Architecture and dynamics of the jasmonic acid gene regulatory network

Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. To advance our understanding of the architecture and dynamic regulation of the JA gene regulatory network, we performed a high-resolution RNA-seq time series of methyl JA-treated Arabidopsis thaliana at 15 time points over a 16-h period. Computational analysis showed that methyl JA (MeJA) induces a burst of transcriptional activity, generating diverse expression patterns over time that partition into distinct sectors of the JA response targeting specific biological processes. The presence of transcription factor (TF) DNA binding motifs correlated with specific TF activity during temporal MeJA-induced transcriptional reprogramming. Insight into the underlying dynamic transcriptional regulation mechanisms was captured in a chronological model of the JA gene regulatory network. Several TFs, including MYB59 and bHLH27, were uncovered as early network components with a role in pathogen and insect resistance. Analysis of subnetworks surrounding the TFs ORA47, RAP2.6L, MYB59, and ANAC055, using transcriptome profiling of overexpressors and mutants, provided insights into their regulatory role in defined modules of the JA network. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints and validates previously unknown regulators, and provides a valuable resource for functional studies on JA signaling components in plant defense and development

Gene regulatory network induced by Western flower thrips in Arabidopsis: Effect of hormone signaling, thrips development and spatial context

Herbivorous thrips are considered as one of the most economically important pests worldwide. They cause direct damage by feeding on plants of at least 60 families including many vegetable and ornamental crops, and indirect damage by transferring devastating plant viruses. Their high and parthenogenetic reproductive capacity and hidden lifestyle (pupation in the soil, thigmotactic behavior) make thrips hard to control. Current pest management control relies mainly on the use of chemical pesticides, to which thrips can develop resistance. Exploiting the natural defense mechanisms of plants against thrips can provide the opportunity towards more sustainable resistance breeding. The major aim of this PhD research was to explore the molecular mechanisms underlying natural defenses of the model plant Arabidopsis thaliana (Arabidopsis) in response to the Western flower thrips (Frankliniella occidentalis). To achieve this, several non-destructive bioassays were designed to assess thrips performance on single Arabidopsis leaves or whole plants. Using RNA-sequencing in a high-density time series, combined with bioinformatic analyses, we were able to capture the transcriptional dynamics and chronology of genes within the gene regulatory network that were induced in single Arabidopsis leaves upon thrips infestation. We confirmed that jasmonic acid (JA) is the predominant phytohormone modulating the induced defense response against thrips as (1) most up-regulated genes showed an overrepresentation of bHLH TF binding motifs which correlated with the activation of JA-associated processes, (2) JA-insensitive mutant coi1-34 and the MYC triple mutant myc2,3,4 showed significantly more feeding damage and a higher number of oviposited eggs compared to the Col-0 wild-type and (3) the novel regulators discovered in the thrips-induced gene regulatory network (GRN), although having distinct roles in the thrips-GRN, are closely connected to the JA pathway. However, depending on the thrips developmental stage, the predominant JA-induced response is modulated differently. For example, L1 larvae induced a relatively higher expression level of the ethylene (ET)-coregulated JA-inducible ERF-branch marker gene PDF1.2, which correlated with defense repression, while the older developmental larval stages activated higher levels of the abscisic acid (ABA)-coregulated JA-inducible MYC-branch marker gene VSP2, which was associated with enhanced plant resistance. Interestingly, although herbivory by L2 stage larvae of thrips mainly activated the expression of the MYC-branch marker gene VSP2 in the locally infested leaves, the ERF-branch marker gene PDF1.2 was mainly activated in the systemic, undamaged leaves of Arabidopsis, which correlated with enhanced preference of subsequently attacking thrips for the youngest systemic leaf tissue. In contrast, the tissue-chewing caterpillar Mamestra brassicae induced relatively higher levels of VSP2 in the local as well as the systemic, undamaged leaves of Arabidopsis, which was associated with enhanced deterrence of subsequently attacking thrips. Collectively, the work described in this thesis provides a better understanding of thrips-induced plant defense responses, which can facilitate the development of more sustainable thrips-resistance breeding

A Universal Framework for Claim Portability in Self-Sovereign Identity Applications

Self-sovereign identity (SSI) provides users of the internet control over their own data by letting them store it on their own device or in a decentralized way, such as on a blockchain. The Super App is an SSI application currently under development by the Delft Blockchain Lab, but it still lacks one of the core features of SSI, which is interoperability. In SSI applications, the user will be in control over their identity when an issuer attests to it. Services can request confirmation about the identity of a user through a verifiable claim, to which the user can reply with this attestation. This research first focuses on building a claim portability framework, which means these verifiable claims and attestations can be communicated between the Super App and other applications. This framework is designed using a public key infrastructure, as that is already present in the Super App. Before sending a claim or attestation, it is signed by the sender and encrypted with the public key of the intended receiver for security purposes. The Super App currently lacks infrastructure to assign issuers of attestations, so a Trusted Issuer registry will have to be stored somewhere in the network. To contest the adoption problem that currently exists in many SSI solutions, the usability has been evaluated as it plays a significant part in adoption. For this, some mock-up user interfaces were created and evaluated by users through a survey and some suggestions were made for improvements.CSE3000 Research ProjectComputer Science and Engineerin

Gene regulatory network induced by Western flower thrips in Arabidopsis: Effect of hormone signaling, thrips development and spatial context

Herbivorous thrips are considered as one of the most economically important pests worldwide. They cause direct damage by feeding on plants of at least 60 families including many vegetable and ornamental crops, and indirect damage by transferring devastating plant viruses. Their high and parthenogenetic reproductive capacity and hidden lifestyle (pupation in the soil, thigmotactic behavior) make thrips hard to control. Current pest management control relies mainly on the use of chemical pesticides, to which thrips can develop resistance. Exploiting the natural defense mechanisms of plants against thrips can provide the opportunity towards more sustainable resistance breeding. The major aim of this PhD research was to explore the molecular mechanisms underlying natural defenses of the model plant Arabidopsis thaliana (Arabidopsis) in response to the Western flower thrips (Frankliniella occidentalis). To achieve this, several non-destructive bioassays were designed to assess thrips performance on single Arabidopsis leaves or whole plants. Using RNA-sequencing in a high-density time series, combined with bioinformatic analyses, we were able to capture the transcriptional dynamics and chronology of genes within the gene regulatory network that were induced in single Arabidopsis leaves upon thrips infestation. We confirmed that jasmonic acid (JA) is the predominant phytohormone modulating the induced defense response against thrips as (1) most up-regulated genes showed an overrepresentation of bHLH TF binding motifs which correlated with the activation of JA-associated processes, (2) JA-insensitive mutant coi1-34 and the MYC triple mutant myc2,3,4 showed significantly more feeding damage and a higher number of oviposited eggs compared to the Col-0 wild-type and (3) the novel regulators discovered in the thrips-induced gene regulatory network (GRN), although having distinct roles in the thrips-GRN, are closely connected to the JA pathway. However, depending on the thrips developmental stage, the predominant JA-induced response is modulated differently. For example, L1 larvae induced a relatively higher expression level of the ethylene (ET)-coregulated JA-inducible ERF-branch marker gene PDF1.2, which correlated with defense repression, while the older developmental larval stages activated higher levels of the abscisic acid (ABA)-coregulated JA-inducible MYC-branch marker gene VSP2, which was associated with enhanced plant resistance. Interestingly, although herbivory by L2 stage larvae of thrips mainly activated the expression of the MYC-branch marker gene VSP2 in the locally infested leaves, the ERF-branch marker gene PDF1.2 was mainly activated in the systemic, undamaged leaves of Arabidopsis, which correlated with enhanced preference of subsequently attacking thrips for the youngest systemic leaf tissue. In contrast, the tissue-chewing caterpillar Mamestra brassicae induced relatively higher levels of VSP2 in the local as well as the systemic, undamaged leaves of Arabidopsis, which was associated with enhanced deterrence of subsequently attacking thrips. Collectively, the work described in this thesis provides a better understanding of thrips-induced plant defense responses, which can facilitate the development of more sustainable thrips-resistance breeding

VIH2 Regulates the Synthesis of Inositol Pyrophosphate InsP8 and Jasmonate-Dependent Defenses in Arabidopsis

Diphosphorylated inositol polyphosphates, also referred to as inositol pyrophosphates, are important signaling molecules that regulate critical cellular activities in many eukaryotic organisms, such as membrane trafficking, telomere maintenance, ribosome biogenesis, and apoptosis. In mammals and fungi, two distinct classes of inositol phosphate kinases mediate biosynthesis of inositol pyrophosphates: Kcs1/IP6K- and Vip1/PPIP5K-like proteins. Here, we report that PPIP5K homologs are widely distributed in plants and that Arabidopsis thaliana VIH1 and VIH2 are functional PPIP5K enzymes. We show a specific induction of inositol pyrophosphate InsP8 by jasmonate and demonstrate that steady state and jasmonate-induced pools of InsP8 in Arabidopsis seedlings depend on VIH2. We identify a role of VIH2 in regulating jasmonate perception and plant defenses against herbivorous insects and necrotrophic fungi. In silico docking experiments and radioligand binding-based reconstitution assays show high-affinity binding of inositol pyrophosphates to the F-box protein COI1-JAZ jasmonate coreceptor complex and suggest that coincidence detection of jasmonate and InsP8 by COI1-JAZ is a critical component in jasmonate-regulated defenses

Thrips advisor : exploiting thrips-induced defences to combat pests on crops

Plants have developed diverse defence mechanisms to ward off herbivorous pests. However, agriculture still faces estimated crop yield losses ranging from 25% to 40% annually. These losses arise not only because of direct feeding damage, but also because many pests serve as vectors of plant viruses. Herbivorous thrips (Thysanoptera) are important pests of vegetable and ornamental crops worldwide, and encompass virtually all general problems of pests: they are highly polyphagous, hard to control because of their complex lifestyle, and they are vectors of destructive viruses. Currently, control management of thrips mainly relies on the use of chemical pesticides. However, thrips rapidly develop resistance to these pesticides. With the rising demand for more sustainable, safer, and healthier food production systems, we urgently need to pinpoint the gaps in knowledge of plant defences against thrips to enable the future development of novel control methods. In this review, we summarize the current, rather scarce, knowledge of thrips-induced plant responses and the role of phytohormonal signalling and chemical defences in these responses. We describe concrete opportunities for breeding resistance against pests such as thrips as a prototype approach for next-generation resistance breeding

Thrips advisor : exploiting thrips-induced defences to combat pests on crops

Plants have developed diverse defence mechanisms to ward off herbivorous pests. However, agriculture still faces estimated crop yield losses ranging from 25% to 40% annually. These losses arise not only because of direct feeding damage, but also because many pests serve as vectors of plant viruses. Herbivorous thrips (Thysanoptera) are important pests of vegetable and ornamental crops worldwide, and encompass virtually all general problems of pests: they are highly polyphagous, hard to control because of their complex lifestyle, and they are vectors of destructive viruses. Currently, control management of thrips mainly relies on the use of chemical pesticides. However, thrips rapidly develop resistance to these pesticides. With the rising demand for more sustainable, safer, and healthier food production systems, we urgently need to pinpoint the gaps in knowledge of plant defences against thrips to enable the future development of novel control methods. In this review, we summarize the current, rather scarce, knowledge of thrips-induced plant responses and the role of phytohormonal signalling and chemical defences in these responses. We describe concrete opportunities for breeding resistance against pests such as thrips as a prototype approach for next-generation resistance breeding