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Aim: Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time.

Methods: Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture.

Results: SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time.

Conclusion: A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.

 

Driven by increasing greenhouse gas (GHG) concentrations in the atmosphere, extreme weather events have become more frequent and their impacts on human lives have become more severe. Therefore, the need for short-term GHG mitigations is urgent. Recently, methane has been recognized as an important mitigation target due to its high global warming potential (GWP). However, methane’s low concentration in the atmosphere and stable molecular structure make its removal from the air highly challenging. This review first discusses the fundamental aspects of the challenges in atmospheric methane removal and then briefly reviews the existing research strategies following the mechanisms of natural methane sinks. Although still in its infancy, recent research on methane removal from the air holds great potential for slowing down global warming. At the same time, it is important to carefully examine the energy consumption of these methane removal strategies and whether they will be able to achieve net GHG reduction. In addition, due to the scale of methane removal from the air, any potential solution’s environmental impacts must be carefully evaluated before it can be implemented in practice.

 

We present a mathematical model based on ordinary differential equations to investigate the spatially homogeneous state of tumor growth under virotherapy. The model emphasizes the interaction among the tumor cells, the oncolytic viruses, and the host immune system that generates both innate and adaptive immune responses. We conduct a rigorous equilibrium analysis and derive threshold conditions that determine the growth or decay of the tumor under various scenarios. Numerical simulation results verify our analytical predictions and provide additional insight into the tumor growth dynamics. 

Dataset discovery from data lakes is essential in many real application scenarios. In this paper, we propose Starmie, an end-to-end framework for dataset discovery from data lakes (with table union search as the main use case). Our proposed framework features a contrastive learning method to train column encoders from pre-trained language models in a fully unsupervised manner. The column encoder of Starmie captures the rich contextual semantic information within tables by leveraging a contrastive multi-column pre-training strategy. We utilize the cosine similarity between column embedding vectors as the column unionability score and propose a filter-and-verification framework that allows exploring a variety of design choices to compute the unionability score between two tables accordingly. Empirical results on real table benchmarks show that Starmie outperforms the best-known solutions in the effectiveness of table union search by 6.8 in MAP and recall. Moreover, Starmie is the first to employ the HNSW (Hierarchical Navigable Small World) index to accelerate query processing of table union search which provides a 3,000X performance gain over the linear scan baseline and a 400X performance gain over an LSH index (the state-of-the-art solution for data lake indexing). 

Complex systems can exhibit sudden transitions or regime shifts from one stable state to another, typically referred to as critical transitions. It becomes a great challenge to identify a robust warning sufficiently early that action can be taken to avert a regime shift. We employ landscape-flux theory from nonequilibrium statistical mechanics as a general framework to quantify the global stability of ecological systems and provide warning signals for critical transitions. We quantify the average flux as the nonequilibrium driving force and the dynamical origin of the nonequilibrium transition while the entropy production rate as the nonequilibrium thermodynamic cost and thermodynamic origin of the nonequilibrium transition. Average flux, entropy production, nonequilibrium free energy, and time irreversibility quantified by the difference in cross-correlation functions forward and backward in time can serve as early warning signals for critical transitions much earlier than other conventional predictors. We utilize a classical shallow lake model as an exemplar for our early warning prediction. Our proposed method is general and can be readily applied to assess the resilience of many other ecological systems. The early warning signals proposed here can potentially predict critical transitions earlier than established methods and perhaps even sufficiently early to avert catastrophic shifts.