Familial Left Ventricular Non-Compaction Is Associated with a Rare P.V407I Variant in Bone Morphogenetic Protein 10
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Identification of the Binding Partners for Hspb2 and Cryab Reveals
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity. -
TBX20 Loss-Of-Function Mutation Contributes to Double Outlet Right Ventricle
1058 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 35: 1058-1066, 2015 TBX20 loss-of-function mutation contributes to double outlet right ventricle YUN PAN1*, RUI GENG1*, NING ZHOU1, GUI-FEN ZHENG1, HONG ZHAO1, JUAN WANG2, CUI-MEI ZHAO2, XING-BIAO QIU3, YI-QING YANG3-5 and XING-YUAN LIU1 Departments of 1Pediatrics and 2Cardiology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065; 3Department of Cardiology, 4Cardiovascular Research Laboratory and 5Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China Received November 30, 2014; Accepted January 20, 2015 DOI: 10.3892/ijmm.2015.2077 Abstract. Congenital heart disease (CHD), the most prevalent nant pattern with complete penetrance. The missense mutation birth defect in humans worldwide, is still a leading non-infec- was absent in 400 control chromosomes and the altered amino tious cause of infant morbidity and mortality. Increasing acid was completely conserved evolutionarily across species. evidence demonstrates that genetic risk factors play a key role Functional analysis revealed that mutant TBX20 had a signifi- in the pathogenesis of CHD, and more than 50 genes have cantly diminished transcriptional activity compared with its been linked to various types of CHD. Nevertheless, CHD is wild-type counterpart. To the best of our knowledge, this study a heterogeneous disorder and the genetic components under- is the first to report the association of TBX20 loss-of-function pinning CHD in an overwhelming majority of cases remain mutation with increased susceptibility to DORV in humans, unknown. In the present study, the entire coding exons and which provides novel insight into the molecular mechanisms flanking introns of the TBX20 gene, which codes for a T-box responsible for CHD, suggesting potential implications for the transcription factor essential for the proper development of the antenatal prophylaxis of CHD. -
Myocardin Is Sufficient and Necessary for Cardiac Gene Expression in Xenopus Eric M
Research article 987 Myocardin is sufficient and necessary for cardiac gene expression in Xenopus Eric M. Small1,*,†, Andrew S. Warkman1,*, Da-Zhi Wang2, Lillian B. Sutherland3, Eric N. Olson3 and Paul A. Krieg1,‡ 1Department of Cell Biology and Anatomy, University of Arizona Health Sciences Center, 1501 N. Campbell Avenue, PO Box 245044, Tucson, AZ, 85724, USA 2Carolina Cardiovascular Biology Center, Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, NC 27599-7126, USA 3Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA *These authors contributed equally to this work †Present address: Cardiovascular Research, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada ‡Author for correspondence (e-mail: [email protected]) Accepted 14 December 2004 Development 132, 987-997 Published by The Company of Biologists 2005 doi:10.1242/dev.01684 Summary Myocardin is a cardiac- and smooth muscle-specific co- expression. Inhibition of myocardin activity in Xenopus factor for the ubiquitous transcription factor serum embryos using morpholino knockdown methods results in response factor (SRF). Using gain-of-function approaches inhibition of cardiac development and the absence of in the Xenopus embryo, we show that myocardin is expression of cardiac differentiation markers and severe sufficient to activate transcription of a wide range of disruption of cardiac morphological processes. We cardiac and -
MOCHI Enables Discovery of Heterogeneous Interactome Modules in 3D Nucleome
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome Dechao Tian1,# , Ruochi Zhang1,# , Yang Zhang1, Xiaopeng Zhu1, and Jian Ma1,* 1Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA #These two authors contributed equally *Correspondence: [email protected] Contact To whom correspondence should be addressed: Jian Ma School of Computer Science Carnegie Mellon University 7705 Gates-Hillman Complex 5000 Forbes Avenue Pittsburgh, PA 15213 Phone: +1 (412) 268-2776 Email: [email protected] 1 Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The composition of the cell nucleus is highly heterogeneous, with different constituents forming complex interactomes. However, the global patterns of these interwoven heterogeneous interactomes remain poorly understood. Here we focus on two different interactomes, chromatin interaction network and gene regulatory network, as a proof-of-principle, to identify heterogeneous interactome modules (HIMs), each of which represents a cluster of gene loci that are in spatial contact more frequently than expected and that are regulated by the same group of transcription factors. HIM integrates transcription factor binding and 3D genome structure to reflect “transcriptional niche” in the nucleus. We develop a new algorithm MOCHI to facilitate the discovery of HIMs based on network motif clustering in heterogeneous interactomes. By applying MOCHI to five different cell types, we found that HIMs have strong spatial preference within the nucleus and exhibit distinct functional properties. Through integrative analysis, this work demonstrates the utility of MOCHI to identify HIMs, which may provide new perspectives on the interplay between transcriptional regulation and 3D genome organization. -
WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Discovery and Systematic Characterization of Risk Variants and Genes For
medRxiv preprint doi: https://doi.org/10.1101/2021.05.24.21257377; this version posted June 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . 1 Discovery and systematic characterization of risk variants and genes for 2 coronary artery disease in over a million participants 3 4 Krishna G Aragam1,2,3,4*, Tao Jiang5*, Anuj Goel6,7*, Stavroula Kanoni8*, Brooke N Wolford9*, 5 Elle M Weeks4, Minxian Wang3,4, George Hindy10, Wei Zhou4,11,12,9, Christopher Grace6,7, 6 Carolina Roselli3, Nicholas A Marston13, Frederick K Kamanu13, Ida Surakka14, Loreto Muñoz 7 Venegas15,16, Paul Sherliker17, Satoshi Koyama18, Kazuyoshi Ishigaki19, Bjørn O Åsvold20,21,22, 8 Michael R Brown23, Ben Brumpton20,21, Paul S de Vries23, Olga Giannakopoulou8, Panagiota 9 Giardoglou24, Daniel F Gudbjartsson25,26, Ulrich Güldener27, Syed M. Ijlal Haider15, Anna 10 Helgadottir25, Maysson Ibrahim28, Adnan Kastrati27,29, Thorsten Kessler27,29, Ling Li27, Lijiang 11 Ma30,31, Thomas Meitinger32,33,29, Sören Mucha15, Matthias Munz15, Federico Murgia28, Jonas B 12 Nielsen34,20, Markus M Nöthen35, Shichao Pang27, Tobias Reinberger15, Gudmar Thorleifsson25, 13 Moritz von Scheidt27,29, Jacob K Ulirsch4,11,36, EPIC-CVD Consortium, Biobank Japan, David O 14 Arnar25,37,38, Deepak S Atri39,3, Noël P Burtt4, Maria C Costanzo4, Jason Flannick40, Rajat M 15 Gupta39,3,4, Kaoru Ito18, Dong-Keun Jang4, -
Genetic and Genomics Laboratory Tools and Approaches
Genetic and Genomics Laboratory Tools and Approaches Meredith Yeager, PhD Cancer Genomics Research Laboratory Division of Cancer Epidemiology and Genetics [email protected] DCEG Radiation Epidemiology and Dosimetry Course 2019 www.dceg.cancer.gov/RadEpiCourse (Recent) history of genetics 2 Sequencing of the Human Genome Science 291, 1304-1351 (2001) 3 The Human Genome – 2019 • ~3.3 billion bases (A, C, G, T) • ~20,000 protein-coding genes, many non-coding RNAs (~2% of the genome) • Annotation ongoing – the initial sequencing in 2001 is still being refined, assembled and annotated, even now – hg38 • Variation (polymorphism) present within humans – Population-specific – Cosmopolitan 4 Types of polymorphisms . Single nucleotide polymorphisms (SNPs) . Common SNPs are defined as > 5% in at least one population . Abundant in genome (~50 million and counting) ATGGAACGA(G/C)AGGATA(T/A)TACGCACTATGAAG(C/A)CGGTGAGAGG . Repeats of DNA (long, short, complex, simple), insertions/deletions . A small fraction of SNPs and other types of variation are very or slightly deleterious and may contribute by themselves or with other genetic or environmental factors to a phenotype or disease 5 Different mutation rates at the nucleotide level Mutation type Mutation rate (per generation) Transition on a CpG 1.6X10-7 Transversion on a CpG 4.4X10-8 Transition: purine to purine Transition out of CpG 1.2X10-8 Transversion: purine to pyrimidine Transversion out of CpG 5.5X10-9 Substitution (average) 2.3X10-8 A and G are purines Insertion/deletion (average) 2.3X10-9 C and T are pyrimidines Mutation rate (average) 2.4X10-8 . Size of haploid genome : 3.3X109 nucleotides . -
TBX20 Loss-Of-Function Mutation Responsible for Familial Tetralogy Of
Int. J. Med. Sci. 2017, Vol. 14 323 Ivyspring International Publisher International Journal of Medical Sciences 2017; 14(4): 323-332. doi: 10.7150/ijms.17834 Research Paper TBX20 loss-of-function mutation responsible for familial tetralogy of Fallot or sporadic persistent truncus arteriosus Ri-Tai Huang1*, Juan Wang2*, Song Xue1, Xing-Biao Qiu3, Hong-Yu Shi3, Ruo-Gu Li3, Xin-Kai Qu3, Xiao-Xiao Yang3, Hua Liu3, Ning Li3, Yan-Jie Li3, Ying-Jia Xu3, Yi-Qing Yang3,4,5 1. Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 1630 Dongfang Road, Shanghai 200127, China; 2. Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, China; 3. Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China; 4. Department of Cardiovascular Research Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China; 5. Department of Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China. * These two authors contributed equally to this work. Corresponding author: Dr. Ying-Jia Xu, Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China. E-mail: [email protected]; Prof. Yi-Qing Yang, Department of Cardiovascular Research Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China. E-mail: [email protected]. © Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). -
Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis
Getting “Under the Skin”: Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis by Kristen Monét Brown A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Epidemiological Science) in the University of Michigan 2017 Doctoral Committee: Professor Ana V. Diez-Roux, Co-Chair, Drexel University Professor Sharon R. Kardia, Co-Chair Professor Bhramar Mukherjee Assistant Professor Belinda Needham Assistant Professor Jennifer A. Smith © Kristen Monét Brown, 2017 [email protected] ORCID iD: 0000-0002-9955-0568 Dedication I dedicate this dissertation to my grandmother, Gertrude Delores Hampton. Nanny, no one wanted to see me become “Dr. Brown” more than you. I know that you are standing over the bannister of heaven smiling and beaming with pride. I love you more than my words could ever fully express. ii Acknowledgements First, I give honor to God, who is the head of my life. Truly, without Him, none of this would be possible. Countless times throughout this doctoral journey I have relied my favorite scripture, “And we know that all things work together for good, to them that love God, to them who are called according to His purpose (Romans 8:28).” Secondly, I acknowledge my parents, James and Marilyn Brown. From an early age, you two instilled in me the value of education and have been my biggest cheerleaders throughout my entire life. I thank you for your unconditional love, encouragement, sacrifices, and support. I would not be here today without you. I truly thank God that out of the all of the people in the world that He could have chosen to be my parents, that He chose the two of you. -
Findings from Chick Embryo Studies
Journal of Cardiovascular Development and Disease Review Mechanosensitive Pathways in Heart Development: Findings from Chick Embryo Studies Maha Alser 1,2, Samar Shurbaji 1 and Huseyin C. Yalcin 1,* 1 Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar; [email protected] (M.A.); [email protected] (S.S.) 2 College of Health and Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar * Correspondence: [email protected]; Tel.: +974-4403-7719 Abstract: The heart is the first organ that starts to function in a developing embryo. It continues to undergo dramatic morphological changes while pumping blood to the rest of the body. Genetic regulation of heart development is partly governed by hemodynamics. Chick embryo is a major animal model that has been used extensively in cardiogenesis research. To reveal mechanosensitive pathways, a variety of surgical interferences and chemical treatments can be applied to the chick embryo to manipulate the blood flow. Such manipulations alter expressions of mechanosensitive genes which may anticipate induction of morphological changes in the developing heart. This paper aims to present different approaches for generating clinically relevant disturbed hemodynamics conditions using this embryonic chick model and to summarize identified mechanosensitive genes using the model, providing insights into embryonic origins of congenital heart defects. Keywords: chick embryo; hemodynamics; mechanobiology; mechanosensitive pathways; surgical interferences; left atrial ligation; outflow tract banding; vitelline vein ligation; chemical treatment; gene expression Citation: Alser, M.; Shurbaji, S.; Yalcin, H.C. Mechanosensitive Pathways in Heart Development: Findings from Chick Embryo Studies. 1. Introduction J. Cardiovasc. Dev. -
Genetic Differences Between Extreme and Composite Constitution Types from Whole Exome Sequences Reveal Actionable Variations
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.24.059006; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Genetic differences between extreme and composite constitution types from whole exome sequences reveal actionable variations Tahseen Abbas3,4,#, Rintu Kutum1,3,4,#, Rajesh Pandey1,#, Pushkar Dakle1, Ankita Narang1, Vijeta Manchanda1, Rutuja Patil1,5, Dheeraj Aggarwal5, Gourja Bansal1, Pooja Sharma1, Gaura Chaturvedi1,2,4, Bhushan Girase5, Ankita Srivastava5, Sanjay Juvekar5, Debasis Dash3,4,*, Bhavana Prasher1,2,4,*, Mitali Mukerji1,2,4,* 1Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, India. 2Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi, India 3Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi, India 4Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Delhi, India 5Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India # Lead authors * Corresponding authors: [email protected]; [email protected]; [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.24.059006; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Personalized medicine relies on successful identification of genome-wide variations that governs inter-individual differences in phenotypes and system level outcomes. In Ayurveda, assessment of composite constitution types “Prakriti” forms the basis for risk stratification, predicting health and disease trajectories and personalized recommendations. -
A Novel TBX20 Loss‑Of‑Function Mutation Contributes to Adult‑Onset Dilated Cardiomyopathy Or Congenital Atrial Septal Defect
MOLECULAR MEDICINE REPORTS 14: 3307-3314, 2016 A novel TBX20 loss‑of‑function mutation contributes to adult‑onset dilated cardiomyopathy or congenital atrial septal defect YI-MENG ZHOU1*, XIAO-YONG DAI1*, RI-TAI HUANG2, SONG XUE2, YING-JIA XU3, XING-BIAO QIU3 and YI-QING YANG3-5 1Department of Emergency Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090; 2Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127; Departments of 3Cardiology, 4Cardiovascular Research Laboratory and 5Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China Received July 11, 2015; Accepted July 22, 2016 DOI: 10.3892/mmr.2016.5609 Abstract. Dilated cardiomyopathy (DCM) is the most transcriptional activity in contrast to its wild-type counterpart. prevalent form of primary cardiomyopathy in humans and Furthermore, the mutation abolished the synergistic activation is a leading cause of heart failure and sudden cardiac death. between TBX20 and NK2 homeobox 5, or between TBX20 Genetic abnormalities have been demonstrated to be a major and GATA binding protein 4. The observations of the current contributor to the development of DCM. However, DCM is a study expand the mutation spectrum of TBX20 associated genetically heterogeneous disease, and the genetic basis under- with DCM and congenital heart disease (CHD), which provide lying DCM in a significant proportion of patients remains novel insight into the molecular mechanisms underlying DCM unclear. In the current study, the coding exons and splicing and CHD, suggesting the potential implications for the effec- junction sites of the T-Box 20 (TBX20) gene, which encodes a tive and personalized treatment of these diseases.