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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Plant-Enhanced Degradation Of Munitions by Engineered TERrestrial microbes (PEDOMETER) (Final Report)

LLNL led two major Technical Areas (TAs) within the PEDOMETER program: TA3 focused on biocontainment and TA4 focused on developing electrochemical TNT degradation sensors and testbeds. A key takeaway from our work is the importance of chassis host strain choice for kill switch design and actuator choice. Genetic instability of the kill switch circuit is a major barrier toward establishing a kill switch, which is host dependent. Addition of a host down-selection step to regulator and actuator screening stages would be beneficial to hasten kill switch development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Unraveling the Dynamics of Nucleosome Arrays

The organization of genomic DNA into chromatin is a fundamental determinant of genome stability, regulation, and cellular function. Nucleosomes, the basic repeating units of chromatin, assemble into higher-order structures whose organization and heterogeneity remain difficult to characterize using conventional ensemble-averaged techniques. A key need in the field is the development of experimental approaches capable of directly visualizing nucleosome assemblies and their structural variability at the single-molecule level. This LDRD Lab-Wide project focused on establishing and evaluating atomic force microscopy (AFM)–based approaches for the characterization of nucleosome assemblies. The work emphasized experimental workflows for preparing, imaging, and assessing multi-nucleosome systems, rather than isolated single nucleosomes. Through method development and exploratory measurements, the project demonstrated the feasibility of applying scanning probe microscopy to investigate chromatin-relevant assemblies and provided preliminary insight into the strengths and limitations of this approach for future quantitative studies. Results and lessons learned from this effort were disseminated to the broader scientific community through multiple national conference presentations, helping to position LLNL for continued work in chromatin and genome organization research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Host-Directed, Bioelectronic Immunomodulation for Protection Against Emerging Pathogens

Acute care of patients with severe infections often relies on systemic administration of pharmaceuticals and monitoring of complex physiological symptoms to identify immune system dysfunction, which can lead to increased mortality. Furthermore, determining disease-specific treatment plans often leads to a delay in patient care. To address this, we proposed an immune modulation system that electrically detects and responds to a patient’s immune system status, creating an agnostic means of treating illness and infection. Two pieces of hardware were developed for this task: a minimally-invasive sensor and a vagus nerve stimulator. Stimulation of the vagus nerve is known to modulate the immune system. The sensor is a microfabricated, silicon-based microneedle array capable of interfacing with interstitial fluid to detect small molecules such as inflammatory proteins (cytokines) and pharmaceuticals (vancomycin). Process optimization to manufacture the needles refined the silicon etch process, creating needle patches long enough to penetrate skin and reach interstitial fluid. The needles were tested for mechanical strength and stability, and did not shatter when inserted into skin models. The needles are coated with a thin film metal, turning them into electrodes for electrochemical sensing of our target molecules. We hybridized aptamers to the surface of the electrode to act as the sensing layer and were able to detect changes in the conformation of the aptamer electrochemically in the presence of the target molecule. The stimulator was a cuff electrode that encircled the vagus nerve. Rodent studies were conducted in which rodents were exposed to an inflammatory event and vagus nerve stimulation (VNS) was applied. It was demonstrated that optimized electrical stimulation of the vagus nerve created measurably different levels of cytokines in blood samples, and certain cytokines released during the inflammatory event were either upregulated or downregulated. In sum, this project successfully developed new platforms and technologies that can, with further development, enable better temporal insight into biomarker changes in the body, letting healthcare providers know of possible immune system dysfunction before they are detected physiologically. We also demonstrated the value of VNS and its possible use in treating immune system response to inflammation and illness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Protein engineering for critical metal recovery beyond REEs

Achieving decarbonization and electrification goals will require expanded production of critical minerals (CM), including Li, Co, Cu, rare earths, Ni, and graphite, whose supply chains are geopolitically vulnerable. Problematically, current extraction and separation processes pose severe environmental burdens that impede the development of a diversified domestic supply chain and undercut the environmental benefits of energy technologies [1, 2]. The development of efficient, economical, and environmentally sustainable processing technologies is thus important for meeting the CM demand of the emerging energy technology market. To this end, we have recently developed an all-aqueous protein-based process for rare earth element (REE) extraction and separation. To extend our protein-based approach to critical metals beyond REEs, the goal of this project was to develop a protein discovery and engineering pipeline to generate a panel of proteins that selectively bind target critical metals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Investigation of encapsulin nanocompartment systems as a scaffold for biomaterials synthesis in Rhodococcus species (Annual Report 2025)

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcus species. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., alkene, inorganic nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Inter-Kingdom Viral Interactions

Please cite as : Josué A. Rodríguez-Ramos, Amy E. Zimmerman, Ruonan Wu, Sheryl Bell, Trinidad Alfaro, Kirsten Hofmockel, William C. Nelson. 2025. Inter-Kingdom Viral Interactions. [Data Set] PNNL DataHub. This data is published under a CC0 license. The authors encourage data reuse and request attribution by referencing the above citations for the data package and associated manuscript. Deciphering viral ecology in soils is challenging due to their high physiochemical and community complexity. To enhance detection of sub-communities of DNA and RNA viruses, we applied fractionation approaches to soils collected across a moisture gradient from a grassland field experiment. Analyses included metagenomics and metatranscriptomics of size-fractionated extracellular viruses (i.e., DNA and RNA viromes), metagenomics of bacteria/archaea- or eukaryote-enriched samples, and whole soil metatranscriptomes with rRNA-depletion or polyadenylation enrichment. While RNA virome and whole soil RNA methods captured similar viral diversity, RNA viromes identified longer, higher-quality genomes. Further, we showed that significantly more DNA viruses were active in higher moisture than lower moisture samples, whereas responses by overall diversity vary by genome type (DNA versus RNA genomes). Finally, we demonstrate the power of fractionation approaches for identifying distinct viral communities that infect unique hosts, which has significant implications for ecological investigations, particularly related to interkingdom interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Large-scale prediction of outer-membrane multiheme cytochromes uncovers hidden diversity of electroactive bacteria and underlying pathways

Multi-heme cytochromes (MHCs), together with accessory proteins like porins and periplasmic cytochromes, enable microbes to transport electrons between the cytoplasmic membrane and extracellular substrates (e.g., minerals, electrodes, other cells). Extracellular electron transfer (EET) has been described in multiple systems; yet, the broad phylogenetic and mechanistic diversity of these pathways is less clear. One commonality in EET-capable systems is the involvement of MHCs, in the form of porin-cytochrome complexes, pili-like cytochrome polymers, and lipid-anchored extracellular cytochromes. Here, we put forth MHCscan—a software tool for identifying MHCs and identifying potential EET capability. Using MHCscan, we scanned ~60,000 bacterial and 2,000 archaeal assemblies, and identify a diversity of MHCs, many of which represent enzymes with no known function, and many found within organisms not previously known to be electroactive. In total, our scan identified ~1,400 unique enzymes, each encoding more than 10 heme-binding motifs. In our analysis, we also find evidence for modularity and flexibility in MHC-dependent EET pathways, and suggest that MHCs may be far more common than previously recognized, with many facets yet to be discovered. We present MHCscan as a lightweight and user-friendly software tool that is freely available: https://github.com/Arkadiy-Garber/MHCscan.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Improving the explanation capabilities of advisory systems

A major limitation of current advisory systems (e.g., intelligent tutoring systems and expert systems) is their restricted ability to give explanations. The goal of our research is to develop and evaluate a flexible explanation facility, one that can dynamically generate responses to questions not anticipated by the system's designers and that can tailor these responses to individual users. To achieve this flexibility, we are developing a large knowledge base, a viewpoint construction facility, and a modeling facility. In the long term we plan to build and evaluate advisory systems with flexible explanation facilities for scientists in numerous domains. In the short term, we are focusing on a single complex domain in biological science, and we are working toward two important milestones: (1) building and evaluating an advisory system with a flexible explanation facility for freshman-level students studying biology, and (2) developing general methods and tools for building similar explanation facilities in other domains.

Porter, Bruce↗
NASA NTRS1993

Improving the explanation capabilities of advisory systems

A major limitation of current advisory systems (e.g., intelligent tutoring systems and expert systems) is their restricted ability to give explanations. The goal of our research is to develop and evaluate a flexible explanation facility, one that can dynamically generate responses to questions not anticipated by the system's designers and that can tailor these responses to individual users. To achieve this flexibility, we are developing a large knowledge base, a viewpoint construction facility, and a modeling facility. In the long term we plan to build and evaluate advisory systems with flexible explanation facilities for scientists in numerous domains. In the short term, we are focusing on a single complex domain in biological science, and we are working toward two important milestones: (1) building and evaluating an advisory system with a flexible explanation facility for freshman-level students studying biology; and (2) developing general methods and tools for building similar explanation facilities in other domains.

Porter, Bruce↗
NASA NTRS2014

SporeSat

Project Overview: SporeSat is a fundamental space biology science space mission to investigate biophysical mechanisms of plant gravity sensing using a "lab-on-a-chip" experimental approach. The unicellular germinating Ceratopteris richardii fern spore will be studied in outer space. Science Objective: SporeSat shall determine gravity thresholds for calcium ion (Ca2+) channel activation in wild-fern spores. Why This is Important: Ion channels are critical to the functioning of biological organisms, including humans. Ion channels are key components of the nervous system as well as cardiac, skeletal, and smooth muscle function, transport of nutrients and ions, T-cell activation, and pancreatic beta-cell insulin release. Ion channels are often the target of the search for new drugs.

Space Biology↗
DOE OSTI2026

Data from: "Reply to ‘The challenge of defining effectively-no-snow’"

This repository contains the data and code associated with the paper titled "Reply to ‘The challenge of defining effectively-no-snow’" published in Nature Reviews Earth and Environment, 2026. In this reply, we argue that the 10th percentile of peak SWE (Snow Water Equivalent), which we propose in the original article, can be used as intended given it's a standardized, impact-based benchmark for comparing snow conditions across regions, not as a literal measure of snow absence. We present new evidence with SNOwpack TELemetry (SNOTEL) data showing that years meeting the threshold are overwhelmingly associated with subsequent drought (given United States Drought Monitor conditions), supporting its hydrologic and societal relevance. We conclude that while the distinction between "effectively no snow" and "zero snow" should be clearly communicated, the original definition remains appropriate for assessing impacts on snow-dependent water systems. The file code_nree_ML_reply_2026.Rmd contains the main processing scripts which analyze the SNOTEL data. Data from the US Drought Monitor was downloaded at: https://usdmdataservices using the Get Drought Severity Statistics By Area Percent' option, saved to the *_HUC4_delineated.csv files (Hydrologic Unit Code), which are labeled accordingly. 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.

EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > SNOW/ICE↗
DOE OSTI2024

Global Corn Heat Stress: Mean and SD of Degree Days Above 29°C based on NEX-GDDP-CMIP6 Climate Projections

Description This global dataset provides the estimated mean and standard deviation (SD) of corn heat stress (degree days above 29°C) for a set of climate models in NEX-GDDP-CMIP6 at 0.25-degree resolution. The NEX-GDDP-CMIP6 dataset is comprised of global downscaled climate scenarios derived from the General Circulation Model (GCM) runs conducted under the Coupled Model Intercomparison Project Phase 6 (CMIP6). The current dataset includes: Long-Term Average Degree Days Above 29°C- Historical Long-Term Average Degree Days Above 29°C- SSP245 Long-Term Standard Deviation of Degree Days Above 29°C- Historical Long-Term Standard Deviation of Degree Days Above 29°C- SSP245 The mean and SD are calculated over 1985-2014 for the historical period and over 2035-2064 for future projections. A full description of methods, including growing season, daily temperature distribution, and statistical coefficients, can be found in Haqiqi (2024). The source climate data are obtained from https://ds.nccs.nasa.gov/thredds2/catalog/catalog.html and are described in Thrasher et al (2022). The codes used to create this dataset are available at https://github.com/ihaqiqi/dd29c_nex_cmip6. Acknowledgments This work was supported by the US Department of Energy, Office of Science, Biological and Environmental Research Program, Earth and Environmental Systems Modeling, MultiSector Dynamics under Cooperative Agreement DE-SC0022141. The data processing, computation, and storage were completed on Purdue Anvil supercomputer and cyberinfrastructure supported by the National Science Foundation HDR award # 2118329: "NSF Institute for Geospatial Understanding through an Integrative Discovery Environment (I-GUIDE)". References Haqiqi. I. (2024). Trade can buffer climate-induced risks and volatilities in crop supply. Environmental Research: Food Systems. https://doi.org/10.1088/2976-601X/ad7d12 Thrasher, B., Wang, W., Michaelis, A., Melton, F., Lee, T., & Nemani, R. (2022). NASA global daily downscaled projections, CMIP6. Scientific Data, 9(1), 262. https://doi.org/10.1038/s41597-022-01393-4

Climate Change↗
DOE OSTI2025

Time-lapse imagery in 2017 and 2018 at the Lower Montane site in the East River Watershed, Colorado

Time-lapse imagery was collected using an automated RGB camera mounted on a pole at the base of the northeast-facing hillslope at the Lower Montane site in the East River Watershed, Colorado. The imagery was intended to support a better understanding of plant dynamics and their controls during the growing season. The dataset includes RGB images archived in four zip files (containing imagery in JPEG format), corresponding to photos taken from the hillslope and the adjacent floodplain during 2017 and 2018. A fifth zip file contains a few AVI movies that compare imagery between the two years. The AVI files can be read with most media players applications. The archive contains a total of five *.zip files and three csv metadata files (flmd.csv, dd.csv, and 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.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Groundwater and river water elevations and temperature from 2017 to 2022 across Meander Z in the East River Watershed, Colorado

This dataset includes groundwater and river water elevations and temperature data collected in the East River watershed located in the Upper Colorado River Basin. The data were collected in order to investigate the coupling between hydrology and biogeochemical processes in the floodplain. Data was collected at ten groundwater locations in Meander Z (MZ), located just upstream of the confluence with Brush Creek and two river locations directly adjacent to Meander Z from 2017-2019. From 2019-2022, data was collected at five groundwater locations in Meander Z. Note that location names, not location identifiers (IDs), are used in the related publication Dewey et al. (2022). Both location IDs and names are included in data files. Files in this dataset include the main data files for each location zipped into a single folder (waterlevel_data.zip), an installation methods file describing sensor installation (InstallationMethods.csv), a file containing field metadata including GPS (Global Positioning System) coordinates and ground surface elevations (transducers_locations.csv). This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. This dataset conforms to the ESS-DIVE hydrological reporting format. 2026-04-27 Update: The river water elevation data files (ER-MZR1.csv and ER-MZR2.csv) were corrected. The data for these two locations were inadvertently swapped in the original published data. 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.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Meteorological Variables and Energy Fluxes at the Pumphouse Site, Crested Butte, CO 2017-2019

This data contains output from the pumphouse eddy covariance tower that includes shortwave radiation, longwave radiation, net radiation, air temperature, relative humidity, as well as sensible, latent, and ground heat fluxes. Also included is calculated evapotranspiration from the latent heat flux and the latent heat of vaporization. All data are on a daily timestep and displayed in Mountain Time. The data has been processed, and Quality Assurance / Quality Control (QA/QC) was done, but any daily gaps in the data have not been filled in. This research was funded by the Department of Energy and performed as part of the Watershed Function Scientific Focus Area. This research aimed to constrain evapotranspiration in a high-elevation catchment.The dataset includes one comma-separated values (CSV) data file (EddyCovariance_MeteorlogicalVariables_CrestedButtePumphouse.csv). Additionally, three metadata CSV files are included: (1) location metadata file (locations.csv), which contains location metadata and coordinates; (2) a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata; and (3) a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.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.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1994

Science observed: The mass-extinction debates

The upheaval triggered in 1980 by the Alvarez-Berkeley group impact hypothesis transformed the literature of mass extinctions from an unfocused, sporadic collection of papers that virtually ignored extraterrestrial causes and treated endogenous ones only sparingly better to an integrated, diverse body of literature. Research programs organized seemingly overnight spawned collaborative teams whose members, often from distant, isolated disciplines, redirected their careers in order to address the captivating, high-stakes issues. The initial, generally skeptical, cool reception of the impact hypothesis might have been predicted for any of a number of reasons: such an instantaneous catastrophe contravened earth science's reigning philosophy of uniformitarianism; it was formulated from a form of evidence - siderophile element anomalies - alien to the community charged with its appraisal; it advanced a causal mechanism that was improbable in terms of canonical knowledge; and it was proffered mainly by specialists alien to earth and biological science, especially paleobiology. Early on it became clear that irrespective of which causal hypothesis was chosen, the chosen one would be the strongest predictor of how the chooser would select and apply standards in assessing evidence bearing on all such hypothesis. Less strong correlation also appeared between disciplinary speciality and the assessment of evidence. Such correlations varied with the level of specialization; the most robust correlations appeared in the broadest areas of science practice. The gestalt (mindset) seemingly engendered by the embrace of an extinction hypothesis overrode, or was stronger than, the intellectual predispositions attributable to disciplinary specialty.

Glen, W.↗
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↗