Intestine of Zebrafish: Regionalization, Characterization and Stem Cells
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Wo 2010/075007 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 1 July 2010 (01.07.2010) WO 2010/075007 A2 (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/68 (2006.01) G06F 19/00 (2006.01) kind of national protection available): AE, AG, AL, AM, C12N 15/12 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (21) International Application Number: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US2009/067757 HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (22) International Filing Date: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 11 December 2009 ( 11.12.2009) ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (25) Filing Language: English SE, SG, SK, SL, SM, ST, SV, SY, TJ, TM, TN, TR, TT, (26) Publication Language: English TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 12/3 16,877 16 December 2008 (16.12.2008) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, (71) Applicant (for all designated States except US): DODDS, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, W., Jean [US/US]; 938 Stanford Street, Santa Monica, TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE, CA 90403 (US). -
University of Copenhagen, Copenhagen, Denmark, Citation: Pereira J, Johnson WE, O’Brien SJ, 8
Evolutionary genomics and adaptive evolution of the hedgehog gene family (Shh, Ihh and Dhh) in vertebrates Pereira, Joana; Johnson, Warren E.; O'Brien, Stephen J.; Jarvis, Erich D; Zhang, Guojie; Gilbert, M. Thomas P.; Vasconcelos, Vitor; Antunes, Agostinho Published in: PloS one DOI: 10.1371/journal.pone.0074132 Publication date: 2014 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Pereira, J., Johnson, W. E., O'Brien, S. J., Jarvis, E. D., Zhang, G., Gilbert, M. T. P., Vasconcelos, V., & Antunes, A. (2014). Evolutionary genomics and adaptive evolution of the hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. PloS one, 9(12), [e74132]. https://doi.org/10.1371/journal.pone.0074132 Download date: 24. sep.. 2021 RESEARCH ARTICLE Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates Joana Pereira1¤, Warren E. Johnson2, Stephen J. O’Brien3,4, Erich D. Jarvis5, Guojie Zhang6, M. Thomas P. Gilbert7, Vitor Vasconcelos1,8, Agostinho Antunes1,8* 1. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal, 2. Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia, United States of America, 3. Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia, 4. Oceanographic Center, N. Ocean Drive, Nova Southeastern University, Ft. Lauderdale, Florida, United States of America, 5. Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America, 6. BGI-Shenzhen, Beishan Industrial Zoon, Yantian District, Shenzhen, China, 7. -
Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2006 Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene Yutao Liu University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Life Sciences Commons Recommended Citation Liu, Yutao, "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino- like Mouse Models: Tracking the Role of the Hairless Gene. " PhD diss., University of Tennessee, 2006. https://trace.tennessee.edu/utk_graddiss/1824 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Yutao Liu entitled "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Life Sciences. Brynn H. Voy, Major Professor We have read this dissertation and recommend its acceptance: Naima Moustaid-Moussa, Yisong Wang, Rogert Hettich Accepted for the Council: Carolyn R. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
S1 Supplemental Materials Supplemental Methods Supplemental Figure 1. Immune Phenotype of Mcd19 Targeted CAR T and Dose Titratio
Supplemental Materials Supplemental Methods Supplemental Figure 1. Immune phenotype of mCD19 targeted CAR T and dose titration of in vivo efficacy. Supplemental Figure 2. Gene expression of fluorescent-protein tagged CAR T cells. Supplemental Figure 3. Fluorescent protein tagged CAR T cells function similarly to non-tagged counterparts. Supplemental Figure 4. Transduction efficiency and immune phenotype of mCD19 targeted CAR T cells for survival study (Figure 2D). Supplemental Figure 5. Transduction efficiency and immune phenotype of CAR T cells used in irradiated CAR T study (Fig. 3B-C). Supplemental Figure 6. Differential gene expression of CD4+ m19-humBBz CAR T cells. Supplemental Figure 7. CAR expression and CD4/CD8 subsets of human CD19 targeted CAR T cells for Figure 5E-G. Supplemental Figure 8. Transduction efficiency and immune phenotype of mCD19 targeted wild type (WT) and TRAF1-/- CAR T cells used for in vivo study (Figure 6D). Supplemental Figure 9. Mutated m19-musBBz CAR T cells have increased NF-κB signaling, improved cytokine production, anti-apoptosis, and in vivo function. Supplemental Figure 10. TRAF and CAR co-expression in human CD19-targeted CAR T cells. Supplemental Figure 11. TRAF2 over-expressed h19BBz CAR T cells show similar in vivo efficacy to h19BBz CAR T cells in an aggressive leukemia model. S1 Supplemental Table 1. Probesets increased in m19z and m1928z vs m19-musBBz CAR T cells. Supplemental Table 2. Probesets increased in m19-musBBz vs m19z and m1928z CAR T cells. Supplemental Table 3. Probesets differentially expressed in m19z vs m19-musBBz CAR T cells. Supplemental Table 4. Probesets differentially expressed in m1928z vs m19-musBBz CAR T cells. -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
Early Diagnosis of Colorectal Cancer Via Plasma Proteomic Analysis of CRC and Advanced Adenomatous Polyp
Gastroenterology and Hepatology From Bed to Bench. ORIGINAL ARTICLE ©2019 RIGLD, Research Institute for Gastroenterology and Liver Diseases Early diagnosis of colorectal cancer via plasma proteomic analysis of CRC and advanced adenomatous polyp Setareh Fayazfar1, Hakimeh Zali2, Afsaneh Arefi Oskouie1, Hamid Asadzadeh Aghdaei3, Mostafa Rezaei Tavirani4, Ehsan Nazemalhosseini Mojarad5 1Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran 2School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran 3Basic and Molecular Epidemiology of Gastroenterology Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran 4Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran 5Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran ABSTRACT Aim: This paper aimed to identify new candidate biomarkers in blood for early diagnosis of CRC. Background: Colorectal cancer (CRC) is the third most widespread malignancies increasing globally. The high mortality rate associated with colorectal cancer is due to the delayed diagnosis in an advanced stage while the metastasis has occurred. For better clinical management and subsequently to reduce mortality of CRC, early detection biomarkers are in high demand. -
Supplemental Table 1: Genes That Show Altered Expression in Hepg2 Cells in the Presence of Exogenously Added Let-7
Supplemental Table 1: Genes that show altered expression in HepG2 cells in the presence of exogenously added let-7 Gene Title Gene Symbol RefSeq Transcriptp- IDvalue(TREAp-TMENTvalue(Let7bS) - negativLog2 Reatio control1) (Let7b - negativp-value(Let7be control1) - negativLog2 Reatio control2) (Let7b - negative control2) aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase) AKR1D1 NM_005989 3.28E-12 2.52E-12 -3.85007 3.59E-12 -3.73727 lin-28 homolog B (C. elegans) LIN28B NM_001004317 6.13E-15 8.29E-15 -3.29879 1.55E-15 -3.79656 high mobility group AT-hook 2 /// high mobility group AT-hook 2 HMGA2 NM_001015886 /// NM_0034833.74E-14 /// NM_0034844.29E-14 -3.06085 4.56E-14 -3.04538 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 HECW2 NM_020760 1.27E-13 6.65E-13 -2.94724 4.47E-12 -2.50907 cell division cycle 25A CDC25A NM_001789 /// NM_2015672.01E-11 7.32E-11 -2.88831 1.99E-11 -3.22735 hypothetical protein FLJ21986 FLJ21986 NM_024913 1.05E-09 5.19E-10 -2.80277 1.18E-09 -2.61084 solute carrier family 2 (facilitated glucose transporter), member 3 SLC2A3 NM_006931 1.59E-13 3.49E-13 -2.78111 1.84E-12 -2.41734 Transcribed locus --- --- 2.58E-13 1.08E-13 -2.59794 1.69E-13 -2.50248 Hypothetical protein LOC145786 LOC145786 --- 4.23E-12 1.07E-11 -2.58849 3.00E-12 -2.88135 Dicer1, Dcr-1 homolog (Drosophila) DICER1 NM_030621 /// NM_1774381.06E-08 4.37E-09 -2.5442 4.49E-09 -2.53796 mannose-binding lectin (protein C) 2, soluble (opsonic defect) MBL2 NM_000242 9.73E-10 1.48E-09 -2.53211 9.84E-10 -2.62363 cell -
FAM20B (N-14): Sc-164312
SAN TA C RUZ BI OTEC HNOL OG Y, INC . FAM20B (N-14): sc-164312 BACKGROUND SOURCE Chromosome 1 is the largest human chromosome spanning about 260 million FAM20B (N-14) is an affinity purified goat polyclonal antibody raised against base pairs and making up 8% of the human genome. There are about 3,000 a peptide mapping near the N-terminus of FAM20B of human origin. genes on chromosome 1, and considering the great number of genes there are also a large number of diseases associated with chromosome 1. Notably, the PRODUCT rare aging disease Hutchinson-Gilford progeria is associated with the LMNA Each vial contains 200 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide gene which encodes lamin A. When defective, the LMNA gene product can and 0.1% gelatin. build up in the nucleus and cause characteristic nuclear blebs. The mechanism of rapidly enhanced aging is unclear and is a topic of continuing exploration. Blocking peptide available for competition studies, sc-164312 P, (100 µg The MUTYH gene is located on chromosome 1 and is partially responsible for peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). familial adenomatous polyposis. Stickler syndrome, Parkinsons, Gaucher dis - ease and Usher syndrome are also associated with chromosome 1. A break - APPLICATIONS point has been identified in 1q which disrupts the DISC1 gene and is linked FAM20B (N-14) is recommended for detection of FAM20B of mouse, rat and to schizophrenia. Aberrations in chromosome 1 are found in a variety of can - human origin by Western Blotting (starting dilution 1:200, dilution range cers including head and neck cancer, malignant melanoma and multiple myelo - 1:100-1:1000), immunofluorescence (starting dilution 1:50, dilution range ma. -
High-Throughput Bioinformatics Approaches to Understand Gene Expression Regulation in Head and Neck Tumors
High-throughput bioinformatics approaches to understand gene expression regulation in head and neck tumors by Yanxiao Zhang A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in The University of Michigan 2016 Doctoral Committee: Associate Professor Maureen A. Sartor, Chair Professor Thomas E. Carey Assistant Professor Hui Jiang Professor Ronald J. Koenig Associate Professor Laura M. Rozek Professor Kerby A. Shedden c Yanxiao Zhang 2016 All Rights Reserved I dedicate this thesis to my family. For their unfailing love, understanding and support. ii ACKNOWLEDGEMENTS I would like to express my gratitude to Dr. Maureen Sartor for her guidance in my research and career development. She is a great mentor. She patiently taught me when I started new in this field, granted me freedom to explore and helped me out when I got lost. Her dedication to work, enthusiasm in teaching, mentoring and communicating science have inspired me to feel the excite- ment of research beyond novel scientific discoveries. I’m also grateful to have an interdisciplinary committee. Their feedback on my research progress and presentation skills is very valuable. In particular, I would like to thank Dr. Thomas Carey and Dr. Laura Rozek for insightful discussions on the biology of head and neck cancers and human papillomavirus, Dr. Ronald Koenig for expert knowledge on thyroid cancers, Dr. Hui Jiang and Dr. Kerby Shedden for feedback on the statistics part of my thesis. I would like to thank all the past and current members of Sartor lab for making the lab such a lovely place to stay and work in. -
Functional Analysis of Structural Variation in the 2D and 3D Human Genome
FUNCTIONAL ANALYSIS OF STRUCTURAL VARIATION IN THE 2D AND 3D HUMAN GENOME by Conor Mitchell Liam Nodzak A dissertation submitted to the faculty of The University of North Carolina at Charlotte in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics and Computational Biology Charlotte 2019 Approved by: Dr. Xinghua Mindy Shi Dr. Rebekah Rogers Dr. Jun-tao Guo Dr. Adam Reitzel ii c 2019 Conor Mitchell Liam Nodzak ALL RIGHTS RESERVED iii ABSTRACT CONOR MITCHELL LIAM NODZAK. Functional analysis of structural variation in the 2D and 3D human genome. (Under the direction of DR. XINGHUA MINDY SHI) The human genome consists of over 3 billion nucleotides that have an average distance of 3.4 Angstroms between each base, which equates to over two meters of DNA contained within the 125 µm3 volume diploid cell nuclei. The dense compaction of chromatin by the supercoiling of DNA forms distinct architectural modules called topologically associated domains (TADs), which keep protein-coding genes, noncoding RNAs and epigenetic regulatory elements in close nuclear space. It has recently been shown that these conserved chromatin structures may contribute to tissue-specific gene expression through the encapsulation of genes and cis-regulatory elements, and mutations that affect TADs can lead to developmental disorders and some forms of cancer. At the population-level, genomic structural variation contributes more to cumulative genetic difference than any other class of mutation, yet much remains to be studied as to how structural variation affects TADs. Here, we study the func- tional effects of structural variants (SVs) through the analysis of chromatin topology and gene activity for three trio families sampled from genetically diverse popula- tions from the Human Genome Structural Variation Consortium. -
Functional Annotation of Genes Overlapping Copy Number Variants in Autistic Patients: Focus on Axon Pathfinding
136 Current Genomics, 2010, 11, 136-145 Functional Annotation of Genes Overlapping Copy Number Variants in Autistic Patients: Focus on Axon Pathfinding Silvia Sbacchi1, Francesco Acquadro2, Ignazio Calò1, Francesco Calì3 and Valentino Romano*,1,3 1Dipartimento di Oncologia Sperimentale e Applicazioni Cliniche, Università degli Studi di Palermo, Palermo; 2Molecular Cytogenetics Group, Centro Nacional de Investigaciones Oncologicas (C.N.I.O.), and Centro de Investiga- ciones de Enfermidades Raras (CIBERER), Madrid, Spain; 3Associazione Oasi Maria SS. (I.R.C.C.S.), Troina (EN), Italy Abstract: We have used Gene Ontology (GO) and pathway analyses to uncover the common functions associated to the genes overlapping Copy Number Variants (CNVs) in autistic patients. Our source of data were four published studies [1- 4]. We first applied a two-step enrichment strategy for autism-specific genes. We fished out from the four mentioned stud- ies a list of 2928 genes overall overlapping 328 CNVs in patients and we first selected a sub-group of 2044 genes after excluding those ones that are also involved in CNVs reported in the Database of Genomic Variants (enrichment step 1). We then selected from the step 1-enriched list a sub-group of 514 genes each of which was found to be deleted or dupli- cated in at least two patients (enrichment step 2). The number of statistically significant processes and pathways identified by the Database for Annotation, Visualization and Integrated Discovery and Ingenuity Pathways Analysis softwares with the step 2-enriched list was significantly higher compared to the step 1-enriched list. In addition, statistically significant GO terms, biofunctions and pathways related to nervous system development and function were exclusively identified by the step 2-enriched list of genes.