A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast

Deciphering gene regulatory mechanisms through the analysis of high-throughput expression data is a challenging computational problem. Previous computational studies have used large expression datasets in order to resolve fine patterns of coexpression, producing clusters or modules of potentially coregulated genes. These methods typically examine promoter sequence information, such as DNA motifs or transcription factor occupancy data, in a separate step after clustering. We needed an alternative and more integrative approach to study the oxygen regulatory network in Saccharomyces cerevisiae using a small dataset of perturbation experiments. Mechanisms of oxygen sensing and regulation underlie many physiological and pathological processes, and only a handful of oxygen regulators have been identified in previous studies. We used a new machine learning algorithm called MEDUSA to uncover detailed information about the oxygen regulatory network using genome-wide expression changes in response to perturbations in the levels of oxygen, heme, Hap1, and Co2+. MEDUSA integrates mRNA expression, promoter sequence, and ChIP-chip occupancy data to learn a model that accurately predicts the differential expression of target genes in held-out data. We used a novel margin-based score to extract significant condition-specific regulators and assemble a global map of the oxygen sensing and regulatory network. This network includes both known oxygen and heme regulators, such as Hap1, Mga2, Hap4, and Upc2, as well as many new candidate regulators. MEDUSA also identified many DNA motifs that are consistent with previous experimentally identified transcription factor binding sites. Because MEDUSA's regulatory program associates regulators to target genes through their promoter sequences, we directly tested the predicted regulators for OLE1, a gene specifically induced under hypoxia, by experimental analysis of the activity of its promoter. In each case, deletion of the candidate regulator resulted in the predicted effect on promoter activity, confirming that several novel regulators identified by MEDUSA are indeed involved in oxygen regulation. MEDUSA can reveal important information from a small dataset and generate testable hypotheses for further experimental analysis. Supplemental data are included

Advancing How We Learn from Biodesign to Mitigate Risks with Next-Generation Genome Engineering

In the last decade, the unprecedented simplicity and flexibility of the CRISPR-Cas system has made it the dominant transformative tool in gene and genome editing. However, this democratized technology is both a boon and a bane, for which we have yet to understand the full potential to investigate and rewrite genomes (also named “genome biodesign”). Rapid CRISPR advances in a range of applications in basic research, agriculture, and clinical applications pose new risks and raise several biosecurity concerns. In such a fast-moving field of research, we emphasize the importance of properly communicating the quality and accuracy of results and recommend new reporting requirements for results derived from next-generation genome engineering

Advancing How We Learn from Biodesign to Mitigate Risks with Next-Generation Genome Engineering

In the last decade, the unprecedented simplicity and flexibility of the CRISPR-Cas system has made it the dominant transformative tool in gene and genome editing. However, this democratized technology is both a boon and a bane, for which we have yet to understand the full potential to investigate and rewrite genomes (also named “genome biodesign”). Rapid CRISPR advances in a range of applications in basic research, agriculture, and clinical applications pose new risks and raise several biosecurity concerns. In such a fast-moving field of research, we emphasize the importance of properly communicating the quality and accuracy of results and recommend new reporting requirements for results derived from next-generation genome engineering

Apport de la microbalance à quartz dans l'étude de l'influence des ions sulfate, chlorure et magnésium sur la cinétique d'entartrage

Dans le présent travail, nous avons fait appel à la microbalance à quartz électrochimique pour étudier l'influence des ions chlorure, sulfate et magnésium sur la cinétique d'entartrage de l'or au contact d'eaux synthétiques. Les résultats chronoélectrogravimétriques permettent l'évaluation des étapes de germination et de croissance cristalline. Des analyses infrarouge des dépôts formés permettent de lier la nature des espèces identifiées aux paramètres cinétiques, en particulier en présence d'ions SO$_{4}^{2-}$ ou Mg2+. Des effets de seuil sont mis en évidence pour chaque type d'ion étudié. Ils sont essentiellement attribués à des phénomènes d'accumulation d'espèces sur le métal ou sur les produits superficiels, comme l'indique l'étude de l'effet du potentiel d'électrode et de la concentration des espèces en solution

Uncovering the Missing Link between Molecular Electrochemistry and Electrocatalysis: Mechanism of the Reduction of Benzyl Chloride at Silver Cathodes

Herein, the traditional views that contrast the important areas of electrocatalysis and molecular electrochemistry are challenged. By extending Laviron\u2019s seminal concept, we show that these two domains only represent idealized limits of a much broader continuum. More importantly, we show that electrochemical systems that apparently behave experimentally as if under diffusion control (i.e. systems that obey the founding molecular electrochemistry paradigm) may be controlled by electrocatalytic steps, that is, in which the activation of electroactive substrates exclusively occurs through adsorbed intermediates. This analysis is supported through quantitative experimental and theoretical investigations on the reduction of benzyl chloride at silver electrodes. At silver cathodes, the reduction wave of benzyl chloride as monitored at the usual scan rates is dramatically shifted to more positive potentials by about 0.5 V versus that at inert (e.g. glassy carbon) electrodes. This approach, which is based on the use of fast-scan cyclic voltammetry and simulations (KISSA-1D), combined with our previous results from surface-enhanced Raman spectroscopy (SERS) and density functional theory (DFT) analysis, allow us to fully unravel the mechanistic origin of this dramatic effect and quantitatively validate this mechanism, which has eluded many research groups until now. In practice, this example provides a missing link between the traditional areas of electrocatalysis and molecular electrochemistry. Furthermore, it bridges the chemical areas of organometallic/inorganic catalysis and electrochemical activation by showing that the inner-sphere concept, as developed by Taube and Myers for inorganic reactions, applies perfectly to electrochemical reactions of molecular substrate

The Werner syndrome gene product (WRN): a repressor of hypoxia-inducible factor-1 activity

Hypoxia-inducible factor-1 (HIF-1) is a decisive element for the transcriptional regulation of genes essential for adaptation to low oxygen conditions. HIF-1 is also implicated in the molecular mechanisms of ageing. Here, we show that the cellular depletion of WRN protein (by siRNA targeting) leads to increased HIF-1 complex stabilization and activation. HIF-1 activation in the absence of WRN involves the generation of mitochondrial reactive oxygen species (mtROS) since SkQ1, a mitochondrial-targeted antioxidant, and stigmatellin, an inhibitor of mitochondrial complex III, blocked increased HIF-1 levels. Ascorbate, an essential co-factor involved in HIF-1 stability, was decreased in WRN-depleted cells. Interestingly, expression levels of GLUT1, a known dehydroascorbic acid transporter, were also decreased in WRN-depleted cells. Ascorbate supplementation of WRN-depleted cells led to a dose-dependent inhibition of HIF-1 activation. These results indicate that WRN protein regulates HIF-1 activation by affecting mitochondrial ROS production and intracellular ascorbate levels. This work provides a novel mechanistic link between HIF-1 activity and different age-associated pathologies