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Author Sebbenn, A.M.; Blanc-Jolivet, C.; Mader, M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Honorio Coronado, E.N.; García-Dávila, C.; Tysklind, N.; Troispoux, V.; Delcamp, A.; Degen, B.
Title Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia Type Journal Article
Year 2019 Publication Conservation Genetics Resources Abbreviated Journal Conserv. Gen. Res.
Volume 11 Issue 3 Pages 341-343
Keywords DNA fingerprints; Geographical origin; Jacaranda copaia; MassARRAY; MiSeq; RADSeq; Tropical timber
Abstract Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin.
Address BIOGECO, INRA, Univ. Bordeaux, Cestas, 33610, France
Corporate Author Thesis
Publisher Springer Netherlands Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 18777252 (Issn) ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number EcoFoG @ webmaster @ Serial 907
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Author Chaves, C.L.; Blanc-Jolivet, C.; Sebbenn, A.M.; Mader, M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Honorio Coronado, E.N.; Garcia-Davila, C.; Tysklind, N.; Troispoux, V.; Massot, M.; Degen, B.
Title Nuclear and chloroplastic SNP markers for genetic studies of timber origin for Hymenaea trees Type Journal Article
Year 2019 Publication Conservation Genetics Resources Abbreviated Journal Conserv. Gen. Res.
Volume 11 Issue 3 Pages 329-331
Keywords DNA fingerprints; Geographical origin; MiSeq; RADSeq
Abstract We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed. © 2018, Springer Nature B.V.
Address Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brazil
Corporate Author Thesis
Publisher Springer Netherlands Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 18777252 (Issn) ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number EcoFoG @ webmaster @ Serial 908
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Author Tysklind, N.; Blanc-Jolivet, C.; Mader, M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Honorio Coronado, E.N.; García-Dávila, C.R.; Sebbenn, A.M.; Caron, H.; Troispoux, V.; Guichoux, E.; Degen, B.
Title Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species Type Journal Article
Year 2019 Publication Conservation Genetics Resources Abbreviated Journal Conserv. Gen. Res.
Volume 11 Issue 3 Pages 337-339
Keywords Carapa guianensis; Carapa surinamensis; DNA-fingerprints; Geographical origin; MassARRAY; MiSeq; RADSeq; Tropical timber
Abstract Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping.
Address BIOGECO, INRA, University Bordeaux, Cestas, 33610, France
Corporate Author Thesis
Publisher Springer Netherlands Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 18777252 (Issn) ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number EcoFoG @ webmaster @ Serial 909
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Author Honorio Coronado, E.N.; Blanc-Jolivet, C.; Mader, M.; García-Dávila, C.R.; Sebbenn, A.M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Tysklind, N.; Troispoux, V.; Massot, M.; Degen, B.
Title Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia Type Journal Article
Year 2019 Publication Conservation Genetics Resources Abbreviated Journal Conserv. Genet. Res.
Volume 11 Issue 3 Pages 333-336
Keywords
Abstract We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1877-7260 ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number EcoFoG @ webmaster @ Honorio Coronado2019 Serial 906
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Author Fouquet, A.; Dubut, V.; Hataway, R.; Scotti-Saintagne, C.; Scotti, I.; Noonan, B.
Title Isolation and characterisation of 19 microsatellite loci from the Amazonian frog Adenomera andreae (Amphibia: Anura: Leptodactylidae) Type Journal Article
Year 2009 Publication Conservation Genetics Resources Abbreviated Journal Conserv. Genet. Res.
Volume 1 Issue 1 Pages 217-220
Keywords Biomedicine
Abstract Nineteen novel microsatellite loci were isolated from Adenomera andreae, a widespread Amazonian frog considered to be a species complex. Three multiplex kits were optimized. Genetic diversity was assessed in 66 individuals sampled in three populations along the West of the Approuague River catchment (French Guiana). We also tested the multiplex kits in four other Adenomera and nine Leptodactylus species with 43.4 and 17.5% success respectively.
Address
Corporate Author Thesis
Publisher Springer Netherlands Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1877-7252 ISBN Medium
Area Expedition Conference
Notes Approved no
Call Number EcoFoG @ eric.marcon @ Serial 185
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Author Touchard, A.; Dauvois, M.; Arguel, M.-J.; Petitclerc, F.; Leblanc, M.; Dejean, A.; Orivel, J.; Nicholson, G.M.; Escoubas, P.
Title Elucidation of the unexplored biodiversity of ant venom peptidomes via MALDI-TOF mass spectrometry and its application for chemotaxonomy Type Journal Article
Year 2014 Publication Journal of Proteomics Abbreviated Journal J. Proteomics
Volume 105 Issue Pages 217-231
Keywords Ant venom; Chemotaxonomy; Maldi-Tof Ms; Peptide; Peptidome; Ponerinae; ant venom; cytochrome c oxidase; ant; article; biodiversity; chemotaxonomy; correlational study; DNA sequence; French Guiana; Hymenoptera; matrix assisted laser desorption ionization time of flight mass spectrometry; mitochondrial gene; nonhuman; Odontomachus biumbonatus; Odontomachus haematodus; Odontomachus hastatus; Odontomachus mayi; Odontomachus scalptus; Pachcondyla apicalis; Pachcondyla arhuaca; Pachcondyla commutata; Pachcondyla constricta; Pachcondyla crassinola; Pachcondyla goeldii; Pachcondyla inversa; Pachcondyla marginata; Pachcondyla procidua; Pachcondyla stigma; Pachcondyla verenae; Pachcondyla villosa; peptidomics; phylogeny; priority journal; Animalia; Formicidae; Hymenoptera; Odontomachus; Pachycondyla; Pachycondyla apicalis; Pachycondyla stigma; Ponerinae
Abstract The rise of integrative taxonomy, a multi-criteria approach used in characterizing species, fosters the development of new tools facilitating species delimitation. Mass spectrometric (MS) analysis of venom peptides from venomous animals has previously been demonstrated to be a valid method for identifying species. Here we aimed to develop a rapid chemotaxonomic tool for identifying ants based on venom peptide mass fingerprinting. The study focused on the biodiversity of ponerine ants (Hymenoptera: Formicidae: Ponerinae) in French Guiana. Initial experiments optimized the use of automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to determine variations in the mass profiles of ant venoms using several MALDI matrices and additives. Data were then analyzed via a hierarchical cluster analysis to classify the venoms of 17 ant species. In addition, phylogenetic relationships were assessed and were highly correlated with methods using DNA sequencing of the mitochondrial gene cytochrome c oxidase subunit 1. By combining a molecular genetics approach with this chemotaxonomic approach, we were able to improve the accuracy of the taxonomic findings to reveal cryptic ant species within species complexes. This chemotaxonomic tool can therefore contribute to more rapid species identification and more accurate taxonomies. Biological significance: This is the first extensive study concerning the peptide analysis of the venom of both Pachycondyla and Odontomachus ants. We studied the venoms of 17 ant species from French Guiana that permitted us to fine-tune the venom analysis of ponerine ants via MALDI-TOF mass spectrometry. We explored the peptidomes of crude ant venom and demonstrated that venom peptides can be used in the identification of ant species. In addition, the application of this novel chemotaxonomic method combined with a parallel genetic approach using COI sequencing permitted us to reveal the presence of cryptic ants within both the Pachycondyla apicalis and Pachycondyla stigma species complexes. This adds a new dimension to the search for means of exploiting the enormous biodiversity of venomous ants as a source for novel therapeutic drugs or biopesticides. This article is part of a Special Issue entitled: Proteomics of non-model organisms. © 2014 Elsevier B.V.
Address Neurotoxin Research Group, School of Medical and Molecular Biosciences, University of Technology, Sydney, NSW, Australia
Corporate Author Thesis
Publisher Elsevier Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 18767737 (Issn) ISBN Medium
Area Expedition Conference
Notes Cited By (since 1996):1; Export Date: 30 July 2014; Correspondence Address: Touchard, A.; UMR-EcoFoG, Campus Agronomique, BP 316, 97379 Kourou Cedex, France; email: axel.touchard@ecofog.gf; Chemicals/CAS: cytochrome c oxidase, 72841-18-0, 9001-16-5 Approved no
Call Number EcoFoG @ webmaster @ Serial 555
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Author Cachet, N.; Ho-A-Kwie, F.; Rivaud, M.; Houel, E.; Deharo, E.; Bourdy, G.; Jullian, V.
Title Picrasin K, a new quassinoid from Quassia amara L. (Simaroubaceae) Type Journal Article
Year 2012 Publication Phytochemistry Letters Abbreviated Journal Phytochem. Lett.
Volume 5 Issue 1 Pages 162-164
Keywords Malaria; P. falciparum; Quassia amara; Quassinoids; Simaroubaceae
Abstract A new quassinoid Picrasin K 1 was isolated from a decoction made of Quassia amara leaves, traditionally used in French Guyana to treat malaria. The structure and relative stereochemistry of 1 was determined through extensive NMR analysis. Picrasin K showed a low activity against Plasmodium falciparum in vitro (IC 50 = 8 μM), and a similar low activity on human cancerous cells line (IC 50 = 7 μM on MCF-7 cells line). © 2011 Phytochemical Society of Europe. Published by Elsevier B.V. All rights reserved.
Address CNRS, UMR Ecofog, Université des Antilles et de la Guyane, Cayenne, France
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 18743900 (Issn) ISBN Medium
Area Expedition Conference
Notes Export Date: 8 March 2012; Source: Scopus; doi: 10.1016/j.phytol.2011.12.001; Language of Original Document: English; Correspondence Address: Jullian, V.; UMR-152 Pharma-Dev, IRD, Université Paul Sabatier Toulouse 3, 31062 Toulouse, France; email: jullian@cict.fr Approved no
Call Number EcoFoG @ webmaster @ Serial 382
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Author Revel, N.; Alvarez, N.; Gibernau, M.; Espíndola, A.
Title Investigating the relationship between pollination strategies and the size-advantage model in zoophilous plants using the reproductive biology of Arum cylindraceum and other European Arum species as case studies Type Journal Article
Year 2012 Publication Arthropod-Plant Interactions Abbreviated Journal Arthropod-Plant Interact.
Volume 6 Issue 1 Pages 35-44
Keywords Araceae; Flower evolution; Plant-insect interactions; Reproductive strategy; Sex allocation
Abstract The size-advantage model (SAM) explains the temporal variation of energetic investment on reproductive structures (i. e. male and female gametes and reproductive organs) in long-lived hermaphroditic plants and animals. It proposes that an increase in the resources available to an organism induces a higher relative investment on the most energetically costly sexual structures. In plants, pollination interactions are known to play an important role in the evolution of floral features. Because the SAM directly concerns flower characters, pollinators are expected to have a strong influence on the application of the model. This hypothesis, however, has never been tested. Here, we investigate whether the identity and diversity of pollinators can be used as a proxy to predict the application of the SAM in exclusive zoophilous plants. We present a new approach to unravel the dynamics of the model and test it on several widespread Arum (Araceae) species. By identifying the species composition, abundance and spatial variation of arthropods trapped in inflorescences, we show that some species (i. e. A. cylindraceum and A. italicum) display a generalist reproductive strategy, relying on the exploitation of a low number of dipterans, in contrast to the pattern seen in the specialist A. maculatum (pollinated specifically by two fly species only). Based on the model presented here, the application of the SAM is predicted for the first two and not expected in the latter species, those predictions being further confirmed by allometric measures. We here demonstrate that while an increase in the female zone occurs in larger inflorescences of generalist species, this does not happen in species demonstrating specific pollinators. This is the first time that this theory is both proposed and empirically tested in zoophilous plants. Its overall biological importance is discussed through its application in other non-Arum systems. © 2011 Springer Science+Business Media B.V.
Address CNRS-UMR 8172 Ecologie des Forêts de Guyane, BP 709, 97387 Kourou, France
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 18728855 (Issn) ISBN Medium
Area Expedition Conference
Notes Export Date: 21 March 2012; Source: Scopus; doi: 10.1007/s11829-011-9164-1; Language of Original Document: English; Correspondence Address: Espíndola, A.; Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland; email: MariaAnahi.Espindola@unil.ch Approved no
Call Number EcoFoG @ webmaster @ Serial 384
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Author Siebicke, L.; Steinfeld, G.; Foken, T.
Title CO2-gradient measurements using a parallel multi-analyzer setup Type Journal Article
Year 2011 Publication Atmospheric Measurement Techniques Abbreviated Journal Atmos. Meas. Tech.
Volume 4 Issue 3 Pages 409-423
Keywords
Abstract Accurate CO2 concentration gradient measurements are needed for the computation of advective flux terms, which are part of the full Net Ecosystem Exchange (NEE) budget equation. A typical draw back of current gradient measurement designs in advection research is the inadequate sampling of complex flow phenomena using too few observation points in space and time. To overcome this draw back, a new measurement design is presented which allows the parallel measurement of several sampling points at a high frequency. Due to the multi-analyzer nature of the design, inter-instrument bias becomes more of a concern compared to conventional setups. Therefore a statistical approach is presented which allows for accurate observations of concentration gradients, which are typically small in relation to analyzer accuracy, to be obtained. This bias correction approach applies a conditional, time dependent signal correction. The correction depends on a mixing index based on cross correlation analysis, which characterizes the degree of mixing of the atmosphere between individual sample points. The approach assumes statistical properties of probability density functions (pdf) of concentration differences between a sample point and the field average which are common to the pdf's from several sample points. The applicability of the assumptions made was tested by Large Eddy Simulation (LES) using the model PALM and could be verified for a test case of well mixed conditions. The study presents concentration time series before and after correction, measured at a 2 m height in the sub-canopy at the FLUXNET spruce forest site Waldstein-Weidenbrunnen (DE-Bay), analyzes the dependence of statistical parameters of pdf's from atmospheric parameters such as stratification, quantifies the errors and evaluates the performance of the bias correction approach. The improvements that are achieved by applying the bias correction approach are one order of magnitude larger than possible errors associated with it, which is a strong incentive to use the correction approach. In conclusion, the presented bias correction approach is well suited for – but not limited to – horizontal gradient measurements in a multi-analyzer setup, which would not have been reliable without this approach. Finally, possible future improvements of the bias correction approach are outlined and further fields of application indicated.
Address [Siebicke, L.; Foken, T.] Univ Bayreuth, Dept Micrometeorol, Bayreuth, Germany, Email: lukas.siebicke@ecofog.gf
Corporate Author Thesis
Publisher Copernicus Gesellschaft Mbh Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 1867-1381 ISBN Medium
Area Expedition Conference
Notes ISI:000288911000002 Approved no
Call Number EcoFoG @ webmaster @ Serial 303
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Author Zaremski, A.; Gastonguay, L.; Zaremski, C.; Chaffanel, F.; Le Floch, G.; Beauchene, J.
Title Capacity of tropical forest soils of french guiana and réunion for depolluting the woods impregnated with biocides Type Journal Article
Year 2013 Publication Bois et Forets des Tropiques Abbreviated Journal Bois Forets Tropiques
Volume 67 Issue 318 Pages 51-58
Keywords Bioremediation; Copper chromium arsenic(CCA) wood-destroying fungi; Depollution; Loss of mass; Pentachlorophenol(PCP); Treated timber; Tropical soil
Abstract Wood material for a long time was treated with fungicides or insecticides whose impact on the soil after leaching constitutes a real environmental problem. Nowadays, most of the studies on degradation of these toxic products was carried out with microorganisms which have been isolated in the laboratory. The present study sought to refine the knowledge vis-à-vis these microorganisms, especially wood-destroying fungi degrading pollutants in situ, from which few data are actually available. To decontaminate treated wood, the capacity of wooddestroying microorganisms from tropical forest soils of French Guiana and Reunion was evaluated to degrade toxic biocides. These are pentachlorophenol (PCP) and copper- chromium arsenic based compounds (CCA). Monitoring the degradation of samples of red pine, Pinus resinosa, shows that soils of French Guiana are more efficient than those of Reunion Island in terms of microbial activity vis-àvis these two biocides. A significant difference in loss of mass in specimens of red pine treated with CCA and PCP can range from single to double (respectively 18% and 30%). These findings confirm that CCA is less leacher and less degradable than the PCP by microorganisms in the soil. According to the scale of mass loss in laboratory tests, the wood so treated would be classified very not durable after three years of contact with soil, while the treatment is expected to be very durable.
Address Cirad Umr Ecofog, BP 701, 97387 Kourou cedex, France
Corporate Author Thesis
Publisher Lavoisier Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (down) 17775760 (Issn) ISBN Medium
Area Expedition Conference
Notes Export Date: 12 May 2014; Source: Scopus; Language of Original Document: French Approved no
Call Number EcoFoG @ webmaster @ Serial 540
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