Peptide Aggregation and Neurotoxicity in Alzheimer's Disease
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Supplementary Data
Supplementary Data for Quantitative Changes in the Mitochondrial Proteome from Subjects with Mild Cognitive Impairment, Early Stage and Late Stage Alzheimer’s disease Table 1 - 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Table 2 - MCI mitochondrial samples, Protein Summary Table 3 - MCI mitochondrial samples, Experiment 1 Table 4 - MCI mitochondrial samples, Experiment 2 Table 5 - MCI mitochondrial samples, Experiment 3 Table 6 - EAD Mitochondrial Study, Protein Summary Table 7 - EAD Mitochondrial Study, Experiment 1 Table 8 - EAD Mitochondrial Study, Experiment 2 Table 9 - EAD Mitochondrial Study, Experiment 3 Table 10 - LAD Mitochondrial Study, Protein Summary Table 11 - LAD Mitochondrial Study, Experiment 1 Table 12 - LAD Mitochondrial Study, Experiment 2 Table 13 - LAD Mitochondrial Study, Experiment 3 Supplemental Table 1. 112 unique, non-redundant proteins identified and quantified in at least two of the three analytical replicates for all three disease stages. Description Data MCI EAD LAD AATM_HUMAN (P00505) Aspartate aminotransferase, mitochondrial precursor (EC Mean 1.43 1.70 1.31 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transaminase 2) [MASS=47475] SEM 0.07 0.09 0.09 Count 3.00 3.00 3.00 ACON_HUMAN (Q99798) Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) Mean 1.24 1.61 1.19 (Citrate hydro-lyase) (Aconitase) [MASS=85425] SEM 0.05 0.17 0.18 Count 3.00 2.00 3.00 ACPM_HUMAN (O14561) Acyl carrier protein, mitochondrial -
Ovulation-Selective Genes: the Generation and Characterization of an Ovulatory-Selective Cdna Library
531 Ovulation-selective genes: the generation and characterization of an ovulatory-selective cDNA library A Hourvitz1,2*, E Gershon2*, J D Hennebold1, S Elizur2, E Maman2, C Brendle1, E Y Adashi1 and N Dekel2 1Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA 2Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel (Requests for offprints should be addressed to N Dekel; Email: [email protected]) *(A Hourvitz and E Gershon contributed equally to this paper) (J D Hennebold is now at Division of Reproductive Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon 97006, USA) Abstract Ovulation-selective/specific genes, that is, genes prefer- (FAE-1) homolog, found to be localized to the inner entially or exclusively expressed during the ovulatory periantral granulosa and to the cumulus granulosa cells of process, have been the subject of growing interest. We antral follicles. The FAE-1 gene is a -ketoacyl-CoA report herein studies on the use of suppression subtractive synthase belonging to the fatty acid elongase (ELO) hybridization (SSH) to construct a ‘forward’ ovulation- family, which catalyzes the initial step of very long-chain selective/specific cDNA library. In toto, 485 clones were fatty acid synthesis. All in all, the present study accom- sequenced and analyzed for homology to known genes plished systematic identification of those hormonally with the basic local alignment tool (BLAST). Of those, regulated genes that are expressed in the ovary in an 252 were determined to be nonredundant. -
18S Rrna Is a Reliable Normalisation Gene for Real Time PCR Based On
Kuchipudi et al. Virology Journal 2012, 9:230 http://www.virologyj.com/content/9/1/230 METHODOLOGY Open Access 18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells Suresh V Kuchipudi1*, Meenu Tellabati1, Rahul K Nelli1, Gavin A White2, Belinda Baquero Perez1, Sujith Sebastian1, Marek J Slomka3, Sharon M Brookes3, Ian H Brown3, Stephen P Dunham1 and Kin-Chow Chang1 Abstract Background: One requisite of quantitative reverse transcription PCR (qRT-PCR) is to normalise the data with an internal reference gene that is invariant regardless of treatment, such as virus infection. Several studies have found variability in the expression of commonly used housekeeping genes, such as beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), under different experimental settings. However, ACTB and GAPDH remain widely used in the studies of host gene response to virus infections, including influenza viruses. To date no detailed study has been described that compares the suitability of commonly used housekeeping genes in influenza virus infections. The present study evaluated several commonly used housekeeping genes [ACTB, GAPDH, 18S ribosomal RNA (18S rRNA), ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide (ATP5B) and ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) (ATP5G1)] to identify the most stably expressed gene in human, pig, chicken and duck cells infected with a range of influenza A virus subtypes. Results: The relative expression stability of commonly used housekeeping genes were determined in primary human bronchial epithelial cells (HBECs), pig tracheal epithelial cells (PTECs), and chicken and duck primary lung-derived cells infected with five influenza A virus subtypes. -
Systematic Identification of Housekeeping Genes Possibly Used As References in Caenorhabditis Elegans by Large-Scale Data Integration
cells Article Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration 1, 1, 1 1 1 1 1 Jingxin Tao y, Youjin Hao y, Xudong Li , Huachun Yin , Xiner Nie , Jie Zhang , Boying Xu , Qiao Chen 2 and Bo Li 1,* 1 College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; [email protected] (J.T.); [email protected] (Y.H.); [email protected] (X.L.); [email protected] (H.Y.); [email protected] (X.N.); [email protected] (J.Z.); [email protected] (B.X.) 2 Scientific Research Office, Chongqing Normal University, Chongqing 401331, China; [email protected] * Correspondence: [email protected]; Tel.: +86-23-6591-0315 These authors contributed equally to this work. y Received: 24 January 2020; Accepted: 11 March 2020; Published: 24 March 2020 Abstract: For accurate gene expression quantification, normalization of gene expression data against reliable reference genes is required. It is known that the expression levels of commonly used reference genes vary considerably under different experimental conditions, and therefore, their use for data normalization is limited. In this study, an unbiased identification of reference genes in Caenorhabditis elegans was performed based on 145 microarray datasets (2296 gene array samples) covering different developmental stages, different tissues, drug treatments, lifestyle, and various stresses. As a result, thirteen housekeeping genes (rps-23, rps-26, rps-27, rps-16, rps-2, rps-4, rps-17, rpl-24.1, rpl-27, rpl-33, rpl-36, rpl-35, and rpl-15) with enhanced stability were comprehensively identified by using six popular normalization algorithms and RankAggreg method. -
Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
Analysis of the Stability of 70 Housekeeping Genes During Ips Reprogramming Yulia Panina1,2*, Arno Germond1 & Tomonobu M
www.nature.com/scientificreports OPEN Analysis of the stability of 70 housekeeping genes during iPS reprogramming Yulia Panina1,2*, Arno Germond1 & Tomonobu M. Watanabe1 Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of cell state known to be associated with profound changes, has been overlooked. In this study we analyzed the expression patterns of the most comprehensive list to date of housekeeping genes during iPS reprogramming of a mouse neural stem cell line N31. Our results show that housekeeping genes’ expression fuctuates signifcantly during the iPS reprogramming. Clustering analysis shows that ribosomal genes’ expression is rising, while the expression of cell-specifc genes, such as vimentin (Vim) or elastin (Eln), is decreasing. To ensure the robustness of the obtained data, we performed a correlative analysis of the genes. Overall, all 70 genes analyzed changed the expression more than two-fold during the reprogramming. The scale of this analysis, that takes into account 70 previously known and newly suggested genes, allowed us to choose the most stable of all genes. We highlight the fact of fuctuation of housekeeping genes during iPS reprogramming, and propose that, to ensure robustness of qPCR experiments in iPS cells, housekeeping genes should be used together in combination, and with a prior testing in a specifc line used in each study. We suggest that the longest splice variants of Rpl13a, Rplp1 and Rps18 can be used as a starting point for such initial testing as the most stable candidates. -
Peroxisomal Functions in the Lung and Their Role in the Pathogenesis of Lung Diseases
Aus dem Institut für Anatomie und Zellbiologie der Justus-Liebig-Universität Gießen Leiter: Prof. Dr. Eveline Baumgart-Vogt Peroxisomal functions in the lung and their role in the pathogenesis of lung diseases Habilitationsschrift zur Erlangung der Venia legendi des Fachbereichs Medizin der Justus-Liebig-Universität Gießen vorgelegt von Srikanth Karnati Gießen 2018 Die nachfolgende Arbeit nimmt Bezug auf folgende Originalarbeiten: 1. Karnati S*, Graulich T, Oruqaj G, Pfreimer S, Seimetz M, Stamme C, Mariani TJ, Weissmann N, Mühlfeld C, Baumgart-Vogt E (2016). Postnatal development of the secretory cells of the distal airways, the bronchiolar club cells in the mouse lung: stereological and molecular biological studies. Cell and Tissue Research. Jun;364(3):543- 57. 2. Karnati S, Baumgart-Vogt E (2009) PeroXisomes in airway epithelia and future prospects of these organelles for pulmonary cell biology. Histochem Cell Biol. Apr: 131(4):447-54. 3. Karnati S, Lüers G, Pfreimer S and Baumgart-Vogt E (2013) Manganese SuperoXide dismutase 2 (MnSOD) is localized to mitochondria but not in peroXisomes. Histochemistry and Cell Biology, Aug:140(2):105-17 4. Karnati S, Palaniswamy S, Alam MR, Oruqaj G, Stamme C, Baumgart-Vogt E (2015) C22- bronchial and T7-alveolar epithelial cell lines of the immortomouse are eXcellent murine cell culture model systems to study pulmonary peroXisome biology and metabolism. Histochemistry and Cell Biology Mar;145(3):287-304. 5. Oruqaj G§, Karnati S§, Vijayan V, Kotarkonda LK, Boateng E, Zhang W, Ruppert C, Günther A, Shi W, Baumgart-Vogt E (2015) Compromised peroXisomes in idiopathic pulmonary fibrosis, a vicious cycle inducing a higher fibrotic response via TGF-β signaling. -
A Common Analgesic Enhances the Anti-Tumour Activity of 5-Aza-2’- Deoxycytidine Through Induction of Oxidative Stress
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.31.017947; this version posted April 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A common analgesic enhances the anti-tumour activity of 5-aza-2’- deoxycytidine through induction of oxidative stress Hannah J. Gleneadie1,10, Amy H. Baker1, Nikolaos Batis2, Jennifer Bryant2, Yao Jiang3, Samuel J.H. Clokie4, Hisham Mehanna2, Paloma Garcia5, Deena M.A. Gendoo6, Sally Roberts5, Alfredo A. Molinolo7, J. Silvio Gutkind8, Ben A. Scheven1, Paul R. Cooper1, Farhat L. Khanim9 and Malgorzata Wiench1, 5,*. 1School of Dentistry, Institute of Clinical Studies, College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B5 7EG, UK; 2Institute of Head and Neck Studies and Education (InHANSE), The University of Birmingham, Birmingham, B15 2TT, UK; 3School of Biosciences, The University of Birmingham, Birmingham, B15 2TT, UK; 4West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s Hospital, Birmingham, B15 2TG, UK; 5Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK; 6Centre for Computational Biology, Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, B15 2TT, UK; 7Moores Cancer Center and Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA; 8Department of Pharmacology and Moores Cancer -
Supplement 1A Steffensen Et
Liver Wild-type Knockout C T C T 1 2 4 7 8 9 1 2 4 5 7 9 1 1 1 1 1 1 C C C T T T C C C T T T W W W W W W K K K K K K IMAGE:793166 RIKEN cDNA 6720463E02 gene IMAGE:1447421 ESTs, Weakly similar to ZF37 MOUSE ZINC FINGER PROTEIN 37 [M.musculus] IMAGE:934291 RIKEN cDNA 2810418N01 gene IMAGE:1247525 small EDRK-rich f2actor IMAGE:1449402 expressed sequence AW321064 IMAGE:1279847 ESTs IMAGE:518737 expressed sequence AW049941 IMAGE:860231 a disintegrin and metalloproteinase domain 17 IMAGE:642836 CD86 antigen IMAGE:1003885 phosphoribosyl pyrophosphate sy1nthetase IMAGE:524862 RIKEN cDNA 5730469D23 gene IMAGE:1264473 protein inhibitor of activat1ed STAT IMAGE:847035 RIKEN cDNA 4833422F06 gene IMAGE:374550 requiem IMAGE:976520 nuclear receptor coact4ivator IMAGE:1264311 Unknown IMAGE:976735 expressed sequence AI987692 IMAGE:976659 cathepsLin IMAGE:1477580 RIKEN cDNA 1600010J02 gene IMAGE:1277168 ribosomal protein, large, P1 IMAGE:524842 RIKEN cDNA 0710008D09 gene IMAGE:373019 split hand/foot delete1d gene IMAGE:404428 expressed sequence AI413851 IMAGE:619810 RIKEN cDNA 1700003F10 gene IMAGE:1749558 caspase 3, apoptosis related cysteine protease IMAGE:718718 RIKEN cDNA 2810003F23 gene IMAGE:819789 Unknown IMAGE:524474 ATP-binding cassette, sub-family A ABC1, member IMAGE:804950 Mus musculus, Similar to ribosomal protein S20, clone MGC:6876 IMAGE:2651405, mRNA, complete cds IMAGE:806143 gap junction membrane channel prot2ein beta IMAGE:1745887 expressed sequence AI836376 IMAGE:779426 RIKEN cDNA 5230400G24 gene IMAGE:1125615 Unknown IMAGE:535025 DNA -
Guideline to Reference Gene Selection for Quantitative Real-Time PCR
BBRC Biochemical and Biophysical Research Communications 313 (2004) 856–862 www.elsevier.com/locate/ybbrc Guideline to reference gene selection for quantitative real-time PCR Aleksandar Radonicc,a Stefanie Thulke,a Ian M. Mackay,b Olfert Landt,d Wolfgang Siegert,a and Andreas Nitschea,c,d,* a Charite—Campus Charite Mitte, II. Medizinische Klinik mit Schwerpunkt Onkologie und Ha€matologie, Humboldt Universita€t, Berlin, Germany b Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children’s Hospital, Brisbane, Australia c Robert Koch Institut, Berlin, Germany d TIB MOLBIOL, Berlin, Germany Received 18 November 2003 Abstract Today, quantitative real-time PCR is the method of choice for rapid and reliable quantification of mRNA transcription. However, for an exact comparison of mRNA transcription in different samples or tissues it is crucial to choose the appropriate reference gene. Recently glyceraldehyde 3-phosphate dehydrogenase and b-actin have been used for that purpose. However, it has been reported that these genes as well as alternatives, like rRNA genes, are unsuitable references, because their transcription is significantly regulated in various experimental settings and variable in different tissues. Therefore, quantitative real-time PCR was used to determine the mRNA transcription profiles of 13 putative reference genes, comparing their transcription in 16 different tissues and in CCRF-HSB-2 cells stimulated with 12-O-tetradecanoylphorbol-13-acetate and ionomycin. Our results show that “Classical” reference genes are indeed unsuitable, whereas the RNA polymerase II gene was the gene with the most constant ex- pression in different tissues and following stimulation in CCRF-HSB-2 cells. -
Cell Type-Specific Analysis of Human Interactome and Transcriptome Shahin Mohammadi Purdue University
Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations January 2016 Cell Type-specific Analysis of Human Interactome and Transcriptome Shahin Mohammadi Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Recommended Citation Mohammadi, Shahin, "Cell Type-specific Analysis of Human Interactome and Transcriptome" (2016). Open Access Dissertations. 1371. https://docs.lib.purdue.edu/open_access_dissertations/1371 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School Form 30 Updated 12/26/2015 PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared By Shahin Mohammadi Entitled CELL TYPE-SPECIFIC ANALYSIS OF HUMAN INTERACTOME AND TRANSCRIPTOME For the degree of Doctor of Philosophy Is approved by the final examining committee: Ananth Grama Wojciech Szpankowski Chair David Gleich Jennifer Neville Markus Lill To the best of my knowledge and as understood by the student in the Thesis/Dissertation Agreement, Publication Delay, and Certification Disclaimer (Graduate School Form 32), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy of Integrity in Research” and the use of copyright material. Approved by Major Professor(s): Ananth Grama William Gorman, Assistant to the Department Head 11/1/2016 Approved by: Head of the Departmental Graduate Program Date CELL TYPE-SPECIFIC ANALYSIS OF HUMAN INTERACTOME AND TRANSCRIPTOME A Dissertation Submitted to the Faculty of Purdue University by Shahin Mohammadi In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2016 Purdue University West Lafayette, Indiana ii I dedicate this thesis to my mom, whose role in my life I can not even begin to describe. -
Live Imaging of Nascent RNA Dynamics Reveals Distinct Types of Transcriptional Pulse Regulation
Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation Tetsuya Muramotoa,1, Danielle Cannona,2, Marek Gierlinski b,c, Adam Corrigana,2, Geoffrey J. Bartonb,c, and Jonathan R. Chubba,2,3 aDivision of Cell and Developmental Biology, bDivision of Biological Chemistry and Drug Discovery, and cWellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom Edited by Sanjay Tyagi, University of Medicine and Dentistry of New Jersey, Newark, NJ, and accepted by the Editorial Board March 21, 2012 (received for review October 25, 2011) Transcription of genes can be discontinuous, occurring in pulses or have different fluctuation kinetics. However, available data on bursts. It is not clear how properties of transcriptional pulses vary transcription bursts and pulses imply active transcriptional states between different genes. We compared the pulsing of five house- last more in the range of minutes, even for strongly transcribed keeping and five developmentally induced genes by direct imaging genes (1). To describe the dynamics of transcription pulses it is of single gene transcriptional events in individual living Dictyoste- therefore necessary to directly observe pulses of RNA production, lium cells. Each gene displayed its own transcriptional signature, which requires using high-affinity RNA–protein interactions to differing in probability of firing and pulse duration, frequency, and deliver fluorescent signals to nascent RNA (15, 16). The resultant intensity. In contrast to the prevailing view from both prokary- accumulation of fluorescence at the site of transcription is viewed otes and eukaryotes that transcription displays binary behavior, under a microscope as a fluorescent spot, which appears and dis- strongly expressed housekeeping genes altered the magnitude of appears (pulses) at irregular intervals when imaged in living cells.