Dmrt1, a Gene Related to Worm and Fly Sexual Regulators, Is Required for Mammalian Testis Differentiation
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INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of tftis reproduction is dependent upon the quality of the copy sutHnitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. in the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with smal overlaps. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9* black and white photographic prints are available for any photographs or Uustrations appearing in this copy for an additional charge. Contact UMI directly to order. ProQuest Information and Learning 300 North Zeeb Road, Atm Arbor, Ml 48106-1346 USA 800-521-0600 UMT MOLECULAR ANALYSIS OF L7/PCP-2 MESSENGER RNA AND ITS INTERACTING PROTEINS DISSERTATION Presented in Partial Fulfillment of the Requirements for The Degree Doctor of Philosophy in Ohio State Biochemistry Program of The Ohio State University By Xulun Zhang, M.S. ***** The Ohio State University 2001 Dissertation Committee: Approved by Professor John D. -
Further Delineation of Chromosomal Consensus Regions in Primary
Leukemia (2007) 21, 2463–2469 & 2007 Nature Publishing Group All rights reserved 0887-6924/07 $30.00 www.nature.com/leu ORIGINAL ARTICLE Further delineation of chromosomal consensus regions in primary mediastinal B-cell lymphomas: an analysis of 37 tumor samples using high-resolution genomic profiling (array-CGH) S Wessendorf1,6, TFE Barth2,6, A Viardot1, A Mueller3, HA Kestler3, H Kohlhammer1, P Lichter4, M Bentz5,HDo¨hner1,PMo¨ller2 and C Schwaenen1 1Klinik fu¨r Innere Medizin III, Zentrum fu¨r Innere Medizin der Universita¨t Ulm, Ulm, Germany; 2Institut fu¨r Pathologie, Universita¨t Ulm, Ulm, Germany; 3Forschungsdozentur Bioinformatik, Universita¨t Ulm, Ulm, Germany; 4Abt. Molekulare Genetik, Deutsches Krebsforschungszentrum, Heidelberg, Germany and 5Sta¨dtisches Klinikum Karlsruhe, Karlsruhe, Germany Primary mediastinal B-cell lymphoma (PMBL) is an aggressive the expression of BSAP, BOB1, OCT2, PAX5 and PU1 was extranodal B-cell non-Hodgkin’s lymphoma with specific clin- added to the spectrum typical of PMBL features.9 ical, histopathological and genomic features. To characterize Genetically, a pattern of highly recurrent karyotype alterations further the genotype of PMBL, we analyzed 37 tumor samples and PMBL cell lines Med-B1 and Karpas1106P using array- with the hallmark of chromosomal gains of the subtelomeric based comparative genomic hybridization (matrix- or array- region of chromosome 9 supported the concept of a unique CGH) to a 2.8k genomic microarray. Due to a higher genomic disease entity that distinguishes PMBL from other B-cell non- resolution, we identified altered chromosomal regions in much Hodgkin’s lymphomas.10,11 Together with less specific gains on higher frequencies compared with standard CGH: for example, 2p15 and frequent mutations of the SOCS1 gene, a notable þ 9p24 (68%), þ 2p15 (51%), þ 7q22 (32%), þ 9q34 (32%), genomic similarity to classical Hodgkin’s lymphoma was þ 11q23 (18%), þ 12q (30%) and þ 18q21 (24%). -
Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7 -
Retinoic Acid Induces Sertoli Cell Paracrine Signals for Spermatogonia Differentiation but Cell Autonomously Drives Spermatocyte Meiosis
Retinoic acid induces Sertoli cell paracrine signals for spermatogonia differentiation but cell autonomously drives spermatocyte meiosis Mathilde Raverdeaua, Aurore Gely-Pernota, Betty Féreta, Christine Dennefelda, Gérard Benoitb, Irwin Davidsona, Pierre Chambona,1, Manuel Marka,c, and Norbert B. Ghyselincka,1 aInstitut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7104, Institut National de la Santé et de la Recherche Médicale Unité 964, Université de Strasbourg, F-67404 Illkirch Cedex, France; bCentre de Génétique et de Physiologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5534, Université de Lyon 1, F-69622 Villeurbanne Cedex, France; and cHôpitaux Universitaires de Strasbourg, F-67091 Strasbourg Cedex, France Contributed by Pierre Chambon, August 29, 2012 (sent for review July 26, 2012) Direct evidence for a role of endogenous retinoic acid (RA), the active a recent study showing that female GC can enter meiosis in a fetal metabolite of vitamin A in the initial differentiation and meiotic entry ovary devoid of RA has challenged this model (6). of spermatogonia, and thus in the initiation of spermatogenesis is still During embryonic development RA usually acts in a paracrine lacking. RA is synthesized by dedicated enzymes, the retinaldehyde manner, one cell type controlling its synthesis, whereas a neigh- dehydrogenases (RALDH), and binds to and activates nuclear RA bor cell type responds to the signal (7). In cells synthesizing RA, receptors (RARA, RARB, and RARG) either within the RA-synthesizing conversion of retinol to its active metabolite depends upon ret- cells or in the neighboring cells. -
DM Domain Proteins in Sexual Regulation 875 Transformation Marker Prf4 (Containing the Mutant Rol-6 Allele Green fluorescent Protein (GFP) Coding Region
Development 126, 873-881 (1999) 873 Printed in Great Britain © The Company of Biologists Limited 1999 DEV5283 Similarity of DNA binding and transcriptional regulation by Caenorhabditis elegans MAB-3 and Drosophila melanogaster DSX suggests conservation of sex determining mechanisms Woelsung Yi1 and David Zarkower1,2,* 1Biochemistry, Molecular Biology and Biophysics Graduate Program, and 2Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA *Author for correspondence (e-mail: [email protected]) Accepted 17 December 1998; published on WWW 2 February 1999 SUMMARY Although most animals occur in two sexes, the molecular transcription, resulting in expression in both sexes, and the pathways they employ to control sexual development vary vitellogenin genes have potential MAB-3 binding sites considerably. The only known molecular similarity upstream of their transcriptional start sites. MAB-3 binds between phyla in sex determination is between two genes, to a site in the vit-2 promoter in vitro, and this site is mab-3 from C. elegans, and doublesex (dsx) from required in vivo to prevent transcription of a vit-2 reporter Drosophila. Both genes contain a DNA binding motif called construct in males, suggesting that MAB-3 is a direct a DM domain and they regulate similar aspects of sexual repressor of vitellogenin transcription. This is the first development, including yolk protein synthesis and direct link between the sex determination regulatory peripheral nervous system differentiation. Here we show pathway and sex-specific structural genes in C. elegans, and that MAB-3, like the DSX proteins, is a direct regulator of it suggests that nematodes and insects use at least some of yolk protein gene transcription. -
A W-Linked DM-Domain Gene, DM-W, Participates in Primary Ovary Development in Xenopus Laevis
A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis Shin Yoshimoto*, Ema Okada*, Hirohito Umemoto*, Kei Tamura*, Yoshinobu Uno†, Chizuko Nishida-Umehara†, Yoichi Matsuda†, Nobuhiko Takamatsu*, Tadayoshi Shiba*, and Michihiko Ito*‡ *Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan; and †Division of Genome Dynamics, Creative Research Initiative ‘‘Sousei,’’ Hokkaido University, North10 West8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan Communicated by Satoshi Omura,¯ The Kitasato Institute, Tokyo, Japan, December 27, 2007 (received for review September 11, 2007) In the XX/XY sex-determining system, the Y-linked SRY genes of In some species of amphibians, sex determination is controlled most mammals and the DMY/Dmrt1bY genes of the teleost fish genetically (13), even though the animals’ sex chromosomes are medaka have been characterized as sex-determining genes that morphologically indistinguishable from the autosomes. The trigger formation of the testis. However, the molecular mechanism South African clawed frog Xenopus laevis uses the ZZ/ZW of the ZZ/ZW-type system in vertebrates, including the clawed frog system, which was demonstrated by backcrosses between sex- Xenopus laevis, is unknown. Here, we isolated an X. laevis female reversed and normal individuals (14), but its sex chromosomes genome-specific DM-domain gene, DM-W, and obtained molecular have not yet been identified. Moreover, as with other animals evidence of a W-chromosome in this species. The DNA-binding that use the ZZ/ZW system, no sex-determining gene(s) has domain of DM-W showed a strikingly high identity (89%) with that been identified. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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 The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
The Staurotypus Turtles and Aves Share the Same Origin of Sex Chromosomes but Evolved Different Types of Heterogametic Sex Determination
The Staurotypus Turtles and Aves Share the Same Origin of Sex Chromosomes but Evolved Different Types of Heterogametic Sex Determination Taiki Kawagoshi1, Yoshinobu Uno1, Chizuko Nishida2, Yoichi Matsuda1,3* 1 Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan, 2 Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan, 3 Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan Abstract Reptiles have a wide diversity of sex-determining mechanisms and types of sex chromosomes. Turtles exhibit temperature- dependent sex determination and genotypic sex determination, with male heterogametic (XX/XY) and female heterogametic (ZZ/ZW) sex chromosomes. Identification of sex chromosomes in many turtle species and their comparative genomic analysis are of great significance to understand the evolutionary processes of sex determination and sex chromosome differentiation in Testudines. The Mexican giant musk turtle (Staurotypus triporcatus, Kinosternidae, Testudines) and the giant musk turtle (Staurotypus salvinii) have heteromorphic XY sex chromosomes with a low degree of morphological differentiation; however, their origin and linkage group are still unknown. Cross-species chromosome painting with chromosome-specific DNA from Chinese soft-shelled turtle (Pelodiscus sinensis) revealed that the X and Y chromosomes of S. triporcatus have homology with P. sinensis chromosome 6, which corresponds to the chicken Z chromosome. We cloned cDNA fragments of S. triporcatus homologs of 16 chicken Z-linked genes and mapped them to S. triporcatus and S. salvinii chromosomes using fluorescence in situ hybridization. Sixteen genes were localized to the X and Y long arms in the same order in both species. -
Ubiquitin-Dependent Regulation of a Conserved DMRT Protein Controls
RESEARCH ARTICLE Ubiquitin-dependent regulation of a conserved DMRT protein controls sexually dimorphic synaptic connectivity and behavior Emily A Bayer1, Rebecca C Stecky1, Lauren Neal1, Phinikoula S Katsamba2, Goran Ahlsen2, Vishnu Balaji3, Thorsten Hoppe3,4, Lawrence Shapiro2, Meital Oren-Suissa5, Oliver Hobert1,2* 1Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States; 2Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, United States; 3Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; 4Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; 5Weizmann Institute of Science, Department of Neurobiology, Rehovot, Israel Abstract Sex-specific synaptic connectivity is beginning to emerge as a remarkable, but little explored feature of animal brains. We describe here a novel mechanism that promotes sexually dimorphic neuronal function and synaptic connectivity in the nervous system of the nematode Caenorhabditis elegans. We demonstrate that a phylogenetically conserved, but previously uncharacterized Doublesex/Mab-3 related transcription factor (DMRT), dmd-4, is expressed in two classes of sex-shared phasmid neurons specifically in hermaphrodites but not in males. We find dmd-4 to promote hermaphrodite-specific synaptic connectivity and neuronal function of phasmid sensory neurons. Sex-specificity of DMD-4 function is conferred by a novel mode of *For correspondence: posttranslational regulation that involves sex-specific protein stabilization through ubiquitin binding [email protected] to a phylogenetically conserved but previously unstudied protein domain, the DMA domain. A Competing interest: See human DMRT homolog of DMD-4 is controlled in a similar manner, indicating that our findings may page 25 have implications for the control of sexual differentiation in other animals as well. -
G Protein-Coupled Estrogen Receptor Is Not Required for Sex Determination Or Ovary
bioRxiv preprint doi: https://doi.org/10.1101/373092; this version posted July 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: G protein-coupled estrogen receptor is not required for sex determination or ovary function in zebrafish Authors: Camerron M. Crowder1,$, Shannon N. Romano1,* and Daniel A. Gorelick2,# Affiliations: 1Department of Pharmacology & Toxicology, University of Alabama at Birmingham, Birmingham Alabama, USA 2Center for Precision Environmental Health, Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA *present address: Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA $present address: Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham Alabama, USA #corresponding author: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/373092; this version posted July 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT Estrogens regulate vertebrate development and function through binding to nuclear estrogen receptors alpha and beta (ERa, ERb) and the G protein-coupled estrogen receptor (GPER). Studies in mutant animal models demonstrated that ERa and ERb are required for normal ovary development and function.