Patrick Lambert | Institut National de la Recherche Agronomique (original) (raw)
Papers by Patrick Lambert
The Plant journal : for cell and molecular biology, Jan 25, 2018
Double-flowers with supernumerary petals have been selected by humans for their attractive appear... more Double-flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants including peach, a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in 5 segregating progenies delimited Di2 to an interval spanning 150,858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic re-sequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait and showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical...
BMC genomics, Jun 6, 2017
Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the ag... more Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3-5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, s...
Theor Appl Genet, 2002
The genetic diversity of apricot ( Prunus armeniaca; 2n = 16) was studied using AFLP markers. For... more The genetic diversity of apricot ( Prunus armeniaca; 2n = 16) was studied using AFLP markers. Forty seven apricot cultivars were selected from the following geographic regions: Europe, North America, North Africa, Turkey, Iran and China. Five EcoRI- MseI AFLP primer combinations revealed 416 legible bands, of which 379 were polymorphic markers. A similarity matrix was prepared using the simple matching coefficient of similarity. A UPGMA dendrogram demonstrated a gradient of decreasing genetic diversity of varieties from the former USSR to Southern Europe. This is coherent with the historical dissemination of apricot from its center of origin in Asia. The American cultivars were intermediate demonstrating a different genetic base than the European and/or Mediterranean cultivars. Euclidean distances from the first ten Factorial Component Analysis coordinate axes were used to generate a tree using the Ward algorithm. The results of these analyses were evaluated based on the known geographic origins and agronomic characteristics of the cultivars studied. Four cultivar groups were identified: Diversification, Geographically Adaptable, Continental Europe and Mediterranean Basin. To evaluate the relationship of the common apricot with some closely related species, one or two accessions of the following related species or sub-species from within the section Armeniaca were included in the analysis: Prunus armeniaca var. ansu, Prunus mume, Prunus brigantiaca, Prunus dasycarpa, and Prunus holosericea. A Neighbour Joining dendrogram was made using the similarity matrix. The P. holosericea accession fell well within the cultivar group, thus supporting its classification as a variant of P. armeniaca. The P. armeniaca var. ansu accession was sister to the common apricot cluster with a bootstrap value of 96%. P. mume was farther removed. P. brigantiaca was the most-distant from the common apricots. P. dasycarpa was intermediate between P. brigantiaca and P. mume, in accord with its plum-apricot hybrid origin. The results have a direct application for the selection of new breeding progenitors.
Journal of experimental botany, May 1, 2016
Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and pr... more Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs co...
Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in tempe... more Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programs is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. To address this limitation, about 1,300 peach cultivars were genotyped with the 9K peach SNP chip (Verde et al. 2012) in the frame of FruitBreedomics project. This germplasm was chosen to be representative of the genetic diversity present in five germplasm collection in Europe and in China. Out of the 8144SNPs present in the chip, about 4300 were positively genotyped and used for the further analysis. The average number of hetero...
ABSTRACT Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops... more ABSTRACT Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Every year new varieties are released from breeding programmes trying to meet the requirements imposed by the market. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programmes is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. FruitBreedomics is a European project conceived with the strategic goal to improve the efficiency of fruit breeding by bridging the gap between scientific knowledge and application in breeding. In the frame of this project, and with the goal of obtaining SNP closely linked to agronomic interesting traits, the 9K peach SNP chip (Illumina Inc.) developed by the International Peach SNP Consortium (IPSC) has been used in both segregating populations and in germplasm collections. This chip, containing 8144 SNPs scattered on the 8 peach chromosomes, has been used in about 1,500 individuals belonging to seventeen Prunus crosses (12 peach x peach and 5 interspecific) and in 1,300 peach cultivars from different origins, including some of the founders of the current breeding programs.
BMC genomics, Jun 6, 2017
Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activ... more Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A tot...
Advances in Experimental Medicine and Biology
In order to study the organization of the genome of porcine epidemic diarrhoea virus (PEDV), we c... more In order to study the organization of the genome of porcine epidemic diarrhoea virus (PEDV), we constructed a cDNA library in a phage expression vector by using poly(A) RNA from PEDV-infected Vero cells. An anti-PEDV hyperimmune serum was used to probe the library. The first isolated clone mapped within the N gene and was subsequently used for rescreening the library. The selected clones allowed us to establish the sequence of the 3'-most 7.4 kb of the PEDV genome. Analysis of the cDNA sequences revealed a 3'-coterminal nested structure, which is typical of Coronaviridae and the presence of a hexameric sequence XUA(A/G)AC upstream of each coding region. The amino acid sequences deduced from four of the five ORFs identified showed the characteristic features of the structural proteins S, M, sM and N. Only one ORF located between the S and M genes was found to potentially encode a non-structural polypeptide. Our data lead us to conclude that PEDV is a member of Coronaviridae and belongs to the same genetic subset as TGEV, FIPV and HCV 229E.
Advances in Experimental Medicine and Biology
Tree Genetics & Genomes, 2011
The green peach aphid (GPA), Myzus persicae (Sulzer), is a widespread pest insect that significan... more The green peach aphid (GPA), Myzus persicae (Sulzer), is a widespread pest insect that significantly reduces yield in peach orchards [Prunus persica (L.) Batsch]. Chemical control of the GPA population in the orchards showed little efficiency because of the development of resistance to most classes of insecticides. Biological control partially gave convincing results. Breeding for resistant peach cultivars is therefore a serious option to take into account for the development of sustainable pest management. Among the few available resistance cultivars, the rootstock peach "Rubira ® " shows a strong induced antixenosis-type GPA resistance. This was demonstrated segregating as a single dominant gene. In order to investigate the genetic basis of resistance and develop molecular tools useful in breeding programs, a F 2 population derived from "Rubira ® " also segregating for leaf color was grown and scored for GPA resistance under contrasted environmental conditions. A SSR-based genetic linkage map composed of 120 SSR loci spanned over a distance of 497.8 cM was then established. The GPA resistance mapped to a single locus at the bottom end of linkage group 1. We propose to name Rm2 the dominant allele of the underlying gene. Additionally, a reciprocal translocation was identified near the Gr gene controlling leaf color. The red-leaf parent "Rubira ® " was demonstrated responsible for the translocation. This study provides the basis for future molecular analysis for the use of Rm2 in peach breeding programs against GPA in peach orchards.
Several reasons may account for the decline of American (Anguilla rostrata) and European (Anguill... more Several reasons may account for the decline of American (Anguilla rostrata) and European (Anguilla anguilla) eel populations. This study aims at developing a better understanding of eel reproductive biology, and to investigate the effects of contaminants on their reproductive capacity. Eels bioaccumulate contaminants during their long continental growth phase, then once they initiate their reproductive migration, fasting silver eels will exclusively rely on their energy stores and constituents for swimming and gonad development. Sexually maturing eels may therefore become particularly vulnerable to contaminant effects. We have undertaken artificial maturation of female downstream migrants from various locations in Quebec and France, and measured ovarian development together with neuro-endocrine parameters, body energy reserves, and contaminant levels. In this presentation, we examine and compare for both eel species the relative expression of genes encoding for cerebral releasing hormones (GnRH1, GnRH2), pituitary gonadotropins (LHβ, FSHβ), ERα estradiol receptor and hepatic vitellogenin, as measured by quantitative PCR. We will discuss the role of the brain-pituitary-gonadal-hepatic axis in eel ovarian development, as well as the possible influence of contaminants on these endpoints.
The IRIM group is a consortium of French teams working on Multimedia Indexing and Retrieval. This... more The IRIM group is a consortium of French teams working on Multimedia Indexing and Retrieval. This paper describes our participation to the TRECVID 2010 semantic indexing and instance search tasks. For the semantic indexing task, we evaluated a number of different descriptors and tried different fusion strategies, in particular hierarchical fusion. The best IRIM run has a Mean Inferred Average Precision of 0.0442, which is above the task median performance. We found that fusion of the classification scores from different classifier types improves the performance and that even with a quite low individual performance, audio descriptors can help. For the instance search task, we used only one of the example images in our queries. The rank is nearly in the middle of the list of participants. The experiment showed that HSV features outperform the concatenation of HSV and Edge histograms or the Wavelet features.
2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2011
We propose a straightforward intensity-based dissolve detection method which is able to cope with... more We propose a straightforward intensity-based dissolve detection method which is able to cope with the particular constraints of the artistic animated movie domain. It uses the hypothesis that during a dissolve, the amount of fading-out and fading-in pixels should be high. Instead of just applying a global threshold, as most of the existing approaches do, we use a twin-threshold approach coped with shape analysis of the signal. This approach allows to reduce false detections caused by steep intensity uctuations as well as to retrieve dissolves caught up in other visual effects. Experimental tests show that whether classic approaches tends to fail, the proposed method provides a good detection even for very complex content setups (e.g. global movement, temporal discontinuity).
PLOS ONE, 2015
Species can respond to climate change by tracking appropriate environmental conditions in space, ... more Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold temperatures deserved more attention in terms of modelling, but further in conservation planning as well.
The Plant journal : for cell and molecular biology, Jan 25, 2018
Double-flowers with supernumerary petals have been selected by humans for their attractive appear... more Double-flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants including peach, a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in 5 segregating progenies delimited Di2 to an interval spanning 150,858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic re-sequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait and showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical...
BMC genomics, Jun 6, 2017
Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the ag... more Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3-5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, s...
Theor Appl Genet, 2002
The genetic diversity of apricot ( Prunus armeniaca; 2n = 16) was studied using AFLP markers. For... more The genetic diversity of apricot ( Prunus armeniaca; 2n = 16) was studied using AFLP markers. Forty seven apricot cultivars were selected from the following geographic regions: Europe, North America, North Africa, Turkey, Iran and China. Five EcoRI- MseI AFLP primer combinations revealed 416 legible bands, of which 379 were polymorphic markers. A similarity matrix was prepared using the simple matching coefficient of similarity. A UPGMA dendrogram demonstrated a gradient of decreasing genetic diversity of varieties from the former USSR to Southern Europe. This is coherent with the historical dissemination of apricot from its center of origin in Asia. The American cultivars were intermediate demonstrating a different genetic base than the European and/or Mediterranean cultivars. Euclidean distances from the first ten Factorial Component Analysis coordinate axes were used to generate a tree using the Ward algorithm. The results of these analyses were evaluated based on the known geographic origins and agronomic characteristics of the cultivars studied. Four cultivar groups were identified: Diversification, Geographically Adaptable, Continental Europe and Mediterranean Basin. To evaluate the relationship of the common apricot with some closely related species, one or two accessions of the following related species or sub-species from within the section Armeniaca were included in the analysis: Prunus armeniaca var. ansu, Prunus mume, Prunus brigantiaca, Prunus dasycarpa, and Prunus holosericea. A Neighbour Joining dendrogram was made using the similarity matrix. The P. holosericea accession fell well within the cultivar group, thus supporting its classification as a variant of P. armeniaca. The P. armeniaca var. ansu accession was sister to the common apricot cluster with a bootstrap value of 96%. P. mume was farther removed. P. brigantiaca was the most-distant from the common apricots. P. dasycarpa was intermediate between P. brigantiaca and P. mume, in accord with its plum-apricot hybrid origin. The results have a direct application for the selection of new breeding progenitors.
Journal of experimental botany, May 1, 2016
Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and pr... more Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs co...
Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in tempe... more Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programs is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. To address this limitation, about 1,300 peach cultivars were genotyped with the 9K peach SNP chip (Verde et al. 2012) in the frame of FruitBreedomics project. This germplasm was chosen to be representative of the genetic diversity present in five germplasm collection in Europe and in China. Out of the 8144SNPs present in the chip, about 4300 were positively genotyped and used for the further analysis. The average number of hetero...
ABSTRACT Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops... more ABSTRACT Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Every year new varieties are released from breeding programmes trying to meet the requirements imposed by the market. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programmes is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. FruitBreedomics is a European project conceived with the strategic goal to improve the efficiency of fruit breeding by bridging the gap between scientific knowledge and application in breeding. In the frame of this project, and with the goal of obtaining SNP closely linked to agronomic interesting traits, the 9K peach SNP chip (Illumina Inc.) developed by the International Peach SNP Consortium (IPSC) has been used in both segregating populations and in germplasm collections. This chip, containing 8144 SNPs scattered on the 8 peach chromosomes, has been used in about 1,500 individuals belonging to seventeen Prunus crosses (12 peach x peach and 5 interspecific) and in 1,300 peach cultivars from different origins, including some of the founders of the current breeding programs.
BMC genomics, Jun 6, 2017
Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activ... more Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A tot...
Advances in Experimental Medicine and Biology
In order to study the organization of the genome of porcine epidemic diarrhoea virus (PEDV), we c... more In order to study the organization of the genome of porcine epidemic diarrhoea virus (PEDV), we constructed a cDNA library in a phage expression vector by using poly(A) RNA from PEDV-infected Vero cells. An anti-PEDV hyperimmune serum was used to probe the library. The first isolated clone mapped within the N gene and was subsequently used for rescreening the library. The selected clones allowed us to establish the sequence of the 3'-most 7.4 kb of the PEDV genome. Analysis of the cDNA sequences revealed a 3'-coterminal nested structure, which is typical of Coronaviridae and the presence of a hexameric sequence XUA(A/G)AC upstream of each coding region. The amino acid sequences deduced from four of the five ORFs identified showed the characteristic features of the structural proteins S, M, sM and N. Only one ORF located between the S and M genes was found to potentially encode a non-structural polypeptide. Our data lead us to conclude that PEDV is a member of Coronaviridae and belongs to the same genetic subset as TGEV, FIPV and HCV 229E.
Advances in Experimental Medicine and Biology
Tree Genetics & Genomes, 2011
The green peach aphid (GPA), Myzus persicae (Sulzer), is a widespread pest insect that significan... more The green peach aphid (GPA), Myzus persicae (Sulzer), is a widespread pest insect that significantly reduces yield in peach orchards [Prunus persica (L.) Batsch]. Chemical control of the GPA population in the orchards showed little efficiency because of the development of resistance to most classes of insecticides. Biological control partially gave convincing results. Breeding for resistant peach cultivars is therefore a serious option to take into account for the development of sustainable pest management. Among the few available resistance cultivars, the rootstock peach "Rubira ® " shows a strong induced antixenosis-type GPA resistance. This was demonstrated segregating as a single dominant gene. In order to investigate the genetic basis of resistance and develop molecular tools useful in breeding programs, a F 2 population derived from "Rubira ® " also segregating for leaf color was grown and scored for GPA resistance under contrasted environmental conditions. A SSR-based genetic linkage map composed of 120 SSR loci spanned over a distance of 497.8 cM was then established. The GPA resistance mapped to a single locus at the bottom end of linkage group 1. We propose to name Rm2 the dominant allele of the underlying gene. Additionally, a reciprocal translocation was identified near the Gr gene controlling leaf color. The red-leaf parent "Rubira ® " was demonstrated responsible for the translocation. This study provides the basis for future molecular analysis for the use of Rm2 in peach breeding programs against GPA in peach orchards.
Several reasons may account for the decline of American (Anguilla rostrata) and European (Anguill... more Several reasons may account for the decline of American (Anguilla rostrata) and European (Anguilla anguilla) eel populations. This study aims at developing a better understanding of eel reproductive biology, and to investigate the effects of contaminants on their reproductive capacity. Eels bioaccumulate contaminants during their long continental growth phase, then once they initiate their reproductive migration, fasting silver eels will exclusively rely on their energy stores and constituents for swimming and gonad development. Sexually maturing eels may therefore become particularly vulnerable to contaminant effects. We have undertaken artificial maturation of female downstream migrants from various locations in Quebec and France, and measured ovarian development together with neuro-endocrine parameters, body energy reserves, and contaminant levels. In this presentation, we examine and compare for both eel species the relative expression of genes encoding for cerebral releasing hormones (GnRH1, GnRH2), pituitary gonadotropins (LHβ, FSHβ), ERα estradiol receptor and hepatic vitellogenin, as measured by quantitative PCR. We will discuss the role of the brain-pituitary-gonadal-hepatic axis in eel ovarian development, as well as the possible influence of contaminants on these endpoints.
The IRIM group is a consortium of French teams working on Multimedia Indexing and Retrieval. This... more The IRIM group is a consortium of French teams working on Multimedia Indexing and Retrieval. This paper describes our participation to the TRECVID 2010 semantic indexing and instance search tasks. For the semantic indexing task, we evaluated a number of different descriptors and tried different fusion strategies, in particular hierarchical fusion. The best IRIM run has a Mean Inferred Average Precision of 0.0442, which is above the task median performance. We found that fusion of the classification scores from different classifier types improves the performance and that even with a quite low individual performance, audio descriptors can help. For the instance search task, we used only one of the example images in our queries. The rank is nearly in the middle of the list of participants. The experiment showed that HSV features outperform the concatenation of HSV and Edge histograms or the Wavelet features.
2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2011
We propose a straightforward intensity-based dissolve detection method which is able to cope with... more We propose a straightforward intensity-based dissolve detection method which is able to cope with the particular constraints of the artistic animated movie domain. It uses the hypothesis that during a dissolve, the amount of fading-out and fading-in pixels should be high. Instead of just applying a global threshold, as most of the existing approaches do, we use a twin-threshold approach coped with shape analysis of the signal. This approach allows to reduce false detections caused by steep intensity uctuations as well as to retrieve dissolves caught up in other visual effects. Experimental tests show that whether classic approaches tends to fail, the proposed method provides a good detection even for very complex content setups (e.g. global movement, temporal discontinuity).
PLOS ONE, 2015
Species can respond to climate change by tracking appropriate environmental conditions in space, ... more Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold temperatures deserved more attention in terms of modelling, but further in conservation planning as well.