Genetic Variation in Offspring Indirectly Influences the Quality of Maternal Behaviour in Mice David George Ashbrook*, Beatrice Gini, Reinmar Hager*
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Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Enzyme DHRS7
Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d. -
Table S6. Names and Functions of 44 Target Genes and 4 Housekeeping Genes Assessed for Gene Expression Measurements
Table S6. Names and functions of 44 target genes and 4 housekeeping genes assessed for gene expression measurements. Gene Gene name Function Category Reference CD45 CD45 (leukocyte common antigen) Regulation of T-cell and B-cell antigen receptor signaling Adaptive NCBI, UniProt HIVEP2 Human immunodeficiency virus typeI enhancer2 Transcription factor, V(D)J recombination, MHC enhancer binding Adaptive (Diepeveen et al. 2013) HIVEP3 Human immunodeficiency virus typeI enhancer3 Transcription factor, V(D)J recombination, MHC enhancer binding Adaptive (Diepeveen et al. 2013) IgM-lc Immunoglobulin light chain Recognition of antigen or pathogen Adaptive NCBI, UniProt Integ-Bt Integrin-beta 1 Cell signaling and adhesion of immunoglobulin Adaptive NCBI, UniProt Lymph75 Lymphocyte antigen 75 Directs captured antigens to lymphocytes Adaptive (Birrer et al. 2012) Lympcyt Lymphocyte cytosolic protein 2 Positive role in promoting T-cell development and activation Adaptive NCBI, UniProt TAP Tap-binding protein (Tapasin) Transport of antigenic peptides, peptide loading on MHC I Adaptive NCBI, UniProt AIF Allograft inflammation factor Inflammatory responses, allograft rejection, activation of macrophages Innate (Roth et al. 2012) Calrcul Calreticulin Chaperone, promotes phagocytosis and clearance of apoptotic cells Innate NCBI, UniProt Cf Coagulation factor II Blood clotting and inflammation response Innate (Birrer et al. 2012) IL8 Interleukin 8 Neutrophil chemotactic factor, phagocytosis, inflammatory activity Innate NCBI, UniProt Intf Interferon induced transmembrane protein 3 Negative regulation of viral entry into host cell, antiviral response Innate NCBI, UniProt Kin Kinesin Intracellular transport Innate (Roth et al. 2012) LectptI Lectin protein type I Pathogen recognition receptors (C-type lectin type I) Innate NCBI, UniProt LectpII Lectin protein type II Pathogen recognition receptors (C-type lectin type II) Innate NCBI, UniProt Nramp Natural resistance-assoc macrophage protein Macrophage activation Innate (Roth et al. -
Mygene.Info R Client
MyGene.info R Client Adam Mark, Ryan Thompson, Chunlei Wu May 19, 2021 Contents 1 Overview ..............................2 2 Gene Annotation Service ...................2 2.1 getGene .............................2 2.2 getGenes ............................2 3 Gene Query Service ......................3 3.1 query ..............................3 3.2 queryMany ...........................4 4 makeTxDbFromMyGene....................5 5 Tutorial, ID mapping .......................6 5.1 Mapping gene symbols to Entrez gene ids ........6 5.2 Mapping gene symbols to Ensembl gene ids .......7 5.3 When an input has no matching gene ...........8 5.4 When input ids are not just symbols ............8 5.5 When an input id has multiple matching genes ......9 5.6 Can I convert a very large list of ids?............ 11 6 References ............................. 11 MyGene.info R Client 1 Overview MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It’s designed with simplicity and performance emphasized. mygene is an easy-to-use R wrapper to access MyGene.Info services. 2 Gene Annotation Service 2.1 getGene • Use getGene, the wrapper for GET query of "/gene/<geneid>" service, to return the gene object for the given geneid. > gene <- getGene("1017", fields="all") > length(gene) [1] 1 > gene["name"] [[1]] NULL > gene["taxid"] [[1]] NULL > gene["uniprot"] [[1]] NULL > gene["refseq"] [[1]] NULL 2.2 getGenes • Use getGenes, the wrapper for POST query of "/gene" service, to return the list of gene objects for the given character vector of geneids. > getGenes(c("1017","1018","ENSG00000148795")) DataFrame with 3 rows and 7 columns 2 MyGene.info R Client query _id X_version entrezgene name <character> <character> <integer> <character> <character> 1 1017 1017 4 1017 cyclin dependent kin. -
Solar and Ultraviolet Radiation
SOLAR AND ULTRAVIOLET RADIATION Solar and ultraviolet radiation were considered by a previous IARC Working Group in 1992 (IARC, 1992). Since that time, new data have become available, these have been incorpo- rated into the Monograph, and taken into consideration in the present evaluation. 1. Exposure Data 1.1 Nomenclature and units For the purpose of this Monograph, the Terrestrial life is dependent on radiant energy photobiological designations of the Commission from the sun. Solar radiation is largely optical Internationale de l’Eclairage (CIE, International radiation [radiant energy within a broad region Commission on Illumination) are the most of the electromagnetic spectrum that includes relevant, and are used throughout to define ultraviolet (UV), visible (light) and infrared the approximate spectral regions in which radiation], although both shorter wavelength certain biological absorption properties and (ionizing) and longer wavelength (microwaves biological interaction mechanisms may domi- and radiofrequency) radiation is present. The nate (Commission Internationale de l’Eclairage, wavelength of UV radiation (UVR) lies in the 1987). range of 100–400 nm, and is further subdivided Sources of UVR are characterized in radio- into UVA (315–400 nm), UVB (280–315 nm), metric units. The terms dose (J/m2) and dose rate and UVC (100–280 nm). The UV component (W/m 2) pertain to the energy and power, respec- of terrestrial radiation from the midday sun tively, striking a unit surface area of an irradi- comprises about 95% UVA and 5% UVB; UVC ated object (Jagger, 1985). The radiant energy and most of UVB are removed from extraterres- delivered to a given area in a given time is also trial radiation by stratospheric ozone. -
Kin Discrimination Promotes Horizontal Gene Transfer Between Unrelated Strains in Bacillus Subtilis
ARTICLE https://doi.org/10.1038/s41467-021-23685-w OPEN Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis ✉ Polonca Stefanic 1,5,6 , Katarina Belcijan1,5, Barbara Kraigher 1, Rok Kostanjšek1, Joseph Nesme2, Jonas Stenløkke Madsen2, Jasna Kovac 3, Søren Johannes Sørensen 2, Michiel Vos 4 & ✉ Ines Mandic-Mulec 1,6 Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically 1234567890():,; distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low related- ness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with acti- vation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context. 1 Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia. -
Gene Networks Activated by Specific Patterns of Action Potentials in Dorsal Root Ganglia Neurons Received: 10 August 2016 Philip R
www.nature.com/scientificreports OPEN Gene networks activated by specific patterns of action potentials in dorsal root ganglia neurons Received: 10 August 2016 Philip R. Lee1,*, Jonathan E. Cohen1,*, Dumitru A. Iacobas2,3, Sanda Iacobas2 & Accepted: 23 January 2017 R. Douglas Fields1 Published: 03 March 2017 Gene regulatory networks underlie the long-term changes in cell specification, growth of synaptic connections, and adaptation that occur throughout neonatal and postnatal life. Here we show that the transcriptional response in neurons is exquisitely sensitive to the temporal nature of action potential firing patterns. Neurons were electrically stimulated with the same number of action potentials, but with different inter-burst intervals. We found that these subtle alterations in the timing of action potential firing differentially regulates hundreds of genes, across many functional categories, through the activation or repression of distinct transcriptional networks. Our results demonstrate that the transcriptional response in neurons to environmental stimuli, coded in the pattern of action potential firing, can be very sensitive to the temporal nature of action potential delivery rather than the intensity of stimulation or the total number of action potentials delivered. These data identify temporal kinetics of action potential firing as critical components regulating intracellular signalling pathways and gene expression in neurons to extracellular cues during early development and throughout life. Adaptation in the nervous system in response to external stimuli requires synthesis of new gene products in order to elicit long lasting changes in processes such as development, response to injury, learning, and memory1. Information in the environment is coded in the pattern of action-potential firing, therefore gene transcription must be regulated by the pattern of neuronal firing. -
Mygene.Info R Client
MyGene.info R Client Adam Mark, Ryan Thompson, Chunlei Wu May 19, 2021 Contents 1 Overview ..............................2 2 Gene Annotation Service ...................2 2.1 getGene .............................2 2.2 getGenes ............................2 3 Gene Query Service ......................3 3.1 query ..............................3 3.2 queryMany ...........................4 4 makeTxDbFromMyGene....................5 5 Tutorial, ID mapping .......................6 5.1 Mapping gene symbols to Entrez gene ids ........6 5.2 Mapping gene symbols to Ensembl gene ids .......7 5.3 When an input has no matching gene ...........8 5.4 When input ids are not just symbols ............8 5.5 When an input id has multiple matching genes ......9 5.6 Can I convert a very large list of ids?............ 11 6 References ............................. 11 MyGene.info R Client 1 Overview MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It’s designed with simplicity and performance emphasized. mygene is an easy-to-use R wrapper to access MyGene.Info services. 2 Gene Annotation Service 2.1 getGene • Use getGene, the wrapper for GET query of "/gene/<geneid>" service, to return the gene object for the given geneid. > gene <- getGene("1017", fields="all") > length(gene) [1] 1 > gene["name"] [[1]] NULL > gene["taxid"] [[1]] NULL > gene["uniprot"] [[1]] NULL > gene["refseq"] [[1]] NULL 2.2 getGenes • Use getGenes, the wrapper for POST query of "/gene" service, to return the list of gene objects for the given character vector of geneids. > getGenes(c("1017","1018","ENSG00000148795")) DataFrame with 3 rows and 7 columns 2 MyGene.info R Client query _id X_version entrezgene name <character> <character> <integer> <character> <character> 1 1017 1017 4 1017 cyclin dependent kin. -
Identification of Expression Qtls Targeting Candidate Genes For
ISSN: 2378-3648 Salleh et al. J Genet Genome Res 2018, 5:035 DOI: 10.23937/2378-3648/1410035 Volume 5 | Issue 1 Journal of Open Access Genetics and Genome Research RESEARCH ARTICLE Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics Salleh MS1,2, Mazzoni G2, Nielsen MO1, Løvendahl P3 and Kadarmideen HN2,4* 1Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark Check for 2Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark updates 3Department of Molecular Biology and Genetics-Center for Quantitative Genetics and Genomics, Aarhus University, AU Foulum, Tjele, Denmark 4Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark *Corresponding author: Kadarmideen HN, Department of Applied Mathematics and Computer Science, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark, E-mail: [email protected] Abstract body weight gain and net merit). The eQTLs and biological pathways identified in this study improve our understanding Background: Residual feed intake (RFI) is the difference of the complex biological and genetic mechanisms that de- between actual and predicted feed intake and an important termine FE traits in dairy cattle. The identified eQTLs/genet- factor determining feed efficiency (FE). Recently, 170 can- ic variants can potentially be used in new genomic selection didate genes were associated with RFI, but no expression methods that include biological/functional information on quantitative trait loci (eQTL) mapping has hitherto been per- SNPs. formed on FE related genes in dairy cows. In this study, an integrative systems genetics approach was applied to map Keywords eQTLs in Holstein and Jersey cows fed two different diets to eQTL, RNA-seq, Genotype, Data integration, Systems improve identification of candidate genes for FE. -
Bioinformatics - 2 - Investigation of C
Advanced Skills in Biochemistry: Bioinformatics - 2 - Investigation of C. elegans protein kinase polypeptides Exercise 1 The purpose of this workshop is to familarise you with some of the databases and tools that are available for the analysis of proteins. For the purposes of this exercise, you will again be investigating the family of catalytic subunits of the cyclic AMP-dependent protein kinase (PK-A) in the free-living nematode, C. elegans. 1. The C. elegans polypeptide sequences we are interested in are encoded by the F47F2.1 gene on the X chromosome and the kin-1 gene on chromosome 1. In addition, we need the sequence of the mouse PK-A - catalytic subunit. The easiest way of obtaining each of these sequences is by making use of the Sequence Retrieval System (SRS). You should therefore visit the SRS Homepage: http://srs6.ebi.ac.uk/ 2. From the home page, select the Library Page tab. Then, under the UniProt Universal Protein Resource section, select the UniProtKB and UniParc databases. Then select the Standard Query Form. You should then carry out separate searches for the following accession numbers (i.e. select AccessionNumber from the drop-down menu in place of the default AllText): P05132, UPI000002AC77 and Q7JP68. These searches should find records for the polypeptide sequence for the mouse -catalytic subunit, the polypeptide sequence of the catalytic subunit encoded by the kin-1 gene and the F47F2.1b polypeptide sequence. Each of the records should be saved locally (e.g. on the desktop). 3. You should now prepare a simple text -
Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/ Differentiation Program
ORIGINAL RESEARCH published: 24 August 2021 doi: 10.3389/fonc.2021.707066 Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/ Differentiation Program Tian-Tian Xu 1, Xiao-Wen Zeng 1, Xin-Hong Wang 2, Lu-Xi Yang 1, Gang Luo 1* and Ting Yu 1* 1 Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China, 2 Department of Oral Pathology and Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China Disturbance in the proteolytic process is one of the malignant signs of tumors. Proteolysis Edited by: Eva Csosz, is highly orchestrated by cysteine cathepsin and its inhibitors. Cystatin-B (CSTB) is a University of Debrecen, Hungary general cysteine cathepsin inhibitor that prevents cysteine cathepsin from leaking from Reviewed by: lysosomes and causing inappropriate proteolysis. Our study found that CSTB was Csongor Kiss, downregulated in both oral squamous cell carcinoma (OSCC) tissues and cells University of Debrecen, Hungary Gergely Nagy, compared with normal controls. Immunohistochemical analysis showed that CSTB was University of Debrecen, Hungary mainly distributed in the epithelial structure of OSCC tissues, and its expression intensity *Correspondence: was related to the grade classification. A correlation analysis between CSTB and clinical Gang Luo [email protected] prognosis was performed using gene expression data and clinical information acquired Ting Yu from The Cancer Genome Atlas (TCGA) database. Patients with lower expression levels of [email protected] CSTB had shorter disease-free survival times and poorer clinicopathological features Specialty section: (e.g., lymph node metastases, perineural invasion, low degree of differentiation, and This article was submitted to advanced tumor stage). -
Karyomegalic Interstitial Nephritis and DNA Damage-Induced Polyploidy in Fan1 Nuclease-Defective Knock-In Mice
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION Fancd2 ubiquitylation (K561) causes defective ICL repair Karyomegalic interstitial (Garcia-Higuera et al. 2001; Knipscheer et al. 2009; Deans nephritis and DNA damage- and West 2011). Fan1 is a 5′ flap endonuclease recruited to sites where induced polyploidy in Fan1 replisomes stall—for example, at ICLs—in a manner that requires Fancd2 ubiquitylation (Kratz et al. 2010; Liu et al. nuclease-defective knock-in 2010; MacKay et al. 2010; Smogorzewska et al. 2010). The mice nuclease activities of Fan1 are mediated by a C-terminal “ ” 1 1 VRR_nuc domain (Iyer et al. 2006), which is conserved Christophe Lachaud, Meghan Slean, in all orthologs as far back as yeasts. Fan1 also has a SAP- Francesco Marchesi,2 Claire Lock,3 Edward Odell,3 type DNA-binding domain and a UBZ4-type ubiquitin- Dennis Castor,1,4 Rachel Toth,1 binding domain, which interacts with ubiquityl-Fancd2, and John Rouse1 thereby recruiting Fan1 to sites of replisome stalling. Fan1 is required for efficient ICL repair, but, surprisingly, 1MRC Protein Phosphorylation and Ubiquitylation Unit, College this does not require interaction with ubiquityl-Fancd2 of Life Sciences, Sir James Black Centre, University of Dundee, (Lachaud et al. 2016). Similarly, genetic analyses in worms Dundee DD1 5EH, United Kingdom 2School of Veterinary and human cells showed that Fan1 and Fancd2 mutations Medicine, College of Medical, Veterinary, and Life Sciences, are not epistatic with respect to hypersensitivity to ICL- University of Glasgow, Glasgow G61 1QH, United Kingdom inducing drugs, suggesting that the two genes are not 3Department of Head and Neck Pathology, Guy’s Hospital, equivalent in function when it comes to ICL repair (Yosh- London SE1 9RT, United Kingdom ikiyo et al.