Case Report 12Q14 Microdeletions: Additional Case Series with Confirmation of a Macrocephaly Region
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Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Benefits of Exome Sequencing in Children with Suspected Isolated
G C A T T A C G G C A T genes Article Benefits of Exome Sequencing in Children with Suspected Isolated Hearing Loss Roxane Van Heurck 1, Maria Teresa Carminho-Rodrigues 1, Emmanuelle Ranza 1, Caterina Stafuzza 2, Lina Quteineh 1, Corinne Gehrig 1, Eva Hammar 1, Michel Guipponi 1, Marc Abramowicz 1, Pascal Senn 2 , Nils Guinand 2, Helene Cao-Van 2 and Ariane Paoloni-Giacobino 1,* 1 Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; [email protected] (R.V.H.); [email protected] (M.T.C.-R.); [email protected] (E.R.); [email protected] (L.Q.); [email protected] (C.G.); [email protected] (E.H.); [email protected] (M.G.); [email protected] (M.A.) 2 Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; [email protected] (C.S.); [email protected] (P.S.); [email protected] (N.G.); [email protected] (H.C.-V.) * Correspondence: [email protected] Abstract: Purpose: Hearing loss is characterized by an extensive genetic heterogeneity and remains a common disorder in children. Molecular diagnosis is of particular benefit in children, and permits the early identification of clinically-unrecognized hearing loss syndromes, which permits effective clinical management and follow-up, including genetic counselling. Methods: We performed whole-exome Citation: Van Heurck, R.; sequencing with the analysis of a panel of 189 genes associated with hearing loss in a prospective Carminho-Rodrigues, M.T.; Ranza, E.; cohort of 61 children and 9 adults presenting mainly with isolated hearing loss. -
A Yeast Phenomic Model for the Gene Interaction Network Modulating
Louie et al. Genome Medicine 2012, 4:103 http://genomemedicine.com/content/4/12/103 RESEARCH Open Access A yeast phenomic model for the gene interaction network modulating CFTR-ΔF508 protein biogenesis Raymond J Louie3†, Jingyu Guo1,2†, John W Rodgers1, Rick White4, Najaf A Shah1, Silvere Pagant3, Peter Kim3, Michael Livstone5, Kara Dolinski5, Brett A McKinney6, Jeong Hong2, Eric J Sorscher2, Jennifer Bryan4, Elizabeth A Miller3* and John L Hartman IV1,2* Abstract Background: The overall influence of gene interaction in human disease is unknown. In cystic fibrosis (CF) a single allele of the cystic fibrosis transmembrane conductance regulator (CFTR-ΔF508) accounts for most of the disease. In cell models, CFTR-ΔF508 exhibits defective protein biogenesis and degradation rather than proper trafficking to the plasma membrane where CFTR normally functions. Numerous genes function in the biogenesis of CFTR and influence the fate of CFTR-ΔF508. However it is not known whether genetic variation in such genes contributes to disease severity in patients. Nor is there an easy way to study how numerous gene interactions involving CFTR-ΔF would manifest phenotypically. Methods: To gain insight into the function and evolutionary conservation of a gene interaction network that regulates biogenesis of a misfolded ABC transporter, we employed yeast genetics to develop a ‘phenomic’ model, in which the CFTR-ΔF508-equivalent residue of a yeast homolog is mutated (Yor1-ΔF670), and where the genome is scanned quantitatively for interaction. We first confirmed that Yor1-ΔF undergoes protein misfolding and has reduced half-life, analogous to CFTR-ΔF. Gene interaction was then assessed quantitatively by growth curves for approximately 5,000 double mutants, based on alteration in the dose response to growth inhibition by oligomycin, a toxin extruded from the cell at the plasma membrane by Yor1. -
Dissertationes Medicinae Universitatis Tartuensis 178
DISSERTATIONES MEDICINAE UNIVERSITATIS TARTUENSIS 178 DISSERTATIONES MEDICINAE UNIVERSITATIS TARTUENSIS 178 RITA TEEK The genetic causes of early onset hearing loss in Estonian children Department of Paediatrics, University of Tartu, Tartu, Estonia Dissertation is accepted for commencement of the degree of Doctor of Medical Sciences on September 22, 2010 by the Council of the Faculty of Medicine, University of Tartu, Estonia. Supervisors: Professor Katrin Õunap, MD, PhD, Department of Paediatrics, University of Tartu, Tartu, Estonia The Late Professor Mart Kull, MD, PhD, Department of Oto-Rhino-Laryngology, University of Tartu, Tartu, Estonia (2005–2008) Reviewers: Assistant Professor Gunnar Tasa, MD, PhD, Department of General and Molecular Pathology, University of Tartu, Tartu, Estonia Assistant Professor Oivi Uibo, MD, PhD, Department of Paediatrics, University of Tartu, Tartu, Estonia Opponent: Professor Lisbeth Tranebjærg, MD, PhD, Department of Audiology, H:S Bispebjerg Hospital, and Wilhelm Johannsen Centre of Functional Genomics Institute of Cellular and Molecular Medicine, ICMM, University of Copenhagen, The Panum Institute, Denmark Commencement: November 24, 2010 ISSN 1024–395x ISBN 978–9949–19–478–0 (trükis) ISBN 978–9949–19–479–7 (PDF) Autoriõigus: Rita Teek, 2010 Tartu Ülikooli Kirjastus www.tyk.ee Tellimuse nr. 570 To my patients and their families CONTENTS LIST OF ORIGINAL PUBLICATIONS ...................................................... 9 ABBREVIATIONS OF HEARING LOSS STUDY GROUPS AND PATIENTS .................................................................................................... -
An Evaluation of Host Factors As Novel Therapeutic Targets During Influenza Infection Using RNA Technologies
California State University, San Bernardino CSUSB ScholarWorks Electronic Theses, Projects, and Dissertations Office of aduateGr Studies 6-2018 An Evaluation of Host Factors as Novel Therapeutic Targets During Influenza Infection Using RNA Technologies Michael Ryan Haden Thompson California State University - San Bernardino Follow this and additional works at: https://scholarworks.lib.csusb.edu/etd Part of the Virology Commons Recommended Citation Thompson, Michael Ryan Haden, "An Evaluation of Host Factors as Novel Therapeutic Targets During Influenza Infection Using RNA Technologies" (2018). Electronic Theses, Projects, and Dissertations. 721. https://scholarworks.lib.csusb.edu/etd/721 This Thesis is brought to you for free and open access by the Office of aduateGr Studies at CSUSB ScholarWorks. It has been accepted for inclusion in Electronic Theses, Projects, and Dissertations by an authorized administrator of CSUSB ScholarWorks. For more information, please contact [email protected]. AN EVALUATION OF HOST FACTORS AS NOVEL THERAPEUTIC TARGETS DURING INFLUENZA INFECTION USING RNA TECHNOLOGIES _____________________ A Thesis Presented to the Faculty of California State University, San Bernardino _____________________ In Partial Fulfillment of the Requirements for the Degree Master of Science in Biology _____________________ by Michael Ryan Haden Thompson June 2018 AN EVALUATION OF HOST FACTORS AS NOVEL THERAPEUTIC TARGETS DURING INFLUENZA INFECTION USING RNA TECHNOLOGIES _____________________ A Thesis Presented to the Faculty of California State University, San Bernardino _____________________ By Michael Ryan Haden Thompson June 2018 Approved by: Dr. Laura L Newcomb, Committee Chair, Biology Dr. Nicole Bournias-Vardiabasis, Committee Member Dr. Daniel Nickerson, Committee Member © 2018 Michael Ryan Haden Thompson ABSTRACT Influenza A is a single-stranded, multi-segmented, negative sense RNA virus of the family Orthomyxoviridae and is the causative agent of seasonal Influenza. -
The Loss of Photosynthetic Pathways in the Plastid and Nuclear Genomes of the Non- Photosynthetic Mycoheterotrophic Eudicot Monotropa Hypopitys Nikolai V
The Author(s) BMC Plant Biology 2016, 16(Suppl 3):238 DOI 10.1186/s12870-016-0929-7 RESEARCH Open Access The loss of photosynthetic pathways in the plastid and nuclear genomes of the non- photosynthetic mycoheterotrophic eudicot Monotropa hypopitys Nikolai V. Ravin*, Eugeny V. Gruzdev, Alexey V. Beletsky, Alexander M. Mazur, Egor B. Prokhortchouk, Mikhail A. Filyushin, Elena Z. Kochieva, Vitaly V. Kadnikov, Andrey V. Mardanov and Konstantin G. Skryabin From The International Conference on Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2016) Novosibirsk, Russia. 29 August-2 September 2016 Abstract Background: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary. Transition to a non-photosynthetic lifestyle is expected also to relax the selective pressure on photosynthetic machinery in the nuclear genome, however, the corresponding changes are less known. Results: Here we report the complete sequence of the plastid genome of Monotropa hypopitys, an achlorophyllous obligately mycoheterotrophic plant belonging to the family Ericaceae. The plastome of M. hypopitys is greatly reduced in size (35,336 bp) and lacks the typical quadripartite structure with two single-copy regions and an inverted repeat. -
Mir-17-92 Fine-Tunes MYC Expression and Function to Ensure
ARTICLE Received 31 Mar 2015 | Accepted 22 Sep 2015 | Published 10 Nov 2015 DOI: 10.1038/ncomms9725 OPEN miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth Marija Mihailovich1, Michael Bremang1, Valeria Spadotto1, Daniele Musiani1, Elena Vitale1, Gabriele Varano2,w, Federico Zambelli3, Francesco M. Mancuso1,w, David A. Cairns1,w, Giulio Pavesi3, Stefano Casola2 & Tiziana Bonaldi1 The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 30 untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c- MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 30 UTR shortening at different stages of tumorigenesis. 1 Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy. 2 Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Therapeutic Targeting of Nuclear Transport
cells Review Controlling the Gatekeeper: Therapeutic Targeting of Nuclear Transport Friederike K. Kosyna * and Reinhard Depping Institute of Physiology, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-451-3101-7322; Fax: +49-451-3101-7304 Received: 25 October 2018; Accepted: 17 November 2018; Published: 21 November 2018 Abstract: Nuclear transport receptors of the karyopherin superfamily of proteins transport macromolecules from one compartment to the other and are critical for both cell physiology and pathophysiology. The nuclear transport machinery is tightly regulated and essential to a number of key cellular processes since the spatiotemporally expression of many proteins and the nuclear transporters themselves is crucial for cellular activities. Dysregulation of the nuclear transport machinery results in localization shifts of specific cargo proteins and associates with the pathogenesis of disease states such as cancer, inflammation, viral illness and neurodegenerative diseases. Therefore, inhibition of the nuclear transport system has future potential for therapeutic intervention and could contribute to the elucidation of disease mechanisms. In this review, we recapitulate clue findings in the pathophysiological significance of nuclear transport processes and describe the development of nuclear transport inhibitors. Finally, clinical implications and results of the first clinical trials are discussed for the most promising nuclear transport inhibitors. Keywords: nuclear transport; exportin; importin; karyopherin; chromosome region maintenance 1 (CRM1); cancer; drug; nuclear transport inhibitor 1. Introduction The cytoplasm and the nucleoplasm are separated by the nuclear envelope in eukaryotic cells. Spatially segregation of essential cellular processes requires tight control of large molecule exchange such as RNAs, proteins, or ribonucleoprotein particles through this double membrane. -
Downloaded the “Top Edge” Version
bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 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 4.0 International license. 1 Drosophila models of pathogenic copy-number variant genes show global and 2 non-neuronal defects during development 3 Short title: Non-neuronal defects of fly homologs of CNV genes 4 Tanzeen Yusuff1,4, Matthew Jensen1,4, Sneha Yennawar1,4, Lucilla Pizzo1, Siddharth 5 Karthikeyan1, Dagny J. Gould1, Avik Sarker1, Yurika Matsui1,2, Janani Iyer1, Zhi-Chun Lai1,2, 6 and Santhosh Girirajan1,3* 7 8 1. Department of Biochemistry and Molecular Biology, Pennsylvania State University, 9 University Park, PA 16802 10 2. Department of Biology, Pennsylvania State University, University Park, PA 16802 11 3. Department of Anthropology, Pennsylvania State University, University Park, PA 16802 12 4 contributed equally to work 13 14 *Correspondence: 15 Santhosh Girirajan, MBBS, PhD 16 205A Life Sciences Building 17 Pennsylvania State University 18 University Park, PA 16802 19 E-mail: [email protected] 20 Phone: 814-865-0674 21 1 bioRxiv preprint doi: https://doi.org/10.1101/855338; this version posted December 6, 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 4.0 International license. 22 ABSTRACT 23 While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non- 24 neuronal phenotypes, functional studies evaluating these regions have focused on the molecular 25 basis of neuronal defects. -
The Pathological Consequences of Impaired Genome Integrity in Humans; Disorders of the DNA Replication Machinery
The pathological consequences of impaired genome integrity in humans; disorders of the DNA replication machinery Article (Accepted Version) O'Driscoll, Mark (2017) The pathological consequences of impaired genome integrity in humans; disorders of the DNA replication machinery. Journal of Pathology, 241 (2). pp. 192-207. ISSN 0022-3417 This version is available from Sussex Research Online: http://sro.sussex.ac.uk/id/eprint/65956/ This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher’s version. Please see the URL above for details on accessing the published version. Copyright and reuse: Sussex Research Online is a digital repository of the research output of the University. Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available. Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. http://sro.sussex.ac.uk The pathological consequences of impaired genome integrity in humans; disorders of the DNA replication machinery. -
2021 Code Changes Reference Guide
Boston University Medical Group 2021 CPT Code Changes Reference Guide Page 1 of 51 Background Current Procedural Terminology (CPT) was created by the American Medical Association (AMA) in 1966. It is designed to be a means of effective and dependable communication among physicians, patients, and third-party payers. CPT provides a uniform coding scheme that accurately describes medical, surgical, and diagnostic services. CPT is used for public and private reimbursement systems; development of guidelines for medical care review; as a basis for local, regional, and national utilization comparisons; and medical education and research. CPT Category I codes describe procedures and services that are consistent with contemporary medical practice. Category I codes are five-digit numeric codes. CPT Category II codes facilitate data collection for certain services and test results that contribute to positive health outcomes and quality patient care. These codes are optional and used for performance management. They are alphanumeric five-digit codes with the alpha character F in the last position. CPT Category III codes represent emerging technologies. They are alphanumeric five-digit codes with the alpha character T in the last position. The CPT Editorial Panel, appointed by the AMA Board of Trustees, is responsible for maintaining and updating the CPT code set. Purpose The AMA makes annual updates to the CPT code set, effective January 1. These updates include deleted codes, revised codes, and new codes. It’s important for providers to understand the code changes and the impact those changes will have to systems, workflow, reimbursement, and RVUs. This document is meant to assist you with this by providing a summary of the changes; a detailed breakdown of this year’s CPT changes by specialty, and HCPCS Updates for your reference.