VOLUME THREE HUNDRED AND NINETEEN INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY International Review of Cell and Molecular Biology Series Editors GEOFFREY H BOURNE JAMES F DANIELLI KWANG W JEON MARTIN FRIEDLANDER JONATHAN JARVIK 1949e1988 1949e1984 1967e 1984e1992 1993e1995 Editorial Advisory Board PETER L BEECH ROBERT A BLOODGOOD BARRY D BRUCE DAVID M BRYANT KEITH BURRIDGE HIROO FUKUDA MAY GRIFFITH KEITH LATHAM WALLACE F MARSHALL BRUCE D MCKEE MICHAEL MELKONIAN KEITH E MOSTOV ANDREAS OKSCHE MADDY PARSONS TERUO SHIMMEN ALEXEY TOMILIN GARY M WESSEL VOLUME THREE HUNDRED AND NINETEEN INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY Edited by KWANG W JEON Department of Biochemistry University of Tennessee Knoxville, Tennessee AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 225 Wyman Street, Waltham, MA 02451, USA 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA 125 London Wall, London EC2Y 5AS, UK The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK First edition 2015 Copyright © 2015 Elsevier Inc All rights reserved No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein) Notices Knowledge and best practice in this field are constantly changing As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein ISBN: 978-0-12-802278-8 ISSN: 1937-6448 For information on all Academic Press publications visit our website at http://store.elsevier.com/ CONTRIBUTORS Sandra L Accari Professional and Continuing Education, Turitea Campus, Massey University, Palmerston North, New Zealand Martin Altvater Institute of Biochemistry (IBC), Department of Biology (D-BIOL), ETH Zurich; Molecular Life Science (MLS) Graduate School, Zurich, Switzerland Simone Bergmann Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany Sunil K Chauhan Schepens Eye Research Institute & Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA Thomas G Cotter Tumour Biology Laboratory, School of Biochemistry and Cell Biology, Bioscience Research Institute, University College Cork, Cork, Ireland Ute Fischer Institute of Biochemistry (IBC), Department of Biology (D-BIOL), ETH Zurich, Zurich, Switzerland Paul R Fisher Discipline of Microbiology, La Trobe University, Melbourne, VIC, Australia Stefan Gerhardy Institute of Biochemistry (IBC), Department of Biology (D-BIOL), ETH Zurich; Biomolecular Structure and Mechanism (BSM) Graduate School, Zurich, Switzerland William R Jeffery Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA; Department of Biology, University of Maryland, College Park, MD, USA Kishore R Katikireddy Schepens Eye Research Institute & Mass Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA Ikeda Lal LV Prasad Eye Institute, Hyderabad, Telangana, India Jung Weon Lee Department of Pharmacy, Research Institute of Pharmaceutical Sciences, Tumor Microenvironment Global Core Research Center, Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul, Korea ix j x Contributors Dilip Kumar Mishra Department of Ocular Pathology, LV Prasad Eye Institute, Hyderabad, Telangana, India Purnima Nerurkar Institute of Biochemistry (IBC), Department of Biology (D-BIOL), ETH Zurich; Molecular Life Science (MLS) Graduate School, Zurich, Switzerland Vikram Govind Panse Institute of Biochemistry (IBC), Department of Biology (D-BIOL), ETH Zurich, Zurich, Switzerland Charanya Ramachandran Sudhakar and Sreekanth Ravi Stem Cell Biology Laboratory, Prof Brien Holden Eye Research Centre, C-TRACER, LV Prasad Eye Institute, Hyderabad, Telangana, India Eileen G Russell Tumour Biology Laboratory, School of Biochemistry and Cell Biology, Bioscience Research Institute, University College Cork, Cork, Ireland Virender S Sangwan Center for Ocular Regeneration, Dr Paul Dubord Chair in Cornea, LV Prasad Eye Institute, Hyderabad, Telangana, India Sabina Schütz Institute of Biochemistry (IBC), Department of Biology (D-BIOL), ETH Zurich; Molecular Life Science (MLS) Graduate School, Zurich, Switzerland Sachin Shukla Sudhakar and Sreekanth Ravi Stem Cell Biology Laboratory, Prof Brien Holden Eye Research Centre, C-TRACER, LV Prasad Eye Institute, Hyderabad, Telangana, India Vivek Singh Sudhakar and Sreekanth Ravi Stem Cell Biology Laboratory, Prof Brien Holden Eye Research Centre, C-TRACER, LV Prasad Eye Institute, Hyderabad, Telangana, India Michael Steinert Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Lower Saxony, Germany Christine Weirich Institute of Biochemistry (IBC), Department of Biology (D-BIOL), ETH Zurich, Zurich, Switzerland CHAPTER ONE From Single Cells to Engineered and Explanted Tissues: New Perspectives in Bacterial Infection Biology Simone Bergmann* and Michael Steinert* Institute of Microbiology, Technische Universit€at Braunschweig, Braunschweig, Lower Saxony, Germany *Corresponding authors: E-mail: simone.bergmann@tu-bs.de; m.steinert@tu-braunschweig.de Contents Introduction 2D Cell Culture 2.1 Culture of Immortalized Cell Lines versus Primary Cell Culture 2.2 Protozoa as Alternative Infection Models 2.3 Coculture Infection Models 2.3.1 Coculture-based generation of tissue barriers 2.3.2 Coculture of adherent cells and neutrophiles in suspension 3D Cell Culture 3.1 Benefits and Limitations of 3D Scaffold 10 11 13 14 15 3.1.1 Coculture-based reconstruction of BBB with matrix scaffold 3.1.2 Requirements of 3D tissue models generating aireliquid surface 3.2 MicrogravitydVariations of 3D Cell Culture Models Organ Equivalents and Tissue Explants 4.1 Organoids and Tissue Equivalents Providing Complex Cell Systems “En Miniature” 4.2 Tissue ExplantsdPiece of Reality 4.3 Integration of Microfluidic Systems in 2D and 3D Cell Culture Concluding Remarks and Future Perspectives Acknowledgments References 17 18 19 21 22 24 26 30 31 31 Abstract Cell culture techniques are essential for studying hostepathogen interactions In addition to the broad range of single cell type-based two-dimensional cell culture models, an enormous amount of coculture systems, combining two or more different cell types, has been developed These systems enable microscopic visualization and molecular analyses of bacterial adherence and internalization mechanisms and also provide a suitable setup for various biochemical, immunological, and pharmacological applications International Review of Cell and Molecular Biology, Volume 319 ISSN 1937-6448 http://dx.doi.org/10.1016/bs.ircmb.2015.06.003 © 2015 Elsevier Inc All rights reserved j Simone Bergmann and Michael Steinert The implementation of natural or synthetical scaffolds elevated the model complexity to the level of three-dimensional cell culture Additionally, several transwell-based cell culture techniques are applied to study bacterial interaction with physiological tissue barriers For keeping highly differentiated phenotype of eukaryotic cells in ex vivo culture conditions, different kinds of microgravity-simulating rotary-wall vessel systems are employed Furthermore, the implementation of microfluidic pumps enables constant nutrient and gas exchange during cell cultivation and allows the investigation of long-term infection processes The highest level of cell culture complexity is reached by engineered and explanted tissues which currently pave the way for a more comprehensive view on microbial pathogenicity mechanisms INTRODUCTION Most basic studies on hostepathogen interaction have been focused on cultured and, frequently, immortalized cell lines or animal experiments (Mizgerd and Skerrett, 2008) The first reports highlighting the suitability of in vitro cell culture models to study pathogenesis of microorganisms were published in the early 1970s and focused on virusehost cell interactions (Todaro et al., 1971) As early as in 1976, Taylor-Robinson (1976) described the use of ciliated tracheal epithelium of animals to study mycoplasma pneumonia infections Since then, in vitro cell culture models became increasingly popular in infection biology as they combine several advantages Compared to animal models they are cost-effective and accessible, they allow experimental flexibility including high-throughput platforms and they exhibit a high reproducibility Moreover, the vast innovations in cell biology such as microscopic imaging, genetic, biochemical, and immunologic technologies allowed deep insights in host cell responses elicited by microbes This includes the exploitation of host cell components during adherence, invasion, replication, and evasion of pathogens Meanwhile, several tissue culture collections and companies offer a broad list of different immortalized cell lines and primary cells derived from human and different animal species thereby allowing cell type-specific investigations The central key point in cell culture-based infection biology is the level of complexity which can be reached by an in vitro cell culture model in regard to differentiation and reactivity, to adequately mimic the situation in a complex host organism In order to improve the value of data obtained from cell culture models, the methods have been optimized and adapted to special scientific questions Many examples derived from different scientific Cell Culture Techniques in Infection Biology disciplines approved that simplified models enhance the probability to elucidate crucial or new specific interactions of individual components by excluding the vast amount of overlaying interactions A prerequisite for this, however, is that conclusions drawn from model systems take into account the fact that certain properties are not represented in the model Thus, it is widely accepted that the suitability of a specific cell culture-based model to generate reliable data, which can be superimposed for the situation in vivo, has to be validated for every single scientific question To overcome the limitation of isolated and often immortalized cells, models of higher complexity have been generated during the last decades of years Figure depicts the increase in model complexity and outlines Figure Schematic illustration of different cell culture models presented in this review The cell culture models are roughly categorized in two-dimensional (2D) cell culture, three-dimensional (3D) cell culture with scaffolding materials, and organoids and tissue explants The cell culture models are distributed vertically according to the level of complexity, reaching from cellular level to tissue level The transwell models are composed of a two chamber system separated by a porous membrane In most of the applied transwell cell culture systems, different cell types are cultivated on the upper and the lower site of the membrane Several bloodebrain barrier (BBB) models also implement scaffolding materials such as extracellular matrix (ECM) components for cell culture The rotary vessel culture enabled cell cultivation in microgravity environment Simone Bergmann and Michael Steinert the structure of this review Beginning with monolayer cultures and protozoa-based models as paradigms for simple two-dimensional (2D) cell culture, we will discuss the benefits and limitations of established cell culture models applied in infection biology Following the line of increasing complexity, several cocultivation techniques, transwell-based tissue models, and culture systems with implementation of scaffolds will be presented in the second part The current highest level in complexity is reached in reconstructional systems on the tissue level and includes the generation of tissue aggregates, the cultivation of organoids and the use of organ-specific ex vivo tissue explants Based on selected examples, the advantages and restrictions of these complex three-dimensional (3D) systems will be commented within the last chapter of this review 2D CELL CULTURE In many experimental setups, the creation of a functional host cell surface is sufficient to study initial interactions with bacterial pathogens such as adherence, invasion, and induction of signal transduction processes For decades of years 2D cell monolayers grown on solid, impermeable plastic or glass surfaces have been applied as simple and cost-effective strategy to analyze principle mechanisms of bacterialehost cell interactions Numerous in vitro cell culture systems have been confirmed as suitable to provide information about specific bacterial virulence factors involved and also elucidated the induction of many fold intracellular processes, such as signaling cascades and cytoskeletal rearrangements on the host side (Table 1) Depending on the physiological niche of the bacteria, pulmonary cells are cultivated and infected with typical lung pathogens like Legionella pneumophila and Streptococcus pneumoniae; gastrointestinal cells are used for infection studies with Helicobacter and Salmonella, and skin fibroblasts are chosen for infection with causative agents of wound infections like staphylococcidjust giving a few examples These studies generated impressive transmission electron microscopic pictures and opened up the field for more detailed cell culture infection analyses Several immunofluorescence staining procedures have been developed, which can be applied after infection of eukaryotic cell monolayers with pathogenic bacteria These procedures enable a microscopic visualization and also a differential quantification of adhered and internalized bacteria (Bergmann et al., 2009, 2013; Elm et al., 2004; Jensch et al., 2010; L€ uttge et al., 2012; Agarwal et al., 2013, Ciona Regeneration, Stem Cells, and Aging 275 AGING AND OS REGENERATION The regenerative abilities of Ciona decline with age Regenerative aging of the NC and OS has been observed in both natural marine environments and laboratory cultures (Dahlberg et al., 2009; Auger et al., 2010; Jeffery, 2012, 2015c) In wild collected adults, regeneration capacity during the life cycle was evaluated using size (e.g., distal to proximal length) as a proxy for age Under favorable conditions, wild Ciona adults grow continuously during a life span of about 1e1.5 years (Berrill, 1947; Millar, 1952; Dybern, 1965; Peterson et al., 1995) NC ablation or OS amputation of different sized animals resulted in the discovery of an inverse relationship between body length (age) and the rate of regeneration (Dahlberg et al., 2009; Auger et al., 2010): larger (older) animals regenerate much more slowly than smaller (younger) animals (Figure 8(A)) A similar decline in regeneration rate as a function of age also occurs in laboratory cultures in which animals of precisely known age are grown from fertilized eggs (Jeffery, 2015c) Despite a decrease in the rate of regeneration during the adult life cycle, the regenerative processes involved, for example OPO replacement, are still completed with accuracy This situation changes as animals reach an age threshold, when the capacity for regeneration disappears (Jeffery, 2012) OS regeneration is compromised in the oldest animals collected in the wild or cultured in the laboratory (Jeffery, 2012, 2015c) The old animals show morphological and reproductive abnormalities relative to their younger counterparts They exhibit a thickened and withered tunic, a reduction in gamete production, and have malformed and larger OPOs Moreover, the pharynx and siphons of these animals appear to be inflamed due to the overproduction of orange pigment cells, a condition that is possibly related to stress (Parrinello et al., 2010) When the siphons of old animals are amputated at any position, the rate of regeneration is either very slow or it does not occur at all, even after a month or more of observation (Figure 8(B)) Even though there is no net siphon growth after amputation in old animals, OPO replacement still occurs, although it shows several differences from normal replacement in younger animals (Jeffery, 2012) First, when the oral siphons of old animals are amputated in the tube, OPO replacement occurs, but multiple OPOs are formed in the place of the original single OPO Thus, siphon tube regeneration in old animals resembles siphon base regeneration in younger animals This difference could be due to the 276 William R Jeffery (B) (A) (C) (D) (E) (F) Figure Aging and oral siphon (OS) regeneration (A) The time required for oral siphon pigment organ (OPO) replacement increases during the life cycle A: From Auger et al (2010) (B) Lack of OS growth in an old animal subjected to two consecutive cycles of amputation (C) Oral siphon pigment organ (OPO) replacement has been arrested at an intermediate stage as a line of mixed orange (black in print versions) and yellow (white in print versions) pigment cells (arrows) (D) Cell proliferation determined by phosphohistone H3 antibody staining in the regeneration blastema of middle-aged animals and in the siphon stump of old animals The number of proliferating cells is significantly higher in the region above the siphon amputation plane (AeA) compared to the region below it in middle-aged animals but not in old animals Asterisks represent significant differences N is shown below each bar BeD: From Jeffery (2012) (EF) Lymph node cells stained with PIWI stem cell marker in transverse vessels (TV) in the branchial sac of middle age (E) but not old (F) animals E, F From Jeffery (2015c) Ciona Regeneration, Stem Cells, and Aging 277 abundance of differentiated orange pigment cells both in the siphons and elsewhere in the body of old animals Second, OPO replacement is arrested when old animals are subjected to an additional cycle of siphon amputation After two consecutive cycles of amputation, large numbers of orange pigment cells differentiate in the siphon stump, and the pigment cell masses line up along the wound epidermis, which seems to be formed normally, but the orange pigment cells not condense into distinct pigment spots or form OPOs Instead, they arrest in lines along the siphon rim and later mix with similar lines of yellow pigment responsible for interOPO pigment band formation (Figure 8(B) and (C)) Lastly, when the amputated siphon stumps of old animals are excised and cultured as explants in vitro, the OPO regeneration bands overproduce orange pigment cells, but they not move distally to form OPOs, as occurs in siphon explants derived from young animals (Figure 4(I)) Therefore, although orange pigment cells still differentiate, and in fact are overproduced, OPO replacement is defective, suggesting that aging disrupts morphogenetic processes in old animals The formation of a blastema of proliferating cells plays an important role in OS regeneration, contributing the precursors of new muscle and nerve cells during siphon growth (Auger et al., 2010) As described above, the blastema is formed by stem cells that migrate from the branchial sac early during regeneration and reform the OPO without undergoing cell division and progenitor cells that proliferate in the branchial sac and migrate into the blastema later during regeneration (Jeffery, 2015c) Although OPO replacement can occur (albeit defectively) in old animals, they not develop a blastema of proliferating cells (Figure 8(D)) (Jeffery, 2012) Accordingly, old animals not replace muscle cells and regain the ability for siphon contraction There is no information available about the effects of age on nerve cell replacement The absence of a blastema in old animals suggests that defects might occur in the production or migration of proliferating cells Branchial sac stem cells have been compared in young and old animals following OS amputation by EdU pulse labeling and expression of AP and PIWI stem cell markers (Jeffery, 2015c) The structure of the branchial sac and distribution of proliferating cells appear to be abnormal in old animals (Millar, 1952; Jeffery, 2015c) Furthermore, the branchial sac of old animals shows much lower levels of AP- and PIWI-labeled adult stem cells compared to their younger counterparts Thus, a reduction in stem cell number, the failure of stem cells to produce progenitor cells, and/or the inability of progenitor 278 William R Jeffery cells to migrate into the injured siphons may be responsible for regenerative aging It is also possible that the injured siphon stumps of old animals not produce a normal signal for the attraction of progenitor cells to the regeneration blastema Based on all the information currently available about siphon regeneration, stem cells, and aging, a model has been suggested to explain the gradual decline and eventual abrupt cessation of regenerative capacity of the Ciona OS (Jeffery, 2015c) The model states (1) that all of the branchial sac stem cells that are used in growth (and potentially in regeneration) are produced early during the adult life cycle, (2) after a maximal number of stem cells is reached, they slowly lose potency or disappear as animals age, and (3) during old age, no additional stem cells are available for further growth or, if necessary, regeneration A test of this model would entail the experimental reduction and elevation of stem cell number, and approaches to accomplish this are currently under development CONCLUDING REMARKS AND PERSPECTIVES We suggest that new animal models are needed to study the relationship between regeneration and aging As well as being able to reveal the principles underlying regenerative aging, these models should also help us understand how and why regeneration has been lost during the evolution of some animals, including ourselves Ultimately, using information gleaned from these models, we might find ways to reverse the loss of regenerative potential that is imposed during aging and evolution Ciona is an animal that fills the need for a model in regenerative aging Although many avenues of regenerative biology research need to be explored further in Ciona, in recent years there has been progress in deciphering the underpinnings of regeneration In Ciona, it is possible to study regeneration in a small part of the animal while also observing related changes in the entire animal, thus allowing both short- and long-distance regeneration processes to be analyzed This approach led to the discovery of the Ciona branchial sac stem cell niche and its long-distance contribution to the regenerating siphon (Jeffery, 2015c) Most of the insights described in this article are derived from experiments on OS regeneration, however, Ciona also promises to be an excellent model to study the regeneration capacity of other organs, such as the brain and heart, and these studies should be vigorously pursued in the future Although Ciona Regeneration, Stem Cells, and Aging 279 some vertebrates, namely amphibians, show partial brain regeneration (Endo et al., 2007), no chordate group other than the tunicates can regenerate an entire brain after its complete removal Thus, insights about vertebrate brain regeneration may be gained from studying the capacity for complete brain regeneration in Ciona We have described recent results showing that adult stem cells are instrumental in Ciona regeneration and aging Similar properties of stem cells have been observed in other animals (e.g., Conboy and Rando, 2005; Sharpless and Schatten, 2009; Waterstrat and Van Zant, 2009) It is remarkable that all stages in the life and function of adult stem cells, from their initial formation during metamorphosis (or perhaps even during embryogenesis) to their possible depletion or decay during old age, are accessible for study in Ciona This attribute is likely to have important impacts on understanding the life history of adult stem cells Molecular analysis of Ciona regeneration is still being developed This approach will be fostered by the existence of molecular and genomic tools that have been pioneered for studying the development of this organism (Stolfi and Christiaen, 2012) Thus, it will be imperative to take advantage of these tools in future studies to reveal the molecular basis of regenerative aging ACKNOWLEDGMENTS This article was prepared under the auspices of a grant from the National Institutes of Heath (AG037918) and Frederick and Betsy Bang and Laura and Arthur Colwin Fellowships from the Marine Biological Laboratory, Woods Hole, MA REFERENCES Akhmadieva, A.V., Shukalyuk, A.I., Aleksandrova, Y.N., 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in ascidians In: Bosch, T.C.G (Ed.), Stem Cells: From Hydra to Man, Chapter Springer, New York, pp 95e112 Voog, J., Jones, D.L., 2010 Stem cells and the niche: a dynamic duo Cell Stem Cell 6, 103e115 Waterstrat, A., Van Zant, G., 2009 Effects of aging on hematopoietic stem and progenitor cells Curr Opin Immunol 21, 408e413 Weissman, I.L., 2000 Stem cells: units of development, units of regeneration, and units in evolution Cell 100, 157e168 Whittaker, J.R., 1975 Siphon regeneration in Ciona Nature 255, 224e225 INDEX Note: Page numbers with “f ” and “t” denote figures and tables, respectively A Acanthamoeba castellanii, 9–10 Acinetobacter baumannii, 23–24 Adult stem cells, 269–271 branchial sac stem cells, 270f, 271 multiple stem cells, 269–271, 270f Aging, 241 Akt, 231–232 Aldehyde dehydrogenase (ALDH), 156–157 Alkaline phosphatase (AP), 269–270 AlkB protein demethylates, 174–175 Allogeneic transplantation, 80–81 Amine oxidase (LSD1/KDM1), 167–170, 172f Amniotic membrane transplantation (AMT), 73 Antioxidant systems, 226 ARX1, 119 Atherosclerosis, 236–237 ATM protein kinase, 234 B BBB See Blood-brain barrier (BBB) Biological materials collagen-based materials, 61–62 fibrin, 60–61 silk fibroin-based materials, 62–63 Blastema, formation of, 277 Blood-brain barrier (BBB), 11 coculture-based reconstruction of, 17–18 complexity of, 12 Blood-cerebrospinal fluid barrier (BCSFB), 11 Bombyx mori (BM), 62–63 Brain microvascular endothelial cells (BMECs), 11 in vitro models, 12 Branchial sac stem cells, 270f, 271 C Ca2+/calmodulin-dependent protein kinase II (CaMKII), 234 Calu-3 cells, 13–14 cAMP-dependent protein kinase, 232 Cancer, 241–242 Candida albicans, 11 CD63 (Tspan30), 149–150 CD151 (Tspan24), 148–149 Cell-based therapies, 53–58 embryonic stem cell (ESC), 54 induced pluripotent stem cell (iPSC), 54–55 mesenchymal stem cells See Mesenchymal stem cell (MSC) Cell culture models, 3f key points, 2–3 organ equivalents and tissue explants, 21–29 complex cell systems “En Miniature”, 22–24 piece of reality, 24–26 2D and 3D cell culture, microfluidic systems in, 26–29 three-dimensional (3D) cell culture, 14–21 air–liquid surface, requirements of, 18–19 BBB, coculture-based reconstruction of, 17–18 benefits and limitations, 15–19 microgravity-variations of, 19–21 two-dimensional (2D) cell culture, 4–14 alternative infection models, protozoa as, 9–10 bacterial pathogens, 4, 5t–6t coculture infection models See Coculture infection models fluorescence staining, immortalized cell lines vs primary cell culture, 7–9 Cellular organoids, 21–22 Cellular spheroids, 21–22 cGMP-dependent protein kinase, 235 Chlamydia trachomatis, 19–21 Chromatography, 176–177 283 j 284 Ciona intestinalis adult stem cells, 269–271 branchial sac stem cells, 270f, 271 multiple stem cells, 269–271, 270f life cycle/adult organization and growth, 257–260, 258f oral siphon (OS) aging, 275–278, 276f model, 260–262, 261f regeneration See Oral siphon (OS), regeneration partial body regeneration, 260 stem/progenitor cell mobilization and deployment, 271–274, 272f–273f Circular debridement wounds, 77–78 Circular muscle bands, 267–268 Citrobacter freundii, 11 CLET See Cultivated limbal epithelial transplantation (CLET) Coculture infection models, 10–14 suspension, adherent cells and neutrophiles in, 13–14 tissue barriers, coculture-based generation of, 11–13 Collagen, 15–17 COMET See Cultivated oral mucosal epithelial transplantation (COMET) Conjunctival basal cells, 49–50 Conjunctival epithelium, 49–50 Corneal cells, 57 Corneal epithelium, 48 Corneal wound healing, 77–80, 79t Cross-linking collagen, 61–62 Cultivated limbal epithelial transplantation (CLET), 82f results, 83–84, 83f, 85t–87t surgical steps, 82 Cultivated oral mucosal epithelial transplantation (COMET) results, 90, 90t surgical technique, 89–90 Cysteine residues, 222–224, 223f Cytoplasmic maturation, 124–130 pre-40S subunits, 127–130 pre-60S subunits, 124–127, 124f Index D Dictyostelium discoideum, 9–10 Double-stranded b helix (DSBH) fold, 166 Drosophila melanogaster, 177 Dual TUDOR domains, 190 E ECM1, 119 Embryonic stem cell (ESC), 46–47, 54 Endostyle, 259 Engineering limbal niche, 67–68, 69t–72t Enterohemorrhagic Escherichia coli (EHEC), 22–23 Enteropathogenic Escherichia coli (EPEC), 22–23 EpiAirwayTM See Epithelial airway tissue model (EpiAirwayTM) Epithelial airway tissue model (EpiAirwayTM), 18–19 Epithelial cells culture, 15–17 Epithelial–mesenchymal transition (EMT), 142–150, 149f, 153–154, 156–157 liver fibrosis See Liver fibrosis zebrafish, muscle cells in, 145–146 Ethylenediamine tetra-acetic acid (EDTA), 81–82 Eukaryotic ribosome biogenesis, experimental approaches to, 109–110 cytoplasmic maturation, 124–130 pre-40S subunits, 127–130 pre-60S subunits, 124–127, 124f export, 114–124 pre-40S subunits, 121–124 pre-60S subunits, 117–121, 118f shared export factors, 115–117 nuclear maturation, 111–114 pre-40S subunits, 113–114 pre-60S subunits, 111–113 90S preribosome assembly, 110–111, 110f ribosomal RNAs (rRNAs), 108 synthesis, 108 Extracellular matrix, 151 F Factor-inhibiting HIF-1 alpha, 166, 167f Flow cytometry analysis, 285 Index Fluorescence staining, Forkhead boxO (FOXO) transcription factors, 235 Four-point-one, ezrin, radixin and moesin (FERM), 151 Fractionation, 176–177 Francisella tularensis, 19–21 G Gle2-binding sequence (GLEBS), 120 Glycocalyx forms, 49 Golgi complex, 15–17 H Hartmannella vermiformis, 9–10 Henle’s crypt, 49–50 Hepatocyte growth factor (HGF), 145 Herpes simplex virus (HSV), 80 Histone demethylase subgroups, 176–210 JARID subgroup, 193–199 JHDM2 (JMJD1) subgroup, 182–187 JmjC-domain-only, 208–210 Jumonji histone demethylase (JHDM1) subgroup, 176–182, 177f Jumonji histone demethylase (JHDM2) subgroup, 182–187 Jumonji histone demethylase (JHDM3) subgroup, 187–193 PHF2/PHF8/KIAA1718 subgroup, 203–208 UTX/UTY/JMJD3 subgroup, 199–203 H3K9 methylation mark, 183–185 human amniotic membrane (hAM), 58–60 Human embryonic stem cell (hESC), 30–31 Human epidermal equivalent (HEE), 30–31 Human limbal epithelial cells, 68 Human malignant choroid plexus papilloma cells (HIBCPP), 13–14 Human Rio2 (hRio2), 122 Human umbilical vein endothelial cells (HUVEC), 12–13 HUVEC See Human umbilical vein endothelial cells (HUVEC) Hydrophilic siloxane hydrogel contact lenses, 63–64 Hypertension, 239–240 I induced pluripotent stem cell (iPSC), 30–31, 54–55 Inflammation, 237–238 Inhibitory kB (IkB), 234 Intracellular loop (ICL), 151 iPSC See induced pluripotent stem cell (iPSC) J JARID subgroup, 193–199 JARID2-Jumonji, 199 KDM5A, 193–195, 194f KDM5B, 195–196, 197f KDM5C, 196–199 JHDM2 (JMJD1) subgroup, 182–187 Jumonji C (JmjC) domain-containing proteins, 208–210 double-stranded b helix (DSBH) fold, 166 factor-inhibiting HIF-1 alpha, 166, 167f histone demethylases, 174–210, 175f demethylase subgroups, 176–210 histone demethylation and demethylases peptidylarginine deiminase (PADI4/ PAD4) and amine oxidase (LSD1/ KDM1), 167–170, 172f histone modification and methylation, 167–171, 168t–169t arginine residues, 170, 171f JMJD6, 208–209 KDM8, 209–210 plant histone demethylation nondemethylating roles, 210–211 plant histone demethylases, 211, 212f Jumonji histone demethylase (JHDM1) subgroup, 176–182, 177f Epe1, 182 Jhd1, 181 KDM2A/KDM2B, 178–181, 179f Jumonji histone demethylase (JHDM2) subgroup, 182–187 KDM3A, 183–185, 184f KDM3B, 185–186 KDM3C, 186–187 286 Jumonji histone demethylase (JHDM3) subgroup, 187–193 KDM4A, 189–191, 190f KDM4B, 191 KDM4C, 191–192 yeast KDM4 members, 192–193 K Kap123, 111 L Legionella pneumophila, 4–7, 24–25 Leptomycin B (LMB), 115 Limbal/corneal epithelial cells chemical and mechanical injury of, 74–75, 75f, 76t, 77f genetic defects of, 73–74 Limbal stem cell deficiency (LSCD), 50–52, 56–58, 57f–58f, 73–80 corneal wound healing, 77–80, 79t limbal/corneal epithelial cells, chemical and mechanical injury of, 74–75, 75f, 76t, 77f limbal/corneal epithelial cells, genetic defects of, 73–74 Limbus, 50–53, 51f–53f Listeria monocytogenes, 11 Liver fibrosis cross-talk between tetraspanins, 148–150, 149f TGFb1 signaling, 147–148 Longitudinal muscle bands, 267–268 LSCD See Limbal stem cell deficiency (LSCD) Lymph nodes, 270–271, 270f M Manual superficial keratectomy (MSK), 77–78 Melanoma cells culture, 15–17 Mesenchymal stem cell (MSC) corneal reconstruction, 56 LSCD, 56–58, 57f–58f Messenger ribonucleic acid (mRNA), 146 Mex67-Mtr2 heterodimer, 115–116 Microfluidic cell culture, 26–28 Index MIDAS interacting domains (MIDOs), 112–113 Motile nonfeeding larva, 257–258 MSC See Mesenchymal stem cell (MSC) Mucins, 49 Mucus-secreting goblet cells, 49–50 Multiple stem cells, 269–271, 270f N Neisseria meningitides, 13–14 Neural complex (NC), 259 Neural ganglion, 264 Neurodegenerative diseases, 238 Neuroinflammation, 238 N-glycosylation, 156–157 Nmd3, 118–119 Nonkeratinized stratified limbal epithelium, 50–52 Nonreceptor kinases Akt, 231–232 ATM protein kinase, 234 Ca2+/calmodulin-dependent protein kinase II (CaMKII), 234 cAMP-dependent protein kinase, 232 cGMP-dependent protein kinase, 235 inhibitory kB (IkB), 234 MAPK, 233–234 Src family kinases, 232–233 Non-small cell lung cancer (NSCLC), 153–154 Nuclear export signal (NES), 115 Nuclear factor-Like (Nrf2), 235–236 Nuclear maturation, 111–114 pre-40S subunits, 113–114 pre-60S subunits, 111–113 Nuclear pore complex (NPC), 114–115 Nucleolar ribosome assembly, 111 O Obesity, 240–241 Ocular mucus, 49 Ocular surface reconstruction anatomy and pathology, 47 conjunctival epithelium, 49–50 limbus, 50–53, 51f–53f preocular tear film, 49 cell-based therapies for, 53–58 287 Index embryonic stem cell (ESC), 54 induced pluripotent stem cell (iPSC), 54–55 mesenchymal stem cells See Mesenchymal stem cell (MSC) embryonic stem cell (ESC), 46–47 limbal stem cells (LSCs), 46–47 LSCD, animal models for, 73–80 corneal wound healing, 77–80, 79t limbal/corneal epithelial cells, chemical and mechanical injury of, 74–75, 75f, 76t, 77f limbal/corneal epithelial cells, genetic defects of, 73–74 new material technologies, 58–68 biological materials See Biological materials engineering limbal niche, 67–68, 69t–72t human amniotic membrane (hAM), 58–60 synthetic materials See Synthetic materialss ophthalmology, 47 overview, 80–81 surgical techniques cultivated limbal epithelial transplantation See Cultivated limbal epithelial transplantation (CLET) cultivated oral mucosal epithelial transplantation See Cultivated oral mucosal epithelial transplantation (COMET) simple limbal epithelial transplantation See Simple limbal epithelial transplantation (SLET) OPO See Oral siphon pigment organ (OPO) Oral siphon (OS) aging, 275–278, 276f model, 260–262, 261f regeneration, 261f, 262–269, 263f, 264t capacity, 260 long-distance regeneration, 267–268 OPO replacement, 264–265 short-distance regeneration, 264t, 265–267, 266f siphon base, 268–269 tip and tube, 264–268 structure, 258f Oral siphon pigment organ (OPO), 260–263, 261f, 263f blastema and siphon nerves, 268 multiple, 268–269 regeneration band, 264, 270–271 OS See Oral siphon (OS) P Palpebral conjunctiva, 49–50 Partial body regeneration, 260 Pathophysiological significance aging, 241 atherosclerosis, 236–237 cancer, 241–242 hypertension, 239–240 inflammation, 237–238 neuroinflammation and neurodegenerative diseases, 238 obesity, 240–241 preeclampsia, 240 type diabetes, 238–239 PAX6 mutation, 73–74 Peptidylarginine deiminase (PADI4/ PAD4), 167–170, 172f PHF2/PHF8/KIAA1718 subgroup, 203–208 KDM7A (KIAA1718), 207–208 KDM7B, 204–207 Piwi gene, 269–270 Plant homeodomain (PHD), 178 Plasma polymer coating, 63–64 Plasmodium falciparum, 28–29 Poly(N-isopropylacrylamide) (PIPAAm), 66–67 Polycomb-group (PcG), 202 Polydimethylsiloxane (PDMS), 26–28 Polyethylene glycol diacrylate (PEGDA), 68 Polymorphnuclear granulocytes (PMNs), 12–13 Preeclampsia, 240 Preocular tear film, 49 288 Preribosomal subunits cytoplasmic maturation, 124–130 pre-40S subunits, 127–130 pre-60S subunits, 124–127, 124f export, 114–124 pre-40S subunits, 121–124 pre-60S subunits, 117–121, 118f shared export factors, 115–117 nuclear maturation, 111–114 pre-40S subunits, 113–114 pre-60S subunits, 111–113 Pre-60S maturation, 125 Primary porcine choroid plexus epithelial cells (PCPEC), 13–14 Progenitor cell mobilization, 271–274, 272f–273f R Rea1, 112–113 Reactive oxygen species (ROS), 223f antioxidant systems, 226 cysteine residues, 222–224, 223f forkhead boxO (FOXO) transcription factors, 235 future perspectives, 246 measurement, 245–246 nuclear factor-Like (Nrf2), 235–236 pathophysiological significance aging, 241 atherosclerosis, 236–237 cancer, 241–242 hypertension, 239–240 inflammation, 237–238 neuroinflammation and neurodegenerative diseases, 238 obesity, 240–241 preeclampsia, 240 type diabetes, 238–239 redox regulation, 228–235 nonreceptor kinases See Nonreceptor Kinases protein tyrosine phosphatases, 228, 229f receptor tyrosine kinases See Receptor tyrosine kinases signaling mechanism, 227 Index signaling molecules, 226–227 source of, 224–226, 225f treatment strategies, 242–244 Receptor tyrosine kinases, 228–230 epidermal growth factor receptor (EGFR), 230 fibroblast growth factor receptors (FGFRs), 231 insulin receptor kinase (IRK), 230–231 platelet-derived growth factor receptor (PDGFR), 228–230 vascular endothelial growth factor receptor (VEGFR), 230 Recombinant human type III collagen (RHCIII), 61–62 Redox regulation, 228–235 nonreceptor kinases See Nonreceptor Kinases protein tyrosine phosphatases, 228, 229f receptor tyrosine kinases See Receptor tyrosine kinases Regenerative aging, 256–257 Ribosomal RNAs (rRNAs) See Eukaryotic ribosome Rotating cell culture systems (RCCS), 21–23 Rotating wall vessel (RWV), 19–21 RPMI 2650 epithelial cells, 19 Rrp12, 116–117 RWV See Rotating wall vessel (RWV) S Saccharomyces cerevisiae, 177 Schizosaccharomyces pombe, 177 Signal recognition particle (SRP), 125 Signal transducer and activator of transcription (STAT), 152 Simple limbal epithelial transplantation (SLET) results, 84–89, 88f surgical technique, 84 SLET See Simple limbal epithelial transplantation (SLET) Src family kinases, 232–233 Staphylococcus aureus, 28–29 Stem cell-based therapy, 80–81 Stevens–Johnson syndrome (SJS), 50–52 289 Index Streptococcus pneumoniae, 11 Streptococcus pyogenes, 15–17 Surface-coated lenses, 63–64 Symblepharon, 82 Synthetic materials, 63–67 contact lenses, 63–64 polylactic glycolic acid (PLGA), 64–66, 65f–66f thermoresponsive substrate, 66–67 T Tails, 167–170 Tear film, 49 Tetraspanin CD151, 148–149, 149f Tetratricopeptide repeats (TPR), 200 Three-dimensional (3D) cell culture, 14–21 air–liquid surface, requirements of, 18–19 BBB, coculture-based reconstruction of, 17–18 benefits and limitations, 15–19 microgravity-variations of, 19–21 Transepithelial electrical resistance (TEER), 12 Transmembrane 4-L six family member (TM4SF5), 143f drug resistance, 153–155 epithelial–mesenchymal transition, 143–150 liver fibrosis See Liver fibrosis zebrafish, muscle cells in, 145–146 metastatic potential direct migration, FAK activation for, 150–152 invasion, c-Src regulation of, 152–153 self-renewal capacity, 156–157 tetraspanin enriched microdomains, component of, 142–143, 144f Trithorax (TrxG), 202 Trojan Horse mechanisms, 11 Two-dimensional (2D) cell culture, 4–14 alternative infection models, protozoa as, 9–10 bacterial pathogens, 4, 5t–6t coculture infection models See Coculture infection models fluorescence staining, immortalized cell lines vs primary cell culture, 7–9 Type diabetes, 238–239 Tyrosine kinase inhibitors (TKIs), 153 U Ubiquitin-associated (UBA), 115–116 UTX/UTY/JMJD3 subgroup, 199–203 KDM6A, 199–203 KDM6A (UTX), 200–202 KDM6B (JMJD3), 202–203 V Visual acuity, 84–89 W Weibel–Palade bodies, Wound epidermis forms, 262–263 ... internalization mechanisms and also provide a suitable setup for various biochemical, immunological, and pharmacological applications International Review of Cell and Molecular Biology, Volume 319 ISSN 1937-6448... Models for LSCD 5.1 LSCD due to Genetic Defects of Limbal/Corneal Epithelial Cells 67 73 73 International Review of Cell and Molecular Biology, Volume 319 ISSN 1937-6448 http://dx.doi.org/10.1016/bs.ircmb.2015.07.001... replication, and evasion of pathogens Meanwhile, several tissue culture collections and companies offer a broad list of different immortalized cell lines and primary cells derived from human and different