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.
Modeled surface-atmosphere fluxes from paired sites in the Upper Great Lakes Region using neural networks
Here we use a long-term record of carbon cycling from six paired sites plus a seventh reference site that are all spatially close to each other, with an average of ∼11 km separation. The goal is to use field observations from one of the paired sites, along with observations from the second site that can be measured easily, in order to estimate carbon cycling at the second site using artificial intelligence methods.
Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics
Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.
Hanseniaspora smithiae sp. nov., a novel apiculate yeast species from Patagonian forests that lacks the typical genomic domestication signatures for fermentative environments
During a survey of Nothofagus trees and their parasitic fungi in Andean Patagonia (Argentina), genetically distinct strains of Hanseniaspora were obtained from the sugar-containing stromata of parasitic Cyttaria spp.
Contributions of environmental and maternal transmission to the assembly of leaf fungal endophyte communities
We used amplicon sequencing to track switchgrass (Panicum virgatum) LFEs in a greenhouse and field experiment as communities assembled from seed endophytes and rain fungi (integration of wet and dry aerial dispersal) in germinating seeds, seedlings, and adult plants.
Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories
Here, we measured fitness costs of over 4000 overexpressed genes in 15 Saccharomyces cerevisiae strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE).
Relevance of the unfolded protein response to spaceflight-induced transcriptional reprogramming in Arabidopsis
To contribute to the understanding of how plants respond to spaceflight stress, we examined the significance of the unfolded protein response (UPR), a conserved signaling cascade that responds to a number of unfavorable environmental stresses, in the model plant Arabidopsis thaliana.
QTL x environment interactions underlie ionome divergence in switchgrass
We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens.
A facile spectroscopic method for measuring lignin content in lignocellulosic biomass
A facile spectroscopic method, our CASA (Cysteine-Assisted Sulfuric Acid) method, was developed to quantify the lignin content of lignocellulosic biomass, based on an extraordinary system in which biomass samples are fully dissolved in 72% H2SO4 containing cysteine at 24 °C in 60 min.
A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1
Here, we describe the isolation of an exceptional lignocellulose-degrading fungus that produces new oxidase activity with no cofactor requirements.
Genome-resolved metagenomics of a photosynthetic bioreactor performing biological nutrient removal
We present a genome-resolved metagenomics data set consisting of 86 metagenome-assembled genome sequences from a photosynthetically operated lab-scale bioreactor simulating EBPR.
Efficient synthesis of pinoresinol, an important lignin dimeric model compound
The synthetic yield and isolation efficiency of racemic pinoresinol from coniferyl alcohol by conventional radical coupling methods is sub-optimal. In this work, a facile and efficient synthetic approach was developed to synthesize pinoresinol with much higher yield.
Predictive models of genetic redundancy in Arabidopsis thaliana
Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties.
A genome-scale phylogeny of the kingdom Fungi
To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages.
Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples
By carrying out a phylogenomic analysis of 77 isolates, we find that C. tropicalis genomes range from very homozygous to highly heterozygous. We show that the heterozygous isolates are hybrids, most likely formed by mating between different parents.
Accuracy, Bias, and Improvements in Mapping Crops and Cropland across the United States Using the USDA Cropland Data Layer
We used state- and land cover class-specific accuracy statistics from the USDA from 2008 to 2016 to comprehensively characterize the performance of the CDL across space and time. We estimated nationwide area-weighted accuracies for the CDL for specific crops as well as for the aggregated classes of cropland and non-cropland.
Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops
Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus).
Quantifying and correcting for pre-assay CO2 loss in short-term carbon mineralization assays
Soils can lose carbon (C) as they dry and, if soil samples vary in moisture content at sampling, differential C loss during the pre-assay dry-down period may complicate the assay’s interpretations. We examined the impact of pre-assay CO2 loss in a long-cultivated agricultural soil at initial moisture contents of 30 %, 50 %, and 70 % water-filled pore space (WFPS).
Eudicot Nutshells: Cell-Wall Composition and Biofuel Feedstock Potential
In the context of understanding the general character of phylogenetically diverse eudicot species, we provide a chemical analysis of the lignin in the shells of commonly eaten nuts and detail the chemical composition of their lignins.
A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR
We performed a large-scale systems-level analysis of the protein-DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high-throughput enhanced yeast one-hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR.
