0.01 Sequence Description Accession #Fold Change P-Value Solute Carrier Fa
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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 -
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. -
Overexpressed Nup88 Stabilized Through Interaction with Nup62 Promotes NFB
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063057; this version posted May 4, 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. Overexpressed Nup88 stabilized through interaction with Nup62 promotes NFB dependent pathways in cancer Usha Singh1, Atul Samaiya2, and Ram Kumar Mishra1,* 1 Nups and Sumo Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Madhya Pradesh, 462066, India. 2 Department of Surgical Oncology, Bansal Hospital, Bhopal, Madhya Pradesh, 462016, India * To whom correspondence should be addressed. Corresponding Author: Phone – +91-755-2691407 Fax - +91-755-2692392 Email- [email protected] Keywords Nup88; NFB; Head and neck cancer; ubiquitination; cell proliferation; inflammation 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063057; this version posted May 4, 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. Abstract Nuclear pores control nucleo-cytoplasmic trafficking and directly or indirectly regulate vital cellular processes. Nup88, important for Crm1 mediated nuclear export process, is overexpressed in many cancers. A positive correlation exists between progressive stages of cancer and Nup88 expression. However, links between Nup88 overexpression and head and neck cancer are insignificant, and mechanistic details are non-existent. Here, we report that Nup88 exhibits positive correlation in head and neck cancer in addition to elevated Nup62 levels. We demonstrate that Nup88 interacts with Nup62 in a cell-cycle and glycosylation independent manner. -
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. -
HCC and Cancer Mutated Genes Summarized in the Literature Gene Symbol Gene Name References*
HCC and cancer mutated genes summarized in the literature Gene symbol Gene name References* A2M Alpha-2-macroglobulin (4) ABL1 c-abl oncogene 1, receptor tyrosine kinase (4,5,22) ACBD7 Acyl-Coenzyme A binding domain containing 7 (23) ACTL6A Actin-like 6A (4,5) ACTL6B Actin-like 6B (4) ACVR1B Activin A receptor, type IB (21,22) ACVR2A Activin A receptor, type IIA (4,21) ADAM10 ADAM metallopeptidase domain 10 (5) ADAMTS9 ADAM metallopeptidase with thrombospondin type 1 motif, 9 (4) ADCY2 Adenylate cyclase 2 (brain) (26) AJUBA Ajuba LIM protein (21) AKAP9 A kinase (PRKA) anchor protein (yotiao) 9 (4) Akt AKT serine/threonine kinase (28) AKT1 v-akt murine thymoma viral oncogene homolog 1 (5,21,22) AKT2 v-akt murine thymoma viral oncogene homolog 2 (4) ALB Albumin (4) ALK Anaplastic lymphoma receptor tyrosine kinase (22) AMPH Amphiphysin (24) ANK3 Ankyrin 3, node of Ranvier (ankyrin G) (4) ANKRD12 Ankyrin repeat domain 12 (4) ANO1 Anoctamin 1, calcium activated chloride channel (4) APC Adenomatous polyposis coli (4,5,21,22,25,28) APOB Apolipoprotein B [including Ag(x) antigen] (4) AR Androgen receptor (5,21-23) ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 (4) ARHGAP35 Rho GTPase activating protein 35 (21) ARID1A AT rich interactive domain 1A (SWI-like) (4,5,21,22,24,25,27,28) ARID1B AT rich interactive domain 1B (SWI1-like) (4,5,22) ARID2 AT rich interactive domain 2 (ARID, RFX-like) (4,5,22,24,25,27,28) ARID4A AT rich interactive domain 4A (RBP1-like) (28) ARID5B AT rich interactive domain 5B (MRF1-like) (21) ASPM Asp (abnormal -
Towards Relating the Evolution of the Gene Repertoire in Mammals to Tissue Specialisation
Towards Relating the Evolution of the Gene Repertoire in Mammals to Tissue Specialisation Shiri Freilich Wolfson College This dissertation is submitted to the University of Cambridge for the degree of Doctor of Philosophy 21 December 2006 To Leon, who was the wind blowing in my sails, in the deep blue sea of this journey of ours. This Thesis is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This Thesis does not exceed the specified length limit of 300 pages as defined by the Biology Degree Committee. This Thesis has been typeset in 12pt font according to the specifications defined by the Board of Graduate Studies and the Biology Degree Committee. 3 Summary: Towards Relating the Evolution of the Gene Repertoire in Mammals to Tissue Specialisation The sequencing efforts of recent years have provided a rich source of data for investigating how gene content determines similarity and uniqueness in a species’ phenotype. Work described in this PhD Thesis attempts to relate innovations in the gene repertoire along the mammalian lineage to the most obvious phenotypic characteristic of animals: the appearance of highly differentiated tissue types. Several different approaches, outlined below, have been followed to address some aspects of this problem. Initially, a comprehensive study of the pattern of expansion of the complement of enzymes in various species was performed in order to obtain a better view of the principles underlying the expansion of the gene repertoire in mammals. Although several studies have described a tendency toward an increase in sequence redundancy in mammals, not much is known about the way such sequence redundancy reflects functional redundancy. -
Antigen-Specific Memory CD4 T Cells Coordinated Changes in DNA
Downloaded from http://www.jimmunol.org/ by guest on September 24, 2021 is online at: average * The Journal of Immunology The Journal of Immunology published online 18 March 2013 from submission to initial decision 4 weeks from acceptance to publication http://www.jimmunol.org/content/early/2013/03/17/jimmun ol.1202267 Coordinated Changes in DNA Methylation in Antigen-Specific Memory CD4 T Cells Shin-ichi Hashimoto, Katsumi Ogoshi, Atsushi Sasaki, Jun Abe, Wei Qu, Yoichiro Nakatani, Budrul Ahsan, Kenshiro Oshima, Francis H. W. Shand, Akio Ametani, Yutaka Suzuki, Shuichi Kaneko, Takashi Wada, Masahira Hattori, Sumio Sugano, Shinichi Morishita and Kouji Matsushima J Immunol Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Author Choice option Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Freely available online through http://www.jimmunol.org/content/suppl/2013/03/18/jimmunol.120226 7.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Permissions Email Alerts Subscription Author Choice Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 24, 2021. Published March 18, 2013, doi:10.4049/jimmunol.1202267 The Journal of Immunology Coordinated Changes in DNA Methylation in Antigen-Specific Memory CD4 T Cells Shin-ichi Hashimoto,*,†,‡ Katsumi Ogoshi,* Atsushi Sasaki,† Jun Abe,* Wei Qu,† Yoichiro Nakatani,† Budrul Ahsan,x Kenshiro Oshima,† Francis H. -
Nup88 (22): Sc-136009
SANTA CRUZ BIOTECHNOLOGY, INC. Nup88 (22): sc-136009 BACKGROUND APPLICATIONS The nuclear pore complex (NPC) mediates bidirectional macromolecular Nup88 (22) is recommended for detection of Nup88 of mouse, rat and human traffic between the nucleus and cytoplasm in eukaryotic cells and is com- origin by Western Blotting (starting dilution 1:200, dilution range 1:100- prised of more than 100 different subunits. Many of the subunits belong to 1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml a family called nucleoporins (Nups), which are characterized by the pres- of cell lysate)] and immunofluorescence (starting dilution 1:50, dilution range ence of O-linked-N-acetylglucosamine moieties and a distinctive pentapep- 1:50-1:500). tide repeat (XFXFG). Nup88 (nucleoporin 88 kDa) is a 741 amino acid protein Suitable for use as control antibody for Nup88 siRNA (h): sc-75980, Nup88 that localizes to the nucleus and functions as an essential component of siRNA (m): sc-75981, Nup88 shRNA Plasmid (h): sc-75980-SH, Nup88 shRNA the nuclear pore complex. Expressed ubiquitously, Nup88 is subject to phos- Plasmid (m): sc-75981-SH, Nup88 shRNA (h) Lentiviral Particles: sc-75980-V phorylation by ATM or ATR and is upregulated in malignant neoplasms and and Nup88 shRNA (m) Lentiviral Particles: sc-75981-V. precancerous dysplasias, suggesting a role in tumorigenesis. The gene encod- ing Nup88 maps to human chromosome 17p13.2, which comprises over 2.5% Molecular Weight of Nup88: 88 kDa. of the human genome and encodes over 1,200 genes. Positive Controls: IMR-32 cell lysate: sc-2409, HeLa whole cell lysate: sc-2200 or A-431 whole cell lysate: sc-2201. -
Eukaryotic Genome Annotation
Comparative Features of Multicellular Eukaryotic Genomes (2017) (First three statistics from www.ensembl.org; other from original papers) C. elegans A. thaliana D. melanogaster M. musculus H. sapiens Species name Nematode Thale Cress Fruit Fly Mouse Human Size (Mb) 103 136 143 3,482 3,555 # Protein-coding genes 20,362 27,655 13,918 22,598 20,338 (25,498 (13,601 original (30,000 (30,000 original est.) original est.) original est.) est.) Transcripts 58,941 55,157 34,749 131,195 200,310 Gene density (#/kb) 1/5 1/4.5 1/8.8 1/83 1/97 LINE/SINE (%) 0.4 0.5 0.7 27.4 33.6 LTR (%) 0.0 4.8 1.5 9.9 8.6 DNA Elements 5.3 5.1 0.7 0.9 3.1 Total repeats 6.5 10.5 3.1 38.6 46.4 Exons % genome size 27 28.8 24.0 per gene 4.0 5.4 4.1 8.4 8.7 average size (bp) 250 506 Introns % genome size 15.6 average size (bp) 168 Arabidopsis Chromosome Structures Sorghum Whole Genome Details Characterizing the Proteome The Protein World • Sequencing has defined o Many, many proteins • How can we use this data to: o Define genes in new genomes o Look for evolutionarily related genes o Follow evolution of genes ▪ Mixing of domains to create new proteins o Uncover important subsets of genes that ▪ That deep phylogenies • Plants vs. animals • Placental vs. non-placental animals • Monocots vs. dicots plants • Common nomenclature needed o Ensure consistency of interpretations InterPro (http://www.ebi.ac.uk/interpro/) Classification of Protein Families • Intergrated documentation resource for protein super families, families, domains and functional sites o Mitchell AL, Attwood TK, Babbitt PC, et al. -
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 -
Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7, -
(19) United States (12) Patent Application Publication (10) Pub
US 20120149714A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0149714 A1 Heise et al. (43) Pub. Date: Jun. 14, 2012 (54) EFFECTS OF INHIBITORS OF FGFR3 ON (60) Provisional application No. 60/748,944, ?led on Dec. GENE TRANSCRIPTION 8, 2005. (76) Inventors: Carla Heise, Benicia, CA (US); Publication Classi?cation Esther Masih-Khan, Ontario (CA); 51 I Cl Edward Moler Walnut Creek CA ( ) nt' ' (US); Michael. Rowe,’ Oakland,’ CA A61K 31/497 (2006.01) (US),_ Keith. Stewart, Scottsdale, G01N 33/53 (2006.01) AZ (US) Suzanne Trudel Ontario G01N 33/566 (200601) (CA) ’ ’ C12Q 1/68 (2006.01) (52) US. Cl. ................ .. 514/253.07; 435/611; 435/612; (21) Appl. No.: 13/400,833 435/79; 435/792; 436/501 (22) Filed: Feb. 21, 2012 (57) ABSTRACT Related U‘s‘ Application Data Methods of utilizing blomarkers to 1dent1fy patients for treat ment or to momtor response to treatment are taught herein. (62) Division of application No, 12/096,222, ?led on Jun, Alterations in levels of gene expression of the biomarkers, 19, 2008, now Pat. No. 8,158,360, ?led as application particularly in response to FGFR3 inhibition, are measured No. PCT/US2006/061766 on Dec. 7, 2006. and identi?cations or adjustments may be made accordingly. US 2012/0149714 A1 Jun. 14, 2012 EFFECTS OF INHIBITORS OF FGFR3 ON [0007] An individual’s response to a particular treatment or GENE TRANSCRIPTION predisposition to disease and the correlation to a particular gene of interest has been documented. It is noW believed that BACKGROUND OF THE INVENTION cancer chemotherapy is limited by the predisposition of spe ci?c populations to drug toxicity or poor drug response.