The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium gra... more The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulin gene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type.
GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specifi... more GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mito-chondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github. com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).
Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of ... more Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of CryIVD toxin of Bacillus thuringiensis subsp. israelensis to proteins of 148 kDa in Anopheles stephensi and of 78 kDa in Tipula oleracea, both species being susceptible to CryIVD. Binding of CryIVD with BBMVs of A. stephensi resulted in a stronger signal than with BBMVs of T. oleracea. Likewise, larvae of A. stephensi are 10,000-fold more susceptible to the CryIVD toxin than are larvae of T. oleracea. Binding was also found with six proteins ranging in size from 48 to 110 kDa in BBMVs from the lepidopteran species Manduca sexta, but CryIVD was not toxic for M. sexta larvae. No binding of trypsinated CryIVD to BBMV proteins was observed. With the lepidopteran-specific toxin CryIA(b), no binding to dipteran BBMVs was found. Binding of CryIA(b) to nine different BBMV proteins ranging in size from 71 to 240 kDa was observed in M. sexta. The major binding signal was observed with a protein of 240 kDa for CryIA(b).
Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium... more Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium oxysporum f. sp. cubense -Foc) under greenhouse conditions have been reported. Here, we report a standardised rapid and reliable greenhouse bioassay for this pathosystem. This is indispensable for banana phenotyping, particularly since the occurrence of tropical race 4 (TR4), which is a significant threat for the global Cavendish-based banana export industry. Using a double-pot system, hardened 3-months-old tissue-culture plants of 'Grand Naine' (AAA, Cavendish subgroup) were individually inoculated with three TR4 isolates and one race 1 isolate with known pathogenicity on 'Silk' (AAB) bananas. All TR4 isolates caused similar symptoms and no differences regarding incubation period or severity were observed. In addition, all TR4 isolates were successfully recovered from the symptomatic rhizomes on Komada medium.
Please be patient while the object screen loads. Changez de vue : Choisir un site UCL FUNDP FUSL... more Please be patient while the object screen loads. Changez de vue : Choisir un site UCL FUNDP FUSL FUCaM. ...
Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of ... more Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of CryIVD toxin of Bacillus thuringiensis subsp. israelensis to proteins of 148 kDa in Anopheles stephensi and of 78 kDa in Tipula oleracea, both species being susceptible to CryIVD. Binding of CryIVD with BBMVs of A. stephensi resulted in a stronger signal than with BBMVs of T. oleracea. Likewise, larvae of A. stephensi are 10,000-fold more susceptible to the CryIVD toxin than are larvae of T. oleracea. Binding was also found with six proteins ranging in size from 48 to 110 kDa in BBMVs from the lepidopteran species Manduca sexta, but CryIVD was not toxic for M. sexta larvae. No binding of trypsinated CryIVD to BBMV proteins was observed. With the lepidopteran-specific toxin CryIA(b), no binding to dipteran BBMVs was found. Binding of CryIA(b) to nine different BBMV proteins ranging in size from 71 to 240 kDa was observed in M. sexta. The major binding signal was observed with a protein of 240 kDa for CryIA(b).
International Symposium on Recent Advances in Banana Crop Protection for Sustainable Production and Improved Livelihoods, 2009
Mycosphaerella leaf spots and nematodes threaten banana cultivation worldwide. The Mycosphaerella... more Mycosphaerella leaf spots and nematodes threaten banana cultivation worldwide. The Mycosphaerella disease complex involves three related ascomycetous fungi: Mycosphaerella fijiensis, M. musicola and M. eumusae. The exact distribution of these three species and their disease epidemiology remain unclear, since their symptoms and life cycles are rather similar. Diagnosing these diseases and the respective causal agents is based on the presence of host symptoms and fungal fruiting structures, but is time consuming and not conducive to preventive management. In the present study, we developed rapid and robust species-specific diagnostic tools to detect and quantify M. fijiensis, M. musicola and M. eumusae. Conventional species-specific PCR primers were developed based on the actin gene that detected as little as 100, 1 and 10 pg/µl DNA from, respectively, M. fijiensis, M. musicola and M. eumusae. Furthermore, TaqMan real-time quantitative PCR assays that were developed based on the ß-tubulin gene detected quantities as low as 1 pg/µl DNA of each species from pure cultures and 1.6 pg/µl DNA/mg of M. fijiensis from dry leaf tissue. The efficacy of the tests was validated using naturally infected banana leaves. Similar technology has been used to develop a quantitative PCR assay for the banana burrowing nematode, Radopholus similis, which is currently being validated
International ISHS-ProMusa Symposium on Global Perspectives on Asian Challenges, 2011
Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium... more Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium oxysporum f. sp. cubense -Foc) under greenhouse conditions have been reported. Here, we report a standardised rapid and reliable greenhouse bioassay for this pathosystem. This is indispensable for banana phenotyping, particularly since the occurrence of tropical race 4 (TR4), which is a significant threat for the global Cavendish-based banana export industry. Using a double-pot system, hardened 3-months-old tissue-culture plants of 'Grand Naine' (AAA, Cavendish subgroup) were individually inoculated with three TR4 isolates and one race 1 isolate with known pathogenicity on 'Silk' (AAB) bananas. All TR4 isolates caused similar symptoms and no differences regarding incubation period or severity were observed. In addition, all TR4 isolates were successfully recovered from the symptomatic rhizomes on Komada medium.
International ISHS-ProMusa Symposium on Global Perspectives on Asian Challenges, 2011
Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of Fusarium wilt, the devastating dis... more Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of Fusarium wilt, the devastating disease that ruined the ‘Gros Michel’ (AAA)-based banana production in the first half of the 20th century. The occurrence of a new variant in Southeast Asia that overcomes the resistance in Cavendish clones such as ‘Grand Naine’ (AAA) is a major concern to current banana
Background: Genome comparisons between closely related species often show non-conserved regions a... more Background: Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more entire chromosomes. The origin and biological relevance of these non-conserved regions are still largely unknown. Here we used the genome of Fusarium graminearum to elucidate the significance of non-conserved regions.
A quantitative detection tool was developed to enable the monitoring of fumonisin-producing fungi... more A quantitative detection tool was developed to enable the monitoring of fumonisin-producing fungi in food and feed commodities. To this end, a quantitative PCR (TaqMan) was developed that targets a conserved region in the polyketide synthase gene fum1, which is involved in the biosynthesis of fumonisin. Hence, this method specifically detected isolates from the fumonisin-producing species Fusarium verticillioides, F. proliferatum, F. nygamai and F. globosum whereas isolates of the fumonisin non-producing species F. equiseti, F. graminearum, F. oxysporum, F. semitectum and F. subglutinans that commonly occur on maize were not detected. Moreover, a few fumonisin non-producing F. verticillioides isolates did not generate any fluorescent signals and were therefore not detected. The correlation between quantitative PCR and mycotoxin content was determined using field samples collected at homestead farms in South Africa. Among 40 samples from the Eastern Cape collected in 2005 a good corr...
¶these authors contributed equally to this research. ★ Corresponding authors. Plant Dis. ; Publis... more ¶these authors contributed equally to this research. ★ Corresponding authors. Plant Dis. ; Published online as . Accepted for publication.
The nephropathogenic Escherichia coli strain P673 was shown to harbor two plasmids with molecular... more The nephropathogenic Escherichia coli strain P673 was shown to harbor two plasmids with molecular sizes of 70 and 41 megadaltons, respectively. The 70-megadalton plasmid, pCW1, coded for tetracycline resistance, whereas hemolysin production was coded by the 41-megadalton plasmid, pCW2. Plasmid pCW1 proved to be self-transmissible, in contrast to pCW2. Transfer of the hemolysin character was associated with the appearance of a 110-megadalton plasmid, pCW3. The incompatibility of pCW3 with both native plasmids and restriction enzyme analysis led to the conclusion that pCW3 is a cointegrate of pCW1 and pCW2, pCW2, carrying the hemolytic determinant, is involved in the nephropathogenic character of strain P673, because (i) elimination of pCW2 from P673 was associated with a loss of virulence and (ii) the nephropathogenicity of the avirulent mutant could be restored by reintroduction of pCW2 DNA as part of a cointegrate structure.
The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium gra... more The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulin gene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type.
GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specifi... more GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mito-chondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github. com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).
Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of ... more Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of CryIVD toxin of Bacillus thuringiensis subsp. israelensis to proteins of 148 kDa in Anopheles stephensi and of 78 kDa in Tipula oleracea, both species being susceptible to CryIVD. Binding of CryIVD with BBMVs of A. stephensi resulted in a stronger signal than with BBMVs of T. oleracea. Likewise, larvae of A. stephensi are 10,000-fold more susceptible to the CryIVD toxin than are larvae of T. oleracea. Binding was also found with six proteins ranging in size from 48 to 110 kDa in BBMVs from the lepidopteran species Manduca sexta, but CryIVD was not toxic for M. sexta larvae. No binding of trypsinated CryIVD to BBMV proteins was observed. With the lepidopteran-specific toxin CryIA(b), no binding to dipteran BBMVs was found. Binding of CryIA(b) to nine different BBMV proteins ranging in size from 71 to 240 kDa was observed in M. sexta. The major binding signal was observed with a protein of 240 kDa for CryIA(b).
Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium... more Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium oxysporum f. sp. cubense -Foc) under greenhouse conditions have been reported. Here, we report a standardised rapid and reliable greenhouse bioassay for this pathosystem. This is indispensable for banana phenotyping, particularly since the occurrence of tropical race 4 (TR4), which is a significant threat for the global Cavendish-based banana export industry. Using a double-pot system, hardened 3-months-old tissue-culture plants of 'Grand Naine' (AAA, Cavendish subgroup) were individually inoculated with three TR4 isolates and one race 1 isolate with known pathogenicity on 'Silk' (AAB) bananas. All TR4 isolates caused similar symptoms and no differences regarding incubation period or severity were observed. In addition, all TR4 isolates were successfully recovered from the symptomatic rhizomes on Komada medium.
Please be patient while the object screen loads. Changez de vue : Choisir un site UCL FUNDP FUSL... more Please be patient while the object screen loads. Changez de vue : Choisir un site UCL FUNDP FUSL FUCaM. ...
Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of ... more Ligand-blotting experiments on dipteran brush border membrane vesicles (BBMVs) showed binding of CryIVD toxin of Bacillus thuringiensis subsp. israelensis to proteins of 148 kDa in Anopheles stephensi and of 78 kDa in Tipula oleracea, both species being susceptible to CryIVD. Binding of CryIVD with BBMVs of A. stephensi resulted in a stronger signal than with BBMVs of T. oleracea. Likewise, larvae of A. stephensi are 10,000-fold more susceptible to the CryIVD toxin than are larvae of T. oleracea. Binding was also found with six proteins ranging in size from 48 to 110 kDa in BBMVs from the lepidopteran species Manduca sexta, but CryIVD was not toxic for M. sexta larvae. No binding of trypsinated CryIVD to BBMV proteins was observed. With the lepidopteran-specific toxin CryIA(b), no binding to dipteran BBMVs was found. Binding of CryIA(b) to nine different BBMV proteins ranging in size from 71 to 240 kDa was observed in M. sexta. The major binding signal was observed with a protein of 240 kDa for CryIA(b).
International Symposium on Recent Advances in Banana Crop Protection for Sustainable Production and Improved Livelihoods, 2009
Mycosphaerella leaf spots and nematodes threaten banana cultivation worldwide. The Mycosphaerella... more Mycosphaerella leaf spots and nematodes threaten banana cultivation worldwide. The Mycosphaerella disease complex involves three related ascomycetous fungi: Mycosphaerella fijiensis, M. musicola and M. eumusae. The exact distribution of these three species and their disease epidemiology remain unclear, since their symptoms and life cycles are rather similar. Diagnosing these diseases and the respective causal agents is based on the presence of host symptoms and fungal fruiting structures, but is time consuming and not conducive to preventive management. In the present study, we developed rapid and robust species-specific diagnostic tools to detect and quantify M. fijiensis, M. musicola and M. eumusae. Conventional species-specific PCR primers were developed based on the actin gene that detected as little as 100, 1 and 10 pg/µl DNA from, respectively, M. fijiensis, M. musicola and M. eumusae. Furthermore, TaqMan real-time quantitative PCR assays that were developed based on the ß-tubulin gene detected quantities as low as 1 pg/µl DNA of each species from pure cultures and 1.6 pg/µl DNA/mg of M. fijiensis from dry leaf tissue. The efficacy of the tests was validated using naturally infected banana leaves. Similar technology has been used to develop a quantitative PCR assay for the banana burrowing nematode, Radopholus similis, which is currently being validated
International ISHS-ProMusa Symposium on Global Perspectives on Asian Challenges, 2011
Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium... more Several disease resistance screening protocols for Fusarium wilt of banana (causal agent Fusarium oxysporum f. sp. cubense -Foc) under greenhouse conditions have been reported. Here, we report a standardised rapid and reliable greenhouse bioassay for this pathosystem. This is indispensable for banana phenotyping, particularly since the occurrence of tropical race 4 (TR4), which is a significant threat for the global Cavendish-based banana export industry. Using a double-pot system, hardened 3-months-old tissue-culture plants of 'Grand Naine' (AAA, Cavendish subgroup) were individually inoculated with three TR4 isolates and one race 1 isolate with known pathogenicity on 'Silk' (AAB) bananas. All TR4 isolates caused similar symptoms and no differences regarding incubation period or severity were observed. In addition, all TR4 isolates were successfully recovered from the symptomatic rhizomes on Komada medium.
International ISHS-ProMusa Symposium on Global Perspectives on Asian Challenges, 2011
Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of Fusarium wilt, the devastating dis... more Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of Fusarium wilt, the devastating disease that ruined the ‘Gros Michel’ (AAA)-based banana production in the first half of the 20th century. The occurrence of a new variant in Southeast Asia that overcomes the resistance in Cavendish clones such as ‘Grand Naine’ (AAA) is a major concern to current banana
Background: Genome comparisons between closely related species often show non-conserved regions a... more Background: Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more entire chromosomes. The origin and biological relevance of these non-conserved regions are still largely unknown. Here we used the genome of Fusarium graminearum to elucidate the significance of non-conserved regions.
A quantitative detection tool was developed to enable the monitoring of fumonisin-producing fungi... more A quantitative detection tool was developed to enable the monitoring of fumonisin-producing fungi in food and feed commodities. To this end, a quantitative PCR (TaqMan) was developed that targets a conserved region in the polyketide synthase gene fum1, which is involved in the biosynthesis of fumonisin. Hence, this method specifically detected isolates from the fumonisin-producing species Fusarium verticillioides, F. proliferatum, F. nygamai and F. globosum whereas isolates of the fumonisin non-producing species F. equiseti, F. graminearum, F. oxysporum, F. semitectum and F. subglutinans that commonly occur on maize were not detected. Moreover, a few fumonisin non-producing F. verticillioides isolates did not generate any fluorescent signals and were therefore not detected. The correlation between quantitative PCR and mycotoxin content was determined using field samples collected at homestead farms in South Africa. Among 40 samples from the Eastern Cape collected in 2005 a good corr...
¶these authors contributed equally to this research. ★ Corresponding authors. Plant Dis. ; Publis... more ¶these authors contributed equally to this research. ★ Corresponding authors. Plant Dis. ; Published online as . Accepted for publication.
The nephropathogenic Escherichia coli strain P673 was shown to harbor two plasmids with molecular... more The nephropathogenic Escherichia coli strain P673 was shown to harbor two plasmids with molecular sizes of 70 and 41 megadaltons, respectively. The 70-megadalton plasmid, pCW1, coded for tetracycline resistance, whereas hemolysin production was coded by the 41-megadalton plasmid, pCW2. Plasmid pCW1 proved to be self-transmissible, in contrast to pCW2. Transfer of the hemolysin character was associated with the appearance of a 110-megadalton plasmid, pCW3. The incompatibility of pCW3 with both native plasmids and restriction enzyme analysis led to the conclusion that pCW3 is a cointegrate of pCW1 and pCW2, pCW2, carrying the hemolytic determinant, is involved in the nephropathogenic character of strain P673, because (i) elimination of pCW2 from P673 was associated with a loss of virulence and (ii) the nephropathogenicity of the avirulent mutant could be restored by reintroduction of pCW2 DNA as part of a cointegrate structure.
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