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High-resolution molecular networks from novel 'omics' approaches elucidate survival strategies in organisms from land to sea


Molecular networks drive nearly all cellular processes. With the advent of omics technologies involving next-generation sequencing and mass spectrometry, we have started to uncover highly complex gene, protein, and biochemical networks that underlie survival mechanisms like growth and stress tolerance.However, the study of cell wide of protein-protein interactions that importantly link genomic, transcriptomic, and proteomic data to cellular activity has been hindered by technical limitations, and the need to survey and track billions of possible combinatorial protein interactions. Moreover, many omics technologies have not yet been developed or applied to non-model organisms, particularly to ecologically and economically important species that may be negatively impacted by climate change. To address these shortcomings, I developed a modified yeast two-hybrid technology called CrY2H-seq that enables massively multiplexed protein interaction screening through a Cre-lox reporter and next generation sequencing, and demonstrated its applications for generating interactome resources by screening a comprehensive set of Arabidopsis transcription factors. Lastly, I applied metabolomics analysis to investigate how ocean acidification might impact the Dungeness crab. I found transcription factor families preferentially interact with others, and relationships among families supported by recent independent studies may drive mechanisms underlying reproductive development and hormone signaling. I also found that metabolomes of developing Dungeness crab show treatment specific responses to low oxygen and low pH seawater treatments. Taken all together, the new biological insight gained from these novel omics approaches can valuably be used to inform targeted future experiments aimed at optimizing crop cultivation and predicting how economically and economically important species might response to future environmental stress.

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