DOCSLIB.ORG

The Contribution of Extrachloroplastic Factors and Plastid Gene Expression

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

The contribution of extrachloroplastic factors and plastid gene expression to chloroplast development and abiotic stress tolerance Dissertation Zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) an der Fakultät für Biologie der Ludwig-Maximilians-Universität München vorgelegt von Duorong Xu Munich, 2020 Gutachter: 1. PD Dr. Tatjana Kleine 2. Prof. Dr. Peter Geigenberger Datum der Abgabe: 23.04.2020 Datum der mündlichen Prüfung: 16.07.2020 II Eidesstattliche Erklärung Ich versichere hiermit an Eides statt, dass die vorgelegte Dissertation von mir selbstständig und ohne unerlaubte Hilfe angefertigt wurde. Des Weiteren erkläre ich, dass ich nicht anderweitig ohne Erfolg versucht habe, eine Dissertation einzureichen oder mich der Doktorprüfung zu unterziehen. Die folgende Dissertation liegt weder ganz, noch in wesentlichen Teilen einer anderen Prüfungskommission vor. München, 23. April 2020 Duorong Xu Statutory declaration I declare that I have authored this thesis independently, that I have not used other than the declared (re)sources. As well I declare, that I have not submitted a dissertation without success and not passed the oral exam. The present dissertation (neither the entire dissertation nor parts) has not been presented to another examination board. Munich, 23. April 2020 Duorong Xu III Contents Statutory declaration ............................................................................................................................... III Contents ................................................................................................................................................... IV Abbreviations ........................................................................................................................................... VI Declaration of contribution as a co-author ........................................................................................ VIII Summary .................................................................................................................................................. IX Zusammenfassung ................................................................................................................................. XI 1. Introduction ........................................................................................................................................... 1 1.1 Photosynthesis ................................................................................................................................... 1 1.2 Origin, structure and biogenesis of chloroplasts ........................................................................... 2 1.2.1 Chloroplast biogenesis .................................................................................................................. 6 1.2.2 Thylakoid complexes ..................................................................................................................... 7 1.3 Retrograde signaling ....................................................................................................................... 10 1.3.1 Tetrapyrrole signaling and gun mutants .................................................................................... 11 1.3.2 Plastid gene expression .............................................................................................................. 13 1.4 Abiotic stress and chloroplasts ...................................................................................................... 14 2. Aim of the thesis ................................................................................................................................. 16 3. Results ................................................................................................................................................. 18 3.1 Chapter 1 Extrachloroplastic PP7L functions in chloroplast development and abiotic stress tolerance ..... 18 3.2 Chapter 2 VENOSA4, a human dNTPase SAMHD1 homolog, contributes to chloroplast development and abiotic stress tolerance .......................................................................................................................... 38 3.3 Chapter 3 Arabidopsis thaliana mTERF10 and mTERF11, but not mTERF12, are involved in the response to salt stress ............................................................................................................................................ 48 3.4 Chapter 4 Cellulose defects in the Arabidopsis secondary cell wall promote early chloroplast development .................................................................................................................................................................. 67 4. Discussion ........................................................................................................................................... 83 4.1 The role of PP7L in chloroplast development .............................................................................. 83 IV 4.2 VEN4 participates in regulating dNTP metabolism .................................................................... 84 4.3 Perturbed OGE lead to altered salt stress responses in plant.................................................. 85 4.4 Cell wall integrity modulates nuclear gene expression in Arabidopsis seedling .................... 86 References .............................................................................................................................................. 88 Supplemental information ..................................................................................................................... 98 Supplemental information – Chapter 1 ............................................................................................... 98 Supplemental information – Chapter 2 ............................................................................................. 104 Supplemental information – Chapter 3 ............................................................................................. 111 Supplemental information – Chapter 4 ............................................................................................. 114 Acknowledgement ................................................................................................................................ 119 Curriculum vitae.................................................................................................................................... 120 V Abbreviations ABA Abscisic acid ADP Adenosine diphosphate ATP Adenosine triphosphate Ces Cellulose synthase Chl Chlorophyll Col-0 Arabidopsis ecotype Columbia DNA Deoxyribonucleic acid dNTP Deoxynucleoside triphosphate EMS Ethyl methane sulfonate ETC Electron transport chain FNR Ferredoxin-NADP+ reductase Fv/Fm Maximum quantum yield of PSII GFP Green fluorescent protein GLK GOLDEN 2-LIKE (GLK) transcription factors gun genomes uncoupled mutant Gya Billion years ago kbp Kilo-base pair LHC Light harvesting complex LHCB Light-harvesting complex II LIN Lincomycin MS Murashige and Skoog medium mTERF Mitochondrial transcription termination factor NADH Nicotinamide adenine dinucleotide NEP Nuclear-encoded RNA polymerase NF Norflurazon OEC Oxygen-evolving complex P680 Photosystem II primary donor P700 Primary electron donor PC Plastocyanin PEP Plastid-encoded RNA polymerase PGE Plastid gene expression PhANGs Photosynthesis-associated nuclear-encoded genes PPR Pentatricopeptide repeat PQH2 Plastoquinone PSI Photosystem I PSII Photosystem II PTM Plant homeodomain (PHD) transcription factor VI RC Reaction center RNA Ribonucleic acid ROS Reactive oxygen species Sig Sigma VII Declaration of contribution as a co-author Chapter 1: Duorong Xu, Giada Marino, Andreas Klingl, Beatrix Enderle, Elena Monte, Joachim Kurth, Andreas Hiltbrunner, Dario Leister, Tatjana Kleine (2019). Extrachloroplastic PP7L functions in chloroplast development and abiotic stress tolerance. Plant Physiol 180: 323–341 Research was designed by T.K. and D.X.; the pp7l:En-1 mutant was confirmed by J.K.; most of the experiments were performed by D.X.; G.M. realized the shot-gun proteomics experiment; A.K. provided TEM pictures; B.E. performed phyB western- blot analysis; T.K., D. X., G.M., D.L., A.H., and E.M. analyzed the data; T.K. wrote the manuscript with input primarily from D.L., A.H., and E.M., and then all authors; the whole study was supervised by T.K.; all authors read and approved the article. Chapter 2: Duorong Xu, Dario Leister, Tatjana Kleine (2020). VENOSA4, a human dNTPase SAMHD1 homolog, contributes to chloroplast development and abiotic stress tolerance. Plant Physiol 182: 721–729 Research was designed by T.K. and D.X. Most of the experiments were performed by D.X. D.X. and T.K. analyzed the data. T.K. wrote the manuscript with input from D.L. and D.X. The whole study was supervised by T.K. All authors read and approved the article. Chapter 3: Duorong Xu, Dario Leister and Tatjana Kleine (2017). Arabidopsis thaliana mTERF10 and mTERF11, but not mTERF12, are involved in the response to salt stress. Front Plant Sci 8: 1213 Research was designed by TK. Research was performed by DX and TK. The manuscript was prepared by DX, DL, and TK. Chapter 4: Durorong Xu, Ravi Dhiman, Adriana Garibay, Hans-Peter Mock, Dario Leister, Tatjana Kleine (2020). Cellulose defects in the Arabidopsis secondary cell wall promote early chloroplast development. Plant J 101: 156–170 Conceptualization: T.K., D.X.; Experiments: D.X., R.D., A.G., H.-P.
Recommended publications
  • A Bioinformatics Analysis of the Arabidopsis Thaliana Epigenome Ikhlak Ahmed

    A Bioinformatics Analysis of the Arabidopsis Thaliana Epigenome Ikhlak Ahmed

    A bioinformatics analysis of the arabidopsis thaliana epigenome Ikhlak Ahmed To cite this version: Ikhlak Ahmed. A bioinformatics analysis of the arabidopsis thaliana epigenome. Agricultural sciences. Université Paris Sud - Paris XI, 2011. English. NNT : 2011PA112230. tel-00684391 HAL Id: tel-00684391 https://tel.archives-ouvertes.fr/tel-00684391 Submitted on 2 Apr 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 2011 PhD Thesis Ikhlak Ahmed Laboratoire: CNRS UMR8197 - INSERM U1024 Institut de Biologie de l'ENS(IBENS) Ecole Doctorale : Sciences Du Végétal A Bioinformatics analysis of the Arabidopsis thaliana Epigenome Supervisors: Dr. Chris Bowler and Dr. Vincent Colot Jury Prof. Dao-Xiu Zhou President Prof. Christian Fankhauser Rapporteur Dr. Raphaël Margueron Rapporteur Dr. Chris Bowler Examiner Dr. Vincent Colot Examiner Dr. Allison Mallory Examiner Dr. Michaël Weber Examiner Acknowledgement I express my deepest gratitude to my supervisors Dr. Chris Bowler and Dr. Vincent Colot for the support, advice and freedom that I enjoyed working with them. I am very thankful to Chris Bowler who trusted in me and gave me the opportunity to come here and work in the excellent possible conditions. I have no words to express my thankfulness to Vincent Colot for his enthusiastic supervision and the incredibly valuable sessions we spent together that shaped my understanding of DNA methylation.
  • Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts

    Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts

    Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing
  • Research Article Determining the Traditional Chinese Medicine (TCM)

    Research Article Determining the Traditional Chinese Medicine (TCM)

    Hindawi Evidence-Based Complementary and Alternative Medicine Volume 2021, Article ID 9991533, 13 pages https://doi.org/10.1155/2021/9991533 Research Article Determining the Traditional Chinese Medicine (TCM) Syndrome with the Best Prognosis of HBV-Related HCC and Exploring the Related Mechanism Using Network Pharmacology Zhulin Wu , Chunshan Wei , Lianan Wang , and Li He e Fourth Clinical Medical College of Guangzhou University of Chinese Medicine (Shenzhen Traditional Chinese Medicine Hospital), Shenzhen 518033, China Correspondence should be addressed to Chunshan Wei; [email protected] Received 17 March 2021; Revised 4 June 2021; Accepted 21 June 2021; Published 30 June 2021 Academic Editor: Chunpeng Wan Copyright © 2021 Zhulin Wu et al. *is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. In traditional Chinese medicine (TCM), TCM syndrome is a key guideline, and Chinese materia medicas are widely used to treat hepatitis B virus- (HBV-) related hepatocellular carcinoma (HCC) according to different TCM syndromes. However, the prognostic value of TCM syndromes in HBV-related HCC patients has never been studied. Methods. A retrospective cohort of HBV-related HCC patients at Shenzhen Traditional Chinese Medicine Hospital from December 2005 to October 2017 was analyzed. *e prognostic value of TCM syndromes in HBV-related HCC patients was assessed by Kaplan–Meier survival curves and Cox analysis, and the TCM syndrome with the best prognosis of HBV-related HCC patients was determined. To further study the relevant mechanisms, key Chinese materia medicas (KCMMs) for the TCM syndrome with the best prognosis were summarized, and network pharmacology was also performed.
  • Strong Synaptic Transmission Impact by Copy Number Variations in Schizophrenia

    Strong Synaptic Transmission Impact by Copy Number Variations in Schizophrenia

    Strong synaptic transmission impact by copy number variations in schizophrenia Joseph T. Glessnera, Muredach P. Reillyb, Cecilia E. Kima, Nagahide Takahashic, Anthony Albanoa, Cuiping Houa, Jonathan P. Bradfielda, Haitao Zhanga, Patrick M. A. Sleimana, James H. Florya, Marcin Imielinskia, Edward C. Frackeltona, Rosetta Chiavaccia, Kelly A. Thomasa, Maria Garrisa, Frederick G. Otienoa, Michael Davidsond, Mark Weiserd, Abraham Reichenberge, Kenneth L. Davisc,JosephI.Friedmanc, Thomas P. Cappolab, Kenneth B. Marguliesb, Daniel J. Raderb, Struan F. A. Granta,f,g, Joseph D. Buxbaumc, Raquel E. Gurh, and Hakon Hakonarsona,f,g,1 aCenter for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104; bPenn Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104; cConte Center for the Neuroscience of Mental Disorders and Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, 10029; dSheba Medical Center, Tel Hashomer, 52621, Israel; eMount Sinai and Institute of Psychiatry, King’s College, London, SE5 8AF, United Kingdom; fDivision of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104; gDepartment of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104; and hSchizophrenia Center, Neuropsychiatry Division, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104 Edited by James R. Lupski, Baylor College of Medicine, Houston, TX, and accepted by the Editorial Board April 13, 2010 (received for review January 7, 2010) Schizophrenia is a psychiatric disorder with onset in late adoles- contribute to the complex etiology underlying various psychiatric cence and unclear etiology characterized by both positive and ne- and neurodevelopmental disorders (13, 14). Whereas rare recurrent gative symptoms, as well as cognitive deficits.
  • Open Moore Sarah P53network.Pdf

    Open Moore Sarah P53network.Pdf

    THE PENNSYLVANIA STATE UNIVERSITY SCHREYER HONORS COLLEGE DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY A SYSTEMATIC METHOD FOR ANALYZING STIMULUS-DEPENDENT ACTIVATION OF THE p53 TRANSCRIPTION NETWORK SARAH L. MOORE SPRING 2013 A thesis submitted in partial fulfillment of the requirements for a baccalaureate degree in Biochemistry and Molecular Biology with honors in Biochemistry and Molecular Biology Reviewed and approved* by the following: Dr. Yanming Wang Associate Professor of Biochemistry and Molecular Biology Thesis Supervisor Dr. Ming Tien Professor of Biochemistry and Molecular Biology Honors Advisor Dr. Scott Selleck Professor and Head, Department of Biochemistry and Molecular Biology * Signatures are on file in the Schreyer Honors College. i ABSTRACT The p53 protein responds to cellular stress, like DNA damage and nutrient depravation, by activating cell-cycle arrest, initiating apoptosis, or triggering autophagy (i.e., self eating). p53 also regulates a range of physiological functions, such as immune and inflammatory responses, metabolism, and cell motility. These diverse roles create the need for developing systematic methods to analyze which p53 pathways will be triggered or inhibited under certain conditions. To determine the expression patterns of p53 modifiers and target genes in response to various stresses, an extensive literature review was conducted to compile a quantitative reverse transcription polymerase chain reaction (qRT-PCR) primer library consisting of 350 genes involved in apoptosis, immune and inflammatory responses, metabolism, cell cycle control, autophagy, motility, DNA repair, and differentiation as part of the p53 network. Using this library, qRT-PCR was performed in cells with inducible p53 over-expression, DNA-damage, cancer drug treatment, serum starvation, and serum stimulation.
  • Analyzing the Mirna-Gene Networks to Mine the Important Mirnas Under Skin of Human and Mouse

    Analyzing the Mirna-Gene Networks to Mine the Important Mirnas Under Skin of Human and Mouse

    Hindawi Publishing Corporation BioMed Research International Volume 2016, Article ID 5469371, 9 pages http://dx.doi.org/10.1155/2016/5469371 Research Article Analyzing the miRNA-Gene Networks to Mine the Important miRNAs under Skin of Human and Mouse Jianghong Wu,1,2,3,4,5 Husile Gong,1,2 Yongsheng Bai,5,6 and Wenguang Zhang1 1 College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China 2Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China 3Inner Mongolia Prataculture Research Center, Chinese Academy of Science, Hohhot 010031, China 4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 5Department of Biology, Indiana State University, Terre Haute, IN 47809, USA 6The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA Correspondence should be addressed to Yongsheng Bai; [email protected] and Wenguang Zhang; [email protected] Received 11 April 2016; Revised 15 July 2016; Accepted 27 July 2016 Academic Editor: Nicola Cirillo Copyright © 2016 Jianghong Wu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Genetic networks provide new mechanistic insights into the diversity of species morphology. In this study, we have integrated the MGI, GEO, and miRNA database to analyze the genetic regulatory networks under morphology difference of integument of humans and mice. We found that the gene expression network in the skin is highly divergent between human and mouse.
  • Global Transcriptome Analysis of Subterranean Pod and Seed in Peanut

    Global Transcriptome Analysis of Subterranean Pod and Seed in Peanut

    www.nature.com/scientificreports OPEN Global transcriptome analysis of subterranean pod and seed in peanut (Arachis hypogaea L.) unravels the complexity of fruit development under dark condition Hao Liu1, Xuanqiang Liang1, Qing Lu1, Haifen Li1, Haiyan Liu1, Shaoxiong Li1, Rajeev Varshney2, Yanbin Hong1* & Xiaoping Chen1* Peanut pods develop underground, which is the most salient characteristic in peanut. However, its developmental transcriptome remains largely unknown. In the present study, we sequenced over one billion transcripts to explore the developmental transcriptome of peanut pod using Illumina sequencing. Moreover, we identifed and quantifed the abundances of 165,689 transcripts in seed and shell tissues along with a pod developmental gradient. The dynamic changes of diferentially expressed transcripts (DETs) were described in seed and shell. Additionally, we found that photosynthetic genes were not only pronouncedly enriched in aerial pod, but also played roles in developing pod under dark condition. Genes functioning in photomorphogenesis showed distinct expression profles along subterranean pod development. Clustering analysis unraveled a dynamic transcriptome, in which transcripts for DNA synthesis and cell division during pod expansion were transitioning to transcripts for cell expansion and storage activity during seed flling. Collectively, our study formed a transcriptional baseline for peanut fruit development under dark condition. Abbreviations P0 Aerial peg P1 Subterranean peg PSD Pod seed PSH Pod shell PEs Paired-end
  • Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine Max L.)

    Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine Max L.)

    plants Article Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.) Taeklim Lee 1,2,†, Kyung Do Kim 3,† , Ji-Min Kim 1, Ilseob Shin 1, Jinho Heo 1,4, Jiyeong Jung 1, Juseok Lee 4, Jung-Kyung Moon 5 and Sungteag Kang 1,* 1 Department of Crop Science and Biotechnology, Dankook University, Cheonan 31116, Korea; [email protected] (T.L.); [email protected] (J.-M.K.); [email protected] (I.S.); [email protected] (J.H.); [email protected] (J.J.) 2 Seed Management Office, Gyeonggi-do Provincial Government, Yeoju 12668, Korea 3 Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058, Korea; [email protected] 4 Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; [email protected] 5 National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk 55365, Korea; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: The depletion of the stratospheric ozone layer is a major environmental issue and has increased the dosage of ultraviolet-B (UV-B) radiation reaching the Earth’s surface. Organisms are negatively affected by enhanced UV-B radiation, and especially in crop plants this may lead to severe yield losses. Soybean (Glycine max L.), a major legume crop, is sensitive to UV-B radiation, and therefore, it is required to breed the UV-B-resistant soybean cultivar. In this study, 688 soybean Citation: Lee, T.; Kim, K.D.; Kim, germplasms were phenotyped for two categories, Damage of Leaf Chlorosis (DLC) and Damage of J.-M.; Shin, I.; Heo, J.; Jung, J.; Lee, J.; Leaf Shape (DLS), after supplementary UV-B irradiation for 14 days.

  • In Vivo CRISPR Screens Identify E3 Ligase Cop1 As a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target

    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.09.418012; this version posted December 10, 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. In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target Xiaoqing Wang1,2,3,4,10, Collin Tokheim2,3,4,10, Binbin Wang2,10, Shengqing Stan Gu1,2,3,4,10, Qin Tang1,2,4,5, Yihao Li1,4, Nicole Traugh2,6, Yi Zhang2,3,4, Ziyi Li2, Boning Zhang1,2,3,4, Jingxin Fu2,3, Tengfei Xiao1,4, Wei Li2,3,4,7, Clifford A. Meyer2,3,4, Jun Chu2,8, Peng Jiang2,3,4,9, Paloma Cejas4, Klothilda Lim4, Henry Long4, Myles Brown1,4,*, and X. Shirley Liu2,3,4,* 1, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215. 2, Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215. 3, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215. 4, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215. 5, Current address: Salk Institute for Biological Studies, San Diego, CA 92037. 6, Current address: Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111. 7, Current address: Children's National Medical Center, George Washington University, Washington, DC 20010. 8, Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University Of Chinese Medicine, Hefei, Anhui, China, 230038. 9, Current address: Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 10, These authors contributed equally.
  • Prelamin a Influences a Program of Gene Expression in Regulation of Cell Cycle Control Christina N

    Prelamin a Influences a Program of Gene Expression in Regulation of Cell Cycle Control Christina N

    East Tennessee State University Digital Commons @ East Tennessee State University Electronic Theses and Dissertations Student Works 5-2012 Prelamin A Influences a Program of Gene Expression In Regulation of Cell Cycle Control Christina N. Bridges East Tennessee State University Follow this and additional works at: https://dc.etsu.edu/etd Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons Recommended Citation Bridges, Christina N., "Prelamin A Influences a Program of Gene Expression In Regulation of Cell Cycle Control" (2012). Electronic Theses and Dissertations. Paper 1213. https://dc.etsu.edu/etd/1213 This Dissertation - Open Access is brought to you for free and open access by the Student Works at Digital Commons @ East Tennessee State University. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Digital Commons @ East Tennessee State University. For more information, please contact [email protected]. Prelamin A Influences a Program of Gene Expression in the Regulation of Cell Cycle Control _____________________ A dissertation presented to the faculty of the Department of Biochemistry & Molecular Biology East Tennessee State University In partial fulfillment of the requirements for the degree Doctor of Philosopy in Biomedical Sciences _____________________ by Christina Norton Bridges May 2012 _____________________ Antonio E. Rusiñol, Chair Douglas P. Thewke Sharon E. Campbell Deling Yin Robert V. Schoborg Keywords: Prelamin A, Lamin A, Cell Cycle, Quiescence, Senescence, FoxO, p27, Progeria, Pin1 ABSTRACT Prelamin A Influences a Program of Gene Expression In Regulation of Cell Cycle Control by Christina Norton Bridges The A-type lamins are intermediate filament proteins that constitute a major part of the eukaryotic nuclear lamina—a tough, polymerized, mesh lining of the inner nuclear membrane, providing shape and structural integrity to the nucleus.
  • Genes by Expressed Sequence Tag Profiling Genome-Wide Analysis Of

    Genes by Expressed Sequence Tag Profiling Genome-Wide Analysis Of

    The Journal of Immunology Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling Cosmas C. Giallourakis,*,†,1 Yair Benita,*,†,‡,1 Benoit Molinie,*,† Zhifang Cao,*,†,‡ Orion Despo,*,† Henry E. Pratt,*,† Lawrence R. Zukerberg,x Mark J. Daly,{,k John D. Rioux,# and Ramnik J. Xavier*,†,‡,{,k Profiling studies of mRNA and microRNA, particularly microarray-based studies, have been extensively used to create compendia of genes that are preferentially expressed in the immune system. In some instances, functional studies have been subsequently pursued. Recent efforts such as the Encyclopedia of DNA Elements have demonstrated the benefit of coupling RNA sequencing analysis with information from expressed sequence tags (ESTs) for transcriptomic analysis. However, the full characterization and identification of transcripts that function as modulators of human immune responses remains incomplete. In this study, we demonstrate that an integrated analysis of human ESTs provides a robust platform to identify the immune transcriptome. Be- yond recovering a reference set of immune-enriched genes and providing large-scale cross-validation of previous microarray stud- ies, we discovered hundreds of novel genes preferentially expressed in the immune system, including noncoding RNAs. As a result, we have established the Immunogene database, representing an integrated ESTroad map of gene expression in human immune cells, which can be used to further investigate the function of coding and noncoding genes in the immune system. Using this approach, we have uncovered a unique metabolic gene signature of human macrophages and identified PRDM15 as a novel overexpressed gene in human lymphomas. Thus, we demonstrate the utility of EST profiling as a basis for further deconstruction of physiologic and pathologic immune processes.
  • Identification of Candidate Biomarkers and Pathways Associated with Type 1 Diabetes Mellitus Using Bioinformatics Analysis

    Identification of Candidate Biomarkers and Pathways Associated with Type 1 Diabetes Mellitus Using Bioinformatics Analysis

    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.08.447531; this version posted June 9, 2021. 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. Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2021.06.08.447531; this version posted June 9, 2021. 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 Type 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein-protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were then performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway.