DOCSLIB.ORG

Transcriptional and Morphological Changes During Thyroxine-Induced Metamorphosis of the Mexican Axolotl and Axolotl-Tiger Salamander Hybrids

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Transcriptional and Morphological Changes During Thyroxine-Induced Metamorphosis of the Mexican Axolotl and Axolotl-Tiger Salamander Hybrids University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2009 TRANSCRIPTIONAL AND MORPHOLOGICAL CHANGES DURING THYROXINE-INDUCED METAMORPHOSIS OF THE MEXICAN AXOLOTL AND AXOLOTL-TIGER SALAMANDER HYBRIDS Robert Bryce Page University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Page, Robert Bryce, "TRANSCRIPTIONAL AND MORPHOLOGICAL CHANGES DURING THYROXINE- INDUCED METAMORPHOSIS OF THE MEXICAN AXOLOTL AND AXOLOTL-TIGER SALAMANDER HYBRIDS" (2009). University of Kentucky Doctoral Dissertations. 774. https://uknowledge.uky.edu/gradschool_diss/774 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Robert Bryce Page The Graduate School University of Kentucky 2009 TRANSCRIPTIONAL AND MORPHOLOGICAL CHANGES DURING THYROXINE-INDUCED METAMORPHOSIS OF THE MEXICAN AXOLOTL AND AXOLOTL-TIGER SALAMANDER HYBRIDS ________________________________ ABSTRACT OF DISSERTATION _________________________________ A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Arts and Sciences at the University of Kentucky By Robert Bryce Page Lexington, Kentucky Director: Dr. S. Randal Voss, Associate Professor of Biology Lexington, Kentucky 2009 Copyright © Robert Bryce Page 2009 ABSTRACT OF DISSERTATION TRANSCRIPTIONAL AND MORPHOLOGICAL CHANGES DURING THYROXINE-INDUCED METAMORPHOSIS OF THE MEXICAN AXOLOTL AND AXOLOTL-TIGER SALAMANDER HYBRIDS For nearly a century, amphibian metamorphosis has served as an important model of how thyroid hormones regulate vertebrate development. Consequently metamorphosis has been studied in a number of ways including: morphologically, developmentally, ecologically, and from an endocrine perspective. Over the last two decades, much has been learned about the molecular basis of anuran (frog) metamorphosis. However, very little is known about the molecular underpinnings of urodele (salamander) metamorphosis. Using the axolotl and axolotl hybrids as models, I present some of the first studies on the gene expression changes that occur during urodele metamorphosis. In Chapter 1, the motivation for the research described in the subsequent chapters is presented and the literature is briefly reviewed. In Chapter 2, the first microarray analysis of urodele metamorphosis is presented. This analysis shows that hundreds of genes are differentially expressed during thyroid hormone-induced metamorphic skin remodeling. Chapter 3 extends the analysis presented in Chapter 2 by showing that the transcriptional patterns associated with metamorphic skin remodeling are robust even when the concentration of thyroid hormone used to induce metamorphosis is varied by an order of magnitude. Chapter 4 makes use of the differentially expressed genes identified in Chapters 2 and 3 to articulate the first model of urodele metamorphosis to integrate changes in morphology, gene expression, and histology. In addition, Chapter 4 outlines a novel application for piecewise linear regression. In turn, Chapter 5 makes use of the model presented in Chapter 4 to demonstrate that full siblings segregating profound variation in metamorphic timing begin to diverge in phenotype early during larval development. In Chapter 6 the conclusions drawn from the research are summarized and future directions are suggested. KEYWORDS: Amphibian Metamorphosis, Mexican Axolotl, Morphometrics, Thyroid Hormone, Transcription Robert Bryce Page 29 October 2009 TRANSCRIPTIONAL AND MORPHOLOGICAL CHANGES DURING THYROXINE-INDUCED METAMORPHOSIS OF THE MEXICAN AXOLOTL AND AXOLOTL-TIGER SALAMANDER HYBRIDS By Robert Bryce Page S. Randal Voss Director of Dissertation Brian C. Rymond Director of Graduate Studies 29 October 2009 RULES FOR THE USE OF DISSERTATIONS Unpublished dissertations submitted for the Doctor’s degree and deposited in the University of Kentucky Library are as a rule open for inspection, but are to be used only with due regard to the rights of the authors. Bibliographical references may be noted, but quotations or summaries of parts may be published only with the permission of the author, and with the usual scholarly acknowledgments. Extensive copying or publication of the dissertation in whole or in part also requires the consent of the Dean of the Graduate School of the University of Kentucky. A library that borrows this dissertation for use by its patrons is expected to secure the signature of each user. Name Date ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ DISSERTATION Robert Bryce Page The Graduate School University of Kentucky 2009 TRANSCRIPTIONAL AND MORPHOLOGICAL CHANGES DURING THYROXINE-INDUCED METAMORPHOSIS OF THE MEXICAN AXOLOTL AND AXOLOTL-TIGER SALAMANDER HYBRIDS _________________________________ DISSERTATION _________________________________ A dissertation submitted in partial fulfillment of the the requirements for the degree of Doctor of Philosophy in the College of Arts and Sciences at the University of Kentucky By Robert Bryce Page Lexington, Kentucky Director: Dr. S. Randal Voss, Associate Professor of Biology Lexington, Kentucky 2009 Copyright © Robert Bryce Page 2009 FOR MY PARENTS, RICHARD C. AND ANNE M. PAGE ACKNOWLEDGMENTS After doing something as involved as a doctoral dissertation in the natural sciences, it’s hard to know where to begin when it comes to thanking people. This is particularly true when one has well over half a decade invested in getting into a doctoral program in the first place. Therefore I’d like to thank people who helped put me in this position through their academic mentorship during my time at institutions other than the University of Kentucky including: Carlos Camp, Lu Elrod, Bob Jaeger, Paul Leberg, Joe Neigel, and David Marsh. After I arrived at the University of Kentucky, a number of people have been helpful in different ways. In particular, I’d like to thank Randal Voss for taking me on as a graduate student and exposing me to the worlds of functional and comparative genomics. In addition, Phil Crowley and David Weisrock have continuously provided good advice and lent a kind ear. Arny Stromberg and Craig Sargent have both consistently taken time out of their days to discuss statistical issues, and this has undoubtedly improved the content of this dissertation. Finally, I’d like to thank the graduate students, techs, and additional scientists that have been collaborators during my time at the University of Kentucky. In particular thanks are due to: Chris Beachy, Meredith Boley, Kevin Kump, James Monaghan, Sri Putta, Amy Samuels, Jeramiah Smith, and John Walker. Like most trying endeavors, completing a doctoral degree in the natural sciences is not something that can be done without the continuous support of loved ones (or at least if it can be… I’m glad that I didn’t have to do it). My long-time partner Paige McMurry has provided unending support and put up with me for countless hours when I was absolutely no fun to be around. Likewise my parents, Richard C. and Anne M. Page have provided incredible support and understanding throughout this entire process. Finally, I’d like to thank several of my friends who have provided support and served as much needed distractions from my dissertation research including: Emily Bruner, Carol Dyer, Chris Ewing, Ira Fahrnam, Damon Ivey, Ian Henneberger, Joe Henneberger, Jason McAlister, Byran McCord, Dave McLeroy, Mike See, and Dave Smith. You are all reminders to me that the most important things that we build and achieve in our lifetimes are meaningful relationships with other human beings. iii TABLE OF CONTENTS Acknowledgments.............................................................................................................. iii List of Tables ..................................................................................................................... vi List of Figures ................................................................................................................... vii List of Files ........................................................................................................................ ix Chapter One: Introduction ...................................................................................................1 Overview ..................................................................................................................1 Background and motivation .....................................................................................2 Chapter Two: Microarray analysis identifies keratin
Load more

Recommended publications
  • 140503 IPF Signatures Supplement Withfigs Thorax
    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Cloud-Clone 16-17
    Cloud-Clone - 2016-17 Catalog Description Pack Size Supplier Rupee(RS) ACB028Hu CLIA Kit for Anti-Albumin Antibody (AAA) 96T Cloud-Clone 74750 AEA044Hu ELISA Kit for Anti-Growth Hormone Antibody (Anti-GHAb) 96T Cloud-Clone 74750 AEA255Hu ELISA Kit for Anti-Apolipoprotein Antibodies (AAHA) 96T Cloud-Clone 74750 AEA417Hu ELISA Kit for Anti-Proteolipid Protein 1, Myelin Antibody (Anti-PLP1) 96T Cloud-Clone 74750 AEA421Hu ELISA Kit for Anti-Myelin Oligodendrocyte Glycoprotein Antibody (Anti- 96T Cloud-Clone 74750 MOG) AEA465Hu ELISA Kit for Anti-Sperm Antibody (AsAb) 96T Cloud-Clone 74750 AEA539Hu ELISA Kit for Anti-Myelin Basic Protein Antibody (Anti-MBP) 96T Cloud-Clone 71250 AEA546Hu ELISA Kit for Anti-IgA Antibody 96T Cloud-Clone 71250 AEA601Hu ELISA Kit for Anti-Myeloperoxidase Antibody (Anti-MPO) 96T Cloud-Clone 71250 AEA747Hu ELISA Kit for Anti-Complement 1q Antibody (Anti-C1q) 96T Cloud-Clone 74750 AEA821Hu ELISA Kit for Anti-C Reactive Protein Antibody (Anti-CRP) 96T Cloud-Clone 74750 AEA895Hu ELISA Kit for Anti-Insulin Receptor Antibody (AIRA) 96T Cloud-Clone 74750 AEB028Hu ELISA Kit for Anti-Albumin Antibody (AAA) 96T Cloud-Clone 71250 AEB264Hu ELISA Kit for Insulin Autoantibody (IAA) 96T Cloud-Clone 74750 AEB480Hu ELISA Kit for Anti-Mannose Binding Lectin Antibody (Anti-MBL) 96T Cloud-Clone 88575 AED245Hu ELISA Kit for Anti-Glutamic Acid Decarboxylase Antibodies (Anti-GAD) 96T Cloud-Clone 71250 AEK505Hu ELISA Kit for Anti-Heparin/Platelet Factor 4 Antibodies (Anti-HPF4) 96T Cloud-Clone 71250 CCA005Hu CLIA Kit for Angiotensin II
    [Show full text]
  • Keratin 17 Regulates Nuclear Morphology and Chromatin Organization Justin T
    © 2020. Published by The Company of Biologists Ltd | Journal of Cell Science (2020) 133, jcs254094. doi:10.1242/jcs.254094 SHORT REPORT Keratin 17 regulates nuclear morphology and chromatin organization Justin T. Jacob1,*, Raji R. Nair1,2, Brian G. Poll1,‡, Christopher M. Pineda2, Ryan P. Hobbs§,1, Michael J. Matunis1,3 and Pierre A. Coulombe1,2,4,5,¶ ABSTRACT et al., 2006; Jacob et al., 2018). We and others recently discovered Keratin 17 (KRT17; K17), a non-lamin intermediate filament protein, that select keratins and other non-lamin IF proteins can localize to the α was recently found to occur in the nucleus. We report here on nucleus, contain functional importin -dependent nuclear K17-dependent differences in nuclear morphology, chromatin localization signal (NLS) sequences, and participate in nuclear organization, and cell proliferation. Human tumor keratinocyte cell processes, such as transcriptional control of gene expression, cell lines lacking K17 exhibit flatter nuclei relative to normal. Re-expression cycle progression, and protection from senescence (Escobar-Hoyos of wild-type K17, but not a mutant form lacking an intact nuclear et al., 2015; Hobbs et al., 2015, 2016; Kumeta et al., 2013; Zhang localization signal (NLS), rescues nuclear morphology in KRT17-null et al., 2018; Zieman et al., 2019). cells. Analyses of primary cultures of skin keratinocytes from a mouse Before these findings, the generally accepted notion was that, strain expressing K17 with a mutated NLS corroborated these findings. with the exception of type V nuclear lamins, IF proteins strictly Proteomics screens identified K17-interacting nuclear proteins with reside in the cytoplasm (Hobbs et al., 2016).
    [Show full text]
  • The Correlation of Keratin Expression with In-Vitro Epithelial Cell Line Differentiation
    The correlation of keratin expression with in-vitro epithelial cell line differentiation Deeqo Aden Thesis submitted to the University of London for Degree of Master of Philosophy (MPhil) Supervisors: Professor Ian. C. Mackenzie Professor Farida Fortune Centre for Clinical and Diagnostic Oral Science Barts and The London School of Medicine and Dentistry Queen Mary, University of London 2009 Contents Content pages ……………………………………………………………………......2 Abstract………………………………………………………………………….........6 Acknowledgements and Declaration……………………………………………...…7 List of Figures…………………………………………………………………………8 List of Tables………………………………………………………………………...12 Abbreviations….………………………………………………………………..…...14 Chapter 1: Literature review 16 1.1 Structure and function of the Oral Mucosa……………..…………….…..............17 1.2 Maintenance of the oral cavity...……………………………………….................20 1.2.1 Environmental Factors which damage the Oral Mucosa………. ….…………..21 1.3 Structure and function of the Oral Mucosa ………………...….……….………...21 1.3.1 Skin Barrier Formation………………………………………………….……...22 1.4 Comparison of Oral Mucosa and Skin…………………………………….……...24 1.5 Developmental and Experimental Models used in Oral mucosa and Skin...……..28 1.6 Keratinocytes…………………………………………………….….....................29 1.6.1 Desmosomes…………………………………………….…...............................29 1.6.2 Hemidesmosomes……………………………………….…...............................30 1.6.3 Tight Junctions………………………….……………….…...............................32 1.6.4 Gap Junctions………………………….……………….….................................32
    [Show full text]
  • Gene Expression Profiling of Intrahepatic Cholangiocarcinoma
    DOI:http://dx.doi.org/10.7314/APJCP.2013.14.1.557 Gene Expression Profiling of Intrahepatic Cholangiocarcinoma RESEARCH ARTICLE Gene Expression Profiling of Intrahepatic Cholangiocarcinoma Ittisak Subrungruang1, Charin Thawornkuno2, Porntip Chawalitchewinkoon- Petmitr3, Chawalit Pairojkul4,6, Sopit Wongkham5,6, Songsak Petmitr2* Abstract Intrahepatic cholangiocarcinoma (ICC) is ranked as one of the top five causes of cancer-related deaths. ICC in Thai patients is associated with infection with the liver fluke,Opisthorchis viverrini, but the molecular basis for development remains unclear. The present study employed a microarray approach to compare gene expression profiles of ICCs and normal liver tissues from the same patients residing in Northeast Thailand, a region with a high prevalence of liver fluke infection. In ICC samples, 2,821 and 1,361 genes were found to be significantly up- and down-regulated respectively (unpaired t-test, p<0.05; fold-change ≥2.0). For validation of the microarray results, 7 up-regulated genes (FXYD3, GPRC5A, CEACAM5, MUC13, EPCAM, TMC5, and EHF) and 3 down- regulated genes (CPS1, TAT, and ITIH1) were selected for confirmation using quantitative RT-PCR, resulting in 100% agreement. The metallothionine heavy metal pathway contains the highest percentage of genes with statistically significant changes in expression. This study provides exon-level expression profiles in ICC that should be fruitful in identifying novel genetic markers for classifying and possibly early diagnosis of this highly fatal type of cholangiocarcinoma. Keywords: Intrahepatic cholangiocarcinoma - gene expression profile - metallothione heavy metal pathway Asian Pacific J Cancer Prev, 14 (1), 557-563 Introduction using cDNA microarray have been generated, showing that O.
    [Show full text]
  • Loss of Keratin 13 in Oral Carcinoma in Situ: a Comparative Study of Protein and Gene Expression Levels Using Paraffin Sections
    Modern Pathology (2012) 25, 784–794 784 & 2012 USCAP, Inc. All rights reserved 0893-3952/12 $32.00 Loss of keratin 13 in oral carcinoma in situ: a comparative study of protein and gene expression levels using paraffin sections Hiroko Ida-Yonemochi1,2,3, Satoshi Maruyama3, Takanori Kobayashi3, Manabu Yamazaki1, Jun Cheng1 and Takashi Saku1,3 1Division of Oral Pathology, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; 2Division of Anatomy and Cell Biology of the Hard Tissue, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan and 3Oral Pathology Section, Department of Surgical Pathology, Niigata University Hospital, Niigata, Japan Immunohistochemical loss of keratin (K)13 is one of the most valuable diagnostic criteria for discriminating carcinoma in situ (CIS) from non-malignancies in the oral mucosa while K13 is stably immunolocalized in the prickle cells of normal oral epithelium. To elucidate the molecular mechanism for the loss of K13, we compared the immunohistochemical profiles for K13 and K16 which is not expressed in normal epithelia, but instead enhanced in CIS, with their mRNA levels by in-situ hybridization in formalin-fixed paraffin sections prepared from 23 CIS cases of the tongue, which were surgically removed. Reverse transcriptase-PCR was also performed using RNA samples extracted from laser-microdissected epithelial fragments of the serial paraffin sections in seven of the cases. Although more enhanced expression levels for K16 were confirmed at both the protein and gene levels in CIS in these seven cases, the loss of K13 was associated with repressed mRNA levels in four cases, but not in the other three cases.
    [Show full text]
  • Chemical Agent and Antibodies B-Raf Inhibitor RAF265
    Supplemental Materials and Methods: Chemical agent and antibodies B-Raf inhibitor RAF265 [5-(2-(5-(trifluromethyl)-1H-imidazol-2-yl)pyridin-4-yloxy)-N-(4-trifluoromethyl)phenyl-1-methyl-1H-benzp{D, }imidazol-2- amine] was kindly provided by Novartis Pharma AG and dissolved in solvent ethanol:propylene glycol:2.5% tween-80 (percentage 6:23:71) for oral delivery to mice by gavage. Antibodies to phospho-ERK1/2 Thr202/Tyr204(4370), phosphoMEK1/2(2338 and 9121)), phospho-cyclin D1(3300), cyclin D1 (2978), PLK1 (4513) BIM (2933), BAX (2772), BCL2 (2876) were from Cell Signaling Technology. Additional antibodies for phospho-ERK1,2 detection for western blot were from Promega (V803A), and Santa Cruz (E-Y, SC7383). Total ERK antibody for western blot analysis was K-23 from Santa Cruz (SC-94). Ki67 antibody (ab833) was from ABCAM, Mcl1 antibody (559027) was from BD Biosciences, Factor VIII antibody was from Dako (A082), CD31 antibody was from Dianova, (DIA310), and Cot antibody was from Santa Cruz Biotechnology (sc-373677). For the cyclin D1 second antibody staining was with an Alexa Fluor 568 donkey anti-rabbit IgG (Invitrogen, A10042) (1:200 dilution). The pMEK1 fluorescence was developed using the Alexa Fluor 488 chicken anti-rabbit IgG second antibody (1:200 dilution).TUNEL staining kits were from Promega (G2350). Mouse Implant Studies: Biopsy tissues were delivered to research laboratory in ice-cold Dulbecco's Modified Eagle Medium (DMEM) buffer solution. As the tissue mass available from each biopsy was limited, we first passaged the biopsy tissue in Balb/c nu/Foxn1 athymic nude mice (6-8 weeks of age and weighing 22-25g, purchased from Harlan Sprague Dawley, USA) to increase the volume of tumor for further implantation.
    [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]
  • Supplementary Material Contents
    Supplementary Material Contents Immune modulating proteins identified from exosomal samples.....................................................................2 Figure S1: Overlap between exosomal and soluble proteomes.................................................................................... 4 Bacterial strains:..............................................................................................................................................4 Figure S2: Variability between subjects of effects of exosomes on BL21-lux growth.................................................... 5 Figure S3: Early effects of exosomes on growth of BL21 E. coli .................................................................................... 5 Figure S4: Exosomal Lysis............................................................................................................................................ 6 Figure S5: Effect of pH on exosomal action.................................................................................................................. 7 Figure S6: Effect of exosomes on growth of UPEC (pH = 6.5) suspended in exosome-depleted urine supernatant ....... 8 Effective exosomal concentration....................................................................................................................8 Figure S7: Sample constitution for luminometry experiments..................................................................................... 8 Figure S8: Determining effective concentration .........................................................................................................
    [Show full text]
  • Transcriptome Profiling and Differential Gene Expression In
    G C A T T A C G G C A T genes Article Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis Dominique J. Wiener 1,* ,Kátia R. Groch 1 , Magdalena A.T. Brunner 2,3, Tosso Leeb 2,3 , Vidhya Jagannathan 2 and Monika M. Welle 3,4 1 Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Science, Texas A&M University, College Station, TX 77843, USA; [email protected] 2 Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; [email protected] (M.A.T.B.); [email protected] (T.L.); [email protected] (V.J.) 3 Dermfocus, Vetsuisse Faculty, University Hospital of Bern, 3010 Bern, Switzerland; [email protected] 4 Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland * Correspondence: [email protected]; Tel.: +1-979-862-1568 Received: 30 June 2020; Accepted: 3 August 2020; Published: 4 August 2020 Abstract: The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction.
    [Show full text]
  • Toward Unraveling the Complexity of Simple Epithelial Keratins in Human Disease
    Toward unraveling the complexity of simple epithelial keratins in human disease M. Bishr Omary, … , Pavel Strnad, Shinichiro Hanada J Clin Invest. 2009;119(7):1794-1805. https://doi.org/10.1172/JCI37762. Review Series Simple epithelial keratins (SEKs) are found primarily in single-layered simple epithelia and include keratin 7 (K7), K8, K18–K20, and K23. Genetically engineered mice that lack SEKs or overexpress mutant SEKs have helped illuminate several keratin functions and served as important disease models. Insight into the contribution of SEKs to human disease has indicated that K8 and K18 are the major constituents of Mallory-Denk bodies, hepatic inclusions associated with several liver diseases, and are essential for inclusion formation. Furthermore, mutations in the genes encoding K8, K18, and K19 predispose individuals to a variety of liver diseases. Hence, as we discuss here, the SEK cytoskeleton is involved in the orchestration of several important cellular functions and contributes to the pathogenesis of human liver disease. Find the latest version: https://jci.me/37762/pdf Review series Toward unraveling the complexity of simple epithelial keratins in human disease M. Bishr Omary,1 Nam-On Ku,1,2 Pavel Strnad,3 and Shinichiro Hanada1,4 1Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA. 2Department of Biomedical Sciences, Graduate School, Yonsei University, Seoul, Republic of Korea. 3Department of Internal Medicine I, University Medical Center Ulm, Ulm, Germany. 4Division of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, Japan. Simple epithelial keratins (SEKs) are found primarily in single-layered simple epithelia and include keratin 7 (K7), K8, K18–K20, and K23.
    [Show full text]