A Prevalence of Imprinted Genes Within the Total Transcriptomes of Human Tissues and Cells
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Product Datasheet C9orf85 Overexpression Lysate NBL1-08604 Unit Size: 0.1 mg Store at -80C. Avoid freeze-thaw cycles. Protocols, Publications, Related Products, Reviews, Research Tools and Images at: www.novusbio.com/NBL1-08604 Updated 3/17/2020 v.20.1 Earn rewards for product reviews and publications. Submit a publication at www.novusbio.com/publications Submit a review at www.novusbio.com/reviews/destination/NBL1-08604 Page 1 of 2 v.20.1 Updated 3/17/2020 NBL1-08604 C9orf85 Overexpression Lysate Product Information Unit Size 0.1 mg Concentration The exact concentration of the protein of interest cannot be determined for overexpression lysates. Please contact technical support for more information. Storage Store at -80C. Avoid freeze-thaw cycles. Buffer RIPA buffer Target Molecular Weight 18.1 kDa Product Description Description Transient overexpression lysate of chromosome 9 open reading frame 85 (C9orf85) The lysate was created in HEK293T cells, using Plasmid ID RC208807 and based on accession number NM_182505. The protein contains a C- MYC/DDK Tag. Gene ID 138241 Gene Symbol C9ORF85 Species Human Notes HEK293T cells in 10-cm dishes were transiently transfected with a non-lipid polymer transfection reagent specially designed and manufactured for large volume DNA transfection. Transfected cells were cultured for 48hrs before collection. The cells were lysed in modified RIPA buffer (25mM Tris-HCl pH7.6, 150mM NaCl, 1% NP-40, 1mM EDTA, 1xProteinase inhibitor cocktail mix, 1mM PMSF and 1mM Na3VO4, and then centrifuged to clarify the lysate. Protein concentration was measured by BCA protein assay kit.This product is manufactured by and sold under license from OriGene Technologies and its use is limited solely for research purposes. -
Two Spatially Distinct Kinesin-14 Pkl1 and Klp2 Generate Collaborative
bioRxiv preprint doi: https://doi.org/10.1101/205815; this version posted October 19, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Two spatially distinct Kinesin-14 Pkl1 and Klp2 generate collaborative inward forces against Kinesin-5 Cut7 in S. pombe Masashi Yukawa*, Yusuke Yamada, Tomoaki Yamauchi and Takashi Toda* Laboratory of Molecular and Chemical Cell Biology, Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan. * To whom correspondence should be addressed: Tel/Fax: +81 82 424 7754; E-mail: [email protected], Tel/Fax: +81 82 424 7868; E-mail: [email protected] Running title: Inward forces exerted by Kinesin-14s Keywords: fission yeast/force generation/kinesin/mitotic bipolar spindle/spindle pole body Abbreviations used: GFP-binding protein, GBP; Msd1-Wdr8-Pkl1 complex, MWP complex; spindle pole body, SPB; temperature sensitive, ts; the γ-tubulin complex, γ-TuC 1 bioRxiv preprint doi: https://doi.org/10.1101/205815; this version posted October 19, 2017. 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. SUMMARY STATEMENT Proper force-balance generated by Kinesin-5 and Kinesin-14 is crucial for spindle bipolarity. Two fission yeast Kinesin-14s localize to different structures, thereby collaboratively producing inward forces against Kinesin-5-mediated outward force. ABSTRACT Kinesin motors play central roles in bipolar spindle assembly. -
Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 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. Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome Edward L. Huttlin1*, Raphael J. Bruckner1,3, Jose Navarrete-Perea1, Joe R. Cannon1,4, Kurt Baltier1,5, Fana Gebreab1, Melanie P. Gygi1, Alexandra Thornock1, Gabriela Zarraga1,6, Stanley Tam1,7, John Szpyt1, Alexandra Panov1, Hannah Parzen1,8, Sipei Fu1, Arvene Golbazi1, Eila Maenpaa1, Keegan Stricker1, Sanjukta Guha Thakurta1, Ramin Rad1, Joshua Pan2, David P. Nusinow1, Joao A. Paulo1, Devin K. Schweppe1, Laura Pontano Vaites1, J. Wade Harper1*, Steven P. Gygi1*# 1Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA. 2Broad Institute, Cambridge, MA, 02142, USA. 3Present address: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA. 4Present address: Merck, West Point, PA, 19486, USA. 5Present address: IQ Proteomics, Cambridge, MA, 02139, USA. 6Present address: Vor Biopharma, Cambridge, MA, 02142, USA. 7Present address: Rubius Therapeutics, Cambridge, MA, 02139, USA. 8Present address: RPS North America, South Kingstown, RI, 02879, USA. *Correspondence: [email protected] (E.L.H.), [email protected] (J.W.H.), [email protected] (S.P.G.) #Lead Contact: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Transcriptional Control of Tissue-Resident Memory T Cell Generation
Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells. -
Comprehensive Identification of Genes Driven by ERV9-Ltrs Reveals TNFRSF10B As a Re-Activatable Mediator of Testicular Cancer Cell Death
Cell Death and Differentiation (2016) 23, 64–75 & 2016 Macmillan Publishers Limited All rights reserved 1350-9047/16 www.nature.com/cdd Comprehensive identification of genes driven by ERV9-LTRs reveals TNFRSF10B as a re-activatable mediator of testicular cancer cell death U Beyer1,2,5, SK Krönung1,5, A Leha3, L Walter4 and M Dobbelstein*,1 The long terminal repeat (LTR) of human endogenous retrovirus type 9 (ERV9) acts as a germline-specific promoter that induces the expression of a proapoptotic isoform of the tumor suppressor homologue p63, GTAp63, in male germline cells. Testicular cancer cells silence this promoter, but inhibitors of histone deacetylases (HDACs) restore GTAp63 expression and give rise to apoptosis. We show here that numerous additional transcripts throughout the genome are driven by related ERV9-LTRs. 3' Rapid amplification of cDNA ends (3’RACE) was combined with next-generation sequencing to establish a large set of such mRNAs. HDAC inhibitors induce these ERV9-LTR-driven genes but not the LTRs from other ERVs. In particular, a transcript encoding the death receptor DR5 originates from an ERV9-LTR inserted upstream of the protein coding regions of the TNFRSF10B gene, and it shows an expression pattern similar to GTAp63. When treating testicular cancer cells with HDAC inhibitors as well as the death ligand TNF-related apoptosis-inducing ligand (TRAIL), rapid cell death was observed, which depended on TNFRSF10B expression. HDAC inhibitors also cooperate with cisplatin (cDDP) to promote apoptosis in testicular cancer cells. ERV9-LTRs not only drive a large set of human transcripts, but a subset of them acts in a proapoptotic manner. -
Two Spatially Distinct Kinesin-14 Proteins, Pkl1 and Klp2, Generate Collaborative Inward Forces Against Kinesin-5 Cut7 in S
© 2018. Published by The Company of Biologists Ltd | Journal of Cell Science (2018) 131, jcs210740. doi:10.1242/jcs.210740 RESEARCH ARTICLE Two spatially distinct kinesin-14 proteins, Pkl1 and Klp2, generate collaborative inward forces against kinesin-5 Cut7 in S. pombe Masashi Yukawa*, Yusuke Yamada, Tomoaki Yamauchi and Takashi Toda* ABSTRACT bioinformatics analysis indicates the existence of additional groups Kinesin motors play central roles in bipolar spindle assembly. In many (Wickstead et al., 2010). In general, N-kinesins and C-kinesins eukaryotes, spindle pole separation is driven by kinesin-5, which possess microtubule plus end- and minus end-directed motilities generates outward force. This outward force is balanced by respectively, whereas M-kinesins are microtubule depolymerases. antagonistic inward force elicited by kinesin-14 and/or dynein. In As proposed originally (Vale et al., 1985), kinesin molecules act as fission yeast, two kinesin-14 proteins, Pkl1 and Klp2, play an cellular power plants by generating directional forces across opposing role against the kinesin-5 motor protein Cut7. However, microtubules through repeated ATPase cycles. how the two kinesin-14 proteins coordinate individual activities During mitosis, a number of distinct kinesin molecules engage remains elusive. Here, we show that although deletion of either pkl1 with bipolar spindle assembly, thereby ensuring coordinated or klp2 rescues temperature-sensitive cut7 mutants, deletion of only chromosome segregation; these kinesins are collectively called pkl1 can bypass the lethality caused by cut7 deletion. Pkl1 is tethered mitotic kinesins (Sharp et al., 2000b; Tanenbaum and Medema, to the spindle pole body, whereas Klp2 is localized along the spindle 2010; Yount et al., 2015). -
Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades. -
Inter-Population Differences in Retrogene Loss and Expression in Humans
RESEARCH ARTICLE Inter-population Differences in Retrogene Loss and Expression in Humans Michał Kabza1*, Magdalena Regina Kubiak1, Agnieszka Danek2, Wojciech Rosikiewicz1, Sebastian Deorowicz2, Andrzej Polański2, Izabela Makałowska1* 1 Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland, 2 Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland * [email protected] (MK); [email protected] (IM) a11111 Abstract Gene retroposition leads to considerable genetic variation between individuals. Recent studies revealed the presence of at least 208 retroduplication variations (RDVs), a class of polymorphisms, in which a retrocopy is present or absent from individual genomes. Most of OPEN ACCESS these RDVs resulted from recent retroduplications. In this study, we used the results of Citation: Kabza M, Kubiak MR, Danek A, Rosikiewicz Phase 1 from the 1000 Genomes Project to investigate the variation in loss of ancestral (i.e. ń W, Deorowicz S, Pola ski A, et al. (2015) Inter- shared with other primates) retrocopies among different human populations. In addition, we population Differences in Retrogene Loss and Expression in Humans. PLoS Genet 11(10): examined retrocopy expression levels using RNA-Seq data derived from the Ilumina Body- e1005579. doi:10.1371/journal.pgen.1005579 Map project, as well as data from lymphoblastoid cell lines provided by the Geuvadis Con- Editor: Takashi Gojobori, National Institute of sortium. We also developed a new approach to detect novel retrocopies absent from the Genetics, JAPAN reference human genome. We experimentally confirmed the existence of the detected retro- Received: June 3, 2015 copies and determined their presence or absence in the human genomes of 17 different populations. -
Genome-Wide Profiling of Druggable Active Tumor Defense Mechanisms to Enhance Cancer Immunotherapy
bioRxiv preprint doi: https://doi.org/10.1101/843185; this version posted November 15, 2019. 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. Genome-wide profiling of druggable active tumor defense mechanisms to enhance cancer immunotherapy Rigel J. Kishton1,2,*,#, Shashank J. Patel1,2,†,*, Suman K. Vodnala1,2, Amy E. Decker3, Yogin Patel1,2, Madhusudhanan Sukumar1,2, Tori N. Yamamoto1,2,4, Zhiya Yu1,2, Michelle Ji1,2, Amanda N. Henning1,2, Devikala Gurusamy1,2, Douglas C. Palmer1,2, Winifred Lo1, Anna Pasetto1, Parisa Malekzadeh1, Drew C. Deniger1, Kris C. Wood3, Neville E. Sanjana5,6, Nicholas P. Restifo1,2, #, § 1Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA 2Center for Cell-Based Therapy, National Cancer Institute, Bethesda, MD 20892, USA 3Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC, USA 4Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA 5New York Genome Center, New York, NY 10013 USA 6Department of Biology, New York University, New York, NY 10003, USA *These authors contributed equally to this work. †Present address: NextCure Inc., Beltsville, MD 20705, USA §Present address: Lyell Immunopharma, South San Francisco, CA 94080, USA #Corresponding authors. NPR: [email protected]. RJK: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/843185; this version posted November 15, 2019. 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. -
Símbolos, Siglas E Abreviaturas
UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL DEPARTAMENTO DE GENÉTICA PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA E BIOLOGIA MOLECULAR AVALIAÇÃO CITOGENÔMICA EM INDIVÍDUOS COM CARDIOPATIAS CONGÊNITAS CONOTRUNCAIS Káren Regina Silva de Souza Dissertação submetida ao Programa de Pós- Graduação em Genética e Biologia Molecular da UFRGS como requisito parcial para a obtenção do grau de Mestre em Genética e Biologia Molecular Orientadora: Profa Dra. Mariluce Riegel Porto Alegre Março de 2015 Este trabalho foi desenvolvido no Laboratório de Citogenética Molecular do Hospital de Clínicas de Porto Alegre e teve como fontes financiadoras o Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq/476783/2013-5) e Fundação de Amparo à Pesquisa do Rio Grande do Sul (FAPERGS/Edital PQG 001/2013). AGRADECIMENTOS ______________________________________________________________________________ Agradeço, primeiramente, a minha orientadora Profa Dra. Mariluce Riegel, sem sua paciência, profissionalismo e companheirismo este trabalho não teria sido possível. Agradeço por sua orientação e compreensão durante todas as etapas deste estudo. Agradeço a meus pais, José Nilton e Hilda Regina, por seu apoio em todas as etapas da minha vida e por sempre acreditarem em mim e me proporcionarem a possibilidade de escolher o caminho que eu gostaria de trilhar. Agradeço a meu marido André, por sua paciência e amor infinito. Agradeço a minhas irmãs Carla e Helena por serem companheiras de todas as horas. Agradeço a equipe dos Laboratórios de Citogenética do Serviço de Genética Médica e de Citogenética Molecular por fazerem parte da minha rotina tornando todos os dias de trabalho mais agradáveis. A Dra. Janaina Huber, cardiologista do Instituto de Cardiologia do Rio Grande do Sul/Fundação Universitária, pelo trabalho em colaboração. -
Wo 2010/065567 A2
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 10 June 2010 (10.06.2010) WO 2010/065567 A2 (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 36/889 (2006.01) A61K 31/16 (2006.01) kind of national protection available): AE, AG, AL, AM, A61K 36/736 (2006.01) A61K 31/05 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, A61K 31/166 (2006.01) A61P 5/00 (2006.01) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (21) International Application Number: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, PCT/US2009/066294 KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (22) International Filing Date: ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, 1 December 2009 (01 .12.2009) NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TJ, TM, TN, TR, TT, (25) Filing Language: English TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 61/1 18,945 1 December 2008 (01 .12.2008) US GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, (71) Applicant (for all designated States except US): LIFES¬ TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE, PAN EXTENSION LLC [US/US]; 933 First Colonial ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Road, Suite 114, Virginia Beach, VA 23454 (US).