -
Structural and Functional Diversity of Caspase Homologues in Non-Metazoan Organisms
Protoplasma DOI 10.1007/s00709-017-1145-5 REVIEW ARTICLE Structural and functional diversity of caspase homologues in non-metazoan organisms Marina Klemenčič1,2 & Christiane Funk1 Received: 1 June 2017 /Accepted: 5 July 2017 # The Author(s) 2017. This article is an open access publication Abstract Caspases, the proteases involved in initiation and supports the role of metacaspases and orthocaspases as im- execution of metazoan programmed cell death, are only pres- portant contributors to cell homeostasis during normal physi- ent in animals, while their structural homologues can be ological conditions or cell differentiation and ageing. found in all domains of life, spanning from simple prokary- otes (orthocaspases) to yeast and plants (metacaspases). All members of this wide protease family contain the p20 do- Keywords Algae . Cyanobacteria . Cell death . Cysteine main, which harbours the catalytic dyad formed by the two protease . Metacaspase . Orthocaspase amino acid residues, histidine and cysteine. Despite the high structural similarity of the p20 domain, metacaspases and orthocaspases were found to exhibit different substrate speci- ficities than caspases. While the former cleave their substrates Introduction after basic amino acid residues, the latter accommodate sub- strates with negative charge. This observation is crucial for BOut of life’s school of war: What does not destroy me, the re-evaluation of non-metazoan caspase homologues being makes me stronger.^ wrote the German philosopher involved in processes of programmed cell death. In this re- Friedrich Nietzsche in his book Twilight of the Idols or view, we analyse the structural diversity of enzymes contain- how to philosophize with a hammer. Even though ing the p20 domain, with focus on the orthocaspases, and reformatted to more common use, this phrase has been summarise recent advances in research of orthocaspases and used to describe the dual nature of caspase homologues metacaspases of cyanobacteria, algae and higher plants. -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
C-Terminal Region (ARP58987 P050) Data Sheet
CASP3 antibody - C-terminal region (ARP58987_P050) Data Sheet Product Number ARP58987_P050 Product Name CASP3 antibody - C-terminal region (ARP58987_P050) Size 50ug Gene Symbol CASP3 Alias Symbols CPP32; CPP32B; SCA-1 Nucleotide Accession# NM_032991 Protein Size (# AA) 277 amino acids Molecular Weight 12kDa Product Format Lyophilized powder NCBI Gene Id 836 Host Rabbit Clonality Polyclonal Official Gene Full Name Caspase 3, apoptosis-related cysteine peptidase Gene Family CASP This is a rabbit polyclonal antibody against CASP3. It was validated on Western Blot by Aviva Systems Biology. At Aviva Systems Biology we manufacture rabbit polyclonal antibodies on a large scale (200-1000 Description products/month) of high throughput manner. Our antibodies are peptide based and protein family oriented. We usually provide antibodies covering each member of a whole protein family of your interest. We also use our best efforts to provide you antibodies recognize various epitopes of a target protein. For availability of antibody needed for your experiment, please inquire (). Peptide Sequence Synthetic peptide located within the following region: NLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFG CASP3 is a protein which is a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic residues to produce two subunits, Description of Target large and small, that dimerize to form the active enzyme. This protein cleaves and activates caspases 6, 7 and 9, and the protein itself is processed by caspases 8, 9 and 10. It is the predominant caspase involved in the cleavage of amyloid-beta 4A precursor protein, which is associated with neuronal death in Alzheimer's disease. -
Comparative Study of Apoptosis-Related Gene Loci in Human, Mouse and Rat Genomes
ISSN 1672-9145 Acta Biochimica et Biophysica Sinica 2005, 37(5): 341–348 CN 31-1940/Q Comparative Study of Apoptosis-related Gene Loci in Human, Mouse and Rat Genomes Yan-Bin YIN, Yong ZHANG, Peng YU, Jing-Chu LUO, Ying JIANG*, and Song-Gang LI* Center of Bioinformatics, National Laboratory of Genetic Engineering and Protein Engineering, College of Life Sciences, Peking University, Beijing 100871, China Downloaded from Abstract Many genes are involved in mammalian cell apoptosis pathway. These apoptosis genes often contain characteristic functional domains, and can be classified into at least 15 functional groups, according to previous reports. Using an integrated bioinformatics platform for motif or domain search from three public mammalian proteomes (International Protein Index database for human, mouse, and rat), we system- atically cataloged all of the proteins involved in mammalian apoptosis pathway. By localizing those proteins http://abbs.oxfordjournals.org/ onto the genomes, we obtained a gene locus centric apoptosis gene catalog for human, mouse and rat. Further phylogenetic analysis showed that most of the apoptosis related gene loci are conserved among these three mammals. Interestingly, about one-third of apoptosis gene loci form gene clusters on mammal chromosomes, and exist in the three species, which indicated that mammalian apoptosis gene orders are also conserved. In addition, some tandem duplicated gene loci were revealed by comparing gene loci clusters in the three species. All data produced in this work were stored in a relational database and may be viewed at http://pcas.cbi.pku.edu.cn/database/apd.php. at Institute of Zoology, CAS on November 2, 2011 Key words apoptosis; gene cluster; comparative genomics; bioinformatics Apoptosis is a regulated program by which cells destroy between mouse and human, they revealed that most themselves [1]. -
FLIP and the Death Effector Domain Family
Oncogene (2008) 27, 6216–6227 & 2008 Macmillan Publishers Limited All rights reserved 0950-9232/08 $32.00 www.nature.com/onc REVIEW FLIP and the death effector domain family JW Yu and Y Shi Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA Death effector domains (DEDs) are protein interaction and stress that impinge on the mitochondria or modules found in a number of proteins known to regulate ‘extrinsically’ from extracellular ligands that activate apoptosis from death receptors. The core DED family death receptors at the cell surface. In either scenario, members that orchestrate programmed cell death from each pathway critically relies on the action of a family of death receptors include the adaptor protein FADD, the cysteine proteases known as caspases to initiate and initiator caspases procaspases-8 and -10 and the regulatory execute the cell death process through a two-step protein c-FLIP. Through homotypic DED interactions, cascade (Riedl and Shi, 2004). In the apoptotic these proteins assemble into the death-inducingsignaling proteolytic cascade, the initiator caspases (caspases-2, complex (DISC) to regulate initiator caspase activation -8, -9 and -10) cleave and consequently activate the and launch the apoptotic proteolytic cascade. A consider- effector caspases (caspases-3, -6 and -7), and the effector able body of evidence, however, is revealingthat the same caspases in turn cleave a large array of substrates to core group of DED-containing proteins also paradoxically dismantle and package the cell into apoptotic bodies. promotes survival and proliferation in lymphocytes and Activation of initiator caspases for both the intrinsic possibly other cell types. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Elabscience®
Tel:240-252-7368(USA) Fax:240-252-7376(USA) www.elabscience.com ® E-mail:[email protected] Elabscience Elabscience Biotechnology Inc. DEDD Polyclonal Antibody Catalog No. E-AB-67706 Reactivity H,M,R Storage Store at -20°C. Avoid freeze / thaw cycles. Host Rabbit Applications IHC Isotype IgG Note: Centrifuge before opening to ensure complete recovery of vial contents. Images Immunogen Information Immunogen Recombinant fusion protein of human DEDD (NP_001034801.1). GeneID 9191 Swissprot O75618 Synonyms DEDD,CASP8IP1,DEDD1,DEFT,FLDED1,KE05 Immunohistochemistry of paraffin- Product Information embedded Rat lung using DEDD Buffer PBS with 0.02% sodium azide, 50% glycerol, pH7.3. Polyclonal Antibody at dilution of Purify Affinity purification 1:100 (40x lens). Dilution IHC 1:50-1:100 Background This gene encodes a protein that contains a death effector domain (DED). DED is a protein-protein interaction domain shared by adaptors, Immunohistochemistry of paraffin- regulators and executors of the programmed cell death pathway. embedded Human esophagus using Overexpression of this gene was shown to induce weak apoptosis. Upon DEDD Polyclonal Antibody at dilution stimulation, this protein was found to translocate from cytoplasm to of 1:100 (40x lens). nucleus and colocalize with UBTF, a basal factor required for RNA polymerase I transcription, in the nucleolus. At least three transcript variants encoding the same protein have been found for this gene. Immunohistochemistry of paraffin- embedded Mouse kidney using DEDD Polyclonal Antibody at dilution of 1:100 (40x lens). For Research Use Only Focus on your research Thank you for your recent purchase. If you would like to learn more about antibodies,please visit www.elabscience.com. -
Substantial Conformational Change Mediated by Charge-Triad Residues of the Death Effector Domain in Protein-Protein Interactions
Substantial Conformational Change Mediated by Charge-Triad Residues of the Death Effector Domain in Protein-Protein Interactions Edward C. Twomey1,2,3, Dana F. Cordasco1,2, Stephen D. Kozuch2, Yufeng Wei1* 1 Institute of NeuroImmune Pharmacology, Seton Hall University, South Orange, New Jersey, United States of America, 2 Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey, United States of America, 3 Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, New York, United States of America Abstract Protein conformational changes are commonly associated with the formation of protein complexes. The non-catalytic death effector domains (DEDs) mediate protein-protein interactions in a variety of cellular processes, including apoptosis, proliferation and migration, and glucose metabolism. Here, using NMR residual dipolar coupling (RDC) data, we report a conformational change in the DED of the phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) protein in the complex with a mitogen-activated protein (MAP) kinase, extracellular regulated kinase 2 (ERK2), which is essential in regulating ERK2 cellular distribution and function in cell proliferation and migration. The most significant conformational change in PEA-15 happens at helices a2, a3, and a4, which also possess the highest flexibility among the six-helix bundle of the DED. This crucial conformational change is modulated by the D/E-RxDL charge-triad motif, one of the prominent structural features of DEDs, together with a number of other electrostatic and hydrogen bonding interactions on the protein surface. Charge- triad motif promotes the optimal orientation of key residues and expands the binding interface to accommodate protein- protein interactions. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing