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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

4D structural changes and pore network model of biomass during pyrolysis

Biochar is an engineered carbon-rich substance used for soil improvement, environmental management, and other diverse applications. To date, the understanding of how biomass affects biochar microstructure has been limited due to the complexity of analysis involved in tracing the changes in the physical structure of biomass as it undergoes thermochemical conversion. In this study, we used synchrotron x-ray micro-tomography to visualize changes in the internal structure of biochar from diverse feedstock (miscanthus straw pellets, wheat straw pellets, oilseed rape straw pellets, and rice husk) during pyrolysis by collecting a sequence of 3D scans at 50 °C intervals during progressive heating from 50 °C to 800 °C. The results show a strong dependence of biochar porosity on feedstock as well as pyrolysis temperature, with observed porosity in the range of 7.41–60.56%. Our results show that the porosity, total surface area, pore volume, and equivalent diameter of the largest pore increases with increasing pyrolysis temperature up to about 550 °C. The most dramatic development of pore structure occurred in the temperature range of 350–450 °C. This understanding is pivotal for optimizing biochar’s properties for specific applications in soil improvement, environmental management, and beyond. By elucidating the nuanced variations in biochar’s physical characteristics across different production temperatures and feedstocks, this research advances the practical application of biochar, offering significant benefits in agricultural, environmental, and engineering contexts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2026

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 1. Evaluating Above- and Below-ground Controls of Flow Persistence in a Forested Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in a forested catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, ground penetrating radar (GPR), continuous self-potential (SP) monitoring, electromagnetic (EM) imaging, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Contains two subfolders: Synthetic and Field_Application subfolder. Synthetic subfolder contains the ATS XML input script (can be opened using any code editor) for the four synthetic hydrological cases tested (Connected and gaining, Connected and losing, Disconnected and losing, and dry stream). It also includes other experimental cases to test the influence of precipitation and concentration gradient. For each synthetic case, the flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.mph can be opened with the commercial software COMSOL and requires a license) is executed using the ATS output data to simulate the potential field. It also includes the Synthetic_model_plot.ipynb (can be opened using any code editor) to visualize the SP result and generate manuscript figures. The data subfolder contains mesh files to run both the ATS (.exo and .stl files can be viewed using Paraview; .h5 files can be opened using HDFView software and h5py Python package) and COMSOL models. Field_Application subfolder contains two subfolders: ES_MDA_inversion and Final_Model. ES_MDA_inversion contains the Python script (.py can be opened using any code editor) and SP observation data used to run the Ensemble Smoother with Multiple Data Assimilation (ES-MDA) inversion sequence to get the optimal model parameters. The Final_model subfolder contains the ATS XML input scripts, data files, output data for the two SP sites. The same workflow steps outlined for the Synthetic subfolder apply here. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) EM Contains the CSV file of the EM data from the DUALEM-42, including spatial coordinates (x, y, z), apparent conductivity, and in-phase measurements at 2 m coil separations for horizontal coplanar (HCP) and perpendicular (PRP) geometries. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion (.resipy can be opened with the open-source ResIPy software). 6) GPR Includes GPR field datasets collected at 100 MHz and 250 MHz antenna frequencies, along with the processing/interpretation project file (GPR_process.gpz can be viewed using EKKO_Project 6, a commercial software by Sensors & Software that requires a license). 7) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 8) SP Contains the SP data collected in field at the two SP sites (one in the perennial reach and the other in the intermittent reach), provided as DAT files. 9) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). It also includes DTW.ipynb, a Jupyter notebook containing the code for the dynamic time warping (DTW) with sliding window to evaluate SP signal synchronicity.

ATS↗
DOE OSTI2022

Passive spiral galaxies deeply captured by Subaru Hyper Suprime-Cam

Abstract This paper presents a thousand passive spiral galaxy samples at z = 0.01–0.3 based on a combined analysis of the Third Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP PDR3) and the GALEX–SDSS–WISE Legacy Catalog (GSWLC-2). Among 54871 gri galaxy cutouts taken from the HSC-SSP PDR3 over 1072 deg2, we conducted a search with deep-learning morphological classification for candidates of passive spirals below the star-forming main sequence derived by ultraviolet to mid-infrared spectral energy distribution fitting in the GSWLC-2. We then classified the candidates into 1100 passive spirals and 1141 secondary samples based on visual inspections. Most of the latter cases are considered to be passive ringed S0 or pseudo-ringed galaxies. The remaining secondary samples have ambiguous morphologies, including two peculiar objects with diamond-shaped stellar wings. The selected passive spirals have a similar distribution to the general quiescent galaxies on the EWHδ–Dn4000 diagram and concentration indices. Moreover, we detected an enhanced passive fraction of spiral galaxies in X-ray clusters. Passive spirals in galaxy clusters are preferentially located in the midterm or late infall phase on the phase–space diagram, supporting the ram pressure scenario, which has been widely advocated in previous studies. The source catalog and gri-composite images are available on the HSC-SSP PDR3 website 〈https://hsc.mtk.nao.ac.jp/ssp/data-release/〉. Future updates, including integration with a citizen science project dedicated to the HSC data, will achieve more effective and comprehensive classifications.

Shimakawa, Rhythm (ORCID:0000000344422750)↗
DOE OSTI2018

Structure- and Physics-Preserving Reductions of Power Grid Models

The large size of multiscale, distribution and transmission, power grids hinders fast systemwide estimation and real-time control and optimization of operations. This paper studies graph reduction methods of power grids that are favorable for fast simulations and follow-up applications. While the classical Kron reduction has been successful in reduced order modeling of power grids with traditional, hierarchical design, the selection of reference nodes for the reduced model in a multiscale, distribution and transmission, network becomes ambiguous. In this work we extend the use of the iterative Kron reduction by utilizing the electric grid's graph topology for the selection of reference nodes, consistent with the design features of multiscale networks. Additionally, we propose further reductions by aggregation of coherent subnetworks of triangular meshes, based on the graph topology and network characteristics, in order to preserve currents and build another power-flow equivalent network. Our reductions are achieved through the use of iterative aggregation of subgraphs that include general tree structures, lines, and triangles. Important features of our reduction algorithms include that (i) the reductions are either equivalent to the Kron reduction or otherwise produce a power-flow equivalent network; (ii) due to the mentioned power-flow equivalence, the reduced network can model the dynamic of the swing equations for a lossless, inductive, steady state network; (iii) the algorithms efficiently utilize hash tables to store the sequential reduction steps. The third feature allows for easy reintroduction of detailed models into the reduced, conceptual network and makes the final reduced order model backward compatible with a sequence of intermediate, partially reduced networks with varying resolution---the ordered sequence of iterative reductions corresponds to a sequence of reduced order models. The performance of our graph reduction algorithms and features of the reduced grids are discussed on a real-word transmission and distribution grid. We produce visualizations of the reduced models through open source libraries and release our reduction algorithms with example code and toy data.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2019

From chiral anomaly to two-fluid hydrodynamics for electronic vortices

Highlights: • Chiral transformations with account for chiral anomaly were applied to the CDW model. • Two-fluid hydrodynamics was constructed of the order parameter and the normal liquid. • Topologically nontrivial dynamics appears under applied fields or charge injection. • Spontaneous spacetime vorticity under the driving current was modeled numerically. • Periodic sequence of amplitude nodes with 2π phase increments was demonstrated. - Abstract: Many recent experiments addressed manifestations of electronic crystals, particularly the charge density waves, in nano-junctions, under electric field effect, at high magnetic fields, together with real space visualizations by STM and micro X-ray diffraction. This activity returns the interest to stationary or transient states with static and dynamic topologically nontrivial configurations: electronic vortices as dislocations, instantons as phase slip centers, and ensembles of microscopic solitons. Describing and modeling these states and processes calls for an efficient phenomenological theory which should take into account the degenerate order parameter, various kinds of normal carriers and the electric field. Here we notice that the commonly employed time-depend Ginzburg–Landau approach suffers with violation of the charge conservation law resulting in unphysical generation of particles which is particularly strong for nucleating or moving electronic vortices. We present a consistent theory which exploits the chiral transformations taking into account the principle contribution of the fermionic chiral anomaly to the effective action. The resulting equations clarify partitions of charges, currents and rigidity among subsystems of the condensate and normal carriers. On this basis we perform the numerical modeling of a spontaneously generated coherent sequence of phase slips – the spacetime vortices – serving for the conversion among the injected normal current and the collective one.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

A Knowledge Graph Approach for the Secondary Use of Cancer Registry Data

Population-based central cancer registries collect valuable structured and unstructured data primarily for cancer surveillance and research, enhancing insights into clinical features associated with cancer occurrence, cancer treatment, and cancer outcomes to guide interventions which reduce the cancer burden. Cancer registries primarily collect data on (1) cancer type (case or tumor); (2) patient demographics such as age, gender, and residential address at time of diagnosis; (3) planned first course of treatment; and (4) date of last contact, vital status, and cause of death. Cancer registry data is dynamic, structured data, which is extracted from many unstructured sources such as electronic healthcare records, and consolidated for reporting and other purposes. While available advanced analytic tools such as SEER*Stat have the ability to build SAS queries, we, however, explore an innovative knowledge graph approach to organizing cancer registry data for advanced analytics and visualization, which has unique advantages over approaches of existing tools. This innovative knowledge graph approach semantically enriches the data and easily enables linkage with third-party data, which can better explain variation in outcomes. We have developed a prototype knowledge graph based on data from the Louisiana Tumor Registry and other publicly available datasets including Behavioral Risk Factor Surveillance System, Clinical Trials, DBpedia, GeoNames, Rural-Urban Continuum Codes, and Semantic MEDLINE. The resource description framework (RDF) data model was selected to represent our knowledge graph, which contains more than 25 billion triples and is ~4TB in storage size. To exhibit the benefits of the knowledge graph approach, we used scenario specific queries, which find the relationships between cancer treatment sequences and outcomes. To illustrate its ease of use in iterative analysis, the knowledge graph was linked to external datasets for performing complex queries across multiple datasets. In addition, we used knowledge graphs to identify data discrepancies and to handle schema changes. Finally, we visualized the knowledge graph to discover data patterns. Our results demonstrate this graph-based solution enables cancer researchers to execute complex queries and more easily perform iterative analyses to improve understanding of cancer registry data. In the future, we would like to use high-performance computing (HPC) resources for faster-generating hypotheses with clinical potential from our knowledge graph.

Hasan, S M Shamimul↗
DOE OSTI2021

TX$^2$: Transformer eXplainability and eXploration

The Transformer eXplainability and eXploration (Martindale & Stewart, 2021), or TX 2 software package, is a library designed for artificial intelligence researchers to better understand the performance of transformer models (Vaswani et al., 2017) used for sequence classification. The tool is capable of integrating with a trained transformer model and a dataset split into training and testing populations to produce an ipywidget (Project Jupyter Contributors, 2021) dashboard with a number of visualizations to understand model performance with an emphasis on explainability and interpretability. The TX 2 package is primarily intended to integrate into a workflow centered around Jupyter Notebooks (Kluyver et al., 2016), and currently assumes the use of PyTorch (Paszke et al., 2019) and Hugging Face transformers library (Wolf et al., 2020). The dashboard includes visualization and data exploration features to aid researchers, including an interactive UMAP embedding graph (McInnes et al., 2018) to understand classification clusters, a word salience map that can be updated as researchers alter textual entries in near real time, a set of tools to understand word frequency and importance based on the clusters in the UMAP embedding graph, and a set of traditional confusion matrix analysis tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Event-modeled Risk Assessment Using Linked Diagrams

Event Modeling Risk Assessment using Linked Diagrams (EMRALD) is a software tool developed at INL for researching the capabilities of dynamic PRA (Probabilistic Risk Assessment). In order to promote the effective use of dynamic PRA by the general community, EMRALD focuses on the following key aspects: Simplifying the modeling process by providing a structure that corresponds to traditional PRA modeling methods Providing a user interface (UI) that makes it easy for the user to model and visualize complex interactions Allowing the user to couple with other analysis applications such as physics based simulations. This includes one-way communication for most applications and two-way loose coupling for customizable applications Providing the sequence and timing of events that lead to the specified outcomes when calculating results Traditional aspects of components with basic events, fault trees, and event trees are all captured in a dynamic framework of state diagrams, which are displayed.

Prescott, SteveR↗
DOE OSTI2023

CPViz: Visualizing clinical pathways represented in higher-order networks

To improve clinical care practice, it is important to understand the variability of clinical pathways executed in different contexts (e.g., pathways in different geographical locations, demographics, and phenotypic groups). A common way of representing clinical pathways is through network-based representations that capture trajectories of treatment steps. However, first-order networks, which are based on the Markovian property and the de facto standard model to represent transitions between steps, often fail to capture real trajectories. This paper introduces a visual analytic tool to explore and compare pathways represented in higher-order networks. Because each higher node in the network is a subtrajectory (i.e., partial or full history of treatment steps), the tool can display true sequences of treatment steps and compute the similarity of the two networks in a space of higher-order nodes. The tool also highlights areas in which the two networks are similar and dissimilar and how a certain subtrajectory is realized differently in different pathways. The paper demonstrates the tool's usefulness by applying it to multiple antidepressant pharmacotherapy pathways for veterans diagnosed with major depressive disorder and by illustrating heterogeneity in prescription patterns across pathways.

Chae, Junghoon↗
DOE OSTI2026

Hyporheic zone, river, and groundwater metagenome resolved genomes and rpS3 genes in East River Watershed, Colorado USA Summer 2020, 2021

Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from water filter collected across 8 locations along the East River Watershed, CO, and 1 nearby groundwater well. The purpose was to look for connectivity and similarities across the network and to see the impact of the groundwater. As a part of Lawrence Berkeley National Laboratory (LBNL) Watershed Science Focus Area (SFA), we assessed community composition and strain similarities between the sites and we also compared it to previous metagenomic studies within the watershed looking at floodplain (Matheus Carnevali et al. 2021) and hillslope (Lavy et al. 2019) microbiomes. Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from filters across 8 locations during August 2020 and July 2021. This resulted in 32 samples. The groundwater sample was sequenced at UC Berkley's QB3. The other 31 samples were sequenced at University of Maryland. Metagenomes were assembled using four autobinners and the best bins were selected using dasTool. The genomes were dereplicated at 95% with dRep and the subset of winning genomes were manually curated based on visual inspection of taxonomic profile, GC content, coverage, and a set of 51 bacterial single copy genes (BSCG), and 38 archaeal signal copy genes (ASCG). The dataset includes a zip file of 311 genomes (HZ_River_SW_MAGS_Dereplicated_95.zip). The dataset additionally includes a zipped file of ribosomal protein small subunit 3 (rpS3) proteins from the hyporheic zone and river data (rpS3_Proteins_HZ_River.zip), a metadata file used to register associated samples with IGSNs (International Generic Sample Numbers) (samples.csv), a location metadata file (locations.csv). This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

DNA↗
DOE OSTI2019

A Comprehensive Methodology to Evaluate Losses and Process Variations in Silicon Solar Cell Manufacturing

Novel, high-throughput metrology methods are used in this paper for detailed performance loss analysis of approximately 400 industrial crystalline silicon solar cells, all coming from the same production line. The characterization sequence combines traditional global cell measurements (e.g., current-voltage, Suns-VOC) with camera-based cell imaging of voltage distribution and power dissipation from photoluminescence and lock-in thermography, respectively. Spatial variations in current collection are visualized using a high-speed external quantum efficiency and reflectance measurement technique. A nondestructive transfer length method (TLM) measurement technique is also implemented, featuring circular TLM structures hidden within the busbars of the cells. The variance of individual loss parameters and their impact on cell performance are quantified for this large group of cells. Based on correlations performed across parameters, recombination losses in the bulk and rear surface of the cell are shown to be the primary limiting factor for the cell efficiency. The nature of these distributions and correlations provide important insights about loss mechanisms in industrial solar cells, helping to prioritize efforts for optimizing the performance of the production line. Additionally, many of the parameters extracted from these techniques can be tied back to incoming material quality issues (e.g., poor bulk carrier lifetime, nonuniform wafer doping) and to individual unit processes (e.g., texturing, phosphorus diffusion, silicon nitride deposition, metallization), allowing the data to be used directly for process control in manufacturing. All of the datasets are made available for download.

14 SOLAR ENERGY↗
DOE OSTI2024

HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies

Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

First Report and Molecular Variability of Belonolaimus longicaudatus Associated with Turfgrass in Maryland

Abstract Turfgrass is a crop used extensively in athletic fields and golf courses in Maryland. A soil sample collected in July 2023 from an athletic field in Baltimore County, Maryland, part of a turfgrass nematode survey, containedBelonolaimus longicaudatus. In the southeastern United States,B. longicaudatusis an economically important pathogen of warm season turfgrass. The density was four individuals/100 cm 3 of soil, and no visual symptoms were observed in the bermudagrass field. Morphological features and morphometrics of males and females were consistent withB. longicaudatusand placed the Maryland population in a subclade that was geographically represented by populations from north and west Florida, Texas, and South Carolina. Sequencing of the internal transcribed spacer region ITS1 and ITS2 and 28S large ribosomal subunit D2-23 expansion region confirmed the species' identity. Phylogenetic trees and parsimony network analysis placed the Maryland isolate in a large grouping ofB. longicaudatuspopulations including those from Alabama, Delaware, Florida, Indiana, Mississippi, South Carolina, and Texas. To our knowledge, this is the first report ofB. longicaudatusin Maryland.

Zoology↗
DOE OSTI2023

Comparative Genomics Using the Integrated Microbial Genomes and Microbiomes (IMG/M) System: A Deinococcus Use Case

The Integrated Microbial Genomes and Microbiomes (IMG/M) system is a web-based platform that provides access to the wealth of public sequence data arising from diverse environments and enables the user to answer biological questions. In this review, we explore IMG’s tools and features using genome data for genus Deinococcus isolates as well as metagenome-assembled genomes (MAGs). Here, we use various comparative genomic and visualization tools to investigate this genus and address specific research questions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

RCSB Protein Data Bank 1D tools and services

Abstract Motivation Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Results Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. Availabilityand implementation https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC

AbstractThe folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

Zhao, Yanyan (ORCID:0000000323021763)↗
DOE OSTI2024

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Abstract Background Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. Results Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. Conclusions We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

59 BASIC BIOLOGICAL SCIENCES↗