1
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Benham PM, Cicero C, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, King BL, Thomas WK, Kovach AI, Nachman MW, Bowie RCK. Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery. Genome Biol Evol 2024; 16:evae067. [PMID: 38566597 DOI: 10.1093/gbe/evae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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2
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Soos BL, Ballinger A, Weinstein M, Foreman H, Grampone J, Weafer S, Aylesworth C, King BL. Color-Flu Fluorescent Reporter Influenza A Viruses Allow for In Vivo Studies of Innate Immune Function in Zebrafish. Viruses 2024; 16:155. [PMID: 38275965 PMCID: PMC10818453 DOI: 10.3390/v16010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Influenza virus infection can cause severe respiratory disease and is estimated to cause millions of illnesses annually. Studies on the contribution of the innate immune response to influenza A virus (IAV) to viral pathogenesis may yield new antiviral strategies. Zebrafish larvae are useful models for studying the innate immune response to pathogens, including IAV, in vivo. Here, we demonstrate how Color-flu, four fluorescent IAV strains originally developed for mice, can be used to study the host response to infection by simultaneously monitoring infected cells, neutrophils, and macrophages in vivo. Using this model, we show how the angiotensin-converting enzyme inhibitor, ramipril, and mitophagy inhibitor, MDIVI-1, improved survival, decreased viral burden, and improved the respiratory burst response to IAV infection. The Color-flu zebrafish larvae model of IAV infection is complementary to other models where the dynamics of infection and the response of innate immune cells can be visualized in a transparent host in vivo.
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Affiliation(s)
- Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Alec Ballinger
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Mykayla Weinstein
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Haley Foreman
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Julianna Grampone
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Samuel Weafer
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Connor Aylesworth
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Benjamin L. King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
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3
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Soos BL, Ballinger A, Weinstein M, Foreman H, Grampone J, Weafer S, Aylesworth C, King BL. Multi-spectral Fluorescent Reporter Influenza A Viruses Allow for in vivo Studies of Innate Immune Function in Zebrafish. bioRxiv 2023:2023.10.31.564888. [PMID: 37961402 PMCID: PMC10634972 DOI: 10.1101/2023.10.31.564888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Influenza virus infection can cause severe respiratory disease and is estimated to cause millions of illnesses annually. Studies of the contribution of the innate immune response to influenza A virus (IAV) to viral pathogenesis may yield new antiviral strategies. Zebrafish larvae are useful models to study the innate immune response to pathogens, including IAV, in vivo. Here, we demonstrate how Color-flu, four fluorescent IAV strains originally developed for mice, can be used to study host-virus interactions by simultaneously monitoring virus particles, neutrophils, and macrophages in vivo. Using this model, we show how the angiotensin-converting enzyme inhibitor, ramipril, and mitophagy inhibitor, MDIVI-1, improved survival, decreased viral burden, and improved the respiratory burst response to IAV infection. The Color-flu zebrafish model of IAV infection is complementary to other models as it is the only model where interactions between virus particles and host cells in an intact vertebrate can be visualized in vivo.
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Affiliation(s)
- Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Alec Ballinger
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Mykayla Weinstein
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Haley Foreman
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Julianna Grampone
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Samuel Weafer
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Connor Aylesworth
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, USA
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4
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Sullivan C, de Oliveira S, Kikuchi K, King BL. Editorial: Zebrafish: An emerging model to study the cellular dynamics of inflammation in development, regeneration, and disease. Front Cell Dev Biol 2023; 10:1102381. [PMID: 36699004 PMCID: PMC9870062 DOI: 10.3389/fcell.2022.1102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Affiliation(s)
- Con Sullivan
- College of Arts and Sciences, University of Maine at Augusta, Bangor, ME, United States,*Correspondence: Con Sullivan,
| | | | - Kazu Kikuchi
- National Cerebral and Cardiovascular Center, Suita, Japan
| | - Benjamin L. King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States
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5
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Kimble M, Allers S, Campbell K, Chen C, Jackson LM, King BL, Silverbrand S, York G, Beard K. medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata. Bioinformatics 2022; 38:4589-4597. [PMID: 35960154 PMCID: PMC9524998 DOI: 10.1093/bioinformatics/btac556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/23/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software. RESULTS We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019). AVAILABILITY AND IMPLEMENTATION The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- M Kimble
- To whom correspondence should be addressed.
| | - S Allers
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - K Campbell
- School of Computing and Information Science, University of Maine, Orono, ME 04469, USA
| | - C Chen
- School of Computing and Information Science, University of Maine, Orono, ME 04469, USA
| | - L M Jackson
- Advanced Research Computing, Security and Information Management, University of Maine, Orono, ME 04469, USA,Maine EPSCoR, University of Maine, Orono, ME 04469, USA
| | - B L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - S Silverbrand
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - G York
- Environmental DNA Laboratory, Coordinated Operating Research Entities, University of Maine, Orono, ME 04469, USA
| | - K Beard
- School of Computing and Information Science, University of Maine, Orono, ME 04469, USA
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6
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Smith AM, Dykeman CA, King BL, Yin VP. Retraction Notice to: Modulation of TNFα Activity by the microRNA Let-7 Coordinates Zebrafish Heart Regeneration. iScience 2022; 25:104363. [PMID: 35774531 PMCID: PMC9236889 DOI: 10.1016/j.isci.2022.104363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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7
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Smith AM, Dykeman CA, King BL, Yin VP. Retraction Notice to: Modulation of TNFa Activity by the microRNA Let-7 Coordinates Zebrafish Heart Regeneration. iScience 2022; 25:104362. [PMID: 35774532 PMCID: PMC9236885 DOI: 10.1016/j.isci.2022.104362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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8
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Raut P, Weller SR, Obeng B, Soos BL, West BE, Potts CM, Sangroula S, Kinney MS, Burnell JE, King BL, Gosse JA, Hess ST. Cetylpyridinium chloride (CPC) reduces zebrafish mortality from influenza infection: Super-resolution microscopy reveals CPC interference with multiple protein interactions with phosphatidylinositol 4,5-bisphosphate in immune function. Toxicol Appl Pharmacol 2022; 440:115913. [PMID: 35149080 PMCID: PMC8824711 DOI: 10.1016/j.taap.2022.115913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 01/12/2023]
Abstract
The COVID-19 pandemic raises significance for a potential influenza therapeutic compound, cetylpyridinium chloride (CPC), which has been extensively used in personal care products as a positively-charged quaternary ammonium antibacterial agent. CPC is currently in clinical trials to assess its effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) morbidity. Two published studies have provided mouse and human data indicating that CPC may alleviate influenza infection, and here we show that CPC (0.1 μM, 1 h) reduces zebrafish mortality and viral load following influenza infection. However, CPC mechanisms of action upon viral-host cell interaction are currently unknown. We have utilized super-resolution fluorescence photoactivation localization microscopy to probe the mode of CPC action. Reduction in density of influenza viral protein hemagglutinin (HA) clusters is known to reduce influenza infectivity: here, we show that CPC (at non-cytotoxic doses, 5-10 μM) reduces HA density and number of HA molecules per cluster within the plasma membrane of NIH-3T3 mouse fibroblasts. HA is known to colocalize with the negatively-charged mammalian lipid phosphatidylinositol 4,5-bisphosphate (PIP2); here, we show that nanoscale co-localization of HA with the PIP2-binding Pleckstrin homology (PH) reporter in the plasma membrane is diminished by CPC. CPC also dramatically displaces the PIP2-binding protein myristoylated alanine-rich C-kinase substrate (MARCKS) from the plasma membrane of rat RBL-2H3 mast cells; this disruption of PIP2 is correlated with inhibition of mast cell degranulation. Together, these findings offer a PIP2-focused mechanism underlying CPC disruption of influenza and suggest potential pharmacological use of this drug as an influenza therapeutic to reduce global deaths from viral disease.
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Affiliation(s)
- Prakash Raut
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Sasha R Weller
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Bright Obeng
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Brandy L Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Bailey E West
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Christian M Potts
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Suraj Sangroula
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Marissa S Kinney
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - John E Burnell
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - Julie A Gosse
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA.
| | - Samuel T Hess
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA.
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Kilroy EA, Ignacz AC, Brann KL, Schaffer CE, Varney D, Alrowaished SS, Silknitter KJ, Miner JN, Almaghasilah A, Spellen TL, Lewis AD, Tilbury K, King BL, Kelley JB, Henry CA. Beneficial impacts of neuromuscular electrical stimulation on muscle structure and function in the zebrafish model of Duchenne muscular dystrophy. eLife 2022; 11:62760. [PMID: 35324428 PMCID: PMC8947762 DOI: 10.7554/elife.62760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/10/2022] [Indexed: 12/20/2022] Open
Abstract
Neuromuscular electrical stimulation (NMES) allows activation of muscle fibers in the absence of voluntary force generation. NMES could have the potential to promote muscle homeostasis in the context of muscle disease, but the impacts of NMES on diseased muscle are not well understood. We used the zebrafish Duchenne muscular dystrophy (dmd) mutant and a longitudinal design to elucidate the consequences of NMES on muscle health. We designed four neuromuscular stimulation paradigms loosely based on weightlifting regimens. Each paradigm differentially affected neuromuscular structure, function, and survival. Only endurance neuromuscular stimulation (eNMES) improved all outcome measures. We found that eNMES improves muscle and neuromuscular junction morphology, swimming, and survival. Heme oxygenase and integrin alpha7 are required for eNMES-mediated improvement. Our data indicate that neuromuscular stimulation can be beneficial, suggesting that the right type of activity may benefit patients with muscle disease.
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Affiliation(s)
- Elisabeth A Kilroy
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States
| | - Amanda C Ignacz
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States
| | - Kaylee L Brann
- School of Biology and Ecology, University of Maine, Orono, United States
| | - Claire E Schaffer
- School of Biology and Ecology, University of Maine, Orono, United States
| | - Devon Varney
- School of Biology and Ecology, University of Maine, Orono, United States
| | | | - Kodey J Silknitter
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States
| | - Jordan N Miner
- Department of Chemical and Biomedical Engineering, University of Maine, Orono, United States
| | - Ahmed Almaghasilah
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States
| | - Tashawna L Spellen
- School of Biology and Ecology, University of Maine, Orono, United States
| | - Alexandra D Lewis
- School of Biology and Ecology, University of Maine, Orono, United States
| | - Karissa Tilbury
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States.,Department of Chemical and Biomedical Engineering, University of Maine, Orono, United States
| | - Benjamin L King
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States.,Department of Molecular and Biomedical Sciences, University of Maine, Orono, United States
| | - Joshua B Kelley
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States.,Department of Molecular and Biomedical Sciences, University of Maine, Orono, United States
| | - Clarissa A Henry
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, United States.,School of Biology and Ecology, University of Maine, Orono, United States
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10
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Wilczek MP, Armstrong FJ, Geohegan RP, Mayberry CL, DuShane JK, King BL, Maginnis MS. The MAPK/ERK Pathway and the Role of DUSP1 in JCPyV Infection of Primary Astrocytes. Viruses 2021; 13:v13091834. [PMID: 34578413 PMCID: PMC8473072 DOI: 10.3390/v13091834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
JC polyomavirus (JCPyV) is a neuroinvasive pathogen causing a fatal, demyelinating disease of the central nervous system (CNS) known as progressive multifocal leukoencephalopathy (PML). Within the CNS, JCPyV predominately targets two cell types: oligodendrocytes and astrocytes. The underlying mechanisms of astrocytic infection are poorly understood, yet recent findings suggest critical differences in JCPyV infection of primary astrocytes compared to a widely studied immortalized cell model. RNA sequencing was performed in primary normal human astrocytes (NHAs) to analyze the transcriptomic profile that emerges during JCPyV infection. Through a comparative analysis, it was validated that JCPyV requires the mitogen-activated protein kinase, extracellular signal-regulated kinase (MAPK/ERK) pathway, and additionally requires the expression of dual-specificity phosphatases (DUSPs). Specifically, the expression of DUSP1 is needed to establish a successful infection in NHAs, yet this was not observed in an immortalized cell model of JCPyV infection. Additional analyses demonstrated immune activation uniquely observed in NHAs. These results support the hypothesis that DUSPs within the MAPK/ERK pathway impact viral infection and influence potential downstream targets and cellular pathways. Collectively, this research implicates DUSP1 in JCPyV infection of primary human astrocytes, and most importantly, further resolves the signaling events that lead to successful JCPyV infection in the CNS.
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Affiliation(s)
- Michael P. Wilczek
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (M.P.W.); (F.J.A.); (R.P.G.); (C.L.M.); (J.K.D.); (B.L.K.)
| | - Francesca J. Armstrong
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (M.P.W.); (F.J.A.); (R.P.G.); (C.L.M.); (J.K.D.); (B.L.K.)
| | - Remi P. Geohegan
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (M.P.W.); (F.J.A.); (R.P.G.); (C.L.M.); (J.K.D.); (B.L.K.)
| | - Colleen L. Mayberry
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (M.P.W.); (F.J.A.); (R.P.G.); (C.L.M.); (J.K.D.); (B.L.K.)
| | - Jeanne K. DuShane
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (M.P.W.); (F.J.A.); (R.P.G.); (C.L.M.); (J.K.D.); (B.L.K.)
| | - Benjamin L. King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (M.P.W.); (F.J.A.); (R.P.G.); (C.L.M.); (J.K.D.); (B.L.K.)
- Graduate School in Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Melissa S. Maginnis
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (M.P.W.); (F.J.A.); (R.P.G.); (C.L.M.); (J.K.D.); (B.L.K.)
- Graduate School in Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
- Correspondence:
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11
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Wood ZT, Wiegardt AK, Barton KL, Clark JD, Homola JJ, Olsen BJ, King BL, Kovach AI, Kinnison MT. Meta-analysis: Congruence of genomic and phenotypic differentiation across diverse natural study systems. Evol Appl 2021; 14:2189-2205. [PMID: 34603492 PMCID: PMC8477602 DOI: 10.1111/eva.13264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/17/2023] Open
Abstract
Linking genotype to phenotype is a primary goal for understanding the genomic underpinnings of evolution. However, little work has explored whether patterns of linked genomic and phenotypic differentiation are congruent across natural study systems and traits. Here, we investigate such patterns with a meta-analysis of studies examining population-level differentiation at subsets of loci and traits putatively responding to divergent selection. We show that across the 31 studies (88 natural population-level comparisons) we examined, there was a moderate (R 2 = 0.39) relationship between genomic differentiation (F ST ) and phenotypic differentiation (P ST ) for loci and traits putatively under selection. This quantitative relationship between P ST and F ST for loci under selection in diverse taxa provides broad context and cross-system predictions for genomic and phenotypic adaptation by natural selection in natural populations. This context may eventually allow for more precise ideas of what constitutes "strong" differentiation, predictions about the effect size of loci, comparisons of taxa evolving in nonparallel ways, and more. On the other hand, links between P ST and F ST within studies were very weak, suggesting that much work remains in linking genomic differentiation to phenotypic differentiation at specific phenotypes. We suggest that linking genotypes to specific phenotypes can be improved by correlating genomic and phenotypic differentiation across a spectrum of diverging populations within a taxon and including wide coverage of both genomes and phenomes.
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Affiliation(s)
- Zachary T. Wood
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
| | - Andrew K. Wiegardt
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Kayla L. Barton
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Jonathan D. Clark
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Brian J. Olsen
- Maine Center for Genetics in the EnvironmentOronoMEUSA
- Department of Wildlife, Fisheries, and Conservation BiologyUniversity of MaineOronoMEUSA
| | - Benjamin L. King
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Michael T. Kinnison
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
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12
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Sullivan C, Soos BL, Millard PJ, Kim CH, King BL. Modeling Virus-Induced Inflammation in Zebrafish: A Balance Between Infection Control and Excessive Inflammation. Front Immunol 2021; 12:636623. [PMID: 34025644 PMCID: PMC8138431 DOI: 10.3389/fimmu.2021.636623] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
The inflammatory response to viral infection in humans is a dynamic process with complex cell interactions that are governed by the immune system and influenced by both host and viral factors. Due to this complexity, the relative contributions of the virus and host factors are best studied in vivo using animal models. In this review, we describe how the zebrafish (Danio rerio) has been used as a powerful model to study host-virus interactions and inflammation by combining robust forward and reverse genetic tools with in vivo imaging of transparent embryos and larvae. The innate immune system has an essential role in the initial inflammatory response to viral infection. Focused studies of the innate immune response to viral infection are possible using the zebrafish model as there is a 4-6 week timeframe during development where they have a functional innate immune system dominated by neutrophils and macrophages. During this timeframe, zebrafish lack a functional adaptive immune system, so it is possible to study the innate immune response in isolation. Sequencing of the zebrafish genome has revealed significant genetic conservation with the human genome, and multiple studies have revealed both functional conservation of genes, including those critical to host cell infection and host cell inflammatory response. In addition to studying several fish viruses, zebrafish infection models have been developed for several human viruses, including influenza A, noroviruses, chikungunya, Zika, dengue, herpes simplex virus type 1, Sindbis, and hepatitis C virus. The development of these diverse viral infection models, coupled with the inherent strengths of the zebrafish model, particularly as it relates to our understanding of macrophage and neutrophil biology, offers opportunities for far more intensive studies aimed at understanding conserved host responses to viral infection. In this context, we review aspects relating to the evolution of innate immunity, including the evolution of viral pattern recognition receptors, interferons and interferon receptors, and non-coding RNAs.
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Affiliation(s)
- Con Sullivan
- College of Arts and Sciences, University of Maine at Augusta, Bangor, ME, United States
| | - Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States
| | - Paul J Millard
- Department of Environmental and Sustainable Engineering, University at Albany, Albany, NY, United States
| | - Carol H Kim
- Department of Biomedical Sciences, University at Albany, Albany, NY, United States.,Department of Biological Sciences, University at Albany, Albany, NY, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
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13
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Hartig EI, Zhu S, King BL, Coffman JA. Chronic cortisol exposure in early development leads to neuroendocrine dysregulation in adulthood. BMC Res Notes 2020; 13:366. [PMID: 32746894 PMCID: PMC7398215 DOI: 10.1186/s13104-020-05208-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 07/28/2020] [Indexed: 01/30/2023] Open
Abstract
Objective Chronic early life stress can affect development of the neuroendocrine stress system, leading to its persistent dysregulation and consequently increased disease risk in adulthood. One contributing factor is thought to be epigenetic programming in response to chronic cortisol exposure during early development. We have previously shown that zebrafish embryos treated chronically with cortisol develop into adults with constitutively elevated whole-body cortisol and aberrant immune gene expression. Here we further characterize that phenotype by assessing persistent effects of the treatment on cortisol tissue distribution and dynamics, chromatin accessibility, and activities of glucocorticoid-responsive regulatory genes klf9 and fkbp5. To that end cortisol levels in different tissues of fed and fasted adults were measured using ELISA, open chromatin in adult blood cells was mapped using ATAC-seq, and gene activity in adult blood and brain cells was measured using qRT-PCR. Results Adults derived from cortisol-treated embryos have elevated whole-body cortisol with aberrantly regulated tissue distribution and dynamics that correlate with differential activity of klf9 and fkbp5 in blood and brain.
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Affiliation(s)
| | - Shusen Zhu
- MDI Biological Laboratory, Salisbury Cove, Maine, USA
| | - Benjamin L King
- MDI Biological Laboratory, Salisbury Cove, Maine, USA.,Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.,Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - James A Coffman
- MDI Biological Laboratory, Salisbury Cove, Maine, USA. .,Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.
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14
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Smith AM, Dykeman CA, King BL, Yin VP. RETRACTED: Modulation of TNFα Activity by the microRNA Let-7 Coordinates Zebrafish Heart Regeneration. iScience 2019; 17:225-229. [PMID: 31307002 PMCID: PMC6629608 DOI: 10.1016/j.isci.2019.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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15
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Smith AM, Dykeman CA, King BL, Yin VP. Modulation of TNFα Activity by the microRNA Let-7 Coordinates Zebrafish Heart Regeneration. iScience 2019; 15:1-15. [PMID: 31026665 PMCID: PMC6482333 DOI: 10.1016/j.isci.2019.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/24/2022] Open
Abstract
The adult zebrafish is capable of regenerating heart muscle, resolving collagen tissue, and fully restoring heart function throughout its life. In this study, we show that the highly upregulated, epicardium-enriched microRNA let-7i functions in wound closure and cardiomyocyte proliferation. RNA sequencing experiments identified upregulated expression of members of the tumor necrosis factor (TNF) signaling pathway in the absence of let-7. Importantly, co-suppression of TNF and let-7 activity rescued epicardium migration and cardiomyocyte proliferation defects induced by depletion of let-7 alone. Sensitizing animals to low levels of TNF activity before injury culminated in repressed cardiomyocyte proliferation and wound closure defects, suggesting that levels of inflammation at the onset of injury are critical for heart regeneration. Our studies indicate that injury-induced reduction in TNF signaling by let-7 in the epicardium creates a pro-regenerative environment for cardiomyocyte proliferation during adult heart regeneration.
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Affiliation(s)
- Ashley M Smith
- Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Christina A Dykeman
- Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Benjamin L King
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA; Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Viravuth P Yin
- Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA.
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16
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Goodale BC, Hampton TH, Ford EN, Jackson CE, Shaw JR, Stanton BA, King BL. Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress. Aquat Toxicol 2019; 206:142-153. [PMID: 30476744 PMCID: PMC6298807 DOI: 10.1016/j.aquatox.2018.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model as a result of its ability to acclimate to rapid environmental changes and adapt to polluted habitats. MicroRNAs (miRNAs) are highly conserved small RNAs that regulate gene expression and play critical roles in stress responses in a variety of organisms. Global miRNA expression in killifish and the potential roles miRNA have in environmental acclimation have yet to be characterized. Accordingly, we profiled miRNA expression in killifish gill for the first time and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms. Killifish respond to large fluctuations in salinity with rapid changes in gene expression and protein trafficking to maintain osmotic balance, followed by a secondary phase of gene and protein expression changes that enable remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit gene expression responses in killifish gill, as well the ability of killifish to acclimate to a rapid increase in salinity. Thus, we examined the individual and combined effects of salinity and arsenic on miRNA expression in killifish gill. Using small RNA sequencing, we identified 270 miRNAs expressed in killifish, and found that miR-135b was differentially expressed in response to arsenic and at 24 h following transfer to salt water. Predicted targets of miR-135b are involved in ion transport, cell motility and migration, GTPase mediated signal transduction and organelle assembly. Consistent with previous studies of these two environmental stressors, we found a significant interaction (i.e., arsenic dependent salinity effect), whereby killifish exposed to arsenic exhibited an opposite response in miR-135b expression at 24 h post hyperosmotic challenge compared to controls. By examining mRNA expression of predicted miRNA targets during salinity acclimation and arsenic exposure, we found that miR-135b targets were significantly more likely to decrease during salinity acclimation than non-targets. Our identification of a significant interaction effect of arsenic and salinity on miR-135b expression supports the hypothesis that arsenic alters upstream regulators of stress response networks, which may adversely affect the killifish response to osmotic stress. The characterization of miRNAs in this ecotoxicological model will be a valuable resource for future studies investigating the role of miRNAs in response to environmental stress.
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Affiliation(s)
- Britton C Goodale
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States.
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Emily N Ford
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA 01119, United States
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, United States
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Hersh TA, Dimond AL, Ruth BA, Lupica NV, Bruce JC, Kelley JM, King BL, Lutton BV. A role for the CXCR4-CXCL12 axis in the little skate, Leucoraja erinacea. Am J Physiol Regul Integr Comp Physiol 2018; 315:R218-R229. [PMID: 29641231 PMCID: PMC6139610 DOI: 10.1152/ajpregu.00322.2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The interaction between C-X-C chemokine receptor type 4 (CXCR4) and its cognate ligand C-X-C motif chemokine ligand 12 (CXCL12) plays a critical role in regulating hematopoietic stem cell activation and subsequent cellular mobilization. Extensive studies of these genes have been conducted in mammals, but much less is known about the expression and function of CXCR4 and CXCL12 in non-mammalian vertebrates. In the present study, we identify simultaneous expression of CXCR4 and CXCL12 orthologs in the epigonal organ (the primary hematopoietic tissue) of the little skate, Leucoraja erinacea. Genetic and phylogenetic analyses were functionally supported by significant mobilization of leukocytes following administration of Plerixafor, a CXCR4 antagonist and clinically important drug. Our results provide evidence that, as in humans, Plerixafor disrupts CXCR4/CXCL12 binding in the little skate, facilitating release of leukocytes into the bloodstream. Our study illustrates the value of the little skate as a model organism, particularly in studies of hematopoiesis and potentially for preclinical research on hematological and vascular disorders.
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Affiliation(s)
- Taylor A Hersh
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - Alexandria L Dimond
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
| | - Brittany A Ruth
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
| | - Noah V Lupica
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - Jacob C Bruce
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - John M Kelley
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
- Beth Israel Deaconess Medical Center, Program in Placebo Studies, Harvard Medical School , Boston, Massachusetts
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, Maine
| | - Bram V Lutton
- Mount Desert Island Biological Laboratory , Bar Harbor, Maine
- School of Arts and Sciences, Endicott College , Beverly, Massachusetts
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18
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King BL, Rosenstein MC, Smith AM, Dykeman CA, Smith GA, Yin VP. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. NPJ Regen Med 2018; 3:10. [PMID: 29872545 PMCID: PMC5973935 DOI: 10.1038/s41536-018-0049-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 12/16/2022] Open
Abstract
Regeneration is an endogenous process of tissue repair that culminates in complete restoration of tissue and organ function. While regenerative capacity in mammals is limited to select tissues, lower vertebrates like zebrafish and salamanders are endowed with the capacity to regenerate entire limbs and most adult tissues, including heart muscle. Numerous profiling studies have been conducted using these research models in an effort to identify the genetic circuits that accompany tissue regeneration. Most of these studies, however, are confined to an individual injury model and/or research organism and focused primarily on protein encoding transcripts. Here we describe RegenDbase, a new database with the functionality to compare and contrast gene regulatory pathways within and across tissues and research models. RegenDbase combines pipelines that integrate analysis of noncoding RNAs in combination with protein encoding transcripts. We created RegenDbase with a newly generated comprehensive dataset for adult zebrafish heart regeneration combined with existing microarray and RNA-sequencing studies on multiple injured tissues. In this current release, we detail microRNA-mRNA regulatory circuits and the biological processes these interactions control during the early stages of heart regeneration. Moreover, we identify known and putative novel lncRNAs and identify their potential target genes based on proximity searches. We postulate that these candidate factors underscore robust regenerative capacity in lower vertebrates. RegenDbase provides a systems-level analysis of tissue regeneration genetic circuits across injury and animal models and addresses the growing need to understand how noncoding RNAs influence these changes in gene expression.
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Affiliation(s)
- Benjamin L. King
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
| | - Michael C. Rosenstein
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Present Address: RockStep Solutions, Portland, ME 04101 USA
| | - Ashley M. Smith
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Christina A. Dykeman
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Grace A. Smith
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- University of Maine Honors College, University of Maine, Orono, ME 04469 USA
| | - Viravuth P. Yin
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
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19
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Soundararajan R, Stearns TM, Czachor A, Fukumoto J, Turn C, Westermann-Clark E, Breitzig M, Tan L, Lockey RF, King BL, Kolliputi N. Global gene profiling of aging lungs in Atp8b1 mutant mice. Aging (Albany NY) 2017; 8:2232-2252. [PMID: 27689529 PMCID: PMC5076460 DOI: 10.18632/aging.101056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/10/2016] [Indexed: 12/18/2022]
Abstract
Objective Recent studies implicate cardiolipin oxidation in several age-related diseases. Atp8b1 encoding Type 4 P-type ATPases is a cardiolipin transporter. Mutation in Atp8b1 gene or inflammation of the lungs impairs the capacity of Atp8b1 to clear cardiolipin from lung fluid. However, the link between Atp8b1 mutation and age-related gene alteration is unknown. Therefore, we investigated how Atp8b1 mutation alters age-related genes. Methods We performed Affymetrix gene profiling of lungs isolated from young (7-9 wks, n=6) and aged (14 months, 14 M, n=6) C57BL/6 and Atp8b1 mutant mice. In addition, Ingenuity Pathway Analysis (IPA) was performed. Differentially expressed genes were validated by quantitative real-time PCR (qRT-PCR). Results Global transcriptome analysis revealed 532 differentially expressed genes in Atp8b1 lungs, 157 differentially expressed genes in C57BL/6 lungs, and 37 overlapping genes. IPA of age-related genes in Atp8b1 lungs showed enrichment of Xenobiotic metabolism and Nrf2-mediated signaling pathways. The increase in Adamts2 and Mmp13 transcripts in aged Atp8b1 lungs was validated by qRT-PCR. Similarly, the decrease in Col1a1 and increase in Cxcr6 transcripts was confirmed in both Atp8b1 mutant and C57BL/6 lungs. Conclusion Based on transcriptome profiling, our study indicates that Atp8b1 mutant mice may be susceptible to age-related lung diseases.
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Affiliation(s)
- Ramani Soundararajan
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Alexander Czachor
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Jutaro Fukumoto
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Christina Turn
- University of Florida College of Medicine, Gainesville, FL 32608, USA
| | - Emma Westermann-Clark
- Division of Allergy and Immunology, Department of Internal Medicine, James A Haley Veterans Hospital, Tampa, FL 33612, USA
| | - Mason Breitzig
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Lee Tan
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Richard F Lockey
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Narasaiah Kolliputi
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Sanford NN, Catalano PJ, Enzinger PC, King BL, Bueno R, Martin NE, Hong TS, Wo JY, Mamon HJ. A retrospective comparison of neoadjuvant chemoradiotherapy regimens for locally advanced esophageal cancer. Dis Esophagus 2017; 30:1-8. [PMID: 28475728 DOI: 10.1093/dote/dox025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/06/2017] [Indexed: 12/11/2022]
Abstract
Preoperative chemoradiotherapy (CRT) with carboplatin/paclitaxel has been shown to increase survival in patients with esophageal cancer, including gastroesophageal junction (GE) junction cancer, over surgery alone; however, there have been no studies comparing the different neoadjuvant CRT regimens. We retrospectively evaluated the long-term results of trimodality therapy for patients with locally advanced esophageal cancer treated on several chemotherapy regimens. Between 1999 and 2014, 215 patients with locally advanced esophageal cancer underwent neoadjuvant CRT followed by surgical resection. The median age was 62 years (range 21-84), 80.5% were men and 86% had adenocarcinoma. The following chemotherapy regimens were administered: cisplatin/5FU (14.9%), cisplatin/irinotecan (35.8%), carboplatin/paclitaxel (35.8%), and other (9.7%). The majority of patients (92.1%) received a radiation dose of 50.4 Gy. Predictors of toxicities and surgical complications were assessed using logistic regression. Overall survival (OS) and recurrence-free survival (RFS) were estimated using the Kaplan-Meier method and proportional hazards regression was used to model time-to-event outcomes. The median follow-up among surviving patients was 4.1 years (range 0.4,13). The median OS was 3.0 years from time of diagnosis and OS was 36.8% at 5 years. RFS was 34.9% at 5 years. After neoadjuvant CRT, 34.7% of patients achieved a pathologic complete response including 60.7% of squamous cell carcinoma patients and 18.4% of adenocarcinoma patients (P < 0.001) and 66% were downstaged. Of the variables examined, pathologic stage, preoperative baseline cardiac comorbidity, postoperative cardiac or pulmonary complications, and chemotherapy regimen were associated with OS. Using cisplatin and 5FU as the reference regimen, patients treated with carboplatin/paclitaxel had significantly improved OS (HR = 0.47, P = 0.017 after adjusting for surgery type, radiation modality, baseline cardiac comorbidity, and preoperative stage) with 5-year OS rate of 66%. The most common surgical complications were cardiac in 61 patients (28.5%) and pulmonary in 52 patients (24.3%). Cardiac complications were associated with age (OR 1.05, P = 0.007) and cardiac comorbidity (OR 2.6, P = 0.02) and pulmonary complications with female gender (OR 3.98, P < 0.001). Forty-four patients (20.5%) required readmission within 30 days of discharge, and readmission was associated with cardiac comorbidity (OR 2.7, P = 0.017). Three patients died within 30 days of surgery. We observed an association between neoadjuvant carboplatin/paclitaxel and improved overall survival that requires confirmation in a prospective randomized trial.
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Affiliation(s)
| | - P J Catalano
- Departments of Biostatistics and Computational Biology
| | | | - B L King
- Departments of Radiation Oncology
| | - R Bueno
- Thoracic Surgery, Brigham and Women's Hospital
| | | | - T S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, United States
| | - J Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, United States
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21
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Reid NM, Jackson CE, Gilbert D, Minx P, Montague MJ, Hampton TH, Helfrich LW, King BL, Nacci DE, Aluru N, Karchner SI, Colbourne JK, Hahn ME, Shaw JR, Oleksiak MF, Crawford DL, Warren WC, Whitehead A. The landscape of extreme genomic variation in the highly adaptable Atlantic killifish. Genome Biol Evol 2017; 9:659-676. [PMID: 28201664 PMCID: PMC5381573 DOI: 10.1093/gbe/evx023] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/30/2017] [Accepted: 02/04/2017] [Indexed: 12/22/2022] Open
Abstract
Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.
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Affiliation(s)
- Noah M Reid
- Department of Environmental Toxicology, University of California, Davis, CA 95616
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405
| | - Don Gilbert
- Biology Department, Indiana University, Bloomington, IN 47405
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108
| | - Michael J Montague
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Dartmouth College Geisel School of Medicine, Hanover, NH 03755
| | - Lily W Helfrich
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Benjamin L King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672
| | - Diane E Nacci
- US Environmental Protection Agency, Office of Research and Development, Narragansett, RI, 02882
| | - Neel Aluru
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - John K Colbourne
- School of Biosciences, University of Birmingham, United Kingdom, B15 2TT
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405
| | - Marjorie F Oleksiak
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149
| | - Douglas L Crawford
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis, CA 95616
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Frevel M, King BL, Kolb DS, Boswell RP, Shoemaker RS, Janicek JC, Cole RC, Poole HM, Longhofer SL. Clodronate disodium for treatment of clinical signs of navicular disease – a double-blinded placebo-controlled clinical trial. PFERDEHEILKUNDE 2017. [DOI: 10.21836/pem20170308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Affiliation(s)
- Benjamin L King
- MDI Biological Laboratory, Kathryn W Davis Center for Regenerative Biology & Medicine, Salisbury Cove, ME 04672, USA
| | - Viravuth P Yin
- MDI Biological Laboratory, Kathryn W Davis Center for Regenerative Biology & Medicine, Salisbury Cove, ME 04672, USA
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Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database. Environ Health Perspect 2016; 124:1592-1599. [PMID: 27170236 PMCID: PMC5047769 DOI: 10.1289/ehp174] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/11/2016] [Accepted: 04/26/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Exposure science studies the interactions and outcomes between environmental stressors and human or ecological receptors. To augment its role in understanding human health and the exposome, we aimed to centralize and integrate exposure science data into the broader biological framework of the Comparative Toxicogenomics Database (CTD), a public resource that promotes understanding of environmental chemicals and their effects on human health. OBJECTIVES We integrated exposure data within the CTD to provide a centralized, freely available resource that facilitates identification of connections between real-world exposures, chemicals, genes/proteins, diseases, biological processes, and molecular pathways. METHODS We developed a manual curation paradigm that captures exposure data from the scientific literature using controlled vocabularies and free text within the context of four primary exposure concepts: stressor, receptor, exposure event, and exposure outcome. Using data from the Agricultural Health Study, we have illustrated the benefits of both centralization and integration of exposure information with CTD core data. RESULTS We have described our curation process, demonstrated how exposure data can be accessed and analyzed in the CTD, and shown how this integration provides a broad biological context for exposure data to promote mechanistic understanding of environmental influences on human health. CONCLUSIONS Curation and integration of exposure data within the CTD provides researchers with new opportunities to correlate exposures with human health outcomes, to identify underlying potential molecular mechanisms, and to improve understanding about the exposome. CITATION Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. 2016. Advancing exposure science through chemical data curation and integration in the Comparative Toxicogenomics Database. Environ Health Perspect 124:1592-1599; http://dx.doi.org/10.1289/EHP174.
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Affiliation(s)
- Cynthia J. Grondin
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Address correspondence to C.J. Grondin, North Carolina State University, Department of Biological Sciences, Campus Box 7617, Raleigh, NC 27695-7617 USA. Telephone: (919) 515-1509. E-mail:
| | - Allan Peter Davis
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Thomas C. Wiegers
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Benjamin L. King
- Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA
| | - Jolene A. Wiegers
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - David M. Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Jane A. Hoppin
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Carolyn J. Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
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25
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Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res 2016; 45:D972-D978. [PMID: 27651457 PMCID: PMC5210612 DOI: 10.1093/nar/gkw838] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/09/2016] [Indexed: 12/19/2022] Open
Abstract
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between chemicals and gene products, and their relationships to diseases. Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate expanded networks and predict novel associations. Today, core CTD includes more than 30.5 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, Gene Ontology (GO) annotations, pathways, and gene interaction modules. In this update, we report a 33% increase in our core data content since 2015, describe our new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduce a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies). These advancements centralize and contextualize real-world chemical exposures with molecular pathways to help scientists generate testable hypotheses in an effort to understand the etiology and mechanisms underlying environmentally influenced diseases.
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Affiliation(s)
- Allan Peter Davis
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Cynthia J Grondin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Robin J Johnson
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Daniela Sciaky
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Benjamin L King
- Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Roy McMorran
- Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Jolene Wiegers
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas C Wiegers
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Carolyn J Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
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Abstract
Chronic early-life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid-induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on both larvae and adults. Treated larvae had elevated whole-body cortisol and glucocorticoid signaling, and upregulated genes associated with defense response and immune system processes. In adulthood the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol, and constitutively mis-expressed genes involved in defense response and its regulation. Adults derived from cortisol-treated embryos displayed defective tailfin regeneration, heightened basal expression of pro-inflammatory genes, and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro-inflammatory adult phenotype, at the expense of immunoregulation and somatic regenerative capacity.
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Affiliation(s)
- Ellen I Hartig
- MDI Biological Laboratory, Kathryn W. Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, 04672, USA
| | - Shusen Zhu
- MDI Biological Laboratory, Kathryn W. Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, 04672, USA
| | - Benjamin L King
- MDI Biological Laboratory, Kathryn W. Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, 04672, USA
| | - James A Coffman
- MDI Biological Laboratory, Kathryn W. Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, 04672, USA
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27
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King BL, Yin VP. A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration. PLoS One 2016; 11:e0157106. [PMID: 27355827 PMCID: PMC4927183 DOI: 10.1371/journal.pone.0157106] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/24/2016] [Indexed: 01/25/2023] Open
Abstract
Background Although regenerative capacity is evident throughout the animal kingdom, it is not equally distributed throughout evolution. For instance, complex limb/appendage regeneration is muted in mammals but enhanced in amphibians and teleosts. The defining characteristic of limb/appendage regenerative systems is the formation of a dedifferentiated tissue, termed blastema, which serves as the progenitor reservoir for regenerating tissues. In order to identify a genetic signature that accompanies blastema formation, we employ next-generation sequencing to identify shared, differentially regulated mRNAs and noncoding RNAs in three different, highly regenerative animal systems: zebrafish caudal fins, bichir pectoral fins and axolotl forelimbs. Results These studies identified a core group of 5 microRNAs (miRNAs) that were commonly upregulated and 5 miRNAs that were commonly downregulated, as well as 4 novel tRNAs fragments with sequences conserved with humans. To understand the potential function of these miRNAs, we built a network of 1,550 commonly differentially expressed mRNAs that had functional relationships to 11 orthologous blastema-associated genes. As miR-21 was the most highly upregulated and most highly expressed miRNA in all three models, we validated the expression of known target genes, including the tumor suppressor, pdcd4, and TGFβ receptor subunit, tgfbr2 and novel putative target genes such as the anti-apoptotic factor, bcl2l13, Choline kinase alpha, chka and the regulator of G-protein signaling, rgs5. Conclusions Our extensive analysis of RNA-seq transcriptome profiling studies in three regenerative animal models, that diverged in evolution ~420 million years ago, reveals a common miRNA-regulated genetic network of blastema genes. These comparative studies extend our current understanding of limb/appendage regeneration by identifying previously unassociated blastema genes and the extensive regulation by miRNAs, which could serve as a foundation for future functional studies to examine the process of natural cellular reprogramming in an injury context.
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Affiliation(s)
- Benjamin L. King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island, Biological Laboratory, Salisbury Cove, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, United States of America
| | - Viravuth P. Yin
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island, Biological Laboratory, Salisbury Cove, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, United States of America
- * E-mail:
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28
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Lee EC, Kim H, Ditano J, Manion D, King BL, Strange K. Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis. PLoS One 2016; 11:e0154156. [PMID: 27111894 PMCID: PMC4844114 DOI: 10.1371/journal.pone.0154156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 04/09/2016] [Indexed: 11/19/2022] Open
Abstract
Protein function is controlled by the cellular proteostasis network. Proteostasis is energetically costly and those costs must be balanced with the energy needs of other physiological functions. Hypertonic stress causes widespread protein damage in C. elegans. Suppression and management of protein damage is essential for optimal survival under hypertonic conditions. ASH chemosensory neurons allow C. elegans to detect and avoid strongly hypertonic environments. We demonstrate that mutations in osm-9 and osm-12 that disrupt ASH mediated hypertonic avoidance behavior or genetic ablation of ASH neurons are associated with enhanced survival during hypertonic stress. Improved survival is not due to altered systemic volume homeostasis or organic osmolyte accumulation. Instead, we find that osm-9(ok1677) mutant and osm-9(RNAi) worms exhibit reductions in hypertonicity induced protein damage in non-neuronal cells suggesting that enhanced proteostasis capacity may account for improved hypertonic stress resistance in worms with defects in osmotic avoidance behavior. RNA-seq analysis revealed that genes that play roles in managing protein damage are upregulated in osm-9(ok1677) worms. Our findings are consistent with a growing body of work demonstrating that intercellular communication between neuronal and non-neuronal cells plays a critical role in integrating cellular stress resistance with other organismal physiological demands and associated energy costs.
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Affiliation(s)
- Elaine C. Lee
- MDI Biological Laboratory, Salisbury Cove, ME, 04672, United States of America
- University of Connecticut, Storrs, CT, 06269, United States of America
| | - Heejung Kim
- MDI Biological Laboratory, Salisbury Cove, ME, 04672, United States of America
| | - Jennifer Ditano
- MDI Biological Laboratory, Salisbury Cove, ME, 04672, United States of America
| | - Dacie Manion
- MDI Biological Laboratory, Salisbury Cove, ME, 04672, United States of America
| | - Benjamin L. King
- MDI Biological Laboratory, Salisbury Cove, ME, 04672, United States of America
| | - Kevin Strange
- MDI Biological Laboratory, Salisbury Cove, ME, 04672, United States of America
- * E-mail:
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29
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Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol Evol 2016; 8:330-44. [PMID: 26733575 PMCID: PMC4779606 DOI: 10.1093/gbe/evv261] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.
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Affiliation(s)
- James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Ireland School of Earth Sciences, University of Bristol, United Kingdom
| | - Mario Dos Reis
- Department of Genetics, Evolution and Environment, University College London, United Kingdom School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Siavash Mirarab
- Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego
| | - Raymond J Moran
- Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds
| | - Sean Parker
- School of Earth Sciences, University of Bristol, United Kingdom
| | | | - Benjamin L King
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds
| | - Robert J Asher
- Museum of Zoology, University of Cambridge, United Kingdom
| | - Tandy Warnow
- Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, United Kingdom School of Biological Sciences, University of Bristol, United Kingdom
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30
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King BL, Shi LF, Kao P, Clusin WT. Calcium activated K⁺ channels in the electroreceptor of the skate confirmed by cloning. Details of subunits and splicing. Gene 2015; 578:63-73. [PMID: 26687710 DOI: 10.1016/j.gene.2015.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/07/2015] [Indexed: 12/22/2022]
Abstract
Elasmobranchs detect small potentials using excitable cells of the ampulla of Lorenzini which have calcium-activated K(+) channels, first described in 1974. A distinctive feature of the outward current in voltage clamped ampullae is its apparent insensitivity to voltage. The sequence of a BK channel α isoform expressed in the ampulla of the skate was characterized. A signal peptide is present at the beginning of the gene. When compared to human isoform 1 (the canonical sequence), the largest difference was absence of a 59 amino acid region from the S8-S9 intra-cellular linker that contains the strex regulatory domain. The ampulla isoform was also compared with the isoform predicted in late skate embryos where strex was also absent. The BK voltage sensors were conserved in both skate isoforms. Differences between the skate and human BK channel included alternative splicing. Alternative splicing occurs at seven previously defined sites that are characteristic for BK channels in general and hair cells in particular. Skate BK sequences were highly similar to the Australian ghost shark and several other vertebrate species. Based on alignment of known BK sequences with the skate genome and transcriptome, there are at least two isoforms of Kcnma1α expressed in the skate. One of the β subunits (β4), which is known to decrease voltage sensitivity, was also identified in the skate genome and transcriptome and in the ampulla. These studies advance our knowledge of BK channels and suggest further studies in the ampulla and other excitable tissues.
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Affiliation(s)
- Benjamin L King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, United States
| | - Ling Fang Shi
- Department of Medicine, Stanford University Medical School, Stanford, CA 94305, United States
| | - Peter Kao
- Department of Medicine, Stanford University Medical School, Stanford, CA 94305, United States
| | - William T Clusin
- Department of Medicine, Stanford University Medical School, Stanford, CA 94305, United States.
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31
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Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet 2015; 49:213-42. [PMID: 26473382 DOI: 10.1146/annurev-genet-120213-092023] [Citation(s) in RCA: 361] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database--MirGeneDB ( http://mirgenedb.org )--to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.
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Affiliation(s)
- Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research
| | - Tyler Billipp
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
| | - Liam E Peck
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | | | - James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland.,School of Earth Sciences, University of Bristol, BS8 1TQ Bristol, United Kingdom
| | - Benjamin L King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672
| | - James M Newcomb
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | - Lorenzo F Sempere
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research.,Department of Gastroenterological Surgery.,Institute of Clinical Medicine
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424 Oslo, Norway.,Department of Informatics, University of Oslo, Blindern, N-0318 Oslo, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
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32
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Hanke N, King BL, Vaske B, Haller H, Schiffer M. A Fluorescence-Based Assay for Proteinuria Screening in Larval Zebrafish (Danio rerio). Zebrafish 2015; 12:372-6. [PMID: 26125680 DOI: 10.1089/zeb.2015.1093] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Analysis of genes compromising the glomerular filtration barrier in rodent models using transgenic or knockdown approaches is time- and resource-consuming and often leads to unsatisfactory results. Therefore, it would be beneficial to have a selection tool indicating that your gene of interest is in fact associated with proteinuria. Zebrafish (Danio rerio) is a rapid screening tool to study effects in glomerular filtration barrier integrity after genetic manipulation. We use either injection of high-molecular-weight dextrans or a transgenic fluorescent fish line [Tg(l-fabp:DBP:EGFP)] expressing a vitamin D-binding protein fused with eGFP for indirect detection of proteinuria. A loss of high-molecular-weight proteins from the circulation of the fish into the urine can be identified by monitoring fluorescence intensity in the zebrafish eye. Paired with an optimized analysis method, this assay provides an effective screening solution to detect filtration barrier damage with proteinuria before moving to a mammalian system.
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Affiliation(s)
- Nils Hanke
- 1 Division of Nephrology, Hannover Medical School , Hannover, Germany
| | - Benjamin L King
- 2 Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - Bernhard Vaske
- 3 Division of Biometry, Hannover Medical School , Hannover, Germany
| | - Hermann Haller
- 1 Division of Nephrology, Hannover Medical School , Hannover, Germany .,2 Mount Desert Island Biological Laboratory , Bar Harbor, Maine
| | - Mario Schiffer
- 1 Division of Nephrology, Hannover Medical School , Hannover, Germany .,2 Mount Desert Island Biological Laboratory , Bar Harbor, Maine
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33
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Carrier TJ, King BL, Coffman JA. Gene Expression Changes Associated With the Developmental Plasticity of Sea Urchin Larvae in Response to Food Availability. Biol Bull 2015; 228:171-80. [PMID: 26124444 PMCID: PMC4706744 DOI: 10.1086/bblv228n3p171] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Planktotrophic sea urchin larvae are developmentally plastic: in response to food scarcity, development of the juvenile rudiment is suspended and larvae instead develop elongated arms, thus increasing feeding capacity and extending larval life. Here, data are presented on the effect of different feeding regimes on gene expression in larvae of the green sea urchin Strongylocentrotus droebachiensis. These data indicate that during periods of starvation, larvae down-regulate genes involved in growth and metabolic activity while up-regulating genes involved in lipid transport, environmental sensing, and defense. Additionally, we show that starvation increases FoxO activity and that in well-fed larvae rapamycin treatment impedes rudiment growth, indicating that the latter requires TOR activity. These results suggest that the developmental plasticity of echinoplutei is regulated by genes known to control aging and longevity in other animals.
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Affiliation(s)
- Tyler J Carrier
- MDI Biological Laboratory, Salisbury Cove, Maine 04672; and School of Marine Sciences, University of Maine, Orono, Maine 04469
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34
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Shaw JR, Hampton TH, King BL, Whitehead A, Galvez F, Gross RH, Keith N, Notch E, Jung D, Glaholt SP, Chen CY, Colbourne JK, Stanton BA. Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes. Mol Biol Evol 2014; 31:3002-15. [PMID: 25158801 PMCID: PMC4209136 DOI: 10.1093/molbev/msu241] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Many organisms survive fluctuating and extreme environmental conditions by manifesting multiple distinct phenotypes during adulthood by means of developmental processes that enable phenotypic plasticity. We report on the discovery of putative plasticity-enabling genes that are involved in transforming the gill of the euryhaline teleost fish, Fundulus heteroclitus, from its freshwater to its seawater gill-type, a process that alters both morphology and function. Gene expression that normally enables osmotic plasticity is inhibited by arsenic. Gene sets defined by antagonistic interactions between arsenic and salinity show reduced transcriptional variation among individual fish, suggesting unusually accurate and precise regulatory control of these genes, consistent with the hypothesis that they participate in a canalized developmental response. We observe that natural selection acts to preserve canalized gene expression in populations of killifish that are most tolerant to abrupt salinity change and that these populations show the least variability in their transcription of genes enabling plasticity of the gill. We found that genes participating in this highly canalized and conserved plasticity-enabling response had significantly fewer and less complex associations with transcriptional regulators than genes that respond only to arsenic or salinity. Collectively these findings, which are drawn from the relationships between environmental challenge, plasticity, and canalization among populations, suggest that the selective processes that facilitate phenotypic plasticity do so by targeting the regulatory networks that gives rise to the response. These findings also provide a generalized, conceptual framework of how genes might interact with the environment and evolve toward the development of plastic traits.
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Affiliation(s)
- Joseph R Shaw
- The School of Public and Environmental Affairs, Indiana University, Bloomington The Center for Genomics and Bioinformatics, Indiana University, Bloomington The Mount Desert Island Biological Laboratory, Salisbury Cove, ME Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Thomas H Hampton
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, United Kingdom Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Benjamin L King
- The Mount Desert Island Biological Laboratory, Salisbury Cove, ME
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis
| | - Fernando Galvez
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Robert H Gross
- Department of Biological Sciences, Dartmouth College, Hanover, NH
| | - Nathan Keith
- The School of Public and Environmental Affairs, Indiana University, Bloomington
| | - Emily Notch
- The Mount Desert Island Biological Laboratory, Salisbury Cove, ME Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Dawoon Jung
- The Mount Desert Island Biological Laboratory, Salisbury Cove, ME Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Stephen P Glaholt
- The School of Public and Environmental Affairs, Indiana University, Bloomington
| | - Celia Y Chen
- Department of Biological Sciences, Dartmouth College, Hanover, NH
| | - John K Colbourne
- The Center for Genomics and Bioinformatics, Indiana University, Bloomington The Mount Desert Island Biological Laboratory, Salisbury Cove, ME Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Bruce A Stanton
- The Mount Desert Island Biological Laboratory, Salisbury Cove, ME Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH
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Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Res 2014; 43:D914-20. [PMID: 25326323 PMCID: PMC4384013 DOI: 10.1093/nar/gku935] [Citation(s) in RCA: 284] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ten years ago, the Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) was developed out of a need to formalize, harmonize and centralize the information on numerous genes and proteins responding to environmental toxic agents across diverse species. CTD's initial approach was to facilitate comparisons of nucleotide and protein sequences of toxicologically significant genes by curating these sequences and electronically annotating them with chemical terms from their associated references. Since then, however, CTD has vastly expanded its scope to robustly represent a triad of chemical–gene, chemical–disease and gene–disease interactions that are manually curated from the scientific literature by professional biocurators using controlled vocabularies, ontologies and structured notation. Today, CTD includes 24 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, Gene Ontology annotations, pathways and interaction modules. In this 10th year anniversary update, we outline the evolution of CTD, including our increased data content, new ‘Pathway View’ visualization tool, enhanced curation practices, pilot chemical–phenotype results and impending exposure data set. The prototype database originally described in our first report has transformed into a sophisticated resource used actively today to help scientists develop and test hypotheses about the etiologies of environmentally influenced diseases.
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Affiliation(s)
- Allan Peter Davis
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Cynthia J Grondin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Kelley Lennon-Hopkins
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | | | - Daniela Sciaky
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Benjamin L King
- Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Thomas C Wiegers
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Carolyn J Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
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Wyffels J, King BL, Vincent J, Chen C, Wu CH, Polson SW. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. F1000Res 2014; 3:191. [PMID: 25309735 PMCID: PMC4184313 DOI: 10.12688/f1000research.4996.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2014] [Indexed: 12/02/2022] Open
Abstract
Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods) and actinoptergii (ray-finned fish including teleosts) taxa, but limited for chondrichthyan fishes. In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish,
Leucoraja erinacea, the little skate. SkateBase (
http://skatebase.org) serves as the skate genome project portal linking data, research tools, and teaching resources.
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Affiliation(s)
- Jennifer Wyffels
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Benjamin L King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, 04672, USA
| | - James Vincent
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Chuming Chen
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Cathy H Wu
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Shawn W Polson
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
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37
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Field DJ, Gauthier JA, King BL, Pisani D, Lyson TR, Peterson KJ. Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles. Evol Dev 2014; 16:189-96. [PMID: 24798503 PMCID: PMC4215941 DOI: 10.1111/ede.12081] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using microRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister-relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super-alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.
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Affiliation(s)
- Daniel J. Field
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Benjamin L. King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Queen’s Road, Bristol BS8 1RJ, United Kingdom and School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, United Kingdom
| | - Tyler R. Lyson
- Smithsonian National Museum of Natural History, 10 Street and Constitution Avenue, Washington, DC 20013, USA
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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Davis AP, Wiegers TC, Roberts PM, King BL, Lay JM, Lennon-Hopkins K, Sciaky D, Johnson R, Keating H, Greene N, Hernandez R, McConnell KJ, Enayetallah AE, Mattingly CJ. A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions. Database (Oxford) 2013; 2013:bat080. [PMID: 24288140 PMCID: PMC3842776 DOI: 10.1093/database/bat080] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Improving the prediction of chemical toxicity is a goal common to both environmental health research and pharmaceutical drug development. To improve safety detection assays, it is critical to have a reference set of molecules with well-defined toxicity annotations for training and validation purposes. Here, we describe a collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88 629 articles relating over 1 200 pharmaceutical drugs to their potential involvement in cardiovascular, neurological, renal and hepatic toxicity. In 1 year, CTD biocurators curated 2 54 173 toxicogenomic interactions (1 52 173 chemical–disease, 58 572 chemical–gene, 5 345 gene–disease and 38 083 phenotype interactions). All chemical–gene–disease interactions are fully integrated with public CTD, and phenotype interactions can be downloaded. We describe Pfizer’s text-mining process to collate the articles, and CTD’s curation strategy, performance metrics, enhanced data content and new module to curate phenotype information. As well, we show how data integration can connect phenotypes to diseases. This curation can be leveraged for information about toxic endpoints important to drug safety and help develop testable hypotheses for drug–disease events. The availability of these detailed, contextualized, high-quality annotations curated from seven decades’ worth of the scientific literature should help facilitate new mechanistic screening assays for pharmaceutical compound survival. This unique partnership demonstrates the importance of resource sharing and collaboration between public and private entities and underscores the complementary needs of the environmental health science and pharmaceutical communities. Database URL: http://ctdbase.org/
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Affiliation(s)
- Allan Peter Davis
- Department of Biological Sciences, 3510 Thomas Hall, North Carolina State University, Raleigh, NC 27695-7617, USA, Computational Sciences Center of Emphasis, 200 Cambridgepark Drive, Pfizer Inc., Cambridge, MA 02139, USA, Department of Bioinformatics, P.O. Box 35, Old Bar Harbor Road, MDI Biological Laboratory, Salisbury Cove, ME 04672, USA, Compound Safety Prediction, MS 8118-B3, Eastern Point Road, Pfizer Inc., Groton, CT 06340, USA, Computational Sciences Center of Emphasis, Pfizer Inc., Ramsgate Road, Sandwich, Kent CT13 9NJ, UK, Computational Sciences Center of Emphasis, 558 Eastern Point Road, Pfizer Inc., Groton, CT 06340, USA and Drug Safety Research and Development, 558 Eastern Point Road, Pfizer Inc., Groton, CT 06340, USA
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Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, Pisani D, Donoghue PCJ, Peterson KJ. miRNAs: small genes with big potential in metazoan phylogenetics. Mol Biol Evol 2013; 30:2369-82. [PMID: 23913097 DOI: 10.1093/molbev/mst133] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
microRNAs (miRNAs) are a key component of gene regulatory networks and have been implicated in the regulation of virtually every biological process found in multicellular eukaryotes. What makes them interesting from a phylogenetic perspective is the high conservation of primary sequence between taxa, their accrual in metazoan genomes through evolutionary time, and the rarity of secondary loss in most metazoan taxa. Despite these properties, the use of miRNAs as phylogenetic markers has not yet been discussed within a clear conceptual framework. Here we highlight five properties of miRNAs that underlie their utility in phylogenetics: 1) The processes of miRNA biogenesis enable the identification of novel miRNAs without prior knowledge of sequence; 2) The continuous addition of miRNA families to metazoan genomes through evolutionary time; 3) The low level of secondary gene loss in most metazoan taxa; 4) The low substitution rate in the mature miRNA sequence; and 5) The small probability of convergent evolution of two miRNAs. Phylogenetic analyses using both Bayesian and parsimony methods on a eumetazoan miRNA data set highlight the potential of miRNAs to become an invaluable new tool, especially when used as an additional line of evidence, to resolve previously intractable nodes within the tree of life.
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Affiliation(s)
- James E Tarver
- Department of Biological Sciences, Dartmouth College, Hanover, NH
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Peterson KJ, Su YH, Arnone MI, Swalla B, King BL. MicroRNAs support the monophyly of enteropneust hemichordates. J Exp Zool B Mol Dev Evol 2013; 320:368-74. [PMID: 23703796 DOI: 10.1002/jez.b.22510] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/28/2013] [Accepted: 04/06/2013] [Indexed: 01/24/2023]
Abstract
Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic interrelationships amongst the constituent taxa. Although the monophyly and interrelationships among the three principal groups-the chordates, the echinoderms, and the hemichordates-are well established, as are the internal relationships among the echinoderm and chordate taxa, the interrelationships among the principal groups of hemichordates-the harrimaniid enteropneusts, the ptychoderid enteropneusts, and the pterobranchs-remain unresolved. Depending on the study some find enteropneusts paraphyletic with pterobranchs (e.g., Cephalodiscus) more closely related to the harrimaniid enteropneusts (e.g., Saccoglossus) than either are to the ptychoderid enteropneusts (e.g., Ptychodera), whereas other studies support a monophyletic Enteropneusta. To try and resolve between these two competing hypotheses, we turned to microRNAs, small ∼22 nt non-coding RNA genes that have been shown to shed insight into particularly difficult phylogenetic questions. Using deep sequencing we characterized the small RNA repertoires of two hemichordate species, Cephalodiscus hodgsoni and Ptychodera flava, and the crinoid echinoderm Antedon mediterranea, and combined our results with the described complements of the hemichordate Saccoglossus kowalevskii, the sea urchin Strongylocentrotus purpuratus, and the starfish Patiria miniata. Our data unambiguously support the monophyly of Enteropneusts as S. kowalevskii shares 12 miRNA sequences with P. flava that are not present in the C. hodgsoni or A. mediterranea libraries, and have never been reported from another metazoan taxon. Thus, these data resolve the phylogenetic position of pterobranchs, ultimately allowing for a better understanding of body plan evolution throughout the deuterostomes.
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Affiliation(s)
- Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ. Ranking transitive chemical-disease inferences using local network topology in the comparative toxicogenomics database. PLoS One 2012; 7:e46524. [PMID: 23144783 PMCID: PMC3492369 DOI: 10.1371/journal.pone.0046524] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 09/05/2012] [Indexed: 11/19/2022] Open
Abstract
Exposure to chemicals in the environment is believed to play a critical role in the etiology of many human diseases. To enhance understanding about environmental effects on human health, the Comparative Toxicogenomics Database (CTD; http://ctdbase.org) provides unique curated data that enable development of novel hypotheses about the relationships between chemicals and diseases. CTD biocurators read the literature and curate direct relationships between chemicals-genes, genes-diseases, and chemicals-diseases. These direct relationships are then computationally integrated to create additional inferred relationships; for example, a direct chemical-gene statement can be combined with a direct gene-disease statement to generate a chemical-disease inference (inferred via the shared gene). In CTD, the number of inferences has increased exponentially as the number of direct chemical, gene and disease interactions has grown. To help users navigate and prioritize these inferences for hypothesis development, we implemented a statistic to score and rank them based on the topology of the local network consisting of the chemical, disease and each of the genes used to make an inference. In this network, chemicals, diseases and genes are nodes connected by edges representing the curated interactions. Like other biological networks, node connectivity is an important consideration when evaluating the CTD network, as the connectivity of nodes follows the power-law distribution. Topological methods reduce the influence of highly connected nodes that are present in biological networks. We evaluated published methods that used local network topology to determine the reliability of protein-protein interactions derived from high-throughput assays. We developed a new metric that combines and weights two of these methods and uniquely takes into account the number of common neighbors and the connectivity of each entity involved. We present several CTD inferences as case studies to demonstrate the value of this metric and the biological relevance of the inferences.
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Affiliation(s)
- Benjamin L. King
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, United States of America
| | - Allan Peter Davis
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Michael C. Rosenstein
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, United States of America
| | - Thomas C. Wiegers
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Carolyn J. Mattingly
- North Carolina State University, Raleigh, North Carolina, United States of America
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Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res 2012; 41:D1104-14. [PMID: 23093600 PMCID: PMC3531134 DOI: 10.1093/nar/gks994] [Citation(s) in RCA: 287] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types. CTD now contains over 15 million toxicogenomic relationships. To navigate this sea of data, we added several new features, including DiseaseComps (which finds comparable diseases that share toxicogenomic profiles), statistical scoring for inferred gene-disease and pathway-chemical relationships, filtering options for several tools to refine user analysis and our new Gene Set Enricher (which provides biological annotations that are enriched for gene sets). To improve data visualization, we added a Cytoscape Web view to our ChemComps feature, included color-coded interactions and created a 'slim list' for our MEDIC disease vocabulary (allowing diseases to be grouped for meta-analysis, visualization and better data management). CTD continues to promote interoperability with external databases by providing content and cross-links to their sites. Together, this wealth of expanded chemical-gene-disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.
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Affiliation(s)
- Allan Peter Davis
- Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA.
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Collin GB, Marshall JD, King BL, Milan G, Maffei P, Jagger DJ, Naggert JK. The Alström syndrome protein, ALMS1, interacts with α-actinin and components of the endosome recycling pathway. PLoS One 2012; 7:e37925. [PMID: 22693585 PMCID: PMC3365098 DOI: 10.1371/journal.pone.0037925] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 04/30/2012] [Indexed: 01/26/2023] Open
Abstract
Alström syndrome (ALMS) is a progressive multi-systemic disorder characterized by cone-rod dystrophy, sensorineural hearing loss, childhood obesity, insulin resistance and cardiac, renal, and hepatic dysfunction. The gene responsible for Alström syndrome, ALMS1, is ubiquitously expressed and has multiple splice variants. The protein encoded by this gene has been implicated in ciliary function, cell cycle control, and intracellular transport. To gain better insight into the pathways through which ALMS1 functions, we carried out a yeast two hybrid (Y2H) screen in several mouse tissue libraries to identify ALMS1 interacting partners. The majority of proteins found to interact with the murine carboxy-terminal end (19/32) of ALMS1 were α-actinin isoforms. Interestingly, several of the identified ALMS1 interacting partners (α-actinin 1, α-actinin 4, myosin Vb, rad50 interacting 1 and huntingtin associated protein1A) have been previously associated with endosome recycling and/or centrosome function. We examined dermal fibroblasts from human subjects bearing a disruption in ALMS1 for defects in the endocytic pathway. Fibroblasts from these patients had a lower uptake of transferrin and reduced clearance of transferrin compared to controls. Antibodies directed against ALMS1 N- and C-terminal epitopes label centrosomes and endosomal structures at the cleavage furrow of dividing MDCK cells, respectively, suggesting isoform-specific cellular functions. Our results suggest a role for ALMS1 variants in the recycling endosome pathway and give us new insights into the pathogenesis of a subset of clinical phenotypes associated with ALMS.
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Affiliation(s)
- Gayle B. Collin
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Jan D. Marshall
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Benjamin L. King
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, United States of America
| | - Gabriella Milan
- Department of Medical and Surgical Sciences, University of Padua, Padua, Italy
| | - Pietro Maffei
- Department of Medical and Surgical Sciences, University of Padua, Padua, Italy
| | - Daniel J. Jagger
- UCL Ear Institute, University College London, London, United Kingdom
| | - Jürgen K. Naggert
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail:
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Walker MB, King BL, Paigen K. Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species. PLoS One 2012; 7:e35274. [PMID: 22563380 PMCID: PMC3338513 DOI: 10.1371/journal.pone.0035274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 03/14/2012] [Indexed: 11/22/2022] Open
Abstract
Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent [1], [2], [3]. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity. Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml) describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters) in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes. With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.
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Affiliation(s)
| | - Benjamin L. King
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, United States of America
| | - Kenneth Paigen
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail:
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Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, Huang H, Kingham BF, Page ST, Rendino MF, Thomas WK, Udwary DW, Wu CH. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford) 2012; 2012:bar064. [PMID: 22434832 PMCID: PMC3308154 DOI: 10.1093/database/bar064] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.
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Affiliation(s)
- Qinghua Wang
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
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Lyson TR, Sperling EA, Heimberg AM, Gauthier JA, King BL, Peterson KJ. MicroRNAs support a turtle + lizard clade. Biol Lett 2012; 8:104-7. [PMID: 21775315 PMCID: PMC3259949 DOI: 10.1098/rsbl.2011.0477] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 06/27/2011] [Indexed: 11/12/2022] Open
Abstract
Despite much interest in amniote systematics, the origin of turtles remains elusive. Traditional morphological phylogenetic analyses place turtles outside Diapsida-amniotes whose ancestor had two fenestrae in the temporal region of the skull (among the living forms the tuatara, lizards, birds and crocodilians)-and allied with some unfenestrate-skulled (anapsid) taxa. Nonetheless, some morphological analyses place turtles within Diapsida, allied with Lepidosauria (tuatara and lizards). Most molecular studies agree that turtles are diapsids, but rather than allying them with lepidosaurs, instead place turtles near or within Archosauria (crocodilians and birds). Thus, three basic phylogenetic positions for turtles with respect to extant Diapsida are currently debated: (i) sister to Diapsida, (ii) sister to Lepidosauria, or (iii) sister to, or within, Archosauria. Interestingly, although these three alternatives are consistent with a single unrooted four-taxon tree for extant reptiles, they differ with respect to the position of the root. Here, we apply a novel molecular dataset, the presence versus absence of specific microRNAs, to the problem of the phylogenetic position of turtles and the root of the reptilian tree, and find that this dataset unambiguously supports a turtle + lepidosaur group. We find that turtles and lizards share four unique miRNA gene families that are not found in any other organisms' genome or small RNA library, and no miRNAs are found in all diapsids but not turtles, or in turtles and archosaurs but not in lizards. The concordance between our result and some morphological analyses suggests that there have been numerous morphological convergences and reversals in reptile phylogeny, including the loss of temporal fenestrae.
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Affiliation(s)
- Tyler R. Lyson
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Erik A. Sperling
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Alysha M. Heimberg
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Benjamin L. King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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Abstract
Hox proteins are a metazoan-specific family of transcription factors that are required for developmental patterning. The genomic arrangement of Hox genes into four paralogous clusters is a primitive feature of jawed vertebrates. By using high-throughput sequencing, we demonstrate the absence of all HoxC transcripts from embryos of the shark Scyliorhinus canicula and the skate Leucoraja erinacea and the absence of all HoxC genes and two HoxC-associated microRNAs from the genome of L. erinacea. These data suggest a loss of the entire HoxC cluster in elasmobranch fishes and represent evidence for the natural deletion of an entire Hox cluster in vertebrates.
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Affiliation(s)
- Benjamin L King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA.
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48
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Howell GR, Walton DO, King BL, Libby RT, John SWM. Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data. BMC Genomics 2011; 12:429. [PMID: 21864367 PMCID: PMC3171729 DOI: 10.1186/1471-2164-12-429] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/24/2011] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND We introduce Glaucoma Discovery Platform (GDP), an online environment for facile visualization and interrogation of complex transcription profiling datasets for glaucoma. We also report the availability of Datgan, the suite of scripts that was developed to construct GDP. This reusable software system complements existing repositories such as NCBI GEO or EBI ArrayExpress as it allows the construction of searchable databases to maximize understanding of user-selected transcription profiling datasets. DESCRIPTION Datgan scripts were used to construct both the underlying data tables and the web interface that form GDP. GDP is populated using data from a mouse model of glaucoma. The data was generated using the DBA/2J strain, a widely used mouse model of glaucoma. The DBA/2J-Gpnmb+ strain provided a genetically matched control strain that does not develop glaucoma. We separately assessed both the retina and the optic nerve head, important tissues in glaucoma. We used hierarchical clustering to identify early molecular stages of glaucoma that could not be identified using morphological assessment of disease. GDP has two components. First, an interactive search and retrieve component provides the ability to assess gene(s) of interest in all identified stages of disease in both the retina and optic nerve head. The output is returned in graphical and tabular format with statistically significant differences highlighted for easy visual analysis. Second, a bulk download component allows lists of differentially expressed genes to be retrieved as a series of files compatible with Excel. To facilitate access to additional information available for genes of interest, GDP is linked to selected external resources including Mouse Genome Informatics and Online Medelian Inheritance in Man (OMIM). CONCLUSION Datgan-constructed databases allow user-friendly access to datasets that involve temporally ordered stages of disease or developmental stages. Datgan and GDP are available from http://glaucomadb.jax.org/glaucoma.
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Howell GR, Macalinao DG, Sousa GL, Walden M, Soto I, Kneeland SC, Barbay JM, King BL, Marchant JK, Hibbs M, Stevens B, Barres BA, Clark AF, Libby RT, John SWM. Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. J Clin Invest 2011; 121:1429-44. [PMID: 21383504 DOI: 10.1172/jci44646] [Citation(s) in RCA: 329] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 01/05/2011] [Indexed: 12/11/2022] Open
Abstract
Glaucoma is one of the most common neurodegenerative diseases. Despite this, the earliest stages of this complex disease are still unclear. This study was specifically designed to identify early stages of glaucoma in DBA/2J mice. To do this, we used genome-wide expression profiling of optic nerve head and retina and a series of computational methods. Eyes with no detectable glaucoma by conventional assays were grouped into molecularly defined stages of disease using unbiased hierarchical clustering. These stages represent a temporally ordered sequence of glaucoma states. We then determined networks and biological processes that were altered at these early stages. Early-stage expression changes included upregulation of both the complement cascade and the endothelin system, and so we tested the therapeutic value of separately inhibiting them. Mice with a mutation in complement component 1a (C1qa) were protected from glaucoma. Similarly, inhibition of the endothelin system with bosentan, an endothelin receptor antagonist, was strongly protective against glaucomatous damage. Since endothelin 2 is potently vasoconstrictive and was produced by microglia/macrophages, our data provide what we believe to be a novel link between these cell types and vascular dysfunction in glaucoma. Targeting early molecular events, such as complement and endothelin induction, may provide effective new treatments for human glaucoma.
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Affiliation(s)
- Gareth R Howell
- The Howard Hughes Medical Institute, Bar Harbor, Maine 04609, USA
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Lee Y, Smith RS, Jordan W, King BL, Won J, Valpuesta JM, Naggert JK, Nishina PM. Prefoldin 5 is required for normal sensory and neuronal development in a murine model. J Biol Chem 2010; 286:726-36. [PMID: 20956523 DOI: 10.1074/jbc.m110.177352] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular chaperones and co-chaperones are crucial for cellular development and maintenance as they assist in protein folding and stabilization of unfolded or misfolded proteins. Prefoldin (PFDN), a ubiquitously expressed heterohexameric co-chaperone, is necessary for proper folding of nascent proteins, in particular, tubulin and actin. Here we show that a genetic disruption in the murine Pfdn5 gene, a subunit of prefoldin, causes a syndrome characterized by photoreceptor degeneration, central nervous system abnormalities, and male infertility. Our data indicate that a missense mutation in Pfdn5, may cause these phenotypes through a reduction in formation of microtubules and microfilaments, which are necessary for the development of cilia and cytoskeletal structures, respectively. The diversity of phenotypes demonstrated by models carrying mutations in different PFDN subunits suggests that each PFDN subunit must confer a distinct substrate specificity to the prefoldin holocomplex.
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Affiliation(s)
- YongSuk Lee
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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