Search for: All records

Ocean metabolism constitutes a complex, multiscale ensemble of biochemical reaction networks harbored within and between the boundaries of a myriad of organisms. Gaining a quantitative understanding of how these networks operate requires mathematical tools capable of solving in silico the resource allocation problem each cell faces in real life. Toward this goal, stoichiometric modeling of metabolism, such as flux balance analysis, has emerged as a powerful computational tool for unraveling the intricacies of metabolic processes in microbes, microbial communities, and multicellular organisms. Here, we provide an overview of this approach and its applications, future prospects, and practical considerations in the context of marine sciences. We explore how flux balance analysis has been employed to study marine organisms, help elucidate nutrient cycling, and predict metabolic capabilities within diverse marine environments, and highlight future prospects for this field in advancing our knowledge of marine ecosystems and their sustainability. 

Synthetic biology is creating genetically engineered organisms at an increasing rate for many potentially valuable applications, but this potential comes with the risk of misuse or accidental release. To begin to address this issue, we have developed a system called GUARDIAN that can automatically detect signatures of engineering in DNA sequencing data, and we have conducted a blinded test of this system using a curated Test and Evaluation (T&E) data set. GUARDIAN uses an ensemble approach based on the guiding principle that no single approach is likely to be able to detect engineering with perfect accuracy. Critically, ensembling enables GUARDIAN to detect sequence inserts in 13 target organisms with a high degree of specificity that requires no subject matter expert (SME) review.