Functional annotation of proteins for signaling network inference in non-model species.

Molecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence. We annotate kinases and phosphatases in Glycine max. We use the functional annotations from our neural network, Bayesian inference principles, and high resolution phosphoproteomics to infer phosphorylation signaling cascades in soybean exposed to cold, and identify Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature regulators. Importantly, the signaling cascade inference does not rely upon known kinase motifs or interaction data, enabling de novo identification of kinase-substrate interactions. Conclusively, our neural network shows generalization and scalability, as such we extend our predictions to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum. Taken together, we develop a signaling inference approach for non-model species leveraging our predicted kinases and phosphatases.

Dryland irrigation increases accumulation rates of pedogenic carbonate and releases soil abiotic CO2.

Agricultural fields in drylands are challenged globally by limited freshwater resources for irrigation and also by elevated soil salinity and sodicity. It is well known that pedogenic carbonate is less soluble than evaporate salts and commonly forms in natural drylands. However, few studies have evaluated how irrigation loads dissolved calcium and bicarbonate to agricultural fields, accelerating formation rates of secondary calcite and simultaneously releasing abiotic CO2 to the atmosphere. This study reports one of the first geochemical and isotopic studies of such "anthropogenic" pedogenic carbonates and CO2 from irrigated drylands of southwestern United States. A pecan orchard and an alfalfa field, where flood-irrigation using the Rio Grande river is a common practice, were compared to a nearby natural dryland site. Strontium and carbon isotope ratios show that bulk pedogenic carbonates in irrigated soils at the pecan orchard primarily formed due to flood-irrigation, and that approximately 20-50% of soil CO2 in these irrigated soils is calcite-derived abiotic CO2 instead of soil-respired or atmospheric origins. Multiple variables that control the salt buildup in this region are identified and impact the crop production and soil sustainability regionally and globally. Irrigation intensity and water chemistry (irrigation water quantity and quality) dictate salt loading, and soil texture governs water infiltration and salt leaching. In the study area, agricultural soils have accumulated up to 10 wt% of calcite after just about 100 years of cultivation. These rates will likely increase in the future due to the combined effects of climate variability (reduced rainfall and more intense evaporation), use of more brackish groundwater for irrigation, and reduced porosity in soils. The enhanced accumulation rates of pedogenic carbonate are accompanied by release of large amounts of abiotic CO2 from irrigated drylands to atmosphere. Extensive field studies and modelling approaches are needed to further quantify these effluxes at local, regional and global scales.