Mouse Models of Congenital Cataract
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Appendix 4. Top 50 Highest Expressed Genes in Epithelial Cells Based on RPKM Values
Appendix 4. Top 50 highest expressed genes in epithelial cells based on RPKM values Gene Description E_RPKM F_RPKM E_counts F_counts FC* p_value symbol Cryaa Crystallin, alpha A 29,373.3 177,267.7 366,616.4 6,264,319. 17.09 9.11E-118 1 RP23– Long intergenic non-coding RNA 11,888.5 2702.4 261,760.9 134,763.0 −1.94 1 81C12.3 Cryab Crystallin, alpha B 5673.3 10,124.2 65,971.7 333,597.9 5.06 2.71E-43 mt-Nd1 NADH dehydrogenase, subunit 1 5655.6 1798.9 53,082.3 47,748.1 −1.11 0.838775756 Cryba1 Crystallin, beta A1 5622.0 155,230.3 43,420.9 3,380,176. 77.85 1.34E-240 5 Crybb3 Crystallin, beta B3 4743.1 37,636.3 34,717.7 736,007.9 21.20 4.45E-135 Cryga Crystallin, gamma A 2333.2 83,496.3 10,854.5 1,162,864. 107.1 5.89E-270 6 3 Sparc Secreted acidic cysteine rich 2257.4 809.8 39,749.7 34,033.9 −1.17 0.462853166 glycoprotein Slc2a1 Solute carrier family 2, member 1 1832.8 162.9 43,031.4 10,654.8 −4.04 1.67E-05 Hsp90ab1 Heat shock protein 90 kDa alpha, class 1480.7 1139.7 18,998.2 35,901.2 1.89 3.84E-05 B member 1 Igfbp7 Insulin-like growth factor binding 1464.6 428.3 15,428.3 12,626.8 −1.22 0.154954147 protein 7 mt-Nd2 NADH-ubiquinone oxidoreductase 1450.9 615.2 14,644.7 17,789.5 1.21 0.833748849 chain 2 Eef1a1 Eukaryotic translation elongation 1389.1 587.5 11,489.2 12,607.2 1.10 0.754135917 factor 1 alpha 1 Crybb1 Crystallin, beta B1 1376.6 34,662.8 11,455.5 820,406.2 71.62 5.82E-233 Htra3 HtrA serine peptidase 3 1338.6 162.0 23,197.6 6433.9 −3.61 3.93E-05 Gnb2l1 Guanine nucleotide-binding protein 1293.3 670.1 14,495.1 21,652.1 1.49 0.001685952 -
CRYGB Rabbit Pab
Leader in Biomolecular Solutions for Life Science CRYGB Rabbit pAb Catalog No.: A14569 Basic Information Background Catalog No. Crystallins are separated into two classes: taxon-specific, or enzyme, and ubiquitous. A14569 The latter class constitutes the major proteins of vertebrate eye lens and maintains the transparency and refractive index of the lens. Since lens central fiber cells lose their Observed MW nuclei during development, these crystallins are made and then retained throughout 21kDa life, making them extremely stable proteins. Mammalian lens crystallins are divided into alpha, beta, and gamma families; beta and gamma crystallins are also considered as a Calculated MW superfamily. Alpha and beta families are further divided into acidic and basic groups. 20kDa Seven protein regions exist in crystallins: four homologous motifs, a connecting peptide, and N- and C-terminal extensions. Gamma-crystallins are a homogeneous group of Category highly symmetrical, monomeric proteins typically lacking connecting peptides and terminal extensions. They are differentially regulated after early development. Four Primary antibody gamma-crystallin genes (gamma-A through gamma-D) and three pseudogenes (gamma-E, gamma-F, gamma-G) are tandemly organized in a genomic segment as a Applications gene cluster. Whether due to aging or mutations in specific genes, gamma-crystallins WB have been involved in cataract formation. Cross-Reactivity Mouse, Rat Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 1419 P07316 Immunogen Recombinant fusion protein containing a sequence corresponding to amino acids 80-135 of human CRYGB (NP_005201.2). Synonyms CRYGB;CRYG2;CTRCT39 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. -
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins
International Journal of Molecular Sciences Article Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins M. Quadir Siddiqui 1,† , Maulik D. Badmalia 1,† and Trushar R. Patel 1,2,3,* 1 Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; [email protected] (M.Q.S.); [email protected] (M.D.B.) 2 Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada 3 Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada * Correspondence: [email protected] † These authors contributed equally to the work. Abstract: Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and func- tions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share Citation: Siddiqui, M.Q.; Badmalia, similarities with transcriptional regulators and have positively charged electrostatic patches, which M.D.; Patel, T.R. -
Variants in PAX6, PITX3 and HSF4 Causing Autosomal Dominant Congenital Cataracts ✉ ✉ Vanita Berry 1,2 , Alex Ionides2, Nikolas Pontikos 1,2, Anthony T
www.nature.com/eye ARTICLE OPEN Variants in PAX6, PITX3 and HSF4 causing autosomal dominant congenital cataracts ✉ ✉ Vanita Berry 1,2 , Alex Ionides2, Nikolas Pontikos 1,2, Anthony T. Moore2, Roy A. Quinlan3 and Michel Michaelides 1,2 © Crown 2021 BACKGROUND: Lens development is orchestrated by transcription factors. Disease-causing variants in transcription factors and their developmental target genes are associated with congenital cataracts and other eye anomalies. METHODS: Using whole exome sequencing, we identified disease-causing variants in two large British families and one isolated case with autosomal dominant congenital cataract. Bioinformatics analysis confirmed these disease-causing mutations as rare or novel variants, with a moderate to damaging pathogenicity score, with testing for segregation within the families using direct Sanger sequencing. RESULTS: Family A had a missense variant (c.184 G>A; p.V62M) in PAX6 and affected individuals presented with nuclear cataract. Family B had a frameshift variant (c.470–477dup; p.A160R*) in PITX3 that was also associated with nuclear cataract. A recurrent missense variant in HSF4 (c.341 T>C; p.L114P) was associated with congenital cataract in a single isolated case. CONCLUSIONS: We have therefore identified novel variants in PAX6 and PITX3 that cause autosomal dominant congenital cataract. Eye; https://doi.org/10.1038/s41433-021-01711-x INTRODUCTION consistent with early developmental effects as would be Cataract the opacification of the eye lens is the most common, but anticipated for PAX6 and PITX3 transcription factors. Recently, treatable cause of blindness in the world (https://www.who.int/ we have found two novel mutations in the transcription factors publications-detail/world-report-on-vision). -
Noninvasive Sleep Monitoring in Large-Scale Screening of Knock-Out Mice
bioRxiv preprint doi: https://doi.org/10.1101/517680; this version posted January 11, 2019. 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-ND 4.0 International license. Noninvasive sleep monitoring in large-scale screening of knock-out mice reveals novel sleep-related genes Shreyas S. Joshi1*, Mansi Sethi1*, Martin Striz1, Neil Cole2, James M. Denegre2, Jennifer Ryan2, Michael E. Lhamon3, Anuj Agarwal3, Steve Murray2, Robert E. Braun2, David W. Fardo4, Vivek Kumar2, Kevin D. Donohue3,5, Sridhar Sunderam6, Elissa J. Chesler2, Karen L. Svenson2, Bruce F. O'Hara1,3 1Dept. of Biology, University of Kentucky, Lexington, KY 40506, USA, 2The Jackson Laboratory, Bar Harbor, ME 04609, USA, 3Signal solutions, LLC, Lexington, KY 40503, USA, 4Dept. of Biostatistics, University of Kentucky, Lexington, KY 40536, USA, 5Dept. of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA. 6Dept. of Biomedical Engineering, University of Kentucky, Lexington, KY 40506, USA. *These authors contributed equally Address for correspondence and proofs: Shreyas S. Joshi, Ph.D. Dept. of Biology University of Kentucky 675 Rose Street 101 Morgan Building Lexington, KY 40506 U.S.A. Phone: (859) 257-2805 FAX: (859) 257-1717 Email: [email protected] Running title: Sleep changes in knockout mice bioRxiv preprint doi: https://doi.org/10.1101/517680; this version posted January 11, 2019. 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. -
Supp Table 1.Pdf
Upregulated genes in Hdac8 null cranial neural crest cells fold change Gene Symbol Gene Title 134.39 Stmn4 stathmin-like 4 46.05 Lhx1 LIM homeobox protein 1 31.45 Lect2 leukocyte cell-derived chemotaxin 2 31.09 Zfp108 zinc finger protein 108 27.74 0710007G10Rik RIKEN cDNA 0710007G10 gene 26.31 1700019O17Rik RIKEN cDNA 1700019O17 gene 25.72 Cyb561 Cytochrome b-561 25.35 Tsc22d1 TSC22 domain family, member 1 25.27 4921513I08Rik RIKEN cDNA 4921513I08 gene 24.58 Ofa oncofetal antigen 24.47 B230112I24Rik RIKEN cDNA B230112I24 gene 23.86 Uty ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome 22.84 D8Ertd268e DNA segment, Chr 8, ERATO Doi 268, expressed 19.78 Dag1 Dystroglycan 1 19.74 Pkn1 protein kinase N1 18.64 Cts8 cathepsin 8 18.23 1500012D20Rik RIKEN cDNA 1500012D20 gene 18.09 Slc43a2 solute carrier family 43, member 2 17.17 Pcm1 Pericentriolar material 1 17.17 Prg2 proteoglycan 2, bone marrow 17.11 LOC671579 hypothetical protein LOC671579 17.11 Slco1a5 solute carrier organic anion transporter family, member 1a5 17.02 Fbxl7 F-box and leucine-rich repeat protein 7 17.02 Kcns2 K+ voltage-gated channel, subfamily S, 2 16.93 AW493845 Expressed sequence AW493845 16.12 1600014K23Rik RIKEN cDNA 1600014K23 gene 15.71 Cst8 cystatin 8 (cystatin-related epididymal spermatogenic) 15.68 4922502D21Rik RIKEN cDNA 4922502D21 gene 15.32 2810011L19Rik RIKEN cDNA 2810011L19 gene 15.08 Btbd9 BTB (POZ) domain containing 9 14.77 Hoxa11os homeo box A11, opposite strand transcript 14.74 Obp1a odorant binding protein Ia 14.72 ORF28 open reading -
Relative Impact of Multi-Layered Genomic Data on Gene Expression
Sohn et al. BMC Systems Biology 2013, 7(Suppl 6):S9 http://www.biomedcentral.com/1752-0509/7/S6/S9 RESEARCH Open Access Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors Kyung-Ah Sohn1†, Dokyoon Kim2,3†, Jaehyun Lim2,4, Ju Han Kim2,4* From 24th International Conference on Genome Informatics (GIW 2013) Singapore, Singapore. 16-18 December 2013 Abstract Background: The emerging multi-layers of genomic data have provided unprecedented opportunities for cancer research, especially for the association study between gene expressions and other types of genomic features. No previous approaches, however, provide an adequate statistical framework for or global analysis on the relative impact of different genomic feature layers to gene expression phenotypes. Methods: We propose an integrative statistical framework based on a sparse regression to model the impact of multi-layered genomic features on gene expression traits. The proposed approach can be regarded as an integrative expression Quantitative Traits Loci approach in which not only the genetic variations of SNPs or copy number variations but also other features in both genomic and epigenomic levels are used to explain the expression of genes. To highlight the validity of the proposed approach, the TCGA ovarian cancer dataset was analysed as a pilot task. Results: The analysis shows that our integrative approach has consistently superior power in predicting gene expression levels compared to that from each single data type-based analysis. Moreover, the proposed method has the advantage of producing a substantially reduced number of spurious associations. We provide an interesting characterization of genes in terms of its genomic association patterns. -
A Comprehensive Analysis of the Expression of Crystallins in Mouse Retina Jinghua Xi Washington University School of Medicine in St
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2003 A comprehensive analysis of the expression of crystallins in mouse retina Jinghua Xi Washington University School of Medicine in St. Louis Rafal Farjo University of Michigan - Ann Arbor Shigeo Yoshida University of Michigan - Ann Arbor Timothy S. Kern Case Western Reserve University Anand Swaroop University of Michigan - Ann Arbor See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Xi, Jinghua; Farjo, Rafal; Yoshida, Shigeo; Kern, Timothy S.; Swaroop, Anand; and Andley, Usha P., ,"A comprehensive analysis of the expression of crystallins in mouse retina." Molecular Vision.9,. 410-419. (2003). https://digitalcommons.wustl.edu/open_access_pubs/1801 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Jinghua Xi, Rafal Farjo, Shigeo Yoshida, Timothy S. Kern, Anand Swaroop, and Usha P. Andley This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/1801 Molecular Vision 2003; 9:410-9 <http://www.molvis.org/molvis/v9/a53> © 2003 Molecular Vision Received 28 May 2003 | Accepted 19 August 2003 | Published 28 August 2003 A comprehensive analysis of the expression of crystallins in mouse retina Jinghua Xi,1 Rafal Farjo,3 Shigeo Yoshida,3 Timothy S. Kern,5 Anand Swaroop,3,4 Usha P. Andley1,2 Departments of 1Ophthalmology and Visual Sciences and 2Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. -
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, -
RNA Sequencing and Bioinformatics Analysis of Human Lens Epithelial
Wang et al. BMC Ophthalmology (2021) 21:152 https://doi.org/10.1186/s12886-021-01915-5 RESEARCH ARTICLE Open Access RNA sequencing and bioinformatics analysis of human lens epithelial cells in age-related cataract Zhongying Wang1†, Dongmei Su2†, Shanhe Liu1, Guiqian Zheng1, Gaobo Zhang1, Tingsong Cui1,XuMa2*, Zhaoyi Sun1* and Shanshan Hu1* Abstract Background: Age-related cataract (ARC) is the main cause of blindness in older individuals but its specific pathogenic mechanism is unclear. This study aimed to identify differentially expressed genes (DEGs) associated with ARC and to improve our understanding of the disease mechanism. Methods: Anterior capsule samples of the human lens were collected from ARC patients and healthy controls and used for RNA sequencing to detect DEGs. Identified DEGs underwent bioinformatics analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Subsequently, reverse transcription quantitative RT-qPCR was used to validate the different expression levels of selected genes. Results: A total of 698 up-regulated DEGs and 414 down-regulated DEGs were identified in ARC patients compared with controls by transcriptome analysis. Through GO and KEGG bioinformatics analysis, the functions of significantly DEGs and their possible molecular mechanisms were determined. Sequencing results were verified by RT-qPCR as being accurate and reliable. Conclusions: This study identified several genes associated with ARC, which improves our knowledge of the disease mechanism. Keywords: Age-related cataract, Differentially expressed genes, Bioinformatics analysis, Pathogenic genes Background alternative effective methods are necessary to prevent and Age-related cataract (ARC) is a common visual disorder treat the occurrence and development of ARC. -
Related Macular Degeneration and Cutis Laxa
UvA-DARE (Digital Academic Repository) Genetic studies of age-related macular degeneration Baas, D.C. Publication date 2012 Document Version Final published version Link to publication Citation for published version (APA): Baas, D. C. (2012). Genetic studies of age-related macular degeneration. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:05 Oct 2021 G������ S������ �� A��-������� M������ D����������� D����������� M������ G������ S������ �� A��-������� | 2012 D�������� C. B��� G������ S������ �� A��-������� M������ D����������� D�������� C. B��� cover.indd 1 31-10-12 08:36 Genetic Studies of Age-related Macular Degeneration Dominique C. Baas Chapter 0.indd 1 23-10-12 19:24 The research described in this thesis was conducted at the Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences, Department of Clinical and Molecular Ophthalmogenetics, Amsterdam, The Netherlands. -
Congenital Eye Disorders Gene Panel
Congenital eye disorders gene panel Contact details Introduction Regional Genetics Service Ocular conditions are highly heterogeneous and show considerable phenotypic overlap. 1 in Levels 4-6, Barclay House 2,500 children in the UK are diagnosed as blind or severely visually impaired by the time they 37 Queen Square reach one year old. As many as half of these cases are likely to be inherited and remain undiagnosed due to the vast number of genes involved in these conditions. Many congenital London, WC1N 3BH eye disorders causing visual impairment or blindness at birth or progressive visual impairment T +44 (0) 20 7762 6888 also include syndromic conditions involving additional metabolic, developmental, physical or F +44 (0) 20 7813 8578 sensory abnormalities. Gene panels offer the enhanced probability of diagnosis as a very large number of genes can be interrogated. Samples required Ocular birth defects include all inheritance modalities. Autosomal dominant and recessive 5ml venous blood in plastic EDTA diseases as well as X-linked dominant and recessive diseases are seen. These conditions can bottles (>1ml from neonates) also be caused by de novo variants. Prenatal testing must be arranged Referrals in advance, through a Clinical Genetics department if possible. Patients presenting with a phenotype appropriate for the requested sub-panel Amniotic fluid or CV samples Referrals will be accepted from clinical geneticists and consultants in ophthalmology. should be sent to Cytogenetics for Prenatal testing dissecting and culturing, with instructions to forward the sample Prenatal diagnosis may be offered as appropriate where pathogenic variants have been to the Regional Molecular Genetics identified in accordance with expected inheritance pattern and where appropriate parental laboratory for analysis testing and counselling has been conducted.