DOCSLIB.ORG

Identification of QTL for Resistance Against Two Fungal Pathogens, Pyrenophora Teres F

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Identification of QTL for Resistance Against Two Fungal Pathogens, Pyrenophora Teres F Fluturë Novakazi Institut für Resistenzforschung und Stresstoleranz Identification of QTL for resistance against two fungal pathogens, Pyrenophora teres f. teres and Bipolaris sorokiniana, in a barley (Hordeum vulgare L.) diversity set Dissertationen aus dem Julius Kühn-Institut Julius Kühn-Institut Bundesforschungsinstitut für Kulturpflanzen Kontakt | Contact: Fluturë Novakazi Beethovenstraße 24 18069 Rostock Die Schriftenreihe ,,Dissertationen aus dem Julius Kühn-lnstitut“ veröffentlicht Doktorarbeiten, die in enger Zusammenarbeit mit Universitäten an lnstituten des Julius Kühn-lnstituts entstan- den sind. The publication series „Dissertationen aus dem Julius Kühn-lnstitut“ publishes doctoral disser- tations originating from research doctorates and completed at the Julius Kühn-Institut (JKI) either in close collaboration with universities or as an outstanding independent work in the JKI research fields. Der Vertrieb dieser Monographien erfolgt über den Buchhandel (Nachweis im Verzeichnis liefer- barer Bücher - VLB) und OPEN ACCESS unter: https://www.openagrar.de/receive/openagrar_mods_00005667 The monographs are distributed through the book trade (listed in German Books in Print - VLB) and OPEN ACCESS here: https://www.openagrar.de/receive/openagrar_mods_00005667 Wir unterstützen den offenen Zugang zu wissenschaftlichem Wissen. Die Dissertationen aus dem Julius Kühn-lnstitut erscheinen daher OPEN ACCESS. Alle Ausgaben stehen kostenfrei im lnternet zur Verfügung: http://www.julius-kuehn.de Bereich Veröffentlichungen. We advocate open access to scientific knowledge. Dissertations from the Julius Kühn-lnstitut are therefore published open access. All issues are available free of charge under http://www.julius-kuehn.de (see Publications). Bibliografische Information der Deutschen Nationalbibliothek Die Deutsche Nationalbibliothek verzeichnet diese Publikation In der Deutschen Nationalbibliografie: detaillierte bibliografische Daten sind im lnternet über http://dnb.d-nb.de abrufbar. Bibliographic information published by the Deutsche Nationalbibliothek (German National Library) The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available in the Internet at http://dnb.dnb.de. ISBN 978-3-95547-097-5 DOI 10.5073/dissjki.2020.006 Herausgeber l Editor Julius Kühn-lnstitut, Bundesforschungsinstitut für Kulturpflanzen, Quedlinburg, Deutschland Julius Kühn-lnstitut, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany © Der Autor/ Die Autorin 2020. Dieses Werk wird unter den Bedingungen der Creative Commons Namensnennung 4.0 International Lizenz (CC BY 4.0) zur Verfügung gestellt (https://creativecommons.org/licenses/by/4.0/deed.de). © The Author(s) 2020. This work is distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/deed.en). Institute of Agronomy and Plant Breeding I, Department of Plant Breeding, Justus Liebig University, Giessen and Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Quedlinburg ___________________________________________________________________________ Identification of QTL for resistance against two fungal pathogens, Pyrenophora teres f. teres and Bipolaris sorokiniana, in a barley (Hordeum vulgare L.) diversity set ___________________________________________________________________________ Inaugural Dissertation for a Doctorate Degree in Agricultural Sciences - Dr. agr - In the Faculty Agricultural Sciences, Nutritional Sciences and Environmental Management Submitted by Fluturë Novakazi born in Prishtina, Kosovo Giessen 2020 Approved by the Faculty Agricultural Sciences, Nutritional Sciences and Environmental Management, Justus Liebig University Giessen Examining Committee: First Reviewer: Prof. Dr. Rod Snowdon Second Reviewer: Prof. Dr. Frank Ordon Examiner: Prof. Dr. Matthias Frisch Examiner: PD Dr. Annaliese Mason Chair of the Examining Committee: Prof. Dr. Gesine Lühken Date of Defence: May 11th , 2020 “So long, and thanks for all the fish.“ Douglas Adams Contents List of abbreviations II List of publications V 1 Summary 1 2 Introduction 3 2.1 Barley 3 2.2 Net Blotch of Barley 7 2.3 Spot Blotch of Barley 12 2.4 Marker systems and genome-wide association studies 14 3 Aims 20 4 Genetic analysis of a worldwide barley collection for resistance to net form of net blotch disease (Pyrenophora teres f. teres) 21 5 Genome-wide association studies in a barley diversity set reveal a limited number of loci for resistance to spot blotch 40 6 Discussion 56 6.1 Candidate genes located in regions identified for net blotch resistance 56 6.2 Resistant accessions 66 References 71 Appendix VII Contributions to meetings and conferences XLVI Acknowledgement XLVIII Erklärung XLIX ~ I ~ List of abbreviations List of abbreviations °C degree Celsius AFLP amplified fragment length polymorphism apaf apoptotic protease-activating factor Avr gene avirulence gene bp base pairs Bs Bipolaris sorokiniana Btr1/ 2 brittle rachis gene CC-NBS-LRR/ CNL coiled-coil nucleotide binding site LRR DNA deoxyribonucleic acid Eam8 early maturity 8 gene ET ethylene ETI effector triggered immunity GBS genotyping-by-sequencing GWAS genome-wide association studies h hours HC gene high-confidence gene HR hypersensitive response HSP heat shock protein IBSC International Barley genome Sequencing Consortium JA jasmonic acid K kinship LC gene low-confidence gene LD linkage disequilibrium LRR leucine-rich repeat ~ II ~ List of abbreviations MAGIC multi-parent advanced generation inter-cross MAMPs microbe-associated molecular patterns MAPK mitogen-activated protein kinase MAS marker-assisted selection Mat-a Praematurum-a gene Mbp mega base pairs Mlo mildew resistance locus o MTA marker-trait association NADPH nicotinamide adenine dinucleotide phosphate NAM nested association mapping NB nucleotide-binding NETS necrotrophic effector-triggered susceptibility NFNB net form of net blotch NGS next generation sequencing NO nitric oxide NPR1 non-expressor of pathogen-related nud nudum/ naked kernel gene PAMPs pathogen-associated molecular patterns PCA principle component analysis PCD programmed cell death PCR polymerase chain reaction Ppd-H1 Photoperiod-H1 gene PR proteins pathogenesis-related proteins PRR pattern recognition receptors PTI pattern triggered immunity Ptm Pyrenophora teres f. maculata ~ III ~ List of abbreviations Ptt Pyrenophora teres f. teres Q-matrix population structure matrix qPCR quantitative PCR QTL quantitative trait locus R gene resistance gene R protein disease resistance protein RAPD randomly amplified polymorphic DNA RFLP restriction fragment length polymorphism ROS reactive oxygen species RT-PCR real time PCR SA salicylic acid SAR systemic acquired resistance SFNB spot form of net blotch SNP single nucleotide polymorphism SSR simple sequence repeats TF transcription factor thresh-1 threshability gene TIR-NBS-LRR/ TNL toll interleukin receptor nucleotide binding site LRR Vrn vernalisation gene Vrs1 six-rowed spike gene ~ IV ~ List of publications List of publications This thesis is based on the following peer-reviewed publications: Novakazi F, Afanasenko O, Anisimova A, Platz GJ, Snowdon R, Kovaleva O, Zubkovich A, Ordon F, 2019. Genetic analysis of a worldwide barley collection for resistance to net form of net blotch disease (Pyrenophora teres f. teres). Theoretical and Applied Genetics, 132 (9): 2633-2650, https://doi.org/10.1007/s00122-019-03378-1. Novakazi F, Afanasenko O, Lashina N, Platz GJ, Snowdon R, Loskutov I, Ordon F, 2019. Genome- wide association studies in a barley (Hordeum vulgare) diversity set reveal a limited number of loci for resistance to spot blotch (Bipolaris sorokiniana). Plant Breeding, 00: 1-15, https://doi.org/10.1111/pbr.12792. ~ V ~ List of publications ~ VI ~ Summary 1 Summary Barley is worldwide the fourth most important cereal crop and is cultivated in near desert to sub- arctic conditions. The majority of production, around 70 %, is used for animal feed, 20 % are used for malting and the rest for human consumption, with regional differences. Pests and diseases constantly result in high yield losses. Two worldwide important fungal foliar diseases of barley are Pyrenophora teres f. teres (Ptt) and Bipolaris sorokiniana (Bs), the causal agents of net blotch and spot blotch, respectively. Yield losses are on average around 40 % and can amount to over 70 % in years with epidemics. Both pathogens are highly variable and the occurrence of new pathogenic strains demands for breeding of resistant cultivars. In order to identify new resistance sources, a diverse barley set comprising 449 accessions originating from over 50 different regions all over the world, expressing different levels of resistance against both pathogens, was screened. Seedling resistance was tested under controlled greenhouse conditions with three isolates of each pathogen. Adult plant resistance was tested in field trials at three and two locations for Ptt and Bs, respectively. Phenotypic results showed a wide range of the level of resistance and significant differences between accessions were observed in all trials. The set was genotyped using the Illumina iSelect 50k barley SNP chip. After filtering for quality control parameters, i.e. failure rates < 10%, heterozygous calls < 12.5% and minor allele frequency > 5%, 33,318 polymorphic, mapped SNPs were left for further genome-wide association studies
Load more

Recommended publications
  • The Bone Marrow Niche in the Pathogenesis of Multiple Myeloma a Role for Wnt Signaling and Adrenomedullin
    A role for Wnt signaling and Adrenomedullin and signaling Wnt for A role Myeloma Multiple of niche in the pathogenesis marrow The bone The bone marrow niche in the pathogenesis of Multiple Myeloma A role for Wnt signaling and Adrenomedullin pracownia DTP i grafiki www.przygotowalniaDTP.pl ISBN 978-83-63861-16-2 Kinga Anna Kocemba okladka_nowa.indd 1-3 2014-01-20 11:57:46 The bone marrow niche in the pathogenesis of Multiple Myeloma A role for Wnt signaling and Adrenomedullin The bone marrow niche in the pathogenesis of Multiple Myeloma A role for Wnt signaling and Adrenomedullin Kinga Anna Kocemba The research described in this thesis was funded by the Dutch Cancer Society Editing Przygotowalnia Pracownia DTP i Grafiki Graphic design and typesetting Przygotowalnia Pracownia DTP i Grafiki Cover: Antelope Canyon, Arizona, USA by Kinga Anna Kocemba © Copyright by Kinga Anna Kocemba ISBN 978-83-63861-16-2 Amsterdam–Kraków 2014 Pracownia DTP i Grafiki ul. Łużycka 71c/9 30–693 Kraków [email protected] www.przygotowalniaDTP.pl Moim rodzicom To my parents The bone marrow niche in the pathogenesis of Multiple Myeloma A role for Wnt signaling and Adrenomedullin academisch proefschrift ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam op gezag van de Rector Magnificus prof. dr. D.C. van den Boom ten overstaan van een door het college voor promoties ingestelde commissie, in het openbaar te verdedigen in de Agnietenkapel op donderdag 6 maart 2014, te 14:00 uur door Kinga Anna Kocemba geboren te Oświęcim, Polen Promotiecommissie promotor Prof.
    [Show full text]
  • Effects of Altered Expression of the Sumo Conjugating Enzyme, UBC9 on Mitosis, Meiosis and Conjugation in Tetrahymena Thermophila Qianyi Yang Purdue University
    Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations Fall 2014 Effects of altered expression of the sumo conjugating enzyme, UBC9 on mitosis, meiosis and conjugation in Tetrahymena thermophila Qianyi Yang Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Yang, Qianyi, "Effects of altered expression of the sumo conjugating enzyme, UBC9 on mitosis, meiosis and conjugation in Tetrahymena thermophila" (2014). Open Access Dissertations. 395. https://docs.lib.purdue.edu/open_access_dissertations/395 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School Form 30 (Revised 08/14) PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared By Qianyi Yang Entitled EFFECTS OF ALTERED EXPRESSION OF THE SUMO CONJUGATING ENZYME, UBC9 ON MITOSIS, MEIOSIS AND CONJUGATION IN TETRAHYMENA THERMOPHILA Doctor of Philosophy For the degree of Is approved by the final examining committee: James D. Forney Scott D. Briggs Mark C. Hall Clifford F. Weil To the best of my knowledge and as understood by the student in the Thesis/Dissertation Agreement, Publication Delay, and Certification/Disclaimer (Graduate School Form 32), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy
    [Show full text]
  • S1 SUPPORTING INFORMATION Comparative Proteomic Analysis
    SUPPORTING INFORMATION Comparative proteomic analysis unveils critical pathways underlying the role of nitrogen fertilizer treatment in American elderberry Bo Yang1, Andrew L. Thomas2, and C. Michael Greenlief 1, † 1Department of Chemistry, University of Missouri, Columbia, Missouri 65211, USA 2Division of Plant Sciences, Southwest Research Center, University of Missouri, Mt. Vernon, Missouri 65712, USA †Corresponding author: C. Michael Greenlief Phone: 573-882-3288; Fax: 573-882-2754; E-mail: [email protected] TABLE OF CONTENTS Figure S1. Scatter graph of relative spots volumes detected on 2-DE gels Figure S2. Representative 2-DE maps of differentially expressed proteins Figure S3. PCA analysis of differentially expressed proteins Figure S4. Mercator protein functional categorization of each genotype Table S1. Statistical analysis of differentially expressed proteins Table S2. Protein report for MALDI-TOF/TOF Table S3. Protein report for LC-MS/MS Table S4. Identification of altered proteins after 56 kg N/ha treatment Table S5. Identification of altered proteins after 112 kg N/ha treatment Table S6. Identification of altered proteins after 169 kg N/ha treatment S1 Figure S1. Scatter graph based on the ratios of relative spots volumes detected in the master gel (y-axis) and the respective replicates (x-axis). (A-D): 0, 56, 112 and 169 kg N/ha treated Adams II. (E-H): 0, 56, 112 and 169 kg N/ha treated Bob Gordon. (I-L): 0, 56, 112 and 169 kg N/ha treated Wyldewood. A B C S2 D E F G S3 H I J K S4 L S5 Figure S2. Representative 2-DE maps of proteins extracted from American elderberry leaves.
    [Show full text]
  • Investigation of Candidate Genes and Mechanisms Underlying Obesity
    Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between
    [Show full text]
  • Noelia Díaz Blanco
    Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
    [Show full text]
  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2014/0304845 A1 Loboda Et Al
    US 201403.04845A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0304845 A1 Loboda et al. (43) Pub. Date: Oct. 9, 2014 54) ALZHEMIERS DISEASE SIGNATURE Publicationublication ClassificatiClassification MARKERS AND METHODS OF USE (51) Int. Cl. (71) Applicant: MERCKSHARP & DOHME CORP, CI2O I/68 (2006.01) Rahway, NJ (US) AOIK 67/027 (2006.01) (52) U.S. Cl. (72) Inventors: SIES yet.sS); CPC .......... CI2O I/6883 (2013.01); A0IK 67/0275 Icnaei NepoZnyn, Yeadon, (2013.01) le.East,Italia; David J. Stone, Wyncote, USPC .............. 800/12:536/23.5:536/23.2:506/17 (US); Keith Tanis, Quakertown, PA (US); William J. Ray, Juniper, FL (US) (57) ABSTRACT (21) Appl. No.: 14/354,622 Methods, biomarkers, and expression signatures are dis 1-1. closed for assessing the disease progression of Alzheimer's (22) PCT Filed: Oct. 26, 2012 disease (AD). In one embodiment, BioAge (biological age), NdStress (neurodegenerative stress), Alz (Alzheimer), and (86). PCT No.: PCT/US12A62218 Inflame (inflammation) are used as biomarkers of AD pro S371 (c)(1), gression. In another aspect, the invention comprises a gene (2), (4) Date: Apr. 28, 2014 signature for evaluating disease progression. In still another Related U.S. Application Data abiliticises in (60) Provisional application No. 61/553,400, filed on Oct. used to identify animal models for use in the development and 31, 2011. evaluation of therapeutics for the treatment of AD. Patent Application Publication Oct. 9, 2014 Sheet 1 of 16 US 2014/0304845 A1 Y : : O O O O O O O O D O v v CN On cy Patent Application Publication Oct.
    [Show full text]
  • Transcriptomic Signature of Drought Response in Pearl Millet
    www.nature.com/scientificreports OPEN Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and Received: 4 September 2017 Accepted: 4 February 2018 development of web-genomic Published: xx xx xxxx resources Sarika Jaiswal1, Tushar J. Antala2, M. K. Mandavia2, Meenu Chopra1, Rahul Singh Jasrotia1, Rukam S. Tomar2, Jashminkumar Kheni2, U. B. Angadi1, M. A. Iquebal1, B. A. Golakia2, Anil Rai1 & Dinesh Kumar1 Pearl millet, (Pennisetum glaucum L.), an efcient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortifcation combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but feld-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 diferentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the frst web-based genomic resource (http://webtom. cabgrid.res.in/pmdtdb/) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in feld condition.
    [Show full text]
  • Supp Table 6.Pdf
    Supplementary Table 6. Processes associated to the 2037 SCL candidate target genes ID Symbol Entrez Gene Name Process NM_178114 AMIGO2 adhesion molecule with Ig-like domain 2 adhesion NM_033474 ARVCF armadillo repeat gene deletes in velocardiofacial syndrome adhesion NM_027060 BTBD9 BTB (POZ) domain containing 9 adhesion NM_001039149 CD226 CD226 molecule adhesion NM_010581 CD47 CD47 molecule adhesion NM_023370 CDH23 cadherin-like 23 adhesion NM_207298 CERCAM cerebral endothelial cell adhesion molecule adhesion NM_021719 CLDN15 claudin 15 adhesion NM_009902 CLDN3 claudin 3 adhesion NM_008779 CNTN3 contactin 3 (plasmacytoma associated) adhesion NM_015734 COL5A1 collagen, type V, alpha 1 adhesion NM_007803 CTTN cortactin adhesion NM_009142 CX3CL1 chemokine (C-X3-C motif) ligand 1 adhesion NM_031174 DSCAM Down syndrome cell adhesion molecule adhesion NM_145158 EMILIN2 elastin microfibril interfacer 2 adhesion NM_001081286 FAT1 FAT tumor suppressor homolog 1 (Drosophila) adhesion NM_001080814 FAT3 FAT tumor suppressor homolog 3 (Drosophila) adhesion NM_153795 FERMT3 fermitin family homolog 3 (Drosophila) adhesion NM_010494 ICAM2 intercellular adhesion molecule 2 adhesion NM_023892 ICAM4 (includes EG:3386) intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)adhesion NM_001001979 MEGF10 multiple EGF-like-domains 10 adhesion NM_172522 MEGF11 multiple EGF-like-domains 11 adhesion NM_010739 MUC13 mucin 13, cell surface associated adhesion NM_013610 NINJ1 ninjurin 1 adhesion NM_016718 NINJ2 ninjurin 2 adhesion NM_172932 NLGN3 neuroligin
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • On SARS-Cov-2, Tropical Medicine and Bioinformatics: Analysis of the SARS-Cov-2 Molecular Features and Epitope Prediction for Antibody Or Vaccine Development
    ACTA SCIENTIFIC MICROBIOLOGY (ISSN: 2581-3226) Volume 4 Issue 1 January 2021 Research Article On SARS-CoV-2, Tropical Medicine and Bioinformatics: Analysis of the SARS-Cov-2 Molecular Features and Epitope Prediction for Antibody or Vaccine Development Joshua Angelo Hermida Mandanas* Received: November 24, 2020 Tropical Medicine Scientist and Immunobiologist, Philippine Medical Technology Published: December 08, 2020 Professional/National Lecturer, University of the Philippines Manila, Philippines © All rights are reserved by Joshua Angelo *Corresponding Author: Joshua Angelo Hermida Mandanas, Tropical Medicine Hermida Mandanas. Scientist and Immunobiologist, Philippine Medical Technology Professional/National Lecturer, University of the Philippines Manila, Philippines. Abstract Introduction: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the cause of COVID-19 which is the pandemic as of the current time. It is a global public health emergency and is still on the loose of spreading more infections and deaths. Bioinformat- ics offer extensive visualization and analysis of combined molecular, cellular, biochemical and immunobiologic aspects of SARS-CoV-2 which is indeed vital for antibody and vaccine development. Objectives: This paper presents the SARS-CoV-2 molecular virologic, biochemical, cellular and immunobiologic features and gives a basic B cell linear epitope prediction of the SARS-CoV-2 spike (S) glycoprotein using bioinformatics which both can serve as a guide for development of vaccines or antibody-based treatments. Methods: Several bioinformatic methods were used, from sequence analysis (Uniprot), structural correlation (PDB), molecular mod- elling (UCSF Chimera) and illustration (Biorender), B cell linear epitope prediction tools, conservancy analysis and search of related epitopes (IEDB) together with determination of disordered regions (GlobPlot and DisEMBL).
    [Show full text]
  • Citrate Synthase Polyclonal Antibody Catalog Number:16131-1-AP Featured Product 45 Publications
    For Research Use Only Citrate synthase Polyclonal antibody www.ptglab.com Catalog Number:16131-1-AP Featured Product 45 Publications Catalog Number: GenBank Accession Number: Purification Method: Basic Information 16131-1-AP BC010106 Antigen affinity purification Size: GeneID (NCBI): Recommended Dilutions: 150ul , Concentration: 350 μg/ml by 1431 WB 1:1000-1:8000 Nanodrop and 313 μg/ml by Bradford Full Name: IP 0.5-4.0 ug for IP and 1:500-1:2000 method using BSA as the standard; citrate synthase for WB Source: IHC 1:100-1:400 Calculated MW: IF 1:50-1:500 Rabbit 466 aa, 52 kDa Isotype: Observed MW: IgG 45-50 kDa Immunogen Catalog Number: AG9117 Applications Tested Applications: Positive Controls: IF, IHC, IP, WB,ELISA WB : mouse heart tissue, HeLa cells Cited Applications: IP : mouse heart tissue, IF, IHC, WB IHC : human liver cancer tissue, Species Specificity: human, mouse, rat IF : HepG2 cells, Cited Species: hamster, human, mouse, rat Note-IHC: suggested antigen retrieval with TE buffer pH 9.0; (*) Alternatively, antigen retrieval may be performed with citrate buffer pH 6.0 Citrate synthase (CS), the first and rate-limiting enzyme of the tricarboxylic acid cycle, plays a key role in Background Information regulating energy generation of mitochondrial respiration(PMID:19479947).It belongs to the citrate synthase family. The deduced 466-amino acid protein contains an N-terminal mitochondrial targeting sequence and a motif highly conserved in citrate synthases(PMID:12549038). It can exsit as a dimer(PMID:8749851). Northern blot analysis detected no CS expression in thymus and small intestine(PMID:12549038).
    [Show full text]