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Stewart, R. D.

Publications and source records attributed to Stewart, R. D..

7 recordsLinked to original sources

Harnessing artificial intelligence to automate environmental predictions

Predicting heterogeneous and non-linear processes remains a fundamental challenge in Earth sciences. Here, we present an artificial intelligence (AI)-guided framework that iteratively combines predictive modeling with targeted field sampling to rapidly improve environmental predictions. We demonstrate our workflow by predicting oxygen consumption, a key process of stream metabolism, across the contiguous United States (CONUS). Our approach consisted of 18 iterative loops of measurements and models, combining distributed participatory field sampling, lab analysis, automated machine learning (ML) predictions, and error and distinctiveness analyses to autonomously guide the next sampling at optimal site locations. Through our approach, we increased the predictive power of sediment oxygen consumption across CONUS by over fifteenfold between the first and last iteration. Relative to our last sampling iteration, our first sampling missed sites with high rates and underestimated median oxygen consumption rates by 68%. In addition to identifying areas of high oxygen consumption rates, iterations enabled refinement of laboratory and data handling methods, and engagement with a broad community of field researchers. We conclude that AI-guided iterative loops between targeted sampling and predictive modeling are a powerful and efficient approach for improving predictions of heterogeneous environmental processes.

ecology↗

Leveraging machine learning and citizen science data to describe flowering phenology across South Africa

O_LIPhenology -- the timing of recurring life history events--is strongly linked to climate. Shifts in phenology have important implications for trophic interactions, ecosystem functioning and community ecology. However, data on plant phenology can be time consuming to collect and current records are biased across space and taxonomy. C_LIO_LIHere, we explore the performance of Convolutional Neural Networks (CNN) for classifying flowering phenology on a very large and taxonomically diverse dataset of citizen science images. We analyse >1.8 million iNaturalist records for plants listed in the National Botanical Gardens within South Africa, a country famed for its floristic diversity ([~]21,000 species) but poorly represented in phenological databases. C_LIO_LIWe were able to correctly classify images with >90% accuracy. Using metadata associated with each image, we then reconstructed the timing of peak flower production and length of the flowering season for the 6,986 species with >5 iNaturalist records. C_LIO_LIOur analysis illustrates how machine learning tools can leverage the vast wealth of citizen science biodiversity data to describe large-scale phenological dynamics. We suggest such approaches may be particularly valuable where data on plant phenology is currently lacking. C_LI

ecology↗

Refinement of the "Candidatus Accumulibacter" Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration

Members of the "Candidatus Accumulibacter" genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 "Ca. Accumulibacter" species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most "Ca. Accumulibacter" MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the "Ca. Accumulibacter" diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium and high-quality MAGs for 5 of the 18 "Ca. Accumulibacter" species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized "Ca. Accumulibacter" species for which we propose the new species designation "Ca. Accumulibacter jenkinsii" sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, "Ca. A. necessarius" and "Ca. A. propinquus" accounted for more than 40% of the "Ca. Accumulibacter" community, whereas the newly proposed "Ca. A. jenkinsii" accounted for about 5% of the "Ca. Accumulibacter" community. IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the "Candidatus Accumulibacter" genus in pilot-scale plants operating with minimal aeration. We identified the "Ca. Accumulibacter" species enriched under these conditions, including one novel species for which we propose "Ca. Accumulibacter jenkinsii" sp. nov. as its designation. Furthermore, the MAGs obtained for 5 additional "Ca. Accumulibacter" species further refine the phylogeny of the "Ca. Accumulibacter" genus and provide new insight into its diversity within unconventional biological nutrient removal systems.

microbiology↗

Differential effects of high versus low linear energy transfer (LET) radiation on type-I interferon (IFNβ) and TREX1 responses

PurposeCancer cells produce innate immune signals following radiation damage, with STING pathway signaling as a critical mediator. High linear energy transfer (LET) radiations create larger numbers of DNA double-strand breaks (DSBs) per unit dose than low-LET radiations and may therefore be more immunogenic. We studied the dose response characteristics of pro-immunogenic type-I interferon, interferon-beta (IFN{beta}), and its reported suppressor signal, three-prime repair exonuclease 1 (TREX1), in vitro with low-LET x-rays and high-LET fast neutrons. MethodsMerkel cell carcinoma cells (MCC) were irradiated by graded doses of x-rays (1-24 Gy) or fast neutrons (1-8 Gy). IFN{beta} was measured as a function of dose via ELISA assay, and exonuclease TREX1 expression via immunofluorescence microscopy. The Monte Carlo damage simulation (MCDS) was used to model fast neutron relative biological effectiveness for DSB induction (RBEDSB) and compared to laboratory measurements of the RBE for IFN{beta} production (RBEIFN{beta}) and TREX1 upregulation (RBETREX1). RBEIFN{beta} models were also applied to radiation transport simulations to quantify the potential secretion of IFN{beta} in representative clinical beams. ResultsPeak IFN{beta} secretion occurred at 5.7 Gy for fast neutrons and at 14.0 Gy for x-rays, i.e., an effective RBEIFN{beta} of 2.5 {+/-} 0.2. The amplitude (peak value) of secreted IFN{beta} signal did not significantly differ between x-rays and fast neutrons (P > 0.05). TREX1 signal increased linearly with absorbed dose, with a four-fold higher upregulation per unit dose for fast neutrons relative to x-rays (RBETREX1 of 4.0 {+/-} 0.1). Monte Carlo modeling of IFN{beta} suggests Bragg peak-to-entrance ratios of IFN{beta} production of 40, 100, and 120 for proton, alpha, and carbon ion beams, respectively, a factor of 10-20-fold higher compared to their corresponding physical dose peak-to-entrance ratios. The spatial width of the Bragg peak for IFN{beta} production is also a factor of two smaller. ConclusionHigh-LET fast neutrons initiate a larger IFN{beta} response per unit absorbed dose than low-LET x-rays (i.e., RBEIFN{beta} value of 2.5). The RBE value for IFN{beta} is quite similar to data reported in the literature for DSB induction and cellular, post-irradiation micronucleation formation for neutrons and x-rays. The increased IFN{beta} release after high-LET radiation may be a contributing factor in stimulating a systemic anti-tumor, adaptive immune response (abscopal effect). However, our results indicate that TREX1 anti-inflammatory signaling in vitro for MCC cells is larger per unit dose for fast neutrons than for x-rays (RBETREX1 of 4.0). Given these competing effects, additional studies are needed to clarify whether or not high-LET radiations are therapeutically advantageous over low-LET radiation for pro-inflammatory immune signaling in other cell lines in vitro and for in vivo cancer models.

cancer biology↗

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short chain fatty acids, nitrogen recycling and amino acid production. In this study we sequenced DNA from caecal contents samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. We utilised 1.6T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species and 42 novel genera. We compared our genomes to data from eight EU countries and show that these genomes are abundant within European chicken flocks. We also compared the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

microbiology↗

The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics

Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialised stomach adapted to the breakdown of plant-derived complex polysaccharides, and collectively the rumen microbiota encode the thousands of enzymes responsible. Here we present a comprehensive analysis of over 6.5 terabytes of Illumina and Nanopore sequence data, including assembly of 4941 metagenome-assembled genomes, and several single-contig, whole-chromosome assemblies of novel rumen bacteria. We also present the largest dataset of predicted proteins from the rumen, and provide rich annotation against public datasets. Together these data will form an essential part of future studies of rumen microbiome structure and function.

microbiology↗

Open prediction of polysaccharide utilisation loci (PUL) in 5414 public Bacteroidetes genomes using PULpy

Polysaccharide utilisation loci (PUL) are regions within bacterial genomes that encode all the necessary machinery for the cleavage of particular carbohydrates. For the Bacteroidetes phylum, prediction of PUL from genomic data alone involves the identification of carbohydrate-active enzymes (CAZymes) co-localised with susCD gene pairs. Here we present the open prediction of PUL in 5414 public Bacteroidetes genomes, and an open-source pipeline to reproduce or extend the results.

microbiology↗