Strains Used in Whole Organism Plasmodium Falciparum Vaccine Trials Differ in 2 Genome Structure, Sequence, and Immunogenic Potential 3 4 Authors: Kara A
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The N-Cadherin Interactome in Primary Cardiomyocytes As Defined Using Quantitative Proximity Proteomics Yang Li1,*, Chelsea D
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs221606. doi:10.1242/jcs.221606 TOOLS AND RESOURCES The N-cadherin interactome in primary cardiomyocytes as defined using quantitative proximity proteomics Yang Li1,*, Chelsea D. Merkel1,*, Xuemei Zeng2, Jonathon A. Heier1, Pamela S. Cantrell2, Mai Sun2, Donna B. Stolz1, Simon C. Watkins1, Nathan A. Yates1,2,3 and Adam V. Kwiatkowski1,‡ ABSTRACT requires multiple adhesion, cytoskeletal and signaling proteins, The junctional complexes that couple cardiomyocytes must transmit and mutations in these proteins can cause cardiomyopathies (Ehler, the mechanical forces of contraction while maintaining adhesive 2018). However, the molecular composition of ICD junctional homeostasis. The adherens junction (AJ) connects the actomyosin complexes remains poorly defined. – networks of neighboring cardiomyocytes and is required for proper The core of the AJ is the cadherin catenin complex (Halbleib and heart function. Yet little is known about the molecular composition of the Nelson, 2006; Ratheesh and Yap, 2012). Classical cadherins are cardiomyocyte AJ or how it is organized to function under mechanical single-pass transmembrane proteins with an extracellular domain that load. Here, we define the architecture, dynamics and proteome of mediates calcium-dependent homotypic interactions. The adhesive the cardiomyocyte AJ. Mouse neonatal cardiomyocytes assemble properties of classical cadherins are driven by the recruitment of stable AJs along intercellular contacts with organizational and cytosolic catenin proteins to the cadherin tail, with p120-catenin β structural hallmarks similar to mature contacts. We combine (CTNND1) binding to the juxta-membrane domain and -catenin β quantitative mass spectrometry with proximity labeling to identify the (CTNNB1) binding to the distal part of the tail. -
1 Title: Re-Annotation of the Theileria Parva Genome Refines 53% of the Proteome And
bioRxiv preprint doi: https://doi.org/10.1101/749366; this version posted August 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. 1 Title: Re-annotation of the Theileria parva genome refines 53% of the proteome and 2 uncovers essential components of N-glycosylation, a conserved pathway in many 3 organisms 4 Kyle Tretina1, Roger Pelle2, Joshua Orvis1, Hanzel T. Gotia1, Olukemi O. Ifeonu1, Priti 5 Kumari1, Nicholas C. Palmateer1, Shaikh B.A. Iqbal1, Lindsay Fry3,4, Vishvanath M. 6 Nene5, Claudia Daubenberger6, Richard P. Bishop3, Joana C. Silva1,7* 7 Affiliations: 8 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 9 MD, USA 10 2Biosciences eastern and central Africa-International Livestock Research Institute, 11 Nairobi, Kenya 12 3Animal Disease Research Unit, Agricultural Research Service, USDA, Pullman, WA 13 99164-7030, USA 14 4Department of Veterinary Microbiology & Pathology, Washington State University 15 Pullman, WA 99164-7040, USA 16 5International Livestock Research Institute, Nairobi, Kenya 17 6Swiss Tropical and Public Health Institute, Basel, Switzerland & University of Basel, 18 Basel, Switzerland 19 7Department of Microbiology and Immunology, University of Maryland School of 20 Medicine, Baltimore, MD, USA 21 *Corresponding author 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/749366; this version posted August 31, 2019. 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. 24 Abstract (<350 words) 25 Background: Genome annotation remains a significant challenge because of limitations in 26 the quality and quantity of the data being used to inform the location and function of 27 protein-coding genes and, when RNA data are used, the underlying biological complexity 28 of the processes involved in gene expression. -
Aminoacyl-Trna Synthetase Deficiencies in Search of Common Themes
© American College of Medical Genetics and Genomics ARTICLE Aminoacyl-tRNA synthetase deficiencies in search of common themes Sabine A. Fuchs, MD, PhD1, Imre F. Schene, MD1, Gautam Kok, BSc1, Jurriaan M. Jansen, MSc1, Peter G. J. Nikkels, MD, PhD2, Koen L. I. van Gassen, PhD3, Suzanne W. J. Terheggen-Lagro, MD, PhD4, Saskia N. van der Crabben, MD, PhD5, Sanne E. Hoeks, MD6, Laetitia E. M. Niers, MD, PhD7, Nicole I. Wolf, MD, PhD8, Maaike C. de Vries, MD9, David A. Koolen, MD, PhD10, Roderick H. J. Houwen, MD, PhD11, Margot F. Mulder, MD, PhD12 and Peter M. van Hasselt, MD, PhD1 Purpose: Pathogenic variations in genes encoding aminoacyl- with unreported compound heterozygous pathogenic variations in tRNA synthetases (ARSs) are increasingly associated with human IARS, LARS, KARS, and QARS extended the common phenotype disease. Clinical features of autosomal recessive ARS deficiencies with lung disease, hypoalbuminemia, anemia, and renal tubulo- appear very diverse and without apparent logic. We searched for pathy. common clinical patterns to improve disease recognition, insight Conclusion: We propose a common clinical phenotype for recessive into pathophysiology, and clinical care. ARS deficiencies, resulting from insufficient aminoacylation activity Methods: Symptoms were analyzed in all patients with recessive to meet translational demand in specific organs or periods of life. ARS deficiencies reported in literature, supplemented with Assuming residual ARS activity, adequate protein/amino acid supply unreported patients evaluated in our hospital. seems essential instead of the traditional replacement of protein by Results: In literature, we identified 107 patients with AARS, glucose in patients with metabolic diseases. DARS, GARS, HARS, IARS, KARS, LARS, MARS, RARS, SARS, VARS, YARS, and QARS deficiencies. -
Validation of the PARVA C.392A<T Variant in a South African Family
Validation of the PARVA c.392A>T variant in a South African family with severe Arrhythmogenic Right Ventricular Cardiomyopathy Stephen Kamuli Thesis presented for the Degree of MASTER OF SCIENCE In the Department of Medicine UniversityUNIVERSITY OF of CAPE Cape TOWN Town Supervisor: Dr Gasnat Shaboodien Co-supervisor: Professor Bongani Mayosi August 2016 i The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town DECLARATION I, …Stephen Kamuli………………, hereby declare that the work on which this dissertation/thesis is based is my original work (except where acknowledgements indicate otherwise) and that neither the whole work nor any part of it has been, is being, or is to be submitted for another degree in this or any other university. I empower the university to reproduce for the purpose of research either the whole or any portion of the contents in any manner whatsoever. Signature: signature removed Date: 18 August 2016 ii TABLE OF CONTENTS TABLE OF CONTENTS ...................................................................................................................................... I ABSTRACT .................................................................................................................................................... -
Mclean, Chelsea.Pdf
COMPUTATIONAL PREDICTION AND EXPERIMENTAL VALIDATION OF NOVEL MOUSE IMPRINTED GENES A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Chelsea Marie McLean August 2009 © 2009 Chelsea Marie McLean COMPUTATIONAL PREDICTION AND EXPERIMENTAL VALIDATION OF NOVEL MOUSE IMPRINTED GENES Chelsea Marie McLean, Ph.D. Cornell University 2009 Epigenetic modifications, including DNA methylation and covalent modifications to histone tails, are major contributors to the regulation of gene expression. These changes are reversible, yet can be stably inherited, and may last for multiple generations without change to the underlying DNA sequence. Genomic imprinting results in expression from one of the two parental alleles and is one example of epigenetic control of gene expression. So far, 60 to 100 imprinted genes have been identified in the human and mouse genomes, respectively. Identification of additional imprinted genes has become increasingly important with the realization that imprinting defects are associated with complex disorders ranging from obesity to diabetes and behavioral disorders. Despite the importance imprinted genes play in human health, few studies have undertaken genome-wide searches for new imprinted genes. These have used empirical approaches, with some success. However, computational prediction of novel imprinted genes has recently come to the forefront. I have developed generalized linear models using data on a variety of sequence and epigenetic features within a training set of known imprinted genes. The resulting models were used to predict novel imprinted genes in the mouse genome. After imposing a stringency threshold, I compiled an initial candidate list of 155 genes. -
Gene Section Review
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Review PARVB (parvin, beta) Cameron N Johnstone Cancer Metastasis Laboratory, Research Division, Peter MacCallum Cancer Centre, 2 St Andrew's Place, East Melbourne, 3002, Victoria, Australia (CNJ) Published in Atlas Database: April 2010 Online updated version : http://AtlasGeneticsOncology.org/Genes/PARVBID46486ch22q13.html DOI: 10.4267/2042/44936 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2011 Atlas of Genetics and Cytogenetics in Oncology and Haematology Identity DNA/RNA Other names: CGI-56, affixin, beta-parvin Note HGNC (Hugo): PARVB Genethon marker D22S1171 is located at the 5' end of Location: 22q13.31 the gene (Mongroo et al., 2004). Genethon marker Local order: PARVB is located telomeric to the D22S1171 is located between exon 2 and exon 1A of SAMM50 gene and centromeric to the PARVG gene the PARVB gene. at 22q13.31. The PARVA gene is located at 11p15.3. Figure A. Generation of transcript diversity by alternative promoter usage. Horizontal lines above the gene structure indicate human genomic DNA BAC clones. The NCBI accession numbers of the clones, and clone names (in brackets) are shown. Figure adapted from Mongroo et al., 2004. Atlas Genet Cytogenet Oncol Haematol. 2011; 15(1) 34 PARVB (parvin, beta) Johnstone CN Figure B. Human polyA+ RNA Multiple Tissue Northern blot (Origene) probed with full-length PARVB1 cDNA probe radiolabeled to a specific activity of > 5 x 108 cpm / mg (Johnstone C.N., unpublished). The two PARVB mRNA transcripts are indicated. -
Anti-VARS (Aa 994-1102) Polyclonal Antibody (DPAB-DC3179) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Anti-VARS (aa 994-1102) polyclonal antibody (DPAB-DC3179) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Antigen Description Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. The protein encoded by this gene belongs to class-I aminoacyl-tRNA synthetase family and is located in the class III region of the major histocompatibility complex. Immunogen VARS (NP_006286, 994 a.a. ~ 1102 a.a) partial recombinant protein with GST tag. The sequence is AVRLSNQGFQAYDFPAVTTAQYSFWLYELCDVYLECLKPVLNGVDQVAAECARQTLYTCLDVG LRLLSPFMPFVTEELFQRLPRRMPQAPPSLCVTPYPEPSECSWKDP Source/Host Mouse Species Reactivity Human Conjugate Unconjugated Applications WB (Recombinant protein), ELISA, Size 50 μl Buffer 50 % glycerol Preservative None Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. GENE INFORMATION Gene Name VARS valyl-tRNA synthetase [ Homo sapiens (human) ] Official Symbol VARS Synonyms VARS; valyl-tRNA synthetase; G7A; VARS1; VARS2; valine--tRNA ligase; valRS; protein G7a; valyl-tRNA synthetase 2; valine tRNA ligase 1, cytoplasmic; 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved Entrez Gene ID 7407 Protein Refseq NP_006286 UniProt ID A0A024RCN6 Chromosome Location 6p21.3 Pathway Aminoacyl-tRNA biosynthesis; Cytosolic tRNA aminoacylation; tRNA Aminoacylation; Function ATP binding; aminoacyl-tRNA editing activity; valine-tRNA ligase activity; 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 2 © Creative Diagnostics All Rights Reserved. -
Pfswib, a Potential Chromatin Regulator for Var Gene Regulation and Parasite Development in Plasmodium Falciparum Wei‑Feng Wang1,3† and Yi‑Long Zhang2,3*†
Wang and Zhang Parasites Vectors (2020) 13:48 https://doi.org/10.1186/s13071-020-3918-5 Parasites & Vectors RESEARCH Open Access PfSWIB, a potential chromatin regulator for var gene regulation and parasite development in Plasmodium falciparum Wei‑Feng Wang1,3† and Yi‑Long Zhang2,3*† Abstract Background: Various transcription factors are involved in the process of mutually exclusive expression and clonal variation of the Plasmodium multigene (var) family. Recent studies revealed that a P. falciparum SWI/SNF‑related matrix‑associated actin‑dependent regulator of chromatin (PfSWIB) might trigger stage‑specifc programmed cell death (PCD), and was not only crucial for the survival and development of parasite, but also had profound efects on the parasite by interacting with other unknown proteins. However, it remains unclear whether PfSIWB is involved in transcriptional regulation of this virulence gene and its functional properties. Methods: A conditional knockdown system “PfSWIB‑FKBP‑LID” was introduced to the parasite clone 3D7, and an integrated parasite line “PfSWIB‑HA‑FKBP‑LID” was obtained by drug cycling and clone screening. Growth curve analysis (GCA) was performed to investigate the growth and development of diferent parasite lines during 96 h in vitro culturing, by assessing parasitemia. Finally, we performed qPCR assays to detect var gene expression profling in various comparison groups, as well as the mutually exclusive expression pattern of the var genes within a single 48 h life‑cycle of P. falciparum in diferent parasite lines. In addition, RNA‑seq was applied to analyze the var gene expres‑ sion in diferent lines. Results: GCA revealed that conditional knockdown of PfSWIB could interfere with the growth and development of P. -
The Genome 10K Project: a Way Forward
The Genome 10K Project: A Way Forward Klaus-Peter Koepfli,1 Benedict Paten,2 the Genome 10K Community of Scientists,Ã and Stephen J. O’Brien1,3 1Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russian Federation; email: [email protected] 2Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064 3Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida 33004 Annu. Rev. Anim. Biosci. 2015. 3:57–111 Keywords The Annual Review of Animal Biosciences is online mammal, amphibian, reptile, bird, fish, genome at animal.annualreviews.org This article’sdoi: Abstract 10.1146/annurev-animal-090414-014900 The Genome 10K Project was established in 2009 by a consortium of Copyright © 2015 by Annual Reviews. biologists and genome scientists determined to facilitate the sequencing All rights reserved and analysis of the complete genomes of10,000vertebratespecies.Since Access provided by Rockefeller University on 01/10/18. For personal use only. ÃContributing authors and affiliations are listed then the number of selected and initiated species has risen from ∼26 Annu. Rev. Anim. Biosci. 2015.3:57-111. Downloaded from www.annualreviews.org at the end of the article. An unabridged list of G10KCOS is available at the Genome 10K website: to 277 sequenced or ongoing with funding, an approximately tenfold http://genome10k.org. increase in five years. Here we summarize the advances and commit- ments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and futurevision of the landscape of Genome 10K. -
Whole-Exome Sequencing Identifies Causative Mutations in Families
BASIC RESEARCH www.jasn.org Whole-Exome Sequencing Identifies Causative Mutations in Families with Congenital Anomalies of the Kidney and Urinary Tract Amelie T. van der Ven,1 Dervla M. Connaughton,1 Hadas Ityel,1 Nina Mann,1 Makiko Nakayama,1 Jing Chen,1 Asaf Vivante,1 Daw-yang Hwang,1 Julian Schulz,1 Daniela A. Braun,1 Johanna Magdalena Schmidt,1 David Schapiro,1 Ronen Schneider,1 Jillian K. Warejko,1 Ankana Daga,1 Amar J. Majmundar,1 Weizhen Tan,1 Tilman Jobst-Schwan,1 Tobias Hermle,1 Eugen Widmeier,1 Shazia Ashraf,1 Ali Amar,1 Charlotte A. Hoogstraaten,1 Hannah Hugo,1 Thomas M. Kitzler,1 Franziska Kause,1 Caroline M. Kolvenbach,1 Rufeng Dai,1 Leslie Spaneas,1 Kassaundra Amann,1 Deborah R. Stein,1 Michelle A. Baum,1 Michael J.G. Somers,1 Nancy M. Rodig,1 Michael A. Ferguson,1 Avram Z. Traum,1 Ghaleb H. Daouk,1 Radovan Bogdanovic,2 Natasa Stajic,2 Neveen A. Soliman,3,4 Jameela A. Kari,5,6 Sherif El Desoky,5,6 Hanan M. Fathy,7 Danko Milosevic,8 Muna Al-Saffar,1,9 Hazem S. Awad,10 Loai A. Eid,10 Aravind Selvin,11 Prabha Senguttuvan,12 Simone Sanna-Cherchi,13 Heidi L. Rehm,14 Daniel G. MacArthur,14,15 Monkol Lek,14,15 Kristen M. Laricchia,15 Michael W. Wilson,15 Shrikant M. Mane,16 Richard P. Lifton,16,17 Richard S. Lee,18 Stuart B. Bauer,18 Weining Lu,19 Heiko M. Reutter ,20,21 Velibor Tasic,22 Shirlee Shril,1 and Friedhelm Hildebrandt1 Due to the number of contributing authors, the affiliations are listed at the end of this article. -
Expression of Parvin-Β Is a Prognostic Factor for Patients with Urothelial Cell
British Journal of Cancer (2010) 103, 852 – 860 & 2010 Cancer Research UK All rights reserved 0007 – 0920/10 www.bjcancer.com Expression of parvin-b is a prognostic factor for patients with urothelial cell carcinoma of the upper urinary tract 1,2 3 1 4,5 4 6 2,7 ,2,4, C-F Wu , K-F Ng , C-S Chen , P-L Chang , C-K Chuang , W-H Weng , S-K Liao and S-T Pang* 1Department of Surgery, Division of Urology, Chia-Yi Chang Gung Memorial Hospital, Chia-Yi, Taiwan; 2Graduate Institute of Clinical Medical Sciences, Chang Gung University, Kwei-shan, Taoyuan, Taiwan; 3Department of Pathology, Lin-Kou Chang Gung Memorial Hospital, Kwei-shan, Taoyuan, Taiwan; 4 5 Department of Surgery, Division of Urology, Lin-Kou Chang Gung Memorial Hospital, No. 5, Fushing Road, Kwei-Shan, Taoyuan, Taiwan; Chang Gung 6 Bioinformatics Center, Lin-Kou Chang Gung Memorial Hospital, Kwei-shan, Taoyuan, Taiwan; Department of Chemical Engineering and Biotechnology, 7 Graduate Institute of Biotechnology, National Taipei University of Technology, Taipei, Taiwan; Cancer Immunotherapy Program, Taipei Medical University Hospital, Taipei, Taiwan BACKGROUND: Parvin-b (ParvB), a potential tumour suppressor gene, is a focal adhesion protein. We evaluated the role of ParvB in the upper urinary tract urothelial cell carcinoma (UUT-UC). METHODS: ParvB mRNA and proteins levels in UUT-UC tissue were investigated by quantitative real-time polymerase chain reaction and western blot analysis, respectively. In addition, the expression of ParvB in tissues from patients with UUT-UC at different stages was evaluated by immunohistochemistry. Furthermore, biological functions of ParvB in urothelial cancer cells were investigated using a doxycycline-inducible overexpression system and siRNA. -
Capture-Based Enrichment of Theileria Parva DNA
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.11.037309; this version posted April 13, 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. Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo- derived strain and reveals exceptional intra-specific genetic diversity Nicholas C Palmateer1, Kyle Tretina1, Joshua Orvis1, Olukemi O Ifeonu1, Jonathan Crabtree1, Elliott Drabék1, Roger Pelle2, Elias Awino3, Hanzel T Gotia1, James B Munro1, Luke Tallon1, W Ivan Morrison4, Claudia A Daubenberger5,6, Vish Nene3, Donald P Knowles7, Richard P Bishop7, Joana C Silva1,8§ 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA 2Biosciences eastern and central Africa-International Livestock Research Institute, Nairobi, Kenya 3International Livestock Research Institute, Nairobi, Kenya 4The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK 5Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland 6University of Basel, Basel, Switzerland 7Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99163, USA 8Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA §Corresponding author: [email protected] Running title: “Apicomplexan Theileria parva is exceptionally polymorphic” Keywords: Theileria parva, lawrencei, DNA enrichment, genome assembly, polymorphism 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.11.037309; this version posted April 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.