Last updated on 2024-02-11T22:41:43+00:00 by LN Anderson Interferon Experiment IFNaCL001 The purpose of this experiment was to evaluate the host interferon-stimulated cellular response to interferon alpha (IFNα) treatment. Sample data was obtained from human lung adenocarcinoma cells (Calu-3)...
The data accompanies the manuscript that evaluates salinity-associated shifts in organic C thermodynamics, biochemical transformations, and heteroatom content in a first-order coastal watershed in the Olympic Peninsula of Washington state, USA. The files contain raw data including soil chemical...
Citation: Mejia-Rodriguez D, Kim H, Sadler N, Li X, Bohutskyi P, Valiev M, Qian WJ, Cheung MS. PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions. Protein Sci. 2023 Dec;32(12)...
Citation : Reichart NJ, Steiger AK, Van Fossen EM, McClure R, Overkleeft HS, Wright AT. Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing. ISME Commun. 2023 Sep 30;3(1):106. doi: 10.1038/s43705-023...
The research goal of this project is to establish model synthetic microbial communities to understand the rules regulating their biological function in order to utilize them as next generation bioproduction platforms capable of reducing carbon and nitrogen footprints in biomanufacturing processes.
The soil microbiome performs many functions that are key to ecology, agriculture, and nutrient cycling. However, because of the complexity of this ecosystem we do not know the molecular details of the interactions between microbial species that lead to these important functions. Here, we use a...
"Moisture modulates soil reservoirs of active DNA and RNA viruses" Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect...
Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil...
The research goal of this project is to develop new theory and tools that leverage evolutionary perspectives and knowledge of the energetics of reactions to predict the most likely regulation in a given environment. These methods will accelerate exploration, modeling and understanding of cell...
The research goal of this project is to identify and control host functions hijacked during viral infection through use of PNNL ‘omics technologies and modeling capabilities.
We are constructing a streamlined approach to identify phenotype-relevant signatures by integrating various proteomics data. Leveraging protein structures and interaction networks, we will map structural changes and post-translational modifications to identify molecular drivers and subsequently...
By developing explainable, predictive metabolic models of individual microbes, we aim to design consortia that convert light and abundant atmospheric gases into high-value molecules through microbial division of labor.
The research goal of this project is to develop a biologically informed machine learning (ML) model that integrates datasets from different studies, and leverages current biological knowledge in an automated manner, to improve predictions in biological data analysis.
