Browsing ⇒ OBON: Ocean Biomolecular Observing Network by Issue Date

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    • Transcriptome sequencing of 19 diverse species of choanoflagellates. 

      Richter, Daniel; Fozouni, Parinaz; Eisen, Michael; King, Nicole (Station Biologique de Roscoff, Roscoff, France, 2017)
      The origin of animals, which occurred over 600 million years ago, left no evidence in the fossil record. To trace the earliest events in animal prehistory, we compare extant animals to their closest living relatives, the ...

    • Simple 3D imaging of biogenic silica structures by fluorescence microscopy. Version 2. 

      Colin, Sebastien (Station Biologique de Roscoff, Roscoff, France, 2018)
      This protocol describes how to prepare, stain and mount biogenic silica particles (opaline from diatoms, Radiolaria, sponges spicules, phytolith...) for 3D imaging with fluorescence microscopy. The protocol is fast, ...

    • Earth Microbiome Project (EMP) high throughput (HTP) DNA extraction protocol. Version 07112018. 

      Marotz, Lisa; Schwartz, Tara; Thompson, Luke; Humphrey, Greg; Gogul, Grant; Gaffney, James; Amir, Amnon; Knigh, Rob (University of California, San Diego, San Diego, CA, 2018)
      This protocol accompanies the following publication: Marotz, Clarisse, et al. "DNA extraction for streamlined metagenomics of diverse environmental samples." BioTechniques 62.6 (2017):290-293

    • Scanning Electron Microscopy imaging for Opaline Silica Single Cell Skeletons (Polycystines Radiolaria). Version 3. 

      Sandin, Miguel Mendez (Station Biologique de Roscoff, Roscoff, France, 2018)
      Protocol adapted from: Biard, T., Pillet, L., Decelle, J., Poirier, C., Suzuki, N. and Not, F. (2015) Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria). Protist 166, ...

    • Confocal Microscopy imaging for Opaline Silica Single Cell Skeletons (Polycystines Radiolaria). 

      Sandin, Miguel Mendez (Station Biologique de Roscoff, Roscoff, France, 2018)

    • Single cell rDNA amplification of Nassellaria (Radiolaria). 

      Sandin, Miguel Mendez (Station Biologique de Roscoff, Roscoff, France, 2018)

    • EMP Sample Submission Guide. 

      Thompson, Luke; Ackermann, Gail; Humphrey, Greg; Gilbert, Jack; Jansson, Janet; Knight, Rob (NOAA Fisheries Southwest Fisheries Research Center, La Jolla,CA, 2018)
      This protocol was designed for collaborators with the Earth Microbiome Project to contribute samples in a standardized fashion. Raw, frozen samples are submitted in individually labeled tubes, 10 aliquots (identical ...

    • BBI: an R package for the computation of Benthic Biotic Indices from composition data. 

      Cordier, Tristan; Pawlowski, Jan (2018)
      The monitoring of impacts of anthropic activities in marine environments, such as aquaculture, oil-drilling platforms or deep-sea mining, relies on Benthic Biotic Indices (BBI). Several indices have been formalised to ...

    • Quanti-iT™ Pico Green dsDNA Assay (Invitrogen P7589). 

      Poulos, Bonnie (Matthew Sullivan Lab, University of Arizona/Ohio State University, Tucson, AZ, 2019)
      This protocol accompanies the following publication: Ul-Hasan S, Bowers RM, Figueroa-Montiel A, Licea-Navarro AF, Beman JM, Woyke T, et al. (2019) Community ecology across bacteria, archaea and microbial eukaryotes in the ...

    • Microscope video recording. 

      Vaulot, Daniel (Station Biologique de Roscoff, Roscoff, France, 2019)
      Protocol to record videos on SBR Microscope.

    • Expanding "Tara" Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018). 

      Gorsky, Gabriel; Bourdin, Guillaume; Lombard, Fabien; Pedrotti, Maria Luiza; Audrain, Samuel; Bin, Nicolas; Boss, Emmanuel; Bowler, Chris; Cassar, Nicolas; Caudan, Loic; Chabot, Genevieve; Cohen, Natalie R.; Cron, Daniel; De Vargas, Colomban; Dolan, John R.; Douville, Eric; Elineau, Amanda; Flores, J. Michel; Ghiglione, Jean Francois; Haëntjens, Nils; Hertau, Martin; John, Seth G.; Kelly, Rachel L.; Koren, Ilan; Lin, Yajuan; Marie, Dominique; Moulin, Clémentine; Moucherie, Yohann; Pesant, Stéphane; Picheral, Marc; Poulain, Julie; Pujo-Pay, Mireille; Reverdin, Gilles; Romac, Sarah; Sullivan, Mathew B.; Trainic, Miri; Tressol, Marc; Troublé, Romain; Vardi, Assaf; Voolstra, Christian R.; Wincker, Patrick; Agostini, Sylvain; Banaigs, Bernard; Boissin, Emilie; Forcioli, Didier; Furla, Paola; Galand, Pierre E.; Gilson, Eric; Reynaud, Stéphanie; Sunagawa, Shinichi; Thomas, Olivier P.; Thurber, Rebecca Lisette Vega; Zoccola, Didier; Planes, Serge; Allemand, Denis; Karsenti, Eric (2019)
      Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition ...

    • Toward a Global Public Repository of Community Protocols to Encourage Best Practices in Biomolecular Ocean Observing and Research 

      Samuel, Robyn; Meyer, Raïssa; Buttigieg, Pier Luigi; Davies, Neil; Jeffery, Nicholas W.; Samuel, Robyn; Pavloudi, Christina; Pitz, Kathleen Johnson; Sweetlove, Maxime; Theroux, Susanna; van de Kamp, Jodie; Watts, Alison (2021)
      Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over ...

    • A practical guide to DNA-based methods for biodiversity assessment. 

      Bruce, Kat; Blackman, Rosetta C.; Bourlat, Sarah J.; Hellström, Micaela; Bakker, Judith; Bista, Iliana; Bohmann, Kristine; Bouchez, Agnès; Brys, Rein; Clark, Katie; Elbrecht, Vasco; Fazi, Stefano; Fonseca, Vera G.; Hänfling, Bernd; Leese, Florian; Mächler, Elvira; Mahon, Andrew R.; Meissner, Kristian; Panksep, Kristel; Pawlowski, Jan; Schmidt Yáñez, Paul Luis; Seymour, Mathew; Thalinger, Bettina; Valentini, Alice; Woodcock, Paul; Traugott, Michael; Vasselon, Valentin; Deiner, Kristy (Pensoft Advanced Books, Sofia, Bulgaria, 2021)
      This book represents a synthesis of knowledge and best practice in the field of DNA-based biomonitoring at the time of writing. It has been written with end-users of molecular tools in mind, as well as those who are new ...

    • Collection Standand Operating Procedures: Omics size fractionation. Version 1.00. 

      Trano, Anna Chiara (Naples Ecological Research Augmented Observatory (NEREA), Naples, Italy, 2021)
      The NEREA project aims to promote the development of new indicators for ocean health and new models of ocean microbiomes by coupling traditional physical, chemical, and biological measurements with omics approaches (i.e. ...

    • DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review. 

      Gielings, Romy; Fais, Maria; Fontaneto, Diego; Creer, Simon; Costa, Filipe Oliveira; Renema, Willem; Macher, Jan-Niklas (2021)
      Meiofaunal animals, roughly between 0.045 and 1 mm in size, are ubiquitous and ecologically important inhabitants of benthic marine ecosystems. Their high species richness and rapid response to environmental change make ...

    • Interoperable vocabulary for marine microbial flow cytometry. 

      Thyssen, Melilotus; Gregori, Gerald; Creach, Veronique; Lahbib, Soumaya; Dugenne, Mathilde; Aardema, Hedy M.; Artigas, Luis-Felipe; Huang, Bangqin; Barani, Aude; Beaugeard, Laureen; Bellaaj-Zouari, Amel; Beran, Alfred; Casotti, Raffaella; Del Amo, Yolanda; Denis, Michel; Dubelaar, George B.J.; Endres, Sonja; Haraguchi, Lumi; Karlson, Bengt; Lambert, Christophe; Louchart, Arnaud; Marie, Dominique; Moncoiffe, Gwenaëlle; Pecqueur, David; Ribalet, Francoise; Rijkeboer, Machteld; Silovic, Tina; Silva, Ricardo; Marro, Sophie; Sosik, Heidi M.; Sourisseau, Marc; Tarran, Glen; Van Oostende, Nicolas; Zhao, Li; Zheng, Shan (2022)
      The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms ...

    • Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures. 

      Stefanni, S.; Mirimin, L.; Stankovic, D.; Chatzievangelou, D.; Bongiorni, L.; Marini, S.; Modica, M.V.; Manea, E.; Bonofiglio, F.; del Rio Fernandez, J.; Cukrov, N.; Gavrilovic, A.; De Leo, F.C.; Aguzzi, J. (2022)
      Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their ...

    • Environmental DNA protocol development guide for biomonitoring. 

      De Brauwer, M.; Chariton, A.; Clarke, L.J.; Cooper, M.K.; DiBattista, J.; Furlan, E.; Giblot-Ducray, D.; Gleeson, D.; Harford, A.; Herbert, S.; MacDonald, A.J.; Miller, A.; Montgomery, K.; Mooney, T.; Noble, L.M.; Rourke, M.; Sherman, C.D.H.; Stat, M.; Suter, L.; West, K.M.; White, N.; Villacorta-Rath, C.; Zaiko, A.; Trujillo-Gonzalez, A. (National eDNA Reference Centre, Canberra, Australia, 2022)
      The Environmental DNA protocol development guide for biomonitoring (EP guide for biomonitoring) provides harmonised quality control and minimum standard operating procedures. This document is complemented by the Environmental ...

    • Environmental DNA test validation guidelines. 

      De Brauwer, M.; Chariton, A.; Clarke, L.J.; Cooper, M.K.; DiBattista, J.; Furlan, E.; Giblot-Ducray, D.; Gleeson, D.; Harford, A.; Herbert, S.; MacDonald, A.J.; Miller, A.; Montgomery, K.; Mooney, T.; Noble, L.M.; Rourke, M.; Sherman, C.D.H.; Stat, M.; Suter, L.; West, K.M.; White, N.; Villacorta-Rath, C.; Zaiko, A.; Trujillo-Gonzalez, A. (National eDNA Reference Centre, Canberra, Australia, 2022)
      These Environmental DNA test validation guidelines provide harmonised quality control and minimum standard considerations for developing or validating eDNA/eRNA assays for the purpose of single-species or multi-species ...

    • Marine microbiomes: Towards standard methods and best practices. 

      Pesant, Stéphane; Goodwin, Kelly D.; Magalhães, Catarina; Lacoursière-Roussel, Anaïs (Frontiers Media SA, Lausanne, Switzerland, 2023)
      The microbiome is key to understanding and sustaining the services that ocean ecosystems provide (Bolhuis et al., 2020). The marine microbiome—an ensemble of microscopic organisms that inhabit water columns, sediments, ...