Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG... more Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.
Additional file 1. Dynamic visualisation of Arabidopsis thaliana response to Pseudomonas syringae... more Additional file 1. Dynamic visualisation of Arabidopsis thaliana response to Pseudomonas syringae. AtCKN network, cluster 40, GSE56094 experimental data, Pseudomonas syringae pv. tomato DC3000 vs Mock subset. Relative expression between Pseudomonas syringae and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red-induction, blue-repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression following 0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16 and 17.5 hpi are shown.
Additional file 1. 40 putative differences between the WT DNA sequence and published RNA-seq data... more Additional file 1. 40 putative differences between the WT DNA sequence and published RNA-seq data [SRA Accession SRP014619] that were considered to be sequencing errors of the original genome sequence.
Additional file 12. Figures representing western blot analyses of constitutively over-expressed i... more Additional file 12. Figures representing western blot analyses of constitutively over-expressed ilvB1 gene and mms operon (mmsOp).
Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG... more Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.
Additional file 2. Dynamic visualisation of immune signalling network response in potato cv. Dési... more Additional file 2. Dynamic visualisation of immune signalling network response in potato cv. Désirée infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for Désirée plants.
Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Co... more Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato
Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an ... more Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an application in bioinformatics, we first define a generalized subgroup discovery problem. In this setting, a subgroup is interesting if its members are characteristic for their class, even if the classes are not identical. Then we further refine this setting for the case where subsets of objects, for example, subsets of objects that represent different time points or different phenotypes, are contrasted. We show that this allows finding subgroups of objects that could not be found with classical subgroup discovery. To find such subgroups, we propose an approach that consists of two subgroup discovery steps and an intermediate, contrast set definition step. This approach is applicable in various application areas. An example is biology, where interesting subgroups of genes are searched by using gene expression data. We address the problem of finding enriched gene sets that are specific for...
Abstract. The paper presents an approach to computational knowledge discovery through the mechani... more Abstract. The paper presents an approach to computational knowledge discovery through the mechanism of bisociation. Bisociative reasoning is at the heart of creative, accidental discovery (e.g., serendipity), and is focused on finding unexpected links by crossing contexts. Contextualization and linking between highly diverse and distributed data and knowledge sources is therefore crucial for the implementation of bisociative reasoning. In the paper we explore these ideas on the problem of analysis of microarray data. We show how enriched gene sets are found by using ontology information as background knowledge in semantic subgroup discovery. These genes are then contextualized by the computation of probabilistic links to diverse bioinformatics resources. Preliminary experiments with microarray data illustrate the approach. 1
Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an ... more Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an application in bioinformatics, we first define a generalized subgroup discovery problem. In this setting, a subgroup is interesting if its members are characteristic for their class, even if the classes are not identical. Then we further refine this setting for the case where subsets of objects, for example, subsets of objects that represent different time points or different phenotypes, are contrasted. We show that this allows finding subgroups of objects that could not be found with classical subgroup discovery. To find such subgroups, we propose an approach that consists of two subgroup discovery steps and an intermediate, contrast set definition step. This approach is applicable in various application areas. An example is biology, where interesting subgroups of genes are searched by using gene expression data. We address the problem of finding enriched gene sets that are specific for...
Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘... more Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analys...
Beatriz Romero-Rodríguez1, Marko Petek2, Maja Zagorscak2, Álvaro Piedra-Aguilera1, Ana P. Luna1, ... more Beatriz Romero-Rodríguez1, Marko Petek2, Maja Zagorscak2, Álvaro Piedra-Aguilera1, Ana P. Luna1, Kristina Gruden2, Eduardo R. Bejarano1 y Araceli G. Castillo1. 1 Área de Genética. Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-CSIC (IHSM-UMA-CSIC), Campus Teatinos, 29010 Málaga, Spain. 2 Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, 1000 Ljubljana, Slovenia.
Arthropods crop pests are responsible for 20% of global annual crop losses, a figure predicted to... more Arthropods crop pests are responsible for 20% of global annual crop losses, a figure predicted to increase in a changing climate where the ranges of numerous species are projected to expand. At the same time, many insect species are beneficial, acting as pollinators and predators of pest species. For thousands of years, humans have used increasingly sophisticated chemical formulations to control insect pests but, as the scale of agriculture expanded to meet the needs of the global population, concerns about the negative impacts of agricultural practices on biodiversity have grown. While biological solutions, such as biological control agents and pheromones, have previously had relatively minor roles in pest management, biotechnology has opened the door to numerous new approaches for controlling insect pests. In this review, we look at how advances in synthetic biology and biotechnology are providing new options for pest control. We discuss emerging technologies for engineering resistant crops and insect populations and examine advances in biomanufacturing that are enabling the production of new products for pest control.
ABSTRACTColorado potato beetle (CPB) is an agricultural pest of Solanaceous crops, notorious for ... more ABSTRACTColorado potato beetle (CPB) is an agricultural pest of Solanaceous crops, notorious for its rapid resistance development to chemical pesticides. Foliar spraying of dsRNA formulations is a promising innovative technology providing highly specific and environmentally acceptable option for CPB management.We designed dsRNA to silence CPB mesh gene (dsMESH) and performed laboratory feeding trials to assess impacts on beetle survival and development. We compared the effectiveness of in-vivo and in-vitro produced dsRNA in a series of laboratory experiments. We additionally performed a field trial in which the efficacy of dsRNA sprayed onto potato foliage was compared to a spinosad-based insecticide.We showed that dsMESH ingestion consistently and significantly impaired larval growth and decreased larval survival in laboratory feeding experiments. In-vivo produced dsRNA performed similarly as in-vitro synthesised dsRNA in laboratory settings. In the field trial, dsMESH was as effec...
Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG... more Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.
Additional file 1. Dynamic visualisation of Arabidopsis thaliana response to Pseudomonas syringae... more Additional file 1. Dynamic visualisation of Arabidopsis thaliana response to Pseudomonas syringae. AtCKN network, cluster 40, GSE56094 experimental data, Pseudomonas syringae pv. tomato DC3000 vs Mock subset. Relative expression between Pseudomonas syringae and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red-induction, blue-repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression following 0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16 and 17.5 hpi are shown.
Additional file 1. 40 putative differences between the WT DNA sequence and published RNA-seq data... more Additional file 1. 40 putative differences between the WT DNA sequence and published RNA-seq data [SRA Accession SRP014619] that were considered to be sequencing errors of the original genome sequence.
Additional file 12. Figures representing western blot analyses of constitutively over-expressed i... more Additional file 12. Figures representing western blot analyses of constitutively over-expressed ilvB1 gene and mms operon (mmsOp).
Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG... more Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.
Additional file 2. Dynamic visualisation of immune signalling network response in potato cv. Dési... more Additional file 2. Dynamic visualisation of immune signalling network response in potato cv. Désirée infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for Désirée plants.
Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Co... more Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato
Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an ... more Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an application in bioinformatics, we first define a generalized subgroup discovery problem. In this setting, a subgroup is interesting if its members are characteristic for their class, even if the classes are not identical. Then we further refine this setting for the case where subsets of objects, for example, subsets of objects that represent different time points or different phenotypes, are contrasted. We show that this allows finding subgroups of objects that could not be found with classical subgroup discovery. To find such subgroups, we propose an approach that consists of two subgroup discovery steps and an intermediate, contrast set definition step. This approach is applicable in various application areas. An example is biology, where interesting subgroups of genes are searched by using gene expression data. We address the problem of finding enriched gene sets that are specific for...
Abstract. The paper presents an approach to computational knowledge discovery through the mechani... more Abstract. The paper presents an approach to computational knowledge discovery through the mechanism of bisociation. Bisociative reasoning is at the heart of creative, accidental discovery (e.g., serendipity), and is focused on finding unexpected links by crossing contexts. Contextualization and linking between highly diverse and distributed data and knowledge sources is therefore crucial for the implementation of bisociative reasoning. In the paper we explore these ideas on the problem of analysis of microarray data. We show how enriched gene sets are found by using ontology information as background knowledge in semantic subgroup discovery. These genes are then contextualized by the computation of probabilistic links to diverse bioinformatics resources. Preliminary experiments with microarray data illustrate the approach. 1
Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an ... more Subgroup discovery methods find interesting subsets of objects of a given class. Motivated by an application in bioinformatics, we first define a generalized subgroup discovery problem. In this setting, a subgroup is interesting if its members are characteristic for their class, even if the classes are not identical. Then we further refine this setting for the case where subsets of objects, for example, subsets of objects that represent different time points or different phenotypes, are contrasted. We show that this allows finding subgroups of objects that could not be found with classical subgroup discovery. To find such subgroups, we propose an approach that consists of two subgroup discovery steps and an intermediate, contrast set definition step. This approach is applicable in various application areas. An example is biology, where interesting subgroups of genes are searched by using gene expression data. We address the problem of finding enriched gene sets that are specific for...
Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘... more Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analys...
Beatriz Romero-Rodríguez1, Marko Petek2, Maja Zagorscak2, Álvaro Piedra-Aguilera1, Ana P. Luna1, ... more Beatriz Romero-Rodríguez1, Marko Petek2, Maja Zagorscak2, Álvaro Piedra-Aguilera1, Ana P. Luna1, Kristina Gruden2, Eduardo R. Bejarano1 y Araceli G. Castillo1. 1 Área de Genética. Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-CSIC (IHSM-UMA-CSIC), Campus Teatinos, 29010 Málaga, Spain. 2 Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, 1000 Ljubljana, Slovenia.
Arthropods crop pests are responsible for 20% of global annual crop losses, a figure predicted to... more Arthropods crop pests are responsible for 20% of global annual crop losses, a figure predicted to increase in a changing climate where the ranges of numerous species are projected to expand. At the same time, many insect species are beneficial, acting as pollinators and predators of pest species. For thousands of years, humans have used increasingly sophisticated chemical formulations to control insect pests but, as the scale of agriculture expanded to meet the needs of the global population, concerns about the negative impacts of agricultural practices on biodiversity have grown. While biological solutions, such as biological control agents and pheromones, have previously had relatively minor roles in pest management, biotechnology has opened the door to numerous new approaches for controlling insect pests. In this review, we look at how advances in synthetic biology and biotechnology are providing new options for pest control. We discuss emerging technologies for engineering resistant crops and insect populations and examine advances in biomanufacturing that are enabling the production of new products for pest control.
ABSTRACTColorado potato beetle (CPB) is an agricultural pest of Solanaceous crops, notorious for ... more ABSTRACTColorado potato beetle (CPB) is an agricultural pest of Solanaceous crops, notorious for its rapid resistance development to chemical pesticides. Foliar spraying of dsRNA formulations is a promising innovative technology providing highly specific and environmentally acceptable option for CPB management.We designed dsRNA to silence CPB mesh gene (dsMESH) and performed laboratory feeding trials to assess impacts on beetle survival and development. We compared the effectiveness of in-vivo and in-vitro produced dsRNA in a series of laboratory experiments. We additionally performed a field trial in which the efficacy of dsRNA sprayed onto potato foliage was compared to a spinosad-based insecticide.We showed that dsMESH ingestion consistently and significantly impaired larval growth and decreased larval survival in laboratory feeding experiments. In-vivo produced dsRNA performed similarly as in-vitro synthesised dsRNA in laboratory settings. In the field trial, dsMESH was as effec...
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