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3. Beyond the 'Code': A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)

Author

Fox Ramos, Alexander, Alcover, Charlotte, Evanno, Laurent, Litaudon, Marc, DUPLAIS, Christophe, Bernadat, Guillaume, Gallard, Jean-Francois, Jullian, Christophe, Mouray, Elisabeth, Loiseau, Philippe, Pomel, Sébastien, Poupon, Erwan, Champy, Pierre, Beniddir, Mehdi, Ortiz, Sergio, Dali-Yahia, Kamel, Vásquez-Ocmín, Pedro, Grougnet, Raphäel, Grellier, Philippe, Michel, Sylvie, Maciuk, Alexandre, Boutefnouchet, Sabrina, Warren, Alan, Patterson, David, Dunthorn, Micah, Clamp, John, Achilles-Day, Undine E.M., Aescht, Erna, Al-Farraj, Saleh, Al-Quraishy, Saleh, Al-Rasheid, Khaled, Carr, Martin, Day, John, Dellinger, Marc, El-Serehy, Hamed, Fan, Yangbo, Gao, Feng, Gao, Shan, Gong, Jun, Gupta, Renu, Hu, Xiaozhong, Kamra, Komal, Langlois, Gaytha, Lin, Xiaofeng, Lipscomb, Diana, Lobban, Christopher, Luporini, Pierangelo, Lynn, Denis, Ma, Honggang, Ma, Miroslav, Ma, Jacqueline, Ma, Seema, Ma, Robert, Ma, Mercedes, McMiller, Nettie, Montagnes, David, Nikolaeva, Svetlana, Ong'ondo, Geoffrey Odhiambo, Ma, Blanca, Purushothaman, Jasmine, Ma, Pablo, Rotterová, Johana, Ma, Luciana, Shao, Chen, Shen, Zhuo, Shi, Xinlu, Ma, Weibo, Stoeck, Thorsten, La Terza, Antonietta, Vallesi, Adriana, Ma, Mei, Weisse, Thomas, Wiackowski, Krzysztof, Wu, Lei, Xu, Kuidong, Yi, Zhenzhen, Zufall, Rebecca, Agatha, Sabine, Équipe 'Pharmacognosie-Chimie des Substances Naturelles' BioCIS, Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Équipe 'Molécules Fluorées et Chimie Médicinale' BioCIS, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Équipe 'Chimiothérapie Antiparasitaire' BioCIS, Universitat d'Alacant, Laboratorios de Investigación y Desarrollo (LID), Universidad Peruana Cayetano Heredia (UPCH), Chimie Organique, Médicinale et Extractive et Toxicologie Expérimentale (COMETE - UMR 8638), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Paris Descartes - Paris 5 (UPD5), Equipe Pharmacognosie (UMR 8638), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Paris Descartes - Paris 5 (UPD5), National History Museum of London, Department of ecology, Universität Kaiserslautern, Austrian Museum, University of Huddersfield, Computer Science Department [Boston] (Boston University), Boston University [Boston] (BU), Laboratoire de Mecanique des Fluides et d'Acoustique (LMFA), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Wuhan University [China], Institut Charles Sadron (ICS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), School of Biological Sciences [Liverpool], University of Liverpool, Shandong University, Institutions et Dynamiques Historiques de l'Économie et de la Société (IDHES), Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Nanterre (UPN)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris 1 Panthéon-Sorbonne (UP1), Universität Salzburg, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia-FACULTAD DE CIENCIAS Y FILOSOFIA, Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Bio Sci, Univ Liverpool, and École normale supérieure - Cachan (ENS Cachan)-Université Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
0301 basic medicine, Databases, Factual, Cultivation, Best practice, [SDV]Life Sciences [q-bio], Biodiversity, Invertebrados, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Q1, Microbiología, Microbiology, GeneralLiterature_MISCELLANEOUS, taxonomy, 03 medical and health sciences, Documentation, morphology, Ciliophora, systematics, QH426, Phylogeny, molecular phylogeny, ComputingMilieux_MISCELLANEOUS, Grand Challenges, International research, Internet, Ecology, business.industry, Online database, Original Articles, Data science, type specimens, phylogenetics, Metadata, 030104 developmental biology, cultivation, Knowledge base, Original Article, nomenclature, business, information resources
Abstract

© 2017 The International Society of Protistologists.Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.

Published
2017
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4. Journal of Eukaryotic Microbiology / Beyond the 'Code' : a guide to the description and documentation of biodiversity in ciliated protists (Alveolata, Ciliophora)

Author

Warren, Alan, Patterson, David J., Dunthorn, Micah, Clamp, John C., Achilles-Day, Undine E.M., Aescht, Erna, Al-Farraj, Saleh A., Al-Quraishy, Saleh, Al-Rasheid, Khaled, Carr, Martin, Day, John G., Dellinger, Marc, El-Serehy, Hamed A., Fan, Yangbo, Gao, Feng, Gao, Shan, Gong, Jun, Gupta, Renu, Hu, Xiaozhong, Kamra, Komal, Langlois, Gaytha, Lin, Xiaofeng, Lipscomb, Diana, Lobban, Christopher S., and Agatha, Sabine

Subjects
phylogenetics, taxonomy, Cultivation, morphology, nomenclature, systematics, GeneralLiterature_MISCELLANEOUS, molecular phylogeny, information resources, type specimens
Abstract

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.

Published
2017
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5. Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)

Author

Warren, Alan, primary, Patterson, David J., additional, Dunthorn, Micah, additional, Clamp, John C., additional, Achilles-Day, Undine E.M., additional, Aescht, Erna, additional, Al-Farraj, Saleh A., additional, Al-Quraishy, Saleh, additional, Al-Rasheid, Khaled, additional, Carr, Martin, additional, Day, John G., additional, Dellinger, Marc, additional, El-Serehy, Hamed A., additional, Fan, Yangbo, additional, Gao, Feng, additional, Gao, Shan, additional, Gong, Jun, additional, Gupta, Renu, additional, Hu, Xiaozhong, additional, Kamra, Komal, additional, Langlois, Gaytha, additional, Lin, Xiaofeng, additional, Lipscomb, Diana, additional, Lobban, Christopher S., additional, Luporini, Pierangelo, additional, Lynn, Denis H., additional, Ma, Honggang, additional, Macek, Miroslav, additional, Mackenzie-Dodds, Jacqueline, additional, Makhija, Seema, additional, Mansergh, Robert I., additional, Martín-Cereceda, Mercedes, additional, McMiller, Nettie, additional, Montagnes, David J.S., additional, Nikolaeva, Svetlana, additional, Ong'ondo, Geoffrey Odhiambo, additional, Pérez-Uz, Blanca, additional, Purushothaman, Jasmine, additional, Quintela-Alonso, Pablo, additional, Rotterová, Johana, additional, Santoferrara, Luciana, additional, Shao, Chen, additional, Shen, Zhuo, additional, Shi, Xinlu, additional, Song, Weibo, additional, Stoeck, Thorsten, additional, La Terza, Antonietta, additional, Vallesi, Adriana, additional, Wang, Mei, additional, Weisse, Thomas, additional, Wiackowski, Krzysztof, additional, Wu, Lei, additional, Xu, Kuidong, additional, Yi, Zhenzhen, additional, Zufall, Rebecca, additional, and Agatha, Sabine, additional

Published
2017
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6. Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)

Author

Warren, Alan, Patterson, David J., Dunthorn, Micah, Clamp, John C., Achilles Day, Undine E.M., Aescht, Erna, Al-Farraj, Saleh A., Al-Quraishy, Saleh, Al-Rasheid, Khaled, Carr, Martin, G. Day, John, Dellinger, Marc, El-Serehy, Hamed A., Fan, Yangbo, Gao, Feng, Gao, Shan, Gong, Jun, Gupta, Renu, Hu, Xiaozhong, Kamra, Komal, Langlois, Gaytha, Lin, Xiaofeng, Lipscomb, Diana, Lobban, Christopher S., Luporini, Pierangelo, Lynn, Denis H., Ma, Honggang, Macek, Miroslav, Mackenzie-Dodds, Jacqueline, Makhija, Seema, Mansergh, Robert I., Martín Cereceda, María Mercedes, McMiller, Nettie, Montagnes, David J.S., Nikolaeva, Svetlana, Ong'ondo, Geoffrey Odhiambo, Pérez Uz, María Blanca, Purushothaman, Jasmine, Quintela Alonso, Pablo, Rotterová, Johana, Santoferrara, Luciana, Shao, Chen, Shen, Zhuo, Shi, Xinlu, Song, Weibo, Stoeck, Thorsten, Terza, Antonietta La, Vallesi, Adriana, Wang, Mei, Weisse, Thomas, Wiackowski, Krzysztof, Wu, Lei, Xu, Kuidong, Yi, Zhenzhen, Zufall, Rebecca, Agatha, Sabine, Warren, Alan, Patterson, David J., Dunthorn, Micah, Clamp, John C., Achilles Day, Undine E.M., Aescht, Erna, Al-Farraj, Saleh A., Al-Quraishy, Saleh, Al-Rasheid, Khaled, Carr, Martin, G. Day, John, Dellinger, Marc, El-Serehy, Hamed A., Fan, Yangbo, Gao, Feng, Gao, Shan, Gong, Jun, Gupta, Renu, Hu, Xiaozhong, Kamra, Komal, Langlois, Gaytha, Lin, Xiaofeng, Lipscomb, Diana, Lobban, Christopher S., Luporini, Pierangelo, Lynn, Denis H., Ma, Honggang, Macek, Miroslav, Mackenzie-Dodds, Jacqueline, Makhija, Seema, Mansergh, Robert I., Martín Cereceda, María Mercedes, McMiller, Nettie, Montagnes, David J.S., Nikolaeva, Svetlana, Ong'ondo, Geoffrey Odhiambo, Pérez Uz, María Blanca, Purushothaman, Jasmine, Quintela Alonso, Pablo, Rotterová, Johana, Santoferrara, Luciana, Shao, Chen, Shen, Zhuo, Shi, Xinlu, Song, Weibo, Stoeck, Thorsten, Terza, Antonietta La, Vallesi, Adriana, Wang, Mei, Weisse, Thomas, Wiackowski, Krzysztof, Wu, Lei, Xu, Kuidong, Yi, Zhenzhen, Zufall, Rebecca, and Agatha, Sabine

Abstract

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data., U.S. National Science Foundation, National Natural Science Foundation of China, Depto. de Genética, Fisiología y Microbiología, Fac. de Ciencias Biológicas, TRUE, pub

Published
2017

9. Risk assessment for the spread of Serratia marcescens within dental-unit waterline systems using Vermamoeba vermiformis

Author

Lal, Sham, Singhrao, Simarjit Kaur, Achilles-Day, Undine E.M., Morton, Leslie Hugh Glyn, Pearce, Mark, Crean, Stjohn, Lal, Sham, Singhrao, Simarjit Kaur, Achilles-Day, Undine E.M., Morton, Leslie Hugh Glyn, Pearce, Mark, and Crean, Stjohn

Abstract

Vermamoeba vermiformis is associated with the biofilm ecology of dental-unit waterlines (DUWLs). This study investigated whether V. vermiformis is able to act as a vector for potentially pathogenic bacteria and so aid their dispersal within DUWL systems. Clinical dental water was initially examined for Legionella species by inoculating it onto Legionella selective-medium plates. The molecular identity/profile of the glassy colonies obtained indicated none of these isolates were Legionella species. During this work bacterial colonies were identified as a non-pigmented Serratia marcescens. As the water was from a clinical DUWL which had been treated with Alpron™ this prompted the question as to whether S. marcescens had developed resistance to the biocide. Exposure to Alpron™ indicated that this dental biocide was effective, under laboratory conditions, against S. marcescens at up to 1x108 colony forming units/millilitre (cfu/ml). V. vermiformis was cultured for eight weeks on cells of S. marcescens and Escherichia coli. Subsequent electron microscopy showed that V. vermiformis grew equally well on S. marcescens and E. coli (p = 0.0001). Failure to detect the presence of S. marcescens within the encysted amoebae suggests that V. vermiformis is unlikely to act as a vector supporting the growth of this newly isolated, nosocomial bacterium.

Published
2015

11. The CCAP KnowledgeBase: linking protistan and cyanobacterial biological resources with taxonomic and molecular data

Author

Gachon, Claire M.M., primary, Heesch, Svenja, additional, Küpper, Frithjof C., additional, Achilles-Day, Undine E.M., additional, Brennan, Debra, additional, Campbell, Christine N., additional, Clarke, Alison, additional, Dorrell, Richard G., additional, Field, Joanne, additional, Gontarek, Steven, additional, Rad Menendez, Cecilia, additional, Saxon, Rachel J., additional, Veszelovszki, Andrea, additional, Guiry, Michael D., additional, Gharbi, Karim, additional, Blaxter, Mark, additional, and Day, John G., additional

Published
2013
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12. Future algal biofuels: implications of environmental temperature on production strain selection

Author

Day, John G., Burt, Daniel J., Achilles-Day, Undine E.M., and Stanley, Michele S.

Abstract

Current and future economic mass production of microalgae or cyanobacteria will require suitable, preferably relatively high, levels of photosynthetically active radiation (PAR). Most large-scale productions sites, as well as those under development or under consideration, have been located between 40N and 40S raising the possible issue of the algae being periodically, or routinely, subjected to elevated temperatures (>30°C). The effects of environmental temperatures in the range 8–35°C on the marine, oleaginous model alga Nannochloropsis oculatawere assessed. Active growth was observed at all temperatures except 35°C, where cells bleached and died. The implications of elevated temperature regimes were assessed for a variety of potential biofuel producing, biotechnologically relevant freshwater, marine and hyper-saline algae and the implications for their biotechnological exploitability discussed.

Published
2015
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