Leigh Syndrome
Total Page:16
File Type:pdf, Size:1020Kb

Load more
Recommended publications
-
Genome-Wide Association Identifies Candidate Genes That Influence The
Genome-wide association identifies candidate genes that influence the human electroencephalogram Colin A. Hodgkinsona,1, Mary-Anne Enocha, Vibhuti Srivastavaa, Justine S. Cummins-Omana, Cherisse Ferriera, Polina Iarikovaa, Sriram Sankararamanb, Goli Yaminia, Qiaoping Yuana, Zhifeng Zhoua, Bernard Albaughc, Kenneth V. Whitea, Pei-Hong Shena, and David Goldmana aLaboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Rockville, MD 20852; bComputer Science Department, University of California, Berkeley, CA 94720; and cCenter for Human Behavior Studies, Weatherford, OK 73096 Edited* by Raymond L. White, University of California, Emeryville, CA, and approved March 31, 2010 (received for review July 23, 2009) Complex psychiatric disorders are resistant to whole-genome reflects rhythmic electrical activity of the brain. EEG patterns analysis due to genetic and etiological heterogeneity. Variation in dynamically and quantitatively index cortical activation, cognitive resting electroencephalogram (EEG) is associated with common, function, and state of consciousness. EEG traits were among the complex psychiatric diseases including alcoholism, schizophrenia, original intermediate phenotypes in neuropsychiatry, having been and anxiety disorders, although not diagnostic for any of them. EEG first recorded in humans in 1924 by Hans Berger, who documented traits for an individual are stable, variable between individuals, and the α rhythm, seen maximally during states of relaxation with eyes moderately to highly heritable. Such intermediate phenotypes closed, and supplanted by faster β waves during mental activity. appear to be closer to underlying molecular processes than are EEG can be used clinically for the evaluation and differential di- clinical symptoms, and represent an alternative approach for the agnosis of epilepsy and sleep disorders, differentiation of en- identification of genetic variation that underlies complex psychiat- cephalopathy from catatonia, assessment of depth of anesthesia, ric disorders. -
Genome-Wide Analysis of Allele-Specific Expression Patterns in Seventeen Tissues of Korean Cattle (Hanwoo)
animals Article Genome-Wide Analysis of Allele-Specific Expression Patterns in Seventeen Tissues of Korean Cattle (Hanwoo) Kyu-Sang Lim 1 , Sun-Sik Chang 2, Bong-Hwan Choi 3, Seung-Hwan Lee 4, Kyung-Tai Lee 3 , Han-Ha Chai 3, Jong-Eun Park 3 , Woncheoul Park 3 and Dajeong Lim 3,* 1 Department of Animal Science, Iowa State University, Ames, IA 50011, USA; [email protected] 2 Hanwoo Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang 25340, Korea; [email protected] 3 Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea; [email protected] (B.-H.C.); [email protected] (K.-T.L.); [email protected] (H.-H.C.); [email protected] (J.-E.P.); [email protected] (W.P.) 4 Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; [email protected] * Correspondence: [email protected] Received: 26 July 2019; Accepted: 23 September 2019; Published: 26 September 2019 Simple Summary: Allele-specific expression (ASE) is the biased allelic expression of genetic variants within the gene. Recently, the next-generation sequencing (NGS) technologies allowed us to detect ASE genes at a transcriptome-wide level. It is essential for the understanding of animal development, cellular programming, and the effect on their complexity because ASE shows developmental, tissue, or species-specific patterns. However, these aspects of ASE still have not been annotated well in farm animals and most studies were conducted mainly at the fetal stages. Hence, the current study focuses on detecting ASE genes in 17 tissues in adult cattle. -
High-Throughput, Pooled Sequencing Identifies Mutations in NUBPL And
ARTICLES High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency Sarah E Calvo1–3,10, Elena J Tucker4,5,10, Alison G Compton4,10, Denise M Kirby4, Gabriel Crawford3, Noel P Burtt3, Manuel Rivas1,3, Candace Guiducci3, Damien L Bruno4, Olga A Goldberger1,2, Michelle C Redman3, Esko Wiltshire6,7, Callum J Wilson8, David Altshuler1,3,9, Stacey B Gabriel3, Mark J Daly1,3, David R Thorburn4,5 & Vamsi K Mootha1–3 Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes that are involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing and experimental validation to uncover the molecular basis of mitochondrial complex I disorders. We created seven pools of DNA from a cohort of 103 cases and 42 healthy controls and then performed deep sequencing of 103 candidate genes to identify 151 rare variants that were predicted to affect protein function. We established genetic diagnoses in 13 of 60 previously unsolved cases using confirmatory experiments, including cDNA complementation to show that mutations in NUBPL and FOXRED1 can cause complex I deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can be used to identify causal mutations in individual cases. Complex I of the mitochondrial respiratory chain is a large ~1-MDa assembly factors are probably required, as suggested by the 20 factors macromolecular machine composed of 45 protein subunits encoded necessary for assembly of the smaller complex IV9 and by cohort by both the nuclear and mitochondrial (mtDNA) genomes. -
Neurodevelopmental Signatures of Narcotic and Neuropsychiatric Risk Factors in 3D Human-Derived Forebrain Organoids
Molecular Psychiatry www.nature.com/mp ARTICLE OPEN Neurodevelopmental signatures of narcotic and neuropsychiatric risk factors in 3D human-derived forebrain organoids 1 1 1 1 2 2 3 Michael Notaras , Aiman Lodhi , Estibaliz✉ Barrio-Alonso , Careen Foord , Tori Rodrick , Drew Jones , Haoyun Fang , David Greening 3,4 and Dilek Colak 1,5 © The Author(s) 2021 It is widely accepted that narcotic use during pregnancy and specific environmental factors (e.g., maternal immune activation and chronic stress) may increase risk of neuropsychiatric illness in offspring. However, little progress has been made in defining human- specific in utero neurodevelopmental pathology due to ethical and technical challenges associated with accessing human prenatal brain tissue. Here we utilized human induced pluripotent stem cells (hiPSCs) to generate reproducible organoids that recapitulate dorsal forebrain development including early corticogenesis. We systemically exposed organoid samples to chemically defined “enviromimetic” compounds to examine the developmental effects of various narcotic and neuropsychiatric-related risk factors within tissue of human origin. In tandem experiments conducted in parallel, we modeled exposure to opiates (μ-opioid agonist endomorphin), cannabinoids (WIN 55,212-2), alcohol (ethanol), smoking (nicotine), chronic stress (human cortisol), and maternal immune activation (human Interleukin-17a; IL17a). Human-derived dorsal forebrain organoids were consequently analyzed via an array of unbiased and high-throughput analytical approaches, including state-of-the-art TMT-16plex liquid chromatography/mass- spectrometry (LC/MS) proteomics, hybrid MS metabolomics, and flow cytometry panels to determine cell-cycle dynamics and rates of cell death. This pipeline subsequently revealed both common and unique proteome, reactome, and metabolome alterations as a consequence of enviromimetic modeling of narcotic use and neuropsychiatric-related risk factors in tissue of human origin. -
Analysis of Translating Mitoribosome Reveals Functional Characteristics of Translation in Mitochondria of Fungi
ARTICLE https://doi.org/10.1038/s41467-020-18830-w OPEN Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi Yuzuru Itoh 1,2,4, Andreas Naschberger1,4, Narges Mortezaei1,4, Johannes M. Herrmann 3 & ✉ Alexey Amunts 1,2 1234567890():,; Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly inter- mediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF1) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation. 1 Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden. 2 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Solna, Sweden. 3 Cell Biology, University -
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. -
Genetics of Amyotrophic Lateral Sclerosis in the Han Chinese
Genetics of amyotrophic lateral sclerosis in the Han Chinese Ji He A thesis submitted for the degree of Master of Philosophy at The University of Queensland in 2015 The University of Queensland Diamantina Institute 1 Abstract Amyotrophic lateral sclerosis is the most frequently occurring neuromuscular degenerative disorders, and has an obscure aetiology. Whilst major progress has been made, the majority of the genetic variation involved in ALS is, as yet, undefined. In this thesis, multiple genetic studies have been conducted to advance our understanding of the genetic architecture of the disease. In the light of the paucity of comprehensive genetic studies performed in Chinese, the presented study focused on advancing our current understanding in genetics of ALS in the Han Chinese population. To identify genetic variants altering risk of ALS, a genome-wide association study (GWAS) was performed. The study included 1,324 Chinese ALS cases and 3,115 controls. After quality control, a number of analyses were performed in a cleaned dataset of 1,243 cases and 2,854 controls that included: a genome-wide association analysis to identify SNPs associated with ALS; a genomic restricted maximum likelihood (GREML) analysis to estimate the proportion of the phenotypic variance in ALS liability due to common SNPs; and a gene- based analysis to identify genes associated with ALS. There were no genome-wide significant SNPs or genes associated with ALS. However, it was estimated that 17% (SE: 0.05; P=6×10-5) of the phenotypic variance in ALS liability was due to common SNPs. The top associated SNP was within GNAS (rs4812037; p =7×10-7). -
Ncomms8214.Pdf
ARTICLE Received 20 Feb 2015 | Accepted 17 Apr 2015 | Published 26 May 2015 DOI: 10.1038/ncomms8214 OPEN Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast Jing Hou1, Anne Friedrich1, Jean-Sebastien Gounot1 & Joseph Schacherer1 Genetic variation within a species could cause negative epistasis leading to reduced hybrid fitness and post-zygotic reproductive isolation. Recent studies in yeasts revealed chromo- somal rearrangements as a major mechanism dampening intraspecific hybrid fertility on rich media. Here, by analysing a large number of Saccharomyces cerevisiae crosses on different culture conditions, we show environment-specific genetic incompatibility segregates readily within yeast and contributes to reproductive isolation. Over 24% (117 out of 481) of cases tested show potential epistasis, among which 6.7% (32 out of 481) are severe, with at least 20% of progeny loss on tested conditions. Based on the segregation patterns, we further characterize a two-locus Dobzhansky–Mu¨ller incompatibility case leading to offspring respiratory deficiency caused by nonsense mutation in a nuclear-encoding mitochondrial gene and tRNA suppressor. We provide evidence that this precise configuration could be adaptive in fluctuating environments, highlighting the role of ecological selection in the onset of genetic incompatibility and reproductive isolation in yeast. 1 Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, 28 rue Goethe, 67083 Strasbourg, France. Correspondence -
Alterations of Genetic Variants and Transcriptomic Features of Response to Tamoxifen in the Breast Cancer Cell Line
Alterations of Genetic Variants and Transcriptomic Features of Response to Tamoxifen in the Breast Cancer Cell Line Mahnaz Nezamivand-Chegini Shiraz University Hamed Kharrati-Koopaee Shiraz University https://orcid.org/0000-0003-2345-6919 seyed taghi Heydari ( [email protected] ) Shiraz University of Medical Sciences https://orcid.org/0000-0001-7711-1137 Hasan Giahi Shiraz University Ali Dehshahri Shiraz University of Medical Sciences Mehdi Dianatpour Shiraz University of Medical Sciences Kamran Bagheri Lankarani Shiraz University of Medical Sciences Research Keywords: Tamoxifen, breast cancer, genetic variants, RNA-seq. Posted Date: August 17th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-783422/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/33 Abstract Background Breast cancer is one of the most important causes of mortality in the world, and Tamoxifen therapy is known as a medication strategy for estrogen receptor-positive breast cancer. In current study, two hypotheses of Tamoxifen consumption in breast cancer cell line (MCF7) were investigated. First, the effect of Tamoxifen on genes expression prole at transcriptome level was evaluated between the control and treated samples. Second, due to the fact that Tamoxifen is known as a mutagenic factor, there may be an association between the alterations of genetic variants and Tamoxifen treatment, which can impact on the drug response. Methods In current study, the whole-transcriptome (RNA-seq) dataset of four investigations (19 samples) were derived from European Bioinformatics Institute (EBI). At transcriptome level, the effect of Tamoxifen was investigated on gene expression prole between control and treatment samples. -
Proteomic and Metabolomic Analyses of Mitochondrial Complex I-Deficient
THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 24, pp. 20652–20663, June 8, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Proteomic and Metabolomic Analyses of Mitochondrial Complex I-deficient Mouse Model Generated by Spontaneous B2 Short Interspersed Nuclear Element (SINE) Insertion into NADH Dehydrogenase (Ubiquinone) Fe-S Protein 4 (Ndufs4) Gene*□S Received for publication, November 25, 2011, and in revised form, April 5, 2012 Published, JBC Papers in Press, April 25, 2012, DOI 10.1074/jbc.M111.327601 Dillon W. Leong,a1 Jasper C. Komen,b1 Chelsee A. Hewitt,a Estelle Arnaud,c Matthew McKenzie,d Belinda Phipson,e Melanie Bahlo,e,f Adrienne Laskowski,b Sarah A. Kinkel,a,g,h Gayle M. Davey,g William R. Heath,g Anne K. Voss,a,h René P. Zahedi,i James J. Pitt,j Roman Chrast,c Albert Sickmann,i,k Michael T. Ryan,l Gordon K. Smyth,e,f,h b2 a,h,m,n3 David R. Thorburn, and Hamish S. Scott Downloaded from From the aMolecular Medicine Division, gImmunology Division, and eBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, the bMurdoch Childrens Research Institute, Royal Children’s Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia, the cDépartement de Génétique Médicale, Université de Lausanne, 1005 Lausanne, Switzerland, the dCentre for Reproduction and Development, Monash Institute of Medical Research, Clayton, Victoria 3168, Australia, the hDepartment of Medical Biology -
FOXRED1 (D-4): Sc-377010
SANTA CRUZ BIOTECHNOLOGY, INC. FOXRED1 (D-4): sc-377010 BACKGROUND APPLICATIONS FOXRED1 (FAD-dependent oxidoreductase domain-containing protein 1), also FOXRED1 (D-4) is recommended for detection of FOXRED1 of human origin known as FP634, is a 486 amino acid single-pass membrane protein. Utilizing by Western Blotting (starting dilution 1:100, dilution range 1:100-1:1000), FAD as a cofactor, FOXRED1 may act as a chaperone protein essential for the immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml of cell function of mitochondrial complex I. Mutations to FOXRED1 may result in lysate)], immunofluorescence (starting dilution 1:50, dilution range 1:50- mitochondrial complex I deficiency (MT-C1D), which results in a wide range 1:500), immunohistochemistry (including paraffin-embedded sections) of clinical maladies from lethal neonatal disease to adult onset neurodegen- (starting dilution 1:50, dilution range 1:50-1:500) and solid phase ELISA erative disorders. Common phenotypes of MT-C1D include cardiomyopathy, (starting dilution 1:30, dilution range 1:30-1:3000). liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some Suitable for use as control antibody for FOXRED1 siRNA (h): sc-96988, forms of Parkinson disease. FOXRED1 exists as three alternatively spliced FOXRED1 shRNA Plasmid (h): sc-96988-SH and FOXRED1 shRNA (h) isoforms and is encoded by a gene mapping to human chromosome 11q24.2. Lentiviral Particles: sc-96988-V. With approximately 135 million base pairs and 1,400 genes, chromosome 11 makes up around 4% of human genomic DNA and is considered a gene and Molecular Weight of FOXRED1 isoform 1: 54 kDa. -
NDUFA2 Rabbit Pab
Leader in Biomolecular Solutions for Life Science NDUFA2 Rabbit pAb Catalog No.: A8136 Basic Information Background Catalog No. The encoded protein is a subunit of the hydrophobic protein fraction of the A8136 NADH:ubiquinone oxidoreductase (complex 1), the first enzyme complex in the electron transport chain located in the inner mitochondrial membrane, and may be involved in Observed MW regulating complex I activity or its assembly via assistance in redox processes. Mutations 11kDa in this gene are associated with Leigh syndrome, an early-onset progressive neurodegenerative disorder. Alternative splicing results in multiple transcript variants. Calculated MW 8kDa/10kDa Category Primary antibody Applications WB,IHC,IF Cross-Reactivity Human, Mouse, Rat Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 4695 O43678 IHC 1:50 - 1:100 Immunogen 1:50 - 1:200 IF Recombinant fusion protein containing a sequence corresponding to amino acids 1-95 of human NDUFA2 (NP_002479.1). Synonyms NDUFA2;B8;CD14;CIB8 Contact Product Information 400-999-6126 Source Isotype Purification Rabbit IgG Affinity purification [email protected] www.abclonal.com.cn Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using NDUFA2 antibody (A8136) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. Lysates/proteins: 25ug per lane. Blocking buffer: 3% nonfat dry milk in TBST. Detection: ECL Basic Kit (RM00020). Exposure time: 30s. Immunohistochemistry of paraffin- Immunohistochemistry of paraffin- Immunofluorescence analysis of NIH/3T3 embedded human esophagus using embedded human liver cancer using cells using NDUFA2 antibody (A8136) at NDUFA2 antibody (A8136) at dilution of NDUFA2 antibody (A8136) at dilution of dilution of 1:100.