bioRxiv Science⌕ Search

Biology subjects

Guđmundsson, S.

Publications and source records attributed to Guđmundsson, S..

2 recordsLinked to original sources

Convolutional-LSTM Approach for Temporal Catch Hotspots (CATCH): An AI-Driven Model for Spatiotemporal Forecasting of Fisheries Catch Probability Densities

Efficient fisheries management is crucial for sustaining both marine ecosystems and the economies that heavily depend on them, such as Iceland. Current fishing practices involve decisions informed by a combination of personal experience, current data on environmental and oceanographic conditions, reports from other captains, and target species within the constraints of the fishing quota. However, the intricate spatiotemporal dynamics of fish behaviour make it difficult to predict fish stock distributions. Despite technological breakthroughs in fishing vessel data collection, much of the decision-making still relies heavily on subjective judgment, highlighting the need for more robust, data-driven predictive methods. This paper presents CATCH, a convolutional long short-term memory neural network model that forecasts fish stock probability densities over time and space in Icelandic waters. The framework represents the first utilization of large-scale Icelandic fishing fleet data integrating multidimensional inputs like depth, bottom temperature, and catch data to produce accurate, multivariate forecasts. The model demonstrates high accuracy, low error metrics, and strong structural similarity to observed data, generalizing well across key species such as Atlantic cod, haddock, saithe, golden redfish, and Greenland halibut. Its promising results suggest deep learning models have the potential to optimize fisheries operations, enhance sustainability, and support data-driven decision-making.

bioinformatics↗

A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

BackgroundLactobacillus reuteri is a heterofermentative Lactic Acid Bacterium (LAB) that is commonly used for food fermentations and probiotic purposes. Due to its robust properties, it is also increasingly considered for use as a cell factory. It produces several industrially important compounds such as 1,3-propanediol and reuterin natively, but for cell factory purposes, developing improved strategies for engineering and fermentation optimization is crucial. Genome-scale metabolic models can be highly beneficial in guiding rational metabolic engineering. Reconstructing a reliable and a quantitatively accurate metabolic model requires extensive manual curation and incorporation of experimental data.\n\nResultsA genome-scale metabolic model of L. reuteri JCM 1112T was reconstructed and the resulting model, Lreuteri_530, was validated and tested with experimental data. Several knowledge gaps in the metabolism were identified and resolved during this process, including presence/absence of glycolytic genes. Flux distribution between the two glycolytic pathways, the phosphoketolase and Embden-Meyerhof-Parnas pathways, varies considerably between LAB species and strains. As these pathways result in different energy yields, it is important to include strain-specific utilization of these pathways in the model. We determined experimentally that the Embden-Meyerhof-Parnas pathway carried at most 7% of the total glycolytic flux. Predicted growth rates from Lreuteri_530 were in good agreement with experimentally determined values. To further validate the prediction accuracy of Lreuteri_530, the predicted effects of glycerol addition and adhE gene knock-out, which results in impaired ethanol production, were compared to in vivo data. Examination of both growth rates and uptake- and secretion rates of the main metabolites in central metabolism demonstrated that the model was able to accurately predict the experimentally observed effects. Lastly, the potential of L. reuteri as a cell factory was investigated, resulting in a number of general metabolic engineering strategies.\n\nConclusionWe have constructed a manually curated genome-scale metabolic model of L. reuteri JCM 1112T that has been experimentally parameterized and validated and can accurately predict metabolic behavior of this important platform cell factory.

systems biology↗