Genetic Heterogeneity for Recessively Inherited Congenital Cataract Microcornea with Corneal Opacity
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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). -
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. -
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. -
Análise Integrativa De Perfis Transcricionais De Pacientes Com
UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. -
Functional Characterisation of MYT1L, a Brain-Specific Transcriptional Regulator
This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ Functional characterisation of MYT1L, a brain-specific transcriptional regulator Kepa, Agnieszka Maria Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 04. Oct. 2021 Functional characterisation of MYT1L, a brain-specific transcriptional regulator Agnieszka Kępa 2014 A thesis submitted to King’s College London for the degree of Doctor of Philosophy MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry ABSTRACT Abnormalities in brain development and maladaptive plasticity are thought to underlay a range of neurodevelopmental and neurological disabilities and disorders, such as autism spectrum disorders, schizophrenia and learning disability. -
Early-Onset Obesity and Paternal 2Pter Deletion Encompassing the ACP1, TMEM18,Andmyt1l Genes
European Journal of Human Genetics (2014) 22, 471–479 & 2014 Macmillan Publishers Limited All rights reserved 1018-4813/14 www.nature.com/ejhg ARTICLE Early-onset obesity and paternal 2pter deletion encompassing the ACP1, TMEM18,andMYT1L genes Martine Doco-Fenzy*,1, Camille Leroy1, Anouck Schneider2, Florence Petit3, Marie-Ange Delrue4, Joris Andrieux3, Laurence Perrin-Sabourin5, Emilie Landais1, Azzedine Aboura5, Jacques Puechberty2,6, Manon Girard6, Magali Tournaire6, Elodie Sanchez2, Caroline Rooryck4,Agne`s Ameil7, Michel Goossens8, Philippe Jonveaux9, Genevie`ve Lefort2,6, Laurence Taine4, Dorothe´e Cailley4, Dominique Gaillard1, Bruno Leheup10, Pierre Sarda2 and David Genevie`ve2 Obesity is a common but highly, clinically, and genetically heterogeneous disease. Deletion of the terminal region of the short arm of chromosome 2 is rare and has been reported in about 13 patients in the literature often associated with a Prader–Willi-like phenotype. We report on five unrelated patients with 2p25 deletion of paternal origin presenting with early- onset obesity, hyperphagia, intellectual deficiency, and behavioural difficulties. Among these patients, three had de novo pure 2pter deletions, one presented with a paternal derivative der(2)t(2;15)(p25.3;q26) with deletion in the 2pter region and the last patient presented with an interstitial 2p25 deletion. The size of the deletions was characterized by SNP array or array-CGH and was confirmed by fluorescence in situ hybridization (FISH) studies. Four patients shared a 2p25.3 deletion with a minimal critical region estimated at 1.97 Mb and encompassing seven genes, namely SH3HYL1, ACP1, TMEMI8, SNTG2, TPO, PXDN, and MYT1L genes. The fifth patient had a smaller interstitial deletion encompassing the TPO, PXDN, and MYT1L genes. -
The Role of Genetics Mutations in Genes PORCN, TWIST2, HCCS In
ISSN: 2378-3672 Asadi and Jamali. Int J Immunol Immunother 2019, 6:038 DOI: 10.23937/2378-3672/1410038 Volume 6 | Issue 1 International Journal of Open Access Immunology and Immunotherapy REVIEW ARTICLE The Role of Genetics Mutations in Genes PORCN, TWIST2, HCCS in Goltz Syndrome Shahin Asadi1* and Mahsa Jamali2 Check for updates Division of Medical Genetics and Molecular Pathology Research, Molecular Genetics-IRAN-TABRIZ, Iran *Corresponding author: Shahin Asadi, Division of Medical Genetics and Molecular Pathology Research, Molecular Genetics-IRAN-TABRIZ, Iran are usually formed around the nose, the lips, the anal Abstract holes and the genitals of women with Goltz syndrome. Goltz syndrome (focal skin hypoplasia) is a genetic disorder In addition, papillomas may be present in the throat, that primarily affects the skin, skeletal system, eyes and face. People with Goltz syndrome have birth defects. These especially in the esophagus or larynx, and can cause disorders include very thin skin veins (skin hypoplasia), pink swallowing, respiration or sleep poisoning. The papillo- yellow nodules, subcutaneous fat, lack of upper skin layers mas can be removed if necessary by surgery from the (aplasia cutis), small clusters of superficial skin vessels growing regions. People with Goltz syndrome may have (telangiectasia), and veins in dark skin Or bright. Goltz syndrome is caused by mutation genes PORCN, TWIST2, small and abnormal nails on the toes. In addition, hair in HCCS. the scalp of these people can be weak or fragile or not [2] (Figure 2). Keywords Goltz syndrome, PORCN, TWIST2, HCCS genes, Skin and Many people with Goltz syndrome also have hand Skeletal disorders and foot disorders, including abnormalities such as oligodactyly in fingers and toes, fingers and legs (cin- Generalizations of Goltz Syndrome dactyly) or ecd rhodactyly. -
Investigation of Four Genes Responsible for Autosomal Recessive Congenital Cataract and Highly Expressed in the Brain in Four Unrelated Tunisian Families
Open Journal of Ophthalmology, 2012, 2, 64-70 http://dx.doi.org/10.4236/ojoph.2012.23014 Published Online August 2012 (http://www.SciRP.org/journal/ojoph) Investigation of Four Genes Responsible for Autosomal Recessive Congenital Cataract and Highly Expressed in the Brain in Four Unrelated Tunisian Families Manèl Chograni1, Myriam Chaabouni1,2, Faouzi Maazoul2, Habiba Chaabouni Bouhamed1,2* 1Laboratoire de Génétique Humaine, Faculté de Médecine de Tunis, University Tunis Elmanar, Tunis, Tunisia; 2Congenital and Hereditary Disorders Department, Charles Nicolle Hospital, Tunis, Tunisia. Email: *[email protected] Received March 14th, 2012; revised April 28th, 2012; accepted May 11th, 2012 ABSTRACT Purpose: To identify the causative gene for phenotypes associating autosomal recessive congenital cataract, mental re- tardation and congenital cataract, mental retardation and microcephaly in four unrelated Tunisian families. Methods: Four genes (EPHA2, GALK1, GCNT2, and CRYBB1) were selected based on their expression in human brain and their known or putative function. Linkage analysis were performed for the four genes in multiple affected and unaffected families’ members and results were explored by the GeneMapper ID v3.2 software. Results: No linkage was identified for the four studied genes in the four families. Affected members of each family did not share common haplotypes in corresponding candidate regions containing selected gene. Conclusion: Although the four studied genes were reported responsible for autosomal recessive congenital cataract and highly expressed in the human brain, we report no linkage for EPHA2, GALK1, GCNT2, and CRYBB1 genes in four families with congenital cataract, mental retardation and con- genital cataract, mental retardation and microcephaly. Keywords: Congenital Cataract; Mental Retardation; Microcephaly; Autosomal Recessive; Association; Linkage Study 1. -
Chemical Reactions, and Cellular Respiration
Chapter 03 Lecture Outline See separate PowerPoint slides for all figures and tables pre- inserted into PowerPoint without notes. Copyright © McGraw-Hill Education. Permission required for reproduction or display. 1 Energy, Chemical Reactions, and Cellular Respiration • All living organisms require energy to – Power muscle – Pump blood – Absorb nutrients – Exchange respiratory gases – Synthesize new molecules – Establish cellular ion concentrations • Glucose broken down through metabolic pathways – Forms ATP, the “energy currency” of cells 2 3.1a Classes of Energy • Energy – Capacity to do work – Two classes of energy o Potential energy—stored energy (energy of position) o Kinetic energy—energy of motion – Both can be converted from one class to the other 3 3.1a Classes of Energy • Potential energy and the plasma membrane – Concentration gradient exists across plasma membrane o Boundary between inside and outside of cell • Potential energy and electron shells – Electrons move from a higher- to lower-energy shell – Kinetic energy can be harnessed to do work • Potential energy must be converted to kinetic energy before it can do work 4 Conversion of Potential Energy to Kinetic Energy Figure 3.1 5 3.1b Forms of Energy • Chemical energy – One form of potential energy – Energy stored in a molecule’s chemical bonds – Most important form of energy in the human body – Used for o Movement o Molecule synthesis o Establishing concentration gradients – Present in all chemical bonds – Released when bonds are broken during reactions 6 3.1b Forms of -
Murine Pancreatic Tumor Cell Line TD2 Bears the Characteristic Pattern of Genetic Changes with Two Independently Amplified Gene Loci
Oncogene (2003) 22, 6802–6809 & 2003 Nature Publishing Group All rights reserved 0950-9232/03 $25.00 www.nature.com/onc Murine pancreatic tumor cell line TD2 bears the characteristic pattern of genetic changes with two independently amplified gene loci Bettina Schreiner1, Florian R Greten2,3, Dorotthe M Baur4, Alexander A Fingerle4, Ulrich Zechner4, Christian Bo¨ hm5, Michael Schmid5, Horst Hameister1 and Roland M Schmid3,4,* 1Department of Human Genetics, University of Ulm, D-89069 Ulm, Germany; 2Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0636, USA; 3Department of Internal Medicine II, Technical University of Munich, D-81675 Munich, Germany; 4Department of Internal Medicine I, University of Ulm, D-89069 Ulm, Germany; 5Institute of Human Genetics, University of Wu¨rzburg, D-97074 Wu¨rzburg, Germany TGFa/p53 þ /À transgenic mice represent a genetically that lead to final tumor development (Hruban et al., engineered mouse model for pancreatic adenocarcinoma. 2000; Bardeesy et al., 2001). To be able to investigate the The tumors develop a characteristic pattern of secondary different steps of genetic alterations occuring during genetic changes. From one of these tumors, the permanent cancer progression, a transgenic mouse tumor model cell line TD2 was established. Here, we describe in detail was established, in which TGFa is expressed under the the genetic changes by molecular–cytogenetic techniques. regulation of the elastase promoter. This ensures TGFa The original tumor-specific CGH profile has been retained overexpression restricted to pancreatic acinar cells unchanged. The most characteristic aberration pattern (Sandgren et al., 1990, 1991). It has already been shown bears chromosome 11.