Author: "National Research Foundation of South Africa" - Searchworks@Jio Institute Digital Library Search Results

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82 results on '"National Research Foundation of South Africa"'

1. The African-PREDICT Study (PREDICT)

Author: Medical Research Council, South Africa, National Research Foundation of South Africa, GlaxoSmithKline, Medical Research Council, Pfizer, Boehringer Ingelheim, Novartis, Mediclinic Hospital, Roche Diagnostics GmbH, and Alta Schutte, Professor
Published: 2024

2. Exercise, Arterial Modulation and Nutrition in Youth South Africa Study (ExAMIN-Youth)

Author: National Research Foundation of South Africa, Medical Research Council, South Africa, and Ruan Kruger, Professor
Published: 2024

3. Joint Position Sense in Individuals With Anterior Knee Pain

Author: National Research Foundation of South Africa and Dominique Leibbrandt, Dr Dominique Leibbrandt (PhD Physiotherapy), Postdoctoral Researcher in Faculty of Health and Rehabilitation Sciences
Published: 2019

4. Modulated Electro-Hyperthermia Plus Chemo-radiation for Locally Advanced Cervical Cancer Patients in South Africa (mEHT)

Author: National Research Foundation of South Africa, NTP Radioisotopes SOC Ltd, and Jeffrey Kotzen, Senior Radiation Oncologist
Published: 2017

5. Effect of African Leafy Vegetables on Nutritional Status of South African School Children. (ALV)

Author: Medical Research Council, South Africa, Agricultural Research Council of South Africa, Sight and Life, Program to Support Pro-poor Policy Development (PSPPD), National Research Foundation of South Africa, and Marinka van der Hoeven, Mrs Marinka van der Hoeven
Published: 2013

6. Randomised Trial of Two Educational Intervention for Improving Evidence-based Practice Knowledge, Atttitudes and Practice (OTEBP)

Author: National Research Foundation of South Africa and Helen Buchanan, Principal investigator
Published: 2012

7. The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity

Author: Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Agencia Estatal de Investigación. España, Swiss National Science Foundation (SNFS), Austrian Fonds zur Förderung der Wissenschaftlichen Forschung, German Bundesministerium für Bildung und Forschung (BMBF), French National Research Agency, US National Science Foundation, National Research Foundation of South Africa, Australian Research Council, UK Natural Environment Research Council, Hellenic Foundation for Research and Innovation (H.F.R.I.), Vimercati, Giovanni, Probert, Anna F., Volery, Lara, Bernardo Madrid, Rubén, Bertolino, Sandro, Cespedes, Vanessa, Essl, Franz, Evans, Thomas, González Moreno, Pablo, Vilà, Montserrat, Wilson, John R U., Bacher, Sven, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Agencia Estatal de Investigación. España, Swiss National Science Foundation (SNFS), Austrian Fonds zur Förderung der Wissenschaftlichen Forschung, German Bundesministerium für Bildung und Forschung (BMBF), French National Research Agency, US National Science Foundation, National Research Foundation of South Africa, Australian Research Council, UK Natural Environment Research Council, Hellenic Foundation for Research and Innovation (H.F.R.I.), Vimercati, Giovanni, Probert, Anna F., Volery, Lara, Bernardo Madrid, Rubén, Bertolino, Sandro, Cespedes, Vanessa, Essl, Franz, Evans, Thomas, González Moreno, Pablo, Vilà, Montserrat, Wilson, John R U., and Bacher, Sven
Abstract: Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions.
Published: 2022

8. Scientists' warning on invasive alien species

Author: Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Czech Science Foundation, Czech Academy of Sciences, Swiss National Science Foundation (SNFS), Austrian Science Foundation FWF, National Research Foundation of South Africa, New Zealand Ministry of Business, Innovation and Employment, Comisión Nacional de Investigación Científica y Tecnológica (CONICYT). Chile, Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT). Chile, Natural Environment Research Council, Deutsche Forschungsgemeinschaft / German Research Foundation (DFG), Ministerio de Ciencia, Innovación y Universidades (MICINN). España, German Federal Ministry of Education and Research, Vilà, Montserrat, Pyšek, Petr, Hulme, Philip E., Simberloff, Dan, Bacher, Sven, Blackburn, Tim M., Carlton, James T., Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Czech Science Foundation, Czech Academy of Sciences, Swiss National Science Foundation (SNFS), Austrian Science Foundation FWF, National Research Foundation of South Africa, New Zealand Ministry of Business, Innovation and Employment, Comisión Nacional de Investigación Científica y Tecnológica (CONICYT). Chile, Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT). Chile, Natural Environment Research Council, Deutsche Forschungsgemeinschaft / German Research Foundation (DFG), Ministerio de Ciencia, Innovación y Universidades (MICINN). España, German Federal Ministry of Education and Research, Vilà, Montserrat, Pyšek, Petr, Hulme, Philip E., Simberloff, Dan, Bacher, Sven, Blackburn, Tim M., and Carlton, James T.
Abstract: Biological invasions are a global consequence of an increasingly connected world and the rise in human population size. The numbers of invasive alien species – the subset of alien species that spread widely in areas where they are not native, affecting the environment or human livelihoods – are increasing. Synergies with other global changes are exacerbating current invasions and facilitating new ones, thereby escalating the extent and impacts of invaders. Invasions have complex and often immense long-term direct and indirect impacts. In many cases, such impacts become apparent or problematic only when invaders are well established and have large ranges. Invasive alien species break down biogeographic realms, affect native species richness and abundance, increase the risk of native species extinction, affect the genetic composition of native populations, change native animal behaviour, alter phylogenetic diversity across communities, and modify trophic networks. Many invasive alien species also change ecosystem functioning and the delivery of ecosystem services by altering nutrient and contaminant cycling, hydrology, habitat structure, and disturbance regimes. These biodiversity and ecosystem impacts are accelerating and will increase further in the future. Scientific evidence has identified policy strategies to reduce future invasions, but these strategies are often insufficiently implemented. For some nations, notably Australia and New Zealand, biosecurity has become a national priority. There have been long-term successes, such as eradication of rats and cats on increasingly large islands and biological control of weeds across continental areas. However, in many countries, invasions receive little attention. Improved international cooperation is crucial to reduce the impacts of invasive alien species on biodiversity, ecosystem services, and human livelihoods. Countries can strengthen their biosecurity regulations to implement and enforce more effective management
Published: 2020

9. Evaluation of important mineral nutrients and vitamins in polyherbal medicines used for the treatment of tuberculosis in the Eastern Cape Province, South Africa

Author: National Research Foundation of South Africa, Famewo, Elizabeth Bosede; Faculty of Science and Agriculture, University of Fort Hare, Alice 5700, South Africa, Clarke, Anna Maria; Faculty of Science and Agriculture, University of Fort Hare, Alice 5700, South Africa, Afolayan, Anthony Jide; Faculty of Science and Agriculture, University of Fort Hare, Alice 5700, South Africa, National Research Foundation of South Africa, Famewo, Elizabeth Bosede; Faculty of Science and Agriculture, University of Fort Hare, Alice 5700, South Africa, Clarke, Anna Maria; Faculty of Science and Agriculture, University of Fort Hare, Alice 5700, South Africa, and Afolayan, Anthony Jide; Faculty of Science and Agriculture, University of Fort Hare, Alice 5700, South Africa
Abstract: Polyherbal medicines are widely used for the treatment of various diseases in the developing countries. In order to validate their ability in boosting the immune system of tuberculosis patients, the mineral nutrients and vitamins present were determined. Their nutritive properties were analysed using an inductively coupled plasma optical emission spectrometer, while the vitamins were determined using standardized methods. The polyherbal preparations were found to be rich in mineral nutrients and vitamins. Calcium was the highest mineral nutrient detected, while the lowest nutrient was phosphorus. Quantitatively, calcium and magnesium contents in the remedies ranged from 973.30 to 6503.30 mg/100g and 80.00 to 406.00 mg/100g respectively. The amount of phosphorus and potassium was between 20.00 and 263.30 mg/100g; 160.00 and 2050.00 mg/100g respectively. Micro nutrients such as iron, manganese, zinc, aluminium and copper were also detected. Iron was the highest nutrient in the majority of the polyherbal preparations while the lowest value was recorded for copper. However, vitamin C was absent in the herbal preparations while vitamin A and E were detected. These findings indicate that these polyherbal formulations contain the essential mineral nutrients and vitamins that could probably be boosting the immune system of tuberculosis patients.
Published: 2018

10. Blinded by Sight: Divining the Future of Anthropology in Africa

Author: National Research Foundation (NRF), South Africa, Francis B. Nyamnjoh; University of Cape Town, National Research Foundation (NRF), South Africa, and Francis B. Nyamnjoh; University of Cape Town
Abstract: Using the metaphor of the elephant and the three blind men, this paper discusses some elements of the scholarly debate on the postcolonial turn in academia, in and of Africa, and in anthropology in particular. It is a part of the context in which anthropology remains unpopular among many African intellectuals. How do local knowledge practices take up existential issues and epistemological perspectives that may interrogate and enrich more global transcultural debates and scholarly reflexivity? Many an anthropologist still resists opening his or her mind up to life-worlds unfolding themselves through the interplay between everyday practice and the manifold actions and messages of humans, ancestors and non-human agents in sites of emerging meaning-production and innovative world-making. African anthropologists seeking recognition find themselves contested or dismissed by fellow anthropologists for doing “native”, “self” or “insider” anthropology, and are sometimes accused of perpetuating colonial epistemologies and subservience by fellow African scholars who are committed to scholarship driven by the need to valorise ways of being and knowing endogenous to Africa. This essay calls on anthropologists studying Africa to reflect creative diversity and reflexivity in the conceptualisation and implementation of research projects, as well as in how they provide for co-production, collaboration and co-implication within anthropology across and beyond disciplines., Unter Rückgriff auf die Fabel vom Elefanten und den drei weisen Männern diskutiert dieser Beitrag einige Elemente der Debatte zur postkolonialen Wende in der Wissenschaft – innerhalb und außerhalb Afrikas und insbesondere in Bezug auf die Ethnologie. Unter vielen afrikanischen Intellektuellen ist die Ethnologie immer noch unbeliebt. Inwieweit greifen lokale Wissenspraktiken existentielle Fragen und epistemologische Perspektiven auf und stellen damit die globale transkulturelle Debatte und wissenschaftliche Reflexion infrage oder bereichern sie? Viele Ethnologen scheuen sich immer noch, sich gegenüber Lebenswelten zu öffnen, in denen die alltägliche Praxis mit den facettenreichen Handlungen und Botschaften von lebenden Menschen, Vorfahren und nicht-menschlichen Wesen verwoben ist – an Orten, an denen zunehmend neue Bedeutungsformen und innovative Welten entstehen. Afrikanische Ethnologen, die sich um Anerkennung bemühen, machen die Erfahrung, dass sie von anderen Ethnologen infrage gestellt oder abgelehnt werden, weil sie angeblich eine selbstbezogene oder Insider-Ethnologie betreiben, oder dass sie von afrikanischen Wissenschaftlern – die selbst auf Stipendien angewiesen sind und sich daher bemühen, spezifisch afrikanische Lebensarten und Wissenswelten aufzuwerten – beschuldigt werden, sich kolonialen Erkenntnisinteressen zu unterwerfen. Der Autor des Beitrags fordert Ethnologen, die zu Afrika forschen, dazu auf, bei der Konzeptionierung und Durchführung von Forschungsprojekten auf kreative Vielfalt und Reflexivität sowie auf Möglichkeiten der Zusammenarbeit innerhalb der Ethnologie und über die Disziplin hinaus zu setzen.
Published: 2012

11. Introducing educational computer programmes through evaluation: A case in South African disadvantaged schools

Author: National Research Foundation of South Africa., Muwanga-Zake, Johnnie W. F.; University of New England, Australia; jmuwanga@une.edu.au, National Research Foundation of South Africa., and Muwanga-Zake, Johnnie W. F.; University of New England, Australia; jmuwanga@une.edu.au
Abstract: I report on benefits from teacher-participant evaluation and mode of introducing educational computer programmes (ECPs) in disadvantaged schools in South Africa. 26 teachers from 23 schools participated in evaluating a biology computer game designed to motivate and ease conceptual understanding. The evaluation comprised teachers training, which simultaneously provided a platform for introducing the ECP into the schools. The paper recommends that an evaluation of ECPs that includes the value system of end-users (through social dialogue); curriculum issues (learning theories in the ECP and those the education authorities recommend, as well as ECP-curriculum integration); the concepts which the ECP presents; and the compatibility of the ECP with school computers, can provide useful methods of introducing ECPs into curricula of disadvantaged schools.
Published: 2007

12. Learning from the rhetoric of academics

Author: National Research Foundation of South Africa and the Research Council of Norway, Deacon, Andrew; University of Cape Town, South Africa; andrew.deacon@uct.ac.za, WynSculley, Catherine; University of Cape Town, South Africa; catherine.wynsculley@uct.ac.za, National Research Foundation of South Africa and the Research Council of Norway, Deacon, Andrew; University of Cape Town, South Africa; andrew.deacon@uct.ac.za, and WynSculley, Catherine; University of Cape Town, South Africa; catherine.wynsculley@uct.ac.za
Abstract: Seminar presentations, by academics successfully using educational technology to support their courses, form a visible part of many staff development programmes. These events contribute to developing a community of academics that use educational technology and are sharing experiences on its use in supporting teaching and learning. We draw on classic rhetorical analysis to highlight the epideictic or ceremonial form of these presentations we see as exemplary of these events. These presentations tend to be quite distinct from how educational technology research or best practice is disseminated. We argue that this epideictic form is a vital component in emerging communities of practice and, for example, communicates the value of working collaboratively. While the underlying intuition is widely acknowledged, our analysis offers a framework to view these conscious and stylistic choices across learning communities.
Published: 2007

13. ICT provision to disadvantaged urban communities: A study in South Africa and Nigeria

Author: National research foundation in South Africa, Akinsola, Olabode Samuel (OS); Tshwane University of Technology, South Africa; akinsolas@tut.ac.za, Herselman, Marlien Elizabeth; Tshwane University of Technology, South Africa; herselmanme@tut.ac.za, Jacobs, S. J.; Tshwane University of Technology, South Africa; jacobssj@tut.ac.za, National research foundation in South Africa, Akinsola, Olabode Samuel (OS); Tshwane University of Technology, South Africa; akinsolas@tut.ac.za, Herselman, Marlien Elizabeth; Tshwane University of Technology, South Africa; herselmanme@tut.ac.za, and Jacobs, S. J.; Tshwane University of Technology, South Africa; jacobssj@tut.ac.za
Abstract: The focus of this research was to develop a sustainable ICT model in a Nigerian community, by evaluating ICT provision in South Africa?s disadvantaged communities and comparing it with the Nigerian situation; to identify applicable models and service mechanisms; and, to identify pitfalls and risks. This research was conducted by analyzing the problem from four points of view: ICT infrastructure, management, influencing factors and the risks of ICT provision in disadvantaged communities. A literature review was undertaken to discuss those issues. Four ICT centres were involved in the case study. The author argued that bridging the digital divide in disadvantaged communities required adequate knowledge of the underlying causes of the divide, a favourable Government policy, a focus on the benefits of providing ICT, the provision of suitable infrastructure, and a committed management that is prepared to get round the various barriers or risks found in disadvantaged communities.
Published: 2005

14. Measuring Kruger visitors’ place attachment to specific camps

Author: <p>This work is based on the research supported in part by the National Research Foundation of South Africa (Grant Number 114916).</p>, Douglas, Anneli, Wessels, Jan-Albert, Pope, Jenny, Morrison-Saunders, Angus, Hughes, Mike, <p>This work is based on the research supported in part by the National Research Foundation of South Africa (Grant Number 114916).</p>, Douglas, Anneli, Wessels, Jan-Albert, Pope, Jenny, Morrison-Saunders, Angus, and Hughes, Mike
Abstract: Douglas, A., Wessels, J. A., Pope, J., Morrison-Saunders, A., & Hughes, M. (2019). Measuring Kruger visitors’ place attachment to specific camps. Koedoe, 61(1). Available here.

15. Comparison of pivot profile© to frequency of attribute citation: Analysis of complex products with trained assessors

Author: Tormod Næs, Dominique Valentin, Martin Kidd, Jeanne Brand, Melané A. Vivier, Helene Nieuwoudt, Stellenbosch University, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nofima AS, Project IWBT 13/02, the National Research Foundation of South Africa and THRIP for funding project Tp14080888680., and Project IWBT 13/02, the National Research Foundation of South Africa and THRIP for funding project Tp14080888680
Subjects: trained panel, confidence ellipses, Pivot profile, 030309 nutrition & dietetics, pivot profile, Correspondence analysis, correspondence analysis, 03 medical and health sciences, 0404 agricultural biotechnology, cata, Citation analysis, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Statistics, interrater reliability, Mathematics, 0303 health sciences, Nutrition and Dietetics, Complex matrix, CATA, tool, 04 agricultural and veterinary sciences, Explained variation, 040401 food science, Frequency of attribute citation, Reference sample, frequency of attribute citation, agreement, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: Pivot© profile (PP), a method which compares samples to a reference (pivot), has shown profiling potential for complex matrices. However, various aspects require further investigation. This study’s aim was to compare PP to frequency of attribute citation (FC) considering individual judges’ data and sample set complexity. A trained panel analysed three wine sets with different within-set product similarity levels. The stability of the PP sensory space was tested by changing the pivot. PP and FC results were compared using RV coefficients. Confidence ellipses on correspondence analysis (CA) plots were constructed to consider individual judges’ data. CA plots constructed from different pivot PP data sets, were less similar to each other, than to CA plots of FC data, for the set with medium and the set with high within-set variation. The most profound differences were observed for the set with the high within-set variation. PP configurations of the set with low within-set variation, were more similar to each other than to FC configurations. Higher explained variance was obtained with PP than FC, but confidence ellipses overlapped more frequently indicating fewer significant differences between samples. PP and FC data were comparable for the set with medium within-set variation. From this study’s results PP is recommended for wine profiling if medium within-set variation between samples exist but not when sample sets with low or high within-set variation are profiled. PP is recommended over FC for comparative studies where a reference sample is required for example during benchmarking or for aging and shelf-life studies.
Published: 2020
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16. Rediscovery and redescription of Teneriffia quadripapillata Sig Thor (Acari: Trombidiformes: Teneriffiidae)

Author: Edward A. Ueckermann, Juan Carlos De La Paz, David Hernández-Teixidor, Furkan Durucan, Cabildo de Tenerife, and National Research Foundation of South Africa
Subjects: redescription, Insect Science, predatory mites, littoral mites, teneriffiids
Abstract: Teneriffia quadripapillata Sig Thor, the type species of Teneriffia Sig Thor (1911), is redescribed from new material collected on Tenerife, the island which is the type locality in the Canary Islands. Sig Thor’s original material was apparently destroyed., The Cabildo of Tenerife provided collecting permits. DHT is currently funded by the Cabildo de Tenerife, under the TFinnova Programme supported by MEDI and FDCAN funds. The manuscript was edited by Guido Jones, also funded by the Cabildo de Tenerife under the same programme. This work is based on the research supported in part by the National Research Foundation of South Africa (Grant Number 126938). Any opinion, findings and conclusions or recommendations expressed in the material are those of the authors and therefore the NRF does not accept any liability in regard thereto.
Published: 2022
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17. From fossils to mind

Author: de Sousa, A., Beaudet, A., Calvey, T., Bardo, A., Benoit, J., Charvet, C., Dehay, C., Gómez-Robles, A., Gunz, P., https://orcid.org/0000-0002-2350-4450, Heuer, K., van den Heuvel, M., Hurst, S., Lauters, P., Reed, D., Salagnon, M., Sherwood, C., Ströckens, F., Tawane, M., Todorov, O., Toro, R., Wei, Y., de Sousa, Alexandra A [0000-0003-2379-3894], Beaudet, Amélie [0000-0002-9363-5966], Calvey, Tanya [0000-0002-7540-2130], Bardo, Ameline [0000-0003-1840-6423], Gómez-Robles, Aida [0000-0002-8719-2660], Gunz, Philipp [0000-0002-2350-4450], Heuer, Katja [0000-0002-7237-0196], van den Heuvel, Martijn P [0000-0003-1570-1195], Hurst, Shawn [0000-0002-1458-759X], Lauters, Pascaline [0000-0003-3664-3182], Sherwood, Chet C [0000-0001-6711-449X], Todorov, Orlin S [0000-0002-0295-7557], Apollo - University of Cambridge Repository, Bath Spa University, Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), University of Cape Town, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), University of Kent [Canterbury], University of the Witwatersrand [Johannesburg] (WITS), Auburn University (AU), Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (SBRI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University College of London [London] (UCL), Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Neuroanatomie Appliquée et Théorique / Applied and Theoretical Neuroanatomy (NAAT), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Vrije Universiteit Amsterdam [Amsterdam] (VU), Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Institut Royal des Sciences Naturelles de Belgique (IRSNB), University of Texas at Austin [Austin], Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), The George Washington University (GW), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Ditsong National Museum of Natural History [Pretoria, South Africa] (DNMNH), Macquarie University [Sydney], Beijing University of Posts and Telecommunications (BUPT), A.Ba. was funded by the Agence Nationale de la Recherche (grant number: ANR-20-CE27-0009-01). A.Be. was funded by the National Research Foundation of South Africa (Research Development Grants for Y-Rated Researchers (grant number 129336) and the South Africa/France (PROTEA) Joint Research Programme (grant number 129923). C.C.S. was funded by NSF (EF-2021785, DRL-2219759) and NIH (NS092988, AG067419, HG011641). C.J.C. was funded by NIGMS COBRE (grant number 5P20GM103653). J.B. was funded by the NRF African Origins Platform. K.H. and R.T. were supported by the French Agence Nationale de la Recherche, projects NeuroWebLab (ANR-19-DATA-0025) and DMOBE (ANR-21-CE45-0016). K.H. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No101033485 (Individual Fellowship). O.S.T was funded by a Discovery Project Award (project number: DP210101324) funded by the Australian Government. P.G. was funded by the Max Planck Society (grant number M.IF.A.XXXX8103)., ANR-20-CE27-0009,PaleoBRAIN,Ressusciter le cerveau d'Homo erectus et des Néandertaliens(2020), ANR-19-DATA-0025,NeuroWebLab,Un laboratoire de neuroscience collectif: Au delà de FAIR(2019), and ANR-21-CE45-0016,DMOBE,Méchanique dévelopemental de l'évolution du cerveau(2021)
Subjects: [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Archaeology, Fossils, Brain, Artifacts, Phylogeny, [SHS]Humanities and Social Sciences
Abstract: International audience; Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology’s approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.
Published: 2023
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18. New national and regional bryophyte records, 65

Author: L. T. Ellis, C. Ah-Peng, G. Aslan, V. A. Bakalin, A. Bergamini, D. A. Callaghan, P. Campisi, F. M. Raimondo, S. S. Choi, J. Csiky, É. Csikyné Radnai, B. Cykowska-Marzencka, I. V. Czernyadjeva, Yu M. Kalinina, O. M. Afonina, G. Domina, P. Drapela, V. E. Fedosov, E. Fuertes, R. Gabriel, M. Kubová, I. Soares Albergaria, G. Gospodinov, R. Natcheva, A. Graulich, T. Hedderson, E. Hernández-Rodríguez, V. Hugonnot, C. W. Hyun, M. Kırmacı, U. Çatak, S. Kubešová, J. Kučera, C. La Farge, J. Larraín, P. Martin, B. Mufeed, C. N. Manju, K. P. Rajesh, Cs. Németh, J. Nagy, N. Norhazrina, N. Syazwana, S. V. O’Leary, S. J. Park, A. P. Peña-Retes, A. Rimac, A. Alegro, V. Šegota, N. Koletić, N. Vuković, S. Rosadziński, J. A. Rosselló, M. S. Sabovljević, A. D. Sabovljević, A. Schäfer-Verwimp, C. Sérgio, A. V. Shkurko, D. Shyriaieva, V. M. Virchenko, M. Smoczyk, D. Spitale, P. Srivastava, I. Omar, A. K. Asthana, M. Staniaszek-Kik, A. Cienkowska, M.-M. Ștefănuţ, S. Ștefănuţ, G. Tamas, C.-C. Bîrsan, G.-R. Nicoară, M. C. Ion, T. Pócs, G. Kunev, E. I. Troeva, J. van Rooy, P. Wietrzyk-Pełka, M. H. Węgrzyn, G. J. Wolski, D. Bożyk, The Natural History Museum [London] (NHM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Adnan Menderes Üniversitesi, Botanical Garden-Institute, Far-East Branch, Russian Academy of Sciences, Vladivostok, Russia, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Bryophyte Surveys Ltd, Università degli studi di Palermo - University of Palermo, National Institute of Environmental Research [South Korea] (NIER), University of Pecs, Lajos Nagy Grammar School of the Cistercian Order, Polish Academy of Sciences (PAN), Komarov Botanical Institute of Russian Academy of Science, Russian Academy of Sciences [Moscow] (RAS), Lomonosov Moscow State University (MSU), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), University of the Azores, Centre for Ecology, Evolution and Environmental Changes (cE3c) /Azorean Biodiversity Group and Universidade dos Açores - Faculdade de Ciências Agrárias e do Ambiente, Angra do Heroísmo, Açores, Bulgarian Academy of Sciences (BAS), Institute of Biodiversity and Ecosystem Research, University of Cape Town, Department of Biological Sciences, Bolus Herbarium, Université du Québec en Abitibi-Témiscamingue (UQAT), Incheon National University, Biyoloji Bolumu, Moravian Museum, University of South Bohemia, University of Alberta, Pontificia Universidad Católica de Valparaíso (PUCV), The Zamorin's Guruvayurappan College, Szent István University, Universiti Kebangsaan Malaysia, Jeonbuk National University, Univ Nacl Autonoma Mexico, University of Zagreb, Universitat de València (UV), University of Belgrade [Belgrade], Université de Belgrade, Botanical Garden, Centre for Ecology - Evolution and Environmental Changes (cE3c), Universidade de Lisboa (ULISBOA), Natl Acad Sci Ukraine, Museo delle Scienze, Lucknow University, Council of Scientific and Industrial Research [India] (CSIR), University of Lódź, University of Bucharest (UniBuc), Institute of Biology Bucharest of Romanian Academy, Université Eszterházy Károly/Eszterházy Károly Egyetem [Eger, Hungary] (UEK/EKE), Institute of Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences (SB RAS), South African National Biodiversity Institute, University of the Witwatersrand [Johannesburg] (WITS), School of Animal, Plant & Environmental Sciences, Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), The field work in the study was particulary supported by The Rufford Foundation (project ID 27637-1). The work of G. Gospodinov was supported by the Bulgarian Ministry of Education and Science under 249 the National Research Programme ‘Young scientists and postdoctoral students’ approved by 250 DCM no. 577/17.08.2018. Esther Fuertes and Juan Larraín thank Jörn Hentschel for confirming the identity of the Tierra del Fuego specimen of Frullania glomerata. E. Fuertes' research is funded by projects AECI, A-3818-2005, A-6307-2006 y A- 8930-2007 of the Science and Innovation Ministry of Spain. J. Larraín's research is funded by CONICYT postdoctoral grant 3160556. N. Norhazrina and N. Syazwana would like to thank Universiti Kebangsaan Malaysia for supporting this research project through Geran Universiti Penyelidikan (GUP-2018-016 and GGPM-2017-090), and thank L.T. Ellis (BM) for confirming the identity of their collection of Calymperes. The work of S. S. Choi, V. A. Bakalin and S. J. Park was supported by the grant ‘National ecosystem Survey’ from the National Institute of Ecology, while that of S. S. Choi, V. A. Bakalin and C. W. Hyun was supported by the grant ‘Biological Diversity Survey of the Flora of Korean Bryophyta (NIBR201902104)’ from the National Institute of Biological Resources of Ministry of Environment in Korea to C. W. Hyun. Laboratory work of S. S Choi was also supported by the grant ‘National ecosystem Survey’ from the National Institute of Ecology. The study by Yu. M. Kalinina and O. M. Afonina was funded by RFBR, project number 19-34-90033. The work of V. Fedosov was supported by RSF Grant 18-14-00121. T. A. Hedderson is grateful to the National Research Foundation of South Africa for their continued financial support, and to the Himalayan Wildlife Project for their logistical support in Pakistan. The contribution of E. Hernández-Rodríguez and A. P. Peña-Retes is part of the project ‘Effect of forest management on two contrasting groups: mosses and medium and large mammals, Sierra Norte, Oaxaca, Mexico’ supported by Consejo Nacional de Ciencia y Tecnología, Mexico (ID 595991) and The Sigma Xi Grant-in-Aid of Research (ID G201603152071095) through scholarships to E. Hernández-Rodríguez. The work of I. V. Czernyadjeva was supported by Russian Foundation for Basic Research (grants # 18-05-60093) and it was carried out within the framework of the institutional research project (no. АААА-А19-119020690077-4) of the Komarov Botanical Institute of the Russian Academy of Sciences. The work of G. Gospodinov and R. Natcheva was supported by The Bulgarian National Science Fund, project ‘Cryptic species in Bulgarian flora—molecular species delimitation in the Aneura pinguis complex’. Thanks are also due to the Department of Biotechnology, New Delhi for providing financial assistance. S. Ştefănuţ, G. Tamas, C.-C. Bîrsan, G.-R. Nicoară and M. C. Ion acknowledge the support by project no. RO1567-IBB03/2020 through Institute of Biology Bucharest of Romanian Academy. A. V. Shkurko was supported by governmental contract 118021490111-5 of Tsitsin Main Botanical Garden. The contribution by Beata Cykowska-Marzencka has been financially supported by the statutory fund of the W. Szafer Institute of Botany of the Polish Academy of Sciences. The field research in 2017 leading to her results has received funding from the European Union’s Horizon 2020 project INTERACT, under grant agreement No 730938. The laboratory analyses were financed by National Science Centre in Poland (research project No. 2017/27/N/ST10/00862). The work of Paulina Wietrzyk-Pełka was supported by Etiuda project of the National Science Centre in Poland (research project No. 2019/32/T/ST10/00182). M. Kırmacı, G. Aslan and U. Çatak give many thanks to Aydın Adnan Menderes University's scientific research project department (BAP) for supporting their research (FEF 18018) and to Dr Metin Armağan (Adnan Menderes University) for helping during their field trip., European Project: 262693,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,INTERACT(2011), Universiti Kebangsaan Malaysia (UKM), and Universidade de Lisboa = University of Lisbon (ULISBOA)
Subjects: Riccia rhenana, liverworts, bryophytes, Croatia, 0106 biological sciences, Pseudoamblystegium subtile (Hedw.), business.industry, [SDV]Life Sciences [q-bio], Aneura maxima, Bryophytes, Coal mining, Forestry, Plant Science, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Geography, Bryophyte, business, Azores, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany
Abstract: Pseudoamblystegium subtile (Hedw.) Vanderp. & Hedenäs. CONTRIBUTORS: R. Gabriel, M. Kubová, C. Sérgio and I. Soares Albergaria. PORTUGAL, AZORES: Terceira Island, Angra do Heroísmo, municipal garden ‘Jardim Duque da Terceira’, 38° 39′ 24.0′′N, 27°13′ 05.99′′W, 31 m a.s.l, on the base of a shrub, in acidic conditions, 7 April 2017, leg. Michaela Kubová s.n. (AZU). A new understanding of the pleurocarpous moss species Pseudoamblystegium subtile was proposed by Vanderpoorten and Hedenäs (2009). The new genus is separated from the other Amblystegiaceae primarily due to its phylogenetic consistency and is characterised by the possession of leaves with a very short nerve, and erect capsules (Vanderpoorten and Hedenäs 2009). (excerpt) info:eu-repo/semantics/publishedVersion
Published: 2021
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19. Single-Dose Liposomal Amphotericin B Treatment for Cryptococcal Meningitis

Author: Jarvis, Joseph N, Lawrence, David S, Meya, David B, Kagimu, Enock, Kasibante, John, Mpoza, Edward, Rutakingirwa, Morris K, Ssebambulidde, Kenneth, Tugume, Lillian, Rhein, Joshua, Boulware, David R, Mwandumba, Henry C, Moyo, Melanie, Mzinganjira, Henry, Kanyama, Cecilia, Hosseinipour, Mina C, Chawinga, Chimwemwe, Meintjes, Graeme, Schutz, Charlotte, Comins, Kyla, Singh, Achita, Muzoora, Conrad, Jjunju, Samuel, Nuwagira, Edwin, Mosepele, Mosepele, Leeme, Tshepo, Siamisang, Keatlaretse, Ndhlovu, Chiratidzo E, Hlupeni, Admire, Mutata, Constantine, van Widenfelt, Erik, Chen, Tao, Wang, Duolao, Hope, William, Boyer-Chammard, Timothée, Loyse, Angela, Molloy, Síle F, Youssouf, Nabila, Lortholary, Olivier, Lalloo, David G, Jaffar, Shabbar, Harrison, Thomas S, Ambition Study Group, London School of Hygiene and Tropical Medicine (LSHTM), Bostwana Harvard AIDS Institute Partneship Gaborone, National Center for Atmospheric Research [Boulder] (NCAR), University of North Carolina Project-Malawi (UNC Project), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), University of Cape Town, Mycologie moléculaire - Molecular Mycology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Centre National de Référence Mycoses Invasives et Antifongiques - National Reference Center Invasive Mycoses & Antifungals (CNRMA), Institut Pasteur [Paris]-Université Paris Cité (UPC), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Supported by a grant (TRIA2015-1092) through the European and Developing Countries Clinical Trials Partnership, with assistance from the Swedish International Development Cooperation Agency, as well as by funding from the U.K. Department of Health and Social Care, the U.K. Foreign Commonwealth and Development Office, the U.K. Medical Research Council, and Wellcome Trust, through the Joint Global Health Trials scheme (MR/P006922/1). Funding was also provided by the National Institute for Health Research (NIHR) through a Global Health Research Professorship (RP-2017-08-ST2-012, to Dr. Jarvis) with aid from the U.K. government to support global health research. Dr. Meintjes was supported by grants (098316, 214321/Z/18/Z, and 203135/Z/16/Z) from the Wellcome Trust and a grant (64787) from the South African Research Chairs Initiative of the Department of Science and Technology and the National Research Foundation of South Africa. Diagnostic testing in Uganda was supported by a grant (R01NS086312) from the National Institute of Neurological Disorders and Stroke. Dr. Rhein was supported by a grant (K01 TW010268) from the Fogarty International Center. Liposomal amphotericin B (AmBisome) was donated by Gilead Sciences., We thank the trial participants and their families and caregivers, as well as all the clinical, laboratory, and administrative staff at all the sites who were not directly involved in the trial, Andrew Nunn, Sayoki Mfinanga, Robert Peck, and William Powderly for serving on the data and safety monitoring committee, and John Perfect, Andrew Kambugu, Saidi Kapigi, and Douglas Wilson for serving on the trial steering committee. We dedicate the trial to the memory of Siphokazi Hlungulu, who worked as a research nurse and study coordinator for the Cape Town Ambition site for the duration of the trial and died before seeing the results published., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)
Subjects: wl_200, qv_350, General Medicine, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, wc_245
Abstract: BackgroundCryptococcal meningitis is a leading cause of human immunodeficiency virus (HIV)-related death in sub-Saharan Africa. Whether a treatment regimen that includes a single high dose of liposomal amphotericin B would be efficacious is not known.MethodsIn this phase 3 randomized, controlled, noninferiority trial conducted in five African countries, we assigned HIV-positive adults with cryptococcal meningitis in a 1:1 ratio to receive either a single high dose of liposomal amphotericin B (10 mg per kilogram of body weight) on day 1 plus 14 days of flucytosine (100 mg per kilogram per day) and fluconazole (1200 mg per day) or the current World Health Organization-recommended treatment, which includes amphotericin B deoxycholate (1 mg per kilogram per day) plus flucytosine (100 mg per kilogram per day) for 7 days, followed by fluconazole (1200 mg per day) for 7 days (control). The primary end point was death from any cause at 10 weeks; the trial was powered to show noninferiority at a 10-percentage-point margin.ResultsA total of 844 participants underwent randomization; 814 were included in the intention-to-treat population. At 10 weeks, deaths were reported in 101 participants (24.8%; 95% confidence interval [CI], 20.7 to 29.3) in the liposomal amphotericin B group and 117 (28.7%; 95% CI, 24.4 to 33.4) in the control group (difference, -3.9 percentage points); the upper boundary of the one-sided 95% confidence interval was 1.2 percentage points (within the noninferiority margin; P10 colony-forming units (CFU) per milliliter per day in the liposomal amphotericin B group and -0.42 log10 CFU per milliliter per day in the control group. Fewer participants had grade 3 or 4 adverse events in the liposomal amphotericin B group than in the control group (50.0% vs. 62.3%).ConclusionsSingle-dose liposomal amphotericin B combined with flucytosine and fluconazole was noninferior to the WHO-recommended treatment for HIV-associated cryptococcal meningitis and was associated with fewer adverse events. (Funded by the European and Developing Countries Clinical Trials Partnership and others; Ambition ISRCTN number, ISRCTN72509687.).
Published: 2022
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20. Microplastic leachates disrupt the chemotactic and chemokinetic behaviours of an ecosystem engineer (Mytilus edulis)

Author: Marine Uguen, Katy R. Nicastro, Gerardo I. Zardi, Sylvie M. Gaudron, Nicolas Spilmont, Fleurine Akoueson, Guillaume Duflos, Laurent Seuront, Université de Lille, Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Rhodes University, Grahamstown, Centro de Ciências do Mar [Faro] (CCMAR), Universidade do Algarve (UAlg), Sorbonne Université - UFR Sciences de la vie (UFR 927 ), Sorbonne Université (SU), Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Tokyo University of Marine Science and Technology (TUMSAT), and This research was also financially supported by both the European Maritime and Fisheries Fund (FEAMP) and France Filière Pêche through the research project SOLACE (« Resilience of the mussel Mytilus edulis to anthropogenic and climatic stressors »), and by the Fundação para a Ciência e a Tecnologia (FCT, MEC, Portugal, grant number: UIDB/04326/2020) and the National Research Foundation of South Africa (grant number: 64801).
Subjects: Mytilus, Environmental Engineering, Chemodetection, Brachyura, Mytilus edulis, Microplastics, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Public Health, Environmental and Occupational Health, General Medicine, General Chemistry, Polypropylenes, Pollution, Predators, Intertidal species, [SDE]Environmental Sciences, Animals, Environmental Chemistry, [CHIM]Chemical Sciences, Chemical stimulus, Cues, Plastics, Ecosystem, Water Pollutants, Chemical, Blue mussel
Abstract: The massive contamination of the environment by plastics is an increasing global scientific and societal concern. Knowing whether and how these pollutants affect the behaviour of keystone species is essential to identify environmental risks effectively. Here, we focus on the effect of plastic leachates on the behavioural response of the common blue mussel Mytilus edulis, an ecosystem engineer responsible for the creation of biogenic structures that modify the environment and provide numerous ecosystem functions and services. Specifically, we assess the effect of virgin polypropylene beads on mussels' chemotactic (i.e. a directional movement in response to a chemical stimulus) and chemokinetic (i.e. a non-directional change in movement properties such as speed, distance travelled or turning frequency in response to a chemical stimulus) responses to different chemical cues (i.e. conspecifics, injured conspecifics and a predator, the crab Hemigrapsus sanguineus). In the presence of predator cues, individual mussels reduced both their gross distance and speed, changes interpreted here as an avoidance behaviour. When exposed to polypropylene leachates, mussels moved less compared to control conditions, regardless of the cues tested. Additionally, in presence of crab cues with plastic leachates, mussels significantly changed the direction of movement suggesting a leachate-induced loss of their negative chemotaxis response. Taken together, our results indicate that the behavioural response of M. edulis is cue-specific and that its anti-predator behaviour as well as its mobility are impaired when exposed to microplastic leachates, potentially affecting the functioning of the ecosystem that the species supports. info:eu-repo/semantics/publishedVersion
Published: 2022
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21. The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity

Author: Vimercati, Giovanni, Probert, Anna F., Volery, Lara, Bernardo Madrid, Rubén, Bertolino, Sandro, Cespedes, Vanessa, Essl, Franz, Evans, Thomas, González Moreno, Pablo, Vilà, Montserrat, Wilson, John R U., Bacher, Sven, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Agencia Estatal de Investigación. España, Swiss National Science Foundation (SNFS), Austrian Fonds zur Förderung der Wissenschaftlichen Forschung, German Bundesministerium für Bildung und Forschung (BMBF), French National Research Agency, US National Science Foundation, National Research Foundation of South Africa, Australian Research Council, UK Natural Environment Research Council, and Hellenic Foundation for Research and Innovation (H.F.R.I.)
Abstract: Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions. Agencia Estatal de Investigación PCI2018-092939, PCI2018-092986 Swiss National Science Foundation 31003A_179491, 31BD30_184114 Austrian Fonds zur Förderung der Wissenschaftlichen Forschung 4011-B32 German Bundesministerium für Bildung und Forschung 16LC1803A, 01LC1807C French National Research Agency ANR-18-EBI4-0001-06 US National Science Foundation ICER-1852060 National Research Foundation of South Africa 89967 Australian Research Council DP200101680 UK Natural Environment Research Council NE/V007548/1 Hellenic Foundation for Research and Innovation (H.F.R.I.) HFRIFM17-1597
Published: 2022

22. Studying the microbiota of bats: Accuracy of direct and indirect samplings

Author: Muriel Dietrich, Wanda Markotter, Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IRD-Centre National de la Recherche Scientifique (CNRS), University of Pretoria [South Africa], Centers for Disease Control and Prevention, Grant/Award Number: 5NU2GGH001874-02-00, National Research Foundation of South Africa, Grant/Award Number: UID 78566, 91496, 92524 and 98339, Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR), and Univ, Réunion
Subjects: 0106 biological sciences, bats, Zoology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, South Africa, Illumina, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Ecology, Evolution, Behavior and Systematics, Feces, 030304 developmental biology, Nature and Landscape Conservation, Original Research, 0303 health sciences, Ecology, biology, Direct sampling, Sampling (statistics), biology.organism_classification, 6. Clean water, urine, 16S rRNA sequencing, feces, Metagenomics, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Rousettus, Passive sampling
Abstract: International audience; Given the recurrent bat‐associated disease outbreaks in humans and recent advances in metagenomics sequencing, the microbiota of bats is increasingly being studied. However, obtaining biological samples directly from wild individuals may represent a challenge, and thus, indirect passive sampling (without capturing bats) is sometimes used as an alternative. Currently, it is not known whether the bacterial community assessed using this approach provides an accurate representation of the bat microbiota. This study was designed to compare the use of direct sampling (based on bat capture and handling) and indirect sampling (collection of bat's excretions under bat colonies) in assessing bacterial communities in bats. Using high‐throughput 16S rRNA sequencing of urine and feces samples from Rousettus aegyptiacus, a cave‐dwelling fruit bat species, we found evidence of niche specialization among different excreta samples, independent of the sampling approach. However, sampling approach influencedboth the alpha‐ and beta‐diversity of urinary and fecal microbiotas. In particular, increased alpha‐diversity and more overlapping composition between urine and feces samples was seen when direct sampling was used, suggesting that cross‐contamination may occur when collecting samples directly from bats in hand. In contrast, results from indirect sampling in the cave may be biased by environmental contamination. Our methodological comparison suggested some influence of the sampling approach on the bat‐associated microbiota, but both approaches were able to capture differences among excreta samples. Assessment of these techniques opens an avenue to use more indirect sampling, in order to explore microbial community dynamics in bats.
Published: 2019
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23. A one health investigation of pathogenic trypanosomes of cattle in Malawi

Author: Eric Etter, Ilse Vorster, Elizabeth T. Chimera, Geoffrey T. Fosgate, Alain Boulangé, Luis Neves, University of Pretoria [South Africa], Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Eduardo Mondlane University, and The funding for this research was provided by the Borlaug Higher Education for Agricultural Research and Development (BHEARD) program of the United States Agency for International Development (USAID) with partial funding from the National Research Foundation in South Africa (Grant 76734 ).
Subjects: Veterinary medicine, Malawi, Trypanosoma congolense, [SDV]Life Sciences [q-bio], L73 - Maladies des animaux, Serology, 0403 veterinary science, 0302 clinical medicine, Food Animals, Prevalence, Trypanosoma brucei, 2. Zero hunger, Incidence (epidemiology), Santé animale, Incidence, Spatial epidemiology, 04 agricultural and veterinary sciences, Trypanosomose africaine, 3. Good health, One Health, Maladie des animaux, S50 - Santé humaine, Livestock, Trypanosoma, 040301 veterinary sciences, Distribution géographique, 030231 tropical medicine, relation homme-faune, Cattle Diseases, Biology, Trypanosoma theileri, 03 medical and health sciences, Species Specificity, Trypanosomiasis, parasitic diseases, Animals, Transmission des maladies, Bovin, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, business.industry, Trypanosoma brucei rhodesiense, Distribution spatiale, Loop-mediated isothermal amplification, Sleeping sickness, biology.organism_classification, Cross-Sectional Studies, Maladie infectieuse, Animal Science and Zoology, Cattle, business
Abstract: International audience; arasitic protozoan trypanosomes of the genus Trypanosoma cause infections in both man and livestock in Africa. Understanding the current spatial distribution of trypanosomes, herd-level factors associated with Trypanosoma brucei infection as well as local knowledge of African trypanosomosis is key to its prevention and control. A cross-sectional study was performed that sampled 53 livestock farmers and 444 cattle throughout Malawi. Cattle were screened for trypanosomes using serology and molecular techniques. Questionnaires were administered to livestock herders and incidence of hospital diagnosed human trypanosome infections was estimated from reports submitted to the Department of Health Unit. The apparent prevalence of trypanosome species based on molecular detection was low for Trypanosoma brucei (2%; 95 % CI: 1–4 %) and Trypanosoma congolense (3%; 95 % CI: 2–5 %) but higher for Trypanosoma theileri (26 %; 95 % CI: 22–30 %). The central region of the country was identified as being at a higher risk of T.brucei infection. One of the sampled cattle was confirmed as being infected with Trypanosoma brucei rhodesiense. Human trypanosome cases were more frequently reported in the northern region with an estimated incidence of 5.9 cases per 100,000 people in Rumphi District. The control of zoonotic diseases that impact poor livestock herders requires a One Health approach due to the close contact between humans and their animals and the reliance on animal production for a sustainable livelihood.
Published: 2021
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24. Civic Ecology Uplifts Low-Income Communities, Improves Ecosystem Services and Well-Being, and Strengthens Social Cohesion

Author: Rob Slotow, Margaret Burger, Ntswaki Ditlhale, Kirsten Mahood, Rashieda Davids, Mathieu Rouget, University of KwaZulu-Natal (UKZN), School of Agricultural, Earth and Environmental Sciences (SAEES), EnviroHeart Consulting (Pty) Ltd (EnviroHeart Consulting), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), EcoImvelo, Triple-P NPC (Previously i4WATER), School of Life Sciences, University of KwaZulu- Natal, Durban, South Africa, University College of London [London] (UCL), This research is part of the SHEFS-an interdisciplinary research partnership forming part of the Wellcome Trust's funded Our Planet, Our Health programme, with the overall objective to provide novel evidence to define future food systems policies to deliver nutritious and healthy foods in an environmentally sustainable and socially equitable manner. This research was funded by the Wellcome Trust through the Sustainable and Healthy Food Systems (SHEFS) Project (grant no. 205200/Z/16/Z). The South African Research Chairs Initiative of the Department of Science and Technology and the National Research Foundation of South Africa (grant no. 84157) financially supported the research. The funding support of i4Water is also acknowledged for commissioning Rashieda Davids and Margaret Burger to undertake an associated study that facilitated data collection for this study., and University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN)
Subjects: 010504 meteorology & atmospheric sciences, lcsh:TJ807-830, Geography, Planning and Development, Social ecology, Wetland, 010501 environmental sciences, 01 natural sciences, Ecosystem services, environmental management, social-ecological system, Bien-être social, 11. Sustainability, lcsh:Environmental sciences, lcsh:GE1-350, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, geography.geographical_feature_category, sustainable development, Community engagement, Ecology, lcsh:Environmental effects of industries and plants, Livelihood, 6. Clean water, P01 - Conservation de la nature et ressources foncières, Natural capital, lcsh:Renewable energy sources, Management, Monitoring, Policy and Law, 12. Responsible consumption, stewardship, E50 - Sociologie rurale, social–ecological system, 0105 earth and related environmental sciences, Sustainable development, geography, Renewable Energy, Sustainability and the Environment, business.industry, Sociologie rurale, 15. Life on land, social ecology, services écosystémiques, ecosystem service, lcsh:TD194-195, Développement durable, 13. Climate action, Agriculture, business, ecosystem services, Gestion de l'environnement
Abstract: Ecosystem services enhance well-being and the livelihoods of disadvantaged communities. Civic ecology can enhance social&ndash, ecological systems, however, their contributions to ecosystem services are rarely measured. We analysed the outcomes of civic ecology interventions undertaken in Durban, South Africa, as part of the Wise Wayz Water Care programme (the case study). Using mixed methods (household and beneficiary (community members implementing interventions) surveys, interviews, field observations, and workshops), we identified ecosystem service use and values, as well as the benefits of six interventions (solid waste management and removal from aquatic and terrestrial areas, recycling, invasive alien plant control, river water quality monitoring, vegetable production, and community engagement). Ecosystem services were widely used for agriculture, subsistence, and cultural uses. River water was used for crop irrigation, livestock, and recreation. Respondents noted numerous improvements to natural habitats: decrease in invasive alien plants, less pollution, improved condition of wetlands, and increased production of diverse vegetables. Improved habitats were linked to enhanced ecosystem services: clean water, agricultural production, harvesting of wood, and increased cultural and spiritual activities. Key social benefits were increased social cohesion, education, and new business opportunities. We highlight that local communities can leverage natural capital for well-being and encourage policy support of civic ecology initiatives.
Published: 2021
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25. Forest canopy gaps offer a window into the future:The case of subtropical coastal forests within an urban matrix in South Africa

Author: Syd Ramdhani, Olivier Kambol Kambaj, Astika Bhugeloo, Sershen, Kabir Peerbhay, Hawaan Forest Management, uMdoni Trust, Wildlife and Environment Society of Southern Africa, Teddy Govender, and National Research Foundation of South Africa
Subjects: 0106 biological sciences, Abiotic component, Canopy, Tree canopy, 010504 meteorology & atmospheric sciences, Ecology, Biodiversity, Soil Science, Forestry, Subtropics, SD1-669.5, 010603 evolutionary biology, 01 natural sciences, Geography, Species richness, Ecology, Evolution, Behavior and Systematics, Species reintroduction, 0105 earth and related environmental sciences, Global biodiversity
Abstract: Aim of the study: Alien and indigenous species emergence patterns within canopy gaps in urban subtropical forests are poorly understood. This study compared canopy gap floristics in relation to abiotic and physical characteristics across three subtropical urban forests differing in disturbance history. Area of study: Three Northern Coastal Forests of varying disturbance histories located in coastal subtropical urban KwaZulu-Natal (KZN), South Africa (SA). Materials and methods: Closed canopy (n = 15 quadrats per forest ) and four gaps (n = 12 quadrats per forest) from three size classes (‘small’ < 25 m2, ‘medium’ 25 - 45 m2; ‘large’ > 45 m2) were surveyed for the primary least disturbed (PLD), primary highly disturbed (PHD) and transitional highly disturbed (THD) forests using classical vegetation sampling techniques. Soil moisture content and air temperature were measured within each gap. Main results: Cumulatively all forest gaps hosted 198 species. Equivalent number of species (Hill numbers from H = 0 to H = 2) were constantly higher in the PHD forest followed by the PLD forest and lowest in the THD forest. Alien and indigenous plant density were negatively correlated. Species richness was positively correlated with gap size and soil moisture content, and negatively correlated with air temperature. Research highlights: Gap floristic patterns are influenced by size, abiotic factors, disturbance and forest successional status. Floristic, abiotic and physical characteristics of gaps should be monitored within urban forests as these can influence gap infilling in terms of rate, species composition, and alien-indigenous plant interactions across the forest. This can inform management interventions such as species reintroduction and alien clearing. Keywords: conservation; disturbance; gaps; management; Northern Coastal Forest; subtropical; species richness. Abbreviations: SA: South Africa; KZN: KwaZulu-Natal; PLD: Primary Least Disturbed forest; PHD: Primary Highly Disturbed forest; THD: Transitional Highly Disturbed forest; IOCB: Indian Ocean Coastal Belt; New POSA: New Plants of southern Africa website; NEMBA: National Environmental Management: Biodiversity Act.
Published: 2021

26. Surveillance of Antibiotic Resistance of Maltose-Negative Staphylococcus aureus in South African Dairy Herds

Author: Inge-Marie Petzer, Joanne Karzis, Eric Etter, Edward Francis Donkin, Vinny Naidoo, University of Pretoria [South Africa], Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and This research was partly funded by The National Research Foundation (NRF), South Africa
Subjects: 0301 basic medicine, Microbiology (medical), Troupeau laitier, Veterinary medicine, Staphylococcus aureus, antibiotic resistance, medicine.drug_class, [SDV]Life Sciences [q-bio], 030106 microbiology, Antibiotics, Résistance aux antibiotiques, Biology, medicine.disease_cause, L73 - Maladies des animaux, mastitis, Biochemistry, Microbiology, 03 medical and health sciences, Minimum inhibitory concentration, Antibiotic resistance, Ampicillin, Mammite, medicine, regions, Pharmacology (medical), MIC, General Pharmacology, Toxicology and Pharmaceutics, 2. Zero hunger, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, seasons, somatic cell count, lcsh:RM1-950, medicine.disease, 3. Good health, Mastitis, Penicillin, 030104 developmental biology, Infectious Diseases, lcsh:Therapeutics. Pharmacology, Somatic cell count, medicine.drug
Abstract: Antibiotic resistance has been reported since the 1940s in both human and veterinary medicine. Many years of monitoring milk samples in South Africa led to identification of a novel maltose-negative Staphylococcus aureus (S. aureus) strain, which appears to be an emerging pathogen. In this study, the susceptibility of this strain to antibiotics was evaluated over time, during diverse seasons in various provinces and according to somatic cell count (SCC) categories. A data set of 271 maltose-negative S. aureus isolates, from milk samples of 117 dairy herds, was examined using the disk diffusion method, between 2010 and 2017. This study also compared the susceptibility testing of 57 maltose-negative and 57 maltose-positive S. aureus isolated from 38 farms, from three provinces using minimum inhibitory concentration (MIC). The MIC results for the maltose-negative S. aureus isolates showed highest resistance to ampicillin (100%) and penicillin (47.4) and lowest resistance (1.8%) to azithromycin, ciprofloxacin and erythromycin. The maltose-negative S. aureus isolates showed overall significantly increased antibiotic resistance compared to the maltose-positive strains, as well as multidrug resistance. Producers and veterinarians should consider probability of cure of such organisms (seemingly non-chronic) when adapting management and treatment, preventing unnecessary culling.
Published: 2020
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27. How virulent are emerging maize-infecting mastreviruses?

Author: Arvind Varsani, Lara Donaldson, Penelope Hartnady, Jean-Michel Lett, Pierre Lefeuvre, Darren P. Martin, Sohini Claverie, Kehinde A. Oyeniran, Adérito L. Monjane, University of Cape Town, Institute of Infectious Disease & Molecular Medicine (IDM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Norwegian Veterinary Institute [Oslo], Arizona State University [Tempe] (ASU), School of Life Sciences (Arizona State University), Department of Integrative Biomedical Sciences [Cape Town], KAO was supported by the National Research Foundation (NRF) South Africa and The World Academy of Science (TWAS) Grant number 105461. SC, PL and J-ML were supported by the European Union (ERDF, contract GURDT I2016-1731-0006632), the Conseil Regional de La Reunion, the Agropolis Fondation (Labex Agro-Montpellier, E-SPACE project number 1504-004) and CIRAD., and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: endocrine system, medicine.medical_specialty, Genotype, viruses, Virulence, Pathologie végétale, Disease, Genome, Viral, Zea mays, Virus, Crop, 03 medical and health sciences, Mastrevirus, Maladie des plantes, Medical microbiology, Virology, Maize streak virus, medicine, neoplasms, Géminivirus, Phylogeny, H20 - Maladies des plantes, 030304 developmental biology, Plant Diseases, 2. Zero hunger, 0303 health sciences, Géminivirus striure du maïs, biology, 030306 microbiology, General Medicine, Sequence Analysis, DNA, biology.organism_classification, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA, Viral
Abstract: International audience; Maize streak disease (MSD) is one of the most significant biotic constraints on the production of Africa's most important cereal crop. Until recently, the only virus known to cause severe MSD was the A-strain of maize streak virus (MSV/A), a member of the genus Mastrevirus, family Geminiviridae. However, over the past decade, two other mastreviruses, MSV/C and maize streak Reunion virus (MSRV), have been repeatedly found in the absence of MSV/A in maize plants displaying severe MSD symptoms. Here, we report on infectious clones of MSV/C and MSRV and test their ability to cause severe MSD symptoms. Although cloned MSV/C and MSRV genomes could cause systemic symptomatic infections in MSD-sensitive maize genotypes, these infections yielded substantially milder symptoms than those observed in the field. The MSV/C and MSRV isolates that we have examined are therefore unlikely to cause severe MSD on their own. Furthermore, mixed infections of MSRV and MSV/C with other mild MSV strains also consistently yielded mild MSD symptoms. It is noteworthy that MSRV produces distinctive striate symptoms in maize that are similar in pattern, albeit not in severity, to those seen in the field, showing that this virus may contribute to the severe MSD symptoms seen in the field. Therefore, despite not fulfilling Koch's postulates for MSV/C and MSRV as causal agents of severe MSD, we cannot exclude the possibility that these viruses could be contributing to currently emerging maize diseases.
Published: 2020
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28. Scientists' warning on invasive alien species

Author: Philip E. Hulme, Hanno Seebens, Daniel Simberloff, Nicholas E. Mandrak, Llewellyn C. Foxcroft, Jan Pergl, Tim M. Blackburn, Wayne Dawson, Franz Essl, Piero Genovesi, Andrew M. Liebhold, Mark van Kleunen, Helen E. Roy, Jonathan M. Jeschke, Montserrat Vilà, James T. Carlton, Laura A. Meyerson, Aníbal Pauchard, David M. Richardson, Michael J. Wingfield, Petr Pyšek, Sven Bacher, Ingolf Kühn, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Czech Science Foundation, Czech Academy of Sciences, Swiss National Science Foundation (SNFS), Austrian Science Foundation, National Research Foundation of South Africa, New Zealand Ministry of Business, Innovation and Employment, Comisión Nacional de Investigación Científica y Tecnológica (CONICYT). Chile, Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT). Chile, Natural Environment Research Council (NERC). Reino Unido, Deutsche Forschungsgemeinschaft / German Research Foundation (DFG), Ministerio de Ciencia, Innovación y Universidades (MICINN). España, German Federal Ministry of Education and Research, Austrian Science Foundation FWF, and Natural Environment Research Council
Subjects: 0106 biological sciences, Biosecurity, biological invasions, Biodiversity, Introduced species, 01 natural sciences, Ecosystem services, Global change, Phylogeny, Naturalization, 0303 health sciences, Ecology, environmental impacts, Geography, Policy, Habitat, Invasion hotspots, Socioeconomic impacts, Original Article, General Agricultural and Biological Sciences, policy, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, Ecology and Environment, 03 medical and health sciences, ddc:570, biological invasions, biosecurity, global change, environmental impacts, invasion dynamics, invasion hotspots, naturalization, policy, protected areas, socioeconomic impacts, Animals, Ecosystem, Biological invasions, invasion dynamics, global change, 030304 developmental biology, Population Density, socioeconomic impacts, Original Articles, invasion hotspots, Environmental impacts, Rats, Protected areas, naturalization, Disturbance (ecology), Invasion dynamics, Species richness, protected areas, Introduced Species, biosecurity
Abstract: Biological invasions are a global consequence of an increasingly connected world and the rise in human population size. The numbers of invasive alien species – the subset of alien species that spread widely in areas where they are not native, affecting the environment or human livelihoods – are increasing. Synergies with other global changes are exacerbating current invasions and facilitating new ones, thereby escalating the extent and impacts of invaders. Invasions have complex and often immense long-term direct and indirect impacts. In many cases, such impacts become apparent or problematic only when invaders are well established and have large ranges. Invasive alien species break down biogeographic realms, affect native species richness and abundance, increase the risk of native species extinction, affect the genetic composition of native populations, change native animal behaviour, alter phylogenetic diversity across communities, and modify trophic networks. Many invasive alien species also change ecosystem functioning and the delivery of ecosystem services by altering nutrient and contaminant cycling, hydrology, habitat structure, and disturbance regimes. These biodiversity and ecosystem impacts are accelerating and will increase further in the future. Scientific evidence has identified policy strategies to reduce future invasions, but these strategies are often insufficiently implemented. For some nations, notably Australia and New Zealand, biosecurity has become a national priority. There have been long-term successes, such as eradication of rats and cats on increasingly large islands and biological control of weeds across continental areas. However, in many countries, invasions receive little attention. Improved international cooperation is crucial to reduce the impacts of invasive alien species on biodiversity, ecosystem services, and human livelihoods. Countries can strengthen their biosecurity regulations to implement and enforce more effective management strategies that should also address other global changes that interact with invasions. Czech Science Foundation 19-28807X Czech Academy of Sciences RVO 67985939 Swiss National Science Foundation 31BD30_184114, 31003A_179491 Austrian Science Foundation FWF I 3757-B29 National Research Foundation of South Africa IFR2010041400019, IFR160215158271 New Zealand Ministry of Business, Innovation and Employment C09X1611 CONICYT AFB-170008 Fondecyt 1180205 Natural Environment Research Council NE/R016429/1 Deutsche Forschungsgemeinschaft JE 288/9-2, 264740629 Ministerio de Ciencia, Innovación y Universidades PCI2018- 092939 German Federal Ministry of Education and Research 01LC1803A, 01LC1807B, 01LC1807A
Published: 2020

29. Host conservation through their parasites : molecular surveillance of vector-borne microorganisms in bats using ectoparasitic bat flies

Author: Eléonore Genzoni, Philippe Christe, Muriel Dietrich, Laurie Ançay, Wanda Markotter, Loic Brun, Ernest C.J. Seamark, Teresa Kearney, Péter Estók, Laura Clément, Tamara Szentiványi, Olivier Glaizot, Museum of Zoology [Lausanne, Switzerland] (MZL), University of Lausanne (UNIL), University of Pretoria [South Africa], AfricanBats NPC [Pretoria, South Africa], Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR), Ditsong National Museum of Natural History [Pretoria, South Africa] (DNMNH), Université Eszterházy Károly/Eszterházy Károly Egyetem [Eger, Hungary] (UEK/EKE), This work was financially supported in part by the National Research Foundation of South Africa under grant numbers UID 92524, 85756, and 91496 (held by Prof. W. Markotter) as well as the South AfricanResearch Chair in Animal Infectious Diseases (Zoonoses) held by Prof. W. Markotter, grant no. 98339 and the Swiss National Science Foundation grant 31003A_179378 held by Prof. P. Christe., Université de Lausanne = University of Lausanne (UNIL), Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IRD-Centre National de la Recherche Scientifique (CNRS), and Univ, Réunion
Subjects: 0106 biological sciences, Animals, Apicomplexa/isolation & purification, Bartonella/genetics, Bartonella/isolation & purification, Bartonella Infections/epidemiology, Bartonella Infections/microbiology, Chiroptera/microbiology, Chiroptera/parasitology, Conservation of Natural Resources/methods, Diptera/microbiology, Diptera/parasitology, Parasites/isolation & purification, Phylogeny, Population Surveillance/methods, Prevalence, Protozoan Infections, Animal/epidemiology, Protozoan Infections, Animal/parasitology, Spain/epidemiology, Trypanosoma/isolation & purification, Bartonella, Nycteribiidae, Polychromophilus, Trypanosoma, blood-sampling, non-invasive method, 01 natural sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chiroptera, Protozoan Infections, Animal, 0303 health sciences, education.field_of_study, biology, 3. Good health, Infectious Diseases, Population Surveillance, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Research Article, Conservation of Natural Resources, Veterinary (miscellaneous), Population, Zoology, 010603 evolutionary biology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Bartonella Infections, lcsh:RC109-216, Parasites, education, 030304 developmental biology, Host (biology), Diptera, fungi, biology.organism_classification, Parasitology, Spain, Insect Science, Vector (epidemiology), Animal Science and Zoology, Apicomplexa, Blood sampling
Abstract: Most vertebrates host a wide variety of haematophagous parasites, which may play an important role in the transmission of vector-borne microorganisms to hosts. Surveillance is usually performed by collecting blood and/or tissue samples from vertebrate hosts. There are multiple methods to obtain samples, which can be stored for decades if properly kept. However, blood sampling is considered an invasive method and may possibly be harmful to the sampled individual. In this study, we investigated the use of ectoparasites as a tool to acquire molecular information about the presence and diversity of infectious microorganism in host populations. We tested the presence of three distinct vector-borne microorganisms in both bat blood and bat flies: Bartonella bacteria, malaria-like Polychromophilus sp. (Apicomplexa), and Trypanosoma sp. (Kinetoplastea). We detected the presence of these microorganisms both in bats and in their bat flies, with the exception of Trypanosoma sp. in South African bat flies. Additionally, we found Bartonella sp. in bat flies from one population in Spain, suggesting its presence in the host population even if not detected in bats. Bartonella and Polychromophilus infection showed the highest prevalence in both bat and bat fly populations. Single, co-and triple infections were also frequently present in both. We highlight the use of haematophagous ectoparasites to study the presence of infectious microorganism in host blood and its use as an alternative, less invasive sampling method., Conservation des hôtes grâce à leurs parasites : surveillance moléculaire des microorganismes à transmission vectorielle chez les chauves-souris à l’aide de mouches ectoparasites. La plupart des vertébréshébergent une grande variété de parasites hématophages, qui peuvent jouer un rôle important dans la transmission de microorganismes à transmission vectorielle à leurs hôtes. La surveillance est généralement effectuée en prélevant des échantillons de sang et/ou de tissus sur des hôtes vertébrés. Il existe plusieurs méthodes pour obtenir des échantillons, qui peuvent être conservés pendant des décennies dans des bonnes conditions. Cependant, le prélèvement sanguin est considéré comme une méthode invasive et peut éventuellement être nocif pour l’individu prélevé. Dans cette étude, nous avons étudié l’utilisation d’ectoparasites comme outil pour acquérir des informations moléculaires sur la présence et la diversité des microorganismes infectieux dans les populations hôtes. Nous avons testé la présence de trois microorganismes distincts, transmis par des vecteurs, dans le sang et les mouches des chauves-souris : les bactéries Bartonella, Polychromophilus sp. (Apicomplexa) et Trypanosoma sp.(Kinetoplastea). Nous avons détecté la présence de ces microorganismes à la fois chez les chauves-souris et chez leurs mouches des chauves-souris, à l’exception de Trypanosoma sp. chez les chauves-souris sud-africaines. De plus, nous avons trouvé Bartonella sp. chez les mouches des chauves-souris d’une population en Espagne, ce qui suggère sa présence dans la population hôte même si elle n’est pas détectée chez les chauves-souris elles-mêmes. Les infections à Bartonella et Polychromophilus ont montré la prévalence la plus élevée dans les populations de chauves-souris et de mouches des chauves-souris. Des infections simples, doubles et triples étaient également fréquemment présentes dans les deux cas. Nous mettons en évidence l’utilisation d’ectoparasites hématophages pour étudier la présence de microorganismes infectieux dans le sang de l’hôte et son utilisation comme méthode alternative et moins invasive d’échantillonnage.
Published: 2020
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30. Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand

Author: Denis Filloux, Simona Kraberger, Arvind Varsani, Gordon William Harkins, Cécile Richet, Pauline Bernardo, Philippe Roumagnac, Darren P. Martin, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University [Tempe] (ASU), Ohio State University [Columbus] (OSU), University of the Western Cape, University of Cape Town, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury [Christchurch], Structural Biology Research Unit, Department of Clinical Laboratory Sciences, National Research Foundation of South Africa, EU : PIOF-GA-2013-622571, Direction Generale de l'Armement, MEM INRA Metaprogram, and Fondation pour la Recherche : MH425569-MH425573
Subjects: Viral metagenomics, viruses, Amino Acid Motifs, Biology, Poaceae, Virus, DNA sequencing, Plant Viruses, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, chemistry.chemical_compound, South Africa, Virology, Plant virus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Genomic organization, H20 - Maladies des plantes, Genetics, 0303 health sciences, 030306 microbiology, DNA Viruses, Helicase, General Medicine, 3. Good health, chemistry, Capsid, biology.protein, DNA, Circular, DNA, Apiaceae, New Zealand
Abstract: International audience; Advances in molecular techniques used in viral metagenomics coupled with high throughput sequencing is rapidly expanding our knowledge of plant-associated virus diversity. Applying such approaches, we have identified five novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from Poaceae and Apiaceae plant from South Africa and New Zealand. These viruses have a simple genomic organization, including two open reading frames that likely encode a Rep and a capsid protein (CP), a conserved nonanucleotide motif on the apex of a putative stem loop structure, and conserved rolling-circle replication and helicase motifs within their likely Rep: all suggesting that they replicate through rolling-circle replication. The Reps and the CPs putatively encoded by these five novel viruses share low to moderate degrees of similarity (22.1 - 44.6%) with other CRESS DNA viruses.
Published: 2019
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31. Comparative morphological characteristics of three Brettanomyces bruxellensis wine strains in the presence/absence of sulfur dioxide

Author: Benoit Divol, Maret du Toit, Marlie Louw, Hervé Alexandre, Institute for Wine Biotechnology [University of Stellenbosch - Afrique du Sud], University of Stellenbosch [South Africa], Procédés Alimentaires et Microbiologiques ( PAM ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Winetech, THRIP, and National Research Foundation of South Africa
Subjects: 0301 basic medicine, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, 030106 microbiology, Food spoilage, Brettanomyces, Brettanomyces bruxellensis, Wine, Saccharomyces cerevisiae, Microbiology, Cell membrane, 03 medical and health sciences, chemistry.chemical_compound, Microscopy, Electron, Transmission, medicine, Fluorescence microscope, Sulfur Dioxide, Presence absence, Sulfur dioxide, Dekkera, biology, General Medicine, biology.organism_classification, Yeast, medicine.anatomical_structure, Microscopy, Fluorescence, chemistry, Biochemistry, Food Microbiology, Microscopy, Electron, Scanning, Food Science
Abstract: International audience; The red wine spoilage yeast Brettanomyces bruxellensis has been the subject of numerous investigations. Some of these studies focused on spoilage mechanisms, sulfur dioxide tolerance and nutrient requirements. Pseudomycelium formation, although a striking feature of this species, has however been poorly investigated. Furthermore, literature regarding the induction mechanism of pseudomycelium formation in this yeast is limited and lacks clarity, as results published are contradictory. This study elucidates this phenomenon among strains from geographically different areas. Potential environmental cues were investigated, to attain a better understanding of this mechanism and its role as a survival strategy. SO2 was previously reported to induce this morphological change however results obtained in this study did not support this. Nevertheless, the results obtained using scanning and transmission electron microscopy illustrate, for the first time in this yeast, deformity to the cell membrane and alterations to the fibrillar layers in SO2 treated cells. In addition, the SO2 exposed cultures displayed cell size variations, with cells displaying a decrease in length as well as delayed growth, with a prolonged lag phase. Fluorescence microscopy demonstrated a decrease in metabolic activity and the appearance of inclusion body-like structures in the cells following exposure to SO2.
Published: 2016
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32. The Westward Journey of Alfalfa Leaf Curl Virus

Author: Davoodi, Zohreh, Bejerman, Nicolás, Richet, Cecile, Filloux, Denis, Kumari, Safaa G., Chatzivassiliou, Elisavet K., Galzi, Serge, Julian, Charlotte, Samarfard, Samira, Trucco, Veronica, Giolitti, Fabian, Fiallo-Olive, Elvira, Navas-Castillo, Jesús, Asaad, Nader, Moukahel, Abdul Rahman, Hijazi, Jomana, Mghandef, Samia, Heydarnejad, Jahangir, Massumi, Hossein, Varsani, Arvind, Dietzgen, Ralf G., Harkins, Gordon W., Martin, Darren P., Roumagnac, Philippe, Agropolis Fondation, National Research Foundation (South Africa), University of Queensland, Iranian National Science Foundation, Ministerio de Economía y Competitividad (España), European Commission, Instituto Nacional de Tecnología Agropecuaria (Argentina), Queensland Government, Shahid Bahonar University of Kerman, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), International Center for Agricultural Research in the Dry Areas (ICARDA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Agricultural University of Athens, Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), GCSAR, Partenaires INRAE, International Center for Agricultural Research in the Dry Areas, CGIAR, The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University [Tempe] (ASU), Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, University of the Western Cape, Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, Agropolis Fondation (E-Space flagship program) : 1504-004, National Research Foundation of South Africa, Queensland Department of Agriculture and Fisheries, University of Queensland through the Queensland Alliance for Agriculture and Food Innovation, AgriFutures Australia : PRJ-009751, INTA through the PNPV : 1135022, Iran National Science Foundation (INSF) : 96008997, and Ministerio de Economia, Industria y Competitividad (MINECO, Spain) - European Regional Development Fund : AGL2016-75819-C2-2-R
Subjects: geminivirus, Virologie, lcsh:QR1-502, Genome, Viral, Article, lcsh:Microbiology, F30 - Génétique et amélioration des plantes, Plant Viruses, Viral Proteins, Evolutionary history, Alfalfa leaf curl virus, alfalfa, evolutionary history, Virology, virus de la mosaïque de la luzerne, Phylogeny, H20 - Maladies des plantes, Plant Diseases, Recombination, Genetic, Geography, Alfalfa, fungi, Genetic Variation, food and beverages, Sequence Analysis, DNA, Geminiviridae, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA, Viral, Geminivirus, Medicago sativa
Abstract: Alfalfa leaf curl virus (ALCV), which causes severe disease symptoms in alfalfa (Medicago sativa L.) and is transmitted by the widespread aphid species, Aphis craccivora Koch, has been found throughout the Mediterranean basin as well as in Iran and Argentina. Here we reconstruct the evolutionary history of ALCV and attempt to determine whether the recent discovery and widespread detection of ALCV is attributable either to past diagnostic biases or to the emergence and global spread of the virus over the past few years. One hundred and twenty ALCV complete genome sequences recovered from ten countries were analyzed and four ALCV genotypes (ALCV-A, ALCV-B, ALCV-C, and ALCV-D) were clearly distinguished. We further confirm that ALCV isolates are highly recombinogenic and that recombination has been a major determinant in the origins of the various genotypes. Collectively, the sequence data support the hypothesis that, of all the analyzed locations, ALCV likely emerged and diversified in the Middle East before spreading to the western Mediterranean basin and Argentina., This study was funded by the Agropolis Fondation (E-Space flagship program) grant number 1504-004. D.P.M. has received a research grant from the National Research Foundation of South Africa. S.S. and R.G.D. were jointly supported by the Queensland Department of Agriculture and Fisheries and the University of Queensland through the Queensland Alliance for Agriculture and Food Innovation, and by AgriFutures Australia project PRJ-009751. N.B., V.T., and F.G. were partially supported by INTA through the PNPV 1135022 project. J.H. was supported by the Iran National Science Foundation (INSF) under grant number 96008997. J.N.C. and E.F.O. were supported by Grant AGL2016-75819-C2-2-R from the Ministerio de Economía, Industria y Competitividad (MINECO, Spain) co-financed by the European Regional Development Fund.
Published: 2018
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33. New phylogenetic insights toward developing a natural generic classification of African angraecoid orchids (Vandeae, Orchidaceae)

Author: Olivier J. Hardy, Molly B. Edwards, Eberhard Fischer, Vladimir Ječmenica, Barbara S. Carlsward, Porter P. Lowry, Benny Bytebier, Vincent Droissart, Simon Verlynde, Gregory M. Plunkett, Laura N. Azandi, Murielle Simo-Droissart, Tariq Stévart, Florent Martos, Tania D'haijère, Bonaventure Sonké, João N.M. Farminhão, Claire Micheneau, University of Yaoundé [Cameroun], New York Botanical Garden (NYBG), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), New York Botanical Garden, Université Libre de Bruxelles [Bruxelles] (ULB), Missouri Botanical Garden, Missouri Botanical Garden (USA), Laboratoire de Botanique et Ecologie, Université de Yaoundé I [Yaoundé], Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Evolution Biologique et Ecologie, Université de Bruxelles, Herbarieum et Bibliothèque de Botanique africaine, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université de Yaoundé I, Université libre de Bruxelles (ULB), U.S. National Science Foundation [1051547], Belgian Fund for Scientific Research (F.R.S-FNRS) [FRFC 2.4.577.10, MIS 4.519.10], American Orchid Society, National Geographic Society [C303-15], Erasmus Mundus Tropimundo MSc scholarship, FRIA-FNRS, DIVEAC, ECOFAC, Central Africa Regional Program of the Environment (CARPE), 'Sud Expert Plantes' project under the French Ministry of Foreign Affairs [375], 'Akademie der Wissenschaften und Literaur Mainz' (Germany), and National Research Foundation of South Africa
Subjects: 0106 biological sciences, 0301 basic medicine, Paraphyly, DNA, Plant, Campylocentrum, Molecular phylogeny, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Vandeae, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Polyphyly, Angraecinae, Genetics, Paleotropics, Angraecopsis, Orchidaceae, Molecular Biology, Indian Ocean, Ecology, Evolution, Behavior and Systematics, Phylogeny, biology, Bayes Theorem, Sequence Analysis, DNA, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, 030104 developmental biology, Evolutionary biology, Aerangis, Epidendroideae, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Angraecum, Angraecoid orchids
Abstract: International audience; Despite significant progress made in recent years toward developing an infrafamilial classification of Orchidaceae, our understanding of relationships among and within tribal and subtribal groups of epidendroid orchids remains incomplete. To reassess generic delimitation among one group of these epidendroids, the African angraecoids, phylogenetic relationships were inferred from DNA sequence data from three regions, ITS, matK, and the trnL-trnF intergenic spacer, obtained from a broadly representative sample of taxa. Parsimony and Bayesian analyses yielded highly resolved trees that are in clear agreement and show significant support for many key clades within subtribe Angraecinae s.l. Angraecoid orchids comprise two well-supported clades: an African/American group and an Indian Ocean group. Molecular results also support many previously proposed relationships among genera, but also reveal some unexpected relationships. The genera Aerangis, Ancistrorhynchus, Bolusiella, Campylocentrum, Cyrtorchis, Dendrophylax, Eurychone, Microcoelia, Nephrangis, Podangis and Solenangis are all shown to be monophyletic, but Angraecopsis, Diaphananthe and Margelliantha are polyphyletic. Diaphananthe forms three well-supported clades, one of which might represent a new genus, and Rhipidoglossum is paraphyletic with respect to Cribbia and Rhaesteria, and also includes taxa currently assigned to Margelliantha. Tridactyle too is paraphyletic as Eggelingia is embedded within it. The large genus Angraecum is confirmed to be polyphyletic and several groups will have to be recognized as separate genera, including sections Dolabrifolia and Hadrangis. The recently segregated genus Pectinariella (previously recognized as A. sect. Pectinaria) is polyphyletic and its Continental African species will have to be removed. Similarly, some of the species recently transferred to Angraecoides that were previously placed in Angraecum sects. Afrangraecum and Conchoglossum will have to be moved and described as a new genus.
Published: 2018
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34. Adaptive Sampling of Large Deviations

Author: Grégoire Ferré, Hugo Touchette, Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), École des Ponts ParisTech (ENPC), MATHematics for MatERIALS (MATHERIALS), École des Ponts ParisTech (ENPC)-École des Ponts ParisTech (ENPC)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), National Institute for Theoretical Physics (NITheP), Stellenbosch University, G.F. is supported by the Labex Bezout. H.T. was supported by the National Research Foundation of South Africa (Grant nos 90322 and 96199) and Stellenbosch University (Project Funding for New Appointee). This research was also supported in part by the International Centre for Theoretical Sciences (ICTS) during a visit for participating in the program \Large deviation theory in statistical physics: Recent advances and future challenges' (Code: ICTS/Prog-ldt/2017/8)., Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), and École des Ponts ParisTech (ENPC)-École des Ponts ParisTech (ENPC)
Subjects: Adaptive sampling, Statistical Mechanics (cond-mat.stat-mech), Stochastic process, Markov process, FOS: Physical sciences, Statistical and Nonlinear Physics, 01 natural sciences, 010305 fluids & plasmas, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], symbols.namesake, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], 0103 physical sciences, Trajectory, symbols, Rare events, Large deviations theory, Limit (mathematics), Statistical physics, 010306 general physics, Mathematical Physics, Importance sampling, Condensed Matter - Statistical Mechanics
Abstract: We introduce and test an algorithm that adaptively estimates large deviation functions characterizing the fluctuations of additive functionals of Markov processes in the long-time limit. These functions play an important role for predicting the probability and pathways of rare events in stochastic processes, as well as for understanding the physics of nonequilibrium systems driven in steady states by external forces and reservoirs. The algorithm uses methods from risk-sensitive and feedback control to estimate from a single trajectory a new process, called the driven process, known to be efficient for importance sampling. Its advantages compared to other simulation techniques, such as splitting or cloning, are discussed and illustrated with simple equilibrium and nonequilibrium diffusion models., v1: 20 pages, 5 figures; v2: minor typos corrected; v3 typos in Eq. (51) corrected
Published: 2018
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35. Geospatial distribution of Mycobacterium tuberculosis genotypes in Africa

Author: Xia Wang, Antoinette Niehaus, Robin M. Warren, Samantha L. Sampson, Paul D. van Helden, Marnomorney Pillay, Nicolaas C. Gey van Pittius, Nalin Rastogi, Peter R. Mason, Elizabeth M. Streicher, Webster Kasongo, David Couvin, Marcel A. Behr, Marisa Klopper, Violet N. Chihota, Sayoki Mfinanga, Gunilla Källenius, Stellenbosch University, University of the Witwatersrand [Johannesburg] (WITS), University of Cincinnati (UC), Biomedical Research and Training Institute (BRTI), Karolinska Institutet [Stockholm], National Institute for Medical Research - Muhimbili Research Centre (NIMR), University of KwaZulu-Natal (UKZN), Tropical Diseases Research Centre [Zambia] (TDRC), McGill University Health Center [Montreal] (MUHC), Unité de la Tuberculose et des Mycobactéries - WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), and VN Chihota was supported by the Wellcome Trust (Research Leave Grant 01680/Z//00/Z). EM Streicher was supported by the National Research Foundation (NRF) Research Career Advancement Award. SL Sampson is funded by the South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation of South Africa, award number UID 86539. The study was also supported by the South African Medical Research Council (SAMRC). David Couvin was awarded a Ph.D. fellowship by the European Social Funds through the Regional Council of Guadeloupe, while the work done at Institut Pasteur de la Guadeloupe was supported by a FEDER grant, financed by the European Union and Guadeloupe Region (Programme OpeÂrationnel FEDER-Guadeloupe-Conseil Régional 2014-2020, Grant number 2015-FED-192). XW participated in this project through the South African Tuberculosis Bioinformatics Initiative, funded by a Strategic Health Innovation Partnership (SHIP) grant from the South African Department of Science and Technology (DST) and South African Medical Research Council (SAMRC) to Gerhard Walzl.
Subjects: 0301 basic medicine, Databases, Factual, lcsh:Medicine, Distribution (economics), Plant Science, computer.software_genre, Infographics, Plant Roots, Geographical Locations, Mathematical and Statistical Techniques, Genotype, Cluster Analysis, Cameroon, lcsh:Science, Phylogeny, Principal Component Analysis, Multidisciplinary, Geography, Plant Anatomy, Charts, 3. Good health, Actinobacteria, Phylogeography, Biogeography, Physical Sciences, Statistics (Mathematics), Research Article, Computer and Information Sciences, Asia, Geospatial analysis, 030106 microbiology, Biology, Research and Analysis Methods, Mycobacterium tuberculosis, 03 medical and health sciences, Genetics, Humans, Tuberculosis, Statistical Methods, Demography, Evolutionary Biology, Bacteria, Population Biology, business.industry, Data Visualization, Ecology and Environmental Sciences, lcsh:R, Organisms, Biology and Life Sciences, biology.organism_classification, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Root Structure, 030104 developmental biology, Africa, People and Places, Multivariate Analysis, Earth Sciences, lcsh:Q, business, computer, Mathematics, Population Genetics
Abstract: International audience; OBJECTIVE:To investigate the distribution of Mycobacterium tuberculosis genotypes across Africa.METHODS:The SITVIT2 global repository and PUBMED were searched for spoligotype and published genotype data respectively, of M. tuberculosis from Africa. M. tuberculosis lineages in Africa were described and compared across regions and with those from 7 European and 6 South-Asian countries. Further analysis of the major lineages and sub-lineages using Principal Component analysis (PCA) and hierarchical cluster analysis were done to describe clustering by geographical regions. Evolutionary relationships were assessed using phylogenetic tree analysis.RESULTS:A total of 14727 isolates from 35 African countries were included in the analysis and of these 13607 were assigned to one of 10 major lineages, whilst 1120 were unknown. There were differences in geographical distribution of major lineages and their sub-lineages with regional clustering. Southern African countries were grouped based on high prevalence of LAM11-ZWE strains; strains which have an origin in Portugal. The grouping of North African countries was due to the high percentage of LAM9 strains, which have an origin in the Eastern Mediterranean region. East African countries were grouped based on Central Asian (CAS) and East-African Indian (EAI) strain lineage possibly reflecting historic sea trade with Asia, while West African Countries were grouped based on Cameroon lineage of unknown origin. A high percentage of the Haarlem lineage isolates were observed in the Central African Republic, Guinea, Gambia and Tunisia, however, a mixed distribution prevented close clustering.CONCLUSIONS:This study highlighted that the TB epidemic in Africa is driven by regional epidemics characterized by genetically distinct lineages of M. tuberculosis. M. tuberculosis in these regions may have been introduced from either Europe or Asia and has spread through pastoralism, mining and war. The vast array of genotypes and their associated phenotypes should be considered when designing future vaccines, diagnostics and anti-TB drugs.
Published: 2018
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36. Synthesis and opto-structural characterization of reduced graphene oxide and meso-tetrakis(4-phenylsulfonic-acid) porphyrin composites

Author: Omar Bajjou, Mimouna Baitoul, Mohammed Khenfouch, Malik Maaza, Anass Bakour, Bakang Moses Mothudi, Eric Faulques, University of South Africa (UNISA), Laboratory of Solid State Physics Fes, Maroc, Université Sidi Mohamed Ben Abdellah (USMBA), iThemba LABS, Somerset West, National Research Foundation of South Africa, Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), and Université de Nantes (UN)-Université de Nantes (UN)
Subjects: Materials science, Photoluminescence, Scanning electron microscope, Exciton, Oxide, 02 engineering and technology, 010402 general chemistry, Photochemistry, 01 natural sciences, 7. Clean energy, law.invention, chemistry.chemical_compound, symbols.namesake, law, Electrical and Electronic Engineering, Fourier transform infrared spectroscopy, ComputingMilieux_MISCELLANEOUS, Graphene, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Porphyrin, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, chemistry, symbols, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0210 nano-technology, Raman scattering
Abstract: The present paper aims to study the mixing of reduced graphene oxide (RGO) with meso-tetrakis(4-phenylsulfonic-acid)porphyrin [H4TPPS42−] via a covalent functionalization, through a facile synthesis process. The intermolecular interaction was investigated using scanning electron microscope, Raman scattering, Fourier transform infrared spectroscopy, X-ray diffraction. These techniques demonstrated a structural enhancement of the composite, a better conjugation system and the presence of component interaction at the molecular level. UV–Visible absorption, Steady state photoluminescence (PL) as well as time-resolved PL (TRPL) measurements were carried out to further elucidate the nature of electronic interaction between the components. Steady state PL quenching of the porphyrin is in favor of photoinduced electron and/or energy transfer to the RGO. The TRPL results exhibit a decrease in the exciton mean lifetime compared to that of porphyrin’s confirming the presence of significant interaction between H4TPPS42− and RGO, and corroborating the existence of new interbands leading to slower carrier recombination.
Published: 2018
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37. Sulcal pattern variation in extant human endocasts

Author: de Jager, Edwin, van Schoor, Albert, Hoffman, Jakobus, Oettlé, Anna, Fonta, C, Beaudet, Amélie, Fonta, Caroline, University of Pretoria [South Africa], Universität Bielefeld = Bielefeld University, Sefako Makgatho Health Sciences University - Université des sciences de la santé Sefako Makgatho (SMU), Centre de recherche cerveau et cognition (CERCO), Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of the Witwatersrand [Johannesburg] (WITS), National Research Foundation of South Africa (Grant Number: 112186), Centre of Excellence in Palaeosciences, Claude Leon Foundation, and French Institute of South Africa
Subjects: [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology
Abstract: de congrès publié : De Jager EJ, Van Schoor AN, Hoffman JW, Oettle AC, Fonta C, Beaudet A. 2018 Sulcal pattern variation in extant human brain endocasts. American Association for Physical Anthropologists. Austin, April 10-14. American Journal of Physical Anthropology, 165, suppl 63 (poster).
Published: 2018

38. Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhône delta region of France

Author: Serge Galzi, Denis Filloux, Simona Kraberger, Romain Gallet, Philippe Roumagnac, Arvind Varsani, Darren P. Martin, Hugo Fontes, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University [Tempe] (ASU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de recherche pour la conservation des zones humides méditerranéennes, University of Cape Town, Structural Biology Research Unit, Department of Clinical Laboratory Sciences, National Research Foundation of South Africa, and EU : PIOF-GA-2013-622571
Subjects: 0301 basic medicine, Delta, Identification, Vicia, Virologie, ADN, Genome, Nanoviruses, Vicia cracca, cow vetch, Phylogeny, Genetics, biology, General Medicine, 3. Good health, Phylogeography, ssDNA virus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Nanoviridae, France, Reassortant Viruses, DNA, Single-Stranded, Alphavirus, Genome, Viral, génomique, 03 medical and health sciences, Sequence Homology, Nucleic Acid, Virology, Alphasatellite, Plant Diseases, H20 - Maladies des plantes, Génome, Base Sequence, Nanovirus, Virus des végétaux, biology.organism_classification, Sequence identity, 030104 developmental biology, DNA, Viral
Abstract: BGPI : équipe 2 / 7; International audience; Nanoviruses are multi-component plant-infecting single-stranded DNA viruses. Using a viral metagenomics-informed approach, a new nanovirus and two associated alphasatellite molecules have been identified in an uncultivated asymptomatic Vicia cracca plant in the Rhône region of France. This novel nanovirus genome includes eight genomic components (named DNA-R, DNA-S, DNA-M, DNA-C, DNA-N, DNA-U1, DNA-U2 and DNA-U4) and, across all components, shares < 66% pairwise sequence identity with other nanovirus genomes. The two associated alphasatellites share 62% identity with each other and < 81% identity will all other nanovirus-associated alphasatellites.
Published: 2018
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39. Characterization of casein and alpha lactalbumin of African elephant (Loxodonta africana) milk

Author: Diederick Johannes Opperman, H. E. Patterton, Gary Osthoff, Hugh-Georges Patterton, Moses Madende, Patrice Martin, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State [South Africa], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of the Free State (Bloemfontein, Republic of South Africa), National Research Foundation (Pretoria, South Africa), University of the Free State [South Africa] (UFS), and European Project: 315146,EC:FP7:SME,FP7-SME-2012,SWARMONITOR(2012)
Subjects: Whey protein, animal structures, Protein Conformation, [SDV]Life Sciences [q-bio], Elephants, Molecular Sequence Data, casein, African elephant, chemistry.chemical_compound, biology.animal, Casein, alpha-lactalbumin, Genetics, Animals, Amino Acid Sequence, protein structure, Lactose, Peptide sequence, Micelles, lactalbumine alpha, Lactalbumin, chemistry.chemical_classification, milk, caséine, structure de la protéine, biology, Caseins, éléphant d'afrique, Oligosaccharide, lait, Whey Proteins, Biochemistry, chemistry, Alpha-lactalbumin, biology.protein, Female, Animal Science and Zoology, Sequence Alignment, Food Science
Abstract: The current research reports partial characterization of the caseins and alpha-lactalbumin (alpha-LA) of the African elephant with proposed unique structure-function properties. Extensive research has been carried out to understand the structure of the casein micelles. Crystallographic structure elucidation of caseins and casein micelles is not possible. Consequently, several models have been developed in an effort to describe the casein micelle, specifically of cow milk. Here we report the characterization of African elephant milk caseins. The kappa-caseins and beta-caseins were investigated, and their relative ratio was found to be approximately 1:8.5, whereas alpha-caseins were not detected. The gene sequence of beta-casein in the NCBI database was revisited, and a different sequence in the N-terminal region is proposed. Amino acid sequence alignment and hydropathy plots showed that the kappa-casein of African elephant milk is similar to that of other mammals, whereas the beta-casein is similar to the human protein, and displayed a section of unique AA composition and additional hydrophilic regions compared with bovine caseins. Elephant milk is destabilized by 62% alcohol, and it is speculated that the beta-casein characteristics may allow maintenance of the colloidal nature of the casein micelle, a role that was previously only associated with K-casein. The oligosaccharide content of milk was reported to be low in dairy animals but high in some other species such as humans and elephants. In the milk of the African elephant, lactose and oligosaccharides both occur at high levels. These levels are typically related to the content of alpha-LA in the mammary gland and thus point to a specialized carbohydrate synthesis, where the whey protein alpha-LA plays a role. We report the characterization of African elephant alpha-LA. Homology modeling of the alpha-LA showed that it is structurally similar to crystal structures of other mammalian species, which in turn may be an indication that its functional properties, such as lactose synthesis, should not be impaired.
Published: 2015
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40. aprendizaje como 'mundización': descentralizando la educación 'no egológica' de gert biesta

Author: Karin Murris and National Research Foundation of South Africa
Subjects: Philosophy, 05 social sciences, 050301 education, biesta, educación post-humana, física cuántica, feminismo, 06 humanities and the arts, 0603 philosophy, ethics and religion, educação pós-humana, física quântica, Education, 060302 philosophy, education, philosophy, posthumanism, Developmental and Educational Psychology, posthuman education, 0503 education, Humanities
Abstract: O filósofo da educação Gert Biesta apresentou uma conferência no 18th ICPIC em Madri e publicou seu artigo neste Dossier. Neste artigo, os coloco no contexto das atuais conversações transdisciplinares da academia sobre subjetividade pós-humana. Prestando a devida atenção à relação entre o si mesmo e o mundo implicada na proposta de Biesta (uma mudança do “eu” antes do mundo para o “eu” chamado para o mundo), mostro como o pós-humanismo crítico produz uma mudança ontológica mais radical (“eu” como parte do mundo), com implicações para a subjetividade assumida em filosofia para crianças (P4C), e na educação de maneira mais geral. Através da leitura feminista da teoria quântica de Karen Barad exponho a natureza política (ocidental) do “eu” como significador transcendental e através da inclusão de corpos não-humanos, a educação 'não-egológica' proposta por Biesta é descentrada. Concluo que o aprendizado não ocorre no sujeito (com o qual Biesta está também preocupado), nem entre dois ou mais sujeitos humanos e o mundo, mas que é um processo de construção de mundo material-discursivo: uma “mundização” ('worlding', Haraway, 2016). Ilustro minha proposta por uma maneira 'worlding' de trabalhar em filosofia para crianças através do exemplo do conceito de 'animal de estimação' El filósofo de la educación Gert Biesta presentó una conferencia en el 18vo IPIC en Madrid y publicó un artículo en este Dossier. En el presente artículo lo ubico en el contexto de las actuales discusiones transdisciplinarias de la academia sobre subjetividad post humana. Prestando la debida atención a la relación implícita en la propuesta de Biesta entre el sí mismo y el mundo (un cambio del “yo” antes del mundo para el “yo” llamado para el mundo), muestro como el post humanismo crítico produce un cambio ontológico más radical (“yo” como parte del mundo), con implicancias para la subjetividad asumida en filosofía para niños (PC4) y en la educación en general. A través de la lectura feminista de la teoría quántica de Karen Barad expongo la naturaleza política (occidental) del “yo” como significante trascendental y a través de la inclusión de cuerpos no humanos, la educación “no egológica” propuesta por Biesta es descentrada. Concluyo que el aprendizaje no ocurre en el sujeto (con lo cual Biesta también está preocupado) ni entre dos o más sujetos humanos y el mundo, sino que es un proceso de construcción del mundo discursivo-material: una “mundanización” (worlding, Haraway, 2016). Ilustro mi postura como una manera worlding de trabajar en filosofía con niños por medio del ejemplo del concepto de “mascota”. Philosopher of Education, Gert Biesta, presented at the 18th ICPIC conference in Madrid and published his paper in this same Special Issue. In this paper, I put these in the context of current transdisciplinary conversations in academia about posthuman subjectivity. By paying close attention to the self/world relationality implied in what Biesta proposes (a shift from ‘I’ before the world, to ‘I’ called into the world), I show how critical posthumanism produces a more radical ontological shift (‘I’ as part of the world), with implications for the subjectivity assumed in philosophy with children (P4C), and education more generally. By exposing the political (Western) nature of the ‘I’ as transcendental signifier and by including nonhuman bodies, I de-centre the ‘non-egological’ education proposed by Biesta. I conclude that learning does not take place in a subject (which Biesta is also concerned about), nor in between two or more human subjects and the world, but that it is a process of material-discursive world-making: a ‘worlding’ (Haraway, 2016). I illustrate my proposal for a worlding way of working in P4C through an example of the concept ‘pet’.
Published: 2017
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41. The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1

Author: Cornick, Jennifer E., Tastan Bishop, Özlem, Yalcin, Feyruz, Kiran, Anmol M., Kumwenda, Benjamin, Chaguza, Chrispin, Govindpershad, Shanil, Ousmane, Sani, Senghore, Madikay, du Plessis, Mignon, Pluschke, Gerd, Ebruke, Chinelo, McGee, Lesley, Sigaùque, Beutel, Collard, Jean-Marc, Bentley, Stephen D., Kadioglu, Aras, Antonio, Martin, von Gottberg, Anne, French, Neil, Klugman, Keith P., Heyderman, Robert S., Alderson, Mark, Everett, Dean B., PAGe consortium, Malawi Liverpool Wellcome Trust Clinical Research Programme (MLW), Liverpool School of Tropical Medicine (LSTM)-University of Liverpool-Wellcome Trust-University of Malawi, University of Liverpool, Rhodes University, Grahamstown, The Wellcome Trust Sanger Institute [Cambridge], National Institute for Communicable Diseases [Johannesburg] (NICD), University of the Witwatersrand [Johannesburg] (WITS), Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), Medical Research Council Unit The Gambia (MRC), University of Warwick [Coventry], Swiss Tropical and Public Health Institute [Basel], Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Centro de Investigação em Saúde de Manhiça [Maputo, Mozambique] (CISM), London School of Hygiene and Tropical Medicine (LSHTM), Emory University [Atlanta, GA], PATH [Seattle], This work supported by the Bill and Melinda Gates Foundation (Grant No. OPP1023440), Wellcome Trust (Award No. 084679/Z/08/Z), National Research Foundation of South Africa (Grant No. 93690) and the NIH Common Fund Award (H3A Bionet) (Grant No. U41HG006941)., and A full list of PAGe members can be found at http://www.pagegenomes.org/page/consortium
Subjects: Models, Molecular, Vaccination Coverage, Antigenic diversity, MESH: Geography, MESH: Vaccines, Subunit, MESH: Amino Acid Sequence, MESH: Global Health, MESH: Africa, MESH: Virulence, Global Health, Structural diversity, Pneumococcal Vaccines, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Pneumococcal Infections, Variant, MESH: Bacterial Proteins, Geography, Virulence, MESH: Asia, Research Support, Non-U.S. Gov't, MESH: Vaccination Coverage, Protein modelling, Antigenic Variation, Europe, Infectious Diseases, Streptococcus pneumoniae, Vaccines, Subunit, Molecular Medicine, MESH: Antigenic Variation, PCV, MESH: Models, Molecular, MESH: Streptococcus pneumoniae, MESH: Pneumococcal Vaccines, Asia, Antigenic profiling, Pneumococcal disease, Serogroup, Article, Pneumococcal Infections, Bacterial Proteins, Research Support, N.I.H., Extramural, Immunology and Microbiology(all), Journal Article, Humans, Multi-valent, Amino Acid Sequence, Alleles, Antigens, Bacterial, MESH: Humans, MESH: Alleles, Public Health, Environmental and Occupational Health, MESH: Serogroup, MESH: South America, South America, veterinary(all), [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Africa, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Europe, MESH: Antigens, Bacterial
Abstract: International audience; Serotype 1 is one of the most common causes of pneumococcal disease worldwide. Pneumococcal protein vaccines are currently being developed as an alternate intervention strategy to pneumococcal conjugate vaccines. Pre-requisites for an efficacious pneumococcal protein vaccine are universal presence and minimal variation of the target antigen in the pneumococcal population, and the capability to induce a robust human immune response. We used in silico analysis to assess the prevalence of seven protein vaccine candidates (CbpA, PcpA, PhtD, PspA, SP0148, SP1912, SP2108) among 445 serotype 1 pneumococci from 26 different countries, across four continents. CbpA (76%), PspA (68%), PhtD (28%), PcpA (11%) were not universally encoded in the study population, and would not provide full coverage against serotype 1. PcpA was widely present in the European (82%), but not in the African (2%) population. A multi-valent vaccine incorporating CbpA, PcpA, PhtD and PspA was predicted to provide coverage against 86% of the global population. SP0148, SP1912 and SP2108 were universally encoded and we further assessed their predicted amino acid, antigenic and structural variation. Multiple allelic variants of these proteins were identified, different allelic variants dominated in different continents; the observed variation was predicted to impact the antigenicity and structure of two SP0148 variants, one SP1912 variant and four SP2108 variants, however these variants were each only present in a small fraction of the global population (
Published: 2017
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42. A major subtropical fruit pest accumulates in crop fields and spills over to a wild host

Author: Elisa Thébault, F. J. Frank van Veen, Wiebke Lammers, Courtney Moxley, Colleen L. Seymour, Karen J. Esler, Department of Conservation Ecology and Entomology, Stellenbosch University, Kirstenbosch Research Centre, South African National Biodiversity Institute, Centre of Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), DST/NRF Centre of Excellence at the Percy FitzPatrick Institute of African Ornithology, Department of Biological Sciences, University of Cape Town, Mare Curie International Research Staff Exchange Scheme [318929], National Research Foundation of South Africa [90139], South African Department of Science and Technology [0054/2013], Institut d'écologie et des sciences de l'environnement de Paris (IEES), and Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Polyphagous pests, [SDV]Life Sciences [q-bio], Population, medicine.disease_cause, Related plant hosts, 010603 evolutionary biology, 01 natural sciences, Crop, Pest control, Infestation, medicine, Anacardiaceae, Mangifera, education, 2. Zero hunger, education.field_of_study, Ecology, biology, Agroforestry, business.industry, Vegetation, 15. Life on land, biology.organism_classification, 010602 entomology, Agronomy, Spatiotemporal variability, Animal Science and Zoology, Population reservoir, business, Agronomy and Crop Science, Sclerocarya birrea, Agroecology
Abstract: Wild plant species are often considered a source of crop pests in mixed landscapes but this view rarely considers pest spillover in the opposite direction (from crop fields to natural vegetation), or spatiotemporal variability in resources between crop and wild habitats. We investigate how infestation of mango crop ( Mangifera indica , Anacardiaceae) and a related wild host (marula, Sclerocarya birrea , Anacardiaceae) by a major subtropical fruit crop pest ( Ceratitis cosyra , Diptera: Tephritidae) varies with distance from the boundary between crop and natural vegetation. We determined how infestation of marula is associated with proximity to mango crops at field and landscape scales over two fruiting seasons on three farms in north-eastern South Africa. This is one of few studies to date to consider pest spillover from crop fields to natural vegetation and the only one performed in a biodiverse region with relatively little habitat transformation. Over three sampling periods, C. cosyra infestation of marula always decreased with distance from mango fields. At the landscape scale, marula alongside crop fields were 30 times more likely to be infested than in distant vegetation (1.3–6 km from mango), suggesting that spillover occurs from crop fields to natural vegetation. During late mango and marula fruiting, twice as many flies infested marula than mango. However, over the two months post-mango fruiting, up to 25 times more C. cosyra were trapped in mango fields than in bordering natural vegetation. Although pests spillover from crop fields into natural vegetation to use marula as an alternate host, biological control in the natural vegetation may eliminate this habitat as a pest reservoir outside the crop season. Other nearby crops may be more important than wild hosts for maintaining C. cosyra out of mango season. Landscape planning should consider proximity and arrangement of fields containing crops that host shared pests at different times of the year.
Published: 2017
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43. What crop type for atmospheric carbon sequestration : results from a global data analysis

Author: Isack Mathew, Macdex Mutema, Vincent Chaplot, Hussein Shimelis, University of KwaZulu-Natal (UKZN), School of Agricultural, Earth & Environmental Sciences, Centre for Water Resources Research (CWRR), Biogéochimie-Traceurs-Paléoclimat (BTP), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Water Research Commission of South Africa (WRC), National Research Foundation of South Africa (NRF), University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636))
Subjects: 0106 biological sciences, Inorganic carbon, Atmospheric carbon cycle, chemistry.chemical_element, Biomass, 01 natural sciences, Crop, chemistry.chemical_compound, Total inorganic carbon, Climate change, 2. Zero hunger, Ecology, World, fungi, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, Agronomy, chemistry, 13. Climate action, Carbon dioxide, Soil water, Shoot, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Animal Science and Zoology, Land rehabilitation, Agronomy and Crop Science, Carbon, 010606 plant biology & botany
Abstract: International audience; Sequestration of atmospheric carbon (C) into soils is a strategy to compensate for anthropogenic emissions of carbon dioxide. The response of SOCs to crop types is yet to be determined under different environments. The objectives of this study were to elucidate the impact of crop type on the allocation of atmospheric C to shoots and roots, and ultimately to the soils and to determine its association with soil carbon stocks. Three hundred and eighty-nine field trials were compared to determine allocation of biomass and C in plants and SOCs under fields of different crop types. Grasses had the highest plant biomass production (19.80 ± 1.16 Mg ha−1 yr−1), followed by cereals (9.44 ± 0.45 Mg ha−1 yr−1), fibre (7.90 ± 1.00 Mg ha−1 yr−1), legumes (3.29 ± 0.63 Mg ha−1 yr−1), and oil crops (3.05 ± 1.16 Mg ha−1 yr−1) showing significant differences (p < 0.05). Maize (6.3 ± 0.34 Mg C ha−1 yr−1) had the highest plant C amongst summer crops, while wheat (2.2 ± 0.35 Mg C ha−1 yr−1) had the highest plant C amongst winter crops. In all the studies, crops allocated more C to their shoots than roots yielding root C: shoot C (Rc/Sc) ratios below magnitude. The greatest C allocation to roots was in grasses (Rc/Sc = 1.19 ± 0.08), followed by cereals (0.95 ± 0.03), legumes (0.86 ± 0.04), oil crops (0.85 ± 0.08), and fibre crops (0.50 ± 0.07). There was evidence that high plant C stocks were found in crops grown under carbon rich clayey soils of tropical humid areas. Natural grasses and cereals should be promoted as they appeared to yield greater potential for atmospheric carbon sequestration in plants and soils. Overall, the study evaluated the relative potential of the main crop types to sequester atmospheric C useful in screening of crop types for carbon efficiency and for development of plant C models.
Published: 2017
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44. Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Reunion

Author: Emmanuel Fernandez, Arvind Varsani, Jack C. Comstock, Philippe Rott, Wardatou Boukari, Jane E. Polston, Philippe Roumagnac, Ricardo I. Alcalá-Briseño, Jean-Heinrich Daugrois, Simona Kraberger, Denis Filloux, Jean-Michel Lett, Darren P. Martin, Rott, Philippe C., IFAS, Everglades Research & Education Center, University of Florida [Gainesville] (UF), IFAS, Plant pathology Department, The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University [Tempe] (ASU), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Sugarcane Field Station, USDA-ARS : Agricultural Research Service, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, Observatory, University of Cape Town, Structural Biology Research Unit, Department of Clinical Laboratory Sciences, Florida Sugar Cane League : 00107475, F000057, USDA National Institute of Food and Agriculture : Hatch/Rott FLA-BGL-005404, Region Reunion, European Union (FEDER) : 1.03, National Research Foundation of South Africa, EU grant FP7-PEOPLE-IOF : PIOF-GA-2013-622571, University of Florida [Gainesville], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Germplasm, Identification, Virologie, Sequence Homology, Saccharum officinarum, sugarcane, Cluster Analysis, Cloning, Molecular, Guadeloupe, pathologie végétale, Phylogeny, Phylogenetic tree, biology, Microbiology and Parasitology, Microbiologie et Parasitologie, Saccharum, Infectious Diseases, Geminiviridae, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Florida, virologie végétale, Saccharum spp, Sugarcane striate virus, génomique, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Mastrevirus, Phylogenetics, Virology, Botany, lcsh:RC109-216, Virus classification, H20 - Maladies des plantes, Génome, Whole Genome Sequencing, Host (biology), Research, pays tropical, Sequence Analysis, DNA, Virus des végétaux, Taxonomie, biology.organism_classification, mastrevirus, 030104 developmental biology, DNA, Viral, Sugarcane, Reunion, canne à sucre
Abstract: Background In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion. Conclusions As these virus isolates share
Published: 2017
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45. Genome sequences of a capulavirus infecting Plantago lanceolata in the Aland archipelago of Finland

Author: Hanna Susi, Mikko J. Frilander, Pauline Bernardo, Denis Filloux, Anna-Liisa Laine, Philippe Roumagnac, Kata Farkas, Darren P. Martin, Arvind Varsani, Simona Kraberger, Metapopulation Research Centre [Helsinki] (MRC), University of Helsinki, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury [Christchurch], Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA), Institute of Biotechnology, Albanova University Center-Royal Institute of Technology [Stockholm] (KTH ), Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Structural Biology Research Unit, Department of Clinical Laboratory Sciences, The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University [Tempe] (ASU), INRA, Departement Santedes Plantes et Environnement : AAP SPE 2015, National Research Foundation of South Africa, EU grant : PIOF-GA-2013-622571, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), University of Canterbury, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, Viral metagenomics, Séquence nucléotidique, viruses, Genomics, plantago lanceolata, Genome, Virus, 03 medical and health sciences, finlande, Virology, Botany, Plantago, pathologie végétale, Finland, Géminivirus, Plant Diseases, H20 - Maladies des plantes, Genomic organization, geography, Génome, geography.geographical_feature_category, biology, Virus des végétaux, Taxonomie, General Medicine, biology.organism_classification, Geminiviridae, 030104 developmental biology, Metagenomics, maladie virale, Archipelago, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Espèce nouvelle, virologie végétale, protection des cultures, séquence de gènes
Abstract: The discovery and full-genome sequences of two isolates of a fourth capulavirus species are reported. The viruses were discovered during a viral metagenomics survey of uncultivated Plantago lanceolata plants in the Åland archipelago of south western Finland. The newly discovered viruses apparently produce no symptoms in P. lanceolata. They have a genome organization that is very similar to that of the three known capulavirus species and additionally share between 62.9 and 67.1% genome-wide sequence identity with the isolates of these species. It is therefore proposed that these viruses be assigned to a new capulavirus species named “Plantago lanceolata latent virus”.
Published: 2017
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46. Photoluminescence and dynamics of excitation relaxation in graphene oxide-porphyrin nanorods composite

Author: Mohammed Khenfouch, Jany Wéry, Malik Maaza, Mimouna Baitoul, Laboratory of Solid State Physics Fes, Maroc, Université Sidi Mohamed Ben Abdellah (USMBA), iThemba LABS, Somerset West, National Research Foundation of South Africa, UNESCO-UNISA, Pretoria, University of South Africa (UNISA), Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), and Université de Nantes (UN)-Université de Nantes (UN)
Subjects: Materials science, Photoluminescence, Exciton, Biophysics, Oxide, Nanotechnology, 02 engineering and technology, White photoluminescence, 010402 general chemistry, 01 natural sciences, Biochemistry, law.invention, Porphyrin, chemistry.chemical_compound, law, Absorption (electromagnetic radiation), Graphene oxide, Optical absorption, Graphene, General Chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, chemistry, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Nanorods, Nanorod, 0210 nano-technology, Luminescence
Abstract: International audience; Generally, porphyrin nanostructured materials are known by playing many roles such as photoconductors, photovoltaics and capable of light induced charging. Also their combination with acceptors like graphene, the rising two dimension material, added exciting physical and chemical properties. In this work, Morphology, optical absorption and photoluminescence properties were investigated in order to elucidate the interaction between the few layered graphene oxide (FGO) and pophyrin nanorods. Reporting on the photoluminescence (PL) of both porphyrin nanorods and FGO/porphyrin nanorods composite, synthesized via a self-assembly method, we have experimentally demonstrated the generation of a new photoluminescence band giving rise to a white light. This luminescence was studied by the analysis of its origins and dynamics which show a huge change of exciton life time found to be longer after the interaction with graphene oxide (GO) sheets. (C) 2013 Elsevier B.V. All rights reserved.
Published: 2014
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47. Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale

Author: Bernardo, Pauline, Charles-Dominique, Tristan, Barakat, Mohamed, Ortet, Philippe, Fernandez, Emmanuel, Filloux, Denis, Hartnady, Penelope, Rebelo, Tony, Cousins, Stephen, Mesléard, François, Cohez, Damien, Yavercovski, Nicole, Varsani, Arvind, Harkins, Gordon, Peterschmitt, Michel, Malmstrom, Carolyn, Martin, Darren, Roumagnac, Philippe, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Xishuangbanna Tropical Botanical Garden, Kirstenbosch Research Centre, South African National Biodiversity Institute, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de recherche de la Tour du Valat, Aix Marseille Université (AMU), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Station Biologique de la Tour du Valat, Electron Microscopy Unit, University of Cape Town, National Research Foundation of South Africa, EU grant FP7-PEOPLE-IOF : PIOF-GA-2013-622571, MSU AgBioResearch, NSF : DEB-08343140, Direction Generale de l'Armement, MEM INRA Metaprogram, Fondation pour la Recherche, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, and Arizona State University [Tempe] (ASU)
Subjects: Climate, Agriculture, Biodiversity, Plants, Plant Viruses, South Africa, [SDE]Environmental Sciences, Original Article, France, Metagenomics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, Ecosystem, H20 - Maladies des plantes
Abstract: International audience; Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km 2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.
Published: 2016
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48. Structural and photophysical studies of few layers of reduced graphene oxide functionalized with Sn(IV) tetrakis (4-pyridyl)porphyrin dichloride

Author: Omar Bajjou, Anass Bakour, Mimouna Baitoul, Mohammed Khenfouch, Malik Maaza, Eric Faulques, Laboratory of Solid State Physics Fes, Maroc, Université Sidi Mohamed Ben Abdellah (USMBA), Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), iThemba LABS, Somerset West, and National Research Foundation of South Africa
Subjects: Photoluminescence, Materials science, Scanning electron microscope, Oxide, 02 engineering and technology, 010402 general chemistry, Photochemistry, 01 natural sciences, 7. Clean energy, Photoinduced electron transfer, law.invention, chemistry.chemical_compound, law, Materials Chemistry, Thin film, ComputingMilieux_MISCELLANEOUS, Graphene, Mechanical Engineering, Metals and Alloys, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Porphyrin, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, chemistry, Mechanics of Materials, X-ray crystallography, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0210 nano-technology
Abstract: Reduced graphene oxide has attracted great interest owing to its exceptional properties, and its combination with Porphyrins has many potential applications in optoelectronics, light emitting diodes and dye-sensitized solar cells, because of the long excited-state lifetimes and delocalizable electron density on the porphyrin. Few layers of reduced graphene oxide (FRGO) were synthesized and functionalized with Sn(IV) tetrakis(4-pyridyl) porphyrin dichloride (SnTPyP 2+ ). The structural and photophysical properties of the solution-cast thin films prepared from this composite were investigated by means of Scanning electron microscopy, X-ray diffraction, Raman scattering, FT-Infrared, UV–vis absorption, steady state Photoluminescence (PL), and time resolved PL (TR-PL). The results showed strong interactions between these hybrids components and successful deposition of the porphyrin on the FRGO layers. Moreover, a steady state PL quenching of the SnTPyP 2+ -FRGO composite film indicated an important interaction suggesting a photoinduced electron transfer between SnTPyP 2+ and FRGO. The TR-PL measurements of the photogenerated charges lifetimes showed major change for the SnTPyP 2+ after its interaction with the FRGO, resulting in a decrease in the PL mean lifetime.
Published: 2016
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49. The harlequin ladybird, Harmonia axyridis: global perspectives on invasion history and ecology

Author: Alexandra Magro, Artur Gil, A.J.M. Loomans, Cang Hui, Katie M. Murray, Sandra Viglášová, Paul S. van Wielink, Axel Vandereycken, Arnaud Estoup, Susana Clusella-Trullas, Benoit Facon, Annette Herz, May-Guri Saethre, Zdenka Martinkova, Richard Comont, Isabel Borges, Dirk Maes, Sergey K. Ryndevich, Thomas Guillemaud, Helen E. Roy, António O. Soares, Marina J. Orlova-Bienkowskaja, Mary M. Gardiner, Alexander Ok Lukashuk, Tim Adriaens, William D. Hutchison, Ingrid A. Minnaar, Patrick De Clercq, John J. Sloggett, Peter M. J. Brown, Alois Honek, Marc Kenis, Audrey A. Grez, Hans Peter Ravn, Tania Zaviezo, Nick Berkvens, Wolfgang Rabitsch, Danny Haelewaters, Riaan Stals, Zihua Zhao, Ján Kulfan, John E. Losey, Peter Zach, Andy G. Howe, Eric Lombaert, I. A. Zakharov, Lori Lawson Handley, Oldrich Nedved, Robert L. Koch, Steph L. Rorke, Matthew C. Tinsley, Gabriele Rondoni, René Eschen, Naoya Osawa, Edward W. Evans, Gilles San Martin, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Anglia Ruskin University (ARU), Research Institute for Nature and Forest (INBO), Research Institute for Agricultural, Fisheries and Food (ILVO), University of the Azores, Centre for Ecology, Evolution and Environmental Changes (cE3c) / Azorean Biodiversity Group and Universidade dos Açores, Departamento de Ciências e Engenharia do Ambiente, Açores, Stellenbosch University, Centre for Invasion Biology, Department of Botany and Zoology, Bumblebee Conservation Trust, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Crop Protection, Centre for Agricultural and Biosciences International Europe - Switzerland (CABI Europe - Switzerland), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Utah State University (USU), Ohio State University [Columbus] (OSU), Ohio Agricultural Research and Development Center, Universidad de Chile = University of Chile [Santiago] (UCHILE), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Crop Res Inst, Div Crop Genet & Breeding, Prague, Czech Republic, Partenaires INRAE, Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, University of Minnesota System, Institute of Forest Ecology - SAS, University of Hull [United Kingdom], National Plant Protection Organization (NPPO), Cornell University [New York], Berezinskiy Biosphere Reserve, Belarus, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Stirling, Department of Biological and Environmental Sciences, University of Stirling, Walloon Agricultural Research Centre, Department of Botany and Zoology, Centre of Excellence for Invasion Biology, University of South Bohemia, Institute of Entomology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Kyoto University [Kyoto], Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Environment Agency Austria, Department of Agricultural, Food and Environmental Sciences, University of Perugia (DSA3), Università degli Studi di Perugia (UNIPG), The paper had its origin at a workshop on 'Drivers, impacts, mechanisms and adaptation in insect invasions' hosted by the DST-NRF Centre of Excellence for Invasion Biology in Stellenbosch, South Africa, in November 2014. Additional financial support was provided by HortGro, the National Research Foundation of South Africa, Stellenbosch University, and SubTrop. We thank all our collaborators, and particularly the volunteer community, who have contributed to research around the world on H. axyridis. The number of references included reflects the range of inspiring studies on H. axyridis from so many people-we look forward to new and continued collaborations in the future. We are grateful to the editors of this special issue for inviting this review and providing an opportunity to explore ideas through the 'Invasive Insects Workshop funding (NRF South Africa, CIB)'. We also thank the anonymous reviewers for all their useful comments and reflections. The UK Ladybird Survey and associated coauthors are supported by the Biological Records Centre (part of the Centre for Ecology & Hydrology), which receives support from both the Natural Environment Research Council and the Joint Nature Conservation Committee. The IOBC WPRS and Global Working Groups 'Benefits and Risks of Exotic Biological Control Agents' and the COST Action TD1209 'Alien Challenge' have facilitated discussions and collaborations on H. axyridis. This study was supported by the French Agropolis Fondation (Labex Agro-Montpellier, BIOFIS Project Number 1001-001) and by a grant from the ERA-Net BiodivERsA, with the national funders ANR (France), DFG (Germany) and BELSPO (Belgium), as part of the 2012-2013 BiodivERsA call for research proposals. Support has been also received from FONDECYT 1140662 (Chile). The study of M.J. Orlova-Bienkowskaja and I. A. Zakharov was supported by Russian Science Foundation, Project No. 16-16-00079. Gabriele Rondoni acknowledges financial support from Fondazione Cassa di Risparmio di Perugia. Riaan Stals acknowledges funding from the Department of Science and Technology, South Africa. The research of Peter Zach and colleagues was funded by the project VEGA 2/0035/13 and VEGA 2/0052/15. A. Honek and Z. Martinkova were supported by grants GACR 14-26561S and COST CZ LD14084. Research in Switzerland is funded by the Swiss Federal Office for the Environment. Hans Peter Ravn was supported by the Villum Foundation. Danny Haelewaters acknowledges funding from the David Rockefeller Center for Latin American Studies at Harvard University and from the Mycological Society of America., Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, Research Institute for Nature and Forest, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Julius Kühn Institute (JKI), CABI Europe Switzerland, Universität der Bundeswehr München [Neubiberg], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Grad Sch Agr, Lab Forest Ecol, Department of Biodiversity and Nature Conservation, NEMOD Biotherapeutics GmbH & Co. KG, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile (UC), RS: FSE MSP, and Maastricht Science Programme
Subjects: 0106 biological sciences, Range (biology), Ecology (disciplines), ADALIA-BIPUNCTATA, Population, Biodiversity, INTRAGUILD PREDATION, Generalist and specialist species, NATURAL ENEMIES, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, 1ST RECORD, Competitive interactions, MYZUS-PERSICAE HOMOPTERA, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Apex predator, education.field_of_study, APHIS-GLYCINES, Ecology, biology, PALLAS COLEOPTERA-COCCINELLIDAE, Biocontrol, 15. Life on land, biology.organism_classification, Harmonia axyridis, 010602 entomology, MULTICOLORED ASIAN LADYBIRD, Coccinellidae, Invasion history, Species traits, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, BEETLE COLEOPTERA, BIOLOGICAL-CONTROL, Intraguild predation
Abstract: International audience; The harlequin ladybird, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae), is native to Asia but has been intentionally introduced to many countries as a biological control agent of pest insects. In numerous countries, however, it has been introduced unintentionally. The dramatic spread of H. axyridis within many countries has been met with considerable trepidation. It is a generalist top predator, able to thrive in many habitats and across wide climatic conditions. It poses a threat to biodiversity, particularly aphidophagous insects, through competition and predation, and in many countries adverse effects have been reported on other species, particularly coccinellids. However, the patterns are not consistent around the world and seem to be affected by many factors including landscape and climate. Research on H. axyridis has provided detailed insights into invasion biology from broad patterns and processes to approaches in surveillance and monitoring. An impressive number of studies on this alien species have provided mechanistic evidence alongside models explaining large-scale patterns and processes. The involvement of citizens in monitoring this species in a number of countries around the world is inspiring and has provided data on scales that would be otherwise unachievable. Harmonia axyridis has successfully been used as a model invasive alien species and has been the inspiration for global collaborations at various scales. There is considerable scope to expand the research and associated collaborations, particularly to increase the breadth of parallel studies conducted in the native and invaded regions. Indeed a qualitative comparison of biological traits across the native and invaded range suggests that there are differences which ultimately could influence the population dynamics of this invader. Here we provide an overview of the invasion history and ecology of H. axyridis globally with consideration of future research perspectives. We reflect broadly on the contributions of such research to our understanding of invasion biology while also informing policy and people.
Published: 2016
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50. Thermally driven sign switch of static dielectric constant of VO 2 thin film

Author: J. B. Kana Kana, Guillaume Vignaud, Alain Gibaud, Malik Maaza, Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), Le Mans Université (UM), iThemba LABS, Somerset West, and National Research Foundation of South Africa
Subjects: Phase transition, Materials science, Physics::Optics, 02 engineering and technology, Dielectric, 01 natural sciences, Inorganic Chemistry, Condensed Matter::Materials Science, Vanadium dioxide, Optics, Ellipsometry, Phase (matter), 0103 physical sciences, Electrical and Electronic Engineering, Physical and Theoretical Chemistry, Thin film, 010306 general physics, Spectroscopy, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], Static dielectric constant, business.industry, Organic Chemistry, 021001 nanoscience & nanotechnology, Atomic and Molecular Physics, and Optics, Electronic, Optical and Magnetic Materials, Optoelectronics, Condensed Matter::Strongly Correlated Electrons, 0210 nano-technology, business, Sign (mathematics)
Abstract: Smart multifunctional materials exhibiting phase transition and tunable optical and/electrical properties provide a new direction towards engineering switchable devices. Specifically, the reversible, tunable and sign switch dielectric constants via external temperature stimuli observed in vanadium dioxide (VO2) make it a candidate of choice for tunable and switchable technologies devices. Here we report new aspect of the metal-insulator transition (MIT) through the sign switch of the static dielectric constant eS of pure VO2. As it is shown, the static dielectric constant showed an abrupt change from positive at T 70 °C. eS > 0 confirms the insulating phase where charges are localized while eS
Published: 2016
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