Automatic Generation of Attacker Contracts in Solidity

Smart contracts on the Ethereum blockchain continue to suffer from well-published problems. A particular example is the well-known smart contract reentrancy vulnerability, which continues to be exploited. In this article, we present preliminary work on a method which, given a smart contract that may be vulnerable to such a reentrancy attack, proceeds to attempt to automatically derive an "attacker" contract which can be used to successfully attack the vulnerable contract. The method uses property-based testing to generate, semi-randomly, large numbers of potential attacker contracts, and then proceeds to check whether any of them is a successful attacker. The method is illustrated using a case study where an attack is derived for a vulnerable contract

Seed tolerance to deterioration in arabidopsis is affected by virus infection

[EN] Seed longevity is the period during which the plant seed is able to germinate. This property is strongly influenced by environment conditions experienced by seeds during their formation and storage. In the present study we have analyzed how the biotic stress derived from the infection of Cauliflower mosaic virus (CaMV), Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV) and Alfalfa mosaic virus (AMV) affects seed tolerance to deterioration measuring germination rates after an accelerated aging treatment. Arabidopsis wild type plants infected with AMV and CMV rendered seeds with improved tolerance to deterioration when compared to the non -inoculated plants. On the other hand, CaMV infection generated seeds more sensitive to deterioration. No seeds were obtained from TuMV infected plants. Similar pattern of viral effects was observed in the double mutant athb22 athb25, which is more sensitive to accelerated seed aging than wild type. However, we observed a significant reduction of the seed germination for CMV (65% vs 55%) and healthy (50% vs 30%) plants in these mutants. The seed quality differences were overcomed using the A. thaliana athb25-1D dominant mutant, which over accumulated gibberellic acid (GA), except for TuMV which generated some siliques with low seed tolerance to deterioration. For AMV and TuMV (in athb25-1D), the seed quality correlated with the accumulation of the messengers of the gibberellin 3-oxidase family, the mucilage of the seed and the GA1. For CMV and CaMV it was not a good correlation suggesting that other factors are affecting seed viability. (C) 2017 Elsevier Masson SAS. All rights reserved.We thank L. Corachan and I. Martinez for their excellent technical assistance. This work was supported by grant BI02014-54862-R from the Spanish Direccion General de Investigacion Cientifica y Tecnica (DGICYT) and the Prometeo Program GV2014/010 from the Generalitat Valenciana.Bueso Rodenas, E.; Serrano Salom, R.; Pallas, V.; Sanchez Navarro, JA. (2017). Seed tolerance to deterioration in arabidopsis is affected by virus infection. Plant Physiology and Biochemistry. 116:1-8. https://doi.org/10.1016/j.plaphy.2017.04.020S1811

Uncovering salt tolerance mechanisms in pepper plants: a physiological and transcriptomic approach.

[EN] Background Pepper is one of the most cultivated crops worldwide, but is sensitive to salinity. This sensitivity is dependent on varieties and our knowledge about how they can face such stress is limited, mainly according to a molecular point of view. This is the main reason why we decided to develop this transcriptomic analysis. Tolerant and sensitive accessions, respectively called A25 and A6, were grown for 14 days under control conditions and irrigated with 70 mM of NaCl. Biomass, different physiological parameters and differentially expressed genes were analysed to give response to differential salinity mechanisms between both accessions. Results The genetic changes found between the accessions under both control and stress conditions could explain the physiological behaviour in A25 by the decrease of osmotic potential that could be due mainly to an increase in potassium and proline accumulation, improved growth (e.g. expansins), more efficient starch accumulation (e.g. BAM1), ion homeostasis (e.g. CBL9, HAI3, BASS1), photosynthetic protection (e.g. FIB1A, TIL, JAR1) and antioxidant activity (e.g. PSDS3, SnRK2.10). In addition, misregulation of ABA signalling (e.g. HAB1, ERD4, HAI3) and other stress signalling genes (e.g. JAR1) would appear crucial to explain the different sensitivity to NaCl in both accessions. Conclusions After analysing the physiological behaviour and transcriptomic results, we have concluded that A25 accession utilizes different strategies to cope better salt stress, being ABA-signalling a pivotal point of regulation. However, other strategies, such as the decrease in osmotic potential to preserve water status in leaves seem to be important to explain the defence response to salinity in pepper A25 plants.This work was financed by the INIA (Spain) and the Ministerio de Ciencia, Innovacion y Universidades (RTA2017-00030-C02-00) and the European Regional Development Fund (ERDF). Lidia Lopez-Serrano is a beneficiary of a doctoral fellowship (FPI-INIA).Lopez-Serrano, L.; Calatayud, Á.; López Galarza, SV.; Serrano Salom, R.; Bueso Rodenas, E. (2021). Uncovering salt tolerance mechanisms in pepper plants: a physiological and transcriptomic approach. BMC Plant Biology. 21(1):1-17. https://doi.org/10.1186/s12870-021-02938-2S11721

Comparative analysis of wild-type accessions reveals novel determinants of Arabidopsis seed longevity

Understanding the genetic factors involved in seed longevity is of paramount importance in agricultural and ecological contexts. The polygenic nature of this trait suggests that many of them remain undiscovered. Here, we exploited the contrasting seed longevity found amongst Arabidopsis thaliana accessions to further understand this phenomenon. Concentrations of glutathione were higher in longer-lived than shorter-lived accessions, supporting that redox poise plays a prominent role in seed longevity. However, high seed permeability, normally associated with shorter longevity, is also present in long-lived accessions. Dry seed transcriptome analysis indicated that the contribution to longevity of stored messenger RNA (mRNAs) is complex, including mainly accession-specific mechanisms. The detrimental effect on longevity caused by other factors may be counterbalanced by higher levels of specific mRNAs stored in dry seeds, for instance those of heat-shock proteins. Indeed, loss-of-function mutant analysis demonstrated that heat-shock factors HSF1A and 1B contributed to longevity. Furthermore, mutants of the stress-granule zinc-finger protein TZF9 or the spliceosome subunits MOS4 or MAC3A/MAC3B, extended seed longevity, positioning RNA as a novel player in the regulation of seed viability. mRNAs of proteins with putative relevance to longevity were also abundant in shorter-lived accessions, reinforcing the idea that resistance to ageing is determined by multiple factors.Peer reviewe

Peptidyl-prolyl cis-trans isomerase ROF2 modulates intracellular pH homeostasis in Arabidopsis

[EN] Intracellular pH must be kept close to neutrality to be compatible with cellular functions, but the mechanisms of pH homeostasis and the responses to intracellular acidification are mostly unknown. In the plant Arabidopsis thaliana, we found that intracellular acid stress generated by weak organic acids at normal external pH induces expression of several chaperone genes, including ROF2, which encodes a peptidyl-prolyl cis-trans isomerase of the FK506-binding protein class. Loss of function of ROF2, and especially double mutation of ROF2 and the closely related gene ROF1, results in acid sensitivity. Over-expression of ROF2 confers tolerance to intracellular acidification by increasing proton extrusion from cells. The activation of the plasma membrane proton pump (H+-ATPase) is indirect: over-expression of ROF2 activates K+ uptake, causing depolarization of the plasma membrane, which activates the electrogenic H+ pump. The depolarization of ROF2 over-expressing plants explains their tolerance to toxic cations such as lithium, norspermidine and hygromycin B, whose uptake is driven by the membrane potential. As ROF2 induction and intracellular acidification are common consequences of many stresses, this mechanism of pH homeostasis may be of general importance for stress tolerance.This work was supported by grants BFU2008-00604 from the Ministerio de Ciencia e Innovacion (Madrid, Spain) and PROMETEO/2010/ 038 of the 'Conselleria de Educacion' (Valencia, Spain). We thank Dr Eugenio Grau (Sequencing Service, Instituto de Biologia Molecular y Celular de Plantas, Valencia, Spain) for sequencing of the various genes, and Dr Vicente Fornes (Instituto de Tecnologia Quimica, Valencia, Spain) for assistance with atomic absorption spectrophotometry. None of the authors has a conflict of interest to declare.Bissoli, G.; Niñoles Rodenes, R.; Fresquet Corrales, S.; Palombieri, S.; Bueso Ródenas, E.; Rubio, L.; Garcia-Sanchez, MJ.... (2012). Peptidyl-prolyl cis-trans isomerase ROF2 modulates intracellular pH homeostasis in Arabidopsis. Plant Journal. 70(4):704-716. https://doi.org/10.1111/j.1365-313X.2012.04921.xS70471670

PRX2 and PRX25, peroxidases regulated by COG1, are involved in seed longevity in Arabidopsis

[EN] Permeability is a crucial trait that affects seed longevity and is regulated by different polymers including proanthocyanidins, suberin, cutin and lignin located in the seed coat. By testing mutants in suberin transport and biosynthesis, we demonstrate the importance of this biopolymer to cope with seed deterioration. Transcriptomic analysis of cog1-2D, a gain-of-function mutant with increased seed longevity, revealed the upregulation of several peroxidase genes. Reverse genetics analysing seed longevity uncovered redundancy within the seed coat peroxidase gene family; however, after controlled deterioration treatment, seeds from the prx2 prx25 double and prx2 prx25 prx71 triple mutant plants presented lower germination than wild-type plants. Transmission electron microscopy analysis of the seed coat of these mutants showed a thinner palisade layer, but no changes were observed in proanthocyanidin accumulation or in the cuticle layer. Spectrophotometric quantification of acetyl bromide-soluble lignin components indicated changes in the amount of total polyphenolics derived from suberin and/or lignin in the mutant seeds. Finally, the increased seed coat permeability to tetrazolium salts observed in the prx2 prx25 and prx2 prx25 prx71 mutant lines suggested that the lower permeability of the seed coats caused by altered polyphenolics is likely to be the main reason explaining their reduced seed longevityRenard, J.; Martínez-Almonacid, I.; Sonntag, A.; Molina, I.; Moya-Cuevas, J.; Bissoli, G.; Muñoz-Bertomeu, J.... (2020). PRX2 and PRX25, peroxidases regulated by COG1, are involved in seed longevity in Arabidopsis. Plant Cell & Environment. 43(2):315-326. https://doi.org/10.1111/pce.13656S315326432Almagro, L., Gómez Ros, L. V., Belchi-Navarro, S., Bru, R., Ros Barceló, A., & Pedreño, M. A. (2008). Class III peroxidases in plant defence reactions. 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M., Menard, G., Trick, M., Dechirico, S., Corbineau, F., … Penfield, S. (2017). Awake1, an ABC-Type Transporter, Reveals an Essential Role for Suberin in the Control of Seed Dormancy. Plant Physiology, 174(1), 276-283. doi:10.1104/pp.16.01556Francoz, E., Ranocha, P., Nguyen-Kim, H., Jamet, E., Burlat, V., & Dunand, C. (2015). Roles of cell wall peroxidases in plant development. Phytochemistry, 112, 15-21. doi:10.1016/j.phytochem.2014.07.020Franke, R., Briesen, I., Wojciechowski, T., Faust, A., Yephremov, A., Nawrath, C., & Schreiber, L. (2005). Apoplastic polyesters in Arabidopsis surface tissues – A typical suberin and a particular cutin. Phytochemistry, 66(22), 2643-2658. doi:10.1016/j.phytochem.2005.09.027Franke, R., & Schreiber, L. (2007). Suberin — a biopolyester forming apoplastic plant interfaces. Current Opinion in Plant Biology, 10(3), 252-259. doi:10.1016/j.pbi.2007.04.004GoffL TrapnellC&KelleyD(2014)CummeRbund: Analysis exploration manipulation and visualization of Cufflinks high‐throughput sequencing data. R package version 2.22.0.Gou, M., Hou, G., Yang, H., Zhang, X., Cai, Y., Kai, G., & Liu, C.-J. (2016). The MYB107 Transcription Factor Positively Regulates Suberin Biosynthesis. Plant Physiology, 173(2), 1045-1058. doi:10.1104/pp.16.01614Graça, J. (2015). Suberin: the biopolyester at the frontier of plants. Frontiers in Chemistry, 3. doi:10.3389/fchem.2015.00062Haughn, G., & Chaudhury, A. (2005). Genetic analysis of seed coat development in Arabidopsis. Trends in Plant Science, 10(10), 472-477. doi:10.1016/j.tplants.2005.08.005Herrero, J., Fernández-Pérez, F., Yebra, T., Novo-Uzal, E., Pomar, F., Pedreño, M. Á., … Zapata, J. M. (2013). Bioinformatic and functional characterization of the basic peroxidase 72 from Arabidopsis thaliana involved in lignin biosynthesis. Planta, 237(6), 1599-1612. doi:10.1007/s00425-013-1865-5Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357-360. doi:10.1038/nmeth.3317Kosma, D. K., Murmu, J., Razeq, F. M., Santos, P., Bourgault, R., Molina, I., & Rowland, O. (2014). At MYB 41 activates ectopic suberin synthesis and assembly in multiple plant species and cell types. The Plant Journal, 80(2), 216-229. doi:10.1111/tpj.12624Kunieda, T., Shimada, T., Kondo, M., Nishimura, M., Nishitani, K., & Hara-Nishimura, I. (2013). Spatiotemporal Secretion of PEROXIDASE36 Is Required for Seed Coat Mucilage Extrusion in Arabidopsis  . The Plant Cell, 25(4), 1355-1367. doi:10.1105/tpc.113.110072Lee, Y., Rubio, M. C., Alassimone, J., & Geldner, N. (2013). A Mechanism for Localized Lignin Deposition in the Endodermis. Cell, 153(2), 402-412. doi:10.1016/j.cell.2013.02.045Liang, M., Davis, E., Gardner, D., Cai, X., & Wu, Y. (2006). Involvement of AtLAC15 in lignin synthesis in seeds and in root elongation of Arabidopsis. Planta, 224(5), 1185-1196. doi:10.1007/s00425-006-0300-6Li-Beisson, Y., Shorrosh, B., Beisson, F., Andersson, M. X., Arondel, V., Bates, P. D., … Ohlrogge, J. (2013). Acyl-Lipid Metabolism. The Arabidopsis Book, 11, e0161. doi:10.1199/tab.0161Mandel, T., Candela, H., Landau, U., Asis, L., Zilinger, E., Carles, C. C., & Williams, L. E. (2016). Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways. Development. doi:10.1242/dev.129973Milne, I., Stephen, G., Bayer, M., Cock, P. J. A., Pritchard, L., Cardle, L., … Marshall, D. (2012). Using Tablet for visual exploration of second-generation sequencing data. Briefings in Bioinformatics, 14(2), 193-202. doi:10.1093/bib/bbs012Molina, I., Bonaventure, G., Ohlrogge, J., & Pollard, M. (2006). The lipid polyester composition of Arabidopsis thaliana and Brassica napus seeds. Phytochemistry, 67(23), 2597-2610. doi:10.1016/j.phytochem.2006.09.011Molina, I., Ohlrogge, J. B., & Pollard, M. (2007). Deposition and localization of lipid polyester in developing seeds of Brassica napus and Arabidopsis thaliana. The Plant Journal, 53(3), 437-449. doi:10.1111/j.1365-313x.2007.03348.xMoreira‐Vilar F C. Siqueira‐Soares R deC Finger‐Teixeira A. Oliveira de D. M. Ferro AP Rocha daG J. Ferrarese M deLL Santos dosW. D. Ferrarese‐Filho O(2014).The Acetyl Bromide Method Is Faster Simpler and Presents Best Recovery of Lignin in Different Herbaceous Tissues than Klason and Thioglycolic Acid Methods. PLoS ONE 9:e110000.https://doi.org/10.1371/journal.pone.0110000Oñate-Sánchez, L., & Vicente-Carbajosa, J. (2008). DNA-free RNA isolation protocols for Arabidopsis thaliana, including seeds and siliques. BMC Research Notes, 1(1), 93. doi:10.1186/1756-0500-1-93Østergaard, L., Teilum, K., Mirza, O., Mattsson, O., Petersen, M., Welinder, K. G., … Henriksen, A. (2000). 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A Tomato Peroxidase Involved in the Synthesis of Lignin and Suberin. Plant Physiology, 122(4), 1119-1128. doi:10.1104/pp.122.4.1119Rains, M. K., Gardiyehewa de Silva, N. D., & Molina, I. (2017). Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues. Tree Physiology, 38(3), 340-361. doi:10.1093/treephys/tpx060Russell, W. R., Burkitt, M. J., Scobbie, L., & Chesson, A. (2005). EPR Investigation into the Effects of Substrate Structure on Peroxidase-Catalyzed Phenylpropanoid Oxidation. Biomacromolecules, 7(1), 268-273. doi:10.1021/bm050636oSano, N., Rajjou, L., North, H. M., Debeaujon, I., Marion-Poll, A., & Seo, M. (2015). Staying Alive: Molecular Aspects of Seed Longevity. Plant and Cell Physiology, 57(4), 660-674. doi:10.1093/pcp/pcv186Shigeto, J., Itoh, Y., Hirao, S., Ohira, K., Fujita, K., & Tsutsumi, Y. (2015). Simultaneously disrupting AtPrx2 , AtPrx25 and AtPrx71 alters lignin content and structure in Arabidopsis stem. Journal of Integrative Plant Biology, 57(4), 349-356. doi:10.1111/jipb.12334Shigeto, J., Kiyonaga, Y., Fujita, K., Kondo, R., & Tsutsumi, Y. (2013). Putative Cationic Cell-Wall-Bound Peroxidase Homologues in Arabidopsis, AtPrx2, AtPrx25, and AtPrx71, Are Involved in Lignification. Journal of Agricultural and Food Chemistry, 61(16), 3781-3788. doi:10.1021/jf400426gSoliday, C. L., Dean, B. B., & Kolattukudy, P. E. (1978). Suberization: Inhibition by Washing and Stimulation by Abscisic Acid in Potato Disks and Tissue Culture. Plant Physiology, 61(2), 170-174. doi:10.1104/pp.61.2.170Tobimatsu, Y., Chen, F., Nakashima, J., Escamilla-Trevino, L. L., Jackson, L., Dixon, R. A., & Ralph, J. (2013). Coexistence but Independent Biosynthesis of Catechyl and Guaiacyl/Syringyl Lignin Polymers in Seed Coats. The Plant Cell, 25(7), 2587-2600. doi:10.1105/tpc.113.113142Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., & Pachter, L. (2012). 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Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences

Background : Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but the specific and cooperative contributions of the MAPKs in these signalling events are largely unclear.[br/] Results: In this work, we analyse the behaviour of MPK3, MPK4 and MPK6 mutants in early and late immune responses triggered by the MAMP flg22 from bacterial flagellin. A genome-wide transcriptome analysis reveals that 36% of the flg22-upregulated genes and 68% of the flg22-downregulated genes are affected in at least one MAPK mutant. So far MPK4 was considered as a negative regulator of immunity, whereas MPK3 and MPK6 were believed to play partially redundant positive functions in defence.[br/] Our work reveals that MPK4 is required for the regulation of approximately 50% of flg22-induced genes and we identify a negative role for MPK3 in regulating defence gene expression, flg22-induced salicylic acid accumulation and disease resistance to Pseudomonas syringae. Among the MAPK-dependent genes, 27% of flg22-upregulated genes and 76% of flg22-downregulated genes require two or three MAPKs for their regulation. The flg22-induced MAPK activities are differentially regulated in MPK3 and MPK6 mutants, both in amplitude and duration, revealing a highly interdependent network.[br/] Conclusions : These data reveal a new set of distinct functions for MPK3, MPK4 and MPK6 and indicate that the plant immune signalling network is choreographed through the interplay of these three interwoven MAPK pathways

New insights into short-term water stress tolerance through transcriptomic and metabolomic analyses on pepper roots

In the current climate change scenario, water stress is a serious threat to limit crop growth and yields. It is necessary to develop tolerant plants that cope with water stress and, for this purpose, tolerance mechanisms should be studied. NIBER® is a proven water stress- and salt-tolerant pepper hybrid rootstock (Gisbert-Mullor et al., 2020; López-Serrano et al., 2020), but tolerance mechanisms remain unclear. In this experiment, NIBER® and A10 (a sensitive pepper accession (Penella et al., 2014)) response to short-term water stress at 5 h and 24 h was studied in terms of gene expression and metabolites content in roots. GO terms and gene expression analyses evidenced constitutive differences in the transcriptomic profile of NIBER® and A10, associated with detoxification systems of reactive oxygen species (ROS). Upon water stress, transcription factors like DREBs and MYC are upregulated and the levels of auxins, abscisic acid and jasmonic acid are increased in NIBER®. NIBER® tolerance mechanisms involve an increase in osmoprotectant sugars (i.e., trehalose, raffinose) and in antioxidants (spermidine), but lower contents of oxidized glutathione compared to A10, which indicates less oxidative damage. Moreover, the gene expression for aquaporins and chaperones is enhanced. These results show the main NIBER® strategies to overcome water stress

Identification of novel seed longevity genes related to oxidative stress and seed coat by genome wide association studies and reverse genetics

[EN] Seed longevity is a polygenic trait of relevance for agriculture and for understanding the effect of environment on the ageing of biological systems. In order to identify novel longevity genes, we have phenotyped the natural variation of 270 ecotypes of the model plant,Arabidopsis thaliana, for natural ageing and for three accelerated ageing methods. Genome-wide analysis, using publicly available single-nucleotide polymorphisms (SNPs) data sets, identified multiple genomic regions associated with variation in seed longevity. Reverse genetics of 20 candidate genes in Columbia ecotype resulted in seven genes positive for seed longevity (PSAD1,SSLEA,SSTPR,DHAR1,CYP86A8,MYB47andSPCH) and five negative ones (RBOHD,RBOHE,RBOHF,KNAT7andSEP3). In this uniform genetic background, natural and accelerated ageing methods provided similar results for seed-longevity in knock-out mutants. The NADPH oxidases (RBOHs), the dehydroascorbate reductase (DHAR1) and the photosystem I subunit (PSAD1) highlight the important role of oxidative stress on seed ageing. The cytochrome P-450 hydroxylase, CYP86A8, and the transcription factors, MYB47, KNAT7 and SEP3, support the protecting role of the seed coat during seed ageing.Ministerio de Ciencia, Innovacion y Universidades, Grant/Award Number: BIO2017-88898-PRenard, J.; Niñoles Rodenes, R.; Martínez-Almonacid, I.; Gayubas, B.; Mateos-Fernández, R.; Bissoli, G.; Bueso Rodenas, E.... (2020). Identification of novel seed longevity genes related to oxidative stress and seed coat by genome wide association studies and reverse genetics. Plant Cell & Environment. 43(10):2523-2539. https://doi.org/10.1111/pce.13822S25232539431

Subtyping treatment-seeking gaming disorder patients

Background and aims: Gaming Disorder (GD) is characterized by a pattern of persistent and uncontrolled gaming behavior that causes a marked impairment in important areas of functioning. The evolution of the worldwide incidence of this disorder warrants further studies focused on examining the existence of different subtypes within clinical samples, in order to tailor treatment. This study explored the existence of different profiles of patients seeking treatment for GD through a data-driven approach. Methods: The sample included n = 107 patients receiving treatment for GD (92% men and 8% women) ranging between 14 and 60 years old (mean age = 24.1, SD = 10). A two-step clustering analysis approach explored the existence of different underlying GD profiles based on a broad set of indicators, including sociodemographic features, clinical course of the condition (e.g., onset or evolution), psychopathological symptoms, and personality traits. Results: Two GD profiles emerged. The first cluster grouped together patients who presented with a lower psychological impact (n = 72, 66.1%), whereas the second cluster comprised patients with a higher psychological impact (n = 35, 32.7%). Cluster comparisons revealed that those patients presenting the higher impact were older, with a later onset of pathological gaming patterns, and more pronounced psychopathological symptoms and dysfunctional personality profiles. Conclusions: GD severity is influenced by specific demographic, clinical, and psychopathological factors. The identification of two separate profiles provides empirical evidence that contributes to the conceptualization of this disorder, as well as to the development of reliable and valid screening tools and effective intervention plans focused on the precise characteristics of the treatment-seeking patients