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Vandepas LE, Stefani C, Domeier PP, Traylor-Knowles N, Goetz FW, Browne WE, Lacy-Hulbert A. Extracellular DNA traps in a ctenophore demonstrate immune cell behaviors in a non-bilaterian. Nat Commun 2024; 15:2990. [PMID: 38582801 PMCID: PMC10998917 DOI: 10.1038/s41467-024-46807-6] [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: 04/11/2022] [Accepted: 03/08/2024] [Indexed: 04/08/2024] Open
Abstract
The formation of extracellular DNA traps (ETosis) is a first response mechanism by specific immune cells following exposure to microbes. Initially characterized in vertebrate neutrophils, cells capable of ETosis have been discovered recently in diverse non-vertebrate taxa. To assess the conservation of ETosis between evolutionarily distant non-vertebrate phyla, we observed and quantified ETosis using the model ctenophore Mnemiopsis leidyi and the oyster Crassostrea gigas. Here we report that ctenophores - thought to have diverged very early from the metazoan stem lineage - possess immune-like cells capable of phagocytosis and ETosis. We demonstrate that both Mnemiopsis and Crassostrea immune cells undergo ETosis after exposure to diverse microbes and chemical agents that stimulate ion flux. We thus propose that ETosis is an evolutionarily conserved metazoan defense against pathogens.
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Affiliation(s)
- Lauren E Vandepas
- NRC Research Associateship Program, Seattle, WA, USA.
- Northwest Fisheries Science Center, National Oceanographic and Atmospheric Administration, Seattle, WA, 98112, USA.
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA.
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
| | - Caroline Stefani
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Phillip P Domeier
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, 33149, USA
| | - Frederick W Goetz
- Northwest Fisheries Science Center, National Oceanographic and Atmospheric Administration, Seattle, WA, 98112, USA
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Adam Lacy-Hulbert
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
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2
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Young BD, Williamson OM, Kron NS, Andrade Rodriguez N, Isma LM, MacKnight NJ, Muller EM, Rosales SM, Sirotzke SM, Traylor-Knowles N, Williams SD, Studivan MS. Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing. BMC Genomics 2024; 25:226. [PMID: 38424480 PMCID: PMC10905781 DOI: 10.1186/s12864-024-10092-w] [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: 10/02/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available, opening the door for a wide array of 'omics-based research. Here we present a new de-novo genome assembly for the endangered Caribbean star coral, Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our new de-novo assembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additional O. faveolata fragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affecting O. faveolata, as well as its increasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other 'omics analyses to aid in the conservation of this species.
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Affiliation(s)
- Benjamin D Young
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA.
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
| | - Olivia M Williamson
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
| | - Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
| | - Natalia Andrade Rodriguez
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
| | - Lys M Isma
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
| | - Nicholas J MacKnight
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | | | - Stephanie M Rosales
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | | | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
| | | | - Michael S Studivan
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
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3
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Boohar RT, Vandepas LE, Traylor-Knowles N, Browne WE. Phylogenetic and Protein Structure Analyses Provide Insight into the Evolution and Diversification of the CD36 Domain "Apex" among Scavenger Receptor Class B Proteins across Eukarya. Genome Biol Evol 2023; 15:evad218. [PMID: 38035778 PMCID: PMC10715195 DOI: 10.1093/gbe/evad218] [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: 12/27/2022] [Revised: 11/07/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023] Open
Abstract
The cluster of differentiation 36 (CD36) domain defines the characteristic ectodomain associated with class B scavenger receptor (SR-B) proteins. In bilaterians, SR-Bs play critical roles in diverse biological processes including innate immunity functions such as pathogen recognition and apoptotic cell clearance, as well as metabolic sensing associated with fatty acid uptake and cholesterol transport. Although previous studies suggest this protein family is ancient, SR-B diversity across Eukarya has not been robustly characterized. We analyzed SR-B homologs identified from the genomes and transcriptomes of 165 diverse eukaryotic species. The presence of highly conserved amino acid motifs across major eukaryotic supergroups supports the presence of a SR-B homolog in the last eukaryotic common ancestor. Our comparative analyses of SR-B protein structure identify the retention of a canonical asymmetric beta barrel tertiary structure within the CD36 ectodomain across Eukarya. We also identify multiple instances of independent lineage-specific sequence expansions in the apex region of the CD36 ectodomain-a region functionally associated with ligand-sensing. We hypothesize that a combination of both sequence expansion and structural variation in the CD36 apex region may reflect the evolution of SR-B ligand-sensing specificity between diverse eukaryotic clades.
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Affiliation(s)
- Reed T Boohar
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Lauren E Vandepas
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, USA
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, Florida, USA
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4
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Connelly MT, Snyder G, Palacio-Castro AM, Gillette PR, Baker AC, Traylor-Knowles N. Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression. Mol Ecol 2023; 32:4677-4694. [PMID: 37317893 DOI: 10.1111/mec.17049] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
Corals are important models for understanding invertebrate host-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral-bacteria associations are needed. Coral-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-building corals Pocillopora meandrina and P. verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-associated bacteria.
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Affiliation(s)
- Michael T Connelly
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Grace Snyder
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Ana M Palacio-Castro
- University of Miami Cooperative Institute for Marine and Atmospheric Studies, Miami, Florida, USA
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
| | - Phillip R Gillette
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Andrew C Baker
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
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5
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Young BD, Rosales SM, Enochs IC, Kolodziej G, Formel N, Moura A, D'Alonso GL, Traylor-Knowles N. Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata. PLoS One 2023; 18:e0286293. [PMID: 37228141 DOI: 10.1371/journal.pone.0286293] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.
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Affiliation(s)
- Benjamin D Young
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, United States of America
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Miami, Florida, United States of America
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Stephanie M Rosales
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Miami, Florida, United States of America
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Ian C Enochs
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Graham Kolodziej
- Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Miami, Florida, United States of America
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Nathan Formel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Amelia Moura
- Coral Restoration Foundation, Tavernier, Florida, United States of America
| | | | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, United States of America
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6
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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7
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Eliachar S, Snyder GA, Barkan SK, Talice S, Otolenghi A, Jaimes-Becerra A, Sharoni T, Sultan E, Hadad U, Levy O, Moran Y, Gershoni-Yahalom O, Traylor-Knowles N, Rosental B. Heat stress increases immune cell function in Hexacorallia. Front Immunol 2022; 13:1016097. [PMID: 36618389 PMCID: PMC9815446 DOI: 10.3389/fimmu.2022.1016097] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Climate change induced heat stress has increased coral bleaching events worldwide. Differentially regulated immune genes are one of the primary responses to heat stress suggesting that immune activation is critical. However, the cellular immune mechanisms of coral bleaching is currently unknown, and it is still not known if the immune response documented during heat stress is a consequence of bleaching or is directly caused by the heat stress itself. To address this question, we have used two model system sea anemones (Order: Actiniaria): Exaiptasia diaphana and Nematostella vectensis. E. diaphana is an established sea anemone model for algal symbiont interaction, while N. vectensis is an established sea anemone model that lacks the algal symbiont. Here, we examined the effect of increased temperature on phagocytic activity, as an indication of immune function. Our data shows that immune cell activity increases during heat stress, while small molecule pinocytosis remains unaffected. We observed an increase in cellular production of reactive oxygen species with increasing temperatures. We also found that the cellular immune activity was not affected by the presence of the Symbiodiniaceae. Our results suggest that the immune activity observed in heat-stress induced bleaching in corals is a fundamental and basic response independent of the bleaching effect. These results establish a foundation for improving our understanding of hexacorallian immune cell biology, and its potential role in coral bleaching.
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Affiliation(s)
- Shir Eliachar
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Grace Ann Snyder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Shany Klara Barkan
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Shani Talice
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Aner Otolenghi
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Adrian Jaimes-Becerra
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ton Sharoni
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eliya Sultan
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Uzi Hadad
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orly Gershoni-Yahalom
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,*Correspondence: Nikki Traylor-Knowles, ; Benyamin Rosental,
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel,*Correspondence: Nikki Traylor-Knowles, ; Benyamin Rosental,
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8
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Traylor-Knowles N, Browne WE, Mydlarz LD, Palmer CV, Rosental B. Editorial: Innate Immunity in Early Diverging Metazoans. Front Immunol 2022; 13:816550. [PMID: 35173730 PMCID: PMC8841359 DOI: 10.3389/fimmu.2022.816550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/13/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Sciences, Miami, FL, United States
- *Correspondence: Nikki Traylor-Knowles,
| | - William E. Browne
- Department of Biology, University of Miami, Cox Science Building, Miami, FL, United States
| | - Laura D. Mydlarz
- Department of Biology, University of Texas Arlington, Arlington, TX, United States
| | | | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer Sheva, Israel
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9
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Traylor-Knowles N, Emery M. Analysis of Spatial Gene Expression at the Cellular Level in Stony Corals. Methods Mol Biol 2022; 2450:359-371. [PMID: 35359318 PMCID: PMC9761507 DOI: 10.1007/978-1-0716-2172-1_19] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Scleractinians, or stony corals, are colonial animals that possess a high regenerative capacity and a highly diverse innate immune system. As such they present the opportunity to investigate the interconnection between regeneration and immunity in a colonial animal. Understanding the relationship between regeneration and immunity in stony corals is of further interest as it has major implications for coral reef health. One method for understanding the role of innate immunity in scleractinian regeneration is in situ hybridization using RNA probes. Here we describe a protocol for in situ hybridization in adult stony corals using a digoxigenin (DIG)-labeled RNA antisense probe which can be utilized to investigate the spatial expression of immune factors during regeneration.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
| | - Madison Emery
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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10
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Snyder GA, Eliachar S, Connelly MT, Talice S, Hadad U, Gershoni-Yahalom O, Browne WE, Palmer CV, Rosental B, Traylor-Knowles N. Functional Characterization of Hexacorallia Phagocytic Cells. Front Immunol 2021; 12:662803. [PMID: 34381444 PMCID: PMC8350327 DOI: 10.3389/fimmu.2021.662803] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Phagocytosis is the cellular defense mechanism used to eliminate antigens derived from dysregulated or damaged cells, and microbial pathogens. Phagocytosis is therefore a pillar of innate immunity, whereby foreign particles are engulfed and degraded in lysolitic vesicles. In hexacorallians, phagocytic mechanisms are poorly understood, though putative anthozoan phagocytic cells (amoebocytes) have been identified histologically. We identify and characterize phagocytes from the coral Pocillopora damicornis and the sea anemone Nematostella vectensis. Using fluorescence-activated cell sorting and microscopy, we show that distinct populations of phagocytic cells engulf bacteria, fungal antigens, and beads. In addition to pathogenic antigens, we show that phagocytic cells engulf self, damaged cells. We show that target antigens localize to low pH phagolysosomes, and that degradation is occurring within them. Inhibiting actin filament rearrangement interferes with efficient particle phagocytosis but does not affect small molecule pinocytosis. We also demonstrate that cellular markers for lysolitic vesicles and reactive oxygen species (ROS) correlate with hexacorallian phagocytes. These results establish a foundation for improving our understanding of hexacorallian immune cell biology.
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Affiliation(s)
- Grace A Snyder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Shir Eliachar
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Michael T Connelly
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Shani Talice
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Uzi Hadad
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Orly Gershoni-Yahalom
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, United States
| | - Caroline V Palmer
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
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11
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Davies SW, Putnam HM, Ainsworth T, Baum JK, Bove CB, Crosby SC, Côté IM, Duplouy A, Fulweiler RW, Griffin AJ, Hanley TC, Hill T, Humanes A, Mangubhai S, Metaxas A, Parker LM, Rivera HE, Silbiger NJ, Smith NS, Spalding AK, Traylor-Knowles N, Weigel BL, Wright RM, Bates AE. Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science. PLoS Biol 2021; 19:e3001282. [PMID: 34129646 PMCID: PMC8205123 DOI: 10.1371/journal.pbio.3001282] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Success and impact metrics in science are based on a system that perpetuates sexist and racist “rewards” by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals’ meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change. This Essay argues that success and impact metrics in science are based on a system that perpetuates sexist and racist ‘rewards’ by prioritizing citations and impact factors; the authors advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail: (SWD); (HMP); (AEB)
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
- * E-mail: (SWD); (HMP); (AEB)
| | - Tracy Ainsworth
- School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julia K. Baum
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Colleen B. Bove
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Sarah C. Crosby
- Harbor Watch, Earthplace, Inc., Westport, Connecticut, United States of America
| | - Isabelle M. Côté
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anne Duplouy
- The University of Helsinki, Organismal and Evolutionary Biology Research Program, Helsinki, Finland
| | - Robinson W. Fulweiler
- Department of Earth and Environment & Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Alyssa J. Griffin
- Department of Earth & Planetary Sciences & Bodega Marine Laboratory, University of California, Davis, California, United States of America
| | - Torrance C. Hanley
- Marine Science Center, Northeastern University, Nahant, Massachusetts, United States of America
| | - Tessa Hill
- Department of Earth & Planetary Sciences & Bodega Marine Laboratory, University of California, Davis, California, United States of America
| | - Adriana Humanes
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Anna Metaxas
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura M. Parker
- School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Hanny E. Rivera
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Nyssa J. Silbiger
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Nicola S. Smith
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ana K. Spalding
- School of Public Policy, College of Liberal Arts, Oregon State University, Corvallis, Oregon, United States of America
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Nikki Traylor-Knowles
- University of Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, Florida, United States of America
| | - Brooke L. Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Rachel M. Wright
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Amanda E. Bates
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, New Foundland, Canada
- * E-mail: (SWD); (HMP); (AEB)
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12
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Nowotny JD, Connelly MT, Traylor-Knowles N. Author Correction: Novel methods to establish whole‑body primary cell cultures for the cnidarians Nematostella vectensis and Pocillopora damicornis. Sci Rep 2021; 11:11473. [PMID: 34040038 PMCID: PMC8155171 DOI: 10.1038/s41598-021-90241-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- James D Nowotny
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.,Biology Department, University of Maryland, 4094 Campus Drive, College Park, MD, 20742, USA
| | - Michael T Connelly
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
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Abstract
Coral reefs are one of the most important ecosystems in the world but least understood from a cellular level. In this issue of Cell, Levy et al. unravel the single-cell gene expression of the coral holobiont and open the doors to better understand the novel diversity of cell types.
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Affiliation(s)
- Nikki Traylor-Knowles
- University of Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, FL, USA.
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14
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Fulweiler RW, Davies SW, Biddle JF, Burgin AJ, Cooperdock EHG, Hanley TC, Kenkel CD, Marcarelli AM, Matassa CM, Mayo TL, Santiago-Vàzquez LZ, Traylor-Knowles N, Ziegler M. Rebuild the Academy: Supporting academic mothers during COVID-19 and beyond. PLoS Biol 2021; 19:e3001100. [PMID: 33690708 PMCID: PMC7942998 DOI: 10.1371/journal.pbio.3001100] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The issues facing academic mothers have been discussed for decades. Coronavirus Disease 2019 (COVID-19) is further exposing these inequalities as womxn scientists who are parenting while also engaging in a combination of academic related duties are falling behind. These inequities can be solved by investing strategically in solutions. Here we describe strategies that would ensure a more equitable academy for working mothers now and in the future. While the data are clear that mothers are being disproportionately impacted by COVID-19, many groups could benefit from these strategies. Rather than rebuilding what we once knew, let us be the architects of a new world.
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Affiliation(s)
- Robinson W. Fulweiler
- Departments of Earth and Environment, Boston, Massachusetts, United States of America
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Sarah W. Davies
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Jennifer F. Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America
| | - Amy J. Burgin
- Department of Environmental Studies and Ecology & Evolutionary Biology, Kansas Biological Survey, University of Kansas, Lawrence, Kansas, United States of America
| | - Emily H. G. Cooperdock
- Department of Earth Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Torrance C. Hanley
- Marine Science Center, Northeastern University, Nahant, Massachusetts, United States of America
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Amy M. Marcarelli
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Catherine M. Matassa
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Talea L. Mayo
- Department of Mathematics, Emory University, Atlanta, Georgia, United States of America
| | - Lory Z. Santiago-Vàzquez
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, Texas, United States of America
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida, United States of America
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
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15
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Bonacolta AM, Connelly MT, M Rosales S, Del Campo J, Traylor-Knowles N. The starlet sea anemone, Nematostella vectensis, possesses body region-specific bacterial associations with spirochetes dominating the capitulum. FEMS Microbiol Lett 2021; 368:6070651. [PMID: 33417693 DOI: 10.1093/femsle/fnab002] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Sampling of different body regions can reveal highly specialized bacterial associations within the holobiont and facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. Here, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct microhabitats. This sampling design allowed us to uncover a capitulum-specific dominance of spirochetes within N. vectensis. Bacteria from the family Spirochaetaceae made up 66% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. A phylogenetic analysis of the predominant spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described genus Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this clade. This suggests a prevalent and yet uncharacterized association between N. vectensis and spirochetes from the order Spirochaetales.
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Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Michael T Connelly
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Stephanie M Rosales
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL 33149, USA
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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16
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Young BD, Serrano XM, Rosales SM, Miller MW, Williams D, Traylor-Knowles N. Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events. PLoS One 2020; 15:e0228514. [PMID: 33091033 PMCID: PMC7580945 DOI: 10.1371/journal.pone.0228514] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 01/15/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Coral disease outbreaks are expected to increase in prevalence, frequency and severity due to climate change and other anthropogenic stressors. This is especially worrying for the Caribbean branching coral Acropora palmata which has already seen an 80% decrease in cover primarily due to disease. Despite the importance of this keystone species, there has yet to be a characterization of its transcriptomic response to disease exposure. In this study we provide the first transcriptomic analysis of 12 A. palmata genotypes and their symbiont Symbiodiniaceae exposed to disease in 2016 and 2017. Year was the primary driver of gene expression variance for A. palmata and the Symbiodiniaceae. We hypothesize that lower expression of ribosomal genes in the coral, and higher expression of transmembrane ion transport genes in the Symbiodiniaceae indicate that a compensation or dysbiosis may be occurring between host and symbiont. Disease response was the second driver of gene expression variance for A. palmata and included a core set of 422 genes that were significantly differentially expressed. Of these, 2 genes (a predicted cyclin-dependent kinase 11b and aspartate 1-decarboxylase) showed negative Log2 fold changes in corals showing transmission of disease, and positive Log2 fold changes in corals showing no transmission of disease, indicating that these may be important in disease resistance. Co-expression analysis identified two modules positively correlated to disease exposure, one enriched for lipid biosynthesis genes, and the other enriched in innate immune genes. The hub gene in the immune module was identified as D-amino acid oxidase, a gene implicated in phagocytosis and microbiome homeostasis. The role of D-amino acid oxidase in coral immunity has not been characterized but could be an important enzyme for responding to disease. Our results indicate that A. palmata mounts a core immune response to disease exposure despite differences in the disease type and virulence between 2016 and 2017. These identified genes may be important for future biomarker development in this Caribbean keystone species.
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Affiliation(s)
- Benjamin D. Young
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - Xaymara M. Serrano
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanographic and Atmospheric Administration, Miami, Florida, United States of America
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America
| | - Stephanie M. Rosales
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America
| | - Margaret W. Miller
- Southeast Fisheries Science Center, NOAA-National Marine Fisheries Service, Miami, FL, United States of America
- SECORE International, Miami, FL, United States of America
| | - Dana Williams
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America
- Southeast Fisheries Science Center, NOAA-National Marine Fisheries Service, Miami, FL, United States of America
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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17
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Walters BM, Connelly MT, Young B, Traylor-Knowles N. The Complicated Evolutionary Diversification of the Mpeg-1/Perforin-2 Family in Cnidarians. Front Immunol 2020; 11:1690. [PMID: 32849589 PMCID: PMC7424014 DOI: 10.3389/fimmu.2020.01690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/24/2020] [Indexed: 11/13/2022] Open
Abstract
The invertebrate innate immune system is surprisingly complex, yet our knowledge is limited to a few select model systems. One understudied group is the phylum Cnidaria (corals, sea anemones, etc.). Cnidarians are the sister group to Bilateria and by studying their innate immunity repertoire, a better understanding of the ancestral state can be gained. Corals in particular have evolved a highly diverse innate immune system that can uncover evolutionarily basal functions of conserved genes and proteins. One rudimentary function of the innate immune system is defense against harmful bacteria using pore forming proteins. Macrophage expressed gene 1/Perforin-2 protein (Mpeg-1/P2) is a particularly important pore forming molecule as demonstrated by previous studies in humans and mice, and limited studies in non-bilaterians. However, in cnidarians, little is known about Mpeg-1/P2. In this perspective article, we will summarize the current state of knowledge of Mpeg-1/P2 in invertebrates, analyze identified Mpeg-1/P2 homologs in cnidarians, and demonstrate the evolutionary diversity of this gene family using phylogenetic analysis. We will also show that Mpeg-1 is upregulated in one species of stony coral in response to lipopolysaccharides and downregulated in another species of stony coral in response to white band disease. This data presents evidence that Mpeg-1/P2 is conserved in cnidarians and we hypothesize that it plays an important role in cnidarian innate immunity. We propose that future research focus on the function of Mpeg-1/P2 family in cnidarians to identify its primary role in innate immunity and beyond.
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Affiliation(s)
- Brian M. Walters
- Department of Biology, University of Miami, Coral Gables, FL, United States
| | - Michael T. Connelly
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Coral Gables, FL, United States
| | - Benjamin Young
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Coral Gables, FL, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Coral Gables, FL, United States
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18
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Connelly MT, McRae CJ, Liu PJ, Traylor-Knowles N. Lipopolysaccharide treatment stimulates Pocillopora coral genotype-specific immune responses but does not alter coral-associated bacteria communities. Dev Comp Immunol 2020; 109:103717. [PMID: 32348787 DOI: 10.1016/j.dci.2020.103717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Corals are comprised of a coral host and associated microbes whose interactions are mediated by the coral innate immune system. The diversity of immune factors identified in the Pocillopora damicornis genome suggests that immunity is linked to maintaining microbial symbioses while also being able to detect pathogens. However, it is unclear which immune factors respond to specific microbe-associated molecular patterns and how these immune reactions simultaneously affect coral-associated bacteria. To investigate this, fragments of P. damicornis and P. acuta colonies from Taiwan were subjected to lipopolysaccharide (LPS) treatment to stimulate immune responses and measure bacteria community shifts. RNA-seq revealed genotype-specific immune responses to LPS involving the upregulation of immune receptors, transcription factors, and pore-forming toxins. Bacteria 16S sequencing revealed significantly different bacteria communities between coral genotypes but no differences in bacteria communities were caused by LPS. Our findings confirm that Pocillopora corals activate conserved immune factors in response to LPS and identify transcription factors coordinating Pocillopora corals' immune responses. Additionally, the strong effect of coral genotype on gene expression and bacteria communities highlights the importance of coral genotype in the investigation of coral host-microbe interactions.
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Affiliation(s)
- Michael T Connelly
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33145, USA
| | - Crystal J McRae
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada; Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 974, Taiwan
| | - Pi-Jen Liu
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 944, Taiwan; National Museum of Marine Biology and Aquarium, Pingtung, 944, Taiwan
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33145, USA.
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19
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Snyder GA, Browne WE, Traylor-Knowles N, Rosental B. Fluorescence-Activated Cell Sorting for the Isolation of Scleractinian Cell Populations. J Vis Exp 2020. [PMID: 32538898 DOI: 10.3791/60446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Coral reefs are under threat due to anthropogenic stressors. The biological response of coral to these stressors may occur at a cellular level, but the mechanisms are not well understood. To investigate coral response to stressors, we need tools for analyzing cellular responses. In particular, we need tools that facilitate the application of functional assays to better understand how cell populations are reacting to stress. In the current study, we use fluorescence-activated cell sorting (FACS) to isolate and separate different cell populations in stony corals. This protocol includes: (1) the separation of coral tissues from the skeleton, (2) creation of a single cell suspension, (3) labeling the coral cells using various markers for flow cytometry, and (4) gating and cell sorting strategies. This method will enable researchers to work on corals at the cellular level for analysis, functional assays, and gene expression studies of different cell populations.
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Affiliation(s)
- Grace A Snyder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami
| | | | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami;
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, and Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev;
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20
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Abstract
Innate immunity is an ancient physiological response critical for protecting metazoans from invading pathogens. It is the primary pathogen defense mechanism among invertebrates. While innate immunity has been studied extensively in diverse invertebrate taxa, including mollusks, crustaceans, and cnidarians, this system has not been well characterized in ctenophores. The ctenophores comprise an exclusively marine, non-bilaterian lineage that diverged early during metazoan diversification. The phylogenetic position of ctenophore lineage suggests that characterization of the ctenophore innate immune system will reveal important features associated with the early evolution of the metazoan innate immune system. Here, we review current understanding of the ctenophore immune repertoire and identify innate immunity genes recovered from three ctenophore species. We also isolate and characterize Mnemiopsis leidyi cells that display macrophage-like behavior when challenged with bacteria. Our results indicate that ctenophores possess cells capable of phagocytosing microbes and that two distantly related ctenophores, M. leidyi and Hormiphora californiensis, possess many candidate innate immunity proteins.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA
| | - Lauren E Vandepas
- Benaroya Research Institute, 1201 9th Avenue, Seattle, WA 98101, USA.,Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Building, 1301 Memorial Drive, Miami, FL 33146, USA
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21
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Rosales SM, Miller MW, Williams DE, Traylor-Knowles N, Young B, Serrano XM. Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays. Sci Rep 2019; 9:18279. [PMID: 31797896 PMCID: PMC6892807 DOI: 10.1038/s41598-019-54855-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 07/23/2019] [Accepted: 11/07/2019] [Indexed: 12/17/2022] Open
Abstract
In recent decades coral gardening has become increasingly popular to restore degraded reef ecosystems. However, the growth and survivorship of nursery-reared outplanted corals are highly variable. Scientists are trying to identify genotypes that show signs of disease resistance and leverage these genotypes in restoring more resilient populations. In a previous study, a field disease grafting assay was conducted on nursery-reared Acropora cervicornis and Acropora palmata to quantify relative disease susceptibility. In this study, we further evaluate this field assay by investigating putative disease-causing agents and the microbiome of corals with disease-resistant phenotypes. We conducted 16S rRNA gene high-throughput sequencing on A. cervicornis and A. palmata that were grafted (inoculated) with a diseased A. cervicornis fragment. We found that independent of health state, A. cervicornis and A. palmata had distinct alpha and beta diversity patterns from one another and distinct dominant bacteria. In addition, despite different microbiome patterns between both inoculated coral species, the genus Sphingomonadaceae was significantly found in both diseased coral species. Additionally, a core bacteria member from the order Myxococcales was found at relatively higher abundances in corals with lower rates of disease development following grafting. In all, we identified Sphingomonadaceae as a putative coral pathogen and a bacterium from the order Myxococcales associated with corals that showed disease resistant phenotypes.
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Affiliation(s)
- Stephanie M Rosales
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanographic and Atmospheric Administration, Miami, Florida, USA.
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, USA.
| | - Margaret W Miller
- SECORE International, Miami, FL, 33145, USA
- Southeast Fisheries Science Center, NOAA-National Marine Fisheries Service, Miami, FL, USA
| | - Dana E Williams
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, USA
- Southeast Fisheries Science Center, NOAA-National Marine Fisheries Service, Miami, FL, USA
| | - Nikki Traylor-Knowles
- University of Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, USA
| | - Benjamin Young
- University of Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, USA
| | - Xaymara M Serrano
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanographic and Atmospheric Administration, Miami, Florida, USA
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, USA
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22
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Abstract
It is well understood that heat stress causes bleaching in corals. Much work has focused on the way heat stress disrupts corals’ symbiotic relationship with endosymbiotic algal dinoflagellate, Symbiodiniaceae, a process called bleaching. However, the damage to the coral tissue that occurs during the bleaching process and, importantly, the factors that contribute to subsequent recovery, are not well understood. I hypothesize that the host tissue damage created by heat stress initiates cascades of wound healing factors that maintain epithelial integrity. These factors may be found to contribute to the coral’s potential capacity to recover. In this study, I present evidence that heat stress causes damage to the coral host tissue and that collagen is present in the gastrodermis of heat-stressed corals. I found that, during the early stages of bleaching, an important transcription factor for wound healing, Grainyhead, is expressed throughout the gastrodermis, where the cellular and tissue rearrangements occur. Lastly, using phylogenetics, I found that cnidarian Grainyhead proteins evolved three distinct groups and that evolution of this protein family likely happened within each taxonomic group. These findings have important implications for our study of coral resiliency in the face of climate change.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami, Rosenstiel School of Marine and Atmospheric Sciences, Miami, FL, United States of America
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23
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Cunning R, Bay RA, Gillette P, Baker AC, Traylor-Knowles N. Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Sci Rep 2018; 8:16134. [PMID: 30382153 PMCID: PMC6208414 DOI: 10.1038/s41598-018-34459-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [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: 05/09/2018] [Accepted: 10/19/2018] [Indexed: 12/22/2022] Open
Abstract
Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral ‘core’ genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.
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Affiliation(s)
- R Cunning
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA. .,Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, 1200 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - R A Bay
- Department of Evolution and Ecology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - P Gillette
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - A C Baker
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - N Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
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24
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Abstract
Corals are important ocean invertebrates that are critical for overall ocean health as well as human health. However, due to human impacts such as rising ocean temperatures and ocean acidification, corals are increasingly under threat. To tackle these challenges, advances in cell and molecular biology have proven to be crucial for diagnosing the health of corals. Modifying some of the techniques commonly used in human medicine could greatly improve researchers' ability to treat and save corals. To address this, a protocol for in situ hybridization used primarily in human medicine and evolutionary developmental biology has been adapted for use in adult corals under stress. The purpose of this method is to visualize the spatial expression of an RNA probe in adult coral tissue that has been embedded in paraffin and sectioned onto glass slides. This method focuses on removal of the paraffin and rehydration of the sample, pretreatment of the sample to ensure permeability of the sample, pre-hybridization incubation, hybridization of the RNA probe, and visualization of the RNA probe. This is a powerful method when using non-model organisms to discover where specific genes are expressed, and the protocol can be easily adapted for other non-model organisms. However, the method is limited in that it is primarily qualitative, because expression intensity can vary depending on the amount of time used during the visualization step and the concentration of the probe. Furthermore, patience is required, as this protocol can take up to 5 days (and in many cases, longer) depending on the probe being used. Finally, non-specific background staining is common, but this limitation can be overcome.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami, Rosenstiel School of Marine and Atmospheric Sciences;
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25
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Rosental B, Kozhekbaeva Z, Fernhoff N, Tsai JM, Traylor-Knowles N. Coral cell separation and isolation by fluorescence-activated cell sorting (FACS). BMC Cell Biol 2017; 18:30. [PMID: 28851289 PMCID: PMC5575905 DOI: 10.1186/s12860-017-0146-8] [Citation(s) in RCA: 28] [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] [Received: 11/15/2016] [Accepted: 08/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Generalized methods for understanding the cell biology of non-model species are quite rare, yet very much needed. In order to address this issue, we have modified a technique traditionally used in the biomedical field for ecological and evolutionary research. Fluorescent activated cell sorting (FACS) is often used for sorting and identifying cell populations. In this study, we developed a method to identify and isolate different cell populations in corals and other cnidarians. METHODS Using fluorescence-activated cell sorting (FACS), coral cell suspension were sorted into different cellular populations using fluorescent cell markers that are non-species specific. Over 30 different cell markers were tested. Additionally, cell suspension from Aiptasia pallida was also tested, and a phagocytosis test was done as a downstream functional assay. RESULTS We found that 24 of the screened markers positively labeled coral cells and 16 differentiated cell sub-populations. We identified 12 different cellular sub-populations using three markers, and found that each sub-population is primarily homogeneous. Lastly, we verified this technique in a sea anemone, Aiptasia pallida, and found that with minor modifications, a similar gating strategy can be successfully applied. Additionally, within A. pallida, we show elevated phagocytosis of sorted cells based on an immune associated marker. CONCLUSIONS In this study, we successfully adapted FACS for isolating coral cell populations and conclude that this technique is translatable for future use in other species. This technique has the potential to be used for different types of studies on the cellular stress response and other immunological studies.
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Affiliation(s)
- Benyamin Rosental
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pathology, Hopkins Marine Station, Stanford University, 120 Ocean View Blvd, Pacific Grove, CA, 93950, USA.
| | - Zhanna Kozhekbaeva
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Florida, 33149, USA
| | - Nathaniel Fernhoff
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jonathan M Tsai
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nikki Traylor-Knowles
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Florida, 33149, USA.
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26
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Traylor-Knowles N, Rose NH, Sheets EA, Palumbi SR. Early Transcriptional Responses during Heat Stress in the Coral Acropora hyacinthus. Biol Bull 2017; 232:91-100. [PMID: 28654330 DOI: 10.1086/692717] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Corals respond to heat pulses that cause bleaching with massive transcriptional change, but the immediate responses to stress that lead up to these shifts have never been detailed. Understanding these early signals could be important for identifying the regulatory mechanisms responsible for bleaching and how these mechanisms vary between more and less resilient corals. Using RNA sequencing (RNAseq) and sampling every 30 minutes during a short-term heat shock, we found that components of the transcriptome were significantly upregulated within 90 min and after a temperature increase of +2 °C. The developmental transcription factor, Krüppel-like factor 7, was highly expressed within 60 min, and stress-related transcription factors such as Elk-3 were highly expressed starting at 240 min. The sets of genes enriched for early transcriptional response to heat stress included heat shock proteins, small GTPases, and proteasome genes. Retrovirus-related Pol polyproteins from transposons were significantly expressed throughout the whole experiment. Lastly, we propose a model for early transcriptional regulation of protein degradation and cell adhesion response that may ultimately lead to the bleaching and stress response.
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27
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Traylor-Knowles N, Rose NH, Palumbi SR. The cell specificity of gene expression in the response to heat stress in corals. ACTA ACUST UNITED AC 2017; 220:1837-1845. [PMID: 28254881 DOI: 10.1242/jeb.155275] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 12/30/2016] [Accepted: 02/23/2017] [Indexed: 12/21/2022]
Abstract
Previous transcriptional studies in heat-stressed corals have shown that many genes are responsive to generalized heat stress whereas the expression patterns of specific gene networks after heat stress show strong correlations with variation in bleaching outcomes. However, where these specific genes are expressed is unknown. In this study, we employed in situ hybridization to identify patterns of spatial gene expression of genes previously predicted to be involved in general stress response and bleaching. We found that tumor necrosis factor receptors (TNFRs), known to be strong responders to heat stress, were not expressed in gastrodermal symbiont-containing cells but were widely expressed in specific cells of the epidermal layer. The transcription factors AP-1 and FosB, implicated as early signals of heat stress, were widely expressed throughout the oral gastrodermis and epidermis. By contrast, a G protein-coupled receptor gene (GPCR) and a fructose bisphosphate aldolase C gene (aldolase), previously implicated in bleaching, were expressed in symbiont-containing gastrodermal cells and in the epidermal tissue. Finally, chordin-like/kielin (chordin-like), a gene highly correlated to bleaching, was expressed solely in the oral gastrodermis. From this study, we confirm that heat-responsive genes occur widely in coral tissues outside of symbiont-containing cells. Joint information about expression patterns in response to heat and cell specificity will allow greater dissection of the regulatory pathways and specific cell reactions that lead to coral bleaching.
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Affiliation(s)
- Nikki Traylor-Knowles
- Hopkins Marine Station, Stanford University, 120 Oceanview Blvd, Pacific Grove, CA 93950, USA
| | - Noah H Rose
- Hopkins Marine Station, Stanford University, 120 Oceanview Blvd, Pacific Grove, CA 93950, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Stanford University, 120 Oceanview Blvd, Pacific Grove, CA 93950, USA
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28
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Traylor-Knowles N. Distinctive wound-healing characteristics in the corals Pocillopora damicornis and Acropora hyacinthus found in two different temperature regimes. Mar Biol 2016; 163:231. [PMID: 27812225 PMCID: PMC5067285 DOI: 10.1007/s00227-016-3011-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/06/2016] [Indexed: 05/27/2023]
Abstract
Wound healing is a critical physiological function needed for survival in all marine organisms. However, it is particularly critical in organisms like corals, which cannot escape predators. In this study, I characterized the gross morphology of wound healing in Pocillopora damicornis and Acropora hyacinthus found in two pools with distinct previously documented temperature profiles in Ofu, American Samoa. I observed differences between healing rates of A. hyacinthus versus P. damicornis, but no significant difference in healing rates between A. hyacinthus colonies found in different environmental regimes. Both coral species exhibit very distinct healing phenotypes, where A. hyacinthus develops a pink pigmentation and P. damicornis forms an algal/sand plug. The algal/sand plug appeared in corals found in the highly variable pool more quickly than in the corals from the moderately variable pool. Lastly, P. damicornis appeared to never fully heal during this two-week study, indicating that it is a slower healer despite predation pressure.
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Affiliation(s)
- Nikki Traylor-Knowles
- Hopkins Marine Station, Stanford University, 120 Oceanview Blvd, Pacific Grove, CA 93950 USA
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
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29
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Traylor-Knowles N, Palumbi SR. Translational environmental biology: cell biology informing conservation. Trends Cell Biol 2014; 24:265-7. [PMID: 24766840 DOI: 10.1016/j.tcb.2014.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 02/06/2023]
Abstract
Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA.
| | - Stephen R Palumbi
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
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30
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Abstract
Reef corals are highly sensitive to heat, yet populations resistant to climate change have recently been identified. To determine the mechanisms of temperature tolerance, we reciprocally transplanted corals between reef sites experiencing distinct temperature regimes and tested subsequent physiological and gene expression profiles. Local acclimatization and fixed effects, such as adaptation, contributed about equally to heat tolerance and are reflected in patterns of gene expression. In less than 2 years, acclimatization achieves the same heat tolerance that we would expect from strong natural selection over many generations for these long-lived organisms. Our results show both short-term acclimatory and longer-term adaptive acquisition of climate resistance. Adding these adaptive abilities to ecosystem models is likely to slow predictions of demise for coral reef ecosystems.
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Affiliation(s)
- Stephen R Palumbi
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA.
| | - Daniel J Barshis
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Nikki Traylor-Knowles
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Rachael A Bay
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
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31
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DuBuc TQ, Traylor-Knowles N, Martindale MQ. Initiating a regenerative response; cellular and molecular features of wound healing in the cnidarian Nematostella vectensis. BMC Biol 2014; 12:24. [PMID: 24670243 PMCID: PMC4229989 DOI: 10.1186/1741-7007-12-24] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [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: 01/15/2014] [Accepted: 03/12/2014] [Indexed: 11/17/2022] Open
Abstract
Background Wound healing is the first stage of a series of cellular events that are necessary to initiate a regenerative response. Defective wound healing can block regeneration even in animals with a high regenerative capacity. Understanding how signals generated during wound healing promote regeneration of lost structures is highly important, considering that virtually all animals have the ability to heal but many lack the ability to regenerate missing structures. Cnidarians are the phylogenetic sister taxa to bilaterians and are highly regenerative animals. To gain a greater understanding of how early animals generate a regenerative response, we examined the cellular and molecular components involved during wound healing in the anthozoan cnidarian Nematostella vectensis. Results Pharmacological inhibition of extracellular signal-regulated kinases (ERK) signaling blocks regeneration and wound healing in Nematostella. We characterized early and late wound healing events through genome-wide microarray analysis, quantitative PCR, and in situ hybridization to identify potential wound healing targets. We identified a number of genes directly related to the wound healing response in other animals (metalloproteinases, growth factors, transcription factors) and suggest that glycoproteins (mucins and uromodulin) play a key role in early wound healing events. This study also identified a novel cnidarian-specific gene, for a thiamine biosynthesis enzyme (vitamin B synthesis), that may have been incorporated into the genome by lateral gene transfer from bacteria and now functions during wound healing. Lastly, we suggest that ERK signaling is a shared element of the early wound response for animals with a high regenerative capacity. Conclusions This research describes the temporal events involved during Nematostella wound healing, and provides a foundation for comparative analysis with other regenerative and non-regenerative species. We have shown that the same genes that heal puncture wounds are also activated after oral-aboral bisection, indicating a clear link with the initiation of regenerative healing. This study demonstrates the strength of using a forward approach (microarray) to characterize a developmental phenomenon (wound healing) at a phylogenetically important crossroad of animal evolution (cnidarian-bilaterian ancestor). Accumulation of data on the early wound healing events across numerous systems may provide clues as to why some animals have limited regenerative abilities.
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Affiliation(s)
| | | | - Mark Q Martindale
- University of Florida, Whitney Marine Laboratory, 9505 Oceanshore Boulevard, St, Augustine, FL 32080, USA.
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32
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Abstract
Reef-building corals form bio-diverse marine ecosystems of high societal and economic value, but are in significant decline globally due, in part, to rapid climatic changes. As immunity is a predictor of coral disease and thermal stress susceptibility, a comprehensive understanding of this new field will likely provide a mechanistic explanation for ecological-scale trends in reef declines. Recently, several strides within coral immunology document defence mechanisms that are consistent with those of both invertebrates and vertebrates, and which span the recognition, signalling and effector response phases of innate immunity. However, many of these studies remain discrete and unincorporated into the wider fields of invertebrate immunology or coral biology. To encourage the rapid development of coral immunology, we comprehensively synthesize the current understanding of the field in the context of general invertebrate immunology, and highlight fundamental gaps in our knowledge. We propose a framework for future research that we hope will stimulate directional studies in this emerging field and lead to the elucidation of an integrated network of coral immune mechanisms. Once established, we are optimistic that coral immunology can be effectively applied to pertinent ecological questions, improve current prediction tools and aid conservation efforts.
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Affiliation(s)
- C V Palmer
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia.
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33
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Traylor-Knowles N, Granger BR, Lubinski TJ, Parikh JR, Garamszegi S, Xia Y, Marto JA, Kaufman L, Finnerty JR. Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis. BMC Genomics 2011; 12:585. [PMID: 22126435 PMCID: PMC3339375 DOI: 10.1186/1471-2164-12-585] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [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: 02/16/2011] [Accepted: 11/29/2011] [Indexed: 11/21/2022] Open
Abstract
Background Motivated by the precarious state of the world's coral reefs, there is currently a keen interest in coral transcriptomics. By identifying changes in coral gene expression that are triggered by particular environmental stressors, we can begin to characterize coral stress responses at the molecular level, which should lead to the development of more powerful diagnostic tools for evaluating the health of corals in the field. Furthermore, the identification of genetic variants that are more or less resilient in the face of particular stressors will help us to develop more reliable prognoses for particular coral populations. Toward this end, we performed deep mRNA sequencing of the cauliflower coral, Pocillopora damicornis, a geographically widespread Indo-Pacific species that exhibits a great diversity of colony forms and is able to thrive in habitats subject to a wide range of human impacts. Importantly, P. damicornis is particularly amenable to laboratory culture. We collected specimens from three geographically isolated Hawaiian populations subjected to qualitatively different levels of human impact. We isolated RNA from colony fragments ("nubbins") exposed to four environmental stressors (heat, desiccation, peroxide, and hypo-saline conditions) or control conditions. The RNA was pooled and sequenced using the 454 platform. Description Both the raw reads (n = 1, 116, 551) and the assembled contigs (n = 70, 786; mean length = 836 nucleotides) were deposited in a new publicly available relational database called PocilloporaBase http://www.PocilloporaBase.org. Using BLASTX, 47.2% of the contigs were found to match a sequence in the NCBI database at an E-value threshold of ≤.001; 93.6% of those contigs with matches in the NCBI database appear to be of metazoan origin and 2.3% bacterial origin, while most of the remaining 4.1% match to other eukaryotes, including algae and amoebae. Conclusions P. damicornis now joins the handful of coral species for which extensive transcriptomic data are publicly available. Through PocilloporaBase http://www.PocilloporaBase.org, one can obtain assembled contigs and raw reads and query the data according to a wide assortment of attributes including taxonomic origin, PFAM motif, KEGG pathway, and GO annotation.
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34
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Marquez EC, Traylor-Knowles N, Novillo-Villajos A, Callard IP. Novel cDNA sequences of aryl hydrocarbon receptors and gene expression in turtles (Chrysemys picta and Pseudemys scripta) exposed to different environments. Comp Biochem Physiol C Toxicol Pharmacol 2011; 154:305-17. [PMID: 21763458 PMCID: PMC3176672 DOI: 10.1016/j.cbpc.2011.06.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/24/2011] [Accepted: 06/27/2011] [Indexed: 10/18/2022]
Abstract
Reproductive changes have been observed in painted turtles from a site with known contamination located on Cape Cod, MA, USA. We hypothesize that these changes are caused by exposure to endocrine-disrupting compounds and that genes involved in reproduction are affected. The aryl hydrocarbon receptor (AHR) is an orphan receptor that is activated by environmental contaminants. AHR mRNA was measured in turtles exposed to soil collected from a contaminated site. Adult turtles were trapped from the study site (Moody Pond, MP) or a reference site and exposed to laboratory environments containing soil from either site. The red-eared slider was used to assess neonatal exposure to soil and water from the sites. The environmental exposures occurred over a 13-month period. Juveniles showed an age-dependent increase in brain AHR1. Juvenile turtles exposed to the MP environment had elevated gonadal AHR1. Adult turtles exposed to the MP environment showed significantly decreased brain AHR2. The painted turtle AHR is the first complete reptile AHR cDNA sequence. Phylogenetic analysis of the painted turtle AHR showed that it clusters with other AHR2s. Partial AHR1 and partial AHR2 cDNA sequences were cloned from the red-eared slider. MEME analysis identified 18 motifs in the turtle AHRs, showing high conservation between motifs that overlapped functional regions in both AHR isoforms.
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Affiliation(s)
| | | | | | - Ian P. Callard
- Boston University Department of Biology, Boston, MA, 02215, USA
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Marquez EC, Traylor-Knowles N, Novillo-Villajos A, Callard IP. Cloning of estrogen receptor alpha and aromatase cDNAs and gene expression in turtles (Chrysemys picta and Pseudemys scripta) exposed to different environments. Comp Biochem Physiol C Toxicol Pharmacol 2011; 154:213-25. [PMID: 21664488 DOI: 10.1016/j.cbpc.2011.05.008] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 05/19/2011] [Accepted: 05/25/2011] [Indexed: 11/22/2022]
Abstract
Reproductive changes have been observed in painted turtles (Chrysemys picta) from a site with known contamination located on Cape Cod, MA, USA. We hypothesize that these changes are caused by exposure to endocrine-disrupting compounds and that genes playing a significant role in reproduction are affected. cDNA sequences were determined for estrogen receptor alpha and aromatase in the painted turtle. These genes were measured in our study animals using quantitative PCR. Adult turtles were trapped from our study site (Moody Pond, MP) or a reference site (Washburn Pond) and exposed to laboratory environments containing soil from either site. The red-eared slider (Pseudemys scripta), a pond turtle closely related to the painted turtle, was used to assess neonatal exposure to soil and water from the sites. Our results show an increase in hepatic estrogen receptor, which suggests exposure to estrogenic contaminants. Female turtles from MP appear to have a long-term effect on hepatic ER. Other findings were apparent age-dependent differences in expression of aromatase and ER in the brains of neonate and year-old juvenile turtles. Phylogenetic analyses of the cDNA sequences further support the hypothesis that turtles are in a sister clade to birds and crocodilians.
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Affiliation(s)
- Emily C Marquez
- Boston University, Department of Biology, 5 Cummington St., Boston, MA 02215, USA
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Traylor-Knowles N, Hansen U, Dubuc TQ, Martindale MQ, Kaufman L, Finnerty JR. The evolutionary diversification of LSF and Grainyhead transcription factors preceded the radiation of basal animal lineages. BMC Evol Biol 2010; 10:101. [PMID: 20398424 PMCID: PMC2873413 DOI: 10.1186/1471-2148-10-101] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [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: 05/23/2009] [Accepted: 04/18/2010] [Indexed: 11/10/2022] Open
Abstract
Background The transcription factors of the LSF/Grainyhead (GRH) family are characterized by the possession of a distinctive DNA-binding domain that bears no clear relationship to other known DNA-binding domains, with the possible exception of the p53 core domain. In triploblastic animals, the LSF and GRH subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of DNA binding. For example, Grainyhead (GRH) homologs are expressed primarily in the epidermis, and they appear to play an ancient role in maintaining the epidermal barrier. By contrast, LSF homologs are more widely expressed, and they regulate general cellular functions such as cell cycle progression and survival in addition to cell-lineage specific gene expression. Results To illuminate the early evolution of this family and reconstruct the functional divergence of LSF and GRH, we compared homologs from 18 phylogenetically diverse taxa, including four basal animals (Nematostella vectensis, Vallicula multiformis, Trichoplax adhaerens, and Amphimedon queenslandica), a choanoflagellate (Monosiga brevicollis) and several fungi. Phylogenetic and bioinformatic analyses of these sequences indicate that (1) the LSF/GRH gene family originated prior to the animal-fungal divergence, and (2) the functional diversification of the LSF and GRH subfamilies occurred prior to the divergence between sponges and eumetazoans. Aspects of the domain architecture of LSF/GRH proteins are well conserved between fungi, choanoflagellates, and metazoans, though within the Metazoa, the LSF and GRH families are clearly distinct. We failed to identify a convincing LSF/GRH homolog in the sequenced genomes of the algae Volvox carteri and Chlamydomonas reinhardtii or the amoebozoan Dictyostelium purpureum. Interestingly, the ancestral GRH locus has become split into two separate loci in the sea anemone Nematostella, with one locus encoding a DNA binding domain and the other locus encoding the dimerization domain. Conclusions In metazoans, LSF and GRH proteins play a number of roles that are essential to achieving and maintaining multicellularity. It is now clear that this protein family already existed in the unicellular ancestor of animals, choanoflagellates, and fungi. However, the diversification of distinct LSF and GRH subfamilies appears to be a metazoan invention. Given the conserved role of GRH in maintaining epithelial integrity in vertebrates, insects, and nematodes, it is noteworthy that the evolutionary origin of Grh appears roughly coincident with the evolutionary origin of the epithelium.
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Sullivan JC, Wolenski FS, Reitzel AM, French CE, Traylor-Knowles N, Gilmore TD, Finnerty JR. Two alleles of NF-kappaB in the sea anemone Nematostella vectensis are widely dispersed in nature and encode proteins with distinct activities. PLoS One 2009; 4:e7311. [PMID: 19806194 PMCID: PMC2751831 DOI: 10.1371/journal.pone.0007311] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [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: 05/11/2009] [Accepted: 08/06/2009] [Indexed: 12/22/2022] Open
Abstract
Background NF-κB is an evolutionarily conserved transcription factor that controls the expression of genes involved in many key organismal processes, including innate immunity, development, and stress responses. NF-κB proteins contain a highly conserved DNA-binding/dimerization domain called the Rel homology domain. Methods/Principal Findings We characterized two NF-κB alleles in the sea anemone Nematostella vectensis that differ at nineteen single-nucleotide polymorphisms (SNPs). Ten of these SNPs result in amino acid substitutions, including six within the Rel homology domain. Both alleles are found in natural populations of Nematostella. The relative abundance of the two NF-κB alleles differs between populations, and departures from Hardy-Weinberg equilibrium within populations indicate that the locus may be under selection. The proteins encoded by the two Nv-NF-κB alleles have different molecular properties, in part due to a Cys/Ser polymorphism at residue 67, which resides within the DNA recognition loop. In nearly all previously characterized NF-κB proteins, the analogous residue is fixed for Cys, and conversion of human RHD proteins from Cys to Ser at this site has been shown to increase DNA-binding ability and increase resistance to inhibition by thiol-reactive compounds. However, the naturally-occurring Nematostella variant with Cys at position 67 binds DNA with a higher affinity than the Ser variant. On the other hand, the Ser variant activates transcription in reporter gene assays more effectively, and it is more resistant to inhibition by a thiol-reactive compound. Reciprocal Cys<->Ser mutations at residue 67 of the native Nv-NF-κB proteins affect DNA binding as in human NF-κB proteins, e.g., a Cys->Ser mutation increases DNA binding of the native Cys variant. Conclusions/Significance These results are the first demonstration of a naturally occurring and functionally significant polymorphism in NF-κB in any species. The functional differences between these alleles and their uneven distribution in the wild suggest that different genotypes could be favored in different environments, perhaps environments that vary in their levels of peroxides or thiol-reactive compounds.
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Affiliation(s)
- James C. Sullivan
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Francis S. Wolenski
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Adam M. Reitzel
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Courtney E. French
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Nikki Traylor-Knowles
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Thomas D. Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - John R. Finnerty
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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Reitzel AM, Sullivan JC, Traylor-Knowles N, Finnerty JR. Genomic survey of candidate stress-response genes in the estuarine anemone Nematostella vectensis. Biol Bull 2008; 214:233-254. [PMID: 18574101 DOI: 10.2307/25470666] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Salt marshes are challenging habitats due to natural variability in key environmental parameters including temperature, salinity, ultraviolet light, oxygen, sulfides, and reactive oxygen species. Compounding this natural variation, salt marshes are often heavily impacted by anthropogenic insults including eutrophication, toxic contamination, and coastal development that alter tidal and freshwater inputs. Commensurate with this environmental variability, estuarine animals generally exhibit broader physiological tolerances than freshwater, marine, or terrestrial species. One factor that determines an organism's physiological tolerance is its ability to upregulate "stress-response genes" in reaction to particular stressors. Comparative studies on diverse organisms have identified a number of evolutionarily conserved genes involved in responding to abiotic and biotic stressors. We used homology-based scans to survey the sequenced genome of Nematostella vectensis, the starlet sea anemone, an estuarine specialist, to identify genes involved in the response to three kinds of insult-physiochemical insults, pathogens, and injury. Many components of the stress-response networks identified in triploblastic animals have clear orthologs in the sea anemone, meaning that they must predate the cnidarian-triploblast split (e.g., xenobiotic receptors, biotransformative genes, ATP-dependent transporters, and genes involved in responding to reactive oxygen species, toxic metals, osmotic shock, thermal stress, pathogen exposure, and wounding). However, in some instances, stress-response genes known from triploblasts appear to be absent from the Nematostella genome (e.g., many metal-complexing genes). This is the first comprehensive examination of the genomic stress-response repertoire of an estuarine animal and a member of the phylum Cnidaria. The molecular markers of stress response identified in Nematostella may prove useful in monitoring estuary health and evaluating coastal conservation efforts. These data may also inform conservation efforts on other cnidarians, such as the reef-building corals.
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Affiliation(s)
- Adam M Reitzel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA
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