Gene Expression Profile of Catsper3 and Catsper4 During Postnatal Development of Mouse Testis
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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. -
Identification of Key Genes and Pathways Involved in Response To
Deng et al. Biol Res (2018) 51:25 https://doi.org/10.1186/s40659-018-0174-7 Biological Research RESEARCH ARTICLE Open Access Identifcation of key genes and pathways involved in response to pain in goat and sheep by transcriptome sequencing Xiuling Deng1,2†, Dong Wang3†, Shenyuan Wang1, Haisheng Wang2 and Huanmin Zhou1* Abstract Purpose: This aim of this study was to investigate the key genes and pathways involved in the response to pain in goat and sheep by transcriptome sequencing. Methods: Chronic pain was induced with the injection of the complete Freund’s adjuvant (CFA) in sheep and goats. The animals were divided into four groups: CFA-treated sheep, control sheep, CFA-treated goat, and control goat groups (n 3 in each group). The dorsal root ganglions of these animals were isolated and used for the construction of a cDNA= library and transcriptome sequencing. Diferentially expressed genes (DEGs) were identifed in CFA-induced sheep and goats and gene ontology (GO) enrichment analysis was performed. Results: In total, 1748 and 2441 DEGs were identifed in CFA-treated goat and sheep, respectively. The DEGs identi- fed in CFA-treated goats, such as C-C motif chemokine ligand 27 (CCL27), glutamate receptor 2 (GRIA2), and sodium voltage-gated channel alpha subunit 3 (SCN3A), were mainly enriched in GO functions associated with N-methyl- D-aspartate (NMDA) receptor, infammatory response, and immune response. The DEGs identifed in CFA-treated sheep, such as gamma-aminobutyric acid (GABA)-related DEGs (gamma-aminobutyric acid type A receptor gamma 3 subunit [GABRG3], GABRB2, and GABRB1), SCN9A, and transient receptor potential cation channel subfamily V member 1 (TRPV1), were mainly enriched in GO functions related to neuroactive ligand-receptor interaction, NMDA receptor, and defense response. -
Ion Channels
UC Davis UC Davis Previously Published Works Title THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels. Permalink https://escholarship.org/uc/item/1442g5hg Journal British journal of pharmacology, 176 Suppl 1(S1) ISSN 0007-1188 Authors Alexander, Stephen PH Mathie, Alistair Peters, John A et al. Publication Date 2019-12-01 DOI 10.1111/bph.14749 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California S.P.H. Alexander et al. The Concise Guide to PHARMACOLOGY 2019/20: Ion channels. British Journal of Pharmacology (2019) 176, S142–S228 THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels Stephen PH Alexander1 , Alistair Mathie2 ,JohnAPeters3 , Emma L Veale2 , Jörg Striessnig4 , Eamonn Kelly5, Jane F Armstrong6 , Elena Faccenda6 ,SimonDHarding6 ,AdamJPawson6 , Joanna L Sharman6 , Christopher Southan6 , Jamie A Davies6 and CGTP Collaborators 1School of Life Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK 2Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK 3Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK 4Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, A-6020 Innsbruck, Austria 5School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK 6Centre for Discovery Brain Science, University of Edinburgh, Edinburgh, EH8 9XD, UK Abstract The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. -
Nicotine Dependece
Alma Mater Studiorum – Università di Bologna DOTTORATO DI RICERCA IN Biologia Cellulare e Molecolare Ciclo XXX Settore Concorsuale: 05/I1 Settore Scientifico Disciplinare: BIO/18 GENETICA Investigation of genetic risk variants for nicotine dependence and cluster headache Presentata da: Cinzia Cameli Coordinatore Dottorato Supervisore Prof. Giovanni Capranico Prof.ssa Elena Maestrini Co-supervisore Dott.ssa Elena Bacchelli Esame finale anno 2018 TABLE OF CONTENTS ABSTRACT......................................................................................................................... 4 INTRODUCTION ................................................................................................................ 6 CHAPTER 1 Nicotine dependence ...................................................................................... 6 1.1 Biological mechanisms ............................................................................................................ 6 1.2 Nicotinic acetylcholine receptors ............................................................................................ 8 1.2.1 Protein structure ............................................................................................................. 8 1.2.2 Localization and function of neuronal nAChRs ............................................................. 10 1.2.3 α7 nAChRs ..................................................................................................................... 12 1.3 The genetics of nicotine dependence .................................................................................. -
Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer
Epigenetic mechanisms are involved in the oncogenic properties of ZNF518B in colorectal cancer Francisco Gimeno-Valiente, Ángela L. Riffo-Campos, Luis Torres, Noelia Tarazona, Valentina Gambardella, Andrés Cervantes, Gerardo López-Rodas, Luis Franco and Josefa Castillo SUPPLEMENTARY METHODS 1. Selection of genomic sequences for ChIP analysis To select the sequences for ChIP analysis in the five putative target genes, namely, PADI3, ZDHHC2, RGS4, EFNA5 and KAT2B, the genomic region corresponding to the gene was downloaded from Ensembl. Then, zoom was applied to see in detail the promoter, enhancers and regulatory sequences. The details for HCT116 cells were then recovered and the target sequences for factor binding examined. Obviously, there are not data for ZNF518B, but special attention was paid to the target sequences of other zinc-finger containing factors. Finally, the regions that may putatively bind ZNF518B were selected and primers defining amplicons spanning such sequences were searched out. Supplementary Figure S3 gives the location of the amplicons used in each gene. 2. Obtaining the raw data and generating the BAM files for in silico analysis of the effects of EHMT2 and EZH2 silencing The data of siEZH2 (SRR6384524), siG9a (SRR6384526) and siNon-target (SRR6384521) in HCT116 cell line, were downloaded from SRA (Bioproject PRJNA422822, https://www.ncbi. nlm.nih.gov/bioproject/), using SRA-tolkit (https://ncbi.github.io/sra-tools/). All data correspond to RNAseq single end. doBasics = TRUE doAll = FALSE $ fastq-dump -I --split-files SRR6384524 Data quality was checked using the software fastqc (https://www.bioinformatics.babraham. ac.uk /projects/fastqc/). The first low quality removing nucleotides were removed using FASTX- Toolkit (http://hannonlab.cshl.edu/fastxtoolkit/). -
1 1 2 3 Cell Type-Specific Transcriptomics of Hypothalamic
1 2 3 4 Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to 5 weight-loss 6 7 Fredrick E. Henry1,†, Ken Sugino1,†, Adam Tozer2, Tiago Branco2, Scott M. Sternson1,* 8 9 1Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 10 20147, USA. 11 2Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, 12 Cambridge CB2 0QH, UK 13 14 †Co-first author 15 *Correspondence to: [email protected] 16 Phone: 571-209-4103 17 18 Authors have no competing interests 19 1 20 Abstract 21 Molecular and cellular processes in neurons are critical for sensing and responding to energy 22 deficit states, such as during weight-loss. AGRP neurons are a key hypothalamic population 23 that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific 24 transcriptomics can be used to identify pathways that counteract weight-loss, and here we 25 report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived 26 young adult mice. For comparison, we also analyzed POMC neurons, an intermingled 27 population that suppresses appetite and body weight. We find that AGRP neurons are 28 considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell 29 type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion 30 channels, neuropeptides, and receptors. Combined with methods to validate and manipulate 31 these pathways, this resource greatly expands molecular insight into neuronal regulation of 32 body weight, and may be useful for devising therapeutic strategies for obesity and eating 33 disorders. -
Novel Voltage Dependent Ion Channel Fusions and Method of Use Thereof
(19) TZZ¥ZZ _T (11) EP 3 056 902 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 17.08.2016 Bulletin 2016/33 G01N 33/542 (2006.01) C07K 14/705 (2006.01) (21) Application number: 15155202.3 (22) Date of filing: 16.02.2015 (84) Designated Contracting States: (72) Inventors: AL AT BE BG CH CY CZ DE DK EE ES FI FR GB • Ruigrok, Hermanus GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO 33200 Bordeaux (FR) PL PT RO RS SE SI SK SM TR • Percherancier, Yann Designated Extension States: 33140 Villenave d’Ornon (FR) BA ME •Veyret,Bernard 33600 PESSAC (FR) (71) Applicants: • UNIVERSITE DE BORDEAUX (74) Representative: Lecca, Patricia S. 33000 Bordeaux (FR) Cabinet Lecca • CENTRE NATIONAL DE LA RECHERCHE 21, rue de Fécamp SCIENTIFIQUE 75012 Paris (FR) 75794 Paris Cedex 16 (FR) • Institut Polytechnique de Bordeaux 33402 Talence Cedex (FR) (54) Novel voltage dependent ion channel fusions and method of use thereof (57) The present invention relates to novel volt- izing candidate molecules or physical parameters for age-dependent ion channel fusion subunits, and to a their ability to activate or inhibit voltage-dependent ion functional bioluminescence resonance energy transfer channels. (BRET) assay for screening in real time and character- EP 3 056 902 A1 Printed by Jouve, 75001 PARIS (FR) EP 3 056 902 A1 Description FIELD OF THE INVENTION 5 [0001] The present invention relates to novel voltage-dependent ion channel fusion subunits, and to a functional bioluminescence resonance energy transfer (BRET) assay for screening in real time and characterizing candidate mol- ecules or physical parameters for their ability to activate or inhibit voltage-dependent ion channels. -
(C) Hit Agreement Between Seeding Densities
(a) Morphological space (b) Identification of hits (c) Hit agreement between 1500 cells per well 1500 cells per well seeding densities DMSO 8 1.00 Pentamidine 1.00 Wiskostatin Hydroxychloroquine Imatinib 0.75 0.75 4 Gefitinib Compound DMSO Pentamidine 0.50 0.50 0 Vinblastine UMAP2 Wiskostatin Vinblastine 0.25 0.25 Vinblastine −4 Plate at 1500 cells/well Robust Hellinger Distance Wiskostatin Pentamidine 0.00 DMSO 0.00 −4 0 4 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 UMAP1 FDR−corrected p−value Plate at 750 cells/well Supp. Figure 1: BioProfiling.jl profiles of plates seeded at 750 and 1500 cells per well curated with are similar. (a) UMAP embedding preserving the cosine distance between the mor-phological profiles aggregated per field of view in the plate seeded with 1500 cells per well. Two out of four dimensions are represented. (b) Robust Hellinger distance and Ro-bust Morphological Perturbation Value (FDR-corrected p-value) of each compound in the plate seeded with 1500 cells per well compared to DMSO. Vertical dotted line indicates an FDR threshold of 0.1 and all compounds on its left are defined as morphological hits. (c) FDR-corrected p-value of the significance of morphological changes induced by each compound in both plates. Dotted lines indicate an FDR threshold of 0.1. CompoundName MOA Targets RMPV750 RMPV1500 (+)-Butaclamol hydrochloride 0.2479179 0 (+)-Cyclazocine 0.0288018 0.0012478 ["ABCC1", "ABCC2", "FPR1", (+/-)-Sulfinpyrazone ["Uricosuric blocker"] "SLC22A12"] 0.0019172 0.015413 (-)-JQ1 0.0003682 0 (-)-Perillic -
Comparative Genomic Analysis Suggests That the Sperm-Specific
Romero and Nishigaki Zoological Letters (2019) 5:25 https://doi.org/10.1186/s40851-019-0141-3 RESEARCHARTICLE Open Access Comparative genomic analysis suggests that the sperm-specific sodium/proton exchanger and soluble adenylyl cyclase are key regulators of CatSper among the Metazoa Francisco Romero and Takuya Nishigaki* Abstract Background: CatSper is a sperm-specific calcium ion (Ca2+) channel, which regulates sperm flagellar beating by tuning cytoplasmic Ca2+ concentrations. Although this Ca2+ channel is essential for mammalian fertilization, recent bioinformatics analyses have revealed that genes encoding CatSper are heterogeneously distributed throughout the eukaryotes, including vertebrates. As this channel is activated by cytoplasmic alkalization in mammals and sea urchins, it has been proposed that the sperm-specific Na+/H+ exchanger (sNHE, a product of the SLC9C gene family) positively regulates its activity. In mouse, sNHE is functionally coupled to soluble adenylyl cyclase (sAC). CatSper, sNHE, and sAC have thus been considered functionally interconnected in the control of sperm motility, at least in mouse and sea urchin. Results: We carried out a comparative genomic analysis to explore phylogenetic relationships among CatSper, sNHE and sAC in eukaryotes. We found that sNHE occurs only in Metazoa, although sAC occurs widely across eukaryotes. In animals, we found correlated and restricted distribution patterns of the three proteins, suggesting coevolution among them in the Metazoa. Namely, nearly all species in which CatSper is conserved also preserve sNHE and sAC. In contrast, in species without sAC, neither CatSper nor sNHE is conserved. On the other hand, the distribution of another testis-specific NHE (NHA, a product of the SLC9B gene family) does not show any apparent association with that of CatSper. -
A Polycystin-1 Controls Postcopulatory Reproductive Selection in Mice
A polycystin-1 controls postcopulatory reproductive selection in mice Keith A. Sutton*, Melissa K. Jungnickel*, and Harvey M. Florman*† *Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655 Edited by Ryuzo Yanagimachi, University of Hawaii, Honolulu, HI, and approved April 17, 2008 (received for review January 22, 2008) Pkdrej, a member of the polycystin-1 gene family, is expressed only a candidate subunit of the receptor that initiates acrosome in the male germ line. Male mice that are homozygous for a reactions (18, 19). Additional polycystin-1 proteins are also targeted mutation in the Pkdrej allele (Pkdrejtm/tm) are fertile in present and may participate in the signal transduction mecha- unrestricted mating trials, but exhibit lower reproductive success nism that leads to exocytosis (19, 20). An acrosome reaction is when competing with wild-type males in sequential mating trials also required for mammalian fertilization. In this case, sperm and in artificial insemination of mixed-sperm populations. Follow- first undergo a process of physiological reprogramming, or ing mating, sperm from Pkdrejtm/tm mice require >2 h longer than capacitation, within the female reproductive tract (16, 21). those of wild-type males to be detected within the egg/cumulus Acrosome reactions are triggered following contact of capaci- complex in the oviduct. Sperm from mice of both genotypes are tated sperm with the egg coat, or zona pellucida (ZP), by the able to capacitate in vitro. However, one of the component pro- agonist glycoprotein ZP3 (16, 22). Given the proposed role of cesses of capacitation, the ability to undergo a zona pellucida– polycystin-1 proteins in echinoderm acrosome reactions, it was evoked acrosome reaction, develops more slowly in sperm from suggested that Pkdrej is a candidate component of a ZP3- Pkdrejtm/tm animals than in sperm from wild-type males. -
Transforming Growth Factor ß1-Mediated Functional Inhibition Of
Myelodysplastic Syndromes SUPPLEMENTARY APPENDIX Transforming growth factor 1- mediated functional inhibition of mesenchymal stromal celβls in myelodysplastic syndromes and acute myeloid leukemia Stefanie Geyh, 1* Manuel Rodríguez-Paredes, 1,2 * Paul Jäger, 1 Annemarie Koch, 1 Felix Bormann, 2 Julian Gutekunst, 2 Christoph Zilkens, 3 Ulrich Germing, 1 Guido Kobbe, 1 Frank Lyko, 2 Rainer Haas 1 and Thomas Schroeder 1 1Department of Hematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty; 2Division of Epigenetics, DKFZ- ZMBH Alliance, German Cancer Research Center, Heidelberg and 3Department of Orthopedic Surgery, University of Duesseldorf, Medical Faculty, Germany *SG and MR-P contributed equally to this work. ©2018 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2017.186734 Received: December 19, 2017. Accepted: May 14, 2018. Pre-published: May 17, 2018. Correspondence: [email protected] Figure S1 Downregulated genes Downregulated genes Upregulated Figure S1. Heatmaps showing the 50 most upregulated and downregulated genes between the 3 healthy MSC controls and the 9 RCMD-, RAEB- and AML-derived MSC samples. Color scale depicts the rlog-transformed FPKM values for each gene and every sample. Figure S2 Downregulated genes Downregulated genes Upregulated Figure S2. Heatmaps showing the 50 most upregulated and downregulated genes between the 3 healthy MSC controls and the 3 RCMD, RAEB and AML MSC samples, respectively. Color scales depict the rlog-transformed FPKM values for each gene and every sample. Figure S3 A. B. 0.0015 *** ** <-3 -2 0.0010 RCMD RAEB AML -1 0 1 0.0005 Log2FC LTF 2 CCL26/GAPDH INHBB >3 0.0000 TGFB2 y S h D ML M A ealt ll LTF H a EGF 0.003 *** ** INHBB TGFB2 0.002 INHBB IGFBP7 0.001 GDF11 LIF/GAPDH BMP1 0.000 y L th M TNFSF12 l A FGF13 ea ll MDS H a FGF13 0.0015 * TNFSF10 TNFSF10 0.0010 0.0005 SPP1/GAPDH 0.0000 y th l AML ea H all MDS Figure S3. -
The Concise Guide to PHARMACOLOGY 2015/16
Edinburgh Research Explorer The Concise Guide to PHARMACOLOGY 2015/16 Citation for published version: CGTP Collaborators, Alexander, SP, Catterall, WA, Kelly, E, Marrion, N, Peters, JA, Benson, HE, Faccenda, E, Pawson, AJ, Sharman, JL, Southan, C & Davies, JA 2015, 'The Concise Guide to PHARMACOLOGY 2015/16: Voltage-gated ion channels', British Journal of Pharmacology, vol. 172, no. 24, pp. 5904-5941. https://doi.org/10.1111/bph.13349 Digital Object Identifier (DOI): 10.1111/bph.13349 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: British Journal of Pharmacology General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 28. Sep. 2021 S.P.H. Alexander et al. The Concise Guide to PHARMACOLOGY 2015/16: Voltage-gated ion channels. British Journal of Pharmacology (2015) 172, 5904–5941 THE CONCISE GUIDE TO PHARMACOLOGY 2015/16: Voltage-gated