GLBRC Data Sets
Highlighted below are a variety of published studies that include data sets that might be of interest to the scientific community and have been deposited in online data repositories. Only data sets published in GLBRC-approved repositories following the FAIR Guiding Principles are highlighted. More information can be found on our guidelines page.
GLBRC Sustainability Data Catalog
This Data Catalog is a collection of data from GLBRC's Sustainability research carried out in Michigan and Wisconsin. The Data Catalog summarizes each data table in order to allow the GLBRC community to better understand the data that have been collected and encourage collaboration.
Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway
Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains.
Metagenomes and metagenome-assembled genomes from microbial communities fermenting ultrafiltered milk permeate
Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs).
Exploring the meta-regulon of the CRP/FNR family of global transcriptional regulators in a partial-nitritation anammox microbiome
We defined the meta-regulon of a PNA microbiome by combining existing knowledge of how the CRP/FNR family of bacterial TFs respond to stimuli, with metatranscriptomic analyses to characterize gene expression changes during aeration cycles.
Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms
In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts.
Metagenomes from 25 low-abundance microbes in a partial nitritation anammox microbiome
Microbial communities using anammox bacteria to remove nitrogen are increasingly important in wastewater treatment. We report on 25 metagenome-assembled genomes of low-abundance microbes from a partial nitritation anammox bioreactor system that have not been described previously. These data add to the body of information about this important wastewater treatment system.
Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars
We used a common garden experiment to investigate variation in 12 mature switchgrass cultivar soil microbiomes and, furthermore, to examine how root traits and soil conditions influence microbiome structure. We found that average root diameter varied up to 33% among cultivars and that the cultivars also associated with distinct soil microbiomes.
An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function
Examination of the phenotypic impact of network perturbation using deletion mutant data from the baker’s yeast Saccharomyces cerevisiae, which were obtained from previously published studies, suggests that fitness in diverse environments is affected by orthologous gene neighborhood and connectivity.
Soil origin and plant genotype modulate switchgrass aboveground productivity and root microbiome assembly
This study aims to fill important knowledge gaps and to serve as a foundation for switchgrass biomass promotion through microbe selection with an ultimate goal of facilitating sustainable bioenergy crop production.
Transcriptional competition shapes proteotoxic ER stress resolution
Here, we identified the abscisic acid-related regulator G-class bZIP TF2 (GBF2) and the cis-regulatory element G-box as regulatory components of the plant UPR led by the mTFs, bZIP28 and bZIP60.
Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans
In this work, we built a genome-scale metabolic model of N. aromaticivorans, iNovo479, to guide the engineering of strains for aromatic conversion into products. iNovo479 predicted product yields from single or multiple aromatics, and the impact of combinations of aromatic and non-aromatic substrates on product yields.
Land-based climate solutions for the United States
We detail a simplified scenario for the United States that illustrates the benefits of combining approaches. We assign a portion of non-forested former cropland to bioenergy sufficient to meet projected mid-century transportation needs, with the remainder assigned to nature-based solutions such as reforestation.
Identification and characterization of a set of monocot BAHD monolignol transferases
We identified putative FMT and PMT enzymes in sorghum (Sorghum bicolor) and switchgrass (Panicum virgatum) and have compared their activities to those of known monolignol transferases. The putative FMT enzymes produced both monolignol ferulate and monolignol p-coumarate conjugates, whereas the putative PMT enzymes produced monolignol p-coumarate conjugates.
Rapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM)
To achieve rapid and high-throughput targeted methods, here we show that nLC separations can be eliminated and replaced with direct infusion shotgun proteome analysis (DISPA) using high-field asymmetric waveform ion mobility spectrometry (FAIMS) with PRM.
Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway
Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway.
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds
In this study, we developed a reliable high-throughput (HT) platform for yeast morphological profiling using drug-hypersensitive strains to minimize compound use, HT microscopy to speed up data generation and analysis, and a generalized linear model to predict targets with high reliability.
Environmental outcomes of the US Renewable Fuel Standard
Biofuels are included in many proposed strategies to reduce anthropogenic greenhouse gas emissions and limit the magnitude of global warming. The US Renewable Fuel Standard is the world’s largest existing biofuel program, yet despite its prominence, there has been limited empirical assessment of the program’s environmental outcomes.
Soils of the GLBRC Marginal Land Expeirment (MLE) Sites
The Great Lakes Bioenergy Research Center (GLBRC) Marginal Land Experiment (MLE) was established in 2013 at various sites in Wisconsin and Michigan to evaluate the potential use of low productivity or abandoned agricultural fields for low input bioenergy feedstocks.
Boosting climate change mitigation potential of perennial lignocellulosic crops grown on marginal lands
Here, we show the potential GHG mitigation of fertilizing switchgrass (Panicum virgatum) at the NF rate that minimizes net GHG emissions across 7.1 million ha of marginal lands in the Midwest US, with long-term production advantages surpassing emitted GHG by 0.66 Mg CO2e ha−1 yr−1 on the aggregate.
Modeling temporal and hormonal regulation of plant transcriptional response to wounding
Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation.
