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null (Ed.)Abstract Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic and synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility and histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.more » « less
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Abstract Research on public views of biotechnology has centered on genetically modified (GM) foods. However, as the breadth of biotechnology applications grows, a better understanding of public concerns about non-agricultural biotechnology products is needed in order to develop proactive strategies to address these concerns. Here, we explore the perceived benefits and risks associated with five biotechnology products and how those perceptions translate into public opinion about the use and regulation of biotechnology in the United States. While we found greater support for non-agricultural biotechnology product, 70% of individuals surveyed showed no or little variation in their support across the products, indicating opinions about early GM products may be influencing the acceptance of emerging biotechnologies. We identified five common patterns of opinions about biotechnology and used machine learning models to integrate a wide range of factors and predict a respondent’s opinion group. While the model was particularly good at identifying individuals supportive of biotechnology, differentiating between individuals from the non- and conditionally-supportive opinion groups was more challenging, emphasizing the complexity of public opinions of emerging biotechnology products.