Transcriptomics unravels the adaptive molecular mechanisms of Brettanomyces bruxellensis under SO2 stress in wine condition

CITATION: Valdetara, F. et al. 2020. Transcriptomics unravels the adaptive molecular mechanisms of Brettanomyces bruxellensis under SO2 stress in wine condition. Food Microbiology, 90. doi:10.1016/j.fm.2020.103483.The original publication is available at https://www.sciencedirect.com/journal/food-microbiologySulfur dioxide is generally used as an antimicrobial in wine to counteract the activity of spoilage yeasts, including Brettanomyces bruxellensis. However, this chemical does not exert the same effectiveness on different B. bruxellensis yeasts since some strains can proliferate in the final product leading to a negative sensory profile due to 4-ethylguaiacol and 4-ethylphenol. Thus, the capability of deciphering the general molecular mechanisms characterizing this yeast species’ response in presence of SO2 stress could be considered strategic for a better management of SO2 in winemaking. A RNA-Seq approach was used to investigate the gene expression of two strains of B. bruxellensis, AWRI 1499 and CBS 2499 having different genetic backgrounds, when exposed to a SO2 pulse. Results revealed that sulphites affected yeast culturability and metabolism, but not volatile phenol production suggesting that a phenotypical heterogeneity could be involved for the SO2 cell adaptation. The transcriptomics variation in response to SO2 stress confirmed the strain-related response in B. bruxellensis and the GO analysis of common differentially expressed genes showed that the detoxification process carried out by SSU1 gene can be considered as the principal specific adaptive response to counteract the SO2 presence. However, nonspecific mechanisms can be exploited by cells to assist the SO2 tolerance; namely, the metabolisms related to sugar alcohol (polyols) and oxidative stress, and structural compounds.https://www.sciencedirect.com/science/article/pii/S0740002020300721?via%3DihubPublishers versio

SUPPA2:fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Supplementary methods. (PDF 315 kb

Deep learning for drug design : modeling molecular shapes

Designing novel drugs is a complex process which requires finding molecules in a vast chemical space that bind to a specific biomolecular target and have favorable physio-chemical properties. Machine learning methods can leverage previous data and use it for new predictions helping the processes of selection of molecule candidate without relying exclusively on experiments. Particularly, deep learning can be applied to extract complex patterns from simple representations. In this work we leverage deep learning to extract patterns from three-dimensional representations of molecules. We apply classification and regression models to predict bioactivity and binding affinity, respectively. Furthermore, we show that it is possible to predict ligand properties for a particular protein pocket. Finally, we employ deep generative modeling for compound design. Given a ligand shape we show that we can generate similar compounds, and given a protein pocket we can generate potentially binding compounds.El disseny de drogues novells es un procés complex que requereix trobar les molècules adequades, entre un gran ventall de possibilitats, que siguin capaces d’unir-se a la proteïna desitjada amb unes propietats fisicoquímiques favorables. Els mètodes d’aprenentatge automàtic ens serveixen per a aprofitar dades antigues sobre les molècules i utilitzar-les per a noves prediccions, ajudant en el procés de selecció de molècules potencials sense la necessitat exclusiva d’experiments. Particularment, l’aprenentatge profund pot sera plicat per a extreure patrons complexos a partir de representacions simples. En aquesta tesi utilitzem l’aprenentatge profund per a extreure patrons a partir de representacions tridimensionals de molècules. Apliquem models de classificació i regressió per a predir la bioactivitat i l’afinitat d’unió, respectivament. A més, demostrem que podem predir les propietats dels lligands per a una cavitat proteica determinada. Finalment, utilitzem un model generatiu profund per a disseny de compostos. Donada una forma d’un lligand demostrem que podem generar compostos similars i, donada una cavitat proteica, podem generar compostos que potencialment s’hi podràn unir

Deep learning for drug design : modeling molecular shapes

Designing novel drugs is a complex process which requires finding molecules in a vast chemical space that bind to a specific biomolecular target and have favorable physio-chemical properties. Machine learning methods can leverage previous data and use it for new predictions helping the processes of selection of molecule candidate without relying exclusively on experiments. Particularly, deep learning can be applied to extract complex patterns from simple representations. In this work we leverage deep learning to extract patterns from three-dimensional representations of molecules. We apply classification and regression models to predict bioactivity and binding affinity, respectively. Furthermore, we show that it is possible to predict ligand properties for a particular protein pocket. Finally, we employ deep generative modeling for compound design. Given a ligand shape we show that we can generate similar compounds, and given a protein pocket we can generate potentially binding compounds.El disseny de drogues novells es un procés complex que requereix trobar les molècules adequades, entre un gran ventall de possibilitats, que siguin capaces d’unir-se a la proteïna desitjada amb unes propietats fisicoquímiques favorables. Els mètodes d’aprenentatge automàtic ens serveixen per a aprofitar dades antigues sobre les molècules i utilitzar-les per a noves prediccions, ajudant en el procés de selecció de molècules potencials sense la necessitat exclusiva d’experiments. Particularment, l’aprenentatge profund pot sera plicat per a extreure patrons complexos a partir de representacions simples. En aquesta tesi utilitzem l’aprenentatge profund per a extreure patrons a partir de representacions tridimensionals de molècules. Apliquem models de classificació i regressió per a predir la bioactivitat i l’afinitat d’unió, respectivament. A més, demostrem que podem predir les propietats dels lligands per a una cavitat proteica determinada. Finalment, utilitzem un model generatiu profund per a disseny de compostos. Donada una forma d’un lligand demostrem que podem generar compostos similars i, donada una cavitat proteica, podem generar compostos que potencialment s’hi podràn unir

Benchmarking molecular feature attribution methods with activity cliffs

Feature attribution techniques are popular choices within the explainable artificial intelligence toolbox, as they can help elucidate which parts of the provided inputs used by an underlying supervised-learning method are considered relevant for a specific prediction. In the context of molecular design, these approaches typically involve the coloring of molecular graphs, whose presentation to medicinal chemists can be useful for making a decision of which compounds to synthesize or prioritize. The consistency of the highlighted moieties alongside expert background knowledge is expected to contribute to the understanding of machine-learning models in drug design. Quantitative evaluation of such coloring approaches, however, has so far been limited to substructure identification tasks. We here present an approach that is based on maximum common substructure algorithms applied to experimentally-determined activity cliffs. Using the proposed benchmark, we found that molecule coloring approaches in conjunction with classical machine-learning models tend to outperform more modern, deep-learning-based alternatives. However, none of the tested feature attribution methods sufficiently and consistently generalized when confronted with unseen examples

Benchmarking Molecular Feature Attribution Methods with Activity Cliffs

Feature attribution techniques are popula r choices within the explainable artificial intelligence toolbox, as they can help elucidate which parts of the provided inputs used by an underlying supervised-learning method are considered relevant for a specific prediction. In the context of molecular design, these approaches typically involve the coloring of molecular graphs, whose presentation to medicinal chemists can be useful for making a decision of which compounds to synthesize or prioritize. The consistency of the highlighted moieties alongside expert background knowledge is expected to contribute to the understanding of machine-learning models in drug design. Quantitative evaluation of such coloring approaches, however, has so far been limited to substructure identification tasks. We here present an approach that is based on maximum common substructure algorithms applied to experimentally-determined activity cliffs. Using the proposed benchmark, we found that molecule coloring approaches in conjunction with classical machine-learning models tend to outperform more modern, graph-neural-network alternatives. The provided benchmark data are fully open sourced, which we hope will facilitate the testing of newly developed molecular feature attribution techniques.ISSN:1549-9596ISSN:0095-2338ISSN:1520-514

Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment

Graph neural networks are able to solve certain drug discovery tasks such as molecular property prediction and de novo molecule generation. However, these models are considered \u27black-box\u27 and \u27hard-to-debug\u27. This study aimed to improve modeling transparency for rational molecular design by applying the integrated gradients explainable artificial intelligence (XAI) approach for graph neural network models. Models were trained for predicting plasma protein binding, cardiac potassium channel inhibition, passive permeability, and cytochrome P450 inhibition. The proposed methodology highlighted molecular features and structural elements that are in agreement with known pharmacophore motifs, correctly identified property cliffs, and provided insights into unspecific ligand-target interactions. The developed XAI approach is fully open-sourced and can be used by practitioners to train new models on other clinically-relevant endpoints

Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment

Graph neural networks are able to solve certain drug discovery tasks such as molecular property prediction and de novo molecule generation. However, these models are considered “black-box” and “hard-to-debug”. This study aimed to improve modeling transparency for rational molecular design by applying the integrated gradients explainable artificial intelligence (XAI) approach for graph neural network models. Models were trained for predicting plasma protein binding, hERG channel inhibition, passive permeability, and cytochrome P450 inhibition. The proposed methodology highlighted molecular features and structural elements that are in agreement with known pharmacophore motifs, correctly identified property cliffs, and provided insights into unspecific ligand–target interactions. The developed XAI approach is fully open-sourced and can be used by practitioners to train new models on other clinically relevant endpoints. © 2021 American Chemical SocietyISSN:1549-9596ISSN:0095-2338ISSN:1520-514

SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPPA2 achieves higher accuracy compared to other methods, especially at low sequencing depth and short read length. We use SUPPA2 to identify novel Transformer2-regulated exons, novel microexons induced during differentiation of bipolar neurons, and novel intron retention events during erythroblast differentiation.This work was supported by the MINECO and FEDER with grants BIO2014-52566-R and BIO2017-85364-R, by AGAUR with grants SGR2014-1121 and SGR2017-1020, by BBSRC (BB/P006612/1), and by Breast Cancer Now (2014NovPR355). GH is a BBSRC-funded PhD student