Differential 3' Processing of Specific Transcripts Expands Regulatory
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Genetic Characterization of Endometriosis Patients: Review of the Literature and a Prospective Cohort Study on a Mediterranean Population
International Journal of Molecular Sciences Article Genetic Characterization of Endometriosis Patients: Review of the Literature and a Prospective Cohort Study on a Mediterranean Population Stefano Angioni 1,*, Maurizio Nicola D’Alterio 1,* , Alessandra Coiana 2, Franco Anni 3, Stefano Gessa 4 and Danilo Deiana 1 1 Department of Surgical Science, University of Cagliari, Cittadella Universitaria Blocco I, Asse Didattico Medicna P2, Monserrato, 09042 Cagliari, Italy; [email protected] 2 Department of Medical Science and Public Health, University of Cagliari, Laboratory of Genetics and Genomics, Pediatric Hospital Microcitemico “A. Cao”, Via Edward Jenner, 09121 Cagliari, Italy; [email protected] 3 Department of Medical Science and Public Health, University of Cagliari, Cittadella Universitaria di Monserrato, Asse Didattico E, Monserrato, 09042 Cagliari, Italy; [email protected] 4 Laboratory of Molecular Genetics, Service of Forensic Medicine, AOU Cagliari, Via Ospedale 54, 09124 Cagliari, Italy; [email protected] * Correspondence: [email protected] (S.A.); [email protected] (M.N.D.); Tel.: +39-07051093399 (S.A.) Received: 31 January 2020; Accepted: 2 March 2020; Published: 4 March 2020 Abstract: The pathogenesis of endometriosis is unknown, but some evidence supports a genetic predisposition. The purpose of this study was to evaluate the recent literature on the genetic characterization of women affected by endometriosis and to evaluate the influence of polymorphisms of the wingless-type mammalian mouse tumour virus integration -
VU Research Portal
VU Research Portal Genetic architecture and behavioral analysis of attention and impulsivity Loos, M. 2012 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Loos, M. (2012). Genetic architecture and behavioral analysis of attention and impulsivity. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 28. Sep. 2021 Genetic architecture and behavioral analysis of attention and impulsivity Maarten Loos 1 About the thesis The work described in this thesis was performed at the Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands. This work was in part funded by the Dutch Neuro-Bsik Mouse Phenomics consortium. The Neuro-Bsik Mouse Phenomics consortium was supported by grant BSIK 03053 from SenterNovem (The Netherlands). -
(12) United States Patent (10) Patent No.: US 7.873,482 B2 Stefanon Et Al
US007873482B2 (12) United States Patent (10) Patent No.: US 7.873,482 B2 Stefanon et al. (45) Date of Patent: Jan. 18, 2011 (54) DIAGNOSTIC SYSTEM FOR SELECTING 6,358,546 B1 3/2002 Bebiak et al. NUTRITION AND PHARMACOLOGICAL 6,493,641 B1 12/2002 Singh et al. PRODUCTS FOR ANIMALS 6,537,213 B2 3/2003 Dodds (76) Inventors: Bruno Stefanon, via Zilli, 51/A/3, Martignacco (IT) 33035: W. Jean Dodds, 938 Stanford St., Santa Monica, (Continued) CA (US) 90403 FOREIGN PATENT DOCUMENTS (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 WO WO99-67642 A2 12/1999 U.S.C. 154(b) by 158 days. (21)21) Appl. NoNo.: 12/316,8249 (Continued) (65) Prior Publication Data Swanson, et al., “Nutritional Genomics: Implication for Companion Animals'. The American Society for Nutritional Sciences, (2003).J. US 2010/O15301.6 A1 Jun. 17, 2010 Nutr. 133:3033-3040 (18 pages). (51) Int. Cl. (Continued) G06F 9/00 (2006.01) (52) U.S. Cl. ........................................................ 702/19 Primary Examiner—Edward Raymond (58) Field of Classification Search ................... 702/19 (74) Attorney, Agent, or Firm Greenberg Traurig, LLP 702/23, 182–185 See application file for complete search history. (57) ABSTRACT (56) References Cited An analysis of the profile of a non-human animal comprises: U.S. PATENT DOCUMENTS a) providing a genotypic database to the species of the non 3,995,019 A 1 1/1976 Jerome human animal Subject or a selected group of the species; b) 5,691,157 A 1 1/1997 Gong et al. -
GATA2 Regulates Mast Cell Identity and Responsiveness to Antigenic Stimulation by Promoting Chromatin Remodeling at Super- Enhancers
ARTICLE https://doi.org/10.1038/s41467-020-20766-0 OPEN GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super- enhancers Yapeng Li1, Junfeng Gao 1, Mohammad Kamran1, Laura Harmacek2, Thomas Danhorn 2, Sonia M. Leach1,2, ✉ Brian P. O’Connor2, James R. Hagman 1,3 & Hua Huang 1,3 1234567890():,; Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage- determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes. 1 Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA. 2 Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA. 3 Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, ✉ CO 80045, USA. email: [email protected] NATURE COMMUNICATIONS | (2021) 12:494 | https://doi.org/10.1038/s41467-020-20766-0 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-20766-0 ast cells (MCs) are critical effectors in immunity that at key MC genes. -
The Mosaic Genome of Indigenous African Cattle As a Unique Genetic Resource for African
1 The mosaic genome of indigenous African cattle as a unique genetic resource for African 2 pastoralism 3 4 Kwondo Kim1,2, Taehyung Kwon1, Tadelle Dessie3, DongAhn Yoo4, Okeyo Ally Mwai5, Jisung Jang4, 5 Samsun Sung2, SaetByeol Lee2, Bashir Salim6, Jaehoon Jung1, Heesu Jeong4, Getinet Mekuriaw 6 Tarekegn7,8, Abdulfatai Tijjani3,9, Dajeong Lim10, Seoae Cho2, Sung Jong Oh11, Hak-Kyo Lee12, 7 Jaemin Kim13, Choongwon Jeong14, Stephen Kemp5,9, Olivier Hanotte3,9,15*, and Heebal Kim1,2,4* 8 9 1Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, 10 Seoul National University, Seoul, Republic of Korea. 11 2C&K Genomics, Seoul, Republic of Korea. 12 3International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia. 13 4Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. 14 5International Livestock Research Institute (ILRI), Nairobi, Kenya. 15 6Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum 16 North, Sudan. 17 7Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 18 Sweden. 19 8Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia. 20 9The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The 21 University of Edinburgh, Easter Bush Campus, Midlothian, UK. 1 22 10Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju, 23 Republic of Korea. 24 11International Agricultural Development and Cooperation Center, Jeonbuk National University, 25 Jeonju, Republic of Korea. 26 12Department of Animal Biotechnology, College of Agriculture & Life Sciences, Jeonbuk National 27 University, Jeonju, Republic of Korea. 28 13Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National 29 University, Jinju, Republic of Korea. -
WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T
(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 WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, C12N 1/19 (2006.01) C12Q 1/02 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, C12N 15/81 (2006.01) C07K 14/47 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (21) International Application Number: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, PCT/US20 15/049674 MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (22) International Filing Date: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 11 September 2015 ( 11.09.201 5) SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/050,045 12 September 2014 (12.09.2014) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant: WHITEHEAD INSTITUTE FOR BIOMED¬ DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, ICAL RESEARCH [US/US]; Nine Cambridge Center, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Cambridge, Massachusetts 02142-1479 (US). -
Quantitative Trait Loci Mapping of Macrophage Atherogenic Phenotypes
QUANTITATIVE TRAIT LOCI MAPPING OF MACROPHAGE ATHEROGENIC PHENOTYPES BRIAN RITCHEY Bachelor of Science Biochemistry John Carroll University May 2009 submitted in partial fulfillment of requirements for the degree DOCTOR OF PHILOSOPHY IN CLINICAL AND BIOANALYTICAL CHEMISTRY at the CLEVELAND STATE UNIVERSITY December 2017 We hereby approve this thesis/dissertation for Brian Ritchey Candidate for the Doctor of Philosophy in Clinical-Bioanalytical Chemistry degree for the Department of Chemistry and the CLEVELAND STATE UNIVERSITY College of Graduate Studies by ______________________________ Date: _________ Dissertation Chairperson, Johnathan D. Smith, PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, David J. Anderson, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Baochuan Guo, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Stanley L. Hazen, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Renliang Zhang, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Aimin Zhou, PhD Department of Chemistry, Cleveland State University Date of Defense: October 23, 2017 DEDICATION I dedicate this work to my entire family. In particular, my brother Greg Ritchey, and most especially my father Dr. Michael Ritchey, without whose support none of this work would be possible. I am forever grateful to you for your devotion to me and our family. You are an eternal inspiration that will fuel me for the remainder of my life. I am extraordinarily lucky to have grown up in the family I did, which I will never forget. -
Next-Generation Sequencing of Small Rnas from Inner Ear Sensory
Rudnicki et al. BMC Genomics 2014, 15:484 http://www.biomedcentral.com/1471-2164/15/484 RESEARCH ARTICLE Open Access Next-generation sequencing of small RNAs from inner ear sensory epithelium identifies microRNAs and defines regulatory pathways Anya Rudnicki1†, Ofer Isakov2†, Kathy Ushakov1, Shaked Shivatzki1, Inbal Weiss1,3, Lilach M Friedman1, Noam Shomron2 and Karen B Avraham1* Abstract Background: The mammalian inner ear contains sensory organs, the organ of Corti in the cochlea and cristae and maculae in the vestibule, with each comprised of patterned sensory epithelia that are responsible for hearing and balance. The development, cell fate, patterning, and innervation of both the sensory and nonsensory regions of the inner ear are governed by tight regulation involving, among others, transcription factors and microRNAs (miRNAs). In humans, mutations in specific miRNA genes are associated with hearing loss. In mice, experimental reduction or mutations of miRNAs in the inner ear leads to severe developmental and structural abnormalities. A comprehensive identification of miRNAs in the sensory epithelia and their gene targets will enable pathways of auditory and vestibular function to be defined. Results: In this study, we used Next-Generation Sequencing (NGS) to identify the most prominent miRNAs in the inner ear and to define miRNA-target pairs that form pathways crucial for the function of the sensory epithelial cells. NGS of RNA from inner ear sensory epithelial cells led to the identification of 455 miRNAs in both cochlear and vestibular sensory epithelium, with 30 and 44 miRNAs found in only cochlea or vestibule, respectively. miR-6715-3p and miR-6715-5p were defined for the first time in the inner ear. -
MPA-Induced Gene Expression and Stromal and Parenchymal Gene Expression Profiles in Luminal Murine Mammary Carcinomas with Different Hormonal Requirements
Breast Cancer Res Treat DOI 10.1007/s10549-010-1185-4 PRECLINICAL STUDY MPA-induced gene expression and stromal and parenchymal gene expression profiles in luminal murine mammary carcinomas with different hormonal requirements Sebastia´n Giulianelli • Jason I. Herschkowitz • Vyomesh Patel • Caroline A. Lamb • J. Silvio Gutkind • Alfredo Molinolo • Charles M. Perou • Claudia Lanari Received: 27 August 2010 / Accepted: 17 September 2010 Ó Springer Science+Business Media, LLC. 2010 Abstract Over the past several years, we have been tumor stroma. Eighty-five percent of these genes were interested in understanding the mechanisms by which upregulated, whereas the remaining 15% were downregu- mammary carcinomas acquire hormone independence. We lated in C4-HI relative to their expression in the C4-HD demonstrated that carcinoma associated fibroblasts partic- tumor stroma. Several matrix metallopeptidases were ipate in the ligand-independent activation of progesterone overexpressed in the C4-HI tumor microenvironment. On receptors inducing tumor growth. In this study, we used the other hand, 1100 genes were specifically expressed in DNA microarrays to compare the gene expression profiles the tumor parenchyma. Among them, the 29% were of tumors from the MPA mouse breast cancer model, one upregulated, whereas the remaining 71% were downregu- hormone-dependent (C4-HD) and one hormone-indepen- lated in C4-HI relative to C4-HD tumor epithelium. Steap, dent (C4-HI), using whole tumor samples or laser-captured Pdgfc, Runx2, Cxcl9, and Sdf2 were among the genes with purified stromal and epithelial cells obtained from the high expression in the C4-HI tumor parenchyma. Interest- same tumors. The expression of selected genes was vali- ingly, Fgf2 was one of the few genes upregulated by MPA dated by immunohistochemistry and immunofluorescence in C4-HD tumors, confirming its pivotal role in regulating assays. -
Pathway and Network Analysis for Mrna and Protein Profiling Data
Pathway and network analysis for mRNA and protein profiling data Bing Zhang, Ph.D. Professor of Molecular and Human Genetics Lester & Sue Smith Breast Center Baylor College of Medicine [email protected] VU workshop, 2016 Gene expression DNA Transcription Transcriptome Transcriptome RNA mRNA decay profiling Translation Proteome Protein Proteome Protein degradation profiling Phenotype Networks VU workshop, 2016 Overall workflow of gene expression studies Biological question Experimental design Microarray RNA-Seq Shotgun proteomics Image analysis Reads mapping Peptide/protein ID Signal intensities Read counts Spectral counts; Intensities Data Analysis Experimental Hypothesis validation VU workshop, 2016 Data matrix Samples probe_set_id HNE0_1 HNE0_2 HNE0_3 HNE60_1 HNE60_2 HNE60_3 1007_s_at 8.6888 8.5025 8.5471 8.5412 8.5624 8.3073 1053_at 9.1558 9.1835 9.4294 9.2111 9.1204 9.2494 117_at 7.0700 7.0034 6.9047 9.0414 8.6382 9.2663 121_at 9.7174 9.7440 9.6120 9.7581 9.7422 9.7345 1255_g_at 4.2801 4.4669 4.2360 4.3700 4.4573 4.2979 1294_at 6.3556 6.2381 6.2053 6.4290 6.5074 6.2771 Genes 1316_at 6.5759 6.5330 6.4709 6.6636 6.6438 6.4688 1320_at 6.5497 6.5388 6.5410 6.6605 6.5987 6.7236 1405_i_at 4.3260 4.4640 4.1438 4.3462 4.3876 4.6849 1431_at 5.2191 5.2070 5.2657 5.2823 5.2522 5.1808 1438_at 7.0155 6.9359 6.9241 7.0248 7.0142 7.0971 1487_at 8.6361 8.4879 8.4498 8.4470 8.5311 8.4225 1494_f_at 7.3296 7.3901 7.0886 7.2648 7.6058 7.2949 1552256_a_at 10.6245 10.5235 10.6522 10.4205 10.2344 10.3144 1552257_a_at 10.3224 10.1749 10.1992 10.2464 10.2191 -
Signatures of Adaptive Evolution in Platyrrhine Primate Genomes 5 6 Hazel Byrne*, Timothy H
1 2 Supplementary Materials for 3 4 Signatures of adaptive evolution in platyrrhine primate genomes 5 6 Hazel Byrne*, Timothy H. Webster, Sarah F. Brosnan, Patrícia Izar, Jessica W. Lynch 7 *Corresponding author. Email [email protected] 8 9 10 This PDF file includes: 11 Section 1: Extended methods & results: Robust capuchin reference genome 12 Section 2: Extended methods & results: Signatures of selection in platyrrhine genomes 13 Section 3: Extended results: Robust capuchins (Sapajus; H1) positive selection results 14 Section 4: Extended results: Gracile capuchins (Cebus; H2) positive selection results 15 Section 5: Extended results: Ancestral Cebinae (H3) positive selection results 16 Section 6: Extended results: Across-capuchins (H3a) positive selection results 17 Section 7: Extended results: Ancestral Cebidae (H4) positive selection results 18 Section 8: Extended results: Squirrel monkeys (Saimiri; H5) positive selection results 19 Figs. S1 to S3 20 Tables S1–S3, S5–S7, S10, and S23 21 References (94 to 172) 22 23 Other Supplementary Materials for this manuscript include the following: 24 Tables S4, S8, S9, S11–S22, and S24–S44 1 25 1) Extended methods & results: Robust capuchin reference genome 26 1.1 Genome assembly: versions and accessions 27 The version of the genome assembly used in this study, Sape_Mango_1.0, was uploaded to a 28 Zenodo repository (see data availability). An assembly (Sape_Mango_1.1) with minor 29 modifications including the removal of two short scaffolds and the addition of the mitochondrial 30 genome assembly was uploaded to NCBI under the accession JAGHVQ. The BioProject and 31 BioSample NCBI accessions for this project and sample (Mango) are PRJNA717806 and 32 SAMN18511585. -
2020.02.09.940890V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.09.940890; this version posted February 10, 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. Vezatin is required for the retrograde axonal transport of endosomes in Drosophila and zebrafish Michael A. Spinner1, Katherine Pinter2, Catherine M. Drerup2, and Tory G. Herman1* 1. Institute of Molecular Biology, University of Oregon Eugene, OR USA 2. Unit on Neuronal Cell Biology, NICHD, National Institutes of Health Bethesda, MD USA *To whom correspondence should be addressed Running title: Vezatin is required for retrograde endosomal transport Keywords: Vezatin, CG7705, retrograde axonal transport, endosome Tory Herman, Ph.D. Institute of Molecular Biology 1370 Franklin Blvd University of Oregon Eugene, OR 97403 Tel: 541-346-5043 email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.09.940890; this version posted February 10, 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 Active transport of organelles within axons is critical for neuronal health. Retrograde axonal transport, in particular, relays neurotrophic signals received by axon terminals to the nucleus and circulates new material among en passant synapses. The single retrograde motor, cytoplasmic dynein, is linked to diverse cargos by adaptors that promote dynein motility. Here we identify Vezatin as a new, cargo-specific regulator of retrograde axonal transport. Loss-of- function mutations in the Drosophila vezatin-like (vezl) gene prevent signaling endosomes containing activated BMP receptors from initiating transport out of motor neuron terminal boutons.