Ryan McClure
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View article: Community Dynamics Drive Calcium Carbonate Production in an Enriched Consortium of Soil Microbes
Community Dynamics Drive Calcium Carbonate Production in an Enriched Consortium of Soil Microbes Open
Recently, there has been a focus on using soil microbes as a means to store carbon in the soil in the form of calcium carbonate, outcomes of which include soil stabilization and biocementation. The molecular processes involved in microbial…
View article: Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish
Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish Open
Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studie…
View article: Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil
Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil Open
Soil microorganisms interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat have posed a challenge to elucidating such i…
View article: Describing the Persistence Landscape for Introducing Microbes into Complex Communities
Describing the Persistence Landscape for Introducing Microbes into Complex Communities Open
The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the …
View article: Gut microbiome changes with micronutrient supplementation in children with attention–deficit/hyperactivity disorder: the MADDY study
Gut microbiome changes with micronutrient supplementation in children with attention–deficit/hyperactivity disorder: the MADDY study Open
Micronutrients have demonstrated promise in managing inattention and emotional dysregulation in children with attention-deficit/hyperactivity disorder (ADHD). One plausible pathway by which micronutrients improve symptoms is the gut microb…
View article: pnnl-predictive-phenomics/csc009cyc
pnnl-predictive-phenomics/csc009cyc Open
Using the genome annotation as input, Pathway-tools generates a database containing all the information that can be inferred from the genome. The Pathway/Genome database (PGDB) can subsequently be curated manually. Licensed under the CC-BY…
View article: EVT 16s Data and Large Supplementary Files
EVT 16s Data and Large Supplementary Files Open
Soil microorganisms often interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat has posed a challenge to elucidating s…
View article: pnnl-predictive-phenomics/csc052cyc
pnnl-predictive-phenomics/csc052cyc Open
Using the genome annotation as input, Pathway-tools generates a database containing all the information that can be inferred from the genome. The Pathway/Genome database (PGDB) can subsequently be curated manually Licensed under the CC-BY-…
View article: pnnl-predictive-phenomics/csc040cyc
pnnl-predictive-phenomics/csc040cyc Open
Using the genome annotation as input, Pathway-tools generates a database containing all the information that can be inferred from the genome. The Pathway/Genome database (PGDB) can subsequently be curated manually
View article: pnnl-predictive-phenomics/csc043cyc
pnnl-predictive-phenomics/csc043cyc Open
Organism-specific Pathway/Genome databases enable the analysis, visualization and interrogation of metabolism, regulation, and genetics. Licensed under the CC-BY-4.0 license
View article: Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities
Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities Open
Ensuring the efficient engineering of microbially induced calcium carbonate precipitation (MICP) is crucial for a variety of environmental and civil engineering applications, such as soil stabilization and carbon sequestration. Addressing …
View article: Diverse PFAS produce unique transcriptomic changes linked to developmental toxicity in zebrafish
Diverse PFAS produce unique transcriptomic changes linked to developmental toxicity in zebrafish Open
Per- and polyfluoroalkyl substances (PFAS) are a widespread and persistent class of contaminants posing significant environmental and human health concerns. Comprehensive understanding of the modes of action underlying toxicity among struc…
View article: Genomic fingerprints of the world’s soil ecosystems
Genomic fingerprints of the world’s soil ecosystems Open
Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate ch…
View article: Molecular-Level Dysregulation of Insulin Pathways and Inflammatory Processes in Peripheral Blood Mononuclear Cells by Circadian Misalignment
Molecular-Level Dysregulation of Insulin Pathways and Inflammatory Processes in Peripheral Blood Mononuclear Cells by Circadian Misalignment Open
Circadian misalignment due to night work has been associated with an elevated risk for chronic diseases. We investigated the effects of circadian misalignment using shotgun protein profiling of peripheral blood mononuclear cells taken from…