The Flatworm Macrostomum Lignano Is a Powerful Model Organism for Ion Channel and Stem Cell Research
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Electrical Synapses Are Drivers of Neural Plasticity Through Passage of Small Molecules
Electrical Synapses are Drivers of Neural Plasticity Through Passage of Small Molecules Lisa Voelker A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2019 Reading Committee: Jihong Bai, Chair Linda Buck Cecilia Moens Program Authorized to Offer Degree: Molecular and Cellular Biology ©Copyright 2019 Lisa Voelker 2 University of Washington Abstract Electrical Synapses are Drivers of Neural Plasticity through Passage of Small Molecules Lisa Voelker Chair of the Supervisory Committee: Jihong Bai Department of Biochemistry In order to respond to changing environments and fluctuations in internal states, animals adjust their behavior through diverse neuromodulatory mechanisms. In this study we show that electrical synapses between the ASH primary quinine-detecting sensory neurons and the neighboring ASK neurons are required for modulating the aversive response to the bitter tastant quinine in C. elegans. Mutant worms that lack the electrical synapse proteins INX-18 and INX-19 become hypersensitive to dilute quinine. Cell-specific rescue experiments indicate that inx-18 operates in ASK while inx-19 is required in both ASK and ASH for proper quinine sensitivity. Imaging analyses find that INX-19 in ASK and ASH localizes to the same regions in the nerve ring, suggesting that both sides of ASK-ASH electrical synapses contain INX-19. While inx-18 and inx-19 mutant animals have a similar behavioral phenotype, several lines of evidence suggest the proteins encoded by these genes play different roles in modulating the aversive quinine response. First, INX-18 and INX-19 localize 3 to different regions of the nerve ring, indicating that they are not present in the same synapses. -
New Group of Transmembrane Proteins Associated with Desiccation Tolerance in the Anhydrobiotic Midge Polypedilum Vanderplanki Taisiya A
www.nature.com/scientificreports OPEN New group of transmembrane proteins associated with desiccation tolerance in the anhydrobiotic midge Polypedilum vanderplanki Taisiya A. Voronina1,6, Alexander A. Nesmelov1,6, Sabina A. Kondratyeva1, Ruslan M. Deviatiiarov1, Yugo Miyata2, Shoko Tokumoto3, Richard Cornette2, Oleg A. Gusev1,4,5, Takahiro Kikawada2,3* & Elena I. Shagimardanova1* Larvae of the sleeping chironomid Polypedilum vanderplanki are known for their extraordinary ability to survive complete desiccation in an ametabolic state called “anhydrobiosis”. The unique feature of P. vanderplanki genome is the presence of expanded gene clusters associated with anhydrobiosis. While several such clusters represent orthologues of known genes, there is a distinct set of genes unique for P. vanderplanki. These include Lea-Island-Located (LIL) genes with no known orthologues except two of LEA genes of P. vanderplanki, PvLea1 and PvLea3. However, PvLIL proteins lack typical features of LEA such as the state of intrinsic disorder, hydrophilicity and characteristic LEA_4 motif. They possess four to fve transmembrane domains each and we confrmed membrane targeting for three PvLILs. Conserved amino acids in PvLIL are located in transmembrane domains or nearby. PvLEA1 and PvLEA3 proteins are chimeras combining LEA-like parts and transmembrane domains, shared with PvLIL proteins. We have found that PvLil genes are highly upregulated during anhydrobiosis induction both in larvae of P. vanderplanki and P. vanderplanki-derived cultured cell line, Pv11. Thus, PvLil are a new intriguing group of genes that are likely to be associated with anhydrobiosis due to their common origin with some LEA genes and their induction during anhydrobiosis. Anhydrobiosis is the ability of an organism to survive complete desiccation in the ametabolic state. -
Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics
GBE Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics Marisa C.W. Lim1,*, Christopher C. Witt2, Catherine H. Graham1,3,andLilianaM.Davalos 1,4 1Department of Ecology and Evolution, Stony Brook University 2 Museum of Southwestern Biology and Department of Biology, University of New Mexico Downloaded from https://academic.oup.com/gbe/article-abstract/11/6/1552/5494706 by guest on 08 June 2019 3Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland 4Consortium for Inter-Disciplinary Environmental Research, Stony Brook University *Corresponding author: E-mail: [email protected]. Accepted: May 12, 2019 Data deposition: The raw read data have been deposited in the NCBI Sequence Read Archive under BioProject: PRJNA543673, BioSample: SAMN11774663-SAMN11774674, SRA Study: SRP198856. All scripts used for analyses are available on Dryad: doi:10.5061/dryad.v961mb4. Abstract High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. -
Multifaceted Roles of the Transmembrane Nuclear Envelope Protein, Samp1
!" #$"% "$&$$ ' () * ( +",-& . /01( ( /231( 4 /5 1 &.3 6 7&3 (3 7 3 3 ("& (583( & 583( " 835 4( &"9 ( " & " 3 :. ;( &< ( " &3 5 ( 4 " &35#5"# ( " &. " &. ( ( 4 & #$"% =>> && > ? @ == = = "A"B", 3-C%BC"%,ACD%%! 3-C%BC"%,ACD%B$ ! " ("$,C" Multifaceted roles of the transmembrane nuclear envelope protein, Samp1 Mohammed Hakim Jaffer Ali Abstract The eukaryotic nuclear envelope (NE), separates the nucleoplasm from cytoplasm and is made up of two concentric lipid membranes, the outer and the inner nuclear membranes (ONM and INM), the nuclear pore complexes (NPCs) and an underlying filamentous nuclear lamina. The INM contains hundreds of unique transmembrane proteins of which only a handful have been characterized. In this thesis, I aimed to understand the functional organization of proteins in the nuclear envelope and I focused on investigating the functions of a recently identified INM transmembrane protein, Samp1. We have developed a novel and robust approach, MCLIP, to identify specific protein- protein interactions taking place in live cells. Using MCLIP, we have shown that Samp1 interacts with proteins of the LINC complex, -
Influence of Temperature on the Development, Reproduction and Regeneration in the Flatworm Model Organism Macrostomum Lignano
bioRxiv preprint doi: https://doi.org/10.1101/389478; this version posted August 10, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Influence of temperature on the development, reproduction and regeneration in the flatworm model organism Macrostomum lignano Jakub Wudarski1, Kirill Ustyantsev2, Lisa Glazenburg1, Eugene Berezikov1* 1 European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands; 2 Institute of Cytology and Genetics, Prospekt Lavrentyeva 10, 630090, Novosibirsk, Russia. * Correspondence: [email protected] Abstract The free-living marine flatworm Macrostomum lignano is a powerful model organism to study mechanisms of regeneration and stem cell regulation due to its convenient combination of biological and experimental properties, including the availability of transgenesis methods, which is unique among flatworm models. However, due to its relatively recent introduction in research, there are still many biological aspects of the animal that are not known. One of such questions is the influence of the culturing temperature on Macrostomum biology. Here we systematically investigated how different culturing temperatures affect the development time, reproduction rate, regeneration, heat shock response, and gene knockdown efficiency by RNA interference in M. lignano. We used marker transgenic lines of the flatworm to accurately measure the regeneration endpoint and to establish the stress response threshold for temperature shock. We found that compared to the culturing temperature of 20oC commonly used for M. -
Characterization of Innexin Gene Expression and Functional Roles of Gap-Junctional Communication in Planarian Regeneration
Developmental Biology 287 (2005) 314 – 335 www.elsevier.com/locate/ydbio Characterization of innexin gene expression and functional roles of gap-junctional communication in planarian regeneration Taisaku Nogi, Michael Levin * Department of Cytokine Biology, The Forsyth Institute, 140 The Fenway, Boston, MA 02115, USA Department of Oral and Developmental Biology, Harvard School of Dental Medicine, 140 The Fenway, Boston, MA 02115, USA Received for publication 17 January 2005, revised 20 August 2005, accepted 1 September 2005 Available online 21 October 2005 Abstract Planaria possess remarkable powers of regeneration. After bisection, one blastema regenerates a head, while the other forms a tail. The ability of previously-adjacent cells to adopt radically different fates could be due to long-range signaling allowing determination of position relative to, and the identity of, remaining tissue. However, this process is not understood at the molecular level. Following the hypothesis that gap-junctional communication (GJC) may underlie this signaling, we cloned and characterized the expression of the Innexin gene family during planarian regeneration. Planarian innexins fall into 3 groups according to both sequence and expression. The concordance between expression-based and phylogenetic grouping suggests diversification of 3 ancestral innexin genes into the large family of planarian innexins. Innexin expression was detected throughout the animal, as well as specifically in regeneration blastemas, consistent with a role in long-range signaling relevant to specification of blastema positional identity. Exposure to a GJC-blocking reagent which does not distinguish among gap junctions composed of different Innexin proteins (is not subject to compensation or redundancy) often resulted in bipolar (2-headed) animals. -
The Free-Living Flatworm Macrostomum Lignano
ARTICLE IN PRESS Experimental Gerontology xxx (2009) xxx–xxx Contents lists available at ScienceDirect Experimental Gerontology journal homepage: www.elsevier.com/locate/expgero Review The free-living flatworm Macrostomum lignano: A new model organism for ageing research Stijn Mouton a,*, Maxime Willems a, Bart P. Braeckman b, Bernhard Egger c, Peter Ladurner c, Lukas Schärer d, Gaetan Borgonie a a Nematology Unit, Department of Biology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium b Laboratory for Ageing Physiology and Molecular Evolution, Department of Biology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium c Ultrastructural Research and Evolutionary Biology, Institute of Zoology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria d Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland article info abstract Article history: To study the several elements and causes of ageing, diverse model organisms and methodologies are Received 5 September 2008 required. The most frequently used models are Saccharomyces cerevisiae, Caenorhabditis elegans, Drosoph- Received in revised form 6 November 2008 ila melanogaster and rodents. All have their advantages and disadvantages and allow studying particular Accepted 28 November 2008 aspects of the ageing process. During the last few years, several ageing studies focussed on stem cells and Available online xxxx their role in tissue homeostasis. Here we present a new model organism which can study this relation where other model systems fail. The flatworm Macrostomum lignano possesses a dynamic population Keywords: of likely totipotent somatic stem cells known as neoblasts. Several characteristics qualify M. lignano as Flatworm a suitable model system for ageing studies in general and more specifically for gaining more insight in Macrostomum lignano Ageing the causal relation between stem cells, ageing and rejuvenation. -
Macrostomum Lignano Jakub Wudarski1, Kirill Ustyantsev2, Lisa Glazenburg1 and Eugene Berezikov1*
Wudarski et al. Zoological Letters (2019) 5:7 https://doi.org/10.1186/s40851-019-0122-6 RESEARCH ARTICLE Open Access Influence of temperature on development, reproduction and regeneration in the flatworm model organism, Macrostomum lignano Jakub Wudarski1, Kirill Ustyantsev2, Lisa Glazenburg1 and Eugene Berezikov1* Abstract Background: The free-living marine flatworm Macrostomum lignano is a powerful model organism for use in studying mechanisms of regeneration and stem cell regulation due to its combination of biological and experimental properties, including the availability of transgenesis methods, which is unique among flatworm models. However, due to its relatively recent introduction in research, many aspects of this animal’s biology remain unknown. One such question is the influence of culture temperature on Macrostomum biology. Results: We systematically investigated how different culture temperatures affect development time, reproduction rate, regeneration, heat shock response, and gene knockdown efficiency by RNA interference (RNAi) in M. lignano. We used marker transgenic lines to accurately measure the regeneration endpoint, and to establish the stress response threshold for temperature shock. We found that compared to the culture temperature of 20 °C commonly used for M. lignano, temperatures of 25 °C–30 °C substantially increase the speed of development and regeneration, lead to faster manifestation of RNAi phenotypes, and increase reproduction rate without detectable negative consequences for the animal, while temperatures above 30 °C elicit a heat shock response. Conclusions: We show that altering temperature conditions can be used to reduce the time required to establish M. lignano cultures, perform RNAi experiments, store important lines, and optimize microinjection procedures for transgenesis. -
Transcriptomic Profiling of Ca Transport Systems During
cells Article Transcriptomic Profiling of Ca2+ Transport Systems during the Formation of the Cerebral Cortex in Mice Alexandre Bouron Genetics and Chemogenomics Lab, Université Grenoble Alpes, CNRS, CEA, INSERM, Bâtiment C3, 17 rue des Martyrs, 38054 Grenoble, France; [email protected] Received: 29 June 2020; Accepted: 24 July 2020; Published: 29 July 2020 Abstract: Cytosolic calcium (Ca2+) transients control key neural processes, including neurogenesis, migration, the polarization and growth of neurons, and the establishment and maintenance of synaptic connections. They are thus involved in the development and formation of the neural system. In this study, a publicly available whole transcriptome sequencing (RNA-Seq) dataset was used to examine the expression of genes coding for putative plasma membrane and organellar Ca2+-transporting proteins (channels, pumps, exchangers, and transporters) during the formation of the cerebral cortex in mice. Four ages were considered: embryonic days 11 (E11), 13 (E13), and 17 (E17), and post-natal day 1 (PN1). This transcriptomic profiling was also combined with live-cell Ca2+ imaging recordings to assess the presence of functional Ca2+ transport systems in E13 neurons. The most important Ca2+ routes of the cortical wall at the onset of corticogenesis (E11–E13) were TACAN, GluK5, nAChR β2, Cav3.1, Orai3, transient receptor potential cation channel subfamily M member 7 (TRPM7) non-mitochondrial Na+/Ca2+ exchanger 2 (NCX2), and the connexins CX43/CX45/CX37. Hence, transient receptor potential cation channel mucolipin subfamily member 1 (TRPML1), transmembrane protein 165 (TMEM165), and Ca2+ “leak” channels are prominent intracellular Ca2+ pathways. The Ca2+ pumps sarco/endoplasmic reticulum Ca2+ ATPase 2 (SERCA2) and plasma membrane Ca2+ ATPase 1 (PMCA1) control the resting basal Ca2+ levels. -
Stem Cells and Ion Channels
Stem Cells International Stem Cells and Ion Channels Guest Editors: Stefan Liebau, Alexander Kleger, Michael Levin, and Shan Ping Yu Stem Cells and Ion Channels Stem Cells International Stem Cells and Ion Channels Guest Editors: Stefan Liebau, Alexander Kleger, Michael Levin, and Shan Ping Yu Copyright © 2013 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “Stem Cells International.” All articles are open access articles distributed under the Creative Com- mons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Nadire N. Ali, UK Joseph Itskovitz-Eldor, Israel Pranela Rameshwar, USA Anthony Atala, USA Pavla Jendelova, Czech Republic Hannele T. Ruohola-Baker, USA Nissim Benvenisty, Israel Arne Jensen, Germany D. S. Sakaguchi, USA Kenneth Boheler, USA Sue Kimber, UK Paul R. Sanberg, USA Dominique Bonnet, UK Mark D. Kirk, USA Paul T. Sharpe, UK B. Bunnell, USA Gary E. Lyons, USA Ashok Shetty, USA Kevin D. Bunting, USA Athanasios Mantalaris, UK Igor Slukvin, USA Richard K. Burt, USA Pilar Martin-Duque, Spain Ann Steele, USA Gerald A. Colvin, USA EvaMezey,USA Alexander Storch, Germany Stephen Dalton, USA Karim Nayernia, UK Marc Turner, UK Leonard M. Eisenberg, USA K. Sue O’Shea, USA Su-Chun Zhang, USA Marina Emborg, USA J. Parent, USA Weian Zhao, USA Josef Fulka, Czech Republic Bruno Peault, USA Joel C. Glover, Norway Stefan Przyborski, UK Contents Stem Cells and Ion Channels, Stefan Liebau, -
Ion Channels
UC Davis UC Davis Previously Published Works Title THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels. Permalink https://escholarship.org/uc/item/1442g5hg Journal British journal of pharmacology, 176 Suppl 1(S1) ISSN 0007-1188 Authors Alexander, Stephen PH Mathie, Alistair Peters, John A et al. Publication Date 2019-12-01 DOI 10.1111/bph.14749 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California S.P.H. Alexander et al. The Concise Guide to PHARMACOLOGY 2019/20: Ion channels. British Journal of Pharmacology (2019) 176, S142–S228 THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels Stephen PH Alexander1 , Alistair Mathie2 ,JohnAPeters3 , Emma L Veale2 , Jörg Striessnig4 , Eamonn Kelly5, Jane F Armstrong6 , Elena Faccenda6 ,SimonDHarding6 ,AdamJPawson6 , Joanna L Sharman6 , Christopher Southan6 , Jamie A Davies6 and CGTP Collaborators 1School of Life Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK 2Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK 3Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK 4Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, A-6020 Innsbruck, Austria 5School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK 6Centre for Discovery Brain Science, University of Edinburgh, Edinburgh, EH8 9XD, UK Abstract The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. -
The Regenerative Flatworm Macrostomum Lignano, a Model
Int. J. Dev. Biol. 62: 551-558 (2018) https://doi.org/10.1387/ijdb.180077eb www.intjdevbiol.com The regenerative flatwormMacrostomum lignano, a model organism with high experimental potential STIJN MOUTON#, JAKUB WUDARSKI#, MAGDA GRUDNIEWSKA and EUGENE BEREZIKOV* European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands ABSTRACT Understanding the process of regeneration has been one of the longstanding sci- entific aims, from a fundamental biological perspective, as well as within the applied context of regenerative medicine. Because regeneration competence varies greatly between organisms, it is essential to investigate different experimental animals. The free-living marine flatworm Macros- tomum lignano is a rising model organism for this type of research, and its power stems from a unique set of biological properties combined with amenability to experimental manipulation. The biological properties of interest include production of single-cell fertilized eggs, a transparent body, small size, short generation time, ease of culture, the presence of a pluripotent stem cell popula- tion, and a large regeneration competence. These features sparked the development of molecular tools and resources for this animal, including high-quality genome and transcriptome assemblies, gene knockdown, in situ hybridization, and transgenesis. Importantly, M. lignano is currently the only flatworm species for which transgenesis methods are established. This review summarizes