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Comparative uptake, translocation, and plant mediated transport of Tc-99, Cs-133, Np-237, and U-238 in Savannah River Site soil columns for the grass species Andropogon virginicus
Here, this study examines the ability of the grass species Andropogon virginicus to alter the subsurface transport and redistribution of a suite of radionuclides ( 99 Tc, 133 Cs (stable analog for 135 Cs and 137 Cs), 237 Np, 238 U) with varying chemical behaviors in a Savannah River Site soil via the use of vegetated and unvegetated soil columns. After an acclimation period, a small volume of solution containing all radionuclides was introduced into the columns via Rhizon© pore water sampling tubes. Plants were grown for an additional 4 weeks before shoots were harvested, and columns were prepared for sampling. Plant presence led to decreased radionuclide release from the columns, mainly due to radionuclide specific combinations of system hydrology differences resulting from plant transpiration as well as plant uptake. For the most mobile radionuclides, 99 Tc followed by 237 Np, plant presence resulted in significantly different soil concentration profiles between vegetated and unvegetated columns, including notable upward migration for 237 Np in columns with plants. Additionally, plant uptake of 99 Tc was the greatest of all the radionuclides, with plant tissues containing an average of 44 % of the 99 Tc, while plant uptake only accounted for <2 % of 237 Np and <0.5 % of 133 Cs and 238 U in the system. Although overall plant uptake of 133 Cs and 238 U were similar, the majority of 133 Cs taken up by plants was associated with 133 Cs already available in the aqueous phase while 238 U uptake was mainly associated with the solid phase, meaning that plant activity resulted in a fraction of the native 238 U being mobilized and thus, made available for plant uptake. Overall, this study quantified the influence of several plant-mediated physical and biogeochemical factors that have significant influence on radionuclide mobility and transport in this complex system which can be further utilized in future system or site-specific environmental transport and risk assessment models.
A proteomic meta-analysis refinement of plasma extracellular vesicles
Extracellular vesicles play major roles in cell-to-cell communication and are excellent biomarker candidates. However, studying plasma extracellular vesicles is challenging due to contaminants. Here, we performed a proteomics meta-analysis of public data to refine the plasma EV composition by separating EV proteins and contaminants into different clusters. We obtained two clusters with a total of 1717 proteins that were depleted of known contaminants and enriched in EV markers with independently validated 71% true-positive. These clusters had 133 clusters of differentiation (CD) antigens and were enriched with proteins from cell-to-cell communication and signaling. We compared our data with the proteins deposited in PeptideAtlas, making our refined EV protein list a resource for mechanistic and biomarker studies. As a use case example for this resource, we validated the type 1 diabetes biomarker proplatelet basic protein in EVs and showed that it regulates apoptosis of β cells and macrophages, two key players in the disease development. Our approach provides a refinement of the EV composition and a resource for the scientific community.
Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins
A challenge for design of protein–small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.
Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients
Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25–50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.
Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.
Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes
Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.
Plant Growth Study: Growth of Three Plant Species in 100-OL-1 Operable Unit Soils
Soil contamination from historical application of lead arsenate pesticides persists in the 100-OL-1 Operable Unit (OU) of the U.S. Department of Energy’s Hanford Site in Benton County, Washington. A remedial investigation used a portable X-ray fluorescence analyzer to estimate and map the concentrations of metals in surface soil in the 133 decision units comprising the OU. There is variability in lead and arsenic concentrations among the non-contiguous decision units, and an incomplete understanding of the ecological and human risks from soil contamination. While general screening criteria for lead are reported in literature, limited information is available on the impacts of heavy metals on site-specific plant and animal life. To address this information gap, a study on plant growth in Hanford soils was conducted using native bluegrass (Poa secunda), invasive cheatgrass (Bromus tectorum), and buttercrunch lettuce (Lactuca sativa). The latter is included because it is a common species used in plant growth studies. Soil samples were collected from a single general location within the 100-OL-1 OU, prepared, and categorized as having low, medium, or high concentrations of lead and arsenic, with the high concentration soil having concentrations of up to 3,400 and 790 mg/kg lead and arsenic, respectively. Additionally, a synthetic soil was prepared and used as a control, in accordance with standard plant growth protocols. Fifty-four seeds of each plant species were planted in each of the four soil types following the procedure outlined by the Washington State Department of Ecology. Germination rates and biomass measurements were recorded for 20 days. Both bluegrass and lettuce germination rates appeared to be reduced at the highest lead and arsenic concentrations (Pb: 3400 mg/kg, As: 790 mg/kg), while cheatgrass germination rates were unaffected. Total biomass for all species appeared to be related to the relative concentrations of lead and arsenic in the soil. Results of this growth study agree reasonably well with previous Hanford Site plant growth studies and provide additional data for assessing ecological risk at the Hanford Site.
The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment
Plant adaptation to terrestrial life started 450 million years ago and has played a major role in the evolution of life on Earth. The genetic mechanisms allowing this adaptation to a diversity of terrestrial constraints have been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome-environment association study and a pangenome. We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants. We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration
Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.