ALLERDET: A novel web app for prediction of protein allergenicity.

Allergic diseases are increasing around the world with unprecedented complexity and severity. One of the reasons is that genetically modified crops produce new potentially allergenic proteins. From this starting point, many researchers have paid attention to the development of tools to predict the allergenicity of new proteins. In this study, a novel approach is introduced for the prediction of food allergens based on Artificial Intelligence techniques: a pairwise sequence alignment with the FASTA program for feature extraction and the use of the Deep Learning technique known as Restricted Boltzmann Machines in combination with the Decision Tree method for the prediction process. The developed tool, called ALLERDET (publicly available at http://allerdet.frangam.com), overcomes the state-of-the-art methods. The performance of our method is: 98.46% sensitivity, 94.37% specificity and 97.26% accuracy), on a data set built from several publicly available sources.

Optimizing the Simplicial-Map Neural Network Architecture.

Simplicial-map neural networks are a recent neural network architecture induced by simplicial maps defined between simplicial complexes. It has been proved that simplicial-map neural networks are universal approximators and that they can be refined to be robust to adversarial attacks. In this paper, the refinement toward robustness is optimized by reducing the number of simplices (i.e., nodes) needed. We have shown experimentally that such a refined neural network is equivalent to the original network as a classification tool but requires much less storage.

Two-hidden-layer feed-forward networks are universal approximators: A constructive approach.

It is well-known that artificial neural networks are universal approximators. The classical existence result proves that, given a continuous function on a compact set embedded in an n-dimensional space, there exists a one-hidden-layer feed-forward network that approximates the function. In this paper, a constructive approach to this problem is given for the case of a continuous function on triangulated spaces. Once a triangulation of the space is given, a two-hidden-layer feed-forward network with a concrete set of weights is computed. The level of the approximation depends on the refinement of the triangulation.

The Gcn2-eIF2α pathway connects iron and amino acid homeostasis in Saccharomyces cerevisiae.

In eukaryotic cells, amino acid biosynthesis is feedback-inhibited by amino acids through inhibition of the conserved protein kinase Gcn2. This decreases phosphorylation of initiation factor eIF2α, resulting in general activation of translation but inhibition of translation of mRNA for transcription factor (TF) Gcn4 in yeast or ATF4 in mammals. These TFs are positive regulators of amino acid biosynthetic genes. As several enzymes of amino acid biosynthesis contain iron-sulfur clusters (ISCs) and iron excess is toxic, iron and amino acid homeostasis should be co-ordinated. Working with the yeast Saccharomyces cerevisiae, we found that amino acid supplementation down-regulates expression of genes for iron uptake and decreases intracellular iron content. This cross-regulation requires Aft1, the major TF activated by iron scarcity, as well as Gcn2 and phosphorylatable eIF2α but not Gcn4. A mutant with constitutive activity of Gcn2 (GCN2c ) shows less repression of iron transport genes by amino acids and increased nuclear localization of Aft1 in an iron-poor medium, and increases iron content in this medium. As Aft1 is activated by depletion of mitochondrial ISCs, it is plausible that the Gcn2-eIF2α pathway inhibits the formation of these complexes. Accordingly, the GCN2c mutant has strongly reduced activity of succinate dehydrogenase, an iron-sulfur mitochondrial enzyme, and is unable to grow in media with very low iron or with galactose instead of glucose, conditions where formation of ISCs is specially needed. This mechanism adjusts the uptake of iron to the needs of amino acid biosynthesis and expands the list of Gcn4-independent activities of the Gcn2-eIF2α regulatory system.

Effects of salinity and drought on growth, ionic relations, compatible solutes and activation of antioxidant systems in oleander (Nerium oleander L.).

Nerium oleander is an ornamental species of high aesthetic value, grown in arid and semi-arid regions because of its drought tolerance, which is also considered as relatively resistant to salt; yet the biochemical and molecular mechanisms underlying oleander's stress tolerance remain largely unknown. To investigate these mechanisms, one-year-old oleander seedlings were exposed to 15 and 30 days of treatment with increasing salt concentrations, up to 800 mM NaCl, and to complete withholding of irrigation; growth parameters and biochemical markers characteristic of conserved stress-response pathways were then determined in stressed and control plants. Strong water deficit and salt stress both caused inhibition of growth, degradation of photosynthetic pigments, a slight (but statistically significant) increase in the leaf levels of specific osmolytes, and induction of oxidative stress-as indicated by the accumulation of malondialdehyde (MDA), a reliable oxidative stress marker-accompanied by increases in the levels of total phenolic compounds and antioxidant flavonoids and in the specific activities of ascorbate peroxidase (APX) and glutathione reductase (GR). High salinity, in addition, induced accumulation of Na+ and Cl- in roots and leaves and the activation of superoxide dismutase (SOD) and catalase (CAT) activities. Apart from anatomical adaptations that protect oleander from leaf dehydration at moderate levels of stress, our results indicate that tolerance of this species to salinity and water deficit is based on the constitutive accumulation in leaves of high concentrations of soluble carbohydrates and, to a lesser extent, of glycine betaine, and in the activation of the aforementioned antioxidant systems. Moreover, regarding specifically salt stress, mechanisms efficiently blocking transport of toxic ions from the roots to the aerial parts of the plant appear to contribute to a large extent to tolerance in Nerium oleander.

Long-Term Effect of a Leonardite Iron Humate Improving Fe Nutrition As Revealed in Silico, in Vivo, and in Field Experiments.

Novel, cheap and ecofriendly fertilizers that solve the usual iron deficiency problem in calcareous soil are needed. The aim of this work is to study the long-term effect of an iron leonardite fertilizer on citrus nutrition taking into account a properly characterization, kinetic response with a ligand competition experiment, efficiency assessment using Saccharomyces cerevisiae strain and finally, in field conditions with citrus as test plants. Its efficiency was compared with the synthetic iron chelate FeEDDHA. Leonardite iron humate (LIH) is mainly humic acid with a high-condensed structure where iron is present as ferrihydrite and Fe3+ polynuclear compounds stabilized by organic matter. Iron and humic acids form aggregates that decrease the iron release from these kinds of fertilizers. Furthermore, LIH repressed almost 50% of the expression of FET3, FTR1, SIT1, and TIS11 genes in Saccharomyces cerevisiae cells, indicating increasing iron provided in cells and improved iron nutrition in citrus.

Identification of a GCC transcription factor responding to fruit colour change events in citrus through the transcriptomic analyses of two mutants.

BACKGROUND: External ripening in Citrus fruits is morphologically characterized by a colour shift from green to orange due to the degradation of chlorophylls and the accumulation of carotenoid pigments. Although numerous genes coding for enzymes involved in such biochemical pathways have been identified, the molecular control of this process has been scarcely studied. In this work we used the Citrus clementina mutants 39B3 and 39E7, showing delayed colour break, to isolate genes potentially related to the regulation of peel ripening and its physiological or biochemical effects. RESULTS: Pigment analyses revealed different profiles of carotenoid and chlorophyll modification in 39B3 and 39E7 mutants. Flavedo from 39B3 fruits showed an overall delay in carotenoid accumulation and chlorophyll degradation, while the flavedo of 39E7 was devoid of the apocarotenoid ß-citraurin among other carotenoid alterations. A Citrus microarray containing about 20,000 cDNA fragments was used to identify genes that were differentially expressed during colour change in the flavedo of 39B3 and 39E7 mutants respect to the parental variety. The results highlighted 73 and 90 genes that were respectively up- and down-regulated in both mutants. CcGCC1 gene, coding for a GCC type transcriptional factor, was found to be down-regulated. CcGCC1 expression was strongly induced at the onset of colour change in the flavedo of parental clementine fruit. Moreover, treatment of fruits with gibberellins, a retardant of external ripening, delayed both colour break and CcGCC1 overexpression. CONCLUSIONS: In this work, the citrus fruit ripening mutants 39B3 and 39E7 have been characterized at the phenotypic, biochemical and transcriptomic level. A defective synthesis of the apocarotenoid ß-citraurin has been proposed to cause the yellowish colour of fully ripe 39E7 flavedo. The analyses of the mutant transcriptomes revealed that colour change during peel ripening was strongly associated with a major mobilization of mineral elements and with other previously known metabolic and photosynthetic changes. The expression of CcGCC1 was associated with peel ripening since CcGCC1 down-regulation correlated with a delay in colour break induced by genetic, developmental and hormonal causes.

Characterization of hemizygous deletions in citrus using array-comparative genomic hybridization and microsynteny comparisons with the poplar genome.

BACKGROUND: Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background. RESULTS: Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues. CONCLUSION: In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with Populus trichocarpa than with the phylogenetically closer Arabidopsis thaliana. This work corroborates the potential of Citrus genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement.

Lithium treatment induces a hypersensitive-like response in tobacco.

Treatment of tobacco ( Nicotiana tabacum L.) plants with lithium induces the formation of necrotic lesions and leaf curling as in the case of incompatible pathogen interactions. Further similarities at the molecular level include accumulation of ethylene and of salicylic and gentisic acids, and induced expression of pathogenesis-related PR-P, PR5 and PR1 genes. With the exception of PR1 induction, lithium produced the same effects in transgenic tobacco plants that do not accumulate salicylate because of overexpression of the bacterial hydroxylase gene nahG. On the other hand, inhibition of ethylene biosynthesis with aminoethoxyvinylglycine prevented lithium-induced cell death and PR5 expression. These results suggest that lithium triggers a hypersensitive-like response where ethylene signalling is essential.