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...
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Project
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.
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Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and...
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"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...
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...
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Publication
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...
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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.
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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...
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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...
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Project
The research goal of this project is to build and understand model communities that show carbon storage phenotypes
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The research goal of this project is to develop computational methods to predict cell regulation phenotypes using small molecule and proteome data to understand outcomes in complex biological systems.
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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.
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The science objective of this project is to apply structural proteomics technologies to map the molecular interactome.
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The research objective of this project is to develop an integrative and automated multi-PTM profiling capability with deep proteome coverage.
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The research goal of this project is to use stimuli-specific, synthetic nanobodies to target functional mediators without prior knowledge of the response networks or manipulating the biological system.
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