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Mammola S, Adamo M, Antić D, Calevo J, Cancellario T, Cardoso P, Chamberlain D, Chialva M, Durucan F, Fontaneto D, Goncalves D, Martínez A, Santini L, Rubio-Lopez I, Sousa R, Villegas-Rios D, Verdes A, Correia RA. Drivers of species knowledge across the tree of life. eLife 2023; 12:RP88251. [PMID: 37846960 PMCID: PMC10581686 DOI: 10.7554/elife.88251] [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] [Indexed: 10/18/2023] Open
Abstract
Knowledge of biodiversity is unevenly distributed across the Tree of Life. In the long run, such disparity in awareness unbalances our understanding of life on Earth, influencing policy decisions and the allocation of research and conservation funding. We investigated how humans accumulate knowledge of biodiversity by searching for consistent relationships between scientific (number of publications) and societal (number of views in Wikipedia) interest, and species-level morphological, ecological, and sociocultural factors. Across a random selection of 3019 species spanning 29 Phyla/Divisions, we show that sociocultural factors are the most important correlates of scientific and societal interest in biodiversity, including the fact that a species is useful or harmful to humans, has a common name, and is listed in the International Union for Conservation of Nature Red List. Furthermore, large-bodied, broadly distributed, and taxonomically unique species receive more scientific and societal attention, whereas colorfulness and phylogenetic proximity to humans correlate exclusively with societal attention. These results highlight a favoritism toward limited branches of the Tree of Life, and that scientific and societal priorities in biodiversity research broadly align. This suggests that we may be missing out on key species in our research and conservation agenda simply because they are not on our cultural radar.
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Affiliation(s)
- Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of HelsinkiHelsinkiFinland
- National Biodiversity Future CenterPalermoItaly
| | - Martino Adamo
- National Biodiversity Future CenterPalermoItaly
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Dragan Antić
- University of Belgrade - Faculty of BiologyBelgradeSerbia
| | - Jacopo Calevo
- Royal Botanic GardensLondonUnited Kingdom
- School of Molecular and Life Sciences, Curtin UniversityPerthAustralia
| | - Tommaso Cancellario
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of HelsinkiHelsinkiFinland
| | - Dan Chamberlain
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Matteo Chialva
- National Biodiversity Future CenterPalermoItaly
- Department of Life Sciences and Systems Biology, University of TurinTorinoItaly
| | - Furkan Durucan
- Department of Aquaculture, Isparta University of Applied SciencesIspartaTurkey
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
- National Biodiversity Future CenterPalermoItaly
| | - Duarte Goncalves
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of PortoMatosinhosPortugal
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Luca Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Iñigo Rubio-Lopez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research CouncilVerbaniaItaly
| | - Ronaldo Sousa
- CBMA – Centre of Molecular and Environmental Biology, Department of Biology, University of MinhoMinhoPortugal
| | | | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias NaturalesMadridSpain
| | - Ricardo A Correia
- Helsinki Lab of Interdisciplinary Conservation Science (HELICS), Department of Geosciences and Geography, University of HelsinkiHelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS), University of HelsinkiHelsinkiFinland
- CESAM – Centre for Environmental and Marine Studies, University of AveiroAveiroPortugal
- Biodiversity Unit, University of TurkuTurkuFinland
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Moreno-Martín P, Mourín M, Verdes A, Álvarez-Campos P. Morphological and molecular study of Syllinae (Annelida, Syllidae) from Bermuda, with the description of five new species. R Soc Open Sci 2023; 10:230638. [PMID: 37621663 PMCID: PMC10445030 DOI: 10.1098/rsos.230638] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Although polychaetes from the Bermuda Archipelago have been studied since the beginning of the twentieth century, syllids have been particularly neglected in this area, which is surprising considering this family is usually a dominant group in marine benthic ecosystems. To fill this knowledge gap, we have carried out an extensive analysis of Bermudan Syllidae, combining morphological and molecular data including four nuclear and mitochondrial markers (cytochrome c oxidase subunit I, 18S rRNA, 16S rRNA and 28S rRNA). We have identified and established the phylogenetic position of five new species, Haplosyllis anitae n. sp., Haplosyllis guillei n. sp., Haplosyllis larsi n. sp., Haplosyllis vassiae n. sp. and Syllis laiae n. sp., together with Haplosyllis cf. cephalata. Overall, our results extend the knowledge on the diversity of Syllidae in Bermuda, increasing the number of species present in the area to 25. Our results also recover Opisthosyllis and Syllis as non-monophyletic genera, for which traditional diagnostic morphological features do not accurately reflect their evolutionary histories, and thus we propose that these groups should be reorganized based on molecular characters.
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Affiliation(s)
- Paula Moreno-Martín
- Centro de Investigación en Biodiversidad y Cambio global (CIBC-UAM), Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Mar Mourín
- Centro de Investigación en Biodiversidad y Cambio global (CIBC-UAM), Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Aida Verdes
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales de Madrid, Consejo Superior de Investigaciones Científicas, MNCN-CSIC, Madrid, Spain
| | - Patricia Álvarez-Campos
- Centro de Investigación en Biodiversidad y Cambio global (CIBC-UAM), Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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del Olmo I, Verdes A, Álvarez‐Campos P. Distinct patterns of gene expression during regeneration and asexual reproduction in the annelid Pristina leidyi. J Exp Zool B Mol Dev Evol 2022; 338:405-420. [PMID: 35604322 PMCID: PMC9790225 DOI: 10.1002/jez.b.23143] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/03/2022] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
Regeneration, the ability to replace lost body parts, is a widespread phenomenon in the animal kingdom often connected to asexual reproduction or fission, since the only difference between the two appears to be the stimulus that triggers them. Both developmental processes have largely been characterized; however, the molecular toolkit and genetic mechanisms underlying these events remain poorly unexplored. Annelids, in particular the oligochaete Pristina leidyi, provide a good model system to investigate these processes as they show diverse ways to regenerate, and can reproduce asexually through fission under laboratory conditions. Here, we used a comparative transcriptomics approach based on RNA-sequencing and differential gene expression analyses to understand the molecular mechanisms involved in anterior regeneration and asexual reproduction. We found 291 genes upregulated during anterior regeneration, including several regeneration-related genes previously reported in other annelids such as frizzled, paics, and vdra. On the other hand, during asexual reproduction, 130 genes were found upregulated, and unexpectedly, many of them were related to germline development during sexual reproduction. We also found important differences between anterior regeneration and asexual reproduction, with the latter showing a gene expression profile more similar to that of control individuals. Nevertheless, we identified 35 genes that were upregulated in both conditions, many of them related to cell pluripotency, stem cells, and cell proliferation. Overall, our results shed light on the molecular mechanisms that control anterior regeneration and asexual reproduction in annelids and reveal similarities with other animals, suggesting that the genetic machinery controlling these processes is conserved across metazoans.
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Affiliation(s)
- Irene del Olmo
- Department of Biology (Zoology)Universidad Autónoma de MadridMadridSpain
| | - Aida Verdes
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de MadridMadridSpain
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von Reumont BM, Anderluh G, Antunes A, Ayvazyan N, Beis D, Caliskan F, Crnković A, Damm M, Dutertre S, Ellgaard L, Gajski G, German H, Halassy B, Hempel BF, Hucho T, Igci N, Ikonomopoulou MP, Karbat I, Klapa MI, Koludarov I, Kool J, Lüddecke T, Ben Mansour R, Vittoria Modica M, Moran Y, Nalbantsoy A, Ibáñez MEP, Panagiotopoulos A, Reuveny E, Céspedes JS, Sombke A, Surm JM, Undheim EAB, Verdes A, Zancolli G. Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research. Gigascience 2022; 11:6588117. [PMID: 35640874 PMCID: PMC9155608 DOI: 10.1093/gigascience/giac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.
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Affiliation(s)
- Bjoern M von Reumont
- Goethe University Frankfurt, Institute for Cell Biology and Neuroscience, Department for Applied Bioinformatics, 60438 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany.,Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Naira Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbeli ave. 22, 0028 Yerevan, Armenia
| | - Dimitris Beis
- Developmental Biology, Centre for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 11527, Greece
| | - Figen Caliskan
- Department of Biology, Faculty of Science and Letters, Eskisehir Osmangazi University, TR-26040 Eskisehir, Turkey
| | - Ana Crnković
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Maik Damm
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Hannah German
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Trg Republike Hrvatske 14, 10000 Zagreb, Croatia
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nasit Igci
- Nevsehir Haci Bektas Veli University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 50300 Nevsehir, Turkey
| | - Maria P Ikonomopoulou
- Madrid Institute for Advanced Studies in Food, Madrid,E28049, Spain.,The University of Queensland, St Lucia, QLD 4072, Australia
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
| | - Ivan Koludarov
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Tim Lüddecke
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany.,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35392 Gießen, Germany
| | - Riadh Ben Mansour
- Department of Life Sciences, Faculty of Sciences, Gafsa University, Campus Universitaire Siidi Ahmed Zarrouk, 2112 Gafsa, Tunisia
| | - Maria Vittoria Modica
- Dept. of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Via Po 25c, I-00198 Roma, Italy
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - María Eugenia Pachón Ibáñez
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain.,CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexios Panagiotopoulos
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece.,Animal Biology Division, Department of Biology, University of Patras, Patras, GR-26500, Greece
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Javier Sánchez Céspedes
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain.,CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Andy Sombke
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eivind A B Undheim
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Postboks 1066 Blindern 0316 Oslo, Norway
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Verdes A, Taboada S, Hamilton BR, Undheim EAB, Sonoda GG, Andrade SCS, Morato E, Isabel Marina A, Cárdenas CA, Riesgo A. Evolution, expression patterns and distribution of novel ribbon worm predatory and defensive toxins. Mol Biol Evol 2022; 39:6580756. [PMID: 35512366 PMCID: PMC9132205 DOI: 10.1093/molbev/msac096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Indexed: 11/17/2022] Open
Abstract
Ribbon worms are active predators that use an eversible proboscis to inject venom into their prey and defend themselves with toxic epidermal secretions. Previous work on nemertean venom has largely focused on just a few species and has not investigated the different predatory and defensive secretions in detail. Consequently, our understanding of the composition and evolution of ribbon worm venoms is still very limited. Here, we present a comparative study of nemertean venom combining RNA-seq differential gene expression analyses of venom-producing tissues, tandem mass spectrometry-based proteomics of toxic secretions, and mass spectrometry imaging of proboscis sections, to shed light onto the composition and evolution of predatory and defensive toxic secretions in Antarctonemertes valida. Our analyses reveal a wide diversity of putative defensive and predatory toxins with tissue-specific gene expression patterns and restricted distributions to the mucus and proboscis proteomes respectively, suggesting that ribbon worms produce distinct toxin cocktails for predation and defense. Our results also highlight the presence of numerous lineage-specific toxins, indicating that venom evolution is highly divergent across nemerteans, producing toxin cocktails that might be finely tuned to subdue different prey. Our data also suggest that the hoplonemertean proboscis is a highly specialized predatory organ that seems to be involved in a variety of biological functions besides predation, including secretion and sensory perception. Overall, our results advance our knowledge into the diversity and evolution of nemertean venoms and highlight the importance of combining different types of data to characterize toxin composition in understudied venomous organisms.
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Affiliation(s)
- Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN), CSIC, Madrid, Spain.,Department of Life Sciences, Natural History Museum, London, UK
| | - Sergi Taboada
- Department of Life Sciences, Natural History Museum, London, UK.,Departament of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Brett R Hamilton
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia.,Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gabriel G Sonoda
- Departmento de Genética e Biología Evolutiva, University of Sao Paulo, Sao Paulo, Brazil
| | - Sonia C S Andrade
- Departmento de Genética e Biología Evolutiva, University of Sao Paulo, Sao Paulo, Brazil
| | - Esperanza Morato
- CBMSO Protein Chemistry Facility, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Isabel Marina
- CBMSO Protein Chemistry Facility, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN), CSIC, Madrid, Spain.,Department of Life Sciences, Natural History Museum, London, UK
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Verdes A, Álvarez-Campos P, Nygren A, San Martín G, Deheyn DD, Gruber DF, Holford M. Molecular phylogeny and evolution of bioluminescence in Odontosyllis (Annelida, Syllidae). INVERTEBR SYST 2022. [DOI: 10.1071/is22007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Modica MV, Ahmad R, Ainsworth S, Anderluh G, Antunes A, Beis D, Caliskan F, Serra MD, Dutertre S, Moran Y, Nalbantsoy A, Oukkache N, Pekar S, Remm M, von Reumont BM, Sarigiannis Y, Tarallo A, Tytgat J, Undheim EAB, Utkin Y, Verdes A, Violette A, Zancolli G. Corrigendum to: The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics. Gigascience 2021; 10:6489122. [PMID: 34966929 PMCID: PMC8716359 DOI: 10.1093/gigascience/giab102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2318 Hamar, Norway
| | - Stuart Ainsworth
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, L3 5QA, Liverpool, UK
| | - Gregor Anderluh
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, 4450-208 Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Dimitris Beis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 115 27 Athens, Greece
| | - Figen Caliskan
- Eskisehir Osmangazi University, Faculty of Science and Letters, Department of Biology, TR-26040 Eskisehir, Turkey
| | - Mauro Dalla Serra
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via De Marini 6 - Torre di Francia, 16149 Genova, Italy
| | - Sebastien Dutertre
- IBMM, Universite de Montpellier, CNRS, ´ ENSCM, Place Eugene Bataillon, 34095 Montpellier, France
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram 9190401 Jerusalem, Israel
| | - Ayse Nalbantsoy
- Ege University, Bioengineering Department, 180 Bornova, 35040 Izmir, Turkey
| | - Naoual Oukkache
- Institut Pasteur of Morocco, 1 Place Louis Pasteur, 20100 Casablanca, Morocco
| | - Stano Pekar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czechia
| | - Maido Remm
- Department of Bioinformatics, University of Tartu, IMCB, Riia 23, 51010, Tartu, Estonia
| | - Bjoern Marcus von Reumont
- Department of Insect Biotechnology, Justus Liebig University, Winchester Str. 2, 35394 Giessen, Germany.,LOEWE Center for Translational Biodiversity Genomics, Senckenberganlage 25 D-60325 Frankfurt/Main, Germany
| | - Yiannis Sarigiannis
- Department of Life and Health Sciences, University of Nicosia, 46 Makedonitissas Avenue, CY-2417 Nicosia, Cyprus
| | - Andrea Tarallo
- Department of Research infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Jan Tytgat
- Department of of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Eivind Andreas Baste Undheim
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 1066 Blindern, 0316 Oslo, Norway
| | - Yuri Utkin
- Laboratory of Molecular Toxinology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russian Federation
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Cient´ıficas, Calle de Jose Guti ´ errez ´ Abascal 2, 28006 Madrid, Spain.,Department of Life Science, Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - Aude Violette
- Alphabiotoxine Laboratory, B-7911 Montroeul-au-Bois, Belgium
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, UNIL Sorge Le Biophore, CH - 1015 Lausanne, Switzerland
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Verdes A, Arias MB, Junoy J, Schwartz ML, Kajihara H. Species delimitation and phylogenetic analyses reveal cryptic diversity within Cerebratulus marginatus (Nemertea: Pilidiophora). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1950231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Aida Verdes
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Calle José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - María Belén Arias
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Juan Junoy
- Departamento de Ciencias de la Vida, AP 20 Campus Universitario, Universidad de Alcalá, Alcalá de Henares, 28805, Spain
| | - Megan L. Schwartz
- Department Sciences and Mathematics, University of Washington, 1900 Commerce Avenue, Tacoma, 98420, WA, USA
| | - Hiroshi Kajihara
- Faculty of Science, Hokkaido University, Kita-ku N10 W8, Sapporo, 060-0810, Japan
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Modica MV, Ahmad R, Ainsworth S, Anderluh G, Antunes A, Beis D, Caliskan F, Serra MD, Dutertre S, Moran Y, Nalbantsoy A, Oukkache N, Pekar S, Remm M, von Reumont BM, Sarigiannis Y, Tarallo A, Tytgat J, Undheim EAB, Utkin Y, Verdes A, Violette A, Zancolli G. The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics. Gigascience 2021; 10:6187861. [PMID: 33764467 PMCID: PMC7992391 DOI: 10.1093/gigascience/giab019] [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: 02/02/2021] [Revised: 02/24/2021] [Accepted: 02/28/2021] [Indexed: 11/29/2022] Open
Abstract
Venom research is a highly multidisciplinary field that involves multiple subfields of
biology, informatics, pharmacology, medicine, and other areas. These different research
facets are often technologically challenging and pursued by different teams lacking
connection with each other. This lack of coordination hampers the full development of
venom investigation and applications. The COST Action CA19144–European Venom Network was
recently launched to promote synergistic interactions among different stakeholders and
foster venom research at the European level.
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Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2318 Hamar, Norway
| | - Stuart Ainsworth
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, L3 5QA, Liverpool, UK
| | - Gregor Anderluh
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, 4450-208 Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Dimitris Beis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 115 27 Athens, Greece
| | - Figen Caliskan
- Eskisehir Osmangazi University, Faculty of Science and Letters, Department of Biology, TR-26040 Eskisehir, Turkey
| | - Mauro Dalla Serra
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via De Marini 6 - Torre di Francia, 16149 Genova, Italy
| | - Sebastien Dutertre
- IBMM, Université de Montpellier, CNRS, ENSCM, Place Eugene Bataillon, 34095 Montpellier, France
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram 9190401 Jerusalem, Israel
| | - Ayse Nalbantsoy
- Ege University, Bioengineering Department, 180 Bornova, 35040 Izmir, Turkey
| | - Naoual Oukkache
- Institut Pasteur of Morocco, 1 Place Louis Pasteur, 20100 Casablanca, Morocco
| | - Stano Pekar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czechia
| | - Maido Remm
- Department of Bioinformatics, University of Tartu, IMCB, Riia 23, 51010, Tartu, Estonia
| | - Bjoern Marcus von Reumont
- Department of Insect Biotechnology, Justus Liebig University, Winchester Str. 2, 35394 Giessen, Germany.,LOEWE Center for Translational Biodiversity Genomics, Senckenberganlage 25 D-60325 Frankfurt/Main, Germany
| | - Yiannis Sarigiannis
- Department of Life and Health Sciences, University of Nicosia, 46 Makedonitissas Avenue, CY-2417 Nicosia, Cyprus
| | - Andrea Tarallo
- Department of Research infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Jan Tytgat
- Department of of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Eivind Andreas Baste Undheim
- Centre for Ecological and Evolutionary Synthesis,Department of Biosciences, University of Oslo, 1066 Blindern, 0316 Oslo, Norway
| | - Yuri Utkin
- Laboratory of Molecular Toxinology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russian Federation
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Calle de José Gutiérrez Abascal 2, 28006 Madrid, Spain.,Department of Life Science, Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - Aude Violette
- Alphabiotoxine Laboratory, B-7911 Montroeul-au-Bois, Belgium
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, UNIL Sorge Le Biophore, CH - 1015 Lausanne, Switzerland
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Álvarez-Campos P, Kenny NJ, Verdes A, Fernández R, Novo M, Giribet G, Riesgo A. Delegating Sex: Differential Gene Expression in Stolonizing Syllids Uncovers the Hormonal Control of Reproduction. Genome Biol Evol 2019; 11:295-318. [PMID: 30535381 PMCID: PMC6350857 DOI: 10.1093/gbe/evy265] [Citation(s) in RCA: 9] [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] [Accepted: 12/09/2018] [Indexed: 12/31/2022] Open
Abstract
Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed generally at the posterior end of the animal. When stolons mature, they detach from the adult and gametes are released into the water column. The process is synchronized within each species, and it has been reported to be under environmental and endogenous control, probably via endocrine regulation. To further understand reproduction in syllids and to elucidate the molecular toolkit underlying stolonization, we generated Illumina RNA-seq data from different tissues of reproductive and nonreproductive individuals of Syllis magdalena and characterized gene expression during the stolonization process. Several genes involved in gametogenesis (ovochymase, vitellogenin, testis-specific serine/threonine-kinase), immune response (complement receptor 2), neuronal development (tyrosine-protein kinase Src42A), cell proliferation (alpha-1D adrenergic receptor), and steroid metabolism (hydroxysteroid dehydrogenase 2) were found differentially expressed in the different tissues and conditions analyzed. In addition, our findings suggest that several neurohormones, such as methyl farnesoate, dopamine, and serotonin, might trigger stolon formation, the correct maturation of gametes and the detachment of stolons when gametogenesis ends. The process seems to be under circadian control, as indicated by the expression patterns of r-opsins. Overall, our results shed light into the genes that orchestrate the onset of gamete formation and improve our understanding of how some hormones, previously reported to be involved in reproduction and metamorphosis processes in other invertebrates, seem to also regulate reproduction via stolonization.
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Affiliation(s)
- Patricia Álvarez-Campos
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Spain
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
- Department of Biological & Medical Sciences, Oxford Brookes University, Headington Campus, Gipsy Lane, Oxford, United Kingdom
| | - Nathan J Kenny
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
| | - Aida Verdes
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Spain
- Department of Biology, The Graduate Center, City University of New York
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Rosa Fernández
- Bioinformatics & Genomics Unit, Center for Genomic Regulation, Barcelona, Spain
| | - Marta Novo
- Facultad de Biología, Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Ana Riesgo
- Department of Biology, The Graduate Center, City University of New York
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11
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Verdes A, Simpson D, Holford M. Are Fireworms Venomous? Evidence for the Convergent Evolution of Toxin Homologs in Three Species of Fireworms (Annelida, Amphinomidae). Genome Biol Evol 2018; 10:249-268. [PMID: 29293976 PMCID: PMC5778601 DOI: 10.1093/gbe/evx279] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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] [Accepted: 12/23/2017] [Indexed: 12/14/2022] Open
Abstract
Amphinomids, more commonly known as fireworms, are a basal lineage of marine annelids characterized by the presence of defensive dorsal calcareous chaetae, which break off upon contact. It has long been hypothesized that amphinomids are venomous and use the chaetae to inject a toxic substance. However, studies investigating fireworm venom from a morphological or molecular perspective are scarce and no venom gland has been identified to date, nor any toxin characterized at the molecular level. To investigate this question, we analyzed the transcriptomes of three species of fireworms-Eurythoe complanata, Hermodice carunculata, and Paramphinome jeffreysii-following a venomics approach to identify putative venom compounds. Our venomics pipeline involved de novo transcriptome assembly, open reading frame, and signal sequence prediction, followed by three different homology search strategies: BLAST, HMMER sequence, and HMMER domain. Following this pipeline, we identified 34 clusters of orthologous genes, representing 13 known toxin classes that have been repeatedly recruited into animal venoms. Specifically, the three species share a similar toxin profile with C-type lectins, peptidases, metalloproteinases, spider toxins, and CAP proteins found among the most highly expressed toxin homologs. Despite their great diversity, the putative toxins identified are predominantly involved in three major biological processes: hemostasis, inflammatory response, and allergic reactions, all of which are commonly disrupted after fireworm stings. Although the putative fireworm toxins identified here need to be further validated, our results strongly suggest that fireworms are venomous animals that use a complex mixture of toxins for defense against predators.
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Affiliation(s)
- Aida Verdes
- Department of Chemistry, Hunter College Belfer Research Center, and The Graduate Center, Program in Biology, Chemistry and Biochemistry, City University of New York
- Department of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Spain
| | - Danny Simpson
- Department of Population Health, New York University School of Medicine
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, and The Graduate Center, Program in Biology, Chemistry and Biochemistry, City University of New York
- Department of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
- Department of Biochemistry, Weill Cornell Medical College, Cornell University
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12
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Verdes A, Holford M. Beach to Bench to Bedside: Marine Invertebrate Biochemical Adaptations and Their Applications in Biotechnology and Biomedicine. Results Probl Cell Differ 2018; 65:359-376. [PMID: 30083928 DOI: 10.1007/978-3-319-92486-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ocean covers more than 70% of the surface of the planet and harbors very diverse ecosystems ranging from tropical coral reefs to the deepest ocean trenches, with some of the most extreme conditions of pressure, temperature, and light. Organisms living in these environments have been subjected to strong selective pressures through millions of years of evolution, resulting in a plethora of remarkable adaptations that serve a variety of vital functions. Some of these adaptations, including venomous secretions and light-emitting compounds or ink, represent biochemical innovations in which marine invertebrates have developed novel and unique bioactive compounds with enormous potential for basic and applied research. Marine biotechnology, defined as the application of science and technology to marine organisms for the production of knowledge, goods, and services, can harness the enormous possibilities of these unique bioactive compounds acting as a bridge between biological knowledge and applications. This chapter highlights some of the most exceptional biochemical adaptions found specifically in marine invertebrates and describes the biotechnological and biomedical applications derived from them to improve the quality of human life.
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Affiliation(s)
- Aida Verdes
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Madrid, Spain.
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY, USA.
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, City University of New York, New York, NY, USA.
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, USA.
- The Graduate Center, Program in Biology, Chemistry and Biochemistry, City University of New York, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
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13
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Verdes A, Gruber DF. Glowing Worms: Biological, Chemical, and Functional Diversity of Bioluminescent Annelids. Integr Comp Biol 2017; 57:18-32. [DOI: 10.1093/icb/icx017] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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14
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Álvarez-Campos P, Verdes A. Syllids inhabiting holdfasts of Lessonia spicata in Central Chile: diversity, systematics, and description of three new species. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1285364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Patricia Álvarez-Campos
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Aida Verdes
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Department of Biology, The Graduate Center, City University of New York, 365 5th Ave, New York, NY, 10010, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
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15
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Verdes A, Anand P, Gorson J, Jannetti S, Kelly P, Leffler A, Simpson D, Ramrattan G, Holford M. From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins. Toxins (Basel) 2016; 8:117. [PMID: 27104567 PMCID: PMC4848642 DOI: 10.3390/toxins8040117] [Citation(s) in RCA: 32] [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: 03/03/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022] Open
Abstract
Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics methodologies, including genomics, transcriptomics, and proteomics; (3) chemical and recombinant synthesis of promising peptide toxins; (4) structural characterization through experimental and computational methods; (5) determination of teretoxin bioactivity and molecular function through biological assays and computational modeling; (6) optimization of peptide toxin affinity and selectivity to molecular target; and (7) development of strategies for effective delivery of venom peptide therapeutics. While our research focuses on terebrids, the venomics approach outlined here can be applied to the discovery and characterization of peptide toxins from any venomous taxa.
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Affiliation(s)
- Aida Verdes
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Prachi Anand
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Juliette Gorson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Stephen Jannetti
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Patrick Kelly
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Abba Leffler
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine 550 1st Avenue, New York, NY 10016, USA.
| | - Danny Simpson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Tandon School of Engineering, New York University 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Girish Ramrattan
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Mandë Holford
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
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16
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Verdes A, Cho W, Hossain M, Brennan PLR, Hanley D, Grim T, Hauber ME, Holford M. Nature's Palette: Characterization of Shared Pigments in Colorful Avian and Mollusk Shells. PLoS One 2015; 10:e0143545. [PMID: 26650398 PMCID: PMC4674117 DOI: 10.1371/journal.pone.0143545] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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] [Received: 08/18/2015] [Accepted: 11/05/2015] [Indexed: 11/21/2022] Open
Abstract
Pigment-based coloration is a common trait found in a variety of organisms across the tree of life. For example, calcareous avian eggs are natural structures that vary greatly in color, yet just a handful of tetrapyrrole pigment compounds are responsible for generating this myriad of colors. To fully understand the diversity and constraints shaping nature's palette, it is imperative to characterize the similarities and differences in the types of compounds involved in color production across diverse lineages. Pigment composition was investigated in eggshells of eleven paleognath bird taxa, covering several extinct and extant lineages, and shells of four extant species of mollusks. Birds and mollusks are two distantly related, calcareous shell-building groups, thus characterization of pigments in their calcareous structures would provide insights to whether similar compounds are found in different phyla (Chordata and Mollusca). An ethylenediaminetetraacetic acid (EDTA) extraction protocol was used to analyze the presence and concentration of biliverdin and protoporphyrin, two known and ubiquitous tetrapyrrole avian eggshell pigments, in all avian and molluscan samples. Biliverdin was solely detected in birds, including the colorful eggshells of four tinamou species. In contrast, protoporphyrin was detected in both the eggshells of several avian species and in the shells of all mollusks. These findings support previous hypotheses about the ubiquitous deposition of tetrapyrroles in the eggshells of various bird lineages and provide evidence for its presence also across distantly related animal taxa.
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Affiliation(s)
- Aida Verdes
- The Graduate Center, City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Wooyoung Cho
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
| | - Marouf Hossain
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
| | - Patricia L. R. Brennan
- Department of Psychology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Daniel Hanley
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc, Czech Republic
| | - Tomáš Grim
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc, Czech Republic
| | - Mark E. Hauber
- The Graduate Center, City University of New York, New York, New York, United States of America
- Department of Psychology, Hunter College, City University of New York, New York, New York, United States of America
| | - Mandë Holford
- The Graduate Center, City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
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17
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Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). BMC Genomics 2015; 16:445. [PMID: 26059236 PMCID: PMC4462082 DOI: 10.1186/s12864-015-1565-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce. Results We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids for our homology search, and Gene Ontology (GO) terms and InterPro IDs were assigned to 32,500 of these ORFs. We used this de novo assembled transcriptome to recover major signaling pathways and housekeeping genes. We also identify a suite of H. carunculata genes related to reproduction and immune response. Conclusions We provide a comprehensive catalogue of annotated genes for Hermodice carunculata and expand the knowledge of reproduction and immune response genes in annelids, in general. Overall, this study vastly expands the available genomic data for H. carunculata, of which previously consisted of only 279 nucleotide sequences in NCBI. This underscores the utility of Illumina sequencing for de novo transcriptome assembly in non-model organisms as a cost-effective and efficient tool for gene discovery and downstream applications, such as phylogenetic analysis and gene expression profiling. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1565-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shaadi Mehr
- Biological Science Department, State University of New York, College at Old Westbury, Old Westbury, NY, 11568, USA. .,American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - Aida Verdes
- Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
| | - Rob DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA.
| | - John Sparks
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,American Museum of Natural History, Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, NY, 10024, USA.
| | - Vincent Pieribone
- John B. Pierce Laboratory, Cellular and Molecular Physiology, Yale University, New Haven, CT 06519, USA.
| | - David F Gruber
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park W at 79th St, New York, NY, 10024, USA. .,Baruch College and The Graduate Center, Department of Natural Sciences, City University of New York, New York, NY, 10010, USA.
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18
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Gorson J, Ramrattan G, Verdes A, Wright EM, Kantor Y, Rajaram Srinivasan R, Musunuri R, Packer D, Albano G, Qiu WG, Holford M. Molecular Diversity and Gene Evolution of the Venom Arsenal of Terebridae Predatory Marine Snails. Genome Biol Evol 2015; 7:1761-78. [PMID: 26025559 PMCID: PMC4494067 DOI: 10.1093/gbe/evv104] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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] [Indexed: 11/16/2022] Open
Abstract
Venom peptides from predatory organisms are a resource for investigating evolutionary processes such as adaptive radiation or diversification, and exemplify promising targets for biomedical drug development. Terebridae are an understudied lineage of conoidean snails, which also includes cone snails and turrids. Characterization of cone snail venom peptides, conotoxins, has revealed a cocktail of bioactive compounds used to investigate physiological cellular function, predator-prey interactions, and to develop novel therapeutics. However, venom diversity of other conoidean snails remains poorly understood. The present research applies a venomics approach to characterize novel terebrid venom peptides, teretoxins, from the venom gland transcriptomes of Triplostephanus anilis and Terebra subulata. Next-generation sequencing and de novo assembly identified 139 putative teretoxins that were analyzed for the presence of canonical peptide features as identified in conotoxins. To meet the challenges of de novo assembly, multiple approaches for cross validation of findings were performed to achieve reliable assemblies of venom duct transcriptomes and to obtain a robust portrait of Terebridae venom. Phylogenetic methodology was used to identify 14 teretoxin gene superfamilies for the first time, 13 of which are unique to the Terebridae. Additionally, basic local algorithm search tool homology-based searches to venom-related genes and posttranslational modification enzymes identified a convergence of certain venom proteins, such as actinoporin, commonly found in venoms. This research provides novel insights into venom evolution and recruitment in Conoidean predatory marine snails and identifies a plethora of terebrid venom peptides that can be used to investigate fundamental questions pertaining to gene evolution.
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Affiliation(s)
- Juliette Gorson
- Hunter College and The Graduate Center, City University of New York Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York
| | - Girish Ramrattan
- Hunter College and The Graduate Center, City University of New York
| | - Aida Verdes
- Hunter College and The Graduate Center, City University of New York Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York
| | - Elizabeth M Wright
- Hunter College and The Graduate Center, City University of New York Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York
| | - Yuri Kantor
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia Visiting Professor, Muséum National d'Histoire Naturelle, Paris, France
| | | | - Raj Musunuri
- Department of Bioinformatics, New York University Polytechnic School of Engineering
| | - Daniel Packer
- Hunter College and The Graduate Center, City University of New York
| | - Gabriel Albano
- Estação de Biologia Marítima da Inhaca (EBMI), Faculdade de Ciencias, Universidade Eduardo Mondlane, Distrito Municipal KaNyaka, Maputo, Mozambique
| | - Wei-Gang Qiu
- Hunter College and The Graduate Center, City University of New York
| | - Mandë Holford
- Hunter College and The Graduate Center, City University of New York Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York
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19
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Fecheyr-Lippens DC, Igic B, D'Alba L, Hanley D, Verdes A, Holford M, Waterhouse GIN, Grim T, Hauber ME, Shawkey MD. The cuticle modulates ultraviolet reflectance of avian eggshells. Biol Open 2015; 4:753-9. [PMID: 25964661 PMCID: PMC4571098 DOI: 10.1242/bio.012211] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 04/01/2015] [Accepted: 04/13/2015] [Indexed: 12/03/2022] Open
Abstract
Avian eggshells are variedly coloured, yet only two pigments, biliverdin and protoporphyrin IX, are known to contribute to the dramatic diversity of their colours. By contrast, the contributions of structural or other chemical components of the eggshell are poorly understood. For example, unpigmented eggshells, which appear white to the human eye, vary in their ultraviolet (UV) reflectance, which may be detectable by birds. We investigated the proximate mechanisms for the variation in UV-reflectance of unpigmented bird eggshells using spectrophotometry, electron microscopy, chemical analyses, and experimental manipulations. We specifically tested how UV-reflectance is affected by the eggshell cuticle, the outermost layer of most avian eggshells. The chemical dissolution of the outer eggshell layers, including the cuticle, increased UV-reflectance for only eggshells that contained a cuticle. Our findings demonstrate that the outer eggshell layers, including the cuticle, absorb UV-light, probably because they contain higher levels of organic components and other chemicals, such as calcium phosphates, compared to the predominantly calcite-based eggshell matrix. These data highlight the need to examine factors other than the known pigments in studies of avian eggshell colour.
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Affiliation(s)
| | - Branislav Igic
- Department of Biology, University of Akron, Akron, OH 44325, USA
| | - Liliana D'Alba
- Department of Biology, University of Akron, Akron, OH 44325, USA
| | - Daniel Hanley
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc 771 46, Czech Republic
| | - Aida Verdes
- Department of Chemistry, Hunter College and the Graduate Center, City University of New York, New York, NY 10021, USA
| | - Mande Holford
- Department of Chemistry, Hunter College and the Graduate Center, City University of New York, New York, NY 10021, USA
| | | | - Tomas Grim
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc 771 46, Czech Republic
| | - Mark E Hauber
- Department of Psychology, Hunter College and the Graduate Center, City University of New York, New York, NY 10065, USA
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Álvarez-Campos P, Fernández-Leborans G, Verdes A, San Martín G, Martin D, Riesgo A. The tag-along friendship: epibiotic protozoans and syllid polychaetes. Implications for the taxonomy of Syllidae (Annelida), and description of three new species ofRhabdostylaandCothurnia(Ciliophora, Peritrichia). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12168] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Patricia Álvarez-Campos
- Departamento de Biología (Zoología); Facultad de Ciencias; Universidad Autónoma de Madrid; Cantoblanco 28049 Madrid Spain
| | - Gregorio Fernández-Leborans
- Departamento de Zoología; Facultad de Biología; Universidad Complutense de Madrid; C/ José Antonio Novais, 12 28040 Madrid Spain
| | - Aida Verdes
- Department of Natural Sciences; Baruch College; City University of New York; 55 Lexington Avenue New York NY 10010 USA
| | - Guillermo San Martín
- Departamento de Biología (Zoología); Facultad de Ciencias; Universidad Autónoma de Madrid; Cantoblanco 28049 Madrid Spain
| | - Daniel Martin
- Department d'Ecologia Marina; Centre d‘Estudis Avançats de Blanes; CEAB-CSIC; c/ Accés a la cala St Francesc, 14 17300 Blanes Spain
| | - Ana Riesgo
- Departamento de Biología Animal; Facultad de Biología; Universitat de Barcelona; Av. Diagonal 643 08028 Barcelona Spain
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