A Cdh1–Foxm1–Apc Axis Controls Muscle Development And
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Detailed Review Paper on Retinoid Pathway Signalling
1 1 Detailed Review Paper on Retinoid Pathway Signalling 2 December 2020 3 2 4 Foreword 5 1. Project 4.97 to develop a Detailed Review Paper (DRP) on the Retinoid System 6 was added to the Test Guidelines Programme work plan in 2015. The project was 7 originally proposed by Sweden and the European Commission later joined the project as 8 a co-lead. In 2019, the OECD Secretariat was added to coordinate input from expert 9 consultants. The initial objectives of the project were to: 10 draft a review of the biology of retinoid signalling pathway, 11 describe retinoid-mediated effects on various organ systems, 12 identify relevant retinoid in vitro and ex vivo assays that measure mechanistic 13 effects of chemicals for development, and 14 Identify in vivo endpoints that could be added to existing test guidelines to 15 identify chemical effects on retinoid pathway signalling. 16 2. This DRP is intended to expand the recommendations for the retinoid pathway 17 included in the OECD Detailed Review Paper on the State of the Science on Novel In 18 vitro and In vivo Screening and Testing Methods and Endpoints for Evaluating 19 Endocrine Disruptors (DRP No 178). The retinoid signalling pathway was one of seven 20 endocrine pathways considered to be susceptible to environmental endocrine disruption 21 and for which relevant endpoints could be measured in new or existing OECD Test 22 Guidelines for evaluating endocrine disruption. Due to the complexity of retinoid 23 signalling across multiple organ systems, this effort was foreseen as a multi-step process. -
A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author J Dent Res Manuscript Author . Author manuscript; Manuscript Author available in PMC 2017 October 01. Published in final edited form as: J Dent Res. 2017 October ; 96(11): 1322–1329. doi:10.1177/0022034517716914. A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts L.M. Moreno Uribe1, T. Fomina2, R.G. Munger3, P.A. Romitti4, M.M. Jenkins5, H.K. Gjessing2,6, M. Gjerdevik2,6, K. Christensen7, A.J. Wilcox8, J.C. Murray9, R.T. Lie2,6,*, and G.L. Wehby10,* 1Department of Orthodontics and Dows Institute, College of Dentistry, University of Iowa, Iowa City, IA, USA 2Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway 3Department of Nutrition and Food Sciences, Utah State University, Logan, UT, USA 4Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA 5National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA 6Norwegian Institute of Public Health, Bergen and Oslo, Norway 7Department of Public Health, University of Southern Denmark; Department of Clinical Genetics and Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark 8Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA 9Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA 10Departments of Health Management and Policy, Economics, and Preventive and Community Dentistry, and Public Policy Center, University of Iowa, Iowa City, IA, USA Abstract Prior genome-wide association studies for oral clefts have focused on clinic-based samples with unclear generalizability. -
Differentiation of the Human PAX7
© 2020. Published by The Company of Biologists Ltd | Development (2020) 147, dev187344. doi:10.1242/dev.187344 HUMAN DEVELOPMENT TECHNIQUES AND RESOURCES ARTICLE Differentiation of the human PAX7-positive myogenic precursors/satellite cell lineage in vitro Ziad Al Tanoury1,2,3, Jyoti Rao2,3, Olivier Tassy1,Bénédicte Gobert1,4, Svetlana Gapon2, Jean-Marie Garnier1, Erica Wagner2, Aurore Hick4, Arielle Hall5, Emanuela Gussoni5 and Olivier Pourquié1,2,3,6,* ABSTRACT SC derive from the paraxial mesoderm, the embryonic tissue that Satellite cells (SC) are muscle stem cells that can regenerate adult forms the vertebral column and skeletal muscles (Chal and Pourquié, muscles upon injury. Most SC originate from PAX7+ myogenic 2017; Gros et al., 2005; Hutcheson et al., 2009; Kassar-Duchossoy precursors set aside during development. Although myogenesis has et al., 2005; Lepper and Fan, 2010; Relaix et al., 2005; Schienda et al., + been studied in mouse and chicken embryos, little is known about 2006). Pax3 myogenic precursors arise from the dorsal epithelial + human muscle development. Here, we report the generation of human compartment of the somite called the dermomyotome. Pax3 cells of induced pluripotent stem cell (iPSC) reporter lines in which fluorescent the dermomyotome lips activate Myf5, then downregulate Pax3 and proteins have been introduced into the PAX7 and MYOG loci. We use delaminate and differentiate into elongated post-mitotic myocytes single cell RNA sequencing to analyze the developmental trajectory of expressing myogenin (Myog) to form the first embryonic muscles + the iPSC-derived PAX7+ myogenic precursors. We show that the called myotomes (Chal and Pourquié, 2017). At the same time, Pax3 PAX7+ cells generated in culture can produce myofibers and self- myogenic precursors delaminate from the lateral edge of the renew in vitro and in vivo. -
Predicting FOXM1-Mediated Gene Regulation Through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines
International Journal of Molecular Sciences Article Predicting FOXM1-Mediated Gene Regulation through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines 1, , 2, 1 3,4 Keunsoo Kang * y, Yoonjung Choi y, Hoo Hyun Kim , Kyung Hyun Yoo and Sungryul Yu 5,* 1 Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea; [email protected] 2 Deargen Inc., Daejeon 34051, Korea; [email protected] 3 Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea; [email protected] 4 Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea 5 Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Korea * Correspondence: [email protected] (K.K.); [email protected] (S.Y.); Tel.: +82-41-550-3456 (K.K.); +82-43-649-1418 (S.Y.) These authors contributed equally to the work. y Received: 22 June 2020; Accepted: 24 August 2020; Published: 26 August 2020 Abstract: Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. However, the mechanism by which FOXM1 controls the common gene set in different cellular contexts is unclear. In this study, a comprehensive meta-analysis of genome-wide FOXM1 binding sites in ECC-1, GM12878, K562, MCF-7, and SK-N-SH cell lines was conducted to predict FOXM1-driven gene regulation. Consistent with previous studies, different TF binding motifs were identified at FOXM1 binding sites, while the NFY binding motif was found at 81% of common FOXM1 binding sites in promoters of cell cycle-related genes. -
PAX7 Balances the Cell Cycle Progression Via Regulating Expression of Dnmt3b and Apobec2 in Differentiating Pscs
cells Article PAX7 Balances the Cell Cycle Progression via Regulating Expression of Dnmt3b and Apobec2 in Differentiating PSCs Anita Florkowska , Igor Meszka, Joanna Nowacka, Monika Granica , Zuzanna Jablonska, Magdalena Zawada, Lukasz Truszkowski , Maria A. Ciemerych and Iwona Grabowska * Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; a.fl[email protected] (A.F.); [email protected] (I.M.); [email protected] (J.N.); [email protected] (M.G.); [email protected] (Z.J.); [email protected] (M.Z.); [email protected] (L.T.); [email protected] (M.A.C.) * Correspondence: [email protected] Abstract: PAX7 transcription factor plays a crucial role in embryonic myogenesis and in adult muscles in which it secures proper function of satellite cells, including regulation of their self renewal. PAX7 downregulation is necessary for the myogenic differentiation of satellite cells induced after muscle damage, what is prerequisite step for regeneration. Using differentiating pluripotent stem cells we documented that the absence of functional PAX7 facilitates proliferation. Such action is executed by the modulation of the expression of two proteins involved in the DNA methylation, i.e., Dnmt3b and Apobec2. Increase in Dnmt3b expression led to the downregulation of the CDK inhibitors and Citation: Florkowska, A.; Meszka, I.; facilitated cell cycle progression. Changes in Apobec2 expression, on the other hand, differently Nowacka, J.; Granica, M.; Jablonska, impacted proliferation/differentiation balance, depending on the experimental model used. Z.; Zawada, M.; Truszkowski, L.; Ciemerych, M.A.; Grabowska, I. -
Role of Fzr1 in Embryogenesis
ROLE OF FZR1 IN EMBRYOGENESIS SEAH KAY YI MICHELLE BSC. (HONS I) PH.D THESIS Statement of Originality This thesis contains no material which has been accepted for the award for any other Degree or Diploma in any University or other tertiary institution and, to the best of my knowledge and belief, contains no material previously published or written by another person, except where due reference has been made in the text. I give consent to this copy of my thesis, when deposited in the University library, being made available for loan and photocopying subject to the provisions of the Copyright Act 1968. Seah Kay Yi Michelle 17th December 2012 Page | ii Acknowledgements I would like to sincerely express my appreciation and gratitude to my supervisors, Keith and Janet for giving me this opportunity and to share their wisdom and guidance throughout my PhD. I would also like to extend my thanks to all the lab members including Evan, Jess, Julie, Kyra, Nicole, Phoebe, Simon, Sophia, Suzanne and Yan. Thank you for your company and help throughout my PhD, it has made this an enjoyable experience in the lab. To my family especially Popo, Mummy and Daddy, thank you for the endless love, support and understanding that you have showered upon me. For that, I will be eternally grateful. Thank you for moulding me into the person that I am today, for without all of you, I will not be where I am today. I love you and will always be your little girl. To Clara, my BFF, thank you for your encouragements and to always be there for me. -
Loss of the Mammalian APC/C Activator FZR1 Shortens G1 and Lengthens S Phase but Has Little Effect on Exit from Mitosis
4208 Research Article Loss of the mammalian APC/C activator FZR1 shortens G1 and lengthens S phase but has little effect on exit from mitosis Reinhard Sigl1, Cornelia Wandke1, Veronika Rauch1, Jane Kirk2, Tim Hunt2 and Stephan Geley1,* 1Division of Molecular Pathophysiology, Biocenter, Innsbruck Medical University, Innsbruck, Austria 2Clare Hall Laboratories, Cancer Research UK, South Mimms, England, UK *Author for correspondence ([email protected]) Accepted 10 September 2009 Journal of Cell Science 122, 4208-4217 Published by The Company of Biologists 2009 doi:10.1242/jcs.054197 Summary The anaphase-promoting complex/cyclosome (APC/C) is knockdown of p53 in U2OS cells with inducible FZR1 siRNA essential for progression through mitosis. At anaphase onset, also failed to restore their proliferative capacity. Thus, the the APC/C requires the activator protein CDC20 to target proliferation defects are a direct consequence of the genetic securin and cyclin B1 for proteasome-dependent degradation, damage inflicted by loss of FZR1 function and are largely but then depends on the CDC20-related protein FZR1 (also independent of p53. In summary, mammalian FZR1 is not known as CDH1) to remain active until the onset of the next S required for the completion of mitosis, but is an important phase. To investigate the role of FZR1 in mammalian cells, we regulator of G1 phase and is required for efficient DNA used RNAi in human cell lines and conditional gene targeting replication in human and mouse somatic cells. in mouse embryonic fibroblasts. In neither case was FZR1 required for exit from mitosis, but in cells lacking FZR1, the Supplementary material available online at G1 phase was shortened and the S phase was prolonged. -
Comparison of Gene Expression Response to Neutron and X-Ray Irradiation Using Mouse Blood Constantinos G
Broustas et al. BMC Genomics (2017) 18:2 DOI 10.1186/s12864-016-3436-1 RESEARCHARTICLE Open Access Comparison of gene expression response to neutron and x-ray irradiation using mouse blood Constantinos G. Broustas1, Yanping Xu2, Andrew D. Harken2, Guy Garty2 and Sally A. Amundson1* Abstract Background: In the event of an improvised nuclear device detonation, the prompt radiation exposure would consist of photons plus a neutron component that would contribute to the total dose. As neutrons cause more complex and difficult to repair damage to cells that would result in a more severe health burden to affected individuals, it is paramount to be able to estimate the contribution of neutrons to an estimated dose, to provide information for those making treatment decisions. Results: Mice exposed to either 0.25 or 1 Gy of neutron or 1 or 4 Gy x-ray radiation were sacrificed at 1 or 7 days after exposure. Whole genome microarray analysis identified 7285 and 5045 differentially expressed genes in the blood of mice exposed to neutron or x-ray radiation, respectively. Neutron exposure resulted in mostly downregulated genes, whereas x-rays showed both down- and up-regulated genes. A total of 34 differentially expressed genes were regulated in response to all ≥1 Gy exposures at both times. Of these, 25 genes were consistently downregulated at days 1 and 7, whereas 9 genes, including the transcription factor E2f2, showed bi-directional regulation; being downregulated at day 1, while upregulated at day 7. Gene ontology analysis revealed that genes involved in nucleic acid metabolism processes were persistently downregulated in neutron irradiated mice, whereas genes involved in lipid metabolism were upregulated in x-ray irradiated animals. -
Phosphorylation of the Anaphase Promoting Complex
www.nature.com/scientificreports OPEN Phosphorylation of the Anaphase Promoting Complex activator FZR1/CDH1 is required for Meiosis II entry in mouse male germ cell Nobuhiro Tanno1,2, Shinji Kuninaka2, Sayoko Fujimura3, Kazumasa Takemoto1, Kaho Okamura1, Naoki Takeda4, Kimi Araki4,5, Masatake Araki4, Hideyuki Saya2 & Kei-ichiro Ishiguro1 ✉ FZR1/CDH1 is an activator of Anaphase promoting complex/Cyclosome (APC/C), best known for its role as E3 ubiquitin ligase that drives the cell cycle. APC/C activity is regulated by CDK-mediated phosphorylation of FZR1 during mitotic cell cycle. Although the critical role of FZR1 phosphorylation has been shown mainly in yeast and in vitro cell culture studies, its biological signifcance in mammalian tissues in vivo remained elusive. Here, we examined the in vivo role of FZR1 phosphorylation using a mouse model, in which non-phosphorylatable substitutions were introduced in the putative CDK- phosphorylation sites of FZR1. Although ablation of FZR1 phosphorylation did not show substantial consequences in mouse somatic tissues, it led to severe testicular defects resulting in male infertility. In the absence of FZR1 phosphorylation, male juvenile germ cells entered meiosis normally but failed to enter meiosis II or form diferentiated spermatids. In aged testis, male mutant germ cells were overall abolished, showing Sertoli cell-only phenotype. In contrast, female mutants showed apparently normal progression of meiosis. The present study demonstrated that phosphorylation of FZR1 is required for temporal regulation of APC/C activity at meiosis II entry, and for maintenance of spermatogonia, which raised an insight into the sexual dimorphism of FZR1-regulation in germ cells. Anaphase promoting complex/Cyclosome (APC/C) controls timely transitions of mitotic cell cycle phases by pro- moting ubiquitylation and degradation of many key cell cycle regulators1. -
An OTX2-PAX3 Signaling Axis Regulates Group 3 Medulloblastoma Cell Fate
ARTICLE https://doi.org/10.1038/s41467-020-17357-4 OPEN An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate Jamie Zagozewski1, Ghazaleh M. Shahriary 1, Ludivine Coudière Morrison1, Olivier Saulnier 2,3, Margaret Stromecki1, Agnes Fresnoza4, Gareth Palidwor5, Christopher J. Porter 5, Antoine Forget6,7, Olivier Ayrault 6,7, Cynthia Hawkins2,8,9, Jennifer A. Chan10, Maria C. Vladoiu2,3,9, Lakshmikirupa Sundaresan2,3, Janilyn Arsenio11,12, Michael D. Taylor 2,3,9,13, Vijay Ramaswamy 2,3,14,15 & ✉ Tamra E. Werbowetski-Ogilvie 1 1234567890():,; OTX2 is a potent oncogene that promotes tumor growth in Group 3 medulloblastoma. However, the mechanisms by which OTX2 represses neural differentiation are not well characterized. Here, we perform extensive multiomic analyses to identify an OTX2 regulatory network that controls Group 3 medulloblastoma cell fate. OTX2 silencing modulates the repressive chromatin landscape, decreases levels of PRC2 complex genes and increases the expression of neurodevelopmental transcription factors including PAX3 and PAX6. Expression of PAX3 and PAX6 is significantly lower in Group 3 medulloblastoma patients and is cor- related with reduced survival, yet only PAX3 inhibits self-renewal in vitro and increases survival in vivo. Single cell RNA sequencing of Group 3 medulloblastoma tumorspheres demonstrates expression of an undifferentiated progenitor program observed in primary tumors and characterized by translation/elongation factor genes. Identification of mTORC1 signaling as a downstream effector of OTX2-PAX3 reveals roles for protein synthesis pathways in regulating Group 3 medulloblastoma pathogenesis. 1 Regenerative Medicine Program, Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada. 2 The Arthur and Sonia Labatt Brain Tumour Research Center, The Hospital for Sick Children, Toronto, ON, Canada. -
Effects of Estrogen Receptor Activation on Post-Exercise Muscle Satellite Cell Proliferation
Wilfrid Laurier University Scholars Commons @ Laurier Theses and Dissertations (Comprehensive) 2009 Effects of Estrogen Receptor Activation on Post-Exercise Muscle Satellite Cell Proliferation Kareem Bunyan Wilfrid Laurier University Follow this and additional works at: https://scholars.wlu.ca/etd Part of the Exercise Science Commons Recommended Citation Bunyan, Kareem, "Effects of Estrogen Receptor Activation on Post-Exercise Muscle Satellite Cell Proliferation" (2009). Theses and Dissertations (Comprehensive). 928. https://scholars.wlu.ca/etd/928 This Thesis is brought to you for free and open access by Scholars Commons @ Laurier. It has been accepted for inclusion in Theses and Dissertations (Comprehensive) by an authorized administrator of Scholars Commons @ Laurier. For more information, please contact [email protected]. Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 OttawaONK1A0N4 Canada Canada Your file Votre r&ference ISBN: 978-0-494-54223-1 Our file Notre reference ISBN: 978-0-494-54223-1 NOTICE: AVIS: The author has granted a non L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. -
Biocreative 2012 Proceedings
Proceedings of 2012 BioCreative Workshop April 4 -5, 2012 Washington, DC USA Editors: Cecilia Arighi Kevin Cohen Lynette Hirschman Martin Krallinger Zhiyong Lu Carolyn Mattingly Alfonso Valencia Thomas Wiegers John Wilbur Cathy Wu 2012 BioCreative Workshop Proceedings Table of Contents Preface…………………………………………………………………………………….......... iv Committees……………………………………………………………………………………... v Workshop Agenda…………………………………………………………………………….. vi Track 1 Collaborative Biocuration-Text Mining Development Task for Document Prioritization for Curation……………………………………..……………………………………………….. 2 T Wiegers, AP Davis, and CJ Mattingly System Description for the BioCreative 2012 Triage Task ………………………………... 20 S Kim, W Kim, CH Wei, Z Lu and WJ Wilbur Ranking of CTD articles and interactions using the OntoGene pipeline ……………..….. 25 F Rinaldi, S Clematide and S Hafner Selection of relevant articles for curation for the Comparative Toxicogenomic Database…………………………………………………………………………………………. 31 D Vishnyakova, E Pasche and P Ruch CoIN: a network exploration for document triage………………………………................... 39 YY Hsu and HY Kao DrTW: A Biomedical Term Weighting Method for Document Recommendation ………... 45 JH Ju, YD Chen and JH Chiang C2HI: a Complete CHemical Information decision system……………………………..….. 52 CH Ke, TLM Lee and JH Chiang Track 2 Overview of BioCreative Curation Workshop Track II: Curation Workflows….…………... 59 Z Lu and L Hirschman WormBase Literature Curation Workflow ……………………………………………………. 66 KV Auken, T Bieri, A Cabunoc, J Chan, Wj Chen, P Davis, A Duong, R Fang, C Grove, Tw Harris, K Howe, R Kishore, R Lee, Y Li, Hm Muller, C Nakamura, B Nash, P Ozersky, M Paulini, D Raciti, A Rangarajan, G Schindelman, Ma Tuli, D Wang, X Wang, G Williams, K Yook, J Hodgkin, M Berriman, R Durbin, P Kersey, J Spieth, L Stein and Pw Sternberg Literature curation workflow at The Arabidopsis Information Resource (TAIR)…..……… 72 D Li, R Muller, TZ Berardini and E Huala Summary of Curation Process for one component of the Mouse Genome Informatics Database Resource …………………………………………………………………………....